1.4 - Proteins

What is the general structure of an

amino acid?

-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

Describe how to test for proteins in a

sample.

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.

How many amino acids are there and

how do they differ from one another?

20

differ only by side ‘R’ group

How do dipeptides and polypeptides

form?

● Condensation reaction

forms peptide bond

(-CONH-) & eliminates

molecule of water

● Dipeptide: 2 amino acids

● Polypeptide: 3 or more

amino acids

How many levels of protein structure are

there?

4

Define ‘primary structure’ of a protein.

● Sequence, number & type of amino

acids in the polypeptide.

● Determined by sequence of codons on

mRNA.

Define ‘secondary structure’ of a protein.

Hydrogen bonds form between O 𝛿-

(slightly negative) attached to ‒C=O & H

𝛿+ (slightly positive) attached to ‒NH.

Describe the 2 types of secondary

protein structure.

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

Define ‘tertiary structure’ of a protein.

Name the bonds present.

3D structure formed by further folding of

polypeptide

● disulfide bridges

● ionic bonds

● hydrogen bonds

Describe each type of bond in the tertiary

structure of proteins.

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

Define ‘quaternary structure’ of a protein.

● 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.

Describe the structure and function of

globular proteins.

● Spherical & compact.

● Hydrophilic R groups face outwards & hydrophobic

R groups face inwards = usually water-soluble.

● Involved in metabolic processes e.g. enzymes &

haemoglobin.

Describe the structure and function of

fibrous proteins.

● Can form long chains or fibres

● insoluble in water.

● Useful for structure and support e.g.

collagen in skin.

Outline how chromatography could be

used to identify the amino acids in a

mixture.

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 R f values & match to database

What are enzymes?

● 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.

Explain the induced fit model of enzyme

action.

● 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.

How have models of enzyme action

changed?

● 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.

How could a student identify the

activation energy of a metabolic reaction

from an energy level diagram?

Difference between free

energy of substrate & peak

of curve.

Name 5 factors that affect the rate of

enzyme-controlled reactions.

● enzyme concentration

● substrate concentration

● concentration of inhibitors

● pH

● temperature

How does substrate concentration affect

rate of reaction?

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.

How does enzyme concentration affect

rate of reaction?

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.

How does temperature affect rate of

reaction?

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).

How does pH affect rate of reaction?

Enzymes have a narrow optimum

pH range.

Outside range, H + / OH - ions

interact with H-bonds & ionic

bonds in 3° structure =

denaturation.

Contrast competitive and

non-competitive inhibitors.

Outline how to calculate rate of reaction

from a graph.

● calculate gradient of line or gradient of

tangent to a point.

● initial rate: draw tangent at t = 0.

Outline how to calculate rate of reaction

from raw data.

Change in concentration of product or

reactant / time.

Why is it advantageous to calculate initial

rate?

Represents maximum rate of reaction

before concentration of reactants

decreases & ‘end product inhibition’