BCM9 Flashcards
What is the Pka of the amino group?
9.6
What is the Pka of the carboxyl group?
2.2
What are AA referred to as?
amphoteric
What is the isoelectric point?
pH at which protein has no over all charge
What does a high pKa mean?
it is less likley to dissociate
What is the rule for determining if an AA is charged?
if Narg + Nlys > Nasp + Nglu
= charged at neutral pH and pka > 7
What is the corn law?
- put h behind carbon
CO - R - N
if clockwise it is the l form
Where are D amino acids found?
peptidoglycan
What are the amino acids with a postively charged side chain at neutral ph?
arginine
lysine
- histinde = partially positive
what are the amino acids with a negatively charged side chain at neutral ph?
aspartic acid
glumatic acid
pka of aspartic acid?
4.1
pka of glutamic acid?
4.1
pka of histine
6.1
pka of argine
12.5
pka of lysine
10.8
why is histine only partially charged at ph7?
as imidazole ring loses proton above ph6..1
what is the guanidium group?
NHC(NH2)2
where is a guanidium group found?
arigine
What is found on the side chain of glutamic acid?
carboxylate group
which is stabilised by resonance
how is guanidium group stabilised?
resonance
What are the 5 amino acids with polar uncharged side chains
asparagine
threonine
serine
glutamine
what ate the 8 amino acids with hydrophobic side chains?
alanine phenyl alanine leucine isoleucine valine methionine tyrosine tryptophan
what are the 3 amino acids containing aromatic rings?
phenylalanine
tyrosine
tryptophan
what do not form in the cytosol?
disulfide bonds
what are disulfide bonds used for?
help rigidity where proteins would become unorganised
eg. outside of cell in changing pH or temp
what do disulfide bonds form between?
two cysteine residues
what is a peptide bond?
-CONH
where does the equilbrium lie to in peptide bond formation?
the left
what catalyses peptide bond formation?
ribosome
what cataylses peptide bond hydrolysis?
proteases or proteinases
eg. trypsin, chymotrypsin, collagenase
draw and name the mechanism that occurs in peptide bond formation?
addition elimination
- nucleophillic attach of carbony by lone pair of electrion from amino group
- results in h20 elimination
what is the reality of peptide bond formation mechanism?
both carboylate ion and amino group will be charged
extra proton on amino group transfered to carboxylate during the reaction
the o- acts as a nucelophile on one of the hydrogens
what defines a condensation reaction?
water eliminated
- protein residues = lack water
what is the peptide bond?
- draw structures
a resonance hybrid structure between two competeting structures = double bond character
delocalisation of pi electron over entire peptide boind rather than simply over the c=o bond
-
why is NHCO bond planar?
restricted rotation around around NH-CO bond
due to double bond characteristic of NH CO
which conformation frorm is favoured in peptide bonds and by what amount?
why?
draw
trans 1000:1
or there could be steric clashes or r groups
what conformation from is favoured in prolines?
and by what amount
trans 15:1
what are 4 other AA acids found in the cell and where?
ornithine - urea cycle
citrulline - urea
selenocysteine - rare, few proteins
homocysteine - cysteine + extra ch2
give examples of amino acid neurotransmitters
glutamate
GABA
what does neurotransmitter gaba do?
inhibitory neurotransmitter
release opens cl- channels
what does glutamate do?
release leads of opening of cation channels and depolarisation of the membrane
What amino acids can be post translationally modified by phosphorylation?
serine
threonine
tyrosine
residues
which amino acids can be glycosylated and where?
serine threonine asparagine side chains in endoplasmic reticulum and golgi body
what is the most common post translational modification?
acetylation of amino group and N terminal resudies
give examples of 4 post translational modifications
- myristoylation - add lipid for membrane proteins
- ubiquinination and sumoylation and acetylation of lysine
- thrombin cleaves fibrogen to fibrin
- transglutaminase cross link lysine and glutamine
