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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
What is secondary structure of a protein
The shape of a protein chain
26
2 options for secondary structure
alpha-helix | beta-pleated sheets
27
How is secondary structure held together
H bonding | Between C=O and N-H groups
28
What is the tertiary shape of a protein
Alpha-helix or beta-pleated sheet folded into a complex 3D shape
29
How is tertiary structure held together
H bonding Ionic interactions between R groups Disulfide bridges van der Waals forces of attraction
30
Why is tertiary structure important
The shape of protein molecules vital in their function
31
How can AA be bond to each other
H bonding Ionic interactions Disulfide bridges
32
What is wool - how is it held together
Protein fibre with secondary alpha-helix structure - H bonds
33
What does wool's structure and bonding mean for its properties
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
What is TLC plate made of
Plastic sheet coated with silica, SiO2 | This is the stationary phase
35
Describe how to carry out TLC
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
Why does TLC separate AA
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
What do you often have to do to enable AA to be seen on chromatogram
Spray with ninhydrin or shine UV light on them
38
How to calculate Rf value
Distance moved by substance / Distance moved by solvent front
39
How can Rf values be used to check AA
Compare experimental values with accepted values
40
What is 2D TLC
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
Benefits of 2D TLC
Separates spots of AA more | Gives 2 Rf values for each AA
42
How to find primary structure of protein
Reflux with 6M HCl 24 hours | Carry out TLC
43
How to find secondary and / or tertiary structure of a protein
X-Ray | Diffraction
44
What is an enzyme
Protein based catalysts that speed up reactions in the body
45
How many reactions can 1 enzyme catalyse
1
46
Structure of enzyme
Globular protein containing an active site
47
How does its structure help the function of the enzyme
Lock and Key - reactants fit directly into active site
48
How else do they increase RoR
Reacting molecules form temporary bonds to enzymes - weakens bonds in molecules, promotes electron movement and lowers activation energy
49
What does stereospecificity of enzymes mean
Active sites are so selective of the shape of the substrates that only reactions involving 1 enantiomer can be catalysed
50
What does stereospecificity mean for most naturally occurring molecules
Means they can only occur as 1 enantiomer due stereospecific enzymes
51
How are enzymes denatured
Change in temperature or pH
52
How does enzyme inhibition work
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
Example of drug which works through enzyme inhibition
Penicillin
54
Benefits of modelling new molecules on computers
Understand factors that affect shapes of complex proteins
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 - can be combined differently
57
What constitutes a nucleotide
Phosphate ion Sugar Base
58
What forms between adjacent nucleotides
Hydrogen bonding
59
Which bases pair up between nucleotides
A and T | G and C
60
How does DNA polymerise
OH on phosphate group and OH on number 3 carbon of 2-deoxyribose react to eliminate H2O
61
What kind of polymer is DNA
Condensation polymer chain --> backbone of phosphate and sugar molecules with bases attached
62
What defines properties of DNA
Order of bases
63
Why does DNA have a double helix shape
Exists as 2 strands | H bonding between bases of 2 strands
64
Why is it important that DNA is exactly copied when cells divide
Because it codes for proteins and makes all cells
65
How is DNA exactly copied when cells divide
``` 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
How does the body se information stored in DNA
Template for arranging AA into protein chains
67
What is cisplatins function
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
Why are Cl- ions able to be replaced by N on the base
N atoms on the G base have lone pairs that co-ordinately bond to Pt ion N atoms better ligands than Cl-
69
Drawbacks of cisplatin
Affects healthy cells that are replicating quickly - hair loss
70
What happens when excess bromomethane is added to AA
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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