Viruses• Viruses are nucleic acids

(DNA/RNA) wrapped in protein

• Typically the protein coat, or capsid, of an individual virus particle, or virion, is composed of multiple copies of one or several types of protein subunits, or capsomeres. Some viruses contain enzymes, and some have an outer membranous envelope. Many viruses have striking geometrically regular shapes

Virus Shapes3 main shapes:• Icosohedron/polyhedron: 20 triangular

sections (HIV)• Spiral: RNA surrounded by capsomere

proteins• Bacteriophage: spaceship• Others (ebola)

Types of Viruses• Viruses depend on the

host cells that they infect to reproduce. When found outside of host cells, viruses exist as a protein coat or capsid, sometimes enclosed within a membrane. The capsid encloses either DNA or RNA which codes for the virus elements.

Sizes of Viruses

Nucleic AcidPlus/Minus strand designation mRNA = +polarity

mRNA 5’ GAC UCG AGC 3’+DNA 5’ GAC TCG AGC 3’-DNA 5’ CTG AGC TCG 3’+RNA 5’ GAC UCG AGC 3’ (operates like mRNA)

-RNA 5’ CUG AGC UCG 3’ (euk. cells don’t have enz)

ssDNA(+)-DNA+mRNARetrovirus= RNAdsDNA using reverse transcriptase

Reverse transcription of retroviruses

Reverse Transcriptase 2 Classification of Viruses (reference)

Exceptions

• Viroids circular ssRNA material, infectious to plants, escaped introns???

• Prions proteinaceous infectious particles, no n.a. Against dogma of molecular biology

Scrapie (sheep), kuru (Papau New Guinea), bovine spongiform encephalitis (Mad Cow Disease), and Creutzfeldt-Jakob disease.

Harmful Viruses• Viruses are notorious for

the plethora of diseases they cause, including influenza, rabies, AIDS, polio, herpes, ebola, measles, mumps, chicken pox, warts, small pox -->

Lewandowsky-Lutz/ 2Epidermodysplasia verruciformis,

herpes Warts

Helpful Viruses• Viruses carry out natural "genetic

engineering": by incorporating genetic material into its host

• This is known as transduction, and in some cases it may serve as a means of evolutionary change

• Certain varieties of flowers have been developed using viruses to alter the genetic code.

• Dr Patrick Lee uses reovirus to kill brain cancer cells transplanted into laboratory mice, while sparing normal, healthy cells. Clinical trials involving reovirus in people are now underway.

• Virus Rap

Helpful Viruses• A good virus• Most of us go out of our way to avoid viruses. But

Dr Patrick Lee - formerly of the University of Calgary and now at Dalhousie University - spends a lot of time in the company of a very common virus known as a reovirus. Normally this bug causes nothing more serious than a mild infection. But Dr Lee’s team discovered that the reovirus has the ability to kill brain cancer cells transplanted into laboratory mice, while sparing normal, healthy cells. Clinical trials involving reovirus in people are now underway.

How do they get in?• Lambda phage Replication

• Replication of a Positive (+) Sense Strand of Lytic RNA Phage

• T4 Replication• Entry into Animal Cell • Release of Enveloped Viruses• Replication of Retrovirus• Influenza

Essential knowledge 3.C.3: Viral replication results in genetic variation, and viral infection can introduce

genetic variation into the hosts.

b. The reproductive cycles of viruses facilitate transfer of genetic information.1. Viruses transmit DNA or RNA when they infect a host cell.

• Transduction in bacteria (Specialized Transduction)• Transposons present in incoming DNA

2. Some viruses are able to integrate into the host DNA and establish a latent (lysogenic) infection. These latent viral genomes can result in new properties for the host such as increased pathogenicity in bacteria.

LO 3.29 The student is able to construct an explanation of how viruses introduce genetic variation in host organisms.

Lysogenic Cycle• When it comes into contact

with a host cell, a virus can insert its genetic material into its host, literally taking over the host's functions. An infected cell produces more viral protein and genetic material instead of its usual products. Some viruses may remain dormant inside host cells for long periods, causing no obvious change in their host cells (a stage known as the lysogenic phase).

Lytic Cycle• when a dormant virus is

stimulated, it enters the lytic phase: new viruses are formed, self-assemble, and burst out of the host cell, killing the cell and going on to infect other cells

• Attachmententryreplicationassemblylysis & release

• 1, 2, 3

Essential knowledge 3.C.3: Viral replication results in genetic variation, and viral infection can introduce

genetic variation into the hosts.

a. Viral replication differs from other reproductive strategies and generates genetic variation via various mechanisms.

