Topic 1 - Module 1 Flashcards
What sub-group of amino acids can often act as chelators of metal ions due to it being highly polar?
Give both names.
Acidic AA: Aspartic acid and glutamate
Which amino acid has only one amine functional group, and has its protonated form predominating at physiological pH of 7.4?
Basic AA: Lysine
Which amino acid is predominantly positively charged at physiological pH of 7.4 and also will remain neutral at extremely high pH?
Basic AA: Arginine
Which amino acid is classified as a tertiary amine with an aromatic ring? And also remains highly populated in both protonated and deprotonated forms?
Basic AA: Histidine
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.
uncharged polar side chains: the amides, Asparagine and Glutamine.
Give two examples of chiral, non-reactive amino acids.
Hydroxyls: Serine, Ser (S) and Threonine, Thr (T)
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.
Aromatic side-chains: Phenylalanine, Tyrosine or Trytophan
Explain why tyrosine is useful in biochemical reactions when Phenylalanine is less useful.
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.
Explain the significance of the conjugated bonds in aromatic rings.
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
Which amino acid has an indole ring? Draw the amino acid.
Tryptophan
Define aliphatic side chains and explain their significance
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)
Give two examples of ‘beta-branched’ amino acids.
Valine and Isoleucine
Which amino acid is the structural isomer of Leucine?
Isoleucine (Ile)
Which amino acid contains a cyclic 5-membered ring, and isn’t actually an amino acid?
Proline - an imino acid due to no NH group
Which amino acid doesn’t have side chains (no reactive groups)?
Explain the structural significance of this AA.
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)
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.
Sulphur containing side chains, cysteine or methionine
Explain the difference between interchain and intrachain disulphide bonds.
interchain: sulfide link between two different AA chains (polypeptides)
Intrachain: sulfide link between two different locations along the same polypeptide chain.
Why are biochemical reactions defined as favourable?
when more bond energy is released compared to the bond energy needed to break the bond. (output > input)
What is a nucleotide and how is it different to a nucleoside?
nucleotide: base + sugar + phosphate
nucleoside: base + sugar
What is the structural significance of ADP^3- ?
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.
What is the chemical definition of the hydrolysis of phosphoanhydride bonds and why?
Exergonic, due to the formation of stronger bonds and the release of Pi (stable due to multiple resonance forms)
In both exergonic and endergonic reactions, what should the value of gibbs free energy be?
Exergonic: negative, endergonic; positive
Define Gibbs free energy
The energy of the reaction available to do work
What value of Gibbs free energy is needed for the reaction to be spontaneous?
Negative value (delta G < 0)
What is the more favourable orientation of alpha-carbons relative to their side chains?
Trans-orientation.
Due to there being less steric clashes (from Va der Waals repulsion) between side chains
Which amino acid side chain can exhibit equal porportions residues in both trans and cis orientation?
Proline.
Why are psi and phi angles significant in peptide chains?
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.
What type of chemical interaction is critically dependent on carbon and hydrogen having very similar relative electronegativity?
Their resulting hydrophobic effect.
Given that the pKa of a carboxylate group is 4.5, what will its most highly populated state be at pH = 7?
The most highly populated state is likely to be negatively charged due to its acidic nature of the AA residue.
If the pKa of a guanidinium group is 12.5, what will occur when the pH is less than 12.5?
The highly populated state of this group will be positively charged, as it is acidic.
What are L-amino acids?
They are naturally occurring isomers, derived from L-glyceraldehyde.
What is the omega angle?
Looking from C(i) to N(i+1) - aka looking along the peptide bond.
Trans is -180 degrees, Cis is 0 degrees.
What is the phi angle?
Looks along the N(i) to C(alpha) to observe angle between C(i - 1) and C(i)
What is the psi angle?
Looking along C(alpha) and C(i) bond, observe angle between N(i) and N(i+1)
Under what conditions will Cysteine form disulphide bonds?
Under oxidising conditions it will form disulphide bonds in solution.
Under reducing cell conditions, disulphide bonds will be broken, forming -SH residues instead.
