1.4 Proteins

Question 1

What are proteins made up of?

Answer 1

Amino acids are the monomers from which proteins are made
20 amino acids are common in all organisms - differ only in their R group

Question 2

What is the structure of amino acid?

Answer 2

• Amine group
• Carboxyl group
• R group (variable side chain)

Question 3

What does a condensation reaction between 2 amino acids form?

Answer 3

Peptide bond

Question 4

What is the primary structure?

Answer 4

Sequence of amino acids in a polypeptide chain

Question 5

What is the secondary structure?

Answer 5

• Hydrogen bonding between amino acids (between carbonyl O of one and amino H of another)
• Causes polypeptide chain to fold into a repeating pattern (eg/ alpha helix or beta pleated sheet)

Question 6

What is the tertiary structure?

Answer 6

• Overall 3D structure of a polypeptide held together by interactions between amino acid side chains:
  
  • Ionic bonds/disulfide bridges/hydrogen bonds

Question 7

What is the quaternary structure?

Answer 7

• Some proteins are made of 2+ polypeptide chains
• Held together by more hydrogen, ionic and disulfide bonds

Question 8

What is the Biuret test?

Answer 8

1. Add Biuret solution: sodium hydroxide + copper (I) sulfate
2. Protein present: purple colour (negative = stays blue)
3. Detects presence of peptide bonds

Question 9

What are enzymes?

Answer 9

Biological catalysts - lowers the activation energy -> speeds up rate of reaction

Question 10

Describe the lock and key model?

Answer 10

• Active site is a fixed shape/doesn’t change shape; it is complementary to one substrate
• After a successful collision, an enzyme-substrate complex forms leading to a reaction

Question 11

Describe the induced fit model?

Answer 11

1. Before reaction, enzyme active site not completely complementary to substrate/doesn’t fit substrate
2. Active site shape changes as substrate binds and E-S complex forms
3. This stresses/distorts bonds in substrate making the reaction more likely to happen

Question 12

How specific are enzymes?

Answer 12

Have a specific shaped tertiary structure and active site
- Active site is complementary to a specific substrate
- Only this substrate can bind to the active site, inducing fit and forming an enzyme-substrate complex

Question 13

How does enzyme concentration affect rate of reaction?

Answer 13

Increasing enzyme concentration -> rate of reaction increases
- Enzyme concentration = limiting factor
- More enzymes -> more available active sites
- More successful E-S collisions and E-S complexes
At a certain point, rate of reaction plateus
- Substrate concentration = limiting factor (all substrates in use)

Question 14

How does substrate concentration affect rate of reaction?

Answer 14

Increasing substrate concentration -> rate of reaction increases
- Substrate concentration = limiting factor
- More successful E-S collisions and E-S complexes
At a certain point, rate of reaction plateus
- Enzyme concentration = limiting factor (all active sites saturated)

Question 15

How does temperature affect rate of reaction?

Answer 15

Increasing the temperature up to optimum temp. -> rate of reaction increases
- Increase in kinetic energy
- More successful E-S collisions and E-S complexes
Increasing temp. above optimum -> rate of reaction falls
- Enzyme denature; tertiary structure and active site change shape
- Fewer E-S collisions and E-S complexes
Rate of reaction 0 when all enzymes denatured

Question 16

How does pH affect rate of reaction?

Answer 16

pH above/below optimum pH -> rate of reaction decreases
- Enzymes denature; tertiary structure and active site changes shape/hydrogen/ionic bonds break
- Complementary substrate can no longer bind to active site
- Fewer E-S collisions and E-S complexes
pH = -log10[H+]

Question 17

How do competitive inhibitors affect rate of reaction?

Answer 17

Competitive inhibitors decrease rate of reaction
- Similar shape to substrate
- Competes for/binds to/blocks active site so substrates can’t bind
- Fewer E-S complexes
- Increasing substrate concentration reduces effect of inhibitor

Question 18

How do non-competitive inhibitors affect rate of reaction?

Answer 18

Non-cometitive inhibitors decrease rate of reaction
- Binds to site away from the active site (allosteric site)
- Enzyme tertiary structure/active sit change shape so substrate can’t bind to active site
- Fewer E-S complexes
- Increasing substrate concentration has no effect on rate of reaction as it causes permanent change to active site

Question 19

Describe how proteins are digested in the human gut?

Answer 19

1. Hydrolysis of peptide bonds
2. Endopeptidases break polypeptides into smaller peptide chains
3. Exopeptidases remove terminal amino acids
4. Dipeptidases hydrolyse dipeptides into amino acids