1. Viruses have highly efficient replicative capabilities that allow for rapid evolution and acquisition of new phenotypes. Viral Recombination , 1918 Spanish Flu, 2, 3

2. Viruses replicate via a component assembly model allowing one virus to produce many progeny simultaneously via the lytic cycle.

3. Virus replication allows for mutations to occur through usual host pathways.4. RNA viruses lack replication error-checking mechanisms, and thus have higher rates

of mutation.5. Related viruses can combine/recombine information if they infect the same host cell. (

Antigenic Shift)6. HIV is a well-studied system where the rapid evolution of a virus within the host

contributes to the pathogenicity of viral infection.

LO 3.30 The student is able to use representations and appropriate models to describe how viral replication introduces genetic variation in the viral population.

Life Cycle of HIV HIV Life Cycle 2 HIV Replication Future of HIV

Vaccines

• Constructing a Vaccine

• Engineering the Avian Flu

• 1918 Flu

• Malarial Vaccine • Virus Rap

Lysogenic Cycle vs Lytic Cycle

• Attachmententryreplicationassemblylysis & release

Eubacteria “true bacteria”• Typical “monerans” found

where humans live• Evolution of the 3 Domains

                     

   

Archaea “archaic/old”extremophiles

• Methanogens• Thermophiles• Acidophiles• Halophiles• Alkaliphiles• Psychrophiles• Xerophiles• Barophiles

• Archae vs Bacteria

Bacteria Characteristics• Bacteria are

distinguished from other living things because of their cell structure:

• All bacterial cells have a cell wall surrounding a cell membrane, inside of which lies the unbound nuclear matter and other material.

• Bacteria have extra genomic DNA that is round and called a “plasmid”

• Plasmid Cloning

Bacteria: Classified by Shape• There are three types of bacterial cells, based on

shape: spherical (coccus), rodlike (bacillus), and spiral (spirillum).

• Some bacteria have flagella for locomotion and some have pili to transfer DNA (conjugation) and to stick to substrates of host cells

Bacterial Chemotaxis

Harmful Bacteria• A number of bacteria

cause disease, these are called pathogenic bacteria.

• They can cause diseases of plants, animals, fungi, protists and other bacteria

• E. coli infection

• Salmonella infection

• Some bacterial diseases include: strep throat, scarlet fever, toxic shock syndrome, pneumonia, ear infections, gonorrhea, syphilis, Tuberculosis

• Bacteria can also be used by some countries to harm other countries in an act called bioterrorism

Eczema w/ 2o infection

Helpful Bacteria• actinomycetes,

produce antibiotics such as streptomycin and nocardicin

• live symbiotically in the guts of animals

• put the tang in yogurt and the sour in sourdough bread, cheese = spoiled milk

Symbiotic bacteria assist in digestion

• break down dead (and living) organic matter

• Bioremediation

• used in genetic engineering

• Nitrogen Fixation roots of certain plants, converting nitrogen into a usable form (nitrate).

Wound infectionDefinition

of

wound

infection•1992

US

Centre

for

Disease

Control

•Defined

the

following:

•Surgical

site

infections

•Superficial

incisional

infection

•Deep

incisional

infections

•Organ

space

infections

•Surgical

site

infections

must

fulfill

the

following

criteria

•Infection

must

occur

within

30

days

of

surgery

•Infection

must

involve

only

the

skin

and

subcutaneous

tissue

•There

must

be

at

least

one

of

the

following

•Purulent

discharge

from

a

superficial

infection

•Organisms

isolated

from

aseptically

obtained

wound

culture

•Must

be

at

least

one

of

the

following

signs

of

infection

•Pain

or

tenderness

•Localised

swelling

•Redness

or

heat

Predisposing

factors•General

factors

•Age,

obesity,

malnutrition

•Endocrine

and

metabolic

disorders

•Hypoxia,

anaemia

•Malignant

disease

•Immunosupression

•Local

factors

•Necrotic

tissue

•Foreign

bodies

•Tissue

ischaemia

•Haematoma

formation

•Poor

surgical

technique

•Microbiological

contamination

•Type

and

virulence

of

organism

•Size

of

bacte

riological

dose

•Antibiotic

resistance

Aerobic

pathogens

in

wound

infections•Staphylococcus

aureus

(17%)

•Enterococci

(13%)

•Coagulase-negative

staphylococci

(12%)

•Escherichia

coli

(10%)

