Topic 1 - Module 1

Question 1

What sub-group of amino acids can often act as chelators of metal ions due to it being highly polar?
Give both names.

Answer 1

Acidic AA: Aspartic acid and glutamate

Question 2

Which amino acid has only one amine functional group, and has its protonated form predominating at physiological pH of 7.4?

Answer 2

Basic AA: Lysine

Question 3

Which amino acid is predominantly positively charged at physiological pH of 7.4 and also will remain neutral at extremely high pH?

Answer 3

Basic AA: Arginine

Question 4

Which amino acid is classified as a tertiary amine with an aromatic ring? And also remains highly populated in both protonated and deprotonated forms?

Answer 4

Basic AA: Histidine

Question 5

What sub-group of amino acids are known to be mostly chemically unreactive (despite being polar in nature) due to its trigonal planar structure (flatness)?
Give two examples.
Note: can also de-amidate to its acidic forms.

Answer 5

uncharged polar side chains: the amides, Asparagine and Glutamine.

Question 6

Give two examples of chiral, non-reactive amino acids.

Answer 6

Hydroxyls: Serine, Ser (S) and Threonine, Thr (T)

Question 7

Each carbon exhibit a trigonal planar shape, and when combined, will form a flat, hexagonal structure, hence will have multiple resonance forms.
Give two examples of amino acids in this sub-group.

Answer 7

Aromatic side-chains: Phenylalanine, Tyrosine or Trytophan

Question 8

Explain why tyrosine is useful in biochemical reactions when Phenylalanine is less useful.

Answer 8

Tyrosine has a hydroxyl group (-OH) and when deprotonated can form hydrogen bonds with other molecules such as chelates and cofactors, which makes it useful in comparison to Phe, which doesn’t have any functional groups.

Question 9

Explain the significance of the conjugated bonds in aromatic rings.

Answer 9

The extensive network of double carbon bonds (C=C) creates a pool of delocalised electrons, which is what enables:

• absorption of UV and fluorescent light,
• electron-rich charge transfers

making them sensitive to their environment.

Therefore: makes them useful as probes for detecting proteins in solutions

Question 10

Which amino acid has an indole ring? Draw the amino acid.

Answer 10

Tryptophan

Question 11

Define aliphatic side chains and explain their significance

Answer 11

an organic compound containing carbon and hydrogen joined together in straight chains, branched chains, or non-aromatic rings.

Given that they are non-polar, they are able to react favorably with other non-polar groups/hydrophobic groups (biochemical substances)

Question 12

Give two examples of ‘beta-branched’ amino acids.

Answer 12

Valine and Isoleucine

Question 13

Which amino acid is the structural isomer of Leucine?

Answer 13

Isoleucine (Ile)

Question 14

Which amino acid contains a cyclic 5-membered ring, and isn’t actually an amino acid?

Answer 14

Proline - an imino acid due to no NH group

Question 15

Which amino acid doesn’t have side chains (no reactive groups)?
Explain the structural significance of this AA.

Answer 15

Glycine, without a side chain:

• will make it have less steric clashes, such as increased rotational freedom (greater phi and psi angles).
• can form both LH and RH turns (due to lack of bulky chains)

Question 16

What amino acid sub-group will undergo redox reactions depending on cell environment? (inside or outside cell) Provide an example of an AA in this sub-group.

Answer 16

Sulphur containing side chains, cysteine or methionine

Question 17

Explain the difference between interchain and intrachain disulphide bonds.

Answer 17

interchain: sulfide link between two different AA chains (polypeptides)
Intrachain: sulfide link between two different locations along the same polypeptide chain.

Question 18

Why are biochemical reactions defined as favourable?

Answer 18

when more bond energy is released compared to the bond energy needed to break the bond. (output > input)

Question 19

What is a nucleotide and how is it different to a nucleoside?

Answer 19

nucleotide: base + sugar + phosphate
nucleoside: base + sugar

Question 20

What is the structural significance of ADP^3- ?

Answer 20

ATP has 4 negative charges spread along the phosphate group, compared to ADP with only 3, hence ATP is said to have higher charge density than ADP, structurally, ADP is more stable than ATP.

Question 21

What is the chemical definition of the hydrolysis of phosphoanhydride bonds and why?

Answer 21

Exergonic, due to the formation of stronger bonds and the release of Pi (stable due to multiple resonance forms)

Question 22

In both exergonic and endergonic reactions, what should the value of gibbs free energy be?

Answer 22

Exergonic: negative, endergonic; positive

Question 23

Define Gibbs free energy

Answer 23

The energy of the reaction available to do work

Question 24

What value of Gibbs free energy is needed for the reaction to be spontaneous?

Answer 24

Negative value (delta G < 0)

Question 25

What is the more favourable orientation of alpha-carbons relative to their side chains?

Answer 25

Trans-orientation.

Due to there being less steric clashes (from Va der Waals repulsion) between side chains

Question 26

Which amino acid side chain can exhibit equal porportions residues in both trans and cis orientation?

Answer 26

Proline.

Question 27

Why are psi and phi angles significant in peptide chains?

Answer 27

They are the two angles that determine the extent of free rotation (conformational freedom) between two AA side chains, and hence, is what dictates the amount of protein folding that occurs.

Question 28

What type of chemical interaction is critically dependent on carbon and hydrogen having very similar relative electronegativity?

Answer 28

Their resulting hydrophobic effect.

Question 29

Given that the pKa of a carboxylate group is 4.5, what will its most highly populated state be at pH = 7?

Answer 29

The most highly populated state is likely to be negatively charged due to its acidic nature of the AA residue.

Question 30

If the pKa of a guanidinium group is 12.5, what will occur when the pH is less than 12.5?

Answer 30

The highly populated state of this group will be positively charged, as it is acidic.

Question 31

What are L-amino acids?

Answer 31

They are naturally occurring isomers, derived from L-glyceraldehyde.

Question 32

What is the omega angle?

Answer 32

Looking from C(i) to N(i+1) - aka looking along the peptide bond.
Trans is -180 degrees, Cis is 0 degrees.

Question 33

What is the phi angle?

Answer 33

Looks along the N(i) to C(alpha) to observe angle between C(i - 1) and C(i)

Question 34

What is the psi angle?

Answer 34

Looking along C(alpha) and C(i) bond, observe angle between N(i) and N(i+1)

Question 35

Under what conditions will Cysteine form disulphide bonds?

Answer 35

Under oxidising conditions it will form disulphide bonds in solution.

Under reducing cell conditions, disulphide bonds will be broken, forming -SH residues instead.