From Gene to Protein

From Gene to Protein

 Genes specify proteins via
transcription and translation
• How was the fundamental relationship between
genes and proteins discovered?
– In 1902, British physician Archibald Garrod first
suggested that genes dictate phenotypes through
enzymes that catalyze specific chemical reactions

– Linking genes to enzymes required understanding that

cells synthesize and degrade molecules in a series of
steps, a metabolic pathway
Nutritional Mutants in Neurospora:
Scientific Inquiry
• George Beadle and Edward Tatum exposed bread mold to
X-rays, creating mutants that were unable to survive on
minimal media

• Using crosses, they and their coworkers identified three

classes of arginine-deficient mutants, each lacking a
different enzyme necessary for synthesizing arginine

• They developed a one gene–one enzyme hypothesis,

which states that each gene dictates production of a
specific enzyme
Figure 17.2
Precursor Results Table Classes of Neurospora crassa

Enzyme A Wild type Class I mutants Class II mutants Class III mutants

Ornithine Minimal
medium
Enzyme B (MM)
(control)
Citrulline
Enzyme C MM +
ornithine
Arginine

Condition
MM +
citrulline

MM +
Growth: arginine
No growth:
Wild-type (control)
Mutant cells
cells growing cannot grow
and dividing and divide Can grow with Can grow on Can grow only
Summary ornithine, Require arginine
or without any on citrulline or
of results citrulline, to grow
Control: Minimal medium supplements arginine
or arginine

Gene Class I mutants Class II mutants Class III mutants

(codes for (mutation in (mutation in (mutation in
enzyme) Wild type gene A) gene B) gene C)
Precursor Precursor Precursor Precursor
Gene A Enzyme A Enzyme A Enzyme A Enzyme A

Ornithine Ornithine Ornithine Ornithine

Gene B Enzyme B Enzyme B Enzyme B Enzyme B

Citrulline Citrulline Citrulline Citrulline

Gene C Enzyme C Enzyme C Enzyme C Enzyme C

Arginine Arginine Arginine Arginine

© 2014 Pearson Education, Inc.

 Basic Principles of
Transcription and Translation
• RNA is the bridge between genes and the proteins for
which they code

• Transcription is the synthesis of RNA using

information in DNA

• Transcription produces messenger RNA (mRNA)

• Translation is the synthesis of a polypeptide, using

information in the mRNA

• Ribosomes are the sites of translation

• A primary transcript is the initial RNA
transcript from any gene prior to processing

• The central dogma is the concept that cells

are governed by a cellular chain of command:

DNA RNA Protein

Figure 17.3

Nuclear
envelope

TRANSCRIPTION
DNA

Pre-mRNA
RNA PROCESSING

mRNA
DNA
TRANSCRIPTION

mRNA
Ribosome TRANSLATION Ribosome
TRANSLATION

Polypeptide Polypeptide

(a) Bacterial cell (b) Eukaryotic cell

 Genetic Code:
Codons -Triplets of Bases

• triplet code: series of three-nucleotide words

– smallest units of uniform length that can code
for all 20 amino acids

• during translation, the mRNA base triplets,

called codons, are read in the 5′ to 3′ direction

• each codon specifies the amino acid to be

placed at the corresponding position along a
polypeptide
Figure 17.4

DNA
template 3′ 5′ DNA
strand A C C A A A C C G A G T molecule

T G G T T T G G C T C A
3′ Gene 1
5′
TRANSCRIPTION
Gene 2
U G G U U U G G C U C A
mRNA 5′ 3′
Codon
TRANSLATION

Protein Trp Phe Gly Ser

Gene 3
Amino acid
Figure 17.5
Second mRNA base
U C A G
UUU UCU UAU UGU U
Phe Tyr Cys
UUC UCC UAC UGC C
U Ser
UUA UCA UAA Stop UGA Stop A
Leu

Third mRNA base (3′ end of codon)

Trp
First mRNA base (5′ end of codon)
UUG UCG UAG Stop UGG G

CUU CCU CAU CGU U

His
CUC CCC CAC CGC C
C Leu Pro Arg
CUA CCA CAA CGA A
Gln
CUG CCG CAG CGG G

AUU ACU AAU AGU U

Asn Ser
AUC Ile ACC AAC AGC C
A Thr
AUA ACA AAA AGA A
Lys Arg
Met or
AUG start ACG AAG AGG G

