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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
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.
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.
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.
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
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.
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.
Ei ole sijaa tytöille, siinä yksi puoli asian selvitystä, joka lyhyesti ja
suoraan ilmaisee yhden niistä perusaatteista, joita on otettu
kasvatuksen järjestämisessäkin ohjeeksi. Mutta tämän syyn rinnalla
ja sen täytteenä löydämme kohta toisen. Se tosin ei ole niin selvästi
sanottu eikä kenties aina niin selvästi ajateltukaan, vaan sen jälkiä ei
ole vaikea huomata. Tämä kuuluu: Mitä tyttö tekee vapailla liikkeillä,
paljolla juoksulla ja voimia kehittävillä ruumiin harjoituksilla? Ei tyttö
sellaista tarvitse, hän voipi käyskennellä sisällä luokkahuoneessa
pulpettien välissä tai käytävissä, se on tytölle sopivaa. — Ja eihän
hän tarvitse raitista ilmaakaan niinkuin pojat, vai miten?
Näin välinpitämättömästi lasta kohdellaan ruumiillisessa
katsannossa, kun sokeasti heittäydytään vanhain ennakkoluulojen
johdatettavaksi. Ajattelemattomasti kodissa ja> koulussa uhrataan
lapsi tytön tähden, niinkuin sitte edelleen elämässä uhrataan ihminen
naisen tähden. Ei ole muka sopiva että naisella on vahva ruumis,
joka antaisi voimaa ja ryhtiä sen liikkeille ja väkevyyttä työnteossa.
Sentähden on ryöstettävä nuorelta tytöltä se mitä hän sitten
ihmisenä elämässä tarvitsee. Pidetäänhän kohtuullinen
jaksamattomuus ja arkamaisuus ikäänkuin ansiollisena
ominaisuutena tytölle.
Eikä ole syytä moitteesen ettei tämä olisi onnistunut. Sen osoittaa
kylläksi se ruumiin puolesta kutistunut nainen, jonka sivistynyt sääty
on yhteiskunnalle kasvattanut. Vertaa häntä rahvaan naiseen, niin
näet heti eroituksen. Nuo vaaleat kasvot, jotka todistavat huonoa
verta; nuo heikot jäsenet, jotka useimmin eivät totiseen työhön
kelpaa eikä sitä kestä; tuo ampiaisvartalo, joka tuskin pääsee sen
verta taipumaan että noukkisi tuokkosellisen marjoja maasta, eikö ne
kantele kasvatuksesta? Eikö se ole hävettävä todistus
kevytmielisyydestä, johon kasvattajat ja yhteiskunta ovat tehneet
itsensä velkapäiksi, kun armottomien ja jumalattomien oppien
eksymyksessä ovat estävästi vaikuttaneet luonnon kulkuun?
Aina viime aikoihin on nuori tyttö usein isän tahdosta tai muiden
omaisten toivomuksesta talutettu vihkituoliin, jossa hän on pantu
sanomaan "tahdon", sentähden että isä ja äiti sanoivat tahdon. Hän
on luvannut rakastaa myötä- ja vastoinkäymisessä, vaikka hänen
sydämmensä oli kylmä kuin kivi. Vanhemmat ja muut todistajat ovat
seisoneet tyynenä vieressä, siten osoittaen hyväksymistänsä.
laulaa Franzén.
"Talon tyttären täytyy osata tehdä selko niistä kaluista, joita hän on
korjannut laimiinlyöjän perässä. Hänen pitää tietää mistä paikasta
isä ensin takkiansa hakee, kun hän lähtee ulos, ja kantaa se joka
kerta sille paikalle. Hänen pitää panna merkki siihen paikkaan
kirjassa, mihin veli lopetti lukunsa, että tämä pian löytäisi paikan, kun
hän taas ottaa kirjan käteensä. Ja pikkuveljen puuhevonen pitää
hänen asettaa nurkkaan seisomaan, että poikanen kävelyltä takaisin
tullessa voipi iloissaan huudahtaa; Hei, Polleni, siinä seisot taas
syömässä seimelläsi".