Biochemistry Flashcards
How does an enzyme change the thermodynamics of a reaction?
It doesn’t! Enzymes ONLY change the kinetics of a reaction, not heat, and not enthalpy.
What are the 6 classifications of enzymes?
LILHOT: Ligase, Isomerase, Lyase, Hydrolase, Oxidoreductase, and Transferase
What do oxidoreductases do?
Catalyze oxidation/reduction rxns
What do transferases do?
Catalyze a transfer of a functional group from one molecule to another molecule
How are transferases named?
trans{functional group}ase, or [functional group] transferase
What is kinase?
A transferase enzyme that transfers a phosphate group from ATP
What classification is polymerase?
Transferase: they transfer nuecleotides onto DNA or RNA
What do hydrolases do?
Catalyze cleavage of a molecule into 2 parts by the addition of H2O and the reverse rxn of dehydration synthesis by removing H2O
How do you name hydrolases?
[substrate] hydrolase, or [substrate]ase (EX: peptidase, nuclease, lipase)
What is a proteinogenic amino acid?
The 20 “common” amino acids that we traditionally think of. The amino and carboxyl groups are both attached to the alpha carbon (alpha amino acids).
What is the common optical activity of all amino acids used in eukaryotes?
L
What is the common chiral configuration for amino acids?
What is the exception?
S, except cysteine which is R
What are the nonpolar nonaromatic amino acids?
Glycine, alanine, valine, leucine, isoleucine, methionine, proline
What is the side chain of glycine?
H
What is the side chain of alanine?
methyl
What is the side chain of valine?
isopropyl
What is the side chain of leucine?
isobutyl
What is the side chain of isoleucine?
sec-butyl
What is the side chain of methionine?
ethyl-sulfur-methyl (in one long chain)
What is the side chain of proline?
5 member ring including the alpha carbon and nitrogen
What are the aromatic amino acids?
tryptophan, phenylalanine, tyrosine
What is the side chain of tryptophan?
“W” double ring
What is the side chain of phenylalanine?
phenyl group
What is the side chain of tyrosine?
phenol group
What are the polar amino acids?
serine, threonine, asparagine, glutamine, cysteine
What is the side chain for serine?
a carbon followed by a hydroxyl
What is the side chain of threonine?
2 carbons w/ a hydroxyl branched off the 1st
What is the side chain of asparagine?
a carbon followed by an amide group
What is the side chain of glutamine?
2 carbons followed by an amide group
What is the side chain of cysteine?
a carbon followed by a thiol group
What are the acidic amino acids?
aspartic acid and glutamic acid
What are the basic amino acids?
lysine, histidine, and arganine
What is the side chain of aspartic acid?
a carbon followed by a carboxyl group
What is the side chain of glutamic acid?
2 carbons followed by a carboxyl group
What is the side chain of lysine?
4 cabons followed by an amino group
What is the side chain of histidine?
a carbon connecting an imidazole
What is the side chain of arganine?
3 carbons followed by a monster with 3 amino groups built in; this is the mother of basic AA’s because the + is stabilized through resonance
What are the 5 ways that enzymes lower activation energy?
transition state stabilization, microenviroment adjustments, adjusting substrate proximity, transient covalent bonding, and reactant destabilization
How does an enzyme effect Gibbs free energy of a rxn?
it doesn’t
What are the theoretical models for enzyme substrate binding? Which one is better?
Lock and Key, and Induced Fit Model
The induced fit model is better
What do lyases do?
They cleave a molecule without the addition of water. They can also catalyze the reverse rxn and synthesize stuff
How do you name a lyase?
[substrate] lyase, or [product] synthase
What does an isomerase do?
transfers the position of a functional group within a molec
How do you name an isomerase?
[substrate] isomerase, or [substrate]ase
What does a ligase do?
catalyse synthesizes by fusing large molecules together using ATP (MUST HAVE ATP)
How do you name a ligase?
[substrate] synthase (also use for lyases), or [substrate] synthetase (SPECIFIC FOR LIGASE)
Which class of enzymes MUST use ATP?
ligases
What is the Michaelis-Menten eqn?
vel = (Vmax*[S])/(Km+[S])