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

amino acids, proteins and dna Flashcards

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
what are the two options for the secondary structure
alpha helix or beta pleated sheets
26
how is secondary structure held together
hydrogen bonding between C=O and N-H groups
27
what is tertiary shape of protein
a-helix or b-pleated sheet folded into complex 3D shape
28
how is tertiary structure held together
hydrogen bonding ionic interactions between R groups disulfide bridges VdW forces
29
why is tertiary structure important
shape of protein molecules is vital in their function
30
how can amino acids bond/be attracted to each other
hydrogen bonding ionic interactions between groups on side chains disulfide bridges
31
what is wool and how is it held together
protein fibre with secondary alpha-helix structure held together by hydrogen bonds
32
what does wool's structure and bonding mean for wool's properties
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
what is a TLC plate made of
plastic sheet coated with silica, SiO2 this is the stationary phase
34
describe how you would carry out TLC
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
why does TLC separate amino acids
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
what do you often have to do to enable the amino acids to be seen on the chromatogram
spray with ninhydrin (amino acids are colourless, ninhydrin turns spots purple) or shine UV light on them
37
how do you calculate an Rf value
distance moved by that substance divided by the distance moved by the solvent front
38
how can Rf values verify which amino acid is which
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
how can Rf values verify which amino acid is which
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
what is 2D TLC
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
what are the benefits of 2D TLC
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
how do you find primary structure of a protein
reflux 6M HCl and reflux 24 hours carry out TLC to find number and type of amino acids present
42
how do you find the secondary and/or tertiary structure of protein
various techniques e.g. x-ray diffraction
43
what is an enzyme
protein based catalysts that speed up reactions in the body by factors of up to 10^10
44
how many reactions is each enzyme designed to catalyse
one reaction - they are very specialised
45
what is the structure of an enzyme
globular protein with a creft/crevice in it known as active site very particular shape
46
how does its structure help the function of the enzyme
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
how else do enzymes increase the rate of reaction
reacting molecules form temporary bonds (via intermolecular forces) to the enzyme this weakens the bonds in the molecules, promotes movement and lowers Ea
48
what does the stereospecificity of enzymes mean
active sites are so selective of the shape of substrates that only reactions involving one enantiomer are catalysed
49
what does stereospecificity mean for most naturally occurring molecules
most naturally occurring molecules only occur as one enantiomer due to stereospecific enzymes
50
how are enzymes denatured
change in temp or pH
51
how does enzyme inhibition work
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
example of a drug that works through enzyme inhibition
penicillin
53
what are benefits of modelling new molecules on computers
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
what does dna stand for
deoxyribonucleic acid
55
what does dna do
present in all cells and is a blueprint from which all organisms are made
56
what structure does dna take
a polymer with 4 monomers; they can be combined differently
57
what constitutes a nucleotide
phosphate ion 2-deoyxyribose sugar a base (ACGT)
58
how does dna polymerise
OH on phosphate group and OH on number 3 carbon of 2-deoxyribose react to eliminate a molecule of H2O
59
what forms between bases of adjacent nucleotides
hydrogen bonding
59
what kind of polymer does the polymerisation of dna lead to
condensation polymer chain --> backbone of phosphate and sugar molecules, with bases attached
60
what defines the properties of the dna molecule
order of the bases
61
why does dna have double helix shape
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
why is it important that DNA is exactly copied when cells divide
because it codes for proteins and makes all cells
63
how is dna is exactly copied when cells divide
- 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
how does the body use information that is stored in dna
template for arranging amino acids into protein chains --> codes for proteins recipe for proteins that make up all living things; enzymes, flesh etc
65
structure of cisplatin
2 (Cl) --- Pt ---- 2 (NH3)
66
what is cisplatin's function? how does it do this
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
why are Cl- ions able to be replaced by N on the base
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
what are the drawbacks of using cisplatin
affects healthy cells that are replicating quickly, e.g. hair follicles --> lose hair during chemotherapy thought to damage kidneys
69
what happens when excess bromomethane is added to an amino acid
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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