Molecular Microbiology

Molecular Information
Flow and Protein
Processing
 DNA and Genetic Information Flow
• Functional unit of genetic information is the gene.
• Genes are part of genetic elements: large molecules
and/or chromosomes.
• Nucleic acids: contain genetic information via
nucleotides (monomers of nucleic acids)
• DNA (genetic blueprint) and RNA (transcription product)
are polynucleotides.
• Informational macromolecules include nucleic acids and
proteins.
 DNA and Genetic Information Flow

• Properties of the double helix

• Backbone of DNA chain is alternating phosphates and
the pentose sugar deoxyribose.
• Phosphodiester bonds connect 3ʹ-carbon of one sugar
to 5ʹ-carbon of the adjacent sugar.
• Primary structure: sequence of nucleotides that
encodes genetic information
 DNA and Genetic Information Flow

• Size, shape, and supercoiling

• Size is expressed in base pairs.
• 1000 base pairs = 1 kilobase pair = 1 kbp
• one million base pairs = 1 megabase pair = 1Mbp
• E. coli genome = 4.64 Mbp
• Linear DNA length is several hundred times longer than
cell, so supercoiling compacts DNA to accommodate
genome.
 DNA and Genetic Information Flow

• Size, shape, and supercoiling

• Topoisomerases insert and remove supercoils.
• negative supercoiling: twisted in opposite sense relative
to right-handed double helix; found in most cells
• DNA gyrase: introduces supercoils into DNA via double-
strand breaks
• positive supercoiling: helps prevent DNA melting at high
temperatures
 DNA and Genetic Information Flow
• Central dogma: Genetic information flow can be divided
into three stages, DNA to RNA to protein.
• Replication: DNA is duplicated by DNA polymerase.
• Transcription: Information from DNA is transferred to RNA by
RNA polymerase.
• mRNA (messenger RNA): encodes polypeptides
• Translation: Information in RNA is used to build polypeptides.
• tRNA (transfer RNA): convert mRNA to amino acid sequence of
protein
• rRNA (ribosomal RNA): catalytic and structural ribosome
components
 DNA and Genetic Information Flow
• Eukaryotes
• Each gene is transcribed individually into a single mRNA.
• Replication and transcription occur in nucleus.
• RNAs must be exported outside nucleus for translation.
• Prokaryotes
• Multiple genes may be transcribed in one mRNA.
• Coupled transcription and translation occur, producing proteins
at maximal rate.
• Some viruses violate central dogma.
Genetic Elements:
Chromosomes and
Plasmids
 Genetic Elements: Chromosomes and
Plasmids

• Chromosome: main genetic element in prokaryotes

• Other genetic elements include virus genomes,
plasmids, organellar genomes, and transposable
elements.
• Most Bacteria and Archaea have single circular
chromosome carrying all/most genes.
• Eukaryotes: two or more linear chromosomes
 Genetic Elements: Chromosomes and
Plasmids
• Viruses contain either RNA or DNA genomes.
• can be linear or circular
• can be single- or double-stranded
• Plasmids: double-stranded DNA that replicate
separately from chromosome
• usually circular
• generally beneficial for the cell (e.g., antibiotic resistance)
• NOT extracellular, unlike viruses
 Genetic Elements: Chromosomes and
Plasmids

• Transposable elements
• segments of DNA that can move from one site to
another site on the same or a different DNA molecule
• inserted into other DNA molecules (e.g., chromosomes,
plasmids, viral genomes)
 Genetic Elements: Chromosomes and
Plasmids
• Chromosomal gene arrangements and the operon
• Some features of the Escherichia coli K-12 chromosome
• about five Mbp in size
• Almost 4300 possible protein-encoding genes make up 88
percent of the genome.
• compact relative to eukaryotes
• Many genes encoding enzymes of a single biochemical
pathway are clustered into operons, transcribed to form
single mRNA and regulated as a unit.
 Genetic Elements: Chromosomes and
Plasmids
• Plasmids
• found in many Bacteria and Archaea
• genetic information encoded on plasmids not essential for
cell function under all conditions
• may confer a selective growth advantage under certain
conditions
• range in size from one kbp to more than one Mbp; typically
less than five percent of the size of the chromosome (Figure
4.9)
• Some cells contain multiple plasmids.
• abundance (copy number) variable (one or a few to 100+
copies)
 Genetic Elements: Chromosomes and
Plasmids

