The Molecular Basis of Inheritance
Figure 16.7a, c
C
T
A
A
T
CG
GC
A
C G
AT
AT
A T
TA
C
TA0.34 nm
3.4 nm
(a) Key features of DNA structure
G
1 nm
G
(c) Space-filling model
T
1962: Nobel Prize in Physiology and Medicine
James D.Watson
Francis H.Crick
Maurice H. F.Wilkins
What about?Rosalind Franklin
Watson, J.D. and F.H. Crick, “Molecular Structure of Nucleic Acids: A Structure for Deoxynucleic Acids”. Nature 171 (1953), p. 738.
The Structure of DNA• DNA is composed of four nucleotides,
each containing: adenine, cytosine, thymine, or guanine.
• The amounts of A = T, G = C, and purines = pyrimidines [Chargaff’s Rule].
• DNA is a double-stranded helix with antiparallel strands [Watson and Crick].
• Nucleotides in each strand are linked by 5’-3’ phosphodiester bonds
• Bases on opposite strands are linked by hydrogen bonding: A with T, and G with C.
The Basic Principle: Base Pairing to a Template Strand
• The relationship between structure and function is manifest in the double helix
• Since the two strands of DNA are complementary each strand acts as a template for building a new strand in replication
DNA replication• The parent molecule unwinds, and two new
daughter strands are built based on base-pairing rules
(a) The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C.
(b) The first step in replication is separation of the two DNA strands.
(c) Each parental strand now serves as a template that determines the order of nucleotides along a new, complementary strand.
(d) The nucleotides are connected to form the sugar-phosphate backbones of the new strands. Each “daughter” DNA molecule consists of one parental strand and one new strand.
ACTAG
ACTAG
ACTAG
ACTAG
TGATC
TGATC
ACTAG
AC
T
A
G
TGATC
TGATC
TGATC
T
G
A
TC
DNA Replication is “Semi-conservative”
• Each 2-stranded daughter molecule is only half new
• One original strand was used as a template to make the new strand
DNA Replication• The copying of DNA is remarkable in its speed and accuracy• Involves unwinding the double helix and synthesizing two
new strands.• More than a dozen enzymes and other proteins participate
in DNA replication• The replication of a DNA molecule begins at special sites
called origins of replication, where the two strands are separated
Origins of Replication• A eukaryotic chromosome may have hundreds or
even thousands of replication origins
Replication begins at specific siteswhere the two parental strandsseparate and form replicationbubbles.
The bubbles expand laterally, asDNA replication proceeds in bothdirections.
Eventually, the replicationbubbles fuse, and synthesis ofthe daughter strands iscomplete.
1
2
3
Origin of replication
Bubble
Parental (template) strandDaughter (new) strand
Replication fork
Two daughter DNA molecules
In eukaryotes, DNA replication begins at many sites along the giantDNA molecule of each chromosome.
In this micrograph, three replicationbubbles are visible along the DNA ofa cultured Chinese hamster cell (TEM).
(b)(a)
0.25 µm
Mechanism of DNA Replication• DNA replication is catalyzed by DNA polymerase which needs an RNA primer• RNA primase synthesizes primer on DNA strand• DNA polymerase adds nucleotides to the 3’ end of the growing strand
Mechanism of DNA Replication• Nucleotides are added by complementary base pairing with the
template strand• The substrates, deoxyribonucleoside triphosphates, are
hydrolyzed as added, releasing energy for DNA synthesis.
The Mechanism of DNA Replication• DNA synthesis on the leading strand is continuous • The lagging strand grows the same general direction as the leading
strand (in the same direction as the Replication Fork). However, DNA is made in the 5’-to-3’ direction
• Therefore, DNA synthesis on the lagging strand is discontinuous• DNA is added as short fragments (Okasaki fragments) that are
subsequently ligated together
DNA polymerase I degrades the RNA primer and replaces it with DNA
The Mechanism of DNA Replication• Many proteins assist in DNA replication
• DNA helicases unwind the double helix, the template strands are stabilized by other proteins
• Single-stranded DNA binding proteins make the template available
• RNA primase catalyzes the synthesis of short RNA primers, to which nucleotides are added.
