The Genome Flashcards
1
Q
what is semi conservative replication?
A
new DNA strand is made from a template (parent) strand and one newly synthesised strand
Watson and Crick suggested how DNA replicates itself
2
Q
how is DNA replication bidirectional?
A
DNA is replicated in two sections
more efficient
Replication goes in both directions at origin point
3
Q
how can DNA replication be unidirectional?
A
multiple replication origins in one bubble
4
Q
what phase of the cell cycle does DNA replicate?
A
S Phase
cell focusses on replicating DNA only
5
Q
what are the key features of the replication bubble?
A
origin of replication- where replication starts
replisome- moves through DNA until two meet at the termination site, then dissociate
termination site- replisome meets so replication stops
6
Q
what does topoisomerase do?
A
unwinds double helix before replication fork
cuts phosphate backbone of one strand and joins back after unwinding
relieves tension built up by unwinding before Helicase
7
Q
what does DNA Helicase do?
A
binds to origin of replication of relaxed DNA strand
uses energy from ATP to break hydrogen bonds between complementary bases
moves down the strand so DNA becomes single stranded
8
Q
what bases are most commonly used at the origin of replication? why?
A
A-T rich sequences
less hydrogen bonds between bases so requires less energy
9
Q
what is the function of single stranded binding proteins?
A
stop single stranded DNA from coiling (complementary bases on the same strand base pairing)
10
Q
are single stranded binding proteins enzymes? why?
A
no
they are co-operative proteins to straighten strands
11
Q
what is the function of Polymerase III in DNA replication?
A
catalyses formation of phosphodiester bonds between nucleotides
releases two phosphate groups
adds nucleotide to 3’ end (OH)
proofreads DNA strand
12
Q
where does the free-flowing nucleotide come from?
A
a nucleoside triphosphate (ATP, TTP, GTP, CTP)
13
Q
what is the RNA primer? what is its function in DNA replication?
A
short piece of RNA that is complementary to the DNA bases
made up of 10 nucleotides
annealed to start of template strand for DNA polymerase III to bind to, to start forming phosphodiester bonds
14
Q
what is the function of primase?
A
makes the RNA primer for DNA polymerase
15
Q
what is the function of DNA Polymerase I in DNA replication?
A
“cleans up” the DNA strand by removing the RNA primer and replacing it with DNA
works on short distances
16
Q
what is the function of DNA ligase?
A
seals the gap left by DNA polymerase I
joins Okazaki fragments made on the lagging strand?
17
Q
what is DNA lagging?
A
one template strand can be replicated in a 5’ to 3’ fashion= leading strand
other strand can’t be= lagging strand
Okazaki fragments (small DNA fragments) make up the lagging strand to keep it 5’ to 3’
18
Q
what is continuous replication?
A
replication on the leading strand
19
Q
what is discontinuous replication?
A
DNA replication of the lagging strand using Okazaki fragments
20
Q
what are the nine ways DNA can be damaged?
A
DNA Polymerase III mishaps
vulnerability when single stranded
depurination
deamination
base oxidation
base alkylation
UV light
DNA adducts
anti-cancer drugs
21
Q
how can single stranded DNA be damaged?
A
bases are exposed after DNA helicase so no hydrogen bonds to protect them
22
Q
how can DNA Polymerase III mishaps damage DNA?
A
can bind uncomplimentary bases together, resulting in helix distortion and deletions/insertions
23
Q
what is depurination? how does it cause DNA damage?
A
removes purine base from nucleotide
caused by random collisions in cytoplasm
24
Q
what is deamination? how does it cause DNA damage?
