Proteins and enzymes

Question 1

Which amino acid is at the start of any protein ?

Answer 1

Met bc of its unreactive side chain

Often not present in mature protein

Question 2

Useful property of cysteine

Answer 2

Side chain can form various metal ion complexes

Question 3

Where do disulphide bonds occur

Answer 3

Between 2 cysteine residues in or between chains

Question 4

7 descriptive characteristics of amino acids

Answer 4

1. Aromatic
2. Acidic (negatively charged )
3. Basic (positively charged)
4. Polar and uncharged
5. Non-polar
6. hydrophobic
7. hydrophilic

Question 5

What bonds/interactions do R groups contribute to ?

how do these stabilise protein structure

Answer 5

H bonds ( if there are N-H / C=O bonds present )

Hydrophobic / hydrophilic associations

salt bridges (between acidic and basic R groups)

responsible for 2/3/4 structure

Question 6

Define macromolecule

Answer 6

Very large molecule consisting of several thousand atoms covalently bonded

Question 7

How does pH affect a proteins structure?

Question 8

Which type of proteins are disulphide bonds more commonly found in and why ?

Answer 8

More common in extra cellular proteins due to the oxidising environment outside the cell

environment in cell is reducing

Question 9

Features of peptide bond

Answer 9

Planar NH-CO region

restricted rotation of N-C

delocalisation of π electrons over entire bond rather than just over C=O

Question 10

Secondary structure

Answer 10

Alpha helix and beta pleated sheet maximise H bonding in order to minimise steric repulsion (by causing the side chains to extend outwards)

In alpha helixes H bonds occur between N-H and C=O in same chain (in AA that are close to each other)

in beta pleated sheets H bonds occur between N-H and C=O in adjacent chains (AA are far apart in primary structure )

proteins with beta pleated sheets may have both parallel and anti parallel strands

Question 11

what does the phrase “modular nature of proteins” mean

Answer 11

proteins consist of structural and functional folds - some folds are there to maintain the proteins shape whereas other fold are resposnisble for serving a function

Question 12

Define domain

Answer 12

Specific part within the tertiary structure that serves a function

domains are found in larger proteins

very different proteins may share the same domains - converse differently common functions

active site of enzymes are an example of domains

Question 13

structural motifs

Answer 13

2⁰ structures linked by loops in specific 3D arrangements

a common three-dimensional structure that appears in a variety of different, evolutionarily unrelated molecules.

Question 14

Bonds responsible for tertiary structure

Answer 14

Question 15

How can pH affect a protein structure

Question 16

List 5 ways in which protein alterations can lead to disease:

Answer 16

1. dysfunctional/absent protein
2. interfering with a metabolic pathway
   
   1. loss of product ; accumulation of precursor
3. dysfunction of regulatory protein/receptor
4. protein aggregation
   
   1. e.g alzheimers and hungtingtons
5. loss of defence against infection

Question 17

Name two advantages of having a homo-oligomeric protein

Answer 17

Protein composed of several identical polypetpide chains

1. bigger size - tertiary structure more stable
2. each subunit has an active site - faster RoR

Question 18

define oligemerisation state

Answer 18

number of polypeptide chains

Question 19

associations in quaternary structure

Answer 19

subunits usually interact non-covalently

closely packed non-polar side chains - more hydrophilic than interior of subunit but less than areas not involved in binding

H bonds between backbones and side chains

Question 20

what does cooperativity mean ?

Answer 20

when thr different polypetide chains within a protein work together to perform the overall function of the protein

Question 21

features of fibrous proteins

Answer 21

polypeptide does not fold on itself

normally display one type of secondary structure

long rod

strong

play structural role

Question 22

features of globular proteins

Answer 22

polypeptide backbone does fold onto itself

exhibit regular secondary structure interspaces with stretches devoid of recognisable structure

compact spherical

usually play metabolic role

soluble in polar/hydrophilic environment

Question 23

How is the structure of secreted proteins adapted for their function

Answer 23

They contain a N-terminal leader - a short sequence of AA that enables those proteins to find their correct location outside the cell membrane

Question 24

How are transmembrane proteins adapted for their function ?

