Replication, Transcription & Translation

Ira Humairah, dr,M.Si.

Biochemistry Dept.

RNA
polymerase

DNA
RNA
 What is Genetics?
• Genetics – study of how traits are passed from parent
to offspring
 What are traits determined by?
• Traits are determined by the genes on the
chromosomes. A gene is a segment of DNA that
determines a trait.
 DNA – genetic blueprint
• Deoxyribonucleic
acid (DNA)

• Located in the
nucleus

• rapped up in
structures called
chromosomes.

• 46 Chromosomes -
23 Pairs in every
cell

Meet the Gene Machine

 What is a locus?
• A locus describes the region of a
chromosome where a gene is
located
• 11p15.5 is the locus for the human
insulin gene
 11 is the chromosome number
 p indicates the short arm of the
chromosome
 15.5 is the number assigned to a
particular region on a chromosome.

• When chromosomes are stained in

the lab, light and dark bands
appear, and each band is
numbered. The higher the number,
the farther away the band is from
the centromere.
 Genes
• Genes are the basic physical and functional
units of heredity
• Each gene is located on a particular region of a
chromosome and has a specific ordered
sequence of nucleotides (the building blocks
of DNA).
 Genes

• A gene: DNA sequence that is needed to encode

amino acid sequence of a protein

• Composed of exons, introns and different control

elements

• Exon – protein coding sequence

• Intron – intervening sequence
DNA Replication
Replication = DNA copies itself exactly
 (Occurs within the nucleus)

 Any mistake in copying = mutation

 DNA mutation = chromosomal mutation

 1953 article in Nature
Watson and Crick
 Double helix structure of DNA

“It has not escaped our notice that the specific pairing we have
postulated immediately suggests a possible copying mechanism for the
genetic material.” Watson & Crick
Directionality of DNA
• You need to number
PO4 nucleotide
the carbons!
• it matters!

N base

5 CH2
This will be O
IMPORTANT!!
4 ribose 1

3 2
OH
 5
The DNA backbone PO4
• Putting the DNA backbone
together base
5 CH2
• refer to the 3 and 5 ends of the DNA
• the last trailing carbon
O
4 1
C
3 2
O
–O P O

O base
Sounds trivial, but…
this will be 5 CH2
IMPORTANT!! O
4 1

3 2
OH
3
Anti-parallel strands
• Nucleotides in DNA backbone are
bonded from phosphate to sugar
between 3 & 5 carbons
• DNA molecule has “direction”
5 3
• complementary strand runs in opposite
direction

3 5
 Bonding in DNA
hydrogen
bonds
5 3

covalent
phosphodiester
bonds

3
5

….strong or weak bonds?

How do the bonds fit the mechanism for copying DNA?
Base pairing in DNA
• Purines
• adenine (A)
• guanine (G)
• Pyrimidines
• thymine (T)
• cytosine (C)
• Pairing
• A:T
• 2 bonds
• C:G
• 3 bonds
Copying DNA
• Replication of DNA
• base pairing allows each strand to
serve as a template for a new
strand
• new strand is 1/2 parent template &
1/2 new DNA
 Let’s meet
the team…
DNA Replication
• Large team of enzymes coordinates replication
Replication: 1st step
• Unwind DNA
• helicase enzyme
• unwinds part of DNA helix
• stabilized by single-stranded binding proteins

helicase

single-stranded binding proteins replication fork

 Replication: 2nd step
 Build daughter DNA
strand
 add new
complementary bases
 DNA polymerase III

But…
Where’s the
We’re missing
DNA ENERGY
something!
for the bonding!
Polymerase III What?
 Energy of Replication
Where does energy for bonding usually come from?
We come
with our own
energy!
You energy
remember
ATP!
energy
Are there
otherenergy
other ways
to get energy
nucleotides?
out
You of it?
bet!

