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Chapter Introduction

The Genetic Code: Using Information

9.1 Genetic Material

9.2 Importance of Proteins

Transcription

9.3 RNA Synthesis

9.4 RNA Processing

Protein Synthesis

9.5 Translation

9.6 Transport and Modification of Proteins

9.7 Translation Errors

Viruses

9.8 Genetic Information and Viruses

9.9 Impact of Viruses

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A Explain the connection between DNA and RNA in protein synthesis; describe the genetic code and its role in protein synthesis.

Learning Outcomes

By the end of this chapter you will be able to:

B Explain why proteins are important to biological systems.

C Identify the stages of transcription and explain what occurs during each stage.

D Summarize the events that occur in RNA processing.


E Identify the stages of translation and explain what occurs during each stage.

Learning Outcomes

By the end of this chapter you will be able to:

F Describe posttranslational modification and transport of proteins.

G Infer the consequences of RNA translation errors.

H Explain the relationship between viruses and host cells and describe the impact of viruses on living systems.


Does a cell express all of its genetic information all the time?

Expressing Genetic Information How does an organism use

the information stored in its genetic material?

A colored scanning electron micrograph of a group of human chromosomes (x6,875)


Expressing Genetic Information• Living organisms store information

in their genetic material.

• In a process called gene expression, organisms read and use the encoded information by directing the synthesis of proteins.

• When a virus infects a cell, the virus takes control of gene expression in the cell.

A colored scanning electron micrograph of a group of human chromosomes (x6,875)



• Genetic material consists of two nucleic acids—DNA and RNA—that are involved in gene expression.


9.1 Genetic Material

• Gene expression depends on two features of their molecular structure:

1. nucleic acids consist of a long strand of repeating subunits that act as letters in a code

2. the subunit bases of one strand pair with the bases of another strand


• Living cells store genetic information in DNA which specifies the primary structures of proteins.

9.1 Genetic Material (cont.)

• By determining the primary structure of each protein, DNA indirectly dictates protein function.

• Proteins, in turn, carry out important cell activities.

• When a gene becomes active, an enzyme makes a temporary RNA copy of the information the DNA contains.



• Messenger RNA (mRNA) is the temporary copy of a gene that encodes a protein.

• The process of making an mRNA molecule is called transcription.



• In translation, the mRNA molecule provides the pattern that determines the order in which amino acids are added to the protein being made.

• Protein synthesis takes place on ribosomes which are made of proteins and ribosomal RNA (rRNA).

• Each amino acid that will be used in making the protein is attached to transfer RNA (tRNA).


Information stored in DNA is copied to mRNA, which in turn directs the synthesis of a particular protein.


• The genetic code describes how a sequence of bases in DNA or RNA translates into the sequence of amino acids in a protein.

• The nucleotides serve as the four “letters” of the DNA “alphabet.”

• A genetic code requires at least 20 different code words—one for each amino acid.




• Three nucleotides are grouped at a time allowing 64 triplet combinations, such as CTG, TAC, and ACA.

• Each nucleotide triplet in DNA directs a particular triplet to be formed in mRNA during transcription.

• In translation, a second base-pairing step is essential for reading the genetic code.




• A triplet in mRNA, called a codon, pairs with a triplet on a tRNA molecule, called an anticodon, carrying the correct amino acid.



A molecule of transfer RNA (tRNA) with a specific amino acid attached reads each codon of a messenger RNA (mRNA) during protein synthesis (translation).


The genetic code is written in nucleotide triplets, or codons, in a strand of mRNA. Each triplet codon specifies an amino acid. For example, UGG codes for the amino acid tryptophan. Several amino acids have more than one codon. Some triplets are “punctuation” telling the system to start or stop translation.


• Many proteins, such as keratin, collagen, and myosin, serve as the material that makes up cell structures or tissues.

9.2 Importance of Proteins


The feathers responsible for the appearance of this Raggiana bird of paradise, Poradisaea raggiana, are composed mostly of the protein keratin.


• Some proteins are enzymes, essential catalysts that make the chemical reactions of living systems happen fast enough to be useful.

• Proteins, such as hemoglobin, bind to specific molecules.

9.2 Importance of Proteins (cont.)



• Protein hormones, such as insulin, play a key role in communication within an organism.

• Hormones are chemical signals given off by cells in one part of an organism that regulate behavior of cells in another part of the organism.




• A protein’s structure determines its function, and information expressed from the code in DNA determines the structures of proteins.

