Chapter 8 Genetics

Chapter 8
Microbial Genetics
Copyright 2010 Pearson Education, Inc.
Lectures prepared by Christine L. Case
Terminology
Genetics: The study of what genes are, how they
carry information, how information is expressed, and
how genes are replicated
Gene: A segment of DNA that encodes a functional
product, usually a protein
Chromosome: Structure containing DNA that
physically carries hereditary information; the
chromosomes contain the genes
Genome: All the genetic information in a cell
Terminology
Phenotype: Expression of the genes
Genotype: The genes of an organism
Genomics: The molecular study of genomes
Proteomics: The study of proteins produced by an
organism.
Bioinformatics: Understanding the function of
genes through computer-assisted analysis
Genetic Map of the Chromosome of E.

coli
E. coli has about 4.6
million base pairs of
DNA in 1 covalently
closed circular
chromosome
A human cell has
about 3 billion base
pairs in 46 linear
chromosomes
E coli has 1/1000 the
DNA a human cell
does
Figure 8.1b
DNA
Polymer of nucleotides:
Adenine, thymine,
cytosine, and guanine
"Backbone" is
deoxyribose-phosphate
Strands are held together
by hydrogen bonds
between AT and CG
Strands are antiparallel
Run in opposite directions
Are reverse-complementary
Figure 8.3b
DNA Synthesis
Figure 8.4
DNA Synthesis
DNA is copied by DNA polymerase
Replication fork begins at oriC with binding of DnaA
Elongates in the 5' 3' direction
Initiated by an RNA primer
Leading strand is synthesized continuously
Lagging strand is synthesized discontinuously
Okazaki fragments
RNA primers are removed and Okazaki fragments joined
by a DNA polymerase and DNA ligase
Replication is semi-conservative
New molecule has one original DNA strand and one
newly synthesized strand
DNA Synthesis
Figure 8.5
Replication of Bacterial DNA
Bidirectional
replication
theta structure
Figure 8.6
Rolling Circle Replication

Unidirectional replication
Products include:
ss- linear DNA
ss- circular DNA
ss- linear DNA tandem
repeats
ds- linear DNA
ds- circular DNA
ds- linear DNA tandem
repeats
Enzymes Involved in DNA Synthesis

Helicaseunwinds dsDNA
Single strand binding proteinsmaintain ssDNA
PrimaseRNA polymerase activity that synthesizes
a short stretch of complementary RNA used as
primer for DNA Polymerase
DNA dependent, DNA Polymerase 5 isoforms in
Bacteria, 15(?) in eukaryotes
Gyrase/TopoisomeraseRelaxes supercoiling.
DNA LigaseRepairs gaps in phosphodiester
backbone
Table 8.1
DNA Polymerase in E coli

DNA Polymerase I
Removes and replaces primers
DNA Polymerase II
DNA repair
DNA Polymerase III

Elongates DNA (normal replication)
DNA Polymerase IV
DNA repair
DNA Polymerase V
Trans-lesion synthesis (DNA repair)
Table 8.1
The Process of Transcription
Figure 8.7
The Process of Transcription
ANIMATION Transcription: Overview

ANIMATION Transcription: Process
Figure 8.7
Transcription
DNA is transcribed to make RNA (mRNA, tRNA, and
rRNA)
Transcription begins when RNA polymerase binds to
the promoter sequence
Transcription proceeds in the 5' 3' direction
Transcription stops when it reaches the
terminator sequence
Eukaryotes: 1 mRNA = 1 product = monocistronic
Prokaryotes:1 mRNA = 1 products = polycistronic
RNA Processing in Eukaryotes
Little to no
splicing, 5-cap,
or
polyadenylation
in prokaryotes!
Figure 8.11
Inhibitors of Nucleic Acid Synthesis