And we
leave behind a
TTP
GTP
CTP
ATP nucleotide! TMP
AMP
ADP
GMP
CMP
modified nucleotide
Energy of Replication
• The nucleotides arrive as nucleosides
• DNA bases with P–P–P
• P-P-P = energy for bonding
• DNA bases arrive with their own energy source for
bonding
• bonded by enzyme: DNA polymerase III

ATP GTP TTP CTP

 5 3

Replication energy
DNA
• Adding bases
Polymerase III
• can only add nucleotides to
3 end of a growing DNA strand energy
DNA
• need a “starter” nucleotide to
bond to Polymerase III
• strand only grows
energy
53 DNA
Polymerase III

energy DNA
Polymerase III
B.Y.O. ENERGY!
The energy rules 3 5
the process
5 3 5 need “primer” bases to add on to 3

energy
no energy


to bond
energy
energy

energy
energy

ligase
energy

energy

3 5 3 5
 Okazaki

Leading & Lagging strands

Limits of DNA polymerase
III
can only build onto 3 end of 5



an existing DNA strand 3 5 5 3
5
3
5
Lagging strand
3
ligase
growing
3
5 replication fork
Leading strand

Lagging strand

3 5

3
DNA polymerase III
 Okazaki fragments
 joined by ligase Leading strand
 “spot welder” enzyme  continuous synthesis
 Replication fork / Replication bubble
3 5

5 3

DNA polymerase III

leading strand
5
3
3 5
5 5
5 3 3
lagging strand

3 5
5
3 lagging strand leading strand growing
5
growing 3 replication fork 5
5
replication fork 5 3
leading strand lagging strand
3
5
5 5
 Starting DNA synthesis: RNA primers
Limits of DNA polymerase
III
 can only build onto 3 end of 5

an existing DNA strand 3 5 3

5
3
3 5

growing
3 primase
5 replication fork DNA polymerase III

RNA 5

RNA primer 3

 built by primase
 serves as starter sequence
for DNA polymerase III
 Replacing RNA primers with DNA
DNA polymerase I
 removes sections of RNA DNA polymerase I
primer and replaces with 5

DNA nucleotides 3

3
5 ligase
growing
3
5 replication fork

RNA 5

3

But DNA polymerase I still

can only build onto 3 end of
an existing DNA strand
 Houston, we
have a problem!

Chromosome erosion
All DNA polymerases can
only add to 3 end of an DNA polymerase I
existing DNA strand 5

3

3
5
growing
3
5 replication fork DNA polymerase III

RNA 5

Loss of bases at 5 ends 3

in every replication
 chromosomes get shorter with each replication
 limit to number of cell divisions?
Replication fork
DNA
polymerase III lagging strand
DNA
polymerase I
3’
Okazaki primase
fragments 5’
5’ ligase
3’ 5’ SSB

3’ helicase

DNA
polymerase III
5’ leading strand
3’
direction of replication
SSB = single-stranded binding proteins
 DNA polymerases
• DNA polymerase III
• 1000 bases/second! Roger Kornberg
• main DNA builder 2006
• DNA polymerase I
• 20 bases/second
• editing, repair & primer removal

DNA polymerase III Arthur Kornberg

enzyme 1959
Editing & proofreading DNA
• 1000 bases/second =
lots of typos!
• DNA polymerase I
• proofreads & corrects typos
• repairs mismatched bases
• removes abnormal bases
• repairs damage
throughout life
• reduces error rate from
1 in 10,000 to
1 in 100 million bases
Fast & accurate!
• It takes E. coli <1 hour to copy
5 million base pairs in its single chromosome
• divide to form 2 identical daughter cells
• Human cell copies its 6 billion bases & divide into daughter
cells in only few hours
• remarkably accurate
• only ~1 error per 100 million bases
• ~30 errors per cell cycle
What does it really look like?

4
Assembling the New Bases

• The term semiconservative replication means that in the new DNA

molecule there is one old and one new strand.

• This is seen in the figure below.

DNA Replication
• Since the DNA molecule is very large, there must be a way to copy it faster than
just unwinding from one end to the other!

• This happens when the DNA molecule separates at many sites, forming
thousands of replication bubbles. This allows parts of the DNA message to be
replicated simultaneously in many locations.

