Amino Acids / Proteins Flashcards
What are the substituents bonded to the a-carbon of an amino acid?
amino group
carboxylic acid group
hydrogen
R group
Which amino acid is achiral?
Glycine - because its R group is just H
Which enantiomer of amino acids is present in proteins?
L-amino acids
How do you determine the absolute configuration of an amino acid?
View the amino acids along the H-aC bond.
In which direction do the substituents read CORN.
Which direction do the substituends read CORN in the L-isomer?
Clockwise
Hydrophobic amino acids
Glycine
Alanine
Proline
Valine
Leucine
Isoleucine
Methionine
Which amino acid contains a secondary amino group?
Proline, as amino group forms part of non-aromatic 5 membered ring of R group.
What effect does proline have on protein structure? Why?
Rigidity of proline due to 5 membered ring limits the conformation of polypeptide regions containing proline.
Which amino acids contain S?
Methionine - thioether (-S-)
Cysteine - sulfhydryl (-SH)
What is the hydrophobic effect?
Non-polar hydrophobic side chains have a tendency to cluster together, excluding water. This has an important stabilising effect on the larger structure of water soluble proteins.
Aromatic amino acids
Phenylalanine
Tyrosine
Tryptophan
Which of the aromatic amino acids are most and least hydrophobic?
Most hydrophobic - phenylalanine.
Least hydrophobic - tryptophan. Slightly polar due to NH group in ring.
Polar amino acids
Serine (-OH)
Threonine (-OH)
Cysteine (-SH)
Asparagine (carboxamide)
Glutamine (carboxamide)
Basic amino acids
Positively charged R groups:
Lysine
Arginine
Histidine
Acidic amino acids
Negatively charged R groups:
Aspartate (aspartic acid)
Glutamate (glutamic acid)
both contain COOH groups that are deprotonated at physiological pH
Henderson Hasselbalch equation
pH = pKa + log([A-]/[HA])
When pH<pKa…
[HA]>[A-]
When [A-]>[HA]…
pH>pKa
pKa of basic amino acids is…
… high
basic amino acids accept protons - positively charged at physiological pH.
pKa of acidic amino acids is …
… low
acidic amino acids release protons - negatively charged at physiological pH.
pI
Isoelectric point - pH at which the amino acid is fully ionised with no net electric charge - NH2 group is protonated, COOH group deprotonated.
pKR
pKa of an amino acid R side group
O-linked glycosylation
sugar attached at -OH of serine or threonine
N-linked glycosylation
sugar attached to -NH2 of asparagine
hydroxylation
oxidation of C-H to C-OH on proline or lysine
phosphorylation
transfer of phosphate group from ATP to -OH group on serine or threonine
which enzymes catalyse phosphorylation and de-phosphorylation
phosphorylation catalysed by kinase enzymes
de-phosphorylation catalysed by phosphatase enzymes
acetylation
transfer of an acetyl group from AcetylCoA to -NH3+ on lysine
example of a protein that is regulated by acetylation + enzymes involved
histones
acetylation catalysed by histone acetyltransferase
deacetylation catalysed by histone deacetylase
acetylation neutralises positive charge of lysine residues - reduces the histones ability to bind to negatively charged DNA
which residues can be methylated
lysine or arginine
