enzymes

Question 1

define enzymes

Answer 1

a catalyst that changes the rate of a reaction without being changed in the process

Question 2

Properties of enzymes x4

Answer 2

• They are highly specific for which substrate they bind to and which product is formed
  
  • There activity can be regulated and the activity can vary depending on the concentration of the substrate it is working on and other molecules
  • Nearly all enzymes= globular proteins [ some RNA catalyst have been found though #ribozymes]
  • Enzymes are made in a way where they are endogenous to the naturally occurring enzyme that may be found in the body [#look the same as the naturally occurring enzyme]

Question 3

Definition of enzyme active site and it is usually a what on the enzyme

Answer 3

region of the enzyme that binds to the substrate and converts it into a product- usually a crevice [indentation]

Question 4

What polarity does the active site typically have- does this have a benefit

Answer 4

hydrophobic - predominantly nonpolar- enhances binding

Question 5

how is substrate bound to active site [forces]

Answer 5

multiple weak forces - [electrostatic, hydrophobic, hydrogen bonds] & some have reversible covalent bonds

Question 6

once substrate and enzyme bind what is the product and what does this cause

Answer 6

enzyme-substrate complex is formed and the catalytically active A.A. which bind -> substrate and cause change its change into product - product is then released

Question 7

once product is formed and released what happens

Answer 7

catalytic cycle begins again

Question 8

how does the substrate bind to the Active site

Answer 8

• Interactions occur between the A.A. side groups which holds the substrate in place
  
  • The A.A in active site actively participates in the enzymes catalysis

Question 9

describe lock and key model

Answer 9

• Shape of substrate + enzymes active site fit together like a lock and key
  
  • 2 shapes = rigid + fixed [#don’t change in shape]
    They are Perfectly complement - don’t change in shape

Question 10

describe induced fit model

Answer 10

• When the substrate binds it induces a conformational change

Question 11

can some enzymes show different features of both molecules

Answer 11

yes- they have some complementarity and some complementary changes- give 2 scenarios

Question 12

what determines an enzymes specifity

Answer 12

properties and spatial arrangement of A.A. residues determines enzyme specificity - i.e. which molecules can bind
- If there’s small A.A. - bulky substrate can fit in
- Large A.A. residues - mean small substrate can fit

Question 13

how is specificity determined

Answer 13

• Determined by changes in a few A.A. in the active site

Question 14

give 3 e.g.s of digestive enzymes and where are they made

Answer 14

• Trypsin
  
  • Chymotrypsin
    Elastase
    Pancrease

Question 15

what are the digestive enzymes called- why are they called this

Answer 15

serine proteases - They have serine residues [involved in catalysis]
- They are proteases as they catalyse the hydrolysis of peptide bonds in protein [i.e. substrate is also made of A.A.]
- The Enzymes cleave peptide bonds in their substrate [which are proteins] - cause slight conformational
- There specificity is based on nature of A.A in residues [complementary bind]

Question 16

explain the enzyme specificity of chymotrypsin

Answer 16

• The enzyme cleaves on the carboxyl side of the bulk aromatic + hydrophobic substrate A.A.
  
  • Enzyme’s A.A. has small chains which gives access to bulky side chains of substrates

Question 17

enzyme specificity of trypsin

Answer 17

• Enzyme cleaves to carboxyl side of positively charged Lysine + Arginine
  
  • This is due to the negatively charged asparagine it has in its active site - this interacts with arginine’s + lysine’s positive side chain [#substrates]

Question 18

enzyme specificity of elastase

Answer 18

• Cleaves the carboxyl groups of small uncharged side chains of substrates
  
  • Enzyme possess A.A. residues with large side chains so larger molecules cannot fit
  • Alanine and glycine however can fit

Question 19

what determines an enzymes specificity

Answer 19

• Shape + A.A. content at the active site determines which substrate can bind [#specicity]
  
  • Each enzyme = usually substrate specific

Question 20

what 2 stages are in a biochemical reaction

Answer 20

1. Substrate is converted to transition state [halfway] molecule becomes distorted to an electronic conformation [energy require here is + because energy is being taken in]
   
   2. Transition state = converted to a product

Question 21

energy hump [activation energy]

Answer 21

is a barrier to chemical reactions

Question 22

whats an enzymes main function

Answer 22

Enzymes main function is to reduce the activation energy and increase rate of reactions sometimes by factor of 10^7 -> 10^14 this 10^14 means that because of the enzyme the reaction that would take a matter of years only takes 1 second

Question 23

free energy charge is determined by what?