• DNA polymerase adds new nucleotides , while DNA ligase joints the DNA
segments together.

• Video DNA Replication Process - Free Science Videos and Lectures.flv

 Transcription, and Translation

• Before a cell can divide, the DNA in the

nucleus of the cell must be duplicated.

• Since the DNA molecule consists of two

complimentary stands, if those two
strands separate and the right conditions
are present, two new stands that are the
compliments of the originals will be
produced.

• Each new DNA molecule will consist of

one old stand, and a new complimentary
strand.

• The gray strands in the figure to the

right are new strands in the process of
being assembled.
 Gene Expression

• There are 4 major events that occur durin

the process of gene expression
– Transcription
– RNA processing
– Translation
– Protein processing
 Central Dogma

• One gene – one protein

 Central Dogma

• This is the same for bacteria to humans

• DNA is the genetic instruction or gene
• DNA  RNA is called Transcription
• RNA  Protein is called Translation
A Gene is a Transcription Unit
Promoter Terminator
Regulatory
sequence

DNA

Transcription

mRNA 5 3

Many
Start Stop
codons
codon codon
Ribosomal-
binding site
 The Discovery of Cells

before
nucleus

true
nucleus
 Prokaryotic Gene Structure

Stop Codon
TAA, TAG,
+1 ATG Stop Codon
TGA ATG
DNA Coding Sequence = ORF 1 Coding Sequence = ORF 2

USE/Promoter 5’ UTR = Leader Protein A Spacer = 5’UTR Protein B

/Operator sequence of 2nd cistron

Cistron 1 Cistron 2

Regulatory Sequences Structural or Coding Sequences Termination

sequence

Regulatory and Coding Sequence Unit = Operon

 Prokaryotic Gene Structure
Stop Codon Stop Codon
+1 ATG TAA, TAG, TGA ATG TAA, TAG, TGA

DNA Coding Sequence= ORF Coding Sequence= ORF

USE/Promoter Protein A Protein B Terminator

5’ UTR = Leader Spacer = 5’UTR
/Operator sequence sequence
of 2nd cistron

Cistron 1 Cistron 2

5’ UTR = Leader
sequence Spacer

Polycistronic
ORF Protein A
mRNA ORF Protein B

+1 AUG AUG
Stop Codon Stop Codon
UAA, UAG, UGA UAA, UAG, UGA
 Eukaryotic Gene Structure
Start Codon Stop Codon
ATG TAA, TAG, TGA

Exon1 Exon2 Exon3

Promoter/
Enhancer 5’ UTR 3’ UTR

Exon1 Exon2 Exon3

Start Codon Stop Codon

polyA tail
Exon1 AAAAAAAA
Exon2Exon3
5’ UTR 3’ UTR
 Protein Synthesis
• The information content of DNA is in the form of
specific sequences of nucleotides along the DNA
strands
• The DNA inherited by an organism leads to specific
traits by dictating the synthesis of proteins
• The process by which DNA directs protein synthesis,
gene expression includes two stages, called
transcription and translation
 Transcription and Translation

• Cells are governed by a cellular chain of command

– DNA RNA protein
• Transcription
– Is the synthesis of RNA under the direction of DNA
– Produces messenger RNA (mRNA)
• Translation
– Is the actual synthesis of a polypeptide, which occurs under
the direction of mRNA
– Occurs on ribosomes
 Transcription and Translation
• In a eukaryotic cell the nuclear envelope separates transcription
from translation
• Extensive RNA processing occurs in the nucleus

Nuclear
envelope

TRANSCRIPTION DNA

Pre-mRNA
RNA PROCESSING

mRNA

Ribosome

TRANSLATION
(b) Eukaryotic cell. The nucleus provides a separate
Polypeptide compartment for transcription. The original RNA
transcript, called pre-mRNA, is processed in various
ways before leaving the nucleus as mRNA.
 Transcription initiation

DNA acts as a template for RNA synthesis

Synthesis by RNA polymerase -RNA Pol

RNA Pol I makes tRNA and rRNA

RNA Poly II makes mRNA in nucleus

 Control of transcription

Transcription initiation by RNA Pol II requires

general transcription factors (Fig 6-16)
 Control of transcription
(Fig. 6-16)
Transcription start site usually a TATA box (not always)

TBP (TATA-binding protein) binds, changing DNA structure

(Fig 6-18).

