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organic chemistry bsc > Molecules of life > Flashcards

Molecules of life Flashcards

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1
Q

what type of amino acids are usually found in nature

A

alpha amino acids

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2
Q

how many different r groups are there

A

20

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3
Q

define chiral

A

Chiral compounds have non-superimposable mirror images called
enantiomers

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4
Q

what are amino acid enantiomers labelled as

A

Amino acid enantiomers are labelled as D and L (small capital letters)

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5
Q

what determines if the enantiomers are L or D

A

The D enantiomer rotates polarised light clockwise (dextro) (+) the L enantiomer of rotates polarised light anticlockwise (laevo) (-).

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6
Q

which natural amino acid is not found in its L form

A

glycine

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7
Q

what are the general properties of amino acids

A

The amino group is basic (pKa ~ 9-10), and the carboxylate group is acidic (pKa ~ 2)
At physiological pH (~ 7.4), amino acids exist as zwitterions or dipolar ions

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8
Q

what are the names of the 9 non-polar amino acids

A

glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tryptophan

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9
Q

what are the names of the 6 uncharged polar side chains

A

serine, threonine, asparagine, glutamine, tyrosine and cysteine

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10
Q

what are the names of the 5 charged polar side chains

A

lysine, arginine, histidine, aspartic acid, glutamic acid

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11
Q

what is the 3 and 1 letter code for glycine

A

3 letter Gly
1 letter G

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12
Q

what are the 3 and 1 letter codes for alanine

A

3 letter Ala
1 letter A

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13
Q

what is the 3 and 1 letter code for valine

A

3 letter Val
1 letter V

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14
Q

what is the 3 and 1 letter code for leucine

A

3 letter Leu
1 letter L

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15
Q

what is the 3 and 1 letter code for isoleucine

A

3 letter ile
1 letter i

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16
Q

what is the 3 and 1 letter code for methionine

A

3 letter met
1 letter M

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17
Q

what is the 3 and 1 letter code for proline

A

3 letter Pro
1 letter P

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18
Q

what is the 3 and 1 letter code for phenylalanine

A

3 letter Phe
1 letter F

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19
Q

what is the 3 and 1 letter code of tryptophan

A

3 letter Trp
1 letter W

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20
Q

what is the 3 and 1 letter codes for serine

A

3 letter ser
1 letter S

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21
Q

what is the 3 and 1 letter codes for threonine

A

3 letter code Thr
1 letter code T

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22
Q

what is the 3 and 1 letter codes for asparagine

A

3 letter Asn
1 letter N

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23
Q

what is the 3 and 1 letter codes for glutamine

A

3 letter Gln
1 letter Q

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24
Q

what is the 3 and 1 letter codes for tyrosine

A

3 letter tyr
1 letter Y

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25
Q

what is the 3 and 1 letter codes for cysteine

A

3 letter cys
1 letter C

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26
Q

what are disulfide bonds and what can they connect

A

Disulfide bond are formed between the thiol (-SH) groups of cysteine residues – they occur most commonly in extracellular
proteins. Disulphide bonds can connect Cys residues in the same peptide chain (intra-chain) or link different peptide chains (inter-chain).

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27
Q

what is the 3 and 1 letter code for lysine

A

3 letter lys
1 letter K

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28
Q

what is the 3 and 1 letter codes for arginine

A

3 letter Arg
1 letter R

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29
Q

what is the 3 and 1 letter codes for histidine

A

3 letter his
1 letter H

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30
Q

what is the 3 and 1 letter code for aspartic acid

A

3 letter asp
1 letter D

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31
Q

what is the 3 and 1 letter code for glutamic acid

A

3 letter Glu
1 letter E

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32
Q

what are D amino acids used for

A

bacterial polypeptides; enzymatically synthesized rather than ribosomally synthesized (stable to peptidases)

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33
Q

what happens when two amino acids react together

A

the reaction of two amino acids is a condensation reaction with the elimination of water to produce a dipeptide, this results in an amide/peptide bond formation. The reaction is very slow without an enzyme catalyst or chemical activation

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34
Q

what is the difference between peptides and proteins

A

peptides have between 2-50 amino acids whereas proteins have more than 50 amino acids

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35
Q

what are the two sides of an amino acid called

A

N - terminus
C - terminus

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36
Q

what is the structure of an amide bond

A

peptide/ amide bonds are sp2 hybridised (trigonal planar) with partial double bond character.
the peptide unit is nearly always trans
the bonds between the alpha carbon and the carbonyl and the alpha carbon and the nitrogen are pure single bonds which are free to rotate
small peptides form flexible chains

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37
Q

where is rotation possible in peptides

A

rotation only possible about 2 bonds on the main chain
alpha carbon - carbon
alpha carbon - nitrogen

