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Lecture 03 v2: Basics of Biological Chemistry - Biology


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Figure 1. Atoms are the building blocks of molecules found in the universe—air, soil, water, rocks—and also the cells of all living organisms. In this model of an organic molecule, the atoms of carbon (black), hydrogen (white), nitrogen (blue), oxygen (red), and sulfur (yellow) are shown in proportional atomic size. The silver rods represent chemical bonds. (credit: modification of work by Christian Guthier)

The Structure of an atom

An atom is the smallest unit of matter that retains all of the chemical properties of an element. Elements are forms of matter with specific chemical and physical properties that cannot be broken down into smaller substances by ordinary chemical reactions.

The chemistry discussed in BIS2A requires us to use a model for an atom. While there are more sophisticated models, the atomic model used in this course makes the simplifying assumption that the standard atom is composed of three subatomic particles, the proton, the neutron, and the electron. Protons and neutrons have a mass of approximately one atomic mass unit (a.m.u.). One atomic mass unit is approximately 1.660538921 x 10-27kg—roughly 1/12 of the mass of a carbon atom (see table below for more precise value). The mass of an electron is 0.000548597 a.m.u. or 9.1 x 10-31kg. Neutrons and protons reside at the center of the atom in a region call the nucleus while the electrons orbit around the nucleus in zones called orbitals, as illustrated below. The only exception to this description is the hydrogen (H) atom, which is composed of one proton and one electron with no neutrons. An atom is assigned an atomic number based on the number of protons in the nucleus. Neutral carbon (C), for instance has six neutrons, six protons, and six electrons. It has an atomic number of six and a mass of slightly more than 12 a.m.u.

Table 1. Charge, mass, and location of subatomic particles

Protons, neutrons, and electrons
ChargeMass (a.m.u.)Mass (kg)Location
Proton+1~11.6726 x 10-27nucleus
Neutron0~11.6749 x 10-27nucleus
Electron–1~09.1094 x 10-31orbitals

Table 1 reports the charge and location of three subatomic particles—the neutron, proton, and electron. Atomic mass unit = a.m.u. (a.k.a. dalton [Da])—this is defined as approximately one twelfth of the mass of a neutral carbon atom or 1.660538921 x 10−27 kg. This is roughly the mass of a proton or neutron.

Figure 2. Elements, such as helium depicted here, are made up of atoms. Atoms are made up of protons and neutrons located within the nucleus and electrons surrounding the nucleus in regions called orbitals. (Note: This figure depicts a Bohr model for an atom—we could use a new open source figure that depicts a more modern model for orbitals. If anyone finds one please forward it.)
Source:(https://commons.wikimedia.org/wiki/F...um_atom_QM.svg)
By User: Yzmo (Own work) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/)], via Wikimedia Commons

Relative sizes and distribution of elements

The typical atom has a radius of one to two angstroms (Å). 1Å = 1 x 10-10m. The typical nucleus has a radius of 1 x 10-5Å or 10,000 smaller than the radius of the whole atom. By analogy, a typical large exercise ball has a radius of 0.85m. If this were an atom, the nucleus would have a radius about 1/2 to 1/10 of your thinnest hair. All of that extra volume is occupied by the electrons in regions called orbitals. For an ideal atom, orbitals are probabilistically defined regions in space around the nucleus in which an electron can be expected to be found.

For additional basic information on atomic structure click here.
For additional basic information on orbitals here.

Video clips

For a review of atomic structure check out this Youtube video: atomic structure.

The properties of living and nonliving materials are determined to a large degree by the composition and organization of their constituent elements. Five elements are common to all living organisms: Oxygen (O), Carbon (C), Hydrogen (H), Phosphorous (P), and Nitrogen (N). Other elements like Sulfur (S), Calcium (Ca), Chloride (Cl), Sodium (Na), Iron (Fe), Cobalt (Co), Magnesium, Potassium (K), and several other trace elements are also necessary for life, but are typically found in far less abundance than the "top five" noted above. As a consequence, life's chemistry—and by extension the chemistry of relevance in BIS2A—largely focuses on common arrangements of and reactions between the "top five" core atoms of biology.

Figure 3. A table illustrating the abundance of elements in the human body. A pie chart illustrating the relationships in abundance between the four most common elements.
Credit: Data from Wikipedia (http://en.wikipedia.org/wiki/Abundan...mical_elements); chart created by Marc T. Facciotti

The Periodic Table

The different elements are organized and displayed in the periodic table. Devised by Russian chemist Dmitri Mendeleev (1834–1907) in 1869, the table groups elements that, due to some commonalities of their atomic structure, share certain chemical properties. The atomic structure of elements is responsible for their physical properties including whether they exist as gases, solids, or liquids under specific conditions and and their chemical reactivity, a term that refers to their ability to combine and to chemically bond with each other and other elements.

In the periodic table, shown below, the elements are organized and displayed according to their atomic number and are arranged in a series of rows and columns based on shared chemical and physical properties. In addition to providing the atomic number for each element, the periodic table also displays the element’s atomic mass. Looking at carbon, for example, its symbol (C) and name appear, as well as its atomic number of six (in the upper right-hand corner indicating the number of protons in the neutral nucleus) and its atomic mass of 12.11 (sum of the mass of electrons, protons, and neutrons).

Figure: The periodic table shows the atomic mass and atomic number of each element. The atomic number appears above the symbol for the element and the approximate atomic mass appears to the left.
Source: By 2012rc (self-made using inkscape) [Public domain], via Wikimedia Commons Modified by Marc T. Facciotti - 2016

Electronegativity

Molecules are collections of atoms that are associated with one another through bonds. It is reasonable to expect—and the case empirically—that different atoms will exhibit different physical properties, including abilities to interact with other atoms. One such property, the tendency of an atom to attract electrons, is described by the chemical concept and term, electronegativity. While several methods for measuring electronegativity have been developed, the one most commonly taught to biologists is the one created by Linus Pauling.

A description of how Pauling electronegativity can be calculated is beyond the scope of BIS2A. What is important to know, however, is that electronegativity values have been experimentally and/or theoretically determined for nearly all elements in the periodic table. The values are unitless and are reported relative to the standard reference, hydrogen, whose electronegativity is 2.20. The larger the electronegativity value, the greater tendency an atom has to attract electrons. Using this scale, the electronegativity of different atoms can be quantitatively compared. For instance, by using Table 1 below, you could report that oxygen atoms are more electronegative than phosphorous atoms.

Table 1. Pauling electronegativity values for select elements of relevance to BIS2A as well as elements at the two extremes (highest and lowest) of the electronegativity scale.

Attribution: Marc T. Facciotti (original work)

The utility of the Pauling electronegativity scale in BIS2A is to provide a chemical basis for explaining the types of bonds that form between the commonly occurring elements in biological systems and to explain some of the key interactions that we observe routinely. We develop our understanding of electronegativity-based arguments about bonds and molecular interactions by comparing the electronegativities of two atoms. Recall, the larger the electronegativity, the stronger the "pull" an atom exerts on nearby electrons.

We can consider, for example, the common interaction between oxygen (O) and hydrogen (H). Let us assume that O and H are interacting (forming a bond) and write that interaction as O-H, where the dash between the letters represents the interaction between the two atoms. To understand this interaction better, we can compare the relative electronegativity of each atom. Examining the table above, we see that O has an electronegativity of 3.44, and H has an electronegativity of 2.20.

Based on the concept of electronegativity as we now understand it, we can surmise that the oxygen (O) atom will tend to "pull" the electrons away from the hydrogen (H) when they are interacting. This will give rise to a slight but significant negative charge around the O atom (due to the higher tendency of the electrons to be associated with the O atom). This also results in a slight positive charge around the H atom (due to the decrease in the probability of finding an electron nearby). Since the electrons are not distributed evenly between the two atoms AND, by consequence, the electric charge is also not evenly distributed, we describe this interaction or bond as polar. There are two poles in effect: the negative pole near the oxygen and the positive pole near the hydrogen.

To extend the utility of this concept, we can now ask how an interaction between oxygen (O) and hydrogen (H) differs from an interaction between sulfur (S) and hydrogen (H). That is, how does O-H differ from S-H? If we examine the table above, we see that the difference in electronegativity between O and H is 1.24 (3.44 - 2.20 = 1.24) and that the difference in electronegativity between S and H is 0.38 (2.58 – 2.20 = 0.38). We can therefore conclude that an O-H bond is more polar than an S-H bond. We will discuss the consequences of these differences in subsequent chapters.

Figure 2. The periodic table with the electronegativities of each atom listed.

Attribution: By DMacks (https://en.wikipedia.org/wiki/Electronegativity) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

An examination of the periodic table of the elements (Figure 2) illustrates that electronegativity is related to some of the physical properties used to organize the elements into the table. Certain trends are apparent. For instance, those atoms with the largest electronegativity tend to reside in the upper right hand corner of the periodic table, such as Fluorine (F), Oxygen (O) and Chlorine (Cl), while elements with the smallest electronegativity tend to be found at the other end of the table, in the lower left, such as Francium (Fr), Cesium (Cs) and Radium (Ra).

The main use of the concept of electronegativity in BIS2A will therefore be to provide a conceptual grounding for discussing the different types of chemical bonds that occur between atoms in nature. We will focus primarily on three types of bonds: Ionic Bonds, Covalent Bonds and Hydrogen Bonds.

Bond types

In BIS2A, we focus primarily on three different bond types: ionic bonds, covalent bonds, and hydrogen bonds. We expect students to be able to recognize each different bond type in molecular models. In addition, for commonly seen bonds in biology, we expect student to provide a chemical explanation, rooted in ideas like electronegativity, for how these bonds contribute to the chemistry of biological molecules.

Ionic bonds

Ionic bonds are electrostatic interactions formed between ions of opposite charges. For instance, most of us know that in sodium chloride (NaCl) positively charged sodium ions and negatively charged chloride ions associate via electrostatic (+ attracts -) interactions to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge. The origins of these interactions may arise from the association of neutral atoms whose difference in electronegativities is sufficiently high. Take the example above. If we imagine that a neutral sodium atom and a neutral chlorine atom approach one another, it is possible that at close distances, due to the relatively large difference in electronegativity between the two atoms, that an electron from the neutral sodium atom is transferred to the neutral chlorine atom, resulting in a negatively charged chloride ion and a positively charged sodium ion. These ions can now interact via an ionic bond.

Figure 1. The formation of an ionic bond between sodium and chlorine is depicted. In panel A, a sufficient difference in electronegativity between sodium and chlorine induces the transfer of an electron from the sodium to the chlorine, forming two ions, as illustrated in panel B. In panel C, the two ions associate via an electrostatic interaction. Attribution: By BruceBlaus (own work) [CC BY-SA 4.0 (http://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons

This movement of electrons from one atom to another is referred to as electron transfer. In the example above, when sodium loses an electron, it now has 11 protons, 11 neutrons, and 10 electrons, leaving it with an overall charge of +1 (summing charges: 11 protons at +1 charge each and 10 electrons at -1 charge each = +1). Once charged, the sodium atom is referred to as a sodium ion. Likewise, based on its electronegativity, a neutral chlorine (Cl) atom tends to gain an electron to create an ion with 17 protons, 17 neutrons, and 18 electrons, giving it a net negative (–1) charge. It is now referred to as a chloride ion.

We can interpret the electron transfer above using the concept of electronegativity. Begin by comparing the electronegativities of sodium and chlorine by examining the periodic table of elements below. We see that chlorine is located in the upper-right corner of the table, while sodium is in the upper left. Comparing the electronegativity values of chlorine and sodium directly, we see that the chlorine atom is more electronegative than is sodium. The difference in the electronegativity of chlorine (3.16) and sodium (0.93) is 2.23 (using the scale in the table below). Given that we know an electron transfer will take place between these two elements, we can conclude that differences in electronegativities of ~2.2 are large enough to cause an electron to transfer between two atoms and that interactions between such elements are likely through ionic bonds.

Figure 2. The periodic table of the elements listing electronegativity values for each element. The elements sodium and chlorine are boxed with a teal boundary. Attribution: By DMacks (https://en.wikipedia.org/wiki/Electronegativity) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia CommonsModified by Marc T. Facciotti

Note: possible discussion

The atoms in a 5 in. x 5 in. brick of table salt (NaCl) sitting on your kitchen counter are held together almost entirely by ionic bonds. Based on that observation, how would you characterize the strength of ionic bonds?

Now consider that same brick of table salt after having been thrown into an average backyard swimming pool. After a couple of hours, the brick would be completely dissolved, and the sodium and chloride ions would be uniformly distributed throughout the pool. What might you conclude about the strength of ionic bonds from this observation?

Propose a reason why NaCl's ionic bonds in air might be behaving differently than those in water? What is the significance of this to biology?

For additional information:

Check out the link from the Khan Academy on ionic bonds.

Covalent bonds

We can also invoke the concept of electronegativity to help describe the interactions between atoms that have differences in electronegativity too small for the atoms to form an ionic bond. These types of interactions often result in a bond called a covalent bond. In these bonds, electrons are shared between two atoms—in contrast to an ionic interaction in which electrons remain on each atom of an ion or are transferred between species that have highly different electronegativities.

We start exploring the covalent bond by looking at an example where the difference in electronegativity is zero. Consider a very common interaction in biology, the interaction between two carbon atoms. In this case, each atom has the same electronegativity, 2.55; the difference in electronegativity is therefore zero. If we build our mental model of this interaction using the concept of electronegativity, we realize that each carbon atom in the carbon-carbon pair has the same tendency to "pull" electrons to it. In this case, when a bond is formed, neither of the two carbon atoms will tend to "pull" (a good anthropomorphism) electrons from the other. They will "share" (another anthropomorphism) the electrons equally, instead.

Aside: bounding example

The two examples above—(1) the interaction of sodium and chlorine, and (2) the interaction between two carbon atoms—frame a discussion by "bounding," or asymptotic analysis (see earlier reading). We examined what happens to a physical system when considering two extremes. In this case, the extremes were in electronegativity differences between interacting atoms. The interaction of sodium and chlorine illustrated what happens when two atoms have a large difference in electronegativities, and the carbon-carbon example illustrated what happens when that difference is zero. Once we create those mental goal posts describing what happens at the extremes, it is then easier to imagine what might happen in between—in this case, what happens when the difference in electronegativity is between 0 and 2.2. We do that next.

When the sharing of electrons between two covalently bonded atoms is nearly equal, we call these bonds nonpolar covalent bonds. If by contrast, the sharing of electrons is not equal between the two atoms (likely due to a difference in electronegativities between the atoms), we call these bonds polar covalent bonds.

In a polar covalent bond, the electrons are unequally shared by the atoms and are attracted to one nucleus more than to the other. Because of the unequal distribution of electrons between atoms in a polar covalent bond, a slightly positive (indicated by δ+) or slightly negative (indicated by δ–) charge develops at each pole of the bond. The slightly positive (δ+) charge will develop on the less electronegative atom, as electrons get pulled more towards the slightly more electronegative atom. A slightly negative (δ–) charge will develop on the more electronegative atom. Since there are two poles (the positive and negative poles), the bond is said to possess a dipole.

Examples of nonpolar covalent and polar covalent bonds in biologically relevant molecules

Nonpolar covalent bonds

Molecular oxygen

Molecular oxygen (O2) is made from an association between two atoms of oxygen. Since the two atoms share the same electronegativity, the bonds in molecular oxygen are nonpolar covalent.

Methane

Another example of a nonpolar covalent bond is the C-H bond found in the methane gas (CH4). Unlike the case of molecular oxygen where the two bonded atoms share the same electronegativity, carbon and hydrogen do not have the same electronegativity; C = 2.55 and H = 2.20—the difference in electronegativity is 0.35.

Figure 3. Molecular line drawings of molecular oxygen, methane, and carbon dioxide. Attribution: Marc T. Facciotti (own work)

Some of you may now be confused. If there is a difference in electronegativity between the two atoms, is the bond not by definition polar? The answer is both yes and no and depends on the definition of polar that the speaker/writer is using. Since this is an example of how taking shortcuts in the use of specific vocabulary can sometimes lead to confusion, we take a moment to discuss this here. See the mock exchange between a student and an instructor below for clarification:

1. Instructor: "In biology, we often say that the C-H bond is nonpolar."

2. Student: "But there is an electronegativity difference between C and H, so it would appear that C should have a slightly stronger tendency to attract electrons. This electronegativity difference should create a small, negative charge around the carbon and a small, positive charge around the hydrogen."

3. Student: "Since there is a differential distribution of charge across the bond, it would seem that, by definition, this should be considered a polar bond."

4. Instructor: "In fact, the bond does have some small polar character."

5. Student: "So, then it's polar? I'm confused."

6. Instructor: "It has some small amount of polar character, but it turns out that for most of the common chemistry that we will encounter that this small amount of polar character is insufficient to lead to "interesting" chemistry. So, while the bond is, strictly speaking, slightly polar, from a practical standpoint it is effectively nonpolar. We therefore call it nonpolar."

7. Student: "That's needlessly confusing; how am I supposed to know when you mean strictly 100% nonpolar, slightly polar, or functionally polar when you use the same word to describe two of those three things?"

8. Instructor: "Yup, it sucks. The fix is that I need to be as clear as I can when I talk with you about how I am using the term "polarity." I also need to inform you that you will find this shortcut (and others) used when you go out into the field, and I encourage you to start learning to recognize what is intended by the context of the conversation.

A real-world analogy of this same problem might be the use of the word "newspaper". It can be used in a sentence to refer to the company that publishes some news, OR it can refer to the actual item that the company produces. In this case, the disambiguation is easily made by native English speakers, as they can determine the correct meaning from the context; non-native speakers may be more confused. Don't worry; as you see more examples of technical word use in science, you'll learn to read correct meanings from contexts too."

Aside:

How large should the difference in electronegativity be in order to create a bond that is "polar enough" that we decide to call it polar in biology? Of course, the exact value depends on a number of factors, but as a loose rule of thumb, we sometimes use a difference of 0.4 as a guesstimate.

This extra information is purely for your information. You will not be asked to assign polarity based on this criteria in BIS2A. You should, however, appreciate the concept of how polarity can be determined by using the concept of electronegativity. You should also appreciate the functional consequences of polarity (more on this in other sections) and the nuances associated with these terms (such as those in the discussion above).

Polar covalent bonds

The polar covalent bond can be illustrated by examining the association between O and H in water (H2O). Oxygen has an electronegativity of 3.44, while hydrogen has an electronegativity of 2.20. The difference in electronegativity is 1.24. It turns out that this size of electronegativity difference is large enough that the dipole across the molecule contributes to chemical phenomenon of interest.

This is a good point to mention another common source of student confusion regarding the use of the term polar. Water has polar bonds. This statement refers specifically to the individual O-H bonds. Each of these bonds has a dipole. However, students will also hear that water is a polar molecule. This is also true. This latter statement is referring to the fact that the sum of the two bond dipoles creates a dipole across the whole molecule. A molecule may be nonpolar but still have some polar bonds.

Figure 4. A water molecule has two polar O-H bonds. Since the distribution of charge in the molecule is asymmetric (due to the number and relative orientations of the bond dipoles), the molecule is also polar. The element name and electronegativities are reported in the respective sphere. Facciotti (own work)

For additional information, view this short video to see an animation of ionic and covalent bonding.

The continuum of bonds between covalent and ionic

The discussion of bond types above highlights that in nature you will see bonds on a continuum from completely nonpolar covalent to purely ionic, depending on the atoms that are interacting. As you proceed through your studies, you will further discover that in larger, multi-atom molecules, the localization of electrons around an atom is also influenced by multiple factors. For instance, other atoms that are also bonded nearby will exert an influence on the electron distribution around a nucleus in a way that is not easily accounted for by invoking simple arguments of pairwise comparisons of electronegativity. Local electrostatic fields produced by other non-bonded atoms may also have an influence. Reality is always more complicated than are our models. However, if the models allow us to reason and predict with "good enough" precision or to understand some key underlying concepts that can be extended later, they are quite useful.

Key bonds in BIS2A

In BIS2A, we are concerned with the chemical behavior of and bonds between atoms in biomolecules. Fortunately, biological systems are composed of a relatively small number of common elements (e.g., C, H, N, O, P, S, etc.) and some key ions (e.g., Na+, Cl-, Ca2+, K+, etc.). Start recognizing commonly occurring bonds and the chemical properties that we often see them showing. Some common bonds include C-C, C-O, C-H, N-H, C=O, C-N, P-O, O-H, S-H, and some variants. These will be discussed further in the context of functional groups. The task is not as daunting as it seems.

Hydrogen Bonds

When hydrogen forms a polar covalent bond with an atom of higher electronegativity, the region around the hydrogen will have a fractional positive charge (termed δ+). When this fractional positive charge encounters a partial negative charge (termed δ-) from another electronegative atom to which the hydrogen is NOT bound, AND it is presented to that negative charge in a suitable orientation, a special kind of interaction called a hydrogen bond can form. While chemists are still debating the exact nature of the hydrogen bond, in BIS2A, we like to conceive of it as a weak electrostatic interaction between the δ+ of the hydrogen and the δ- charge on an electronegative atom. We call the molecule that contributes the partially charged hydrogen atom "the hydrogen bond donor" and the atom with the partial negative charge the "hydrogen bond acceptor." You will be asked to start learning to recognize common biological hydrogen bond donors and acceptors and to identify putative hydrogen bonds from models of molecular structures.

