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Week 3
Inter-chain interactions
• Quanternary structure of proteins
– interaction between 2 or more polypeptides
– Disulfide bridges
• cysteine -S-S- cysteine
• --CH2-S-S-CH2-• see Fig. 5-22
Disulfide bridges
• Bridge between two cysteines
• catalyzed by endoplasmic reticulum
enzymes
• broken by reducing agents, e.g.,
mercaptoethanol and dithiothreitol
– CH2-S - S-CH2 - ------> -CH2 -SH + HS-CH2-
Enzymes
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Catalytic proteins
not permenantly changed during catalysis
need native structure to be active
do not alter Keq or delta Go
lower activation energy of reaction
– see Figures 3-12 and 3-14
Factors affecting enzymes
• Temperature
– increases thermal motion of atoms
– disrupts hydrogen bonds
• pH
– change protonation patterns of amino acids
which affects ionic bonds
• Ion concentration
– interferes with ionic bonds between amino
acids
Enyzme-substrate interactions
• Enzyme like a “glove” and substrate like a
“ball”
– substrate fits in the active site of the enzyme
like a ball fits in the glove.
– See Figure 5-24 and 5-27
• E+S ---> ES -->EP --> E + P
– E-enzyme; S-substrate; P-product
Parameters of enzymes
• See Figure 5-30
• V is the velocity of the enzyme
• Vmax is the maximum velocity of enzyme
– can be in the order of 1000’s substrate
molecules per second!
• Km is a measure of the affinity of an enzyme
for its substrate
– lower the Km the greater the affinity
– Km= substrate concentration at 1/2 Vmax
Michaelis-Menten Equation
• V=Vmax [S/(S+Km)]
• Transform above equation = LineweaverBurk plot
– 1/V = (Km/Vmax) x (1/S) + (1/Vmax)
– equation for a straight line
• where 1/Vmax= y intercept
• and (1/S) = x-intercept
– X-intercept = -1/Km
Enzyme regulation
• Allosteric proteins
– proteins with second binding site for “affector
molecules”
• protein changes conformation when affector
molecule binds to the allosteric site
• see Figure 5-34
• Feedback inhibition - negative feedback
– see Figure 5-32
• Feedback stimulation - positive feedback
Enzyme regulation
• Phosphorylated vs dephosphorylated state
– kinase adds phosphate group
– phosphatase removes phosphate group
– See Figure 5-36
• GTP-binding
– See Figure 5-38
Enzyme cofactors
• Co-enzymes
– NAD+, FAD
• Prosthetic groups
– heme, biotin, retinal
• metallic cations
– Zn++, Mg++, Fe++, Fe+++, Cu++, Na+, and K+
Protein analysis
• Refer to Panels 5-4, 5-5 & 5-6 of your text
Enyzme nomenclature