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38
Q

how is an alpha helix formed

A

The a helix is a rod like structure
The peptide main chain forms the inner part of the rod, the side chains extend out from the rod
Stabilised by hydrogen bonds between every main chain C=O and the N-H group four residues ahead in the sequence
Can have left or right handed turn – right handed in proteins

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39
Q

what is a beta sheet and how is it formed

A

The b sheet is made from almost fully
extended peptide chains called b
strands. The structure is stabilised by hydrogen
bonds between strands. Strands can run in the same direction (parallel sheet) or opposite
(antiparallel sheet)
Structures with 2-5 strands per sheet
are common

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40
Q

what is a beta turn

A

secondaryprotein structure characterized by a tight turn of the polypeptide chain. it ususally involves 4 amino acid residues and often helps to reverse the diraction of the protein chain. they are crutial for protein folding and stability

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41
Q

where are disulphide bonds found and what do they do

A

Disulfide bonds are formed between
two cysteine residues
Disulfide bonds from crosslinks within
the peptide backbone or peptide chains

42
Q

how doe we determine the primary structure of proteins

A

chemical degradation

43
Q

what is chemical degradation and how does it work

A

Acid hydrolysis (6M HCl, heat up to 100-110C for >24 hr)followed by amino acid analysis gives the amino acid composition
The amino acids are reacted with a chromogenic or fluorescence label then identified by HPLC or ion exchange chromatography / comparison with standard

44
Q

what is edman sequencing

A

The N terminal amino acid residue reacts with phenyl isothiocyanate, treatment with two different acids produces a phenyl thiohydantoin (PTH)
Analysis of PTH derivative by highperformance liquid chromatography reveals the amino acid at this position
The process can be repeated until all the amino acid residues are analysed

45
Q

what are the 7 function of proteins and describe these

A
  1. Structural – form bigger structures, involved in movement and organisation
  2. Storage – biological reserves of metal ions and amino acids
  3. Transport – moving essential molecules (e.g. O2)
  4. Enzymes – catalyse chemical reactions e.g. bond forming, bond breaking, oxidation, and reduction
  5. Signalling – required for information processing within cells
  6. Antibodies – bind to foreign matter in vivo
  7. Transcription factors – bind to specific sites on DNA and are involved in gene activation
46
Q

what does GFP stand for and why is it used

A

green fluorescent protein it is used to tag other proteins and make them visible

47
Q

What does GPCRs stand for and what do they do

A

G-protein coupled receptors
they are transmembrane receptors that sense a molecule outside a cell and produce a signal on the inside of the cell
a very large superfamily of proteins
important drug targets

48
Q

what are the 5 techniques of purifying proteins

A
  1. ultracentrifugation
  2. gel filtration chromatography
  3. ion-exchange chromatography
  4. affinity chromatography
  5. gel electrophoresis
49
Q

outline centrifugation

A

Centrifugation separates biological
macromolecules on the basis of their relative
buoyancy
Samples are spun at high speed on a short rotor producing a
centrifugal force

50
Q

outline gel filtration chromatography

A

gelfiltration chromatography is used to separate molecules based on size. The sample passes thrrough a column packed with porous beads and therefor takes longer to travel through the column while larger molecules move quickly

51
Q

outline affinity chromatography

A

Proteins can be separated on the basis of a
specific interaction with another molecule
bound to a column of beads
Proteins that interact stick to the beads, others
do not and are washed off
Purified protein is then released from the
column

52
Q

outline ion exchange chromatography

A

Proteins can be separated on the basis of their
net charge by ion exchange chromatography
Proteins with a net positive charge bind to a
column of beads containing carboxylate groups
Proteins are eluted with increasing
concentrations of sodium chloride solution
Proteins with the least charge elute first, highly
charged proteins last

53
Q

outline gel electrophoresis

A

Charged molecules move in an electric field – electrophoresis
The velocity of migration (v) depends on the field strength (E), the net charge on the protein (z) and on the radius of the sphere (r) and the viscosity of the medium (h)
The medium used is PolyAcrylamide Gel
This can be used to separate DNA, RNA, and proteins.

54
Q

what is denaturing SDS PAGE

A

denaturing SDS-PAGE is a method to separate proteins based on their molecular weight. it involves denaturing using SDS which unfolds them and gives them a uniform negative chare. the proteins are then separated on a polyacrylic gel matrix by applying an electric current. small proteins migrate faster toward the positive while larger ones move slowly

55
Q

outline mass spectroscopy

A

The proteins samples are mixed with an organic acid and then dried on a metal
target.Light from a laser ionizes the proteins, which “fly” down a tube to a detector.
Their time of flight is inversely proportional to their mass and directly proportional to the charge on the protein.

