Chapter 3-theory Flashcards
what are amino acids
the building blocks of proteins
what are proteins
linear polymers of amino acids
what are all proteins produced from
20 standard amino acids
what do all living organisms make there proteins from
the same pool of amino acids
how does 20 building blocks enable sequence diversity
for example a peptide of three residues could be produces 8000 ways
a protein on 100 residues has 1.3x10130 possible sequences
what is the advantages of making biomolecules as polymers of smaller, simpler building blocks
1) simplicity of chemistry
(one type of reaction for polymerization, a second type of reaction for degration)
2) recycling
(biomolecs can be digested back to component building blocks which are reusable for production of other biomolecs)
3) diversity
(the vast number of varying lengths and sequences)
what are the common features of amino acids
a hydrogen
central alpha C
Amino group
carboxyl group
side R chain
how do amino acids differ
the side chain group
how are amino acids constructed except glycine
the alph carbon is bonded to four different groups, this creates chiral caneter
how do amino acids have stereoisomers
the four different groups occupy unique spatial arrangements giving stereoisomers labelled as the L and D isomers
what stereoisomer are proteins made from
biologically proteins are made almost exclusively from L amino acids
what are the groups that amino acids are grouped into based off there properties
non-polar aliphatic
aromatic
polar, uncharges
polar, positively charges
polar, negatively charged
what are some characteristics of the non-polar, aliphatic amino acids
-mainly hydrocarbon side chains
-residues with non-polar chains are often buried in the core of the protein
what are the amino acids that fit into non-polar, aliphatic amino acids (7)
glycine
alanine
valine
leucine
isoleucine
proline
methionine
what are some unusual amino acid characteristics of nonpolar, aliphatic amino acids
glycine-only one thats not a cyro C and smallest acid
proline-has a ring
methionine-has a S group present
what amino acids are in the aromatics
tyrosine
phenylalanine
tryptophan
what is the largest amino acid
tryptophan
what is a phosphoralation
it is a type of post-translational modification
-phosphoryl groups are added by kinases to specific, hydroxyl-group containing amino acids (tyr, ser, thr)
what is post translation modification phosphorylation
phosphorylation is when certain amino acids can be covalently modified after their incorporation into a protein (post-translation)
in post translational modification what removes the phosphatases
phosphoryl
in post translational modification what adds the phosphatases
kinase
are post translational modifications reservable
yes
what amino acids are in the polar, uncharged group
cysteine
asparagine
glutamin
serine
threonine
what can two cystines do
they can form covalent linkages called disulphide bond
disulfide bonds important…
for stabilization of some protein structures
why can cystine form a disulphide bond
because the S is at the end of the amino acid
what polar, uncharged amino acids can be modified through phosphoralation
serine
threonine
how do disulphide bonds form
through the oxidation of the sulfhydryl groups of two cysteine residues to for, a covalent linkage
what do disulphides do
they stabilize protein structures
cystine residue forming a disulphide bond must…
be within close proximity in space within the protein structure
are disulphide bonds intra or inter-molecular
they can be both
what is the effects of cooking an egg
heat+protein=protein starting to unfold and get tangled and ppt out of solution
what amino acids are in the positively charged group
lysine
arginine
histidine
what is the most polar group
the positively charged group
what amino acids in the polar group carry a + charge at physiological pH
lysine
arginine
if histidine isnt + charges at biological pH why is in the + group
-because it has the potential to carry a + charge
-its imidazole has a pKa of 6 (near physiological pH) (that fraction will be +1 and the rest will carry a net 0 charge)
-cell pH=7
-10:1=90% unprotinated
what does histidine do in enzymatic reactions
it serves as a proton accepter/donor
what amino acids are in the negatively charged group
aspartate
glutamate
what is is glutamate responsible for
-for one of the five basic tastes (umami)
-it is used for a flavor enhancer (monosodium glutamate (MSG))
what can aspartate and glutamate also be called
glutamic acid
aspartimic acid
what does it mean that every amino acid has diprotic
every amino acid has at least two groups that accept and donate protons
what do triprotic amino acids have
ionizable groups in their side chains (lys, arg, his, asp, glu, cys and tyr)
what do diprotics have
two buffering groups
what do triprotics have
three buffering regions
what are the ionizable groups in the amino acids
carboxyl group
amino group
side chains off the triprotic amino acids
what does each ionizable group have
a specific pKa
what is the pKa
the pH at which that group changes its protonation state
when pH is below the pKa…
the protonated form predominates (HA)
when pH is above pKa…
the unprotonated form predominates (A-)
what groups do all amino acids have and what are there pKa
carboxyl (pKa=2.0)
amino (pKa=10.0)
at a pH of 7.4 what form will carboxyl and amine group be in
COO- and NH3+ forms
what is the acids and conj base forms of carboxyl
COOH (acid)
COO- + H+ (conj base)
what is zwitterion
dipolar ion of and amino acid
what is the isoelectric point (pI) of an amino acid
it is the average of the pKas on either side of where the net charge is equal to zero
it is the pH at which the net charge on the molecule is equal to 0
how do you calculate the pI
it is the average of the pKas on either side of where the net charge is equal to zero
pI=(pKa 1 + pKa 2) /2