GUU GCU GAU GGU U

Asp
GUC GCC GAC GGC C
G Val Ala Gly
GUA GCA GAA GGA A
Glu
GUG GCG GAG GGG G
© 2014 Pearson Education, Inc.
Figure 17.6

(a) Tobacco plant expressing (b) Pig expressing a jellyfish

a firefly gene gene
Figure 17.7-3
Promoter Transcription unit

5′ 3′
3′ 5′
Start point
RNA polymerase
1 Initiation

5′ 3′
3′ 5′
Unwound RNA Template strand of DNA
DNA transcript
2 Elongation
Rewound
5′ DNA 3′
3′
3′ 5′
5′ Direction of
RNA transcription
transcript (“downstream”)
3 Termination
5′ 3′
3′ 5′
5′ 3′
Completed RNA transcript

© 2014 Pearson Education, Inc.

 RNA Polymerase Binding and
Initiation of Transcription
• Promoters signal the transcriptional start point
and usually extend several dozen nucleotide pairs
upstream of the start point
• Transcription factors mediate the binding of
RNA polymerase and the initiation of transcription
• The completed assembly of transcription factors
and RNA polymerase II bound to a promoter is
called a transcription initiation complex
• A promoter called a TATA box is crucial in
forming the initiation complex in eukaryotes
 1 A eukaryotic promoter
includes a TATA box
Promoter
Template
5′ 3′
3′ 5′
TATA box Start point Template
DNA strand
2 Several transcription factors must
Transcription bind to the DNA before RNA
factors polymerase II can do so.
5′ 3′
3′ 5′

3 Additional transcription factors bind to

the DNA along with RNA polymerase II,
forming the transcription initiation complex.
RNA polymerase II
Transcription factors

5′ 3′
3′ 5′ 5′

RNA transcript
Transcription initiation complex
 Elongation of the RNA Strand
• As RNA polymerase moves along the DNA, it
untwists the double helix, 10 to 20 bases at a
time

• Transcription progresses at a rate of 40

nucleotides per second in eukaryotes

• A gene can be transcribed simultaneously by

several RNA polymerases

• Nucleotides are added to the 3′ end of the

growing RNA molecule
Figure 17.9
Nontemplate
strand of DNA
RNA nucleotides
RNA
polymerase

A T C C A A
3′ 5′
C
3′ end

C A U C C A

5′ 3′
T A G G T T

5′ Direction of transcription
Template
strand of DNA
Newly made
RNA
Termination of Transcription
• The mechanisms of termination are different in
bacteria and eukaryotes

• In bacteria, the polymerase stops transcription at

the end of the terminator and the mRNA can be
translated without further modification

• In eukaryotes, RNA polymerase II transcribes the

polyadenylation signal sequence; the RNA
transcript is released 10–35 nucleotides past this
polyadenylation sequence
 Eukaryotic cells modify RNA after transcription
Enzymes in eukaryotic nucleus modify pre-mRNA before genetic
messages are dispatched to the cytoplasm

modifications share several functions:

facilitate the export of mRNA
protect mRNA from hydrolytic enzymes
help ribosomes attach to the 5′ end

A modified guanine 50–250 adenine

nucleotide added to nucleotides added
the 5′ end to the 3′ end
Region that includes Polyadenylation
protein-coding segments signal
5′ 3′
G P P P AAUAAA AAA…AAA

Start Stop
5′ Cap 5′ UTR 3′ UTR Poly-A tail
codon codon
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Split Genes and RNA Splicing
• Introns: long noncoding stretches of nucleotides that lie between
coding regions

• Exons: expressed - usually translated into amino acid sequences

• RNA splicing removes introns and joins exons, creating an mRNA

molecule with a continuous coding sequence

Pre-mRNA Intron Intron

5′ Cap Poly-A tail

1–30 31–104 Introns cut out 105–146

and exons
spliced together
mRNA
5′ Cap Poly-A tail
1–146
5′ UTR 3′ UTR
Coding
segment
 RNA transcript (pre-mRNA)
5′
RNA splicing is carried Exon 1 Intron Exon 2
out by spliceosomes
Protein
Other
snRNA
Spliceosomes consist of a proteins
snRNPs
variety of proteins and
several small nuclear Spliceosome
ribonucleoproteins
(snRNPs) that recognize 5′
the splice sites