Hydrogen bonds are common in biology both within and between all types of biomolecules. Hydrogen bonds are also critical interactions between biomolecules and their solvent, water.

Figure 1: Two water molecules are depicted forming a hydrogen bond (drawn as a dashed blue line). The water molecule on top "donates" a partially charged hydrogen while the water molecule on the bottom accepts that partial charge by presenting a complementary negatively charged oxygen atom.

Attribution: Marc T. Facciotti (original work)

Water

Water is a unique substance whose special properties are intimately tied to the processes of life. Life originally evolved in a watery environment, and most of an organism’s cellular chemistry and metabolism occur inside the water-solvated contents of the cell. Water solvates or "wets" the cell and the molecules in it, plays a key role as reactant or product in an innumerable number of biochemical reactions, and mediates the interactions between molecules in and out of the cell. Many of water’s important properties derive from the molecule's polar nature, which can be tracked down to the polar molecules whose dipole originates from its polar covalent bonds between hydrogen and oxygen.

In BIS2A, the ubiquitous role of water in nearly all biological processes is easy to overlook by getting caught up in the details of specific processes, proteins, the roles of nucleic acids, and in your excitement for molecular machines (it'll happen). It turns out, however, that water plays key roles in all of those processes and we will need to continuously stay aware of the role that water is playing if we are to develop a more functional understanding. Be on the lookout and also pay attention when your instructor points this out.

In a liquid state, individual water molecule interact with one another through a network of dynamic hydrogen bonds that are being constantly forming and breaking. Water also interacts with other molecules that have charged functional groups and/or functional groups with hydrogen bond donors or acceptors. A substance with sufficient polar or charged character may dissolve or be highly miscible in water is referred to as being hydrophilic (hydro- = “water”; -philic = “loving”). By contrast, molecules with more nonpolar characters such as oils and fats do not interact well with water and separate from it rather than dissolve in it, as we see in salad dressings containing oil and vinegar (an acidic water solution). These nonpolar compounds are called hydrophobic (hydro- = “water”; -phobic = “fearing”). We will consider the some of the energetic components of these types of reactions in other another chapter.

Figure 1. In a liquid state water forms a dynamic network of hydrogen bonds between individual molecules. Shown are one donor-acceptor pair.
Attribution: Marc T. Facciotti (original work)

Water's solvent properties

Since water is a polar molecule with slightly positive and slightly negative charges, ions and polar molecules can readily dissolve in it. Therefore, water is referred to as a solvent, a substance capable of dissolving other polar molecules and ionic compounds. The charges associated with these molecules will form hydrogen bonds with water, surrounding the particle with water molecules. This is referred to as a sphere of hydration, or a hydration shell and serves to keep the particles separated or dispersed in the water.

When ionic compounds are added to water, the individual ions interact with the polar regions of the water molecules, and the ionic bonds are likely disrupted in the process called dissociation. Dissociation occurs when atoms or groups of atoms break off from molecules and form ions. Consider table salt (NaCl, or sodium chloride). A dry block of NaCl is held together by ionic bonds and is difficult to dissociate. When NaCl crystals are added to water, however, the molecules of NaCl dissociate into Na+ and Clions, and spheres of hydration form around the ions. The positively charged sodium ion is surrounded by the partially negative charge of the water molecule’s oxygen. The negatively charged chloride ion is surrounded by the partially positive charge of the hydrogen on the water molecule. One may imagine a model in which the ionic bonds in the crystal are "traded" for many smaller scale ionic bonds with the polar groups on water molecules.

Figure 2. When table salt (NaCl) is mixed in water, spheres of hydration are formed around the ions. This figure depicts a sodium ion (dark blue sphere) and a chloride ion (light blue sphere) solvated in a "sea" of water. Note how the dipoles of the water molecules surrounding the ions are aligned such that complementary charges/partial charges are associating with one another (i.e., the partial positive charges on the water molecules align with the negative chloride ion whereas the partial negative charges on the oxygen of water align with the positively charged sodium ion).
Attribution: Ting Wang - UC Davis (original work modified by Marc T. Facciotti)

Note: possible discussion

Consider the model of water dissolving a salt crystal presented above. Describe in your own words how this model can be used to explain what is happening at the molecular level when enough salt is added to a volume of water that the salt no longer dissolves (the solution reaches saturation). Work together to craft a common picture.

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What is the role of Acid/Base Chemistry in Bis2A?

We have learned that the behavior of chemical functional groups depends greatly on the composition, order and properties of their constituent atoms. As we will see, some of the properties of key biological functional groups can be altered depending on the pH (hydrogen ion concentration) of the solution that they are bathed in.

For example, some of the functional groups on the amino acid molecules that make up proteins can exist in different chemical states depending on the pH. We will learn that the chemical state of these functional groups in the context of a protein can have have a profound effect on the shape of protein or its ability to carry out chemical reactions. As we move through the course we will see numerous examples of this type of chemistry in different contexts.

pH is formally defined as:

[ pH = log_{10} [H^+]]

In the equation above, the square brackets surrounding (H^+) indicate concentration. If necessary, try a math review at wiki logarithm or kahn logarithm. Also see: concentration dictionary or wiki concentration.

Hydrogen ions are spontaneously generated in pure water by the dissociation (ionization) of a small percentage of water molecules into equal numbers of hydrogen (H+) ions and hydroxide (OH-) ions. While the hydroxide ions are kept in solution by their hydrogen bonding with other water molecules, the hydrogen ions, consisting of naked protons, are immediately attracted to un-ionized water molecules, forming hydronium ions (H30+).

Still, by convention, scientists refer to hydrogen ions and their concentration as if they were free in this state in liquid water. This is another example of a shortcut that we often take - it's easier to write H+ rather than H3O+. We just need to realize that this shortcut is being taken; otherwise confusion will ensue.

Figure 1: Water spontaneously dissociates into a proton and hydroxyl group. The proton will combine with a water molecule forming a hydronium ion.
Attribution: Marc T. Facciotti

The pH of a solution is a measure of the concentration of hydrogen ions in a solution (or the number of hydronium ions). The number of hydrogen ions is a direct measure of how acidic or how basic a solution is.

The pH scale is logarithmic and ranges from 0 to 14 (Figure 2). We define pH=7.0 as neutral. Anything with a pH below 7.0 is termed acidic and any reported pH above 7.0 is termed alkaline or basic. Extremes in pH in either direction from 7.0 are usually considered inhospitable to life, although examples exist to the contrary. pH levels in the human body usually range between 6.8 and 7.4, except in the stomach where the pH is more acidic, typically between 1 and 2.

Watch this video for a straightforward explanation of pH and its logarithmic scale.

Figure 2: The pH scale ranging from acidic to basic with various biological compounds or substances that exist at that particular pH. Facciotti

For additional information:

Watch this video for an alternative explanation of pH and its logarithmic scale.

The concentration of hydrogen ions dissociating from pure water is 1 × 10-7 moles H+ ions per liter of water.

1 mole (mol) of a substance (which can be atoms, molecules, ions, etc), is defined as being equal to 6.02 x 1023 particles of the substance. Therefore, 1 mole of water is equal to 6.02 x 1023 water molecules. The pH is calculated as the negative of the base 10 logarithm of this unit of concentration. The log10 of 1 × 10-7 is -7.0, and the negative of this number yields a pH of 7.0, which is also known as neutral pH.

Non-neutral pH readings result from dissolving acids or bases in water. High concentrations of hydrogen ions yields a low pH number, whereas low levels of hydrogen ions result in a high pH.

This inverse relationship between pH and the concentration of protons confuses many students - take the time to convince yourself that you "get it."

An acid is a substance that increases the concentration of hydrogen ions (H+) in a solution, usually by having one of its hydrogen atoms dissociate. For example, we have learned that the carboxyl functional group is an acid. The hydrogen atom can dissociate from the oxygen atom resulting in a free proton and a negatively charged functional group. A base provides either hydroxide ions (OH) or other negatively charged ions that combine with hydrogen ions, effectively reducing the H+ concentration in the solution and thereby raising the pH. In cases where the base releases hydroxide ions, these ions bind to free hydrogen ions, generating new water molecules. For example, we have learned that the amine functional group is a base. The nitrogen atom will accept hydrogen ions in solution, thereby reducing the number of hydrogen ions which raises the pH of the solution.

Figure 3: The carboxylic acid group acts as an acid by releasing a proton into solution. This increases the number of protons in solution and thus decreases the pH. The amino group acts as a base by accepting hydrogen ions from solution, decreasing the number of hydrogen ions in solutions, thus increasing the pH.
Attribution: Erin Easlon

Additional pH resources

Here are some additional links on pH and pKa to help learn the material. Note that there is an additional module devoted to pKa.

PKa

pKa is defined as the negative log10 of the dissociation constant of an acid, its Ka. Therefore, the pKa is a quantitative measure of how easily or how readily the acid gives up its proton [H+] in solution and thus a measure of the "strength" of the acid. Strong acids have a small pKa, weak acids have a larger pKa.

The most common acid we will talk about in BIS2A is the carboxylic acid functional group. These acids are typically weak acids, meaning that they only partially dissociate (into H+ cations and RCOO- anions) in neutral solution. HCL (hydrogen chloride) is a common strong acid, meaning that it will fully dissociate into H+ and Cl-.

Note that the key difference in the figure below between a strong acid or base and a weak acid or base is the single arrow (strong) versus a double arrow (weak). In the case of the single arrow you can interpret that by imagining that nearly all reactants have been converted into products. Moreover, it is difficult for the reaction to reverse backwards to a state where the protons are again associated with the molecule there were associated with before. In the case of a weak acid or base, the double-sided arrow can be interpreted by picturing a reaction in which:

  1. both forms of the conjugate acid or base (that is what we call the molecule that "holds" the proton - i.e. CH3OOH and CH3OO-, respectively in the figure) are present at the same time and
  2. the ratio of those two quantities can change easily by moving the reaction in either direction.

Figure 1. An example of strong acids and strong bases in their protonation and deprotonation states. The value of their pKa is shown on the left. Facciotti

Electronegativity plays a role in the strength of an acid. If we consider the hydroxyl group as an example, the greater electronegativity of the atom or atoms (indicated R) attached to the hydroxyl group in the acid R-O-H results in a weaker H-O bond, which is thus more readily ionized. This means that the pull on the electrons away from the hydrogen atom gets greater when the oxygen atom attached to the hydrogen atom is also attached to another electronegative atom. An example of this is HOCL. The electronegative Cl polarizes the H-O bond, weakening it and facilitating the ionization of the hydrogen. If we compare this to a weak acid where the oxygen is bound to a carbon atom (as in carboxylic acids) the oxygen is bound to the hydrogen and carbon atom. In this case, the oxygen is not bound to another electronegative atom. Thus the H-O bond is not further destabilized and the acid is considered a weak acid (it does not give up the proton as easily as a strong acid).

Figure 2. The strength of the acid can be determined by the electronegativity of the atom the oxygen is bound to. For example, the weak acid Acetic Acid, the oxygen is bound to carbon, an atom with low electronegativity. In the strong acid, Hypochlorous acid, the oxygen atom is bound to an even more electronegative Chloride atom.
Attribution: Erin Easlon

In Bis2A you are going to be asked to relate pH and pKa to each other when discussing the protonation state of an acid or base, for example, in amino acids. How can we use the information given in this module to answer the question: Will the functional groups on the amino acid Glutamate be protonated or deprotonated at a pH of 2, at a pH of 8, at a pH of 11?

In order to start answering this question we need to create a relationship between pH and pKa. The relationship between pKa and pH is mathematically represented by Henderson-Hasselbach equation shown below, where [A-] represents the deprotonated form of the acid and [HA] represents the protonated form of the acid.

Figure 3. The Henderson-Hasselbach equation

A solution to this equation is obtained by setting pH = pKa. In this case, log([A-] / [HA]) = 0, and [A-] / [HA] = 1. This means that when the pH is equal to the pKa there are equal amounts of protonated and deprotonated forms of the acid. For example, if the pKa of the acid is 4.75, at a pH of 4.75 that acid will exist as 50% protonated and 50% deprotonated. This also means that as the pH rises, more of the acid will be converted into the deprotonated state and at some point the pH will be so high that the majority of the acid will exist in the deprotonated state.

Figure 4. This graph depicts the protonation state of acetic acid as the pH changes. At a pH below the pKa, the acid is protonated. At a pH above the pKa the acid is deprotonated. If the pH equals the pKa, the acid is 50% protonated and 50% deprotonated. Attribution: Ivy Jose

In BIS2A, we will be looking at the protonation state and deprotonation state of amino acids. Amino acids contain multiple functional groups that can be acids or bases. Therefore their protonation/deprotonation status can be more complicated. Below is the relationship between the pH and pKa of the amino acid Glutamic Acid. In this graph we can ask the question we posed earlier: Will the functional groups on the amino acid Glutamate be protonated or deprotonated at a pH of 2, at a pH of 8, at a pH of 11?

Figure 5. This graph depicts the protonation state of glutamate as the pH changes. At a pH below the pKa for each functional group on the amino acid, the functional group is protonated. At a pH above the pKa for the functional group it is deprotonated. If the pH equals the pKa, the functional group is 50% protonated and 50% deprotonated.
Attribution: Ivy Jose

Note: Possible discussion

  1. What is the overall charge of free Glutamate at a pH of 5?
  2. What is the overall charge of free Glutamate at a pH of 10?

Chemical reactions

Chemical reactions occur when two or more atoms bond together to form molecules or when bonded atoms are broken apart. The substances that "go into" a chemical reaction are called the reactants (by convention, these are usually listed on the left side of a chemical equation), and the substances that are found to "come out" of the reaction are known as the products (by convention, these are usually found on the right side of a chemical equation). An arrow linking the reactants and products is typically drawn between them to indicate the direction of the chemical reaction. By convention, for one-way reactions, reactants are listed on the left and products on the right of the single-headed arrow. However, you should be able to identify reactants and products of one-way reactions that are written in any orientation (e.g., right-to-left, top-to-bottom, diagonal right-to-left, around a circular arrow, etc.)

[underbrace{2H_2O_2}_{ ext{hydrogen peroxide}} → underbrace{2H_2O}_{ ext{water}} + underbrace{O_2}_{ ext{oxygen}}]

Note: practice

Identify the reactants and products of the reaction involving hydrogen peroxide above.

Note: possible discussion

When we write (H_2O_2) to represent the molecule hydrogen peroxide, it is a model representing an actual molecule. What information about the molecule is immediately communicated by this molecular formula? That is, what do you know about the molecule just by looking at the term (H_2O_2)?

What information is not explicitly communicated about this molecule by looking only at the formula?

Some chemical reactions, such as the one shown above, proceed mostly in one direction. When we depict reactions with a single-headed (unidirectional) arrow, we are implying that the reaction is essentially irreversible. However, all reactions can technically proceed in both directions. Reversible reactions are those that can proceed in either direction. In reversible reactions, reactants are turned into products, but when the concentration of product goes beyond a certain threshold (a characteristic particular to a specific reaction), some of these products will be converted back into reactants. This back and forth continues until a certain relative balance between reactants and products occurs—a state called equilibrium. These situations of reversible reactions are often denoted by a chemical equation with a double-headed arrow pointing towards both the reactants and products. You will find a continuum of chemical reactions; some proceed mostly in one direction and nearly never reverse, while others change direction easily, depending on various factors like the relative concentrations of reactants and products. That is, you will find reactions with all sorts of equilibrium points.

Note: use of vocabulary

You may have realized that the terms "reactants" and "products" are relative to the direction of the reaction. If you have a reaction that is reversible, though, the products of running the reaction in one direction become the reactants of the reverse. You can label the same compound with two different terms. That can be a bit confusing. So, what is one to do in such cases? The answer is that if you want to use the terms "reactants" and "products," you must be clear about the direction of the reaction that you are referring to.

Let's look at an example of a reversible reaction in biology. In human blood, excess hydrogen ions (H+) bind to bicarbonate ions (HCO3-), forming an equilibrium state with carbonic acid (H2CO3). This reaction is readily reversible. If carbonic acid were added to this system, some of it would be converted to bicarbonate and hydrogen ions, as the chemical system seeks equilibrium.

[HCO_3^−+ H^+ ightleftharpoons H_2CO_3 label{2}]

The examples above examine "idealized" chemical systems as they might occur in a test tube. In biological systems, however, equilibrium for a single reaction is rarely obtained as it might be in the lab. In biological systems, reactions do not occur in isolation. The concentrations of the reactants and/or products are constantly changing, often with a product of one reaction being a reactant for another reaction. These linked reactions form what are known as biochemical pathways. The immediate example above illustrates this and another caveat. While the reaction between the bicarbonate/proton and carbonic acid is highly reversible, it turns out that physiologically this reaction is usually "pulled" towards the formation of carbonic acid. Why? As shown below, carbonic acid becomes a reactant for another biochemical reaction: its conversion to CO2 and H2O. This conversion reduces the concentration of H2CO3, thus pulling the reaction between bicarbonate and H+ to the right. Moreover, a third reaction, the removal of CO2 and H2 from the system, also pulls the reaction further to the right. These kinds of reactions are important contributors to maintaining the H+ homeostasis of our blood.

Characteristic Chemical Reactions

All chemical reactions begin with a reactant—the general term for the one or more substances that enter into the reaction. Sodium and chloride ions, for example, are the reactants in the production of table salt. The one or more substances produced by a chemical reaction are called the product. **Note that there is some "hidden" excitement in the story about table salt involving water that we'll see soon.**

In chemical reactions, the atoms and elements present in the reactant(s) must all also be present in the product(s). Similarly, there can be nothing present in the products that was not present in the reactants. This is because chemical reactions are governed by the law of conservation of mass, which states that matter cannot be created nor destroyed in a chemical reaction. This means that when you examine a chemical reaction, you must try to account for everything that goes in AND make sure that you can find it all in the stuff that comes out!

Just as you can express mathematical calculations in equations such as 2 + 7 = 9, you can use chemical equations to show how reactants become products. By convention, chemical equations are typically read or written from left to right. Reactants on the left are separated from products on the right by a single- or double-headed arrow indicating the direction in which the chemical reaction proceeds. For example, the chemical reaction in which one atom of nitrogen and three atoms of hydrogen produce ammonia would be written as:

[N + 3H→NH_3.]

Correspondingly, the breakdown of ammonia into its components would be written as:

[NH3→N + 3H.]

Note that in either direction, you find 1 N and 3 Hs on both sides of the equation.

Reversibility

In theory, any chemical reaction can proceed in either direction under the right conditions. Reactants may synthesize into a product that later reverts back to a reactant. Reversibility is also a quality of exchange reactions. For instance, A+BC→AB+C could then reverse to AB+C→A+BC. This reversibility of a chemical reaction is indicated with a double arrow: A+BC⇄AB+C.

Synthesis reactions

Many macromolecules are made from smaller subunits, or building blocks, called monomers. Monomers covalently link to form larger molecules known as polymers. Often, the synthesis of polymers from monomers will also produce water molecules as products of the reaction. This type of reaction is known as dehydration synthesis or condensation reaction.

Figure 1. In the dehydration synthesis reaction depicted above, two molecules of glucose are linked together to form the disaccharide maltose. In the process, a water molecule is formed.

Attribution: Marc T. Facciotti (original work)

In a dehydration synthesis reaction (Figure 1), the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water. At the same time, the monomers share electrons and form covalent bonds. As additional monomers join, this chain of repeating monomers forms a polymer. Different types of monomers can combine in many configurations, giving rise to a diverse group of macromolecules. Even one kind of monomer can combine in a variety of ways to form several different polymers; for example, glucose monomers are the constituents of starch, glycogen, and cellulose.

In the carbohydrate monomer example above, the polymer is formed by a dehydration reaction; this type of reaction is also used to add amino acids to a growing peptide chain and nucleotides to the growing DNA or RNA polymer. Visit the modules on Amino Acids, Lipids, and Nucleic Acids to see if you can identify the water molecules that are removed when a monomer is added to the growing polymer.

Figure 2. This depicts, using words, (decorated with functional groups colored in red) a generic dehydration synthesis/condensation reaction.

Attribution: Marc T. Facciotti (original work)

Hydrolysis reactions

Polymers are broken down into monomers in a reaction known as hydrolysis. A hydrolysis reaction includes a water molecule as a reactant (Figure 3). During these reactions, a polymer can be broken into two components: one product carries a hydrogen ion (H+) from the water, while the second product carries the water's remaining hydroxide (OH–).

Figure 3. In the hydrolysis reaction shown here, the disaccharide maltose is broken down to form two glucose monomers with the addition of a water molecule. Note that this reaction is the reverse of the synthesis reaction shown in Figure 1 above.

Attribution: Marc T. Facciotti (original work)

Figure 4. This depicts using words (decorated with functional groups colored in red) a generic hydrolysis reaction.

