Prokaryotic Transcription

Transcription stops when the transcription

bubble encounters terminator sequences
– this often includes a series of A-T base
pairs

In prokaryotes, transcription and translation

are often coupled – occurring at the same
time
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Eukaryotic Transcription
RNA polymerase I transcribes rRNA.
RNA polymerase II transcribes mRNA and
some snRNA.
RNA polymerase III transcribes tRNA and
some other small RNAs.
Each RNA polymerase recognizes its own
promoter.
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Eukaryotic Transcription Eukaryotic pre-mRNA Splicing

In eukaryotes, the primary transcript must be
Initiation of transcription of mRNA requires a modified by:
series of transcription factors
– addition of a 5’ cap
– transcription factors – proteins that act – addition of a 3’ poly-A tail
to bind RNA polymerase to the promoter
– removal of non-coding sequences
and initiate transcription
(introns)

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 Mutation: Altered Genes
Point mutations alter a single base.
– base substitution mutations – substitute
one base for another
• transitions or transversions
• also called missense mutations
– nonsense mutations – create stop codon
– frameshift mutations – caused by
insertion or deletion of a single base
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Mutation: Altered Genes Mutation: Altered Genes

triplet repeat expansion mutations involve
a sequence of 3 DNA nucleotides that are
repeated many times
triplet repeats are associated with some
human genetic diseases
– the abnormal allele causing the disease
contains these repeats whereas the
normal allele does not
Chromosomal mutations change the
structure of a chromosome.
– deletions – part of chromosome is lost
– duplication – part of chromosome is
copied
– inversion – part of chromosome in
reverse order
– translocation – part of chromosome is
moved to a new location
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Mutation: Altered Genes

Too much genetic change (mutation) can be
harmful to the individual.

However, genetic variation (caused by

mutation) is necessary for evolutionary
change of the species.

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 Translation
There are fewer tRNAs than codons.
Wobble pairing allows less stringent pairing
between the 3’ base of the codon and the
5’ base of the anticodon.
This allows fewer tRNAs to accommodate all
codons.
Translation
Elongation continues until the ribosome
encounters a stop codon.
Stop codons are recognized by release
factors which release the polypeptide from
the ribosome.

43
Translation 44

In eukaryotes, translation may occur on

ribosomes in the cytoplasm or on
ribosomes of the RER.
Signal sequences at the beginning of the
polypeptide sequence bind to the signal
recognition particle (SRP)
The signal sequence and SRP are
recognized by RER receptor proteins.

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Translation
The signal sequence/SRP holds the
ribosome on the RER.
As the polypeptide is synthesized it passes
through a pore into the interior of the
endoplasmic reticulum.

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 tRNA and Ribosomes
The ribosome has two primary functions:
– decode the mRNA
– form peptide bonds
peptidyl transferase is the enzymatic
component of the ribosome which forms
peptide bonds between amino acids
Translation
In prokaryotes, initiation of translation
requires the formation of the initiation
complex including
– an initiator tRNA charged with N-
formylmethionine
– the small ribosomal subunit
– mRNA strand
The ribosome binding sequence of mRNA
is complementary to part of rRNA
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37

Translation
Elongation of translation involves the
addition of amino acids
– a charged tRNA binds to the A site if its
anticodon is complementary to the
codon at the A site
– peptidyl transferase forms a peptide
bond
– the ribosome moves down the mRNA in
39
a 5’ to 3’ direction
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 Eukaryotic pre-mRNA Splicing
The spliceosome is the organelle
tRNA molecules carry amino acids to the
responsible for removing introns and
splicing exons together.
Small ribonucleoprotein particles (snRNPs)
within the spliceosome recognize the intron-
exon boundaries
– introns – non-coding sequences
– exons – sequences that will be translated
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tRNA and Ribosomes
ribosome for incorporation into a
polypeptide
– aminoacyl-tRNA synthetases add
amino acids to the acceptor arm of tRNA
– the anticodon loop contains 3
nucleotides complementary to mRNA
codons
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tRNA and Ribosomes

The ribosome has multiple tRNA binding
sites:
– P site – binds the tRNA attached to the
growing peptide chain
– A site – binds the tRNA carrying the
next amino acid
– E site – binds the tRNA that carried the
last amino acid
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 The Nature of Genes
The central dogma of molecular biology
states that information flows in one
direction:
DNA RNA protein
Transcription is the flow of information from
DNA to RNA.
Translation is the flow of information from
RNA to protein.
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The Genetic Code

Deciphering the genetic code required
determining how 4 nucleotides (A, T, G, C)
could encode more than 20 amino acids.
Francis Crick and Sydney Brenner
determined that the DNA is read in sets of
3 nucleotides for each amino acid.

