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nucleic acids pt 2 - transcription, there's an OH group on the 3rd…
nucleic acids pt 2 - transcription
transciption
need
dna is very important
blueprint of activity of cell and behaviour
storehouse of vital ingormatinon across generations
but dna is house arrest - can't get out of nucleus
because its double stranded - can't come out of the nucleopore
but no need to ge tout of the nucleus since it controls things from there
so it never lleaves the nucleus
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time
when does the dna divide
in the synthesis phase
preparation for transcription in g1 and g2 phase (before s phase)
of the interphase
in g2 its double, in g1 phase, its only single
sites
in 2 sites
where ends
terminator site
where transcription is just initated
promoter region
where the start codon is
strands
mrna is a form of rna
when rna enters, only rna
when out of the nucleoplasm - becomes mrna coz. its been copied
5 to 3 - sense/ coding
3 to.5 template
mrna is identical to ciding, but complementary to template
mrna has a sequence of bases with identical to ciding dtrand
but has uracil
definition
process by which synthesises of mrna from a dna template in the nucleus
transcription means copying
sequence of nitrogenous bases
fm the template strand 3'to 5'
so 5'3' direction of
copies fm anti sense strand, identical to sense strand
then moves into cytoplasm
can never take place without dna dependant - rna polymerase
rnap
entire process of synthesis and transcription
controlled by the enzyme
copying fm the strand of dna
transcription unit
segment of dna that transcribes the rna to form the mrna
3 maj sites
promoter
location
upstream to the structural gene
LOCATED AT 3 END OF TEMPLATE strand or 5 end of coding strand
important because this is where rnap can bind
has a functional sequence of bases, (present on the promoter region) recognised by rnap - consensus sequence
enables rnap to sttach on it
depending on where located - you can identify where
wherever rnao attached to its always the 3 end of template
doesn't attach to ciding strand
to consesus sequence of protomer
5' TATAAT ^3'
pribnow box
for prokaryots
functional sequence of nitrogenous bases fm 5 to 3 which starts with TATA and goes on TATAAT
terminator site
location
downstream
5 end of template and 3 of coding
place where transcription ends
structural
beteweeen terminator and promoter
functional unit of inheritance
sequence on nucleotides codes for
represents functional nuit of dna, has a sequence o nucletoides for specicif polyppetide
dna becomes fucntional when. it can code
aka cistron
its a gene
mechanism of transcription
3 major stages
initiation, elongation, termination
each has substages
initiation
1 activation of ribonucleotides
nucleoplasm has diff types of ribo/deoxy nucleotides
trnascription - protein synthesis
ribo for synthesis
cytosine monophosphate, guanlylic, adenylic, uracil acid
have to be activated
by conversion fm mono to triphosphate
adenosine monophosphate -> adenosine triphosphate
phosphorylates - adds 2 phosphate groups
nucleoside monophosphate or nucleotide
to ribonucleoside triphosphate
2 recognition of promoter region
area wrapped around actamer - not available for synthesis
but whole thing is needed
histones prevent
all histones will dissolve, then dna strands are left
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3 exposure of bases
dn abonds to promoter, localised unwinding of double stranses dna at the replication fork
dna strand gets denatured - so unwinding, formation of replicatiojn forks in 2 places
2 strands drift apart forming a bubble called transcription bubble
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h bonds break - 2 strands move away fm each other/ get separated forming bubble
elongation
base pairing
activated ribonucleotides
rnap bound to antisense/ template strand
all bases exposed on antisense, new ribonucleoside triphos/ actiated nucleotides
where a - u, where c - g
place where unwinding occurred, RNAP guides bases to form the RNA.
lot of energy very active - structure is unstable
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ligase - phosphate on 5th carbon to OH on 3rd carbon of another sugar
pohosphaester bond form
RNAP doesn't need any glue like ligase
RNAP can do anything!!
