1
Q
why is genetics important in society
A
health, medicine, family life, ethics, insurance law
2
Q
what are the 3 rules mendelian discovered for inheritance
A
the law of segregation
the law of independent assortment
chromosome behavior in meiosis
3
Q
what did mendel work of peas lead to disscover
A
the discovery of dominant and recessive traits
the conce[t of the gene
the formulation of the basic laws of inheritance
4
Q
what did people belivie about inheritance before mendel
A
traits were blended
5
Q
what is a character
A
is a heritable feature of an individual
6
Q
what is a trait
A
a variant from of a character ( the phenotype )
7
Q
what is the law of segregation
A
the two froms of a gene present in each parent segregate independently
8
Q
how did medle fomrualte the law of segregation
A
by studing the results of monohybrid crosses
9
Q
what is a monohybrid cross
A
a cross between two true breeding individyals differing in one character
10
Q
what did mendle observe from monohybrid crosses
A
all F1 progeny( offspring) resemble one of the parents
both of the origional parental traits appeared in the f2 generation
the ration in F2 was 3:1
the same pattern of inheritance was seen for all 7 of the characters he studied
11
Q
what were mendles conculsions from the monohybrid crosses
A
one trait is dominant and the other is reccessive
the heritable factor for the recessive trait had not been in the F1- just masked by the presence of the fcator for the dominat trait
12
Q
what are the main points of medles model
A
1- variation in inherited characteristics are due to the existance of alternative versions of heritable factors- alleles
For each character, an organism inherits two alleles, one from each
parent
If the two alleles differ, then the dominant allele determines the
organism’s appearance (its phenotype)
The alleles do not blend when present in the same individual – they
remain discrete
The two alleles segregate (separate) during gamete formation - and
end up in different gametes
13
Q
what is mendles law of segregation
A
the two forms of a gene alleles present in each parent segregate independelnty
each parent has two alleles but only one is passed to an individual via the gamete
each offspring recives one allele from one parent and the pther allele from the other parent
14
Q
what is a punnett square
A
a diagrammatic device for predicitng the outcomes of crosses between parents of knwon genotypes
15
Q
what is a testcross
A
a method for determiing the genotype of an individual with the dominant phenotype of a trait
it involves crossing it with a homozygous reccessive individual
16
Q
what do the results of a test cross tell you
A
if 100% one colour that it was homozygous dominant
if 50/50 it was heterozygous
17
Q
what is mendels law of indepednent assortment
A
Each pair of alleles assort independently of each other pair of alleles during gamete formation
18
Q
what does the law of indepenednt assortment relate to
A
the situationn where the inheritance of two or more different pairs of alleles is being studied
19
Q
how did mendle formulate the law of independent assortment
A
mendle formulated the law by following the inheritance of two characters at the same time ‘
a cross involving parents differening in two characters is called a dihybrid cross
20
Q
what is the result og a dihybrif cross between 2 heterzygous
and in what ratio
A
two new phenotypes in addition to the two parental phenotypes ‘the new phenotypes are called recombinants
9:3:3:1
21
Q
what would happen if indepednent assortment did not occur
A
alleles would be inherited togther
F2 would have no recombiantn phenotypes - only parental
22
Q
mitosis occurs in ….. cells
meiosis occurs in …….
A
somatic
germ line
23
Q
what is synapsis unique to
A
meiosis
24
Q
what are two chromosomes of a homologous pair from
A
inherited from different parents
25
what is a chromatid
one of the two identical strands of a newly replicated chromosomes
26
what is a sister chromatids
two identical chromatids held togther by a common centromere following replication
27
what did sutton observe
he made the link between the behaviour of chromosomes during meiosis and mendles laws
the observed that:
- chromosomes occur in pairs of somatic cells
- chromosome pairs segregate equallt into gametes '
- different chromosome pairs assort independenty
28
what is the chromosome theory of inherticane
mendles heritable factors are located at sepcific position s- loci- on chromsomes
it is the chromosomes that undergo seregation and indepeendent assortment
29
what is a gene
units of heredity and determine traits
each gene is located at a particular locus on a chromosome
genes can exist in different roms, one of each member of a pair of homologous chromosomes
we inherit one allele form each parent
30
how does chromosome behaviour in meiosis explain mendles law of segregation
the two forms of a gene present in each parent segregate independenty
this occurs becase each allele is on a different member of a a homologous pair of chromosomes and moves to opposite poles in anaphase1
31
how does chromosome behaviour in meiosis explain mendles law of independent assortment
eahc pair of alleles assorts independently of each other pair of alleles during gamete formation
this is explained by the random way that the homologous pairs of chromosomes line up on the metaphase plate during meiosis 1
32
what 4 distinct processes contribite to genetic variation
mutations
independent assortment of chromosomes during meiosis 1
crossing over between homologus chromosomes during meisosi 1
random fertilization of ova by sperm
33
how does independent assortment and random fertilization promote genetic varitaion
the choice of which sperm fuses with which egg is random
with 23 pairs of chromsomes, indepenednt assortment means no of possibke combinations of chromsomes types is 2^23
therefore 2^46 combinations of offspring with just one couple
in additon the process of crossing over adds even more varitation
34
what is a recombiant phenotype
one where the combination of phenotypes can occur through either of the parents
recombinant phenotypes can pccur through either:
independent assortment
crossing over
35
what is crossing over
the process of genetic recombination that gives rise to new combinations of linked genes
36
when does crossing over occur
during the pachytene phase of prophase 1
37
what does crossing over begin with
synapsis - pairing of homologous chromosomes
38
what is the synaptonemal complex
a protein zipper that holds homologus chromosomes togther in the tetrad
39
what leads to crossing over between homologous chromosomes
formation of synaotinemal complex
40
what is the point at wich crossing over takes place called
chiasma
41
what is the result of crossing over
recombinant chromosomes with new combinatinos of lined genes
42
what is recombinat frequency
the percentage of the progeny that inherit a combination of alleles that differs from either parent
43
how do you calculate recombinatin frequency
no. of recombinats / total no. og progeny
x 100
44
how are recombination frequencies estimated
by studying the results of a testcross
the recombination frequnecy between two genes depending on wether the genes are on the same or different chromsomes
for genes on different chromosomes, the recombination frequenct will be 50 %
45
what are the results of a testcross when the genes are on the same chromosomes
parental over 50% and recombiant less that 50%
recombiant only occurs if crossing over occurs - which makes it less common
46
how is the normal allele / wild type usually noted
+ in superscript
47
what are the 2 possile arrangements of the alleles in a double heterozygote
coupling heterozygote
+ on the same chromosome
repuksion heterozygote
+ ( wild type) on different chromomes
in each case the largest phenotypic classes on the progeny will be the parental classes
48
what does recombiant probability also tell you
the relative distance of genes
49
why dont map distances add up for recombient frequencies
the bigger distance - underestimated the percentage
thus us because the further apart there is also more probability of multiple crossingover taking place
50
why are recombination frequnecies greater than 50 % no t possible
multiple corss overs
51
the three point cross
what do the largest and smallest numbers represent
the largest indicate the parental types and te smallest are the result of a double crossover
52
what causes deviations from mendekiam ratios
sex linkage
incomplete dominance
codominance
pleiotropy
polygenic inheritance
epistasis
53
what is sex linkage
the make fly only needs one copy of mutant X to have the reccessibe phenotype
males alwyas get their X chromosomes from their mothers
54
what is incomplete dominace
