Lecture 1

Epigenetics
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Melton lab experiments to reprogram pancreatic cells to insulin-producing

beta cells

Innate versus adaptive immunity

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antigens and antibodies

o antibody specificity depends on shape
why cowpox virus can be used to vaccinate against smallpox

Binding
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expressions for Keq

dissociation: RL R + L, expression for Kd
o What does the value of Kd indicate about the affinity between R and
L? What does it indicate about the relative values of [R] (or [L])and
[RL]?
o measuring Kd using a semipermeable membrane
initial and final states
calculate Kd by counting free R, free L, and RL
what is true about free L at equilibrium (final state)?

Lecture 2: Specificity
Molecular bonds:
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Covalent bonds
o Stability, geometry that determines the shape of molecule, ideal
distance between atoms
o Single and double bonds
Implications for rotation (change in shape of molecule)
o Polar covalent bonds
Electron distribution
Non-covalent bonds
o Hydrogen
directionality
o Ionic
o Van der Waals
Change in energy (attraction vs repulsion) as distance
between atoms changes
o Hydrophobic
Relative strength of non-covalent bonds
o Which are affected by water?
o Effect of temperature on each type of bond
o Effect of pH

Building blocks of macromolecules (should recognize structures):

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sugars polysaccharides

fatty acids fats, lipids, membranes

o saturated and unsaturated
amino acids proteins
o R groups can be acidic, basic, uncharged polar, nonpolar
o Peptide bonds
nucleotides nucleic acids
o components of nucleotide: sugar, base, phosphate

Condensation reactions
Difference between specificity and affinity
Fractional occupancy
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equation
what is the fractional occupancy when the ligand concentration is equal to
Kd?

Definitions of acid, base, pH

Henderson- Haselbalch equation
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what happens when pKA=pH? When pH>pKA? When pH<pKA?

Lecture 3: Thermodynamics
Equilibrium:

For :
o
o

What is the forward rate? Backward rate? What are their relative
values at equilibrium?
What is Keq?

Three laws of thermodynamics

Gibbs Free Energy:
-

G in terms of the free energy of products and reactants

What does G<0 indicate?
G = H-T S
o Which is enthalpy term? When does it indicate a reaction that is
exothermic? Endothermic?
o Which is entropy term?
What is the relationship of S to W (# of permutations)?
When W increases, what happens to G?
How is S related to probability distribution? Which distribution
will maximize S?

How does probability distribution relate to concept of

constraints?
o Boltzmann Distribution
o Use G = H-T S to explain hydrophobic bonds (i.e. organization
of fatty acids into lipid membranes or micelles)
How does G relate to the standard free energy?
o What is the standard free energy? Under what conditions is it
calculated?
How does G relate to Keq?
What is the value of G at equilibrium?
Explain how reactions with a positive value of G occur

Lecture 4: Protein Structure & Function

primary, secondary, tertiary, and quaternary protein structure: be able to define
each term and know the forces involved at each level
thermodynamics of protein folding: calculate G, know which force/s contribute to
the enthalpy and which force/s contribute to the entropy
structures: peptide bond, N- and C- termini of a protein, -helix, -sheet
amino acids: side chain chemistry, N- and C-termini, formation of peptide bonds
protein structure: -helix, -sheet, structural motifs, how structure determines
function
chaperones
reversible and irreversible protein denaturation
Lecture 5: Protein Structure 2 - Myoglobin & Hemoglobin
multivalent binding: independent versus cooperative binding at multiple sites,
fractional occupancy and the Hill equation, thermodynamics of binding
hemoglobin: comparison to myoglobin, heme group and oxygen binding,
physiological function of hemoglobin, saturation as a function of oxygen pressure
(equation and standard curve), factors that affect oxygen binding and how
saturation changes in each case, sequential and concerted models of cooperative
binding, deoxygenated versus oxygenated conformational states, sickle cell anemia
Lecture 6: Bioenergetics & Enzymes
energy of reaction rates: dependence on activation energy (concept and equation),
enzyme catalysis, forward and backward directions
enzymes: definition, substrate specificity, turnover number, competitive versus noncompetitive inhibition, lock and key versus induced fit binding models, reversible
versus irreversible inhibition, allosteric enzymes, reversible activation

Michaelis-Menten kinetics:
reaction rates controlled by [substrate], [enzyme], and enzyme activity
four assumptions that must be hold to make the model valid
equation and plots to describe model as both V versus [S] and 1/[V] and 1/
[S]V, affects of
competitive and non-competitive inhibition
conceptual definition of Km and Vmax
Lecture 7 & 8
DNA vs. RNA:

Nucleotide (phosphate + sugar + base)

Ribose vs deoxyribose
Adenine, guanine, cytosine, Thymine/uracil
Pyramidine vs purine
5 to 3 polarity
Antiparallel
Double helix and basepairing

DNA Replication:

Replication origin
Replication fork
DNA polymerase (proofread function)
Template
Okazaki Fragments
RNA primers / RNA primase
Nuclease
Repair Polymerase
DNA ligase
DNA helicase
DNA single-strand binding proteins
Protein clamp / slide clamp

Telomere/ telomerase
Mechanisms of fixing replication errors (DNA repair)
Transcription:

Where does this occur?

mRNA, tRNA, rRNA
RNA polymerase (vs. DNA polymerase)
Sigma factor
Transcription is 5 -> 3, so DNA template is 3 -> 5
Bacterial mRNA vs. eukaryotic mRNA
o Post-processing/maturation? (and WHERE does this occur in cell?)

o
o
o
o

Protein synthesis during mRNA synthesis?

Exons and introns?
Operons?
5 methyl cap, poly A tail?

Translation:

Where does translation occur?

Codon (= 3 nucleotides, on mRNA)
Anticodon (tRNA)
Wobble pairing (what is this, and what position in codon, anticodon)
How is ATP involved in translation?
Ribosome
o Large and small subunits
o 3 sites on ribosome: E, P, A (what happens at each site?)
Initiation factors and initiation sequence of events
Elongation factors sequence of events involving E, P, A sites ans tRNA
Termination factors
Polyribosome (polysome)

Translation