Chapter 15b: Viruses Cnt

Phage DNA

*Phage DNA =* the DNA from the virus that goes into the cell and takes it over (almost like a parasite)

Two Mechanisms of Latency of Human Viruses

1. Virus *integrates into host genome* and may remain dormant for long periods of time ex) HIV 2. Other viruses can exist as *episomes* - genetic elements that replicate independently but occasionally integrate into host DNA ex) Herpes simplex type I and II, varicella zoster (chicken pox)

Phage

A virus using the host cell to replicate

The incorporation of tetracycline resistance genes that are picked up from outside the cell is an example of: a. Natural competency b. DNA uptake c. Transformation d. Horizontal gene transfer e. All of the above

All of the above

You visit your neighborhood doctor after learning you have acquired swine flu. Despite your pleading she steadfastly refuses to prescribe a course of antibiotics. Why is she doing this? a. Viruses are not alive b. Viruses are unaffected by antibiotics c. Overuse and misuse of antibiotics can lead to widespread resistance d. All medication carry some risk of adverse side effects e. All of the above

All of the above

Reverse Transcriptase: a. Is a viral enzyme b. Copies RNA into DNA c. Is found in the human immunodeficiency virus d. Is critical for retroviral replication e. All of the above

All of the above ***the reverse process of transcription (so going from RNA into DNA)

Types of Plasmids: Fertility Plasmids (F Factors)

Allow bacteria to mate

~Note~

Bacterial DNA is not wound around histone proteins to form nucleosomes (like eukaryotes)

A naturally competent bacterium can do the following: a. Reproduce sexually b. Bind and uptake DNA fragments c. Form a sex pilus d. Reproduce via genetic exchange with other bacteria e. Resist antibiotics

Bind and uptake DNA fragments

F Factors

Carry several genes that are *required for conjugation* and also may carry genes that confer growth advantage

Typical bacterial chromosome must be ____ about 1,000-fold

Compacted

Only _____ with competence factors are capable of transformation

Competent cells

Types of Plasmids: Resistance Plasmids (R Factors)

Confer resistance against antibiotics and other types of toxins

Types of Plasmids: Degradative Plasmids

Enable the bacterium to digest and utilize an unusual substance

Types of Plasmids: Col-Plasmids

Encode colicines, which are proteins that kill other bactiera

F+ and F-: Which has a F factor, and which doesn't?

F+ has an F factor, F- does not

During the lysogenic cycle viral particles are actively being manufacture and assembled a. True b. False

False **this is the lytic cycle **lytic = actively making copies of the virus **lycogenic = having genetic material integrate and waiting for a good time for the virus to be made

Gene Transfer Between Bacteria MULTIPLE QS ON THIS SLIDE ON THE EXAM

Genetic diversity in bacteria - from mutations or genetic transfer 1. Conjugation Direct physical interation transfers genetic material from donor to recipient cell 2. Transformation DNA released from a dead bacterium into the environment is taken up by another bacteria 3. Transduction A virus transfers genetic information from one bacterium to another

Plasmids aren't usually necessary for survival but can provide _____

Growth advantages

~Note!!!~

Horizontal Gene Transfer is the Transfer of Genes Between the Same or Different Species • Vertical gene transfer is when genes are passed from one generation to the next among individuals of the same species • Roughly *17% of genes* in E coli and Salmonella have been acquired by horizontal transfer during the past 100 million years • Medical relevance of horizontal gene transfer is profound -ex) acquired *antibiotic resistance*

~Note~

Integrase doesn't always happen, only happens during lycogenic cycle

Lysogenic Cycle

Integration, replication, and excision

~Note: Bio Principle~

Living Organisms grow and develop After cell division, a bacterial cell increases in size

Proteins important in forming _____

Loop domains **compacts DNA about 10-fold

~Note~

Lysogeny/latency in bacteriophages = when host cell replicates, also copies prophage

Episome:

Plasmid that can integrate into bacterial chromosome

In addition to the circular chromosome bacteria often have small extrachomosomal rings of DNA celled: a. Plasmids b. Endospores c. Includions d. Plastids e. Histones

Plasmids

_____ occur naturally in many strains of bacteria and in a few types of eukaryotic cells, such as yeast

Plasmids

AZT is a reverse transcriptase inhibitor, how does this drug prevent the replication of a retrovirus? a. Prevents the cutting and assembly of viral capsid proteins b. Blocks the integration of viral genes into the host cell's genome c. Prevents the copying of RNA into DNA d. Blocks viral exocytosis from the host cell e. Inhibits viral binding and uncoating

Prevents the copying of RNA into DNA **B would = inhibiting integrase

Plasmids own origin of replication that allows it to be ______ of the bacterial chromosome

Replicated independently

~Note~

Reverse transcriptase lacks proofreading function: • Makes more errors • Tends to create mutant strains of HIV • Makes it difficult to create vaccine

____ are made by F+ cells that bind specifically to F- cells

Sex pili

_____ that exist independently of the bacterial chromosome

Small, circular pieces of DNA

Lytic Cycle

Synthesis, assembly, and release

~Note~

Temperate phages have a lysogenic cycle, but virulent phages do not -Environmental conditions influence integration and length of latency

Integration occurs when: a. The virus uncoats and enters a host cell b. The virus binds to the surface of a host cell c. The viral genes are incorporated into the host cell's genome d. The viral genes direct the synthesis of viral polypeptides e. The viral genes are packaged into newly constructed viral capsids

The viral genes are incorporated into the host cell's genome

DNA Supercoiling

Topoisomerases twist the DNA and control degree of supercoiling

Bacterial genes beings transferred by a virus is termed: a. Transformation b. Conjugation c. Transduction d. Contamination e. Transmutation

