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Chapter 18 - Genetics of Viruses and Bacteria Questions 1. The proteins that encapsulate the genetic material of a virus is known as the _____________.

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Presentation on theme: "Chapter 18 - Genetics of Viruses and Bacteria Questions 1. The proteins that encapsulate the genetic material of a virus is known as the _____________."— Presentation transcript:

1 Chapter 18 - Genetics of Viruses and Bacteria Questions 1. The proteins that encapsulate the genetic material of a virus is known as the _____________. 2. Draw a general structure of a eukaryotic virus and label parts. 3. An individual protein of the structure mentioned in question number 1 is known as a _______________. 4. A bacteriophage can reproduce via two different life cycles known as the ________________ and _________________. 5. The genetic material of viruses can be ______, ______, _____ or ______. 6. This general structure is found to be part of some viruses like Influenza and not part of other viruses like Adenovirus.

2 Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… Viruses : Packaged Genes

3 Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… What is a virus? - A small [20 to 250nm in diameter] infectious agent that requires a host cell to replicate (make more of itself). **1/1000 th the diameter of a eukaryotic cell. If the classroom was a cell, a virus would be about the size of a paperclip. 2. General Structure SEM of adenovirus 3. Host Range - Each virus can only infect a specific range of cell types Ex. HIV can only infect CD4+ Helper T- cells 1. Obligate intracellular parasite Nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope

4 Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… Size Comparison Virus: 20 to 250nm (.02 to.25um ) Prokaryote: 1 to 10um Eukaryote: 10 to 100um

5 Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… 1. All viruses contain genetic material (DNA or RNA) encapsulated by a protein coat called a capsid. 18  250 mm 70–90 nm (diameter) 20 nm 50 nm (a) Tobacco mosaic virus (b) Adenoviruses RNA DNA Capsomere Glycoprotein Capsomere of capsid 80–200 nm (diameter) 50 nm (c) Influenza viruses RNA Glycoprotein Membranous envelope Capsid 80  225 nm 50 nm (d) Bacteriophage T4 DNA Head Tail fiber Tail sheath CAPSID 2. An individual protein in the capsid is called a capsomere. 3. Bacteriophage (phage) have the most complex capsids

6 Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… Influenza looks different…it has an envelope. What’s up with that? 18  250 mm 70–90 nm (diameter) 20 nm 50 nm (a) Tobacco mosaic virus (b) Adenoviruses RNA DNA Capsomere Glycoprotein Capsomere of capsid 80–200 nm (diameter) 50 nm (c) Influenza viruses RNA Glycoprotein Membranous envelope Capsid 80  225 nm 50 nm (d) Bacteriophage T4 DNA Head Tail fiber Tail sheath

7 Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… 1. Only some viruses have cell membrane-like envelopes 80–200 nm (diameter) 50 nm (c) Influenza viruses RNA Glycoprotein Membranous envelope Capsid Envelopes 2. The envelope is derived (comes from) the cell membrane of the host cell Ex. Influenza (shown right)

8 Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… Simplified viral reproductive cycle How do viruses replicate (reproduce)? Viruses Hijack Cells They gain access and use the enzymes, ribosomes, and small molecules (ATP, nucleotides, amino acids, phospholipids, etc…) of host cells.

9 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 1. Bacterial virus (bacteriophage or just phage) T4 Phage infecting E. coli Let’s begin with the best understood virus: How do they reproduce?