The RNAs of the

spliceosome also catalyze
the splicing reaction
Spliceosome
components
Cut-out
intron
mRNA
5′
Exon 1 Exon 2
 The Functional & Evolutionary
Importance of Introns
• some introns contain sequences that may regulate
gene expression

• alternative RNA splicing uses different parts as

exons

• proteins often have modular architecture

consisting of discrete regions called domains
– often, different exons code for the different
domains in a protein
 Gene
DNA
Exon 1 Intron Exon 2 Intron Exon 3

Transcription

RNA processing

Translation

Domain 3

Domain 2

Domain 1

Polypeptide
Molecular Components of
Translation
• A cell translates an Polypeptide
Amino
acids
mRNA message
into protein with the tRNA with
amino acid
help of transfer attached
Ribosome
RNA (tRNA)

• tRNAs transfer
amino acids to the tRNA

growing polypeptide Anticodon

in a ribosome
5′ Codons 3′
mRNA
The Structure and Function Amino acid
attachment site
3′

of Transfer RNA 5′

•Molecules of tRNA are not identical

Hydrogen
•Each carries a specific amino acid on bonds

one end
Anticodon

•Each has an anticodon on the other (a) Two-dimensional structure

Amino acid
end 5′
3′
attachment site

Hydrogen
bonds

A tRNA molecule consists of a single RNA

strand that is only about 80 nucleotides long Anticodon
3′
Anticodon
5′

(c) Symbol used

(b) Three-dimensional structure in this book
• Accurate translation requires two steps:

– First: a correct match between a tRNA and

an amino acid, done by the enzyme
aminoacyl-tRNA synthetase

– Second: a correct match between the tRNA

anticodon and an mRNA codon

• Flexible pairing at the third base of a codon is

called wobble and allows some tRNAs to
bind to more than one codon
Figure 17.16-3
1 Amino acid Tyrosine (Tyr)
and tRNA (amino acid)
enter active
site. Tyrosyl-tRNA
synthetase

Tyr-tRNA

Aminoacyl-tRNA
A U A synthetase
ATP

Complementary AMP + 2 P i tRNA

tRNA anticodon

3 Aminoacyl 2 Using ATP, Amino

tRNA synthetase acid
released. catalyzes
covalent
bonding.

Computer model
© 2014 Pearson Education, Inc.
Ribosomes
• Ribosomes facilitate specific coupling of tRNA
anticodons with mRNA codons in protein
synthesis

• The two ribosomal subunits (large and small) are

made of proteins and ribosomal RNA (rRNA)

• Bacterial and eukaryotic ribosomes are

somewhat similar but have significant
differences: some antibiotic drugs specifically
target bacterial ribosomes without harming
eukaryotic ribosomes
Figure 17.17
Growing
polypeptide Exit tunnel
tRNA
molecules

Large
EP subunit
A

Small
subunit

5′
mRNA 3′

(a) Computer model of functioning ribosome

Growing
polypeptide Next amino
P site (Peptidyl-tRNA Amino end
binding site) Exit tunnel acid to be
added to
A site (Aminoacyl- polypeptide
tRNA binding site) chain
E site
(Exit site)
E P A Large E tRNA
mRNA 3′
subunit
mRNA
binding Small 5′ Codons
site subunit

(b) Schematic model showing binding sites (c) Schematic model with mRNA and tRNA
© 2014 Pearson Education, Inc.
 Building a Polypeptide

• The three stages of translation:

– Initiation
– Elongation
– Termination

• All three stages require protein “factors” that

aid in the translation process
Figure 17.18

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

Pi
Initiator +
tRNA GTP GDP
E A
mRNA
5′ 5′ 3′
3′
Start codon
Small
ribosomal
mRNA binding site subunit Translation initiation complex

1 Small ribosomal subunit binds 2 Large ribosomal subunit

to mRNA. completes the initiation
complex.

© 2014 Pearson Education, Inc.

