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Chemistry > 3.13 amino acids > Flashcards

3.13 amino acids Flashcards

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1
Q

what two groups do amino acids contain

A

an amine group and a carboxylic acid group

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2
Q

what are the amino and carboxylic acid group attached to in alpha amino acids

A

the same carbon

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3
Q

why are amino acids amphoteric

A

they react with acids and bases

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4
Q

what happes to an amino acid when it reacts with an acid

A

the lone pair on the N of the NH2 group accepts a H+ ion

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5
Q

when happens to an amino acid when it reacts with a base

A

the lone pair on the OH- of the base takes the H off to COOH group to leave COO- and H2O

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6
Q

isoelectric point

A

the pH at which the molecule has no net electrical charge

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7
Q

what does the amino acid exist as at the isoelectric point

A

a dipolar ion or zwitter ion

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8
Q

when do zwitterions form

A

when the carboxyl group of one amino acid donates a proton to the amine group of another amino acid molecule

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9
Q

what is the pH of a zwitterion the same as

A

its isoelectric point

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10
Q

how does an amino acid behave at a pH that is lower than its isoelectric point

A

as a base and accepts H+ ions

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11
Q

how does an amino acid behave at a pH that is higher than its isoelectric point

A

as an acid and donates H+ ions

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12
Q

what is the structure of an amino acid

A

crystalline solids

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13
Q

what do amino acids have as a result of their crystalline structure

A

relatively high melting points

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14
Q

what do zwiterions form with eachother that require a lot of energy to break

A

ionic bonds

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15
Q

what do amino acids dissolve well in

A

water

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16
Q

what do amino acids dissolve poorly in

A

non polar solvents

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17
Q

why do amino acids dissolve readily in polar solvents

A

the zwitterions react with polar solvent molecules

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18
Q

what is a peptide

A

a compound made of amino acids joined by peptide links

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19
Q

how are peptide links formed

A

in a condensation reaction between amino acids

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20
Q

what is removed in a condensation reaction between amino acids

A

water

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21
Q

what are the remains of an amino acid after a condensation reactions called

A

an amino acid residue

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22
Q

how can two different amino acids join together

A

in two different ways to give two different dipeptides

eg alanine and glycine- ALAGLY/GLYALA

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23
Q

in what conditions can peptides be hydrolysed under

A

acidic or alkaline

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24
Q

acid hydrolysis: reagents:

A

dilute acid

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25
Q

acid hydrolysis: conditions:

A

heat and reflux

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26
Q

acid hydrolysis: products

A

amino acids but with NH3+ group

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27
Q

alkaline hydrolsis: reagents:

A

dilute alkali

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28
Q

alkaline hydrolsis: conditions:

A

heat and reflux

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29
Q

alkaline hydrolsis: products

A

amino acids but with COO- group

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30
Q

what does the structure of the products in acid and alkali hydrolysis depend on

A

the pH of the hydrolysis mixture

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31
Q

how can the mixture of amino acids be separated after hydrolysis

A

TLC

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32
Q

what do different amino acids have

A

different sidechains

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33
Q

what is chosen to separate the amino acids in tlc

A

a suitable stationary phase

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34
Q

how can separated amino acids be seen in tlc

A

if plate is sprayed with ninhydrin

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35
Q

when can 2D tlc be used to separate amino acids

A

if the two amino acids have very similar Rf values in a particular solvent

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36
Q

2D TLC: what shape is the plate thats used

A

square

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37
Q

2D TLC: where is the mixture spotted

A

in one corner and a chromatogram is run in the usual way so spots are separated along one edge of the plate

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38
Q

2D TLC: how many degrees is plate turned

A

through 90 degrees

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39
Q

2D TLC: what happens aafter tlc plate has been turned 90 degreen

A

the chromatogram is run again with a different ssolvent

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40
Q

what does 2D TLC give

A

2 rf volues for each spot (one for each slvent)

