Microbiology with Diseases by Body

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 CHAPTER
Microbial Genetics
7

Chapter Outline
The Structure and Replication of Genomes (pp. 197–205)
The Structure of Nucleic Acids
The Structure of Prokaryotic Genomes
The Structure of Eukaryotic Genomes
DNA Replication

Gene Function (pp. 205–219)

The Relationship Between Genotype and Phenotype
The Transfer of Genetic Information
The Events in Transcription
Translation
Regulation of Genetic Expression

Mutations of Genes (pp. 219–227)

Types of Mutations
Effects of Point Mutations
Mutagens
Frequency of Mutation
DNA Repair
Identifying Mutants, Mutagens, and Carcinogens

Genetic Recombination and Transfer (pp. 227–233)

Horizontal Gene Transfer Among Prokaryotes
Transposons and Transposition

Chapter Summary
The Structure and Replication of Genomes (pp. 197–205)
Genetics is the study of inheritance and inheritable traits. Genes are composed of specific
sequences of nucleotides that code for polypeptides or RNA molecules. A genome is the sum
of all the genetic material in a cell or virus. Prokaryotic and eukaryotic cells use DNA as their
genetic material; some viruses use DNA, and other viruses use RNA.

Copyright © 2015 Pearson Education, Inc. 41

The Structure of Nucleic Acids
Nucleic acids are polymers of nucleotides (a phosphate attached to a pentose sugar, which is
in turn attached to one of five nitrogenous). The double helix of DNA is two polymer strands
of DNA held together by hydrogen bonds between complementary bases of nucleic acids
called base pairs (bp). In DNA, adenine bonds with thymine, and guanine bonds with
cytosine. One end of a DNA strand is called the 5' end because it terminates in a phosphate
group attached to a 5' carbon; the opposite end of the strand is called the 3' end because it
terminates with a hydroxyl group bound to a 3' carbon of deoxyribose. The two strands are
antiparallel, meaning they are oriented in opposite directions to each other: One strand runs
in a 3' to 5' direction, whereas the other runs in a 5' to 3' direction. The lengths of DNA mole-
cules are expressed in base pairs. Cellular genomes are of extraordinary size relative to the
cell itself.

The Structure of Prokaryotic Genomes

Both bacterial and archaeal genomes consist of one or two chromosomes, which are typically
circular molecules of DNA associated with protein and RNA molecules, localized in a region
of the cytoplasm called the nucleoid. Prokaryotes are haploid with a single copy of each
chromosome. The DNA is extensively folded, coiled, and supercoiled by DNA gyrase. Some
prokaryotes have two or more chromosomes. Archaeal chromosomes are wrapped around
histone proteins. Prokaryotic cells may also contain one or more extrachromosomal DNA
molecules called plasmids, which contain genes that regulate nonessential life functions such
as bacterial conjugation (fertility plasmids); resistance to one or more antimicrobial drugs,
heavy metals, or toxins (resistance plasmids); bacteriocin plasmids carry genes for toxins that
kill competing bacteria; and virulence plasmids carry code for virulence structures, enzymes,
or toxins.

The Structure of Eukaryotic Genomes

Eukaryotic genomes are typically composed of multiple linear chromosomes, which are
contained in the -nuclear envelope. Many eukaryotes are diploid, having two copies of each
chromosome. The DNA of eukaryotic chromosomes is wrapped around proteins called
histones, to form nucleosomes (“beads”) that bind to other proteins to form chromatin
fibers. Loosely packed DNA, euchromatin, are regions where genes are active. Tightly
packed DNA is heterochromatin. Prior to mitosis, highly condensed chromosomes are visible
on light microscopes. Eukaryotic cells also contain extrachromosomal DNA in mitochondria,
chloroplasts, and plasmids.

