Nucleic acids L1 L2 Flashcards
(105 cards)
1
Q
what is the biochemical role of nucleotides
A
Chemical energy (metabolism)
Product of photphosphorylation and cellular respiration
Used by enzymes, and structural proteins and biosynthetic reactions (motility and cell division)
Signal transduction pathways and 2nd messenger systems (cAMP)
2
Q
what is the biochemical role of nucleic acids
A
Fundamental process of information transfer (genetics)
DNA the genetic information within cells
RNA serves in expression of information through transcription and translation (protein synthesis)
3
Q
what is photophosphorylation
A
use of light energy from photosynthesis to provide the energy to convert ADP to ATP
4
Q
what can nucleotides be used by
A
enzymes
structural proteins
biosynthetic reactions
5
Q
what is a nucleoside
A
sugar and base
6
Q
what is a nucleotide
A
sugar, base and phosphate
7
Q
what is a nucleic acid
A
polynucleotides, linear polymers of nucleotides: of sugar, base and phosphate
linked by phosphodiester bridges
8
Q
what joins base and sugar
A
glycosidic bond in beta conformation
9
Q
where is a nucleotide derived from
A
when phosphoric acid is esterified to a sugar OH group of a nucleoside
10
Q
what are the types of nucleic acids
A
DNA
RNA
11
Q
what does a pyrimidine contain
A
6 membered heterocyclic rings containing 2 nitrogen atoms
12
Q
what does a purine contain
A
2 rings of atoms (1 resembling the pyrimidine ring and the other an imidazole ring)
13
Q
which bases are purines
A
adenine
guanine
14
Q
which bases are pyrimidine
A
cytosine
uracil
thymine
15
Q
what is the ribose sugar like
A
5 carbon sugar usually in furanose form
16
Q
what is the deoxyribose sugar like
A
5 carbon sugar usually in furanose form except that on C2’ the OH group replaced with H
17
Q
what is furanose
A
collective term for a 5 membered ring structure, with 4 carbon atoms and one oxygen atom
18
Q
what is the difference between ribose and deoxyribose
A
carbon 2 of deoxyribose the OH group is replaced with a lone hydrogen
19
Q
how is a sugar linked to a purine base
A
linked via a n-glycosyl (glycosidic N) bond between carbon 1 of the sugar and nitrogen 9 of adenosine
20
Q
what happens to adenosine when bound through a glycosidic bond
A
becomes adenonine
21
Q
how is a sugar linked to a pyrimidine base
A
glycosidic N bond, but the bond is situated between carbon 1 of the sugar and nitrogen 1 of the base
22
Q
where are phosphates added on to nucleosides
A
5’ carbon of sugar
23
Q
what linked polynucleotides sugar phosphate backbone
A
phosphodiester bonds
24
Q
what types of DNA are there
A
Some viruses are single stranded DNA
Viruses, bacteria, mitochondria, chloroplasts are double stranded loop
most eukaryotic cells are double stranded linear
25
what was Erwin Chargaffs findings
four bases commonly found in DNA (ATCG) don't occur in equimolar amounts and that the amounts vary across different species
he did note that certain bases paired together lead to base pairing
26
what did Waston and Crick find
took advantage of Chargraffs rule and x-ray diffraction studies on the structure of DNA to conclude that DNA was a complementary double helix
two strands held together by bonding interactions between unique base pairs always consisting of a purine in one strand and a pyrimidine in the other
DNA is essentially 2 antiparallel chains (2 chains that run in opposite directions). The sequence of bases in one DNA strand is complementary to the bases in the other.
