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EXAM WRITING TIPS Time Management

Arrive at least 5 minutes before the exam Give 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 Management
Define key terms Mention as many keywords as possible in logical format No more than 4 to 5 sentences required per answer Double-check your math Attempt 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 Management


Please refrain from suspicious behavior such as looking in the direction of another students 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.

IMPORTANT LECTURE POINTS

Characteristics of living organisms Types of organic molecules Functional groups and number of bonds for each atom of C, H, O, N, P, S Covalent bonds and noncovalent interactions Dielectric constant and forces between particles Dipole moment, polarizable molecules, london dispersion forces Hydrogen bond acceptors and donors Water as the solvent of life, trend of density

LECTURE POINTS
Amphipathic molecules Equilibrium constant Henderson-Hasselbalch equation and pKa Isoelectric point, buf fers, zwitterions Thermodynamic laws and Gibbs free energy Distinguish enthalpy vs. entropy -driven reactions, keeping in mind Temperature Where does energy come from in the breaking of a diphosphate bond? Enzymes, activation energy, rate, transition state 20 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 , hydrophilic/ hydrophobi c , disulfide bridges ( cystine ) Which 2 amino acids have more than one chiral center ? Why cant peptide bonds rotate? Which 6 atoms are within a plane? Which amino acid can form a cis conformati on peptide bond? Phi and psi angle of rotations: why do Ramachandran diagrams only show cer tain 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 1 3 stand for? Know how to interpret a helical wheel. How can pH per turb 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 -parallel Beta turns: distinguish types I and II, understand why they are important for beta sheets Gamma turns: which residues form H bonds compared to beta turns? Tertiary and quaternary structures Agents that disrupt protein structures Steps of protein folding and chaperones Zymogens and proteases: ways by which zymogens are processed into functional proteins, examples Reversible ligand binding

LECTURE POINTS
Association constant, dissociation constant, af finity and Myoglobin and hemoglobin (maternal and fetal): dif ferences, especially af finity and P 50 Prosthetic groups, apoproteins, holoprotein Distal and proximal histidines Sigmoidal curve Cooperative binding (and the role of the proximal histidine) and allosteric regulation, homotropic vs heterotropic modulation of Hb T and R (high O 2 af finity) state BPG, CO 2 , pH (from cell metabolism), Bohr ef fect ( pKa of His146 and binding to Asp94)

LECTURE POINTS
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 V 0 , V max , K cat and K m 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.h tml