1.4 - Proteins

Question 1

What is the general structure of an amino acid?

Answer 1

• COOH carboxylic acid group
• NH2 amine group
• R variable region consisting of carbon chains & other functional groups

Question 2

Describe how to test for proteins in a sample.

Answer 2

Use the Biuret test which confirms the presence of a peptide bond.
1) To make test solution alkaline, add a few drops of sodium hydroxide solution.
2) Add copper (II) sulfate solution.
Negative result: solution remains blue
Positive result: solution changes to purple

Question 3

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

Answer 3

20
Only differ in R group

Question 4

How do dipeptides and polypeptides form?

Answer 4

Condensation reaction forms peptide bonds whilst releasing a water molecule.
Dipeptide = 2 amino acids
Polypeptide = 3 +

Question 5

How do dipeptides and polypeptides form?

Answer 5

Condensation reaction forms peptide bonds whilst releasing a water molecule.
Dipeptide = 2 amino acids
Polypeptide = 3 +

Question 6

What are the levels of protein structure?

Answer 6

Primary, secondary, tertiary & quaternary

Question 7

Define ‘primary structure’ of a protein.

Answer 7

Primary structure is the sequence, number & type of amino acids in the polypeptide chain.
Determined by sequence of codons on mRNA

Question 8

Define ‘secondary structure’ of a protein.

Answer 8

Hydrogen bonds form between amino acids in the polypeptide chain, automatically making it coil into an alpha helix, or fold into a beta pleated sheet.

Question 9

Define ‘tertiary structure’ of a protein.

Answer 9

Hydrogen & ionic bonds, and disulfide bridges form between parts of the polypeptide chain.

Question 10

Describe disulfide bridges in the tertiary structure of proteins.

Answer 10

Strong covalent S-S bonds between molecules of the amino acid cysteine

Question 11

Describe ionic bonds in the tertiary structure of proteins

Answer 11

Relatively strong bonds between charged R groups.
pH changes causes ionic bonds to break.

Question 12

Describe hydrogen bonds in the tertiary structure of proteins.

Answer 12

Numerous & easily broken.

Question 13

Define ‘quaternary structure’ of a protein.

Answer 13

Some proteins are made of several polypeptide chains held together by bonds. The quaternary structure is the protein’s final 3D structure.

Question 14

Describe the structure of globular proteins.

Answer 14

• Spherical & compact
• Hydrophilic R groups face outwards & hydrophobic R groups face inwards, so usually water soluble

Question 15

Describe the function of globular proteins.

Answer 15

Involved in metabolic processes (e.g. enzymes & haemoglobin)

Question 16

Describe the structure of fibrous proteins.

Answer 16

Can form long chains of fibres
Insoluble in water

Question 17

Describe the function of fibrous proteins.

Answer 17

Useful for structure & support (e.g. collagen in skin)

Question 18

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

Answer 18

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 substances based on relative attraction to paper & solubility in solvent.
3) Use revealing agent or UV light to see spots.
4) Calculate retention factor (Rf) values & match database.

Question 19

How is the retention factor value calculated in chromatography?

Answer 19

By dividing the distance travelled by the component by the distance travelled by the solvent.

Question 20

What are enzymes?

Answer 20

Biological catalysts that are responsible for speeding up metabolic reactions both at a cellular level and for the organism as a whole (intra & extracellular)

Question 21

Explain the induced fit model of enzyme action.

Answer 21

Shape of active site isn’t directly complementary to substrate, but is flexible.
As the substrate binds, the active site changes shape slightly in order to form an enzyme-substrate complex.
This puts strain on bonds in the substrate, lowering activation energy.

Question 22

How have models of enzyme action changed?

Answer 22

Initially lock & key model: rigid shape of active site complementary to only 1 substrate.
Now, induced fit model: also explains why binding at allosteric sites can change shape of active site.

Question 23

How could a student identify the activation energy of a metabolic reaction from an energy level diagram?

Answer 23

Difference between free energy of substrate & peak of curve.

Question 24

Name 5 factors that affect enzyme activity.

Answer 24

• Enzyme concentration
• Substrate concentration
• Concentration of inhibitors
• pH
• Temperature

Question 25

How does substrate concentration affect rate of reaction?

Answer 25

The higher the substrate concentration, the faster the rate of reaction, as increases the chance of collisions between enzymes & substrates.
Only true up until ‘saturation’ point, when enzyme concentration becomes a limiting factor, as all active sites are full.
Substrate concentration naturally decreases with time as reactions take place, as they are used up. So therefore, rate of reaction will also decrease.

Question 26

How does enzyme concentration affect rate of reaction?

Answer 26

The higher the enzyme concentration, the faster the rate of reaction, as there are more enzymes to collide and form E-S complexes.
If amount of substrate is limited, there will be more than enough enzymes to deal with all available substrates, so adding more enzymes has no further effect.

Question 27

How does temperature affect rate of reaction?

Answer 27

As temp rises, enzymes have more kinetic energy, so vibrate more, meaning they are more likely to collide and form E-S complexes.
After optimum temp, too much kinetic energy breaks bonds in the enzyme, changing active site shape. The enzyme is denatured.

Question 28

How does pH affect rate of reaction?

Answer 28

All enzymes have optimum pH value (in humans, mostly 7)
Above and below optimum pH, H+ & 0H- ions found in acids and alkalis can affect ionic & hydrogen bonds that maintain enzymes tertiary structure.
Active site changes shape, so enzyme denatures.

Question 29

Why is pepsin unlike most enzymes found in humans?

Answer 29

It has an optimum pH of 2, which is useful as it works in the stomach (acidic environment).

Question 30

What are competitive inhibitors?

Answer 30

Molecules similar in shape to that of the substrate,
Compete with substrate ti bind to active site,
But no reaction takes place.
Instead they block the active site,
So no substrate can fit in and form an E-S complex.

Question 31

How does concentration of competitive inhibitors affect rate of reaction?

Answer 31

Depends on relative concentration of competitive inhibitors to substrate.
Higher conc of inhibitor = most active sites blocked.
Higher conc of substrate = most active sites are joined in E-S complexes to substrate.
However, competitive inhibitors only temporarily block active sites, as are released.

Question 32

What are non-competitive inhibitors?

Answer 32

Molecules that bind to allosteric site of enzymes (away from active site),
Causing active site to change shape,
So substrate molecules can no longer bind to it.
They have a different shape to the substrate.

Question 33

How does the concentration of non-competitive inhibitors affect the rate of reaction?

Answer 33

Permanently cause the active site to change shape, so increasing conc of substrate won’t make a difference to reation rate, as they can no longer bind to active site.
Permanently lowers rate of reaction.

Question 34

Contrast competitive and non-competitive inhibitors.

Answer 34

Competitive have similar shape to substrate, non don’t.
Competitive bind to active site, non bind to allosteric.
Competitive are released so are impermanent, non permanently change shape of enzyme.
Competitive’s effect decreases as substrate conc is added, non’s effect remains the same.

Question 35

Outline how to calculate rate of reaction from a graph.

Answer 35

Calculate gradient of line or gradient of tangent to a point.

Question 36

Outline how to calculate rate of reaction from raw data.

Answer 36

Change in concentration of product

Question 37

Why is it advantageous to calculate initial rate?

Answer 37

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

Question 38

What is ‘end-product inhibition’ ?

Answer 38

When the final product inhibits an enzyme involved in the initial reactions.