• Collagen exists as long fibers that bind cells together in tissues.



A scanning electron micrograph of human pancreatic connective tissue (collagen), x39,000.

• Many enzymes, such as lysozyme, have cavities or pockets that bind only specific substrate molecules.



• Gene expression begins with RNA synthesis—when the transcription enzyme RNA polymerase joins RNA nucleotides according to the base sequence in DNA.

Transcription

9.3 RNA Synthesis

• Prokaryotes have one type of RNA polymerase.

• Eukaryotes have three RNA polymerases, each responsible for making different types of RNA.


• In eukaryotes, protein synthesis takes place outside the nucleus; however, mRNA, tRNA, and rRNA are built in the nucleus.

9.3 RNA Synthesis (cont.)

• During protein synthesis, two ribosomal subunits bind to each other and an mRNA to form an intact ribosome.

Transcription


Each type of RNA carries out a different function in protein synthesis. This figure uses a linear symbol for mRNA to emphasize that its sequence corresponds to the linear sequence of amino acids in a protein. In reality, the mRNA is folded and twisted rather than being straight or rigid.


• Only one strand of the DNA, the coding or template strand, directs the synthesis of RNA.


Transcription

Each DNA nucleotide pairs with a particular RNA nucleotide. This pairing is the basis of the genetic code. Note that in RNA, uracil (U) replaces the thymine (T) of DNA.


• Transcription takes place in three stages:

1. Initiation—the enzyme RNA polymerase attaches to a specific region of the DNA

2. Elongation of the RNA—RNA polymerase partially unwinds the DNA, exposing the coding strand of the gene

3. Termination—RNA polymerase reaches the terminator region, or the end of the DNA to be transcribed and the enzyme and primary transcript are released from the DNA


Transcription


The three stages in transcription of RNA from a DNA template


• In prokaryotes, new mRNA is translated and broken down by enzymes within a few minutes.

9.4 RNA Processing

• In eukaryotes, mRNA can last from minutes to days, depending partly on how the primary transcript is processed.

Transcription

A transmission electron micrograph of an unidentified operon of the bacterium Escherichia coli, x72,600. Ribosomes attach to mRNA, and protein synthesis begins even before transcription is complete.


• All three types of RNA are processed in the nucleus of eukaryotes before they leave the nucleus.

• Enzymes add additional nucleotides and chemically modify or remove others.

9.4 RNA Processing (cont.)

Transcription



Transcription

• Enzymes attach a cap of chemically modified guanine nucleotides (methyl-guanine, or mG) to the starting end of the mRNA molecule.


• Other enzymes then replace part of the opposite end with a tail of 100–200 adenine nucleotides called a poly-A tail.


Transcription


• The final step in mRNA processing involves removal of some internal segments of the RNA that do not code for protein called introns.

• The parts of the transcript that remain (and code for protein) are called exons.


Transcription


• The process of removing introns and rejoining cut ends is called splicing.


Transcription

• If introns are left in RNA, the consequences can be serious.


• An important step in the processing of tRNA is the chemical modification of several nucleotides and folding into a cloverleaf shape.


Transcription

Mature tRNA resembles a cloverleaf (a), with the amino-acid binding site at the end of a stem and the anticodon at the loop on the opposite end. Base pairing between parallel parts of the tRNA molecule stabilizes the cloverleaf shape. The three-dimensional structure of the molecule is roughly L-shaped (b).


• Ribosomal RNA is not involved in coding.

• The primary rRNA transcript is spliced and modified to produce mature rRNA molecules.


Transcription



• On ribosomes, protein synthesis translates the codon sequence of mRNA into the amino-acid sequence of a protein.

Protein Synthesis

9.5 Translation

• tRNA anticodons pair with the mRNA codons that encodes a particular amino acid.

• Attachment of the correct amino acid to its tRNA molecule is called tRNA charging.

• A molecule of ATP provides the energy to form this bond.


• Charged tRNA, mRNA, and the growing polypeptide chain come together at specific binding sites on a ribosome.

9.5 Translation (cont.)

• At these sites, tRNA anticodons base-pair with mRNA codons, positioning the amino acids they carry so that they can bond to the growing polypeptide chain.

Protein Synthesis


• One of the binding sites, the P site, holds the tRNA carrying the growing polypeptide chain.

• The A site holds the tRNA carrying the next amino acid to be added to the chain.

• Next to the P site is the exit site, or E site.

