nucleotides and nucleic acids Flashcards
(138 cards)
1
Q
elements in nucleotides
A
carbon
hydrogen
oxygen
nitrogen
phosphorus
2
Q
what are nucleotides a monomer of
A
nucleic acids (DNA/RNA)
3
Q
what are nucleotides components of?
A
cofactors (coenzyme NAD/FAD)
ATP,ADP,AMP
4
Q
components of nucleotides
A
phosphate group
pentose (5C) sugar
nitrogenous base
5
Q
describe joining nucleotides together
A
when one nucleotide makes a linkage with another nucleotide the phosphate group which already has one phosphoester bond makes a second ester bond. this is called a phosphodiester bond
6
Q
what is Pi
A
PO4 3-
inorganic ion/inorganic phosphate
7
Q
pentose sugars and where they are found
A
ribose: found in RNA and ATP
deoxyribose: found in DNA
8
Q
purine and pyrimidine bases
A
purine= adenine, guanine
pyrimidine= cytosine, thymine, uracil
9
Q
purine structure
A
5 & 6 sided ring structures
10
Q
pyrimidine structure
A
6 sided rings
11
Q
what are phosphorylated nucleotides
A
ADP and ATP
nucleotides (sugar, phosphate base) with extra phosphate groups
12
Q
ATP properties
A
small molecule, soluble in water as energy-requiring processes occur in solution
relatively unstable so cannot be stored easily therefore constantly made and broken down
releases energy in small quantities
13
Q
property of phosphate bonds in ATP
A
bonds take small amount of energy to break and release relatively more energy in this process
14
Q
when does hydrolysis of ATP occur
A
during energy-requiring processes
15
Q
reverse of hydrolysis of ATP?
A
condendsation/ phosphorylation
16
Q
amount of energy released by first 2 phosphate bonds?
A
30.5kJ mol-1
17
Q
amount of energy released by third phosphate
A
14.2kJ mol-1
18
Q
where is DNA found
A
in nucleus of eukaryotes (chromosomes made of DNA)
in mitochondria and chloroplasts of eukaryotes
found free in cytoplasm, in circular chromosome and plasmids of prokaryotes
found in some viruses
19
Q
DNA function
A
hereditary material of life
made of genes -> code for proteins -> determine characteristics
20
Q
structure of DNA and who discovered it (BRIEF)
A
double helix (Watson and crick 1953)
21
Q
describe DNA double helix
A
composed of 2 antiparallel polynucleotide strands each coiled into a helix
helical chain held together by complementary base pairing of bases of neighbouring chains
2 helices run in opposite directions e.g. antiparallel
22
Q
width of DNA double helix
A
2nm
23
Q
length of 10 base pairs on DNA double helix
A
3.4nm
24
Q
what are DNA bases held together by
A
hydrogen bonds
25
Chargaff's ratio of bases in DNA practical steps
extract DNA (blend cells, add salt, detergent and cold water)
add protease and ice cold ethanol
add strong acid treatment
separate bases via paper chromatography
use spectrophotometry
26
use of spectrophotometry in Chargaff's practical
used to determine the amount of each base as they absorb different wavelengths of light
27
function of protease in chargaffs practical
digests histones
28
function of ice cold ethanol in chargaffs practical
to precipitate
29
function of strong acid treatment in chargaffs practical
hydrolyse DNA and release bases
30
what are the names of the 2 strands of DNA
coding/sense strand
non-coding/antisense strand
31
what does antiparallel mean
2 strands run in opposite directions
32
what does each strand of DNA have at each end
phosphate attached to C5 at one end (5')
an OH group attached to C3 at the other end (3')
33
A pairs with T and C pairs with G. what does this lead to?
gives equal length rungs on DNA ladder as a purine always binds with a pyrimidine
34
what kind of bonds hold the 2 strands together
ease of being broken and why?
hydrogen bonds
can also be broken relatively easily to allow molecule to unzip for transcription and replication (helices enzyme)
35
what do the strong phosphodiester bonds of sugar phosphate backbone mean?