• R plasmids
• resistance plasmids; confer resistance to antibiotics or
other growth inhibitors (Figure 4.10)
• widespread and well-studied group of plasmids
• Several antibiotic resistance genes can be on one
R plasmid (e.g., R100).
 Genetic Elements: Chromosomes and
Plasmids
• In several pathogenic bacteria, virulence factors (e.g.,
ability to attach or produce toxins) are encoded by
plasmid genes.
• Bacteriocins can be encoded on plasmids.
• proteins that inhibit or kill closely related species or different
strains of the same species
• Rhizobia require plasmid-encode functions to fix
nitrogen.
• Metabolism (e.g., hydrocarbon degradation)
• Important for conjugation (horizontal gene transfer)
 Copying the Genetic
Blueprint: DNA Replication
 Copying the Genetic Blueprint: DNA
Replication
• Templates, Enzymes, and the Replication Fork
• Bidirectional Replication, the Replisome, and
Proofreading
 Templates, Enzymes, and the Replication
Fork
• DNA replication is semiconservative.
• Each of the two resulting double helices has one parental
(template) strand and one new strand.
DNA Replication: Synthesis
 Templates, Enzymes, and the Replication
Fork
• DNA polymerases catalyze polymerization of
deoxynucleotides.
• Five different DNA polymerases (DNA Pol I-V) in E. coli
• DNA Pol III is primary enzyme replicating chromosomal DNA
(DNA Pol I), which plays lesser role.
• Others repair damage.
• DNA polymerases require a primer: a short stretch of
RNA.
• Primer made from RNA by primase.
 Templates, Enzymes, and the Replication
Fork
• Connecting DNA fragments on the lagging strand
• DNA synthesis on lagging strand continues until it reaches
previously synthesized DNA.
• DNA polymerase I removes the RNA primer and replaces it
with DNA.
• DNA ligase seals nicks in the DNA.
Bidirectional Replication, the Replisome,
and Proofreading

• DNA synthesis is bidirectional in prokaryotes

because of circular chromosome.
• two replication forks moving in opposite directions
• DNA Pol III adds 1000 nucleotides per second.
Bidirectional Replication, the Replisome,
and Proofreading
• Replisome: complex of multiple proteins involved in
replication
• DNA replication is extremely accurate.
• Proofreading helps to ensure high fidelity.
• Mutation (changes in DNA sequence) rates in cells are 10–8 to
10–11 errors per base inserted.
• DNA Pol I and Pol III can detect mismatch through
incorrect hydrogen bonding and remove with 3'→5'
exonuclease.
• Proofreading occurs in prokaryotes, eukaryotes, and
viral DNA replication systems.
RNA Synthesis:
Transcription
 RNA Synthesis: Transcription

• Transcription in Bacteria
• Transcription in Archaea and Eukarya
 Transcription in Bacteria

• Transcription (DNA to RNA) is carried out by RNA

polymerase.
• RNA polymerase uses DNA as template.
• RNA precursors are ATP, GTP, CTP, and UTP.
• chain growth 5ʹ to 3ʹ, just as in DNA replication
• only one strand transcribed
• no priming needed
 Transcription in Bacteria

• RNA polymerases and the promoter sequence

• RNA polymerase has five different subunits.
• Sigma factor of RNA polymerase recognizes initiation sites on
DNA called promoters
 Transcription in Bacteria
• Transcriptional units: DNA segments transcribed into 1
RNA molecule bounded by initiation and termination
sites
• Most genes encode proteins, but some RNAs are not
translated (e.g., rRNA, tRNA).
• three types of rRNA: 16S, 23S, and 5S + tRNA
Figure 4.22
 Transcription in Bacteria
• Termination of RNA synthesis governed by specific DNA
sequences
• example: GC-rich sequence with inverted repeat and central
nonrepeating segment
• Rho-dependent termination: Rho protein recognizes specific
DNA sequences and causes a pause in the RNA polymerase,
releasing RNA and RNA polymerase.
Figure 4.24
Protein Synthesis:
Translation
 Protein Synthesis: Translation

