Download Document

Chapter 17
From Gene to Protein
PowerPoint Lectures for
Biology, Seventh Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Proteins
• Proteins have many structures,
resulting in a wide range of
functions
• Proteins do most of the work in cells
and act as enzymes
• Proteins are made of monomers
called amino acids
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• An overview of protein functions
5.1
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Enzymes
– Are a type of protein that acts as a catalyst,
speeding up chemical reactions
Active site is
available for
a molecule of
substrate, the
reactant on which the
enzyme acts.
2
1
Substrate
binds to
enzyme.
Substrate
(sucrose)
Enzyme
(sucrase)
Glucose
OH
H O
Fructose
Figure 5.16
H 2O
3 Substrate is converted
to products.
4 Products are
released.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Amino acids
– Are organic molecules possessing both
carboxyl and amino groups
– Differ in their properties due to differing
side chains, called R groups
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Twenty Amino Acids
• 20 different amino acids make up proteins
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
H
Glycine (Gly)
O–
C
H3N
C
H
+
O–
C
CH2
O
H 3N
C
H
Valine (Val)
Alanine (Ala)
CH
CH3
CH3
O
CH3
CH3
C
+
O–
O
C
H
Leucine (Leu)
H3C
H3N
+
O–
CH2
CH
C
O
C
H
Isoleucine (Ile)
O–
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
C
H
CH2
O
H3N+
C
O–
Methionine (Met)
C
H
C
O–
Phenylalanine (Phe)
Figure 5.17
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
CH2
O
H3N+
C
H
O
C
H2C
CH2
H2
N
C
O
C
H
O–
Tryptophan (Trp)
Proline (Pro)
O–
OH
OH
Polar
H3N
+
CH2
C
O
C
H
CH
H3N
O–
Serine (Ser)
C
+
O
C
H3N
O–
H
+
CH2
C
H
O
C
CH2
H3N
O–
C
+
O
C
H
Electrically
charged
H3N
+
C
+
O–
O–
O
NH3+
NH2
C
CH2
C
CH2
CH2
CH2
CH2
CH2
CH2
O
H
O–
H3N
+
CH2
C
O
C
H
O–
H3N
+
CH2
C
H
Aspartic acid
(Asp)
O–
+
CH2
C
O
C
H
O–
Glutamine
(Gln)
Asparagine
(Asn)
C
C
C
H3N
Basic
O
C
CH2
O
H
Acidic
–O
CH2
H3N
Tyrosine
(Tyr)
Cysteine
(Cys)
Threonine (Thr)
C
NH2 O
C
SH
CH3
OH
NH2 O
Glutamic acid
(Glu)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
O–
Lysine (Lys)
NH2+
H3N
+
CH2
O
C
NH+
H3N
+
CH2
C
H
NH
CH2
O
C C
O–
H
O
C
O–
Arginine (Arg)
Histidine (His)
Amino Acid Polymers
• Amino acids
– Are linked by peptide bonds
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Polypeptides
• Polypeptides
– Are polymers (chains) of amino acids
• A protein
– Consists of one or more polypeptides
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Protein Conformation and Function
• A protein’s specific conformation (shape)
determines how it functions
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Four Levels of Protein Structure
• Primary structure
+H
3N
Amino
end
– Is the unique
sequence of amino
acids in a polypeptide
Amino
acid
subunits
Gly ProThrGly
Thr
Gly
Glu
Cys LysSeu
LeuPro
Met
Val
Lys
Val
Leu
Asp
AlaVal ArgGly
Ser
Pro
Ala
Glu Lle
Leu Ala
Gly
Asp
Thr
Lys
Ser
Lys TrpTyr
lle
Ser
Pro Phe
His Glu
AlaThrPhe Val
Asn
His
Ala
Glu
Val
Thr
Asp
Tyr
Arg
Ser
Arg
Gly Pro
lle
Ala
Ala
Leu
Leu
Ser
Pro
SerTyr
Tyr
Ser
Thr
Thr
Ala
Val
Val
Glu
Thr Pro Lys
Asn
Figure 5.20
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
c
o
o–
Carboxyl end
• Secondary structure
– Is the folding or coiling of the polypeptide into
a repeating configuration
– Includes the  helix and the  pleated sheet
 pleated sheet
Amino acid
subunits
O H H
C C N
C N
H
R
R
O
C
C
R
N H
C
H
R
O C
O C
N H
N H
N H
O C
O C
H
H C R H C R
H C R
C
R
N H O C
N H
O C
O C
H
C
O
N H
N
C
C
H
R
H
R
C
R
O H H
C C N
C C N
O H H
R
R
O H H
C C N
C C N
OH H
R
O
O
C
H
H
C
H
N HC N H C N H C N
C
H
H
C
O
C
O
R
R
H
 helix
Figure 5.20
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
R
R
O H H
C C N
C C N
OH H
R
O
C
H
H
NH C N
C
H
O C
R
R
C C
O
R
H
C
N HC N
H
O C
• Tertiary structure
– Is the overall three-dimensional shape of a
polypeptide
– Results from interactions between amino
Hydrophobic
acids and R groups
Hydrogen
bond
CH22
CH
O
H
O
H 3C
CH
CH3
H 3C
CH3
CH
interactions and
van der Waals
interactions
Polypeptide
backbone
HO C
CH2
CH2 S S CH2
Disulfide bridge
O
CH2 NH3+-O C CH2
Ionic bond
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Quaternary structure
– Is the overall protein structure that results
from the aggregation of two or more
polypeptide subunits
Polypeptide
chain
Collagen
 Chains
Iron
Heme
 Chains
Hemoglobin
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Review of Protein Structure
+H
3N
Amino end
Amino acid
subunits
helix
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Sickle-Cell Disease: A Simple Change in
Primary Structure
• Sickle-cell disease
