1. VIRUSES and PROKARYOTES
Sections 28.1 and 28.2

2. ARE VIRUSES CONSIDERED “LIVING”? WHAT ARE SOME VIRUSES YOU KNOW?

3. What is a VIRUS?
VIRUS: nonliving strand of genetic ​material within a protein coat​
not considered "living" - lacks ​characteristics of life ​
no organelles, cannot make proteins, cannot move, cannot replication by themselves 

5. So how big is a VIRUS? electron microscopes needed to study them ​
range from 5 to 300 nanometers (nanometer = 1 billionth of a meter)​
10,000 cold viruses needed to cover a period in textbook

6. Where do VIRUSES come from?
Most likely theory: came from parts of cells (genes are similar to cellular genes) ​
somehow developed ability to exist outside of cells ​

7. Structure of Viruses CAPSID: the outermost layer of ALL viruses ​
made of proteins ​
often surrounded by outer membrane envelope (made of plasma membrane)
Genetic material located inside capsid​
can be DNA or RNA, NEVER BOTH!​
classified based on type of nucleic acid they carry 

9. Viruses are classified based on three criteria:
Type of nucleic acid and whether it’s single or double-stranded
Viral size and shape
Presence or absence of outer envelope

10. How do we become infected?
known as obligate intracellular parasites
Although they can infect a variety of cells, each type of virus is very specific.
Tobacco mosaic virus only infects plants
Rabies only infects mammals
Hypothesis: Viral nucleic acids are derived from host-cell genomes, which means that viruses evolved after the appearance of cells and are still evolving today!​

11. Viral Replication ​Viruses are host-cell specific:
Portions of capsid (spikes on envelope) bind in a lock-and-key manner to receptor on host-cell plasma membrane
viral nucleic acid takes over metabolic control of the host cells, producing more viruses
Bacteriophages (or phages): viruses that parasitize bacteria

12. The Lytic Cycle
Occurs when the host cell makes copes of the viral RNA or DNA. ​ ​
1. Attachment: Capsid combines with receptor on bacterial cell wall in lock-and-key manner
2. Penetration: Viral enzyme digests away part of cell wall, and viral DNA enters bacterial cell

13. 3. Biosynthesis: Virus deactivates host’s genes that don’t contribute to replication, then begins viral DNA replication and production of capsid protein subunits
4. Maturation: Viral DNA and capsids are combined, producing viral particles, and lysozyme is produced
5. Release: lysozyme affects cell wall, allowing viruses to be released; destroys the bacterial cell

14. Generally causes active infections (symptoms appear 1-4 days after exposure) ​
EXAMPLES: Common cold and influenza

15. The Lysogenic Cycle
Occurs when viral DNA enters the nucleus of the host cell. ​
1. Attachment: see lytic cycle for details
2. Penetration: see lytic cycle for details
3. Integration: Viral DNA becomes part of the bacterial DNA (doesn’t destroy it like in lytic cycle)

16. 4. Prophage: viral DNA is latent (doesn’t affect the host)
Prophage replicated with host DNA
All daughter cells carry viral DNA
Could be dormant for months or years
5. Activation: environmental factors (ex. UV light) causes prophage to enter the biosynthesis stage (lytic cycle) and continue to maturation and release

17. EXAMPLES: Herpes Simplex I (orally)

18. Replication of Animal Viruses
Replication of animal viruses is very similar to bacteriophages.
If the virus has an envelope...
Glycoprotein spikes get virus to stick to plasma membrane receptors
Capsid and viral genome penetrate host cell
Virus gets uncoated as capsid removed

19. Biosynthesis occurs
Viral release by budding
As virus buds, it develops a plasma envelope
Envelope components (ex. glycoproteins) allow virus to enter host cell
Doesn’t always end in cell death

20. Then what’s a RETROVIRUS?
RETROVIRUS: viruses that contain RNA instead of DNA, and have a complex replication cycle ​(ex. HIV)
Contains reverse transcriptase – enzyme that carries out RNA to cDNA transcription
cDNA – DNA copy of viral genome
after replication, cDNA becomes part of host genome
when DNA is transcribed, new viruses are produced (biosynthesis, maturation, release) by budding

22. REPLICATION CYCLE OF RETROVIRUSES
 ​1. HIV attaches to cell​
virus moves into cytoplasm and releases viral RNA ​
2. Reverse Transcriptase synthesizes DNA using viral RNA as template ​
3. DNA moves into host's nucleus and integrates into chromosome ​
could lie inactive for years ​
4. (When activated) RNA is transcribe from viral DNA and host creates new HIV particles 

24. Viral Infections
Cold/unfluenza, herpes virus, hepatitis viruses, and HIV
Viroids: naked strands of DNA not covered by capsids
like viruses, they direct cell to make more viroids
found in several crop diseases

25. Last but not least, how do PRIONS fit into this?
PRION (proteinaceous infectious particle): protein particles that can cause other proteins to become prions (leads to an infection or disease) ​
normally exist in cells (coil-shaped)
mutations cause misfolding (shaped like a piece of paper folded many times)​
associated with transmissible spongiform encephalopathies ​
EX.: Mad Cow Disease, Scrapie, and Creutzfeldtz- Jakob disease  

26. How do PRIONS infect us? cause normal proteins to mutate ​
infect nerve cells in the
brain, making them burst ​
creates spaces in brains,
like a sponge ​
How does this relate to us? ​
abnormal proteins found in the brains/spinal cords of cattle ​
hypothesis that prions could contaminate beef ​

27. Domains BACTERIA and ARCHAEA
28.2 Prokaryotic Cells
Domains BACTERIA and ARCHAEA

28. Structure No cytoplasmic organelles except for ribosomes
Nucleiod: no nuclear envelope, contains chromosomes
Contain plasmids, which are used to carry foreign DNA into other prokaryotes
Cell wall that has amino sugars cross-linked by peptide chain

29. Surrounded by capsule
Move using flagella or fimbraie (short, hair-like appendages)
Interior: cytoplasm, ribosomes, nucleiod
Exterior: flagella, fimbriae, capsule/slime layer, cell wall, plasma membrane

31. Method of Reproduction
Binary Fission: asexual method of reproduction where the original cell divides into 2 identical daughter cells
Prior to division: Single circular chromosome made of double-stranded DNA
Begins with duplication of chromosome...

32. 2 identical chromosomes attach to inside of plasma membrane
Cell elongates, pushing chromosomes to opposite ends
Plasma membrane pinches together in the middle and cell wall forms
End Result: 2 identical cells

34. 3 methods of genetic recombination have been seen in bacteria...
Conjugation: male cell passes DNA to female cell by way of sex pilus
Transformation: bacterium binds to and takes up DNA released into the medium by dead bacteria
Transduction: bacteriophages carry portions of DNA from one bacterium to another

35. Endospores: portion of cytoplasm and a chromosome copy dehydrate and are protected by 3 heavy spore coasts
Endospore released as cell deteriorates
When conditions are better, endospore absorbs water and grows out of spore coats
Becomes a typical bacterial cell and will reproduce by binary fission

37. Feeding Method
Photosynthetic: use light as an energy source to produce food
Chemosynthetic: oxidize inorganic compounds to obtain energy needed to produce food
Saprotrophs: carry on external digestion of organic matter and absorb resulting nutrients across plasma membrane
Decomposers: break down organic matter, making inorganic nutrients available ot photosynthesizers

38. Obligate anaerobes: unable to grow in the presence of oxygen
Facultative anaerobes: can grow either in the presence or absence of oxygen
Most bacteria are aerobic and require oxygen to live.