Rifampin
Inhibits RNA polymerase (bacterial transcription)
Effective against Mycobacteria
Quinolones/Fluoroquinolones
Ciprofloxin
Inhibits DNA Gyrase (replication of bacterial DNA)
Nucleoside analogs
AZT (Zidovudine or azidothymidine)
Inhibits DNA replication and transcription
Translation
mRNA is translated in
codons (three
nucleotides)
Translation of mRNA
begins at the start
codon: AUG
Translation ends at
nonsense codons:
UAA, UAG, UGA
64 sense codons on
mRNA encode the 20
amino acids
Figure 8.2
The Genetic Code

The genetic code is
degenerate
tRNA carries the
complementary
anticodon
ANIMATION Translation:
Overview
Genetic Code
Process
Figure 8.2
Simultaneous Transcription &

Translation in Prokaryotes
Figure 8.10
The Process of Translation

Ribosome assembly
begins at an internal
ribosome entry site called
a Shine-Delgarno
sequence in prokaryotes
Ribosome
assembly
begins at the 5
cap in
eukaryotes
Figure 8.9

Methionine in Eukarya and Archaea
N-Formyl Methionine in Bacteria
Figure 8.9
Figure 8.9
Figure 8.9
Figure 8.9
Figure 8.9
Figure 8.9
Figure 8.9
Regulation of Gene Expression

Gene expression - when the molecule the
gene codes for has been produced.
Some genes are constitutive in that they are
always expressed. Not genetically regulated.
Others are genetically regulated by repression or
induction.
Operon = a group of genes consisting of a
promoter and operator sites, and structural genes
which code for proteins. The product of the
regulatory gene (I) regulates the operon.
Operon
In prokaryotes, genes involved in the same metabolic pathway are
often clustered together in regions called operons.
ANIMATION Operons: Overview

Figure 8.12

repression: A repressor (protein) blocks
transcription by binding to an operator. Synthesis
stops.
induction: The synthesis of enzymes in the
presence of an inducer.
In the absence of an inducer, a repressor binds to the
operator of an operon, and turns off transcription. When
present, an inducer binds to the repressor and inactivates
it.

lac = lactose, a disaccharide of glucose and
galactose
The lac operon is an inducible operon
tryp=Tryptophan is an amino acid.

The tryp operon is a repressible operon
ANIMATION Operons: Induction

ANIMATION Operons: Repression
The lac operon
Theoperatorsite
Structural genes
Lactosescarce,glucosepresent
The lac operon
Lactosepresent,glucosescarce
Catabolite Repression
Theinhibitionofthelacoperonbyglucoseiscalled
cataboliterepression
Lactose present, no
glucose
Lactose + glucose
present
Figure 8.15
The abundance of glucose regulates many
operons
other catabolites such as Lactose
motility (flagella)
biofilm formation
etc
(a) Growth on glucose or lactose alone
(b) Growth on glucose and lactose

combined
Figure 8.14
TheTrypOperon
TheTrypOperon
Anexampleof
autoregulation
Mutation
A change in the genetic material

Mutations may be neutral, beneficial, or harmful
Mutagen: Agent that causes mutations
Spontaneous mutations: Occur in the absence of a
mutagen
Mutation
Base substitution
(point mutation)
Missense mutation
Change in one base

Result in change in
amino acid
Figure 8.17a, b
Mutation
Nonsense mutation
Results in a nonsense
codon
Figure 8.17a, c
Mutation
Frameshift mutation
Insertion or deletion of
one or more nucleotide
pairs
Figure 8.17a, d
The Frequency of Mutation

Spontaneous mutation rate = 1 in 109 replicated
base pairs or 1 in 106 replicated genes
Mutagens increase rate significantly
Strong mutagens can have antimicrobial activity
ANIMATION Mutations: Types

Chemical Mutagens
Types include:
Base analogs
Alkylation/halogenation
Intercalation
Cross-linking
Oxidation/reduction
ANIMATION Mutagens
Figure 8.19b
Radiation
Ionizing radiation (X rays and gamma rays) causes
the formation of ions that can react with nucleotides
and the deoxyribose-phosphate backbone
Causes oxidative damage, abasic sites, and DNA strand
breaks
UV radiation causes covalent bond formation

between adjacent thymines (thymine dimers)
Repair
Photolyases separate thymine dimers
Base Excision repair
Nucleotide excision repair (NER)
ANIMATION Mutations: Repair