Recruits transcription factor II proteins (TFIIA, B, …)

then RNA Pol II

Collectively the transcription initiation complex

 Control of transcription

Since DNA is wrapped around histones, how does

RNA Pol gain access to the promoter?

How does RNA Pol know where to bind?

 Control of transcription
(Fig. 6-19)

Transcription initiation also requires:

•activators
•mediators (or co-activators),
•chromatin-remodeling proteins

Activators increase the likelihood of successful

transcription initiation
 Transcription
• Transcription is the DNA-
directed synthesis of RNA
• RNA synthesis
– Is catalyzed by RNA
polymerase, which pries the
DNA strands apart and hooks
together the RNA nucleotides
– Follows the same base-pairing
rules as DNA, except that in
RNA, uracil substitutes for
thymine
 RNA

 RNA: ribonucleic acid

 Carries out protein synthesis
 Differences from DNA:
 different sugar (ribose)
 single strand
 different base
 no thymine
 URACIL instead
3 Types of RNA:
• Messenger RNA:
(mRNA) carries
nucleotide sequence
from nucleus to
ribosome
• Transfer RNA: (tRNA)
picks up amino acid in
cytoplasm and carries
them to ribosome
• Ribosomal RNA:
(rRNA)found in
ribosome, joins mRNA
and tRNA; forms
protein
Major players in transcription

• mRNA- type of
RNA that encodes
information for the
synthesis of
proteins and
carries it to a
ribosome from the
nucleus
 Major players in transcription

• RNA polymerase-
complex of enzymes
with 2 functions:
– Unwind DNA
sequence
– Produce primary
transcript by stringing
together the chain of
RNA nucleotides
 RNA vs. DNA
DNA RNA
• Double stranded • Single stranded
• Deoxyribose sugar • Ribose sugar
• Bases: C,G A,T • Bases: C,G,A,U

Both contain a sugar, phosphate, and base.

 RNA
• RNA is single stranded, not double stranded like DNA
• RNA is short, only 1 gene long, where DNA is very long and contains
many genes
• RNA uses the sugar ribose instead of deoxyribose in DNA
• RNA uses the base uracil (U) instead of thymine (T) in DNA.

Table 17.1
 Synthesis of an RNA Transcript

• The stages of Promoter

Transcription unit

transcription are 5
3
DNA
3
5

Start point
– Initiation RNA polymerase 1 Initiation. After RNA polymerase binds to
the promoter, the DNA strands unwind, and
– Elongation the polymerase initiates RNA synthesis at the

– Termination start point on the template strand.

5 3
3 5
Template strand of
Unwound RNA DNA
DNA transcript
2 Elongation. The polymerase moves downstream, unwinding the
DNA and elongating the RNA transcript 5  3 . In the wake of
Rewound transcription, the DNA strands re-form a double helix.

RNA
5 3
3 3 5
5

RNA
transcript
3 Termination. Eventually, the RNA
transcript is released, and the
polymerase detaches from the DNA.

5 3
3 5

5 3
Completed RNA
transcript
 Synthesis of an RNA Transcript - Initiation

TRANSCRIPTION DNA 1 Eukaryotic promoters

RNA PROCESSING Pre-mRNA
mRNA

• Promoters signal the initiation TRANSLATION Ribosome

Polypeptide
of RNA synthesis Promoter

5 T A T A A AA 3
• Transcription factors help 3 AT A T T T T

TATA box
5
Start point Template
eukaryotic RNA polymerase DNA strand

recognize promoter sequences 2 Several transcription

factors
Transcription
factors

5 3
3 5
3 Additional transcription
factors

RNA polymerase II
Transcription factors

5 3
3 5 5
RNA transcript
Transcription initiation complex
 Synthesis of an RNA Transcript - Elongation
• RNA polymerase synthesizes a single strand of RNA against the DNA template strand (anti-
sense strand), adding nucleotides to the 3‟ end of the RNA chain

