INVADERS. Chapter 24: Viruses Objectives: Summarize the discovery of viruses Describe why viruses are not considered living organisms Describe the basic.

INVADERS

Chapter 24: Viruses

Objectives:• Summarize the discovery of viruses• Describe why viruses are not

considered living organisms• Describe the basic structure of viruses• Compare the lytic and lysogenic cycles

of virus replication• Summarize the origin of viruses

Virusnonliving particle that can infect both prokaryotic and eukaryotic cells

Virus Structure-vary in shape and size

All viruses contain two main parts:1) Nucleic Acid (Genome) – Either DNA or RNA2) Capsid – protein coat or lipid protein coat (many different shapes)

– Helical – Tobacco Mosaic Virus (TMV), Rabies, measles– Icosohedreon – Adenovirus, Herpes Simplex, Chicken Pox, Polio– Spherical – Influenza Virus

3) Envelope – bilipid membrane that surrounds the capsid (only some viruses)

– Formed from nuclear membrane or cell membrane as it leave the host cell

– Proteins in the envelope helps new viruses recognize host cell.Examples: Influenza, chicken pox (varicola), HIV

Function of Viruses

1) Cause Disease by infecting the host cell

2) Used in Genetic Research and biotechnology

Characteristics of Viruses

Virus are nonliving!– Are not made of cells– Do not have organelles or cytoplasm– Can’t carry out metabolic processes such as

metabolism and homeostasis– Do not grow through Cell Division– Can’t reproduce outside their host cell

(Need host cells structures to reproduce)

Wendell Stanley was the first scientist to crystallize a virus. This is evidence that viruses are not made of cells and are not alive.

Classification of VirusesA. Genetic Material:

1) RNA or DNA2) Single Stranded or Double Stranded3) Linear or Circular Genetic Information

B. Capsid:1)Shape2)Presence or absence of an envelopeExample: SARS – RNA, Single Stranded, Linear, lollipop-shaped capsid and enveloped (chart pg485)

Classification cont.

- Different viruses infect bacteria, plant and animal hosts

- due to receptor site forming to specific proteins on cell wall or membrane

Bacteriophages – viruses that infect bacteria

How do Viruses Spread

• Air

• Water

• Food

• Bodily Fluids

Obligate intracellular parasites(Viruses)

Viruses replicate only by using the host cellsenzymes and organelles to make moreviruses. Protein synthesis is controlled by the

viral genome and the host cell becomes a virus

makingfactory.

Protein Synthesis review1) Transcription: DNA -> mRNA2) Translation: mRNA -> proteins

Two methods:1) vDNA->mRNA –> make new viruses

(in cytoplasm)

2) DNA – Provirus – (Gets incorporated into Host Cell’s DNA) – Makes new viruses

Replication in DNA viruses

Replication in DNA Viruses

Method 1

1. Virus enters the host cells cytoplasm and takes control of the host cells protein synthesis pathway

2. Enzymes transcribe mRNA from the viral DNA

3.Host ribosomes translate Viral mRNA into viral proteins and enzymes replicate the viral DNA

4.New viral particles are assembled (Capsids and nucleic acids)

Replication in DNA Viruses

Method 21) Viral DNA is injected into the host

cell2) Viral DNA moves into the nucleus

and becomes incorporated into the host cells DNA as a provirus

3) Virus takes over the cell and makes newe viruses as a provirus

Replication in RNA viruses

RNA VirusesRNA 1) The vRNA serves right away as mRNA and

then is translated into proteins (New Viruses)2) Viral RNA is transcribed into mRNA and then is

translated into proteins and new viruses

Retro RNA VirusesContain Reverse Transcriptase which uses RNAas a template to create DNA, which is theninserted into the host cells DNA

Lytic Cycle vs. Lysogenic Cycle Reproduction of viruses

Lytic Cycle: Reproduction of Virulent Virus• Destroy the cell they infectStages:1) Adsorption2) Penetration3) Replication4) Maturation (Assembly)5) Release

Lysogenic Cycle: Reproduction of Temperate Virus• Lays dormant in the host cell before it destroys it• When triggered will go into the lytic cycle

Lytic Cycle – followed when virus is virulent (active)

1. ADSORPTION- virus particle attaches to a host cell.

2. ENTRYThe particle injects its genetic instructions (DNA or RNA) into the hostInjected genetic material ‘hi-jacks’ the cell’s machinery and recruits the host’s enzymes.