– Results from a single amino acid
substitution in the protein
hemoglobin
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Primary
structure
Normal hemoglobin
Val
His Leu Thr Pro Glul Glu
1 2 3 4 5 6 7
Secondary
and tertiary
structures
Red blood
cell shape
Figure 5.21
Val
His
Leu Thr Pro


Molecules do
not associate
with one
another, each
carries oxygen.
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen


Val
Glu
structure 1 2 3 4 5 6 7
Secondary
 subunit and tertiary
structures
Quaternary Hemoglobin A
structure
Function
Sickle-cell hemoglobin
. . . Primary
Quaternary
structure
Function
10 m
...
Exposed
hydrophobic
region
 subunit




10 m
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity
to carry oxygen
is greatly
reduced.
Red blood
cell shape
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Fibers of
abnormal
hemoglobin
deform cell into
sickle shape.
What Determines Protein Conformation?
• Protein conformation Depends on
the physical and chemical
conditions of the protein’s
environment
• Temperature, pH, etc. affect protein
structure
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Denaturation is when a protein
unravels and loses its native
conformation
(shape)
Denaturation
Normal protein
Figure 5.22
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Denatured protein
Renaturation
The Protein-Folding Problem
• Most proteins
– Probably go through several
intermediate states on their way to a
stable conformation
– Denaturated proteins no longer work
in their unfolded condition
– Proteins may be denaturated by
extreme changes in pH, temperature,
salinity or heavy metals
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Chaperonins
– Are protein molecules that assist in the
proper folding of other proteins
Cap
Polypeptide
Correctly
folded
protein
Hollow
cylinder
Steps of Chaperonin
Chaperonin
(fully assembled) Action:
An unfolded poly1
peptide enters the
cylinder from one
Figure 5.23
end.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The cap attaches, causing
The cap comes
3
the cylinder to change shape off, and the
in
properly
such a way that it creates a
folded protein is
hydrophilic environment for
released.
the folding of the polypeptide.
2
What happens if a protein isn’t
folded correctly?
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Prions can be formed – misfolded versions of
normal proteins
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Prions
• Prions are slow-acting, virtually
indestructible infectious proteins that cause
brain diseases in mammals
• Prions propagate by converting normal
proteins into the prion version
• Scrapie in sheep, mad cow disease, and
Creutzfeldt-Jakob disease in humans are all
caused by prions
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Overview: The Flow of Genetic Information
• The information content of DNA
– Is in the form of specific sequences of
nucleotides along the DNA strands
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• 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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The ribosome
– Is part of the cellular machinery for translation,
polypeptide synthesis
Figure 17.1
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 17.1: Genes specify proteins via
transcription and translation
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Evidence from the Study of Metabolic Defects
• In 1909, British physician Archibald Garrod
– Was the first to suggest that genes dictate
phenotypes through enzymes that catalyze
specific chemical reactions in the cell
– DO NOT COPY
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Nutritional Mutants in Neurospora: Scientific Inquiry
• Beadle and Tatum causes bread mold to
mutate with X-rays
– Creating mutants that could not survive on
minimal medium
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Using genetic crosses
– They determined that their mutants fell into three
classes, each mutated in a different gene
EXPERIMENT
RESULTS
Working with the mold Neurospora crassa, George Beadle and Edward Tatum had isolated mutants requiring
arginine in their growth medium and had shown genetically that these mutants fell into three classes, each
defective in a different gene. From other considerations, they suspected that the metabolic pathway of arginine
biosynthesis included the precursors ornithine and citrulline. Their most famous experiment, shown here,
tested both their one gene–one enzyme hypothesis and their postulated arginine pathway. In this experiment,
they grew their three classes of mutants under the four different conditions shown in the Results section below.