where a dominant allele does not completely mask the effect of a recessive allele at the same locus
55
what is the ration of phenotypes in an F2 for incomplete dominance
3:1
56
what is an example of incomplete dominance i humans
familial hypercholesterolaemia
57
what is codominance
where each allele affects the phenotype in separate, distinguishable ways
eg blood type
58
what is the difference beteen incomplete dominance
and codominance
incomplete dominance - blending of trairs and a diluted phenotype where as codominance is no blending , the traitrs appear togther and remain distinct in the heterozygote
59
what is pleitropy
a single gene has multiple effects on the phenotype it is said to be pleiotropic
60
what is polygenic inheritance
where a single trait is determind by multiple genes
61
what is a characteristic of polygenic inheritance
rhe trait shows continuous varitaion in the population '
discontinuous - one gene effectong a trait
continuous - more that one gene effectong a trait
62
what is epistasis
when one gene masks or modifies the espression of another gene it is said to be epistatic to that gene
63
how does epistasis affect the outcome of a dihybrid cross
the ratio of pgenotypes in the f2 is 9:3:4
64
what is cytogenetics
the study of the structure and function of chromosomes
65
what is cytogenetics used for
the screening and diagnosis of inherited chromosomal disorders
66
what is a karyotype
a preparation of chromsomes arranged in size order
67
how do you may a karyotype
draw blood and add a few drops of bloof to a culture flask containing groth medium
add phytohaemagglutinin to stimulate mitosis and incubate
treat with colcemid to stop mitosis in metaphase so the chromosomes are condesed
trensfer cells to tube
pellet cells by centrifugation, add hypotonic somution to lyse cells, transfer to tube containing fixative
drop cells onto microscope slide and stain with giemsa to cause the banding pattern
then examine with microscop eand photograph and arrange the chromosomes inot karyptype
68
what three ways can you identify a chromosome
length
banding pattern
placement of centromere
69
what is it called when the centromere is in the centre
metacentric
70
what is it clled when the cnetrmere is off centre
sub-metacentric
71
what is it called when the centromere is very close to the end
acrocentric
72
what is karyotyping used for
detect changes in chromosome number
to detetct chnages in chromosome structure
73
what is polyploidy
an extra whole set of chromsomes
74
2n= diploid
3n=
4n=
triploid
tetraploid
75
what is aneuploidy
some additional or missing chromosomes
76
what is monosomy and trisomy
monosomy - one chromosome missing
trisomy - one extra chromsome
77
what is the cause of aneuploidy
non dijunction
78
is aneuploidy common and what does it lead to
very common - occurs in 50% of human conceptions
most aneuploidies lead to embryonic death
79
whats the more common type of aneuploidies
sex chromsomes are more comoon
80
what is the only autosomal aneuploidy that permits survival inot adulthood
down syndrome
81
what is downsydrowme formally called and how is it noted
trisomy 21
47,XX, +21
XX or XY
82
what are the chracteristics of downsyndrome
characteristic facial features
short stature
some level of learining disability
heart defetcs
susceptibility to lukaemia and alzheimers disease
83
why does incidence of down syndrome increase with metrnal age
as more time for mutation to occur - as eggs suspended in metaphase
84
how are screening for chromsomal abnormalities carried out
for downsyndrome
blood tests to detetc specific proteins associated with a downs foetus
ultrasound scans to measure the size of the nuchal pad at the name of the foetal neck associated with down syndrome
aminocentesis and karyotyping
85
what is the only viable human monosomy
turners syndrome
45, XO
86
characteristics of turners syndrome
phenotypically female
sterile due to lack of meturation of sex organs
oestrogen replacemnt therapy leads to development of secondary sex characteristics
87
what is klinefelters syndrome
one of the most common genetic abnormalities
47, XXY
88
characteristics of klinefelters syndrome
essentially male, but with some female characteristics
tall stature
sterlie
treated with hormone replacement therapy
silghlty feminized physique, breast development, female type pubic hair pattern
89
what determinds biological sex
the presents or absence of the Y chromsome
90
what allows sepcific chromsomal mutations to be accuratly descirbed
each G band can be given an address
91
what is cri-du-chat syndrome
deletion of part of the short arm of chromsome 5
92
characteristics of cri-du-chat
babies have cat like cry
defetcs in glottis and larynx
wide face with saddle nose
physical and intellectual disability
rage of severity, depending on the extent of the deletion
93
what is prader-willi syndrome
deletion in long arm of chromsome 15
94
prader-willi syndrome symptoms
poor suckling reflexes in infants
uncontrollable eating later i life
obesity
'diabetes
poor sexual development in males
95
when does prader-willis syndrome ony occur
when affected chromsome is inherited from the father due to genomic imprinting
96
what is genomic imprinting
the process that affected certain genes whereby either the meternal or paternal copy fo the gene is silences
97
what is angelmans syndrome
arises if the same segement is missing from the maternally derived chromsome 15
98
characteristics of angelamns syndrome
a happy demeanor
inappropriate outburts of laughter
intellectual disability
sever speech problems
stiff limb movements
seizures
99
what % of down syndrome casses are famililal down syndrome
5%
100
translocation carrier
t(14;21)
explain
one of the chromsomes 21 is attahed tp one of the chromsomes 14
in this case parents have a 1:3 chnace of a affected child
101
what is chronic myelocytic leukaemia
22-9 translocation
spontaneous not heritable
Translocation creates the BCR-ABL fusion gene - an
oncogene that stimulates over-production of white blood cells
CML is most common in middle-aged/elderly
Accounts for 15-20% of all cases of leukaemia
102
what did darwin discover
natural selection theory of evolution
all species of life have decended from a common ancestor over time
103
what did miescher disocver
nucleic acid
104
how did friedrch miescher discover nucelic acid
got pus from used bandaged from soldiers in the crimean war
white blood cells taken and nuclei purifed
extracted nuceli and found a precipitate ruch in phophorus and nitrogen
N rich fraction = protein
P rich fraction = nuceic acid
105
what 3 things are nuceli acids consist of
5 carbon sugar
nitrogenous base
phosphate
106
wha are the two types of nucelic acids
RNA - in nucleoplasm but not in chromosmes
DNA - in chromosomes
107
chromosomes contain DNA and protein, whcih of these did people beilive orgionaly was the genetic material
the proteins.
it was thought that DNA being composed of just 4 bases coudlnt be complex enough to contain the code for life
108
explain frederick griffiths transformation experiments
he used two strauns of streptococcus pneumoniae - one R that is benign and one S that is virtulent
S from - the mice died
R form - the mice lived
S from heat killed - mice lived
S form heat killed, r form - mice died thir blood contaiened live pathogenuc strains of s.pneymoniae
109
interpret griffiths results
Heat killed s form
transfroming principle
to R form
the transformation leads to s form
this showed that genetic material was capable of reprogramming R form cells inot s form disease causing cells
110
what experiments did oswald avery do
osward avery and coworkers built on griffiths experiments by trying to identify the transforming principle
unitl these experiments, it was though it was most likley to be proteins
they subjected the heat killed s-type bacteria to a range of tests to identify the nature of the transforming principle
111
what experiment did hershey chase do
bacteriophage - a type of virus composed of DNA and protein which infects bacterial cells
Electron microscopy studies had shown that the virus itself does not enter cell.
It binds outside of cell, injects it’s “genetic material” and sometime later, cell becomes reprogrammed to produce viral particles.
1- phage protein labelled with S35 result most of the radioactivity in supernatant conatining phage ghosts
2- phage DNA labelled with 32P - results most of the radioactivity in the pellet containing the intact cells
conclusion - DNA is injected inot the cell , not protein
112
what did chargaff do
he reasoned these must contain genetic code as the sugar and phosphate groups were invariant
eamined ratios of these in DNA of various organisms
113
what are the chargaffs rules
Ratio of the four bases is not 1:1:1:1 (suggests it is not simply a structural molecule).