A
amine group is kicked out of cytosine or substituted with oxygen
turns nucleotide into uracil so adenine will bind to it
25
what is base oxidation? how does it cause DNA damage?
oxygen binds to base (G or C)
changes the molecule so incorrect base pairing
26
what is base alkylation? how does it cause DNA damage?
s-adenosyl methionine transfers methyl group
changes shape of nucleotide
electrophile attacked by nucleophile to form alkylated adducts
27
how does UV light damage DNA?
causes covalent linkages between two adjacent pyrimidine bases (crosslinks)
can form thymine dimer
prevents DNA unwinding for replication/transcription
28
how do anti-cancer drugs damage DNA?
topoisomerase inhibitors wait for topoisomerase to cut the strand and then prevents ligation so DNA can't reform and ssDNA breaks
Intercalating agents insert into DNA and cause helix distortion
radiotherapy causes crosslinks to break DNA strands
29
what are the two types of DNA repair?
direct reversal- reversing damage by correcting areas affected
excision repair- cutting out the damage and repairing the gap (DNA ligase)
30
what are the 3 types of mutation?
chromosome mutation
genome mutation
gene mutation
31
what is a mutation?
result of unrepaired DNA
provide allelic variation
heritable changes in genetic material
32
what are gene point mutations?
change in one base
becomes permanent in second round of replication (daughter cells) if not repaired
33
what are the 4 types of gene point mutations?
silent point mutations
neutral point mutations
missense point mutations
nonsense point mutations
34
what are silent point mutations?
change in base pair
mutated genetic code is degenerate so codes for same amino acid as original genetic code
35
what are neutral point mutations?
change in base pair
amino acid is substituted
new genetic code codes for a similar amino acid with similar properties as original genetic code
no detectable change
36
what are missense point mutations?
change in base pair
new genetic code codes for a non-functional protein
37
what are nonsense point mutations?
change in base pair
new genetic code is changed to a stop codon
results in shortened polypeptide
protein wont form
38
in what direction is DNA transcribed?
5' to 3'
39
what is at the 5' end of DNA?
phosphate group
40
what is at the 3' end of DNA?
OH
41
what bases are present in RNA?
uracil
guanine
cytosine
adenine
42
what does RNA polymerase do in transcription?
breaks hydrogen bonds between double stranded DNA to separate one template strand
catalyses formation of phosphodiester bonds between RNA nucleotides
detects promoter region/termination signal
43
what happens to the template strand after RNA polymerase has broken the double helix?
the bases are copied into mRNA base pairs
44
does RNA polymerase require a primer?
no
45
what happens to the two separate DNA strands after they have left RNA polymerase?
DNA retwists and forms another double helix, following base pairing
46
does RNA polymerase have a proofreading mechanism? why?
no
mRNA only a temporary store so isn't necessary
47
what are the two types of prokaryotic RNA polymerase?
core enzyme
holoenzyme
48
what is the core enzyme of RNA polymerase made up of?
two alpha subunits
one beta subunit
one beta prime subunit
49
what is the holoenzyme of RNA polymerase made up of?
two alpha subunits
one beta subunit
one beta prime subunit
one sigma factor
50
what is the promoter region?
specific DNA sequence RNA polymerase looks for to start transcription
51
what are the two types of DNA sequences the promoter region has?
-35 sequences
-10 sequences
52
what is the -10 promoter sequence also known as?
Pribnow Box
53
how are promoter sequences consensus?
bases may change but RNA polymerase can recognise them
54
what is the function for the sigma subunit?
scans the single stranded DNA for -35/-10 sequences
binds to promoter region
55
what happens to the sigma factor after RNA Polymerase begins transcribing?
leaves after 10 nucleotides
turns into core enzyme
56
how is transcription initiated with the nucleotides?
OH group (3') of last nucleotide attacks the phosphate group of the incoming nucleoside triphosphate (nucleophilic)
releases pyrophosphate
57
what is a protein requiring termination site called?
rho dependent
58
what is a termination signal not requiring a protein called?
rho indepentdent
59
if RNA Polymerase can't find the more complex promoter sequences in eukaryotic transcription, what must it use?
general transcription factors
60
what does eukaryotic mRNA contain that prokaryotic mRNA doesn't?
introns
61
what are introns?
non-coding pieces of DNA
62
how are introns removed from mRNA in eukaryotic transcription?
splicing carried out by spliceosomes
63
what are the 3 ways eukaryotic RNA is modified before translation?
