Chapter 1 (Pt. 2) Flashcards
what is a proteome?
all of the proteins expressed by a cell under certain conditions. like a genome for proteins.
how can two different cells in the same organism have differing proteomes?
proteome is based on which genes are active in a cell
what is the subunit of polypeptides?
amino acids
what are polypeptides
polymers that make up proteins
what is the structure of an amino acid? (4)
central alpha carbon
amino group
carboxyl group
variable R group
how many amino acids are there?
20 AAs
what happens to an AA at physiological pH?
amino group protonated, carboxyl group deprotonated
what is the value of physiological pH
7.4
what is the role of peptide bonds?
attach AAs to each other
peptide bonds are formed by which type of reaction?
dehydration
peptide bonds are broken by which type of reaction?
hydrolysis
what are the specific ends of a polypeptide?
C terminus (carboxyl)
N terminus (amino)
describe primary protein structure.
what determines this?
sequence of AAs
genes.
describe secondary protein structure.
what determines this?
local folds in a polypeptide chain.
H bonding between atoms on polypeptide backbone.
what is required for hydrogen bonding?
H binds to F, O, N
which parts of a protein will participate in hydrogen bonding?
carbonyl and amino groups
what is tertiary protein structure.
what determines this?
3D folding pattern of the polypeptide.
due to R group interactions
what are some R group interactions? (5)
ionic
hydrogen
dipole-dipole
london dispersion
hydrophobic
what are disulfide bridges.
what is their role?
in what protein structure are they found?
covalent likages.
hold protein in most stable conf.
tertiary protein structure
folding of a tertiary protein structure positions nonpolar R groups where as a result of hydrophobic interaction?
inside a loop, isolated from water
describe quaternary protein structure.
one large protein with multiple subunits.
what does denaturing proteins mean?
what happens when proteins are denatured?
protein misfolding.
protein loses higher order structures, but primary structure is retained.
name four common denaturation agents
heat
chemicals
pH changes
radiation
protein misfolding causes what?
loss of shape –> loss of function
what three principles govern catalysts
- increase reaction rates
- do not affect spontaneity
- not used up in the reaction
how do catalysts work?
lower activation energy
what is the difference between an enzyme and a catalyst?
same rules apply, enzyme is a biological catalyst.
what are enzymes made of?
proteins
what is the active site made of?
AAs
what does substrate specificity of an enzyme means?
enzyme only binds to certain molecules
what is the enzyme specificity constant?
measure of an enzyme’s efficiency
what does a high specificity constant mean? (2)
- highly efficient enzyme
- enzyme active site has a high substrate affinity
what are the two enzyme models you learned in physiology?
- lock and key model
- induced fit theory
induced theory states that…
enzymes slightly change shape to accomodate substrate
lock and key model states that…
enzymes are rigid. not accurate.
are all enzymes proteins?
no! ex. ribozymes (RNA)
why would knowing about ribozymes be interesting?
they are an RNA enzyme, indicating that not all enzymes are proteins
what are enzyme cofactors?
non-protein molecules that assist enzymes
can you name the two types of enzyme cofactors with some examples of each?
i can.
- organic cofactors: vitamins (coenzymes; vitamin C)
- inorganic cofactors: metal ions (iron, potassium)
what are holoenzymes/
enzyme bound to a cofactor
what are prosthetic groups?
cofactors that bind covalently to their enzyme
what would a holoenzyme look like in a nice little drawing?
it would be the one that has the cofactor or coenzyme bound to the enzyme
what is an enzyme?
a biological catalyst. meaning, it increases reaction rates without affecting spontaneity or being used up in the reaction.
what is an apoenzyme?
enzyme not bound to a cofactor.
what would an apoenzyme look like in a nice little drawing?
the enzyme would not be bound to the cofactor/coenzyme
what factors might affect enzymatic activity?
changes in pH/temp –> change shape –> change function
what does “enzyme inhibition? mean?
interfering or suppressing normal enzyme function
what is the difference between competitive vs. noncompetitive inhibition?
COMPETITIVE: inhibitors compete for active sites. adding substrate can overcome this type of inhibition.
NONCOMPETITIVE: inhibitor binds to allosteric site, which modifies active site. cannot be overcome by adding more substrate, because substrate and inhibitor don’t compete for active site.
ENZYME KINETICS:
what is V?
what is Vmax?
what is [X]?
V: velocity. rate at which reaction occurs.
Vmax: maximum reaction velocity.
how would Vmax be illustrated in a nice little drawing?
substrate has filled up all the enzymes.
what the name of Km?
what does it represent?
Michaeli’s constant.
[X] at 50% of Vmax
large Km = ?
why?
low affinity for substrate.
a lot of substrate was needed to get to 50% of Vmax
small Km = ?
why?
high affinity for substrate
not a lot of substrate was needed to reach 50% of Vmax
what happens to Vmax and Km under COMPETITIVE INHIBITION conditions?
Vmax stays the same
Km increases
what happens to Vmax and Km under NONCOMPETITIVE INHIBITION conditions?
Vmax decreases
Km stays the same
can you name three examples of enzymes?
sure i can! i learned about these in physiology.
phosphatase
phosphorylase
kinase
what type of inhibition can be overcome by adding more substrate?
competitive
what does a low Km imply as opposed to a high Km?
low: high affinity for X
high: low affinity for X
how do enzymes increase reaction rate?
lowering the energy of the transition state, which lowers the activation energy