the integrity of the code (sequence of bases) is protected
36
compare ATP and a DNA molecule
DIFFERENCES
DIFFERENCES
ATP has 3 phosphate groups and a nucleotide has only 1
ATP always has adenine, but nucleotide may have adenine, cytosine, thymine, guanine (25% chance)
ATP is a larger molecule
ATP has ribose, DNA nucleotide has deoxyribose
37
compare ATP and a DNA molecule
SIMILARITIES
SIMILARITIES
phosphoester bond
pentose sugar
nitrogenous base
phosphate group
38
RNA structure
single-stranded
ribs sugar
uracil instead of thymine
39
RNA function
involved in protein synthesis
40
3 different types of RNA
messenger RNA
transfer RNA
ribosomal RNA
41
what % of cellular RNA is messenger RNA
5%
42
messenger RNA
structure
made when
copy of what?
where does it go in the cell
long, single-stranded molecule (1000s of nucleotides long)
made in transcription
copy of coding/sense strand (except U replaces T)
passes out of nuclear pore into the cytoplasm
43
where does the amino acid bind to on transfer RNA
the ACC site
anti-codon (binds to codon on mRNA)
44
where is tRNA made?
nucleus
45
what shape does tRNA fold into?
clover leaf shape
46
what on a tRNA molecule determines which amino acid binds?
anti-codon
47
practical: purification of DNA by precipitation
why does experiment need to be ice cold
decrease activity of DNases in cytoplasm (enzyme that catalyses the hydrolytic cleavage of phosphodiester linkages) (present to destroy viral DNA entering cells)
48
practical: purification of DNA by precipitation
purpose of blending
increases surface area exposed to reagents and disrupts cell walls
49
practical: purification of DNA by precipitation
purpose of detergent
break down cell and nuclear membranes
works as emulsifier: attracts phospholipids of membrane
50
practical: purification of DNA by precipitation
purpose of protease
digest histone proteins associated with DNA
51
practical: purification of DNA by precipitation
purpose of salt
causes the DNA to precipitate in ethanol
52
practical: purification of DNA by precipitation
purpose of ethanol
DNA is soluble in water but not ethanol
53
nucleotide structure
54
ATP structure
55
when does DNA replication occur?
what does it lead to?
in interphase: S phase
leads ti creation of sister chromatids
56
when does DNA replication of chloroplasts and mitochondria occur?
just before organelles and cell divide
57
materials required for DNA replication?
enzymes
intact DNA (both strands act as templates)
activated free nucleotides
energy source (ATP)
58
enzymes required for DNA replication
DNA helicase
DNA polymerase
DNA ligase
59
how are nucleotides activated
they are phosphorylated
60
what is ATP needed for in DNA replication
unwinding DNA and activating nucleotides
61
why is DNA replication semi-conservative?
in each new DNA molecule, 1 old strand is conserved and paired with 1 new strand
62
purpose of DNA helicase
breaks hydrogen bonds between complementary bases
63
purpose of DNA gyrase
unwinds DNA
64
purpose of DNA polymerase
catalyses the formation of phosphodiester bonds joining the new nucleotides in the 5' to 3' direction
before adding next nucleotide, it proofreads the previous pair and can correct & repair if needed
65
DNA ligase purpose
joins Okazaki fragments
66
DNA replication step by step
DNA unwinds (gyrase) and unzips due to action of helicase enzyme which breaks the hydrogen bonds between complementary bases, exposing the DNA bases on both template strands
in the nucleus (nucleoplasm), 2 extra phosphates are added to each free DNA nucleotide to activate them
bases of these nucleotides pair up w/ complementary bases on each of the old strands
DNA polymerase enzyme catalyses the formation of phosphodiester bonds joining new nucleotides in the 5' to 3' direction
2 extra phosphates are broken off and released: this hydrolysis reaction supplies the energy to make the phosphodiester bonds
67
leading strand vs lagging strand in DNA replication
leading strand made continuously
lagging strand is made up of Okazaki fragments joined by DNA ligase
68
in which direction does DNA polymerase move
5' to 3' end
69
what is the conservative model of DNA replication
2 new DNA strands occur together in one of the daughter cells
70
what is the dispersive model of DNA replication
new and old DNA occur together but distributed amongst both strands
71
where are the N atoms found in DNA
in nitrogenous bases
72
which scientists' experiment allows us to differentiate between the 3 models of dna replication
key to this experiment?