• Amino Acids, Polypeptides, and Proteins

• Transfer RNA
• Translation and the Genetic Code
• The Mechanism of Protein Synthesis
 Protein Synthesis: Translation
• Proteins play a major role in cell function
• catalytic proteins (i.e., enzymes)
• structural proteins (e.g., membranes, walls, ribosomes)
• regulatory proteins
• Proteins are polymers of amino acids.
• Amino acids are linked by peptide bonds to form a
polypeptide.
• Proteins are one or more polypeptide(s).
 Transfer RNA
• General structure of RNA
• carries amino acids to translation machinery
• anticodon: three bases on tRNA that recognize codon: three
nucleic acids encoding its cognate (correct)
amino acid
• tRNA and amino acid brought together by aminoacyl-tRNA
synthetases
 Translation and the Genetic Code
• Genetic code: A triplet of nucleic acid bases (codon)
encodes a single amino acid.
• 64 possible codons
• specific codons for starting and stopping translation
• Degenerate code: Multiple codons encode a single amino acid
(64 codons compared with 22 natural amino acids).
 Translation and the Genetic Code
• Start codon: Translation begins with AUG, encodes N-
formylmethionine in Bacteria and methionine in Archaea and
Eukarya.
• Reading frame: Triplet code requires translation to begin at the
correct nucleotide.
• Shine–Dalgarno sequence, or the ribosome-binding site, (RSS)
ensures proper reading frame.
• Stop codons: terminate translation (UAA, UAG, and UGA)
• Open reading frame (ORF): AUG followed by a number of codons
and a stop codon
 The Mechanism of Protein Synthesis
• Three major steps: initiation, elongation, termination
• Needs guanosine triphosphate (GTP) for energy
• Ribosomes: sites of protein synthesis
• thousands of ribosomes per cell
• composed of two subunits (30S and 50S in prokaryotes) to
form 70S ribosome
• combination of rRNA and protein
• E. coli has 52 distinct ribosomal proteins.
• Translation factors (proteins) also essential
 The Mechanism of Protein Synthesis
1. Initiation:
• two ribosomal subunits + formylmethionine tRNA + initiation
factors assemble with mRNA
• begins at an AUG start codon
2. Elongation:
• amino acids brought to the ribosome and added to the growing
polypeptide
• occurs in the A (acceptor) and P (peptide) sites of ribosome
 The Mechanism of Protein Synthesis
3. Termination: occurs when ribosome reaches a stop
codon
• release factors (RF): recognize stop codon and cleave
polypeptide from tRNA
• Ribosome subunits then dissociate.
• Subunits free to form new initiation complex and repeat
process.
 The Hashemite University
Department of Medical Laboratory Sciences
Medical Microbiology

An Introduction
to Viruses
By
Lo’ai Alanagreh, PhD

10/21/20 1
 Learning Goals

• You will know when and how viruses were

discovered.
• You will know that there are good and bad
viruses.
• You will be able to answer the question “are
viruses alive”?
• You will understand the defining features and
structure of viruses.
 We Live and Prosper in a Literal
Cloud of Viruses
• Viruses infect all living things.
• We regularly eat, touch and breathe billions
of virus particles.
• We carry viral genomes as part of our own
genetic material.
 How infected are we?

• HSV-1, HSV-2, VZV, EBV …..

• Once infected, it is for life
We Are Viral
Virus Discovery-Filterable Agents
Virus discovery
 What is A Virus?

An infectious, obligate intracellular parasite comprising

genetic material (DNA or RNA) surrounded by a
protein coat and/or an envelope derived from a host
cell membrane
Viruses Are Amazing
 Viral Structure
• Viruses bear no resemblance to cells
– Lack protein-synthesizing machinery
• Viruses contain only the parts needed to invade
and control a host cell
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Capsid

Covering Envelope (not

found in all viruses)
Virus
particle Nucleic acid molecule(s)
(DNA or RNA)
Central
core Matrix proteins
Enzymes (not found in all *
viruses)
 General Structure of Viruses
• Capsids Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

– All viruses have capsids

(protein coats that Capsid
enclose and protect their
nucleic acid) Nucleic
acid
– The capsid together with
the nucleic acid is the
nucleocapsid (a) Naked Nucleocapsid
Virus

– Some viruses have an Envelope

external covering called

an envelope; those Spike

lacking an envelope are

Capsi
naked d

– Each capsid is made of Nucleic

acid
identical protein subunits *
called capsomers (b) Enveloped Virus
 General Structure of Viruses
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

• Two structural Disc

s
capsid types: Capsomers
Nucleic
acid

– Helical -
continuous helix (a)
of capsomers
forming a
cylindrical
nucleocapsid (b)

– Icosahedral Nucleic
acid
Capsid begins
forming helix.

(c) *
 General Structure of Viruses
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

• Two structural (a) Capsomers

capsid types:
Facet

Capsomers

– Helical - Vertex

– Icosahedral - Nuclei
c
acid

20-sided with 12 (b)

corners
Capsomers

Vertex
Fiber

(c)

*
(d) © Dr. Linda Stannard, UCT/Photo Researchers, Inc.
 General Structure of Viruses
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

• Viral envelope
– Mostly animal viruses Capsid

– Acquired when the Nucleocapsid

virus leaves the host

Nucleic
acid

cell
© Dennis Kunkel/CNRI/Phototake

(a) (b)

Hemagglutinin spike

– Exposed proteins on Neuraminidase spike

the outside of the Matrix protein

envelope, called Lipid bilayer

spikes, are essential

for attachment of the
virus to the host cell (c)
Nucleocapsid

50 nm

Spikes

Nucleocapsi
d

*
Dr. F. A. Murphy/CDC
(d)
 Functions of Capsid/Envelope
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• Protects the nucleic acid

when the virus is outside
of the host cell

• Helps the virus bind to a

cell surface and assists Capsomers
© Dr. Linda Stannard, UCT/Photo Researchers, Inc.