• DNA polymerase III extends the strand in the 5’-to-3’ direction
• DNA polymerase I degrades the RNA primer and replaces it with DNA
• DNA ligase joins the DNA fragments into a continuous daughter strand
Enzymes in DNA replication
Helicase unwinds parental double helix
Binding proteinsstabilize separatestrands
DNA polymerase III binds nucleotides to form new strands
Ligase joins Okazaki fragments and seals other nicks in sugar-phosphate backbone
Primase adds short primer to template strand
DNA polymerase I (Exonuclease) removes RNA primer and inserts the correct bases
Binding proteins prevent single strands from rewinding.
Helicase protein binds to DNA sequences called origins and unwinds DNA strands.
5’ 3’
5’
3’
Primase protein makes a short segment of RNA complementary to the DNA, a primer.
3’ 5’
5’ 3’
Replication
Overall directionof replication
5’ 3’5’
3’
5’
3’
3’ 5’
DNA polymerase enzyme adds DNA nucleotides to the RNA primer.
Replication
DNA polymerase enzyme adds DNA nucleotides to the RNA primer.
5’
5’
Overall directionof replication
5’
3’
5’
3’
3’
3’
DNA polymerase proofreads bases added and replaces incorrect nucleotides.
Replication
5’
5’ 3’
5’ 3’
3’ 5’
3’Overall directionof replication
Leading strand synthesis continues in a 5’ to 3’ direction.
Replication
3’ 5’ 5’
5’ 3’
5’ 3’
3’ 5’
3’Overall directionof replication
Okazaki fragment
Leading strand synthesis continues in a 5’ to 3’ direction.
Discontinuous synthesis produces 5’ to 3’ DNA segments called Okazaki fragments.
Replication
5’ 5’
5’ 3’
5’ 3’
3’ 5’
3’Overall directionof replication
3’
Leading strand synthesis continues in a 5’ to 3’ direction.
Discontinuous synthesis produces 5’ to 3’ DNA segments called Okazaki fragments.
Okazaki fragment
Replication
5’
5’ 3’
5’
3’
3’
5’ 3’
3’
5’ 5’ 3’
Leading strand synthesis continues in a 5’ to 3’ direction.
Discontinuous synthesis produces 5’ to 3’ DNA segments called Okazaki fragments.
Replication
3’
5’
3’ 5’
5’ 3’
5’ 3’
3’
5’ 5’ 3’
Leading strand synthesis continues in a 5’ to 3’ direction.
Discontinuous synthesis produces 5’ to 3’ DNA segments called Okazaki fragments.
Replication
5’
5’
3’ 3’
5’
3’
5’ 3’
5’ 3’
3’
5’
Exonuclease activity of DNA polymerase I removes RNA primers.
Replication
Polymerase activity of DNA polymerase I fills the gaps.
Ligase forms bonds between sugar-phosphate backbone.
3’
5’
3’
5’ 3’
5’ 3’
3’
5’
Replication
Replication Fork Overview
Proofreading• DNA must be faithfully replicated…but
mistakes occur– DNA polymerase (DNA pol) inserts the wrong
nucleotide base in 1/10,000 bases• DNA pol has a proofreading capability and can correct
errors– Mismatch repair: ‘wrong’ inserted base can be
removed– Excision repair: DNA may be damaged by
chemicals, radiation, etc. Mechanism to cut out and replace with correct bases
Mutations
• A mismatching of base pairs, can occur at a rate of 1 per 10,000 bases.
• DNA polymerase proofreads and repairs accidental mismatched pairs.
• Chances of a mutation occurring at any one gene is over 1 in 100,000
• Because the human genome is so large, even at this rate, mutations add up. Each of us probably inherited 3-4 mutations!
Proofreading and Repairing DNA
• DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides
• In mismatch repair of DNA, repair enzymes correct errors in base pairing
• In nucleotide excision DNA repair nucleases cut out and replace damaged stretches of DNA
Nuclease
DNApolymerase
DNAligase
A thymine dimerdistorts the DNA molecule.1
A nuclease enzyme cutsthe damaged DNA strandat two points and thedamaged section isremoved.
2
Repair synthesis bya DNA polymerasefills in the missingnucleotides.
3
DNA ligase seals theFree end of the new DNATo the old DNA, making thestrand complete.
4
Accuracy of DNA Replication
• The chromosome of E. coli bacteria contains about 5 million bases pairs– Capable of copying this DNA in less than an hour
• The 46 chromosomes of a human cell contain about 6 BILLION base pairs of DNA!!– Printed one letter (A,C,T,G) at a time…would fill
up over 900 volumes of Campbell.