Attribution: Marc T. Facciotti (original work)

Dehydration synthesis and hydrolysis reactions are catalyzed, or “sped up,” by specific enzymes. Note that both dehydration synthesis and hydrolysis reactions involve the making and breaking of bonds between the reactants—a reorganization of the bonds between the atoms in the reactants. In biological systems (our bodies included), food in the form of molecular polymers is hydrolyzed into smaller molecules by water via enzyme-catalyzed reactions in the digestive system. This allows for the smaller nutrients to be absorbed and reused for a variety of purposes. In the cell, monomers derived from food may then be reassembled into larger polymers that serve new functions.

Helpful links:

Visit this site to see visual representations of dehydration synthesis and hydrolysis.
Example of Hydrolysis with Enzyme Action is shown in this 3 minute video entitled: Hydrolysis of Sucrose by Sucrase.

Exchange/transfer reactions

We will also encounter reactions termed exchange reactions. In these types of reactions, "parts" of molecules are transferred between one another—bonds are broken to release a part of a molecule and bonds are formed between the released part and another molecule. These enzyme-catalyzed reactions are usually reasonably complex multistep chemical processes.

Figure 5. An exchange reaction in which both synthesis and hydrolysis can occur, chemical bonds are both formed and broken, is depicted using a word analogy.

Chemical equilibrium—Part 1: forward and reverse reactions

Understanding the concept of chemical equilibrium is critical to following several of the discussions that we have in BIS2A and indeed throughout biology and the sciences. It is difficult to completely describe the concept of chemical equilibrium without reference to the energy of a system, but for the sake of simplicity, let’s try anyway and reserve the discussion of energy for another chapter. Let us, rather, begin developing our understanding of equilibrium by considering the reversible reaction below:

Hypothetical reaction #1: A hypothetical reaction involving compounds A, B and D. If we read this from left to right, we would say that A and B come together to form a larger compound: D. Reading the reaction from right to left, we would say that compound D breaks down into smaller compounds: A and B.

We first need to define what is meant by a “reversible reaction.” The term “reversible” simply means that a reaction can proceed in both directions. That is, the things on the left side of the reaction equation can react together to become the things on the right of the equation, AND the things on the right of the equation can also react together to become the things on the left side of the equation. Reactions that only proceed in one direction are called irreversible reactions.

To start our discussion of equilibrium, we begin by considering a reaction that we posit is readily reversible. In this case, it is the reaction depicted above: the imaginary formation of compound D from compounds A and B. Since it is a reversible reaction, we could also call it the decomposition of D into A and B. Let us, however, imagine an experiment in which we watch the reaction proceed from a starting point where only A and B are present.

Example #1: Left-balanced reaction

Hypothetical reaction #1: time course
Concentrationt=0t=1t=5t=10t=15t=20t=25t=30t=35t=40
[A]100908070656260606060
[B]100908070656260606060
[C]0102030453840404040

At time t = 0 (before the reaction starts), the reaction has 100 concentration units of compounds A and B and zero units of compound D. We now allow the reaction to proceed and observe the individual concentrations of the three compounds over time (t=1, 5, 10, 15, 20, 25, 30, 35, and 40 time units). As A and B react, D forms. In fact, one can see D forming from t=0 all the way to t=25. After that time, however, the concentrations of A, B and D stop changing. Once the reaction reaches the point where the concentrations of the components stop changing, we say that the reaction has reached equilibrium. Notice that the concentrations of A, B, and D are not equal at equilibrium. In fact, the reaction seems left balanced so that there is more A and B than D.

Note

****Common student misconception warning****

Many students fall victim to the misconception that the concentrations of a reaction’s reactants and products must be equal at equilibrium. Given that the term equilibrium sounds a lot like the word “equal,” this is not surprising. But as the experiment above tries to illustrate, this is NOT correct!

Example #2: right-balanced reaction

We can examine a second hypothetical reaction, the synthesis of compound J from the compounds E and F.

Hypothetical reaction #2: A hypothetical reaction involving compounds E, F and J. If we read this from left to right, we would say that E and F come together to form a larger compound: J. Reading the reaction from right to left, we would say that compound J breaks down into smaller compounds: E and F.

The structure of hypothetical reaction #2 looks identical to that of hypothetical reaction #1, which we considered above—two things come together to make one bigger thing. We just need to assume, in this case, that E, F, and J have different properties from A, B, and D. Let’s imagine a similar experiment to the one described above and examine this data:

Hypothetical reaction #2: time course


In this case, the reaction also reaches equilibrium. This time, however, equilibrium occurs at around t=30. After that point, the concentrations of E, F, and J do not change. Note again that the concentrations of E, F, and J are not equal at equilibrium. In contrast to hypothetical reaction #1 (the ABD reaction), this time the concentration of J, the thing on the right side of the arrows, is at a higher concentration than E and F. We say that, for this reaction, equilibrium lies to the right.

Four more points need to be made at this juncture.

Point 1: Whether equilibrium for a reaction lies to the left or the right will be a function of the properties of the components of the reaction and the environmental conditions that the reaction is taking place in (e.g., temperature, pressure, etc.).

Point 2: We can also talk about equilibrium using concepts of energy, and we will do this soon, just not yet.

Point 3: While hypothetical reactions #1 and #2 appear to reach a point where the reaction has “stopped,” you should imagine that reactions are still happening even after equilibrium has been reached. At equilibrium the “forward” and “reverse” reactions are just happening at the same rate. That is, in example #2, at equilibrium J is forming from E and F at the same rate that it is breaking down into E and F. This explains how the concentrations of the compounds aren’t changing despite the fact that the reactions are still happening.

Point 4: From this description of equilibrium, we can define something we call the equilibrium constant. Typically, the constant is represented by an uppercase K and may be written as Keq. In terms of concentrations, Keq is written as the mathematical product of the reaction product concentrations (stuff on the right) divided by the mathematical product of the reactant concentrations (stuff on the left). For example, Keq,1 = [D]/[A][B], and Keq,2 = [J]/[E][F]. The square brackets "[]" indicate the “concentration of” whatever is inside the bracket.

Chemical Equilibrium—Part 2: Free Energy

In a previous section, we began a description of chemical equilibrium in the context of forward and reverse rates. Three key ideas were presented:

  1. At equilibrium, the concentrations of reactants and products in a reversible reaction are not changing in time.
  2. A reversible reaction at equilibrium is not static—reactants and products continue to interconvert at equilibrium, but the rates of the forward and reverse reactions are the same.
  3. We were NOT going to fall into a common student trap of assuming that chemical equilibrium means that the concentrations of reactants and products are equal at equilibrium.

Here we extend our discussion and put the concept of equilibrium into the context of free energy, also reinforcing the Energy Story exercise of considering the "Before/Start" and "After/End" states of a reaction (including the inherent passage of time).

Figure 1. Reaction coordinate diagram for a generic exergonic reversible reaction. Equations relating free energy and the equilibrium constant: R = 8.314 J mol-1 K-1 or 0.008314 kJ mol-1 K-1; T is temperature in Kelvin.

Attribution: Marc T. Facciotti (original work)

The figure above shows a commonly cited relationship between ∆G° and Keq: ∆G° = -RTlnKeq. Here, G° indicates the free energy under standard conditions (e.g., 1 atmosphere of pressure, 298K). In the context of an Energy Story, this equation describes the change in free energy of a reaction whose starting condition is out of equilibrium; specifically, all matter at the "start" is in the form of reactants, and the "end" of the reaction is the equilibrium state. Implicit is the idea that the reaction can theoretically proceed to infinite time so that no matter the shape of its energy surface, it can reach equilibrium. One can also consider a reaction where the "starting" state is somewhere between the starting state above and equilibrium and perhaps where the reaction is not at equilibrium. In this case, one can examine the ∆G (not standard conditions) between the "intermediate" starting state and equilibrium by considering the equation ∆G = ∆G° + RTlnQ, where Q is called the reaction quotient. From the standpoint of BIS2A, we will use a simple (a bit incomplete but functional) definition for Q = [Products]st/[Reactants]st at a defined non-equilibrium "starting" condition st. The equation ∆G = ∆G° + RTlnQ can therefore be read as the free energy of the transformation being equal to the free energy associated with the free energy difference for ideal standard condition plus the contribution of free energy that represents the deviation away from the "ideal" starting state represented by the actual starting state and conditions. In both cases, the "final" condition is still equilibrium; we are just changing starting points. One can extend this idea and calculate the free energy difference between two non-equilibrium states, provided they are properly defined, but that's for your chemistry instructor to bother you with. The key point here is that there is a way to both conceive of and compute free energy changes between specifically defined states, not just the standard initial state and equilibrium as the end state.

This takes us to the core summary point. In many biology books, the discussion of equilibrium includes not only the discussion of forward and reverse reaction rates, but also a statement that ∆G = 0 at equilibrium. This often confuses some students because they are also taught that a nonzero ∆G can be associated with a reaction going to equilibrium. We do this each time we report the ∆G of a reaction or examine a reaction coordinate diagram. So, students tend to memorize the "∆G=0 at equilibrium" statement without appreciating where it comes from. The key to closing the apparent disconnect for many is to appreciate that the interpretation of the sometimes seemingly contradictory statements depend a lot on the definition of the starting and ending states used to calculate ∆G. In the case of reporting ∆G for a reaction, the starting state was described in the paragraphs above (in one of two ways—either standard conditions or non-standard, out-of-equilbrium state), and the ending state is some time later, once the reaction has reached equilibrium. Since the starting and ending states are different, ∆G can be nonzero, positive, or negative. By contrast, the statement that concludes "∆G=0 at equilibrium" is considering a different starting state. In this case, the starting state is the system already at equilibrium. The ending state is considered to be sometime later, but still at equilibrium. Since the starting and ending states are ostensibly the same, ∆G = 0.

Buffers

Since changes in pH can dramatically influence the function of many biomolecules, unicellular and multicellular organisms have developed various means of protecting themselves against changes in pH. One of these mechanisms is the use of small molecules that can, based on their chemical properties, be classified as buffers. Buffers are typically small molecules that can reversibly bind and unbind protons in solution. If the pH in an environment is lower than the pKa of a protonatable functional group on the buffer molecule, that group will tend to become protonated and therefore "remove" a proton from solution. Alternatively, if the pH in an environment is higher than the pKa of the same protonatable functional group on the buffer molecule, that group will tend to become or stay deprotonated, lowering the local pH.

of the body carefully maintained in the narrow range required for survival. Maintaining a constant blood pH is critical to a person’s well-being. The buffer maintaining the pH of human blood involves carbonic acid (H2CO3), bicarbonate ion (HCO3–), and carbon dioxide (CO2). When bicarbonate ions combine with free hydrogen ions and become carbonic acid, hydrogen ions are removed, moderating pH changes. Similarly, excess carbonic acid can be converted to carbon dioxide gas and exhaled through the lungs. This prevents too many free hydrogen ions from building up in the blood and dangerously reducing its pH. Likewise, if too much OH– is introduced into the system, carbonic acid will react with it to create bicarbonate, lowering the pH. Without this buffer system, the body’s pH would fluctuate enough to put survival in jeopardy.

Figure 1. This diagram shows the body’s buffering of blood pH levels. The blue arrows show the process of raising pH as more CO2 is made.

Other examples of buffers are antacids used to combat excess stomach acid. Many of these over-the-counter medications work in the same way as blood buffers, usually with at least one ion capable of absorbing hydrogen and moderating pH, bringing relief to those that suffer from “heartburn” after eating. In addition to the many beneficial characteristics of water, its unique properties that contribute to this capacity to balance pH are essential to sustaining life on Earth.

Functional groups

A functional group is a specific group of atoms within a molecule that is responsible for a characteristic of that molecule. Many biologically active molecules contain one or more functional groups. In BIS2A, we will review the major functional groups found in biological molecules. These include the following: hydroxyl, methyl, carbonyl, carboxyl, amino, and phosphate (see Figure 1).

Figure 1. The functional groups shown here are found in many different biological molecules. "R" represents any other atom or extension of the molecule.
Attribution: Marc T. Facciotti (own work adapted from previous image of unknown source)

A functional group may participate in a variety of chemical reactions. Some of the important functional groups in biological molecules are shown above: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl (not shown). These groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids. Functional groups can sometimes be classified as having polar or nonpolar properties depending on their atomic composition and organization. The term polar describes something that has a property that is not symmetric about it—it can have different poles (more or less of something at different places). In the case of bonds and molecules, the property we care about is usually the distribution of electrons and therefore electric charge between the atoms. In a nonpolar bond or molecule, electrons and charge will be relatively evenly distributed. In a polar bond or molecule, electrons will tend to be more concentrated in some areas than others. An example of a nonpolar group is the methane molecule (see discussion in Bond Types Chapter for more detail). Among the polar functional groups is the carboxyl group found in amino acids, some amino acid side chains, and the fatty acids that form triglycerides and phospholipids.

Nonpolar functional groups

Methyl R-CH3

The methyl group is the only nonpolar functional group in our class list above. The methyl group consists of a carbon atom bound to three hydrogen atoms. In this class, we will treat these C-H bonds as effectively nonpolar covalent bonds (more on this in the Bond Types chapter). This means that methyl groups are unable to form hydrogen bonds and will not interact with polar compounds such as water.

Figure 2. The amino acid isoleucine is on the left, and cholesterol is on the right. Each has a methyl group circled in red. Attribution: created by Marc T. Facciotti (own work adapted from Erin Easlon)

The methyl groups highlighted above are found in a variety of biologically relevant compounds. In some cases, the compound can have a methyl group but still be a polar compound overall due to the presence of other functional groups with polar properties (see the discussion on polar functional groups below).

As we learn more about other functional groups, we will add to the list of nonpolar functional groups. Stay alert!

Polar functional groups

Hydroxyl R-OH

A hydroxyl (alcohol group) is an -OH group covalently bonded to a carbon atom. The oxygen atom is much more electronegative than either the hydrogen or the carbon, which will cause the electrons in the covalent bonds to spend more time around the oxygen than around the C or H. Therefore, the O-H and O-C bonds in the hydroxyl group will be polar covalent bonds. Figure 3 depicts the partial charges, δ+ and δ-, that are associated with the hydroxyl group.

Figure 3. The hydroxyl functional group shown here consists of an oxygen atom bound to a carbon atom and a hydrogen atom. These bonds are polar covalent, meaning the electron involved in forming the bonds is not shared equally between the C-O and O-H bonds. Facciotti (own work)

Figure 4. The hydroxyl functional groups can form hydrogen bonds, shown as a dotted line. The hydrogen bond will form between the δ - of the oxygen atom and the δ + of the hydrogen atom. Dipoles are shown in blue arrows. Facciotti (original work)

Hydroxyl groups are very common in biological molecules. Hydroxyl groups appear on carbohydrates (A), on some amino acids (B), and on nucleic acids (C). Can you find any hydroxyl groups in the phospholipid in (D)?

Figure 5. Hydroxyl groups appear on carbohydrates (A, glucose), on some amino acids (B, Serine), and on nucleotides (C, adenosine triphosphate). D is a phospholipid.

Carboxyl R-COOH

Carboxylic acid is a combination of a carbonyl group and a hydroxyl group attached to the same carbon, resulting in new characteristics. The carboxyl group can ionize, which means it can act as an acid and release the hydrogen atom from the hydroxyl group as a free proton (H+). This results in a delocalized negative charge on the remaining oxygen atoms. Carboxyl groups can switch back and forth between protonated (R-COOH) and deprotonated (R-COO-) states depending on the pH of the solution.

The carboxyl group is very versatile. In its protonated state, it can form hydrogen bonds with other polar compounds. In its deprotonated state, it can form ionic bonds with other positively charged compounds. This will have several biological consequences that will be explored more when we discuss enzymes.

Can you identify all the carboxyl groups on the macromolecules shown above in Figure 5?

Amino R-NH3

The amino group consists of a nitrogen atom attached by single bonds to hydrogen atoms. An organic compound that contains an amino group is called an amine. Like oxygen, nitrogen is also more electronegative than both carbon and hydrogen, which results in the amino group displaying some polar character.

Amino groups can also act as bases, which means that the nitrogen atom can bond to a fourth hydrogen atom, as shown in Figure 6. Once this occurs, the nitrogen atom gains a positive charge and can now participate in ionic bonds.

Figure 6. The amine functional group can exist in a deprotonated or protonated state. When protonated, the nitrogen atom is bound to three hydrogen atoms and has a positive charge. The deprotonated form of this group is neutral. Attribution: created by Erin Easlon (own work)

Phosphate R-PO4-

A phosphate group is a phosphorus atom covalently bound to four oxygen atoms and contains one P=O bond and three P-O bonds. The oxygen atoms are more electronegative than the phosphorous atom, resulting in polar covalent bonds. Therefore, these oxygen atoms are able to form hydrogen bonds with nearby hydrogen atoms that also have a δ+(hydrogen atoms bound to another electronegative atom). Phosphate groups also contain a negative charge and can participate in ionic bonds.

Phosphate groups are common in nucleic acids and on phospholipids (the term "phospho" referring to the phosphate group on the lipid). In Figure 7 are images of a nucleotide, deoxyadenosine monphosphate (left), and a phosphoserine (right).

Figure 7. A nucleotide, deoxyadenosine monphosphate, is on the left, and phosphoserine is on the right. Each has a phosphate group circled in red.
Attribution: created by Marc T. Facciotti (own work)


Lecture 03 v2: Basics of Biological Chemistry - Biology

School of Biological Sciences (SBS) at IACS has been founded in May 2018 by reorganization of the erstwhile department of Biological Chemistry as part of the Academic Reform at IACS.

Current research activities at SBS span over a wide-range of biological sciences including cell biology, molecular mechanism of basic cellular processes such as dedifferentiation, neuritogenesis, migration, and cell division coagulation biology /monocytes to macrophage differentiation and cancer signalling, designing and development of task specific functional amphiphiles, gels, vesicles, carbon nanomaterials doped soft nanocomposites, metal nanoparticle doped self-assemblies and other self-assemblies, biocatalysis to biomedicinal applications that includes intracellular cargo (drug/DNA/protein) delivery, biosensing, antimicrobial tissue engineering scaffolds, development of aggregated organic nanoparticle and functionalized carbon dots for biosensing, bio-imaging and drug delivery, developmental biology, to explore the role of tissue rheology in the embryonic development of the zebrafish, role of lipid droplets in the development of zebrafish embryos, development of nucleic acid sensing strategies using bioactive films of Xeno Nucleic Acids (XNAs), and understanding nanoscale biological electron transport, in order to assess the utility of metalloproteins as molecular bioelectronic components, exploring single molecule level structural biology using scanning probe microscopic approach to probe the architecture of protein or protein-nucleic acid supramolecular assemblies, understanding the molecular mechanism of DNA damage response pathways both in the nucleus and mitochondria, to uncover stress induced novel post-translational modification of proteins and evaluate their role in genome maintenance, explore the cellular stress response network with anti-cancer agents in preclinical development self-assembling peptide based functional soft materials for delivering anticancer drugs and biologically important molecules, development of new antibacterial agents based on non-cytotoxic, proteolytically stable peptide gels that are active against both Gram-positive and Gram-negative bacteria and construction of peptide stabilized various metal (gold/silver/copper) nanoclusters with different atomic sizes for cancer cell imaging.


American Sign Language

AMSL-110 American Sign Language I

In this introduction to American Sign Language, students develop visual receptive skills, with a focus on visual memory, visual discrimination, and gestural expressive skills, and learn basic ASL vocabulary and grammatical structures. This course introduces students to the American Deaf Community as a linguistic and cultural minority.

July 07, 2021 - August 13, 2021
Monday Wednesday
06:30 PM - 09:40 PM
ZOOM MEETING

AMSL-111 American Sign Language II

This course continues the work begun in AMSL110 students develop visual receptive skills, with a focus on visual memory, visual discrimination, and gestural expressive skills, and learn basic ASL vocabulary and grammatical structures. Students further their association with the American Deaf Community as a linguistic and cultural minority.

July 07, 2021 - August 13, 2021
Monday Wednesday
06:30 PM - 09:40 PM
ZOOM MEETING


Courses

Introductory survey of macromolecules, cell structure and function, genetics, and molecular biology.

Carolina Core: SCI

Introductory survey of macromolecules, cell structure and function, genetics, and molecular biology. Three lecture hours per week. Restricted to students who have credit for BIOL 101L but lack the lecture.

(Recommended concurrent with BIOL 101). Experimental examination of basic principles of cell biology, genetics and metabolism. Three hours per week.

Carolina Core: SCI

Introductory survey of plant and animal development, physiology, ecology, and evolution.

Carolina Core: SCI

Introductory survey of plant and animal development, physiology, ecology, and evolution. Three lecture hours per week. Restricted to students who have credit for BIOL 102L but lack the lecture.

Experimental examination of structure and function of plant and animal systems, biodiversity, ecology. BIOL 101, 102, 101L and 102L must be completed prior to enrolling in 300-level or above Biology courses.

Carolina Core: SCI

Basic biological concepts and issues for non-biology majors. Credit may not be given for both this course and BIOL 120. Three lecture, two laboratory hours per week.

Carolina Core: SCI

Fundamental principles of human biology. Credit may not be given for both BIOL 110 and BIOL 120. Three lecture hours per week. Not for major credit.

Carolina Core: SCI

Exercises dealing with basic concepts of human biology. Not for major credit.

Carolina Core: SCI

An introduction to plant science for the non-major. This course does not carry major credit, and is not designed as a Plant development, physiology, genetics, evolution, and ecology will be considered. Three lecture hours per week.

