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Chemistry A Level 2023 2 organic > amino acids, proteins and dna > Flashcards

amino acids, proteins and dna Flashcards

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1
Q

what are the two functional groups of amino acids

A

NH2 and COOH
(amine and carboxylic acid)

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2
Q

how many naturally occurring amino acids

A

20

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3
Q

what type of amino acids are found in the body and what does this mean about their structure

A

a-amino acids (alpha) it means that NH2 is always on the carbon next to COOH

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4
Q

are a-amino acids chiral

A

yes, one carbon has 4 different substituents except glycine

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5
Q

which enantiomer do a-amino acids exist as in nature

A

(-) enantiomer

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6
Q

how can amino acids be synthesised industrially

A

RCHO + NH4CN –> RCH(NH2)CN via nucleophilic addition

RCH(NH2)CN + HCl + 2H2O –> RCH(NH2)COOH +NH4Cl
(hydrolysis, HCl is dilute, need to reflux the reaction mixture)

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7
Q

is the product from amino acids being synthesised naturally optically active

A

no, a racemic mixture is formed as the CN- ion can attack from above or below the planar C=O bond with equal likelihood

an equal amount of each enantiomer is formed, so no net effect on plane polarised light

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8
Q

in what form do amino acids exist as solids and what consequences does this have

A

zwitterions (ionic lattice) - high melting and boiling points

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9
Q

what colour solids are most zwitterions at room temperature

A

white solids

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10
Q

do zwitterions dissolve in water? non-polar solvents?

A

yes, but not in non-polar solvents
due to ionic nature/polar bonds

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11
Q

define a zwitterion

A

ions which have both a permanent positive and negative charge, but are neutral overall

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12
Q

how do zwitterions occur in amino acids

A

COOH deprotonated = COO-
NH2 is protonated = NH3+

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13
Q

what happens to amino acids in acidic conditions

A

proton added to NH2 group

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14
Q

what happens to amino acids in alkaline conditions

A

loses a proton from COOH group

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15
Q

what is peptide linkage

A

-CONH-

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16
Q

name of chains of amino acids up to 50 amino acids

A

polypeptide

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17
Q

name of chains of amino acids over to 50 amino acids

A

proteins

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18
Q

what are polypeptides and proteins found in

A

enzymes
wool
hair
muscles

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19
Q

what is the process called by which polypeptides or proteins can be broken down into their constituent amino acids

A

hydrolysis

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20
Q

what conditions needed for hydrolysis to occur

A

6 moldm-3 HCl
reflux for 24 hours

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21
Q

what is the primary structure of a protein

A

sequence of amino acids along protein chain bonded by covalent bonds

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22
Q

how is primary structure of protein represented

A

sequence of 3 letter abbreviations of the amino acids

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23
Q

how can the primary structure of a protein be broken up

A

hydrolysis
6M HCl
24 hour reflux

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24
Q

what is the secondary structure of a protein

A

shape of protein chain

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25
Q

what are the two options for the secondary structure

A

alpha helix or beta pleated sheets

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26
Q

how is secondary structure held together

A

hydrogen bonding between C=O and N-H groups

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27
Q

what is tertiary shape of protein

A

a-helix or b-pleated sheet folded into complex 3D shape

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28
Q

how is tertiary structure held together

A

hydrogen bonding
ionic interactions between R groups
disulfide bridges
VdW forces

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29
Q

why is tertiary structure important

A

shape of protein molecules is vital in their function

30
Q

how can amino acids bond/be attracted to each other

A

hydrogen bonding
ionic interactions between groups on side chains
disulfide bridges

31
Q

what is wool and how is it held together

A

protein fibre with secondary alpha-helix structure held together by hydrogen bonds

32
Q

what does wool’s structure and bonding mean for wool’s properties

A

can be stretched, H bonds extend
release it and returns to original shape
wash too hot and H bonds permanently break so garment loses its shape

33
Q

what is a TLC plate made of

A

plastic sheet coated with silica, SiO2
this is the stationary phase

34
Q

describe how you would carry out TLC

A

spot samples onto a pencil line a few cm above the base of the TLC plate
place this in a beaker or tank, with solvent level below the pencil line
ensure there is a lid on the breaker to keep the inside saturated with solvent vapour
wait until solvent front is almost at the top of the TLC plate; then remove from the beaker and analyse

35
Q

why does TLC separate amino acids

A

solvent carries amino acids up the TLC plate
rate of movement depends on balance between amino acid’s affinity for the solvent (solubility in it) and affinity for the stationary phase (attraction to the silicon with hydrogen bonding)

36
Q

what do you often have to do to enable the amino acids to be seen on the chromatogram

A

spray with ninhydrin (amino acids are colourless, ninhydrin turns spots purple)
or shine UV light on them

37
Q

how do you calculate an Rf value

A

distance moved by that substance divided by the distance moved by the solvent front

38
Q

how can Rf values verify which amino acid is which

A

compare experimental Rf values to known/accepted values in the same solvent

or run pure amino acids in the same solvent and compare results to identify amino acids

