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The Central Dogma of Life.

replication
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 prokaryotes transcription and
translation occur together

DNA
TRANSCRIPTION

mRNA
Ribosome
TRANSLATION

Polypeptide

(a) Prokaryotic cell. In a cell lacking a nucleus, mRNA


produced by transcription is immediately translated
Figure 17.3a without additional processing.
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
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 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
5 3

transcription 3

Start point
DNA
5

are RNA polymerase 1 Initiation. After RNA polymerase binds to


the promoter, the DNA strands unwind, and

Initiation the polymerase initiates RNA synthesis at the


start point on the template strand.
Elongation 5
3
3
5
Template strand of
Unwound
Termination DNA
RNA 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
1 Eukaryotic promoters
Promoters signal the TRANSCRIPTION

RNA PROCESSING
DNA

Pre-mRNA

initiation of RNA mRNA

TRANSLATION Ribosome

synthesis
Polypeptide
Promoter

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

TATA box Start point Template


5

eukaryotic RNA 2
DNA strand
Several transcription

polymerase recognize Transcription


factors

factors
promoter sequences 5 3
3 5
A crucial promoter DNA 3 Additional transcription
factors

sequence is called a
TATA box.
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 EG 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 Overview
Post Termination RNA Processing
Most eukaryotic mRNAs arent 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 As 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 AAAAAA
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)
RNA Processing - Splicing
Ribozymes are catalytic RNA molecules that
function as enzymes and can splice RNA
RNA splicing removes introns and joins exons

5 Exon Intron Exon Intron Exon 3


TRANSCRIPTION DNA Pre-mRNA 5 Cap Poly-A tail
1 30 31 104 105 146
RNA PROCESSING Pre-mRNA

mRNA
Coding Introns cut out and
segment exons spliced together
Ribosome

TRANSLATION

Polypeptide
mRNA 5 Cap Poly-A tail
1 146
3 UTR 3 UTR

Figure 17.10
RNA Processing
RNA Splicing can also be carried out by spliceosomes
RNA transcript (pre-mRNA)
5
Exon 1 Intron Exon 2

Protein
1 Other proteins
snRNA

snRNPs
Spliceosome

2 5

Spliceosome
components
Cut-out
intron
3
mRNA
5
Exon 1 Exon 2
Alternative Splicing (of Exons)
How is it possible that there are millions of
human antibodies when there are only about
30,000 genes?
Alternative splicing refers to the different
ways the exons of a gene may be combined,
producing different forms of proteins within
the same gene-coding region
Alternative pre-mRNA splicing is an important
mechanism for regulating gene expression in
higher eukaryotes
Translation
Translation is the RNA- TRANSCRIPTION DNA

directed synthesis of a TRANSLATION


mRNA
Ribosome

polypeptide Polypeptide

Translation involves Amino


Polypeptide acids
mRNA
Ribosomes - Ribosomal RNA tRNA with
amino acid
Transfer RNA
Ribosome attached
Genetic coding - codons
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
The gene determines the sequence of bases along the length of an
mRNA molecule

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


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 Molecule of tRNA
A specific enzyme called an aminoacyl-tRNA
synthetase joins each amino acid to the correct tRNA

Amino acid Aminoacyl-tRNA


synthetase (enzyme)

P P P Adenosine
1 Active site binds the
amino acid and ATP.
ATP

2 ATP loses two P groups


and joins amino acid as AMP.
P Adenosine

Pyrophosphate P Pi

Pi
Pi
Phosphates
tRNA
3 Appropriate
tRNA covalently
Bonds to amino
Acid, displacing P Adenosine
AMP. AMP
4 Activated amino acid
is released by the enzyme.

Aminoacyl tRNA
(an activated
Figure 17.15 amino acid)
Ribosome
The ribosome has three binding sites for tRNA
The P site
The A site
The E site P site (Peptidyl-tRNA
binding site)
A site (Aminoacyl-
tRNA binding site)
E site
(Exit site)
Large
subunit
E P A

mRNA
binding site Small
subunit

(b) Schematic model showing binding sites. A ribosome has an


mRNA binding site and three tRNA binding sites, known as the A, P,
and E sites. This schematic ribosome will appear in later diagrams.
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
Translation: Initiation
mRNA binds to a ribosome, and the transfer RNA corresponding
to the START codon binds to this complex. Ribosomes are
composed of 2 subunits (large and small), which come together
when the messenger RNA attaches during the initiation process.
Translation: Elongation
Elongation: the ribosome moves down the messenger RNA,
adding new amino acids to the growing polypeptide chain.
The ribosome has 2 sites for binding transfer RNA. The first
RNA with its attached amino acid binds to the first site, and then
the transfer RNA corresponding to the second codon bind to the
second site.
Translation: Elongation
The ribosome then removes the amino acid from the
first transfer RNA and attaches it to the second amino
acid.
At this point, the first transfer RNA is empty: no
attached amino acid, and the second transfer RNA
has a chain of 2 amino acids attached to it.
Translation: Termination
The elongation cycle repeats as the ribosome moves
down the messenger RNA, translating it one codon
and one amino acid at a time.
The process repeats until a STOP codon is reached.
Polyribosomes
A number of ribosomes can translate a single mRNA
molecule simultaneously forming a polyribosome
Polyribosomes enable a cell to make many copies of
a polypeptide very quickly
Completed
Growing polypeptide
polypeptides
Incoming
ribosomal
subunits
Start of End of
mRNA mRNA
(5 end) (3 end)
(a) An mRNA molecule is generally translated simultaneously
by several ribosomes in clusters called polyribosomes.

Ribosomes
mRNA

0.1 m
This micrograph shows a large polyribosome in a prokaryotic
cell (TEM).
Comparing Gene Expression In Prokaryotes And Eukaryotes

In a eukaryotic cell:
The nuclear envelope separates transcription
from translation
Extensive RNA processing occurs in the nucleus

Prokaryotic cells lack a nuclear envelope, allowing


translation to begin while transcription progresses
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
tRNA
CYTOPLASM 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.)
Post-translation
The new polypeptide is now floating loose in the
cytoplasm if translated by a free ribosome.
Polypeptides fold spontaneously into their active
configuration, and they spontaneously join with other
polypeptides to form the final proteins.
Often translation is not sufficient to make a functional
protein, polypeptide chains are modified after
translation
Sometimes other molecules are also attached to the
polypeptides: sugars, lipids, phosphates, etc. All of
these have special purposes for protein function.
Targeting Polypeptides to Specific Locations
Completed proteins are targeted to specific sites
in the cell
Two populations of ribosomes are evident in cells:
free ribsomes (in the cytosol) and bound
ribosomes (attached to the ER)
Free ribosomes mostly synthesize proteins that
function in the cytosol
Bound ribosomes make proteins of the endomembrane
system and proteins that are secreted from the cell
Ribosomes are identical and can switch from free
to bound
Targeting Polypeptides to Specific Locations
Polypeptide synthesis always begins in the cytosol
Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to
attach to the ER
Polypeptides destined for the ER or for secretion are marked by a signal
peptide
A signal-recognition particle (SRP) binds to the signal peptide
The SRP brings the signal peptide and its ribosome to the ER

Ribosomes

mRNA
Signal
peptide ER
Signal- membrane
Signal
recognition
peptide Protein
particle SRP
removed
(SRP) receptor
protein
CYTOSOL

ER LUMEN Translocation
complex