Laboratory exercises, demonstrations, and audio-visual supplements to BIOL 200. Not for major credit. Two hours per week.

(Designed for non-major students.) Genetic principles, emphasizing human heredity. Relevance of recent advances in genetics. Three lecture hours per week.

Carolina Core: SCI

Scientific and social issues concerning the interrelationship of culture and agricultural biotic diversity and technology, climate change, resources management, food security, and human health.

Carolina Core: SCI, VSR

This course will ensure that elementary education majors will understand the fundamental concepts of Biology. Cannot be used for biology major credit.

Functional anatomy of the human body and its relation to disease processes. Not for biology major credit.

The principles of anatomy as demonstrated by microscopic studies and animal dissection. Three hours per week.

Fundamentals of functional human biology and knowledge of contemporary medical problems. Not for major credit.

Functional biology of organ systems in the maintenance of the whole organism homeostatic relationships. Not available for biology major credit. Three lecture and three laboratory hours per week.

Functional anatomy and physiology of the human body, including the integumentary, skeletal, muscular, and nervous systems. Not available for biology major credit. Three lecture hours per week.

Carolina Core: SCI

The principles of anatomy and physiology as demonstrated by microscopic studies, animal dissection, and physiological experiments. One three-hour laboratory per week.

Carolina Core: SCI

Functional anatomy and physiology of the human body, including the cardiovascular, endocrine, excretory, reproductive, digestive, and respiratory systems. Not available for biology major credit. Three lecture hours per week.

Carolina Core: SCI

A continuation of BIOL 243L. One three-hour laboratory per week.

Carolina Core: SCI

An introduction to bacteria and viruses, emphasizing structure, metabolism, and pathogenesis. Discussion of infectious diseases, antigen-antibody relationships, and anti-microbial agents in chemotherapy. Not available for biology major credit. Three lecture hours per week.

Not available for biology major credit. Three hours per week.

Physiology of human systems especially susceptible to disturbance: immunobiology, circulation, excretion, metabolism, endocrinology, and muscle physiology. Not for biology major credit. Intended for pharmacy students.

Basic ecological principles and the impacts of human population growth and technology. Not for major credit.

Carolina Core: SCI

Demonstrations, data analyses, discussions, and films relating to human ecology, resource use, and environmental impact. Not for major credit. Two hours per week.

Carolina Core: SCI

Concepts of evolution, populations, and population interactions communities and ecosystems. Three lecture hours per week.

Graduation with Leadership Distinction: GLD: Research

Experiments, exercises, and demonstrations. Three hours per week.

Principles of eukaryotic cell structure, molecular organization, and physiology. Genome organization and expression. Cell growth, division, and cell-cell interactions. Three lecture hours per week.

Graduation with Leadership Distinction: GLD: Research

Experiments, exercises, and demonstrations. Three hours per week.

Basic principles of transmission and molecular genetics quantitative inheritance recombination biochemical aspects of gene function and regulation developmental genetics and population genetics. Three lecture hours per week.

Observational and experimental examination of principles of genetics and inheritance.

Exploration of current careers in the animal industry including a brief overview of the sciences involved in animal production such as genetics and selection, behavior, physiology, reproduction, and nutrition of cattle (beef and dairy), horses, swine, sheep, poultry, and others.

Participation in preparation and teaching of undergraduate biological sciences laboratories.

Experiential Learning: Experiential Learning Opportunity

Contract approved by instructor, advisor, and department head is required for undergraduate students.

Graduation with Leadership Distinction: GLD: Research

Cellular and molecular mechanisms underlying the development and functions of the nervous system, such as nervous system patterning, neuronal differentiation/migration, formation of neuronal projections, development of synapses, apoptosis, refinement of neuronal circuits, and how cells and neurons respond to signals from the environment.

Phylogenetic and comparative aspects of anatomy, reproduction, and embryology of the vertebrates. Three lecture hours and one three-hour laboratory period per week.

Phylogenetic survey of the major plant divisions consideration of the structure and development of flowering plants.

A survey of plants affecting human health and how they are used historically and in modern times, with emphasis on the biologically active constituents.

Basic introduction to plants, including cellular biology, energetics, structure-function relationships, development, nutrition, and diversity.

Illustration of principles of introductory botany and plant physiology using experiments, exercises, and demonstrations. Three laboratory hours per week.

Principles and methods of measuring production in the sea. Emphasis on the ocean’s role in the global carbon budget. Three lecture hours per week. Scheduled field trips are required.

Cross-listed course: MSCI 450

Functional physiology of human organ systems.

Experiments on organ system functions using different animal models.

Structure, function, and development of human anatomy.

Practical exercises in structure, function, and development of anatomy using digital and animal models.

The taxonomy, morphology, metabolism, genetics, and ecology of microorganisms.

Practical exercises with the taxonomy, morphology, metabolism, genetics, and ecology of microorganisms.

Elements of nutrition and animal feeding in veterinary practice. Three lecture hours per week.

Student seminars and a survey of research in the fields of Biological Sciences.

Methodologies of biological research with emphasis on hypothesis formation, research design, and data collection, and current issues in biology. Two lecture and six laboratory hours per week.

Graduation with Leadership Distinction: GLD: Research

An overview of the microbial world including a survey of the distribution, functioning, and diversity of microorganisms in natural systems. Discusses the crucial roles that microorganisms play in ecosystem function, biogeochemical cycles, and environmental quality.

Cross-listed course: MSCI 503

An introduction to how cell-cell communication, gene expression, cell division, cytoskeletal dynamics, and interactions with the extracellular matrix result in the differentiation, pattern formation, morphogenesis, and growth necessary to generate a new individual.

Descriptive and experimental exercises related to embryology. One three-hour laboratory per week.

Molecular aspects of development from gamete formation through tissue and organ differentiation in plants and animals. Three lecture hours per week.

A series of experimentally oriented laboratory exercises will be performed. One three-hour laboratory per week.

Phylogenetic and comparative aspects of anatomy, physiology, reproduction, and embryology of the invertebrates.

Cross-listed course: MSCI 510

Graduation with Leadership Distinction: GLD: Research

Descriptive and molecular examination of the processes and mechanisms used by plants in organogenesis, differentiation, and morphogenesis. Three lecture hours per week.

Experiments utilizing a genetic approach to the study of plant development. Three laboratory hours per week.

Taxonomy and morphology of fungi cultivation, life histories, and economic importance all classes and major orders considered. Three lecture hours per week. .

Diversity, distribution, physiology, ecology, evolution, and economic importance of marine algal, seagrass, and mangrove communities. Three lecture and three laboratory hours per week. Scheduled field trips are required.

Cross-listed course: MSCI 525

Two lecture and four laboratory hours per week.

Two lecture and four laboratory hours per week.

Two lecture and four laboratory hours per week.

An introduction to the tissues that make up the human body. The microscopic anatomy of tissues is examined and discussed in terms of function and physiology. Three lecture hours and four laboratory hours per week.

Parasites of biological, economic, and public health importance. Three lecture and three laboratory hours per week.

Cross-listed course: ENHS 661, EPID 661

A comparative survey of behavior patterns of animals from protists to humans and the physiological mechanisms underlying behavior.

Observational and experimental methods used in classifying animal behavior patterns and in determining underlying control mechanisms. One three-hour laboratory per week.

Management and conservation of aquatic and marine resources, with emphasis on fisheries. Data procurement and analysis commercial and recreational fisheries sociological, political, legal, and environmental factors that affect fishery management and fish biodiversity.

Cross-listed course: MSCI 535

Phylogeny, morphology, behavior, and ecology of fishes. Three lecture and 3 laboratory hours plus three field trips to be arranged.

Cross-listed course: MSCI 536

Graduation with Leadership Distinction: GLD: Research

Introduction to the practical and scientific aspects of the commercial culture of freshwater and marine organisms. Three lecture hours per week. One all-day field trip required.

Cross-listed course: MSCI 537

The identification of behavioral adaptations of estuarine and marine organisms: their ecology, physiology, development, and evolutionary history field observations.

Cross-listed course: MSCI 538

Graduation with Leadership Distinction: GLD: Research

Description of biological macromolecules and major metabolic pathways.

Cross-listed course: CHEM 550

Experiments and demonstrations illustrating the principles of biochemistry. Three laboratory hours per week.

Cross-listed course: CHEM 550L

An integrative and comparative study of the structure, function, and evolution of the physiological systems of animals. Three lecture hours per week.

Laboratory exercises to illustrate principles from BIOL 543. Three hours per week.

Essentials of modern biochemistry. First semester of a two-semester course. Three lecture hours per week.

Cross-listed course: CHEM 555

Essentials of modern biochemistry and molecular biology. Three lecture hours per week.

Cross-listed course: CHEM 556

A general survey of the major physiological processes in plants. Two lecture and four laboratory hours per week.

Introduction to bacteria and viruses emphasizing ultrastructure, physiology, genetics, and growth. Discussion of public health, industrial, and environmental microbiology. Three lecture hours per week.

Graduation with Leadership Distinction: GLD: Research

Three laboratory hours per week.

An introduction to the principles of population genetics, with emphasis on the origin, maintenance, and significance of genetic variation in natural populations.

Cross-listed course: MSCI 552

Graduation with Leadership Distinction: GLD: Research

Current concepts and applications of genomics, addressing questions from throughout biological inquiry.

Discussion of how physiological factors, like nutritional status, influence systemic signals to alter stem cell activity, and the physiological stimuli that impact stem cell activity in a variety of organisms (from worms to humans).

Interactions of organisms and the environment ecosystem structure and functions. Three lecture hours per week.

Principles of conservation biology. Importance of biodiversity, causes of decline and extinction, and restoration and conversation policy in terrestrial and aquatic ecosystems. 03: 07/05/2019.

Cross-listed course: ENVR 571

Quantitative study of the population, community and evolutionary ecology of freshwater habitats (lakes, ponds, rivers, streams, wetlands). Includes mandatory field trips.

Cross-listed course: ENVR 572

Exploration of how human activities affect marine natural populations, species, communities and ecosystems, including threats to biodiversity approaches to marine conservation and ecological and evolutionary responses to anthropogenic disturbance. 03: 07/05/2019.

Cross-listed course: MSCI 574

Structure, dynamics, and interactions between populations and communities in marine ecosystems. Attendance at designated departmental seminars is required. Three lecture hours per week.

Cross-listed course: MSCI 575

Laboratory and field exercises in coastal environments.

Cross-listed course: MSCI 575L

Interdisciplinary examination of the distribution, reproduction, survival, and historical variation of the principal commercial marine fisheries. 03: 07/05/2019.

Cross-listed course: MSCI 576

Structure, productivity, and biodiversity of coral reefs, emphasizing their sensitivity, stability, and sustainability. Taught as an extended field experience with daily lectures and guided research activities.

Cross-listed course: MSCI 577

This course focuses on quantitative knowledge for interdisciplinary applications in genetics as well as hands-on experience in analyzing genetic data. In this course, students will have programming exercises in using analysis tools to conduct genome-wide analysis, annotation, and interpretation of genetic data using R/Bioconductor packages.

Cross-listed course: STAT 588

Current developments in biological sciences. Readings and research on selected topics. Course content varies and will be announced in the schedule of classes by title.

Survey of current concepts regarding the molecular and genetic factors that regulate the origin and progression of cancer. Readings based on current primary literature.

Advanced study of viruses with regard to biochemical, molecular, pathological, epidemiological, and biotechnological aspects. Focus on animal viruses with particular emphasis on human pathogens.

Focuses on the understanding of how stem cells can be used to make fundamental biological discoveries with a special focus in neuroscience.

Basic immunological concepts including antibody structure, function, and genetics cellular immunology transplantation hypersensitivity autoimmunity and immunity to infectious diseases.

Advanced study of infectious diseases caused by fungi. Etiology, symptoms, and treatment of fungi related illnesses.

Cross-listed course: ENHS 625

Examines the physiology and ecology of phytoplankton, including environmental controls on community composition, primary productivity, and detection and characterization of water quality (eutrophication) and harmful algal blooms.

Cross-listed course: MSCI 627

Biology of birds at molecular, organismal, and population levels, emphasizing unique adaptations of the class of Aves.

Advances in molecular and cellular neurobiology that bring new understanding for human neurological disease.

Descriptive and experimental aspects of the neural basis of behavior, emphasizing cellular and molecular mechanisms. Two lecture and six laboratory hours per week. Three lecture hours per week.

Interactions of microorganisms with each other, with more complex organisms, and with their environments. Three lecture hours per week.

This course examines how the mechanisms by which animals and plants interact with their physical environments influence organismal physiology.

Advanced study of related aspects of biological evolution. Rose of life from physical and chemical precursors, biochemical basis of adaptation to ecological pressures, and biochemical aspects of the origins and maintenance of biodiversity.

A study of the aquatic environment and its biota. Three lecture and four laboratory hours per week.

An advanced course in evolutionary biology, including natural selection, neutral evolution, molecular evolution population genetics, quantitative genetics, sexual selection, speciation, human evolution, and the evolution of disease.

Studies of the principles of genetics and molecular biology as applied to adaptive evolution of genes and genomes.

Speciation as the source of biological diversity. Historical and biological viewpoints. Analysis of concepts of species and models of speciation. Two lectures and one recitation per week.

Studies in molecular biology and genetics with emphasis on the use of newly developed techniques in biotechnology. Three lecture hours per week.

Techniques used in biotechnology will be employed in the context of an experimental project. Twelve laboratory hours per week.

Evolution, systematics, genetics, ecology, and adaptation of mammals. Emphasis on native South Carolina species. Two lectures and one two-hour laboratory per week, plus five field trips to be arranged.

Signaling pathways involved in human diseases, such as cancer, AIDS, autoimmune diseases and diabetes, and cellular processes involving apoptosis, cell cycle, cell-cell adhesion, growth factors, hormones, G protein-couples receptors, cytokines and immune response.

Molecular mechanisms underlying gene action and differentiation in man the genetic bases for human variability and inborn metabolic errors leading to inherited diseases.

An advanced examination of the molecular mechanisms underlying gene action in humans. Current literature illustrating the genotype-phenotype relationship in human disease pathogenesis will be discussed.

Core concepts of biochemistry as applied to human health and disease.

Cross-listed course: CHEM 655

Structure and dynamics of plant populations and communities, including life histories, adaptations, and plant interactions. Three lecture hours per week.

Laboratory and field exercises in plant ecology. Four hours per week.

Physiological, molecular, and genetic examination of induced plant responses to various biotic and abiotic environmental stresses.

Theoretical and practical aspects of scanning and transmission electron microscopy, digital image acquisition and energy dispersive x-ray spectroscopy. Two lecture and one laboratory hour per week, plus a research project to be arranged.


Lecture 03 v2: Basics of Biological Chemistry - Biology

Zoom Link for Class Sessions [LINK]

LECTURE SUMMARIES

Lecture 1 (Jan 25): Overview of Molecular Modeling [PDF] [MP4]

Lecture 2 (Jan 27): Introduction to Molecular Mechanics I [PDF] [MP4]

Lecture 3 (Feb 01): Introduction to Molecular Mechanics II [MP4]

Lecture 4 (Feb 03): Potential Energy Surfaces & Optimization Methods [PDF] [MP4]

Lecture 5 (Feb 08): Basics of Molecular Dynamics Simulation I [PDF] [MP4]

Lecture 6 (Feb 10): Basics of Molecular Dynamics Simulation II [MP4]

Lecture 7 (Feb 15): Computing Properties from Molecular Dynamics I [PDF] [MP4]

Lecture 8 (Feb 17): Computing Properties from Molecular Dynamics II [MP4]

Lecture 9 (Feb 22): Introduction to Monte Carlo Methods I [PDF] [MP4]

Lecture 10 (Feb 24): Introduction to Monte Carlo Methods II [MP4]

Lecture 11 (Mar 01): Methods for Free Energy Calculations [PDF] [MP4]

Lecture 12 (Mar 03): Proteins I: Amino Acids & Secondary Structure [PDF] [MP4]

Lecture 13 (Mar 08): Proteins II: Tertiary Structure, Motifs & Fold Classes [PDF] [MP4]

Lecture 14 (Mar 10): Proteins III: Mechanism of Protein Folding [PDF] [MP4]

Lecture 15 (Mar 15): Electrostatics & Solvation in Biomolecular Systems I [PDF] [MP4]

Lecture 16 (Mar 17): Electrostatics & Solvation in Biomolecular Systems II [MP4]

Lecture 17 (Mar 22): Basics of ab Initio Molecular Orbital Theory I [PDF] [MP4]

Lecture 18 (Mar 24): Basics of ab Initio Molecular Orbital Theory II [MP4]

Lecture 19 (Mar 29): Methods for Treating Electron Correlation [PDF] [MP4]

Lecture 20 (Mar 31): Semi-Empirical Molecular Orbital Methods [PDF] [MP4]

Lecture 21 (Apr 05): Density Functional Theory I [PDF] [MP4]

Lecture 22 (Apr 07): Density Functional Theory II [MP4]

Lecture 23 (Apr 12): QM/MM Methods Frontier Orbital Theory [PDF]

Lecture 24 (Apr 14): Protein Structure Prediction, Engineering & Design [PDF] [MP4]

Lecture 25 (Apr 19): Small Molecule & Protein Docking I [PDF] [MP4]

Lecture 26 (Apr 21): Small Molecule & Protein Docking II [MP4]

Lecture 27 (Apr 26): Computing Binding Rate Constants via Brownian Dynamics [PDF] [MP4]

Lecture 28 (Apr 28): Introduction to Convolutional Neural Networks [PDF] [MP4]

Lecture 29 (May 03): Machine Learning in Computational Chemistry [PDF] [MP4]

READINGS & REFERENCES

Introduction to Using a Linux Terminal Window

Unix for the Beginning Mage, J. Topjian [PDF]

Perspectives on Molecular Modeling

Biomolecular Modeling: Goals, Problems, Perspectives,
W. F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen,
X. Daura, P. Gee, D. P. Geerke, A. Glattli, P. H. Hunenberger, M. A. Kastenholz,
C. Oostenbrink, M. Schenk, D. Trzesniak, N. F. A. van der Vegt and H. B. Yu,
Angewandte Chemie International Edition, 45 , 4064-4092 (2006) [PDF]

Biomolecular Modeling and Simulation: A Field Coming of Age,
T. Schlick, R. Collepardo-Guevara, L. A. Halvorsen, S. Jung and X. Xiao,
Quarterly Reviews of Biophysics, 44 , 191-228 (2011) [PDF]

Molecular Mechanics & Force Fields

Empirical Force Field Models, Chapter 4 from Molecular Modelling:
Principles & Applications, 2nd Edition by A. R. Leach, [PDF]

Biomolecular Force Fields: Where Have We Been, Where Are We Now,,
Where Do We Need To Go and How Do We Get There?, P. Dauber-Osguthorpe
and A. T. Hagler, Journal of Computer-Aided Molecular Design, 33 , 133-203 (2019) [PDF]

Force Field Development Phase II: Relaxation of Physics-Based
Criteria. or Inclusion of More Rigorous Physcs Into the Representation
of Molecular Physics, A. T. Hagler, Journal of Computer-Aided Molecular
Design, 33 , 205-264 (2019) [PDF]

Nonlinear Optimization Methods

Energy Minimization & Related Methods, Chapter 5 from Molecular
Modelling: Principles & Applications, 2nd Edition by A. R. Leach, [PDF]

Optimization Methods in Computational Chemistry, T. Schlick,
Reviews in Computational Chemistry, 3 , 1-71 (1992) [PDF]

Molecular Dynamics Simulation

Simulation Methods & Molecular Dynamics, Chapter 6 & 7 from Molecular
Modelling: Principles & Applications, 2nd Edition by A. R. Leach, [PDF]

Molecular Dynamics, J. Meller,
Encyclopedia of Life Sciences, 1-8 (2001) [PDF]

Introduction to Molecular Dynamics Simulation, M. P. Allen,
Computational Soft Matter, NIC Series, 23 , 1-28 (2004) [PDF]

Molecular Dynamics: Survey of Methods for Simulating
the Activity of Proteins, S. A. Adcock and J. A. McCammon,
Chemical Reviews, 106 , 1589-1615 (2006) [PDF]

History of the Monte Carlo Method

Equation of State Calculations by Fast Computing Machines,
N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller
and E. Teller, Journal of Chemical Physics, 21, 1087-1092 (1953) [PDF]

Perspectives on "Equation of State Calculations by Fast Computing
Machines", W. L. Jorgensen, Theoretical Chemistry Accounts,
103, 225-227 (2000) [PDF]

The Beginning of the Monte Carlo Method,
N. Metropolis, Los Alamos Science, 14, 125-130 (1987) [PDF]

Scientific Uses of the MANIAC, H. L. Anderson,
Journal of Statistical Physics, 43, 731-748 (1986) [PDF]

Monte Carlo Theory and Algorithms

Monte Carlo Simulation Methods, Chapter 8 from Molecular Modelling:
Principles & Applications, 2nd Edition by A. R. Leach, [PDF]

Progress and Outlook in Monte Carlo Simulations, D. N. Theodorou,
Industrial & Engineering Chemistry Research, 49 , 3047-3058 (2010) [PDF]