– Takes a cell a few hours to copy this DNA
– With amazing accuracy – an average of 1 per billion nucleotides
The Central Dogma of Life.
replication
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 prokaryotes transcription and translation occur together
Figure 17.3a
Prokaryotic cell. In a cell lacking a nucleus, mRNAproduced by transcription is immediately translatedwithout additional processing.
(a)
TRANSLATION
TRANSCRIPTION DNA
mRNA
Ribosome
Polypeptide
Transcription and Translation• In a eukaryotic cell the nuclear envelope separates
transcription from translation• Extensive RNA processing occurs in the nucleus
Eukaryotic cell. The nucleus provides a separatecompartment for transcription. The original RNAtranscript, called pre-mRNA, is processed in various ways before leaving the nucleus as mRNA.
(b)
TRANSCRIPTION
RNA PROCESSING
TRANSLATION
mRNA
DNA
Pre-mRNA
Polypeptide
Ribosome
Nuclearenvelope
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
Table 17.1
• 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.
Synthesis of an RNA Transcript
• The stages of transcription are– Initiation– Elongation– Termination
PromoterTranscription unit
RNA polymerase
Start point
53
35
35
53
53
35
53
35
5
5
Rewound
RNA
RNA
transcript
3
3Completed RNA transcript
Unwound
DNA
RNA
transcript
Template strand of DNA
DNA
1 Initiation. After RNA polymerase binds to the promoter, the DNA strands unwind, and the polymerase initiates RNA synthesis at the start point on the template strand.
2 Elongation. The polymerase moves downstream, unwinding theDNA and elongating the RNA transcript 5 3 . In the wake of transcription, the DNA strands re-form a double helix.
3 Termination. Eventually, the RNAtranscript is released, and the polymerase detaches from the DNA.
• Promoters signal the initiation of RNA synthesis
• Transcription factors help eukaryotic RNA polymerase recognize promoter sequences
• A crucial promoter DNA sequence is called a TATA box.
TRANSCRIPTION
RNA PROCESSING
TRANSLATION
DNA
Pre-mRNA
mRNA
Ribosome
Polypeptide
T A T AAA AATAT T T T
TATA box Start point TemplateDNA strand
53
35
Transcriptionfactors
53
35
Promoter
53
355
RNA polymerase IITranscription factors
RNA transcript
Transcription initiation complex
Eukaryotic promoters1
Several transcriptionfactors
2
Additional transcriptionfactors
3
Synthesis of an RNA Transcript - Initiation
Synthesis of an RNA Transcript - Elongation
Elongation
RNApolymerase
Non-templatestrand of DNA
RNA nucleotides
3 end
C A E G C A AU
T A G G T TA
AC
G
U
AT
CA
T C C A A TT
GG
3
5
5
Newly madeRNA
Direction of transcription(“downstream”) Template
strand of DNA
• 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
• 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.
Synthesis of an RNA Transcript - Termination
Transcription Overview
• 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
Post Termination RNA Processing
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 nucleotideadded to the 5 end
50 to 250 adenine nucleotidesadded to the 3 end
Protein-coding segment Polyadenylation signal
Poly-A tail3 UTRStop codonStart codon
5 Cap 5 UTR
AAUAAA AAA…AAA
TRANSCRIPTION
RNA PROCESSING
DNA
Pre-mRNA
mRNA
TRANSLATIONRibosome
Polypeptide
G P P P
5 3
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
Figure 17.10
TRANSCRIPTION
RNA PROCESSING
DNA
Pre-mRNA
mRNA
TRANSLATION
Ribosome
Polypeptide
5 Cap
Exon Intron
1
5
30 31
Exon Intron
104 105 146
Exon 3Poly-A tail
Poly-A tail
Introns cut out andexons spliced together
Codingsegment
5 Cap1 146
3 UTR3 UTR
Pre-mRNA
mRNA
RNA Processing• RNA Splicing can also be carried out by spliceosomes
RNA transcript (pre-mRNA)
Exon 1 Intron Exon 2
Other proteinsProteinsnRNA
snRNPs
Spliceosome
Spliceosomecomponents
Cut-outintronmRNA
Exon 1 Exon 2
