amino acids Flashcards

(40 cards)

1
Q

what is an amino acid?

A

monomeric units of proteins
20 different types
all contain C, H, O and N
same basic structure and an R group

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2
Q

types of side chains

A

non-polar
polar (uncharged)
polar acidic
polar basic
special

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3
Q

non-polar amino acids

A

hydrocarbon chains or rings
hydrophobic

alanine
isoleucine
leucine
methionine
phenylalanine
tryptophan
valine

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4
Q

structure of alanine

A
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5
Q

structure of phenylalanine

A
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6
Q

polar (uncharged) amino acids

A

contains hydroxyl or amide groups
interact with water

serine
threonine
asparagine
glutamine
tyrosine

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7
Q

structure of serine

A
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8
Q

structure of tyrosine

A
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9
Q

polar acidic amino acids

A

contains carboxylic acid group
negatively charged at physiological pH
charged
hydrophilic

aspartic acid
glutamic acid

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10
Q

polar basic amino acids

A

contain basic groups
positively charged at physiological pH
charged
hydrophilic

arginine
histidine
lysine

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11
Q

structure of lysine (polar basic)

A
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12
Q

structure of aspartic acid (polar acidic)

A
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13
Q

special amino acids

A

don’t fit in other groups

cysteine
glycine
proline

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14
Q

structure of cysteine

A
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15
Q

structure of glycine

A
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16
Q

what is an amide?

A

2 amino acids reacted
joined by a peptide bond (covalent)

formed by condensation reaction
releases molecule of water

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17
Q

primary structure proteins

A

sequence of amino acids in a polypeptide chain

determine subsequent structures
determined by code in DNA

18
Q

secondary structure proteins

A

conformations adopted by different parts of a chain
folding of primary structure

hydrogen bonds form between atoms
alpha helix and beta pleated sheet

19
Q

alpha helices

A

hydrogen bonds form between carbon and amino group of 4th amino acid

3.6 amino acids per turn

side chains (r) face outwards

20
Q

beta sheet

A

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

21
Q

tertiary structure proteins

A

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

22
Q

quaternary structure proteins

A

association between different polypeptides

two or more proteins aggregate to form a larger molecule
held by same interactions as tertiary

23
Q

what are fibrous proteins?

A

protein that is NOT folded into a tertiary structure
eg collagen and keratin

24
Q

what is keratin?

A

fibrous protein - no tertiary

usually have a quaternary structure
large portions in secondary
low water solubility

fibroin (beta-keratin)

25
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
26
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
27
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
28
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
29
effects of the ionic strength of environment
high concentration of ions (salts) react more strongly with water than protein hydrogen bonds breaks = protein precipitates
30
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)
31
effects of heavy metals
alkaline pH = negative charge so react with positive charged heavy metal ion reduced reactions with water = precipitate
32
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
33
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)
34
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
35
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
36
agents of denaturation
detergents heat pH
37
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
38
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)
39
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
40
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