the penetration of the (a)

Fred P. Williams, Jr./EPA

viral DNA or RNA into a Envelope Capsid DNA core

suitable host cell

*
© Eye of Science/Photo Researchers, Inc.
(b)
 General Structure of Viruses
• Complex viruses: atypical viruses
– Poxviruses lack a typical capsid and are covered by a
dense layer of lipoproteins
– Some bacteriophages have a polyhedral nucleocapsid
along with a helical tail and attachment fibers
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

240–300 nm
Nucleic
Core Capsid acid
membrane head
200 nm Collar
Nucleic
acid Sheath
Outer
envelope
Soluble
protein Tail
Lateral
antigens fiber
(a) body s

Tail Base plate

pin
s
(c)

*
(b) © Bin Ni, Chisholm Lab, MIT
 Types of Viruses
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A. Complex Viruses B. Enveloped Viruses

Helical Icosahedral

(1) (3) (5)

(2) (4) (6)

C. Nonenveloped Naked Viruses A. Complex viruses:

(1) poxvirus, a large DNA virus
Helical Icosahedral (2) flexible-tailed bacteriophage

B. Enveloped viruses:
With a helical nucleocapsid:
(3) mumps virus
(4) rhabdovirus
With an icosahedral nucleocapsid:
(5) herpesvirus
(8)
(6) HIV (AIDS)

C. Naked viruses:
Helical capsid:
(7) plum poxvirus
Icosahedral capsid:
(8) poliovirus
*
(7) (9) (9) papillomavirus
 Nucleic Acids
• Viral genome – either DNA or RNA but never
both

• Carries genes necessary to invade host cell and

redirect cell’s activity to make new viruses

• Number of genes varies for each type of virus –

few to hundreds

*
 Nucleic Acids
• DNA viruses
– Usually double stranded (ds) but may be single
stranded (ss)
– Circular or linear
• RNA viruses
– Usually single stranded, may be double stranded, may
be segmented into separate RNA pieces
– ssRNA genomes ready for immediate translation are
positive-sense RNA
– ssRNA genomes that must be converted into proper
form are negative-sense RNA

*
 General Structure
• Pre-formed enzymes may be present
– Polymerases – DNA or RNA
– Replicases – copy RNA
– Reverse transcriptase – synthesis of DNA
from RNA (AIDS virus)

*
 How Viruses Are Classified
• Main criteria presently used are structure, chemical
composition, and genetic makeup

• Currently recognized: 3 orders, 63 families, and 263

genera of viruses

• Family name ends in -viridae, i.e.Herpesviridae

• Genus name ends in -virus, Simplexvirus

• Herpes simplex virus I (HSV-I)

*
Human Viruses & Viral Diseases

*
*
 Modes of Viral Multiplication
General phases in animal virus multiplication cycle:
1. Adsorption – binding of virus to specific molecules on
the host cell
2. Penetration – genome enters the host cell
3. Uncoating – the viral nucleic acid is released from the
capsid
4. Synthesis – viral components are produced
5. Assembly – new viral particles are constructed
6. Release – assembled viruses are released by
budding (exocytosis) or cell lysis

*
Animal Virus Multiplication
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Host Cell Cytoplasm

Receptors
Cell membrane
Spikes

1 Adsorption. The virus attaches to its

host cell by specific binding of its 1
spikes to cell receptors.

2 Penetration. The virus is engulfed

into a vesicle and its envelope is
3 Uncoated, thereby freeing the viral
RNA into the cell cytoplasm.
2
3

Nucleus

4 Synthesis: Replication and Protein Production.

RNA
Under the control of viral genes, the cell
synthesizes the basic components of new viruses:
RNA molecules, capsomers, spikes.

New
spikes

New
5 Assembly. Viral spike
capsomer
s proteins are inserted into the
5 cell membrane for the viral
New envelope; nucleocapsid is
RNA
formed from RNA and
capsomers.