5' capping
splicing
polyadenylation
64
what is 5' capping?
addition of a modified GTP (7-methyl guanosine residue)
65
what is polyadenation?
addition of Poly A tail to 3' end
tail of 150 adenine nucleotides
66
what are the 3 main sequences in mRNA?
start codon
codons
stop codons
67
what is a start codon?
AUG
start signal at the beginning of mRNA
so ribosomes always read the code at the same place
68
what does AUG code for?
methionine
69
what is a stop codon?
UAA, UAG, UGA
stops translation as doesn't code for an amino acid
70
what is degenerative genetic code?
codons that code for the same amino acid
71
what is the structure of tRNA?
single stranded (5' end and 3' end )
hydrogen bonding causes "clover lead" shape
anticodons
72
what is the function of tRNA?
converts codon to amino acid by decoding nucleic acid language
carries amino acid to help them form a peptide linkage with each other
73
what are ribosomes made of?
proteins
rRNA
74
what size are prokaryotic ribosomes?
70S
75
how many rRNAs does prokaryotic ribosome's small unit have?
1
76
what is the size of eukaryotic ribosomes?
80S
77
what are the 3 parts of the tRNA binding site?
A site (aminoacyl-tRNA)
P site (peptidyl-tRNA)
E site (exit site)
78
where does mRNA sit in the ribosome during translation?
in between the small and large subunit
79
what is the role of the ribosome in translation?
to bring the mRNA and tRNA together by complementary base pairing
80
how is translation initiated?
initiator tRNA binds AUG at p site of ribosome
small ribosome subunit aligns ribosome on mRNA after finding the Shine-Dalgarno sequence
81
what is the Shine-Dalgarno sequence?
purine rich sequence that base pairs to mRNA so the ribosome knows where the start codon is
82
how does elongation occur in translation?
amino acid binds to A site (carried by tRNA)
peptide bond forms between Met in p site and amino acid in A site
tRNA releases Met
83
what catalyses the peptide bond formation in translation?
large ribosomal subunit and rRNA
ribozymes
84
what translocation occurs in translation?
ribosome moves down one codon
empty tRNA moves into E site
tRNA that was in A site moves to P site
A site now empty so new tRNA moves in
85
how does termination occur in translation?
no tRNA carries stop codon
release factor enters A site so everything is released
86
what are the 5 things released at termination of translation?
polypeptide
ribosomal subunits
tRNA
release factor
mRNA
87
what is the purpose of mitosis?
produce new cells by duplicating an existing cell
88
what are the 4 phases of the cell cycle?
M Phase
G1 phase
S Phase
G2 Phase
89
what occurs during M phase?
nuclear division (mitosis)
cytokinesis (cytoplasmic division)
90
what occurs during G1 phase?
cell growth
mass of organelles/proteins double
monitors internal/external conditions before S phase
91
what is G0 phase?
alternative state when the cell is not planning to divide/replicate?
92
what is S phase?
DNA replicates semi-conservatively
chromatin proteins replicated
activates proteins involved in DNA replication
93
what are miotic checkpoints?
checks the environment at certain points of the cell cycle
stops mismatched/damaged DNA being replicated
94
where are the checkpoints in the Cell Cycle?
end of G1
end of G2
metaphase to anaphase transition to check chromosome alignment
95
how do cancer cells and the checkpoints interact?
cancer cells try to bypass the checkpoints
96
what are the 6 stages of mitosis?
prophase
prometaphase
metaphase
anaphase
telophase
cytokinesis
97
what happens during mitotic prophase?
replicated chromosomes condense
centrosome replicates and moves to opposite poles
miotic spindle (microtubules) assemble between the two poles
98
what happens during mitotic prometaphase?
nuclear envelope breaks down
chromosomes attach to spindle microtubules by kinetochore
kinetochore binds to centromere
chromosomes positioned middle of the cell
99
what happens during mitotic metaphase?
chromosomes align on middle of spindle (equator) between spindle pores
specific microtubules attach sister chromatids to opposite spindle fibres
3rd checkpoint occurs
100
what happens during mitotic anaphase?
