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TRANSCRIPTION AND TRANSLATION
& GENETIC CODE
SUMMARY

Transcription
◦ Initiation
◦ Elongation and termination

Translation
◦ Initiation
◦ Elongation and termination

Mutations
(information storage)
Transcription
(information carrier)
Translation
(active cell machinery)
Transcription is the process of creating an equivalent
RNA copy of a sequence of DNA.
Both RNA and DNA are nucleic acids, which use base
pairs of nucleotides as a complementary language that
can be converted back and forth from DNA to RNA in the
presence of the correct enzymes.
During transcription, a DNA sequence is read by RNA
polymerase,
which
produces
a
complementary,
antiparallel RNA strand.
As opposed to DNA replication, transcription results in
an RNA complement that includes uracil (U) in all
instances where thymine (T) would have occurred in a
DNA complement.
Transcription is the first step leading to gene
expression. The stretch of DNA transcribed into an RNA
molecule is called a transcription unit and encodes at
least one gene.
Transcription can be explained easily in a quick
5 step explanation.
Step 1: DNA unwinds/"unzips" as the Hydrogen
Bonds Break.
Step 2: The free nucleotides of the RNA, pair with
complementary DNA bases.
Step 3: RNA sugar-phosphate
(Aided by RNA Polymerase.)
backbone
forms.
Step 4: Hydrogen bonds of the untwisted RNA+DNA
"ladder" break, then the RNA leaves the nucleus
through the small nucleur pores.
Then goes to the cytoplasm to continue on to
protein processing.
Transcription process
Pre-initiation
In eukaryotes, RNA polymerase, and therefore the initiation of
transcription, requires the presence of a core promoter sequence
in the DNA.
The most common type of core promoter in eukaryotes is a short
DNA sequence known as a TATA box, found -30 base pairs from
the start site of transcription.
The TATA box, as a core promoter, is the binding site for a
transcription factor known as TATA binding protein (TBP), which
is itself a subunit of another transcription factor, called
Transcription Factor II D (TFIID).
Five more transcription factors and RNA polymerase combine
around the TATA box in a series of stages to form a preinitiation
complex. 1.Core Promoter Sequence 2.Transcription Factors
3.DNA Helicase 4.RNA Polymerase 5.Activators and Repressors.
The transcription preinitiation in archaea is essentially
homologous to that of eukaryotes, but is much less complex.
Initiation
In bacteria, transcription begins with the binding of RNA
polymerase to the promoter in DNA.
RNA polymerase is a core enzyme consisting of five subunits: 2 α
subunits, 1 β subunit, 1 β' subunit, and 1 ω subunit.
At the start of initiation, the core enzyme is associated with a
sigma factor (number 70) that aids in finding the appropriate -35
and -10 base pairs downstream of promoter sequences.
Transcription initiation is more complex in eukaryotes.
Eukaryotic RNA polymerase does not directly recognize the core
promoter sequences.
Instead, a collection of proteins called transcription factors
mediate the binding of RNA polymerase and the initiation of
transcription.
Only after certain transcription factors are attached to the
promoter does the RNA polymerase bind to it. The completed
assembly of transcription factors and RNA polymerase bind to
the promoter, forming a transcription initiation complex.
Elongation
One strand of the DNA, the template strand (or noncoding
strand), is used as a template for RNA synthesis.
As transcription proceeds, RNA polymerase traverses the
template strand and uses base pairing complementarity with
the DNA template to create an RNA copy.
Although RNA polymerase traverses the template strand from
3' → 5', the coding (non-template) strand and newly-formed
RNA can also be used as reference points, so transcription can
be described as occurring 5' → 3'.
This produces an RNA molecule from 5' → 3', an exact copy of
the coding strand (except that thymines are replaced with
uracils, and the nucleotides are composed of a ribose (5carbon) sugar where DNA has deoxyribose (one less oxygen
atom) in its sugar-phosphate backbone).
Unlike DNA replication, mRNA transcription can involve
multiple RNA polymerases on a single DNA template and
multiple rounds of transcription (amplification of particular
mRNA), so many mRNA molecules can be rapidly produced
from a single copy of a gene.
Elongation also involves a proofreading mechanism that can
replace incorrectly incorporated bases.
In eukaryotes, this may correspond with short pauses during
transcription that allow appropriate RNA editing factors to
bind.
Termination
Bacteria use
termination.
two
different
strategies
for
transcription
In Rho-independent transcription termination, RNA transcription
stops when the newly synthesized RNA molecule forms a G-C rich
hairpin loop.
When the hairpin forms, the mechanical stress breaks the weak
rU-dA bonds, now filling the DNA-RNA hybrid. This pulls the polyU transcript out of the active site of the RNA polymerase,
effectively terminating transcription.
In the "Rho-dependent" type of termination, a protein factor
called "Rho" destabilizes the interaction between the template
and the mRNA, thus releasing the newly synthesized mRNA from
the elongation complex.
Transcription termination in eukaryotes is less understood but
involves cleavage of the new transcript followed by templateindependent addition of As at its new 3' end, in a process called
polyadenylation.
Non-template
(coding) strand
DNA
3
5
5
RNA
3
5
3
Template strand 3
Phosphodiester bond is
formed by RNA polymerase
after base pairing occurs
5
RNA 5
3
Hydrogen bonds form between
complementary base pairs
DNA template
3
5
Transcription

