Exam 3 TA Review Video

oxidoreductases

class of enzyme that transfers electrons

transferases

class of enzyme that catalyzes group transfer reactions

hydrolases

class of enzyme that catalyzes hydrolysis reactions

lyases

class of enzyme that catalyzes the addition of groups to double bonds, or formation of double bonds by removal of groups

isomerases

class of enzymes that catalyzes the transfer of groups within molecules to yield isomeric forms

ligases

class of enzymes that catalyzes the formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to ATP cleavage

EX ^{double dagger}

Which must be bound more tightly for catalysis to occur? : EX ^{double dagger} or ES?

catalyzed rate / uncatalyzed rate

What is the equation for catalytic power?

lock and key model

model that’s a bit older that says the enzyme already has the exact shape for a substrate to fit.

induced fit model

more accurate model for enzyme catalysis that says an enzyme’s active site may not be perfect for the substrate before binding, but the active site shape kinda changes a little bit once the substrate binds

cofactors

non-protein chemical components required for enzyme activity

coenzymes

organic, non-protein molecules that assist enzymes by carrying chemical groups or electrons (often derived from vitamins)

Are all coenzymes cofactors, or are all cofactors coenzymse?

All coenzymes are cofactors

apoenzyme

the protein portion of an enzyme, typically inactive (without its cofactor / coenzyme)

holoenzyme

the complete, catalytically active enzyme (with its cofactor / coenzyme)

k_-1 could also be written as k₃ and k_-2 could also be written as k₄

Label the following

K_m (Michaelis constant)

term in Michaelis-Menten equation that represents the [S] where V is half of V_max

no

Does K_m depend on enzyme concentration?

steady state assumption

assumption that states the concentration of the ES complex stays constant over time bc rate of ES breakdown = rate of ES formation

Write out the Michaelis-Menten equation

Write out the equation for a Lineweaver-Burk plot in y = mx + b form

first order reaction

What order reaction does the first half of a Michaelis-Menten graph resemble?

zero order reaction

What order reaction does the final half of the Michaelis-Menten graph resemble?

M/s (concentration over time)

What are the units of V₀?

turnover frequency (k_cat)

the number of conversions of S to P over time - allows for the comparison of rate limiting steps and provides information on max catalytic rate

catalytic efficiency

measures how effectively an enzyme converts substrate to product - combines speed with binding affinity (higher ratio = more efficient)

What is the equation for turnover frequency (k_cat)?

What is the equation for catalytic efficiency?

enzyme activity

moles of substrate converted over time - measure of the quantity of active enzyme present under defined conditions

specific activity

irreversible inhibition

when an inhibitor binds to an enzyme permanently disrupting its activity, often by forming a covalent bond; potent inhibitors will mimic the transition state

False; they can be organic or inorganic compounds

True or false: inhibitors are always organic compounds

competitive

Is this competitive, noncompetitive, or uncompetitive?

noncompetitive

Is this competitive, noncompetitive, or uncompetitive?

uncompetitive

Is this competitive, noncompetitive, or uncompetitive?

False; noncompetitive inhibitors can bind to the allosteric site of either the free enzyme or the ES complex

True or False: noncompetitive inhibitors can only bind to the free enzyme

allosteric regulation

What type of enzyme regulation yields sigmoid-shaped kinetics

Ser, Thr, and Tyr

On what three amino acid residues can reversible phosphorylation occur on?

isoenzymes

a type of enzyme regulation where different molecular forms of the same enzyme that catalyze the same reaction but vary in amino acid sequence, allowing precise regulation of enzymea activity

zymogen

inactive precursor forms of enzymes that require biochemical activation, usually by proteolytic cleavage

chymotrypsinogen

example of a zymogen that is converted into the active enzyme form in the small intestine by cleavage at Arg, where it helps digest proteins

chymotrypsin

the active form of chymotrypsinogen

compartmentation

a type of enzyme regulation where enzymes, substrates, and regulatory molecules can be physically separated or located close together

trypsin

What is the enzyme that turns chymotrypsinogen into chymotrypsin?

cooperativity

refers to the interaction between different subunits of an enzyme or protein in response to ligand binding, which affects the binding affinity of other subunits

positive cooperativity

amplifies enzyme activity by increasing the affinity of S to E once the first molecule binds, making it easier for additional molecules to bind

negative cooperativity

lower enzyme activity by reducing affinity of S to E, decreasing the likelihood of further binding after the first molecule attaches

hyperbolic curve

What type of curve does negative cooperativity display?

sigmoidal curve

What type of curve does positive cooperativity display?

MWC Model

explains allosteric proteins existing in relaxed (R) or taut/tense (T) states - all subunits must be in the same state

KNF model

explains how ligand-induced conformation changes could cause subunits to adopt conformations with decreased/increased affinity for the ligand - negative / positive cooperativity

heterotropic effectors

molecule that influence the binding of something other than themselves

homotropic effectors

molecules that influence the binding of themselves

left

an allosteric activator (in cooperativity) shifts the curve to the right or left?

right

an allosteric inhibitor (in cooperativity) shifts the curve to the right or left?

covalent catalysis

mechanism of enzyme catalysis where the enzyme forms a temporary covalent bond with the substrate, creating a more reactive intermediate that facilitates the reaction

Chymotrypsin cleaves carboxyl side of large hydrophobic or aromatic amino acids like Phe, Met, Tyr, and Trp

What is an example of covalent catalysis?

Histidine bc it’s pKa is near 7

What amino acid is often used for acid-base catalysis, and why?

low-barrier H-bond

Special type of H-bond where the proton is more equally shared between the donor and acceptor atoms, rather than being strongly associated with one

60 kJ / mol

What is the approximate energy of a low barrier hydrogen bond?

metal ion catalysis

mechanism of enzyme catalysis where metal ions in an enzyme’s cofactors interact with the substrate, stabilizing the transition state and orienting the substrate for reaction

less than 0.26 nm

What distance do atoms have to be apart for low barrier h bonds to exist

Thermolysin

What is an example of metal ion catalysis?

serine and aspartic acid proteases

What are examples of acid-base catalysis?

acylation

What is an example of covalent catalysis?

formation of glucosyl enzyme intermediate

What is an example of nucleophilic attack catalysis?

hydrolase

What class of enzyme does chymotrypsin belong to?

covalent and acid/base catalysis

What two mechanisms of enzyme catalysis does chymotrypsin use?

serine

What amino acid does chymotrypsin use as a nucleophile?

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