•Pseudomonas

aeruginosa

(8%)

•Enterobacter

species

(8%)

•Proteus

mirabilis

(4%)

•Klebsiella

pneumoniae

(3%)

•Candida

species

(2%)

Prevention

of

wound

infection•Exogenous

•Sterilisation

of

instruments,

sutures

etc

•Positive

pressure

ventilation

of

operating

theatres

•Laminar

air

flow

in

high

risk

areas

•Exclusion

of

staff

with

infections

•Endogenous

•Skin

preparation

•Mechanical

bowel

preparation

•Antibiotic

prophylaxis

•Good

surgical

technique

Wound

infection

rates•Risk

of

wound

infection

varies

with

type

of

surgery

•Infection

rate

can

be

reduced

with

antibiotic

prophylaxis

Clean

surgery•No

viscus

opened

(e.g.

hernia

repair)

•Infection

rate

typically

1-2%

Clean-contaminated•Viscus

opened

but

no

spillage

of

gut

contents

(e.g.

right

hemicolectomy)

•Infection

rate

usually

<10%

Contaminated•Viscus

opened

with

inflammation

or

spillage

of

contents

(e.g.

colectomy

for

obstruction)

•Infection

rate

15-20%

Dirty•Intraperitoneal

abscess

formation

or

visceral

perforation

•Infection

rate

40%

Antibiotic

prophylaxis

•Prophylaxis

is

the

use

of

antibiotics

to

prevent

infection

•Treatment

is

their

use

to

eradicate

established

sepsis.

•Prophylaxis

important

in:

•Surgery

with

a

high

incidence

of

post-operative

infection

(e.g.

colonic

surgery)

•Surgery

where

infection

would

be

hazardous

(e.g.

prosthetic

valves)

•Need

to

consider:

•The

use

of

an

appropriate

antibiotic

based

on

likely

bacteria

and

tissue

penetration

•Cefuroxime

&

metronidazole

for

colonic

surgery

•Benzylpenicillin

for

peripheral

vascular

surgery

•Timing

and

duration

of

administration

•Intravenous

administration

at

induction

•Number

of

doses

-

usually

no

more

than

three

doses

BibliographyHoran

T

C,

Gaynes

R

P,

Martone

W

J,

Jarvis

W

R,

Emon

T

G.

CDC

definitions

of

nosocomial

surgical

site

infections,

1992:

a

modification

of

CDC

definitions

of

surgical

wound

infections.

Am

J

Infect

Control

1992;

20:

271-274.McDonald

M,

Grabsch

E,

Marshall

C,

Forbes

A.

Single-versus

multiple-dose

antimicrobial

prophylaxis

for

major

surgery:

a

systematic

review.

Aust

N

Z

J

Surg

1998;

68:

388-396.

Wound infectionDefinition

of

wound

infection•1992

US

Centre

for

Disease

Control

•Defined

the

following:

•Surgical

site

infections

•Superficial

incisional

infection

•Deep

incisional

infections

•Organ

space

infections

•Surgical

site

infections

must

fulfill

the

following

criteria

•Infection

must

occur

within

30

days

of

surgery

•Infection

must

involve

only

the

skin

and

subcutaneous

tissue

•There

must

be

at

least

one

of

the

following

•Purulent

discharge

from

a

superficial

infection

•Organisms

isolated

from

aseptically

obtained

wound

culture

•Must

be

at

least

one

of

the

following

signs

of

infection

•Pain

or

tenderness

•Localised

swelling

•Redness

or

heat

Predisposing

factors•General

factors

•Age,

obesity,

malnutrition

•Endocrine

and

metabolic

disorders

•Hypoxia,

anaemia

•Malignant

disease

•Immunosupression

•Local

factors

•Necrotic

tissue

•Foreign

bodies

•Tissue

ischaemia

•Haematoma

formation

•Poor

surgical

technique

•Microbiological

contamination

•Type

and

virulence

of

organism

•Size

of

bacte

riological

dose

•Antibiotic

resistance

Aerobic

pathogens

in

wound

infections•Staphylococcus

aureus

(17%)

•Enterococci

(13%)

•Coagulase-negative

staphylococci

(12%)

•Escherichia

coli

(10%)

•Pseudomonas

aeruginosa

(8%)

•Enterobacter

species

(8%)

•Proteus

mirabilis

(4%)

•Klebsiella

pneumoniae

(3%)

•Candida

species

(2%)