DNA Replication
The mechanism of DNA replication is similar in all organisms. DNA replication is a simple
concept: A cell separates the two original strands and uses each strand as a template for the
synthesis of a new complementary strand. The process is semiconservative because each
daughter DNA molecule is composed of one original strand and one new strand.
Deoxyribonucleotide triphosphates are both the building blocks and the source of energy
for DNA replication.
DNA replication starts at a specific nucleotide sequence called an origin; DNA helicase
unzips the double helix, breaking hydrogen bonds between complementary base pairs, to
form a replication fork. DNA polymerases always move in the 5' to 3' direction, so the
leading strand is synthesized toward the replication fork. Synthesis is initiated by a primase,
and continued by DNA polymerase, which proofreads the pairing of new nucleotides. The
lagging strand is discontinuously synthesized in a direction away from the replication fork in
series of Okazaki fragments. It always lags behind the process occurring in the leading strand.

42 INSTRUCTOR MANUAL/TEST BANK FOR MICROBIOLOGY WITH DISEASES BY BODY SYSTEM, 4e Copyright © 2015 Pearson Education, Inc.
 DNA ligase seals the gaps between adjacent Okazaki fragments to form a continuous DNA
strand. DNA replication is bidirectional; that is, it proceeds in both directions from the origin
as two replication forks. Gyrase and topoisomerase enzymes remove supercoils that create
tension in the DNA as it is unwound and would stop the replication process.
After bacterial DNA replication, methylation occurs. In methylation, a cell adds a methyl
group to one or two bases that are part of specific nucleotide sequences. In some cases, genes
that are methylated are “turned off” and are not transcribed, whereas in other cases, they are
“turned on” and are transcribed. In some bacteria, methylated nucleotide sequences play a
role in initiating DNA replication, repairing DNA, or recognizing and protecting against
viral DNA.
Eukaryotic DNA replication is similar to that in bacteria with a few exceptions. Eukaryotic
cells use four DNA polymerases to replicate DNA. Due to the large size of eukaryotic
chromosomes, there are many origins of replication. Okazaki fragments of eukaryotes are
smaller than those of bacteria. Finally, plant and animal cells methylate cytosine bases
exclusively.

Gene Function (pp. 205–219)

To understand gene function, it is necessary to distinguish between an organism’s genotype
and phenotype.

The Relationship Between Genotype and Phenotype

The genotype of an organism is the actual set of genes in its genome, whereas the phenotype
is the physical and functional traits that are a result of expression of those genes, such as the
presence of flagella. Thus, genotype determines phenotype; however, not all genes are active
at all times.

The Transfer of Genetic Information

The central dogma of genetics states that DNA is transcribed to RNA, which is translated to
form polypeptides. That is, transcription of the DNA produces RNA molecules, and trans-
lation of the RNA sequence by ribosomes produces polypeptides.

The Events in Transcription

Cells transcribe five types of RNA from DNA:
1. RNA primer molecules for DNA polymerase to use during DNA replication
2. Messenger RNA (mRNA) molecules, which carry genetic information from chromosomes
to ribosomes
3. Ribosomal RNA (rRNA) molecules, which combine with ribosomal polypeptides to form
ribosomes, the organelles that synthesize polypeptides
4. Transfer RNA (tRNA) molecules, which deliver amino acids to the ribosomes
5. Regulatory RNA molecules, which help regulate gene expression
The transfer of genetic information begins with transcription of the genetic code from a
single strand of DNA to RNA. RNA polymerase binds to a region of DNA called a
promoter near the beginning of a gene sequence. Bacterial sigma factors recognize promot-
ers and control transcription. The RNA polymerase unzips the DNA double helix and synthe-
sizes an RNA strand complementary to the DNA bases of the gene sequence. The process is
similar to DNA synthesis except that ribonucleotides are incorporated into the growing strand

Copyright © 2015 Pearson Education, Inc. CHAPTER 7 Microbial Genetics 43

 and U base pairs with A. Transcription ends when RNA polymerase and the transcript are
released from the DNA. A terminator sequence of the transcribed RNA may destabilize the
bonding between the DNA and RNA, or Rho protein may assist in termination.
Eukaryotic transcription differs from bacterial transcription in several ways. Eukaryotic
cells transcribe RNA in the nucleus, while prokaryotic transcription occurs in the cytosol.
Eukaryotes have three types of nuclear RNA polymerase and multiple transcription factors.
Eukaryotic cells process mRNA before translation. RNA processing involves capping,
polyadenylation, and splicing in which a spliceosome removes non-coding intervening
(intron) sequences from between expressed (exon) sequences.