27
what is chromatin
DNA and protein
28
what are the 'bead' like structures of chromatin seen under a microscope
Nucleosomes- protein core, DNA wrapped around outside
29
what are the primary functions of chromatin
1) package DNA into a smaller volume to fit in the cell
2) reinforce DNA macromolecule to allow mitosis
3) prevent DNA damage
4) control gene expression and DNA replication
30
what are the primary components of chromatin
histones that compact the DNA
31
where is chromatin found
only in eukaryotic cells (cells with defined nuclei)
32
what is the structure of a chromosome
Nucleosomes folded into a fibre DNA binds round
Fibres organised on structural scaffold as superloops
All the nucleosomes together
33
what makes up a nucleosome
8 histones
34
what are the three main types of RNA
tRNA
rRNA
mRNA
35
what is the structure of RNA
Single stranded molecules but can still base pair to form loops and stems
36
what are examples of single stranded polynucleotides
tRNA
rRNA
mRNA
can base pair to form a number of loops and stems
37
what are the RNAs in E. coli
23S, 16S and 5S rRNA
38
which is the smallest RNA
tRNA 75-90 nucleotides
39
which contains 10% uncommon bases
tRNA
40
what is rRNA structure like
very few uncommon bases
41
rRNA role
major component of ribosomes plays a catalytic and structural role in protein synthesis
42
what determines rRNA size
according to their sedimentation behaviour
sedimentation rate of each subunit is affected by its shape as well as mass ( i.e. sedimentation rate is a measure of how fast the particle settles or sediments)
usually done in a test tube in a centrifuge
svedberg unit offers a measure of particle size based on its rate of travel in a tube subjected to high g force
43
how many mRNAs are there in a cell
many hundreds of different types in each cell
| each only as a few copies
44
mRNA chain structure
very few uncommon bases
45
what is mRNAs heterogenous size population
6S-25S
46
what does mRNA have in its structure
non-coding sequences - introns (intervene coding regions, exons)
Poly A tails (100-200 adenylic acid residues attached) at their 3'
Cap at 5'
47
function of poly A tail
poly A tail makes the RNA molecule more stable and prevents its degradation
48
which is more stable DNA or RNA
DNA is generally more stable
49
what chemical factors affect nucleic acids
pH (both acid and alkali)
enzymes
chemical modification of DNA bases
50
what physical factors affect nucleic acids
heat, (breaks bonds)
UV light
salt concentrations, (manipulating ionic structure – alter physical and chemical properties)
51
how does pH affect nucleic acids
affect ionization of amino acids, can have direct impact on how a protein will interact with another protein
52
how can hydroxyl groups affect nucleic acids
Hydroxyl groups in carbohydrates can ionize (polar functional groups)
53
how can electron cloud dispersion affect nucleic acids
Dispersion of electron clouds, pH could change the spread of electrons
54
what is the problem with compacting the DNA
more difficult to access specific sites
55
what enzyme is used to cut DNA
restriction endonucleases
56
what is an example of a polymeric molecule
DNA
57
when is an oligonucleotide formed
when several phosphodiester bond bonds
58
what are phosphodiester groups at physiological pH (7.4)
each phosphodiester group exists as an anion
59
what are nucleic acids at physiological pH (7.4)
highly charged polyanionic molecules
60
what gives nucleic acid chains directionality
One end of a nucleic acid strand has a 5′-hydroxyl group (primary hydroxyl) and the other end has a 3′-hydroxyl group (secondary hydroxyl)
61
which are the non-covalent interactions
van der Waals
ionic
hydrogen bond
62
which are the covalent bonds
C-C
C=C
hydrolysis of ATP phosphoanhydride bond
63
what holds the anti-parallel DNA strands together
weak bonds between complementary base pairs
64
what can separate a few base pairs
only small amounts of energy are needed to separate a few base pairs, and so, DNA can open up to its
single strand confirmation
65
where are glycosidic bonds
Link between the sugar and base
66
where are phosphodiester bonds
Links between the sugar and phosphate groups
| in the DNA backbone very strong, broken by specific nucleases enzyme
67
where are hydrogen bonds
links between the complementary bases of the two polynucleotide strands relatively weak and can be disrupted by different factors such as heat
68
what temperature will denature DNA
90 degrees C
| called DNA melting
69
how can DNA melting process be followed
spectrophotometrically