38
Q

how can Rf values verify which amino acid is which

A

compare experimental Rf values to known/accepted values in the same solvent

or run pure amino acids in the same solvent and compare results to identify amino acids

39
Q

what is 2D TLC

A

uses a square TLC plate
spot the amino acids in one corner, then run TLC in first solvent
flip the plate through 90 degrees and repeat TLC in a second, different solvent

40
Q

what are the benefits of 2D TLC

A

separate the spots more - it is extremely unlikely that 2 amino acids will have identical Rf values in 2 solvents

gives you 2 Rf values for each amino acids; you can be more confident in verifying the identity of the amino acids when comparing to known values, as 2 Rf values can be verified

41
Q

how do you find primary structure of a protein

A

reflux 6M HCl and reflux 24 hours

carry out TLC to find number and type of amino acids present

42
Q

how do you find the secondary and/or tertiary structure of protein

A

various techniques e.g. x-ray diffraction

43
Q

what is an enzyme

A

protein based catalysts that speed up reactions in the body by factors of up to 10^10

44
Q

how many reactions is each enzyme designed to catalyse

A

one reaction - they are very specialised

45
Q

what is the structure of an enzyme

A

globular protein with a creft/crevice in it known as active site
very particular shape

46
Q

how does its structure help the function of the enzyme

A

reacting molecules fit precisely into the active site and are held at exactly the right orientation to react. this is the lock and key hypothesis

47
Q

how else do enzymes increase the rate of reaction

A

reacting molecules form temporary bonds (via intermolecular forces) to the enzyme
this weakens the bonds in the molecules, promotes movement and lowers Ea

48
Q

what does the stereospecificity of enzymes mean

A

active sites are so selective of the shape of substrates that only reactions involving one enantiomer are catalysed

49
Q

what does stereospecificity mean for most naturally occurring molecules

A

most naturally occurring molecules only occur as one enantiomer due to stereospecific enzymes

50
Q

how are enzymes denatured

A

change in temp or pH

51
Q

how does enzyme inhibition work

A

molecule with a very specific shape and structure to the substrate is devised
binds to enzyme’s active site
blocks the active site (does not desorb easily)
substrate cannot adsorb to active site, so reaction cannot be catalysed

52
Q

example of a drug that works through enzyme inhibition

A

penicillin

53
Q

what are benefits of modelling new molecules on computers

A

now we understand factors that affect the shapes of extremely complex proteins, we can model drugs that haven’t been synthesised, predict their properties and design drugs that will treat a range of medical conditions

54
Q

what does dna stand for

A

deoxyribonucleic acid

55
Q

what does dna do

A

present in all cells and is a blueprint from which all organisms are made

56
Q

what structure does dna take

A

a polymer with 4 monomers; they can be combined differently

57
Q

what constitutes a nucleotide

A

phosphate ion
2-deoyxyribose sugar
a base (ACGT)

58
Q

how does dna polymerise

A

OH on phosphate group and OH on number 3 carbon of 2-deoxyribose react to eliminate a molecule of H2O

59
Q

what forms between bases of adjacent nucleotides

A

hydrogen bonding

59
Q

what kind of polymer does the polymerisation of dna lead to

A

condensation polymer chain –> backbone of phosphate and sugar molecules, with bases attached

60
Q

what defines the properties of the dna molecule

A

order of the bases

61
Q

why does dna have double helix shape

A

exists as 2 strands; these 2 strands are held together by hydrogen bonding
the complementary dna molecule has bases that hydrogen bond in the same order to those on another molecule –> double helix shape formed

62
Q

why is it important that DNA is exactly copied when cells divide

A

because it codes for proteins and makes all cells

63
Q

how is dna is exactly copied when cells divide

A
  • hydrogen bonds between base pairs break
    covalent bonds in polymer chains remain intact
  • sequence of bases is maintained
  • separate nucleotide molecules that have been created move to hydrogen bond to their relevant bases
  • they polymerise
  • dna replicated
64
Q

how does the body use information that is stored in dna

A

template for arranging amino acids into protein chains –> codes for proteins

recipe for proteins that make up all living things; enzymes, flesh etc

65
Q

structure of cisplatin

A

2 (Cl) — Pt —- 2 (NH3)

66
Q

what is cisplatin’s function? how does it do this

A

anti-cancer drug
bonds to strands of DNA to distort shape and prevent cell replication
bonds to nitrogen atoms on 2 adjacent G bases
N atoms replace the Cl- ligand substitution reaction

67
Q

why are Cl- ions able to be replaced by N on the base

A

N atoms on the G base have lone pairs of electrons that can co-ordinately bond to the Pt ion; N atoms are better ligands than Cl-, so replace them

68
Q

what are the drawbacks of using cisplatin

A

affects healthy cells that are replicating quickly, e.g. hair follicles –> lose hair during chemotherapy

thought to damage kidneys

69
Q

what happens when excess bromomethane is added to an amino acid

A

Ch3Br is in excess, so every H on the N atom and the lone pair on the N atom is replaced by a CH3 group –> quaternary ammonium ion (makes a salt with Br-)

Chemistry A Level 2023 2 organic (16 decks)

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