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CH 17 Central dogma from genes to proteins

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Overview: The Flow of Genetic Information
The information content of DNA

Is in the form of specific sequences of nucleotides along the DNA strands

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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

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Figure 17.1

The ribosome

Is part of the cellular machinery for translation, polypeptide synthesis

Figure 17.1

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Concept 17.1: Genes specify proteins via transcription and translation

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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

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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

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Figure 17.2

Using genetic crosses

They determined that their mutants fell into three classes, each mutated in a different gene

Figure 17.2

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

EXPERIMENT

RESULTS

Class I

Mutants

Class II

Mutants

Class III

Mutants

Wild type

Minimal

medium

(MM)

(control)

MM +

Ornithine

MM +

Citrulline

MM +

Arginine

(control)

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CONCLUSION

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.)

Class I

Mutants

(mutation

in gene A)

Class II

Mutants

(mutation

in gene B)

Class III

Mutants

(mutation

in gene C)

Wild type

Gene A

Gene B

Gene C

Precursor

Ornithine

Citrulline

Arginine

Enzyme

A

Enzyme

B

Enzyme

C

A

B

C

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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

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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

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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

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Figure 17.3a

In prokaryotes

Transcription and translation occur together

Figure 17.3a

Prokaryotic cell. In a cell lacking a nucleus, mRNA�produced by transcription is immediately translated�without additional processing.

(a)

TRANSLATION

TRANSCRIPTION

DNA

mRNA

Ribosome

Polypeptide

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Figure 17.3b

In eukaryotes

RNA transcripts are modified before becoming true mRNA

Figure 17.3b

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.

(b)

TRANSCRIPTION

RNA PROCESSING

TRANSLATION

mRNA

DNA

Pre-mRNA

Polypeptide

Ribosome

Nuclear

envelope

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Cells are governed by a cellular chain of command

DNA → RNA → protein

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The Genetic Code

How many bases correspond to an amino acid?

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Codons: Triplets of Bases

Genetic information

Is encoded as a sequence of nonoverlapping base triplets, or codons

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Figure 17.4

During transcription

The gene determines the sequence of bases along the length of an mRNA molecule

Figure 17.4

DNA

molecule

Gene 1

Gene 2

Gene 3

DNA strand

(template)

TRANSCRIPTION

mRNA

Protein

TRANSLATION

Amino acid

A

C

A

C

G

A

G

T

U

G

U

G

C

U

C

A

Trp

Phe

Gly

Ser

Codon

3′

5′

3′

5′

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Cracking the Code

A codon in messenger RNA

Is either translated into an amino acid or serves as a translational stop signal

Figure 17.5

Second mRNA base

U

C

A

G

U

C

A

G

UUU

UUC

UUA

UUG

CUU

CUC

CUA

CUG

AUU

AUC

AUA

AUG

GUU

GUC

GUA

GUG

Met or

start

Phe

Leu

lle

Val

UCU

UCC

UCA

UCG

CCU

CCC

CCA

CCG

ACU

ACC

ACA

ACG

GCU

GCC

GCA

GCG

Ser

Pro

Thr

Ala

UAU

UAC

UGU

UGC

Tyr

Cys

CAU

CAC

CAA

CAG

CGU

CGC

CGA

CGG

AAU

AAC

AAA

AAG

AGU

AGC

AGA

AGG

GAU

GAC

GAA

GAG

GGU

GGC

GGA

GGG

UGG

UAA

UAG

Stop

UGA

Stop

Trp

His

Gln

Asn

Lys

Asp

Arg

Ser

Arg

Gly

U

C

A

G

U

C

A

G

U

C

A

G

U

C

A

G

First mRNA base (5′ end)

Third mRNA base (3′ end)

Glu

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Codons must be read in the correct reading frame

For the specified polypeptide to be produced

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Evolution of the Genetic Code

The genetic code is nearly universal

Shared by organisms from the simplest bacteria to the most complex animals

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Figure 17.6

In laboratory experiments

Genes can be transcribed and translated after being transplanted from one species to another

Figure 17.6

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Concept 17.2: Transcription is the DNA-directed synthesis of RNA: a closer look

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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

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Synthesis of an RNA Transcript

The stages of transcription are

Initiation
Elongation
Termination

Figure 17.7

Promoter

Transcription unit

RNA polymerase

Start point

5′

3′

5′

3′

5′

3′

5′

3′

5′

3′

5′

Rewound

RNA

transcript

3′

Completed 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 the

DNA and elongating the RNA transcript 5′ → 3 ′. In the wake of

transcription, the DNA strands re-form a double helix.

