Viruses

 Small infectious particle that consists of nucleic

acid enclosed in a protein coat called a capsid
 Host range
 Number of species and cell types that can be infected

 Structural
 Viral capsids vary in shape and complexcity
 Some have viral envelope derived from the host cell’s
plasma membrane
 Genome
*DNA vs. RNA, single stranded (ss) vs. double
stranded (ds), linear vs. circular.
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Brain and CNS:

Flavivirus—yellow fever
Rhabdovirus—rabies

Skin:
Herpes simplex I—cold sores
Variola virus—smallpox

Respiratory tract:
Influenza virus—flu
Rhinovirus—common cold

Immune system:
Rubella virus—measles
Human immunodeficiency virus—AIDS
Epstein-Barr virus—mononucleosis

Digestive system:
Hepatitis B virus—viral hepatitis
Rotavirus—viral gastroenteritis
Norwalk virus—viral gastroenteritis

Reproductive system:
Herpes simplex II—genital herpes
Papillomavirus—warts, cervical cancer

Blood:
Ebola virus—hemorrhagic fever
Hantavirus—hemorrhagic fever
with renal syndrome

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Over 4,000 different types of viruses
Helical
capsid

45 nm

Protein Nucleic
(a) Tobacco mosaic virus, a nonenveloped virus with a subunit acid (RNA)
helical capsid (capsomer)

Polyhedral capsid

Capsomer

Nucleic acid (DNA)

25 nm
Protein fiber
with a knob
(b) Adenovirus, a nonenveloped virus with a
polyhedral capsid and protein fibers with a knob

Polyhedral
capsid

Viral envelope

Nucleic acid (RNA)

Spike glycoproteins
100 nm

(c) Influenza virus, an enveloped virus with spikes

90 nm
Head
(polyhedral capsid)
Nucleic acid (DNA)
inside capsid
head
Shaft
Tail fiber
Base plate

(d) T4, a bacteriophage

a: © Robley C. Williams/Biological Photo Service; b: Reprinted from R.C. Valentine and H.G. Pereira, “Antigens and structure of the
adenovirus,” Journal of Molecular Biology, 13(2):71–83, © 1965, with permission from Elsevier; c: © Chris Bjornberg/Photo Researchers, Inc.;
3
d: © Omikron/Photo Researchers, Inc.
Reproduction
 Viruses are not alive
 Not cells or composed of cells
 Cannot carry out metabolism on their own
 Viral reproductive cycle can be quite different
among types of viruses
A virus may have alternative cycles.

4
Viral Reproductive Cycle

1. Attachment
2. Entry
3. (integration)
4. Synthesis of viral components
5. Viral assembly
6. Release

5
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Bacterial chromosome

4a New phages can 1 Phage injects its

bind to bacterial DNA into
cells. cytoplasm.

LYTIC
CYCLE

3a Cell lyses and 2a Phage DNA directs

releases the new the synthesis of
phages. many new phages.

6
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Prophage
Integrase

Phage DNA Bacterial

chromosome
Phage DNA Phage DNA
integration excision

E.coli cell

Integration:
1 Attachment: 2 Entry: 3
Phage DNA may integrate into the
The phage binds specifically to The phage injects its DNA into the
bacterial chromosome via integrase.
proteins in the outer bacterial cell bacterial cytoplasm.
The host cell carrying a prophage
membrane. may then undergo repeated divisions,
which is called the lysogenic cycle.
To end the lysogenic cycle and
switch to the lytic cycle, the phage
DNA is excised. Alternatively, the
reproductive cycle may completely
skip the lysogenic cycle and proceed
directly to step 4.

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5 Viral assembly: 6 Release:

4 Synthesis of viral components: Phage components are assembled The viral enzyme called lysozyme
In the lytic cycle, phage DNA with the help of noncapsid proteins causes cell lysis, and new phages
directs the synthesis of viral to make many new phages. are released from the broken cell.
components. During this process,
the phage DNA circularizes, and the
host chromosomal DNA is degraded.

8
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Reverse Viral envelope Spike
transcriptase glycoprotein Helper T cell

Reverse Cytosol
transcriptase
Two copies of viral RNA

Receptors

Viral RNA- DNA

RNA DNA

Integrase
Provirus

Attachment:
1 Spike glycoproteins bind to
receptors on the host cell
plasma membrane.
2 Entry:
The viral envelope fuses with the host
cell membrane, releasing the capsid
and its contents into the cytosol. Integration:
3
Some capsid proteins are removed Viral RNA is reverse transcribed
by cellular enzymes, a process called into double-stranded DNA and
uncoating. This releases the RNA and then integrated into the host cell
reverse transcriptase into the cytosol. chromosome, via integrase. The
integrated provirus may remain
latent for a long period of time.

