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A Level Organic Chemistry > 3.13 Amino Acids, Proteins And DNA > Flashcards

3.13 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 are there in the body

A

20

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3
Q

What type of amino acids are found in the body? What does this mean about their structure

A

Alpha amino acids

It means that NH2 is always on the carbon next to COOH

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4
Q

Draw a general formula for alpha amino acid

A

Slide 10

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5
Q

Are alpha amino acids chiral? Why?

A

Yes, one carbon has 4 different substituents.
Except glycine, where R = H

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6
Q

Which enantiomer do alpha amino acids exist as in nature

A
  • enantiomer
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7
Q

How can amino acids be synthesised industrially

A

RCHO + NH4CN —> RCH(NH2)CN via nucleophilic addition
RCH(NH2)CN + HCI + 2H2O —> RCH(NH2)COOH + NH4CI
(hydrolysis, HCI is dilute) Need to reflux the reaction mixture

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8
Q

Is the product from amino acids being synthesised naturally optically active? Why?

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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9
Q

In what form do amino acids exist as solids? What consequence does this have?

A

Zwitterions (ionic lattice) - high melting and boiling points

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10
Q

What colour solids are most zwitterions at room temperature?

A

White solids

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11
Q

Do zwitterions dissolve in water? Non-polar solvents? Why?

A

Yes, but not in non-polar solvents. Due to ionic nature/polar bonds

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12
Q

Define zwitterion

A

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

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13
Q

How do zwitterions occur in amino acids? Draw a general structure of one

A

COOH is deported —> COO-
NH2 is protonated —> NH3+

slide 28

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14
Q

What happens to amino acids in acidic conditions? Draw this

A

Gains a proton on NH2 group

Slide 30

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15
Q

What happens to amino acids in alkaline conditions?
Draw this

A

Loses a proton from COOH group

Slide 32

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16
Q

What is the peptide linkage?

A

-CONH-

Slide 34

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17
Q

What is a dipeptide? Draw a general one for amino acids

A

Two amino acids bonded together

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18
Q

What name is given to chains of amino acids up to 50 amino acids?

A

Polypeptides

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19
Q

What name is given to chains of amino acid with more than 50?

A

Proteins

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20
Q

What are polypeptides and proteins found in?

A

Enzymes
Wool
Hair
Muscles

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21
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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22
Q

What conditions are needed for hydrolysis to occur?

A

6 mol dm-3 HCI, reflux for 24 hours

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23
Q

What is the primary structure of a protein? How is if bonded

A

The sequence of amino acids along the protein chain. Bonded by covalent bonds

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24
Q

How is the primary structure represented?

A

Sequence of 3 letter abbreviations of the amino acids

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25
Q

How can the primary structure of a protein be broken up

A

Hydrolysis, 6M HCI, 24 hour reflux

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26
Q

What is the secondary structure of a protein?

A

The shape of the protein chain

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27
Q

What are the two options for the secondary structure

A

Alpha - helix shape or beta - pleated sheets

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28
Q

How is the secondary structure held together?

A

Hydrogen bonding, e.g. between C=O and N-H groups

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29
Q

What is the tertiary shape of a protein?

A

Alpha-helix or beta-pleated sheet is folded into a complex 3D shape; this is the tertiary structure

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30
Q

How is the tertiary structure held together?

A

Hydrogen bonding

Ionic interactions between R groups

Sulfer-sulfer bonding (disulfide bridges)

Van der waals forces of attraction

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31
Q

What is the tertiary structure important?

A

The shape of protein molecules is vital in their function - e.g. for enzymes

32
Q

How can amino acids bond/be attracted to each other? (3 main ways)

A

Hydrogen bonding

Ionic interactions between groups on side chains

Sulfur - sulfur bonds/disulfide bridges; 2 S atoms oxidised to form an S-S bond

33
Q

What is wool? How is it held together?

A

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

34
Q

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

A

Can be stretched, H bonds extend.

Release it and it returns to its original shape

Wash too hot and H bonds permanently break so garment loses its shape

35
Q

What is a TLC plate made of?

