Proteins - Biological Molecules

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 & may include other functional groups e.g. benzene ring or -OH (alcohol)
-NH2 amine/ amino group

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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 & 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-) & eliminates molecule of water
● Dipeptide: 2 amino acids
● Polypeptide: 3 or more
amino acids

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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 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

α-helix:
● all N-H bonds on 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 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 to 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 & 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 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 & 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 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

What are enzymes?

Answer 16

● 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 17

How have models of enzyme action changed?

Answer 17

● 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 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.

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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 & peaks at optimum temperature.
Above optimum, ionic & H-bonds in 3° structure break = active site 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 & ionic bonds in 3° structure = denaturation.

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Question 24

Contrast competitive and non-competitive inhibitors.

Answer 24

competitive:
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 & ‘end product inhibition’.

Question 28

State the formula for pH.

Answer 28

pH = -log10[H+]