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BDS year 1 - biochemistry > Amino acids + proteins > Flashcards

Amino acids + proteins Flashcards

1
Q

what makes up most of cell’s dry mass

A

amino acids

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2
Q

how many amino acids are in plants, animals + microbial + how many are encoded by genetic code

A

300

20

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3
Q

what does a alpha carbon mean

A

central Carbon - hydrogen + amine + carboxyl group + variable side chain attached to

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4
Q

what do optical isomers mean

A

same structural formula but different spatial arrangement of atoms
2 enantiomers - mirror images

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5
Q

which amino acid doesn’t have a optical isomer and why

A

glycine

doesn’t have asymmetric carbon - doesn’t have 4 diff gaps attached

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6
Q

what way can most amino acids rotate the polarised light

A

L - rotates light to the left

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7
Q

what does it mean if optical isomers are optically active

A

can rotate the plane of polarised light
L - light to the left
D - light to the right

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8
Q

what are the charges on amino acids

A

dipolar ions = positive + negative charged

but are zwitterions - net charge = 0

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9
Q

what is pK values for carboxylic acid groups

A

2.2 - strong acid

readily donate protons

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10
Q

what is pK value for alpha amino group

A

9.4

readily ionise

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11
Q

what happens to amino groups + carboxylic acid groups on AA at pH 7.4

A

amino acid group protonated - POSITIVE (NH3+)

carboxylic acid grp –> carboxylate (conjugate base)(COO-)

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12
Q

what happens to the amino acid in very acidic conditions

A

net charge is positive

excess number of free protons present from acid

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13
Q

what happens to the amino acid at neutral pH

A

net charge is neutral

it is a zwitterion

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14
Q

what happens if the amino acid net charge is negative

A

it is in Anionic form

its in basic condition

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15
Q

why are amino acids amtopheric

A

they have basic + acidic groups

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16
Q

what happens to the groups on the amino acid at a high pH

A

carboxylic group will lose proton first –> bound more loosely than amino group
COO- + NH2

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17
Q

what happens to the groups on amino acid as the pH decreases

A

NH3+ AND COOH

amino group is protonated

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18
Q

describe the beginning of graph of titration of amino acid

A
    • curve is steep up to pH 2 –> there’s no buffer - so can’t resist pH change
  2. pH 2.34 carboxyl group acts as buffer + loses proton (COO-) –> Ph doesn’t change much = BUFFERING REGION
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19
Q

what is the isoelectric pH of amino acid

A

pH 6.1

net charge of molecule = 0

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20
Q

what is the pKa of carboxylate ion

A

pKa 2.34

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21
Q

what happens to the amino group of the AA at around pH 10 and what is the pKb of the amino group

A

amino group acts as a buffer now

pKb = 9.87

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22
Q

what does it mean if the AA is negatively charged

A

all groups have been ionised

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23
Q

what is the overall trend of the AA graph

A

as the pH increases, AA net charge goes from positive –> negative

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24
Q

how many inflection point are there on the AA titration graph + what do they mean

A

4 inflection points

  1. half zwitterions + half cations (NH3+ , COOH)
  2. all AA are zwitterions
  3. half zwitterions + half anions (NH2 , COO-)
  4. all AA are anions
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25
Q

what does anion mean

A

negative charged NH2 and COO-)

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26
Q

what does cation mean

A

positive charged NH3+ AND COOH

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27
Q

what amino acids are non-polar, neutral + aliphatic inside + outside protein

A 
glycine
alanine
valine
leucine
isoleucine
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28
Q

what amino acid are non - polar, neutral + imino acid (bent chain)

A

proline

29
Q

what amino acids are non polar, neutral + aromatic

A

phenylalanine

tryptophan

30
Q

what amino acids are non- polar, neutral + contain sulphur

A

cysteine

methionine

31
Q

what amino acids are polar, neutral + aromatic –> what is it used for

A

tyrosine

aromatic = site for phosphorylation

32
Q

what amino acids are polar, neutral + contain OH group –> what is used for

A

threonine
serine
OH group –> site for glycosylation

33
Q

what amino acids are polar, neutral + contain NH2 groups + what reason

A

asparagine
glutamine
site for glycosylation

34
Q

what amino acids are polar, acidic + carry negative OH carboxyl group

A

aspartic acid

glutamic acid

35
Q

what amino acids are polar, basic + carry positive NH3 amino group

A

arginine
lysine
histidine

36
Q

what is the isoelectric point

A

point at which AA doesn’t carry net charge

37
Q

what is the formula to work out pI (isoelectric point) + when can you use this formula

