1. Vivacious Viruses
Chapter 19

2. I. Virus Characteristics Smaller than a ribosome
Can form into regular crystals (cells won’t do this)
Made of Nucleic Acid - Genome is made of one of the following:
DNA - double stranded
DNA - single stranded
RNA - double stranded
RNA - single stranded

4. A. Characteristics (cont)
Range from 4 genes to several hundred
Protein coat surrounds nucleic acid
Capsid - protein coat
can be rod shaped (helical), polyhedral or more complex
capsids are made from large numbers of protein subunits called capsomeres

5. A. Characteristics (cont)
Accessory Structures (found in some viruses)
Viral Envelopes - membranes surrounding capsid
come from membrane of their host cell and contain the same proteins, glycoproteins and phospholipids used by host
These envelopes help viruses to infect host without being detected
Bacteriophages - have most complex capsids

7. B. Reproduction of Viruses
Happens only in a host
cell because they have no
ribosomes or enzymes to
reproduce on their own

8. B. Reproduction of Viruses
Host Range - limited amount of host cells that a virus can infect (can be one host or a few related species)
Host identified by “lock and key” fit between proteins on capsid and receptors on outside of host cell
Can be Tissue Specific - eukaryotic viruses may infect only certain tissues of their host
ex. cold - respiratory tissue, HIV - white blood cells only

9. B. Reproduction of Viruses
Methods of Reproduction - virus infects host first and overtakes host cell to make viral nucleic acids and proteins
Host provides the following:
Nucleotides for synthesizing viruses nucleic acid
Enzymes
Ribosomes
tRNA, amino acids, ATP and other parts needed by virus to go through transciption and translation (to make viral proteins)

10. Reproduction of Viruses-
Lytic Cycle - viral reproductive cycle that ends in the death of the host cell (also called virulent virus)
ex. T4 bacteriophage

11. Lytic Cycle (cont)
Phage attaches to cell - uses tail fiber to stick to receptor site on host (e. coli)
DNA is injected through cell wall and membrane into the host cell

12. Empty capsid remains outside the cell and DNA of the host is hydrolyzed (broken up)
Phage overtakes cell using its parts to manufacture viral nucleic acids and proteins. New phages are reassembled inside host cell

13. Phage makes host cell produce lysozyme - an enzyme that digests the host’s cell wall.
Osmosis causes the cell to swell and burst releasing the new phages (may be new ones) Phages go find new host cell to infect

15. Reproduction of Viruses
Lysogenic Cycle - replicates viral genome without killing host cell
If they use both lytic and lysogenic - also called temperate viruses

16. B. Lysogenic Cycle (cont)
Phage binds to host cell and injects DNA
Phage DNA forms a circle inside host - it can now go through either lytic or lysogenic cycle. (If lytic - see previous process)
Viral DNA lines up with host DNA and gets incorporated into the host DNA by crossing over - it is now called a prophage - one of its genes represses the other genes so it’s basically not affecting the host at all at this point
When the host cell replicates and divides, it also replicates the virus and passes it on to its daughter cells

17. B. Lysogenic Cycle (cont)/
At some point, phages will leave the host DNA and return to a lytic cycle. At this point they will destroy their host cell - trigger can be chemicals, radiation or other
Some other viral genes may be expressed when DNA is part of host cell and produce toxins (like botulism, diptheria, scarlet fever)

19. C. Animal Viruses
Vary in type of nucleic acid and presence/absence of viral envelope
Viral Envelopes
Outer membrane (outside capsid) that helps parasite enter host cell
Bind to animal cell
Envelope fuses with plasma membrane and injects virus + capsid into cell
Enzymes of host cell remove capsid, virus overtakes cell (similar to bacteria)

20. C. Animal Viruses Cycle does not always kill the host cell
Some virus envelopes come from nuclear membrane and virus is replicated inside the nucleus of the host (like herpes)
DNA of virus becomes integrated into host DNA and becomes a provirus
Trigger will cause provirus to become active and destroy host cell

22. C. Animal Viruses RNA virus
Classification - by # of strands and how they function in host
Class IV - serve directly as mRNA - can be translated into viral protein as soon as they infect
Class V - RNA of virus serves as template to make mRNA - must be transcribed into mRNA before translation

24. B. RNA viruses in animals
Class VI - Retroviruses - reverse flow of genetic information
Contain enzyme - reverse transcriptase - that transcribes DNA from an RNA template (goes backward)
DNA becomes a provirus in nucleus of host
Viral DNA is now transcribed to RNA (can be mRNA for translation, or can be packaged and sent to new host cells)
HIV is a retrovirus that causes AIDS