56
Q

outline x-ray crystallography

A

A beam of X-rays is shone through the crystal
Part of the beam is scattered or diffracted by
the electrons of each atom in the crystal
The diffraction pattern can be used to
determine the precise location of each atom in
the crystal

57
Q

which bases of purine

A

adenine guanine

58
Q

which bases are pyrimidine

A

uracil, thymine and cytosine

59
Q

what is a nucleoside

A

base and sugar
if adenine is the base the nucleoside is adenosine

60
Q

what is a nucleotide

A

nucleoside and phosphate

61
Q

how are nucleotides linked

A

Nucleotide residues of nucleic acids
are linked by a phosphodiester
backbone
*The phosphate group links the 3’-OH
of one sugar to the 5’-OH of the next
polyanionic at physiological pH

62
Q

which way is the stand written

A

the strand is written from 5 prime to 3 prime

63
Q

how many hydrogen bonds between A and T

A

2

64
Q

how many hydrogen bonds between G and C

A

3

65
Q

forces within the double helix

A
  1. Hydrogen Bonds: Hydrogen bonding between base
    pairs.
  2. Stacking Interactions: van der Waals forces between
    base pairs.
  3. Hydrophobic effects: burying hydrophobic purine
    and pyrimidines within the helix increases stability.
  4. Charge-charge interactions: Electrostatic repulsion
    of the negatively charged phosphates is minimised
    by the presence of ions e.g. Mg2+, and proteins
66
Q

what is the structure of RNA

A

RNA is made of 4 ribonucleotides: G, C, A, U
Can form base pairs G-C and A-U
RNA can hybridise with DNA forming G-C, A-T
and U-A base pairs
Usually single stranded but can form double
helices including a hairpin loop

67
Q

what is the relative stability of DNA

A

DNA is stable to hydrolysis in aqueous solution
Anionic phosphate ester groups repel any
negatively charged nucleophile

68
Q

what is the relative stability of RNA

A

RNA contains a hydroxyl group at the 2 prime position of its ribose sugar making it more susceptibal to hydrolysis compared to DNA

69
Q

what are the 4 important nucleotide derivatives and what are they used for

A

coenzyme A - fatty acid synthesis, enzyme production
ATP - chemical energy in cells
S-adenosyl methionine - cofactor used in enzymes
nicintinamide adenine dinucleotide - cofactor used in many enzymes for redox

70
Q

how is DNA organised

A

DNA is compactly packaged inside the cell, wrapped around histone proteins, and organised into structures called chromosomes
DNA contains the coded instructions that govern life. The code is split into smaller chunks called genes

71
Q

what is the human genome project

A

International team of scientists working together to decode the human genome
World’s largest collaborative biological project. First draft sequence published in 2001, completed 2003
3 billion nucleotides, appx 30,000 genes 98% of our genome is non-coding DNA

72
Q

what is the importance of DNA packaging

A

Packaging enables the long DNA strands to be physically accommodated within a small space in the nucleus.
Packaging serves to protect the genetic material from damage e.g. by UV radiation and oxidative agents.
Packaging regulates access by the transcription machinery to portions of the chromosome.
DNA needs to unwinds off the nucleosome for replication and transcription to occur

73
Q

what is a gene

A

a sequence that codes for a functional molecule

74
Q

how is DNA controlled

A

Every cell in the body contains the same DNA sequence
Specific genes can be switched on and off, allowing for different genes to be
expressed (epigenetics)

75
Q

what is semi-conservative replication

A

One of the stands of each daughter DNA
molecule is newly synthesised the other comes
from the parent

76
Q

outline the experiment which proves semi-conservative replication

A

The experiment that proved this used the 15N
isotope of nitrogen to label DNA in growing
bacteria
The bacteria were transferred to medium
containing the 14N isotope, After one generation the DNA contained half 15N
and half 14N. After a second generation half of the DNA was the 15N and 14N hybrid, the other half was 100% 14N containing

77
Q

what does DNA helicase do

A

unwinds the DNA strand

78
Q

what does DNA polymerase do

A

makes new DNA strand
It catalyses the step-by-step addition of deoxyribonucleotide
units to a growing DNA chain

79
Q

what does RNA primase do

A

makes RNA primers on the lagging strand

80
Q

what does RNase H do

A

removes RNA primers

81
Q

what does DNA ligase do

A

joins the okazaki fragments to create one continuous strand

82
Q

what 5 activated precursors are needed for dna polymerase to work

A

dATP, dGTP, dTTP and dCTP and Mg2+ to work

83
Q

how is chain elongation reaction works

A

DNA polymerase adds deoxyribonucleotide units to the 3’-hydroxyl group of a DNA chain – this is called the primer
A DNA template is essential – this can be single or double stranded if it contains breaks in the
phosphate backbone
The reaction is a nucleophilic attack of the 3’-OH terminus of the primer DNA on the innermost phosphorus atom of a deoxynucleoside triphosphate
The reaction releases a diphosphate unit which is hydrolysed by inorganic pyrophosphatase – this provides the energy for the reaction