9 10

The Genetic Code The Genetic Code

codon: set of 3 nucleotides that specifies a
particular amino acid
reading frame: the series of nucleotides
read in sets of 3 (codon)
– only 1 reading frame is correct for
encoding the correct sequence of amino
acids
Marshall Nirenberg identified the codons
that specify each amino acid.
RNA molecules of only 1 nucleotide and of
specific 3-base sequences were used to
determine the amino acid encoded by
each codon.
The amino acids encoded by all 64 possible
codons were determined.

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13
Gene Expression Overview
template strand: strand of the DNA double
helix used to make RNA
coding strand: strand of DNA that is
complementary to the template strand
RNA polymerase: the enzyme that
synthesizes RNA from the DNA template
15
Gene Expression Overview
• Translation proceeds through
– initiation – mRNA, tRNA, and ribosome
come together
– elongation – tRNAs bring amino acids to
the ribosome for incorporation into the
polypeptide
– termination – ribosome encounters a
stop codon and releases polypeptide
17
The Genetic Code
stop codons: 3 codons (UUA, UGA, UAG)
in the genetic code used to terminate
translation
start codon: the codon (AUG) used to
signify the start of translation
The remainder of the code is degenerate
meaning that some amino acids are
specified by more than one codon.
14
Gene Expression Overview
Transcription proceeds through:
– initiation – RNA polymerase identifies
where to begin transcription
– elongation – RNA nucleotides are added
to the 3’ end of the new RNA
– termination – RNA polymerase stops
transcription when it encounters
terminators in the DNA sequence
16
Gene Expression Overview
Gene expression requires the participation
of multiple types of RNA:
messenger RNA (mRNA) carries the
information from DNA that encodes
proteins
ribosomal RNA (rRNA) is a structural
component of the ribosome
transfer RNA (tRNA) carries amino acids to
the ribosome for translation
18
 Gene Expression Overview
Gene expression requires the participation
of multiple types of RNA:
small nuclear RNA (snRNA) are involved
in processing pre-mRNA
signal recognition particle (SRP) is
composed of protein and RNA and
involved in directing mRNA to the RER
micro-RNA (miRNA) are very small and
their role is not clear yet
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Prokaryotic Transcription
Prokaryotic cells contain a single type of
RNA polymerase found in 2 forms:
– core polymerase is capable of RNA
elongation but not initiation
– holoenzyme is composed of the core
enzyme and the sigma factor which is
required for transcription initiation

20

Prokaryotic Transcription
A transcriptional unit extends from the
promoter to the terminator.
The promoter is composed of
– a DNA sequence for the binding of RNA
polymerase
– the start site (+1) – the first base to be
transcribed

21 22

Prokaryotic Transcription
During elongation, the transcription bubble
moves down the DNA template at a rate of
50 nucleotides/sec.
The transcription bubble consists of
– RNA polymerase
– DNA template
– growing RNA transcript

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 Genes and How They Work
The Nature of Genes
Beadle and Tatum looked for fungal cells
lacking specific enzymes.
– The enzymes were required for the
biochemical pathway producing the
amino acid arginine.
– They identified mutants deficient in each
enzyme of the pathway.

The Nature of Genes The Nature of Genes

Evidence for the function of genes came
from studying fungus.
George Beadle and Edward Tatum, 1941
– studied Neurospora crassa
– used X-rays to damage the DNA in cells
of Neurospora
– looked for cells with a new (mutant)
phenotype caused by the damaged
DNA
3
Early ideas to explain how genes work came
from studying human diseases.
Archibald Garrod studied alkaptonuria, 1902
– Garrod recognized that the disease is
inherited via a recessive allele
– Garrod proposed that patients with the
disease lacked a particular enzyme
These ideas connected genes to enzymes.
2

The Nature of Genes

Beadle and Tatum proposed that each
enzyme of the arginine pathway was
encoded by a separate gene.
They proposed the one gene – one
enzyme hypothesis.
Today we know this as the one gene – one
polypeptide hypothesis.

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