26. E. Viral Diseases in Animals
Causes
Virus could damage or kill cells
Virus may produce toxins that cause symptoms

27. C. Viral Diseases in Animals
Effects depend on ability of affected tissue to make new cells
If virus affects rapidly dividing cells – can have complete recovery (throat)
If virus affects areas where cells have stopped dividing, damage is permanent (like nerve cells - polio virus)

28. 3. Vaccines
Harmless variants of pathogenic microbes that stimulate the immune system to mount defense against virus
sensitizes immune system to the virus so that it reacts vigorously if ever truly exposed to the virus

29. 4. New Viruses Result from a variety of causes
Mutation of existing virus - seen often in RNA viruses because they have no proofreading mechanism
May lead to new varieties that individuals were already immune to (flu)
Spread of existing viruses from one species to another
Dissemination from small population to large population - due to increased travel, blood transfusions,
IV drug use

30. 5. Cancer causing viruses
Oncogenes - genes that trigger cancerous characteristics in cells
Proto-oncogenes - versions of oncogenes found in normal cells - code for proteins that control growth factors and cell division
Virus may trigger proto-oncogenes to turn on causing uncontrolled cell division - Usually only cause cancer in combo with a mutagen

31. F. Plant Viruses stunt growth in plants and diminish crop yields
Horizontal transmission of virus - insects, high winds, injury, freezes - cause plants outer layer of epidermis to become damaged
increases chance of virus to penetrate epidermis and infect plant
farmers transmit from plant to plant using same pruning tools

32. D. Plant Viruses
Vertical transmission - plant inherits viral infection from a parent
Occurs during asexual reproduction or in seeds of sexual reproduction
Virus spreads through plant via plasmodesmata

34. G. Viroids Tiny molecules of naked RNA that infect plants only
Make no proteins but replicate in plant cells and stunt their growth

35. H. Prions
infectious proteins - usually affect brain tissue (mad cow)

36. Breathtaking Bacteria
Chapter 27
Chapter 18

37. I. Major Characteristics
DNA
One, double stranded, circular molecule
Tightly packed into “nucleoid” region
No membrane surrounding it
Plasmids - smaller circular pieces of DNA outside nucleoid region

38. B. Reproduction
Divide by binary fission from single origin of replication
Asexual- no mating involved - Most offspring are genetically identical to parent
Fast process - many can divide every 20 minutes
Relatively high rate of mutation due to speed of reproduction
Mutation rate helps bacterial colonies to survive better

40. C. Genetic Recombination
While bacteria do not reproduce sexually, they are able to have some recombination of genes with other bacteria through one of the following methods:

41. 1. Transformation
Uptake of “naked” foreign DNA from the surrounding environment (like the S-strain/R-strain killing mice)
Live, nonpathogenic cell takes up a piece of DNA that includes the allele to make it pathogenic
Foreign allele is incorporated into the bacterial chromosome and replaces the original allele by crossing over
Many bacteria have receptors on their surface proteins that aid in uptake of naked DNA only from closely related species
Calcium - can be added to bacteria without these receptors (like e.coli) and will artificially stimulate the bacteria to take up naked DNA

43. 2. Transduction
Phages carry bacterial genes from one host to another

44. Transduction (cont.)
When a virus is reassembling in it’s host a small piece of bacterial DNA from host is accidentally packaged into capsid of virus
Phage can attach to another host and inject the bacterial DNA into it
Crossing over incorporates this DNA into the host cell
RANDOM

46. 3. Conjugation
Direct transfer of genetic material between two bacterial cells that are temporarily joined.
bacterial version of “sex”
One way transfer
donor = male - uses sex pili to attach to
recipient = female
bridge forms between two bacteria and DNA can be transferred

47. D. Plasmids
Small, circular, self-replicating DNA molecule separate from bacterial chromosome
Can remain separate from chromosome
Episome: Can become part of bacterial chromosome and replicate with it
No protein coats and can’t exist outside the cell
Generally beneficial to bacteria
Small number of genes that may help bacteria survive in stressful environments

48. 1. F Plasmid Contains 25 genes required for production of sex pili
F+ = cell that contains F plasmid - donaters
F- = cell without F plasmid - recipients
Heritable F+ bacteria give rise to F+ offspring
F+ x F-  F+ (male) replicates it’s DNA, transfers copy to F- (female) converting it to F+ (male). Now the newly converted F+ bacteria can make sex pili and transfer its plasmid to new bacterial cells