Figure 8.20
The Trouble with Mutations--Tuberculosis

Tuberculosis (consumption)
Fifth leading cause of death in WORLD.
Caused by Mycobacterium tuberculosis, a Grampositive rod, aerobe, acid fast
Has mycolic acids (lipid) in cell envelope.
Resistant to drying and disinfectants.
Grows very slowly.
Tuberculosis
Tuberculosis, cont.
Acquire organism by inhalation.
Organism goes to lung.
Is phagocytized by macrophage.
May be killed by macrophage.
If not, other macrophages migrate to lung.
A tubercle is formed, a granuloma of macrophages,
neutrophils, bacteria, and tissue cells in the lung.
Other macrophages ingest M. tuberculosis.
Tuberculosis
Tuberculosis, cont.
Soon macrophages die, releasing bacteria.
The center of tubercle takes on a caseous appearance,
i.e., has the consistency of cheese.
Caseous lesion has bacteria in center surrounded by
tightly packed WBCs.
Bacteria remain viable.
Lesions calcify and are seen on X-rays.
May exist for years.
Tuberculosis
Tuberculosis, cont.
In some people, cells start to multiply.
Results in liquefaction in center of lesion.
M. tuberculosis is released. May reinfect the lung.
Or, M. tuberculosis may get into the blood, and
infection becomes systemic causing miliary
tuberculosis. Cells go to many organs of body.
Symptoms: coughing, loss of weight, weakness.
(Consumption is old name for TB.)
Tuberculosis is a chronic disease.
Tuberculosis
Tuberculosis, cont.
Treatment: streptomycin, isoniazid, rifampin, and
other antimicrobial drugs.
Treatment continues for one to two years.
Detection: by the tuberculin skin test. Are looking for
immune reaction to M. tuberculosis.
No effective vaccine (although some are used)
Problem: drug resistant strains arise
XDR TB (extremely drug resistant TB)

Random DNA mutation selects for strains resistant to
antibiotics
Genetic Transfer
Vertical gene transfer:
Occurs during
reproduction between
generations of cells.
Horizontal gene
transfer: The transfer of
genes between cells of
the same generation.
ANIMATION Horizontal Gene Transfer: Overview

Transformation
Some genera can take up

free DNA from the
environment. DNA may
or may not recombine
with host DNA. Plasmid
DNA may be transferred
this way and remain intact
Figure 8.25
Genetic transfer and recombination, cont.

Plasmids
Small DS circles of DNA in the cytoplasm.
Are about 1-5% the size of the chromosome.
Replicate autonomously.
Are not essential for cell survival.
May integrate into (recombine with)
chromosome of host cell.
Cell may be cured of plasmid.
Plasmid may be transferred to another cell by
transformation or conjugation.
Rare in eukaryotes
Genetic transfer and recombination

Types of plasmids:
dissimilation plasmids Code for enzymes
that degrade unusual compounds.
virulence determinants Code for virulence
determinants, e.g., exotoxins.
F factors Carry genes for sex pili and for
transfer of plasmid to another cell.
Resistance factors (R factors) Code for
proteins to make cell resistant to antibiotics.
Plasmids and MRSA

Staphylococcus aureus G+ cocci
Found on surface of skin, nasal passages, etc
Food infections
Ear infections
Skin infections (boils, pimples, etc)
Surgical/medical procedure infections
Pneumonia
Toxic shock syndrome (systemic infection and shock)
Highly resistant to antibiotics
Methicillin resistant S aureus (MRSA)
A number of R plasmids and transposable elements
Genetic transfer and recombination, cont.