meselsohn and stahl
the different properties of the 2 isotopes of nitrogen (N14 and N15): N14 is lighter than N15 so we can distinguish between them by their mass
73
how was meselsohn and stahls experiment carried out
bacteria were grown in a medium where their nitrogen source sued to synthesise nucleotides and eventually DNA is ammonium ions NH4+ containing heavy N15. after several generated the DNA in these bacteria is heavy
bacteria placed in fresh medium containing light N14 ammonium ions, allowed to divide once so produce generation 1
some allowed to divide again run N14 to produce generation 2
isolate and separate DNA form each regeneration and use centrifugation
74
what is centrifugation
separating molecules based on their density
75
if DNA replication is semi-conservative, all generation 1 bacteria are expected to have hybrid DNA with one heavy strand and one light strand
explain why
DNA replication is semi-conservative bc one old strand is conserved in each DNA molecule
a heavy N15 strand from parent cell conserved and pairs with a new light N14 strand
76
if replication is semi conservative, 2 types of all bacterial DNA are expected to be present in generation 2: light and hybrid. explain why
in gen 1, there is 1 light and 1 heavy strand in each molecule (all hybrid)
if one of these is conserved in gen 2 molecules, some will retain a light strand and some a heavy strand
these will pair w new light strands
77
how do centrifugation results prove DNA replication is semi-conservative
in gen 1, only 1 band of DNA bc all molecules have same density bc all hybrid
in gen2, 2 bands of DNA (some hybrid= denser, some light entirely), is proves that 1 strand from each DNA molecule is conserved
78
if replication had been conservative or dispersive what patterns of DNA bands would be seen in the venture tubes for gen 1 and 2
DISPERSIVE: only 1 band bc all the same density of DNA molecule. band gradually rises up the tube towards position of band of N14 and becomes less dense (larger proportion is N14)
CONSERVATIVE: 2 bands: one light N14 band and one heavy N15 band ( lower than hybrid band)
79
DNA vs RNA sugar
dna deoxyribose
rna ribose
80
dna vs rna bases
dna: adenine guanine thymine cytosine
rna: adenine guanine uracil cytosine
81
dna vs rna ratio of bases
dna : A+C:G+T
1:1
rna: ratio varies
82
dna vs rna occurrence
dna: mainly in nucleus. also in mitochondria and chloroplasts
rna: mainly in nucleus but found throughout the cell
83
dna vs rna shape
dna: doubel helix, 2 antiparallel strands
rna: single-stranded (single helix)
84
dna vs rna number of types
dna= 1 basic form
rna= 3: mRNA, tRNA, rRNA
85
dna vs rna size of molecule
dna is larger, rna is smaller
86
dna vs rna amount
dna: constant for all somatic cells apart from gametes (1/2) and RBC (no nucleus)
rna: vary from cell to cell (e.g. secretory cells, liver cells have lots to make proteins)
87
dna vs rna stability
dna: more stable
rna: less stable bc ribose sugar is more reactive
88
dna vs rna permanence
dna: permanent
rna: may be temporary
89
what % of cellular RNA is rRNA
80%
90
where is rRNA made
nucleolus
91
what is rRNA combined with
ribosomal proteins in the nucleus
92
rRNA structure
large molecule
2 subunits (large and small) come together when mRNA binds
93
rRNA makes up what
ribosomes
94
Eukarya vs Bacteria/Archaea ribosomes
E: 80s (bigger, sediment faster)
B/A: 70s (smaller, sediment slower)
95
2 places in cell where ribosomes are found
on surface of RER
free in cytoplasm
96
what does nucleolus do?
produce rRNA
97
properties required by DNA as genetic code
stores info: storable condensed molecule and carries code
transfers info: code needs to be carried by a messenger (mRNA)
can be reproduced accurately (DNA polymerase= proofreading)
98
what are most chemicals manufactured with the aid of?
enzymes, which are globular proteins
99
example of a conserved protein
hameoglobin (conserved amongst many species)
BUUT not exactly the same: llama Hb is slightly different to adult Hb; bird Hb has 45 amino acids different
100
how does DNA determine the characteristics of a species
determines the proteins which are produced: changes in sequences of bases
sequence of bases determines the sequence of amino acids in a protein
101
how many different amino acids are there which regularly occur in proteins
20
102
how many bases code for an amino acid
therefore what is the code called ?