Ratio is species-specific
Base composition always obeys a strict rule: A=T and G=C (Chargaff’s Rule)
114
what are the pyrimidines
single ringed
cytosine and thymine
115
what are purines
double ringed
adenine
guanine
116
what are the conclusions from the X ray diffraction experiments on determining dna structure
dna is a helic
it is 2 nm wide
length of each turn is 3.4nm
distance between repeating units is 0.34nm
so 10 nucelotide pairs per turn
117
what does hydrogen bonding ensure in dna
specific base pairing
A-T base pair have 2 h bonds weaker
G-C base pairs 3 H bonds stronger
118
what dection do dna stramds run in
they run antiparralel
in the 5' to 3' direction
119
what did watson and crick suggest about dna replication
each strand of DNA can act as a template for the synthesis of a new complementary strande
semi conservative replication
120
what were the meselson stahl experiments
1- bacteria cultured in medium 15N ( heavy )
2- bacteria transferred to medium with 14N ( lighter)
3- dna sample centrifuged after first replication
they saw that all dna of intermediate density so 1 ligth strand and 1 heavy strand. so semi conservative replication
121
what does DNA polymerase require to work
single stranded template DNA
all 4 nucleoside triphsphates
free 3' hydroxyl ( primer )
122
what direction does DNA polymerase work
5' to 3'
123
what does DNA polymerase do
inserts complemntary nucleotides
uses energy from breaking phosphate bonds
proof reading ability can remove incorrectly inserted nucelotides
124
where does replication begin
at origins of replication froming a bubble which meet to form two daughter dna molecules
125
each replication fork has what 2 strands
leading and lagging strands
126
what are the 3 phases of dna replication
initiation
elongation
termination
127
explain replication of the leading strand ; initiation
1- the origin of replication is recognized by initiator proteins that open up the double helix and recruit helicase
2- helicase unwinds and separates the two strands
3- single stranded binding proteins prevent DNA strands from re annealing
4- rna primer synthesised and added by primase
128
dna polymerase can only add nucleotides to ....
an existing 3' group end
129
explain replication of the leading strand : elongation
1- after the RNA primer is sythesiszed, the sliding clamp is recruited
2- dna polymerase III associates with dna via the sliding clamp
3- each base in the parental dna is read by the dna polymerase, complementary bases added to the growing strand in a 5' to 3' directiom
the leading strand is sythesised continuously
130
explain replication of the leading strand ; termination
replication complexes are disassembled
rna primers are removed and replaced with dna
dna ligase connects adjacent strands
131
when does termination of dna replication occur
- dna polymerase encounters nda that has been replicated
- two different replication forks meet
- the replication fork reachest the end of a linear chromosome
132
explain replication of the lagging strand ; inititation
the origin of replication is recognised by initator proteins that open up the double helix and recruit helicases
2- helicase unwids and separates the two strands
3- single stranded binding proteins prevent dna stands from re annealing
4- rna primer synthesised ad added by primase
133
explain replication of the lagging strand; elongation
1- after the rna primer is synthesized, the slidng clamp is recruited
2- dna polymerase associated with dna via the sliding clamp
3- each base in the parental dna is read by the dna polymerase, complementary bases added to the growing strand in the 5' to 3' direction
but lagging strand must be synthesised discontinuosly
4- lagging strands synthesised in sections known as 'okazaki frangments ' At end of first “Okazaki fragment”, DNA polymerase and sliding clamp dissociate from DNA.
5- rna primer for fragment 2 synthesised and added by primase
134
explain replication of lagging strand ; termination
dna pol1 rplaces rna with dna
dna ligase joins okazaki fragments ''
135
what does helicase do
unwinds the helix to open it up
136
what does dsingle strand binding proteins do
hold helix open
137
what do primase do
synthesises the rna primers needed for initiation of dna synthesis
138
what does dna polymerase 111 do
extends the dan or rna strand from the 3' end copying the template
in prokaryotes; similar proteins do the same job in eukaryotes)
139
what does dna polymerase 1 do
in prokaryotes; similar proteins do the same job in eukaryotes)
removes the rna primer and fills in gaps between okazaki fragments
140
what does dna ligase do
seals the gaps between okazaki fragments
141
what did archibold garrod do
the first to connect inherited human disorders with medles law of inheritance
he studied alkaptonuria
142
what is an inborn errors of metabolism
disease where the patient is unable to carry out a particular biochemical reaction
143
what is alkaptonuria
urine darkens from yellow to brown to black after it is exposed to the air
144
what did garrod observe with alkaptonuria
urine containes large amounts of homogentisic acid
alkaptonuria is inherited in a mendelian fashion ( autosomal recessive)
145
what did gerrad hypothesis on alkaptonuria
alkatonuria patients lack the enzyme necessary for breaking down homogentisic acid
lack od the enzyme is due to defect in a gene
146
conclusions from garrods alkaptonuria experiments
defects in genetic material can lead to specific diseases which can be inherited
mendelian genetics inheritance can be observed in humans
lack of an enzyme is due to a defect in a gene
147
explain beadle and tatums 'one gene on enzyme' experiments
beadle and tatum were also interested in how genetic chnages may effect matabolism
had been using drosphila as model organism but, due to their complexity , was difficult to prove a single gene was responsible for a particular chemical reaction
using simple organism neurospora led to the nobel prize
148
descibe the nurospora organism
They have a haploid stage of life cycle (where they have just one set of genes) and therefore genetic changes easy to study as recessive traits will appear in offspring.
Most higher organisms have diploid genomes: identifying new recessive mutations requires at least two generations of crosses
149
why is neuro spora an easy system ti test for defect in metabolic pathways
Normal (“wild-type”) Neurospora can grow without many nutrients because it has enzymes to generate it’s own e.g. amino acids.
Their theory was that if they damaged the DNA for one of these enzymes, then the cells would not be able to grow without the particular nutrient.
Could easily test for this by growing Neurospora on defined media which lacked one or more specific nutrients.
150
to test if genes were responsible for specific chemical reactions , what did beadle tatum do and identify
they irradiated neurosora with x rays ( known to cause mutations )
thwy identified a series of auxotrophic mutans
151
what are auxotrophs
are mutant strains that cannot synthesize a particular molecule required for growth (such as arginine) – therefore they will only grow if they are supplied with that molecule.
152
how can you screen for auxotrophic mutants
1- culture individual spores on comlete medium
2- transfer to minimal medium to identify possible auxotrophs
3- test candidates for growth on minimal medium spplimented with different classes of nutrients ( vitamins aa or nucelotides )
4. Test candidates for growth on MM supplemented with individual amino acids (or vitamins or nucleotides)
5- identify the amino acid that allows your mutant to grow
153
what are the three clasess of arganine auxotroph identified by srb and horowitz
Class I mutants grow on:
MM + ornithine
MM + citrulline
MM + arginine
Class II mutants grow on:
MM + citrulline
MM + arginine
Class III mutants grow on:
MM + arginine (only)
154
what is the 'one gene - one enzyme ' hypothesis
beadle and tatum poropsed that each enzyme in a pathway was controlled by one gene
role of a gene is to encode an enzyme- and that for each anzyme there is a gene
155
how did the idea of ' one gene - one enzyme' develop to 'one gene one polypeptide'
‘One Gene - One Enzyme’ Hypothesis…
But… not all gene products are enzymes.
As knowledge of proteins grew it became clear not all proteins were enzymes. For example there are many structural proteins.
