Chapter 10 Gene expression, Transcription and Translation

Chapter 10 – The Expression of Genetic Information via
Genes I: Transcription and Translation
Chapter Outline
1. Overview of gene
expression
2. Transcription
3. RNA modifications in
eukaryotes
4. Translation and the genetic
code
5. The machinery of
translation
6. The stages of translation

10.1 Overview of Gene Expression
Section 10.1 Learning
Outcomes
1. Outline the general steps of
gene expression at the
molecular level, which
together constitute the
central dogma
2. Explain how proteins are
largely responsible for
determining an organism's
characteristics

10.1 Overview of Gene Expression
Molecular Gene Expression Involves the Processes of
Transcription and Translation
• At the molecular level, transcription and translation are key
processes of gene expression
• Transcription produces an RNA copy of a gene
• Translation interprets the nucleotide sequence in the messenger
RNA (mRNA) to build a polypeptide with a specific amino acid
sequence
• The cellular locations differ between
prokaryotes and eukaryotes
• Eukaryotes also use an additional step of RNA modification

10.1 Overview of Gene Expression
Molecular Gene Expression Involves the Processes of
Transcription and Translation
• The central dogma describes information flow from DNA to RNA to
protein
• Although DNA  RNA  protein is the most common pathway for
information flow, there are exceptions
• Some genes do not encode polypeptides, rather an RNA is the
final functional product
• Retroviruses use an RNA template to make DNA (RNA  DNA)

10.1 Overview of Gene Expression
The Protein Products of Genes Largely Determine an
Organism’s Characteristics
• Genes provide a “blueprint” for the characteristics of organisms
• Most genes are structural genes that code for polypeptides
• One or several polypeptides function as a protein that plays
some role in the cell
• The activities of proteins determine the structure and functions
of cells, and the cumulative cellular activities determine the
traits of an organism

10.2 Transcription
Section 10.2 Learning
Outcomes
1. Give a molecular definition
for the term gene
2. Sketch the structure of a
typical protein-coding gene,
and label key sequences
3. Outline the 3 stages of
transcription and the role
of RNA polymerase in this
process
4. Compare and contrast
transcription in bacteria
and eukaryotes

10.2 Transcription
• DNA stores information; this information must be accessed at the
molecular level for genes to be expressed
• Transcription copies a discrete unit of information from DNA into RNA
• DNA is not altered by transcription, so the same DNA molecule can
be used again and again as a source of information

10.2 Transcription
At the Molecular Level, a Gene Is Transcribed and
Produces a Functional Product
• A gene can be defined as an organized unit of nucleotide
sequences that enables a segment of DNA to be transcribed into
RNA and ultimately results in the formation of a functional product
• The functional product is often a protein however it can also be
an RNA molecule
• Ex: transfer RNA (tRNA) and ribosomal RNA (rRNA)

10.2 Transcription
At the Molecular Level, a Gene Is Transcribed and
Produces a Functional Product
• A gene is composed of specific base sequences organized in a way
that allows the DNA to be transcribed into RNA
• Important sequences
include the promoter,
transcribed region,
terminator, and
regulatory sequences

10.2 Transcription
During Transcription, RNA Polymerase Uses a DNA
Template to Make RNA
Transcription occurs in 3 stages: initiation, elongation, termination
1. Initiation is a recognition step where the promoter functions
as a recognition site
• In bacteria, sigma factor binds to RNA polymerase and
facilitates the binding of RNA polymerase to the promoter
• DNA strands are separated to form an open complex
2. Elongation occurs as RNA polymerase synthesizes RNA
• The DNA strand that is used as a template is called the
template strand and the opposite DNA strand is called the
coding strand
• The transcript is synthesized in the 5’ to 3’ direction
3. Termination occurs when RNA polymerase reaches a
terminator, releases the transcript, and dissociates from DNA