Figure 17.19-3
Amino end
of polypeptide
1 Codon
E 3′ recognition
mRNA
Ribosome ready for P A
next aminoacyl tRNA 5′ site site GTP

GDP + P i

E E

P A P A

GDP + P i

3 Translocation GTP
2 Peptide bond
formation
E

P A

© 2014 Pearson Education, Inc.

Figure 17.20-3

Release Free
factor polypeptide

5′
3′ 3′
3′
5′ 5′
2 GTP
Stop codon
2 GDP + 2 P i
(UAG, UAA, or UGA)
1 Ribosome reaches a 2 Release factor 3 Ribosomal subunits
stop codon on mRNA. promotes hydrolysis. and other components
dissociate.

© 2014 Pearson Education, Inc.

Polyribosomes Growing
Completed
polypeptide
polypeptides
Incoming
ribosomal
subunits

Start of
mRNA End of
(5′ end) mRNA
(3′ end)
(a)

Ribosomes

mRNA

(b) 0.1 µm
 Protein Folding and
Post-Translational Modifications

• During and after synthesis, a polypeptide chain

spontaneously coils and folds into its three-dimensional
shape

• Proteins may also require post-translational modifications

before doing their job

• Some polypeptides are activated by enzymes that cleave

them

• Other polypeptides come together to form the subunits of

a protein
Targeting Polypeptides to Specific Locations

• 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 and brings the signal peptide and ribosome to the
ER
Figure 17.21

1 2 3 4 5 6
Polypeptide SRP SRP SRP Signal- Completed
synthesis binds to binds to detaches cleaving polypeptide
begins. signal receptor and enzyme cuts folds into
peptide. protein. polypeptide off signal final
synthesis peptide. conformation.
resumes.
Ribosome
mRNA

Signal ER
peptide membrane
Signal
SRP peptide Protein
removed

CYTOSOL SRP receptor

protein
ER LUMEN

Translocation complex

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Mutations of one or a few nucleotides can
affect protein structure and function

• Mutations are changes in the genetic material

of a cell or virus

• Point mutations are chemical changes in just

one base pair of a gene

• The change of a single nucleotide in a DNA

template strand can lead to the production of an
abnormal protein
Figure 17.25

Wild-type β-globin Sickle-cell β-globin

Wild-type β-globin DNA Mutant β-globin DNA

3′ C T C 5′ 3′ C A C 5′
5′ G A G 3′ 5′ G T G 3′

mRNA mRNA
5′ G A G 3′ 5′ G U G 3′

Normal hemoglobin Sickle-cell hemoglobin

Glu Val

© 2014 Pearson Education, Inc.

 Substitutions
• A nucleotide-pair substitution replaces one
nucleotide and its partner with another pair of
nucleotides
• Silent mutations have no effect on the amino
acid produced by a codon because of
redundancy in the genetic code
• Missense mutations still code for an amino
acid, but not the correct amino acid
• Nonsense mutations change an amino acid
codon into a stop codon, nearly always leading
to a nonfunctional protein
 Insertions and Deletions
• Insertions and deletions are additions or
losses of nucleotide pairs in a gene

• These mutations have a disastrous effect on

the resulting protein more often than
substitutions do

• Insertion or deletion of nucleotides may alter

the reading frame, producing a frameshift
mutation
Figure 17.26
Wild type
DNA template strand 3′ T A C T T C A A A C C G A T T 5′
5′ A T G A A G T T T G G C T A A 3′
mRNA 5′ A U G A A G U U U G G C U A A 3′
Protein Met Lys Phe Gly Stop
Amino end Carboxyl end

(a) Nucleotide-pair substitution (b) Nucleotide-pair insertion or deletion

A instead of G Extra A
3′ T A C T T C A A A C C A A T T 5′ 3′ T A C A T T C A A A C C G A T T 5′
5′ A T G A A G T T T G G T T A A 3′ 5′ A T G T A A G T T T G G C T A A 3′
U instead of C Extra U
5′ A U G A A G U U U G G U U A A 3′ 5′ A U G U A A G U U U G G C U A A 3′
Met Lys Phe Gly Met Stop
Stop
Silent Frameshift (1 nucleotide-pair insertion)