3

Termination. Eventually, the RNA

transcript is released, and the

polymerase detaches from the DNA.

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Elongation

RNA

polymerase

Non-template

strand of DNA

RNA nucleotides

3′ end

C

A

E

G

C

A

U

T

A

G

T

A

C

G

U

A

T

C

A

T

C

A

T

G

3′

5′

Newly made

RNA

Direction of transcription

(“downstream”)

Template

strand of DNA

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RNA Polymerase Binding and Initiation of Transcription

Promoters signal the initiation of RNA synthesis
Transcription factors

Help eukaryotic RNA polymerase recognize promoter sequences

Figure 17.8

TRANSCRIPTION

RNA PROCESSING

TRANSLATION

DNA

Pre-mRNA

mRNA

Ribosome

Polypeptide

T

A

T

A

T

A

T

TATA box

Start point

Template

DNA strand

5′

3′

5′

Transcription

factors

5′

3′

5′

Promoter

5′

3′

5′

RNA polymerase II

Transcription factors

RNA transcript

Transcription initiation complex

Eukaryotic promoters

1

Several transcription

factors

2

Additional transcription

factors

3

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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

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Termination of Transcription

The mechanisms of termination

Are different in prokaryotes and eukaryotes

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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

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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

Figure 17.9

A modified guanine nucleotide

added to the 5′ end

50 to 250 adenine nucleotides

added to the 3′ end

Protein-coding segment

Polyadenylation signal

Poly-A tail

3′ UTR

Stop codon

Start codon

5′ Cap

5′ UTR

AAUAAA

AAA…AAA

TRANSCRIPTION

RNA PROCESSING

DNA

Pre-mRNA

mRNA

TRANSLATION

Ribosome

Polypeptide

G

P

5′

3′

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Split Genes and RNA Splicing

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

3′

Poly-A tail

Introns cut out and

exons spliced together

Coding

segment

5′ Cap

1

146

3′ UTR

Pre-mRNA

mRNA

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Figure 17.11

Is carried out by spliceosomes in some cases

Figure 17.11

RNA transcript (pre-mRNA)

Exon 1

Intron

Exon 2

Other proteins

Protein

snRNA

snRNPs

Spliceosome

components

Cut-out

intron

mRNA

Exon 1

Exon 2

5′

1

2

3

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Ribozymes

Ribozymes

Are catalytic RNA molecules that function as enzymes and can splice RNA

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The Functional and Evolutionary Importance of Introns

The presence of introns

Allows for alternative RNA splicing

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Figure 17.12

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

Gene

DNA

Exon 1

Intron

Exon 2

Intron

Exon 3

Transcription

RNA processing

Translation

Domain 3

Domain 1

Domain 2

Polypeptide

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Concept 17.4: Translation is the RNA-directed synthesis of a polypeptide: a closer look

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Molecular Components of Translation

A cell translates an mRNA message into protein

With the help of transfer RNA (tRNA)

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Figure 17.13

Translation: the basic concept

Figure 17.13

TRANSCRIPTION

TRANSLATION

DNA

mRNA

Ribosome

Polypeptide

Amino

acids

tRNA with

amino acid

attached

Ribosome

tRNA

Anticodon

mRNA

Trp

Phe

Gly

A

G

C

A

C

G

U

G

U

G

C

Codons

5′

3′

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Molecules of tRNA are not all identical

Each carries a specific amino acid on one end
Each has an anticodon on the other end

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The Structure and Function of Transfer RNA

A tRNA molecule

Consists of a single RNA strand that is only about 80 nucleotides long
Is roughly L-shaped

A

C

Figure 17.14a

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′

C

A

C

G

C

U

A

G

A

C

A

C

U

*

G

C

*

G

U

G

U

*

C

U

*

G

A

G

U

*

A

*

A

G

U

C

A

G

A

C

*

C

G

A

G

A

G

*

G

A

C

U

C

*

A

U

A

G

C

G

5′

Amino acid

attachment site

Hydrogen

bonds

Anticodon

A

43 of 71

Figure 17.14b

(b) Three-dimensional structure

Symbol used

in this book

Amino acid

attachment site

Hydrogen

bonds

Anticodon

A

G

5′

3′

5′

(c)

44 of 71

Figure 17.15

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

Phosphates

tRNA

P

P_i

P

AMP

Aminoacyl tRNA

(an “activated

amino acid”)

Aminoacyl-tRNA

synthetase (enzyme)

Active site binds the

amino acid and ATP.