Prevention

of

wound

infection•Exogenous

•Sterilisation

of

instruments,

sutures

etc

•Positive

pressure

ventilation

of

operating

theatres

•Laminar

air

flow

in

high

risk

areas

•Exclusion

of

staff

with

infections

•Endogenous

•Skin

preparation

•Mechanical

bowel

preparation

•Antibiotic

prophylaxis

•Good

surgical

technique

Wound

infection

rates•Risk

of

wound

infection

varies

with

type

of

surgery

•Infection

rate

can

be

reduced

with

antibiotic

prophylaxis

Clean

surgery•No

viscus

opened

(e.g.

hernia

repair)

•Infection

rate

typically

1-2%

Clean-contaminated•Viscus

opened

but

no

spillage

of

gut

contents

(e.g.

right

hemicolectomy)

•Infection

rate

usually

<10%

Contaminated•Viscus

opened

with

inflammation

or

spillage

of

contents

(e.g.

colectomy

for

obstruction)

•Infection

rate

15-20%

Dirty•Intraperitoneal

abscess

formation

or

visceral

perforation

•Infection

rate

40%

Antibiotic

prophylaxis

•Prophylaxis

is

the

use

of

antibiotics

to

prevent

infection

•Treatment

is

their

use

to

eradicate

established

sepsis.

•Prophylaxis

important

in:

•Surgery

with

a

high

incidence

of

post-operative

infection

(e.g.

colonic

surgery)

•Surgery

where

infection

would

be

hazardous

(e.g.

prosthetic

valves)

•Need

to

consider:

•The

use

of

an

appropriate

antibiotic

based

on

likely

bacteria

and

tissue

penetration

•Cefuroxime

&

metronidazole

for

colonic

surgery

•Benzylpenicillin

for

peripheral

vascular

surgery

•Timing

and

duration

of

administration

•Intravenous

administration

at

induction

•Number

of

doses

-

usually

no

more

than

three

doses

BibliographyHoran

T

C,

Gaynes

R

P,

Martone

W

J,

Jarvis

W

R,

Emon

T

G.

CDC

definitions

of

nosocomial

surgical

site

infections,

1992:

a

modification

of

CDC

definitions

of

surgical

wound

infections.

Am

J

Infect

Control

1992;

20:

271-274.McDonald

M,

Grabsch

E,

Marshall

C,

Forbes

A.

Single-versus

multiple-dose

antimicrobial

prophylaxis

for

major

surgery:

a

systematic

review.

Aust

N

Z

J

Surg

1998;

68:

388-396.

Bacteria are useful in making antibiotics and in biotechnology.

Producers in Geothermal Vents

Reproduction

• Bacteria reproduce asexually by binary fission• Bacterial Conjugation (lateral/horizontal gene exchange)

• Bacterial Transformation (lateral/horizontal gene exchange)

• Bacteria life cycle

BB CheckpointBB#1SB1a. Explain the role of cell organelles for both prokaryotic and eukaryotic cells, including the cell membrane, in maintaining homeostasis and cell reproduction.

BB#8 SB2e. Compare the advantages of sexual reproduction and asexual reproduction in different situations

BB#10 SB3b. Compare how structures and function vary between the six groups (archaebacteria, eubacteria, protists, fungi, plants, and animals).

Kingdom Protista• All protists are eukaryotes.

This means that their cells contain a nucleus, a membrane-bounded structure that encloses the

cell's genetic material. • Some protists are

autotrophs like plants, others are consumers like animals. Unlike plants and animals, however, protists do not have cells organized into specialized tissues.

Protista Classified by Nutrition• The first detailed descriptions of

protists were made in 1676 by the inventor of the microscope, Dutch naturalist Leewenhoek.

• The classification is currently based on the structure and organization of the cell, the presence of organelles, and the pattern of reproduction or life cycles. The five-kingdom system divides the Protista into 27 phyla. However, classifications based on DNA sequences suggest that many protist phyla may be sufficiently large and diverse to be classified as kingdoms.