A

Plastic sheet coated with silica, SiO2. This is the stationary phase. (The solvent is the mobile phase)

36
Q

Describe how you would carry out Thin layer chromatography

A

Spot the 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 beaker to keep the inside saturated with solvent vapour.
Waited until the solvent front is almost at the top of the TLC plate; then remove from the beaker and analyse

37
Q

Why does TLC seperate amino acids (or other molecules)?

A

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

38
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 their spots purple) or shine UV light on them

39
Q

How do you calculate an Rf value?

A

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

40
Q

How can Rf values verify which amino acids is which?

A

Compare the 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

41
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 90degree and repeat TLC In a second, different solvent

42
Q

What are the benefits of 2D TLC

A

Separates 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

43
Q

How do you find the primary structure of a protein?

A

Reflux with 6M HCl and reflux for 24hrs

Carry out TLC to find the number and type of amino acids present

44
Q

How do you find the secondary and/or tertiary structure of a protein?

A

Various techniques, e.g. X-Ray
Diffraction

45
Q

What is an enzyme

A

Protein based catalyst that speeds up reactions in the body by factors of up to 10^10

46
Q

How many reactions is each enzyme designed to catalyse?

A

One reaction - they are very specialised

47
Q

What is the structure of an enzyme?

A

Globular protein with a creft/crevice in it, known as an “active site”. Very particular shape

48
Q

How does its structure help the function of the enzyme? What is the hypothesis known as?

A

The 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

49
Q

How else do enzymes increase the rate of reaction?

A

Reacting molecules from temporary bonds (via intermolecular forces) to the enzyme. This weakens the bonds In the molecules, promotes electron movement and lowers Ea

50
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

51
Q

What does stereospecificity mean for most naturally occurring molecules

A

Most naturally occurring molecules only occur as one enantiomer due to stereospecificic enzymes

52
Q

How Enzymes denatured

A

Change in temp or pH

53
Q

How does enzymes inhibition work?

A

A molecule with a very similar shape and structure to the substrate is devised. Binds to the enzymes active site. Blocks the active site (does not desire easily). Substrate cannot adsorb to the active site, so reaction cannot be catalysed

54
Q

An example of a drug that works through enzyme inhibition

A

Penicillin

55
Q

What are the 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 even been synthesised, predict their properties and design drugs that will treat a range of medical conditions

56
Q

What does DNA stand for?

A

Deoxyribonucleic acid

57
Q

What does DNA do?

A

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

58
Q

What structure does DNA take

A

A polymer with 4 monomers; they can be combined differently

59
Q

What constitutes a nucleotide?

A

A phosphate ion

A sugar (2-deoxyribose)

A base (A(adenine), C(cytosine), G(guanine), T(thymine))

60
Q

Draw a nucleotide

A

Slide 122

61
Q

What forms between bases of adjacent nucleotides

A

Hydrogen bonding

62
Q

Which bases pair up between nucleotides?

A

adenine with Thymine (A and T)
Guanine with Cytosine (C and G)

63
Q

What does DNA polymerase?

A

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

64
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

65
Q

What defines the properties of the DNA molecule

A

The order of the bases

66
Q

Why does DNA have a double helix shape?

A

Exists as 2 strands; these 2 strands are held together by hydrogen bonding (C and G and A and T). The complementary DNA molecule has bases that hydrogen bond in the same order to those on another molecule —> double helix shape is formed

67
Q

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

A

Because it codes for proteins and makes all cells

68
Q

How is DNA is exactly copied when cells divide

A

Hydrogen bonds between base pairs break. Covalent bonds in polymer chains remain intact. The sequence of bases is maintained. Separated nucleotide molecules that have been created move to hydrogen bond to their relevant bases. They polymerise. Thus, DNA is replicated exactly

69
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

70
Q

Draw the structure of cisplatin

A

Slide 142

71
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. It bonds to the N(nitrogen) atoms on 2 adjacent G bases. The N atoms replace the Cl- ligands in a ligands substitution reaction

72
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

73
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

74
Q

What happens when excess bromomethane is added to 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-)

75
Q

What happens If an amino acid is added to an excess of methanol in the presence of concentration sulfuric acid?

A

Excess ester forms with COOH group —> COOCH3

NH2 is protonated by the acid —> NH3+

A Level Organic Chemistry (16 decks)

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