10.2 Transcription
During Transcription, RNA Polymerase Uses a DNA
Template to Make RNA

10.2 Transcription
Transcription in Eukaryotes Involves More Proteins
• The basic features of transcription are similar among all organisms
• Ex: use promoters, initiation, elongation, and termination stages
• Transcription of eukaryotic genes involves more complexity of
protein components
• Eukaryotes have 3 forms of RNA polymerase (I, II, III) whereas
bacteria have a single RNA polymerase
• RNA polymerase II transcribes mRNA from protein-coding genes
• RNA polymerases I and III transcribe non-coding genes such as
genes for tRNAs and rRNAs
• Initiation is also more complex; RNA polymerase II requires 5
general transcription factors

10.3 RNA Modifications in Eukaryotes
Section 10.3 Learning
Outcomes
1. Describe the addition of the
5ʹ cap and the 3ʹ poly A tail
to eukaryotic mRNA
2. Outline the process of
splicing that produces
mature eukaryotic mRNA
3. Explain the function of each
of the 3 RNA modifications

10.3 RNA Modification in Eukaryotes
• In eukaryotes, the product of transcription is a pre-mRNA, an
immature precursor that must be processed to form a mature
(functionally active) mRNA
• Pre-mRNAs undergo 3 key
modifications
1. A 5’ cap is added
2. A 3’ poly A tail is added
3. During splicing, the
introns (intervening
regions) are removed,
and the exons
(expressed regions) are
connected together

10.3 RNA Modifications in Eukaryotes
The Ends of Eukaryotic Pre-mRNA Are Modified by the
Addition of a 5ʹ Cap and a 3ʹ Poly A Tail
• Capping occurs when a modified
form of guanine is covalently
attached to the 5’ end
• The 5’ cap is recognized by a
variety of proteins; it is
needed for the mRNA to exit
the nucleus and bind the
ribosome
• The poly A tail is added to the 3’
end after transcription (via
enzyme activity)
• The poly A tail increases the
stability of the mRNA in the
cytosol

10.3 RNA Modifications in Eukaryotes
Splicing Involves the Removal of Introns and the
Linkage of Exons
• Introns are found in many (but not all) eukaryotic genes
• An average human gene has about 9 introns, each potentially
ranging from dozens to over 100,000 nucleotides
• The spliceosome is a complex that precisely removes introns
• The spliceosome is composed of several different subunits known
as snRNPs; each snRNP (“snurp”) contains small nuclear RNA and a
set of proteins
• The spliceosome can be regulated
so that splicing a given pre-mRNA
can occur in 2 or more ways
• Alternative splicing allows complex
eukaryotes to use the same gene to
make different proteins

10.3 RNA Modifications in Eukaryotes
Splicing Involves the Removal of Introns and the
Linkage of Exons
• Splicing occurs in a series of steps, and the catalytic events of steps
3 and 4 are catalyzed by an RNA component (ribozyme activity)

10.4 Translation and the Genetic Code
Section 10.4 Learning
Outcomes
1. Explain in detail how the
genetic code specifies the
relationship between the
sequence of codons in
mRNA and the amino acid
sequence of a polypeptide
2. Apply the genetic code to
determine the amino acid
sequence of a protein

10.4 Translation and the Genetic Code
The Genetic Code Specifies the Amino Acids
Within a Polypeptide
• The genetic code specifies the relationship between the sequence
of nucleotides in the mRNA and the sequence of amino acids in a
polypeptide
• The code is read in groups of 3 nucleotides called codons
• There are 64 different codons
• 1 start codon
• 3 stop codons
• 61 codons specify amino acids
• The code is redundant, meaning
more than 1 codon can specify
the same amino acid

10.4 Translation and the Genetic Code
The Genetic Code Specifies the Amino Acids
Within a Polypeptide

10.4 Translation and the Genetic Code
During Translation, mRNA Is Used to Make a Polypeptide
with a Specific Amino Acid Sequence
• A bacterial mRNA is depicted below
• The ribosomal-binding site, start codon, coding sequence, and
stop codon are key components for translation
• AUG is the start codon
• UAA, UAG, UGA are the
stop codons

