Syllabus Outline till Christmas

Week Date /Time Event Reading

9 26/9 Lecture 1 Unit Introduction/History of Chapter 1
Microbiology
10 3/10 Lecture 2 Microscopes and Microbial Cell Chapter 1 and 2
Structure
All dates 11 10/10 Lecture 3 Cell structure and function Chapter 2

and times 12 14/10 Lecture 4 Microbial nutrition Chapter 3 (15

are 17/10 (9-10, 11-12,
further reading)
Online Lab
12 Laboratory introduction and training
subject to 2-3, 4-5)
24/10 (9-11, 12-2,
Manual
Lab Manual
13 Laboratory 1
change- 13
3-5, 6-8)
25/10 Lecture 5 Microbial Growth and Control Chapter 5
please
15 7/11 (9-11, 12-2, 3- Laboratory 2 Lab Manual
check your 5, 6-8)

portal! 16 14/11 (9-11, 12-2,

3-5, 6-8)
Laboratory 3 Lab Manual

18 28/11 (9-11, 12-2, LAB EXAM Lab Manual

3-5, 6-8)

20 9/12 Lecture 6 Viruses Chapter 8

Formative MCQ assessment online
Virology
3700BC, which depicts a temple priest
-typical clinical signs of paralytic
poliomyelitis.
Graph 1: Total suspected, probable, and confirmed cases of Ebola virus disease in
Guinea, Liberia, and Sierra Leone, March 25, 2014 – February 14, 2016, by date of
WHO Situation Report, n=28603
http://www.theguardian.com/world/2015/sep/30/ebola-inquest-un-united-nations-world-
health-organisation
 Viruses
• Contain DNA or RNA
• Contain a protein coat
• Some are enclosed by an envelope
• Some viruses have spikes
• Most viruses infect only specific tissue in one
host
• Alive or dead
Fig. 10-21

Nonenveloped Enveloped Nonenveloped Enveloped all ssRNA

partially
dsDNA
ssDNA
Parvovirus Hepadnavirus

Rhabdovirus
dsDNA ssRNA
Picornavirus Togavirus
Papovavirus dsDNA
Orthomyxovirus
dsDNA
Poxvirus
Adenovirus dsRNA Bunyavirus Coronavirus

Reovirus
dsDNA
dsDNA
Herpesvirus
Paramyxovirus
Iridovirus Arenavirus Retrovirus

DNA viruses RNA viruses

Mimivirus
800 nm and a 1.2 Mbp genome

"Bradfordcoccus"

weblogs.nieuwegarde.nl/mieke/index.php
 The Origin of Viruses
3 Major Theories

1) Regressive evolution - viruses are degenerate life-forms which

have lost many functions that other organisms possess & have
only retained the genetic information essential to their parasitic
way of life.

2) Cellular origins - viruses are sub-cellular, functional assemblies of

macromolecules which have escaped their origins inside cells.

3) Independent entities - viruses evolved on a parallel course to

cellular organisms from the self-replicating molecules believed to
have existed in the primitive prebiotic 'RNA world'.
Helical Viruses

Figure 13.4a–b
Polyhedral Viruses

https://science.sciencemag.org/content/362/6414/598

Figure 13.2a–b
Enveloped Viruses

Figure 13.3
Complex Viruses

Figure 13.5a
 Viral Taxonomy
• Family names end in -viridae.
• Genus names end in -virus.
• Viral species: A group of viruses sharing the same
genetic information and ecological niche (host).
Subspecies are designated by a number.

 Herpesviridae
 Herpesvirus
 Human herpes virus HHV-1,
HHV-2, HHV-3
Virus Taxonomy and Phylogeny
• Lack of information on origin and evolutionary
history makes viral classification difficult
• A uniform classification system developed in 1971
by the International Committee for Taxonomy of
Viruses (ICTV)
– most current report ~2,000 viruses, 6 orders,
87 families, 19 subfamilies, and 349 genera
Viral Class DNA viruses

Viral Genome ssDNA dsDNA

Viral Class RNA viruses

ssRNA dsRNA
Viral Genome

RNA DNA
Viral Class viruses

ssRNA dsDNA
Viral Genome (Retroviruses) (Hepadnaviruses)
Virus Classification
• Classification based on numerous characteristics
– nucleic acid type
– presence or absence of envelope
– capsid symmetry
– dimensions of virion and capsid
 Alternative Classification Scheme
• David Baltimore
– focuses on viral genome
and process used to
synthesize viral mRNA
– 7 life cycle groups based on
• double stranded (ds) DNA
• single stranded (ss) DNA
• dsRNA
• ssRNA (+ or – strand)
• retrovirus
Archaeal Viruses
• All known archaeal viruses have dsDNA genomes
(1 exception with ssDNA genome)
– linear or circular
• Unusual morphologies define new virus families
• Life cycles
– lytic and lysogenic viruses
– integrated or free in cytoplasm
Archaeal Viruses
Archaeal Viruses
• Sulfolobus turreted icosahedral
virus (STIV)
– Replicates using host cell
DNA replication,
transcription, translation
machinery
– Icosahedral capsid encasing
a lipid bilayer-enclosed
genome
– Viruses form pyramid-like
structures on the surface of
the host cell to effect release
 The Virosphere and Viral Ecology
• Most of Earth's genetic diversity resides in
viruses
– Most viruses are believed to be bacteriophages
• Viral metagenome: the sum total of all viral
genes in a particular environment
• Most viruses are undiscovered
• Most viral genes have unknown function
Growing Viruses
• Viruses must be grown in living cells.
– Bacteriophages form plaques on a lawn of
bacteria.
1. Pour mixture onto
solidified nutrient
agar plate

Nutrient agar plate

Mixture containing
molten top agar,
bacterial cells, and
diluted phage
suspension Plaques

Sandwich of top agar

and nutrient agar

2. Incubate

Phage
plaques
Lawn of host cells
Growing Viruses
• Animal viruses may
be grown in living
animals or in
embryonated eggs.
http://www.ifpma.org/Influenza/index.aspx?30
Growing Viruses

 Animal and plants viruses may be grown in cell culture.

