Chem 375 Spring 2005 Study guide for Final Exam

Click here for a copy of last year's final exam

Complete answers to practice problems will be posted outside my office in the glass case.

Brief answers to most of the practice exam questions are available here.

Here are links to the 2005 midterms: Exam 1 and Exam 2

The exam will be held Tuesday afternoon 6/7, in SL130, from 1 pm until 3 pm. Bring a calculator. Partial credit for multi-step problems will be given ONLY if you show your work. In some cases full credit will not be given UNLESS you show the logical progression of your work. Some of the problems are designed to test your ability to solve biochemical problems (such as those in recommended as homework in P&C). In addition other problems will be designed to test your ability to use biological and chemical concepts to suggest likely explanations for biochemical phenomena. You will be given copies of relevant pathways that show the structures of intermediates. You will also be given a very barebones schemes for electron transport.

I will have drop-in office hours: Friday 6/3 8:30am-3pm

Monday 6/6 8:30am-5pm

Tuesday 6/7 8:30am- 12 noon.

This list is not guaranteed to be comprehensive, but it is a very good idea to review the in-class assignments, the past exams, the exam practice questions, and the following topics in preparation for the final exam. The exam will be comprehensive with roughly 50% new material (new since the last exam) and 50% “comprehensive” material (covers entire quarter).

“New” Material:

Glycogen metabolism

how is glycogen metabolism regulated (roles of glucagon, epinephrine and insulin and their various effects in muscle and/or liver tissue)? What are the names of the two major catabolic and anabolic enzymes in glycogen metabolism? Familiarize yourself with the phosphorylation/dephosphorylation cascades discussed in lecture.

Gluconeogenesis

source(s) of substrates (i.e. what are feedstocks for the pathway?)

steps from pyruvate to glucose that differ from glycolytic pathway and the corresponding enzyme names

what is role of biotin?

Citric acid cycle

carbon/electron flow in pathway

conversion of pyruvate to AcSCoA via pyruvate dehydrogenase

substrates and products of citric acid cycle enzymes

steps that generate ATP/GTP/NADH/ FADH₂

fates of C atoms from AcSCoA and OAA (e.g., loss of CO₂; “follow the labeled carbon” problems)

cofactors: What chemistries do they perform? Includes: NADH, FAD, CoASH (and AcSCoA), TPP, biotin, lipoic acid.

Lipids: roles in biological systems, general features (i.e., polar head, non-polar fatty acid tails)

Membranes: fluid mosaic model, composition (lipids, proteins), factors affecting fluidity (length, saturation of fatty acid tail)

Membrane transport: mediated and non-mediated transport, saturation kinetics, thermodynamics of transport for charged and non-charged molecules i.e.,

DG = RTlnQ + nzFDY

coupling ATP hydrolysis to transport (calculating overall free energy change for transport reaction, e.g., Na⁺/K⁺ transporter).

It is highly recommended that you look over the handout given in class on this topic and make sure you understand it.

Bioenergetics:

Calculations based on: DG’ = DG°’ + RTlnQ for redox reactions:

DG°’ = -nFDE°’

Look over the handout given earlier in the course that goes through a calculation of DG for the reaction of NADH and oxygen.

Electron transport and oxidative phosphorylation

Mitochondrion inner membrane features (e.g. selective permeability)

How do electrons enter pathway? (complexes I-IV)

How does each complex contribute to the proton gradient?

What are the two major mechanisms for proton translocation in Complexes I, III and IV?

Effects of inhibitors on the pathway.

Prediction of O₂ consumption curves as a function of added compounds

Chemiosmotic theory

ATP synthase (location, catalytic functions, inhibitors, gross structure)

What are “uncouplers”? How do they work? (e.g. DNP)

Fatty acid catabolism

Activation of free fatty acids to form fatty acyl-CoA (at the expense of ATP)

4 steps of b-oxidation (from initial fatty acyl-CoA to AcSCoA + fatty acyl-CoA that is 2 carbons shorter)

Topics for “comprehensive” review:

General: I still expect you to be able to draw amino acid structures because the sidechain structures determine protein structure and function. Know 1-letter code, structures and properties (i.e. sidechain polarity, charge at pH = 7.0) for the 20 biosynthetic amino acids. You are expected to know the names of the enzymes in the glycolytic and gluconeogenic pathways, and in the citric acid cycle.

