Proteins and amino acids Flashcards
number of amino acids
20
contain C H O N sometimes S
basic structure of amino acid
C COOH NH2 (amino group) H R group (differs)
physiological PH NH2 and COOH ionise (NH3 COO)
7 amino acids
non polar hydrophobic
(hydrocarbon chains or rings e.g. CH3)
- Alanine (Ala) (A)
- Isoleucine (Ile) (I)
- Leucine (Leu) (L)
- Methionine (Met) (M)
- Phenylalanine (Phe) (F)
- Tryptophan (Trp) (W)
- Valine (Val) (V)
5 amino acids
polar but uncharged
(hydroxyl or amide groups e.g. OH, NH2)
- Serine (Ser) (S)
- Threonine (Thr) (T)
- Asparagine (Asn (N)
- Glutamine (Gln (Q)
- Tyrosine (Tyr) (Y)
3 amino acids
special cases
- Cysteine (Cys) (C)
- Glycine (Gly) (G)
- Proline (Pro) (P)
2 amino acids
polar acidic - contain carboxylic acid groups. negatively charged at physiological pH. hydrophillic
e.g. COO-
- Aspartic acid (Asp) (D)
2. Glutamic acid (Glu) (E)
3 amino acids
polar basic - basic groups positively charged at physiological pH. hydrophilic
e.g. NH3+
Arginine (Arg) (R)
Histidine (His) (H)
Lysine (Lys) (K)
need to know structure of a few amino acids. see desktop and recall
Non polar
Analine
Phenylalanine
Polar but uncharged
Serine
Tyrosine
Special
Cysteine
Glycine
Polar acidic (-ve charge) Aspartic acid
Polar basic (+ve charge) Lysine
bonding 2 amino acids
Carboxyllic acid reacts with amine
COOH + NH2
forms amide
CONH (C double bonded to O)
Condensation reaction
bond
peptide bond
structure - primary
sequence of amino acids
structure - secondary (2 types)
caused by hydrogen bonds
alpha helix: side chains face out of helix. C=O of one amino acid hydrogen bonded to NH on fourth amino acid away
beta sheet: H bonds between C=O with N-H elsewhere on chain. side chains alternate above and below plain of strand. paralel or antiparallel
structure - Tertiary
bending folding of secondary structure
shape held by interactions between amino acid side chains
H bonding (polarity)
Electrostatic bonding (loose and gain electron)
Disulphide bridges (2 sulphurs)
hydrophobic interactions - non-polar side, hydrophobic side chains associate together. often found in middle of 3D structure
structure - quaternary
2 or more polypeptide chains combined
bonds same as tertiary
structure relating to function
can form lots of shapes and bind to other molecules / with each other = lots of functions
Fibrous proteins e.g. collagen
6 points
- not folded into tertiary
- quaternary
- sheet or helical conformations
- low water solubility
- strong, flexible
- structural function
globular
6 points
- tertiary - compact, highly specific, 3D
- sometimes quaternary
- highly specific shape
- soluble in water
- shape - recognition and binding to other molecules
- function - catalysts. transport. defence. regulation.
Fibroin (b-Keratin)
3 points
- protein in silk
- molecules of fibroin pack alongside, above and below each-other
- anti-parallel B sheets
side chains of alternate amino acids project on opposite sides
a-keratin
- feather, hair, nail, horns, hoof, beak
- a helix
- non helical regions at either end
- helical portion sequence of 7 amino acids. non-polar hydrophobic residues at 1 and 4
- side chains outwards along axis cutting diagonally across helix
List two functions carried out by proteins
structure: keratin, collagen
contractile: actin, myosin
buffers Ka
3 points
- acid dissociation constant Ka reflects level of dissociation
- Ka = [H+][A-] / [HA]
(A- conjugate base) - whenever free acid and conjugate base mixed proportions present ajust until
[H+][A-] / [HA] = Ka
Phosphate buffers
- based on phosphoric cid H3PO4
2. 3 H atoms which can be replaced - dissociates in 3 stages
Bicarbonate buffer
- helps regulate pH of blood
- CO2 dissolves in water = H2CO3. acts as weak acid
- H2CO3 HCO3- + H+
- close control. CO2 controlled by respiration. HCO3- controlled by kidneys
Excergonic reaction
- release energy
2. energy required to start reaction less than energy release by end of reaction
Endergonic reaction
- requires energy
2. energy required to start reaction greater than energy release by reaction
activation energy
- to react molecules must collide
- sometimes energy released in collision enough to start reaction. if not external energy e.g. heat needed
- lower Ea faster reaction
- maximum energy requirement = transition state
enzymes
- catalysts lower Ea by providing alternative transition state
a keratin structure
a helix -> dimer (2 molecules coiled around each other. held together by hydrophobic interactions and disulphide bonds) -> protofilament -> protofibril -> a-keratin filament
3 categories of structure function relationships
fibrous
globular
membrane
Myoglobin
5 points
- stores oxygen
- in muscle
- monomer
- high saturation at normal tissue concentration
- low saturation when oxygen supply to tissues low (released)
Haemoglobin
5 points
- transports oxygen
- in blood
- tetramer
- high saturation in lungs
- low saturation at tissues (Released)
Solubility of proteins
2 points
- proteins held in suspension with water through hydrogen bonds (between polar groups of protein and water)
- disrupting bonds affects solubility
Iso-electric point (PI) of a protein
2 points
- pH at which net charge = 0
2. protein least soluble when pH of solution = PI of protein
Ionic strength of environment
3 points
- high conc of ions (salts) in env
- interact more strongly with water than protein
- break protein water interactions. protein precipitates
Heavy metals
3 points
- alkaline pH proteins tend to have -ve charges on surface
- react with +ve charged hevay metal ion
- if multivalent heavy metal can form larger complexes between proteins
organic acids
- acidic nature increases +ve charges on surface of protein
- react with -ve charge on complex anion (HA -> H+ + A-)
- if anion multivalent can form larger complexes between proteins
Dielectric constant (backwards 3 symbol) 2 points
- a measure of a substances ability to insulate charges from each other. taken as a measure of solvent polarity
- higher dielectric constant = higher polarity. greater ability to stabilise charges
protein denaturation
4 points
- loss of secondary tertiary or quarternary structure
- most common causes - dtergents, heat, pH
- shape changes so much cant carry out normal function
- often exposure of hydrophobic groups causes precipitation
Detergents
3 points
- high affinity for non-polar structures
- disrupt hydrophobic interactions - have higher affinity for non-polar side chains than are between side chains
- exposure of hydrophobic residues disrupts protein structure
Heat
2 points
- extra energy to system. atoms vibrate within structure
2. increasing energy can break bonds
pH
- of a solution is inverse measure of its hydronium ion concentration
- H20 H+ + OH- =
H3O+ - pH = -Log10[H3O+]
- pH changes = ionisation of some amino acid side chains changes
- pH alters ionisation = alters electrostatic bonding. can result in unfolding of tertiary structure
Buffers
4 points
- acid-base conjugate pair. weak acid and conjugate base
- minimise change in pH in response to increase or decrease of [H+ in solution
- strong acid fully dissociates in solution. weak acid only partially dissociates in solution
- works because of need to keep ratio [H+][A-]/[HA]=Ka
important biological buffers
phosphate buffer
bicarbonate buffer