3 bases, so 64 combinations
TRIPLET CODE (degenerate)
103
what does 'degenerate' mean?
more than one triplet codes for most amino acids, so the code contains more information than necessary
104
what is the use of the degenerate coding system
reduces the effect of mutations
e.g. AAA and AAG both code for lysine: so if last adenine mutates to guanine, lysine is still coded for
105
what are nonsense triplets
some triplets don't code for any amino acids
tell ribosomes where to stop "reading" the code
106
what does 'Near-universal code" mean?
almost all living organisms have the same triplets of DNA bases coding for the same amino acid
107
mitochondria exception from universal code and why
AUA codes for methionine, not AUG bc of endosymbiotic theory of the origin of mitochondria (mitochondria used to be unicellular organisms but were taken up by bacteria)
108
what does non-overlapping mean?
each base is only involved in one triplet
e.g. GAGAGCAAG is read as GAG AGC AAG
109
what happens if a base is added or deleted?
causes a frameshift
every triplet after that base is changed, and this could affect every amino acid
110
explain how pairing of nitrogenous bases allows identical copies of DNA to be made
A pairs with T and C pairs with G due to hydrogen bonding
only purines can bind to pyrimidines bc of different sizes
one base van only pair with one other base
111
a DNA molecule contains 2 polynucleotide chains
describe how these 2 chains are held together
hydrogen bonds between the complementary base pairs: 2 between A and T and 3 between G and C
phosphodiester bonds in the backbone
112
types of point mutation
base substitution (missense mutation)
base addition
base deletion
113
estimated frequency of base addition
1 in 10^8 base pairs
114
how does the body decrease the rate of mutations
during replication there are enzymes that proofread and edit out incorrect nucleotides
115
what can mutations be?
neutral (degenerate)
advantageous
negative (abnormal protein e.g. sickle cell anaemia)
116
what can mutations give rise to?
new versions of a gene so a new allele
117
number of hydrogen bonds between bases
AT=2
CG=3
118
'describe the synthesis of haemoglobin starting in the nucleus'
sections to divide this question into?
transcription
translation
folding
119
'describe the synthesis of haemoglobin starting in the nucleus': TRANSCRIPTION
DNA unzips, exposing bases on the Hb genes
H bonds broken, revealing template strand
alpha globin gene and beta globin gene
free activated RNA nucleotides joined to the template strand by complementary base paring (A with T, U with A, C/G)
RNA polymerase moves in 5' to 3' direction
RNA nucleotides joined by RNA polymerase by phosphodiester bonds
enzyme reaches stop codon and detaches
2 transcripts are modified before leaving nucleus via nuclear pores
120
'describe the synthesis of haemoglobin starting in the nucleus': TRANSLATION
each mRNA attached to the small subunit of a ribosome
6 bases (2 codons) exposed
each tRNA is attached to a specific AA
the 1st tRNA AA complex binds to the 1st codon w complementary anticodon (methionine added)
2nd tRNA brings 2nd AA
peptide transferase enzyme catalyses the peptide bond formation
tRNA dissociates from mRNA and ribosome
process repeats until stop codon reached
more ribosomes bind to same mRNA transcripts and translate them
alpha globin and beta globin polypeptide chains are released
121
'describe the synthesis of haemoglobin starting in the nucleus': FOLDING
2 alpha globin chains and 2 beta globin chains make up 1 Hb molecule
each chain folds into its 2ary structure (alpha helices) held by H bonding
folds into 3ary structure held by hydrophobic/philic interactions, ionic bonds, H bonds and disulfide bonds
a ham group is added containing iron (prosthetic group and Hb is conjugated)
2 folded pp chains joined together to form 4ary structure
122
what is a polysome
a group of ribosomes (up to 50) attached to a single strand of mRNA, forming a structure
123
what are the stop codons?