10 Fig Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… Bacteriophage binds to the surface of the bacterium using the tail fibers and injects its DNA into the cell… Bacteriophage reproductive cycle (two methods of reproduction)

11 Fig Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… Lysogenic cycle Bacteriophage reproductive cycle (two methods of reproduction)

12 Fig Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… Lysogenic cycle Lytic cycle Bacteriophage reproductive cycle (two methods of reproduction)

13 Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… Lysogenic cycle Lytic cycle - After the bacteriophage injects its DNA, it might get incorporated into the bacterial chromosome and is now called a prophage. Now when the bacterial cells replicates, the phage DNA replicates with it. - After the bacteriophage injects its DNA or when the prophage jumps out of the DNA, it can hijack the cell and use it (its ribosomes and other enzymes) to make more viral DNA and proteins to in turn make more viral particles. The cell will lyse and the viruses will be released. Temperate Phages - Phages that can do both lytic and lysogenic methods of reproduction Ex. Lambda (λ) phage

14 Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… We observed the switch to be caused by environmental factors like radiation or certain chemicals causing DNA damage, which would promote the lytic phase as the bacterial cell will likely die soon and the phage needs to get out quick. In addition, lytic is favored when nutrients are plentiful allowing the phage to makes lots more of itself, while the lysogenic is favored when nutrients are in low concentration within the bacterium. This makes sense as the virus can lay low until better times. Can’t make more of yourself if the materials are simply not available. What causes a temperate phage like lambda to switch from lysogenic to lytic?

15 Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… Of course. They contain enzymes that attempt to hydrolyze the viral DNA known as restriction enzymes like little molecular scissors. Can prokaryotes defend themselves against this attack?

16 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses Capsid – made of proteins and surrounds the genetic material in the core. A. Anatomy Genetic Material – Can be ssDNA/dsDNA or ssRNA/dsRNA depending on the virus. Codes for polypeptides/proteins needed by the virus to enter and hijack the cell as well as the proteins of the capsid and envelope. Envelope – Phospholipid bilayer similar to a cell membrane with embedded proteins (protein spikes) surrounding the capsid. Not all virus types have envelopes

17 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses Capsid DNA Protein spikes

18 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses They are classified by their genetic material.

19 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses DNA viruses

20 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses B. DNA viruses DNA capsid envelope

21 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses B. DNA viruses Ex. Adenovirus - Causes upper respiratory infections - Symptoms range from those similar to the common cold to bronchitis or pneumonia. (Common cold is caused by rhinovirus, an RNA virus)

22 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses B. DNA viruses Ex2. Herpesviruses (family of related viruses) These can cause: 1. Oral herpes (cold sores) or genital herpes (an STD)

23 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses B. DNA viruses Ex2. Herpesviruses (family of related viruses) These can cause: 2. Chicken pox (varicella zoster virus)

24 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses B. DNA viruses Ex3. Poxvirus (family of related viruses) Can cause: 1. Small pox This is the only human infectious disease to ever be eradicated (removed from the face of the planet) – we did this through extensive vaccination.

25 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses B. DNA viruses Ex4. HPV – Human Papillomavirus 1. Some of these STD viruses can lead to cancers of the cervix, vagina, and anus in women or cancers of the anus and penis in men. 2. Others cause genital warts A. Over 200 different types…many are STDs (sexually transmitted) a. Nearly all cases of cervical cancer are caused by HPV

26 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses B. DNA viruses HPV Vaccine Recommended by CDC for all females and males age 11 to 26.

27 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… What do viruses need to accomplish to continue to exist? 1. Gain access to a cell 2. Use the cell’s workers (ribosomes, RNA polymerase, etc…) to make more of itself. a. Synthesize viral proteins b. Replicate its genome c. Assemble these into new viral particles

28 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… 1. Viral Attachment and Entry a. If the virus does not have an envelope, protein spikes on the capside will act as ligands and bind cell receptors, triggering receptor mediated endocytosis. What is the first thing a virus must be able to do? Life cycle of a DNA virus

29 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… 1. Viral Attachment and Entry b. If it does have an envelope, the protein spikes in the envelope will act as ligands and bind to cell receptors resulting in fusion of the viral membrane and cell membrane, injecting the capsid into the cell… Life cycle of a DNA virus

30 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… 1. Viral Attachment and Entry Protein spikes = the key Cell receptors = door lock In either case, the protein spikes on the surface need to bind receptors to gain access to the cell, which is why specific viruses can only infect specific cells with matching receptors. Analogy: Life cycle of a DNA virus

31 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… A. Viral attachment and entry B. Uncoating The capsid fall apart and the viral DNA enters the nucleus C. Transcription and translation of the viral DNA The viral DNA is transcribed and translated by our workers (our RNA polymerases, ribosomes/tRNAs/etc…) using our ATP made by our mitochondria!! Life cycle of a DNA virus

32 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Life cycle of a DNA virus D. Replication of the viral DNA E. Viral protein sorting Capsid proteins are brought into the nucleus while envelope proteins get into nuclear membrane via endomembrane system.