• As RNA polymerase moves along the DNA it continues to untwist the double helix, exposing
about 10 to 20 DNA bases at a time for pairing with RNA nucleotides

Elongation Non-template
strand of DNA
RNA nucleotides

RNA
polymerase

T C C A A
A
3
3 end
U
A E G C A
5

T A G G T T

Direction of transcription
5 Template
(“downstream”)
strand of DNA

Newly made
RNA
 Synthesis of an RNA Transcript - Termination
• Specific sequences in the DNA signal termination
of transcription
• When one of these is encountered by the
polymerase, the RNA transcript is released from
the DNA and the double helix can zip up again.
Transcription OverviewYouTube -
Transcription.flv
 Post Termination RNA Processing
• Most eukaryotic mRNAs aren‟t ready to be translated into protein directly after being
transcribed from DNA. mRNA requires processing.

• Transcription of RNA processing occur in the nucleus. After this, the messenger RNA
moves to the cytoplasm for translation.

• The cell adds a protective cap to one end, and a tail of A‟s to the other end. These both
function to protect the RNA from enzymes that would degrade

• Most of the genome consists of non-coding regions called introns

– Non-coding regions may have specific chromosomal functions or have regulatory purposes

– Introns also allow for alternative RNA splicing

• Thus, an RNA copy of a gene is converted into messenger RNA by doing 2 things:

– Add protective bases to the ends

– Cut out the introns

 Alteration of mRNA Ends
• Each end of a pre-mRNA molecule is modified in a
particular way
– The 5 end receives a modified nucleotide cap
– The 3 end gets a poly-A tail

A modified guanine nucleotide 50 to 250 adenine nucleotides

added to the 5 end added to the 3 end
TRANSCRIPTION DNA

RNA PROCESSING Pre-mRNA

Protein-coding segment Polyadenylation signal
5
3
mRNA
G P P P AAUAAA AAA…AAA
Ribosome
TRANSLATION
Start codon Stop codon
5 Cap 5 UTR 3 UTR Poly-A tail
Polypeptide
 RNA Processing - Splicing
• The original transcript from
the DNA is called pre-mRNA.

• It contains transcripts of both

introns and exons.

• The introns are removed by a

process called splicing to
produce messenger RNA
(mRNA)

• videoYouTube - -mRNA
Splicing--.flv
mRNA Processing

• Primary transcript is
not mature mRNA
• DNA sequence has
coding regions
(exons) and non-
coding regions
(introns)
• Introns must be
removed before
primary transcript is
mRNA and can leave
nucleus
 RNA Processing
• Proteins often have a modular architecture consisting
of discrete structural and functional regions called
domains
• In many cases different exons code for the different
domains in a protein

Gene
DNA
Exon 1 Intron Exon 2 Intron Exon 3
Transcription
RNA processing
Translation

Domain 3

Domain 2
Domain 1

Figure 17.12 Polypeptide

 Translation
• Conversion of RNA into amino
acid sequence that makes a
protein
• The mRNA leaves the nucleus
and enters the cytoplasm
• Ribosomes attach to mRNA
• tRNA (carrying anti-codon)
picks up the correct amino
acids and carries them to the
mRNA strand forming the
protein
Ex:
– tRNA carries GAU (anti-
codon)& looks for CUA on
mRNA
 Translation
• Translation is the RNA-directed TRANSCRIPTION DNA

synthesis of a polypeptide mRNA

Ribosome

•
TRANSLATION
Translation involves Polypeptide

– mRNA
Amino
– Ribosomes - Ribosomal RNA acids
Polypeptide
– Transfer RNA
– Genetic coding - codons tRNA with
amino acid
Ribosome attached

Gly

tRNA

Anticodon
A A A
U G G U U U G G C

5 Codons 3
mRNA
 The Genetic Code
• Genetic information is encoded as a sequence of nonoverlapping base
triplets, or codons