6 Release. Enveloped viruses bud off

of the membrane, carrying away an 6
envelope with the spikes. This
complete virus or virion is ready to
infect another cell. *
 Adsorption and Host Range
• Virus coincidentally collides with a susceptible host cell and
adsorbs specifically to receptor sites on the membrane
• Spectrum of cells a virus can infect – host range
– Hepatitis B – human liver cells
– Poliovirus – primate intestinal and nerve cells
– Rabies – various cells of many mammals
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Envelope spike
Host cell membrane
Capsid spike

Receptor

Host cell
membrane

Receptor

*
(a) (b)
 Penetration/Uncoating
• Flexible cell membrane is penetrated by the
whole virus or its nucleic acid by:
– Endocytosis – entire virus is engulfed and
enclosed in a vacuole or vesicle
– Fusion – envelope merges directly with
membrane resulting in nucleocapsid’s
entry into cytoplasm

*
Variety in Penetration and Uncoating
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Host cell Free

membrane RNA
Receptors
Uncoating
of
nucleic acid
Receptor- Entry of
spike nucleocapsid
Irreversible Membrane complex
(a) attachment fusion

Uncoating
Host cell step
membrane

Free
Virus in Vesicle, envelope DNA
vesicle and
Specific Engulfmen capsid break down
(b) attachment t

Capsi
d

RNA

Nucleic
acid
Recepto *
r Engulfment into
Adhesion of virus to host Viral RNA is released from
(c)
receptors vesicle vesicle
Replication and Protein Production
• Varies depending on whether the virus is a
DNA or RNA virus
• DNA viruses generally are replicated and
assembled in the nucleus
• RNA viruses generally are replicated and
assembled in the cytoplasm
– Positive-sense RNA contain the message for
translation
– Negative-sense RNA must be converted into
positive-sense message
 Release
• Assembled viruses leave the host Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

cell in one of two ways:

– Budding – exocytosis;
nucleocapsid binds to membrane
which pinches off and sheds the
viruses gradually; cell is not
immediately destroyed
– Lysis – nonenveloped and
complex viruses released when
cell dies and ruptures (b) © Chris Bjornberg/Photo Researchers, Inc.

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Viral
Host cell nucleocapsid
membrane Viral glycoprotein
spikes
Cytoplasm

Capsid

RN
A

Budding Free infectious

virion virion with *
envelope
Viral matrix
(a) protein
 Damage to Host Cell
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Cytopathic effects - virus-

induced damage to cells
1. Changes in size and shape Normal
cell
Multiple
2. Cytoplasmic inclusion nuclei

bodies
3. Inclusion bodies
Giant
4. Cells fuse to form cell

multinucleated cells
5. Cell lysis (a)
CDC CDC

Inclusion
bodies
6. Alter DNA
7. Transform cells into
cancerous cells

*
© Massimo Battaglia, INeMM CNR, Rome Italy
(b)
Effects of Some Human Viruses

*
 Persistent Infections
• Persistent infections - cell harbors the virus and
is not immediately lysed
• Can last weeks or host’s lifetime; several can
periodically reactivate – chronic latent state
– Measles virus – may remain hidden in brain cells for
many years
– Herpes simplex virus – cold sores and genital herpes
– Herpes zoster virus – chickenpox and shingles

*
 Viral Damage
• Some animal viruses enter the host cell and
permanently alter its genetic material resulting in
cancer – transformation of the cell
• Transformed cells have an increased rate of
growth, alterations in chromosomes, and the
capacity to divide for indefinite time periods
resulting in tumors
• Mammalian viruses capable of initiating tumors
are called oncoviruses
– Papillomavirus – cervical cancer
– Epstein-Barr virus – Burkitt’s lymphoma
*
Multiplication Cycle in Bacteriophages
• Bacteriophages – bacterial viruses (phages)
• Most widely studied are those that infect
Escherichia coli – complex structure, DNA
• Multiplication goes through similar stages as
animal viruses
• Only the nucleic acid enters the cytoplasm -
uncoating is not necessary
• Release is a result of cell lysis induced by
viral enzymes and accumulation of viruses -
lytic cycle

*
 Steps in Phage Replication
1. Adsorption – binding of virus to specific
molecules on host cell
2. Penetration – genome enters host cell
3. Replication – viral components are produced
4. Assembly – viral components are assembled
5. Maturation – completion of viral formation
6. Lysis & Release – viruses leave the cell to
infect other cells

*
Multiplication of Bacteriophage
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

E. coli
7 Release of viruses
Bacteriophage host

Bacteria Viral
Lysogenic State l DNA
DNA
1 Adsorption

Viral DNA becomes 2 Penetration 6 Lysis of weakened cell

latent as prophage.

Lytic
Cycle

Spliced
DNA viral
splits genome
3 Duplication of phage 5 Maturation
components; replication of
virus genetic material
Viral Bacterial
DNA DNA molecule

Capsid
DNA
The lysogenic state in bacteria.
The viral DNA molecule is inserted at
specific sites on the bacterial
chromosome. The viral DNA is
+
duplicated along with the regular Tail Tail fibers
genome and can provide adaptive 4 Assembly of Sheath
genes for the host bacterium. new virions

Bacteriophage

Bacteriophage assembly line.

