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AQA A Level Organic Chemistry > 13. Amino acids, Proteins and DNA > Flashcards

13. Amino acids, Proteins and DNA Flashcards

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1
Q

What category do amino acids come under?

A

Amines and acids

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2
Q

What groups do amino acids have?

A

Amino and carbonyl groups

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3
Q

Do amino acids always only have one of each functional group?

A

No - they may also contain other functional groups

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4
Q

Why is the amine group in amino acids basic?

A

It has a tendency to accept protrons

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5
Q

Why is the carboxyl group in amino acids acidic?

A

It has a tendency to donate protons

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6
Q

What are the simplest amino acids?

A

α amino acids

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7
Q

What are α amino acids?

A

Amino acids with the amino group on the C atom adjacent to the carboxyl group (i.e. 2nd C atom)

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8
Q

Example of an α amino acid?

A

Alanine

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9
Q

What types of amino acids are there?

A

Alpha, beta, gamma

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10
Q

IUPAC name of alanine?

A

2-aminopropanoic acid

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11
Q

IUPAC name of aspartic acid?

A

2-amino butadioic acid

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12
Q

IUPAC name of lysine?

A

2,6 - diamino hexanoic acid

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13
Q

IUPAC name of phenylalanine?

A

2-amino 3-phenyl propanoic acid

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14
Q

IUPAC name of serine?

A

2-amino 3-hydroxyl propanoic acid

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15
Q

Which amino acid is not chiral?

A

Glycine

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16
Q

What does it mean that amino acids are chiral?

A

They have an asymmetric C atom and are optically active

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17
Q

What is zwitterion?

A

A dipolar ion

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18
Q

Why is zwitterion formed?

A

As a result of the lone pair of electrons on the nitrogen of amine group being able to accept a proton from the acid group

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19
Q

Do amino acids have both acidic and basic properties?

A

Yes

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20
Q

What is the isoelectric point of an amino acid?

A

The pH where the overall charge on the amino acid is zero

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21
Q

What pH are Zwitterions formed at?

A

Unique pH value for each amino acid

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22
Q

Is Zwitterion an acid-base property?

A

Yes

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23
Q

What will happen, in terms of Zwitterions, in acidic conditions?

A
  • pH is lower than isoelectric point
  • so NH2 group protonated (acting as base)
  • COOH group unchanged
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24
Q

What will happen, in terms of Zwitterions, in basic conditions?

A
  • pH is higher than isoelectric point
  • so COOH group deprotonated (acting as acid)
  • NH2 group unchanged
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25
Q

When naming amino acids, what does the longest chain have to contain?

A

The carboxyl group

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26
Q

In what reaction will two amino acids react together?

A

Condensation reaction

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27
Q

How are two amino acids joined when they react together?

A

Via peptide link - a peptide bond

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28
Q

What compound is formed when two amino acids react?

A

Dipeptide

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29
Q

How are polypeptides formed?

A

If either end of a dipeptide reacts with another amino acid

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30
Q

What are proteins made of?

A

One or more long polypeptide chains

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31
Q

What are condensation polymers of amino acids also called?

A

Proteins

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32
Q

In our bodies, what catalyse the condensation reaction to form proteins?

A

Enzymes

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33
Q

How many levels of structure do proteins have?

A

3 or 4 - primary, secondary, tertiary and quaternary

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34
Q

What forms the primary structure of any protein?

A

The sequence of amino acids in a polypeptide chain

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35
Q

What does the primary structure of a protein determine?

A

Its shape and hence its function

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36
Q

How can the primary structure of a protein be represented?

A

By the sequence of three letter names of the relevant amino acids

(e.g. - gyl - ala - ala - val - leu -)

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37
Q

How is secondary structure of proteins formed?

A

Within the peptide chains, hydrogen bonds form between amino acids at various points - meaning it is not a straight chain

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38
Q

In amino acids, where are there strong dipoles?

A

In the C=O in the carboxyl group, and in the O-H in a hydroxyl group

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39
Q

What can the secondary structure of proteins be in the form of?

A
  • α-helix

* β - pleated sheets (folded structures)

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40
Q

Why the secondary structure of proteins easier to disrupt than the primary structure?

A
  • hydrogen bonds responsible for 2°, covalent for 1°

* hydrogen bonds are IMFs which are weak so easier to disrupt than the primary structure e.g. by heating

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41
Q

How are tertiary structures of proteins be formed?

A

When additional bonds are formed at different positions in the helix or pleated sheet

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42
Q

What bonds can be formed to make tertiary proteins?

A
  • hydrogen bonds
  • disulphide bonds
  • ionic bonds
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43
Q

Do Van der Waals forces exist between proteins?

A

Yes - as they do between all molecules

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44
Q

What do Van der Waals forces mean for proteins?

A

The structure twisting and folding, forming the tertiary structure

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45
Q

What do disulphide bonds form between?

