Amino acids Flashcards
What are the structures of glycine and cysteine
(two i must know to draw)
Look at a photo
What is a residue?
An amino acid as part of a protein e.g. if a protein contains
glycine, that is not “the amino acid glycine” but “a glycine residue”
What is a moiety?
Part of a molecule, basically – does not have to be a functional
group “this moiety interacts with…” “the amide moiety here…”
What amino acids are found in protein (D/L)
Amino acids found in proteins are all L-amino acids (e.g. L-cysteine).
Does Glycine have D/L isomerism?
no optical isomerism so it does not have L/D as it is not asymmetrical
How many structural (proteogenic) amino acids are found and how many are coded for in the genetic code?
- 22 and of these, 21 have codons so are directly coded for in the genetic code. The others are formed post-translation or essentially by chance.
What about D-amino acids
- D-alanine is found in cell walls of the Bacteria, but not usually in proteins.
Give the only example where a D-amino acid is found in a protein in Eukarya that we know?
In the venom of the male duckbill platypus. In one of the proteins there is one D-amino acid and that’s the only time it has been evolved in the whole of the Euskara
What is the intracellular PH of most things and what is the exception?
About pH 7.2
Primary amino and carboxyl groups on side-chains are very important in pH homeostasis.
* One key exception – Acetobacter spp. (used to make vinegar
commercially) have a low intracellular pH, about pH 4
Explain a peptide bond and where is it formed?
Covalent bond from the –COOgroup of one amino acid and –
NH3+ group of another.
* Technically an amide group (-CONH-) but when within a
protein/peptide backbone, it is called a peptide bond.
* Formed in a ribosomes, catalysed by the rRNA component.
Formation eliminates water – thus can be cleaved
hydrolytically but only at extremes of pH (below 1)or if catalysed by an enzyme e.g proteases (trypsin in stomach).
Peptide nomenclature
What can you call a dipeptide of glycine?
What are 6 peptides called and what are they used in?
glycinyl glycinate or diglycine
Hexapeptides commonly used in skincare active ingredients.
Oligopeptides short but with undefined length.
Polypeptide = long, and also a term for a single subunit of a protein.
protein = one or many polypeptides, often with prosthetic groups bound to the structure.
How to lable a heme group
NOT haem its is now heme B
Name aliphatic side-chain amino acids and their properties?
Alanine, isoleucine, leucine, glycine and valine
They are all non-polar and at pH 7.2 and do
not carry a charge on their sidechains.
*All are hydrophobic side-chains –particularly leucine and isoleucine (longer, branched chains).
* isoleucine, leucine and valine are
branched-chain amino acids (BCAAs). Important in nutrition of
the Mammalia.
* glycine is one of the sites at which a fatty acid residue can bind to form proteolipids (not called
“lipoproteins” if in membranes!).
Amino acids – aromatic side-chains
histidine, phenylalanine, tryptophan and tyrosine
- histidine is basic aromatic and basic
polar, carrying a positive charge at pH
7.2. - histidine binds many d-block metals
strongly e.g. Cu(II), Co(II), Ni(II) etc –found in active sites of
enzymes and exploited in His-tagging proteins for
purification. - ‘copper peptides’ used in skincare products, they contain histidine bound to Cu(II) ions.
- phenylalanine and tryptophan are non-polar and are both hydrophobic.
- tyrosine is polar.
- They all absorb UV light (λ 200-300 nm) –used in protein separation technologies.
Amino acids – hydroxyl side-chains
serine and threonine
- Hydroxylated side chains.
- Both are polar and neutral at
pH 7.2. - both are sites at which carbohydrate moieties can bind
to proteins to form glycoproteins. - often found in active sites of enzymes.
- many protease enzymes cut only after these amino acids
(“serine proteases” etc).
Amino acids – thiol side-chains
cysteine and methionine
- both are non-polar and neutral at pH 7.2.
- cysteine is key to the formation of some important bonds
within proteins (disulfide bridges and trisulfide bridges). - methionine is key in many roles as a free amino acid
rather than in proteins. - don’t confuse “cysteine” with
its dimer, “cystine”.
Amino acids – acid side-chains
aspartic acid and glutamic acid
- both are acid-polar and acidic at pH
7.2. - aspartic acid (side-chain) deprotonates at pH 7.2 to aspartate.
- glutamic acid (side-chain) deprotonates at pH 7.2 to glutamate.
- both carry a negative charge
- glutamate is key in umami (旨味) flavours in foods and in
neurotransmission. - aspartate is key in nitrogenous waste production in the Mammalia.
Amino acids – basic side-chains
arginine and lysine
Histidine is sort-of-basic too.
* both are basic-polar and basic at pH 7.2.
* both have positively charged amino groups on the ends of hydrophobic aliphatic chains.
* sold as their hydrochloride salts e.g. lysine hydrochloride
* lysinium ibuprofenate is sold as “ibuprofen lysine” for control of mild pain.
Amino acids – amide side-chains
asparagine and glutamine
- both are polar and neutral at pH 7.2.
- glutamine is the most abundant free amino acid in human blood plasma.
- both are sites at which carbohydrate moieties can bind to
proteins to form glycoproteins. - react in Maillard reactions with reducing sugars at high temperatures – this causes browning of many foods during
cooking.
Amino acids – the odd one out!
proline
- usually classified as a cyclic amino acid or an imino acid.
- contains a pyrrolidine ring (nonaromatic).
- neutral at pH 7.2 and non-polar.
- L-proline is often accumulated in tissues of the viridiplantae and others as a stress metabolic/osmoprotectant.
Amino acids – “the dark horses” in the Eukaraya
selenocysteine and selenomethionine
- selenocysteine is encoded for by an atypical codon important in regulating redox.
- selenomethionine is formed at aa synthesis stage substitution of Se for S essentially randomly.
- tellurocysteine/telluromethionine are found in some members of the fungi grown in high-Te soils.
Amino acids – “the dark horses” in the Archaea and bacteria
pyrrolysine, it is encoded for by an atypical codon in some Archaea and Bacteria.
An amino acids formed directly in the polypeptide chain by posttranslational modifications
Side-chains – ionic interaction
- if a positively and negatively charged side-chain come into
close proximity, an ionic interaction (bond) will form. - if they get close enough, they can react to form a covalent bond like peptide bond but between sidechain –COO- and -NH3 + groups but we call it an isopeptide bond.
Side-chains – hydrophobic interaction
- hydrophobic groups (e.g. phenylalanine residues) in close
proximity tend to cluster together with other hydrophobic groups on the inside of a protein molecule in 3D. - important in tertiary structure of proteins and protein separation (by hydrophobic interaction chromatography.
Side-chains – H bonds and van der Waals
- Polar side-chains that have e.g. –S-H groups, -C=O
groups, >NH groups etc. - van der Waals interactions are weaker but similar interactions, but formed by induced dipoles.
Side-chains – di- and trisulfide bridges
- two thiol groups (-SH) on 3D adjacent cysteine residues react to form a covalent disulfide bridge:
X-SH + HS-X → X-S-S-X + 2H+ - these are the strongest amino acid sidechain interaction, tying with isopeptide bonds.
- if formed between free L-cysteine molecules, the product is cystine.
2 L-cysteine → cystine + 2H+
* there are also trisulfide bridges (even stronger):
