MGD 4-5

Question 1

what is activation energy?

Answer 1

minimum energy substrate must have to react

Question 2

what is transition state?

Answer 2

high energy intermediate that lies between substrate and product (difference)

Question 3

what increases the rate of a reaction?

Answer 3

temperature: increase no. of molecules with activation energy
concentration: increase chance of molecular collisions

Question 4

what are enzymes?

Answer 4

biological catalysts that increase the rate of reaction by lowering the activation energy
facilitate formation of transition state

Question 5

what are important features of enzymes?

Answer 5

highly specific, unchanged after the reaction, do not affect reaction equilibrium, increase rate of reaction, proteins, may require associated cofactors

Question 6

what is the active site of an enzyme?

Answer 6

the place where substrates bind and where the chemical reaction occurs
formed by AA from different parts of primary sequence

Question 7

what are features of active site?

Answer 7

are clefts or crevices (exclude water)
have a complementary shape to substrate - lock and key / induced fit (active site forms after binding of the substrate)
substrates are bound to enzymes by multiple weak covalent bonds

Question 8

what is max reaction rate bound by?

Answer 8

number of enzyme active sites

reaches max velocity - retangular hyperbola (initially a lot of increase, then not so much)

Question 9

what is the michaelis-menten model for enzyme catalysis?

Answer 9

a specific complex between the enzyme and the substrate is a necessary intermediate in catalysis
predicts a plot of velocity VS [S] is rectangular hyperbola

Question 10

what is Vmax?

Answer 10

maximum rate when all enzyme active sites are saturated with substrate

Question 11

what is Km

Answer 11

substrate concentration that gives 1/2 Vmax

Question 12

what does a high and low Km mean?

Answer 12

low Km: high affinity for substrate (reaction rate quickly reached)
high Km: low affinity for substrate

Question 13

Km of hexokinase and glucokinase - what causes the difference?

Answer 13

hexokinase low Km as always active - in all tissues

glucokinase high Km as ony in liver and only activated when glucose levels peak after feeding

Question 14

what are enzyme inhibitors?

Answer 14

molecules that slow down or prevent an enzyme action

Question 15

what are irreversible enzyme inhibitors?

Answer 15

bind v tightly, generally from covalent bonds

e.g. nerve hases e.g. sarin

Question 16

what are reversible enzyme inhibitors?

Answer 16

non-covalent, can freely dissociate

can be competitive (bind at active site) or non-competitive (binds at another site on enzyme)

Question 17

what are the 2 difference in terms of Km and Vmax between competitive and non-competitive reversible inhibitors?

Answer 17

competitive: affects Km (1/2 dissociation constant) but NOT Vmax - can be overcome by enough substrates
non-competitive: affects Vmax but not Km (curve doesn’t peak as high)

Question 18

describe competitive inhibitor

Answer 18

resembles the substrate and binds to the active site, reducing the proportion of enzyme molecules bound to the substrate

Question 19

what are short term regulations of enzyme activity?

Answer 19

1. substrate and product concentration
2. change in enzyme conformation:
   a. allosteric regulation
   b. covalent modification
   c. proteolytic clevage

Question 20

what are long term regulations for enzyme activity?

Answer 20

change in rate of protein synthesis

change in rate of protein degradation

Question 21

explain how substrate and production concentration affects enzyme activity? what are isoenzymes?

Answer 21

substrate avaliability will affect the rate of enzyme activity
isoenzymes are different forms of the same enzyme that have different kinetic properties

Question 22

what is product inhibition? example?

Answer 22

accumulation of product of a reaction inhibits the forward reaction
e.g. G-6-P inhibits hexokinase activity

Question 23

what does an allosteric regulation graph look like?

Answer 23

shows a sigmoidal relationship between rate and substrate concentration, instead of rectangular hyperbola
multi subunit enzymes, can exist in 2 different conformations: T-state (low), R-state (high affinity)
shows sigmoidal because substrate binding to 1 subunit makes subsequent subunits bind easier (cooperative binding)

Question 24

what is allosteric regulation? what are the different types and how do they work?

Answer 24

allosteric activators: increase the proportion of enzymes in R state
allosteric inhibitors: increase the proportion of enzymes in T state
bind somewhere else other than active site which changes the active site to which enhances the binding of the substrate, stabilising the high affinity R state

Question 25

importance of allosteric regulation to phosphofructoinase (step 3 - irreversible)

Answer 25

PKF is allosterically regulated and sets the pace of glycolysis
activated by: AMP
inhibited by: ATP, citrate, H+

Question 26

examples of covalent modification of enzymes through phosphorylation

Answer 26

1. protein kinase - transfer terminal Pi from ATP to OH

2. protein phosphatases - reverse effects of kinase (remove P from porteins)

Question 27

what does amplification by enzyme cascade achieve?

Answer 27

amplification of signals by kinase cascades allows amplification of the initial signal by several orders of magnitude within a few seconds

Question 28

what is amplification by enzyme cascade?

Answer 28

when enzymes activate other enzymes, the number of affected molecules increases geometrically in an enzyme cascade

Question 29

what are examples of enzymes activated by specific proteolytic cleavage?

Answer 29

1. digestive enzymes - synthesised as zymogens in stomach and pancreas
2. protein hormones e.g. insulin (synthesised as inactive precursors)
3. blood clotting
4. programmed cell death (apoptosis) - caspase (8)

Question 30

proteolytic activation of chymotrypsinogen

Answer 30

chymotrypsinogen –(trypsin)–> chymotrypsin (pi)
chymotrypsin (pi) –(chymotrypsin)–> a chymotrypsin
from 1 inactive peptide to 3 active chains (a,b,c)

Question 31

zymogen activation by proteolytic cleavage

Answer 31

by pancreatic protease

activation controlled by trypsin (from trypsinogen)

Question 32

what are endogenous inhibitors of protease activity?

what happens without it?

Answer 32

1. a1-antitrypsin

without it causes emphysema as proteases breakdown walls of elastase

Question 33

what is a long term regulation of protease activity?

Answer 33

1. change in rate of protein synthesis (enzyme induction/repression)
2. change in rate of protein degradation (ubiquitin)