Biochemistry Exam 2

Front 1

Give the formulas for the Michaelis-Menten equation and the Lineweaver-Burk equation. Show a typical kinetic plot that could be obtained using each equation. Why is the Lineweaver-Burk equation preferred for plotting experimental data?

Back 1

The formula for the Michaelis-Menten equation is V=(Vmax*[S])/([S]+Km); and the formula for the Lineweaver-Burk equation is 1/V=(Km+[S])/(Vmax*[S])=((Km/Vmax)*(1/[S]))+(1/Vmax). The Michaelis-Menten equation is a rational function and rational functions can be difficult to work with graphically, so the Michaelis-Menten equation can be transformed into a linear equation, the Lineweaver-Burk equation.

Front 2

How is enzyme catalysis achieved? What does an enzyme actually do to its substrate to catalyze its modification or breakdown? How does an enzyme lower the energy of activation for a reaction? Don’t just say that an enzyme binds substrate to form an ES complex (that doesn’t explain catalysis). Tell me how the enzyme active site interacts with the substrate to speed the rate of a reaction.

Back 2

Generally, enzymes lower the activation energy of a reaction by offering an better pathway for the non-catalyzed reaction to occur. They stabilize a transition state in such a way that allows it to carry out the reaction, but at the same time not associate too tightly so that the products can be easily released after completion. For a given substrate this could mean (but not limited to) binding that allows a perfect position for some kind of molecular attack, the stretching of bonds to ease their breakage or the exclusion of competing molecules from the binding pocket (like H2O). All of these work to lower the gibb's energy for the product, allowing a more efficient pathway for the reaction to occur.

Front 3

Describe the biochemical structure of phosphoglycerols and the function of these compounds in biological membranes. What component of phosphoglycerols contributes to their liquid character?

Back 3

Phosphoglycerols are a component of phospholipids, a type of amphipathic molecule with a glycerol backbone, a phosphate group on its C1 carbon, and 1-2 acyl chains on the C2 and C3 carbon. The phosphate headgroup is polar (due to the phosphate and oxygens) which makes it hydrophillic (water loving since water is polar too). The acyl chains on the other hand can be either a saturated (all single bonds) or unsaturated (has 1 or more double bonds) carbohydrate chain, which makes it hydrophobic (water hating, nonpolar). The liquid characteristics of phosphoglycerols comes from the acyl side chains at C2 and C3. These acyl chains are long and generally have a lot of motion to them, since entropy increases with increasing molecular complexity. The double bonds in the acyl chains gives them kinks which further increases the motion to the acyl chains and increases the spacing between adjacent phospholipids in a membrane. This motion and spacing contributes to a liquid-type medium where other lipids and proteins can laterally diffuse relatively freely.

Front 4

Outline the process of semi-conservative replication and describe the key experiment that supported this mechanism.

Back 4

Semi-conservative replication means that when the double stranded DNA helix was replicated, each of the two double stranded DNA helices consisted of one strand coming from the original helix and one newly synthesized. Meselson and Stahl tested the hypothesis of DNA replication. They cultured bacteria in a 15N medium. They then shifted the bacteria to a 14N medium, DNA was isolated at different times corresponding to replication cycles 0, 1, and 2. After one replication cycle, the DNA was all of intermediate density. After two replication cycles, two bands of DNA were seen, one of intermediate density and one of light density.

Front 5

Outline the fluid mosaic model for biological membranes.

Back 5

Biological membranes are important for rigidity, structure and to form a semi-permeable interface between aqueous environments. However, despite all that, there is still a large liquid like movement in the membrane. This is the basis of the fluid mosaic model. Basically, the membrane is made up of phospholipids (and other lipids like sphingolipids, sterols, etc). These lipids are hydrophillic on one end allowing it interface with the aqueous environment, and hyrdrophobic on the other end... usually because of the long hydrocarbon (Acyl) chains they have. Thus the membrane forms a phospholipid bilayer with the acyl chains of two phospholipid molecule facing towards each other and the head group facing outwards. The entropic motion in the long acyl chains creates spacing between neighboring phospholipids. The longer the chains or the more kinks (double bonds) they have, the more motion and thus more spacing. Of course the membrane has other components to it, more specifically, it has a large amount of proteins (integral) which can insert themselves into the membrane and anchor themselves there. Thus adding a type of mosaic composition to the membrane. The fluidity comes from the spacing freedom of motion of these lipids and proteins within the membrane. Due to the movement of acyl chains, proteins and other lipids can laterally diffuse throughout the membrane. In fact, the membrane is about 100x more viscous than water, but still liquid/fluid like. Yet, even though they adopt this fluidity and liquid like state, they still stand as a strong kind of barrier for the cell.