Answer 23

by free energy difference between starting substrate and product Overall reaction must have a negative free energy [meaning the energy of the reactants = greater than the energy of the products ] if its not negative the reaction will not occur
Enzyme doesn’t affect the overall change in energy rather just speeds it up [in terms of the ratio

Question 24

define enzyme activity, specific activity, Kcat

Answer 24

I Unit is the amount of enzyme that converts 1 micromolar substrate per minute at 25 degrees Celsius at optimal pH
Specific activity = units of enzyme per mg of protein present
Turnover number [kcat]- maximum number of molecules of a substrate that an enzyme can convert to product per catalytic site per unit of time

Question 25

who classifies enzymes

Answer 25

IUBMB - union biochemistry & molecular biology [enzyme commission

Question 26

explain 4 digit numbering system for enzymes

Answer 26

1- Six classification numbers
2- Subclass [type of bound it acts upon]
3- A subclass[tells if cofactor is required + involved]
4- Is the serial number - it’s the order in which the enzyme was added to the list
e.g. alpha Amylase EC 3.2.1.1 - beta amylase EC 3.2.1.2

Question 27

many enzymes require cofactors/coenzymes to carry out their functions

Answer 27

• Many enzymes require cofactors to carry out their particular reaction
  
  • When a metal/coenzyme is covalently attached to the enzyme - this coenzyme/metal is called prosthetic group
  • Complete catalytically-active enzyme with its prosthetic group = HOLOENZYME
  • Protein part of enzyme without its prosthetic group = called apoenzyme
  • Some coenzymes i.e. NAD+ = bound + released by enzyme during the catalytic cycle -i.e. function as co-substrates [part of the product]
  • Many Coenzymes = derived from Vitamin precursors.
  • An inadequate supply of these vitamins leads to deficiency disease

Question 28

When a metal/coenzyme is covalently attached to the enzyme what is it called

Answer 28

a prosthetic group

Question 29

complete catalytically-active enzyme with its prosthetic group is called what?

Answer 29

Holoenzyme

Question 30

protein part of enzyme without its prosthetic group is called what?

Answer 30

apoenzyme

Question 31

some coenzymes like NAD+ are ? during the catalytic cycle this makes them?

Answer 31

Bound and released - co-substrates

Question 32

many coenzymes are derived from?

Answer 32

vitamin precursors

Question 33

what 2 factors affect enzyme activity

Answer 33

Ph and temperature

Question 34

describe pH optimum- describe effects of small changes and large changes- most enzymes are optimum at what ph- give exception

Answer 34

• Each enzyme has an optimum pH- [the rate of the reaction is optimum at this pH]
  
  • Small changes cause small deviations due to change of ionisation [charge] of groups at the active site of the enzyme
  • Large deviations cause the enzyme to be denatured due to weak noncovalent bonds being interfered [these are the bonds that maintain the enzymes 3D structure]
  • Many enzymes are optimum at 7 pH because this is the bodies physiological pH
  • Exception = digestive enzymes i.e. pepsin which optimum ph is near 2 as stomach is acidic so needs to have a low optimum to survive.

Question 35

describe temperature optimum- small and large effects

Answer 35

• Small increase in temp increase the thermal energy of the substrates. This also lowers the energy activation and increase the rate of reaction
  
  • Large increase in temp bonds [weak non-covalent reactions that hold enzyme in it’s 3D form = broken - protein becomes denatured
  • Most mammalian enzymes = 37 degrees - why? Because its physiological temperature

Question 36

Enzyme inhibitors - what are they and what do they do and give 2 examples of them

Answer 36

• Inhibitors are molecules that work directly on enzymes -> lower its catalytic rate
  
  • e.g. normal body metabolites [inhibits a particular enzyme in normal metabolic control
  • foreign substances i.e. drugs/toxins effect enzyme inhibition can be therapeutic or lethal

Question 37

enzyme inhibition can be x or y

Answer 37

inhibition can be reversible or irreversible

Question 38

reversible inhibition of enzymes can be? x3

Answer 38

1. competitive [blocks active site so substrate won’t go in]
   
   2. Non-competitive [change occurs at active site - substrate cant go in
   3. Uncompetitive

Question 39

Isoenzymes are defined as

Answer 39

different forms of an enzyme that catalyse the same reaction

Question 40

These isoenzymes exhibit ? and derived from?

Answer 40

exhibit different physical + kinetic properties i.e. optimum pH
- They are also derived from different genes which occur in different tissues of the body

Question 41

give an example of an isoenzyme and what is does

Answer 41

catalyzes reversible reaction conversion of pyruvate into lactate in the presence of the coenzyme NADH. LDH = tetramer made up of 2 different types of subunits [H & M]

Question 42

LDH is a tetramer made of 2 different subunits which combine to form different subunits give 5 possible isoenzymes

Answer 42

1. H4 [predominantly in heart + red blood cells]
   
   2. M4 [predominantly in skeletal muscle + liver]
   3. H3M [predominantly in heart + RBC]
   4. HM3 [predominantly in liver + skeletal muscle]
   5. H2M2 - in brain and kidney
      - M units = found in skeletal muscle + liver
      - H subunit - found in heart

Question 43

what are the allosteric enzymes

Answer 43

enzymes that change their shape, or
conformation, upon binding of an effector molecule

Question 44

the biological activity of allosteric enzymes = effected by what?

