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EXAM #2 STUDY GUIDE
Chapter 6
1) Conformation
a) Native vs denatured
2) Solvation layer & stability
3) Peptide bond & peptide group
4) Ramanchandran plots
a) Psi vs Phi
5) Secondary structure of proteins
a) Definition
b) Rules for secondary structure
6) *Alpha helix structure
a) Stability & interactions between
R groups
b) Effect of glu, lys, arg; asn, ser, thr,
leu; pro
c) Electric dipole
d) Constraints on structure
7) Beta conformation
a) Beta sheets – parallel and anti-parallel
8) Beta turns
a) Type 1 vs Type 2
9) Tertiary structure
a) Globular vs fibrous
10) *Famous proteins
a) Alpha keratins
b) Intermediate filaments
c) Supertwisted coiled coils
d) Collagen
e) Role of non-standard amino acids
f) Fibroin
g) Myoglobin
11) Supersecondary structures
a) Motifs, folds, domains
12) Protein folding
13) Protein families and superfamilies
14) Quaternary structure
a) Multimer
b) Oligomer
c) Protomer
15) Symmetry
a) Rotational – Cyclic, Dihedral
b) Helical
16) Denaturation/folding
a) Role of chaperonins
Chapter 7
1) Function/structure relationship
2) Ligand/binding site
a) Induced fit
b) Enzymes: substrate/catalytic site
3) Oxygen binding proteins
a) Heme prosthetic group
4) Heme
a) Protoporphyrin IX
b) Porphyrin ring system
c) Iron coordination bonds
d) Ferrous vs ferric states
e) Role of His side chain
f) CO2, NO, CO, O2 binding
5) *Myoglobin – O2 binding
a) Kd for O2
b) Fraction (%) bound
c) Theta (q)
d) pO2
e) P50
f) Oxygen binding curve
6) Protein-ligand interactions and structure
7) *Hemoglobin (Hb)
a) O2 vs CO2 binding
b) Lungs vs tissues
c) Structure (primary, secondary, tertiary
& quaternary)
d) T vs R states
e) DeoxyHb vs OxyHb
f) Bohr effect
g) BPG
8) Co-operative binding effect
a) Binding curve/dissociation curve
b) Concerted vs sequential model
9) Allosteric proteins
a) Homotropic vs heterotropic
10) Hill equation
a) Hill plot
b) Hill coefficient
11) Sickle-cell anemia
a) HbS
12) Examples of complementary interactions
a) Antibody molecules
b) Antigen, immunogen, hapten
c) Epitope
d) MHC molecules
13) *Protein interactions modulated by chemical
energy
a) Myosin (Heavy & light chains)
(1) Heavy & light meromyosin
(2) S1 & S2 fragments
(3) Thick filaments
b) Actin (F vs G)
(1) Thin filaments
Chapter 8
1) Criteria that make enzymes “catalysts”
2) General properties of enzymes
3) Turnover number (kcat)
4) Cofactor vs coenzymes
5) Prosthetic group
a) Holoenzyme
b) Apoenzyme
6) Equilibrium definition
7) Ground state
8) Activation energy (DG?)
9) Standard free energy change (DGo)
a) Biochemical standard free-energy change
(DG’o)
10) Reaction co-ordinate diagrams
a) Function/purpose
b) Axis labels
11) Transition state
a) Reaction intermediates
b) Entropy reduction
c) Desolvation
d) Induced fit
12) Rate-limiting step
13) Binding energy (DGB)
a) Role of covalent bond rearrangement
b) Role of non-covalent bond interactions
14) E-S interaction model
15) *Molecular mechanisms of enzyme catalysis
a) General acid-base catalysis
b) Covalent catalysis
c) Metal ion catalysis
16) Serine proteases
a) *Mechanism of action of chymotrypsin
17) Naming of enzymes
18) Effect of pH, temperature and enzyme
concentration on reaction rate
19) Enzyme kinetics
a) Substrate concentration
b) Vmax
c) Effect of [S] on Vo
20) *Michaelis-Menten Kinetics
a) Equation
b) Assumptions
c) Km
21) Steady state assumption
a) Pre-steady state condition
22) Lineweaver-Burk Equation
a) Double reciprocal plot
b) Equation
c) Axis labels
d) X and Y intercepts
23) kcat/Km (specificity constant)
a) Reason for this ratio
b) Upper limit determination
24) Bisubstrate reactions
a) Reaction pathways: random or specific
order vs ping-pong
25) Reversible enzyme inhibitors
a) Reversible (competitive)
b) Uncompetitive
c) Mixed
d) Effect of inhibitors on Lineweaver-Burk
plot
