Biochemistry entry 3 PUM 2nd year | Quizlet

recommended and systematic name

each enzyme is assigned two names

recommended name

consists of substrate of action with suffix ''ase'' added, description of performed action and original trivial name

systematic name

six major groups with subgroups, suffix ''ase'' is attached, each enzyme gets classficatio number

Oxidoreductase

1. enzyme class that catalyzes oxidation-reduction reaction

lactate dehydrogenase

example for oxidoreductase that turns lactate into pyruvate

transferases

2. Enzyme class that catalyzes transfer C, N, P containing groups

serine hydroxymethyl transferase

example for transferase that turns serine into glycine

hydrolases

3. enzyme class that catalyzes cleavage of bonds by addition of water

urease

example for hydrolase that turns Urea into CO2 + NH3

Lyases

4. enzyme class that catalyzes cleavage of C-C, C-S and certain C-N bonds

pyruvate decarboxylase

example of Lyase that pyruvate into Acetaldehyde

Isomerases

5. enzyme class that catalyzes rearrangement of optical or geometric isomers

Methylmalonyl CoA mutase

example of isomerase that turns Methylmalonyl CoA into Succinyl CoA

Ligases

6. enzyme class that catalyzes bond formation between C and O,S, N coupled to hydrolysis of high energy phosphates

Pyruvate carboxylase

example of Ligase that turns Pyruvate into Oxaloacetate with energy from ATP

ATP

synthetases requires what

no ATP

synthases requires

H2O

phosphotases need what to remove phosphate group

inorganic phosphate

phosphorylase needs what to remove phosphate group

efficient, specific protein catalyst

properties of enzymes

active site

special cleft formed on enzyme molecule by protein folding

substrate enzyme complex (ES)

Substrate binds enzyme to form

substrate binding and catalysis

active site contains amino acids residues whose R groups participate in

induced fit model

though to conformational change enzyme that allows rapid conversion of ES to EP (enzyme product complex)

free enzyme and product

enzyme product complex (EP) dissociates into

10 hoch 3 to 10 hoch 8 times faster

Enzymes catalyze reactions making them how much faster than uncatalized reactions

turn over number Kcat

number of substrate molecules converted to product per enzyme molecule per second

10 hoch 2 to 10 hoch 3 seconds

Kcat of enzymes

one type of chemical reaction

enzymes are highly specific they can only catalyze

set of enzymes synthesized in the cell

determines which reaction can occur in a cell

holoenzyme

enzyme that requires protein and non protein component to have enzymatic activity

apoenzyme

holoenzyme without non protein moiety (inactive)

cofactor

non protein moiety is a metal ion its called

coenzyme

non protein moiety is small organic molecule its called

vitamins

coenzymes are commonly derived from

prosthetic group

when coenzmy is permanently associated to enzyme its called

intracellular

where do most enzymes function

compartmentalization

many enzymes are localized in specific organelles within cells this is called

isolates reaction substrate/product from competing reactions

function of compartmentalization

degradation of complex macromolecules

biochemical pathways that happen in lysosome of cell

DNA/RNA Synthesis

biochemical pathways that happen in nucleus of cell

glcolysis, PP pathway, fatty acid synthesis

biochemical pathways that happen in cytosol

TCA cycle, fatty acid/pyruvate oxidation

biochemical pathways that happen in mitochondria

energy change, how active site chemically facilitates catalysis

two perspectives mechanism of enzyme activity can be viewed

activation energy (Ea)

energy barrier separating reactants and products

reactants and transition state energy (T)

activation energy is the difference between

transition state (T)

high energy intermediate formed during conversion of reactant to product

high Ea

uncatalysed reaction are often slow because of

rate of reaction

determined by amount of molecules that contain sufficient energy to overcome T

faste

enzymes provide alternative reaction pathway with lower Ea which allows reaction to occur

free energy of reactant/product, equilibrium

enzyme does not change

accelerates rate equilibrium is reached

enzyme does not change equilibrium but

active site chemistry

complex molecular machine that employs chemical mechanisms and facilitates substrate product conversion