3. REPLICATION Enzymes make parts for the new virus particles

4. ASSEMBLY -new particles assemble the parts into new viruses

5. RELEASE -Cell explodes (lyses) releasing new viruses which search for a new host cell

Lysogenic Cycle - followed when virus is in latent or temperate state

The steps of the lysogenic cycle:1) Viral nucleic acid enters cell 2) Viral nucleic acid attaches to host cell nucleic acid, creating a prophage 3) Host cell enzyme copies viral nucleic acid4) Cell divides, and virus nucleic acid is in daughter cells 5) At any moment when the virus is "triggered", the viral nucleic acid detaches from the host cell's DNA and enters stage 2 of the lytic cycle.

Common symptoms that appear to "trigger" the viral DNA are hormones, high stress levels (adrenaline), and free energy within the infected cell.

Viral Diseases

• Vector – intermediate host that transfers a pathogen or parasite to another organism– Ex: humans, mosquitos, ticks, fleas.

• Human viral diseases - chickenpox, shingles, viral hepatitis, AIDS, etc…

• Protease inhibitors – drugs that block virus reproduction

• Oncogenes – viral genes that cause cancer by messing with cell division checkpoints

• Proto-oncogene – controls cell growth

Prevention and Treatment

Vaccine – weakened sample of virus or virus parts which triggers your body’s immune system

Attenuated virus – weakened virus that cannot cause disease

Inactivated virus – unable to replicate in host

Natural immunity - antibodies are specialized proteins formed in B cells of immune system

- antibodies block attachment sites of viruses

http://www.pbs.org/wgbh/nova/bioterror/vaccines.html

Disease causing particles even smaller than viruses

Viroids

– short single strand of RNA without a capsid

- interfere with cell processes and cause new viroids to be made

- are found only in plants

Prions

- glycoprotein particle

- able to reproduce in mammalian cells

- Prion diseases: mad cow disease; Creutzfeldt-Jakob disease & kuru (degenerative nerve diseases of the brain)

Genetic engineering

Genetic engineers use viruses to carry desirable genes from one cell to another

Improved agriculture – herbicide tolerant soybeans; rot resistant tomatoes; fast growing fish; meatier chickens

Correcting genetic disorders - experimental; only done in animal with success; not allowed in humans

Pest control – insert genes of plants that create chemical to resist insects into crop plants such as corn

Manufacturing of medicine - human insulin &clotting factors 8 & 9

http://www.pbs.org/wgbh/harvest/engineer/transgen.html

Chapter 23: Bacteria

Archaea and Bacteria

Bacteria Objectives

• Describe the common methods used to identify bacteria

• Identify 3 Archael groups, 5 bacterial groups

Characteristics of Domain Archaea

• Prokaryotic cells• Unicellular• Cell Walls do not contain peptidoglycan• Cell Membranes contain other types of

hydrocarbons in addition to fatty acids• rRNA shows they are more like Eukaryotes• Contain Introns in their DNA• Heterotrophs and Autotrophic Chemotrophs

III. Kingdom Archaebacteria – the most primitive organisms

(archae = ancient)

live in harsh conditions including

- acidic hot springs

- very salty water

- environments with no oxygen

- near undersea volcanic vents

- different from other bacteria

- cell wall composition (pseudomurien)

- Cell membrane

- rRNA

Phyla 1: Methanogens:

- obligate anaerobes (oxygen kills them)

- metabolizes hydrogen gas and CO2 to methane gas

- live in the bottom of swamps, sewage, and inside the digestive tracks of many animals

Helps

- grazing animals process cellulose

- termites process wood

- in industry to treat sewage, purify water.

