Chapter 9 Glossary, Summary, and Practice Questions

 KEY TERMS

alternative RNA splicing a post-transcriptional gene regulation mechanism in eukaryotes in which multiple protein products are produced by a single gene through alternative splicing combinations of the RNA transcript

codon three consecutive nucleotides in mRNA that specify the addition of a specific amino acid or the release of a polypeptide chain during translation

deoxyribose a five-carbon sugar molecule with a hydrogen atom rather than a hydroxyl group in the 2′ position; the sugar component of DNA nucleotides

DNA ligase the enzyme that catalyzes the joining of DNA fragments together

DNA polymerase an enzyme that synthesizes a new strand of DNA complementary to a template strand

double helix the molecular shape of DNA in which two strands of nucleotides wind around each other in a spiral shape

epigenetic describing non-genetic regulatory factors, such as changes in modifications to histone proteins and DNA that control accessibility to genes in chromosomes

exon a sequence present in protein-coding mRNA after completion of pre-mRNA splicing

gene expression processes that control whether a gene is expressed

genetic code the amino acids that correspond to three-nucleotide codons of mRNA

helicase an enzyme that helps to open up the DNA helix during DNA replication by breaking the hydrogen bonds

intron non–protein-coding intervening sequences that are spliced from mRNA during processing

lagging strand during replication of the 3′ to 5′ strand, the strand that is replicated in short fragments and away from the replication fork

leading strand the strand that is synthesized continuously in the 5′ to 3′ direction that is synthesized in the direction of the replication fork

mismatch repair a form of DNA repair in which non-complementary nucleotides are recognized, excised, and replaced with correct nucleotides

mRNA messenger RNA; a form of RNA that carries the nucleotide sequence code for a protein sequence that is translated into a polypeptide sequence

mutation a permanent variation in the nucleotide sequence of a genome

nitrogenous base a nitrogen-containing molecule that acts as a base; often referring to one of the purine or pyrimidine components of nucleic acids

nontemplate strand the strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA

nucleotide excision repair a form of DNA repair in which the DNA molecule is unwound and separated in the region of the nucleotide damage, the damaged nucleotides are removed and replaced with new nucleotides using the complementary strand, and the DNA strand is resealed and allowed to rejoin its complement

Okazaki fragments the DNA fragments that are synthesized in short stretches on the lagging strand

phosphate group a molecular group consisting of a central phosphorus atom bound to four oxygen atoms

post-transcriptional control of gene expression after the RNA molecule has been created but before it is translated into protein

post-translational control of gene expression after a protein has been created

primer a short stretch of RNA nucleotides that is required to initiate replication and allow DNA polymerase to bind and begin replication

promoter a sequence on DNA to which RNA polymerase and associated factors bind and initiate transcription

replication fork the Y-shaped structure formed during the initiation of replication

RNA polymerase an enzyme that synthesizes an RNA strand from a DNA template strand

rRNA ribosomal RNA; molecules of RNA that combine to form part of the ribosome

semiconservative replication the method used to replicate DNA in which the double-stranded molecule is separated and each strand acts as a template for a new strand to be synthesized, so the resulting DNA molecules are composed of one new strand of nucleotides and one old strand of nucleotides

splicing the process of removing introns and reconnecting exons in a pre-mRNA

start codon the AUG (or, rarely GUG) on an mRNA from which translation begins; always specifies methionine

stop codon one of the three mRNA codons that specifies termination of translation

telomerase an enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends

telomere the DNA at the end of linear chromosomes

template strand the strand of DNA that specifies the complementary mRNA molecule

transcription bubble the region of locally unwound DNA that allows for transcription of mRNA

tRNA transfer RNA; an RNA molecule that contains a specific three-nucleotide anticodon sequence to pair with the mRNA codon and also binds to a specific amino acid

CHAPTER SUMMARY

The Structure of DNA

The model of the double-helix structure of DNA was proposed by Watson and Crick. The DNA molecule is a polymer of nucleotides. Each nucleotide is composed of a nitrogenous base, a five-carbon sugar (deoxyribose), and a phosphate group. There are four nitrogenous bases in DNA, two purines (adenine and guanine) and two pyrimidines (cytosine and thymine). A DNA molecule is composed of two strands. Each strand is composed of nucleotides bonded together covalently between the phosphate group of one and the deoxyribose sugar of the next. From this backbone extend the bases. The bases of one strand bond to the bases of the second strand with hydrogen bonds. Adenine always bonds with thymine, and cytosine always bonds with guanine. The bonding causes the two strands to spiral around each other in a shape called a double helix. Ribonucleic acid (RNA) is a second nucleic acid found in cells. RNA is a single-stranded polymer of nucleotides. It also differs from DNA in that it contains the sugar ribose, rather than deoxyribose, and the nucleotide uracil rather than thymine. Various RNA molecules function in the process of forming proteins from the genetic code in DNA.

