Day 11, Lecture 2: Proteins: Enzymes Flashcards
1
Q
Enzymes and the transition state
A
- Enzymes make the transition state
- appears more often in a reaction mixture with the active site (residues involved in catalysis)
- Enzymes stabilize the transition state by forming favorable interactions iwht active site
- An alternative reaction pathway with a lower energy barrier is utilized
2
Q
The vast majority of the interactions of the substrate and the amino acids of the active site are
A
- noncovalent: ionic, hydrogen, van der Waals, and hydrophobic interactions
- Note that Van der Waals and hydrogen my give the enzyme the best specificity
3
Q
Induced fit model of enzymes
A
- Enzymes often undergo a conformational shape change during catalysis (induced fit model) to bring functional groups into play on the substrate. After substrate is converted into products, the enzyme no longer “holds” onto the product and it diffuses away
4
Q
Examples of how some enzymes use cofactors to alter the substrate
A
- Metal ions
- Fe2+, Zn2+, Mn2+
- coenzymes
- diffusible (e.g. the NAD, FAD groups donate/accept H- or 2H)
- Prosthetic groups
- Covalently bound (e.g. biotin group is a CO2 carrier
5
Q
Tay-Sachs disease
A
- common lipid storage disease
- result of complete loss of a single enzyme, hexosaminidase A
- loss leads to lipids accumulating in cells causing severe and ultimately fatal disease by age 3
*
- loss leads to lipids accumulating in cells causing severe and ultimately fatal disease by age 3
6
Q
The majority of drugs are enzyme ____
A
inhibitors
7
Q
Michaelis-Menten Plots
A
- V vs. {S}
- Maximal Velocity, Vmax
- Defined as the reaction rate where enzyme is saturated with substrate
- Michaelis constant, Km
- Defined as the concentration where velocity is 1/2 of Vmax
8
Q
Lineweaver-Burke or Reciprocal Plot
A
9
Q
Irreversible inhibition
A
- Covalent complex of inhibitor and enzyme
- Inactivates enzyme by a reaction of the I with a critical site. (ex. an acetyl group from aspirin reacts with cyclooxygenase; organophosphate nerve gas and pesticides react with the reactive serine of acetylcholinesterase
10
Q
Competitive inhibition
A
- Reversible Inhibition
- Substrate cannot get to the active site when inhibitor is bound at active site- mutually exclusive binding (inhibitor typically resembles substrate)
- Inhibitor works best at low [S]
- inhibitor makes the measured Km value appear higher since more S required for availability to enzyme
11
Q
Noncompetitive inhibition
A
- Reversible inhibition
- Inhibitor and substrate bind simultaneously to the enzyme molecule at different sites and productive catalysis is slowed or prevented (special- allosteric inhibition)
- Works at a different site on enzyme, thus inhibition possible at any [S] (nice choice for a drug)
- Km value same with or without I present (just takes some of the enzyme out of action) but the Vmax is decreased
12
Q
How to treat methanol (wood alcohol) poisoning or ethylene glycol (antifreeze)
A
- Both cause the conversion of the initial compound into toxic metabolites (formaldehyde, formic acid, and oxalic acid) by alcohol dehydrogenase in the body
- Ethanol can be used as a competitive inhibitor to keep the methanol or ethylene glycol from the active site
13
Q
Effect of pH on enzymes
A
- The catalytic groups of enzyme and/or groups of the substrate must be in proper protonation state
- Typically a peak of activity in a certain pH range
- But at pH extremes, global folding problems or precipitation
14
Q
Effect of Temperature on Enzyme activity
A
- All chemical reactions proceed quicker with higher temperature
- but at a certain point, the enzyme can be denatured as the weak bonds that hold proteins together for most part eventually are broken
15
Q
do allosteric enzymes obey typical kinetics
A
No they are sigmoidal and not hyperbolic
16
Q
A