1

ATP loses two P groups

and joins amino acid as AMP.

2

3

Appropriate

tRNA covalently

Bonds to amino

Acid, displacing

AMP.

Activated amino acid

is released by the enzyme.

4

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Ribosomes

Ribosomes

Facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis

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Figure 17.16a

The ribosomal subunits

Are constructed of proteins and RNA molecules named ribosomal RNA or rRNA

Figure 17.16a

TRANSCRIPTION

TRANSLATION

DNA

mRNA

Ribosome

Polypeptide

Exit tunnel

Growing

polypeptide

tRNA

molecules

E

P

A

Large

subunit

Small

subunit

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)

5′

3′

47 of 71

Figure 17.16b

The ribosome has three binding sites for tRNA

The P site
The A site
The E site

Figure 17.16b

E

P

A

P site (Peptidyl-tRNA

binding site)

E site

(Exit site)

mRNA

binding site

A site (Aminoacyl-

tRNA binding site)

Large

subunit

Small

subunit

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)

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Figure 17.16c

Amino end

Growing polypeptide

Next amino acid

to be added to

polypeptide 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)

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Building a Polypeptide

We can divide translation into three stages

Initiation
Elongation
Termination

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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

Large

ribosomal

subunit

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.

2

Initiator tRNA

mRNA

mRNA binding site

Small

ribosomal

subunit

Translation initiation complex

P site

GDP

GTP

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

U

A

C

A

U

G

E

A

3′

5′

3′

5′

3′

5′

Figure 17.17

51 of 71

Elongation of the Polypeptide Chain

In the elongation stage of translation

Amino acids are added one by one to the preceding amino acid

Figure 17.18

Amino end

of polypeptide

mRNA

Ribosome ready for

next aminoacyl tRNA

E

P

A

E

P

A

E

P

A

E

P

A

GDP

GTP

GDP

2

site

5′

3′

TRANSCRIPTION

TRANSLATION

DNA

mRNA

Ribosome

Polypeptide

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.

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

52 of 71

Termination of Translation

The final stage of translation is termination

When the ribosome reaches a stop codon in the mRNA

Figure 17.19

Release

factor

Free

polypeptide

Stop codon

(UAG, UAA, or UGA)

5′

3′

5′

3′

5′

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.

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Polyribosomes

A number of ribosomes can translate a single mRNA molecule simultaneously

Forming a polyribosome

Figure 17.20a, b

Growing

polypeptides

Completed

polypeptide

Incoming

ribosomal

subunits

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)

Ribosomes

mRNA

This micrograph shows a large polyribosome in a prokaryotic

cell (TEM).

0.1 µm

(b)

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Completing and Targeting the Functional Protein

Polypeptide chains

Undergo modifications after the translation process

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Protein Folding and Post-Translational Modifications

After translation

Proteins may be modified in ways that affect their three-dimensional shape

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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

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Proteins destined for the endomembrane system or for secretion

Must be transported into the ER
Have signal peptides to which a signal-recognition particle (SRP) binds, enabling the translation ribosome to bind to the ER

58 of 71

Figure 17.21

The signal mechanism for targeting proteins to the ER

Figure 17.21

Ribosome

mRNA

Signal

peptide

Signal-

recognition

particle

(SRP)

SRP

receptor

protein

Translocation

complex

CYTOSOL

Signal

peptide

removed

ER

membrane

Protein

ERLUMEN

Polypeptide

synthesis begins

on a free

ribosome in

the cytosol.

1

An SRP binds

to the signal

peptide, halting

synthesis

momentarily.

2

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.

3

The SRP leaves, and

the polypeptide resumes

growing, meanwhile

translocating across the

membrane. (The signal

peptide stays attached

to the membrane.)

