Proteins

Question 1

What is the general structure of an amino acid?

Answer 1

• COOH carboxyl group
• R variable side group consists of carbon chain & may include other functional groups
• NH2 amine group

Question 2

Describe how to test for proteins in a sample

Answer 2

1. Add equal volume of NaOH to sample at room temperature
2. Add drop of dilute CuSO4 solution. Swirl to mix = biuret reagent
3. Positive: colour changes from blue to purple
   Negative: 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-) & eliminates molecule of water

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 & 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 form between Oδ- attached to -C=O & Hδ+ attached to -NH

Question 8

Describe the 2 types of secondary protein structure

Answer 8

α-helix
- all N-H bonds on the same side of protein chain
- spiral shape
- H-bonds parallel to helical axis
β-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

Answer 9

3D structure formed by further folding of polypeptide

• disulfide bridges
• ionic bonds
• hydrogen bonds

Question 10

Describe disulfide bridges

Answer 10

Strong covalent S-S bonds between molecules of the amino acid cysteine

Question 11

Describe ionic bonds

Answer 11

Relatively strong bonds between charged R groups (pH changes cause these bonds to break)

Question 12

Describe hydrogen bonds

Answer 12

Numerous & easily broken

Question 13

Define ‘quaternary structure’ of a protein

Answer 13

• Functional proteins may consist of more than one polypeptide
• Precise 3D structure held together by the same types of bond as tertiary structure
• May involve addition of prosthetic groups

Question 14

Describe the structure and function of globular proteins

Answer 14

• spherical & compact
• hydrophilic R groups face outwards & hydrophobic R groups face inwards = usually water-soluble
• involved in metabolic processes

Question 15

Describe the structure and function of fibrous proteins

Answer 15

• can form long chains or fibres
• insoluble in water
• useful for structure and support e.g collagen in skin

Question 16

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

Answer 16

1. Use capillary tube to spot mixture onto pencil origin line & 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 & solubility in solvent
3. Use revealing agent or UV light to see spots
4. Calculate Rf values & match to database

Question 17

What are enzymes?

Answer 17

• Biological catalysts for intra & extracellular reactions
• Specific tertiary structure determines shape of active site, complementary to a specific substrate
• Formation of ES complexes lowers activation energy of metabolic reactions

Question 18

Explain the induced fit model of enzyme action

Answer 18

• Shape of active site is not directly complementary to substrate & is flexible
• Conformational change enables ES complexes to form
• This puts strain on substrate bonds, lowering activation energy

Question 19

How have models of enzyme action changed?

Answer 19

• Initially lock & 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 20

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

Answer 20

Difference between free energy of substrate & peak of curve

Question 21

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

Answer 21

• enzyme concentration
• substrate concentration
• concentration of inhibitors
• pH
• temperature

Question 22

How does substrate concentration affect rate of reaction?

Answer 22

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 23

How does enzyme concentration affect rate of reaction?

Answer 23

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 24

How does temperature affect rate of reaction?

Answer 24

Rate increases as kinetic energy increases & peaks at optimum temperature
Above optimum, ionic & H-bonds in tertiary structure break = active site no longer complementary to substrate - denatured

Question 25

How does pH affect rate of reaction?

Answer 25

Enzymes have a narrow optimum pH range | Outside range, H+/OH- ions interact with H-bonds & ionic bonds in tertiary structure = denatured

Question 26

Contrast competitive and non-competitive inhibitors

Answer 26

- bind to active site vs bind at allosteric binding site - do not stop reaction (when released ES complex forms) vs may permanently stop reaction since active site changed shape - increasing substrate concentration decreases their effect vs increasing substrate concentration has no impact

Question 27

Outline how to calculate rate of reaction from a graph

Answer 27

- calculate gradient of line or gradient of tangent to a point - initial rate: draw tangent at t = 0

Question 28

Outline how to calculate rate of reaction from raw data

Answer 28

Change in concentration of reactant / time