The wild-type strain required only the minimal medium for growth. The three classes of mutants had
different growth requirements
Wild type
Minimal
medium
(MM)
(control)
MM +
Ornithine
MM +
Citrulline
MM +
Arginine
(control)
Figure 17.2
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Class I
Mutants
Class II
Mutants
Class III
Mutants
CONCLUSION
Gene A
From the growth patterns of the mutants, Beadle and Tatum deduced that each mutant was unable
to carry out one step in the pathway for synthesizing arginine, presumably because it lacked the
necessary enzyme. Because each of their mutants was mutated in a single gene, they concluded
that each mutated gene must normally dictate the production of one enzyme. Their results
supported the one gene–one enzyme hypothesis and also confirmed the arginine pathway.
(Notice that a mutant can grow only if supplied with a compound made after the defective step.)
Wild type
Class I
Mutants
(mutation
in gene A)
Precursor
Precursor
Precursor
Precursor
A
A
A
Ornithine
Ornithine
Ornithine
B
B
B
Citrulline
Citrulline
Citrulline
C
C
C
Arginine
Arginine
Arginine
Enzyme
A
Ornithine
Gene B
Enzyme
B
Citrulline
Gene C
Enzyme
C
Arginine
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Class II
Mutants
(mutation
in gene B)
Class III
Mutants
(mutation
in gene C)
• Beadle and Tatum developed the “one gene–
one enzyme hypothesis”
– Which states that the function of a gene is to
dictate the production of a specific enzyme
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
From AP Outline – Do not copy
• Obj. 3.4 TSIAT describe representations and
models illustrating how genetic information is
translated into polypeptides
• 3.6 TSC predict how a change in a specific
DNA or RNA sequence can result in changes
in gene expression.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
From AP Outline – Do not copy
• 3.19 TSIAT describe the connection between
the regulation of gene expression and
observed differences between individuals in a
a population
• 3.25 THS can create a visual representation to
illustrate how changes in a DNA nucelotide
sequence can result in a change in the
polypeptide produced.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Products of Gene Expression: A Developing Story
• As researchers learned more about proteins
– The made minor revision to the one gene–one
enzyme hypothesis
• Genes code for polypeptide chains or for RNA
molecules
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Basic Principles of Transcription and Translation
• 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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• In prokaryotes
– Transcription and translation occur together
TRANSCRIPTION
DNA
mRNA
Ribosome
TRANSLATION
Polypeptide
(a) Prokaryotic cell. In a cell lacking a nucleus, mRNA
produced by transcription is immediately translated
without additional processing.
Figure 17.3a
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• In eukaryotes
– RNA transcripts are modified before becoming
true mRNA
Nuclear
envelope
DNA
TRANSCRIPTION
Pre-mRNA
RNA PROCESSING
mRNA
Ribosome
TRANSLATION
Polypeptide
Figure 17.3b
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
(b) Eukaryotic cell. The nucleus provides a separate
compartment for transcription. The original RNA
transcript, called pre-mRNA, is processed in various
ways before leaving the nucleus as mRNA.
• Cells are governed by a cellular chain of
command
– DNA RNA protein
CENTRAL DOGMA
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Genetic Code
• How many bases correspond to an amino
acid?