Integrase cuts host chromosomal DNA and inserts viral genome.

Integrates as a provirus
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Spike
Capsid proteins glycoproteins

Reverse
transcriptase
Viral RNA

Viral assembly:
5
Capsid proteins enclose 2 RNA
molecules and 2 molecules of 6 Release:
4 Synthesis of viral components:
reverse transcriptase. Capsid Virus buds from the plasma
Proviral DNA directs the synthesis
assembles with spike glycoproteins membrane of the host cell and is
of viral components.
during budding. released. The new viral envelope
is derived from a portion of the
host cell plasma membrane.

10
4. Synthesis of viral components
 Hostcell enzymes such as DNA polymerase make
many copies of the phage DNA and transcribe the
genes within these copies into mRNA

 In the case of HIV, the DNA provirus is not excised

from the host chromosome.
* Translated to make viral proteins
* Serve as genome for new viral particles

11
5. Viral assembly

 Some viruses self-assemble

 Other are too complicated to self-assemble
 Proteins modify capsid proteins or serve as
scaffolding

6. Release
 Phages must lyse their host cell to escape
 Enveloped viruses bud from the host cell 12
Latency in bacteriophage
 Lysogeny / latency in bacteriophages
 When host cell replicates, also copies prophage
 Lysogenic cycle – integration, replication, and
excision
 Lytic cycle – synthesis, assembly, and release
 Temperate phages have a lysogenic cycle,
but virulent phages do not
 Environmental conditions influence integration
and length of latency.

13
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Bacterial chromosome

4a New phages can 1 Phage injects its

bind to bacterial DNA into
cells. cytoplasm. Phage DNA

LYTIC
CYCLE

3a Cell lyses and 2a Phage DNA directs

releases the new the synthesis of
phages. many new phages.

14
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Bacterial chromosome

4b On rare occasions,
a prophage may
be excised from
host chromosome.
4a New phages can 1 Phage injects its
bind to bacterial DNA into
cells. cytoplasm. Phage DNA

LYTIC LYSOGENIC
CYCLE CYCLE

2b Phage DNA 3b Prophage DNA

3a Cell lyses and 2a Phage DNA directs
integrates into is copied when
releases the new the synthesis of
host chromosome. cell divides.
phages. many new phages. or Prophage

15
Latency in human viruses
 Two different mechanisms
1. Virus integrates into host genome and may
remain dormant for long periods of time
 ex: HIV

2. Other viruses can exist as episomes – genetic

elements that replicate independently but
occasionally integrate into host DNA
 ex: Herpes simplex type I and II, varicella zoster
(chicken pox)

16
Origin of viruses
 Many biologists argue that cells evolved
first, before viruses
 Viruses evolved from macromolecules inside living
cells (maybe plasmids)

 Others argue for regressive evolution

 Another theory is that viruses did not evolve
from cells but evolved in parallel with
cellular organisms

17
 Viroids and Prions

Viroids
 Composed solely of a single-stranded circular RNA
molecule a few hundred nucleotides in length

 Infect plant cells

 Some replicate in host cell nucleus, others in chloroplast

 RNA genome does not code for proteins

 Disease mechanism not well understood

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Prions
 Composed entirely of protein
 Disease causing conformation PrPSc
 Normal conformation PrPC
 Normal protein expressed at low levels on surface
of neurons
 Prion converts normal proteins to abnormal form
 Several types of neurodegenerative diseases of
human and livestock
* Group of diseases called transmissible
spongiform encephalopathies (TSE)
19
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PrPSc

1 A prion protein in the

PrPSc conformation enters PrPC
the cell and binds to a
normal protein in the PrPC
conformation.
PrPSc
Original converted
PrPSc from PrPC
molecule

2 The prion protein in

the PrPSc conformation
converts a PrPC protein
into a PrPSc protein.

3 The 2 PrPSc proteins

bind to 2 PrPC proteins
(these will be
converted to PrPSc).

4 Over time, many PrPC

proteins will be converted
to PrPSc proteins, and fibrils
will form.