5
5
5
1
2
3
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
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
Figure 17.12
GeneDNA
Exon 1 Intron Exon 2 Intron Exon 3
TranscriptionRNA processing
Translation
Domain 3
Domain 1
Domain 2
Polypeptide
Translation
• Translation is the RNA-directed synthesis of a polypeptide
• Translation involves – mRNA– Ribosomes - Ribosomal RNA– Transfer RNA – Genetic coding - codons
TRANSCRIPTION
TRANSLATION
DNA
mRNARibosome
Polypeptide
PolypeptideAminoacids
tRNA withamino acidattachedRibosome
tRNA
Anticodon
mRNA
Trp
Phe Gly
A G C
A A A
CC
G
U G G U U U G G C
Codons5 3
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
DNAmolecule
Gene 1
Gene 2
Gene 3
DNA strand(template)
TRANSCRIPTION
mRNA
Protein
TRANSLATION
Amino acid
A C C A A A C C G A G T
U G G U U U G G C U C A
Trp Phe Gly Ser
Codon
3 5
35
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 baseU C A G
U
C
A
G
UUUUUCUUAUUG
CUUCUCCUACUG
AUUAUCAUAAUG
GUUGUCGUAGUG
Met orstart
Phe
Leu
Leu
lle
Val
UCUUCCUCAUCG
CCUCCCCCACCG
ACUACCACAACG
GCUGCCGCAGCG
Ser
Pro
Thr
Ala
UAUUAC
UGUUGCTyr Cys
CAUCACCAACAG
CGUCGCCGACGG
AAUAACAAAAAG
AGUAGCAGAAGG
GAUGACGAAGAG
GGUGGCGGAGGG
UGGUAAUAG Stop
Stop UGA StopTrp
His
Gln
Asn
Lys
Asp
Arg
Ser
Arg
Gly
UCAGUCAGUCAGUCAG
Firs
t mR
NA
bas
e (5
end
)
Third
mR
NA
bas
e (3
end
)
Glu
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,
Two-dimensional structure. The four base-paired regions and three loops are characteristic of all tRNAs, as is the base sequence of the amino acid attachment site at the 3 end. The anticodon triplet is unique to each tRNA type. (The asterisks mark bases that have been chemically modified, a characteristic of tRNA.)
(a)
3
CCACGCUUAAGACACCU*
GC * *
G U G U *CU* G AG
GU**A
*A A GUC
AGACC*
C G A G A G GG*
*GACUC*AUUUAGGCG5
Amino acidattachment site
Hydrogenbonds
Anticodon
A
The “anticodon” is the 3 RNA bases that matches the 3 bases of the codon on the mRNA molecule
Transfer RNA• 3 dimensional tRNA molecule is roughly “L” shaped
(b) Three-dimensional structureSymbol used in the book
Amino acidattachment site
Hydrogen bonds
AnticodonAnticodon
A A G
53
3 5
(c)
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
TRANSLATION
DNA
mRNARibosome
Polypeptide Exit tunnelGrowingpolypeptide
tRNAmolecules
E P A
Largesubunit
Smallsubunit
mRNA
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.
(a)
53
Ribosome• The ribosome has three binding sites for tRNA
– The P site– The A site– The E site
E P A
P site (Peptidyl-tRNAbinding site)
E site (Exit site)
mRNAbinding site
A site (Aminoacyl-tRNA binding site)
Largesubunit
Smallsubunit
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.
(b)
Amino end Growing polypeptide
Next amino acidto be added topolypeptide chain
tRNA
mRNA
Codons
3
5
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.
(c)
Building a Polypeptide
Building a Molecule of tRNA• A specific enzyme called an aminoacyl-tRNA
synthetase joins each amino acid to the correct tRNA
Figure 17.15
Amino acid
ATP
Adenosine
Pyrophosphate
Adenosine
Adenosine
Phosphates
tRNA
P P P
P
P Pi
Pi
Pi
P
AMP
Aminoacyl tRNA(an “activatedamino acid”)
Aminoacyl-tRNAsynthetase (enzyme)
Active site binds theamino acid and ATP. 1
ATP loses two P groupsand joins amino acid as AMP.2
3 AppropriatetRNA covalentlyBonds to aminoAcid, displacingAMP.
Activated amino acidis released by the enzyme.4
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
Largeribosomalsubunit
The arrival of a large ribosomal subunit completes the initiation complex. Proteins called initiationfactors (not shown) are required to bring all the translation components together. GTP provides the energy for the assembly. The initiator tRNA is in the P site; the A site is available to the tRNA bearing the next amino acid.