Monte Carlo Simulations, D. J. Earl and M. W. Deem,
Methods in Molecular Biology, 443 , 25-36 (2008) [PDF]

Monte Carlo Codes, Tools and Algorithms, D. Dubbledam, A. Torres-Knoop
and K. S. Walton, Molecular Simulation, 39 , 1253-1292 (2013) [PDF]

Free Energy Calculations

Free Energy Calculations, Chapter 11 from Molecular Modelling:
Principles & Applications, 2nd Edition by A. R. Leach, [PDF]

Free Energy Calculations in Structure-Based Drug Design, M. R. Shirts,
D. L. Mobley and S. P. Brown, Chapter 5 from Drug Design: Structure- and
Ligand-Based Approaches, by K. M. Merz Jr., D. Ringe and C. H. Reynolds [PDF]

Towards Accurate Free Energy Calculations in Ligand
Protein-Binding Studies, T. Steinbrecher and A. Labahn,
Current Medicinal Chemistry, 17 , 767-785 (2010) [PDF]

Efficient Estimation of Free Energy Differences from Monte Carlo Data,
C. H. Bennett, Journal of Computational Physics, 22 , 245-268 (1976) [PDF]

Accurate Calculation of the Absolute Free Energy of Binding for Drug
Molecules, M. Aldeghi, A. Heifetz, M. J. Bodkin, S. Knapp and P. C. Biggin,
Chemical Science, 7 , 207-218 (2016) [PDF]

Biomolecular Electrostatics and Solvation

Poisson's Equation in Electrostatics, J.-L. Liu, March 2011 [PDF]

Semianalytical Treatment of Solvation for Molecular Mechanics and
Dynamics, W. C. Still, A. Tempczyk, R. C. Hawley and T. Hendrickson,
Journal of the American Chemical Society, 112 , 6127-6129 (1990) [PDF]

Computational Methods for Biomolecular Electrostatics, F. Dong,
B. Olsen and N. A. Baker, Methods in Cell Biology, 84 , 843-870 (2008) [PDF]

Biomolecular Electrostatics and Solvation: A Computational Perspective,
P. Ren, J. Chun, D. G. Thomas, M. J. Schnieders, M. Marcho, J. Zhang
and N. A. Baker, Quarterly Reviews of Biophysics, 45 , 427-491 (2012) [PDF]

Classical Electrostatics for Biomolecular Simulations, G. A. Cisneros,
M. Karttunen, P. Ren and C. Sagui, Chemical Reviews, 114 , 779-814 (2014) [PDF]

Ab Initio Molecular Orbital Theory

Computational Quantum Mechanics & Advanced ab Initio Methods,
Chapters 2 & 3 from Molecular Modeling, 2nd Edition by A. R. Leach [PDF]

Proof of the Variational Theorem, Appendix B from
Introduction to Computational Chemistry, 2nd Edition, by F. Jensen,
John Wiley & Sons, Chichester UK, 2007 [PDF]

Derivation of the Hartree-Fock Equation, Appendix 7 from
Quantum Chemistry, 3rd Edition, by J. P. Lowe and K. A. Peterson,
Elsevier Academic Press, Amsterdam, 2006 [PDF]

The RHF Dissociation Problem, Section 4.3 from Introduction
to Computational Chemistry, 2nd Edition, by F. Jensen,
John Wiley & Sons, Chichester UK, 2007 [PDF]

The Difference Between Configuration Interaction & Coupled Cluster,
Chemistry Stack Exchange Online, February 2017 [PDF]

Derivation of Moeller-Plesset Perturbation Theory,
Gaussian, Inc., 2015-2018 [PDF]

Approximate Molecular Orbital Methods

The Extended Huckel Method, Chapter 10 from
Quantum Chemistry, 3rd Edition by J. P. Lowe and K. A. Peterson [PDF]

Basic Theory of the FMO Method, Chapters 2 & 3
from Frontier Orbitals, by N. T. Anh [PDF]

Klopman-Salem Equation, taken from the Wikipedia page [PDF]

Role of Frontier Orbitals in Chemical Reactions, K. Fukui,
Science, 218 , 747-754 (1982) [Nobel Prize Award Lecture] [PDF]

An Examination of the Nature of Localized Molecular Orbitals and
their Value in Understanding Phenomena that Occur in Organic Chemistry,
J. J. P. Stewart, Journal of Molecular Modeling, 25 , 7 (2019) [PDF]

Density Functional Theory

DFT in a Nutshell, K. Burke and L. O. Wagner,
International Journal of Quantum Chemistry, 113 , 96-101 (2013) [PDF]

An Introduction to Density Functional Theory,
N. M. Harrison, Department of Chemistry, Imperial College, London [PDF]

Obituary: Density Functional Theory (1927-1993), P. M. W. Gill,
Australian Journal of Chemistry, 54 , 661-662 (2001) [PDF]

Density Functional Theory (DFT), Hartree-Fock (HF), and
the Self-Consistent Field, P. M. W. Gill,
Encyclopedia of Computational Chemistry, 1 , 678-689 (1998) [PDF]

Perspective: Fifty Years of Density-Functional Theory
in Chemical Physics, A. D. Becke,
Journal of Chemical Physics, 140 , 18A301 (2014) [PDF]

Can Orbitals Really Be Observed? [Warning! Philosophy. ]

Can Orbitals Really Be Observed in Scanning Tunneling
Microscopy Experiments, B. Q. Pham and M. S. Gordon,
Journal of Physical Chemistry A, 121 , 4851-4852 (2017) [PDF]

Are Orbitals Observable?, P. Mulder,
International Journal for Philosophy of Chemistry, 17 , 24-35 (2011) [PDF]

Measuring Orbitals: Provocation or Reality?, W. H. E. Schwarz,
Angewandte Chemie International Edition, 45 , 1508-1517 (2006) [PDF]

Comparative & Homology Modeling

Protein Structure Modeling with MODELLER, B. Webb and A. Sali,
Methods in Molecular Biology, 1654 , 39-54 (2017) [PDF]

SWISS-MODEL: Homology Modelling of Protein Structures and Complexes,
A. Waterhouse, M. Bertoni, S. Beinert, G. Studer, G. Tauriello,
R. Gumienny, F. T. Heer, T. A. P. de Beer, C. Rempfer, L. Bordoli,
R. Lepore and T. Schwede, Nucleic Acids Research, 46 , W296-303 (2018) [PDF]

The Phyre2 Web Portal for Protein Modeling, Prediction and Analysis,
L. A. Kelley, S. Mezulis, C. M. Yates, M. N. Wass and M. J. E. Sternberg,
Nature Protocols, 10 , 845-858 (2015) [PDF]

Molecular Docking Methods

Challenges and Advances in Computational Docking: 2009 in Review,
E. Yurlev, M. Agostino and P. A. Ramsland,
Journal of Molecular Recognition, 24 , 149-164 (2011) [PDF]

Protein-Ligand Docking in the New Millennium - A Retrospective of 10
Years in the Field, S. F. Sousa, A. J. M Ribeiro, J. T. S. Coimbra,
R. P. P. Neves, S. A. Martins, N. S. H. N. Moorthy, P. A. Fernandes and
M. J. Ramos, Current Medicinal Chemistry, 20 , 2296-2314 (2013) [PDF]

Molecular Docking and Structure-Based Drug Design Strategies,
L. G. Ferreira, R. N. dos Santos, G. Oliva and A. D. Andricopulo,
Molecules, 20 , 13384-13421 (2015) [PDF]

Software for Molecular Docking: A Review, N. S. Pagadala,,
K. Syed and J. Tuszynski, Biophysical Reviews, 9 , 91-102 (2017) [PDF]

Progress in Molecular Docking, J. Fan, A. Fu and L. Zhang,
Quantitative Biology, 7 , 83-89 (2019) [PDF]

AutoDock Search and Scoring Methodology

Automated Docking Using a Lamarckian Genetic Algorithm and an
Empirical Binding Free Energy Function, G. M. Morris, D. S. Goodsell,
R. S. Halliday, R. Huey, W. E. Hart, R. K. Belew and A. J. Olsen,
Journal of Computational Chemistry, 19 , 1639-1662 (1998) [PDF]

A Semiempirical Free Energy Force Field with Charge-Based Desolvation,
R. Huey, G. M. Morris, A. J. Olsen and D. S. Goodsell,
Journal of Computational Chemistry, 28 , 1145-1152 (2007) [PDF]

AutoDock Vina: Improving the Speed and Accuracy of Docking with a New
Scoring Function, Efficient Optimization, and Multithreading, O. Trott
and A. J. Olson, Journal of Computational Chemistry, 31 , 455-461 (2010) [PDF]

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly
Specified Binding Site Flexibility, P. A. Ravindranath, S. Forli,
D. S. Goodsell, A. J. Olson and M. F. Sanner,
PLoS Computational Biology, 11 , e1004586 (2015) [PDF]

Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms
Better Binding Affinity, N. T. Nguyen, T. H. nguyen, T. N. H. Pham,
N. T. Huy, M. V. Bay, M. Q. Pham, P. C. Nam, V. V. Vu and S. T. Ngo,
Journal of Chemical Information and Modeling, 60 , 204-211 (2020) [PDF]

Brownian Dynamics Simulation

Biological Applications of Electrostatic Calculations
and Brownian Dynamics Simulations, J. D. Madura, M. E. Davis,
M. K. Gilson, R. C. Wade, B. A. Luty and J. A. McCammon,
Reviews in Computational Chemistry, 4 , 229-267 (1994) [PDF]

Brownian Dynamics, Molecular Dynamics, and Monte Carlo
Modeling of Colloidal Systems, J. C. Chen and A. S. Kim,
Advances in Colloid and Interface Science, 112 , 159-173 (2004) [PDF]

Brownian Dynamics Simulations of Biological Molecules,
G. A. Huber and J. A. McCammon, Trends in Chemistry, 1 , 727-738 (2019) [PDF]

Convolutional Neural Networks

Simple Introduction to Convolutional Neural Networks,
M. Stewart, Towards Data Science, February 2019 [PDF]

Basic Introduction to Convolutional Neural Network,
H. S. Chatterjee, Towards Data Science, July 2019 [PDF]

A Quick Introduction to Neural Networks,
U. J. J. Walkarn, The Data Science Blog, August 2016 [PDF]

An Intuitive Explanation of Convolutional Neural Networks,
U. J. J. Walkarn, The Data Science Blog, August 2016 [PDF]

Applications of Neural Networks

Fast and Accurate Modeling of Molecular Atomization Energies
with Machine Learning, M. Rupp, A. Tkatchenko, K.-R. Muller
and O. A. von Lilienfeld, Physical Review Letters, 108 , 058301 (2012) [PDF]

Bypassing the Kohn-Sham Equations with Machine Learning,
F. Brockherde, L. Vogt, L. Li, M. E. Tuckerman, K. Burke
and K.-R. Muller, Nature Communications, 8 , 872 (2017) [PDF]

ANI-1: An Extensible Neural Network Potential with DFT Accuracy
at Force Field Computational Cost, J. S. Smith, O. Isayev
and A. E. Roitberg, Chemical Science, 8 , 3192-3203 (2017) [PDF]

SchNet - A Deep Learning Architecture for Molecular and Materials,
K. T. Schutt, H. E. Sauceda, P.-J. Kindermans, A. Tkatchenko
and K.-R. Muller, Journal of Chemical Physics, 148 , 241722 (2018) [PDF]

Improved Protein Structure Prediction Using Potentials from Deep Learning,
A. W. Senior, R. Evans, J. Jumper, J. Kirkpatrick, L. Sifre, T. Green,
C. Qin, A. Zidek, A. W. R. Nelson, A. Bridgland, H. Penedones, S. Petersen,
K. Simonyan, S. Crossan, P. Kohl, D. T. Jones, D. Silver, K. Kavukcuoglu
and D. Hassabis, Nature, 577 , 706-710 (2020) [PDF]

News in Focus - "It Will Change Everything": AI Makes
Gigantic Leap in Solving Protein Structures, E. Callaway,
Nature, 588 , 203-204 (2020) [PDF]

CASP14: What Google DeepMind's AlphaFold2 Really Achieved,
and What It Means for Protein Folding, Biology and Bioinformatics,
C. O. Rubiera, Oxford Protein Informatics Group, December 2020 [PDF]

SOFTWARE RESOURCES

General Information

How to Install Non-AppStore Programs on macOS [PDF]

How to Disable the (Annoying!) Gatekeeper on macOS [PDF]

Avogadro & Avogadro2: Molecular Editors

Avogadro 1.2.0 Software for macOS [DMG]

Avogadro 1.2.0 Software for Windows [EXE]

Avogadro2 1.91 Software for macOS [DMG]

Avogadro2 1.91 Software for Windows [EXE]

Chimera: Extensible Molecular Modeling System

Chimera 1.15 Software for macOS [DMG]

Chimera 1.15 Software for Windows [EXE]

Chimera 1.15 Software for Linux [BIN]

ChimeraX: Next-Generation of Chimera Software

ChimeraX 1.1 Software for macOS [DMG]

ChimeraX 1.1 Software for Windows [EXE]

ChimeraX 1.1 Software for Ubuntu Linux [DEB]

ChimeraX 1.1 Software for RedHat Linux [RPM]

ChimeraX 1.1 Software for Generic Linux [GZIPPED TAR]]

PyMOL: Python-Enhanced Molecular Graphics

PyMOL 1.7.4.5 Software for macOS [DMG]

PyMOL 1.7.4.5 Software for Windows [MSI]

PyMOL 1.7.4.5 Software for Linux [GZIPPED TAR]

VMD: Visual Molecular Dynamics

VMD 1.9.4 Software for macOS (10.10 thru 10.13) [DMG]

VMD 1.9.4 Software for macOS (10.15, Catalina) [DMG]

VMD 1.9.4 Software for macOS (11, Big Sur, Intel) [DMG]

VMD 1.9.4 Software for macOS (11, Big Sur, Apple M1) [DMG]

VMD 1.9.4 Software for Windows [EXE]

VMD 1.9.4 Software for Linux [GZIPPED TAR]

Spartan Student Molecular Modeling

Spartan Student V6 Software for macOS [DMG]

Spartan Student V6 Software for Windows [EXE]

Spartan Student V7 Software for macOS [DMG]

Spartan Student V7 Software for Windows [EXE]

Spartan Student V8 Software for macOS [DMG]

Spartan Student V8 Software for Windows [EXE]

Walking Through Spartan Student (input file for tutorial) [Input]

Tinker: Software Tools for Molecular Design

Tinker 8.8.3 Software for macOS [GZIPPED TAR]

Tinker 8.8.3 Software for Windows [ZIP]

Tinker 8.8.3 Software for Linux [GZIPPED TAR]

FFE: Force Field Explorer

Force Field Explorer 8.7.2 Software for macOS [DMG]

Force Field Explorer 8.7.2 Software for Windows [ZIP]

Force Field Explorer 8.7.2 Software for Linux [GZIPPED SH]

Force Field Explorer Manual [PDF]

APBS: Adaptive Poisson-Boltzmann Solver

APBS 1.3 Software for macOS [GZIPPED TAR]

APBS 1.3 Software for Windows [ZIP]

APBS 1.3 Software for Linux [GZIPPED TAR]

Using PDB2PQR Documentation [HTML]

Gaussian Quantum Chemistry

Gaussian 16 Online Manual [HTML]

GaussView 6 Online Manual [HTML]

Modeller: Comparative Protein Structure Modeling

Modeller 9.21 Software for macOS [DMG]

Modeller 9.21 Software for Windows [ZIP]

Modeller 9.21 Software for Linux (Ubuntu & Debian) [DEB]

Modeller 9.21 Software for Linux (RedHat & CentOS) [RPM]

Modeller 9.21 Installation Instructions [PDF]

Chimera Interface to Modeller [PDF]

Tutorial: Modeling Based on a Single Template [PDF] Files [GZIPPED TAR]

Tutorial: Multiple Templates, Loop Refinement & User Restraints [PDF]

Tutorial: The Alignment-Modeling-Evaluation Cycle [PDF]

Tutorial: Modeling a Sequence after Fold Assignment [PDF]

Tutorial: Use of Cryo-EM Data in Modeling [PDF]

AutoDock4 & MGLTools: Automated Molecular Docking

AutoDock 4.2.6 Software for macOS [TAR]

AutoDock 4.2.6 Software for Windows [ZIP]

AutoDock 4.2.6 Software for Linux [TAR]

AutoDock 4.2.6 Installation for Linux & macOS [PDF]

AutoDock 4.2.6 Installation for Windows [PDF]

MGLTools 1.5.7 Software for macOS (10.14 & earlier only!) [DMG]

MGLTools 1.5.7 Software for Windows [ZIP]

MGLTools 1.5.7 Software for Linux [SCRIPT]

XQuartz 2.7.11 for MacOS (needed by MGLTools on Mac) [DMG]

Tutorial: Docking Indinavir to HIV Protease [PDF]

Tutorial: Docking of BACE1 with an Inhibitor [PDF]

SDA7: Simulation of Diffusional Association

LABORATORY PROJECTS

Suggested Lab Report Format [PDF]

Lab 1 (Jan 29): Unix Tutorial Using Chimera, VMD, FFE & Spartan [Files]

Lab 2 (Feb 05): Conformational Analysis of Alanine Dipeptide [Files]

Lab 3 (Feb 12): Liquid Properties via Molecular Dynamics Simulation [Files]

Lab 4 (Feb 19): Global Optimization of Lennard-Jonesium & Polyalanine [Files]

Lab 5 (Feb 26): Relative Hydration Free Energy of Monovalent Ions [Files]

Lab 6 (Mar 05): Folding Simulations of the TrpCage MiniProtein [Files]

Lab 7 (Mar 19): APBS Poisson-Boltzmann Calculations on Lysozyme [Files]

Lab 8 (Apr 02): Computing the Rotational Barrier in Hydrazine [Files]

Lab 9 (Apr 09): Frontier Molecular Orbital Analysis of Regioselectivity [Files]

Lab 10 (Apr 16): Homology Modeling of a Lactate Dehydrogenase [Files]

Lab 11 (Apr 23): Docking Indinavir to HIV Protease Using AutoDock [Files]

Lab 12 (Apr 30): Diffusional Association of the Barnase-Barstar Complex [Files]


Collin College

BIOL 1322 Nutrition and Diet Therapy
This course introduces general nutritional concepts in health and disease and includes practical applications of that knowledge. Special emphasis is given to nutrients and nutritional processes including functions, food sources, digestion, absorption, and metabolism. Food safety, availability, and nutritional information including food labels, advertising, and nationally established guidelines are addressed. 3 credit hours. (A)

BIOL 1323 Nutrition and Diet Therapy II
Applications of nutrition principles and techniques of nutrition care for healthy individuals and patients/clients at nutritional risk. Nutrition risk screening, interviewing/counseling methods, diet evaluation, basic diet calculations, and documentation. 3 credit hours. (A)

BIOL 1406 Biology for Science Majors I
Lecture: Fundamental principles of living organisms will be studied, including physical and chemical properties of life, organization, function, evolutionary adaptation, and classification. Concepts of cytology, reproduction, genetics, and scientific reasoning are included. Lab: Laboratory activities will reinforce the fundamental principles of living organisms, including physical and chemical properties of life, organization, function, evolutionary adaptation, and classification. Study and examination of the concepts of cytology, reproduction, genetics, and scientific reasoning are included. Lab required. Prerequisites: TSI Math score of 910-949 with a diagnostic score of 5, and TSI college-readiness standard for Reading and Writing or equivalent. 4 credit hours. (A)

BIOL 1407 Biology for Science Majors II
Lecture: The diversity and classification of life will be studied, including animals, plants, protists, fungi, and prokaryotes. Special emphasis will be given to anatomy, physiology, ecology, and evolution of plants and animals. Lab: Laboratory activities will reinforce study of the diversity and classifications of life, including animals, plants, protists, fungi, and prokaryotes. Special emphasis will be given to anatomy, physiology, ecology, and evolution of plants and animals. Lab required. Prerequisite: BIOL 1406. 4 credit hours. (A) Note: This course includes dissection in lab.

BIOL 1408 Biology for Non-Science Majors I
Lecture: Provides a survey of biological principles with an emphasis on humans, including chemistry of life, cells, structure, function, and reproduction. Lab: Laboratory activities will reinforce a survey of biological principles with an emphasis on humans, including chemistry of life, cells, structure, function, and reproduction. Lab required. 4 credit hours. (A)

BIOL 1409 Biology for Non-Science Majors II
Lecture: This course will provide a survey of biological principles with an emphasis on humans, including evolution, ecology, plant and animal diversity, and physiology. Lab: Laboratory activities will reinforce a survey of biological principles with an emphasis on humans, including evolution, ecology, plant and animal diversity, and physiology. Lab required. Prerequisite: BIOL 1408. 4 credit hours. (A) Note: This course includes dissection in lab.

