1. tertiary - compact, highly specific, 3D 2. sometimes quaternary 3. highly specific shape 4. soluble in water 5. shape - recognition and binding to other molecules 6. function - catalysts. transport. defence. regulation.

Proteins and amino acids Flashcards by Erin H

number of amino acids

contain C H O N sometimes S

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basic structure of amino acid

C
COOH
NH2 (amino group)
H
R group (differs)

physiological PH NH2 and COOH ionise (NH3 COO)

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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)

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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)

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3 amino acids

special cases

Cysteine (Cys) (C)
Glycine (Gly) (G)
Proline (Pro) (P)

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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)

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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)

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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

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bonding 2 amino acids

Carboxyllic acid reacts with amine
COOH + NH2

forms amide
CONH (C double bonded to O)

Condensation reaction

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bond

peptide bond

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structure - primary

sequence of amino acids

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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

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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

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structure - quaternary

2 or more polypeptide chains combined

bonds same as tertiary

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structure relating to function

can form lots of shapes and bind to other molecules / with each other = lots of functions

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Fibrous proteins e.g. collagen

6 points

not folded into tertiary
quaternary
sheet or helical conformations
low water solubility
strong, flexible
structural function

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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.

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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

1. requires energy | 2. energy required to start reaction greater than energy release by reaction

activation energy

1. to react molecules must collide 2. sometimes energy released in collision enough to start reaction. if not external energy e.g. heat needed 3. lower Ea faster reaction 4. maximum energy requirement = transition state

enzymes

1. 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

1. stores oxygen 2. in muscle 3. monomer 4. high saturation at normal tissue concentration 5. low saturation when oxygen supply to tissues low (released)

Haemoglobin | 5 points

1. transports oxygen 2. in blood 3. tetramer 4. high saturation in lungs 5. low saturation at tissues (Released)

Solubility of proteins | 2 points

1. proteins held in suspension with water through hydrogen bonds (between polar groups of protein and water) 2. disrupting bonds affects solubility

Iso-electric point (PI) of a protein | 2 points

1. pH at which net charge = 0 | 2. protein least soluble when pH of solution = PI of protein

Ionic strength of environment | 3 points

1. high conc of ions (salts) in env 2. interact more strongly with water than protein 3. break protein water interactions. protein precipitates

Heavy metals | 3 points

1. alkaline pH proteins tend to have -ve charges on surface 2. react with +ve charged hevay metal ion 3. if multivalent heavy metal can form larger complexes between proteins

organic acids

1. acidic nature increases +ve charges on surface of protein 2. react with -ve charge on complex anion (HA -> H+ + A-) 3. if anion multivalent can form larger complexes between proteins

``` Dielectric constant (backwards 3 symbol) 2 points ```

1. a measure of a substances ability to insulate charges from each other. taken as a measure of solvent polarity 2. higher dielectric constant = higher polarity. greater ability to stabilise charges

protein denaturation | 4 points

1. loss of secondary tertiary or quarternary structure 2. most common causes - dtergents, heat, pH 3. shape changes so much cant carry out normal function 4. often exposure of hydrophobic groups causes precipitation

Detergents | 3 points

1. high affinity for non-polar structures 2. disrupt hydrophobic interactions - have higher affinity for non-polar side chains than are between side chains 3. exposure of hydrophobic residues disrupts protein structure

Heat | 2 points

1. extra energy to system. atoms vibrate within structure | 2. increasing energy can break bonds

1. of a solution is inverse measure of its hydronium ion concentration 2. H20 H+ + OH- = H3O+ 3. pH = -Log10[H3O+] 4. pH changes = ionisation of some amino acid side chains changes 5. pH alters ionisation = alters electrostatic bonding. can result in unfolding of tertiary structure

Buffers | 4 points

1. acid-base conjugate pair. weak acid and conjugate base 2. minimise change in pH in response to increase or decrease of [H+ in solution 3. strong acid fully dissociates in solution. weak acid only partially dissociates in solution 4. works because of need to keep ratio [H+][A-]/[HA]=Ka

important biological buffers

phosphate buffer | bicarbonate buffer