Front 6

How do integral membrane proteins differ from peripheral membrane proteins in structure and in the way they are associated with biological membranes? How are the two types of proteins released from the membrane, and how do they behave after they are released?

Back 6

Integral membrane proteins - span the width of the cell membrane, meaning that they have a hydrophobic core that can interact with the hydrophobic acyl chains of the lipid bilayer, thus locking the membrane protein to the membrane. peripheral membrane proteins - associate with the inner leaflet of the phospholipid bilayer through electrostatic interactions or apical monotopic hydrophobic hooks that insert slightly into the bilayer and come out on the same side.Mild denaturating agents can release peripheral membrane proteins since they're not firmly embedded in the membrane. To extract the integral membrane protein, you would need to lyse the cell and use strong denaturing agents and possibly another lipid film intermediate. Since peripheral membrane proteins can dissociate from the membrane at times, releasing it from the membrane doesn't have a drastic conformational effect. Integral membrane proteins on the other hand do since their hydrophobic core would now be exposed to the hydrophillic environment, causing conformational changes to the protein.

Front 7

Describe the differences in structure and function between hemoglobin and myoglobin and explain how the oxygen binding response of hemoglobin aids in its biological function?

Back 7

Myoglobin - a single polypeptide chain containing a heme group that tightly binds to Oxygen. It has a greater affinity to Oxygen than Hemeglobin, however, it's not found in the circulatory system. Hemoglobin - a tetrameric protein that is composed of 4 subunits (a1, a2, b1, b2), each of which is similar to myoglobin and contains a heme group, allowing for the transport of 4 oxygens. It's found in the circulatory system to delivery oxygen to tissues. Hemoglobin has to have the ability to tightly bind to oxygen and also to release it when intended. This is accomplished by a sort of conformational change in the hemeoglobin subunits. A high amount of O2 pressure is needed to attach an Oxygen molecule to the heme group of a single subunit, this is achieved in the capillaries of aveoli. One addition of oxygen allows for a homotropic response where it induces the binding of oxygen to the other subunits... thus encouraging the loading of 4 oxygen molecules to the protein. When this protein is traevlling through the circulatory system, a 2,3-biphosphoglycerate (BPG) molecule can bind to the protein and trigger another conformation change to the protein. This, along with the low O2 encourages the release of oxygen molecules from the heme groups to be taken up by myoglobin.

Front 8

List five kinds of lipids and explain the major role of each lipid type in living organisms.

Back 8

(1) Fatty acids: Used to synthesize triglycerides and phospholipids or catabolized to generate adenosine triphosphate (ATP).

(2) Triglycerides: (fats and oils) Protection, insulation, energy storage.

(3) Phospholipids Major lipid component of cell membranes.

(4) Steroids: (a) Cholesterol Minor component of all animal cell membranes; precursor of bile salts, vitamin D, and steroid hormones. (b) Bile salts Needed for digestion and absorption of dietary lipids. (c) Vitamin D Helps regulate calcium level in the body; needed for bone growth and repair. (d) Adrenocortical hormones: Help regulate metabolism, resistance to stress, and salt and water balance. (e) Sex hormones Stimulate reproductive functions and sexual characteristics.

(5) Eicosanoids (Prostaglandins and leukotrienes) Have diverse effects on modifying responses to hormones, blood clotting, inflammation, immunity, stomach acid secretion, airway diameter, lipid breakdown, and smooth muscle contraction.

Front 9

What does it mean the biological membranes exhibit sidedness and how do the various membrane components exhibit sidedness?

Back 9

Proteins are oriented in the Golgi when they’re glycosylated for extracellular exposure of their added carbohydrate side chain. In this way the membrane associated proteins carry out cell surface or cytosol specific functions. Orientation of each bilayer leaflet is maintained (cytosolic vs non-cytosolic) to alter how each face functions. The outer bilayer leaflet has a different phospholipid/glycolipid content, mainly phosphatidylcholine and sphingomyelin. Whereas phosphatidylethanolamine and phosphatidylserine are the predominant phospholipids of the inner leaflet. Glycolipids make up only 2% of a membrane and are found exclusively in the outer leaflet of the plasma membrane, with their carbohydrate portions exposed on the cell surface. The head groups of both phosphatidylserine and the minor constituent phosphatidylinositol are negatively charged, so their predominance in the inner leaflet results in a net negative charge on the cytosolic face of the plasma membrane.

Front 10

What are transition state intermediates in enzyme reactions? Using chymotrypsin as an example, describe the unstable and semi-stable intermediates in this enzyme reaction.

Back 10

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