84
Q

what are the three steps of PCR

A

Strand separation – the two strands of DNA are separated by heating
Hybridisation of primers – short strands of DNA flanking the 3’ ends of both strands
of DNA are hybridised to the sequences
DNA synthesis – DNA polymerase is added and elongation of both primers occurs

85
Q

what are the applications of PCR

A

The PCR process can be repeated over many cycles to amplify a sequence 20 cycles
This can be used to diagnose diseases, e.g. HIV or tuberculosis, by amplifying and
detecting viral or bacterial DNA sequences
PCR is used in genetic fingerprinting for forensics. DNA isolated from human
samples at a crime scene can be amplified. Dinosaur DNA can be amplified from insects trapped in amber – but the sequences
are too short to be useful

86
Q
A
87
Q

summarize the structure of RNA

A

Ribose (2’-OH)
RNA is made of 4 ribonucleotides: G, C, A, and U
Can form base pairs G-C and A-U
Usually single stranded but can form
double helices including a hairpin loop

88
Q

outline the uses of mRNA

A

mRNA is a short lived molecule
Its base sequence reflects the DNA sequence
mRNA is complementary to its DNA template
mRNA varies in length depending on the gene
The synthesis of mRNA is called transcription

89
Q

how does the RNA polymerase know where to start or stop

A

DNA templates contain promoter sites that bind to RNA polymerase and position it in the correct place to start synthesis
These are on the 5’ side of the DNA (upstream)
Specific DNA sequences stop the synthesis

90
Q

describe the features of the genetic code

A

The genetic code (right) is a non overlapping, comma free, degenerate, triplet code.
Only Met and Trp, two of the least common amino acids in proteins, are specified by a single codon.

91
Q

what is the process of translation

A

The ribosome uses the instructions
from the mRNA and builds a new
protein. The ribosome uses activated amino
acids which are attached to transfer
RNA (tRNA). The ribosome has space for two
tRNA units and catalyzes the
formation of a new peptide bond
between the two amino acids

92
Q

what happens when amino acids are activated

A

Amino acid is activated by reaction
with ATP to form aminoacyl-adenylate
Mixed anhydride then reacts with
tRNA to form aminoacyl-tRNA and
AM

93
Q

what are the common features of transfer RNA

A
  1. Single chains of 73-93 nucleotides
  2. They contain unusual bases
  3. The 5’ end is phosphorylated
  4. The base sequence at the 3’ end is CCA.
    The activated amino acid is attached
    using an ester group to the 3’OH of the
    ribose unit.
  5. Base pairing within tRNA produces a
    distinctive structure with an anti-codon
    loop that recognises the mRNA template.
94
Q

how is tRNA recycled by tRNA synthetases

A

tRNA is recycled by a group of enzymes that
recognise the specific tRNA and add a new
amino acid unit
Each amino acid has it’s own synthetase
These are highly specific reactions
The enzyme must be able to recognise the
matching tRNA and the incoming amino
acid which may only differ by a CH2 group

95
Q

what is the processes involved in protein unfolding

A

conformational entropy
H-bonding to water
+190kCal/mole

96
Q

what is the processes involved in protein folding

A

hydrophobic collapse
intramolecular H-bonding
van der waals interactions
-200kCal/mole

97
Q

how do proteins fold

A

proteins do not fold randomly
protein folding goes through two stages
- hydrophobic collapse to molten globule
- progressive stabilization form in the molten globule at multiple points

98
Q

why do genes mutate and become damaged

A

Inheritance – mutated genes can be inherited from parental genes
Ageing – the normal process of DNA replication during cell division can introduce errors
Environmental Damage
- Radiation – UV and ionising radiation damages DNA
- Chemicals – some chemicals can react covalently with DNA causing damage

99
Q

what is a germline mutations

A

Germline mutations
(Inheritable) – mutations
occur in gametes and passed
onto offspring

100
Q

what is a somatic mutations

A

Somatic mutations (cannot
be inherited) – mutations
occur in a single body cell

101
Q

what happens when genes mutate and become damaged

A
  • Change of DNA sequence – changes protein
    sequence e.g. BRAF
  • Modifications to control regions of genes – altered gene expression
  • Gene deletions – result in severe mental and
    physical disabilities e.g. Prader Willi syndrome
  • Extra genes – result in mental and physical differences e.g. Down’s syndrome (Trisomy 21)
  • Chromosome breakage and translocation – results in mutant genes
102
Q

what are the type of micro mutations within genes

A

Silent – code is degenerate
Missense – codes for another amino acid
Nonsense – codes for STOP
Frameshift – deletion or insertion of one base
changes the meaning of the DNA downstream

organic chemistry bsc (5 decks)

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