1.4 Proteins

Question 1

What is the general structure of an amino acid?

Answer 1

-COOH carboxyl/carboxylic acid group

• R variable side group consists of carbon chain and may include other functional groups e.g. benzene ring or -OH(alcohol)

-NH2 amine/amino group

Question 2

Describe how to test for proteins in a sample

Answer 2

Biuret test confirms presence of peptide bond

1. Add equal volume of sodium hydroxide to sample at room temperature
2. Add drops of dilute copper (II) sulfate solution. Swirl to mix. (Steps 1 and 2 make biuret reagent)
3. Positive result: colour changes from blue to purple
   Negative result : solution remains blue

Question 3

How many amino acids are there and how do they differ from one another?

Answer 3

20

Differ only by side ‘R’ group

Question 4

How do dipeptides and polypeptides form?

Answer 4

Condensation reaction forms peptide bond (-CONH-) and eliminates molecule of water

Dipeptide: 2 amino acids

Polypeptide: 3 or more amino acids

Question 5

How many levels of protein structure are there?

Answer 5

4

Question 6

Define ‘primary structure’ of a protein

Answer 6

Sequence, number and type of amino acids in the polypeptide,determined by sequence of codons on mRNA

Question 7

Define ‘secondary structure’ of a protein

Answer 7

Hydrogen bonds formed between O (slightly negative) attached to -C=O and H (slightly positive) attached to -NH

Question 8

Describe the two types of secondary protein structure

Answer 8

Alpha helix

All N-H bonds on same side of protein chain
Spiral shape
H-bonds parallel to helical axis

Beta pleated sheet
N-H & C=O groups alternate from one side to the other

Question 9

Define ‘tertiary structure’ of a protein. Name the bonds present

Answer 9

3D structure formed by further folding of polypeptide

• disulfide bridges
  -ionic bonds
  -hydrogen bonds

Question 10

Describe each type of bond in the tertiary structure of proteins

Answer 10

Disulfide bridges: strong covalent S-S bonds between molecules of the amino acid cycsteine

Ionic bonds: relatively strong bonds between charged R groups (pH changes cause these to break)

Hydrogen bonds: numerous and easily broken

Question 11

Define ‘quaternary structure’ of a protein

Answer 11

Two or more polypeptide chains

Question 12

Describe the structure and function of globular proteins

Answer 12

Spherical and compact

Hydrophilic R groups face outwards and hydrophobic R groups face inwards = usually water- soluble

Involved in metabolic processes e.g. enzymes and haemoglobin

Question 13

Describe the structure and function of fibrous proteins

Answer 13

Can form long chains or fibres

Insoluble in water

Useful for structure and support e.g. collagen in skin

Question 14

Outline how chromatography could be used to identify the amino acids in a mixture

Answer 14

1. Use capillary tube to spot mixture onto pencil origin line and place chromatography paper in solvent
2. Allow solvent to run until it almost touches other end of paper. Amino acids move different distances based on relative attraction to paper and solubility in solvent
3. Use revealing agent or UV light to see spots
4. Calculate Rf values and match to database

Question 15

What are enzymes

Answer 15

Biological catalysts for intra and extracellular reactions

Specific tertiary structure determines shape of active site, complementary to a specific substrate

Formation of enzyme-substrate (ES) complexes lowers activation energy of metabolic reactions

Question 16

Explain the induce fit model of enzyme action

Answer 16

Shape of active site is not directly complementary to substrate and is flexible

Conformational change enables ES complexes to form

This puts strain on substrate bonds, lowering activation energy

Question 17

How have models of enzymes action changed

Answer 17

Initially lock and key model: rigid shape of active site complementary to only 1 substrate

Currently induced fit model: also explains why binding at allosteric sites can change shape of active site

Question 18

How could a student identify the activation energy of a metabolic reaction from an energy level diagram?

Answer 18

Difference between free energy of substance and peak of curve

Slide 38

Question 19

Name 5 factors that affect the rate of enzyme-controlled reactions

Answer 19

Enzyme concentration
Substrate concentration
Concentration of inhibitors
pH
Temperature

Question 20

How does substrate concentration affect rate of reaction?

Answer 20

Given that enzyme concentration is fixed, rate increases proportionally to substrate concentration

Rate levels off when maximum number of ES complexes form at any given time

Question 21

How does enzyme concentration affect rate of reaction?

Answer 21

Given that substrate is in excess, rate increases proportionally to enzyme concentration

Rate levels off when maximum number of ES complexes form at any given time

Question 22

How does temperature affect rate of reaction?

Answer 22

Rate increases as kinetic energy increases and peaks at optimum temperature

Above optimum, ionic and H-bonds in tertiary structure break meaning the active site is no longer complementary to substrate (denaturation)

Question 23

How does pH affect rate of reaction?

Answer 23

Enzymes have a narrow optimum pH range

Outside range, H+/OH- ions interact with H-bonds and ionic bonds in tertiary structure = denaturation

Question 24

Contrast competitive and non-competitive inhibitors

Answer 24

Competitive inhibitors:
- similar shape to substrate = bind to active site
-Do not stop reaction; ES complex forms when inhibitor is released
-Increasing substrate concentration decreases their effect

Non-competitive inhibitors
-bind at allosteric binding site
-may permanently stop reaction; triggers active site to change shape
-increasing substrate concentration has no impact on their effect

Question 25

Outline how to calculate rate of reaction from a graph

Answer 25

Calculate gradient of line or gradient of tangent to a point

Initial rate: draw tangent at t=0

Question 26

Outline how to calculate rate of reaction from raw data

Answer 26

Change in concentration of product or reactant/ time

Question 27

Why is it advantageous to calculate initial rate?

Answer 27

Represents maximum rate of reaction before concentration of reactants decreases and ‘end product inhibition’

Question 28

State the formula for pH

Answer 28

pH = -log10[H+]