Chapter 12
Genes: Structure
Replication and
Expression
Replication:
 During mitotic
division
information is
duplicated by DNA
replication and is
passed on to next
generation
 daughter cells has
exavcyt replica of
the parent DNA
Role of DNA in Protein synthesis

DNA and protein synthesis
involves:



Transcription- yields a
ribonucleic acid (RNA) copy of
specific genes
Translation- uses information
in messenger RNA (mRNA) to
synthesize a polypeptide.
Protein synthesis is assisted by
RNA (tRNA) and ribosomal RNA
(rRNA)
Nucleic Acids
Nucleic Acid Structure
Deoxyribonucleic Acid (DNA)
polymer of nucleotides
 contains the bases adenine, guanine,
cytosine and thymine
 sugar is deoxyribose
 molecule is usually double stranded




DNA is a double-stranded molecule twisted into a
helix (think of a spiral staircase).
Each spiraling strand, comprised of a sugarphosphate backbone and attached bases, is
connected to a complementary strand by noncovalent hydrogen bonding between paired
bases.
The bases are adenine (A), thymine (T), cytosine
(C) and guanine (G).
A and T are connected by two hydrogen bonds. G
and C are connected by three hydrogen bonds.
DNA Structure – Two
Complementary Strands

base pairing



Adenine (purine) and thymine
(pyrimidine) pair by 2
hydrogen bonds
Guanine (purine) and cytosine
(pyrimidine) pair by 3
hydrogen bonds
major and minor grooves
form when the 2 strands
twist around each other
Nucleic Acid Structure
Ribonucleic Acid (RNA)
 polymer
of nucleotides
 contains the bases adenine,
guanine, cytosine and uracil
 sugar is ribose
 most RNA molecules are single
stranded
RNA Structure

three different types which differ from
each other in function and in structure
 messenger
RNA (mRNA)
 ribosomal RNA (rRNA)
 transfer RNA(tRNA)
The Organization of DNA in Cells
In most bacteria DNA is a
circular, double helix
 further twisting results in
supercoiled DNA


in bacteria the DNA is
associated with basic
proteins

help organize the DNA into a
coiled chromatin like
structure
DNA Replication
DNA Replication
complex process involving
numerous proteins which help
ensure accuracy
 the 2 strands separate, each
serving as a template for
synthesis of a complementary
strand
 synthesis is semi-conservative;
each daughter cell obtains one
old and one new strand

DNA Replication

bidirectional from a single origin of replication
DNA replication (arrows) occurs in
both directions from the origin of
replication in the circular DNA found
in most bacteria.
Rolling Circle Replication

some small circular
genomes (e.g.,
viruses and
plasmids)

replicated by rollingcircle replication

Animation
illustrating DNA
replication by
complementary
base pairing
Genes
Gene Structure
Gene
 the
basic unit of genetic information
 also defined as the nucleic acid sequence
that codes for a polypeptide, tRNA or rRNA
 linear sequence of nucleotides
 codons are found in mRNA and code for
single amino acids

reading frame
 organization
of codons such that they can
be read to give rise to a gene product
Importance of Reading Frame
Figure 12.16
Genes that Code for Proteins

template strand directs RNA synthesis

promoter is located at the start of the gene



is the recognition/binding site for RNA polymerase
functions to orient polymerase
leader sequence is transcribed into mRNA but is not
translated into amino acids

Shine-Delgarno sequence important for initiation of translation
Genes that Code for Proteins
The Coding Region:
 begins with the DNA sequence from 3´-TAC-5´


produces codon AUG which codes for Nformylmethionine, a modified amino acid used to
initiate protein synthesis in bacteria ( check fig.)
coding region ends with a stop codon, immediately
followed by the trailer sequence which contains a
terminator sequence used to stop transcription
Bacterial Gene Structure
Genes That Code for tRNA and
rRNA
• tRNA/rRNA genes
have promoter
(recognition/binding
site for RNA
polymerase), leader (is
transcribed into
mRNA), coding region,
spacer and trailer
regions (contains a
terminator sequence
used to stop
transcription)
during maturation
process.
Figure 12.19a:
leader, spacer, and trailer removed during
maturation process
rRNA genes have promoter, leader,
coding, spacer, and trailer regions
Figure 12.19b:
spacer and trailer regions may encode
tRNA molecules
Fig. 12.20
Transcription
Transcription