formation of phosphoester bond forms fm energy fm pyrophohphatase
to form the RNA chain
enzyme only needs a co factor - co factor is in the form of mg ions mangasese ions
termination
RNAP moves along structural genes
ribonucleitide triphosphates to 3' end of MRNA, RNA DNA hybrid increases length
length increases fm 5' to 3'
can't continue over structural gene, it has to stop
terminator region/site
or just before, it receives a polyadenylation signal
the poly a tail - 200-300 a bases,
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rho factor
before RN initiates transcription, recognises the concensus sequence, using the sigma factor to help identify
sigma factor helps RNAP ti identify on the anti sense 3'5' strand
in prokaryots like ecocholine, rho factor also neede
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depending on requirement, its named
in prokaryots - rho dependent
in euk - rho independent
increase in length of newly formed RNA
3' end
oh on 5' end
elongation takes place in 5'3' direction
reformation of dna double helix
transcribed region of dna
unwindeded so transcription can start
so it needs to be wound back - rewind
becomes double helix again
RNAP does this
it can do everything needed for transcription
RNA processing
completed RNA transcript - biologically inactive - can't function
because it is heterogenous
heterogenous nuclear rna
because it has different lengths, depending on the length of dna
and because it shows the presence of exon and intron
exon - coding part - codes for a specific amino acid - protein
intron - non coding
because of the intron - non coding, it prevents it fm becoming functional
so need to remove the intron
RNA splicing, and join exons together
then it can be biologically functional
8 diff stages
capping
process by which methylated guanosine/ guanine is added to head (5' end) of RNA
formation of g cap
tailing
formation of poly a tail
add 200-300 adenylate residues
towards 3' end of rna
cleaving
completed long rna transcript is cut into number of small pieces
splicing
removing the intron - non coding region - fm the rna
union
joining of the exons to form a functional RNA
addition
enzyme catalysed addition of nucleotides to RNA (terminal region/end of rna)
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folding
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genetic code
sequence of nitrogen bases located on the DNA coding for specific protein/polypeptide chain
cistron - functional part of DNA
gene is a segment of the DNA
codon
triplet sequence of the nitrogen bases on the MRNA
coding for particular amino acid
anti codon
triplet sequence of nitrogen bases that codes for a specific amino acid, but is on the TRNA
complementary to bases of codon/ MRNA
features of genetic code
universal
all living organisms, pro or euk
activity/ behaviour of cell is written in genetic code
if there is protein synthesis, happens
always a triplet
combination of 3 nitrogen bases
identical of sense strand
each triplet codes for an amino acid
genetic code is comma less
no punctuation
any two codes/ codons - it is continuous
initiation
start codon in euk is aug in pro - gug
always begins with an initiation codon on 5' end
aug is methanine
gug - valine
termination/ stop codon
uaa, uag, uga
same for pro and euk
degeneracy
important feature
every triplet sequence codes for an amino acid
only 20
more than 1 triplet sequence coding for one amino acid
aspartic acid - 2 codons for the same one - gau and gac - degeneracy
glycine - 4 codons
serine - 6 codons
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non overlapping
triplet sequence dont overlap
bases dont overlap with other codon
non ambiguous
specific - where it is presnt,
aug codon for methionine
wherever aug is present it only codes for methioinine
collinearity
sequence of bases is linear respect to sense strand and sequence of amino acids in polypeptide chain
sequence is similar
types of rna
t RNA
group of 61 small sized amino acids
accounts for about 10-15% of total RNA by weight
shows the presence of a site that can accept amino acids
2 characteristics
has a site which can accept activates amino acids 3'
another site to recognise the codon
trna has the anticodon - which is complementary
the triplet eequence complementary to mrna
soluble rna, superlatent rna, adapter rna
transport rna
responsible for carrying activated amino acids in cytoplasm to the site od protein synthesis (ribosomes)
characteristics
75-93 nucleotides
4s
molecular weight - 27000-31000 daltons
terminus
like dna, - 2
terminus on 3' end - free Oh group - 3' OH terminus
5' end - monophosphate terminus
base
3' end - presence of triplet nitrogen bases - CCA
on 5' end - guanine
another modified form of rna - RNA is single strandde
polynucloetide chain folds onto itself, internal complementary base pairing happens
resembles a twisted clover leaf in 3D plane
clover leaf model
four parts
3 loops and one stem
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one trna can only carry 2 amino acid
because only one anticodon
code on it - it can only take up that particular amino acid
when rna p recognises termination codon
amino acids for termination are brought in
when those are called for, trna can't recognise it, so protein synthesis stops
synthesis starts when
codon - AUG, anticonod - UAC
aug is methanine
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rrna
characteristics
most abundant - 80% of total rna by weight
important for structural component
ribisomal rna
found in assiciation with proteins
like trna - has a highly coiled structure
mechanism of translation
definition
a change in language
written in triplet sequence of nitrogen bases/ nucleotides
copied onto mrna
conveted into sequence of amino acids
a process where triplet sequence of nitrogen bases on the dna (genetic code) converted to trip bases on mrna ( codon ) finally to sequence of amino aicds on protein/ polypeptide chain
steps
4 steps
1 activation of amino aicds
