chapter 12

Chapter 12 Gene Expression and Regulation

How Is the Information in DNA Used in a Cell?

The link between DNA and protein DNA contains the “molecular blueprint” of

every cell Proteins are the construction workers of the

cell Proteins control cell shape, function,

reproduction, and synthesis of biomolecules Therefore, there must be a flow of information

from DNA to protein


DNA provides instructions for protein synthesis via RNA intermediaries DNA in eukaryotes is kept in the nucleus Protein synthesis occurs at ribosomes in the

cytoplasm RNA differs structurally from DNA in three

ways RNA has the sugar ribose RNA is usually single-stranded RNA contains the nitrogenous base uracil (U)

instead of thymine (T)


DNA provides instructions for protein synthesis via RNA intermediaries There are three types of RNA involved in

protein synthesis Messenger RNA (mRNA) carries a copy of

DNA gene information to the ribosome in the cytoplasm

Ribosomal RNA (rRNA) plus proteins make up the structure of ribosomes

Transfer RNA (tRNA) brings amino acids to the ribosome


DNA provides instructions for protein synthesis via RNA intermediaries RNA occurs in many other roles besides

protein synthesis RNA is used as the genetic material in some

viruses, such as HIV Ribozymes – enzymatic RNA “Regulatory” RNA MicroRNA


Overview : Genetic information is transcribed into RNA and then translated into protein mRNA carries the code for protein synthesis

from DNA to the ribosomes Ribosomal rRNA and proteins form ribosomes Transfer tRNA carries amino acids to the

ribosomes for addition to the growing protein


Overview: Genetic information is transcribed into RNA and then translated into protein DNA directs protein synthesis in a two-step

process1.Transcription - Information in a DNA gene

is copied into RNA (like a court transcription – same language just a copy of information)

2.Translation - the genetic information contained in the mRNA is converted to another language by Messenger RNA, tRNA, amino acids, and a ribosome, to synthesize a protein

Genetic Information Flows from DNA to RNA to Protein

Fig. 12-2

(a) Transcription

Translation of the mRNA produces a protein molecule with an amino acid sequence determined by the nucleotide sequence in the mRNA

(b) Translation

Transcription of thegene produces anmRNA with anucleotide sequencecomplementary to oneof the DNA strands

DNA

messenger RNA

protein

ribosome

(cytoplasm)(nucleus)

gene


The genetic code uses three bases to specify an amino acid The genetic code provides the rules Given that there are 20 amino acids but only

four bases, statistically, the smallest number of bases that could combine to yield a different sequence for each of the 20 amino acids is three A two-base code could produce only 16

combinations The three-base code has the potential to

create 64 combinations


The genetic code uses three bases to specify an amino acid Marshall Nirenberg and Heinrich Matthaei

cracked the genetic code by creating artificial mRNAs of known sequence and observing what proteins they produced For example, an mRNA strand composed

entirely of uracil (UUUUUUUU…) produced a protein consisting entirely of the amino acid phenylalanine

Therefore, they concluded that the triplet UUU is the codon for phenylalanine


The genetic code uses three bases to specify an amino acid Base triplets in DNA (sequence of 3

nucleotides) Codons in mRNA specifies a unique amino

acid in the genetic code Each mRNA also has a start codon (AUG) and

one of three stop codons (UAG, UAA, and UGA)

Some amino acids are specified by as many as six different codons


The genetic code uses three bases to specify an amino acid Decoding the codons of mRNA is the job of

tRNA and ribosomes Each unique tRNA has three exposed bases,

called an anticodon, which are complementary to codon bases in mRNA

How Is the Information in a Gene Transcribed into RNA?

Overview of transcription Transcription of a DNA gene into RNA has three

stages1. Initiation - A promoter region at the

beginning of the gene marks where transcription is to be initiated

2. Elongation - The “body” of the gene corresponds with where elongation of the RNA strand occurs

3. Termination - A termination signal at the end of the gene marks where RNA synthesis is to terminate

Initiation

Fig. 12-3 (1 of 4)

direction oftranscription

promoter

beginning ofgene (3´ end)

gene 1 gene 2gene 3

Initiation: RNA polymerase binds to the promoter region of DNA near the beginning of a gene, separating the double helix near the promoter.

DNA

RNApolymerase

DNA

1

Elongation

Fig. 12-3 (2 of 4)

RNA

DNA template strand

Elongation: RNA polymerase travels along the DNA template strand (blue),

unwinding the DNA double helix and synthesizing RNA by catalyzing the addition of ribose

nucleotides into an RNA molecule (red). The nucleotides in the RNA are complementary to

the template strand of the DNA.

2

DNA RNAC - GG - CT - AA - U

Termination and Conclusion of Transcription

termination signal

4

Termination: At the end of the gene, RNA polymerase encounters a DNA sequence called a termination signal. RNA polymerase detaches from the DNA and releases the RNA molecule.