DNA Gene 2
molecule
Gene 1
Gene 3

DNA strand 3 5
(template) A C C A A A C C G A G T

TRANSCRIPTION

U G G U U U G G C U C A
mRNA 5 3
Codon
TRANSLATION

Protein Trp Phe Gly Ser

Amino acid
 The Genetic Code
• Codons: 3 base code for the production of a specific amino acid,
sequence of three of the four different nucleotides

• Since there are 4 bases and 3 positions in each codon, there are 4 x 4
x 4 = 64 possible codons

• 64 codons but only 20 amino acids, therefore most have more than 1
codon

• 3 of the 64 codons are used as STOP signals; they are found at the
end of every gene and mark the end of the protein

• One codon is used as a START signal: it is at the start of every protein

• Universal: in all living organisms

 The Genetic Code
• A codon in messenger RNA is either translated into an amino acid
or serves as a translational start/stop signal

Second mRNA base

U C A G
UUU UCU UAU UGU U
Phe Tyr Cys
UAC
U UUC UCC
Ser
UGC C
UUA UCA UAA Stop UGA Stop A
Leu UAG Stop UGG Trp G
UUG UCG

Third mRNA base (3 end)

First mRNA base (5 end)

CUU CCU CAU CGU U

His
CUC CCC CAC CGC C
C Leu Pro Arg
CUA CCA CAA CGA A
Gln
CUG CCG CAG CGG G
AUU ACU AAU AGU U
Asn
A
AUC lle ACC AAC AGC Ser C
Thr
AUA ACA AAA AGA A
Lys
AGG Arg G
Met or
AUG start ACG AAG
GUU GCU GAU GGU U
G GUC GCC GAC Asp GGC C
Val Ala Gly
GUA GCA GAA GGA A
GUG GCG GAG Glu GGG G
 Transfer RNA
• Consists of a single RNA strand that is only about 80 nucleotides long
• Each carries a specific amino acid on one end and has an anticodon on
the other end
• A special group of enzymes pairs up the proper tRNA molecules with
their corresponding amino acids.
• tRNA brings the amino acids to the ribosomes,

3
Amino acid A
C
attachment site C
A 5
C G
The “anticodon” is the 3 RNA bases that G C
C G
matches the 3 bases of the codon on the U G
U A
mRNA molecule A U
U C A U
* C A C AG UA A G *
G * C U C
G U G U G
*
C * C G A G
* * U C * A G G
* G AG C
(a) Two-dimensional structure. The four base-paired regions and three G C Hydrogen
loops are characteristic of all tRNAs, as is the base sequence of the U A bonds
amino acid attachment site at the 3 end. The anticodon triplet is * G
A
unique to each tRNA type. (The asterisks mark bases that have been A* C
chemically modified, a characteristic of tRNA.) * U
A G
A
Anticodon
 Transfer RNA
• 3 dimensional tRNA molecule is roughly “L” shaped

5 Amino acid
attachment site
3

Hydrogen
bonds

A AG

3 5
Anticodon
Anticodon
(c) Symbol used
(b) Three-dimensional structure in the book
 Ribosomes
• Ribosomes facilitate the specific coupling of tRNA anticodons with
mRNA codons during protein synthesis
• The 2 ribosomal subunits are constructed of proteins and RNA
molecules named ribosomal RNA or rRNA

TRANSCRIPTION DNA

mRNA
Ribosome
TRANSLATION

Polypeptide
Exit tunnel
Growing
polypeptide
tRNA
molecules
Large
subunit
E
P A

Small
subunit

5
mRNA 3
(a) Computer model of functioning ribosome. This is a model of a bacterial
ribosome, showing its overall shape. The eukaryotic ribosome is roughly
similar. A ribosomal subunit is an aggregate of ribosomal RNA molecules
and proteins.
 Building a Polypeptide
Amino end Growing polypeptide