RNA is synthesized under the direction of
DNA
 RNA
produced has complementary sequence to
the template DNA
 three types of RNA are produced
 mRNA
carries the message for protein synthesis
 tRNA carries amino acids during protein synthesis
 rRNA molecules are components of ribosomes
Transcription in Bacteria…
Definitions to understand protein synthesis:
 in most bacterial RNA polymerases:
 Holoenzyme can begin transcription> What
is Holoenzyme??*
 the
core enzyme is composed of 5 chains and
catalyzes RNA synthesis
 the sigma factor has no catalytic activity but
helps the core enzyme recognize the start of
genes
 *holoenzyme = core enzyme + sigma factor
 only
the holoenzyme can begin transcription
Transcription in Bacteria….
• Transcription in Bacteria is catalyzed by
a single RNA polymerase.
• a reaction similar to that catalyzed by
DNA polymerase for DNA syntehsis.
• ATP,GTP,CTP and UTP are used to
produce a complementary RNA copy of
the template DNA sequence
http://www.vidoemo.co
m/yvideo.php?i=M2FW
VDJEcWuRpVGJ0QTg
&replicationtranscription-andtranslation=
Transcription Process
Transcription Initiation
Promoter

site where
RNA
polymerase
binds to
initiate
transcription
& is not
transcribed
Transcription Elongation
after binding, RNA polymerase
unwinds the DNA
 transcription bubble produced


moves with the polymerase as it
transcribes mRNA from template
strand

within the bubble a temporary
RNA:DNA hybrid is formed
Coupled Transcription and
Translation in Prokaryotes
Proteins
The Genetic Code

mRNA sequence is translated into amino
acid sequence of polypeptide chain
(process = translation).

an understanding of the genetic code is
necessary before translation is studied.
Organization of the Code

code degeneracy
 up
to six different codons can code for a
single amino acid

sense codons
 the

61 codons that specify amino acids
stop (nonsense) codons
 the
three codons used as translation
termination signals
 do not encode amino acids
Translation
Translation
Translation of mRNA into protein:
synthesis of polypeptide is directed by
sequence of nucleotides in mRNA
Ribosome:
 70S ribosomes = 30S + 50S subunit



site of translation
polyribosome (polysome) – complex of mRNA with
several ribosomes
Translation of mRNA into
protein:
Three phases:
•Initiation
•Elongation
•Termination
•During translation, the mRNA is "read"
according to the genetic code which relates the
DNA sequence to the amino acid sequence in
proteins
• Each group of three base pairs in mRNA
constitutes a codon, and each codon specifies a
particular amino acid (hence, it is a triplet code).
•The mRNA sequence is thus used as a
template to assemble—in order—the chain of
amino acids that form a protein.
Transfer RNA (tRNA) and
Amino Acid Activation
The tRNA molecules are adaptor
molecules—they have one end
that can read the triplet code in
the mRNA through
complementary base-pairing, and
another end that attaches to a
specific amino acid
 attachment of amino acid to
tRNA is catalyzed by aminoacyltRNA synthetases