Conclusion of transcription: After termination, the DNA completely rewinds into a double helix. The RNA molecule is free to move from the nucleus to the cytoplasm for translation, and RNA polymerase may move to another gene and begin transcription once again.

DNA

RNA

3

Fig. 12-3 (3 & 4 of 4)

RNA Transcription in Action

Fig. 12-4

growingRNAmolecules

end ofgene

beginningof gene

gene

DNA

How Is the Base Sequence of Messenger RNA Translated

into Protein? Messenger RNA synthesis differs between

prokaryotes and eukaryotes Messenger RNA synthesis in prokaryotes

Genes for related functions are adjacent and are transcribed together

Because prokaryotes have no nuclear membrane, translation and transcription are not separated in space or time

As the mRNA molecule separates from the DNA, ribosomes immediately begin translating it to protein

(a) Gene organization on a prokaryotic chromosome

ribosome

protein

mRNA

DNARNApolymerase

direction of transcription

genes coding enzymes in asingle metabolic pathway

gene 1

gene regulatingDNA sequences gene 2 gene 3

(b) Simultaneous transcription and translation in prokaryotes

DNA

mRNA

ribosome

Messenger RNA Synthesis in Prokaryotic Cells Fig. 12-5


into Protein? Messenger RNA synthesis in eukaryotes

In eukaryotes, the DNA is in the nucleus and the ribosomes are in the cytoplasm

The genes that encode the proteins for a metabolic pathway are not clustered together on the same chromosome

Each gene consists of two or more segments of DNA that encode for protein, called exons, that are interrupted by other segments that are not translated, called introns

(a) Eukaryotic gene structure

DNA

promoter

exons

introns

(b) RNA synthesis and processing in eukaryotes

DNA

Transcription

finished mRNA

pre-mRNA

An RNA cap and tail are added

RNA splicing

Finished mRNA is moved to the cytoplasm for translation

cap tail

introns are cut out andbrokendown

1

3

4

2

Messenger RNA Synthesis in Eukaryotic Cells Fig. 12-6

How Is the Base Sequence of Messenger RNA Translated into Protein?

Possible functions of intron-exon gene structure1. Through alternative splicing of the exons in a

gene, a cell can make multiple proteins from a single gene

2. Fragmented genes may provide a quick and efficient way for eukaryotes to evolve new proteins with new functions

If breaks in chromosomes occur in introns, exons may remain intact and be spliced to other chromosomes in ways that produce new, useful proteins


into Protein? During translation, mRNA, tRNA, and

ribosomes cooperate to synthesize proteins Like transcription, translation has three steps

1. Initiation2. Elongation3. Termination

Translation Is the Process of Protein Synthesis: Initiation

Fig. 12-7 (1-3 of 9)

small ribosomal subunit

tRNA anticodon

methioninetRNA

amino acid

first tRNAbindingsite

catalytic sitesecond tRNA binding site

Initiation:

preinitiationcomplex

metmet

A tRNA with an attached methionine amino acid binds to a small ribosomal subunit, forming a preinitiation complex.

The large ribosomal subunit binds to the small subunit. The methionine tRNA binds to the first tRNA site on the large subunit.

The preinitiation complex binds to an mRNA molecule. The methionine (met) tRNA anticodon (UAC) base-pairs with the start codon (AUG) of the mRNA.

C

A ACC G GG U U U

A

A

ACC G GG U U U

CAU

CAUmRNA

large ribosomalsubunit

U

start codon

1 2 3

met

Translation Is the Process of Protein Synthesis: Elongation

Fig. 12-7 (4-6 of 9)

catalytic site

peptide bond

ribosome moves one codon to the right

Elongation:

The "empty" tRNA is released and theribosome moves down the mRNA, onecodon to the right. The tRNA that is attached to the two amino acids is now inthe first tRNA binding site and the secondtRNA binding site is empty.

The catalytic site on the large subunit catalyzes the formation of a peptide bond linking the amino acids methionine and valine. The two amino acids arenow attached to the tRNA in the second binding site.

The second codon of mRNA (GUU) base-pairs with the anticodon (CAA) of a second tRNA carrying the amino acid valine (val). This tRNA binds to the second tRNA site on the large subunit.

AUA ACC G GG U U U A ACC G GG GU U U

C A A A ACAU

A ACC G GG U U U

C A ACAU

initiator tRNA detaches

C

4 5 6

met

met met

valvalval

CA

U

Translation Is the Process of Protein Synthesis: Elongation and Termination

Fig. 12-7 (7-9 of 9)

Termination:

stop codon

The catalytic site forms a peptide bond between the aminoacids, leaving them attached to the tRNA in the second binding site. The tRNA in the first site leaves, and the ribosome moves one codon over on the mRNA.

This process repeats until a stop codon is reached; the mRNA and the completed peptide are released from the ribosome, and the subunits separate.

