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cells and biomolecules 🧬 > amino acids > Flashcards

amino acids Flashcards

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
Q

types of keratin

A

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
Q

what are globular proteins?

A

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
Q

examples of globular proteins

A

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
Q

factors affecting solubility of proteins

A

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
Q

effects of the ionic strength of environment

A

high concentration of ions (salts)
react more strongly with water than protein
hydrogen bonds breaks = protein precipitates

30
Q

effects of low concentrations

A

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
Q

effects of heavy metals

A

alkaline pH = negative charge
so react with positive charged heavy metal ion
reduced reactions with water = precipitate

32
Q

effects of organic acids

A

increased acidity = more positive charges on surface of protein
react with negative charge on the anion
reduced reactions with water = precipitate

33
Q

what is the iso-electric point? (PI)

A

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
Q

what is the dielectric constant?

A

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
Q

protein denaturation

A

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
Q

agents of denaturation

A

detergents
heat
pH

37
Q

detergents

A

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
Q

heat

A

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
Q

pH

A

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
Q

buffers

A

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

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