Translation
In translation, the sequence of genetic information carried by mRNA is used by ribosomes
to synthesize polypeptides with specific amino acid sequences. To understand how 4 DNA
nucleotides can specify the 21 different amino acids commonly found in proteins requires an
understanding of the genetic code. Scientists define the genetic code as the complete set of
triplets of mRNA nucleotides called codons that code for specific amino acids. These bind to
complementary anticodons on tRNA. The code is redundant; that is, more than one codon is
associated with all the amino acids except methionine and tryptophan. In all organisms the
codon AUG is the start signal, specifying methionine (f-MET in prokaryotes), and in most
organisms 3 codons are stop signals. Prokaryotic mRNA may contain instructions for more
than one polypeptide. Eukaryotic mRNAs contain instructions for a single polypeptide and
only fully processed mRNAs are translated.
Transfer RNAs are about 75 bases in length and fold into a complex three-dimensional
shape. One end of the molecule is an anticodon complementary to mRNA codons. The
other end is an acceptor end to which a specific amino acid is attached by specific enzymes.
Because of “wobble” in the third position of an anticodon, some tRNAs can complement
more than one codon, which provides the mechanism for the redundancy of the genetic
code.
Prokaryotes have 70S ribosomes composed of 50s and 30s subunits and 21 polypeptides,
while eukaryotic 80S ribosomes contain 60s and 40s subunits and an as yet undetermined
number of polypeptides. The smaller subunit of a ribosome is shaped to accommodate three
codons at one time. Each ribosome also has three binding sites that are named for their
function:
1. The A site accommodates a tRNA delivering an amino acid.
2. The P site holds a tRNA and the growing polypeptide.
3. Discharged tRNAs exit from the E site.
Prokaryotic translation proceeds in three stages: In initiation, an initiation complex is
formed. During elongation, tRNAs escorted by elongation factors and GTP sequentially
deliver amino acids as directed by the codons of the mRNA. A ribozyme in the large ribo-
somal subunit catalyzes peptide bond formation between the amino acid at the A site and the
growing polypeptide at the P site. The third stage, termination, does not involve tRNA;
instead, proteins called release factors halt elongation. The ribosome then dissociates into its
subunits. A single mRNA may have many ribosomes bound at different stages of translation,
forming a polyribosome.
Eukaryotic translation is similar to that of bacteria with a few exceptions. The small ribo-
somal subunit in eukaryotes binds to the 5' guanine cap to initiate translation. The first amino
acid in eukaryotic polypeptides is methionine rather than N-formylmethionine. Eukaryotic
translation can occur on the endoplasmic reticulum as well as in the cytosol. Archaeal transla-
tion is similar to the process in eukaryotes except for the lack of ER.

44 INSTRUCTOR MANUAL/TEST BANK FOR MICROBIOLOGY WITH DISEASES BY BODY SYSTEM, 4e Copyright © 2015 Pearson Education, Inc.
Regulation of Genetic Expression
A majority of genes in bacteria are expressed at all times; other genes are regulated so that the
polypeptides they encode are synthesized only when a cell has need of them. Cells may regu-
late synthesis by initiating (induction) or blocking (repression) transcription or by stopping
translation directly.
Transcription-level regulation in prokaryotes often involves operons. An operon consists
of a promoter, an adjacent regulatory element called an operator, and a series of genes whose
expression is controlled by a regulatory gene located elsewhere. Operons coding for more
than one polypeptide are polygenic. Inducible operons such as the lactose (lac) operon are
not usually transcribed and must be activated by inducers. Repressible operons such as the
tryptophan operon are transcribed continually until deactivated by repressors.
Lac operon regulation is complex, involving a repressor protein that binds the operator
sequence and prevents RNA polymerase binding; an inducer (allolactose) that binds repressor
protein and prevents it from binding the operator sequence; and catabolite activator protein
(CAP) that binds the DNA and facilitates the binding of RNA polymerase when cyclic adeno-
sine monophosphate (cAMP) is present.
The tryptophan (trp) operon is normally expressed. When tryptophan is abundant, it acts as
a corepressor, binding inactive repressor protein, activating it. The activated repressor protein
binds the trp operator, preventing RNA polymerase binding and transcription.
Regulatory RNAs control whether mRNA is translated. Translation can be controlled
by micro RNA (miRNA) or short interference RNA (siRNA); miRNA and siRNA
molecules are complementary to a portion of an mRNA and prevent its translation when
bound; miRNAs and regulatory proteins form a miRNA-induced silencing complex (miRISC),
which then binds to mRNA, either blocking translation or cutting the molecule; siRNAs are
double-stranded RNAs that complex with regulatory proteins and cut the target RNA mole-
cule. A riboswitch is a sequence of mRNA that changes shape in response to changes in the
environment, and may favor or block translation of the polypeptide.