Phyla 2: Thermoacidiphiles

- can live in extremely hot and acidic water or deep in the ocean near hydrothermal vents in the ocean floor

- Ex: hot springs of Yellowstone Natl Park, ice of Iceland

- chemotrophs = process sulfur compounds to produce energy

Phyla 3: Halophiles:

- live in extremely salty (saline) environments,

ex: Dead Sea

- use the salt to generate ATP.

IV. Kingdom Eubacteria (Eu = true) “Germs”

• Found almost every where on Earth

• Characteristics: – peptidoglycan in cell wall – may have outer covering of glycocalyx

(sticky sugars) that keeps cells from drying out

1) Composition of the cell wall – identified with Gram staining technique

Gram positive – stains purple – thick outer layer of peptidoglycan

Gram negative – stains pink/red – lipid layer covering thin layer of peptidoglycan

Characteristics used for classifying:

2. Method of getting energy

autotroph – chemotroph or phototroph

heterotroph - free living or parasite

saprophytes – break down other organisms into nutrients

3) Type of metabolism

obligate aerobe – must have oxygen; dies without it

obligate anaerobe – dies if exposed to oxygen; processes ATP by fermentation

facultative anaerobe – uses oxygen when it can but doesn’t need it

4) Shape of bacterial cells

round coccus (cocci)

rod shaped bacillus (bacilli)

spiral shaped spirillus

Domain Bacteria

• Shapes (cont’d)– Spiral-shaped

• Called spirilla

Domain Bacteria

• Occur in many shapes including– Rod-shaped

• Called bacilli

Domain Bacteria

• Shapes (cont’d)– Sphere-shaped

• Called cocci– In chains, called streptococci– In grapelike clusters called

staphylococci

5) How cells grow (prefixes are added to coccus)

a) staphylo – cells grow in clumps

b) strepto - cells grow in chains

c) diplo - cells grow in pairs

6) Motility – movement

a) flagellated – move with flagellum or flagella

b) slime layer allows gliding

c) spirochete - cork-screw rotation

Reproduction – 2 types

Asexual - most common

Binary fission – chromosome replicates cytoplasm, membrane and wall divide into two new cells

Sexual – exchanges genetic info giving variation

a) conjugation – two bacterial cells get side by side and hair-like “pili” connect to provide tube to pass info

b) transformation – living bacterial cell absorbs dead related bacterial DNA and incorporates it into genome

c) transduction – a virus transfers DNA from one bacterium to another

Endospores

- special dehydrated cells formed by some bacteria to survive bad living conditions

- ex: high temperatures, harsh chemicals, radiation, lack of moisture

- dormant as endospore

- when conditions improve cell is revived

- ex. Anthrax

Structure of a Bacterial Cell

Gram positive

- thick outer layer of peptidoglycan (stains purple)

- may be beneficial or cause disease

- may be used to make yogurt, pickles, and buttermilk

- or to make medicines using biotechnology

Ex. Strep throat ; staph infections; tuberculosis

Phyla groups:

Phyla groups:

Gram negative taxa

A) Proteobacteria

• may have symbiotic lifestyle

• ex. Nitrogen fixing bacteria inside legumes (peas, beans, alfalfa, and clover)

• In human and animal intestines, help break down foods (enteric bacteria)

• Some in soil or fresh water and process iron and other minerals as an energy source (chemotrophs)

B) Gram-positive bacteria

- most are gram-positive

- ex: botulism, Lactobacilli (yogurt),

C) Cyanobacteria

• Gram-negative • contain chlorophyll (but not

chloroplasts), perform a plant-like photosynthesis releasing oxygen as a by-product