Sequence in prokaryotes
◦ Initiation phase
 RNA polymerase binds a Sigma protein that in turn
binds to the promoter, upstream from the start site
for a particular gene on DNA.
 Sigma opens up a portion of the DNA helix and
RNA polymerase begins transcription.
HOW TRANSCRIPTION BEGINS
Promoter (on non-template strand)
35 box
10 box
Upstream
DNA
+1 site
Sigma
Active
site
RNA polymerase
1. Initiation begins
Sigma binds to promoter
region of DNA.
Downstream
DNA
HOW TRANSCRIPTION BEGINS
Template strand
Non-template
strand
+1 site
RNA
NTPs
2. Initiation continues
Sigma opens the DNA helix;
transcription begins.
Transcription

Sequence in prokaryotes cont’d
◦ Elongation and termination phase
 Elongation: RNA polymerase adds nucleotides 5’ to
3’ at a rate of ~ 50 nucleotides/second beginning at
start site. Active portion = transcription bubble.
 Completed mRNA strand exits bubble as it is
finished.
 Termination: RNA polymerase stops when the
RNA produces a hairpin loop.
HOW TRANSCRIPTION ENDS
Upstream DNA
Hairpin loop
RNA
polymerase
RNA
RNA
Transcription
termination
signal
DNA
Downstream
DNA
1. RNA polymerase reaches a transcription
2. The RNA hairpin causes the RNA strand
termination signal, which codes for RNA
that forms a hairpin.
to separate from the RNA polymerase,
terminating transcription.
C
G
U
U
G
5’ C A
C
G
G
C
C
G
G
C
G
C
C
G
U U U U OH 3’
Transcription

Sequence in eukaryotes is basically the
same; 3 differences:
◦ 3 types of RNA polymerase –
◦ Promoters are more complex and include
sites for basal transcription factors + others.
Transcription

Sequence in eukaryotes – differences
cont’d
◦ Posttranscriptional modifications
 Addition of a 5’ cap (adenine or guanine + methylGTP and a “poly A tail”.
5 cap
Poly(A) tail
5
3

5
untranslated
region
Coding region
3
untranslated
region
Translation
Translation is the third stage of protein biosynthesis (part of
the overall process of gene expression).
In translation, messenger RNA (mRNA) produced by
transcription is decoded by the ribosome to produce a specific
amino acid chain, or polypeptide, that will later fold into an
active protein.
Translation occurs in the cell's cytoplasm, where the large and
small subunits of the ribosome are located, and bind to the
mRNA.
The ribosome facilitates decoding by inducing the binding of
tRNAs with complementary anticodon sequences to that of the
mRNA.
The tRNAs carry specific amino acids that are chained together
into a polypeptide as the mRNA passes through and is "read" by
the ribosome in a fashion reminiscent to that of a stock ticker
and ticker tape.
Translation in Prokaryotes
◦ Initiation phase
 A small sequence of rRNA on the ribosome binds
to a complementary sequence on the mRNA with
the help of intiation factors.
 *The start codon, AUG is exposed.
 tRNA with a sequence that is complementary to
the codon (=anticodon) attaches to the codon and
releases its amino acid.
Early model of aminoacyl tRNA function
Amino acid
3
5
Serine anticodon
Binding site for
amino acid
Binding site for
mRNA codon
5
3
mRNA
Serine codon
The Code
A specific order of nucleotides or bases
on the DNA.
 Occurs in blocks of 3 bases = codons that
specify which amino acid goes where in a
protein.
 1 codon = one amino acid
 The code is “universal”, i.e. the codons
specify the same amino acids in all
organisms, pretty much.