T instead of C A missing
3′ T A C T T C A A A T C G A T T 5′ 3′ T A C T T C A A C C G A T T 5′
5′ A T G A A G T T T A G C T A A 3′ 5′ A T G A A G T T G G C T A A 3′
A instead of G U missing
5′ A U G A A G U U U A G C U A A 3′ 5′ A U G A A G U U G G C U A A 3′
Met Lys Phe Ser Stop Met Lys Leu Ala
Missense Frameshift (1 nucleotide-pair deletion)

A instead of T T T C missing
3′ T A C A T C A A A C C G A T T 5′ 3′ T A C A A A C C G A T T 5′
5′ A T G T A G T T T G G C T A A 3′ 5′ A T G T T T G G C T A A 3′
U instead of A A A G missing
5′ A U G U A G U U U G G U U A A 3′ 5′ A U G U U U G G C U A A 3′
Met Met Phe Gly Stop
Stop
Nonsense 3 nucleotide-pair deletion
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 Comparing Gene Expression in
Bacteria, Archaea, & Eukarya

• Bacteria & eukarya differ in RNA polymerases,

termination of transcription & ribosomes

• Bacteria can simultaneously transcribe & translate

the same gene

• In eukarya, transcription & translation are

separated by the nuclear envelope

• In archaea, transcription & translation are likely

coupled
 RNA polymerase

DNA
mRNA

Polyribosome

Direction of 0.25 µm
RNA transcription
polymerase
DNA

Polyribosome

Polypeptide
(amino end)

Ribosome

mRNA (5′ end)

Figure 17.24
DNA
TRANSCRIPTION

3′

5′ RNA
RNA
polymerase
transcript
Exon
RNA
RNA transcript
PROCESSING
(pre-mRNA)
Intron Aminoacyl-tRNA
synthetase
NUCLEUS
Amino
acid AMINO ACID
CYTOPLASM
tRNA ACTIVATION

mRNA

3′
A
P Aminoacyl
E
Ribosomal (charged)
subunits tRNA

TRANSLATION
E A
A A A Anticodon
U G G U U U A U G

Codon
Ribosome

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In summary, a gene can be defined as a
region of DNA that can be expressed to
produce a final functional product, either
a polypeptide or an RNA molecule
The final product of an expressed gene can be
which of the following? Find all of the correct
choices.

a) mRNA
b) tRNA
c) rRNA
d) polypeptide
Replication, Transcription, Translation

Of the following, which pertain to replication,

transcription, modification, or translation? Each
can be used once or more than once.
origin anticodon
stop codon promoter
peptide bond terminator sequence
P site tRNA
GTP spliceosome
amino acid synthetase
Complementarity

The template strand of a given gene includes

the sequence 3′-G C C A C G T A T C A G-5′.

a) What is the sequence of the nontemplate strand?

b) What is the mRNA sequence made?

For each one, be sure to indicate 5′ and 3′

ends.
Gene Expression
Which of the following is the best example of
gene expression?

a) A frog adapts to variation in its environmental

temperature.
b) Mouse fur color results from pigment formed by
gene-encoded enzymes.
c) DNA is replicated during the S phase of the cell
cycle.
d) The percent of A versus a alleles in a population is
altered by natural selection.
e) Mutation alters the sequence of a region of DNA.
Genetic Code

These examples
demonstrate the
ability of genes from
one species to be
expressed in a
different species.
This is possible
because of which
property of the
genetic code?
Transcription

Describe what is
occurring at each of
the stages of
transcription (1, 2, 3
in the figure).
How does each stage
move the process
forward?
Eukaryotic Promoters

What components form the transcription

complex at a eukaryotic promoter?
Modification

How and where are modifications made to

eukaryotic mRNA before it goes to the cytosol?
What role do snRNPs play?
Ribosomes

What is represented at
each of the lettered sites,
and what occurs at each
of these sites during
translation?
tRNA

On this model of a tRNA

molecule, identify each of
the following:
a) 5′ and 3′ ends
b) hydrogen bonds
c) unpaired regions
d) anticodon loop
e) binding site for amino
acid
Charging tRNA

Aminoacyl-tRNA synthetase is an enzyme

whose function is to ___________.

To do so, it binds a molecule of amino acid and

a molecule of ___________.

After dephosphorylation, which two molecules

are joined?

For the appropriate tRNA to be joined to the

amino acid, what must occur?