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Codons: Triplets of Bases
• Genetic information
– Is encoded as a sequence of nonoverlapping
base triplets, or codons
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• During transcription
– The gene determines the sequence of bases
along the length of an mRNA molecule
Gene 2
DNA
molecule
Gene 1
Gene 3
DNA strand 3
5
A C C A A A C C G A G T
(template)
TRANSCRIPTION
mRNA
5
U G G U U U G G C U C A
Codon
TRANSLATION
Protein
Figure 17.4
Trp
Amino acid
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Phe
Gly
Ser
3
Cracking the Code
• A codon in messenger RNA
Figure 17.5
Second mRNA base
U
C
A
UAU
UUU
UCU
Tyr
Phe
UAC
UUC
UCC
U
UUA
UCA Ser UAA Stop
UAG Stop
UUG Leu UCG
CUU
CUC
C
CUA
CUG
CCU
CCC
Leu CCA
CCG
Pro
AUU
AUC
A
AUA
AUG
ACU
ACC
ACA
ACG
Thr
GUU
G GUC
GUA
GUG
lle
Met or
start
GCU
GCC
Val
GCA
GCG
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Ala
G
U
UGU
Cys
UGC
C
UGA Stop A
UGG Trp G
U
CAU
CGU
His
CAC
CGC
C
Arg
CAA
CGA
A
Gln
CAG
CGG
G
U
AAU
AGU
Asn
AAC
AGC Ser C
A
AAA
AGA
Lys
Arg
G
AAG
AGG
U
GAU
GGU
C
GAC Asp GGC
Gly
GAA
GGA
A
Glu
GAG
GGG
G
Third mRNA base (3 end)
First mRNA base (5 end)
– Is either translated into an amino acid or serves as
a translational stop signal
• Codons must be read in the correct reading
frame
– For the specified polypeptide to be produced
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Evolution of the Genetic Code
• The genetic code is nearly universal
– Shared by organisms from the simplest
bacteria to the most complex animals
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• In laboratory experiments
– Genes can be transcribed and translated after
being transplanted from one species to
another
Figure 17.6
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 17.2: Transcription is the DNAdirected synthesis of RNA: a closer look
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Molecular Components of Transcription
• 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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Synthesis of an RNA Transcript
• The stages of transcription are
Promoter
– Initiation
Transcription unit
5
3
3
5
Start point
RNA polymerase
– Elongation
– Termination
DNA
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.
1
5
3
Unwound
DNA
3
5
Template strand of
DNA
transcript
2 Elongation. The polymerase moves downstream, unwinding the
DNA and elongating the RNA transcript 5  3 . In the wake of
transcription, the DNA strands re-form a double helix.
Rewound
RNA
RNA
5
3
3
5
3
5
RNA
transcript
3 Termination. Eventually, the RNA
transcript is released, and the
polymerase detaches from the DNA.
5
3
3
5
5
Figure 17.7
Completed RNA
transcript
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
3
Non-template
strand of DNA
Elongation
RNA nucleotides
RNA
polymerase
A
T
C
C
A
A
3
3 end
U
5
A
E
G
C
A
T
A
G
G
T
T
Direction of transcription
(“downstream”)
5
Newly made
RNA
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Template
strand of DNA
RNA Polymerase Binding and Initiation of Transcription
• Promoters signal the initiation of RNA synthesis
• Transcription factors
– Help eukaryotic RNA polymerase recognize
promoter sequences
1 Eukaryotic promoters
TRANSCRIPTION
DNA
RNA PROCESSING
Pre-mRNA
mRNA
TRANSLATION
Ribosome
Polypeptide
Promoter
5
3
3
5
T A T A A AA
AT A T T T T
TATA box
Start point
Template
DNA strand
Several transcription
factors
2
Transcription
factors
5
3
3
5
3 Additional transcription
factors
RNA polymerase II
5
3
Transcription factors
3
5
5
RNA transcript
Figure 17.8
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Transcription initiation complex
Elongation of the RNA Strand
• 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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Termination of Transcription
• The mechanisms of termination
– Are different in prokaryotes and eukaryotes
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 17.3: Eukaryotic cells modify RNA
after transcription
• Enzymes in the eukaryotic nucleus
– Modify pre-mRNA in specific ways before the
genetic messages are dispatched to the
cytoplasm
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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
added to the 5 end
TRANSCRIPTION
RNA PROCESSING
50 to 250 adenine nucleotides
added to the 3 end
DNA
Pre-mRNA
5
mRNA
Protein-coding segment
Polyadenylation signal
3
G P P P
AAUAAA
AAA…AAA
Ribosome
TRANSLATION
5 Cap
5 UTR
Start codon Stop codon
Polypeptide
Figure 17.9
