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Chemistry > CH30 AA, Proteins and DNA > Flashcards

CH30 AA, Proteins and DNA Flashcards

1
Q

Functional groups of amino acids

A

NH2 and COOH

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2
Q

How many naturally occurring AA are there in the body

A

20

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3
Q

What type of AA are found in the body

A

alpha-AA

NH2 is always on the carbon next to COOH

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4
Q

Why are alpha-AA chiral

A

One carbon has 4 different substituents

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5
Q

Which enantiomer do alpha-AA exist as in nature

A

-ve 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, dilute HCl)
Need to reflux the reaction mixture

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7
Q

Is the product from AA being synthesised naturally optically active - why

A

No - racemic mixture formed as CN- can attack from above and below planar C=O bond with equal likelihood

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8
Q

In what form do AA exist as solids

A

Zwitterions (ionic lattice) - High MP and BP

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9
Q

What colour solids are most zwitterions at RT

A

White

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10
Q

Do zwitterions dissolve in water - why

A

Yes - contain polar bonds

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11
Q

Define 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 AA

A

COOH deprotonated - COO-

NH2 protonated - NH3+

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13
Q

What happens to AA in acidic conditions

A

Gains proton on NH2 group

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14
Q

What happens to AA in alkaline conditions

A

Loses a proton from COOH group

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15
Q

What is the peptide linkage

A
  • CONH-
  • C-N-
  • C=O
  • N-H
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16
Q

What is a dipeptide

A

2 amino acids bonded together

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17
Q

Name given to chains of AA up to 50 AA

A

Polypeptides

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18
Q

Name given to chains of AA with more than 50

AA

A

Proteins

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19
Q

What are polypeptides and proteins found in

A

Enzymes
Wool
Hair
Muscles

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20
Q

Process by which polypeptides and proteins are broken down

A

Hydrolysis

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21
Q

Conditions needed for hydrolysis

A

6 mol dm-3 HCl

Reflux for 24 hours

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22
Q

What is primary structure of a protein - how is it bonded

A

Sequence of AA along the protein chain

Bonded by covalent bonds

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23
Q

How is primary structure represented

A

Sequence of 3 letter abbreviations of AA

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24
Q

How can primary structure of protein be broken up

A

Hydrolysis
6M HCl
24 hour reflux

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25
Q

What is secondary structure of a protein

A

The shape of a protein chain

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26
Q

2 options for secondary structure

A

alpha-helix

beta-pleated sheets

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27
Q

How is secondary structure held together

A

H bonding

Between C=O and N-H groups

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28
Q

What is the tertiary shape of a protein

A

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

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29
Q

How is tertiary structure held together

A

H bonding
Ionic interactions between R groups
Disulfide bridges
van der Waals forces of attraction

30
Q

Why is tertiary structure important

A

The shape of protein molecules vital in their function

31
Q

How can AA be bond to each other

A

H bonding
Ionic interactions
Disulfide bridges

32
Q

What is wool - how is it held together

A

Protein fibre with secondary alpha-helix structure - H bonds

33
Q

What does wool’s structure and bonding mean for its properties

A

Can be stretched - H bonds extend
Release it and return to its original shape
Wash too hot and H bonds permanently break so garment loses its shape

34
Q

What is TLC plate made of

A

Plastic sheet coated with silica, SiO2

This is the stationary phase

35
Q

Describe how to carry out TLC

A

Spot samples onto pencil line few cm above base of TLC plate
Place this in beaker with solvent level below pensil line - ensure lid on beaker to avoided solvent vapour escaping
Wait until solvent front almost at top of TLC plate, remove and analyse

36
Q

Why does TLC separate AA

A

Solvent carries AA up TLC plate. Rate of movement depends on AA affinity for solvent (solubility) and affinity for stationary phase (attraction to silicon)

37
Q

What do you often have to do to enable AA to be seen on chromatogram

A

Spray with ninhydrin or shine UV light on them

38
Q

How to calculate Rf value

A

Distance moved by substance / Distance moved by solvent front

39
Q

How can Rf values be used to check AA

A

Compare experimental values with accepted values

40
Q

What is 2D TLC

A

Uses a square TLC plate
Spot AA in 1 corner
Run TLC in first solvent
Flip plate 90 degrees and repeat TLC in a different solvent

41
Q

Benefits of 2D TLC

A

Separates spots of AA more

Gives 2 Rf values for each AA

42
Q

How to find primary structure of protein

A

Reflux with 6M HCl 24 hours

Carry out TLC

43
Q

How to find secondary and / or tertiary structure of a protein

A

X-Ray

Diffraction

44
Q

What is an enzyme

A

Protein based catalysts that speed up reactions in the body

45
Q

How many reactions can 1 enzyme catalyse

46
Q

Structure of enzyme

A

Globular protein containing an active site

47
Q

How does its structure help the function of the enzyme

A

Lock and Key - reactants fit directly into active site

48
Q

How else do they increase RoR

A

Reacting molecules form temporary bonds to enzymes - weakens bonds in molecules, promotes electron movement and lowers activation energy

49
Q

What does stereospecificity of enzymes mean

A

Active sites are so selective of the shape of the substrates that only reactions involving 1 enantiomer can be catalysed

50
Q

What does stereospecificity mean for most naturally occurring molecules

A

Means they can only occur as 1 enantiomer due stereospecific enzymes

51
Q

How are enzymes denatured

A

Change in temperature or pH

52
Q

How does enzyme inhibition work

A

Molecules with very similar shape and structure binds to enzymes active site
Blocks active site
Substrate cannot adsorb to active site and reaction is not catalysed

53
Q

Example of drug which works through enzyme inhibition

A

Penicillin

54
Q

Benefits of modelling new molecules on computers

A

Understand factors that affect shapes of complex proteins

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 - can be combined differently

57
Q

What constitutes a nucleotide

A

Phosphate ion
Sugar
Base

58
Q

What forms between adjacent nucleotides

A

Hydrogen bonding

59
Q

Which bases pair up between nucleotides

A

A and T

G and C

60
Q

How does DNA polymerise

A

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

61
Q

What kind of polymer is DNA

A

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

62
Q

What defines properties of DNA

A

Order of bases

63
Q

Why does DNA have a double helix shape

A

Exists as 2 strands

H bonding between bases of 2 strands

64
Q

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

A

Because it codes for proteins and makes all cells

65
Q

How is DNA exactly copied when cells divide

A 
H bonds between base pairs break
Covalent bonds in polymer chains remain intact
Sequence of bases maintained
Separate nucleotide molecules move to 
H bond with relevant bases 
They polymerise - DNA replicated exactly
66
Q

How does the body se information stored in DNA

A

Template for arranging AA into protein chains

67
Q

What is cisplatins function

A

Anti-cancer drug
Bonds to strands of DNA to distort shape and prevent cell replication
Bonds to N on 2 adjacent G bases
N atoms replace Cl- ligands in ligand substitution reaction

68
Q

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

A

N atoms on the G base have lone pairs that co-ordinately bond to Pt ion
N atoms better ligands than Cl-

69
Q

Drawbacks of cisplatin

A

Affects healthy cells that are replicating quickly - hair loss

70
Q

What happens when excess bromomethane is added to AA

A

CH3BR in excess - every H on N atom and lone pair on N atom replaced by CH3 group
Quaternary ammonium ion

Chemistry (18 decks)

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