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 & 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 & 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

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

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 model of enzyme

action.

Answer 16

● 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 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.

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.

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 & ‘end product inhibition’.

Question 28

State the formula for pH.

Answer 28

pH = -log10[H+]