Biochemistry Ch. 2 Flashcards
Catalysts do no impact delta ____ or ____
Delta H, delta G, or the equilibrium position
Enzymes (raise/lower) activation energy
lower
Enzymes (increase/decrease) the rate of reaction
Increase
Enzymes (do/don’t) alter equilibrium constant
Don’t
List the six categories of enzymes
LIL HOT:
1) Ligase
2) Isomerase
3) Lyase
4) Hydrolase
5) Oxidoreductase
6) Transferase
Define oxidoreductases
Category of enzyme that catalyzes oxidation-reduction reactions
What category of enzymes often has a cofactor that acts as an electron carrier
Oxidoreductases
Define reductant
Electron donor
Define oxidator
Electron acceptor
Enzymes with dehydrogenase or reductase in their names are usually what category of enzymes?
Oxidoreductases
Oxidases have ___ as the final electron receptor
Oxygen
Define transferase
Category of enzymes that catalyze the movement of a functional group from one molecule to another
How does aminotransferase work?
Can convert aspartate and alpha-ketoglutarate to glutamate and oxaloacetate by moving the amino group from aspartate to alpha-ketoglutarate.
Kinases are an example of what category of enzyme?
Kinases
Aminotransferase is any example of what category of enzyme?
Transferase
Define kinase
Catalyze the transfer of a phosphate group (usually from ATP) to another molecule
Define Hydrolase
A category of enzyme that catalyzes the breaking of a compound into 2 molecules using the addition of water
What category of enzyme is phosphatase?
Transferase
Describe the mechanism of phosphatase
Cleaves a phosphate group from another molecule
Peptidase is an example of what category of enzyme?
Hydrolase
Nuclease is an example of what category of enzyme?
Hydrolase
Lipase is an example of what category of enzyme?
Hydrolase
Define peptidase
A hydrolase that breaks down proteins
Define nuclease
A hydrolase that breaks down nucleic acids
Define lipase
A hydrolase that breaks down lipids
Define lyase
A category of enzyme that catalyzes the cleavage of a single molecule into 2 products or can synthesize 3 products into 1 molecule
Lyases do not require ____ as a substrate
water
Define synthase
A lyase that catalyzes the synthesis of 2 products into 1 molecule
List examples of oxidoreductases
Most enzymes with dehydrogenase or reductase in their names
List 2 examples of a transferase
aminotransferase and kinases
List 4 examples of hydrolases
phosphatases, peptidases, nucleases, lipases
Define isomerase
A category of enzyme that catalyzes the rearrangement of bonds within a molecule
Depending on the mechanism of the enzyme, isomerases can also be classified as ________
Oxidoreductases, transferases, lyases
Define ligase
A category of enzyme that catalyzes addition or synthesis reactions. typically between larger molecules
Ligases often require _____
ATP
Synthesis reactions with small molecules are usually catalyzed by ____ while synthesis reactions with large molecules are usually catalyzed by ____
Lyases; ligase
Enzymes can affect the ____ but not the ___ of a reaction
Kinetics; thermodynamics
If a reaction is endergonic, energy is ___ and delta G is ___
required; G>0
If a reaction is exergonic, energy is ___ and delta G is ___
released; G<0
The active site is stabilized by _______
H bonding, ionic interactions, and transient covalent bonds
The ___ part of the induced fit model is endergonic
The substrate changing shape to respond to the enzyme
The ___ part of the induced fit model is exergonic
Release of the enzyme from susbtrate, causing both enzyme and substrate to resume relaxed, non-induced forms
Define cofactor
small inorganic molecules or metal ions that bind to the active site of an enzyme and participate in the catalysis of a reaction
Define co-enzyme
small organic groups that bind to the active site of an enzyme and participate in the catalysis of a reaction
Cofactors are often ingested as ______
dietary minerals
Define apoenzyme
Enzymes without cofactors
Define holoenzyme
Enzymes with cofactors
Define prosthetic groups
Tightly bound cofactors or coenzymes that are necessary for enzyme function
Coenzymes are usually ___ or ___ derivatives
Vitamin
NAD+. FAD, and coenzyme A are examples of ___
coenzymes
List 3 examples of a coenzyme
NAD+. FAD, and coenzyme A
List the water-soluble vitamins that also act as coenzymes
B and ascorbic acid (C) vitamins
List the fat-soluble vitamins that also act as coenzymes
A, D, E, K
Fat soluble vitamins are regulated by _____
Partition coefficients
Define partitions coefficient
Quantify ability of molecule to dissolve in a polar vs non polar environment
Increasing ___ will increase the rate of the reaction (reaction velocity = v) until reaching saturation, at which the enzyme is working at maximum velocity (vmax) and the addition of ____ will not change v
[S]
A reaction cannot go any faster once it’s reached ____
saturation
At saturation, the enzyme is working at ____
maximum velocity ( v max)
At saturation, the only way to increase v max is to ____
Increase enzyme concentration
when the reaction rate is equal to half of Vmax, ___ = ____
Km = [S]
Define Km
the substrate concentration at which half of the enzyme’s active sites are full
High Km indicates ___
low affinity for substrate
Low Km indicates ___
high affinity for substrate
Define Kcat
Number of substrate molecules converted to product per enzyme molecule per second
Define Lineweaver-Burk plot
Double reciprocal graph of the Michaelis-Menten equation
Define Michaelis-Menten plot
Plot showing that as substrate increases the rate of reaction increases, until plateauing at vmax
When would an enzyme demonstrate a sigmoid curve on a Michaelis-Menten plot?