Answer 24

They span the membrane with a stretch of hydrophobic amino acids

Question 25

Define substrate binding site

Answer 25

The site of the enzyme where the substrate binds via hydrophobic/electrostatic interactions and H bonds with the enzymes amino acids

Spatial geometry dictates specificity of binding - steric hindrance and charge repulsion prevent non-complementary substrates from binding

Holds the substrate in the ideal position for the reaction to begin

Question 26

Define active catalytic site

Answer 26

Region where the reaction occurs

Functional groups present here such as co-enzymes , metal ions , amino acid residues

May overlap with substrate binding site but not always

Question 27

what is the Transition state?

Answer 27

high-energy, unstable state (an intermediate form between the substrate and the product with strained electron configuration) occurring during a chemical reaction

Question 28

Describe the induced fit model of enzyme action.

Answer 28

1. (before reaction) active site not complementary to/does

not fit substrate;

2. Shape of active site changes as substrate binds/as

enzyme-substrate complex forms

This occur s by reposition of side chains of AA within SBS

3. Stressing/distorting/bending bonds (in substrate leading to reaction) as binding interactions increase

Not a rigid lock but a dynamic surface

Question 29

Activation energy

Answer 29

• Energy required for reactants to reach transition state

Question 30

Prosthetic groups

Answer 30

tightly bound cofactors or coenzymes that are necessary for enzyme function

Question 31

How can enzymes be used diagnostically ?

Answer 31

Non-serum specific enzymes should not be found in the blood of a healthy person

Non-serum specific enzymes can be released due to cell damage and malignancy

Released enzymes are affected by metabolisms - different serum half-live in different organs

Question 32

define serum half life

Answer 32

time required for the serum concentration of a drug/substance to decrease by 50%

i.e how quickly a substance is metabolised

Question 33

functions of cofactors and coenzymes

Answer 33

Stabilises substrate

Helps position substrate in correct orientation relative to the catalytic residues

Question 34

Define steady state

Answer 34

When [substrate] > [enzyme]

Enzyme working at a consistent rate

Question 35

what does a high K_m value indicate ?

Answer 35

low substrate affinity - high [S] required for catalysis

Question 36

what does a low K_m value indicate ?

Answer 36

high substrate affinity - low [S] needed for catalysis

Question 37

how can you increase V_max?

Answer 37

by increasing the [enzyme]

Question 38

what happens when [S]m ?

Answer 38

RoR is directly proportional to [S]

Question 39

what happens when [S]>K_m ?

Answer 39

all AS become occupied so RoR is now independent of [S]

another factor is now limiting V_max

Question 40

why is K_m useful?

Answer 40

tell us the [S] required to maximise enzyme activity (reach V_max)

Question 41

[S] found inside cells is often near value of Km

why is that ?

Answer 41

allows modulation of enzymatic reactions

this is because near Km, small change in [S] leads to a greater charge in rate of reaction

Question 42

identify the type of inhibtion displayed

Answer 42

competitive

Vmax doesnt change

K_m increased = as more substrate required to reach half V_max

Question 43

Identify the type of inhibition displayed

Answer 43

Non-competitive inhibition

V_max reduced as effect cannot be overcome by increasing [S]

K_m unaffected as inhibitor does not bind to the substrate binding site on enzyme

Question 44

Uncompetitive inhibition

Answer 44

takes place when an enzyme inhibitor binds only to the complex formed between the enzyme and the substrate (the E-S complex). Uncompetitive inhibition typically occurs in reactions with two or more substrates or products.

Question 45

Identify the type of inhibition shown

Answer 45

Uncompetitive inhibition increases K_m and lowers V_max

Question 46

Substrate and product inhibition

Answer 46

Substrates can act as uncompetitive inhibitors - at very high [S] the substrate binds to a second non-catalytic site

end-product of an enzymatic pathway can affect activity of previous enzymes

this allows regulation of metabolic pathways

Question 47

What are suicide inhibitors ?

Answer 47

Similar shape to substrate

Unreactive until bound to the AS

Converted to reactive compound which then combines irreversibly to enzyme AS

Question 48

Homotropic effector

Answer 48

Substrate acts as an effector

usually a positive effector - increases enzyme activity

Question 49

Define heterotrophic effector

Answer 49

Effector is different from the substrate

Question 50

Describe the concerted model

Answer 50

1st substrate molecule has difficulty binding as all subunits in T state

upon binding of 1st molecule , all the adjacent subunits change to R state

enzyme now has much higher affinity

Question 51

How can the sequential model be used to describe inhibition

Answer 51

When inhibitor binds, it maintains the enzyme in the T state

needs increased substrate/activator conc to overcome the effect

Question 52

How do G proteins work?

Answer 52