2
Initiator tRNA
mRNA
mRNA binding site Smallribosomalsubunit
Translation initiation complex
P site
GDPGTP
Start codon
A small ribosomal subunit binds to a molecule of mRNA. In a prokaryotic cell, the mRNA binding site on this subunit recognizes a specific nucleotide sequence on the mRNA just upstream of the start codon. An initiator tRNA, with the anticodon UAC, base-pairs with the start codon, AUG. This tRNA carries the amino acid methionine (Met).
1
Met MetU A CA U G
E A
3
5
5
3
35 35
Elongation of the Polypeptide Chain• In the elongation stage, amino acids are added one
by one to the preceding amino acid
Amino endof polypeptide
mRNA
Ribosome ready fornext aminoacyl tRNA
E
P A
E
P A
E
P A
E
P A
GDPGTP
GTP
GDP
2
2
site site5
3
TRANSCRIPTION
TRANSLATION
DNA
mRNARibosome
Polypeptide
Codon recognition. The anticodon of an incoming aminoacyl tRNA base-pairs with the complementary mRNA codon in the A site. Hydrolysisof GTP increases the accuracy andefficiency of this step.
1
Peptide bond formation. An rRNA molecule of the large subunit catalyzes the formation of a peptide bond between the new amino acid in the A site and the carboxyl end of the growing polypeptide in the P site. This step attaches the polypeptide to the tRNA in the A site.
2
Translocation. The ribosome translocates the tRNA in the A site to the P site. The empty tRNA in the P site is moved to the E site, where it is released. The mRNA moves along with its bound tRNAs,bringing the next codon to be translated into the A site.
3
Termination of 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.
Release factor
Freepolypeptide
Stop codon(UAG, UAA, or UGA)
5
3 35
35
When a ribosome reaches a stop codon on mRNA, the A site of the ribosome accepts a protein called a release factor instead of tRNA.
1 The release factor hydrolyzes the bond between the tRNA in the P site and the last amino acid of the polypeptide chain. The polypeptide is thus freed from the ribosome.
2 3 The two ribosomal subunits and the other components of the assembly dissociate.
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.
• 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.
Translation: Termination
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
Growingpolypeptides
Completedpolypeptide
Incomingribosomalsubunits
Start of mRNA(5 end)
End of mRNA(3 end)
Polyribosome
An mRNA molecule is generally translated simultaneously by several ribosomes in clusters called polyribosomes.
(a)
RibosomesmRNA
This micrograph shows a large polyribosome in a prokaryotic cell (TEM).
0.1 µm
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
RNA polymerase
DNA
Polyribosome
RNApolymerase
Direction oftranscription
mRNA
0.25 m
DNA
Polyribosome
Polypeptide(amino end)
Ribosome
mRNA (5 end)
A summary of transcription and translation in a eukaryotic cell
Figure 17.26
TRANSCRIPTION
RNA is transcribedfrom a DNA template.
DNA
RNApolymerase
RNAtranscript
RNA PROCESSING
In eukaryotes, theRNA transcript (pre-mRNA) is spliced andmodified to producemRNA, which movesfrom the nucleus to thecytoplasm.
Exon
Poly-A
RNA transcript(pre-mRNA)
Intron
NUCLEUSCap
FORMATION OFINITIATION COMPLEX
After leaving thenucleus, mRNA attachesto the ribosome.
CYTOPLASM
mRNA
Poly-A
Growingpolypeptide
Ribosomalsubunits
Cap
Aminoacyl-tRNAsynthetase
Aminoacid
tRNAAMINO ACID ACTIVATION
Each amino acidattaches to its proper tRNAwith the help of a specificenzyme and ATP.
Activatedamino acid
TRANSLATION
A succession of tRNAsadd their amino acids tothe polypeptide chainas the mRNA is movedthrough the ribosomeone codon at a time.(When completed, thepolypeptide is releasedfrom the ribosome.)