A

Amino acids that contain a thiol group (-SH)

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46
Q

How are disulphide bonds formed?

A

The thiol group (-SH) lose their hydrogen atom and a bond is formed between the two sulphur atoms

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47
Q

What type of bond is a disulphide bond?

A

Covalent

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48
Q

What effect will a disulphide bond have on the tertiary structure of a protein?

A

Stabalises the structure

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49
Q

In tertiary protein structures, where are ionic bonds formed?

A

Between any carboxyl and amine groups not involved in forming the peptide forms

50
Q

Why can changes in pH break ionic bonds in tertiary structures?

A

The charges on carboxyl and amine groups are dependent on the conditions

51
Q

How can the sequence of amino acids in a protein be found?

A

By breaking the peptide bond (primary structure) in a hydrolysis reaction

52
Q

What can the hydrolysis of peptide bonds in a protein show?

A

The sequence of amino acids

53
Q

How is the hydrolysis of peptide bonds in a protein carried out?

A

Heating protein under reflux with an acidic or alkaline solution for 24 hours

54
Q

In the hydrolysis of peptide bonds in a protein, what do the conditions (acidic/alkaline) determine?

A

The form the amino acids take after (anion or cation)

55
Q

In acidic hydrolysis of proteins, what form are the amino acids produced in?

A

Cationic form

56
Q

In alkaline hydrolysis of proteins, what form are the amino acids produced in?

A

Anionic form

57
Q

What does the hydrolysis of proteins allow chemists to do?

A

Deduce which amino acids are present in a sample of a protein

58
Q

How can different amino acids in a protein by identified?

A

Thin-layer chromatography (TLC)

59
Q

How does TLC differ from paper chromatography?

A

The paper is replaced by a thin-layer chromatography plate (a piece of plastic or glass)

60
Q

What is the stationary phase in TLC?

A

The thin-layer chromatography plate

61
Q

How does TLC work to identify amino acids?

A
  • amino acid mixture placed onto chromatography plate and allowed to separate
  • compare Rf values
62
Q

What is an Rf value in TLC of amino acids?

A

The distance each amino acid (spot) moves up the plate compared to the solvent

63
Q

In TLC, what is the indicator for when to remove the plate from the tank?

A

When the solvent has almost reached the top

64
Q

How to calculate Rf value?

A

distance spot travelled / distance solvent travelled

65
Q

What happens in TLC if two amino acids have similar Rf values?

A

2-dimensional TLC is used

66
Q

How is 2-dimensional TLC carried out?

A
  1. carry out TLC as normal using a square piece of TLC film and placing the spot in one corner
  2. once amino acids have separated, rotate the TLC film by 90° and run it again using a different solvent
  3. this enables 2 Rf values to be calculated (one of each solvent) and if both values match to those for a known amino acid identification can be more confirmed
67
Q

Are amino acids colourless?

A

Yes

68
Q

As amino acids are colourless, how are the positions they reach identified?

A
  • use of developing agent e.g. iodine or ninhydrin, which reacts with amino acids to form a purple compound
  • or UV light can be shone onto plate to identify amino acids
69
Q

What are enzymes?

A

Usually globular proteins that catalyse chemical reactions in living cells

70
Q

What are substrates?

A

The molecules that enzymes act upon

71
Q

What is an active site?

A

An area on an enzyme which the substrate fits into so that it can interact with the enzyme

72
Q

What is the active site part of?

A

The tertiary structure of the enzyme of the protein

73
Q

What does it mean that the active sites of enzymes are stereospecific?

A

It will only work on one or the other of a pair of enantiomers of a substrate - the other enantiomer will not fit into the active site, meaning the enzyme cannot work on it

74
Q

What are enzyme inhibitors?

A

Molecules that have a similar shape to the substrate

75
Q

What do enzyme inhibitors do?

A

Compete with the substrate to bond with the active site and therefore the appropriate substrate cannot bind - and no reaction follows

76
Q

What does the amount of enzyme inhibition depend on?

A

The concentrations of inhibitors and substrate, and how strongly it bonds to the active site

77
Q

How do antibiotics work?

A

By blocking the active site of an enzyme

78
Q

How is enzyme inhibition utilized in some drugs?

A

If an enzyme that catalyses a harmful reaction can be blocked, then the reaction can be stopped

79
Q

Why might it be especially difficult to find a drug molecule that will fit into the active site?

A

If the molecule is chiral

80
Q

How do chemists use computers in drug development?

A

They use computers to model the shape of the enzyme active sites and predict how well potential drug molecules will interact with it

81
Q

What does DNA stand for?

A

Deoxyribonucleic acid

82
Q

What is DNA?

A

A polymer made up of four different monomers, which are called nucleotides

83
Q

How many components are nucleotides made up of?

A

3

84
Q

What are the 3 components that nucleotides are made up of?