33 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… F. Viral assembly Capsid forms around DNA and then buds out of nucleus picking up its envelope H. Release How the virus, now in the cytoplasm, gets out of the cell is not understood yet. Life cycle of a DNA virus

34 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… This process typically happens over and over and over again until the cell dies…The cell is a virus producing factory. In certain viruses, like Herpes virus, the viral DNA can integrate (become part of) the cell’s DNA (your DNA), and sit quietly similar to the lysogenic cycle of bacteriophages. Almost all adults carry Herpes Simplex 1 virus (oral herpes). DNA integration Life cycle of a DNA virus

35 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses RNA viruses

36 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses C. RNA viruses Ex1. Mumps virus - Member of the paramyxovirus family - Causes the mumps Before infectionAfter infection Extreme swelling of salivary glands Contagious via respiratory secretions (coughing/sneezing/sharing glass/kissing/etc…)

37 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses C. RNA viruses Ex2. Rubella virus - Member of the togavirus family - Causes rubella (German measles) Rash on body Flu-like symptoms Highly Contagious

38 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses C. RNA viruses Ex3. Measles - Highly contagious through respiratory secretion just like mumps - Caused by a member of the paramyxovirus family like mumps Symptoms: Rash on body, cough, runny nose, red eyes, four day fevers

39 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses C. RNA viruses If these viruses are so easily contagious, why haven’t you gotten them? You have all been vaccinated against them (MMR shot) MMR = measles, mumps, rubella

40 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses C. RNA viruses Ex4. Poliomyelitis (polio) - Highly contagious through fecal-oral route (feces to the mouth) - In 1% of infections, virus enter neurons and destroys motor function – lose control of your muscles It is easier than you think…the chef prepares your food and didn’t wash his hands You are vaccinated against this one too…

41 Animal RNA virus life cycle 1. Viral attachment and entry Similar to DNA virus – protein spikes act as ligands for cell receptors. 2. Uncoating Capsid falls apart releasing the RNA 3. RNA synthesis A viral enzyme will make the complementary RNA strand (purple) using the genomic RNA (red) as a template 4. Protein synthesis Complementary RNA can act as mRNA and your ribosomes will translate it, making new viral proteins. Fig a

42 Animal RNA virus life cycle 5. Synthesizing more genomic RNA The complementary strand (purple) can also act as a template to back synthesize the more genomic RNA (red) 6. Assembly The viral proteins and genomic RNA come together to make new viral particles. Some of the viral proteins made were sent through the endomembrane system to the cell membrane. Fig a

43 Animal RNA virus life cycle 7. Exit The capsid/RNA pinch off from the cell, which is how it acquires the envelope with embedded viral proteins. -Notice that the nucleus is not involved. -This process happens again and again until the cell is dead. Fig a -There can be no integration of standard RNA viruses into our genome as RNA cannot be integrated into DNA

44 RNA Capsid Envelope (with glycoproteins) HOST CELL Viral genome (RNA) Template Capsid proteins Glyco- proteins mRNA Copy of genome (RNA) ER Figure 18.8 The reproductive cycle of an enveloped RNA virus Glycoproteins on the viral envelope bind to specific receptor molecules (not shown) on the host cell, promoting viral entry into the cell. 1 Capsid and viral genome enter cell 2 The viral genome (red) functions as a template for synthesis of complementary RNA strands (pink) by a viral enzyme. 3 New copies of viral genome RNA are made using complementary RNA strands as templates. 4 Complementary RNA strands also function as mRNA, which is translated into both capsid proteins (in the cytosol) and glycoproteins for the viral envelope (in the ER). 5 Vesicles transport envelope glycoproteins to the plasma membrane. 6 A capsid assembles around each viral genome molecule. 7 New virus 8