• An uncharged tRNA leaves the E site after its amino acid is added to the growing chain.


Protein Synthesis



Protein Synthesis

A charged tRNA sits in the A site of the ribosome, bound to the correct mRNA codon by base pairing. A second tRNA, carrying a growing polypeptide, is in the P site, bound to the previous mRNA codon. The E site is not shown.

A groove between the large and small subunits of the ribosome accommodates mRNA and the growing polypeptide chain.


• Translation involves initiation, elongation, and termination, the same three stages as transcription.

• Initiation and elongation require energy supplied by GTP (guanosine triphosphate), a molecule closely related to ATP.


Protein Synthesis


• During initiation of translation, the ribosome attaches at a specific site on the mRNA.


Protein Synthesis


• During elongation, peptide bonds join each amino acid with the next in the sequence.

• A charged tRNA whose anticodon matches the next codon on the message enters the A site of the ribosome.


Protein Synthesis


• This positions the amino acid it carries to form a peptide bond with the amino acid attached to the tRNA at the P site.


Protein Synthesis



Protein Synthesis

• When the bond forms, the polypeptide chain transfers to the tRNA at the A site


• The entire ribosome moves down the mRNA to position the next codon at the A site and the uncharged tRNA leaves the E site.

• The A site is now open and available for the next matching tRNA to bring in an amino acid.


Protein Synthesis


• Translation terminates when a stop codon reaches the A site of the ribosome.

• A special protein known as a release factor binds to the stop codon in the A site.

• At this point, the ribosome lets go of the mRNA, the tRNA, and the release factor.


Protein Synthesis



Protein Synthesis

Transcription produces mRNA, tRNA, and rRNA. All three participate in translation.


• Many proteins must be chemically modified and folded into an active tertiary structure to be functional.

9.6 Transport and Modification of Proteins

• Helper, or “chaperone,” proteins often help stabilize the polypeptide as it is folded.

• After translation, the protein must be transported to where it will function.

Protein Synthesis


• Transport can start while the protein is still being translated.

• The process uses a signal that is part of the protein sequence, called the signal sequence.

9.6 Transport and Modification of Proteins (cont.)

Protein Synthesis

• When translation is complete, the new protein is released from the ribosome into the inner ER.

• Proteins to be released from the cell pass from the ER to the vesicles of the Golgi apparatus.


Synthesis of proteins for secretion or insertion in a membrane


• Errors sometimes occur during translation although most are caught and corrected.

9.7 Translation Errors

• The most common translation error results from misreading the nucleotide sequence.

• A frame shift occurs when the start of translation is shifted by one or two nucleotides in either direction.

• The frame changes causing a different sequence of codons and amino acids will result.

Protein Synthesis


9.7 Translation Errors (cont.)

Protein Synthesis

Each time the reading frame shifts, a different amino-acid sequence results.


• Some errors are due to splicing mistakes or changes in the DNA.

• Insufficient amounts of a particular amino acid also can disrupt translation.

• In some cases, translational frame shifts or alternate initiation sites appear to be normal ways in which one mRNA can specify more than one polypeptide.

9.7 Translation Errors (cont.)

Protein Synthesis



• Viruses are tiny particles that have no cells, yet they replicate and evolve.

Viruses

9.8 Genetic Information and Viruses

• Discovered in 1892 by Russian botanist Dmitri Ivanovsky, viruses depend on the gene-expression machinery of the host cells they infect.


• Most viruses consist of little more than a small amount of genetic material and a protective protein coat.

9.8 Genetic Information and Viruses (cont.)

• Some, such as the familiar viruses that cause colds and the T2 bacteriophage that infects bacterial cells, contain DNA.

Viruses

• Other viruses, such as the influenza virus, contain RNA.



Viruses

Bacteriophage T2, which infects bacterial cells, contains DNA surrounded by a protein coat. The elongated structure attaches to bacterial cells and injects DNA.

HIV (human immunodeficiency virus), which infects human cells, is surrounded by a protein and lipid membrane envelope. The genetic material is RNA. HIV also carries two molecules of the enzyme reverse transcriptase, ready to copy the RNA after entry into a host cell.


• The method of replication varies among types of viruses, but the general principle of copying stored genetic information is the same as for cells.

• Viral replication falls into two patterns:


Viruses

– In lytic infections, the host cell’s enzymes replicate the viral DNA.

– In lysogenic infections, the viral DNA (or a DNA copy of the viral RNA) inserts into the cellular DNA which is then copied when the cell replicates.


