chapter 7 gene expression and control

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Chapter 7 Gene Expression and Control

7.1 Ricin and Your Ribosomes

The ability to make proteins is critical to all life processes

Seeds of the castor-oil plant contain the protein ricin, a deadly poison that inactivates ribosomes that assemble proteins

Ricin has been used by assassins, and is banned as a weapon under the Geneva Protocol

Seeds of the castor-oil plant

7.2 DNA, RNA, and Gene Expression

A gene is a DNA sequence that encodes an RNA or protein product in the sequence of its nucleotide bases (A, T, G, C)

In transcription, enzymes use the gene’s DNA sequence as a template to assemble a strand of messenger RNA (mRNA)

In translation, the protein-building information in mRNA is decoded into a sequence of amino acids

The result is a polypeptide chain that folds into a protein

sugar–phosphate backbone

base pair

nucleotide base

deoxyribonucleic acidDNA

ribonucleic acidRNA

DNA and RNA

Gene Expression

Gene expression involves transcription (DNA to mRNA), and translation (mRNA to protein)

Gene expression Process by which the information in a gene becomes

converted to an RNA or protein product

Proteins (enzymes) assemble other molecules and perform many functions that keep the cell alive

7.3 Transcription: DNA to RNA

During transcription, a strand of DNA acts as a template upon which a strand of RNA is assembled from nucleotides

Base-pairing rules in DNA replication apply to RNA synthesis in transcription, but RNA uses uracil in place of thymine

The enzyme RNA polymerase, not DNA polymerase, adds nucleotides to the end of a growing RNA strand

Base Pairing in Transcription

The Process of Transcription

In transcription, RNA polymerase binds to a promoter in the DNA near a gene

Polymerase moves along the DNA, unwinding the DNA so it can read the base sequence

RNA polymerase links RNA nucleotides in the order determined by the base sequence of the gene

The new mRNA is a copy of the gene from which it was transcribed

RNA polymerase

gene region

binding site in DNA

The enzyme RNA polymerase binds to a promoter in the DNA. The binding positions the polymerase near a gene. Only one of the two strands of DNA will be transcribed into RNA.

1

RNA polymerase binds to a promoter

RNA

DNA winding up

DNA unwinding

The polymerase begins to move along the gene and unwind the DNA. As it does, it links RNA nucleotides in the order specified by the nucleotide sequence of the template DNA strand. The DNA winds up again after the polymerase passes. The structure of the “opened” DNA at the transcription site is called a transcription bubble, after its appearance.

2

RNA nucleotides are linked

direction of transcription

Zooming in on the transcription bubble, we can see that RNA polymerasecovalently bonds successive nucleotides into an RNA strand. The new strand is an RNA copy of the gene.

3

RNA nucleotides are linked

Three Genes Being Transcribed

Many polymerases transcribe a gene region at the same time

RNA molecules DNA molecule

RNA Modifications

Eukaryotic cells modify their RNA before it leaves the nucleus Sequences that stay in the RNA are exons Introns are sequences removed during RNA processing

Exons can be spliced together in different combinations, so one gene may encode different proteins

After splicing, a tail of 50 to 300 adenines (poly-A tail) is added to the end of a new mRNA

gene

promoter exon intron exon intron exon

DNAtranscription

newly transcribed RNA

exon intron exon intron exon

exon exon exon

poly-A tail

finished mRNA

Post-transcriptional modification of RNA

ANIMATED FIGURE: Pre-mRNA transcript processing

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ANIMATED FIGURE: Gene transcription details

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ANIMATED FIGURE: Negative control of the lactose operon

7.4 RNA Players in Translation

Three types of RNA are involved in translation: mRNA, rRNA, and tRNA

mRNA produced by transcription carries protein-building information from DNA to the other two types of RNA for translation

mRNA and the Genetic Code

Information in mRNA consists of sets of three nucleotides (codons) that form “words” spelled with bases A, C, G, U

Sixty-four codons, most of which specify amino acids, constitute the genetic code

The sequence of three nucleotides in a base triplet determines which amino acid the codon specifies

The order of codons in mRNA determines the order of amino acids in the polypeptide that will be translated from it

Genetic Code

Twenty amino acids are encoded by the sixty-four codons in the genetic code

Some amino acids are specified by more than one codon

Other codons signal the beginning and end of a protein-coding sequence

Most organisms use the same code

The Genetic Code

a gene region in DNA

transcription

codon codon codon

mRNA

translation

methionine (met)

tyrosine (tyr)

serine (ser)

amino acid sequence

Correspondence between DNA, RNA, and proteins

rRNA and tRNA – the Translators

Ribosomes consist of two subunits of rRNA and structural proteins

Ribosomes and transfer RNAs (tRNA) interact to translate an mRNA into a polypeptide

tRNA has two attachment sites An anticodon base-pairs with an mRNA codon An attachment site binds to an amino acid specified by the

codon

Ribosome Structure

large subunit small subunit intact ribosome

+ =

anticodon

A) Icon and model of the tRNA that carries the amino acid tryptophan. Each tRNA’s anticodon is complementary to an mRNA codon. Each also carries the amino acid specified by that codon.

