3.13 amino acids Flashcards
1
Q
what two groups do amino acids contain
A
an amine group and a carboxylic acid group
2
Q
what are the amino and carboxylic acid group attached to in alpha amino acids
A
the same carbon
3
Q
why are amino acids amphoteric
A
they react with acids and bases
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
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
6
Q
isoelectric point
A
the pH at which the molecule has no net electrical charge
7
Q
what does the amino acid exist as at the isoelectric point
A
a dipolar ion or zwitter ion
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
9
Q
what is the pH of a zwitterion the same as
A
its isoelectric point
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
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
12
Q
what is the structure of an amino acid
A
crystalline solids
13
Q
what do amino acids have as a result of their crystalline structure
A
relatively high melting points
14
Q
what do zwiterions form with eachother that require a lot of energy to break
A
ionic bonds
15
Q
what do amino acids dissolve well in
A
water
16
Q
what do amino acids dissolve poorly in
A
non polar solvents
17
Q
why do amino acids dissolve readily in polar solvents
A
the zwitterions react with polar solvent molecules
18
Q
what is a peptide
A
a compound made of amino acids joined by peptide links
19
Q
how are peptide links formed
A
in a condensation reaction between amino acids
20
Q
what is removed in a condensation reaction between amino acids
A
water
21
Q
what are the remains of an amino acid after a condensation reactions called
A
an amino acid residue
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
23
Q
in what conditions can peptides be hydrolysed under
A
acidic or alkaline
24
Q
acid hydrolysis: reagents:
A
dilute acid
25
acid hydrolysis: conditions:
heat and reflux
26
acid hydrolysis: products
amino acids but with NH3+ group
27
alkaline hydrolsis: reagents:
dilute alkali
28
alkaline hydrolsis: conditions:
heat and reflux
29
alkaline hydrolsis: products
amino acids but with COO- group
30
what does the structure of the products in acid and alkali hydrolysis depend on
the pH of the hydrolysis mixture
31
how can the mixture of amino acids be separated after hydrolysis
TLC
32
what do different amino acids have
different sidechains
33
what is chosen to separate the amino acids in tlc
a suitable stationary phase
34
how can separated amino acids be seen in tlc
if plate is sprayed with ninhydrin
35
when can 2D tlc be used to separate amino acids
if the two amino acids have very similar Rf values in a particular solvent
36
2D TLC: what shape is the plate thats used
square
37
2D TLC: where is the mixture spotted
in one corner and a chromatogram is run in the usual way so spots are separated along one edge of the plate
38
2D TLC: how many degrees is plate turned
through 90 degrees
39
2D TLC: what happens aafter tlc plate has been turned 90 degreen
the chromatogram is run again with a different ssolvent
40
what does 2D TLC give
2 rf volues for each spot (one for each slvent)
41
what are proteins
naturally occuring polymers of amino acids
42
what are amino acids usually joined by
a peptide link
43
what 3 levels of structure do all proteins have
primary, secondary and tertiary
44
what do proteins with more than one polypeptide chain also have
quaternary structure
45
primary structure
the sequence of amino acids in a protein chain
46
how can the primary structure be resprested
using the sequence of 3 letter codes for the amino acid residues in the chain
47
what is the primary structures stbaility
relatively stable
48
secondary structure
a regular 3d structure formed by part of a protein chain such as an a helix or b pleated sheet
49
how is the secondary structure of proteins held together
by h bonding between the delta + H of one peptide link and the lp O of an adjacent peptide linkq
50
why is secondary structure disrupted more easily thn primary
h bonds much weaker than covalent bonds
51
tertiary structur
3d arrangement of a single polypeptide chain
52
what is the tertiary strucure held together by
VDWs and H bonds AND IONIC BONDS AND DISULPHIDE BONDS
53
where do VDWs forces form in teritary structure
between non polar amino acid side chains such
54
where do h bonds form in tertiary structure
between C=O and n-h groups in back bone of protein and between side chains containg groups such as OH
55
where do ionic bods form in tertiary structure
between amino acid side chains containing charrrged groups eg NH3+ and COO-
56
where do disulphine bonds form in tertiary structure
link different part of protin chain together and help stabilise the teritary structure
57
s-s bonds
a covalent bond formed from the thiol groups of a pair of cysteine residues
58
enzymes
a protein based catalyst, whihc speeds up te rate of a particular reaction in a living organism
59
substrate
the compound that an enzyme acts upon
60
what is the region responsible for an enzymes catalytic activity called
an active site
61
which molecules can fit the enxymes active site and bind to the enzyme
