1. INVADERS

2. 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

3. Virus
nonliving particle that can infect both prokaryotic and eukaryotic cells

4. Virus Structure-vary in shape and size
All viruses contain two main parts:
1) Nucleic Acid (Genome) – Either DNA or RNA
2) 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

5. Function of Viruses 1) Cause Disease by infecting the host cell
2) Used in Genetic Research and biotechnology

6. 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.

7. Classification of Viruses
A. Genetic Material:
1) RNA or DNA
2) Single Stranded or Double Stranded
3) Linear or Circular Genetic Information
B. Capsid:
1)Shape
2)Presence or absence of an envelope
Example: SARS – RNA, Single Stranded, Linear, lollipop-shaped capsid and enveloped (chart pg485)

8. - Different viruses infect bacteria, plant and animal hosts
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
e-coli being wiped out by T4 bacteriophages

9. How do Viruses Spread
Air
Water
Food
Bodily Fluids

10. Obligate intracellular parasites (Viruses)
Viruses replicate only by using the host cells
enzymes and organelles to make more
viruses. Protein synthesis is controlled by the viral
genome and the host cell becomes a virus making
factory.
Protein Synthesis review
Transcription: DNA -> mRNA
Translation: mRNA -> proteins

11. Replication in DNA viruses
Two methods:
vDNA->mRNA –> make new viruses (in cytoplasm)
DNA – Provirus – (Gets incorporated into Host Cell’s DNA) – Makes new viruses

12. 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)

13. Replication in DNA Viruses
Method 2
Viral DNA is injected into the host cell
Viral DNA moves into the nucleus and becomes incorporated into the host cells DNA as a provirus
Virus takes over the cell and makes newe viruses as a provirus

14. Replication in RNA viruses
The vRNA serves right away as mRNA and then is translated into proteins (New Viruses)
Viral RNA is transcribed into mRNA and then is translated into proteins and new viruses
Retro RNA Viruses
Contain Reverse Transcriptase which uses RNA
as a template to create DNA, which is then
inserted into the host cells DNA

15. Lytic Cycle vs. Lysogenic Cycle Reproduction of viruses
Lytic Cycle: Reproduction of Virulent Virus
Destroy the cell they infect
Stages:
1) Adsorption
2) Penetration
3) Replication
4) Maturation (Assembly)
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

16. Lytic Cycle – followed when virus is virulent (active)
ADSORPTION- virus particle attaches to a host cell.
ENTRY
The particle injects its genetic instructions (DNA or RNA) into the host
Injected 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

17. 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 acid
4) 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.

19. 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
Vaccination and vector control are the two most effective ways to control viral diseases

20. 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

21. 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)

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

23. Chapter 23: Bacteria
Archaea and Bacteria

24. Bacteria Objectives
Describe the common methods used to identify bacteria
Identify 3 Archael groups, 5 bacterial groups

25. 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

26. 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

27. 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.

28. 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

29. Phyla 3: Halophiles: - live in extremely salty (saline) environments,
ex: Dead Sea
use the salt to generate ATP.

30. 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

31. Characteristics used for classifying:
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
Gram-positive Staph aureus on top, and gram-negative Pseudomonas aeruginosa at the bottom

32. 2. Method of getting energy
autotroph – chemotroph or phototroph
heterotroph - free living or parasite
saprophytes – break down other organisms into nutrients

33. 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
Shape of bacterial cells
round coccus (cocci)
rod shaped bacillus (bacilli)
spiral shaped spirillus

34. Domain Bacteria
Shapes (cont’d)
Spiral-shaped
Called spirilla

35. Domain Bacteria Occur in many shapes including Rod-shaped
Called bacilli

36. Domain Bacteria Shapes (cont’d) Sphere-shaped Called cocci
In chains, called streptococci
In grapelike clusters called
staphylococci

37. 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
Motility – movement
a) flagellated – move with flagellum or flagella
b) slime layer allows gliding
c) spirochete - cork-screw rotation

38. 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

39. 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

40. Structure of a Bacterial Cell

41. Phyla groups:
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

43. 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)

44. B) Gram-positive bacteria
- most are gram-positive
- ex: botulism, Lactobacilli (yogurt),

45. 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)
People used to call it blue-green algae, because they thought it was algae

46. D) Spirochetes
gram negative
spiral shaped
E) Chlamydia (no peptidoglycan)
gram negative
round shape
are parasites to animal cells

47. 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

48. 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

49. 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

50. Protists

51. Habitats: aquatic habitats or moist soil
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

52. 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)

53. 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

54. 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

55. 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”

56. 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

57. 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

58. Brown algae (Phaeophyta)
All cold water marine; all multicellular; include sargassum and kelp

59. 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

60. 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

62. 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

63. Fungi Kingdom · Eukaryotes · Heterotrophic: - most saprophytes
- some parasites
·       Most multicellular;
one is unicellular
·       Most sessile

64. 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

65. 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)

66. ·       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

67. 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)

68. 1.   Common molds (Zygomycota)
·       No septa in hyphae
·       Asexual reproduction - most common
Sexual reproduction spores formed in sporangium
·       Examples: bread mold, fruit molds

69.    Club fungi (Basidiomycota)
·       Reproduce sexually by producing spores in basidium
Located in gills under the cap
·       Examples: mushrooms, bracket fungi, shelf fungi,
Puffballs

70. 2.   Sac Fungi ( Ascomycota)
·       reproduce sexually by means of ascus
bulb like projections that form from the hyphae
·       examples: yeasts, truffles, morels, powdery mildews

71.    Imperfect fungi (deuteronomycota)
·       no sexual reproduction; asexual only
·       examples: the fungus that cause ringworm, athete’s foot, nail infections

72. 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   

73.    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