2 attachment of activated amino acids on trna
3 polypeptide formation (3 sub stages) - poluymerization
initiation
elongation
termination
4 modification of polypeptide chain
raw materials for protein synthesis
ribosomes - protein factories
amino acids - raw materials
codon on mrna, and t RNA
enzymes
1 - amino acyl
trna synthetase
peptide polymerase system
atp
to activate amino acids
converting to amino acyl
WHEN ATP NOT AVAILABLE
HIGHER NUCLEOTIDES - GTP
guanisine triphosphate
purine gives more energy compared to
adenine and guanine
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soluble proteins
termination factor
elongation factor
initiation factor
dissociation
release
cations
they are co factors
enzymes need co factors - cations
mangesium, ammonium and potassium, not manganese here
steps
activation of amino acids
cytoplasm has 20 inactive amino acids
needs to be activated
so carry out phosphorylation
atp de phosphorylated
so it has enough energy to move to T RNA
1 phosphate group removed
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attachment of amino acids
attaches to binding site of tRNA
same which activates can attach cativated to tRNA - forming amino acyl tRNA
amp coming out
complete complex removed
large complex
so amo and eznyme removed
and amino acyl can bind to tRNA with energy relrased fm the pyrophosphate
phosphate added to move the amino acid
activate means adding a phosphate groups for
formation of polypeptide chain
elongation or polymerization
length is increasing - adding the amino acids
tRNA gets the specific amino acid based on codon
many small and simplae molecules added
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EPA model of ribosome
when large fixes onto lid
not always compact
because mRNA passes through that gap`
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tRNA leaves to get another same one
ribosomes move through the mRNA
specific
amino acid at 3' end, phosphate group needs to be removed
oh on 3' end esterification ewith OH in carboxylic group and Oh in 3' end of tRNA
then tRNA
aka adapter RNA
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mutation
hugo de vries
similar to mendel
obsessed with evening primrose
he was the director of a botanical garden in netherlands
had access to mendell's work before everyone
published as his own
2 more scientists did the same, credited mendell
so he changed it and acknowledged mendell
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parent plant made offspring differing in size and leaf structure fm parent
offspring transmitted these to their offspring
made term mutation
any kind of sudden or spontaneous change in hereditary material that cna be inherited
change in hereditary material on the gene
change in sequence of base pairs' nucleotides
change takes place in base pairs of gene
formatioj of phenotype inherited by offspring
decides the asequence of amino acids decides the phenotyoe
code change
altered phenotype
diff protein produced
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causes - 3/ or types
a change in fine structure of gene
gene mutations
nitrogen bases change
gene mutation
change in fine structure of gene
cased by change in number or arrangement of nucleotides
called intragenic mutations
inside the chain
changes that occur
1 or a few nucleotides
sometimes when 1 base pair changes
but still not a minor change
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examples
sickle cell anameia
plant. deficiency
chlorophyll deficiancy
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muton
smallest unit of the gene which can undergo mutation
the nitrogen bases
no of mutons = number of nitrogen bases
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change in the structure of the chromosome
chromosomal aberration
change in number of chromosomes
genomic mutation
causes and types of geen mutations
change in no of nucleotide in the dna seqment
insertion/ deletion of a new nitro base
eg - genetic code in commaless
frameshift
fm point where removed of added
reading frame changes completely
reading frame undergoes a shift
e
eg sickle cell anameia
polypeptide
new chain is midified
could be lethal
muscular dystrophy
autoimmune disorder
individual cells destroy specific cells
born with weak muscles
identify at a yound age
can't walk and is bed ridden
dystrophin has 21
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1 nitro base substituted by another (change in nitro bases)
substitution mutation
one subtrituded by another
replace a purine with pueinr of with pyrimidine
1 purine replaced by purine and pyrimidine by pyrimidine
transition mutation
one other type
but opposite - purine by pyrimidine or vice versa
transversion mutation
2 other types to go to
t
eg sickle cell anaemia
example of all
e
point mutation
change in single nicleotide
3 types
a single nucleotide affected
AAG -> AAAdegeneracy - coz of degeneracy
not expressed
called silent mutations
or same sense mutation
used to be UAG -
so translation stops
nonsense/ termination codon
nonsense mutation
mis-sense mutation
1 or more undergo changes
sometimes a type of gros mutation
rare
change in more than one nucleotide
gros mutation
becuase of change in nucleotide that occurs in translation or transcription
copy error
sickle cell anameia
structure
quartenary structure
four polypeptide chains
2 are same, 1 and 148
heavy and light chains
alpha and beta
glutamic acid is highly water soluble
all rbcs will have normal characteristics
elastic
don't usually stick to each other
independent
only the sixth position changes
in the beta chain
Hb A
normal
sometimes, same sequence in alpha chain and
same sequence in 1 beta chain, other, change in sequence
1 amino acid changes
point mutation
transversioon substitution
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there's an OH group on the 3rd carbon to get added
catcatcatcatcat
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doubt - what is activated and how, why phosphate group is added?