BIOL 1414 Introduction to Biotechnology I
Overview of classical genetics, DNA structure, the flow of genetic information, DNA replication, gene transcription, protein translation. Principles of molecular biology and genetic engineering techniques, including restriction enzymes and their uses, major types of cloning vectors, construction of libraries, Southern and Northern blotting, hybridization, PCR, DNA typing. Applications of these techniques in human health and welfare, medicine, agriculture and the environment. Introduction to the human genome project, gene therapy, molecular diagnostics, forensics, creation and uses of transgenic plants and animal and animal cloning and of the ethical, legal, and social issues and scientific problems associated with these technologies. Relevant practical exercises in the above areas. Lab required. Prerequisites: TSI Math score of 910-949 with a diagnostic score of 5, and TSI college-readiness standard for Reading and Writing or equivalent. 4 credit hours. (A)

BIOL 1415 Introduction to Biotechnology II
Lecture to focus on an integrative approach to study biomolecules with an emphasis on protein structures, functions and uses in the modern bioscience laboratory. Students will investigate the mechanisms involved in the transfer of information from DNA sequences to proteins to biochemical functions. The course will integrate biological and chemical concepts with techniques that are used in research and industry. Critical thinking will be applied in laboratory exercises using inquiry-based approaches, troubleshooting and analyzing experimental data. Lab required. Prerequisite/Concurrent enrollment: BIOL 1414. 4 credit hours. (A)

BIOL 2389 Academic Co-op Biology
Integrates on-campus study with practical hands-on work experience in biology. In conjunction with class seminars, the student will set specific goals and objectives in the study of biology. Contact the Cooperative Work Experience Office. Prerequisite: BIOL 1406 or BIOL 1408. 3 credit hours. (A)

BIOL 2401 Anatomy and Physiology I
Lecture: Anatomy and Physiology I is the first part of a two course sequence. It is a study of the structure and function of the human body including cells, tissues and organs of the following systems: integumentary, skeletal, muscular, nervous and special senses. Emphasis is on interrelationships among systems and regulation of physiological functions involved in maintaining homeostasis.
Lab: The lab provides a hands-on learning experience for exploration of human system components and basic physiology. Systems to be studied include integumentary, skeletal, muscular, nervous, and special senses. Lab required. Prerequisites: TSI Math score of 910-949 with a diagnostic score of 5, and TSI college-readiness standard for Reading and Writing or equivalent. Enrollment in this course is by permission only. Please meet with an academic advisor. BIOL 1406 is strongly recommended. 4 credit hours. (A)

BIOL 2402 Anatomy and Physiology II
Lecture: Anatomy and Physiology II is the second part of a two-course sequence. It is a study of the structure and function of the human body including the following systems: endocrine, cardiovascular, immune, lymphatic, respiratory, digestive (including nutrition), urinary (including fluid and electrolyte balance), and reproductive (including human development and genetics). Emphasis is on interrelationships among systems and regulation of physiological functions involved in maintaining homeostasis. Lab: The lab provides a hands-on learning experience for exploration of human system components and basic physiology. Systems to be studied include endocrine, cardiovascular, immune, lymphatic, respiratory, digestive (including nutrition), urinary (including fluid and electrolyte balance), and reproductive (including human development and genetics). Lab required. Prerequisite: Biology 2401 with a grade of C or better within the last five years. 4 credit hours. (A)

BIOL 2404 Human Anatomy and Physiology Basic
A one-semester survey of the structure and function of the human body, including discussion and study of cells, tissues, organs, and systems. Lab required. 4 credit hours. (A)

BIOL 2406 Environmental Biology
Lecture: Principles of environmental systems and ecology, including biogeochemical cycles, energy transformations, abiotic interactions, symbiotic relationships, natural resources and their management, lifestyle analysis, evolutionary trends, hazards and risks, and approaches to ecological research. Lab: Laboratory activities will reinforce principles of environmental systems and ecology, including biogeochemical cycles, energy transformations, abiotic interactions, symbiotic relationships, natural resources and their management, lifestyle analysis, evolutionary trends, hazards and risks, and approaches to ecological research. Lab required, including field trips. 4 credit hours. (A)

BIOL 2416 Genetics
Study of the principles of molecular and classical genetics, and the function and transmission of hereditary material. Special emphasis on molecular genetics and genetic engineering. Lab required. Prerequisite: BIOL 1406. 4 credit hours. (A)

BIOL 2420 Microbiology for Non-Science Majors
Lecture: This course covers basic microbiology and immunology and is primarily directed at pre-nursing, pre-allied health, and non-science majors. It provides an introduction to historical concepts of the nature of microorganisms, microbial diversity, the importance of microorganisms and acellular agents in the biosphere, and their roles in human and animal diseases. Major topics include bacterial structure as well as growth, physiology, genetics, and biochemistry of microorganisms. Emphasis is on medical microbiology, infectious diseases, and public health. Lab: This course covers basics of culture and identification of bacteria and microbial ecology. This course is primarily directed at pre-nursing and other pre-allied health majors and covers basics of microbiology. Emphasis is on medical microbiology, infectious diseases, and public health. Lab required. Prerequisite: BIOL 2401 with a grade of C or better within the last three years, and Prerequisite/Concurrent enrollment in BIOL 2402 with a grade of C or better within the last three years. 4 credit hours. (A)

BIOL 2421 Microbiology for Science Majors
Lecture: Principles of microbiology, including metabolism, structure, function, genetics, and phylogeny of microbes. The course will also examine the interactions of microbes with each other, hosts, and the environment. Lab: Laboratory activities will reinforce principles of microbiology, including metabolism, structure, function, genetics, and phylogeny of microbes. The course will also examine the interactions of microbes with each other, hosts, and the environment. Lab required. Prerequisites: BIOL 1407 and CHEM 1411. 4 credit hours. (A)


Courses

This course is designed to introduce students to the basic skills necessary for academic success in the discipline of Biology and to provide students with an overview of professions in which the major may be applied. Pass/Fail. (1 unit Fall/Spring)

BIO101-A
Prins, Bruce
09/07/2021 T 5:00 PM - 6:00 PM BUS 124

BIO146 General Biology I with Lab

Topics covered include cell structure and function, genetics, reproduction and development of animal systems. Lecture (3 units) and required laboratory (1 unit). Additional lab fee. (4 units Fall/Spring)

BIO146-A
Koo, Bonjun
05/03/2021 M 9:00 AM - 12:00 PM CBU Virtual SYNC
BIO146-K
Koo, Bonjun
09/07/2021 Th 12:00 PM - 1:00 PM Yeager Center A112
BIO146-L
Koo, Bonjun
09/07/2021 F 10:45 AM - 11:45 AM Yeager Center A112
BIO146-I
Koo, Bonjun
09/07/2021 T 12:00 PM - 1:00 PM Yeager Center A112
BIO146-A
Koo, Bonjun
09/07/2021 Th 10:45 AM - 11:45 AM Yeager Center A112
BIO146-B
Koo, Bonjun
09/07/2021 M 10:45 AM - 11:45 AM Yeager Center A112
BIO146-C
Koo, Bonjun
09/07/2021 Th 10:45 AM - 11:45 AM Yeager Center A112
BIO146-D
Koo, Bonjun
09/07/2021 M 10:45 AM - 11:45 AM Yeager Center A112
BIO146-E
Koo, Bonjun
09/07/2021 W 10:45 AM - 11:45 AM Yeager Center A112
BIO146-F
Koo, Bonjun
09/07/2021 W 12:00 PM - 1:00 PM Yeager Center A112
BIO146-G
Koo, Bonjun
09/07/2021 T 12:00 PM - 1:00 PM Yeager Center A112
BIO146-H
Koo, Bonjun
09/07/2021 T 12:00 PM - 1:00 PM Yeager Center A112
BIO146-J
Koo, Bonjun
09/07/2021 Th 12:00 PM - 1:00 PM Yeager Center A112
BIO146-A
Koo, Bonjun
05/09/2022 M 9:00 AM - 12:00 PM TBA

BIO148 General Biology II with Lab

Includes organismal biology of animals and plants, their behavior, ecology, evolution and adaptations. Lecture (3 units) and required laboratory (1 unit). Additional lab fee. (4 units Spring)

BIO148-A
Shin, Alexandra Nicole
09/07/2021 M 10:45 AM - 11:45 AM TBA
BIO148-B
Shin, Alexandra Nicole
09/07/2021 M 10:45 AM - 11:45 AM TBA

CHE115 General Chemistry I

A study of inorganic chemical systems including properties of atoms, molecules and ions, composition of matter, solutions, stoichiometry, thermochemistry, gas laws, electronic structure of elements, chemical bonding and molecular geometry. Course content is presented at a level required for Chemistry and related science majors. Lecture: 3 units. Prerequisite: CHE 102 or high school chemistry. (3 units Fall/Spring)

CHE115-D
Rigsby, Emily M.
09/07/2021 MWF 9:30 AM - 10:30 AM TBA
CHE115-B
Suzuki, Satoru
09/07/2021 MWF 12:00 PM - 1:00 PM Mission Hall 124
CHE115-C
Schacht, Patrick C.
09/07/2021 MWF 8:15 AM - 9:15 AM Mission Hall 124
CHE115-A
Suzuki, Satoru
09/07/2021 MWF 10:45 AM - 11:45 AM Mission Hall 124
CHE115-A
Tsai, Jones
01/10/2022 MWF 9:30 AM - 10:30 AM BUS 203
CHE115-B
Suzuki, Satoru
01/10/2022 MWF 10:45 AM - 11:45 AM BUS 124

CHE115L General Chemistry I Lab

A laboratory experience designed to illustrate and reinforce topics covered in General Chemistry I and introduce students to laboratory practices, experiments and equipment that are foundational to the study of Chemistry. Additional lab fee. Pre- or Co- Requisite: CHE 115. (1 unit Fall/Spring)

CHE115L-G
Rigsby, Emily M.
09/07/2021 W 12:00 PM - 2:45 PM James Complex 240
CHE115L-I
Ketenbrink, Brittany
09/07/2021 W 6:00 PM - 8:45 PM James Complex 240
CHE115L-E
Ketenbrink, Brittany
09/07/2021 T 11:00 AM - 1:45 PM James Complex 240
CHE115L-D
Ketenbrink, Brittany
09/07/2021 T 7:30 AM - 10:15 AM James Complex 240
CHE115L-H
Rigsby, Emily M.
09/07/2021 W 3:00 PM - 5:45 PM James Complex 240
CHE115L-A
Ketenbrink, Brittany
09/07/2021 M 12:00 PM - 2:45 PM James Complex 240
CHE115L-C
Haynes, Stacy E.
09/07/2021 M 6:00 PM - 8:45 PM James Complex 240
CHE115L-B
Ketenbrink, Brittany
09/07/2021 M 3:00 PM - 5:45 PM James Complex 240
CHE115L-F
Ketenbrink, Brittany
09/07/2021 T 2:00 PM - 4:45 PM James Complex 240
CHE115L-J
Ketenbrink, Brittany
09/07/2021 Th 11:00 AM - 1:45 PM James Complex 240
CHE115L-K
Ketenbrink, Brittany
09/07/2021 Th 2:00 PM - 4:45 PM James Complex 240
CHE115L-A
Ketenbrink, Brittany
01/10/2022 M 12:00 PM - 2:45 PM James Complex 235
CHE115L-B
Ketenbrink, Brittany
01/10/2022 M 3:00 PM - 5:45 PM James Complex 235
CHE115L-C
Ketenbrink, Brittany
01/10/2022 M 6:00 PM - 8:45 PM James Complex 235
CHE115L-D
Ketenbrink, Brittany
01/10/2022 T 2:00 PM - 4:45 PM James Complex 235
CHE115L-E
Ketenbrink, Brittany
01/10/2022 T 5:30 PM - 8:15 PM James Complex 235
CHE115L-F
Ketenbrink, Brittany
01/10/2022 W 3:00 PM - 5:45 PM James Complex 235
CHE115L-G
Ketenbrink, Brittany
01/10/2022 Th 5:30 PM - 8:15 PM James Complex 235
CHE115L-H
Ketenbrink, Brittany
01/10/2022 W 12:00 PM - 2:45 PM James Complex 235

CHE125 General Chemistry II

A continuation of CHE 115 - General Chemistry I including the study of inorganic chemical systems including liquids and solids, solutions, colloids, kinetics, equilibria, acid-base chemistry, thermodynamics, electrochemistry, and nuclear chemistry. Course content is presented at a level required for Chemistry and related science majors. Lecture (3 units). Prerequisite: CHE 115 and 115L. (3 units Fall/Spring/Summer)

CHE125-A
Rigsby, Emily M.
05/10/2021 TTh 10:30 AM - 12:15 PM CBU Virtual SYNC
CHE125-A
Hu, Ying
09/07/2021 MWF 9:30 AM - 10:30 AM TBA
CHE125-A
Hu, Ying
01/10/2022 MWF 9:30 AM - 10:30 AM TBA
CHE125-B
Schacht, Patrick C.
01/10/2022 TTh 12:15 PM - 1:45 PM BUS 202
CHE125-C
Suzuki, Satoru
01/10/2022 MWF 1:15 PM - 2:15 PM Mission Hall 109
CHE125-A
Tsai, Jones
05/09/2022 TTh 10:30 AM - 12:15 PM TBA

CHE125L General Chemistry II Lab

A laboratory experience designed to illustrate and reinforce topics covered in CHE 125 - General Chemistry II and continue to introduce students to laboratory practices, experiments, and equipment that are foundational to the study of Chemistry. Additional lab fee. Prerequisite: CHE 115L. Pre- or Co- Requisite: CHE 125. (1 unit Fall/Spring/Summer)

CHE125L-A
Rigsby, Emily M.
05/10/2021 T 1:15 PM - 4:00 PM James Complex 235
CHE125L-B
Hu, Ying
09/07/2021 F 12:00 PM - 2:45 PM James Complex 235
CHE125L-A
Hu, Ying
09/07/2021 W 2:00 PM - 4:45 PM James Complex 235
CHE125L-A
Hu, Ying
01/10/2022 W 3:00 PM - 5:45 PM James Complex 236
CHE125L-B
Ketenbrink, Brittany
01/10/2022 T 2:00 PM - 4:45 PM James Complex 236
CHE125L-C
Ketenbrink, Brittany
01/10/2022 T 5:30 PM - 8:15 PM James Complex 236
CHE125L-D
Ketenbrink, Brittany
01/10/2022 Th 5:30 PM - 8:15 PM James Complex 236
CHE125L-E
Ketenbrink, Brittany
01/10/2022 Th 7:30 AM - 10:15 AM James Complex 236
CHE125L-F
Ketenbrink, Brittany
01/10/2022 F 3:00 PM - 5:45 PM James Complex 236
CHE125L-G
Ketenbrink, Brittany
01/10/2022 M 12:00 PM - 2:45 PM James Complex 236
CHE125L-A
Tsai, Jones
05/09/2022 T 1:15 PM - 4:00 PM James Complex 236

PHY214 Physics I

A study of mechanics, heat and thermodynamics, waves, sound, and the mathematical methods of physics. Should be taken with PHY 214L - Physics I Lab. Prerequisite: MAT 145 or 245. (3 units Fall/Spring)

PHY214-A
Buchholz, James R
05/03/2021 Th 9:30 AM - 2:30 PM CBU Virtual SYNC
PHY214-A
Buchholz, James R
09/07/2021 MWF 9:30 AM - 10:30 AM Yeager Center A110
PHY214-B
Buchholz, James R
09/07/2021 MWF 10:45 AM - 11:45 AM BUS 124
PHY214-A
STAFF, STAFF
01/10/2022 MWF 8:15 AM - 9:15 AM TBA
PHY214-A
Buchholz, James R
05/09/2022 Th 9:30 AM - 2:30 PM BUS

PHY214L Physics I Lab

This laboratory course, designed to be taken concurrently with PHY 214 - Physics I, emphasizes scientific measuring and reporting techniques. Observational laboratories will reinforce topics in mechanics, including kinematics, Hooke&aposs Law, momentum and inertia, and waves. Additional course ree. Pre- or Co- Requisite: PHY 214. (1 unit Fall/Spring)

PHY214L-A
Buchholz, James R
05/03/2021 Sa 8:00 AM - 12:00 PM James Complex 122
PHY214L-D
Lee, Yeon_Suk
09/07/2021 F 6:00 PM - 8:45 PM James Complex 122
PHY214L-G
Lee, Yeon_Suk
09/07/2021 Th 5:30 PM - 8:15 PM James Complex 122
PHY214L-B
Lee, Yeon_Suk
09/07/2021 F 3:00 PM - 5:45 PM James Complex 122
PHY214L-F
Lee, Yeon_Suk
09/07/2021 T 6:00 PM - 8:45 PM James Complex 122
PHY214L-A
Grant, Ted William
09/07/2021 M 3:00 PM - 5:45 PM James Complex 122
PHY214L-C
Grant, Ted William
09/07/2021 W 3:00 PM - 5:45 PM James Complex 122
PHY214L-E
Chediak, Juan A.
09/07/2021 Th 2:00 PM - 4:45 PM James Complex 122
PHY214L-A
STAFF, STAFF
01/10/2022 T 5:30 PM - 8:45 PM James Complex 122
PHY214L-A
Buchholz, James R
05/09/2022 Sa 8:00 AM - 12:00 PM James Complex 122

PHY224 Physics II

A continuation of Physics I, including a study of electricity, magnetism, electromagnetic waves, optics, and modern physics topics. Should be taken with PHY 224L. Prerequisite: PHY 214. (3 units Spring)

PHY224-A
Buchholz, James R
06/28/2021 Th 9:30 AM - 2:30 PM CBU Virtual SYNC
PHY224-A
Buchholz, James R
01/10/2022 MWF 9:30 AM - 10:30 AM Mission Hall 109
PHY224-B
Buchholz, James R
01/10/2022 MWF 10:45 AM - 11:45 AM Mission Hall 109
PHY224-A
Buchholz, James R
07/05/2022 Th 9:30 AM - 2:30 PM BUS

PHY224L Physics II Lab

This laboratory course, designed to be taken concurrently with Physcis II, emphasizes scientific measuring and reporting techniques. Observational laboratories will reinforce topics in waves, optics, electricity, and thermodynamics. Additional Lab Fee. Pre- or Co- Requisite: PHY 224. (1 unit Spring)

PHY224L-A
Buchholz, James R
06/28/2021 Sa 8:00 AM - 12:00 PM James Complex 121
PHY224L-A
Grant, Ted William
01/10/2022 W 3:00 PM - 5:45 PM James Complex 121
PHY224L-B
Grant, Ted William
01/10/2022 T 5:30 PM - 8:15 PM James Complex 121
PHY224L-C
Grant, Ted William
01/10/2022 M 3:00 PM - 5:45 PM James Complex 121
PHY224L-D
Grant, Ted William
01/10/2022 W 6:00 PM - 8:45 PM James Complex 121
PHY224L-E
Grant, Ted William
01/10/2022 Th 5:30 PM - 8:15 PM James Complex 121
PHY224L-F
Grant, Ted William
01/10/2022 F 4:00 PM - 6:45 PM James Complex 121
PHY224L-A
Buchholz, James R
07/05/2022 Sa 8:00 AM - 12:00 PM James Complex 121

Choose one (1) of the following courses:

MAT145 Mathematical Methods Nat Science

A calculus-based course including an introduction to derivatives and integrals, dimensional analysis, analytical geometry, trigonometry, vectors, experimental error and other topics to provide a mathematical foundation for natural science majors. Prerequisites: MAT 115, 135 or sufficient SAT, ACT or math placement exam scores and appropriate high school mathematics background. (4 units Spring)

MAT145-A
Carothers, Linn E.
05/03/2021 - Online
MAT145-B
Duran, Nathan Felipe
06/28/2021 TTh 5:00 PM - 7:00 PM CBU Virtual SYNC
MAT145-C
Sill, Michael R.
09/07/2021 T 12:00 PM - 1:00 PM TBA
MAT145-B
Cordero, Ricardo J.
09/07/2021 MWF 8:45 AM - 9:45 AM Mission Hall 124
MAT145-B
STAFF, STAFF
01/10/2022 - Online
MAT145-D
STAFF, STAFF
01/10/2022 - Online
MAT145-C
Farnham, Paul T.
01/10/2022 - Online
MAT145-A
Kish, Stephan C
01/10/2022 MWF 12:15 PM - 1:15 PM BUS 123
MAT145-A
Carothers, Linn E.
05/09/2022 - Online
MAT145-B
Carothers, Linn E.
07/05/2022 - Online

MAT245 Analytcl Geometry and Calculus I

Basic concepts of analytical geometry, limits and derivatives, differentials and rates, integration, definite and indefinite integrals, differentiation of logarithmic and exponential functions. Prerequisites: MAT 135, 145, EGR 182, or sufficient SAT, ACT or math placement exam scores and appropriate high school mathematics background. (4 units Fall/Spring)

MAT245-A
Willett, Robert James
05/03/2021 - Online
MAT245-B
Willett, Robert James
06/28/2021 - Online
MAT245-B
Duran, Nathan Felipe
09/07/2021 T 9:30 AM - 10:30 AM TBA
MAT245-A
Cordero, Ricardo J.
09/07/2021 Th 8:15 AM - 9:15 AM Mission Hall 109
MAT245-A
Willett, Robert James
01/10/2022 MWF 8:15 AM - 9:15 AM Health Science Campus ONLN
MAT245-B
Willett, Robert James
01/10/2022 MWF 9:30 AM - 10:30 AM Health Science Campus ONLN
MAT245-A
Willett, Robert James
05/09/2022 - Online
MAT245-B
Willett, Robert James
07/05/2022 - Online