26) Irreversible inhibitors
a) Suicide inactivators
b) Mechanism-based inhibitors
27) Examples of enzyme mechanisms
a) *Chymotrypsin
b) Hexokinase
28) Allosteric enzymes & modulators
a) Feedback inhibition
b) End product inhibition
c) Effect on binding curve
29) Covalent modification
a) Methylation
b) ADP-ribosylation
c) Phosphorylation
30) Zymogens
Chapter 12
1) Functions and structure of biological
membranes
2) Composition of membranes
a) Lipids
b) Proteins
c) Carbohydrates
3) Fluid mosaic model
4) Lipid bilayer structure
a) Micelles
b) Liposomes
5) *Lipid composition
a) Effect on fluidity
b) Paracrystalline structure
c) Transition temperature
d) Unsaturated vs saturated Fas
e) Sterol content and effect on fluidity
6) Lipid movement
a) Thermal (conformational) motion
b) Lateral diffusion
c) Flip-flop
7) Protein movement
a) Free vs anchored
b) Localization in the membrane
(1) Freeze-fracture; labeling
8) Peripheral vs integral membrane proteins
a) Functions
b) Interaction with membrane
c) Association/Dissociation of membrane
proteins
9) Lipid anchors
10) Types of integral membrane proteins
11) Examples of integral membrane proteins
a) Integrins, cadherins, Ig-like proteins,
selectins
12) Solute transport
a) Function of membrane
b) Simple diffusion
c) Facilitated diffusion (passive transport)
d) Active transport
(1) Primary vs secondary transport
e) Cotransport systems
(1) Symport vs antiport
13) Transmembrane electrical gradient
a) Membrane potential (Vm)
b) Electrogenic transport
14) Examples of facilitated diffusion systems
a) Aquaporins
b) GluT1
c) *Chloride/Bicarbonate Exchange protein
15) Transport ATPase
a) 4 different types
b) CFTR & Cystic fibrosis
16) *Na+/K+ ATPase
a) Mechanism
b) Role in glucose transport
17) Ion gradients
a) Lactose uptake
b) Glucose uptake
18) Ionophores
19) Ion-selective channels
a) Characteristics
b) Ligand vs voltage gated
20) *Nicotinic acetylcholine receptor
a) Structure
b) Function (also see Chpt 13)
c) Neuronal Na+ channels
21) Effect of toxins on ion channels
22) Porins
Chapter 13
1) 3 ways cell communicate
2) Cell signaling – definition
3) Hydrophobic vs hydrophilic ligands
a) Differences in receptor locations
4) First vs second messengers
a) Amplification of signal
5) Three types of cell surface receptors
6) *Molecular mechanisms of signal transduction
a) Specificity, amplification, desensitization,
integration
7) Scatchard analysis
a) Purpose
b) Slope intercept form
c) Axis; X and Y intercepts
8) Gated ion channels
a) Vm
b) 4 most common ions
9) *Nicotinic Acetylchloine receptor
a) Also see Chpt 12
b) 3 states of the Ach receptor
10) Gated ion channels in neurons (Fig 13-5)
11) Receptor enzymes
a) Common features
b) Kinases (types)
c) Phosphatases
d) Role/function of phosphorylation
e) PTKs
12) *Insulin Receptor
a) IRS-1
b) Grb-2
c) SH2 domains
d) Signaling pathway
13) Glycogen synthase activation
14) Guanylyl cyclases
a) Membrane-spanning forms
b) Soluble forms
15) *G-protein coupled receptors
a) General characteristics (serpentine receptors)
b) GEFs
c) Gs vs Gi
16) *Beta-Adrenergic receptor system
a) Beta-arrestin
b) Desensitization
c) GRKs
17) PKA
a) Cyclic nucleotide phosphodiesterase
b) Epinephrine cascade
18) Bacterial toxins
19) cAMP as second msgr
20) *Phosphatidylinositol derivatives
a) PLCgamma
b) PIP2
c) IP3/DAG
21) Calcium as second msgr
a) Calmodulin
b) Calmodulin kinase
22) Steroid hormone receptors
a) HREs
* Denotes potential areas for essay questions. May include questions regarding mechanism of action (chymotrypsin); describing the events involved in signaling (nicotinic acetylcholine receptor) etc. May also include a “list and describe” type of question (Molecular mechanisms of signal transduction) or a compare and contrast (how are two things similar and how are those two things different?)
Page updated: October 9, 2003