2 sister chromatids separate to create 2 daughter chromosomes
microtubules get shorter
spindle poles move apart
sister chromatids pulled to opposite poles
101
what happens during mitotic telophase?
chromosomes decondense
new nuclear envelope forms
mitosis ends
contractile ring starts to contract
102
what happens during mitotic cytokinesis?
cytoplasm divides into two
contractile ring (actin and myosin) pinches the cell into two
103
what is produced at the end of mitosis?
two daughter cells with one nucleus
same number of chromosomes as original cell
both daughter cells are genetically identical
104
what is meiosis?
exchange of genetic information between chromosomes
105
what does meiosis produce?
haploid cells that develop into gametes
106
what is a diploid cell?
2 sets of chromosomes
107
what happens during meiotic prophase I?
chromosomes condense and become visible
duplicated centrosome separate
homologous chromosomes recognise and pair up to form a four chromatid structure (bivalent)
meiotic spindle forms
double strand breaks in chromatid DNA
crossing over created chiasmata
108
what occurs during meiotic prometaphase I?
nuclear envelope breaks down
kinetochore microtubules attach to chromosomes
109
what occurs during meiotic metaphase I?
microtubules align each chromosome pair
paired homologous chromosomes at spindle equator are randomly orientated
110
what occurs during meiotic anaphase I?
homologous chromosomes separate
sister chromatids remain attached and move towards opposite poles
111
what occurs during meiotic telophase I?
separated chromosomes (2 sister chromatids) at opposite poles of cell
spindle disassembles
new nuclear envelope forms
112
what is the product of meiosis I?
2 nuclei
each with a haploid of one mixed parental set of separated chromosomes
113
what happens during meiosis II?
sister chromatids are separated to produce haploid daughter cells
genetically different
114
what are the two ways that meiosis produces genetic variation?
independent segregation
crossing over
115
what is independent segregation?
maternal and paternal homologs separate
116
what is crossing over
maternal and paternal homologs exchange DNA segments
reassorts genes of individual chromosomes
117
what is lateral gene transfer?
gene is passed on from the parent to the offspring
analysis of gene sequences finds relationship between bacteria, archaea, eukaryotes
genetic material has been transferred across lineages
118
what is alternative splicing?
introns are removed out of gene sequences so only exons are present after transcription
can make multiple proteins
119
what is exon shuffling?
protein domains added to the beginning or end of ancestral genes to produce new genes/more complex protein
new exon combinations produced by non-homologous recombination
120
what is a chimeric gene?
a gene that is made of pieces derived from 2 or more different ancestral genes
121
what is gene chimerism
two unrelated genes are fused together
122
what is retro-transposition?
genes correspond to sequences in other genomes are interrupted by introns
intron less genes likely to originated by RT
results in non-functional genes
123
what is motif multiplication?
multiplication of specific patterns within genes
124
what is gene duplication?
gene is duplicated with small alteration producing a slightly different protein
must occur at DNA level
125
what is a phenotype?
genetic constitution of an organism and its interaction with the environment
observed characteristic
126
what is a genotype?
set of genes in an individual's DNA
127
how is evolution a populational process?
genotypes replace other genotypes over time
specific gene abundances change over tim
128
what is genetic drift?
change in genotype population can occur by fluctuation
129
what is natural selection/
adaptations to genetic bases due to different characteristic for different environments
130
what is phylogeny?
common ancestors branch into diverse lineages
131
what is speciation
origin or 2 or more species from a single ancestor
occurs due to geographic isolation of different populations of the same species
prevents interbreeding
promoted genetic differentiation
132
what did Mendel study?
basic principles of inheritance by tracking characteristics of true-breeding offspring
133
what were Mendel's results?