| by monitoring the absorbance of the at 260nm
70
what absorbs light in UV region
Nucleotides contain conjugated double bonds
| and these bonds absorb light in the UV region
71
why can single stranded molecules absorb over 260nm
exposure of bases
72
what is the hyperchromic effect
single strand absorbs more than the double stranded as the nitrogenous bases accessible so will absorb more light
means more colour
73
what has a linear response
More conc solution of molecule is the more absorption occurs – linear response
74
what is the Beer Lamberts law
If you have a chemical or a molecule in solution, assuming it has a chromophore (part of its structure will absorb light) if you increasing the concentration of the molecule it will absorb more light
75
in ds DNA what causes a decreased UV absorbance
H-bonds between paired nitrogen bases
in double helix limits resonance behaviour of aromatic ring of the bases = (hypochromic effect)
stacked bases in dsDNA structure facilitate
shielding from light (Conceal or cover up)
results less absorbance
76
why does ss DNA have a higher absorbance
bases of ssDNA are in free form, and no H-bonds exist between
complementary bases which results in 40% higher absorbance in
ssDNA (hyperchromic) at the same concentration
77
how do you calculate the affects of increased temperature on melting point of two substances
normalised absorbance change for specific temperature
absorbance at specific temp - absorbance at room temp / Abs 85 degrees C - absorbance at room temperature
78
how does a lot of CG bases affect thermal stability
Lots of CG = more energy as they can form three hydrogen bonds with their adjacent pair
79
what is a tautomer
molecule that under differing pH conditions a hydrogen atom in the molecule moves from one part to another, if happens in bases it can cause miss matched pairing
80
what will break in mildly acidic conditions
N-glycosyl bond releasing bases from sugar
81
what will break in strongly acidic conditions
(pH 3-4) typically break phosphodiester bonds in both DNA and RNA
Hydrolysing sugar moieties and leaving the bases intact
82
what will break in pH 7-8
alter the tautomeric state of the bases in DNA
83
what will an amino group (-NH2) tautomerize to
imino form (=NH)
84
what will a keto group (-C=O) tautomerize to
enol form (=C-OH)
85
what can tautomers form
non-standard base pairs that fit into the double helix
86
what do purines and pyrimidines exist as
different chemical forms - tautomers
| phenomenon arise due to changes in the position of protons in the bases
87
how do tautomers form
results in the reversal of base pairing rules
88
what can cause purines and pyrimidines to undergo spontaneous alterations
physiological conditions
89
how do some mutagens affect DNA bases
chemically modify causing mis-match
90
what is Xeroderma pigmentosum
inherited condition where thymine-thymine dimers are not repaired
91
what enzymes cleave nucleic acids
exo endonucleases
92
what are exonucleases
cleaves at the ends of a polynucleotide chain
93
what are endonucleases
cleaves within a polynucleotide chain
94
what are nucleases defined by
Substrate (RNA or DNA)
| Product (whether they cut at the 3’ or 5’ end)
95
where do restriction endonucleases typically target
dsDNA substrates and recognise specific base sequence
96
what can the spectral properties of nucleic acids be used for
detection, quantification and assessment of purity
97
what absorption do aromatic amino acids have
280nm max
98
what absorption should pure DNA give
Pure DNA preparations should give an A260nm/280nm ratio of approx. 1.8 (little contamination from other macromolecules)
lower ratios - contamination by proteins
99
what overall charge is DNA
negative
| due to phosphate
100
where will DNA move if there is -ve and +ve electrodes
to +ve as it is -ve
101
how fast does DNA migrate
relative to the size of the DNA fragment (smaller fragments travel faster than larger ones)
102
what happens to DNA in apoptosis
dna is broken down ‘cleaned’, can track the rate of apoptosis in group of cells
103
what is the earliest application of flow cytometry
Cell cycle analysis by quantitation of DNA content
incorporates the use of a DNA-binding dye called propidium iodide (PI)
PI is impermeable to intact membranes,
PI binds to bases in dsDNA and fluoresces
104
what is PCR
technique to amplify a specific region of double-stranded DNA
105
what happens in each PCR cycle
heating to denature double-stranded DNA and cooling to allow annealing of excess primer to template and elongation/extension from the primers by the Taq Polymerase