Elongation and termination phase
 Ribosome moves down 1 codon at a time and
specific tRNA’s bring their amino acids to the chain.
 Amino acids are joined by peptide bonds to form
the protein.
 3 sites on the ribosome (APE): A = tRNA binding
site, P = site of peptide bond formation, E = exit
site for empty tRNA’s.
Diagram of ribosome during translation
Polypeptide grows in amino
to carboxyl direction
(amino acids in green)
Peptide bond
formation occurs
here
Aminoacyl
tRNA
Large
subunit
Anticodon
3
mRNA
5
Small
subunit
The E site
holds a tRNA
that will exit
Codon
The P site holds
the tRNA with
growing polypeptide
attached
The A site
holds an
aminoacyl
tRNA

Prokaryotes cont’d
◦ Elongation and termination phase
 Translation is terminated when the ribosome
reaches a stop codon.
ELONGATION OF POLYPEPTIDES DURING TRANSLATION
Ribosome
tRNA
Peptidyl site
Exit site
Aminoacyl site
mRNA
5
3
5
3
5
3
Start
codon
1. Incoming aminoacyl tRNA
New tRNA moves into A site, where
its anticodon base pairs with the
mRNA codon.
2. Peptide bond formation
3. Translocation
The amino acid attached to the tRNA
in the P site is transferred to the
tRNA in the A site.
Ribosome moves down mRNA. The
tRNA attached to polypeptide chain
moves into P site. The A site is empty.
ELONGATION OF POLYPEPTIDES DURING TRANSLATION
Exit tunnel
5
3
3
5
Elongation cycle
continues
3
5
4. Incoming aminoacyl tRNA
5. Peptide bond formation
6. Translocation
New tRNA moves into A site, where
its anticodon base pairs with the
mRNA codon.
The polypeptide chain attached to
the tRNA in the P site is transferred
to the aminoacyl tRNA in the A site.
Ribosome moves down mRNA. The
tRNA attached to polypeptide chain
moves into P site. Empty tRNA from
P site moves to E site, where tRNA is
ejected. The A site is empty again.
Bacterial ribosomes during translation
Multiple ribosomes
can translate each
mRNA simultaneously
Ribosomes
DNA
In bacteria, transcription and translation are tightly coupled.
5 end
3
of mRNA
Ribosome translates
mRNA as it is being
synthesized by RNA
polymerase
2
2
Protein
1
1
1
Ribosome
RNA polymerase
Start of gene
(3 end of template strand)
End of gene
(5 end of template strand)
mRNA
DNA Transcription and
RNA processing
in nucleus
Mature
mRNA
Mature
mRNA
Ribosome
Translation
in cytoplasm
Protein
Translation

Eukaryotes
◦ Eukaryotic genes contain sequences that do
not contain codons = INTRONS; sequences
that contain codons are EXONS.
◦ mRNA sequences contain the same introns
and exons.
Micrograph of DNA-RNA
hybrid
Interpretation of micrograph
Single-stranded
DNA only
(c) Genes and RNA transcripts differ in length.
Intron
Exon
Size of gene (DNA)
Single-stranded DNA
base paired with mRNA
Size of mature RNA transcript
Translation in Eukaryotes

Eukaryotes cont’d
◦ Introns are removed after mRNA synthesis
and exons are joined together = RNA
splicing.
◦ snRNPs = small nuclear ribonucleoproteins
are the splicers.
◦ Why? Alternate splicing can produce
different proteins from the same gene
sequence. 30,000 genes can be used to
produce 120,000 mRNA’s.
Introns must be removed from RNA transcripts.
Intron 1 Intron 2
DNA
3
Promoter
5
Exon 1
Exon 2
Exon 3
Primary RNA transcript 5
Spliced transcript
3
5
3
Genetic code
The genetic code is the set of rules by which information
encoded in genetic material (DNA or mRNA sequences) is
translated into proteins (amino acid sequences) by living
cells.
The code defines a mapping between tri-nucleotide
sequences, called codons, and amino acids. With some
exceptions, a triplet codon in a nucleic acid sequence
specifies a single amino acid.
Because the vast majority of genes are encoded with exactly
the same code, this particular code is often referred to as
the canonical or standard genetic code, or simply the
genetic code, though in fact there are many variant codes.
Translation starts with a chain initiation codon (start codon).
Unlike stop codons, the codon alone is not sufficient to begin
the process.
Nearby sequences (such as the Shine-Dalgarno sequence in E.
coli) and initiation factors are also required to start translation.
The most common start codon is AUG which is read as
methionine or, in bacteria, as formylmethionine.
Alternative start codons (depending on the organism), include
"GUG" or "UUG", which normally code for valine or leucine,
respectively. However, when used as a start codon, these
alternative start codons are translated as methionine or
formylmethionine.
The three stop codons have been given names: UAG is amber,
UGA is opal (sometimes also called umber), and UAA is ochre.
Stop codons are also called "termination" or "nonsense" codons
and they signal release of the nascent polypeptide from the
ribosome due to binding of release factors in the absence of
cognate tRNAs with anticodons complementary to these stop
signals.
Amino acid
The Genetic Code
Transcription vs. Translation Review
Transcription
 Process by which
genetic information
encoded in DNA is
copied onto messenger
RNA
 Occurs in the nucleus
 DNA
mRNA
Translation
 Process by which
information encoded in
mRNA is used to
assemble a protein at a
ribosome
 Occurs on a Ribosome
 mRNA
protein