Therefore:
‘One Gene – One Protein’
Further work showed some proteins are made of more than one polypeptide chain, for example haemoglobin is formed of alpha and beta polypeptides.
Therefore:
‘One Gene – One Polypeptide’
156
what is rna
a polymer of nucleotides containing ribose sugar and combinations of four bases: adenine, guanine, cytosine and uracil – usually single-stranded
157
what are the pulse-chase experiments provided evidence for messenge rna
15 min label with radioactive uracil
labelled rna in nucelus
15 min label + 90 min chase with non radioactive uracil. labelled rna in cytoplasm
conclusion: rna is made in the nucelus and moves into the cytoplasm
158
what is the central dogma to molecular biology
dna to m rna to protein
159
what is transcription
Transcription is the synthesis of a mRNA molecule using one strand of the DNA as a template such that G pairs with C and A pairs with U
160
what is transciption catalysed by
rna polymerase
161
does rna polymerase reuqire a primer
no
162
what are the 3 stages on transcription
initiation
elongations
termination
163
what happens in transcription - elongation
RNA polymerase moves along the DNA template, unwinding the double helix and catalysing the addition of ribonucleotides to the 3' end of the growing RNA molecule
164
explain transcription - termination
termination signal in the newly produced RNA
rna polymerase detaches
165
similarities in rna polymerase structure between bacteria, archaea and eukaryotes
all multisubunit enzymes with a conserved core
166
prokaryotic rna polymerases
core enzyme
everything except sigma factor
167
prokaryotic rna polymerases-
holoenzyme
core enzyme + sigma subunit
168
prokaryotic rna polymerase - sigma factor binds directly to.... and locates...
dna
locates the transcipritonal start site by recognising the promoter
169
analysis of promoters of many bacterial genes identifies a ....
promoter consensus
170
what does Prokaryotic promoter (for primary sigma factor s70) consists of
two dna elements
35 sequence- consensus sequence TTGACA
10 sequence - consensus sequence TATAAT
171
what made people realise the rna has to be translated into the 20 letters for amino acids
there are only 4 different bases in dna but 20 different amino acids in proteins
id 4 bases 4^3 = 64 'words'
172
groups of 3 bases are called ...
codons
173
what was the first codon to be proved and how
UUU, coding for phenylalanine was the first codon to be proved.
Took artificial mRNA consisting entirely of Uracil and added to a cell-free translation system.
Found that protein consisted entirely of phenylalanines.
174
?/64 codons coded for amino acids
61
175
what are the stop codons
UAA
UAG
UGA
176
what does AUG do
start codon
and also encodes methionine
177
why is the genetic code specific but redundant
Each codon can only specify one amino acid: so it is specific.
But amino acids can be specified by more than one codon: so it is redundant.
178
what does it mean that the geentic code is univversal and what does it indicate
In the main, the same codons are used for the same amino acids from the simplest bacteria right up to complex organisms like humans.
This indicates it must have been established very early during evolution.
179
what does it mean that proton sequence depends on the reading frame
The codons are read by the translation machinery in the 5' to 3' direction along the mRNA.
But there are No “commas” between codons i.e. nothing to say where one codon ends and the next begins.
Any mRNA could be translated as 3 different proteins.
Protein sequence depends on the reading frame.
180
how does translation get the reading frame correct
always begins at the start of methionine and the correct reading frame follows from there
181
what is the structure of tRNA
Approx. 80 nucleotides in length
Single stranded but base pairs form within the chain G-C, A-U etc.
Clover leaf structure further folds to make L-shaped molecule
Anticodon is at one end - base-pairs with codon
Amino acid attachment site is the 3' hydroxyl group at the end of the RNA chain
182
what determines tRNA specificity
each trna is specific for a single amino acid determined by its anticodon
183
what can trna be descibed as
adaptors
184
185
whay enzyme carried out speciifc attachment for trna to the correct amio acid
amio-acyl tRNA synthetases
186
what is the 2 step atachment process for attaching an amino acid to its tRNA
1- ATP hydrolysed and amino acid joined to AMP
2- correct tRNA binds and amino acid transferred from AMP to the tRNA
187
how many tRNAs are ther
40-45
188
how are there 61 amino acid codons but only 40-45 tRNAs
where multiple codons specify the same amino acid, it is often only the 3rd base in the codon that varies.
wobble base pairing
189
what are ribosomes composed of
ribosomal RNA and proteins
190
structure of a ribsoomes
two subunits - large and smallw
191
make sure u can label a ribsome structyre
lec 6 slide 15
192
what do ribosomes do
Binds mRNA and amino acyl-tRNAs
Catalyses stepwise formation of peptide bonds (amino acids added from N terminus to C terminus)
Moves in 5’-3’ direction along mRNA
By recognising the correct start codon, ribosomes ensure correct reading frame is used
193
what 3 stages does protein synthesis occur in give a brief discription for each
Initiation - small subunit binds mRNA and initiator amino acyl-tRNA then large subunit binds
Elongation - peptide bonds are formed as the ribosome moves along the mRNA
Termination - one of the three stop codons enters A-site and the completed protein is released
194
descibe translation - initiation
Small ribosomal subunit binds mRNA near it’s 5’ end (recognises sequence signal just 5’ of AUG start codon).
Initiator tRNA binds to AUG start codon
Large subunit binds so that the initiator tRNA fits into the P-site on the large subunit
Requires energy from GTP hydrolysis and proteins called initiation factors (help stabilise initiator tRNA and to assemble ribosome).
195
descibe transcription - elongatino
Incoming aminoacyl tRNA base pairs with codon in the A-site - requires hydrolysis of GTP
Peptide bond formed between amino group of the new amino acid and the COOH group of the amino acid in the P-site – catalysed by peptidyl transferase
Growing polypeptide chain now in the A-site
Translocation - tRNA in the P-site is ejected and the ribosome moves along the mRNA by precisely one codon – requires hydrolysis of GTP
Growing chain now in the P-site and the A-site is free to accept the next incoming aminoacyl tRNA
196
what is the elongation cycle
codon recognition
peptide bond formation
translocation
ribosome ready for nect amino acyl trna
197
which direction do proteins grow
from amino terminal to carboxy terminal
198
what are peptide bonds catalysed by
peptidyl transferases - an rna enzyme
199
exmplain translocation - termination
Stop codon in A-site
There are no tRNAs for stop codons
Release factor enters A-site instead of amino acyl tRNA
Water added to end of polypeptide chain
Completed polypeptide released from tRNA in P-site
Ribosome dissociates, 2 X GTP hydrolysed
200
what are polyribosomes ( polysomes )
occurs in both eukaryotes and prokaryotes
an mrna molecule is generally translated simultaneously by several ribosomes in clusters called polyribosomes
201
differences of translation in prokaryotes and eukaryotes
pro have 70s ribosmes, euk have 80s
pro have no nuclear membrane so trnascription and translation is coupled. but euk have a nucelar membrane - mrna transported to cytoplasm before translation occurs
pro have no organelles- proteins diffuse though cytoplasm. euk have several diiferent organelles- proteins must be trafficked to correct site
202
Targeting of proteins destined for secretion to the endoplasmic reticulum (in Eukaryotes only)
1- polypeptide sythensis begins on a free ribosome in the cytosol
2- an SRP binds to signal peptide, haulting sythesis momentarily
3- the srp binds to a receptor protein in ER membrane. thsi receptor protein is part of a protein complec that has a membrane pore and a signal cleaving enzyme
4- the srp leaves and polypeptide resumes growing, meanwhile translocating across the membrae. the signal paptide stays attached to the membran e
5- the signal cleaving enzyme cuts off the signal peptide
6- the rest of the compleed peptide leaved the ribosomes and folds into its final conformation
203
how do Protein synthesis inhibitors act as ANTIBIOTICS
A range of compounds have been shown to inhibit translation on prokaryotic 70S ribosomes but not on eukaryotic 80S ribosomes.
