Time ManagementArrive at least 5 minutes before the examGive yourself about 1 minute per MCQ and 3 minutes per short answer (by the half hour mark, you should be done all MCQ)

In excess time, return to difficult questions and check your answers

Use the washroom before or after the exam if possible

EXAM WRITING TIPS

Answer ManagementDefine key termsMention as many keywords as possible in logical format

No more than 4 to 5 sentences required per answer

Double-check your mathAttempt process of elimination or logical deduction. Never leave blanks!

In cases of ambiguity, clarify it with the TA or your professor by raising your hand.

EXAM WRITING TIPS

Behavioral ManagementPlease refrain from suspicious behavior such as looking in the direction of another student’s exam paper.

Please refrain from cheating.Please switch off all communication devices and keep them in your bags.

Please refrain from visiting the washroom excessively as invigilating grad students have to go with every student.

EXAM WRITING TIPS

IMPORTANT LECTURE POINTS

Characteristics of living organismsTypes of organic moleculesFunctional groups and number of bonds for each atom

of C, H, O, N, P, SCovalent bonds and noncovalent interactionsDielectric constant and forces between particlesDipole moment, polarizable molecules, london

dispersion forcesHydrogen bond acceptors and donorsWater as the solvent of life, trend of density

LECTURE POINTS

Amphipathic moleculesEquilibrium constantHenderson-Hasselbalch equation and pKa Isoelectric point, buffers, zwitterionsThermodynamic laws and Gibbs free energyDistinguish enthalpy vs. entropy-driven reactions,

keeping in mind TemperatureWhere does energy come from in the breaking of

a diphosphate bond?Enzymes, activation energy, rate, transition state20 amino acids, L chirality,

hydrophilic/hydrophobic, disulfide bridges (cystine)

Which 2 amino acids have more than one chiral center?

LECTURE POINTS

20 amino acids, L chirality, ampholytes, hydrophil ic/ hydrophobic, disulfide bridges (cystine)

Which 2 amino acids have more than one chiral center? Why can’t peptide bonds rotate? Which 6 atoms are within a

plane? Which amino acid can form a cis conformation peptide bond? Phi and psi angle of rotations: why do Ramachandran diagrams

only show certain combinations of phi and psi for normal proteins?

Distinguish main chain from side chains Conventional directionality of amino acid sequences When calculating overall charge, remember the N and C terminus The metastability of peptide bonds Levels of protein structure and type of interactions at each level Alpha helices: what does 3.6 13 stand for? Know how to interpret a

helical wheel. How can pH perturb the structure of an alpha helix? Which 2 amino acids are not favorable for alpha helices? Why?

LECTURE POINTS

Types of interactions that constitute each type of secondary structure

Beta sheets: distinguish mixed, parallel vs anti-parallelBeta turns: distinguish types I and II, understand why

they are important for beta sheetsGamma turns: which residues form H bonds compared

to beta turns?Tertiary and quaternary structuresAgents that disrupt protein structuresSteps of protein folding and chaperonesZymogens and proteases: ways by which zymogens

are processed into functional proteins, examplesReversible ligand binding

LECTURE POINTS

Association constant, dissociation constant, affinity and θ

Myoglobin and hemoglobin (maternal and fetal): differences, especially affinity and P50

Prosthetic groups, apoproteins, holoproteinDistal and proximal histidinesSigmoidal curveCooperative binding (and the role of the proximal

histidine) and allosteric regulation, homotropic vs heterotropic modulation of Hb

T and R (high O2 affinity) stateBPG, CO2, pH (from cell metabolism), Bohr effect (pKa

of His146 and binding to Asp94)

Cofactors and coenzymes 6 enzyme classes 5 enzyme mechanisms

Serine proteases e.g. chymotrypsin: where do they cleave and what is the role of serine?

Kinetics Relationships between rate, rate constant and activation energy First order kinetics Reaction intermediates, transition state and the rate limiting step V0, Vmax, Kcat and Km Lineweaver Burke Plots Steady state assumption

Transition state analogs, irreversible/reversible inhibition, covalent adducts, competitive/non-competitive/uncompetitive inhibition

Optional: how to derive the Michaelis Menten Equation http://www.bgu.ac.il/~aflaloc/BioHTML/Goodies/DeriveMMEqn.html

LECTURE POINTS