 Continuous cell lines may be maintained indefinitely.

Figure 13.8
Viral Replication
 Multiplication of Bacteriophages (Lytic Cycle)
• Attachment: Phage attaches by tail fibers to host cell.
• Penetration: Phage lysozyme opens cell wall, tail sheath
contracts to force tail core and DNA into cell.
• Biosynthesis: Production of phage DNA and proteins.
• Maturation: Assembly of phage particles.
• Release: Phage lysozyme breaks cell wall.
1

Figure 13.11, steps 1–3, 6–7

4

Figure 13.11, steps 4–5, 8

One-Step Growth Curve
Eclipse Maturation

Nucleic

(plaque-forming units)
Early Protein

Relative virus count

enzymes acid coats

Virus
added Assembly
and
release
Latent period

Time
Fig. 10-10

Tail
fibers

Tail pins

Outer
membrane
Tail
Peptidoglycan lysozyme
Cytoplasmic
membrane
Cytoplasm
T4 genome
Fig. 10-15

Nucleases
DNA polymerase Phage DNA Phage Tail, collar, base Mature phage particle
New sigma factors head plate, and tail T4 lysozyme
proteins fiber proteins production
Infection Phage DNA replication

Early mRNA Middle mRNA Late mRNA Self assembly

Early proteins Middle proteins Late proteins

Lysis

0 5 10 15 20 25
Minutes
 The Hershey-Chase Experiment
• In 1952, Alfred Hershey and Martha Chase performed
experiments showing that DNA is the genetic material of a
phage known as T2
• To determine the source of genetic material in the
phage, they designed an experiment showing that only one of
the two components of T2 (DNA or protein) enters an E. coli cell
during infection
• They concluded that
the injected DNA of
the phage provides the
genetic information
 EXPERIMENT

Radioactive
Phage
protein
Bacterial cell

Batch 1: DNA
radioactive
sulfur (35S)

Radioactive
DNA

Batch 2:
radioactive
phosphorus (32P)
 EXPERIMENT
Empty
Radioactive protein
Phage shell
protein
Bacterial cell

Batch 1: DNA
radioactive Phage
sulfur (35S) DNA

Radioactive
DNA

Batch 2:
radioactive
phosphorus (32P)
 EXPERIMENT
Empty Radioactivity
Radioactive protein (phage
Phage shell protein)
protein
in liquid
Bacterial cell

Batch 1: DNA
radioactive Phage
sulfur (35S) DNA

Centrifuge

Radioactive Pellet (bacterial

DNA cells and contents)

Batch 2:
radioactive
phosphorus (32P)

Centrifuge
Radioactivity
Pellet (phage DNA)
in pellet
The Lysogenic Cycle
Fig. 10-16
Temperate virus
Attachment
DNA
Cell (host)

Injection

Lytic pathway Lysogenic pathway

Viral DNA
replicates

Induction
Coat proteins
synthesized; Viral DNA
virus is integrated
particles into host
assembled DNA
Lysogenized cell
Prophage

Lysis Cell
division
 Latent viral infections

 Virus remains in asymptomatic host cell for

long periods.
 90-95% of population Cold sores
 10-15% show symptoms
 Shingles 10-20%
Table 13.5
• Lytic cycle: Phage causes lysis and death of host cell.
• Lysogenic cycle: Prophage DNA incorporated in host
DNA.
• Immune to reinfection
• Phage conversion
• Specialised transduction
 The CRISPR/Cas System: Bacteria and
Archaea Fight Back
• Clustered Regularly Interspaced Short Palindromic
Repeats
– Repeating sequences of bases found in bacteria and
archaea with varied spacer sequences between them
• Cas proteins interact with CRISPR regions
• Each time the cell is infected but survives, a portion of
the viral DNA is added to the 3’ end of the region (a
history of infection)

45
https://www.ted.com/talk
s/jennifer_doudna_we_c
an_now_edit_our_dna_
but_let_s_do_it_wisely
Prions
 Infectious proteins
 Inherited and transmissible by
 ingestion, transplant, and surgery
 Spongiform encephalopathies:
Sheep scrapie, Creutzfeldt-Jakob disease, Gerstmann-Sträussler-
Scheinker syndrome, fatal familial insomnia, mad cow disease
 PrPC: Normal cellular prion protein, on cell surface
 PrPSc: Scrapie protein; accumulates in brain cells forming plaques
Viroids

 Infectious nucleic acid

 No protein coat
 Infections found in plants
Crossing the Species Barrier

UN 13.3
http://www.theguardian.com/society/2015/nov/02/fda-approval-imlygic-cancer-hunting-viral-treatment

http://www.the-scientist.com/?articles.view/articleNo/44080/title/New-Virus-Discovered-in-Human-Blood/
https://www.youtube.com/watch?v=mMEPV-NTeZs