Conjugation
Requires cell-to-cell contact.
Requires a sex pilus.
Conjugating cells are of opposite mating
types.
Donor carries a functional F factor (F+)
A gene cluster allowing conjugation.
Conjugation may be incomplete
F factor may integrate into host genome
Referred to as Hfr cells.
Bacterial Conjugation
Gram negative
Gram positive
Figure 8.26
Conjugation in E. coli
The F factor gene cluster transfers last.

Transfer must go to completion for target cell to become F+
Figure 8.27a
Figure 8.27b
ANIMATION F Factor
ANIMATION Chromosome Mapping
ANIMATION Conjugation: Overview

ANIMATION Hfr Conjugation
Figure 8.27c
Transduction and E. coli

E. coli is found naturally in the
human large intestine, and
there it is beneficial. However,
the strain designated E. coli
O157:H7 produces Shiga
toxin.
E coli acquires the Shiga
toxin through specialized
bacteriophage transduction
Results of Multiplication of
Bacteriophages
Lytic cycle
Phage causes lysis and death of host cell
Lysogenic cycle
Prophage DNA incorporated in host DNA
Phage conversion
Specialized transduction
ANIMATION Viral Replication: Virulent Bacteriophages

ANIMATION Viral Replication: Temperate Bacteriophages
The Lysogenic Cycle
Figure 13.12
Genetic Evolution--Recombination
Exchange of
genes between
two DNA
molecules
Crossing over
occurs when two
chromosomes
break and rejoin
Figure 8.23
Genetic Evolution--Transposons
Segments of DNA that can move from one region of
DNA to another
Contain insertion sequences for cutting and resealing
DNA (transposase)
Complex transposons carry other genes
Figure 8.30a, b
Transposons
ANIMATION Transposons:
Overview
Insertion Sequences
Complex Transposons
Figure 8.30c
Evolution
Mutation and recombination = evolution
Increase in genetic diversity or change.
Allows for adaptation to new environments.
Causes partial or full duplication of genetic material
(genetic increase)
The Trouble with Microbial Evolution

Genetic change in microorganisms
contributes to:
Antibiotic resistance
Host tropism (change in host species)
Immune evasion (antigenic change)
Increased pathogenicity (ability to cause disease)

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Chapter 8

Copyright 2010 Pearson Education, Inc.

Lectures prepared by Christine L. Case

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Genetic Map of the Chromosome of E.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

Replication of Bacterial DNA

Copyright 2010 Pearson Education, Inc.

Rolling Circle Replication

Copyright 2010 Pearson Education, Inc.

Enzymes Involved in DNA Synthesis

DNA Polymerase in E coli

DNA Polymerase III

The Process of Transcription

Copyright 2010 Pearson Education, Inc.

The Process of Transcription

ANIMATION Transcription: Overview

Copyright 2010 Pearson Education, Inc.

RNA Processing in Eukaryotes

Inhibitors of Nucleic Acid Synthesis

Copyright 2010 Pearson Education, Inc.

The Genetic Code

Simultaneous Transcription &

Copyright 2010 Pearson Education, Inc.

The Process of Translation

The Process of Translation

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The Process of Translation

Copyright 2010 Pearson Education, Inc.

The Process of Translation

Copyright 2010 Pearson Education, Inc.

The Process of Translation

Copyright 2010 Pearson Education, Inc.

The Process of Translation

Copyright 2010 Pearson Education, Inc.

The Process of Translation

Copyright 2010 Pearson Education, Inc.

The Process of Translation

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Regulation of Gene Expression

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ANIMATION Operons: Overview

Regulation of Gene Expression

Copyright 2010 Pearson Education, Inc.

Regulation of Gene Expression

tryp=Tryptophan is an amino acid.

ANIMATION Operons: Induction

The lac operon

Copyright 2010 Pearson Education, Inc.

The lac operon

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Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

(a) Growth on glucose or lactose alone

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(b) Growth on glucose and lactose

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.

A change in the genetic material

Copyright 2010 Pearson Education, Inc.

Copyright 2010 Pearson Education, Inc.