These compounds prevent the growth of bacteria and should not affect human and animal protein synthesis.
BUT 70S ribosomes are also present in mitochondria, thus some antibiotics can have detrimental side effects
204
what is fusidic acid and what does it do
Narrow spectrum steroid antibiotic – principally staphylococci (e.g. MRSA)
Also used in structural studies of ribosome function
Inhibits elongation at the translocation step
Blocks A site for next round of amino-acid incorporation
205
what is a mutation
a perminant chnage in dna of a cell
could be a change in gene position or number
could be a chnage in nucleotide sequence
206
describe mutations in germ line tissues
Mutations in germ-line cells are passed on to offspring
Cause of inherited genetic diseases.
Raw material from which natural selection produces evolutionary change
207
descibe mutations in somatic tissues
Mutations in somatic cells are not passed on to offspring.
Somatic mutations are passed on to all cells descended from the original mutant.
~85% cancers caused by somatic mutations
208
eg of point mutations
subsitution
deltion
209
if a codon was subituted into a stop codon
what is this mutation called
null mutation
no protein is made at all
210
how does sickle cell anaemia arise from base pair substiution
T--> A
glu --> Val
glutamic acid is large, charged and has a hydrophilic side chain
valine is small, non polar with a hydrophobic sidechain
211
what are the 2 catogarieas of casues of mutations
spontaneous
induced
212
what can induced mutations be split into
- give examples for each
chemical - base analogues, modifying agents, intercalating agents
physical- ionising radiation, ultraviolet radiation
212
what does it mean that a mutation is spontaneous
dna replication
213
spontaneous mutations can occur due to ...
inherent instability in DNA
214
what is base tautomerism (spontaneous mutations )
imino form is possible at low frequencies
the nucelotide can change to other conformations
(isomers and tautomers)
so during DNA replication an incorrect base is inserted to from mismatched pair
215
induced mutations occur when..
an outside agent 9 mutagen ) damaged dna
216
what are base analogoues
chemicals that resemble dna bases but pair incorrectly when incorperated in dna
eg. 5 bromouracil is incorporated into DNA as though it were thymine
Once incorporated it tends to rearrange into a form that resembles cytosine.
Upon DNA replication, can result in a point mutation converting a AT bp to a GC bp.
217
give an example of a chemical that removes the amino group from adenine or cytosine
eg. DEAMINATION of C to U
Replication of DNA containing deaminated C results in A being inserted
Daughter strand base pairing changed from CG to TA.
Occurs spontaneously at low rates
Uracil not usually found in DNA
Uracil DNA glycosylase has specific role in removing U from DNA to prevent mutations.
218
what do alkylating agents do
many of these chemicals are mutagens
addition of an ethyl group at o6 position alters the base pairing characteristics
resulting in a point mutation
(chemicals that add hydrocarbon groups to nucelotide bases )
219
what is an intercalating agent
insert between bases and distort dna helix
interfere with replication
tend to cause frame shift mutations
eg. ethidium bromide
220
how is ionising radiation a physical mutagen
ir can damage bases and cause double-stranded breaks
1. ir can directly ionise dna
2. ir can ionise water to produce free radicals which can interact with dna causing dna deformation
221
how does uv act as a mutatgen
pyrimidne dimers
UV irradiation is absorbed specifically by the pyrimidine bases cytosine and thymine.
Covalent bonds can form between adjacent T or C nucleotides – pyrimidine dimers
Blocks DNA synthesis leaving a gap opposite the site of damage.
222
what are the 2 catagories for dna repair pathways
single strand damage
double strand breaks
223
3 types of single strand damage (dna repair pathways )
base excision repair
mismatch repair
nucleotide excision repair
224
2 types of double strand breaks (dna repair pathways )
homologous recombination (G2)
non-homologous end joining (G1)
225
how can pyrimidine dimers be removed
by nucleotide excision repair (NER)
1. thymine dimer distorts dna molecule
2. a nucelase enzyme cuts the damaged dna strand at two points
3. repair synthesis by a dna polymerase fills the gap
4.dna ligase seals the remaiing nick
226
individuals with rare hereditary disorder......... are deficient in NER
xeroderma pigmentosum
227
what is xeroderma pigmentosum characterised by
development og skin cancer at an early age but only on parts of body exposed to sun
228
what is the ames test
rat liver extract
1. with a positble mutagen on a plate ( w. minimal media lacking histidine )
and incubate- high number of reverants (his- to his+) suggestes the mutagent causes mutations
2. also done wihtout the mutagent to form a control plate (had natural reverants )
The test serves as a quick and convenient assay to estimate the carcinogenic potential of a compound because standard carcinogen assays on mice and rats are time-consuming
conclusion- liver extract contained enzymes that may convert non mutagents into mutagens
229
what are the 2 modes of inheritance
autosomal
sex linked
230
what are single gene disorders caused by
point mutations in single genes
231
effect of single gene disorders
1-5% of pop
costing nhs 2 bill a year
high morbidity and mortality in children,
most are currently incurable but treatments inporving
232
what are autosomes
all chromosomes apart from x amd y
233
describe the appearancee of an autosomal recessive pedigree
males and females affected
disease absent from most generations
consanguinity ( sexual relationship with a blood relative ) increases frequency of affected individuals
carries have 25% chance of having an affected child
234
where does CF disorder origionate
in secretory epitherlial tissue
235
symptoms of CF
accumulation of mucus in lungs, pancreas , digestive tract and other organs
multiple effects including: chronic bronchitis, recurrent bacterial infections
236
what does the CF gene (CFTR) code for
a chloride channel
237
what does CFTR stand for
cystic fibrosis transmembrane conductance regulator
it regulated the flow of cl- across the membrane
238
describe the most common mutation causing CF
Deletion of 3 base pairs (bp) results in loss of a Phe (F) residue at position 508
Protein does not fold normally and is more quickly degraded
239
how does a defect in CFTR cause CF
defect in cl- transport causes extracellular mucus to become thicker and stickier
240
treatment for cf
life prolonged by antibiotics and by daily massage to clear mucus from airways
241
explain precision medicines for cystic fibrosis
sequencing of chloride channel gene, they can determine exactly wht mutation the patient has
- there are drugs to imporve the functin of the mutated portein
- gene thera[y
242
drugs to imporve function of mutated portein - cf
these drugs aim to imporve the function of the mutated ion channel, the druf to treat with depends on what effect the particular mutation has e
Other mutations can be treated with combination therapies that bring more of the chloride channels to the surface and help those channels to operate more effectively.
243
gene therapy for treatment of CF
Gene therapy treatments: to provide patients with a copy of the correct chloride channel.
Clinical trials for integrating and non-integrating gene therapies are underway.