Next amino acid

to be added to
polypeptide chain

tRNA

mRNA 3

Codons
5

(c) Schematic model with mRNA and tRNA. A tRNA fits into a binding site when its anticodon base-
pairs with an mRNA codon. The P site holds the tRNA attached to the growing polypeptide. The A
site holds the tRNA carrying the next amino acid to be added to the polypeptide chain. Discharged
tRNA leaves via the E site.
 Building a Polypeptide
• We can divide translation into three stages
– Initiation
– Elongation
– Termination
• The AUG start codon is recognized by methionyl-tRNA or Met
• Once the start codon has been identified, the ribosome
incorporates amino acids into a polypeptide chain
• RNA is decoded by tRNA (transfer RNA) molecules, which each
transport specific amino acids to the growing chain
• Translation ends when a stop codon (UAA, UAG, UGA) is reached
 Initiation of Translation
• The initiation stage of translation brings together mRNA, tRNA
bearing the first amino acid of the polypeptide, and two subunits
of a ribosome

Large
ribosomal
P site subunit
3 U A C 5
5 A U G 3

Initiator tRNA
GTP GDP
E A
mRNA
5 3 5 3
Start codon

mRNA binding site Small Translation initiation complex

ribosomal
subunit

1 2
A small ribosomal subunit binds to a molecule of The arrival of a large ribosomal subunit completes
mRNA. In a prokaryotic cell, the mRNA binding site the initiation complex. Proteins called initiation
on this subunit recognizes a specific nucleotide factors (not shown) are required to bring all the
sequence on the mRNA just upstream of the start translation components together. GTP provides
codon. An initiator tRNA, with the anticodon UAC, the energy for the assembly. The initiator tRNA is
base-pairs with the start codon, AUG. This tRNA in the P site; the A site is available to the tRNA
carries the amino acid methionine (Met). bearing the next amino acid.
 Where oh where can the amino acids be?

• tRNA is transfer RNA, whose

function is to attach to a specific
amino acid and bring that amino
acids to the site where
polypeptides are being
constructed.
• This RNA strand is twisted and
bonded into the shape seen on
the right.
• One end of the molecule attached
to a specific amino acid.
• The other end has an exposed
sequence of 3-bases. These are
called the anticodon.
• How many kinds of tRNA must
there be?
 You must know your base pairs!!

• If you said 20 types of tRNA you are wrong!

• There must be a different tRNA molecule for each of the possible

triplets. This means 64 anticodons.

The anticodons of the tRNAs each have a complimentary codon in

the mRNA. For example the codon AUG would be the compliment
of the anticodon UAC.
 The role of Ribosomes

• The third type of RNA is risosomal

RNA (rRNA).

• Ribosomes are the „decoding‟

units of the cell.

• Each ribosome consists of two

subunits, and is an assemblage of
rRNA and proteins.

• Ribosomes have binding sites for

both tRNA and mRNA molecules.
 Reading the Message

• An mRNA molecule attaches to a

ribosome.
• As the ribosome moves along the
mRNA, 3-base codons are
exposed one at a time.
• A tRNA with an anticodon that is
complimentary to the codon of the
mRNA temporarily bonds with the
mRNA.
• The ribosome positions the
molecules so that this bonding
occurs.
• As the ribosome continues its
journey along the mRNA
additional tRNAs bring their a.a. to
the site of peptide synthesis.
 Elongation of the Polypeptide Chain
• In the elongation stage, amino acids are added one by one to
the preceding amino acid

1 Codon recognition. The anticodon

TRANSCRIPTION DNA
Amino end of an incoming aminoacyl tRNA
mRNA
of polypeptide base-pairs with the complementary
Ribosome
TRANSLATION mRNA codon in the A site. Hydrolysis
Polypeptide
of GTP increases the accuracy and
E efficiency of this step.
mRNA 3
Ribosome ready for P A
next aminoacyl tRNA 5 site site
2 GTP
2 GDP

E E

P A P A

2 Peptide bond formation. An

GDP
3 Translocation. The ribosome rRNA molecule of the large
GTP
subunit catalyzes the formation
translocates the tRNA in the A
of a peptide bond between the
site to the P site. The empty tRNA
new amino acid in the A site and
in the P site is moved to the E site, E
the carboxyl end of the growing
where it is released. The mRNA
polypeptide in the P site. This step
moves along with its bound tRNAs,
P A attaches the polypeptide to the
bringing the next codon to be
tRNA in the A site.
translated into the A site.
 Termination of Translation
• The final stage is termination when the ribosome reaches a stop codon
in the mRNA

