describe essential amino acids for humans
humans can produce 9 amino acids
other essential ones need to be obtained from food
failure to obtain leads to degradation of body, because body does not store amino acids (like with fats/starch)
plants also synthesis amino acids
what are conditional essential amino acids?
they are not essential
except for when ill, stress or deficient
includes arginine, cysteine, glutamine, tyrosine, glycine, ornithine, proline, and serine
what is a amino acid that humans make but plants cant
selenocysteine
it is a better nucleophile then Cys cause has a smaller pKa
is a amino acid found in proteins
what is selenoenzyme + what is its function
proteins made of selenocysteine that has catalytic activity.
- Peroxide removal
- Reduction of thioredoxins
- Selenophosphate synthesis
- Activation + inactivation of thyroid hormones
- Repair of oxidised Met in protein
common characteristics of amino acids
- Tetrahedral alpha carbon
- Carboxyl group
- Hydrogen bound to alpha carbon
- Side chain (varies)
describe amino acids at pH 7
- At pH 7
○ Amino group has pos. Charge
○ Carboxyl group has neg. Charge
○ Zwitterion- When more acidic environment- add a protein, gives a overall pos. Charge
- When go into a basic environment- loss a protein, gives a overall neg. Charge
- When more acidic environment- add a protein, gives a overall pos. Charge
what is pKa
pH at which 50% of ion has dissociated is pKa
describe non-polar amino acids
- Ala, Val, Leu are important in maintaining 3D structure, due to clustering away from water
- Proline is cyclic, induces abrupt change in direction of polypeptide chain
- MET, Trp, Phe, Iie are important for processes that drive peptide chains to fold, due to hydrophobic water-excluding properties
describe uncharged amino acids
- Gly, Ser, Asn, Gln
- Except for glycine, contains a side chain which can form a hydrogen bond with water
- Glycine cant form H bonds because of simple H-R groups
- Its solubility in influenced by polar amine + carboxyl groups, therefore grouped as polar
- Glycerine- very small, so can fit into niches
- Thr, Cys, Tyr- more insoluble in water than non-polar amino acids
-Play a variety of nucleophilic roles in enzyme reactions
describe acidic amino acids
- R-groups contain a carboxyl group (weak acids)
- Exist as COO- at pH 7, so neg. Charge
- Involved in binding metal ions
describe basic amino acids
- Lys, Arg, His
- Net pos. Charge at pH 7
- Lys + arg fully protonated at pH 7
- His only 10% protonated at pKa 6.4
- His also has important role as proton donors + acceptors in enzyme reactions
- Arg + lys involved in electrostatic interactions in protein
- Biological buffers
amino acids that are rare in proteins
- Hydroxylysine + Hydroxyproline- found in connective tissue proteins (collagen + gelatine)
- G-Carboxyglutamate acid- found in blood clotting proteins
- Pyroglutamate acid- found bacteriorhodopsin
describe amino acid spectrophotometric properties
- No amino acids absorb visible lights
- All amino acids absorb infared however
- Determine protein conc. By measuring absorbance at 280nm
describe the stereochemistry of amino acids
- L and R
- Only L-isomer of amino acids occur commonly in nature
- All amino acids BUT glycine are chiral (all amino acids have 4 different groups attached to the alpha carbon)
- R, S nomenclature is superior, since amino acids like isoleucine + threonine (has 2 chiral centers), named unambigously
○ Chiral centers
§ Is an atom that has 4 different groups bonded to it in such a manner, htat it has a non-superimposable mirror image - 2 possible configurations (enantiomers)
- Emantiomers are observed to rotate polarised light in either clockwise or counterclockwise direction (optical activity)
○ D configuration = to the right
○ L configuration = to the left - All amino acids from proteins are in the L configuration
Some amino acids have more chiral carbons
describe the thalidomide case
- In germany, 1957
- Marketed as a sedative with few side effects for pregnant women to avoid morning sickness
- But when given, some it was in S and some was R enantiomers
- S- teratogenic
R- effective sedative