• Gallimaufry, cornucopia, hodge-podge, potpourri

• Auto trophic Protists are called “Algae”. Scientists believe they gave rise to the kingdome Plantae

• Ingestive Heterotrophic protists are called “Proto zoa”. Scientists believe they gave rise to the kingdom Animalia

• Absorptive heterotrophic protists are called “Slimemolds”. Scientists believe they gave rise to the kingdom Fungi

• Protist Rap

Harmful Protists• Produce a nerve poison in

shellfish that kills humans and fish in red tide

• Cause diseases: Chaga’s disease, Malaria, 2, Lyme disease, diarrhea, toxoplasmosis, dysentary, Trypanosomaisis, 2, Leishmaniasis, 2, Toxoplasma, Cryptospiridium, Leishmaniasis, Brain Amoeba

• Cause mold and mildew which can spoil food and cause allergic reactions

• Cause algal blooms which can result in eutrophication

Beneficial Protists• Used as insect pathogens

• Used in ice cream, soups, nori (seaweed in sushi), jello, agar, vitamin supplements, or eaten as a sea vegetable

• Ancient dinoflagellates formed oil deposits

• Bioluminescent

• Diatoms mined for fine abrasives in silver polish and toothpaste and as packing in air and water filters

• Marine phytoplankton make up ~70% of the oxygen on the planet

• Forensic uses: Diatom Detectives

• Algae for Biofuel

BB CheckpointBB#9SB3a. Explain the cycling of energy through the processes of photosynthesis and respiration.

BB#10 SB3b. Compare how structures and function vary between the six groups (archaebacteria, eubacteria, protists, fungi, plants, and animals).

Fungi: Multicellular absorptive heterotrophs

• Though they grow in soil like plants, they are not autotrophic.

• The have cell walls made of the polysaccharide chitin

• What are the cell walls of plants made of? Bacteria?

Fungi AnatomyHyphae basic structural unit of a fungus made up of branching filaments

Mycelium tangled network of fibers

Fruiting body reproductive structure. In Phylum Basidiomycota it is the mushroom itself

Fungi: Classified by ReproductionDivision Zygomycota form zygospores i.e. Rhizopus (bread mold)

Division Ascomycota form ascospores i.e. yeast, morels, ergot, Dutch elm disease

Division Basidiomycota Most commonly known, forms basidiospores i.e. shelf fungi, mushrooms

Division Deuteromycota/ Imperfecti sexual reproduction unknown i.e. Penicillium, Aspergillus

Fungi Life Cycle

Harmful Fungi• Many fungi are parasitic

and cause diseases like ringworm, athletes foot,

• Can rot and contaminate foods

• Can destroy almost every type of product or food aside from some plastics

• Black Mold in Buildings

• Building a House: Recipe for Disaster

• Lungus Fungus

Beneficial Fungi• People eat mushrooms, truffles and

other fungi, citric acid in Coke

• Fungi are decomposers like bacteria and help to recycle organic matter to inorganic = saprophytic

• Yeasts are used in making bread, wine, beer, solvents, cheese.

• Drugs made from fungi cure diseases and stop the rejection of transplanted hearts and other organs.

• Fungi are also grown in large vats to produce flavorings for cooking, vitamins and enzymes for removing stains.

• Beneficial Protists & Fungi

Fungi Engage in Symbiosis

• Parasitic +/-: Mind control

• Mutualistic +/+: Lichens, a pioneer organism, a fungus and algae living together

• The mycorrhizal fungi live as partners with plants, helping them absorb nutrients

• Predatory +/-: Arthrobotrys, a deuteromycete

BB CheckpointBB#9SB3a. Explain the cycling of energy through the processes of photosynthesis and respiration.

BB#10 SB3b. Compare how structures and function vary between the six groups (archaebacteria, eubacteria, protists, fungi, plants, and animals).

ResourcesVirus Links

•Virus Pictures:

•Virus Review:

•Exploring Life:

•Big Picture Book of Viruses:

•AIDS Online:

•Replication of Herpes Animation:

•Influenza Entry Animation:

•Antigenic Shift Animation

•Immuno- biology Animations

•Biological Diversity

Protists •Protist Kingdom: •Phylogenetic Tree: •Protozoa Bio 4 Kids: •Microbe Zoo, Dirtland:

Bacteria Links•Bioterrorism: •Bacterial Cell Walls: •10 Ways a World Will End: Monster Plague•Discovery of the Germ Theory•Antibiotics Tutorial •Anti-antibiotics/Efflux Pump•Immunology Primer •When Worlds Collide, Macro vs. Micro •Immuno- biology Animations

Fungi Links•Fungi Chapter 30•Tom Volk’s Fungi

Virus LinksVirus Pictures:

Virus Review:

Exploring Life:

Big Picture Book of Viruses:

AIDS Online:

Replication of Herpes Animation:

Influenza Entry Animation:

Antigenic Shift Animation

Immuno- biology Animations

Chapter 6 Viruses

Introduction to Plasmids & Viruses

Bozeman Viral ReplicationSuper Flu: Antigenic shift in influenza