Amino acids + proteins Flashcards
what makes up most of cell’s dry mass
amino acids
how many amino acids are in plants, animals + microbial + how many are encoded by genetic code
300
20
what does a alpha carbon mean
central Carbon - hydrogen + amine + carboxyl group + variable side chain attached to
what do optical isomers mean
same structural formula but different spatial arrangement of atoms
2 enantiomers - mirror images
which amino acid doesn’t have a optical isomer and why
glycine
doesn’t have asymmetric carbon - doesn’t have 4 diff gaps attached
what way can most amino acids rotate the polarised light
L - rotates light to the left
what does it mean if optical isomers are optically active
can rotate the plane of polarised light
L - light to the left
D - light to the right
what are the charges on amino acids
dipolar ions = positive + negative charged
but are zwitterions - net charge = 0
what is pK values for carboxylic acid groups
2.2 - strong acid
readily donate protons
what is pK value for alpha amino group
9.4
readily ionise
what happens to amino groups + carboxylic acid groups on AA at pH 7.4
amino acid group protonated - POSITIVE (NH3+)
carboxylic acid grp –> carboxylate (conjugate base)(COO-)
what happens to the amino acid in very acidic conditions
net charge is positive
excess number of free protons present from acid
what happens to the amino acid at neutral pH
net charge is neutral
it is a zwitterion
what happens if the amino acid net charge is negative
it is in Anionic form
its in basic condition
why are amino acids amtopheric
they have basic + acidic groups
what happens to the groups on the amino acid at a high pH
carboxylic group will lose proton first –> bound more loosely than amino group
COO- + NH2
what happens to the groups on amino acid as the pH decreases
NH3+ AND COOH
amino group is protonated
describe the beginning of graph of titration of amino acid
- curve is steep up to pH 2 –> there’s no buffer - so can’t resist pH change
- pH 2.34 carboxyl group acts as buffer + loses proton (COO-) –> Ph doesn’t change much = BUFFERING REGION
what is the isoelectric pH of amino acid
pH 6.1
net charge of molecule = 0
what is the pKa of carboxylate ion
pKa 2.34
what happens to the amino group of the AA at around pH 10 and what is the pKb of the amino group
amino group acts as a buffer now
pKb = 9.87
what does it mean if the AA is negatively charged
all groups have been ionised
what is the overall trend of the AA graph
as the pH increases, AA net charge goes from positive –> negative
how many inflection point are there on the AA titration graph + what do they mean
4 inflection points
- half zwitterions + half cations (NH3+ , COOH)
- all AA are zwitterions
- half zwitterions + half anions (NH2 , COO-)
- all AA are anions
what does anion mean
negative charged NH2 and COO-)
what does cation mean
positive charged NH3+ AND COOH
what amino acids are non-polar, neutral + aliphatic inside + outside protein
glycine alanine valine leucine isoleucine
what amino acid are non - polar, neutral + imino acid (bent chain)
proline
what amino acids are non polar, neutral + aromatic
phenylalanine
tryptophan
what amino acids are non- polar, neutral + contain sulphur
cysteine
methionine
what amino acids are polar, neutral + aromatic –> what is it used for
tyrosine
aromatic = site for phosphorylation
what amino acids are polar, neutral + contain OH group –> what is used for
threonine
serine
OH group –> site for glycosylation
what amino acids are polar, neutral + contain NH2 groups + what reason
asparagine
glutamine
site for glycosylation
what amino acids are polar, acidic + carry negative OH carboxyl group
aspartic acid
glutamic acid
what amino acids are polar, basic + carry positive NH3 amino group
arginine
lysine
histidine
what is the isoelectric point
point at which AA doesn’t carry net charge
what is the formula to work out pI (isoelectric point) + when can you use this formula
pI = (pKa + pKb) / 2
when there are more than 2 ionisable groups
what to do if you want to find pI but have 3 or more ionisable groups on AA
take pK values closest to neutral + use those vlues
how to find pI of glutamic acid
acidic, take lowest pK charges
how to find pI of arginine
basic
take pK charges of 2 highest values
which AA are precursors of nucleotides
aspartate, glycine, glutamine
what is serotonin and which AA is its precursor
it is a neurotransmitter
tryptophan is precursor
In a polypeptide, what is the N terminal and the C terminal
N terminal = free amino group at the first AA in polypeptide
C terminal = free carboxyl group in polypeptide
which terminal is always synthesised first in protein synthesis
N terminal
left to right
what is post translational modification
AA contained in proteins are altered after translation in protein synthesis
what can post translational modifications include
phosphorylation
glycosylation are essential for protein function
what are most common function + uses of protein
growth + repair
enzymes, hormones, DNA, RNA
what is protein folding
protein has more than 1 stable folded conformation, each has its own conformation + function
but only 1 is active
its reversible
what is a prosthetic group
proteins tightly associated with other chemical/non-protein species
helps to perform function
what is the primary structure of a protein
AA sequence
peptide bonds between each AA
determined by our DNA
what is secondary structure of protein
folding/ coiling of polypeptide chain into alpha helix or beta pleated sheet
weak H bonds between H atom + electronegative atoms (N or O)
how many turns in secondary structure for polypeptide chain in alpha helix + how do the bonds form
3.6 amino acids
H atom in peptide bond is shared with 4th AA instead
what is the tertiary structure of protein
3D shape of polypeptide chain
fibrous or globular
what type of bonds are there in terry structure of protein
electrostatic attraction/ salt bridge
van der Waals forces
disulphide bon
hydrophobic interaction
how does electrostatic attraction / salt bridge occur in tertiary structure
between oppositely charged ions or groups
how do van Der Waals forces occur in tertiary structure
weak but needed in close packed interior of proteins + specific shape of enzyme active site
how do disulphide bonds occur in tertiary structure
strong bond between specific cysteine AA
locks protein in configuration
how does hydrophobic interaction occur in tertiary structure
between non-polar hydrophobic AA
what is quaternary structure of protein
combo of more than 1 proteins + involves non-covalent bonds between proteins
give example if 1 protein with 4 polypeptide chains + 1 protein with 3
haemoglobin - 4 polypeptide chains + 4 haem groups
collagen - 3 helical polypeptide chain supercoiled with each other
what are the 3 protein classes
globular
fibrous
membrane associated
what are the characteristics of globular proteins
soluble
enzymes/ antibodies
Tertiary structure when non - polar hydrophobic AA move in + polar hydrophilic AA bound outwards
give 2 examples of globular proteins + give their uses
carbonic anhydrase - large beta pleated sheet in centre + active site has Zn ion —> catalyses hydration of CO2 –> HCO3- + H+
Hb - 4 globular proteins bound together - electrostatic attraction + H bonds + hydrophobic interaction
each protein associated with haem grp contains iron that binds to O2
what are the characteristics of fibrous proteins
wire like structural/storage function used to construct connective tissues + bones repeated AA sequences contains cross links between chains
what is use + nature of keratin
keratin - tough + insoluble
high proportion of small AA (glycine + alanine)
lots of cysteine –> lots disulphide bridge – thermal stable + permanent –> rigid
can assemble into intermediate filaments for cell cytoskeleton
what are 2 examples of fibrous proteins
keratin
collagen
what is use + nature of collagen
secreted by connective tissue cells
most abundant protein in mammals (25%)
what do membrane associated proteins include (where found)
transmembrane proteins integrated in phospholipid bilayer
lipid associated proteins – inner + outer of membrane + proteins
transporters, linkers, receptors, enzymes on cell membrane
