BB1702 amino acids Flashcards
what are the main properties of amino acids?
- 20 different amino acids
- alpha
- have negative and positive charge
- alpha carbon
properties of alpha carbon
- acidic carboxyl group
- basic amino group
- hydrogen connected to carbon
- closer to carboxyl group in proteins
what’s the importance of amino acid structure?
structure correlates to function
what are GABA amino acids?
neurotransmitters in the brain
NH2 attached to y
how can amino acids be organised?
stereoisomers
chiral carbon
enantiomers
what is a stereoisomer?
same molecular formula and bonding but different 3d oritentation of atoms
what is a chiral carbon atom?
carbon with four different groups bonded to it
which amino acid is not chiral?
glycine
what is an enantiomer?
- stereoisomers that are non superimposable mirror images
- can either be L or D
what is an L amino acid?
- consitiuents of proteins
- more soluble than a racemic mixture of D and L, form crystals
- more dominant in solution due to solubility difference
what are D amino acids?
rare
found in bacteria
what is the ionisation behaviour of amino acids?
- can be placed in five groups due to characteristics, depending on their r group
- 7/20 amino acids have readily ionisable side chains, able to donate or accept protons to dacilitate reactions and form ionic bonds
how can amino acids be organised?
- nonpolar aliphatic
- aromatic
- polar uncharged
- positively charged
- negatively charged
properties of non polar aliphatic amino acids?
- R groups consist of hydrocarbon chains, except glycine and methionine
- side chains are hydrophobic as they cluster together rather than contact water
- different sizes and shapes of hydrocarbon side chains enable them to pack together to form compact structures with little empty space
examples of nonpolar aliphatic amino acids?
- glycine
- alanine
- proline
- valine
- leucine
- isoleucine
- methionine
methionine
contains an aliphatic side chain
includes thioether group
isoleucine
side chain includes an additional chiral centre
proline
has a pyrrolidine ring structure
side chain bonded to alpha carbon and nitrogen
cycle structure makes it more conformationally restricted
examples of aromatic amino acids?
phenylalanine
tyrosine
tryptophan
phenylalanine
has a phenyl ring in place of H atom of alanine
purely hydrophobic
tryptophan
indole group, two fused rings containing NH group, joined to methylene, a double ring, benzene and nitrogen
less hydrophobic due to side chain NH group
tyrosine
version of phenylalanine
hydroxyl group attached to hydrophobic side chain
hydroxyl group makes amino acid more hydrophilic and reactive
examples of polar uncharged amino acids?
serine
cysteine
threonine
asparagine
glutamine
serine
version of alanine with hydroxyl group attached
cysteine
similar to serine
contains sulfhydryl
sulfydryl is more reactive than OH, groups may form disulfide bonds
important for stabilising proteins
threonine
contains additional asymmetric centre with one isomer present
asparine and glutamine
both contain terminal carboxamide
side chain of glutamine is one methyl group longer
examples of positvely charged amino acids?
lysine
arginine
histidine
lysine and arginine
long side chains, end with + group at neutral pH
lysine capped by pos amino group
arginine capped by a guanidinium group
histidine
pos charged aromatic and imidazole group
uncharged or pos at neutral pH
found in enzyme active sites
imidazole binds and releases protons in course of enzymatic reaction
examples of negatively charged amino acids
aspartate
glutamate
properties of negatively charged amino acids
side chain lacks a proton at physiological pH
present in acidic form
side chain accepts a proton
apartate and glutamate
come from aspartic acid/asparagine and glutamic acid/glutamine
glutamate vs glutamic acid
glutamic acic:
- COOH
- protonated
- donate to form glutamate
glutamate:
- COO-
- lost protons
- acid
what are peptide bonds
small condensation products of amino acids
smaller than proteins
peptide ends are not the same
have polarity
formation of peptide bond
COO- + NH3 -> CONH + H2O
what is a bronsted lowry acid
proton donor
what is a bronsted lowry base
proton acceptor
acid dissociation constant
stronger the acid, higher the Ka and lower the pKa - more protons, lower pH
weaker acid, low Ka and high pKa - more OH, higher pH
what is a buffer
resist pH changes by addition of small amounts of acid or base
mixture of weak acid and conjugate base
narrow pH range
buffer region is flat and steep in equilibrium
why is it important that pH is monitored by buffers
- almost every biological processes are pH dependent
- small changes in pH produce large change in rate
- cystolic pH near 7, biological molecules in optimal ionic state
what are zwitterions
contain a pos and negative charge
amino acids can act as acids and bases depending on pH environment
how can ionisation state of amino acids vary with pH?
- low pH: lots of H+, fully protonated, acidic, +1 charge, NH3+ and COOH
- increasing pH: H+ increases, zwitterion, COO-, NH3+, 0 charge (isoelectric point)
- high pH: alkali, low H+, high OH-, NH2, COO-, -1 charge, deprotonated
how to work out isoelectric point?
(pK1 + pK2)/2
fill in the gaps:
Formation of a peptide bond produces _____ as a byproduct.
water
fill in the gap
n the following peptide, which amino acid is the N-terminus?
phenylalanine-alanine-glycine-arginine
phenylalanine
fill in the gap:
Of the 20 standard amino acids, only ___________ is not chiral. The reason is that its side chain _________
- glycine
- a hydrogen atom
what do proteins contain?
only L amino acids
how many of the 20 common amino acids have rings in their structures?
5
What do leucine, isoleucine and valine have in common?
they have nonpolar aliphatic side chains
Which amino acids contain a hydroxyl group in their side chain?
serine, threonine, tyrosine
Which amino acids contain an acid group in their side chain?
aspartate, glutamate
which amino acids contain an amide group in their side chain?
asparagine, glutamine
which of the following pairs of amino acids is positively charged at a neutral pH?
lysine, arginine
Which two amino acids contain a sulfur atom?
cysteine, methionine
Which of the following tripeptides would be expected to be the most hydrophobic?
Gly-Tyr-Ala
name aromatic amino acids
phenylalanine, tyrosine, tryptophan
Experiments on denaturation and renaturation after the reduction and reoxidation of the —S—S— bonds in the enzyme ribonuclease have shown that:
he primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure.
Protein folding to a native conformation is highly dependent upon:
- rotation about the alpha-carbon, carbon bond in the backbone
- the polar character of sequences of amino acids
- the relative size of amino acid R-groups
- the rotation about the alpha-carbon, nitrogen bond
Protein folding to a native conformation is not dependent upon:
the rotation about the peptide bond
what is the disulphide bond between two cysteine molecules?
a covalent bond formed by oxidation
The molecular interaction called “hydrophobic effect” is best described as:
the tendency of non-polar molecules to avoid interactions with water and thus aggregate.
The overall three-dimensional structure of a single polypeptide is referred to as
tertiary structure
The term “quaternary” with respect to protein structure means
a multisubunit structure
What important function do molecular chaperones perform?
fold proteins into a native conformation
What level of protein structure is composed of α helices, β sheets, and turns?
secondary
which amino acid residue would most likely be buried in the interior of a water-soluble, globular protein?
phenylalanine
how do you best describe the arrangement of amino acid side chains in an alpha helix?
the side chains point outward away from the helical axis
which bonds within a peptide backbone show free rotation around both bonds?
C α—C and N—C α
Most proteins have a molecular mass between:
10kDa - 500kDa
which sequence best represents the backbone arrangement of two peptide bonds?
C a—C—N—C a—C—N