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41
Q

what are proteins

A

naturally occuring polymers of amino acids

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42
Q

what are amino acids usually joined by

A

a peptide link

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43
Q

what 3 levels of structure do all proteins have

A

primary, secondary and tertiary

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44
Q

what do proteins with more than one polypeptide chain also have

A

quaternary structure

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45
Q

primary structure

A

the sequence of amino acids in a protein chain

46
Q

how can the primary structure be resprested

A

using the sequence of 3 letter codes for the amino acid residues in the chain

47
Q

what is the primary structures stbaility

A

relatively stable

48
Q

secondary structure

A

a regular 3d structure formed by part of a protein chain such as an a helix or b pleated sheet

49
Q

how is the secondary structure of proteins held together

A

by h bonding between the delta + H of one peptide link and the lp O of an adjacent peptide linkq

50
Q

why is secondary structure disrupted more easily thn primary

A

h bonds much weaker than covalent bonds

51
Q

tertiary structur

A

3d arrangement of a single polypeptide chain

52
Q

what is the tertiary strucure held together by

A

VDWs and H bonds AND IONIC BONDS AND DISULPHIDE BONDS

53
Q

where do VDWs forces form in teritary structure

A

between non polar amino acid side chains such

54
Q

where do h bonds form in tertiary structure

A

between C=O and n-h groups in back bone of protein and between side chains containg groups such as OH

55
Q

where do ionic bods form in tertiary structure

A

between amino acid side chains containing charrrged groups eg NH3+ and COO-

56
Q

where do disulphine bonds form in tertiary structure

A

link different part of protin chain together and help stabilise the teritary structure

57
Q

s-s bonds

A

a covalent bond formed from the thiol groups of a pair of cysteine residues

58
Q

enzymes

A

a protein based catalyst, whihc speeds up te rate of a particular reaction in a living organism

59
Q

substrate

A

the compound that an enzyme acts upon

60
Q

what is the region responsible for an enzymes catalytic activity called

A

an active site

61
Q

which molecules can fit the enxymes active site and bind to the enzyme

A

only substrate molecules wit a correct stereochemistry

62
Q

stereopecificity

A

active site can be so selective of the substrate shape that many enzymes only catalyse the reaction of one enantiomer of an optically active compund

63
Q

what does substrate bind to active site using a combination of and what is this called

A

VDW, dipole dipole, h bonds and ionic

lock and key hypothesis

64
Q

What does the induced fit model state that the substrate binding to the active side induces a change in

A

The shame of the active site to allow the substrate to fit perfectly

65
Q

Induced fit model: bonds between enzyme and substrate promote

A

Movement of electrons within the substrate

66
Q

Induced fit model: what does movement of electrons in substrate make easier

A

Breaking and forming bonds

67
Q

Induced fit model: what does ease of breaking and forming bonds lower

A

Activation energy for enzyme catalysed reaction

68
Q

What can lactic acid be oxidised using

A

An enzyme catalase LDH

69
Q

Equation for oxidation of lactic acid

A

H3COHHCOOH > CH3=O HCOOH

70
Q

Why does lactic acid have two enantiomers

A

Due to the presence of a chiral C atom

71
Q

Why can LDH only bind to one of the enantiomers of lactic acid

A

It’s stereospecific

72
Q

What does an inhibitor have a similar shape to

A

The substrate

73
Q

What is the inhibitor able to do due to it being a similar shape to the substrate

A

Bind to the active site and prevent the substrate from binding

74
Q

What does amount of inhibition depend on

A

Relative concs if inhibitor and substrate

75
Q

How do many drugs act

A

By inhibiting the activity of an enzyme that catalyses a harmful reaction

76
Q

What is the modern day drug design known as

A

Structure directed drug design

77
Q

Structure-directed drug design: how can tertiary structure of enzymes be determined