A

pI = (pKa + pKb) / 2

when there are more than 2 ionisable groups

38
Q

what to do if you want to find pI but have 3 or more ionisable groups on AA

A

take pK values closest to neutral + use those vlues

39
Q

how to find pI of glutamic acid

A

acidic, take lowest pK charges

40
Q

how to find pI of arginine

A

basic

take pK charges of 2 highest values

41
Q

which AA are precursors of nucleotides

A

aspartate, glycine, glutamine

42
Q

what is serotonin and which AA is its precursor

A

it is a neurotransmitter

tryptophan is precursor

43
Q

In a polypeptide, what is the N terminal and the C terminal

A

N terminal = free amino group at the first AA in polypeptide

C terminal = free carboxyl group in polypeptide

44
Q

which terminal is always synthesised first in protein synthesis

A

N terminal

left to right

45
Q

what is post translational modification

A

AA contained in proteins are altered after translation in protein synthesis

46
Q

what can post translational modifications include

A

phosphorylation

glycosylation are essential for protein function

47
Q

what are most common function + uses of protein

A

growth + repair

enzymes, hormones, DNA, RNA

48
Q

what is protein folding

A

protein has more than 1 stable folded conformation, each has its own conformation + function
but only 1 is active
its reversible

49
Q

what is a prosthetic group

A

proteins tightly associated with other chemical/non-protein species
helps to perform function

50
Q

what is the primary structure of a protein

A

AA sequence
peptide bonds between each AA
determined by our DNA

51
Q

what is secondary structure of protein

A

folding/ coiling of polypeptide chain into alpha helix or beta pleated sheet
weak H bonds between H atom + electronegative atoms (N or O)

52
Q

how many turns in secondary structure for polypeptide chain in alpha helix + how do the bonds form

A

3.6 amino acids

H atom in peptide bond is shared with 4th AA instead

53
Q

what is the tertiary structure of protein

A

3D shape of polypeptide chain

fibrous or globular

54
Q

what type of bonds are there in terry structure of protein

A

electrostatic attraction/ salt bridge
van der Waals forces
disulphide bon
hydrophobic interaction

55
Q

how does electrostatic attraction / salt bridge occur in tertiary structure

A

between oppositely charged ions or groups

56
Q

how do van Der Waals forces occur in tertiary structure

A

weak but needed in close packed interior of proteins + specific shape of enzyme active site

57
Q

how do disulphide bonds occur in tertiary structure

A

strong bond between specific cysteine AA

locks protein in configuration

58
Q

how does hydrophobic interaction occur in tertiary structure

A

between non-polar hydrophobic AA

59
Q

what is quaternary structure of protein

A

combo of more than 1 proteins + involves non-covalent bonds between proteins

60
Q

give example if 1 protein with 4 polypeptide chains + 1 protein with 3

A

haemoglobin - 4 polypeptide chains + 4 haem groups

collagen - 3 helical polypeptide chain supercoiled with each other

61
Q

what are the 3 protein classes

A

globular
fibrous
membrane associated

62
Q

what are the characteristics of globular proteins

A

soluble
enzymes/ antibodies
Tertiary structure when non - polar hydrophobic AA move in + polar hydrophilic AA bound outwards

63
Q

give 2 examples of globular proteins + give their uses

A

carbonic anhydrase - large beta pleated sheet in centre + active site has Zn ion —> catalyses hydration of CO2 –> HCO3- + H+

Hb - 4 globular proteins bound together - electrostatic attraction + H bonds + hydrophobic interaction
each protein associated with haem grp contains iron that binds to O2

64
Q

what are the characteristics of fibrous proteins

A 
wire like
structural/storage function 
used to construct connective tissues + bones 
repeated AA sequences 
contains cross links between chains
65
Q

what is use + nature of keratin

A

keratin - tough + insoluble
high proportion of small AA (glycine + alanine)
lots of cysteine –> lots disulphide bridge – thermal stable + permanent –> rigid
can assemble into intermediate filaments for cell cytoskeleton

66
Q

what are 2 examples of fibrous proteins

A

keratin

collagen

67
Q

what is use + nature of collagen

A

secreted by connective tissue cells

most abundant protein in mammals (25%)

68
Q

what do membrane associated proteins include (where found)

A

transmembrane proteins integrated in phospholipid bilayer
lipid associated proteins – inner + outer of membrane + proteins
transporters, linkers, receptors, enzymes on cell membrane

BDS year 1 - biochemistry (14 decks)

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