• Ex. Filamentous bacteria (grow in stagnant water)

D) Spirochetes

- gram negative

- spiral shaped

E) Chlamydia (no peptidoglycan)

- gram negative

- round shape

- are parasites to animal cells

Bacteria and Disease

Toxins – poisons produced by some bacteria

1) endotoxin - created inside the bacterial cell and released as the cell dies; usually Gram negative

bacteria

2) exotoxin – secreted by living bacterial cell into surrounding environment (host); usually Gram-positive bacteria

3) enzymes – some bacteria secrete enzymes that break down the surrounding tissue and damage it

Pathogens – bacteria that cause disease

Antibiotics – chemicals that kill bacteria by interfering with cellular functions such as protein or cell wall synthesis

Gram positive bacteria that cause disease need different antibiotics than Gram negative bacteria

Broad spectrum antibiotics affect a wide variety of bacteria within the taxa

Antibiotic Resistance in Bacteria

• most of the population dies, some survive

• Survivors reproduce and are no longer affected by antibiotic

• Occurs when antibiotics are overused or used improperly

Vocabulary list for honors

Taxonomy binomial nomenclature phylogeny

Dichotomous key phylogenetic chart binary fission

Virus capsid antibiotics

Envelope lytic cycle endospore

Lysogenic cycle vaccine conjugation

Natural immunity morphology pathogen

Viroids prions tranformation

Methanogens thermoacidiphiles transduction

Halophiles obligate aerobes saprophyte

Obligate anaerobes facultative anaerobes endotoxin

Chemotrophs phototrophs exotoxin

Protists

V. Kingdom Protista

Basic Characteristics: eukaryotes; most are unicellular; most are heterotrophs

Habitats: aquatic habitats or moist soil

Characteristics used for classification

•how they obtain energy – heterotrophic; autotrophic; saprophytic

•number of cells – unicellular or multicellular

•Motility – ability to move and movement structures

Reproduction

Asexual (most common): Binary fission(unicellular)

Multiple fission (divide into more than 2 cells)

Sexual: Conjugation (genetic information is swapped and stored in a 2nd nucleus)

Protozoans – “animal-like” protists

Characteristics: unicellular; heterotrophs

Phlya Groups:

Sarcodinians – feed and move with pseudopods (streaming cytoplasm) freshwater- amoebas; marine – forminiferans and radiolarians

Ciliaphorans – feed and move using cilia (small whisker –like structures)

Ex. Paramecium, stentor

Zooflagellates (Sarcomastigophora)- move with one or more flagella

May be free-living or parasitic and cause disease

Ex. Trichonympha, trypanosoma, giardia

Sporazoans (Apicomplexa) – no motility structures

All animal parasites; spore-formers; have complex life cycles with two or more host organisms

Ex. Plasmodium

Algae – “plant-like” protists

Characteristics: unicellular or multicellular

All are phototrophs with chloroplasts and pigments

Unicellular phyla are grouped together under the heading phytoplankton

Phlya Groups:

Dinoflagellates (Dinoflagellata)

Unicellular with two unequal sized flagella; marine;some species exhibit bioluminescence (light producing) others produce toxins (Gonyaulax) that cause “red tide”

Euglenophytes (Euglenophyta) have two flagella no cell wall;cell membrane has flexible pellicle; all freshwater habitat; Ex. Euglena

Diatoms (Bacillariophyta) have 2 sided cell walls made of silica (glass) that fit into each other like a petri dish; may have circular, triangular (mostly marine)or rectangular (mostly freshwater) body shapes

Gold Algae (Chrysophyta) contain gold pigments(carotenoids) as well as chlorophyll; most unicellular but some species form colonies

Green algae (Chlorophyta)

contain chlorophyll a & b; have cell walls composed of cellulose;unicellular, colonial, and multicellular species; freshwater and marine habitats as well as moist land

