topic 3 - enzymes

Question 1

how many amino acids do we have

Answer 1

~20

Question 2

what do amino acids do

Answer 2

building blocks of proteins
encoded by genetics

Question 3

what are amino acids made of

Answer 3

central carbon (alpha carbon)
carboxyl group (COO-)
amino group (H3N+)
R group

Question 4

how do peptide bonds between amino acids form

Answer 4

dehydration reaction between 2 amino acids (new bond formed and water released)

Question 5

where is peptide bond found

Answer 5

on backbone between a C double bonded to a O and N

Question 6

what is a peptide made up of

Answer 6

backbone - same repeated pattern of atoms
N terminus and C terminus
variable R groups

Question 7

how to tell if a R group is hydrophobic

Answer 7

lots of non polar bonds
when present on protein - they will be away from water on the inside of the protein

Question 8

how to tell if a R group is hydrophilic

Answer 8

more polar covalent bonds
able to form bonds with water
when present on protein - they will face out towards water

some R groups have +/- charges and can form electrostatic interactions with each other

Question 9

what is the difference between peptide, polypeptide, and protein

Answer 9

peptide = polymer (multiple) of amino acids
polypeptide = >10 amino acids joined together
protein = polypeptide folded into 3D shape

Question 10

what is primary structure

Answer 10

sequence of amino acids in the polypeptide

Question 11

what are the two types of secondary structure

Answer 11

helices and sheets

Question 12

what are helices

Answer 12

stabilised by H bonds
each carbonyl group in the backbone forms a H bond with an amide 4 residues (amino acids) away
regular repeat of H bonds to stabilise the helix

Question 13

what are sheets

Answer 13

adjacent strands can run in the saem direction or opposite direction (antiparallel)
H bonds can form between carbonyl groups in one polypeptide and amide groups in a different part of the polypeptide
main chain stabilised into sheets through H bonds

Question 14

what is tertiary structure

Answer 14

secondary structure folded into the 3D protein shape
due to multiple levels of interaction between the R groups
shape is stabilised through H bonding, ionic interactions (+/- charged R groups), van der waals interactions, R groups with sulphur form covalent bonds (disulphide bond between cysteines)

Question 15

what is quaternary structure

Answer 15

multiple polypeptides folded into 3D shapes (subunits) that interact with each other
gives the protein an overall shape and function

Question 16

what is a subunit

Answer 16

has tertiary structure - within a protein

Question 17

what is the difference between homotrimer and heterotrimer

Answer 17

homotrimer = 3 subunits with the same primary structure
heterotrimer = 3 subunits with different primary structure

Question 18

what is the activation energy

Answer 18

energy barrier that must be overcame before the reaction can proceed
- energy destabilises the bonds in the reactants which allows (under the right conditions) for the formation of bonds that generate the products

Question 19

what is the summit of activation energy

Answer 19

point where bonds in the reactants are breaking and bonds in the products are forming (transition state)

Question 20

what are the ways to speed up a chemical reaction

Answer 20

• increase the temp so that reactants have more energy when they collide with each other
• increase the concen of the reactants so they collide with each other more often
• add a catalyst (enzyme = protein catalyst, ribozyme = RNA catalyst)

all decrease Ea

Question 21

what effect does an enzyme have on delta G

Answer 21

no effect
- no change in delta G, just Ea
- can’t make an endergonic reaction exergonic

Question 22

what is an enzyme

Answer 22

typically large molecule
made of 1+ polypeptide chains folded into a very specific 3D shape
shape determined by sequence of amino acids

Question 23

what is the active site

Answer 23

region that interacts/binds with a specific substrate (reactant)

Question 24

what is the induced fit model (interaction betwen active site and substrate)

Answer 24

• ES (enzyme-substrate) complex forces the reactants into the transition state (can change shape to help break bonds in the substrate)
• by forcing the transition state - enzyme reduces the need for as much Ea
• products are then released and enzyme shape returns to original (ready to bind with next substrate)

Question 25

what does hexokinase do

Answer 25

catalyse a coupled reaction
(hydrolysed ATP and P is being transferred to glucose (in active site))
- speeds up a exergonic reaction (increases reaction rate)

Question 26

how does an enzyme speed up a reaction

Answer 26

• bring reactant molecules close together in the correct orientation
• charge interations - expose reactants to charged environments
• physically distort or strain substrate molecules

Question 27

what does the rate of an enzyme reaction (enzyme kinetics) depend on

Answer 27

temp
concen of substrate
pH
enzyme concen

Question 28

how do cells control/regulate enzyme kinetics

Answer 28

change enzyme concen
increase concen of substrate
cells produce inhibitors / activators (small molecules that bind to enzyme to speed up or turn it off)

Question 29

what is the relationship between enzyme concen and rate

Answer 29

linear relationship

Question 30

what is the relationship between substrate concen and rate

Answer 30

non linear
- reaches saturation level and plateaus (when enzyme concen is constant)
- max velocity of reaction rate (Vmax)

Question 31

what is denaturation

Answer 31

loss of protein structure
- can be partial (reversible) or complete (irreversible)
- caused by heat or pH

Question 32

what is inactivation

Answer 32

loss of protein activity
- often due to denaturation
- can be reversible or irreversible
- highest activity at optimal temp (decrease on both sides of that temp)

Question 33

what is reversible competitive inhibition

Answer 33

• inhibitor is chemically like the substrate
• non covalently binds to the enzyme at the active site (competes with the substrate to bind)
• molecules with the highest concen will outcompete the other

Question 34

what is reversible non competitive inhibition

Answer 34

• inhibitor is not like the substrate
• inhibitor non covalently binds to the enzyme at a different point (away from active site)
• high concen of substrate will not outcompete the inhibitor
• max rate of enzyme reaction will be less than the inhibited rate of the reaction

Question 35

what are allosteric activators

Answer 35

bind to the enzyme away from the active site which will change shape to a more active form
- stabilises the active form of the enzyme to increase activity

Question 36

what are allosteric inhibitors

Answer 36

bind to the enzyme which will change shape to a less active form (bind away from active site) and decrease activity
- stabilises the inactive form of the enzyme

Question 37

what is feedback inhibition

Answer 37

final product of a pathway inhibits an enzyme early in the pathway