Enzymes and Bioenergetics

Question 1

enzymes

Answer 1

catalysts that facilitate reactions in biological settings

consist of amino acids primarily

Question 2

cofactors

Answer 2

non amino acid component often in conjunction with enzymes

inorganic product

Question 3

coenzyme

Answer 3

non-amino acid component used with enzymes
organic
often derived from vital organic compounds obtained from vitamins

Question 4

rate laws

Answer 4

experimentally determined, express reaction rate in terms of reactants concentration

rate =k[A]^m[B]^n
where m and n are reaction order

Question 5

1st order reaction rate

Answer 5

rate = k[S]
depends on substrate concentration

occurs when km»[S]

Question 6

zero order reaction rate

Answer 6

rate = k
does not depend on substrate concentration
occurs when excess substrate and limited enzymes
km<

Question 7

noncompetitive inhibition

Answer 7

binds to allosteric sites, so doesn’t affect Km
however, less product will be made so decreases Vmax

will show on Lineweaver-Burk Plot as increased Y axis and no change in x axis

Question 8

competitive inhibition

Answer 8

will competitively take over binding sites, so Km will increase (takes more to reach same level) = right shift

vmax not effected because Km can still overcome

Question 9

uncompetitive inhibition

Answer 9

only binds to the enzyme-substrate complex
Km decreases at same rate as Vmax decreases

locks the enzyme in place so that the substrate can bind (decreasing Km) but won’t be able to make a product (decreasing Vmax)

Km and Vmax must decrease at the EXACT SAME rate -> will have same slope as uninhibited slope

left shift, upward shift

Question 10

mixed inhibition

Answer 10

can bind to both enzyme or enzyme-substrate complex

Vmax decreases for both

binds allosterically

when binding to enzyme, will increase Km, when binding to enzyme-substrate complex, will decrease Km

Question 11

catalytic efficiency

Answer 11

proportional to 1/slope of Lineweaver-Burk Plot

how effective an enzyme is at converting substrate to product. higher Kcat means increase turnover rate and lower km means higher binding affinity.

kcat/km

Question 12

Mixed inhibitor binding to free enzyme

Answer 12

Km will increase because will take more to reach same level

Question 13

Mixed inhibitor binding to ES complex

Answer 13

Km will decrease because inhibitor will hold enzyme in place for easier access of substrate

Question 14

enzyme activity can be increased by

Answer 14

increasing Kcat which will increase Vmax
decreasing Km to reach rate more quickly
increase catalytic efficiency (kcat/km)

Question 15

Kcat

Answer 15

turnover number = the number of times each enzyme site converts substrate to product per unit time

Vmax/[E]

Question 16

calculating Vmax

Answer 16

Kcat[E]

concentration of enzymes x how fast enzymes are converting substrates to product / unit of time

Question 17

Michaelis-Menten Equation

Answer 17

V0 = Vmax[S]/Km+[S]

Vmax = Kcat[E]

Question 18

zymogens

Answer 18

enzyme in inactive form; must be altered by covalent modifications to become activated

Question 19

hill coefficient

Answer 19

quantitative measurement of cooperativity

n>1 cooperative -> sigmoidal shape
n=1 not cooperative -> hyperbolic shape
n<1 negative cooperativity

Question 20

protease

Answer 20

type of hydrolase that uses water to break peptide bond

Question 21

R-state binding

Answer 21

relaxed state has higher affinity for binding

high cooperativity

Question 22

T-state binding

Answer 22

tense state has low affinity for binding

low cooperativity

Question 23

effects on reaction of a deleterious mutation in an ezyme

Answer 23

increase activation energy
decrease reduction rate
no change to gibbs free energy or equilibrium constant

increase K and Kcat

decrease catalystic efficiency (kcat/Km) and decrease Vmax

Question 24

lock and key theory

Answer 24

proposes the enzyme’s active site is already in the proper structural conformation to allow a substrate to bind readily and form an ES complex

no conformation changes are necessary for catalysis to occur

Question 25

induced fit model

Answer 25

conformation change is induced when the substrate binds the active site, resulting in a formation of a functional ES complex that is said to be in the induced form

binding is highly specific and the conformational change requires energy input

Question 26

apoenzyme

Answer 26

enzymes that require a cofactor and the cofactor is absent

Question 27

holoenzymes

Answer 27

enzymes that require a cofactor and the cofactor is present

Question 28

entropy

Answer 28

the measure of disorder within a system

+ delta S = increased disorder

Question 29

hydrophobic molecules interacting with water

Answer 29

they cannot hydrogen bond with water so water molecules will hydrogen bond with themselves and so they form a rigid, highly ordered network called the solvation layer aroud hydrophobic molecules

this decreases entropy - which is why hydrophobic molecules fold to decrease surface area and hide hydrophobic residues, increasing entropy (disorder)

Question 30

hydrophilic molecules interacting with water

Answer 30

they can hydrogen bond with water and will do so
formation of solvation layers is unnecessary

entropy is increased

Question 31

what amino acids can act as nucleophiles?

Answer 31

amino acids containing thiol (-SH) or hydroxyl (-OH) groups

most common are cysteine and serine

nucleophiles want to give up electrons so are very attracted to positive charge of atomic nuclei

the greater the negativity, the stronger the nucleophile

Question 32

What will increase the nucleophilicity of cysteine?

Answer 32

deprotonation of cysteine results in a negatively charged sulfur which enhances its nucleophilicity

Question 33

transmembrane domain

Answer 33

contains phopholipid bilayers with hydrophilic head groups facing aqueous environment and hydrophobic tails facing inward

only membrane spanning protein domains containing hydrophobic residues are thermodynamically stable because hydrophilic amino acid residues will interact unfavorably with hydrophobic phospholipid tails

Question 34

transmembrane protein

Answer 34

contains hydrophobic transmembrane domains composed of largely non-polar amino acids. They interact favorably with hydrophobic tails of phospholipids in cellular membranes

Question 35

Specific binding

Answer 35

some enzymes are highly specific for a particular substrate

demonstrate high reaction rates with substrate of interest but not with any other molecules

Question 36

Equation for Vo

Answer 36

Vo = Kcat[E][S]/Km+[S]

Kcat[E] = Vmax so

Vo = Vmax[S]/Km+[S]

Question 37

fructose 2,6 biphosphate

Answer 37

activated by insulin, can activate phosphofructokinase 1 which turns fructose 6 phosphate into fructose 1,6 phosphate even there is enough ATP that the forward reaction is inhibited