Prokaryotes contain a single, double-stranded circular chromosome. Eukaryotes contain double-stranded linear DNA molecules packaged into chromosomes. The DNA helix is wrapped around proteins to form nucleosomes. The protein coils are further coiled, and during mitosis and meiosis, the chromosomes become even more greatly coiled to facilitate their movement. Chromosomes have two distinct regions which can be distinguished by staining, reflecting different degrees of packaging and determined by whether the DNA in a region is being expressed (euchromatin) or not (heterochromatin).

DNA Replication

DNA replicates by a semi-conservative method in which each of the two parental DNA strands act as a template for new DNA to be synthesized. After replication, each DNA has one parental or “old” strand, and one daughter or “new” strand.

Replication in eukaryotes starts at multiple origins of replication, while replication in prokaryotes starts from a single origin of replication. The DNA is opened with enzymes, resulting in the formation of the replication fork. Primase synthesizes an RNA primer to initiate synthesis by DNA polymerase, which can add nucleotides in only one direction.

One strand is synthesized continuously in the direction of the replication fork; this is called the leading strand. The other strand is synthesized in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments. This strand is known as the lagging strand. Once replication is completed, the RNA primers are replaced by DNA nucleotides and the DNA is sealed with DNA ligase.

The ends of eukaryotic chromosomes pose a problem, as polymerase is unable to extend them without a primer. Telomerase, an enzyme with an inbuilt RNA template, extends the ends by copying the RNA template and extending one end of the chromosome. DNA polymerase can then extend the DNA using the primer. In this way, the ends of the chromosomes are protected. Cells have mechanisms for repairing DNA when it becomes damaged or errors are made in replication. These mechanisms include mismatch repair to replace nucleotides that are paired with a non-complementary base and nucleotide excision repair, which removes bases that are damaged such as thymine dimers.

Transcription

In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template. Elongation synthesizes new mRNA. Termination liberates the mRNA and occurs by mechanisms that stall the RNA polymerase and cause it to fall off the DNA template. Newly transcribed eukaryotic mRNAs are modified with a cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Eukaryotic mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs are exported from the nucleus to the cytoplasm.

Translation

The central dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is the correspondence between the three-nucleotide mRNA codon and an amino acid. The genetic code is “translated” by the tRNA molecules, which associate a specific codon with a specific amino acid. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three stop codons. This means that more than one codon corresponds to an amino acid. Almost every species on the planet uses the same genetic code.

The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit binds to the mRNA template. Translation begins at the initiating AUG on the mRNA. The formation of bonds occurs between sequential amino acids specified by the mRNA template according to the genetic code. The ribosome accepts charged tRNAs, and as it steps along the mRNA, it catalyzes bonding between the new amino acid and the end of the growing polypeptide. The entire mRNA is translated in three-nucleotide “steps” of the ribosome. When a stop codon is encountered, a release factor binds and dissociates the components and frees the new protein.

How Genes Are Regulated

While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene expression in prokaryotes is regulated only at the transcriptional level, whereas in eukaryotic cells, gene expression is regulated at the epigenetic, transcriptional, post-transcriptional, translational, and post- translational levels.

ART CONNECTION QUESTIONS

• Figure 9.10 You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at

REVIEW QUESTIONS

• Which of the following does cytosine pair with?

• guanine

the replication fork. Which enzyme is most likely to be mutated?

• thymine
• adenine
• a pyrimidine

• Prokaryotes contain a chromosome, and eukaryotes contain chromosomes.
• single-stranded circular; single-stranded linear
• single-stranded linear; single-stranded circular
• double-stranded circular; double-stranded linear
• double-stranded linear; double-stranded circular
• DNA replicates by which of the following models?

• conservative
• semiconservative
• dispersive
• none of the above
• The initial mechanism for repairing nucleotide errors in DNA is .
• mismatch repair
• DNA polymerase proofreading
• nucleotide excision repair
• thymine dimers
• A promoter is .
• a specific sequence of DNA nucleotides
• a specific sequence of RNA nucleotides
• a protein that binds to DNA
• an enzyme that synthesizes RNA
• Portions of eukaryotic mRNA sequence that are removed during RNA processing are .
• exons
• caps
• poly-A tails

CRITICAL THINKING QUESTIONS

• Describe the organization of the eukaryotic chromosome.
• Describe the structure and complementary base pairing of DNA.
• How do the linear chromosomes in eukaryotes ensure that its ends are replicated completely?
• 
  introns
• The RNA components of ribosomes are synthesized in the .
• cytoplasm
• nucleus
• nucleolus
• endoplasmic reticulum
• How long would the peptide be that is translated from this MRNA sequence: 5′-AUGGGCUACCGA-3′?

a. 0

b. 2

c. 3

d. 4

• Control of gene expression in eukaryotic cells occurs at which level(s)?
• only the transcriptional level
• epigenetic and transcriptional levels
• epigenetic, transcriptional, and translational levels
• epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels
• Post-translational control refers to:
• regulation of gene expression after transcription
• regulation of gene expression after translation
• control of epigenetic activation
• period between transcription and translation

• Transcribe and translate the following DNA sequence (nontemplate strand): 5′-ATGGCCGGTTATTAAGCA-3′
• Describe how controlling gene expression will alter the overall protein levels in the cell.