Lytic and lysogenic viral reproduction


• Viruses live at the expense of the host organism and pose a serious threat to cellular life.

9.9 Impact of Viruses

• Antibiotics are useless against viruses.

• Modern technologies such as air travel have, in some cases, made the threat of viral diseases much greater.

Viruses

The Ebola virus (x26,400). This deadly virus occurs in isolated parts of East Africa, but air travel and human migration may cause it to spread to new regions of the world.


• Mechanical harvesting and international shipment of agricultural products can spread viruses that infect valuable crops and animals.

• Disabled viruses are exploited by advanced technologies, such as for delivering DNA in cloning experiments.

9.9 Impact of Viruses (cont.)

Viruses




Summary

• Much of the genetic information encodes the primary structure for proteins.

• Proteins carry out numerous functions, including structural roles, cell signaling as hormones or cell-surface receptors, regulators of gene activity, and many catalytic functions.

• Genetic information is stored in DNA or, in the case of some viruses, as RNA.

• As the information is needed, it is expressed through transcription and translation.

• Regulation of gene expression is essential for different cells to carry out their particular activities.

• In transcription, the coding strand of DNA is read as a template by RNA polymerases to build matching RNA molecules.

• Genetic information serves as a master program to direct cell activities.


Summary (cont.)

• Proteins combine with rRNA to form ribosomes.

• Amino acids are carried by their matching tRNAs to the ribosomes.

• Protein synthesis occurs as the sequence of codons in mRNA is translated into the sequence of amino acids in a protein.

• Newly transcribed proteins must fold into the appropriate three-dimensional structure in order to be functional. Often they are chemically modified, too.

• Proteins must travel to the appropriate location in order to do their job.

• Errors in transcription, RNA processing, or translation can result in poor function or absence of a particular protein.

• Primary RNA transcripts are processed into tRNA, rRNA, or mRNA in the nucleus.


Summary (cont.)

• One group of RNA viruses, the retroviruses, enter the host cell and make a DNA copy of their RNA genes.

• Viruses pose a serious threat to cellular life.

• They are exploited in biological research and for their potential as agents of gene therapy and vaccination.

• A special exception to the usual flow of genetic information is found in RNA viruses which use RNA as the long-term storage of information.


Reviewing Key TermsMatch the term on the left with the correct description.

___ transcription

___ translation

___ codons

___ introns

___ exons

___ RNA polymerase

a. the enzyme-catalyzed assembly of an RNA molecule

b. the basic unit of the genetic code

c. a segment of RNA that is removed before mRNA leaves the nucleus

d. the assembly of a protein on ribosomes using mRNA

e. an enzyme that catalyzes the assembly of an RNA molecule

f. a segment of RNA that remains after mRNA leaves the nucleus

a

d

b

c

f

e


Reviewing Ideas1. Describe the lytic viral reproductive cycle.

In lytic infections, the host cell’s enzymes replicate the viral DNA. Viral genes are transcribed and translated on the host’s ribosomes to make proteins for the outer capsule. New viral particles assemble. When there are many new viruses, the cell lyses (breaks open) and releases them to infect other cells.


Reviewing Ideas2. How will the complementary segment of RNA be coded if

the DNA is coded: GCT TGA AAT GAC? Which amino acids do these codons represent?

The RNA codons would be:CGA ACU UUA CUG

These codons represent the following amino acids (in order):arginine, threonine, leucine, leucine


Using Concepts3. What could happen if an intron is left in RNA?

If introns are left in RNA, the consequences can be serious. For example, a change in one splice site of an intron in betaglobin, a component of the oxygen-carrying blood protein hemoglobin, results in defective hemoglobin.


Using Concepts4. Why are viruses considered nonliving?

Among the most important basic properties of life is the ability to replicate and to evolve which viruses cannot do without help. Viruses depend on the gene-expression machinery of the host cells they infect. Most viruses consist of little more than a bit of DNA or RNA and a protective protein coat. Some viruses that infect animal cells have a membrane envelope, but they do not carry out metabolism or respond to stimuli, as cells do.


Synthesize5. What makes viruses, particularly lysogenic

infections, attractive for genetic research?

Viruses are designed to insert DNA or RNA into host cells. Scientists can disarm viruses by removing the genes that cause disease. Lysogenic infection, since it inserts the viral DNA into the host’s DNA is useful in cloning experiments as well as in vaccine research.



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