Proteins

Question 1

What is the general structure of an amino acid?

Answer 1

• COOH group
• R group
• NH2 amine group

Question 2

Describe how to test for proteins in a sample.

Answer 2

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

Question 3

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

Answer 3

20
Differ only by side ‘R’ group

Question 4

How do dipeptides and polypeptides form?

Answer 4

• condensation reaction forms peptide bond & 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 form between O δ- attached to C=O & Hδ+ attached to -NH

Question 8

Describe the 2 types of secondary protein structure.

Answer 8

α-helix

β-pleated sheet

Question 9

Define tertiary structure of a protein.

Answer 9

3D structure formed by further folding of polypeptide
- disulfide bridges
- ionic bonds
- hydrogen bonds

Question 10

Define quaternary structure of proteins.

Answer 10

• 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 11

Describe the structure and function of globular proteins.

Answer 11

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

Question 12

Describe the structure and function of fibrous proteins.

Answer 12

• can form long chains or fibres
• insoluble in water
• useful for structure and support

Question 13

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

Answer 13

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 14

What are enzymes?

Answer 14

• biological catalyst for intra & extracellular reactions
• specific tertiary structure determines shape of active site, complementary to a specific substrate
• formation of enzyme-substrate complexes lowers activation energy of metabolic reactions.

Question 15

Explain the induced fit model of enzyme action.

Answer 15

• 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 16

How have models of enzyme action changed?

Answer 16

• initially lock and key model
• currently induced fit model: explains why binding at allosteric sites can change shape of active site

Question 17

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

Answer 17

• enzyme conc
• substrate conc
• conc of inhibitors
• pH
• temperature

Question 18

How does substrate concentration affect rate of reaction?

Answer 18

Rate increases proportionally to substrate concentration.
Rate levels off when maximum number of ES complexes for at any given time

Question 19

How does enzyme concentration affect rate of reaction?

Answer 19

Rate increases proportionally to enzyme concentration
Rate levels off when maximum number of ES complexes form at any given time

Question 20

How does temperature affect the rate of reaction?

Answer 20

Rate increases as kinetic energy increases and peaks at optimum temperature.
Above optimum, ionic & H-bonds in 3 degrees structure break = active longer complementary

Question 21

How does pH affect the rate of reaction?

Answer 21

Enzymes have a narrow optimum pH range
Outside range denatures

Question 22

Contrast competitive and non-competitive inhibitors.

Answer 22

Competitive:
- similar shape to substrate = bind to active site
- do not stop reaction; ES complex forms when inhibitor is released
- increased substrate concentration decreases their effect
Non-competitive:
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 23

Outline how to calculate rate of reaction from raw data.

Answer 23

Change in concentration of product or reactant/time.

Question 24

Why is it advantageous to calculate initial rate?

Answer 24

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

Question 25

State the formula for pH.

Answer 25

pH = -log10[H+]