Mutations of Genes (pp. 219–227)

A mutation is a change in the nucleotide sequence of a genome.

Types of Mutations
Mutations range from large changes in an organism’s genome, such as the loss or gain of an
entire chromosome, to point mutations, in which just one or a few nucleotide base pairs are
affected. Mutations can be harmful, without effect, or sometimes beneficial. Point mutations
include the following:
• Substitutions, in which a single nucleotide base pair is substituted for another
• Frameshift mutations, including insertions and deletions of nucleotides, in which
nucleotide triplets subsequent to an insertion or deletion are displaced, creating new
sequences of codons that result in vastly altered polypeptide sequences or causing prema-
ture termination

Effects of Point Mutations

Some base-pair substitutions produce silent mutations: The substitution does not change the
amino acid sequence because of the redundancy of the genetic code. A change in a nucleotide
sequence resulting in a codon that specifies a different amino acid is called a missense

Copyright © 2015 Pearson Education, Inc. CHAPTER 7 Microbial Genetics 45

 mutation; what gets transcribed and translated makes sense, but not the right sense. Depend-
ing on the location of the missense mutation, the change in a polypeptide may be minor or
result in loss of function. In a nonsense mutation, a base-pair substitution changes an amino
acid codon into a stop codon. Nearly all nonsense mutations result in nonfunctional proteins.
Frameshift mutations (insertions or deletions) typically result in drastic missense and non-
sense mutations.

Mutagens
Mutations can be spontaneous or result from recombination. Physical or chemical agents
called mutagens, which include radiation and several types of DNA-altering chemicals,
induce mutations. Errors during DNA replication or repair can also produce mutations.
Ionizing radiation in the form of X-rays and gamma rays can cause mutations. In addition,
nonionizing radiation in the form of ultraviolet light causes adjacent pyrimidine bases to
bond to one another to form pyrimidine dimers. The presence of dimers prevents hydrogen
bonding with the nucleotides in the complementary strand, distorts the sugar-phosphate back-
bone, and prevents proper replication and transcription.
Chemical mutagens include nucleotide analogs, compounds that are structurally similar to
normal nucleotides but, when incorporated into DNA, may interfere with DNA polymerase
function or cause mismatching. Some nucleotide-altering chemicals change the structure of
nucleotides, causing base-pair substitution mutations. Aflatoxins are nucleotide-altering
chemicals that result in missense mutations and cancer. Frameshift mutagens are chemicals
that insert or delete nucleotide base pairs, resulting in frameshift mutations. Benzopyrene,
ethidium bromide, and acridine are examples of frameshift mutagens.

Frequency of Mutation
About 1 of every 10 million genes contains an error. Mutagens typically increase the
mutation rate by a factor of 10–1000 times. Most deleterious mutations result in cell death.
The rare beneficial mutation may be passed on the descendents and become more frequent in
a population. The change in gene frequency in population is evolution.