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
3 UTR
Poly-A tail
Split Genes and RNA Splicing
• RNA splicing
– Removes introns and joins exons
TRANSCRIPTION
RNA PROCESSING
DNA
Pre-mRNA
5 Exon Intron
Pre-mRNA 5 Cap
30
31
1
Coding
segment
mRNA
Ribosome
Intron
Exon
Exon
3
Poly-A tail
104
105
146
Introns cut out and
exons spliced together
TRANSLATION
Polypeptide
mRNA 5 Cap
1
3 UTR
Figure 17.10
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Poly-A tail
146
3 UTR
• Is carried out by spliceosomes in some cases
RNA transcript (pre-mRNA)
5
Intron
Exon 1
Exon 2
Protein
1
Other proteins
snRNA
snRNPs
Spliceosome
2
5
Spliceosome
components
3
Figure 17.11
5
mRNA
Exon 1
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Exon 2
Cut-out
intron
Ribozymes
• Ribozymes
– Are catalytic RNA molecules that function as
enzymes and can splice RNA
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Functional and Evolutionary Importance of Introns
• The presence of introns
– Allows for alternative RNA splicing
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• 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
Transcription
RNA processing
Intron Exon 3
Translation
Domain 3
Domain 2
Domain 1
Figure 17.12
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Polypeptide
• Concept 17.4: Translation is the RNA-directed
synthesis of a polypeptide: a closer look
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Molecular Components of Translation
• A cell translates an mRNA message into
protein
– With the help of transfer RNA (tRNA)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Translation: the basic concept
TRANSCRIPTION
DNA
mRNA
Ribosome
TRANSLATION
Polypeptide
Amino
acids
Polypeptide
tRNA with
amino acid
Ribosome attached
Gly
tRNA
Anticodon
A A A
U G G U U U G G C
Codons
5
Figure 17.13
mRNA
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
3
• Molecules of tRNA are not all identical
– Each carries a specific amino acid on one end
– Each has an anticodon on the other end
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Structure and Function of Transfer RNA
• A tRNA molecule
– Consists of a single RNA strand CAthat is only
C
about 80 nucleotides long
– Is roughly L-shaped
3
A
C
C
A 5
C G
G C
C G
U G
U A
A U
A U
U C
UA
C A C AG
*
G
*
G U G U *
C
C
* *
U C
*
* G AG C
(a) Two-dimensional structure. The four base-paired regions and three
G C
U A
loops are characteristic of all tRNAs, as is the base sequence of the
* G
amino acid attachment site at the 3 end. The anticodon triplet is
A
A*
unique to each tRNA type. (The asterisks mark bases that have been
C
U
*
chemically modified, a characteristic of tRNA.)
A
G
A
Figure 17.14a
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Amino acid
attachment site
Anticodon
C U C
G A G
A G *
*
G
A G G
Hydrogen
bonds
5
3
Amino acid
attachment site
Hydrogen
bonds
A AG
3
Anticodon
(b) Three-dimensional structure
Figure 17.14b
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
5
Anticodon
(c) Symbol used
in this book
• A specific enzyme called an aminoacyl-tRNA
synthetase
– Joins each amino acid to the correct tRNA
Amino acid
P P
Aminoacyl-tRNA
synthetase (enzyme)
1 Active site binds the
amino acid and ATP.
P Adenosine
ATP
2 ATP loses two P groups
and joins amino acid as AMP.
P
Pyrophosphate
Pi
Phosphates
P
Adenosine
Pi
Pi
tRNA
3 Appropriate
tRNA covalently
Bonds to amino
Acid, displacing
AMP.
P Adenosine
AMP
4 Activated amino acid
is released by the enzyme.
Figure 17.15
Aminoacyl tRNA
(an “activated
amino acid”)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Ribosomes
• Ribosomes
– Facilitate the specific coupling of tRNA
anticodons with mRNA codons during protein
synthesis
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The ribosomal subunits
– Are constructed of proteins and RNA
molecules named ribosomal RNA or rRNA
DNA
TRANSCRIPTION
mRNA
Ribosome
TRANSLATION
Polypeptide
Exit tunnel
Growing
polypeptide
tRNA
molecules
Large
subunit
E
P A
Small
subunit
5
mRNA
Figure 17.16a
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.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• 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 (AminoacyltRNA binding site)
E site
(Exit site)
Large
subunit
E
mRNA
binding site
Figure 17.16b
P
A
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.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Amino end
Growing polypeptide
Next amino acid
to be added to
polypeptide chain
tRNA
3
mRNA
5
Codons
(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.