Fibril

40 nm

20
© Eye of Science/Photo Researchers, Inc.
 Genetic Properties of Bacteria

 Genes of bacteria are found in bacterial chromosomes

 Usually a single type of chromosomes

 May have more than one copy of that chromosomes

 Number of copies depends on the bacterial species and

on growth conditions

 Typically 1-4 identical chromosomes

 Nucleoid – region where tightly packed bacterial

21
Bacterial Chromosomes
 Molecules of double-stranded DNA
 -
 Tend to be shorter
 -
 Mostly structural genes
 -

22
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Origin of
replication

Key features

• Most, but not all, bacterial • Several thousand different

species contain circular genes are interspersed
chromosomal DNA. throughout the chromosome.
• A typical chromosome is a • One origin of replication is
few million base pairs in required to initiate DNA
length. replication.
• Most bacterial species
contain a single type of
chromosome, but it may be
present in multiple copies.
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Plasmids
 Small, circular pieces of DNA that exist
independently of the bacterial chromosome

 Occur naturally in many strains of bacteria and in

a few types of eukaryotic cells, such as yeast

 Own origin of replication that allows it to be replicated

independently of the bacterial chromosome

 Not usually necessary for survival but can provide

growth advantages

 Episome – plasmid that can integrate into bacterial

chromosome 24
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Bacterial
chromosome

Plasmids
80 nm

(right): © Stanley Cohen/Photo Researchers, Inc.

25
Five types of plasmids
1. Resistance plasmids (R factors)
 Confer resistance against antibiotics and other types of toxins

2. Degradative plasmids
 Enable the bacterium to digest and utilize an unusual substance

3. Col-plasmids
 Encode colicines, which are proteins that kill other bacteria

4. Virulence plasmids
 Turn a bacterium into a pathogenic strain

5. Fertility plasmids (F factors)

 Allow bacteria to mate
26
Reproduction
 Some species like E. coli can divide every 20-30 minutes

 Single cell can form a bacterial colony in less than a

day

 Reproduce by binary fission – NOT mitosis

 Unless a mutation occurs, each daughter cell contains

an identical copy of the mother cell’s genetic material

 Does not involve genetic contributions from two different

parents

 Palsmids may replicate independently of the bacterial

chromosome 27
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Mother cell
Plasma membrane Cell wall

1 Bacterial chromosome
replicates and cell
Chromosome
enlarges.

2 Cell begins to divide.

3 A cell wall is formed

between the 2 cells.

4 Cell division is
completed.

28
Two daughter cells
 Gene Transfer Between Bacteria

Genetic diversity in bacteria – from mutations or genetic

transfer
1. -conjugation
 Direct physical interaction transfers genetic material
from donor to recipient cell (involves 2 bacteria cells)
2. transformation
 DNA released from a dead bacterium into the environment
is taken up by another bacteria (involves 1 bacteria cell and
naked DNA)
3. transduction
 A virus transfers genetic information from one bacterium
to another (involves 1 bacteria cell and bacteria phase) 29
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Conjugation: Transformation: Transduction:

Donor cell Recipient cell Donor cell Recipient cell Donor cell Recipient cell
(dead) (infected by
a virus)

30
Conjugation

 Only about 5% of E. coli strains found in nature

can act as donor strains
 Donor strains contain a fertility factor (F factor)
that can be transferred to recipient strains
* Some donor strains are Hfr (for High frequency
of recombination)

31
F factors
 Carry several genes that required for conjugation
and also may carry genes that confer growth advantage

 F+ has an F factor, F- does not

 Sex pili are made by F+ cells that bind specifically

to F- cells
* Once contact is made, pill shorten to draw cells closer
together
* One strand of F factor is transferred, other strand
stays in donor
* Both replicate so that donor and recipient now have
complete double stranded F factor
32
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Donor cell Recipient cell

Bacterial
chromosome
F factor

Origin of Sex pilus

transfer

F+
F–
1 The sex pilus shortens and
draws cells closer together.
A conjugation bridge is formed
that provides a passageway
between the two cells. One strand
of the F factor DNA is cut by an
enzyme at the origin of transfer
and begins separating from the
other strand.

Conjugation
bridge

2 Proteins of the donor cell

transfer the separated
DNA strand to the
recipient cell.

3 In the donor cell, the

remaining F factor DNA
strand is used as a
template to synthesize a
complementary strand.

In the recipient cell, an

enzyme joins the ends
of the transferred
DNA strand, and the F+ F+
complementary strand
is made. Each cell now
has a double-stranded
circular F factor.