4

The signal-

cleaving

enzyme

cuts off the

signal peptide.

5

The rest of

the completed

polypeptide leaves

the ribosome and

folds into its final

conformation.

6

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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

60 of 71

Table 17.1

Types of RNA in a Eukaryotic Cell

Table 17.1

61 of 71

Figure 17.22

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

Figure 17.22

DNA

Polyribosome

mRNA

Direction of

transcription

0.25 μm

RNA

polymerase

Polyribosome

Ribosome

DNA

mRNA (5′ end)

RNA polymerase

Polypeptide

(amino end)

62 of 71

In a eukaryotic cell

The nuclear envelope separates transcription from translation
Extensive RNA processing occurs in the nucleus

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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

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Figure 17.23

The change of a single nucleotide in the DNA’s template strand

Leads to the production of an abnormal protein

Figure 17.23

In the DNA, the

mutant template

strand 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 DNA

Wild-type hemoglobin DNA

mRNA

Normal hemoglobin

Sickle-cell hemoglobin

Glu

Val

C

T

C

A

T

G

A

G

U

A

3′

5′

3′

5′

3′

5′

3′

65 of 71

Types of Point Mutations

Point mutations within a gene can be divided into two general categories

Base-pair substitutions
Base-pair insertions or deletions

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Substitutions

A base-pair substitution

Is the replacement of one nucleotide and its partner with another pair of nucleotides
Can cause missense or nonsense

Figure 17.24

Wild type

A

U

G

A

G

U

G

C

U

A

mRNA

5′

Protein

Met

Lys

Phe

Gly

Stop

Carboxyl end

Amino end

3′

A

U

G

A

G

U

G

U

A

Met

Lys

Phe

Gly

Base-pair substitution

No effect on amino acid sequence

U instead of C

Stop

A

U

G

A

G

U

A

G

U

A

Met

Lys

Phe

Ser

Stop

A

U

G

U

A

G

U

G

C

U

A

Met

Stop

Missense

A instead of G

Nonsense

U instead of A

67 of 71

Insertions and Deletions

Insertions and deletions

Are additions or losses of nucleotide pairs in a gene
May produce frameshift mutations

Figure 17.25

mRNA

Protein

Wild type

A

U

G

A

G

U

G

C

U

A

5′

Met

Lys

Phe

Gly

Amino end

Carboxyl end

Stop

Base-pair insertion or deletion

Frameshift causing immediate nonsense

A

U

G

U

A

G

U

G

C

U

A

U

G

A

G

U

G

C

U

A

U

G

U

G

C

U

A

Met

Stop

U

Met

Lys

Leu

Ala

Met

Phe

Gly

Stop

Missing

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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Mutagens

Spontaneous mutations

Can occur during DNA replication, recombination, or repair

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Mutagens

Are physical or chemical agents that can cause mutations

70 of 71

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

71 of 71

Figure 17.26

A summary of transcription and translation in a eukaryotic cell

Figure 17.26

TRANSCRIPTION

RNA is transcribed

from a DNA template.

DNA

RNA

polymerase

RNA

transcript

RNA PROCESSING

In eukaryotes, the

RNA transcript (pre-

mRNA) is spliced and

modified to produce

mRNA, which moves

from the nucleus to the

cytoplasm.

Exon

Poly-A

RNA transcript

(pre-mRNA)

Intron

NUCLEUS

Cap

FORMATION OF

INITIATION COMPLEX

After leaving the

nucleus, mRNA attaches

to the ribosome.

CYTOPLASM

mRNA

Poly-A

Growing

polypeptide

Ribosomal

subunits

Cap

Aminoacyl-tRNA

synthetase

Amino

acid

tRNA

AMINO ACID ACTIVATION

Each amino acid

attaches to its proper tRNA

with the help of a specific

enzyme and ATP.

Activated

amino acid

TRANSLATION

A succession of tRNAs

add their amino acids to

the polypeptide chain

as the mRNA is moved

through the ribosome

one codon at a time.

(When completed, the

polypeptide is released

from the ribosome.)

Anticodon

A

C

A

U

G

U

A

U

G

U

A

C

E

A

Ribosome

1

Poly-A

5′

3′

Codon

2

3

4

5