•The translation of mRNA begins with
the formation of a complex on the mRNA
(Fig. below).
• First, three initiation factor proteins
(known as IF1, IF2, and IF3) bind to the
small subunit of the ribosome.
•This preinitiation complex and a
methionine-carrying tRNA then bind to
the mRNA, near the AUG start codon,
forming the initiation complex.
The Ribosome
•Methionine (Met) is the first amino
acid incorporated into any new
protein, however, it is not always the
first amino acid in translation of
protein.
•In many proteins, methionine is
removed after translation.
• The large ribosomal subunit binds to this
complex, which causes the release of IFs
(initiation factors) once the initiation complex is
formed on the mRNA
•The large subunit of the ribosome has three
sites at which tRNA molecules can bind:
• The A (amino acid) site is the location at which
the aminoacyl-tRNA anticodon base pairs up
with the mRNA codon, ensuring that correct
amino acid is added to the growing polypeptide
chain.
•The P (polypeptide) site is the location at
which the amino acid is transferred from its
tRNA to the growing polypeptide chain.
• Finally, the E (exit) site is the location at
which the "empty" tRNA sits before being
released back into the cytoplasm to bind
another amino acid and repeat the process.
•The initiator methionine tRNA is the only
aminoacyl-tRNA that can bind in the P site
of the ribosome, and the A site is aligned
with the second mRNA codon.
•The ribosome is thus ready to bind the
second aminoacyl-tRNA at the A site, which
will be joined to the initiator methionine by
the first peptide bond.
Elongation of the Polypeptide
Chain
 The next phase in translation is known as the
elongation phase .

Elongation cycle is the sequential addition of amino
acids to growing polypeptide & consists of three phases

aminoacyl-tRNA binding
transpeptidation reaction
Translocation

The above process need several Elongation factors ( EF)


………Elongation
First, the ribosome moves along the
mRNA in the 5'-to-3'direction, which
requires the elongation factor G, in
a process called translocation
…..Elongation Cycle
•The tRNA which corresponds to the second codon
can then bind to the A site, a step that requires
elongation factors (in E. coli, these are called EF-Tu
and EF-Ts) and GTP (guanosine triphosphate ) as
an energy source for this acitivity.
• Upon binding of the tRNA-amino acid complex in
the A site, GTP is cleaved to form guanosine
diphosphate (GDP), then released along with EF-Tu
to be recycled by EF-Ts for the next round.
……….Elongation
•In the next step, peptide bonds between the
now-adjacent first and second amino acids are
formed through a peptidyl transferase activity.
•After the peptide bond is formed, the
ribosome shifts, or translocates, again, thus
causing the tRNA to occupy the E site.
•The tRNA is then released to the cytoplasm to
pick up another amino acid.
•The A site is now empty and ready to receive
the tRNA for the next codon.
….Elongation
•This process is repeated until all the
codons in the mRNA have been read by
tRNA molecules &
• the amino acids attached to the tRNAs
have been linked together in the growing
polypeptide chain in the appropriate order.
•At this point, translation must be
terminated, and the nascent protein must
be released from the mRNA and ribosome.
Final Phase in Elongation Cycle
− Translocation
Three simultaneous events:

peptidyl-tRNA moves from A site to P site
 ribosome moves down one codon
 empty tRNA leaves P site
Termination of Translation/protein synthesis:
• Three termination codons ( Non-sense or
stop codon) that are employed at the end of a
protein-coding sequence in mRNA: UAA,
UAG, and UGA
•No tRNAs recognize these codons.
•Instead, release factors (RFs) helps in
recognition of stop codons.
•Release factors are protein which binds and
facilitates release of the mRNA from the
ribosome and subsequent dissociation of the
ribosome.
Several ribosome can align on one
mRNA strand and forms several
polypeptide chains each with 20 or
more amino acids.

http://www.vidoemo.com/yvideo.php?i=b
mNqSWlEcWuRpNTFoUWs&dnatranslation-animation
Prokaryotic and Eukaryotic
Translation
•The translation process is very similar in
prokaryotes and eukaryotes.
• Although different elongation, initiation, and
termination factors are used, the genetic code
is generally identical.
• In bacteria, transcription and translation take
place simultaneously, and mRNAs are
relatively short-lived.
•In eukaryotes, mRNAs have highly
variable half-lives,
• are subject to modifications, and must
exit the nucleus to be translated.
References
http://student.ccbcmd.edu/biotutorials/dna/
fg12.htmlhttp://www.accessexcellence.org
/RC/VL/GG/dna_molecule.php
 http://www.nature.com/scitable/topicpage
/Reading-the-Genetic-Code-1042

http://www.nature.com/scitable/topicpage
/Translation-DNA-to-mRNA-to-Protein-393