transition state stabilization

active site acts as flexible molecular template that bonds substrate and initiates transition state conversion and stabilizes it to increase concentration

catalytic groups that enhance probability of T state

active site catalysis by providing this

acid-base catalysis

amino acids provide or accept protons

covalent catalysis

in some enzymes catalysation involves transient covalent ES complex formation

mechanisms in chymotrypsin action

histidine of active site gains/looses protons because pK is close to physiologic pH; serine at active site forms transient covalent bond with substrate

temperature, pH, substrate concentration

different enzymes have different responses to Changes in

velocity (v)

number of substrate molecules converted to product per unit time

micro mol of product per second

velocity is expressed as

maximal velocity (Vmax) is reached

rate of enzyme catalyzed reaction increases with substrate concentration until

Michaelis-Menten kinetics

initial reaction velocity (V0) plotted against substrate concentration is hyperbolic

allosteric enzymes

only enzyme type that show sigmoidal curve when initial reaction velocity (V0) is plotted against substrate concentration

35-40 degrees

Optimum temp for human enzymes to function before they get denatured

70 degrees flexion, 10 degrees supination

optimum temp for thermophilic bacteria before they get denatures

enzyme/substrate have ionized/unionized R groups to interact

in terms of pH catalytic process usually requires that

enzyme denturation

pH extremes can lead to

2

optimal pH for pepsin to function

6

optimal pH for trypsin to function

10

optimal pH for Alkaline phosphotase to function

how reaction velocity varies with substrate concentration

michaelis-menten kinetics describes

substrate concentration is much higher than enzyme

1st derived assumption of Michaelis menten kinetics

concentration of ES complex does not change with time (steady-state assumption)

2nd derived assumption of Michaelis menton kinetics

initial reaction velocity (V0) is used to analyze enzyme reaction

3rd derived assumption of Michaelis menten kinetics

Michaelis menten konstant (Km) is characteristic of enzyme and particular substrate

1st conclusion of Michaelis menten kinetics

high Km

low affinity of enzyme for substrate

low Km

high affinity of enzyme for substrate

reaction rate is directly proportional to enzyme concentration

2nd conclusion of Michaelis menten kinetics

velocity reaction approx proportional to substrate concentration (first order)

when substrate << than Km

velocity is constant = Vmax (0 order)

when substrate >> than Km

Linewaever-Burk plot

straight line observed when plotting 1/v0 against 1/substrate

Km and V max

Linewaever-Burk plot can be used to calculate

1/V0 = Km/Vmax (1/[S]) + 1/Vmax

Linewaever-Burk plot equation

inhibitor

any substance that decreases velocity of enzyme catalysation

reversible or irreversible

inhibitor can be

irreversible

inhibitors that bond to enzyme via covalent bond

Lead inhibits Ferrochelactase

example for irreversible inhibitor

reversible

inhibitors that bind to enzyme via covalent and form enzyme-inhibitor complex

competitive and non competitive

types of reversible inhibitors

dilution of enzyme inhibitor complex

results in dissociation of reversible bound inhibitor

competitive inhibition

occurs when reversibly inhibitor binds to same site as substrate

more substrate is needed to archive 1/2 Vmax

presence of reversible inhibitor increases apparent Km

Transition state analogs

stable molecules that approximate structure of transition state (important group of competitive inhibitors)

statins like atorvastatin and procastin

cholesterol lowering agents that competitively inhibit hydroxymethylglutanyl

decrease Vmax

characteristic effect of noncompetitive inhibitors

noncompetitive inhibition

occurs when inhibitor and substrate bind to different sites on enzyme

cannot be overcome by increasing substrate concentration

why do noncompetitive inhibitors decrease Vmax

stays same because it doesn't interfere with substrate binding

effect of noncompetitive inhibitors on Km

penicillin, amoxicillin, ACE, Aspirin

examples for noncompetitive inhibitors