First the capsomers are synthesized by the host
cell. A strand of viral nucleic acid is inserted
during capsid formation. In final assembly, the *
prefabricated components fit together into whole
parts and finally into the finished viruses.
Comparison of Bacteriophage and Animal Virus
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Head

Bacterial
cell wall

Tube

Viral nucleic acid

Cytoplas
m
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

*
© K.G. Murti/Visuals Unlimited
Lysogeny: The Silent Virus Infection
• Not all phages complete the lytic cycle
• Some DNA phages, called temperate phages, undergo
adsorption and penetration but don’t replicate
• The viral genome inserts into bacterial genome and
becomes an inactive prophage – the cell is not lysed
• Prophage is retained and copied during normal cell
division resulting in the transfer of temperate phage
genome to all host cell progeny – lysogeny
• Induction can occur resulting in activation of lysogenic
prophage followed by viral replication and cell lysis
• Why is this property of some viruses so important and
what affect does it have on the spread of some diseases?
*
Lytic and Lysogenic Lifecycles
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

E. coli
7 Release of viruses
Bacteriophage host

Bacteria Viral
Lysogenic State l DNA
DNA
1 Adsorption

Viral DNA becomes 2 Penetration 6 Lysis of weakened cell

latent as prophage.

Lytic
Cycle

Spliced
DNA viral
splits genome
3 Duplication of phage 5 Maturation
components; replication of
virus genetic material
Viral Bacterial
DNA DNA molecule

Capsid
DNA
The lysogenic state in bacteria.
The viral DNA molecule is inserted at
specific sites on the bacterial
chromosome. The viral DNA is
+
duplicated along with the regular Tail Tail fibers
genome and can provide adaptive 4 Assembly of Sheath
genes for the host bacterium. new virions

Bacteriophage

Bacteriophage assembly line.

First the capsomers are synthesized by the host
cell. A strand of viral nucleic acid is inserted
during capsid formation. In final assembly, the *
prefabricated components fit together into whole
parts and finally into the finished viruses.
 Lysogeny
• Lysogeny results in the spread of the virus
without killing the host cell
• Phage genes in the bacterial chromosome can
cause the production of toxins or enzymes that
cause pathology – lysogenic conversion
– Corynebacterium diphtheriae
– Vibrio cholerae
– Clostridium botulinum

*
How do we grow viruses?
Obligate intracellular parasites
– what do they need to grow?

They require appropriate cells to

replicate.
 Techniques in Cultivating and
Identifying Animal Viruses
• Obligate intracellular parasites that require
appropriate cells to replicate
• Methods used:
– Cell (tissue) cultures – cultured cells grow in sheets that
support viral replication and permit observation for
cytopathic effects
– Bird embryos – incubating egg is an ideal system; virus
is injected through the shell
– Live animal inoculation – occasionally used when
necessary

*
Methods for Growing Viruses

Inoculation
of amniotic
Inoculation cavity
of embryo
Air sac
Inoculation of
chorioallantoic
membrane

Amnion

Shell Inoculation of
yolk sac
Allantoic
cavity

Albumin
*
(b)
Medical Importance of Viruses
• Viruses are the most common cause of acute
infections
• Several billion viral infections per year
• Some viruses have high mortality rates
• Possible connection of viruses to chronic
afflictions of unknown cause
• Viruses are major participants in the earth’s
ecosystem – How if viruses are not “alive” ?

*
 Detection and Treatment of
Animal Viral Infections
• More difficult than other agents
• Consider overall clinical picture
• Take appropriate sample
– Infect cell culture – look for characteristic
cytopathic effects
– Screen for parts of the virus
– Screen for immune response to virus (antibodies)
• Antiviral drugs can cause serious side effects

*
 Prions and Other Infectious Particles
Prions - misfolded proteins, contain no nucleic acid
– Extremely resistant to usual sterilization
techniques
– Cause transmissible spongiform
encephalopathies – fatal neurodegenerative
diseases

*
 Prions Diseases
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Common in animals:
• Scrapie in sheep
and goats Brain cell

• Bovine
Prion
spongiform fibrils

encephalopathies
(BSE), a.k.a. mad
cow disease
© James King-Holmes/Institute of Animal Health/Photo Researchers, Inc.

(a)

• Wasting disease in
elk
• Humans –
Creutzfeldt-Jakob
Syndrome (CJS)
*
Dr. Art Davis/CDC

(b)
Other Noncellular Infectious Agents
• Satellite viruses – dependent on other viruses
for replication
– Adeno-associated virus – replicates only in cells
infected with adenovirus
– Delta agent – naked strand of RNA expressed only
in the presence of hepatitis B virus

• Viroids – short pieces of RNA, no protein coat;

only been identified in plants

*
Viral genomes
The Hashemite University
Department of Medical Laboratory Sciences
Medical Virology
Fall 2020
Learning Goals

• You will know examples of human pathogens from each of

the seven genome types.