Ex. Ulva (sea lettuce), volvox, spirogyra

Red algae ( Rhodophyta)

contain red pigment as well as chlorophyll; most species tropical marine; all multicellular; may live in deep water habitats because red pigment helps absorb red lower energy light ex. seaweeds

Brown algae (Phaeophyta)

All cold water marine; all multicellular; include sargassum and kelp

Slime Molds – “Fungi-like” protists

Characteristics: all saprophytes; live in moist soil or moist organic matter

plasmodial slime molds - 2 stage life cycle

feeding stage – (plasmodium) very large digesting mass of cytoplasm that creeps along the decaying material

reproducing stage (fruiting body) stalked structures that hold haploid spores which fuse when living conditions are good or stay dormant if living conditions are bad

Cellular slime molds – 2 stages

feeding – single haploid cells that creep along like an ameoba;

pseudoplasmodium – matting of individual cells in a colony to share nutrients during bad living conditions; they eventually form fruiting bodies that produce more haploid spores which become individual organisms

Water molds

Grow in filaments called hyphae which break down organic matter

Some are parasitic to animals like fish or plants like blight on potatoes

Genetic engineering

Genetic engineers use viruses to carry desirable genes from one cell to another

Examples: improved agriculture; correcting genetic disorders; pest control; manufacturing of medicine

http://www.pbs.org/inthebalance/terrorism/virus-or-bacteria.html

Fungi Kingdom

 ·     Eukaryotes

·      Heterotrophic:

- most saprophytes

- some parasites

·       Most multicellular;

one is unicellular

·       Most sessile

Structure:

• Cell walls made of chitin (tough, flexible carbohydrate)

       Multicellular fungi are made up of hyphae

(small tubules filled with cytoplasm and nuclei)

       Hyphae form an interconnected mass called the mycelium and cytoplasm of all cells flow between the hyphae

       Hyphae may have walls called septa which still have holes for the cytoplasm to flow through

Hyphae produce enzymes that are secreted into the environment and then nutrients are reabsorbed through hyphae

Asexual Reproduction:

3 ways depending on structure

•       Multi-cellular –regeneration; (single celled- mitosis & cell division)

       Budding - new organism forms from small piece of mycelium

       Asexual spore formation from fruiting bodies

Spores spread by wind,

water, animals (*most common)

       Sexual reproduction – positive and negative hyphae fuse together to form spores

Sexual reproduction is possible in the common molds, club fungi, and sac fungi only

Classification:

Classified by structures used for reproduction

Group names are divisions not phyla (used to be

classified as plants):

Common molds (Zygomycota)

Club fungi (Basidiomycota)

Sac Fungi ( Ascomycota)

Imperfect fungi (deuteronomycota)

1.   Common molds (Zygomycota)

       No septa in hyphae

       Asexual reproduction - most common

Sexual reproduction spores formed in sporangium

       Examples: bread mold, fruit molds

   Club fungi (Basidiomycota)

       Reproduce sexually by producing spores in basidium

Located in gills under the cap

       Examples: mushrooms, bracket fungi, shelf fungi,

Puffballs

2.   Sac Fungi ( Ascomycota)

       reproduce sexually by means of ascus

bulb like projections that form from the hyphae

       examples: yeasts, truffles, morels, powdery mildews

   Imperfect fungi (deuteronomycota)

       no sexual reproduction; asexual only

       examples: the fungus that cause ringworm, athete’s foot, nail infections

Impact:

       environment - help to eat up or break down dead organisms

       symbiosis

a)   lichen live with cyanobacteria; fungus offers protection, cyanobacteria offer food

b)plant growth – fungus grows on root tips of some plants; plants get benefit of all ready broken down nutrients as well as extra support; fungus get nutrition from plant   

   human

help as food sources, medicines (penicillin), food processing, genetic engineering of proteins

   disease

destroy plants and trees

property damage to wood structures

human infection