244
main symptoms of sickle cell anaemia
anaemia
joint oain
swollen spleen
frequent severe infections
245
treatment and cure for SCA
treatemnt - regular blood transfusion
cure - bone marrow transplant
246
explain SCA form a single nucleotide subsitution
glutamic acid to valine
leads to incrorrect folding portien
the defective heamaglobin froms long chains of rigid polymers which deform the red blood cell
- mutation occurs in beta-chain of haemoglobin
247
what are the pleiotropic effects of sickle cell
one gene having multiple phenotypic effect s
eg/ 1- breakdown of red blood cells leads to anemia, heart faliure , physical weekenss
eg.2- clumping of cells and clogging of small blood vessels leads to heart faliure, pain and fever , brain damage ( which leads to paralysis, impaired mental function )
248
what is the 'sickle cell trait'
heterozygotes (carriers ) also have a phentoype in low oxygen conditions
- at sea level carriers have normal blood
at hihg altitudes cells have sickle tcells present
carriers are resistant to malaria
249
why is the sickle cell allele maintained in popoulation
having sickle cell trait ( carrier ) confers resistance to malaria
so selection for malaria resistance in carriers
its an example of heterozygote advantage ( where the heteroxygoite is fitter than either of the homozygotes )
250
descibe the appearane of an autosomal dominat pedigree
males and famles affected
affected inidvidualrs have an affected parent
50% chnage of affected parent having affected child
251
main symptoms of huntingtons disease
( autosomal dominant )
jerky movements
personality changes
deterioration of walking, speaking and swallowing abilities
death will result from complications such as choking, infection or heart failure
252
explain the molecular causes of huntintons
large gene mapping studies showed defect on chromosme 4
narrowed down to abnnormalities in the HD gene
HD gene contains CAG repeates 11-34 repeates is normal
huntingtons have 36-125 repeates
253
symptoms of familial hypercholsterolaemia (FH)
autosomal dominant
high levels of cholesterol in the blood from an early age
cholesterol deposits build up in joints
cardiovascular disease
254
treatments of FH
cholesterol lowering drugs
low cholesterol diet
255
what is FH due to
a lack of low density lipoprotein receptor
without LDL recepot the cholesterol accumulates in the blood
( ldl bind to and carries cholesterol in the blood stream )
256
what is FH an example of and how
incomplete dominance
Homozygotes (hh) have a 6-fold increase in blood cholesterol - heart attacks at age of 2
heterozygotes - have a 2 fold increase in blood cholsterol - heart attacks by age 35
257
what is the dominat phenotype caused by (fh)
haploinsufficiency
258
decsribe the appearance of a pedigree of a sex linked recessive trait
Females are carriers, mostly males affected
Carrier female will transmit to 50% of sons (affected) and to 50% of daughters (carriers)
Affected male cannot transmit to sons but will transmit to 100% of daughters (carriers)
259
symptoms of sex linked recessive - haemophilia
uncontrolled bleeding
tendency to extensive bruising
bleeding into joints
260
haemophilia A
mutstion in the gene for factor VIII ( on x chrom )
1 in 5000 males
261
haemophilia B
mutation in gene for factor IX ( on x chrom )
1 in 30,000 males
262
descibe duchenne muscular dystrophy
sex linked recessive
muslce wasting disease
the most frequcuent lethal childehood genetic disease
affected gene codes for a muscle protein called dystrophin
dystrophin gene is very large - so prone to rearrangements
263
what is dystrophin
part of a protein complex that connects the cytoskeleton of a muscle fibre to the surrounding extracellular matrix through the cell membrane.
264
advantages for bacteria for genetics
easily cultured
short generation time 20-30 min
haploid ( if you see a chnage ( mutation) you see it imedialty - in diploid you have to wait till F2 generation)
ecoli ( escherichia coli) used
265
descirbe E.coli
singular circular chromosome
e.coli chromosome is a double stranded circular dna molecule ( 4.6 million base pairs in length and contains around 4500 genes )
we call this single chromosome the genome of e.coli
266
bacterial dna is compacted by....
coiling up in a structure called the nucleoid which ocupies a large fraction of the cell volume
267
what is a bacteriophage
viruses that infect bacteria
they are structurally and functionally diverse
268
lytic( or virulent) bacteriophage life cycle
lytic bacteriophage multiply and then lyse the bacterial cell releasing progeny bacteriophage particles
(T4)
269
temperate ( or lysogenic )bacteriophage life cycle
can integrate into the bacterial chromosome and remain dormant replicating along with the bacterial dna
270
the lytic life cycle of a bacteriophage - detailed decri[tion with example of T4
1- the T4 pahe uses its tail fibers to tick to specific receptors sites on the outer surfave of an ecoli
2- the sheath of the tail contracts, thrusting a hollow core through the wall and mambrnae of the cell. the phae injects its dna into the cell
3- the empty capsid of the phage is left as a ghost outside the cell. the cells dna is hydrolysed
4- the cells metabolic machinery directed by phage dna, produces phae rpoteins, and nucelotides from cell degraded dna is used to make copies of phage genome. three separate sets of proteins assembel to form phage heads,tails and tail fibers
5- phage then directs production of lyzozyme, digests bacterial cell wall , damaged wall so osmosus causes the cell to swell and burst releasing ohage particles
271
temperate phage - explained in detail
the phage attaches to host cell and injects dna - the phage dna circulizes
- this could enter lytic cycle where new phage dna is synthesised and assembled into phages and then the cell lyses releasing the phages'
- ot the phage integrates into the bacterial chromsome becoming a prophage.
the bacterium reproduces normally,copying the prophage and transmitting it to daughter cells
many cell divisions produce a colony of bacteria infected with prophage
ocassionaly, a prophage exits the bacterial chromsosme intiiating lytic cycle
272
gene transfer and recombination occurs through what 3 processes
1- transformation
2- transductino
3- conjuction
273
what is recombination and what does it produce
recombination is defined as the combining of dna from 2 individuals into a single genome
it produces new combinations of alleles
274
what is reansformation
the uptake of naked dna
275
what is transduction - gene transfer in bacteria
trasfer of bacterial genes from one bacteria to another by a bacteriophage
276
what are the 2 types of transduction
generalised- occurs only with virulent phage
specialised: occures only with temperate phage
277
explain the transduction process ( generalized )
phage infects bacterial cell
host dna is hydrolysed into pieces, and phage dna and proteins are made
ocasionally a bacterial dna fragment is packaged in a pahge capsid
transducing phages infect new host cells, where recombination ( crossing over ) can occur
278
describe the transduction processs - specialized
bacterial cell has prophage integrated between genes a and b
ocassionally prophage dna exists incorectly, taking adjoining bacterial dna with it
phage particles carry bacterial dna along with pahge dna
transducong phage infect new host cells where recomination can occur
279
what is conjugation
the ability to form sex pili and to transfer dna by conjunctinon is determined by a plasmid called an F ( for fertilty ) factor
280
explain conjunction
the F factor replicated in synchrony with the bacterial chromsome
the F factor replicates in such a way tha tone end of the DNA molecule passes through the cytoplasmic bridge itno the recipient cell where it circularises
the recipient cell is called an exconjugant
the donor keeps a copy of the F factor
281
what can ocassionaly happen to the F factor
conversion of an F + into an Hfr
( the dna has been integrated )
282
what happens in a conjuction between an Hfr and a F - bacteriym
takes some of the host dna with it into the recipient cell
if it lines up recombination ( crossing over ) can occur betwenn F- chromsome and transferred fragment
283
genes which code for proteins required all the time by the bacterial cell are ,.............. expressed
constitutively
284
other genes are only active ( expressed ) when they are required - ....... genes
regulated
285
gene expressino in bacteria is oftern controlled at what level
intitation and transcription
286
explain the control of tryptophan biosythesis
regulated sythesis of repressible enzymes
th promoter wheere rna sythesise binds is an operator - a repressor can bind here can control gene expression
if tryptophan absernt --> repressor inactive --> operon on ---> makes tryptophan
when tryptophan is pressent tthe repssor is active ,
this is an example of negative regulation - binding of repressor to operator blocks transcription
287
explain contorl of lactose metabolism
regulated sytheisis of inducible enzymes
lactorse absent, repressor active, operon off
lactose present , the cell whants to break it down. the lactose is a inducer. the repressor is inactive, the operon is on
288
explain the similarites and idfferences between lac and trp
both examples of negative regulation
trp operon, expression is off when tryptophan binds to repressor which then binds to the operator.
lac operon, expression is off in the absence of lactose when the repressor binds to the operator.
