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Biochemistry > Proteins and amino acids > Flashcards

Proteins and amino acids Flashcards

1
Q

number of amino acids

A

20

contain C H O N sometimes S

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2
Q

basic structure of amino acid

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

physiological PH NH2 and COOH ionise (NH3 COO)

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3
Q

7 amino acids

non polar hydrophobic

(hydrocarbon chains or rings e.g. CH3)

A
  1. Alanine (Ala) (A)
  2. Isoleucine (Ile) (I)
  3. Leucine (Leu) (L)
  4. Methionine (Met) (M)
  5. Phenylalanine (Phe) (F)
  6. Tryptophan (Trp) (W)
  7. Valine (Val) (V)
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4
Q

5 amino acids

polar but uncharged

(hydroxyl or amide groups e.g. OH, NH2)

A
  1. Serine (Ser) (S)
  2. Threonine (Thr) (T)
  3. Asparagine (Asn (N)
  4. Glutamine (Gln (Q)
  5. Tyrosine (Tyr) (Y)
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5
Q

3 amino acids

special cases

A
  1. Cysteine (Cys) (C)
  2. Glycine (Gly) (G)
  3. Proline (Pro) (P)
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6
Q

2 amino acids

polar acidic - contain carboxylic acid groups. negatively charged at physiological pH. hydrophillic

e.g. COO-

A
  1. Aspartic acid (Asp) (D)

2. Glutamic acid (Glu) (E)

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7
Q

3 amino acids

polar basic - basic groups positively charged at physiological pH. hydrophilic

e.g. NH3+

A

Arginine (Arg) (R)
Histidine (His) (H)
Lysine (Lys) (K)

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8
Q

need to know structure of a few amino acids. see desktop and recall

A

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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9
Q

bonding 2 amino acids

A

Carboxyllic acid reacts with amine
COOH + NH2

forms amide
CONH (C double bonded to O)

Condensation reaction

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10
Q

bond

A

peptide bond

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11
Q

structure - primary

A

sequence of amino acids

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12
Q

structure - secondary (2 types)

A

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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13
Q

structure - Tertiary

A

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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14
Q

structure - quaternary

A

2 or more polypeptide chains combined

bonds same as tertiary

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15
Q

structure relating to function

A

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

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16
Q

Fibrous proteins e.g. collagen

6 points

A
  1. not folded into tertiary
  2. quaternary
  3. sheet or helical conformations
  4. low water solubility
  5. strong, flexible
  6. structural function
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17
Q

globular

6 points

A
  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.
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18
Q

Fibroin (b-Keratin)

3 points

A
  1. protein in silk
  2. molecules of fibroin pack alongside, above and below each-other
  3. anti-parallel B sheets
    side chains of alternate amino acids project on opposite sides
19
Q

a-keratin

A
  1. feather, hair, nail, horns, hoof, beak
  2. a helix
  3. non helical regions at either end
  4. helical portion sequence of 7 amino acids. non-polar hydrophobic residues at 1 and 4
  5. side chains outwards along axis cutting diagonally across helix
20
Q

List two functions carried out by proteins

A

structure: keratin, collagen
contractile: actin, myosin

21
Q

buffers Ka

3 points

A
  1. acid dissociation constant Ka reflects level of dissociation
  2. Ka = [H+][A-] / [HA]
    (A- conjugate base)
  3. whenever free acid and conjugate base mixed proportions present ajust until
    [H+][A-] / [HA] = Ka
22
Q

Phosphate buffers

A
  1. based on phosphoric cid H3PO4

2. 3 H atoms which can be replaced - dissociates in 3 stages

23
Q

Bicarbonate buffer

A
  1. helps regulate pH of blood
  2. CO2 dissolves in water = H2CO3. acts as weak acid
  3. H2CO3 HCO3- + H+
  4. close control. CO2 controlled by respiration. HCO3- controlled by kidneys
24
Q

Excergonic reaction

A
  1. release energy

2. energy required to start reaction less than energy release by end of reaction

25
Q

Endergonic reaction

A
  1. requires energy

2. energy required to start reaction greater than energy release by reaction

26
Q

activation energy

A
  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
27
Q

enzymes

A
  1. catalysts lower Ea by providing alternative transition state
28
Q

a keratin structure

A 
a helix -> 
dimer (2 molecules coiled around each other. held together by hydrophobic interactions and disulphide bonds) -> 
protofilament -> 
protofibril -> 
a-keratin filament
29
Q

3 categories of structure function relationships

A

fibrous
globular
membrane

30
Q

Myoglobin

5 points

A
  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)
31
Q

Haemoglobin

5 points

A
  1. transports oxygen
  2. in blood
  3. tetramer
  4. high saturation in lungs
  5. low saturation at tissues (Released)
32
Q

Solubility of proteins

2 points

A
  1. proteins held in suspension with water through hydrogen bonds (between polar groups of protein and water)
  2. disrupting bonds affects solubility
33
Q

Iso-electric point (PI) of a protein

2 points

A
  1. pH at which net charge = 0

2. protein least soluble when pH of solution = PI of protein

34
Q

Ionic strength of environment

3 points

A
  1. high conc of ions (salts) in env
  2. interact more strongly with water than protein
  3. break protein water interactions. protein precipitates
35
Q

Heavy metals

3 points

A
  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
36
Q

organic acids

A
  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
37
Q 
Dielectric constant (backwards 3 symbol)
2 points
A
  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
38
Q

protein denaturation

4 points

A
  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
39
Q

Detergents

3 points

A
  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
40
Q

Heat

2 points

A
  1. extra energy to system. atoms vibrate within structure

2. increasing energy can break bonds

41
Q

pH

A
  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
42
Q

Buffers

4 points

A
  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
43
Q

important biological buffers

A

phosphate buffer

bicarbonate buffer

Biochemistry (17 decks)

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