Answer 44

by altering
the conformation of its tertiary structure

Question 45

allosteric enzymes tend to have how much subunits

Answer 45

several subunits

Question 46

in some cases the regulatory site which binds the effector molecule and the x are on ? [allosteric enzymes]

Answer 46

active site - are on separate subunits

Question 47

define an allosteric effector

Answer 47

is a substance that modifies the behaviour
of allosteric enzymes; it may be an allosteric inhibitor or
allosteric activator.

Question 48

what does an allosteric activator

Answer 48

increases the rate of enzyme activity,
while an allosteric inhibitor decreases the rate of enzyme
activity.

Question 49

explain competitive inhibition

Answer 49

• its reversible and - reduces the amount of
  enzyme available for
  substrate binding - may be overcome by increasing substrate - molecule goes in there and attaches to active site

Question 50

non-competitive inhibition-reversible

Answer 50

this inhibitor doesn’t bind to the catalytic site rather binds somewhere else to change enzymes shape - binds -> allosteric site or regulatory site

Question 51

distinguish between allosteric inhibition and allosteric activation

Answer 51

both types have molecules that bind @ sites other than active site and one activates the substrate to bind to the same enzyme whilst the other prevents the substrate binding to the same enzyme

Question 52

un-competitive inhibition

Answer 52

is also reversible - intermediate substrate is formed and inhibitor binds to this enzyme substrate - no product is formed

Question 53

some allosteric activator are the s- itself
these types are said to exhibit what charge cooperativity
define this charge cooperativity
describe the binding of substrate molecules

Answer 53

substrate itself- positive cooperativity
a positive charge c- is when binding to one subunit facilitates binding of substrate to another subunit
the first substrate has difficulty binding-> enzyme as all subunits = in conformation with a low affinity for the substrate - [T-conformation i.e. inactive] when the 1st substrate binds @ least 1 adjacent subunit is changed to the high-affinity conformation [R state- relaxed]

Question 54

when does the activator bind to it’s activator site

Answer 54

when the enzyme is in the R configuration- allows substrate to bind

Question 55

when is the inhibitor binding site of an enzyme open- what does this do the the enzyme

Answer 55

when enzyme is in the T [inactive state] -keeps active site closed/ less accessible- enzyme = inactive

Question 56

give an example of an allosteric inhibitor

Answer 56

can be the product of the enzymatic reaction- if there’s too much product it will bind -> allosteric inhibitor site and enzymatic reaction = stopped #negative feedback inhibition

Question 57

give 3 examples of irreversible inhibitors

Answer 57

1. transition-state analogues
2. covalent inhibitors
3. heavy metal inhibitors

Question 58

what are transition-state analogues

Answer 58

• Compounds that resemble the substrate
  when its in the transition-state
• Bind to active site and keep the reaction at
  that point
• Reaction cannot progress and free up active
  site for new substrate molecule
  E.G– Penicillin inhibits the enzyme transpeptidase
• Transpeptidase – catalyses the formation of the peptide cross links in
  peptidoglycan
• Penicillin – has beta lactam ring – resembles the special amino acid found in the peptide links
• Forms irreversible bond with catalytic serine in the transpeptidase active site

Question 59

what are covalent inhibitors

Answer 59

Compounds that react irreversibly with
amino acids in the active site e.g. aspirin* Diisopropyl phosphofluoridate (DFP) is a neurotoxin
* Forms covalent intermediate in Acetylcholinesterase active site
* Acetylcholinesterase = enzyme that degrades the
neurotransmitter acetylcholine (sends messages in the brain) that’s why its called neurotoxin

Question 60

what are heavy metal inhibitors is it specific? give examples

Answer 60

Heavy metals that bind to important amino acids in the active site and prevent them from taking part in substrate binding or
catalysis- usually non-specific- mercury, lead, aluminium and Fe
Lead replaces important metals that act as an enzyme co-factor
* Replaces Ca2+ ions in calmodulin and protein kinase C

Question 61

give 4 examples of reversible inhibitors

Answer 61

• competitive
• non-competitive
• uncompetitive
• allosteric inhibitors

Question 62

irreversible inhibitors examples x3

Answer 62

• transition-state analogues
  -covalent inhibitors
  -heavy metals