Intro To Proteins And Amino acids

Question 1

Protein functions

Answer 1

Speeded up and regulated by an enzyme
Provide support, strength, resilience
Ligand binding roles- bind metabolite for communication/ signal transduction purposes
Storage facility- bind metabolites for storage, nutrient provision
Transport role
Movement functions- contractile proteins
Defensive functions- blood protective proteins
Toxins - defence or offence/ attack functions

Question 2

The central dogma

Answer 2

It is the structure and function of an organisms proteins that act as the final expression of its DNA ie it’s genetic makeup

Question 3

Relationship between organisms DNA and proteins

Answer 3

Storage of the genetic code for the existing collection of proteins that serve current requirements
The potential for different proteins, with potentially different or improved functions, to be available in its descendants in the future.
Although mutations are caused by changes at the DNA level, they are acted on at protein at the protein level. Proteins determine the long term fate of DNA

Question 4

Power of the polymerisation

Answer 4

• cheap and easy. requires less information, less energy and fewer resources to build something large by respectively joining multiple copies of relatively small subunits together than it would by building the same sized molecules from scratch.
• polymerisation provides the potential for enormous structural diversity.
• diversity in the structure of macromolecules leads to diversity of function

Question 5

determinants of function and structure

Answer 5

Length of polymer

Number of different monomers available

Question 6

Configurations of amino acids

Answer 6

In all except glycine, all 4 groups are chiral or asymmetric. Two different arrangements of groups around the c atom are called stereoisomers and enantiomers - mirror like but are non superimposable without breaking bonds (racemized).

Glycine is chiral.

Question 7

Relationship between pH and pKa

Answer 7

If pH

Question 8

Isoelectric point of the amino acid in acid base titration

Answer 8

The pH at which the molecule has zero net charge

Point of inflection observed midway between the two stages of the titration

Question 9

Buffering capacity in titration so

Answer 9

Reduced slope in vicinity of midpoints indicated ability of both carboxylic acid group and amino group to buffer pH
Buffering action effective over pH range of pKa +- 1 pH unit; outside this range pH varies more readily

Question 10

pH and pKa

Answer 10

pH- proton concentration
pKa - equilibrium constant for an ionisation (Ka)
pKa= -logKa

pKa values are fixed, pH can be varied

Question 11

Amino acid classification:

Non- polar aliphatic R- groups

Answer 11

• non- polar/ hydrophobic
• no formally ionisable groups
• no electronegative atoms
• tend to cluster together, stabilising protein structure through hydrophobic interactions
• usually in Core of protein, away from water

Glycine, alanine, valine, leucine, isoleucine, methionine, proline

Question 12

Amino acid classification: Aromatic R groups

Answer 12

• non-polar/ hydrophobic
• cluster together, stabilising protein structure through hydrophobic interactions with other hydrophobic amino acids
• usually in core of protein, away from water

Phenylalanine, tyrosine, tryptophan

Question 13

Amino acid classification: polar uncharged R-groups

Answer 13

• not formally ionised at pH7
• uncharged R groups in this class are more polar and water soluble that the non-polar amino acids
• contain functional groups that form H bonds with water

Serine, threonine, asparagine, glutamine, cysteine

Question 14

Amino acid classification: Acidic R groups (negatively charged at pH7)

Answer 14

• charge state is pH dependent, so they are technically not “negative” amino acids
• one of the two most hydrophilic groups- extremely polar nature due to formal ionisation of R - groups/ side chains
• side chains of these amino acids contain a second carboxylic acid group, with pKa values of about 3.6 and 4.2 respectively

Aspartate, glutamate

Question 15

Classification of amino acids: Basic R groups (positively charged at pH 7)

Answer 15

• charges state is pH dependent
• second of the two most hydrophilic groups- extremely polar nature due to formal ionisation of R groups/ side chains

Lysine, arginine, histidine

*histidine is the only standard amino acid that had an ionisable side chain with a pKa anywhere near neutrality