A
  • phosphate ion - each with a -ve charge, making nucleic acids highly charged
  • 2-deoxyribose
  • nitrogen-containing organic base
85
Q

What makes nucleic acids highly charged?

A

Phosphate ions, each with a negative charge

86
Q

What is 2-deoxyribose?

A

A 5 carbon sugar (pentose)

87
Q

What are the nitrogen containing bases that can be in DNA?

A
  • cytosine
  • thymine
  • adenine
  • guanine
88
Q

How are the phosphate group, base and sugar held together in DNA?

A

Covalent bonds

89
Q

What is formed when nucleotides are joined together?

A

Polynucleotide chains

90
Q

What bonds nucleotides together to form polynucleotide chains?

A

Covalent bonds

91
Q

In what reaction are polynucleotide chains formed?

A

Condensation polymerisation

92
Q

How are sugar-phosphate polymer chains formed?

A

Condensation polymerisation - the OH group of a phosphate group in one nucleotide reacts with the OH group in the 2-deoxyribose of another nucleotide

93
Q

What are the bases attached to in a sugar-phosphate polymer chain?

A

Sugars

94
Q

What do two polynucleotide strands form?

A

DNA

95
Q

How many polynucleotide chains form DNA?

A

2

96
Q

What do two polynucleotide strands spiral together to form?

A

A double helix

97
Q

What is a double helix formed from?

A

Two polynucleotide chains, held together by hydrogen bonds between bases

98
Q

How is a double helix held together?

A

Hydrogen bonds between bases

99
Q

What does adenine always pair with?

A

Thymine

100
Q

What does guanine always pair with?

A

Cytosine

101
Q

What are complimentary base pairings due to?

A

The arrangement of atoms in the base - to bond the atoms have to be the right distance apart

102
Q

How many hydrogen bonds can cytosine and guanine form?

A

3

103
Q

How many hydrogen bonds can adenine and thymine form?

A

2

104
Q

Why would other pairings (i.e. not C-G and A-T) not work?

A

Would put the partially charged atoms too close (they would repel), too far apart or the bonding atoms would not line up correctly

105
Q

Why does the DNA double helix have to twist?

A

So the bases are in the right alignment and the right distance apart for the complementary bases to bond

106
Q

What is cisplatin?

A

A complex with Pt(II) as the central metal ion and two chloride ion ligands and two ammonia ligands

107
Q

What is the shape of cisplatin?

A

Square planar

108
Q

What is cisplatin formed from?

A

Pt(II) as the central metal ion and two chloride ion ligands and two ammonia ligands bonded to it

109
Q

What is the molecular formula for cisplatin?

A

Pt(NH₃)₂Cl₂

110
Q

What would cisplatin be called if the chloride ions were opposite instead of next to each other?

A

Transplatin

111
Q

How does cisplatin work as an anti-cancer drug?

A

By bonding to strands of DNA, distorting their shape and preventing replication of the cancer cells

112
Q

What is cancer?

A

When cells mutate and start dividing uncontrollably to form tumours

113
Q

What must happen in order for a cell to divide?

A

It has to replicate its DNA, which requires the two DNA strands in the double helix to unwind so they can be copied

114
Q

Specifically, how does cisplatin stop DNA from replicating?

A

Both chloride ion ligands in cisplatin are replaced when a nitrogen atom on a guanine base in DNA forms a coordinate bond with the central Pt(II) ion (a ligand substitution reaction)

115
Q

Describe the ligand substitution reaction in which cisplatin stops DNA from replicating

A

Both chloride ion ligands in cisplatin are replaced when a nitrogen atom on a guanine base in DNA forms a coordinate bond with the central Pt(II) ion

(NOTE: the guanine molecules can be from the same strand or opposte strands in the DNA)

116
Q

Why do nitrogen atoms on a guanine base replace chloride ion ligands?

A

They replace chloride ions because they are better ligands

117
Q

What effect does the presence of the cisplatin complex bound to the DNA strands have?

A

Causes the strands to kink, preventing it from unwinding and being copied - in turn preventing cells from replicating

118
Q

What is the effect of cisplatin bonding to DNA in healthy cells?

A

It stops healthy cells from replicating, as it does cancerous cells - problem for cells that frequently replicate

119
Q

What are the adverse effects of cisplatin?

A
  • hair loss
  • suppress immune system
  • kidney damage
120
Q

Why is the effect of cisplatin greater on cancer cells that on normal cells?

A

Cancer cells replicat much faster than normal cells

121
Q

Why is cisplatin still used as an anticancer drug, although it has some adverse effects?

A

The long-term positive side effects outweight the short term negative effects

122
Q

How can side effects of cisplatin be minimised?

A
  • using low dosages
  • targeting the tumour directly - method that delivers drug directly to the cancer cells preventing the chances of it attacking healthy cells

AQA A Level Organic Chemistry (16 decks)

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