Transduction **transformation = uptake of DNA from the outside environment **conjugation = bacterial sex, exchange genes using the sex pili (one bacteria is F+, so its sex pili attaches to the other that's F- and they transfer their DNA)

_____ does not require direct contact between bacterial cells

Transformation

A filter was used to separate 2 colonies of bacteria in a liquid growth medium. The filter's pores are too small to allow bacteria and viruses to cross but are large enough to allow DNA molecules to pass. Suction is applied and the bacteria on one side of the filter begin to acquire the traits of bacteria on the other side of the filter. What process is responsible for this? a. Transformation b. Conjugation c. Mutation d. Alternative splicing e. Transduction

Transformation **not transduction because it says viruses can't cross the filter and transduction is always done with a virus **alternative splicing is removing exons from genetic material **mutation occurs very randomly and usually very spread out **can't be conjugation because they're separated and the bacteria can't go through the filter and get in direct contact with each other

Types of Plasmids: Virulence Plasmids

Turn a bacterium into a pathogenic strain

Viral Reproductive Cycle: Attachment

Usually specific for one kind of cell due to binding to specific molecules on cell surface

Transduction

Viruses that infect bacteria can transfer bacterial genes from one bacterium to another **Usually an error in a phage lytic cycle **Newly assembled phages incorporate piece of host DNA instead

AIDS Can Also Spread: (3)

• *By transfusion* of HIV-infected blood • By sharing of needles among drug users • From *infected mother* to unborn child

Aids Helper Cells

• AIDS is so devastating because the virus destroys a type of white blood cell called a *helper T cell* -Helper T cells play an essential role in the mammalian immune system • When T cells are destroyed by HIV, the immune system is seriously compromised -Patient becomes susceptible to opportunistic infections that would not occur in a healthy person

Viral Reproductive Cycle: Entry

• Bacteriophage inject only DNA into bacteria • HIV fuses with host membrane and entire virus enters • One or several viral genes are expressed immediately • Virus may proceed to synthesis of viral components OR integrate into host chromosome

Genetic Properties of Bacteria

• Genes of bacteria are found in bacterial chromosomes • Usually a single type of chromosome • May have *more than one copy* of that chromosome • Number of copies depends on the bacterial species and on growth conditions • Typically 1-4 identical chromosomes • *Nucleoid* - region where tightly packed bacterial chromosome found

Viral Reproductive Cycle: Synthesis of Viral Components

• Host cell enzymes such as DNA polymerase make many copies of the phage DNA and transcribe the genes within these copies into mRNA • In the case of HIV, the DNA provirus is not excised from the host chromosome. Instead, it is transcribed in the nucleus to produce many copies of viral RNA -Translated to make viral proteins -Serve as genome for new viral particles

~Note: AIDS and HIV~

• Human immunodeficiency virus (HIV) is the causative agent of acquired immune deficiency syndrome (AIDS) • HIV is primarily spread by *sexual contact* between infected and uninfected individuals

~Note~

• In US, the estimated annual number of AIDS related deaths has fallen, due in part to the use of new *antiviral drugs* (can slow down the process but can't remove the virus from the body)

~Note: Transformation~

• Living bacterial cell imports a strand of DNA that another bacterium released into the environment when it died • Competence factors facilitate binding of DNA fragments to the bacterial cell surface, uptake of DNA into the cytoplasm, and incorporation of imported DNA into the bacterial chromosome

Bacterial Chromosomes

• Molecules of double-stranded DNA • Usually circular • Tend to be shorter • Contains a few thousand unique genes • Mostly structural genes • Single origin of replication

~Note: Sex Pili~

• Once contact is made, pili shorten to draw the cells closer together • One strand of F factor is transferred, other strand stay in donor • Both replicate so that donor and recipient now have complete double stranded F factor

Conjugation

• Only about 5% of E coli strains found in nature can act as donor strains • Donor strains contain a fertility factor (F factor) that can be transferred to recipient strains -Some donor strains are Hfr (High Frequency of Recombination)

Viral Reproductive Cycle: Release

• Phages must lyse their host cell to escape • Enveloped viruses bud from the host cell

~Reproduction~

• Some species like E coli can divide every *20-30 minutes* • Single cell can form a bacterial colony in *less than a day* • Reproduce by *binary fission* - NOT mitosis • Unless a mutation occurs, each daughter cell contains an *identical copy* of the mother cell's genetic material • Does not involve genetic contributions from two different parents • Plasmids may replicate independently of the bacterial chromosome

~Note: Latency in Bacteriophage~

• Some viruses can integrate their genomes into a host chromosome • Prophage or provirus can remain inactive or *latent* • Most viral genes silenced

Viral Reproductive Cycle: Viral Assembly

• Some viruses self-assemble • Other are too complicated to self-assemble • Proteins modify capsid proteins or serve as scaffolding

~Note: AIDS Death and Infection Rates~

• Total number of AIDS deaths since 1981 is over 30 million -more than 0.5 million of these deaths occurred in the US • During 2012, around 2.5 million adults and children became newly infected with HIV • Worldwide, nearly 1 in every 100 adults between 15 and 49 is infected • In the US about 55,000 new HIV infections occur each year -70% of new infections are in mean, 30% in women

Viral Reproductive Cycle: Integration

• Viral gene for integrase • Integrase cuts host chromosomal DNA and inserts viral genome • Phage in bacterial DNA called prophage -may excise later and proceed to synthesis • HIV is an RNA virus -Uses viral reverse transcriptase to make complementart DNA strand that will be template for double stranded viral DNA -Integrates as a provirus