100% of the first generation offspring were yellow
75% of the second generation offspring were yellow
134
what did Mendel propose?
genes had a hereditary factor
alleles could be dominant or recessive
135
what are homozygous chromosomes
alleles are the same on each chromosome for a gene
136
136
what are heterozygous chromosomes?
two chromosomes have different alleles for a gene
137
what is the relationship between dominant/recessive alleles on phenotypes in homozygous chromosomes?
dominant allele determines characteristic
recessive allele has no effect on characteristic
138
what is a monohybrid cross used for?
one trait
139
what is a multi-hybrid cross used for?
multiple unrelated traits
140
what is a dihybrid cross used for?
two related traits
141
how are human patterns of inheritance more complex than Mendelian genetics?
some genes have more than two alleles that determine appearance
alleles may not be fully dominant/recessive
gene can produce multiple phenotypes
humans have to small families to have accurate Mendelian ratios
142
what are autosomal recessive disorder
disorder is carried on the recessive allele of a non-sex linked chromosome
phenotypically healthy parents (carriers) are heterozygous
143
what are autosomal dominant disorders?
disorder is carried on the dominant allele of a non-sex linked chromosome
144
what is a sex linked disorder?
allele for a disorder is carried on either the X or Y chromosome
145
what is mitochondrial inheritance?
disorder inherited from small genome in the mitochondria
leads to problems with energy production
146
what is an example of an autosomal recessive disorder?
cystic fibrosis
147
what is an example of an autosomal dominant disorder
Huntington's Disease
148
why are sex-linked disorders more visible in males?
Male sex chromosome= XY
Female sex chromosome= XX
Y chromosome too small so doesn't carry gene
males only need one allele to have disorder
149
why can only females pass on mitochondrial disorders?
because the ovum carries all of the mitochondria that is replicated
150
what is penetrance?
the percentage of individuals with a genotype who exhibit the phenotype
151
what is complete penetrance?
100% of all identical genotypes show the expected phenotype
152
what is incomplete penetrance?
less than 100% of identical genotypes show the expected genotype
153
what is expressivity?
extent to which a given phenotype is expressed at the phenotypic level
154
what is constant expressivity?
100 % of genotypes with no expressivity yield show the expected phenotype
155
what is variable expressivity?
genotypes with an expressivity effect yield a range of phenotypes
156
why do cells have the same genome, but differ?
they switch on/off certain genes
157
what are the two reasons why genes turn on/off
permanent gene expression
external signals
158
what are the genetic switches?
short stretches of regulatory DNA sequences that turn genes on/off
regulatory proteins which bind to specific DNA sequences
159
how do regulatory proteins work?
read the DNA helix
scan for specific promoter sequence to bind to
blocks/unblocks promoter region for RNA polymerase regulation
160
how to bacterial genes regulate in response to food?
switches on genes when organism has to make its own food
switches off genes when food is available in the environment
161
what are operons?
clusters of genes that regulate other genes
162
how many enzymes does tryptophan need to be made?
5
163
what binds to the operon?
the regulatory protein
164
what does the Trp regulatory protein do to turn the gene off?
binds to operator so the promoter region is blocked
RNA polymerase cannot bind to promoter region
so transcription in inhibited
165
what happens when there are high levels of tryptophan in the environment?
regulatory protein binds to operator on promoter region
RNA polymerase can bind to promoter bind
transcription in inhibited
operon is off so tryptophan isn't made
166
what happens when there are low levels of tryptophan in the environment
bacteria needs to make their own
inactive repressor protein falls off operator
RNA polymerase can bind to promoter region
transcription occurs
operon is on
tryptophan is made
167
what is negative regulation?
protein binds to operator and prevents transcription
168
what does the lac operon do?
catalyses the hydrolysation of lactose into glucose and galactose as bacteria can only absorb glucose
169
why is the protein for the lac operon transcription a regulatory repressor?
it will only bind to the operator when lactose levels are low as operon isn't needed
170
what happens to the Lac operon when there are high levels of lactose in the environment?
repressor protein leaves operator
RNA polymerase can find promoter region
Lac operon is on
protein can convert lactose to glucose
171
what happens to the Lac operon if the environment is absent of lactose?
repressor protein binds to operator
RNA polymerase cannot find promoter region
transcription is inhibited
172