Figure 17.16c
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Building a Polypeptide
• We can divide translation into three stages
– Initiation
– Elongation
– Termination
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Ribosome Association and 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
P site
3 U A C 5
5 A U G 3
Initiator tRNA
Large
ribosomal
subunit
GTP
GDP
E
A
mRNA
5
Start codon
mRNA binding site
Figure 17.17
3
Small
ribosomal
subunit
1 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).
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
5
3
Translation initiation complex
2 The arrival of a large ribosomal subunit completes
the initiation complex. Proteins called initiation
factors (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.
Elongation of the Polypeptide Chain
• In the elongation stage of translation
– Amino acids are added one by one to the
preceding amino acid
TRANSCRIPTION
Amino end
of polypeptide
DNA
mRNA
Ribosome
TRANSLATION
Polypeptide
mRNA
Ribosome ready for
next aminoacyl tRNA
E
3
P A
site site
5
1 Codon recognition. The anticodon
of an incoming aminoacyl tRNA
base-pairs with the complementary
mRNA codon in the A site. Hydrolysis
of GTP increases the accuracy and
efficiency of this step.
2 GTP
2 GDP
E
E
P
P
A
GDP
Figure 17.18
3 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.
GTP
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
E
P
A
A
2 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.
Termination of Translation
• The final stage of translation is termination
– When the ribosome reaches a stop codon in
the mRNA
Release
factor
Free
polypeptide
5
3
3
5
5
3
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.
Figure 17.19
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Polyribosomes
• A number of ribosomes can translate a single
mRNA molecule simultaneously
– Forming a polyribosome
Completed
polypeptide
Growing
polypeptides
Incoming
ribosomal
subunits
Start of
mRNA
(5 end)
End of
mRNA
(3 end)
(a) An mRNA molecule is generally translated simultaneously
by several ribosomes in clusters called polyribosomes.
Ribosomes
mRNA
0.1 µm
Figure 17.20a, b
(b) This micrograph shows a large polyribosome in a prokaryotic
cell (TEM).
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Completing and Targeting the Functional Protein
• Polypeptide chains
– Undergo modifications after the translation
process
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Protein Folding and Post-Translational Modifications
• After translation
– Proteins may be modified in ways that affect
their three-dimensional shape
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Targeting Polypeptides to Specific Locations
• Two populations of ribosomes are evident in
cells
– Free and bound
• Free ribosomes in the cytosol
– Initiate the synthesis of all proteins
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Proteins destined for the endomembrane
system or for secretion
– Must be transported into the ER
– Have signal peptides to which a signalrecognition particle (SRP) binds, enabling the
translation ribosome to bind to the ER
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The signal mechanism for targeting proteins to
the ER
1 Polypeptide
synthesis begins
on a free
ribosome in
the cytosol.
2 An SRP binds
to the signal
peptide, halting
synthesis
momentarily.
3 The SRP binds to a
receptor protein in the ER
membrane. This receptor
is part of a protein complex
(a translocation complex)
that has a membrane pore
and a signal-cleaving enzyme.
4 The SRP leaves, and
the polypeptide resumes
growing, meanwhile
translocating across the
membrane. (The signal
peptide stays attached
to the membrane.)
5 The signalcleaving
enzyme
cuts off the
signal peptide.
6 The rest of
the completed
polypeptide leaves
the ribosome and
folds into its final
conformation.
Ribosome
mRNA
Signal
peptide
Signalrecognition
particle
(SRP) SRP
receptor
CYTOSOL protein
ERLUMEN
Translocation
complex
Figure 17.21
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Signal
peptide
removed
ER
membrane
Protein
• Concept 17.5: RNA plays multiple roles in the
cell: a review
• RNA
– Can hydrogen-bond to other nucleic acid
molecules
– Can assume a specific three-dimensional
shape
– Has functional groups that allow it to act as a
catalyst
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Types of RNA in a Eukaryotic Cell
Table 17.1
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 17.6: Comparing gene expression in
prokaryotes and eukaryotes reveals key differences
• Prokaryotic cells lack a nuclear envelope
– Allowing translation to begin while transcription is
still in progress
RNA polymerase
DNA
mRNA
Polyribosome
RNA
polymerase
Direction of
transcription
DNA
Polyribosome
Polypeptide
(amino end)
Ribosome
Figure 17.22
0.25 m
mRNA (5 end)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• In a eukaryotic cell
– The nuclear envelope separates transcription
from translation
– Extensive RNA processing occurs in the
nucleus
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 17.7: Point mutations can affect
protein structure and function
• Mutations
– Are changes in the genetic material of a cell
• Point mutations
– Are changes in just one base pair of a gene
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The change of a single nucleotide in the DNA’s
template strand
– Leads to the production of an abnormal protein
Wild-type hemoglobin DNA
3
Mutant hemoglobin DNA
5
C T
T
In the DNA, the
mutant template
strand has an A where
the wild-type template
has a T.