tRNA for Tryptophan

B) During translation, tRNAs dock at an intact ribosome (for clarity, only the small subunit is shown, in tan). Here, the anticodons of two tRNAs have base-pairedwith complementary codons on an mRNA (red).

tRNAs dock at a ribosome

ANIMATED FIGURE: Structure of a ribosome

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7.5 Translating the Code: RNA to Protein

Translation (second part of protein synthesis) occurs in the cytoplasm of all cells: mRNA is transcribed in the nucleus In the cytoplasm a small ribosomal subunit binds to mRNA Initiator tRNA base-pairs with the first mRNA codon Large ribosomal subunit joins the small subunit Ribosome assembles a polypeptide chain Translation ends when the ribosome encounters a stop

codon

Translation in Eukaryotes

Transcription

ribosome subunitsRNA transport

tRNA

1

Convergence of RNAs

mRNATranslation

polypeptide

2

3

4

Ribosome assembles a polypeptide chain

Ribosome assembles a polypeptide chain

Ribosome assembles a polypeptide chain

ANIMATED FIGURE: Translation

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7.6 Mutated Genes and Their Products

Mutations are permanent changes in the nucleotide sequence of DNA, which may alter a gene product

A mutation that changes a gene’s product may have harmful effects

Example: Mutations that affect the proteins in hemoglobin reduce blood’s ability to carry oxygen

Types of Mutations

Base-pair substitution Type of mutation in which a single base-pair changes Example: Sickle cell anemia

Mutations that shift the reading frame of the mRNA codons: Deletion of one or more base pairs Insertion of one or more base pairs Example: Beta thalassemia

A) Hemoglobin, an oxygen-binding protein in red blood cells. This protein consists of four polypeptides: two alpha globins (blue) and two beta globins (green). Each globin forms a pocket that cradles a type of cofactor called a heme (red ). Oxygen gas binds to the iron atom at the center of each heme.

Mutations in Hemoglobin

B) Part of the DNA (blue), mRNA (brown), and amino acid sequence (green) of human beta globin. Numbers indicate the position of the nucleotide in the coding sequence of the mRNA.

Mutations in Hemoglobin

C) A base-pair substitution replaces a thymine with an adenine. When the altered mRNA is translated, valine replaces glutamic acid as the sixth amino acid of the polypeptide. Hemoglobin with this form of beta globin is called HbS, or sickle hemoglobin.

Mutations in Hemoglobin

D) A deletion of one nucleotide causes the reading frame for the rest of the mRNA to shift. The protein translated from this mRNA is too short and does not assemble correctly into hemoglobin molecules. The result is beta thalassemia,in which a person has an abnormally low amount of hemoglobin.

Mutations in Hemoglobin

E) An insertion of one nucleotide causes the reading frame for the rest of the mRNA to shift. The protein translated from this mRNA is too short and does not assemble correctly into hemoglobin molecules. As in D, the outcome is beta thalassemia.

Mutations in Hemoglobin

glutamic acid valine

A) A base-pair substitution results in the abnormal beta globin chain of sickle hemoglobin (HbS). The sixth amino acid in such chains is valine, not glutamic acid. The difference causes HbS molecules to form rod-shaped clumps that distort normally round blood cells into sickle shapes.

Sickle-Cell Anemia: A Base-Pair Substitution

sickled cell

normal cell

B) Left, the sickled cells clog small blood vessels, causing circulatory problems that result in damage to many organs. Destruction of the cells by the body’s immune system results in anemia. Right, Tionne “T-Boz” Watkins of the music group TLC is a celebrity spokesperson for the Sickle Cell Disease Association of America. She was diagnosed with sickle-cell anemia as a child.

Sickle-Cell Anemia

What Causes Mutations?