10.4 Translation and the Genetic Code
During Translation, mRNA Is Used to Make a Polypeptide
with a Specific Amino Acid Sequence
• The start codon defines the reading frame, the groups of 3
nucleotides that are “read” as codons
• Codons are read in a sequential and non-overlapping manner in
the 5’ to 3’ direction
• Mark the codons in the sequences below – scan for the start codon
(AUG) after the ribosomal binding site to begin
• The second sequence has been modified by the addition of 1
nucleotide; do the codons differ?
5’ –AUAAGGAGGU U A C G A U G C A G C A G G G C U U U A C C – 3’
ribosomal binding site
5’ –AUAAGGAGGU U A C G A U G U C A G C A G G G C U U U A C C – 3’

10.4 Translation and the Genetic Code
DNA Stores Information, Whereas mRNA and tRNA
Access That Information to Make a Polypeptide
• Transfer RNAs (tRNAs) are involved in translating the nucleotide
base sequence of the mRNA into the amino acid sequence of the
polypeptide
• tRNAs contain an anticodon, a 3-base sequence that is
complimentary to an mRNA codon
• Different tRNAs have different
anticodon sequences and each
tRNA carries a specific amino acid
• The mRNA is read in the 5’ to 3’
direction and the polypeptide is
synthesized from the N-terminus to
the C-terminus

10.4 Translation and the Genetic Code
DNA Stores Information, Whereas mRNA and tRNA
Access That Information to Make a Polypeptide

10.5 The Machinery of Translation
Section 10.5 Learning
Outcomes
1. Describe the structure and
function of tRNA
2. Explain how aminoacyl-
tRNA synthetases attach
amino acids to tRNAs
3. Outline the structural
features of bacterial and
eukaryotic ribosomes
4. Discuss how ribosomal RNA
(rRNA) is used to evaluate
evolutionary relationships
among different species

10.5 The Machinery of Translation
• Many components
are necessary for
translation, and
most cells invest a
substantial amount
of energy into
translation

10.5 The Machinery of Translation
Transfer RNAs Share Common Structural Features
• The tRNAs of all species share common
features:
• 2-D cloverleaf structure with 3 loops
and a stem
• Anticodon located in the middle loop
• 3’ single-stranded region is the amino
acid attachment site
• 3-D structure involves additional
folding
• Cells make many different tRNAs, each
encoded by a different gene
• tRNAs are named according to the amino
acid they carry; tRNASer carries serine

10.5 The Machinery of Translation
Aminoacyl-tRNA Synthetases Charge tRNAs by
Attaching an Appropriate Amino Acid
• The enzymes that catalyze the attachment of amino acids to tRNA
molecules are known as aminoacyl-tRNA synthetases
• Cells make 20 distinct types of aminoacyl-tRNA synthetases; each
recognizes just 1 of the 20 different amino acids
• Each enzyme is named for the specific amino acid it attaches
(ex: alanyl-tRNA synthetase recognizes alanine)
• Aminoacyl-tRNA synthetases catalyze reactions involving an amino
acid, a tRNA molecule, and ATP
• When a tRNA has its amino acid attached, it is called a charged
tRNA

10.5 The Machinery of Translation
Aminoacyl-tRNA Synthetases Charge tRNAs by
Attaching an Appropriate Amino Acid

10.5 The Machinery of Translation
Ribosomes Are Composed of rRNA and Proteins
• Ribosomes are the sites of
translation
• Prokaryotic ribosomes are
distinct from eukaryotic
ribosomes, however both share
common structural features
• Both are large complexes
formed from a small subunit
and a large subunit
• Subunits contain 1 or more
rRNA molecules and
numerous proteins

10.5 The Machinery of Translation
Components of Ribosomal Subunits Form Functional
Sites for Translation
• Ribosomes contain 3 discrete sites where tRNA may be located:
• The aminoacyl (A) site
• The peptidyl (P) site
• The exit (E) site