Anticodon
A C C
A A AU G G U U U A U G
U A CE A
Ribosome
1
Poly-A
5
5
3
Codon
2
3 4
5
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
• 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
Targeting Polypeptides to Specific Locations
Ribosomes
mRNASignalpeptide
Signal-recognitionparticle(SRP)
SRPreceptorprotein
CYTOSOL
ER LUMEN Translocationcomplex
Signalpeptideremoved
ERmembrane
Protein
Mutation Causes and Rate• The natural replication of DNA produces occasional errors.
DNA polymerase has an editing mechanism that decreases the rate, but it still exists
• Typically genes incur base substitutions about once in every 10,000 to 1,000,000 cells
• Since we have about 6 billion bases of DNA in each cell, virtually every cell in your body contains several mutations
• Mutations can be harmful, lethal, helpful, silent• However, most mutations are neutral: have no effect• Only mutations in cells that become sperm or eggs—are
passed on to future generations• Mutations in other body cells only cause trouble when they
cause cancer or related diseases
Mutagens• Mutagens are chemical or physical agents that interact
with DNA to cause mutations.• Physical agents include high-energy radiation like X-rays
and ultraviolet light • Chemical mutagens fall into several categories.
– Chemicals that are base analogues that may be substituted into DNA, but they pair incorrectly during DNA replication.
– Interference with DNA replication by inserting into DNA and distorting the double helix.
– Chemical changes in bases that change their pairing properties.• Tests are often used as a preliminary screen of chemicals
to identify those that may cause cancer• Most carcinogens are mutagenic and most mutagens are
carcinogenic.
Viral Mutagens• Scientists have recognized a number of tumor
viruses that cause cancer in various animals, including humans
• About 15% of human cancers are caused by viral infections that disrupt normal control of cell division
• All tumor viruses transform cells into cancer cells through the integration of viral nucleic acid into host cell DNA.
Point mutations• Point mutations involve alterations in the
structure or location of a single gene. Generally, only one or a few base pairs are involved.
• Point mutations can signficantly affect protein structure and function
• Point mutations may be caused by physical damage to the DNA from radiation or chemicals, or may occur spontaneously
• Point mutations are often caused by mutagens
Point Mutation• The change of a single nucleotide in the DNA’s template
strand leads to the production of an abnormal protein
In the DNA, themutant templatestrand has an A where the wild-type template has a T.
The mutant mRNA has a U instead of an A in one codon.
The mutant (sickle-cell) hemoglobin has a valine (Val) instead of a glutamic acid (Glu).
Mutant hemoglobin DNAWild-type hemoglobin DNA
mRNA mRNA
Normal hemoglobin Sickle-cell hemoglobin
Glu Val
C T T C A T
G A A G U A
3 5 3 5
5 35 3
Types of Point Mutations
• Point mutations within a gene can be divided into two general categories– Base-pair substitutions - is the replacement of
one nucleotide and its partner with another pair of nucleotides
– Base-pair insertions or deletions - are additions or losses of nucleotide pairs in a gene
Base-Pair Substitutions• Silent - changes a codon but codes for the same amino acid• Missense - substitutions that change a codon for one amino acid into a
codon for a different amino acid• Nonsense -substitutions that change a codon for one amino acid into a
stop codonWild type
A U G A A G U U U G G C U A AmRNA 5Protein Met Lys Phe Gly Stop
Carboxyl endAmino end
3
A U G A A G U U U G G U U A A
Met Lys Phe Gly
Base-pair substitutionNo effect on amino acid sequence
U instead of C
Stop
A U G A A G U U U A G U U A A
Met Lys Phe Ser Stop
A U G U A G U U U G G C U A A
Met Stop
Missense A instead of G
NonsenseU instead of A
Insertions and Deletions– Are additions or losses of nucleotide pairs in a gene– May produce frameshift mutations that will change the reading
frame of the gene, and alter all codons downstream from the mutation.
mRNAProtein
Wild typeA U G A A G U U U G G C U A A
5Met Lys Phe Gly
Amino end Carboxyl end
Stop
Base-pair insertion or deletionFrameshift causing immediate nonsense
A U G U A A G U U U G G C U A
A U G A A G U U G G C U A A
A U G U U U G G C U A A
Met Stop
U
Met Lys Leu Ala
Met Phe Gly Stop
MissingA A G
Missing
Extra U
Frameshift causing extensive missense
Insertion or deletion of 3 nucleotides:no frameshift but extra or missing amino acid
3
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