only substrate molecules wit a correct stereochemistry
62
stereopecificity
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
what does substrate bind to active site using a combination of and what is this called
VDW, dipole dipole, h bonds and ionic
lock and key hypothesis
64
What does the induced fit model state that the substrate binding to the active side induces a change in
The shame of the active site to allow the substrate to fit perfectly
65
Induced fit model: bonds between enzyme and substrate promote
Movement of electrons within the substrate
66
Induced fit model: what does movement of electrons in substrate make easier
Breaking and forming bonds
67
Induced fit model: what does ease of breaking and forming bonds lower
Activation energy for enzyme catalysed reaction
68
What can lactic acid be oxidised using
An enzyme catalase LDH
69
Equation for oxidation of lactic acid
H3COHHCOOH > CH3=O HCOOH
70
Why does lactic acid have two enantiomers
Due to the presence of a chiral C atom
71
Why can LDH only bind to one of the enantiomers of lactic acid
It’s stereospecific
72
What does an inhibitor have a similar shape to
The substrate
73
What is the inhibitor able to do due to it being a similar shape to the substrate
Bind to the active site and prevent the substrate from binding
74
What does amount of inhibition depend on
Relative concs if inhibitor and substrate
75
How do many drugs act
By inhibiting the activity of an enzyme that catalyses a harmful reaction
76
What is the modern day drug design known as
Structure directed drug design
77
Structure-directed drug design: how can tertiary structure of enzymes be determined
Using x Ray crystallography, NMR and other techniques
78
Structure-directed drug design: how else is it possible to predict the tertiary structure from an enzymes primary structure
Using computer modelling
79
Structure-directed drug design: what can information about the structure of the active sign be used for
To design inhibitor molecules, again using computer modelling
80
What is DNA
Deoxyribonucleic acid
81
DNA is a polymer of four different
Nucleotides
82
What 3 components is each nucleotide made up of
- phosphate ion
- pentose sugar (2-deoxyribose)
- base
83
What are the 4 bases in DNA
Adenine, guanine, cytosine and thymine
84
What does formation of nucleotides involve
Condensation reactions
85
Nucleotides: what does the phosphate ion bond to and what is eliminated
Phosphate ion bonds to deoxyribose and water is eliminated
86
Nucleotides: what does the organise base bond to and what is eliminated
Deoxyribose and water is eliminated
87
What are polynucleotides
Condensation polymers of nucleotides
88
How are phosphodiester bonds formed
The phosphate group of one nucleotide joins to the sugar of another nucleotide
89
What back bone does a polynucleotide have
Sugar phosphate
90
Where do the organic bases attach in polynucleotides
To the sugars
91
Single strand of DNA
Polynucleotide
92
What does DNA exist as
Two polynucleotide standards in the form of a double helix
93
DNA structure: what are the two strands held together by
H bonds between pairs of bases
94
How many h bonds form between A and T
2
95
How many h bonds form between cytosine and guanine
3
96
Why does the H bonding between base pairs lead to a double helix with complementary strands
- 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
Why are other base pair combinations not possible
They wouldn’t place atoms at the correct distance or in correct alignment to H bond properly
98
Genetic code: what does a sequence of bases in certain sections of DNA hold the code for
The amino acid sequence of certain proteins
99
Genetic code: when do the two strands of the double helix separate
When the DNA is transcribed to make an mRNA template for protein synthesis/replicated during cell division
100
Genetic code: whu does strand separation occur without breaking the polynucleotide chain
Because the H bonds between the strands are weaker than the covalent bonds between nucleotides
101
What is cisplatin a complex of
Platinum (II)
102
How to remember structure of cisplatin
Cis means 2 Cl groups and 2 NH3 groups are together
103
What effect does cisplatin have when it binds to DNA
Blocks DNA replication and transcription and triggers programmed cell death
104
Mechanism for hydrolysis of cisplatin
[PtCl2(NH3)2] <> [PtCl(H2O)(NH3)2]+ + Cl-
105
Second step in mechanism of action of cisplatin
Ligand substitution reaction occurs between a nitrogen atom in a guanine base and the platinum ion
106
Third step in mechanism of action of cisplatin
Second nitrogen atom from a nearby guanine bonds to the platinum by replacing the chloride ligand
107
Fourth step in mechanism of action of cisplatin
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
Why does cisplatin have side effects
It binds to DNA in normal cells as well as cancer wells
109
What do patients having chemotherapy also experience
- hair loss
- immune suppression
- anaemia
110
How can the side effects of chemotherapy be reduced
By using the lowest possible dose of cisplatin and by targeting delivery of the drug directly to the cancer cells in