50. 2. Hfr cell F factor becomes part of bacterial chromosome.
During conjugation - F factor replicates and gets transferred to F-, but some of the bacterial chromosome can be taken with it.
Recipient cell is temporarily “diploid” for some genes and crossing over can occur
When bacteria divides, it has the new genes
Any pieces of Hfr DNA left will be degraded

53. 3. R-plasmids
“Resistance” plasmids - contain genes that code for resistance to antibiotics
When a bacterial population is exposed to antibiotics, any “sensitive” bacteria are killed by the antibiotics
Bacteria that contain the R plasmid with resistance to the antibiotic survive
These bacteria then reproduce, increasing the number of antibiotic resistant bacteria (natural selection)
R-plasmids can also be transferred during conjugation and may carry as many as 10 genes for resistance to different antibiotics

54. II. Control of Gene Expression in Bacteria
Purpose
helps individual bacteria cope with changes in their surroundings
ex. E. coli in human intestine - rely on what the host eats for it’s nutrition. Bacteria must be able to turn genes on and off depending on its nutritional needs

55. B. Metabolic control
Regulates which metabolic pathways are turned on and off. Done by one of the following 2 methods.
Adjust activity of enzymes already present in cell. Depends on sensitivity of enzymes to chemical cues
ex. Feedback inhibition - when the end-product starts to accumulate, it will inhibit one or more of the enzymes in the pathway turning it off

56. B. Metabolic control Regulation of gene expression -
Control of enzyme/protein production by controlling transcription and translation (turning genes on and off).
In bacteria - this regulation occurs with Operons

58. C. Operon
contains all the necessary components for controlling a metabolic pathway including:
Operator - on/off switch located in the promoter region of the DNA (before the genes)
Promoter - binding site for RNA polymerase
Transcription unit - all of the genes necessary for a certain metabolic pathway

59. C. Operon
Regulatory gene - occurs somewhere else in the DNA and codes for a repressor (off switch)
Repressor – a protein that switches an operon off. Specific to one operon
Corepressor - binds to repressor and activates it, changes it’s shape so it can bind to the operator and turn the pathway off

60. Negative Control.. The Repressible Operon
This pathway is called repressible because the system is normally on but can be turned off when there is enough resources available for the bacteria
Normally the operon is in the on position, one long mRNA is made for the 5 enzymes required in the pathway. The mRNA will attach to a ribosome, produces the enzymes and the enzymes will make tryptophan

62. 2. Host eats Thanksgiving dinner
Turkey contains lots of tryptophan
Why would the bacteria use its resources/energy to make tryptophan when it can get it from its host? - it doesn’t

63. Trp operon (cont)
Tryptophan is a corepressor in this pathway. It will bind to the repressor molecules (floating in cytoplasm but inactive)
When trp binds to repressor, shape of repressor changes and it becomes active
Active repressor then binds to operator region of DNA and turns the operon OFF
No mRNA is made and the enzymes to make trp are no longer produces

66. After that great turkey dinner is digested by the host and the tryptophan levels decrease again, the repressor becomes inactive again, releases from the operator, and the operon is turned back on

67. E. Negative Control.. The Inducible Operon
In this pathway, the repressor is made in its active form and automatically binds to the operator. The system is normally OFF but can be turned on (induced) when it is needed. (Why make the enzymes to break down lactose if there’s no lactose around)
EX. The lac operon produces 3 enzymes to break down lactose (milk sugar) for energy.

69. Lac operon (cont)
Host drinks a big glass of milk (contains lots of lactose plus some allolactose)
Allolactose binds to the repressor and releases it from the operator region
RNA polymerase can then go on and transcribe the mRNA needed to make the enzymes for breaking down lactose

71. Positive Control of Gene Expression
There is another factor controlling the lac operon
Glucose is the best energy source for the bacteria. Lactose doesn’t provide as much ATP as glucose does.
Enzymes to break down lactose will only be made if lactose is present AND glucose levels are LOW!

72. Positive Control of Gene Expression
cAMP accumulates (when glucose is low)
cAMP binds to a regulatory protein called cAMP receptor protein (CRP)
This complex (cAMP+CRP) is an activator of transcription and binds near the promoter of the operon and makes transcription faster by making it easier for RNA polymerase to bind to promoter
If glucose levels build up, cAMP/CRP will release and transcription will slow down