amino acids Flashcards
what is an amino acid?
monomeric units of proteins
20 different types
all contain C, H, O and N
same basic structure and an R group
types of side chains
non-polar
polar (uncharged)
polar acidic
polar basic
special
non-polar amino acids
hydrocarbon chains or rings
hydrophobic
alanine
isoleucine
leucine
methionine
phenylalanine
tryptophan
valine
structure of alanine
structure of phenylalanine
polar (uncharged) amino acids
contains hydroxyl or amide groups
interact with water
serine
threonine
asparagine
glutamine
tyrosine
structure of serine
structure of tyrosine
polar acidic amino acids
contains carboxylic acid group
negatively charged at physiological pH
charged
hydrophilic
aspartic acid
glutamic acid
polar basic amino acids
contain basic groups
positively charged at physiological pH
charged
hydrophilic
arginine
histidine
lysine
structure of lysine (polar basic)
structure of aspartic acid (polar acidic)
special amino acids
don’t fit in other groups
cysteine
glycine
proline
structure of cysteine
structure of glycine
what is an amide?
2 amino acids reacted
joined by a peptide bond (covalent)
formed by condensation reaction
releases molecule of water
primary structure proteins
sequence of amino acids in a polypeptide chain
determine subsequent structures
determined by code in DNA
secondary structure proteins
conformations adopted by different parts of a chain
folding of primary structure
hydrogen bonds form between atoms
alpha helix and beta pleated sheet
alpha helices
hydrogen bonds form between carbon and amino group of 4th amino acid
3.6 amino acids per turn
side chains (r) face outwards
beta sheet
hydrogen bonds form between carbonyl and amino group
side chains alternate above and below
can be parallel or antiparallel
parallel - chains run in same direction
antiparallel - chains go in opposite directions
tertiary structure proteins
overall 3D configuration
bending and folding of secondary
held by interactions between side chains
hydrogen bonds
electrostatic bonds
disulphide bridges (covalent bonds between sulphurs)
hydrophobic interactions
associate together and repel water
found in middle of 3D structure
folds into molecule with lowest potential energy needed
quaternary structure proteins
association between different polypeptides
two or more proteins aggregate to form a larger molecule
held by same interactions as tertiary
what are fibrous proteins?
protein that is NOT folded into a tertiary structure
eg collagen and keratin
what is keratin?
fibrous protein - no tertiary
usually have a quaternary structure
large portions in secondary
low water solubility
fibroin (beta-keratin)
types of keratin
fibroin (beta keratin)
antiparallel beta sheets
long regions of alternating glycine and alanine = closely packed
creates strong, flexible molecule
alpha keratin (nails and hair)
forms alpha helix (non-helical regions at each end)
helical regions have repeating 7 amino acid sequence
what are globular proteins?
polypeptide chains with tertiary structures
doesn’t always have a quaternary structure
has complex tertiary = specific shape
gives them specific functions
- transport, storage, protection
most soluble
shape allows recognition and binding of other molecules
examples of globular proteins
myoglobin - stores and releases oxygen
haemoglobin - transports oxygen to tissues
quaternary of 2 alpha and 2 beta subunits = 4 oxygen molecules
functions vary due to different structures
factors affecting solubility of proteins
proteins held in suspension in watt by hydrogen bonds
made between polar groups of protein and water
Ionic strength of environment
low concentrations
heavy metals
organic acids
effects of the ionic strength of environment
high concentration of ions (salts)
react more strongly with water than protein
hydrogen bonds breaks = protein precipitates
effects of low concentrations
salts (ions) beneficial to solubility
salts interact with water and protein
increase interactions between water and protein = more soluble (salting in)
up to a certain point where protein precipitates (salting out)
effects of heavy metals
alkaline pH = negative charge
so react with positive charged heavy metal ion
reduced reactions with water = precipitate
effects of organic acids
increased acidity = more positive charges on surface of protein
react with negative charge on the anion
reduced reactions with water = precipitate
what is the iso-electric point? (PI)
the pH at which the net charge is 0
PI = pH
number of negative and positive charges is equal
hydrogen bonds not made = least soluble
pH above PI = protein is negatively charged
pH below PI = protein is positively charged
further from equal = more soluble (more H bonds)
what is the dielectric constant?
measure of substances ability to insulate
charges from each other (taken as a measure of solvent polarity)
high e = higher polarity so greater ability to stabilise charges
ethanol decreases overall polarity so decreases interactions between water and proteins
protein denaturation
disruption to protein structure resulting in unfolding of protein = shape change
cant carry out function
often exposure to hydrophobic groups = precipitation
loss of secondary, tertiary or quaternary = shape change
agents of denaturation
detergents
heat
pH
detergents
have high affinity for non-polar structures
disrupts hydrophobic interactions due to higher affinity
results in exposure of hydrophobic residues to outside = loss of structure
heat
gives extra energy to the system so atoms vibrate more
causes bonds to break and protein unfolds
= loss of structure
vibrations = new bonds can be formed (cross linking)
some bonds require more energy to break
(covalent strongest, hydrophobic weakest)
pH
inverse measure of its hydrogen ion concentration
- measure of hydroxide ions in a solution
- (alkaline = high)
pH alters ionisation = alters electrostatic bonding
results in unfolding of tertiary structure
increased pH = lose positive side chain
decreased pH = lose negative charge
means electrostatic bonds can’t be made
buffers
minimise change is pH in response to increase or decrease of hydrogen ions in a solution
mops up hydrogen ions through dissociation of acid to its conjugate base