Most mutations result from unrepaired DNA polymerase errors during DNA replication

Some natural and synthetic chemicals cause mutations in DNA (example: cigarette smoke)

Insertion mutations may be caused by transposable elements, which move within or between chromosomes

ANIMATED FIGURE: Base-pair substitution

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ANIMATION: Deletion

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ANIMATION: Frameshift mutation

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ANIMATED FIGURE: Sickle-cell anemia

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ANIMATED FIGURE: Controls of eukaryotic gene expression

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ANIMATION: X-chromosome inactivation

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7.7 Eukaryotic Gene Controls

All cells in your body carry the same DNA

Some genes are transcribed by all cells, but most cells are specialized (differentiated) to use only certain genes

Which genes are expressed at a given time depends on the type of cell and conditions

Cell Differentiation

Cells differentiate when they start expressing a unique subset of their genes – controls over gene expression are the basis of differentiation

Differentiation The process by which cells become specialized Occurs as different cell lineages begin to express different

subsets of their genes

Controlling Gene Expression

Controlling gene expression is critical for normal development and function of a eukaryotic body

All steps between transcription and delivery of gene product are regulated

Transcription factor Protein that influences transcription by binding to DNA

Master Genes

Master gene Gene encoding a product that affects the expression of

many other genes Controls an intricate task such as eye formation

Homeotic gene Type of master gene that controls formation of specific

body parts during development

Studying Homeotic Genes

Researchers study the function of a homeotic gene by altering its expression – by introducing a mutation or deleting it entirely (gene knockout) Examples: antennapedia, dunce, tinman, groucho

Many homeotic genes are interchangeable among species Example: eyeless gene in flies and PAX 6 gene in humans

A) A transcription factor—the protein product (gold )of an insect gene called antennapedia attaches to apromoter sequence in a fragment of DNA. In cells ofa fly embryo, the binding starts a cascade of cellularevents that results in the formation of a leg.

Example of gene control

B) Antennapedia is a homeotic gene whose expression in embryonic tissues of the insect thorax causes legs to form. A mutation that causes antennapedia to be expressed in the embryonic tissues of the head causes legs to form there too (left). Compare the head of the normal fly on the right.

Example of gene control

Gene Knockout Experiment: Eyeless

A) A fruit fly with a mutation in its eyeless gene develops with no eyes.

B) Compare the large, round eyes of a normal fruit fly.

C) Eyes form wherever the eyeless gene is expressed in fly embryos. Abnormal expression of the eyeless gene in this fly caused extra eyes to develop on its head and also on its wings.

PAX6 Gene Function

In humans and many other animals, the PAX6 gene affects eye formation

D) Humans, mice, squids, and other animals have a gene called PAX6. In humans, PAX6 mutations result in missing irises, a condition called aniridia (left ). Compare a normal iris (right ). PAX6 is so similar to eyeless that it triggers eye development when expressed in fly embryos.

Sex Chromosome Genes

In mammals, males have only one X chromosome – females have two, but one is tightly condensed into a Barr body and not expressed

According to the theory of dosage compensation, X chromosome inactivation equalizes expression of X chromosome genes between the sexes

X Chromosome Inactivation

A) Barr bodies. The photo on the left shows the nucleus of five XX cells. Inactivated X chromosomes—Barr bodies— appear as red spots. Compare the nucleus of two XY cells in the photo on the right

The Y Chromosome

The human X chromosome carries 1,336 genes

The human Y chromosome carries 307 genes, including SRY— the master gene for male sex determination Triggers formation of testes Testosterone produced by testes controls formation of

male secondary traits

Absence of SRY gene in females triggers development of ovaries, female characteristics

SRY gene expressed no SRY present

penis

vaginal opening

birth approaching

B) An early human embryo appears neither male nor female. SRY gene expression determines whether male reproductive organs develop.

Development of Human Reproductive Organs

Epigenetics

Transcription is affected by chromosome structure

Modifications that suppress gene expression: Adding a methyl group (CH3) to a histone protein Direct methylation of DNA nucleotides

Once a particular nucleotide has become methylated, it usually stays methylated in all of the cell’s descendants

Environmental factors, including the chemicals in cigarette smoke, add more methyl groups

Methyl group attached to a DNA nucleotide

Epigenetics

Methylation of parental chromosomes is normally “reset” in the first cell of the new individual

All parental methyl groups are not removed, so some methylations can be passed to future offspring

Boys are affected by lifestyle of individuals in the father’s line; girls, by individuals in the mother’s line

Heritable changes in gene expression that are not due to changes in underlying DNA sequence are epigenetic

An epigenetic effect

Grandsons of boys who endured a winter of famine tend to live longer than grandsons of boys who overate at the same age

7.8 Ricin and Your Ribosomes (revisited)

Ricin is a ribosome-inactivating protein (RIP)

Toxic RIPs, including ricin, have one polypeptide chain that binds tightly to carbohydrates on plasma membranes

Once inside the cell, a second polypeptide inactivates the ribosomes, and the cell quickly dies

Other RIPs include Shiga toxin (dysentery) and E. coli O157:H7 (food poisoning)

Some RIPs

ricin Shiga toxin E. coli enterotoxin

Digging Into Data: Paternal Grandmother’s Food Supply and Infant Mortality