G U A
The mutant mRNA has
a U instead of an A in
one codon.
3
5
T
C A
mRNA
mRNA
G A
A
5
3
5
3
Normal hemoglobin
Sickle-cell hemoglobin
Glu
Val
Figure 17.23
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The mutant (sickle-cell)
hemoglobin has a valine
(Val) instead of a glutamic
acid (Glu).
Types of Point Mutations
• Point mutations within a gene can be divided
into two general categories
– Base-pair substitutions
– Base-pair insertions or deletions
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Substitutions
• A base-pair substitution
– Is the replacement of one nucleotide and its
partner with another pair of nucleotides
– Can cause missense or nonsense
Wild type
mRNA
Protein
5
A U G
Met
A A G U U U GG C U A A
Lys
Phe
Gly
3
Stop
Amino end
Carboxyl end
Base-pair substitution
No effect on amino acid sequence
U instead of C
A U G A A G U U U G G U U A A
Met
Lys
Missense
Phe
Gly
Stop
A instead of G
A U G A A G U U U A G U U A A
Met
Lys
Phe
Ser
Stop
Nonsense
U instead of A
A U G U A G U U U G G C U A A
Figure 17.24
Met
Stop
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Insertions and Deletions
• Insertions and deletions
– Are additions or losses of nucleotide pairs in a
gene
– May produce frameshift mutations
Wild type
mRNA
Protein
5
A U G A A GU U U G G C U A A
Met
Lys
Gly
Phe
Stop
Amino end
Carboxyl end
Base-pair insertion or deletion
Frameshift causing immediate nonsense
Extra U
AU G U A AG U U U G GC U A
Met
Stop
Frameshift causing
extensive missense
U Missing
A U G A A GU U G G C U A A
Met
Lys
Leu
Ala
Insertion or deletion of 3 nucleotides:
no frameshift but extra or missing amino acid
A A G
Missing
A U G U U U G G C U A A
Figure 17.25
Met
Phe
Gly
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Stop
3
Mutagens
• Spontaneous mutations
– Can occur during DNA replication,
recombination, or repair
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Mutagens
– Are physical or chemical agents that can
cause mutations
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
What is a gene? revisiting the question
• A gene
– Is a region of DNA whose final product is either
a polypeptide or an RNA molecule
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• A summary of transcription and translation in a
eukaryotic cell
DNA
TRANSCRIPTION
1 RNA is transcribed
from a DNA template.
3
5
RNA
transcript
RNA
polymerase
RNA PROCESSING
Exon
2 In eukaryotes, the
RNA transcript (premRNA) is spliced and
modified to produce
mRNA, which moves
from the nucleus to the
cytoplasm.
RNA transcript
(pre-mRNA)
Intron
Aminoacyl-tRNA
synthetase
NUCLEUS
Amino
acid
tRNA
FORMATION OF
INITIATION COMPLEX
CYTOPLASM 3 After leaving the
nucleus, mRNA attaches
to the ribosome.
mRNA
AMINO ACID ACTIVATION
4
Each amino acid
attaches to its proper tRNA
with the help of a specific
enzyme and ATP.
Growing
polypeptide
Activated
amino acid
Ribosomal
subunits
5
TRANSLATION
A succession of tRNAs
add their amino acids to
the polypeptide chain
Anticodon
as the mRNA is moved
through the ribosome
one codon at a time.
(When completed, the
polypeptide is released
from the ribosome.)
5
E
A
AAA
UG GU U U A U G
Codon
Figure 17.26
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Ribosome
How antibiotics work
• Chloramphenicol inhibits peptidyl transferase
• Erythromycin inhibits translocation
• Streptomycin prevents two subunits from
bonding
• Tetracycline – interferes with attachment of
tRNA to ribosome cannot penetrate
mammalian cells very well
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Amoxicillin – interferes with production of cell
wall
• Cipro – inhibits topoisomerases and prevents
DNA replication
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Reverse transcriptase – found in retroviruses
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings