biochem lec 3
what determines a proteins function
its structure
what is pka
pka is the acid dissacotiaon constant expressed on a log scale. it represent the ph at which half of an acids molecules are dissociated (ionized) and half are protonated.
basically how strongly an acid holds onto its proton
lower pka: stronger acid--> more stable base
ph> pka = [HA]< [A-]
more basic
amino acids are chiral molecules meaning
it cannot be superimposed on its mirror image- assymetric
which form of amino acids are incorporated into proteins
the L-form of amino acids is incorporated into proteins
if an amino acid is at pH 14 what is the charge state on the amino and carboxylic acid groups
every amino acid has two ionizable groups (Nh3+/-NH2) and carboxyl group (COOH/COO-)
amino--> pka around 9-10
carboxyl--> pka around 2
at ph 14 which is higher than both pka values the solution has very low H=--> so strong tendency to deprotonate everything
so coo-= -1 and nh2= 0
what is zwitterionic form
positve and negative charges balance out, between the two pka values the amino acid exists as this
what are the hydrophobic amino acids- they lack reactive functional groups and have mainly hydrocarbon side chains
Alanine, valine, leucine, isoleucine, phenylalanine (phe, F), tryptophan (trp, W), methionine (met, M), proline (pro, p)
draw alanine and describe it
aliphatic (molecules or side chains made up of straight or branched carbon chains and not aromatic rings)
hydrophobic- nonpolar
participates in hydrophobic interactions
draw valine and describe it
aliphatic (branched), highly hydrophobic- non polar, hydrophobic interactions
Leucine
1 branch bigger than valine
aliphatic, highly hydrophobic-non polar, hydrophobic interactions
isoleucine (ile, I)
branching at different spot, adjacent to nH3, chiral
aliphatic, highly hydrophobic- non polar, hydrophobic interactions
phenylalanie (F, phe)
phenyl added to alanine
aromatic, highly hydrophobic- polar, hydrophobic interactions
tryptophan (w, trp)
aromatic r group-heterocyclic, hydrophobic/bulky-polar, hydrophobic interactions, forms h bonds-donor in h bonds.
cannot be a h bond acceptor because trigonal plana shape/lone pair in p orpital (delocalized in pi system)
methionene M, met
honourary aliphatic since it has a sulfur so not really but functionally behaves like one
hydrophobic, hydrophobic interaction, sulfur containing (thioether)
proline (pro, p)
aliphatic with distinctive cyclic structure, secondary amino group- connected to two carbons instead of just one and only one hydrogen," imino acid", hydrophobic
what are the polar amino acids, reactive due to presence of functional groups, polar amino acids, have side chains that contain an electronegative atom
serine, threonine, asparagine (Asn, N), glutamine (Gln, Q), Tyrosine (Tyr, Y), histidine (his, H), cysteine(cys, C), Glycine (Gly, G) sorta
glycine (gly, G)
achiral, weakly polar, very small--> flexible
no side chain just H
unique
Serine (s, Ser)
polar, uncharged
has hydroxyl can be a acceptor (O) or donor (H) - 3 h bonds , typically a donor
can be modified (phosphorylation)
Threonine (T, thr)
polar, uncharged
contains hydroxyl group, can form h bonds, typically a donor, can be phosphorylated
has 2 chiral carbons
Tyrosine (tyr, Y)
weakly polar, uncharged
aromatic r group--> phenol--> hydrophobic
hydroxyl group--> h bonds--> typically donor--> can be phosphoryalted--> pkae 10.5
what charge would tyrosine carry at ph 1 vs ph 14
in a ph of 1 will carry charge of + 1, in a ph of 14 would carry charge of -2 (OH and COO both -)
which r groups have ionizable functional groups: neutral, polar or charged, polar
neutral polar, tyr, cys, his
charged, polar: asp, glu , lys, arg
what are the protonation and charge states of tyr, cys, his, asp , glu, lys and arg at ph 7
tyr--> oh protonated--> 0
cys--> sh protonated--> 0
His--> partly protonated-->0
Asp--> Coo- (deprotonated)--> -1
Glu--> Coo- (deprotonated)--> -1
Lys--> NH3+ (protonated) --> +1
Arg--> guanidinium protonated--> =1
acids lose H=--> negative, bases keep H=--> positive
cysteine (c, cys)
polar uncharged
sulfur containg side chain (thiol group-sh)
can form h bond or thiolate anion (s-)
can from disulphide bonds with another cys
how does a disulphide bond happen
between two cys sidechains, 2 cys--> cys + 2h+ + 2e-
occurs in oxidising enviroments (not cytosolic)
covalent bond that creates cross links in proteins
asparagine (N, Asn)
amide containing side chain (carboxamide functional group), polar/uncharged
forms h bonds-- h bond donor (NH2) and acceptor (c=O)
the lone pair on N is in p orbital so it cant act as an acceptor
glutamine (Q, Gln)
amide containg side chain (carboxamide functional group)
polar uncharged
forms h bond--> h bond donor and acceptor
histidine (H, his)
side chain can be acidic or basic and neutral pH (imidazole ring-aromatic)
pka= 6
polar, charged/uncharged
his residues important in many enzyme catalyzed reactions
proton donor(acid)- protonated/acceptor(base)- deporotonated--. hydrogen bonding capability as possible donor or acceptor
what are the charged amino acids
aspartate (asp, D), glutamate(glu, E), Lysine (Lys, K), arginine(arg, R)
Asparatate (D, Asp)
negatively charged side chain at Ph 7--> second carboxyl group, acidic amino acid
very polar
forms h bond--> h bond acceptor
pka 4.0
why is aspartate called aspartic acid at ph 1
at ph 1 the solution is very acidic so both the alpha carboxyl and side chain carboxyl groups are fully protonated--> in its acid form
Glutamate (E, Glu)
negatively charged side chain at ph 7, second carboxyl group, "acidic" amino acid
pka 4
forms h bonds, h bond acceptor
at ph 1 called glutamic acid
at ph 7 exists as a zwitterion
lysine (k, lys)
postively charged side chain at ph 7, "basic amino acid"
pka 10
side chain contains an amino group--> has 2 primary amino groups all together
forms h bond--> donor
very polar
arginine (R, arg)
positively charged side chain at ph 7, guanio group, "basic" amino acid, almsot never deprotonated under physiological conditons
very polar
forms h bonds--> h bond donor
what are the expection of the amino acids whose abbrv isnt the first three letters of their name
asparagine (Asn), glutamine (gln), Isoleucine (Ile), tryptophan (trp)
where are polar side chains found
usually on the proteins surface, can interact with water, includes polar/uncharged and polar/charged amino acids
non polar side chains are usally found buried in the protein core
minimizes interaction with water
where in a protein might you predict to find both leucine and phenyalanine
protein interior
hydrophobic and non polar
which of the following amino acids does not carry a net -2 charge at ph 14. asp, tyr, cys, his , glu
his
if you place the fully protonated form of lysine in aq solution at ph 7 what will happen to ph
lysine gets fully protonated--> + 2 charge
at ph 7 the environment is less acidic that lysines low ph form so some protons will be lost to the water--> +1
donating H= ions to the water makes the solution more acidic so ph drops slightly