UAA
UAG
UGA
124
DNA is mainly found in the nucleus but proteins are synthesised on ribosomes which are free in the cytoplasm or attached to the RER in the cytoplasm. what does this mean needs to happen?
DNA cannot leave the nucleus so the cell makes a copy of the coding strand of a gene (mRNA)
125
steps of transcription
in the nucleus, the gene unwinds and unzips (hydrogen bonds break), exposing the bases on the DNA template strand
free RNA nucleotides (previously activated) pair up via complementary base pairing and formation of temporary hydrogen bonds
RNA polymerrase moves along the mRNA from 5' to 3', catalysing the formation of the phosphodiester bonds between RNA nucleotides until it reaches a stop codon, where the enzyme detaches from the mRNA, which is modified and leaves the nucleus via nuclear pore
126
examples of mRNA modification
SPLICING: introns cut out and removed, exons joined together
at 5' end, guanine cap added (required for initiation of translation)
at 3' end, poly A tail added to stop degradation of the mRNA
127
what does activation of amino acids require
an enzyme: amino-acyl tRNA synthetase. many of these. each specific to amino acids and anti-codons
ATP
tRNA (many anticodons)
amino acids (20 of these)
128
what does joining an amino acid to tRNA form?
amino acid tRNA complex
129
what bond forms during amino acid activation
ester bond between OH of adenine and carboxyl group of amino acid
130
what does the activation of amino acid provide energy for
the energy needed to firm peptide bond
131
RNA polymerase function and link to classification topic
the enzyme that synthesises mRNA from DNA in transcription
different in archaea (10 proteins), eukarya (12 proteins) and bacteria (5 proteins)
archaea and eukarya structures of enzymes are more similar so therefore proof of common ancestor
132
RNA polymerase link to inhibition with example
since it is essential to the life of the cell, RNA polymerase is the target of many poisons and toxins
e.g. deathtrap mushroom= dangerous bc produces poison called Amantin which is a non-competitive inhibitor of RNA polymerase, leading to coma and maybe death
133
requirements for translation
ribosome and mRNA
activated amino acid tRNA complex
soluble proteins-> initiation, elongation and release factors
enzyme: peptide transferase (part of the small subunit of ribosome)
134
function of the ribosome
(ribozyme)
hold mRNA and tRNA in precise positions to allow peptide bonds to form between amino acids
135
rate of transcription/translation
in 1s, a single bacterial ribosome adds 20 amino acids to growing polypeptide chain
human body synthesises 5x10^14 Hb molecules per second
136
what is an initiation codon
complementary tRNA anticodon?
amino acid?
the first codon to be translated from the mRNA is always AUG
a tRNA molecule w/ the complementary anticodon UAC forms a temporary hydrogen bond with this codon
the tRNA molecule has the amino acid methionine attached to it
methionine therefore occurs at the beginning of every chain but it may be removed before the protein is folded into its final shape
137
translation step by step
mRNA binds to the small subunit of the ribosome
first codon to be translated= initiation AUG so tRNA with UAC is attracted w/ methionine
second codon then attracts its complementary anticodon and a second tRNA amino acyl complex is brought to the acyl site. 2 AAs have now been brought in v close contact and a peptide bond is formed between them. this reaction is catalysed by peptide transferase (found in small subunit of ribosome) and energy comes from high energy bond which held the AA onto the tRNA
the tRNA dissociates from the 1st AA and ribosome moves along mRNA strand, exposing the next 3 bases. 3rd tRNA molecule brings 3rd AA, which joins to 2nd AA
process is repeated and a pp chain is assembled
ribosome continues to move along mRNA code until it reaches a stop codon triplet
release factor from the cytoplasm binds to A site and pp is released from the ribosome and it assumes its 2ary and 3ary structures, with aid of chaperone proteins
138
binding sites on a ribosome?
within a ribosome there are 2 tRNA binding sites where the anticodon of the amino acid tRNA complexes are attracted to the codon on the mRNA according to complementary base pairing