289
what is positive regulation
bidning of a molecule to the operator turns on gene expression
290
example - positive regulation of gene expression and explain
cAMP receptro protein
lactose present, glucose scarce ( cAMP high - binds to crp and activates it )
the binding of crp to lac operon activates it
abundant lacmRNA sythesus
as lactose it present the lacrepressor is tunred off
lactorse present ( so repressor turned off )
glucose is abdunant ( cAMP low- so operon of eventhough lactose is present ) lottle lacmRNA synthesis
291
what is bioinformatics
using computer technology to collect store and analyse and disseminate biological data and information
( bioinformatics is compyteraided biology )
292
why do we need bioinformatics
the gwoth if darabases of genetic informations is increasing
and sequecning cost per human is decreasing due to ti
293
example uses of bioinformatics
- genome sequence and annotation
- protein structure and molecular binding
- dna idnetification
- omics studies
294
what does omics mean
suffix used to decreibe the large scale study of various biomolecules
295
what is genomics
DNA imput
eg. whole genome sequencing, microarray
296
what is epigenomics
DNA modification
eg. whole genome bisulfite sequencing
297
what is transcriptomics
rna
eg. rna sequencing
298
what is proteomics
protein
eg. mass spec
299
what is metanolomics
metabolite imput
eg. mass spec
300
why are omic studies useful
diagnose susptced genetic disorder
determine cancer mutation
301
what are some different sequencing technology
- sanger sequencing
- next generation sequencing ( short read and long read )
302
what are some different processing for a DNA imput sample
whole genome sequencing
exome sequencing
gene panel sequencoing
303
what are some different processing for a RNA imput sample
rna sequencing
single cell rna sequencing
spatial transcriptomics
304
what are sequencing reads
the digital outputs of sequencers that comes from reading the physical fragemnts of DNA / RNA
305
sequencer ?
device that can automate the process of determining the dna bases
306
read ?
nucelotide sequneces generated by a sequrncer
307
issues with bioinformatics particularly with beginners
large number of tools available - when to use what
most tools and databases are not very user friendly
the outputs can look intimidating
d
different file formats
308
dna barcoding
allows specific identificatino through a short section of dna - amplified by pcr and then sequenced
cost effective 'genes regions that are similar wihtin the same species and distinct across differnt species
309
commonly used genes for dna barcoding
Animals: MT-CO1, 16S rRNA
Fungi: ITS (internal transcribed spacer)
Bacteria: 16S rRNA or 18S rRNA
310
example uses for dna barcoding
food fraud detection
identificying pollens
pathogen survaillance
311
what is FASTA format
a commonly used simple format for nucelotide / amino acid sequecning
sequence id required, unique, then a space then after the sapve is decription optional
312
'search' in context to databases
Typically you would say you
“search” a database or perform a “search”, to
describe the process of looking for specific
information in a database.
313
'query' in terms if databases
the formal and structured request for data in dtatabases. oftern used interchangably with search
314
'subject' in context of database
the sequences that your query sequence is compared to
315
dna barcoding can be used to build phylogenetic trees - recorded in what format oftern
newick - its designed for computers and hard to read for humans
316
what is phylogenetcis
the study of the eveolutionary history and relationships
317
what is a clade
a group of organisms that included a single ancestor and all of its descendents
318
what is a branch
shows the path of transmission of genetci information from one generation to the next; the longer the lines the more genetic change has occured. the branch lenghts are usually the number og genetic chnages per sitr ( eg, if 1 base difference for a 100 base sequence the length will be 0.01 )
319
clustal file format is a type of what file
alignment file
320
what is the clustal file format
first line starts with the software that generated this alignment
then sequence name followed by up to 60 amino acids or nucelotides per line
* - all identical
: conserved subsitutions ( strong similar the physico-chemical property)
. semi conserved subsitutuipn ( weak similar physio-chemical properties
no match
321
what is sequence alignment
a way of arrange amino acids or nucleotides sequences to identify regions of similarity ( put the sequences next to each other in a way that they line up well )
322
what is a primary key ( database)
a uniqye id for identifiting an entry in a table in a database
minor technical difference to accession number
323
'fields' in a database context
a set of attributes
324
what is genecards
collates information from different datavases and provides links to sources
its a human gene database with extensive information on each gene
325
what is a PDB
protein data bank format is used to store infromation on protein structure
326
abbreviations
nt
nucleotide
327
UTR
untranslated region
328
CDS
coding dna sequence
329
abbreviations
ORF
open reading frame
330
MT
mitochodnrial
331
what are residues
a unit for counting amino acid
332
How many genes in prokaryotes
500 - 4000 genes
333
how many genes in eukaryotes
6000 - 30 000 genes
334
what is the difference between genome organisation in pro and eukaryotes
pro have a small genome , ciruclar dn a
euk have larger genomes, in linear dna organised into chromatin
335
why are eukaryotic genomes generally so large
the number of genes - reflectong the greater complexity of the organism
the amount of non coding dna
336
there are large amounts of non coding dna in eukaryoyic - explain (eukaryotic genomes are generally larger )
in pro most dna codes for proteins
in euk most dna does not code for protein or rna
337
what do non coding sequences consist of
- gene regulatory sequences eg. promoters
- intorns ( non coding sequences within genes )
- sequrnces of no known function ( including repetitive dn a sequences )
338
what are exons and introns
exons - transcribed sequence that is represented in the final mrna
introl - intervevning sequence in the transcribed region that is not represented in the final mrna
339
what are the two types of repetitive sequences
- interspersed repetitve dna
- tandemly repetitive ( satellite dna )
340
what are intersperesed repetitive dna
- repeated units scattered throughout the genomes
Single unit 100-10,000 bp
Copies not necessarily identical, but closely related
Makes up 25-40% of most mammalian genomes
e.g. Alu elements (300 bp repeats) make up 5% of the mammalian genome
341
how were detection of interspersed repeates in human chromsomes observed
using fluorescent tags
FISH: fluorescent in situ hybridization
green fluorescence shows location of Alu repeates sequences around the human genome
342
what is tandemly repetitive ( satellite) dna
and what are the 3 types
can be broadly classified according to the length of a single repetitive region
Regular satellite DNA: 100,000-10 million bp per site
- Minisatellite DNA: 100-100,000 bp per site
- Microsatellite DNA: 10-100 bp per site
343
where is much satellite dna located and what does this suggest
telomeres and centromeres suvgesting a structural role
344
how does satellite dna link to genetic disorders
some genetic disorders are caused by abnormally long strches of repetitive sequence within a gene
345
how was satellite dna detected
using flourecent tags
346
what are chromasoes composed of
chromatin ( protein + dna )
347
what is the fold compaction for dna
10,000 fold compaction
348
why must dna be packed in an organized manner
to be accessible for transcription and replication
349
how is dna packed and organised
association with specific proteins ( histones ) and the formatin of chromatin
350
eahc human chromasome contains a single linear dna double helix. how long ?