DNA Repair
Cells have numerous methods of repairing damaged DNA. Pyrimidine dimers are repaired by
light repair in which cells use DNA photolyase to break the bonds between adjoining
pyrimidine nucleotides. In dark repair, enzymes repair pyrimidine dimers by cutting dam-
aged DNA from the molecule, creating a gap that is repaired by DNA polymerase I and DNA
ligase. In base-excision repair, an enzyme system excises the erroneous base, and DNA
polymerase I fills in the gap. Mismatch repair enzymes scan newly synthesized unmethy-
lated DNA for mismatched bases, which they remove and replace. Once a new DNA strand
is methylated, mismatch repair enzymes cannot correct any errors that remain. When damage
is so extensive that these mechanisms are overwhelmed, bacterial cells resort to an SOS
response involving the production of novel DNA polymerases capable of copying less-than-
perfect DNA. The SOS response introduces changes to the sequence but may produce DNA
sufficiently intact for cells to survive.

Identifying Mutants, Mutagens, and Carcinogens

If a cell does not repair a mutation, it and its descendants are called mutants. In contrast,
cells normally found in nature are called wild-type cells. Researchers have developed
methods to recognize mutants among their wild-type neighbors. These include:

46 INSTRUCTOR MANUAL/TEST BANK FOR MICROBIOLOGY WITH DISEASES BY BODY SYSTEM, 4e Copyright © 2015 Pearson Education, Inc.
 • Positive selection, which involves selecting a mutant by eliminating wild-type
phenotypes.
• Negative selection (also called indirect selection), a process in which a researcher
attempts to culture auxotrophs which have non–wild type nutritional requirements.
Colonies of bacteria are allowed to grow on complete medium and then are replica plated
to a medium lacking one or more nutrients.
• The Ames test is used to identify potential carcinogens (cancer-causing agents). Salmo-
nella auxotrophs are grown in the presence of possible mutagens and then are screened for
reversion to wild type.

Genetic Recombination and Transfer (pp. 227–233)

Genetic recombination refers to the exchange of nucleotide sequences between two DNA
molecules often mediated by segments composed of identical or nearly identical nucleotide
sequences called homologous sequences. DNA molecules that contain new arrangements of
nucleotide sequences are called recombinants.

Horizontal Gene Transfer Among Prokaryotes

Vertical gene transfer is the transmission of genes from parents to offspring. In horizontal
gene transfer, DNA from a donor cell is transmitted to a recipient cell. A recombinant cell
results from genetic recombination between donated and recipient DNA.
Transformation, transduction, and bacterial conjugation are types of horizontal gene
transfer:
• In transformation, a competent recipient cell takes up DNA from the environment.
Competency results from changes in the cell wall and cytoplasmic membrane that allow
extracellular DNA to enter cells. It is found naturally in some genera of bacteria and can
be created artificially in others. It is an important tool of genetic engineering.
• In transduction, a virus such as a bacteriophage (or phage) carries DNA from a donor
cell to a recipient cell. Donor DNA is accidentally incorporated in transducing phages
during assembly. In generalized transduction, the transducing phage carries a random
DNA segment from the donor to the recipient, while in specialized transduction, only spe-
cific host sequences are transferred.
• In conjugation, a bacterium containing an F (fertility) plasmid forms a conjugation pilus
that attaches to an F– recipient bacterium. Plasmid genes are transferred as single-stranded
DNA to the recipient, which synthesizes the complementary strand and becomes F+ as a
result. Hfr (high frequency of recombination) cells result when an F plasmid integrates
into a prokaryotic chromosome. Hfr cells form conjugation pili and transfer chromosomal
sequences as well as plasmid genes.

Transposons and Transposition

Transposons are DNA segments that code for the enzyme transposase and contain palin-
dromic sequences known as inverted repeats (IR) at each end. (A palindrome is a word,
phrase, or sentence that has the same sequence of letters when read backward or forward.)
Transposons move from one location to another in chromosomes and plasmids in eukaryotes
and prokaryotes. Regions of sequence homology are not required for transposition. The
simplest transposons, known as insertion sequences (IS), consist only of inverted repeats
and transposase. Complex transposons contain other genes as well.

Copyright © 2015 Pearson Education, Inc. CHAPTER 7 Microbial Genetics 47