When demonstrating cooperativity among substrate binding sites
Phosphofructokinase-1 is an example of a regulatory enzyme demonstrating ____
Cooperativity
Define Hill’s coefficient
A value that indicates the nature of cooperative binding
If Hill’s coefficient >1, then ___
positively cooperative binding occurs so that after 1 ligand is bound the affinity of the enzyme for further ligands increase
If Hill’s coefficient is < 1, then ____
negatively cooperative binding occurs so that after 1 ligand is bound the affinity of the enzyme for further ligands decreases
If Hill’s = 1, then _____
the enzyme does not exhibit cooperative binding
During cooperative binding, when a substrate binds, subunits transition from the ___ state to the ___ state
Tense (T); relaxed (R)
What is the optimum temperature of an enzyme in the human body?
37C (98.6F and 310K)
What is the optimum pH for most enzymes in the human body?
7.4
Most enzymes in the human body are optimal at a pH of 7.4; what enzymes are the exception, where can you find them, and at what pH do they work?
Pepsin, in the stomach, at pH 2; pancreatic enzymes, in the small intestine, at pH 8.5
How does salinity effect enzymes?
In vitro; disrupt H and ionic bonds, causing denaturation
Define feedback regulation
Molecules further down a metabolic pathway that regulate enzymes higher up the pathway
Define feedforward regulation
Intermediate molecules in a metabolic pathway that regulate enzyme higher up in the pathway
List the 4 types of reversible inhibition
1) competitive
2) noncompetitive
3) mixed
4) uncompetitive
Define competitive inhibition
A type of reversible inhibition in which the inhibitor binds to the same active site as the substrate
How can competitive inhibition be overcome?
By adding more substrate
Competitive inhibition doesn’t impact ___ but does increase ___
Vmax; Km
Define noncompetitive inhibition
A type of reversible inhibition in which the inhibitor binds to the allosteric site, causing conformational change in the enzyme
Noncompetitive inhibition decreases ___ but does not change ____
Vmax, Km
Define mixed inhibition
A type of reversible inhibition in which an inhibitor binds equally to the allosteric site on an enzyme or enzyme-substrate complex with a different affinity for each
Which type of reversible inhibition binds to both the enzyme and enzyme-substrate complex? A) competitive inhibition B) noncompetitive inhibition C) mixed inhibition D) uncompetitive inhibition
A and B
_____ inhibitors have an equal affinity for the enzyme and enzyme-substrate complex
Noncompetitive
Mixed inhibition decreases ___ and can increase or decrease ___
Vmax; Km
When would mixed inhibition cause Km to increase
If the inhibitory preferentially binds to the enzyme
When would mixed inhibition cause Km to decrease
If the inhibitor preferentially binds to the enzyme-substrate complex
Define uncompetitive inhibition
A type of reversible inhibition in which an inhibitor binds to the allosteric site of an enzyme-substrate complex and prevents the release of the substrate from the enzyme
Uncompetitive inhibition lowers ___ and ___
Vmax; Km
How does competitive inhibition effect Vmax and Km?
Does not effect Vmax; increases Km
How does noncompetitive inhibition effect Vmax and Km?
Decreases; does not effect Km
How does mixed inhibition effect Vmax and Km?
Vmax decreases; Km increases or decreases
How does uncompetitive inhibition effect Vmax and Km?
Decreases Vmax; decreases Km
Define irreversible inhibition
The binding of an inhibitor that causes permanent conformation change to the enzyme or when the active site is occupied by the inhibitor for a long time
Allosteric enzymes shift between what two forms?
Active and inactive forms
Enzymes can be covalently modified to by activated or deactivated by what two mechanisms?
phosphorylation or glycosylation
Define glycosylation
Covalent attachment of sugar moieties; can tag an enzyme to be transported with a cell or modify protein activity and selectivity
Define zymogen
inactive forms of enzymes that have a regulatory site preventing the catalytic domain from being bound by the substrate
Trypsinogen is an example of what form of enzyme?
Zymogen
Define caspases
Apoptotic enzymes
Most zymogens have the suffix ___
-ogen
Digestive enzymes are typically examples of what form of enzyme and why>
Zymogens; we want to wait for the enzymes to be activated only when it’s time to digest food so that the enzymes don’t digest the stomach lining