• You will have an overview of how mRNA is produced from

each genome.

• You will understand how infectious viruses are produced

from nucleic acids.
Classification

1. Taxonomic groups – family, subfamily, genus and species

2. The names of virus families (family) are italicized - End in Latin suffix –
viridae
3. The genera (genus) end in the suffix – virus
4. The species – English common name
Classification (Classical)

• Morphology
– Structure of capsid
– Presence or absence of envelope
• Type of host/host structures the virus infected
- Bacteriophages: infect bacterial cells
- Plant viruses: infect plant cells
- Animal viruses, are sub-grouped by the tissues they attack:
1. Dermotrophic: if they infect the skin
2. Neurotrophic: if they infect nerve tissue
Nomenclature of Viruses

Various approaches, (do not obey the binomial nomenclature) derived

from:
1. Named after the diseases
eg. Measles virus, smallpox virus
2. Named after the places where the disease first reported
eg. Newcastle disease virus, Ebola virus
3. Host and signs of disease
eg. Tobacco mosaic virus, Cauliflower mosaic virus
Nomenclature of Viruses

4. Latin and Greek words

eg. Coronaviridae – “crown”
Parvoviridae – “small”
5. Scientist who discover the virus
eg. Epstein-Barr virus
6. How they were originally thought to be contracted
eg. Dengue virus (“evil spirit”), influenza virus (the “influence” of bad air)
7. Combinations of the above
eg. Rous Sarcoma virus
The Baltimore classification system

• The division of the viruses into classes based on genome type and
mode of replication and transcription

• Suggested by David Baltimore – Seven Baltimore classes.

• Major groups of viruses are distinguished first by their nucleic acid

content as either DNA or RNA
The Baltimore classification system

According to the Baltimore classification, viruses are divided into the following seven
classes:
1. dsDNA viruses
2. ssDNA viruses
3. dsRNA viruses
4. (+) sense ssRNA viruses (codes directly for protein)
5. (-) sense ssRNA viruses
6. RNA reverse transcribing viruses
7. DNA reverse transcribing viruses

Where "ds" represents "double strand" and "ss" denotes "single strand".
RNA viruses

From Principles of Virology Flint et al ASM Press

DNA viruses

From Principles of
Virology Flint et al
ASM Press
Class I

• Double-stranded (ds) DNA viruses are in class 1

• The production of mRNA and genome replication in such viruses occurs
as it would from the host genome.
dsDNA Genomes
dsDNA Genomes
Gapped dsDNA Genome
Gapped dsDNA Genome
Class VII

• Double-stranded DNA genome that replicates with RNA intermediate.

• Required reverse transcriptase
• Mechanism producing mRNA is similar in virus Class I
Class II

• Single-stranded(ss) DNA viruses.

• These viruses form a double stranded DNA intermediate during
replication and this intermediate used for transcription.
• RNA polymerase requires double-stranded DNA as template.
ssDNA Genomes
Positive and Negative strand RNA viruses

• The production of mRNA and genome replication is much different with

RNA viruses (Class III-VI).
• mRNA is the complementary base sequence to the template strand of
DNA.
• In virology, mRNA is said to be plus(+) configuration.
• While its complement is said to be the minus (-) configuration.
RNA Genomes

Cells have no RNA-dependent RNA

polymerase (RdRp)
RNA virus genomes encode RdRp

RdRp produces RNA genomes and

mRNA from RNA templates
dsRNA Genomes
ssRNA: (+) Sense Genome
ssRNA: (+) Sense Genomes
Class VI

• Single-stranded RNA genome that replicates with DNA intermediate.

• This RNA virus require reverse transcriptase to copy the information
found in RNA to DNA.
ssRNA: (+) Sense Genomes with
DNA Intermediate
The Remarkable Retroviral
Genome Strategy
ssRNA: (-) Sense Genomes
ssRNA: (-) Sense Genomes
Reassortment-A Consequence of
a Segmented Genome
Ambisense RNA Genomes
Evolution of Viruses:
Orthomyxoviridae as a model
Lo’ai Alanagreh