Acid-base chemistry: what are pK_a and pI? Given a pI predict overall charge on protein as a function of pH. You will be provided with pK_a information (no need to memorize pK_as for amino acids or buffer salts)

Peptides: predicting the location of N & C termini in a peptide. What is an H-bond (hydrogen bond)? What groups are involved in H-bonding interactions? What are the “mainchain” atoms; what are the “sidechain” atoms in a peptide?

Protein Structure: hierarchy of structure (1°-4° structure), secondary structure (know a-helix, b-sheet structures); how is amino acid sequence related to folded structure (patterns observed in amphiphilic helices and strands)? Tertiary structure: how do 2° structural elements interact in folded structure?

Protein Function: focus on myoglobin and hemoglobin: effects of O₂ binding, H⁺ binding, CO₂ binding and BPG binding on R to T transition. Allosteric regulation of protein function. Ligand binding (i.e. the concept of “COMPLEMENTARITY”).

Enzyme Chemistry:

How do enzymes accelerate reactions (GABC, electrostatic stabilization, covalent, proximity effects)? Use RNase A and chymotrypsin as examples that illustrate these different strategies for rate acceleration

thermodynamic vs. kinetic stability (e.g. why isn’t ATP immediately hydrolyzed in cells?)

what is rate acceleration (ratio of k_cat and k_uncat); how is it calculated from DDG^Ŧ ?

what is the difference between DG, DG°’ and DG^Ŧ ? How are each calculated?

Interpretation of energy diagrams (G vs. reaction coordinate; see pages 172-173)

Enzyme Kinetics:

What are V_max, K_M, k_cat and how are they derived from kinetic data?

What are the slope and y-intercept in a Lineweaver-Burk plot?

What is the Michaelis-Menten model? Why is the plot of v₀ vs. [S] hyperbolic?

Predicting whether a mutation in an enzyme active site will affect K_M (i.e. S binding) or k_cat (effects on catalytic step) or both.

Thermodynamics:

DG’ = DG°’ + RTlnQ (how is DG°’ calculated? What values are used in the Q term?)

biochemical vs. chemical standard state (i.e. the different treatment of water and protons)

how is ATP utilized in biochemical reactions

DG°’ = -RTlnK_eq

solving for DG°’ using coupled reactions

Regulation:

feedback inhibition, allostery, covalent modification (zymogens; phosphorylation)

predicting control points in a pathway (e.g., based on DG, etc.)

how is pathway regulation affected by the cellular energy charge?

Glycolysis/Fermentation:

General features of pathways (what are intermediates and products; which steps are subject to regulation, where is ATP consumed/generated; where do redox reactions occur)

carbon/electron/phosphate flow in pathway (prepare by following the fates of the C atoms in glucose in the pathway)

familiarity with mechanisms of enzymes (glucose -> lactate or EtOH), such that products for reactions could be predicted (i.e. “predict products formed if aldolase acted upon subtrate XYZ”)

cofactors: NAD⁺/NADH and TPP (what chemistry does each cofactor perform?)

calculation the “cost” in terms of ATP for a pathway (e.g., “how many ATP are required to synthesize two moles of GAP from F-6-P?”)

The following will not amount to more than 6-10 pts on the final: You may be asked to predict how one compound is converted to another in one or more enzymatic steps. You will not be expected to have mastery of reactions we have not discussed in lecture; however, you will be expected to predict how a reaction on an unfamiliar substrate would proceed if a familiar enzyme were to act on it (i.e. know the general mechanism of an “aldolase” [C-C bond cleavage of a beta-hydroxy keto compound] or “isomerase” [migration of a carbonyl group as in TIM or PGI], TPP-dependent decarboxylation, etc.). Such questions were asked on the 2^nd midterm (last question).