6 cm
351
heterochromatin?
highly condensed during interphase, not actibely transcribed
352
euchromatin?
less condensed during interphase, able to be transcribed
353
what is the basic unit og chromatin
nucleosome
354
histones ?
proteins with positively charged amino acids that bind to the negatively charged dna - they play a key role in chromatin structure
355
how many bp are wrapped aroun each histone
200
356
Higher orders of packing
30 nm of chromatin fiber
looped domains of the 30 nm chromatin fiber
during interphase, most of the chromsomes is in this form ( euchromatin )
357
during meisois and mitosis the chromatin....
condenses
the highly condensed chromatin also occurs during interphase in some regions of the chromsome
358
what is the nucleosome bead
around 200bp of dna double helix wraps around histones ( octamer)
359
why might most regulation of gene expression occur at the transcirptional level
more energy efficient
energy is not wasted making a mrna that is not translated
360
what different contol of genes is there for regulation of genes
it can occur at any step from gene to protein
1- dna unpacking
2- transcriptional contro;
3- rna processing control
4- rna transport and localization control
5- mrna degradatin control
6- trnaslation contorl
7- protein acitvity control
361
what 2 forms of coarse adjustment of gene expressino by chemical modification of chromatin
1- dna methylation
2- histone acetylation
362
descibe dna methylation
- attahcment of methyl groups to dna bases
- triggers formation fo compact chromatin structre
- associated with inactive dna
- accounts for genomic imprinting in mammels
363
describe histone acetrylation
asscoiated with gene activation
- attachemnt of acetyl groups to histones
- acetylated histones grip dna less tightly
- acetylation / deactivation is involved in switching genes on and off
364
what can causes closed chromatin
dna methylated
histones not acetylated
365
what can cause open chromatin
dna unmethylated
histones acetylated
366
what are the 3 different rna polymerases
RNA polymerase I (pol I): ribosomal RNA
RNA polymerase II (pol II): messenger RNA (mRNA)
RNA polymerase III (pol III): small RNAs e.g. tRNA
367
what is a promoted
dna sequences adjacent to the gene ( upstream )
that:
- determine where the transcription fo the gene is intiated
- determine the rate of transcription
368
what is the TATA box
a key part of the promoter
provides the site of initial binding of the transcription intiation machinery
located 10-35 pb upstream of the transciption start site
369
before transciption can start what mist form
preintiation complex must form
370
rna polymerases cannot bind to promotoers on their own - descibe what happens
1- binding of TFIID : includes the TATA-binding protein + TAT-associated proteins
2- sequential additon of other ' general transcription factors ' - first TFIIA and TFIIB
3- then binding of TFIIF + RNA polymerase II
4- follwed by TFIIE + TFIIH to from the preinitiation complex
371
how is the rate of transcirption modulated in eukaryotes
The interaction between the transcription initiation complex and the basal promoter is very inefficient – so would produce very low level of gene expression
The process is regulated by ‘specific transcription factors’ (‘activators’ or ‘repressors)
These bind to ‘proximal control elements’ and ‘distal control elements’ (groupings of which are called ‘enhancers’)
372
how do enhancers worj when tney may be q00s of bps from the promoter
the dna forms to bring distal sequences into proximits with the promoter
373
what is the transactivation domain responsible for
recruiting other proteins into the transcirption factor complex
374
what is the post transcriptional regulation :
processing of the primary transcirpt ( in eukaryotes )
- capping of 5' end
-polyadenylation of 3' end
- splicing to remove introns
375
what is alternative rna splicing
how one gene can code for more than one protein
1 primary transcript - then there are alternative mrna depnding on what is spliced
the regulatory proteins control inton - exon choices by bidinging to regulatory sequences wihtin the primary transcript
different mrnas can be generated in different cell types
376
give an extremme example of alternative splicing
Dscam gene can generate over 30000 different proteins through alternative splicing
Dscam proteins are located on the surface of a growinf neuron
provide cell recognition mechanism that regualted brain dvelopemnt
377
what determination
the process that leads up to the observable differentiation of a cell
378
wwhat is the differentiated states achived through
mainly through transcriptional regulation - involving gene cascades
379
explain a gene cascade
gene 1 is activated - its a transcriptional factor
this goes on to activate the next level of genes in the cascade that are aslo transciptional factors
these go on to activate the cell specific genes
gene one = master regulator gene
380
determination and dfferentiation
precursor cells
maste regulatory gene = off
cell spefic genes = off
signal
determined cell
master regulatory gene= on
ce,l spefiic gene = off
differentated cell
master regulatory gene = on
cell specific gene = on
381
explain deterination and differentiation of muscle cells
Muscle cells develop from embryonic precursor cells with the potential to develop into a number of different cell types
Signals from other cells lead to activation of the myoD master regulatory gene encoding the MyoD transcription factor
Cell determination has now occurred and the cells are called myoblasts
MyoD activates the expression of other muscle-specific transcription factors
These in turn activate genes for muscle proteins (such as myosin) and block cell division – non-dividing myoblasts fuse to form muscle fibres
382
what are the 3 main phases of drosophila development
1- estabilishing the main axes ( anterior, dorsal , posterior, ventral)
( stage called the synsutical blastoderm )
- nuclei divide but cell walls dont form
2- establishing the segemnts - head ( 3 segments) , thorax ( 3 segments ), abdomen ( 9 segments )
3- filling in the details - organs, wingles, legs, eges
383
what is the bicoid mutant
-abnormal larva from bicoid mutant mother
- no anterior end, just two posterior ends
bicoid = two tailed
384
what is an egg polarity gene
these determine the polarity of the egg and therfore the fly
encode proteins or mrna that enter the egg while it is still in the ovary
when the maternal gene is defective, the gg fail to develop normally ( therfore called maternal effect genes )
encode transcription factors which intiate a cascade of gene activations
385
how can you see an egg polarity gene ( eg, bicoid )
a gradient of the bicoid mrna is already establsihed in the unfertilized egg '
leading to a bicoid protein gradient in the early embryo
- nuceli which bicoid protein has been fluorescently labelled you can see a brighter side and a darker side - a gradient
386
what does the bicoid protein gradient determine - what other conclusions did the come to from these experiments
the anterior end of the fly
established the princple that a gradient of molecules can be determine polarity and position
such molecules are called morphogens
bicoid and other morphogens are transcription factors which initiate a cascade of gene activations
387
egg polarity genes like bicoid intiate a gene cascade that regulates drosophila development
explain the stages
egg polairty genes
- 3 classes og segmentation gene
1- gap genes
2- pair rule genes
3- segment polairty genes
homeotic genes
388
what do egg polarity genes do
determine the anterior- posterior axis and induce
389
what do gap genes do
sub-divide the mebryo into broad areas- and induce
390
what do pair genes do
establish pairs of segemnts - and induce
391
what do segment polarity genes do
establish the anterior -posterior acid of each segemnt and induce homeotic genes
392
what do mutations in gap genes produce
a phenotype where part of the embryo is missing
393
what do homeotic genes do
Homeotic genes were first identified as dominant mutations that changed the identity of body parts e.g. Antennapedia in which legs develop in place of antennae
394
There is a series of homeotic Hox genes in Drosophila that determine the identity of embryonic regions along the anterior-posterior axis
what do hox genes encode
transcriptional factors
with a conserved dna binding domain ( the homebox domain )
hox genes occur in cluseters arranged in the same order as the regions they effect ( colinearity )
395
what does it mean that hox gene clusters are conserved between flies and mammals
order of genes similar to flies - and same as order of expession along the anterior - posterior axis
some mammalian hox genes are so similar to fly hox genes that they can be swapped
hox genes probably played an imprtant role in evolution - many differences in morphology between species/phyla appear to be due to evolutionary changes in hox genes
396
BIOL YR1
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