10.5 The Machinery of Translation
Comparisons of Small Subunit rRNAs Provide a Basis
for Establishing Evolutionary Relationships
• Components for translation arose in the ancestor of all living
species; the gene for the small subunit rRNA is found in all species
• Gene evolution involves changes in DNA sequences; each species
accumulates different mutations over time
• Generally, if 2 species diverged a long time ago their gene
sequences are quite different whereas if they diverged a short time
ago, their gene sequences are more similar

10.6 The Stages of Translation
Section 10.6 Learning
Outcomes
1. Explain the 3 stages of
translation and the events
that occur during each
2. Summarize the similarities
and differences between
translation in bacteria and
eukaryotes

10.6 The Stages of Translation
• Like transcription, translation occurs in 3 stages: initiation,
elongation, and termination
• Initiation: an mRNA, the first tRNA, and the ribosomal subunits
assemble into a complex
• Elongation: the ribosome moves in the 5’ to 3’ direction from the
start codon towards the stop codon, synthesizing a polypeptide
• Termination: the ribosome reaches a stop codon and the complex
disassembles, releasing the polypeptide

10.6 The Stages of Translation
Translation is Initiated with the Assembly of
mRNA, tRNA, and Ribosomal Subunits
• Initiation factors are proteins
that help assemble the mRNA,
tRNA, and ribosome into a
functional complex; hydrolysis of
GTP provides an input of energy
• Initiation of translation in bacteria
is depicted in the figure
• The first tRNA carries a
modified methionine and
resides in the P site

10.6 The Stages of Translation
Translation is Initiated with the Assembly of
mRNA, tRNA, and Ribosomal Subunits
• Initiation of translation in eukaryotes
differs in a few ways:
• Instead of a ribosomal-binding
sequence, mRNAs have the 5’
guanosine cap; the cap is recognized
by proteins that promote binding of
the mRNA to the small subunit
• The position of the start codon is
more variable
• The initiator tRNA carries a regular
methionine (not a modified formyl-
methionine)

10.6 The Stages of Translation
Polypeptide Synthesis Occurs During the
Elongation Stage
• The elongation stage involves the
covalent bonding of amino acids to
each other
• Binding occurs due to codon/
anticodon recognition
• Elongation factors hydrolyze GTP to
provide energy to bind tRNA to the
A site

10.6 The Stages of Translation
Termination Occurs When a Stop Codon Is Reached
in the mRNA
• Termination occurs when a stop
codon is reached
• The 3 stop codons (UAA, UAG, UGA)
are recognized by a protein called a
release factor, not a tRNA

10.6 The Stages of Translation
Termination Occurs When a Stop Codon Is Reached
in the mRNA

Chapter 10 Summary
10.1 Overview of gene expression
• Molecular gene expression involves the processes of
transcription and translation
• The protein products of genes largely determine an organism’s
characteristics
10.2 Transcription
• At the molecular level, a gene is transcribed and produces a
functional product
• During transcription, RNA polymerase uses a DNA template to
make RNA
• Transcription in eukaryotes involves more proteins
10.3 RNA modifications in eukaryotes
• The ends of eukaryotic pre-mRNAs are modified by the addition
of a 5’ cap and a 3’ poly A tail
• Splicing involves the removal of introns and linkage of exons

Chapter 10 Summary
10.4 Translation and the genetic code
• The genetic code specifies the amino acids within a polypeptide
• During translation, mRNA is used to make a polypeptide with a
specific amino acid sequence
• DNA stores information, whereas mRNA and tRNA access that
information to make a polypeptide
10.5 The machinery of translation
• Transfer RNAs share common structural features
• Aminoacyl-tRNA synthetases charge tRNAs by attaching an
appropriate amino acid
• Ribosomes are composed of rRNA and proteins
• Components of ribosomal subunits form functional sites (A, P,
and E sites) for translation
• Comparisons of small subunit rRNAs among different species
provide a basis for establishing evolutionary relationships

Chapter 10 Summary
10.6 The stages of translation
• Translation is initiated with the assembly of mRNA, tRNA, and
ribosomal subunits
• Polypeptide synthesis occurs during the elongation stage
• Termination occurs when a stop codon is reached in the mRNA