Release
factor
Free
polypeptide

5
3 3
3
5 5
Stop codon
(UAG, UAA, or UGA)
1 When a ribosome reaches a stop 2 The release factor hydrolyzes 3 The two ribosomal subunits
codon on mRNA, the A site of the the bond between the tRNA in and the other components of
ribosome accepts a protein called the P site and the last amino the assembly dissociate.
a release factor instead of tRNA. acid of the polypeptide chain.
The polypeptide is thus freed
from the ribosome.
 Translation
• The final step in translation is termination. When the
ribosome reaches a STOP codon, there is no
corresponding transfer RNA.
• Instead, a small protein called a “release factor”
attaches to the stop codon.
• The release factor causes the whole complex to fall
apart: messenger RNA, the two ribosome subunits,
the new polypeptide.
• The messenger RNA can be translated many times,
to produce many protein copies.
• Video YouTube - Translation.flv
 Translation
Nucleus

Lysine mRNA
Phenylalanine
tRNA
Methionine

Ribosome

mRNA Start codon

 Translation

Growing polypeptide
chain

Ribosome
tRNA

Lysine
tRNA

mRNA

mRNA
Ribosome
Translation direction
 A summary of transcription and translation in a eukaryotic cell
TRANSCRIPTION DNA
1RNA is transcribed
from a DNA template.
3

5 RNA RNA
transcript polymerase
RNA PROCESSING Exon
2
In eukaryotes, the RNA transcript
RNA transcript (pre- (pre-mRNA)
mRNA) is spliced and Intron
modified to produce
mRNA, which moves Aminoacyl-tRNA
from the nucleus to the synthetase
cytoplasm. NUCLEUS

Amino
FORMATION OF acid
INITIATION COMPLEX AMINO ACID ACTIVATION
CYTOPLASM tRNA
3 After leaving the 4
Each amino acid
nucleus, mRNA attaches attaches to its proper tRNA
to the ribosome. with the help of a specific
enzyme and ATP.
mRNA Growing
polypeptide
Activated
amino acid

Ribosomal
subunits

5
TRANSLATION
5
A succession of tRNAs
E A add their amino acids to
Anticodon the polypeptide chain
A A A
as the mRNA is moved
U G G U U U A U G
through the ribosome
one codon at a time.
Figure 17.26 Codon (When completed, the
polypeptide is released
Ribosome from the ribosome.)
 A Summary of the flow of Genetic
Information in a Cell

• Information is stored in the • rRNA and proteins form

triplet codes (codons) of DNA ribosomes.
nucleotides. • mRNA attaches to a ribosome
• This information is transcribed and the message is decoded
into 3 types of RNA. when the anticodon of a tRNA
• mRNA carries the information is bonded to a mRNA codon.
to assemble a polypeptide. • Subsequent amino acids are
• In the nucleus, introns are attached to the growing
removed and the remaining peptide chain until a stop
exons spliced together to make codon is reach and the chain is
a functional mRNA strand. terminated.
• tRNA molecules attach to • A summary of these events
specific amino acids. can be seen in the next slide.
 Post-translation
• The new polypeptide is now floating loose in
the cytoplasm if translated by a free ribosme.
• It might also be inserted into a membrane, if
translated by a ribosome bound to the
endoplasmic reticulum.
• Polypeptides fold spontaneously into their
active configuration, and they spontaneously
join with other polypeptides to form the final
proteins.
• Sometimes other molecules are also attached
to the polypeptides: sugars, lipids,
phosphates, etc. All of these have special
purposes for protein function.
Proteins Fold as They are Translated
on the Ribosome
Pathway from GEN to
functional protein
1. Packing/unpacking DNA
2. Transcription
3. mRNA processing
4. mRNA transport
5. Translation
6. Protein processing
7. Protein degradation
Any Questions??

2007-2008