3.1.4 Proteins

Question 1

Describe what amino acids are.

Answer 1

Amino acids are the monomers from which proteins are made.

Question 2

What is the general structure of an amino acid?

Answer 2

1. NH2 represents an amine group.
2. COOH represents a carboxyl group.
3. R represents a variable side chain.

Question 3

Describe the formation and product(s) of a peptide bond.

Answer 3

1. A condensation reaction between 2 amino acids forms a peptide bond.
2. Dipeptides are formed by the condensation of two amino acids.
3. Polypeptides are formed by the condensation of many amino acids.
4. A functional protein may contain one or more polypeptides.

Question 4

Primary (1°) structure:

Answer 4

Sequence of amino acids in a polypeptide chain (joined by peptide bonds).

Question 5

Secondary (2°) structure:

Answer 5

Hydrogen bonding between amino acids (between the carboxyl O of one amino acid and the amino H of another).
This causes the polypeptide chain to fold into a repeating pattern e.g. alpha helix or beta pleated sheet

Question 6

Tertiary (3°) structure:

Answer 6

Overall 3D structure of a polypeptide.
Held together by interactions between the amino acid side chains (R groups): Ionic bonds; Disulfide bridges; Hydrogen bonds

Question 7

Quaternary (4°) structure:

Answer 7

Some proteins are made of 2+ polypeptide chains.
Also held together by more hydrogen, ionic and disulfide bonds

Question 8

Describe the test for proteins.

Answer 8

1. Add biuret solution: sodium hydroxide + copper (II) sulfate
2. Protein present: purple colour (no protein present – stay blue).
3. Detects presence of peptide bonds.

Question 9

Describe the nature and function of enzymes and how do they impact reactions?

Answer 9

1. Enzymes are biological catalysts; they catalyse a wide range of intracellular (within cells) and extracellular (outside cells) reactions that determine structures and functions from cellular to whole-organism level.
2. Each enzyme lowers the activation energy of the reaction it catalyses (by creating an alternative pathway) → speed up rate of reaction

Question 10

Lock and Key Model:

Answer 10

1. Outdated.
2. Active site is fixed shape and complementary to one substrate.
3. After a successful collision, an E-S complex forms leading to a reaction

Question 11

Induced fit model:

Answer 11

1. Recently accepted.
2. Before the reaction the enzyme active site is not completely complementary to the substrate.
3. This induces the active site to change shape.
4. This distorts bonds in substrate leading to a reaction.

Question 12

Describe the specificity of an enzyme with regards to its tertiary structure:

Answer 12

1. The properties of an enzyme relate to the tertiary structure of its active site and its ability to combine with complementary substrate(s) to form an enzyme-substrate complex.
2. Enzymes have a specific shaped tertiary structure and active site - Sequence of amino acids (primary structure) determines tertiary structure.
3. Active site is complementary to a specific substrate.
4. Enabling only this substrate to bind to the active site (induce fit) → enzyme-substrate complex.

Question 13

Explain how enzyme concentration affects the rate of reaction.

Answer 13

1. Increasing enzyme conc. → rate of reaction increases.
   Enzyme conc. = limiting factor (substrate in excess).
2. More enzymes → more available active sites.
3. More successful E-S collisions and E-S complexes.
4. At a certain point, rate of reaction plateaus.
5. Substrate conc. = limiting factor (all substrates in use).

Question 14

Explain how substrate concentration affects the rate of an enzyme-catalysed reaction.

Answer 14

1. Increasing substrate conc. → rate of reaction increases.
2. Substrate concentration = limiting factor (too few enzyme molecules to occupy all active sites).
3. More successful E-S collisions and E-S complexes.
4. At a certain point, rate of reaction plateaus.
5. Enzyme conc. = limiting factor (all active sites saturated; excess substrate).

Question 15

Explain how temperature affects the rate of an enzyme-catalysed reaction.

Answer 15

1. Increasing temp. up to optimum → rate of reaction increases.
2. Increase in kinetic energy.
3. More successful E-S collisions and E-S complexes.
4. Increasing temp. above optimum → rate of reaction falls.
5. Enzymes denature; tertiary structure and active site change shape (hydrogen and ionic bonds break).
6. Fewer E-S collisions and E-S complexes (substrate no longer binds to active site).
7. Rate of reaction 0 when all enzymes denatured.

Question 16

Explain how pH affects the rate of an enzyme-catalysed reaction.

Answer 16

1. pH above/below optimum pH → rate of reaction decreases.
2. Enzymes denature; tertiary structure and active site change shape (hydrogen and ionic bonds break).
3. Complementary substrate no longer binds/fits to active site.
4. Fewer E-S collisions and E-S complexes.

Question 17

Explain how concentration of competitive inhibitors affects the rate of an enzyme-catalysed reaction.

Answer 17

1. Similar shape to substrate.
2. Competes for / binds to / blocks active site so substrates can’t bind.
3. Fewer E-S complexes.
4. Increasing substrate conc. reduces effect of inhibitor (level of inhibition dependent on relative concs. of substrate and inhibitor).
5. Decreases rate of reaction

Question 18

Explain how concentration non-competitive inhibitors affects the rate of an enzyme-catalysed reaction.

Answer 18

1. Binds to site away from the active site (allosteric site).
2. Enzyme tertiary structure / active site change shape so substrate can’t bind to active site.
3. Fewer E-S complexes.
4. Increasing substrate concentration has no effect on rate of reaction as causes permanent change to active site.