Upper Division Requirements

BIO313 Genetics

The principles of genetics including Mendelian, nature of genetic materials, chromosome mechanics, genetic recombination, and gene action. Emphasis will be placed on the transmission of genetic factors. Prerequisite: BIO 146 (4 units Fall/Spring)

BIO313-A
Szeto, Daniel P.
09/07/2021 Th 8:15 AM - 9:15 AM BUS 124
BIO313-B
Szeto, Daniel P.
09/07/2021 Th 8:15 AM - 9:15 AM BUS 124
BIO313-D
Szeto, Daniel P.
09/07/2021 Th 8:15 AM - 9:15 AM BUS 124
BIO313-C
Szeto, Daniel P.
09/07/2021 Th 8:15 AM - 9:15 AM BUS 124

BIO330 Cell and Molecular Bio with Lab

An examination of the structure, ultrastructure, organization, and functions of cells, with emphasis on bioenergetics, membranes, organelles, genes and gene regulation, genetic control of cell division and differentiation, structure and function of biological macromolecules, particularly nucleic acids and proteins. Mechanisms of DNA replication and repair, transcription and translation will be studied, in addition to bacteriophage and eukaryotic virus biology, mobile genetic elements and genetic engineering. Lecture: 3 units) Lab: 1 unit. Additional lab fee. Prerequisites: BIO 146 and 148. Recommended: CHE125 and 125L. (4 units Fall/Spring)

BIO330-B
Bideshi, Dennis K.
09/07/2021 W 12:00 PM - 1:00 PM Mission Hall 109
BIO330-C
Bideshi, Dennis K.
09/07/2021 M 12:00 PM - 1:00 PM Mission Hall 109
BIO330-A
Bideshi, Dennis K.
09/07/2021 F 12:00 PM - 1:00 PM Mission Hall 109

CHE351 Organic Chemistry I with Lab

An integrated mechanistic study of the nomenclature, chemical, and stereochemical properties of aliphatic hydrocarbons. Lecture: 3 units. Lab: 1 unit. Additional lab fee. Prerequisites: CHE 125 and 125L. (4 units Fall/Spring/Summer)

CHE351-C
Fossett, Lawrence A
09/07/2021 W 12:00 PM - 1:00 PM Yeager Center A110
CHE351-A
Fossett, Lawrence A
09/07/2021 T 12:00 PM - 1:00 PM Yeager Center A110
CHE351-B
Fossett, Lawrence A
09/07/2021 T 12:00 PM - 1:00 PM Yeager Center A110
CHE351-D
Nalbandian, Jenifer Natee
09/07/2021 M 9:30 AM - 10:30 AM Mission Hall 124
CHE351-E
Nalbandian, Jenifer Natee
09/07/2021 Th 9:30 AM - 10:30 AM Mission Hall 124
CHE351-F
Nalbandian, Jenifer Natee
09/07/2021 Th 9:30 AM - 10:30 AM Mission Hall 124
CHE351-A
Hu, Ying
01/10/2022 M 10:45 AM - 11:45 AM TBA

CHE352 Organic Chemistry II with Lab

A continuation of Chemistry 351 covering the major aliphatic and aromatic functional groups. Includes an introduction to spectroscopy. Lecture (3 units) and required laboratory (1 unit). Additional lab fee. Prerequisite: CHE 351. (4 units Fall/Spring)

CHE352-A
Hu, Ying
09/07/2021 W 10:45 AM - 11:45 AM TBA
CHE352-A
Fossett, Lawrence A
01/10/2022 T 10:45 AM - 11:45 AM TBA
CHE352-B
Fossett, Lawrence A
01/10/2022 T 10:45 AM - 11:45 AM TBA
CHE352-C
Nalbandian, Jenifer Natee
01/10/2022 W 8:15 AM - 9:15 AM Mission Hall 109
CHE352-D
Nalbandian, Jenifer Natee
01/10/2022 Th 8:15 AM - 9:15 AM Mission Hall 109
CHE352-E
Nalbandian, Jenifer Natee
01/10/2022 Th 8:15 AM - 9:15 AM Mission Hall 109

Practicum Requirement

Complete 3 units from the following:

BIO380 Biology Seminar

This course will introduce and reinforce the skills necessary to perform biological research including discussions of the scientific method, literature research, reading scientific journal articles, analyzing scientific data, reporting research findings in both written and visual formats, critiquing original research, and science ethics. It will also explore field work opportunities available for students. Each student will be required to present a research proposal and/or locate and prepare all necessary documents for entering an internship, field work, or research opportunity. Prerequisite: Biology major. (1 unit Spring)

BIO380-A
Antonio, Melissa
09/07/2021 M 3:45 PM - 4:45 PM Yeager Center B222

BIO490 Senior Research in Biology

This class focuses on laboratory research projects and topics of current or historical interest that are not normally covered in other established courses. Content vary from year to year, and determined by both instructor and student&aposs interest. May be repeated for a maximum of eight (8) units. Prerequisites: BIO 148 Sophomore status and permission of Department Chair. (1-4 units Fall/Spring/Summer)

BIO490-A
Prins, Bruce
05/03/2021 - Instructor OFFC
BIO490-B
Heyman, Nathanael
05/03/2021 - Instructor OFFC
BIO490-C
Prins, Bruce
06/28/2021 - Instructor OFFC
BIO490-C
Prins, Bruce
09/07/2021 - Instructor OFFC
BIO490-H
Lanphere, Jacob D.
09/07/2021 - Instructor OFFC
BIO490-E
Szeto, Daniel P.
09/07/2021 - Instructor OFFC
BIO490-I
Shin, Alexandra Nicole
09/07/2021 - Instructor OFFC
BIO490-D
Koo, Bonjun
09/07/2021 - Instructor OFFC
BIO490-F
Heyman, Nathanael
09/07/2021 - Instructor OFFC
BIO490-J
Antonio, Melissa
09/07/2021 - Instructor OFFC
BIO490-A
Bideshi, Dennis K.
09/07/2021 - Instructor OFFC
BIO490-G
Runyan, Stephen A.
09/07/2021 - Instructor OFFC
BIO490-B
Park, Hyun-Woo
09/07/2021 - Instructor OFFC

BIO491 Internship in Biology

Under the advisement of a faculty member and supervising professional, the student will work or otherwise actively participate in a work/volunteer setting related to their major in Biology. This can be in an industrial, research, health care, or other approved setting. Variable (1-4) units can be earned in any one semester. May be repeated for up to 6 total units of credit. Prerequisites: Declared Biology major and Junior or Senior standing. (1-4 units As offered)

BIO499 Biology Capstone

This course is designed to be a culminating exercise for students to reflect upon, evaluate, and assimilate knowledge and experience they have gained by participating in a research or internship opportunity prior to this course. Students will prepare a presentation (both written and oral) that will focus on that experience. Prerequisite: Biology and Biomedical Sciences major and Junior status. (2 units Fall/Spring)

BIO499-A
Antonio, Melissa
09/07/2021 M 2:30 PM - 3:30 PM Yeager Center B222

Concentration Courses (16-20 units)

Students must complete all requirements in one of the following concentrations:

Environmental Science (16 units)

BIO114 General Botany with Lab

A study of the physiology, morphology, reproduction, and a survey of the plant kingdom, including fungi, algae, liverworts, mosses, ferns, gymnosperms and angiosperms. Emphasis will be placed on the development, reproduction and the relevance of plants to humans. Lecture (3 units) and required laboratory (1 unit). Additional lab fee. (4 units Spring)

BIO302 Ecology with Lab

The study of the interrelations of plants and animals in relation to the environment. Field study and local ecology are emphasized. Additional lab fee. Prerequisite: BIO 114, 143, or 146. (4 units Spring)

ENV360 Environmental Chemistry with Lab

Environmental Chemistry is intended to provide the student with an understanding of the key environmental problems our world faces, by exploring the chemistry of our air, water, and soil and integrating this in order to describe human and ecological exposures to chemicals in the environment. Lecture: 3 units. Lab: 1 unit. Additional lab fee. Prerequisites: CHE 125, 125L, and either BIO 146 or BIO 148. (4 units Spring, odd years)

SCI412 Topics Marine Science

This class deals with research projects and topics of current or historical interest which are not normally covered in other established courses. Content variable from year to year. Prerequisite: BIO 148. (1-4 units As offered)

SCI412-B
Lanphere, Jacob D.
08/30/2021 Sa 9:00 AM - 3:00 PM BUS OTHR
SCI412-A
Lanphere, Jacob D.
08/30/2021 Sa 9:00 AM - 3:00 PM BUS OTHR

General Biology (16 units)

BIO114 General Botany with Lab

A study of the physiology, morphology, reproduction, and a survey of the plant kingdom, including fungi, algae, liverworts, mosses, ferns, gymnosperms and angiosperms. Emphasis will be placed on the development, reproduction and the relevance of plants to humans. Lecture (3 units) and required laboratory (1 unit). Additional lab fee. (4 units Spring)

Complete 12 additional upper division units in biology and SCI 412.

Secondary Biology Education (20 units)

BIO114 General Botany with Lab

A study of the physiology, morphology, reproduction, and a survey of the plant kingdom, including fungi, algae, liverworts, mosses, ferns, gymnosperms and angiosperms. Emphasis will be placed on the development, reproduction and the relevance of plants to humans. Lecture (3 units) and required laboratory (1 unit). Additional lab fee. (4 units Spring)

BIO302 Ecology with Lab

The study of the interrelations of plants and animals in relation to the environment. Field study and local ecology are emphasized. Additional lab fee. Prerequisite: BIO 114, 143, or 146. (4 units Spring)

BIO344 Vertebrate Physiology with Lab

Principles of physiology and the function of vertebrate organ systems with emphasis on human. Lecture: 3 units. Lab: 1 unit. Additional lab fee. Prerequisites: BIO 148, CHE 115, and 115L. (4 units Spring)

ENV451 Advanced Geoscience with Lab

An advanced study of the geosciences including the areas of astronomy, meteorology and climate, geology, and oceanography. The laboratory experience is designed to illustrate and reinforce geosciences principles and to introduce basic geosciences laboratory techniques. Lecture: 3 units. Lab: 1 unit. Additional lab fee. Prerequisites: CHE 115 and 115L. (4 units Fall/Spring)

ENV451-A
Lanphere, Jacob D.
09/07/2021 Th 12:15 PM - 1:45 PM Mission Hall 109

PHY301 Astronomy II

The main focus of the course is on complex concepts from extra-solar astrophysics (astronomy outside of our solar system), including star formation, stellar evolution, supernova and stellar remnants, black holes, galaxy formation, dark matter, the large-scale structure of the universe, and the Creation of the universe. The purpose of this course is to provide a broad baseline of conceptual understanding. Student will also learn how to analyze and understand new discoveries in astronomy as they are related directly to the professional astronomical community, in addition to understanding astronomy articles that are presented through more mainstream media. Prerequisites: PHY113, 201, or 214. (3 units Spring, odd years)

PHY301L Astronomy II Lab

This laboratory course focuses on studying the laws of physics related to astronomy. It is intended as an upper division general education course in astronomy. The purpose of this course is to give a broad experiential understanding of the process of analyzing data from telescopes, integrating real astronomical data with astronomical concepts such as the expansion of the universe and supernova explosion. Additional lab fee. Pre- or Co- Requisite: PHY 301. (1 unit Spring, odd years)

Recommended Courses

PHY214D Physics I Discussion

This discussion section is designed to be taken concurrently with PHY 214 - Physics I. Emphasis will be placed on problem solving and computational techniques, and is meant to reinforce topics in mechanics, heat and thermodynamics, waves, sound, and the mathematical methods of physics. Pass/Fail. Concurrent Requisite: PHY 214. (1 unit Fall/Spring)

PHY214D-B
STAFF, STAFF
09/07/2021 Th 4:45 PM - 5:45 PM Building 36 36A2
PHY214D-D
Campbell, Melvin D.
09/07/2021 M 4:45 PM - 5:45 PM Mission Hall 127
PHY214D-F
Campbell, Melvin D.
09/07/2021 W 4:45 PM - 5:45 PM Mission Hall 127
PHY214D-A
Campbell, Melvin D.
09/07/2021 T 4:45 PM - 5:45 PM Building 36 36A2
PHY214D-E
Buchholz, James R
09/07/2021 W 1:15 PM - 2:15 PM James Complex 189
PHY214D-A
STAFF, STAFF
01/10/2022 W 12:00 PM - 1:00 PM TBA

PHY224D Physics II Discussion

This discussion section is designed to be taken concurrently with Physics II. Emphasis will be placed on problem solving and computational techniques, and is meant to reinforce topics in waves, optics, electricity, and thermodynamics. Pass/Fail. Concurrent Requisite: PHY 224. (1 unit Spring)


This program will prepare you for research-intensive jobs in biochemistry, biophysics, microbiology, zoology or doctoral programs in medicine, pharmacy, dentistry, physical therapy and allied health sciences fields.

Courses to Prepare You for Your Career

  • Foundation courses include Research Literature and Techniques or Thesis, depending on option selected
  • Core business analytics courses include Quantitative Biology, Advanced Cell Biology, Molecular Genetics and Human Physiology

Classes

Chemistry classes are listed below. Please visit the MIT Subject Listing for a comprehensive and up-to-the-minute list of our offered classes.

Units must be arranged between the student and the supervising instructor for subjects that have a TBD in the “Units” column. Subjects offered jointly with another department are indicated with a “J”.

5.00 Energy Technology and Policy: From Principles to Practice

Develops analytical skills to lead a successful technology implementation with an integrated approach that combines technical, economical and social perspectives. Considers corporate and government viewpoints as well as international aspects, such as nuclear weapons proliferation and global climate issues. Discusses technologies such as oil and gas, nuclear, solar, and energy efficiency. Limited to 100.

5.000 Dimensions of Geoengineering

Familiarizes students with the potential contributions and risks of using geoengineering technologies to control climate damage from global warming caused by greenhouse gas emissions. Discusses geoengineering in relation to other climate change responses: reducing emissions, removing CO2 from the atmosphere, and adapting to the impacts of climate change. Limited to 100.

5.03 Principles of Inorganic Chemistry I

Presents principles of chemical bonding and molecular structure, and their application to the chemistry of representative elements of the periodic system.

5.04 Principles of Inorganic Chemistry II

Systematic presentation of the chemical applications of group theory. Emphasis on the formal development of the subject and its applications to the physical methods of inorganic chemical compounds. Against the backdrop of electronic structure, the electronic, vibrational, and magnetic properties of transition metal complexes are presented and their investigation by the appropriate spectroscopy described.

5.05 Principles of Inorganic Chemistry III

Principles of main group (s and p block) element chemistry with an emphasis on synthesis, structure, bonding, and reaction mechanisms.

5.061 Principles of Organometallic Chemistry

A comprehensive treatment of organometallic compounds of the transition metals with emphasis on structure, bonding, synthesis, and mechanism.

5.062 Principles of Bioinorganic Chemistry

Delineates principles that form the basis for understanding how metal ions function in biology. Examples chosen from recent literature on a range of topics, including the global biogeochemical cycles of the elements choice, uptake and assembly of metal-containing units structure, function and biosynthesis of complex metallocofactors electron-transfer and redox chemistry atom and group transfer chemistry protein tuning of metal properties metalloprotein engineering and design and applications to diagnosis and treatment of disease.

5.063 Organometallic Compounds in Catalytic Reactions

An exploration of organometallic chemistry from the perspective of catalytic reactions in organic and polymer chemistry.

5.067 Crystal Structure Refinement

Practical aspects of crystal structure determination from data collection strategies to data reduction and basic and advanced refinement problems of organic and inorganic molecules.

5.068 Physical Inorganic Chemistry

Discusses the physical methods used to probe the electronic and geometric structures of inorganic compounds, with additional techniques employed in the characterization of inorganic solids and surfaces. Includes vibrational spectroscopy, solid state and solution magnetochemical methods, Mössbauer spectroscopy, electron paramagnetic resonance spectroscopy, electrochemical methods, and a brief survey of surface techniques. Applications to current research problems in inorganic and solid-state chemistry.

5.069 Crystal Structure Analysis

Introduction to X-ray crystallography: symmetry in real and reciprocal space, space and Laue groups, geometry of diffraction, structure factors, phase problem, direct and Patterson methods, electron density maps, structure refinement, crystal growth, powder methods, limits of diffraction methods, structure data bases.

5.07J Introduction to Biological Chemistry

Chemical and physical properties of the cell and its building blocks. Structures of proteins and principles of catalysis. The chemistry of organic/inorganic cofactors required for chemical transformations within the cell. Basic principles of metabolism and regulation in pathways, including glycolysis, gluconeogenesis, fatty acid synthesis/degradation, pentose phosphate pathway, Krebs cycle and oxidative phosphorylation, DNA replication, and transcription and translation.

5.08J Fundamentals of Chemical Biology

Spanning the fields of biology, chemistry, and engineering, this class introduces students to the principles of chemical biology and the application of chemical and physical methods and reagents to the study and manipulation of biological systems. Topics include nucleic acid structure, recognition, and manipulation protein folding and stability, and proteostasis bioorthogonal reactions and activity-based protein profiling chemical genetics and small-molecule inhibitor screening fluorescent probes for biological analysis and imaging and unnatural amino acid mutagenesis. The class will also discuss the logic of dynamic post-translational modification reactions with an emphasis on chemical biology approaches for studying complex processes including glycosylation, phosphorylation, and lipidation. Students taking the graduate version are expected to explore the subject in greater depth.

5.111 Principles of Chemical Science

Introduction to chemistry, with emphasis on basic principles of atomic and molecular electronic structure, thermodynamics, acid-base and redox equilibria, chemical kinetics, and catalysis. Introduction to the chemistry of biological, inorganic, and organic molecules.

5.112 Principles of Chemical Science

Introduction to chemistry for students who have taken two or more years of high school chemistry or who have earned a score of at least 4 on the ETS Advance Placement Exam. Emphasis on basic principles of atomic and molecular electronic structure, thermodynamics, acid-base and redox equilibria, chemical kinetics, and catalysis. Applications of basic principles to problems in metal coordination chemistry, organic chemistry, and biological chemistry.

5.12 Organic Chemistry I

Introduction to organic chemistry. Development of basic principles to understand the structure and reactivity of organic molecules. Emphasis on substitution and elimination reactions and chemistry of the carbonyl group. Introduction to the chemistry of aromatic compounds.

5.13 Organic Chemistry II

Focuses on synthesis, structure determination, mechanism, and the relationships between structure and reactivity. Selected topics illustrate the role of organic chemistry in biological systems and in the chemical industry.

5.24J Archaeological Science

Pressing issues in archaeology as an anthropological science. Stresses the natural science and engineering methods archaeologists use to address these issues. Reconstructing time, space, and human ecologies provides one focus materials technologies that transform natural materials to material culture provide another. Topics include 14C dating, ice core and palynological analysis, GIS and other remote sensing techniques for site location, organic residue analysis, comparisons between Old World and New World bronze production, invention of rubber by Mesoamerican societies, analysis and conservation of Dead Sea Scrolls.

5.301 Chemistry Laboratory Techniques

Practical training in basic chemistry laboratory techniques. Intended to provide first-year students with the skills necessary to undertake original research projects in chemistry. First-year students only. Enrollment limited.

5.302 Introduction to Experimental Chemistry

Illustrates fundamental principles of chemical science through practical experience with chemical phenomena. Students explore the theoretical concepts of chemistry through the experiments which informed their discovery, and make chemistry happen with activities that are intellectually stimulating and fun. Preference to first-year students.

5.310 Laboratory Chemistry

Introduces experimental chemistry for students who are not majoring in Course 5. Principles and applications of chemical laboratory techniques, including preparation and analysis of chemical materials, measurement of pH, gas and liquid chromatography, visible-ultraviolet spectrophotometry, infrared spectroscopy, kinetics, data analysis, and elementary synthesis. Enrollment limited.

5.351 Fundamentals of Spectroscopy

Students carry out an experiment that introduces fundamental principles of the most common types of spectroscopy, including UV-visible absorption and fluorescence, infrared, and nuclear magnetic resonance. Emphasizes principles of how light interacts with matter, a fundamental and hands-on understanding of how spectrometers work, and what can be learned through spectroscopy about prototype molecules and materials. Students record and analyze spectra of small organic molecules, native and denatured proteins, semiconductor quantum dots, and laser crystals. Satisfies 4 units of Institute Laboratory credit.

5.352 Synthesis of Coordination Compounds and Kinetics

Students carry out an experiment that provides an introduction to the synthesis of simple coordination compounds and chemical kinetics. Illustrates cobalt coordination chemistry and its transformations as detected by visible spectroscopy. Students observe isosbestic points in visible spectra, determine the rate and rate law, measure the rate constant at several temperatures, and derive the activation energy for the aquation reaction. Satisfies 5 units of Institute Laboratory credit.