Hashemite University
• One of the most important
Emerging and
Reemerging infectious
diseases
• Causes high morbidity and
mortality in communities
(epidemic) and worldwide
(pandemic)
• Epidemics are associated
with excess mortality
Orthomyxoviridae
Orthomyxoviridae
Orthomyxoviridae
Characteristics of Influenza Virus
• Types A, B, C, D
• Diameter 80 - 120 nm
• Enveloped
• 12-15k bp
• Single-stranded ssRNA (-)
• Segmented genome, 8 segments in A and B
Characteristics of Influenza Virus
• Influenza A virus infects
– Humans, mammals, birds
– (cause pandemics)
• Influenza virus B infects humans and seals (stable)
• Influenza virus C infects
– Less common
• Influenza D viruses
– primarily affect cattle
– not known to infect or cause illness in people
 Classification of Influenza virus
• Classified on the basis of
– Hemagglutinin (HA)
– Neuraminidase (NA)
• Influenza A and B have these spikes, but
Influenza C has only one type of glycoprotein
spike which is a hemagglutinin and binds to
different receptors
• 18 subtypes of HA and 11 subtypes of NA are
known to exist in animals nearly 188
combinations.
• Ex: H1N1
 Viral Glycoproteins

Form spikes or projections from envelope

consist of about 10-15 monosaccharide units

Viruses attach to surface

Hemagglutinins receptors and facilitates entry
through endocytosis

Helps in the release of viral

Neuraminidase particles from the cells in which
they were made.
 Influenza genome
• hh
 Antigenic Variation

There are two types:

1. antigenic shift.
2. antigenic drift.
These changes in the antigenic
characteristics of influenza viruses
determine the extent and severity of
influenza epidemics.
 Antigenic Drift

• This term denotes MINOR changes in HA and

NA of influenza virus.
• This results from mutation in the RNA
segments coding for either the HA or NA
• This involves no change in serotype; there is
merely an alteration in amino acid sequence of
HA or NA leading to change in antigenicity.
 Antigenic Drift

• Mutation and selection for the most

advantageous variation of the virus
• Due to the high mutation rate in viruses
• Mutations arise very easily simply due to the
error prone RNA polymerase and its lack of
proofreading mechanisms
 Antigenic Shift

• This term denotes MAJOR changes in HA and

NA resulting from reassortment of gene
segments involving two different influenza
viruses.
• When this occurs, worldwide epidemics may
be the consequence since the entire population
is susceptible to the virus.
H1N1 (Swine flu)
(a) The 1918 flu pandemic

0.5 µm

(b) Influenza A (c) Vaccinating ducks

H5N1 virus
 Vaccination

• Vaccines are harmless derivatives of pathogenic

microbes that stimulate the immune system to
mount defenses against the actual pathogen
• Vaccines can prevent certain viral illnesses
• Viral infections cannot be treated by antibiotics
• Antiviral drugs can help to treat, though not cure,
viral infections
Double stranded
DNA viruses
Part I

Lo’ai Alanagreh
The Hashemite University
Adenoviridae
Adenoviridae

• Nonenveloped virus,
icosahedral capsid

• Double-stranded DNA
with linear genome
Transmission

•Aerosols
•Fecal-oral
•Fomites
•Close contact
Adenoviridae

• 60 seortypes
• Divided into 7 groups A-G

• Binds to the epithelial cells in the

• Respiratory
• GI
• Urinary mucosa
• Coxsackie Adenovirus Receptor (CAR)
Mechanisms of pathogenesis
 Clincal manifestation

• Depends on the site of the

infection
• Upper respiratory tract
• Common cold
• Pharyngitis
• Tonsilitis
• Lower respiratory tract
• Pneumonia
 Clincal manifestation

• GI tract -> gastroentertitis

• Urinary tract ->
hemmorhagic cystitis
• Conjuctiva -> pink eye
Clincal manifestation
Clincal manifestation
Clincal manifestation
Diagnosis

•Serotypes: immunoassay
•PCR
Treatment

• supportive care, no antivirals

Herpesviridae
Herpesviridae

• Large, enveloped (nuclear membrane)

• Icosadeltahedral capsid, with linear, double-
stranded DNA genome
• Lytic-latent infections
Diseases caused by Herpesviridae
Viral sub-family

• HHV 1-3 Alpha

• Short reproductive cycle
• Latent in sensory neurons
• Painful skin disease

• HHV 5-7 Beta

• Long reproductive cycle
• Latent in WBC’s

• HHV 4 and 8 Gamma

• Latent in lymphocytes
• Associated with cancer
Herpes Simplex Viruses Type 1
and Type 2

• HSV-1 (oral herpes) – trigeminal ganglion

• HSV-2 (genital herpes) – sacral ganglion
• Neurotropic
Transmission

• Direct contact
• Oral to oral
• Oral to genital
• Genital to oral
Pathogenesis – Herpes Simplex
Viruses Type 1 and Type 2
Herpes Simplex Viruses Type 1
Herpes Simplex Viruses Type 2
Varicella-zoster Virus (VZV)

• Transmission:
• Aerosols
• Close contact with lesions
• Prevention:
• Live attenuated vaccine
• Beginning at 15 months
Pathogenesis – Varicella-zoster
Virus
Diseases Caused by VZV