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Transformation
 Does not require direct contact between bacterial cells

 Living bacterial cell imports a strand of DNA that

another bacterium released into the environment when
it died

 Only competent cells with competence factors are

capable of transformation

 Competence factors facilitate binding of DNA

fragments to the bacterial cell structure, uptake of DNA
into the cytoplasm, and incorporation of important DNA
into the bacterial chromosome.
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Cell surface
receptor
1 tetR
A DNA fragment
containing the tetR gene
binds to a cell surface
receptor.

2 Bacterial enzymes cut tetR

the DNA into smaller
fragments.

3 One strand is degraded, DNA

and a single strand is uptake
imported into the cell by system
a DNA uptake system.

tetR

4 The imported DNA is

incorporated into the
bacterial chromosome,
and the complementary
strand is made. tetR

Transformed cell that is resistant

35
to the antibiotic tetracycline
Transduction

 Viruses that infect bacteria can transfer

bacterial genes from one bacterium to another
 Usually an error in a phase lytic cycle
 Newly assembled (putting the capsules
together) phages incorporate piece of host
DNA instead.

36
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Phage DNA Bacterial

1 Phage P1 infects chromosome
a bacterial cell,
which is his+.

his+
Donor
cell
2 The host DNA is (his+)
hydrolyzed into pieces.

his+

3 New phages are made.

Occasionally a phage
carries a piece of the
host cell chromosome,
such as the his+ gene.

4 The transducing
Transducing
phage injects its DNA his+
phage with
into a new recipient
host DNA
cell, which is his–.
Crossing over his+

5 The transduced DNA

is recombined into the Recipient cell
chromosome of the (his–)
recipient cell, thereby
introducing the Recombinant
his+ gene into the bacterium
chromosome.

his+

The recombinant bacterium has a genotype (his+) that 37

is different from the original recipient bacterial cell (his–).
 Horizontal Gene Transfer Is the Transfer
of Genes Between Different Species

 Vertical gene transfer is when genes are passed

from one generation to the next among individuals
of the same species
 Roughly 17% of genes in E. coli and Salmonella
typhimurium have been acquired by horizontal
transfer during the past 100 million years
 Medical relevance of horizontal gene transfer is
profound – ex: acquired antibiotic resistance
 Structurally, a typical bacterium
usually consists of
 a cytoplasmic mebrane
 Surrounded by a peptidoglycan cell wall
 May have an outer membrane
 a fluid cytoplasm containing
 Nuclear region (nucleoid)
 Ribosomes
 External structures such as pili, glucolyx and
flagella
The Bacterial Cell Wall

 Protection from osmotic lysis

 Provides shape to the bacteria
 In direct contact with the environment
 Pathogenesis
 Cell walls contain peptiglycan cross-linked by
polypeptides.
 Ribosomes, Inclusions and
Endospores
 Ribosomes
 Consist of RNA plus protein

 Sites of protein synthesis

 Inclusions
aggregates of various compounds that are normally
involved in storing energy reserves or building
blocks for the cell.
 Endospores are resistant to
* high temperatures (including boiling)
* most disinfectants, low energy radiation, drying
* the endospores can survive thousands of years until some environmental
stimulus triggers germination .
 Bacterial Flagella
 Usually found on bacilli and some spirals
 Composed of flagellin
 Glycocalyx
 Functions include
– Attachment to surfaces
– Protection from dessication
Table 27.1
The Role of Oxygen in Metabolism
 Prokaryotic metabolism varies with respect to O2
Obligate aerobes require O2 for cellular respiaration
Obligate anaerobes are poisoned by O2 and use fermentation or anaerobic
respiration
Facultative anaerobics can survive woth ot without O2
Metabolic Cooperation
 Cooperation between prokaryotes allows them to use
environmental resources they could not use as
individual cells
 In the cyanobacterium Anabaena, photosynthetic
cells and nitrogen-fixing cells called heterocysts (or
heterocytes) exchange metabolic products
 In some prokaryotic species, metabolic cooperation
occurs in surface-coating colonies called biofilms
 Relevance of Bacteria
-Compost and composting
True bacteria and disease
-Modes of access of disease bacteria
*air, contamination of food, direct contact, fomites,
wounds,bites from insects and other organisms
-Bioremediation
- Research into chemistry of vision
-Dairy industry
-Digestive system aids (Lactobacillus acidophilus)
-Production of metabolic wastes with industrial use
-Food production