5.353 Macromolecular Prodrugs

Students carry out an experiment that builds skills in how to rationally design macromolecules for drug delivery based on fundamental principles of physical organic chemistry. Begins with conjugation of a drug molecule to a polymerizable group through a cleavable linker to generate a prodrug monomer. Continues with polymerization of monomer to produce macromolecular (i.e., polymer) prodrug monomer and polymer prodrugs are fully characterized. Rate of drug release is measured and correlated to the size of the macromolecule as well as the structure of the cleavable linker. Satisfies 4 units of Institute Laboratory credit.

5.361 Recombinant DNA Technology

Students explore the biochemical basis for the efficacy of a blockbuster drug: Gleevec, which is used to treat chronic myelogenous leukemia. Its target, Abl kinase, is produced in E. coli by recombinant DNA technology, purified using affinity chromatography, and analyzed with polyacrylamide gel electrophoresis, UV–vis spectroscopy, and a colorimetric assay. Natural mutations found in Gleevec-resistant cancer patients are introduced into the ABL1 proto-oncogene with PCR-based mutagenesis and analyzed by agarose gel electrophoresis.

5.362 Cancer Drug Efficacy

Students probe the structural basis for the development of resistance to Gleevec by cancer patients. LC–MS is used to quantify the effect of Gleevec on catalysis by wild-type Abl kinase and a Gleevec-resistant variant (Module 4). Other potential drugs are tested as inhibitors of the Abl variant. Molecular graphics software is used to understand catalysis by Abl kinase, its inhibition by Gleevec, and the basis for drug resistance.

5.363 Organic Structure Determination

Introduces modern methods for the elucidation of the structure of organic compounds. Students carry out transition metal-catalyzed coupling reactions, based on chemistry developed in the Buchwald laboratory, using reactants of unknown structure. Students also perform full spectroscopic characterization – by proton and carbon NMR, IR, and mass spectrometry of the reactants – and carry out coupling products in order to identify the structures of each compound. Other techniques include transfer and manipulation of organic and organometallic reagents and compounds, separation by extraction, and purification by column chromatography. Satisfies 4 units of Institute Laboratory credit.

5.371 Continuous Flow Chemistry

Presents the theoretical and practical fundamentals of continuous flow synthesis, wherein pumps, tubes, and connectors are used to conduct chemical reactions instead of flasks, beakers, etc. Focuses on a catalytic reaction that converts natural vegetable oil into biodiesel that can be used in a variety of combustion engines. Provides instruction in several important organic chemistry experimental techniques, including purification by extraction, rotary evaporation, acid-base titration, gas chromatography (GC), and 1 H NMR.

5.372 Chemistry of Renewable Energy

Introduces the electrochemical processes that underlie renewable energy storage and recovery. Students investigate charge transfer reactions at electrode surfaces that are critical to the operation of advanced batteries, fuel cells, and electrolyzers. Develops basic theory behind inner- and outer-sphere charge transfer reactions at interfaces and applies this theory to construct mechanistic models for important energy conversion reactions including the reduction of O2 to water and the reduction of protons to H2. Students will also synthesize new catalytic materials for these reactions and investigate their relative performance.

5.373 Dinitrogen Cleavage

Introduces the research area of small-molecule activation by transition-element complexes. Covers techniques such as glove-box methods for synthesis for exclusion of oxygen and water filtration, reaction mixture concentration, and recrystallization under a dinitrogen atmosphere and under static vacuum. Characterization methods include proton NMR spectroscopy of both paramagnetic and diamagnetic systems, Evans method magnetic susceptibility measurement, UV-Vis spectroscopy, and infrared spectroscopy of a metal-nitrogen triple bond system.

5.381 Quantum Dots

Covers synthesis of a discrete size series of quantum dots, followed by synthesis of a single size of core/shell quantum dots utilizing air-free Schlenk manipulation of precursors. Uses characterization by absorption and fluorescence spectroscopies to rationalize the compositional/size dependence of the shell on the electronic structure of the quantum dots. Students acquire time traces of the fluorescence of single core and core/shell quantum dots using single molecule spectroscopic tools. The fluorescence on/off blinking distribution observed will be fit to a standard model. Students use Matlab for computational modeling of the electron and hole wavefunction in core and core/shell quantum dots. Analyzes several commercial applications of quantum dot technologies.

5.382 Time and Frequency-Resolved Spectroscopy of Photosynthesis

Uses time- and frequency-resolved fluorescence measurements to investigate photosynthetic light harvesting and energy transfer.

5.383 Fast-Flow Peptide and Protein Synthesis

Develops understanding of both the theory and practice of fundamental techniques in biological chemistry, including chemical reactivity (amide-bond formation, solid phase synthesis, disulfide bond formation, and protecting group chemistry) separation science for purification and analysis, such as preparative HPLC and MALDI-TOF MS and protein structure-function relationships (protein folding and binding). Periodically, guest lecturers from the local biotech research community will describe practical applications in industry.

5.39 Research and Communication in Chemistry

Independent research under the direction of a member of the Chemistry Department faculty. Allows students with a strong interest in independent research to fulfill part of the laboratory requirement for the Chemistry Department Program in the context of a research laboratory at MIT. The research must be conducted on the MIT campus and be a continuation of a previous 12-unit UROP project or full-time work over the summer. Instruction and practice in written and oral communication is provided, culminating in a poster presentation of the work at the annual departmental UROP symposium and a research publication-style writeup of the results. Permission of the faculty research supervisor and the Chemistry Education Office must be obtained in advance.

5.43 Advanced Organic Chemistry

Reaction mechanisms in organic chemistry: methods of investigation, relation of structure to reactivity, and reactive intermediates. Photochemistry and organometallic chemistry, with an emphasis on fundamental reactivity, mechanistic studies, and applications in organic chemistry.

5.44 Organometallic Chemistry

Examination of the most important transformations of organotransition-metal species. Emphasizes basic mechanisms of their reactions, structure-reactivity relationships, and applications in synthesis.

5.45 Heterocyclic Chemistry

Provides an introduction to the chemistry of heterocyclic compounds. Surveys synthesis and reactivity of the major classes of heterocyclic organic compounds. Discusses the importance of these molecules in the pharmaceutical and other industries.

5.46 NMR Spectroscopy and Organic Structure Determination

Applications of 1-D and 2-D 1 H and 13 C NMR spectroscopy to organic structure determination.

5.47 Tutorial in Organic Chemistry

Systematic review of basic principles concerned with the structure and transformations of organic molecules. Problem-solving workshop format. The program is intended primarily for first-year graduate students with a strong interest in organic chemistry. Meets during the month of September.

5.511 Synthetic Organic Chemistry I

Introduction to the design of syntheses of complex organic compounds.

5.512 Synthetic Organic Chemistry II

General methods and strategies for the synthesis of complex organic compounds.

5.52 Tutorial in Chemical Biology

Provides an overview of the core principles of chemistry that underlie biological systems. Students will also explore research topics and methods in chemical biology by participating in laboratory rotations, then present on experiments performed during each rotation. Intended for first-year graduate students with a strong interest in chemical biology.

5.53 Molecular Structure and Reactivity

Reaction mechanisms in organic chemistry: methods of investigation, relation of structure to reactivity, and reactive intermediates.

5.54J Frontiers in Chemical Biology

Introduction to current research at the interface of chemistry, biology, and bioengineering. Topics include imaging of biological processes, metabolic pathway engineering, protein engineering, mechanisms of DNA damage, RNA structure and function, macromolecular machines, protein misfolding and disease, metabolomics, and methods for analyzing signaling network dynamics. Lectures are interspersed with class discussions and student presentations based on current literature.

5.56 Molecular Structure and Reactivity II

Application of physical principles and methods to contemporary problems of interest in organic and polymer chemistry.

5.561 Chemistry in Industry

Examination of recent advances in organic, biological, and inorganic and physical chemical research in industry. Taught in seminar format with participation by scientists from industrial research laboratories.

5.601 Thermodynamics I

Basic thermodynamics: state of a system, state variables. Work, heat, first law of thermodynamics, thermochemistry. Second and third law of thermodynamics: entropy and free energy, including the molecular basis for these thermodynamic functions. Equilibrium properties of macroscopic systems. Special attention to thermodynamics related to global energy issues and biological systems. Combination of 5.601 and 5.602 counts as a REST subject.

5.602 Thermodynamics II and Kinetics

Free energy and chemical potential. Phase equilibrium and properties of solutions. Chemical equilibrium of reactions. Rates of chemical reactions. Special attention to thermodynamics related to global energy issues and biological systems. Combination of 5.601 and 5.602 counts as a REST subject.

5.611 Introduction to Spectroscopy

Introductory quantum chemistry particles and waves wave mechanics harmonic oscillator applications to IR, Microwave and NMR spectroscopy. Combination of 5.611 and 5.612 counts as a REST subject.

5.612 Electronic Structure of Molecules

Introductory electronic structure atomic structure and the Periodic Table valence and molecular orbital theory molecular structure, and photochemistry. Meets with 5.61 second half of term. Combination of 5.611 and 5.612 counts as a REST subject.

5.62 Physical Chemistry

Elementary statistical mechanics transport properties kinetic theory solid state reaction rate theory and chemical reaction dynamics.

5.64J Frontiers of Interdisciplinary Science in Human Health and Disease

Introduces major principles, concepts, and clinical applications of biophysics, biophysical chemistry, and systems biology. Emphasizes biological macromolecular interactions, biochemical reaction dynamics, and genomics. Discusses current technological frontiers and areas of active research at the interface of basic and clinical science. Provides integrated, interdisciplinary training and core experimental and computational methods in molecular biochemistry and genomics.

5.68J Kinetics of Chemical Reactions

Experimental and theoretical aspects of chemical reaction kinetics, including transition-state theories, molecular beam scattering, classical techniques, quantum and statistical mechanical estimation of rate constants, pressure-dependence and chemical activation, modeling complex reacting mixtures, and uncertainty/ sensitivity analyses. Reactions in the gas phase, liquid phase, and on surfaces are discussed with examples drawn from atmospheric, combustion, industrial, catalytic, and biological chemistry.

5.697J Computational Chemistry

Addresses both the theory and application of first-principles computer simulations methods (i.e., quantum, chemical, or electronic structure), including Hartree-Fock theory, density functional theory, and correlated wavefunction methods. Covers enhanced sampling, ab initio molecular dynamics, and transition-path-finding approaches as well as errors and accuracy in total and free energies. Discusses applications such as the study and prediction of properties of chemical systems, including heterogeneous, molecular, and biological catalysts (enzymes), and physical properties of materials. Students taking graduate version complete additional assignments.

5.698J Quantum Chemical Simulation

Addresses both the theory and application of first-principles computer simulations methods (i.e., quantum, chemical, or electronic structure), including Hartree-Fock theory, density functional theory, and correlated wavefunction methods. Covers enhanced sampling, ab initio molecular dynamics, and transition-path-finding approaches as well as errors and accuracy in total and free energies. Discusses applications such as the study and prediction of properties of chemical systems, including heterogeneous, molecular, and biological catalysts (enzymes), and physical properties of materials. Students taking graduate version complete additional assignments.

5.70J Statistical Thermodynamics

Develops classical equilibrium statistical mechanical concepts for application to chemical physics problems. Basic concepts of ensemble theory formulated on the basis of thermodynamic fluctuations. Examples of applications include Ising models, lattice models of binding, ionic and non-ionic solutions, liquid theory, polymer and protein conformations, phase transition, and pattern formation. Introduces computational techniques with examples of liquid and polymer simulations.

5.72 Statistical Mechanics

Principles and methods of statistical mechanics. Classical and quantum statistics, grand ensembles, fluctuations, molecular distribution functions, and other topics in equilibrium statistical mechanics. Topics in thermodynamics and statistical mechanics of irreversible processes.

5.73 Introductory Quantum Mechanics I

Presents the fundamental concepts of quantum mechanics: wave properties, uncertainty principles, Schrodinger equation, and operator and matrix methods. Includes applications to one-dimensional potentials (harmonic oscillator), three-dimensional centrosymetric potentials (hydrogen atom), and angular momentum and spin. Approximation methods include WKB, variational principle, and perturbation theory.

5.74 Introductory Quantum Mechanics II

Time-dependent quantum mechanics and spectroscopy. Topics include perturbation theory, two-level systems, light-matter interactions, relaxation in quantum systems, correlation functions and linear response theory, and nonlinear spectroscopy.

5.78 Biophysical Chemistry Techniques

Presents principles of macromolecular crystallography that are essential for structure determinations. Topics include crystallization, diffraction theory, symmetry and space groups, data collection, phase determination methods, model building, and refinement. Discussion of crystallography theory complemented with exercises such as crystallization, data processing, and model building. Meets with 7.71 when offered concurrently. Enrollment limited.

5.83 Advanced NMR Spectroscopy

Offers a classical and quantum mechanical description of nuclear magnetic resonance (NMR) spectroscopy. The former includes key concepts such as nuclear spin magnetic moment, Larmor precession, Bloch equations, the rotating frame, radio-frequency pulses, vector model of pulsed NMR, Fourier transformation in 1D and nD NMR, orientation dependence of nuclear spin frequencies, and NMR relaxation. The latter covers nuclear spin Hamiltonians, density operator and its time evolution, the interaction representation, Average Hamiltonian Theory for multi-pulse experiments, and analysis of some common pulse sequences in solution and solid-state NMR.

5.913 Seminar in Organic Chemistry

Discusses current journal publications in organic chemistry.

5.921 Seminar in Chemical Biology

Discusses topics of current interest in chemical biology.

5.931 Seminar in Physical Chemistry

Discusses topics of current interest in physical chemistry.

5.941 Seminar in Inorganic Chemistry

Discusses current research in inorganic chemistry.

5.95J Teaching College-Level Science and Engineering

Participatory seminar focuses on the knowledge and skills necessary for teaching science and engineering in higher education. Topics include theories of adult learning course development promoting active learning, problem-solving, and critical thinking in students communicating with a diverse student body using educational technology to further learning lecturing creating effective tests and assignments and assessment and evaluation. Students research and present a relevant topic of particular interest. Appropriate for both novices and those with teaching experience.

5.THG Graduate Thesis

Program of research leading to the writing of a PhD thesis to be arranged by the student and an appropriate MIT faculty member.

5.THU Undergraduate Thesis

Program of original research under supervision of a chemistry faculty member, culminating with the preparation of a thesis. Ordinarily requires equivalent of two terms of research with chemistry department faculty member.

5.UR Undergraduate Research

Program of research to be arranged by the student and a departmental faculty member. Research can be applied toward undergraduate thesis.

5.URG Undergraduate Research

Program of research to be arranged by the student and a departmental faculty member. May be taken for up to 12 units per term, not to exceed a cumulative total of 48 units. A 10-page paper summarizing research is required.


Lecture 03 v2: Basics of Biological Chemistry - Biology

1,000 Inspiring Black Scientists in America

Biology Prof. Jill Bargonetti and dept. alumni Eric Jarvis included in list.

Hunter College Chosen as Capstone College

Hunter College has been designated as one of 11 Capstone Colleges in the United States by the Howard Hughes Medical Institute as a result of long-term funding to PI Shirley Raps.

Bratu Lab Images Featured In Cell

Images From Diana Bratu's lab, taken by Dr. Irina Catrina are featured in Cell's Journal Picture Show, called Reproduction.

Program Learning Outcomes For Biology Students

  1. Recognize, critique, design and carry out experiments according to the scientific method
  2. Synthesize and integrate abstract and practical concepts to address biological problems
  3. Discuss mechanisms of life at the organismal level, at the cellular level and molecular/genetic level
  4. Perform quantitative analyses in Biology

Biology Graduate (M.A.) and B.A./M.A. in Biotechnology

  1. Summarize and Articulate Advanced Research and Theoretical Concepts
  2. Use and Interpret Experimental Design from Current Literature in Molecular, Cellular and Developmental Biology
  3. Interpret Experimental Data Independently

Bio. Department News

New Doctoral Students Fall 2020

The New Biology Department Ph.D. New Students Fall 2020

New Doctoral Students Fall 2019

The New Biology Department Ph.D. New Students Fall 2019

Melendez Lab Work Highlighted in DOD Booklet & Published in Scientific Reports

Prof Carmen Melendez's work recently highlighted in a Multiple Sclerosis Research Program of Department of Defense booklet,and published in Scientific Reports

New Doctoral Students Fall 2018

The New Biology Department Ph.D. Students Fall 2018

Access The Gene Center Mail Server

To Access the Gene Center Mail Server Click Here

Hunter's Quantitative Biology Initiative


Hunter College is one of only nine institutions of higher education in the country to offer an interdisciplinary program in quantitative biology. Students majoring in Biology, Chemistry, Computer Science, Mathematics or Statistics can add a quantitative biology concentration to their major. Among the many benefits of this innovative program are access to competitive scholarships, small classes, training by a multidisciplinary team of research scientists and dedicated academics, individual mentoring, the opportunity to participate in research conducted at Hunter and nationally, topnotch preparation for graduate studies and for scientific careers in this new frontier.

To find out more click here.

Financial support available for:

Summer Internship, Graduate School, Post Bac. Experiences, Medical School, M.D./Ph.D. Programs, Postdoctoral Fellowships. Are you interested in a summer internship or perhaps seeking support for graduate school, medical school, an M.D./Ph.D. degree program or a postdoctoral research experience?

Skirball Science Learning Center


The Skirball Science Learning Center (SSLC) provides comprehensive assistance to all Hunter College students in all areas of the natural sciences and technology.
Location: 7th Floor, East Building

Phone (Desk): 212-396-6458

Director: Christina Medina Ramirez (212)-650-3283)

Our Department

Hunter College is located at the intersection of 68 th Street and Lexington ave. in Manhattan's Upper East Side. The Biology department occupies the 8 th and 9 th floors of the Hunter North building. The mission of the Department of Biological Sciences parallels that of Hunter College: to provide a quality education for our undergraduate and graduate students, enabling them to participate productively in their chosen pursuits.

GENTalks: Introduction

GENTalks were designed to be a series of short recorded presentations on novel, exciting and futuristic topics in genomics, that might capture the imagination of students and scientists. These presentations were recorded by students and staff in the studio of the Department of Film and Media Studies at Hunter College. Although the COVID pandemic delayed the editing and timely release of these presentations, we are happy to begin providing this material for our community. We hope you find them stimulating and informative, and we welcome your feedback in writing.

Harvey Lodish: YouTube

The Howard Hughes Medical Institute Undergraduate Science Education Program


CUNY Hunter College has been designated as one of 11 Capstone Colleges in the United States by the Howard Hughes Medical Institute.
This is the result of long-term funding to PI Professor Shirley Raps from Sept. 1, 1993 - Aug. 31, 2017, resulting in &ldquomature and successful&rdquo programs at the college. This includes recruiting a faculty member to create a bioinformatics program, supporting research by junior faculty in biology, curriculum changes and innovations in biology for undergraduates, increasing support for undergraduate research, enhancing science education for teachers and their students at public high schools and middle schools, collaboration with the Manhattan/Hunter Science High School to provide research opportunities for their students, and developing a Science Policy track in the Public Policy Program at Roosevelt House for undergraduates. Hunter is the only public urban college to receive this designation. The other colleges are Barnard, Bryn Mawr, Carleton, Grinnell, Hope, Morehouse, Smith, Spelman, Swarthmore, and Xavier. Further information can be found on the Biology HHMI website.

MARC Program at Hunter

The MARC Programs at Hunter College is supported by the National Institutes of Health (NIH) and are intended to encourage talented undergraduate minority students to pursue a career in research and science. Students in both programs receive a scholarship and financial support for conducting research throughout the academic year in a Hunter College laboratory. For more information click here.

Bio Department Advising Schedule

Students: To talk with a faculty advisor check out the department Spring Advising Schedule

Minority Graduate Student Network

MGSN is a student-run network of graduate students, medical students, and postdocs that aims to retain and increase the number of underrepresented minority students pursuing advanced degrees in STEM and medical fields.

If you’re interested in boosting MGSN activities at your school, helping plan events, or even starting a chapter, we’d love to hear from you. Email us at [email protected] to join our listserv and come to our meetings, networking events, and socials. MGSN provides the following to its members: • Academic/research support • Mentoring opportunities with established scientists • Career and personal development workshops • Mixers to foster networking and collaborations • Community outreach projects www.nycmgsn.org

Biology Club News

Interested in Pursuing a Graduate Degree??

The Biology Club Presents

Q&A Event on the Graduate School Process?

Department Calendar

Hunter RISE Program

The Minority Biomedical Research Support (MBRS) program was initiated at Hunter College in 1981 and in 2000 was changed to the Research Initiative for Scientific Enhancement (RISE) program. RISE provides underrepresented students majoring in biology, biochemistry, psychology and physics opportunities to complete research training. Students participating in the program are provided with financial, research and professional support to prepare them for Ph.D programs in biomedical sciences. The students are involved in research projects with faculty members in the biomedical research field on a year-round basis. ​Since its inception, the RISE program has produced approximately 75 Ph.D.&rsquos. Currently, the program provides financial and professional development support for up to 15 undergraduates and 14 Ph.D. students.​​

To apply click here.

Scholarship Opportunity

SciMON (Science Mathematics Opportunities Network) is an innovative institutional initiative designed to enhance the extraordinary research and mentoring programs available to students who study science and mathematics at Hunter College. For more info click here


Watch the video: 01 Einfuehrung in die Organische Chemie (December 2021).