1.4-Proteins + 1.5-Enzyme Action

Question 1

What is the general structure of of an amino acid?

Answer 1

COOH - carboxylic acid group.
R group - consists of carbon chains and other functional groups.
NH2 - Amino Group

Question 2

Describe how to test for proteins in a sample.

Answer 2

The Biuret test confirms presence of peptide bonds.
1. Add an equal volume of sodium hydroxide to sample at room temperature.
2. Add drops of silute copper (II) sulfate solution. Swirl to mix.
3. Positive result: colour changes from blue to purple.
4. Negative result: solution remains blue.

Question 3

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

Answer 3

20
They only differ by side ‘R’ group.

Question 4

How do dipeptides and polypeptides form?

Answer 4

• Condensation reaction forms peptide binds and eliminates molecule of water.
• Dipeptide: 2 amino acids
• Polypeptides: 3 or more amino acids.

Question 5

How many levels of protein structures are there?

Answer 5

4

Question 6

Define ‘primary structure’ of a protein.

Answer 6

• Sequence, number ad 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 from between O δ- (slightly negative) attached to -C=O & & H δ+ (slightly positive) attached to -NH.

Question 8

Describe the 2 types of secondary protein structure.

Answer 8

a-helix:
- all N-H bonds on the same side of protein chain.
- spiral shape.
- H-bonds parallel to helical axis
B-pleated sheet:
- N-H & C=O 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 cysteine.
• Ionic bonds: relatively strong bonds between charged R groups (pH changes cause these bonds break)
• Hydrogen bonds: numerous & easily broken.

Question 11

Define quaternary structure of a protein.

Answer 11

• 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 e.g. metal ions or phosphate groups.

Question 12

Describe the structure and function of globular proteins.

Answer 12

• Spherical and compact
• Hydrophilic R groups face outwards & hydrophobic R groups face inwards = usually water soluble.
• Involved in metabolic processes e.g. enzymes & haemoglobin.

Question 13

Describe the stucture and function of fibrous proteins.

Answer 13

• Can form long chains of 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 acides in a mixure.

Answer 14

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 the Rf values and match to database.

Question 15

What are enzymes?

Answer 15

• Biological catalysts for intra & 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 induced fit modle 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 the activation energy.

Question 17

How have models of enzyme action changed?

Answer 17

• Initially lock and key model: rigid shape of active site complementary to only 1 substrate.
• Currently induces fit model: also explains why binding at allosteric sites can chage 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 substrate & peak of curve.

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 19

How does substrate concentration affect rate of reaction?

Answer 19

• 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 20

How does enzyme concentration affect rate of reaction?

Answer 20

• Given that substrate is increases proportionally to enzyme contentration.
• Rate levels off when maximum number of ES complexes form at any given time.

Question 21

How does temperature affect rate of reaction?

Answer 21

• Rate increases as kinetic energy increases & peaks at optimum temperature.
• Above optimum, ionic & H-bonds in 3° structure break = active site no longer complementary to substrate (denature).

Question 22

How does pH affect rate of reaction?

Answer 22

• Enzymes have a narrow optimum pH range.
• Outside range, H+/OH- ions interact with H-bonds and ionic bonds in 3° structure = denature.

Question 23

Contrast competitive and now competitive inhibitors.

Answer 23

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 24

Outline how to calculate rate of reaction from a graph.

Answer 24

• Calculate gradient of line or gradient of tangent to a point.
• Initial rate: draw tangent at t=0.

Question 25

Outline how to calculate rate of reaction from raw data.

Answer 25

Change in concentration of product or reactant / time.

Question 26

Why is it an advantage to calculate initial rate?

Answer 26

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

Question 27

Formula of pH

Answer 27

pH = -log₁₀ [H⁺].