A A A A ACC GG U U U

AUA A

A

CC G G

G

GU U

U

U

C A A

completedpeptide

The third codon of mRNA (CAU) base-pairs with the anticodon (GUA) of a tRNA carrying the amino acid histidine (his). This tRNA enters the second tRNA binding site on the large subunit.

AUA A

A

CC G G G

G

G U U

U

U

C A A

7 8 9

met

val his his

val

met

val

met

his

arg

arg

ile

Complementary Base-Pairing Is Critical to the Process of Decoding Genetic Information

Fig. 12-8

template DNA strand

complementaryDNA strand

(a) DNA

gene

codons

anticodons

amino acids

etc.

etc.

etc.

etc.

(b) mRNA

(c) tRNA

methionine glycine valine(d) protein

T A C C C T C A A

A U G G G A G U U

U A C C C U C A A

etc.A T G G G A G T T

Review

1. How is genetic material encoded in DNA and RNA?

2. Distinguish between transcription and translation. (define and locate)

How Do Mutations Affect Protein Function?

Mutations are changes in the base sequence of DNA caused by mistakes during replication or by various environmental factors

Mutations take many forms and can affect protein function in many ways Mutations fall into five categories

Inversions Translocations Deletions Insertions Substitutions


Inversions and translocations These mutations may be relatively benign if

entire genes, including their promoter, are merely moved from one place to another

However, if a gene is split in two, it will no longer code for a complete, functional protein Severe hemophilia is often caused by an

inversion in the gene that encodes a protein required for blood clotting


Deletions and insertions

Depending on how many nucleotides are involved, deletions and insertions can cause a misreading of a gene’s codons during transcription or replication

The codons in THEDOGSAWTHECAT is changed by deletion of the letter “E” to THD OGS AWT HEC AT

Such mutations are called frameshift mutations


Deletions and insertions Proteins that result from deletions and

insertions have a very different amino acid sequence and almost always are nonfunctional

Deletions and insertions of three nucleotides (or a multiple of three) do not cause a shift of the reading frame and, so, may simply subtract or add a harmless amino acid to the protein


Point mutation (nucleotide substitution) A point mutation sometimes does not change

the amino acid sequence of the protein Because many amino acids are encoded by

more than one codon, the mutation may cause the same amino acid to be added

A known point mutation in the beta-globin gene for hemoglobin causes CTC to change to CTT, but since both codons code for glutamic acid, the protein is unchanged


Point mutation (nucleotide substitution) A mutated protein may function normally

In beta-globin, a point mutation of the CTC codon to GTC causes glutamic acid (hydrophilic) to be replaced with glutamine (also hydrophilic), but the resulting protein functions well


Point mutation (nucleotide substitution) Some substitutions cause an altered amino

acid sequence that change protein function dramatically, usually for the worse The substitution of an adenine for a thymine

in the CTC CAC mutation in a hemoglobin gene causes valine (hydrophobic) to replace glutamic acid (hydrophilic)

Placing this hydrophobic amino acid on the outside of the hemoglobin molecule leads to the clumping of hemoglobin and distortion of the red blood cell seen in sickle cell anemia


Point mutation (nucleotide substitution) The point mutation may introduce a premature

stop codon, leading to an mRNA that produces an incomplete protein

Such a mutation in the beta-globin gene prevents production of functional beta-globin protein This leads to beta-thalassemia People with this mutation have only alpha-

globin subunits and require frequent blood transfusions to survive because it doesn’t bind O2 as well.

How Are Genes Regulated?

The human genome contains 20,000 to 30,000 genes

A given cell “expresses” (transcribes) only a small number of genes

Some genes are expressed in all cells, such as genes coding for RNAs, since all cells require proteins


Other genes are expressed only in certain types of cells, at certain times in an organism’s life, or under specific environmental conditions

For example, even though every cell in your body contains the gene for casein, the major protein in milk, this gene is expressed only in certain cells in the breast, only in mature women, and only when a woman is breast-feeding


Regulation of gene expression may occur at three different levels1. Rate of transcription, regulation determines which

genes in a cell are expressed2. Rate of translation, regulation determines how much

protein is made from a particular type of mRNA3. At the level of protein activity, regulation determines

how long the protein lasts in a cell and how rapidly protein enzymes catalyze specific reactions

Although these general principles apply to both prokaryotic and eukaryotic organisms, there are some differences as well

12.5 How Are Genes Regulated?

In eukaryotic cells, transcriptional regulation occurs on at least three levels The individual gene – promoters have several

binding sites Regions of chromosomes – too tightly wound Entire chromosomes

In female mammals, one entire X chromosome is condensed (Barr bodies)


In female mammals, one entire X chromosome is condensed This effect can be observed

in the fur patterns of calico cats The X chromosome of a cat

contains a gene for fur pigmentation

Different patches of skin cells in a cat inactivate different X chromosomes

chapter 12

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