A

Using x Ray crystallography, NMR and other techniques

78
Q

Structure-directed drug design: how else is it possible to predict the tertiary structure from an enzymes primary structure

A

Using computer modelling

79
Q

Structure-directed drug design: what can information about the structure of the active sign be used for

A

To design inhibitor molecules, again using computer modelling

80
Q

What is DNA

A

Deoxyribonucleic acid

81
Q

DNA is a polymer of four different

A

Nucleotides

82
Q

What 3 components is each nucleotide made up of

A
  • phosphate ion
  • pentose sugar (2-deoxyribose)
  • base
83
Q

What are the 4 bases in DNA

A

Adenine, guanine, cytosine and thymine

84
Q

What does formation of nucleotides involve

A

Condensation reactions

85
Q

Nucleotides: what does the phosphate ion bond to and what is eliminated

A

Phosphate ion bonds to deoxyribose and water is eliminated

86
Q

Nucleotides: what does the organise base bond to and what is eliminated

A

Deoxyribose and water is eliminated

87
Q

What are polynucleotides

A

Condensation polymers of nucleotides

88
Q

How are phosphodiester bonds formed

A

The phosphate group of one nucleotide joins to the sugar of another nucleotide

89
Q

What back bone does a polynucleotide have

A

Sugar phosphate

90
Q

Where do the organic bases attach in polynucleotides

A

To the sugars

91
Q

Single strand of DNA

A

Polynucleotide

92
Q

What does DNA exist as

A

Two polynucleotide standards in the form of a double helix

93
Q

DNA structure: what are the two strands held together by

A

H bonds between pairs of bases

94
Q

How many h bonds form between A and T

A

2

95
Q

How many h bonds form between cytosine and guanine

A

3

96
Q

Why does the H bonding between base pairs lead to a double helix with complementary strands

A
  • only thymine has correct atoms in right place to H bind with adenine
  • only guanine has correct atoms in right position to H bond to cyctosine
97
Q

Why are other base pair combinations not possible

A

They wouldn’t place atoms at the correct distance or in correct alignment to H bond properly

98
Q

Genetic code: what does a sequence of bases in certain sections of DNA hold the code for

A

The amino acid sequence of certain proteins

99
Q

Genetic code: when do the two strands of the double helix separate

A

When the DNA is transcribed to make an mRNA template for protein synthesis/replicated during cell division

100
Q

Genetic code: whu does strand separation occur without breaking the polynucleotide chain

A

Because the H bonds between the strands are weaker than the covalent bonds between nucleotides

101
Q

What is cisplatin a complex of

A

Platinum (II)

102
Q

How to remember structure of cisplatin

A

Cis means 2 Cl groups and 2 NH3 groups are together

103
Q

What effect does cisplatin have when it binds to DNA

A

Blocks DNA replication and transcription and triggers programmed cell death

104
Q

Mechanism for hydrolysis of cisplatin

A

[PtCl2(NH3)2] <> [PtCl(H2O)(NH3)2]+ + Cl-

105
Q

Second step in mechanism of action of cisplatin

A

Ligand substitution reaction occurs between a nitrogen atom in a guanine base and the platinum ion

106
Q

Third step in mechanism of action of cisplatin

A

Second nitrogen atom from a nearby guanine bonds to the platinum by replacing the chloride ligand

107
Q

Fourth step in mechanism of action of cisplatin

A

Cisplatin complex causes DNA double helix to kink

Means DNA can’t unwind and can’t be copied coorectly. Damage to DNA triggers apoptosis

108
Q

Why does cisplatin have side effects

A

It binds to DNA in normal cells as well as cancer wells

109
Q

What do patients having chemotherapy also experience

A
  • hair loss
  • immune suppression
  • anaemia
110
Q

How can the side effects of chemotherapy be reduced

A

By using the lowest possible dose of cisplatin and by targeting delivery of the drug directly to the cancer cells in

Chemistry (42 decks)

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