45 Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses C. RNA viruses Ex5. Retrovirus Ex. HIV (human immunodeficiency virus)– you will need to know the details on this one

46 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… - Retro implies Reverse - These viruses have an RNA genome, but use a special enzyme called Reverse Transcriptase to make a DNA copy of the RNA (the reverse of transcription; hence the name) Ex. HIV (human immunodeficiency virus) Retroviruses - A special family of RNA viruses

47 Fig 10.21A Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Retroviruses HIV - Enveloped RNA virus - Capsid houses two identical RNA molecules and the enzyme Reverse Transcriptase as well as others needed for the virus to function. Because our cells do not have the gene for reverse transcriptase… HIV Why do you think the virus needs to carry its own Reverse Transcriptase? Attachment protein is called GP120

48 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Retroviruses HIV How is HIV transmitted? The virus is transmitted through contact of a bodily fluid containing HIV like blood, semen, vaginal fluid, and breast milk with a mucous membrane or the bloodstream. A. ~33 million people are HIV positive in the world. C. ~2.2 million people, 330,000 of which were children, died as a result of the virus last year – 75% of deaths occurred in Sub-Saharan Africa. B. Estimated 1.1 million people are HIV positive in the US.

49 Fig 10.21A Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Retroviruses HIV What disease does HIV cause? - AIDS – Acquired Immune Deficiency Syndrome Therefore, HIV/AIDS does not kill anyone directly, it is the opportunistic infection or cancer that kills the person. Immune system gradually declines leaving the individual susceptible to opportunistic infections like tuberculosis (5 – 10% of Americans test positive for the bacterium that causes tuberculosis, but the immune system keeps it in check and the person is fine)and tumors (many cells that would have caused cancer are destroyed by the immune system).

50 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Retroviruses HIV How does HIV cause AIDS? HIV (blue dots) infects, hijacks and in the end destroys Helper T-cells (red) (special type of cell of the human immune system required for proper function). Let’s look at how HIV infects Helper-T cells…

51 HIV Life Cycle Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Attachment and Entry: HIV envelope glycoprotein GP120 (ligand) binds to the CD4 receptor on the surface of the Helper T-cell resulting in fusion of the viral envelope with the cell membrane thereby allowing the capsid to enter the cell and fall apart releasing the viral RNA and Reverse transcriptase enzymes. GP120

52 Fig 10.21B HIV Life Cycle Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… This figure skips the “attachment and entry” and “uncoating” of the viral particle.

53 Fig 10.21B HIV Life Cycle Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… 1. Reverse Transcriptase makes a DNA copy (blue) of the viral RNA genome (red). 2. Reverse Transcriptase then removes the RNA and synthesizes the complementary DNA strand. 3. Integration: the dsDNA enters the nucleus and gets integrated (inserted) into the DNA.

54 Fig 10.21B HIV Life Cycle Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… 4/5. Transcription/Translation: viral RNA and proteins are synthesized from the provirus (analogous to prophage) DNA. 6. Assembly: viral particles are assembled and bud off the cell This process happens over and over again as long as the Helper T-cell lasts…

55 The reproductive cycle of HIV, a retrovirus Figure mRNA RNA genome for the next viral generation Viral RNA RNA-DNA hybrid DNA Chromosomal DNA NUCLEUS Provirus HOST CELL Reverse transcriptase New HIV leaving a cell HIV entering a cell 0.25 µm HIV Membrane of white blood cell The virus fuses with the cell’s plasma membrane. The capsid proteins are removed, releasing the viral proteins and RNA. 1 Reverse transcriptase catalyzes the synthesis of a DNA strand complementary to the viral RNA. 2 Reverse transcriptase catalyzes the synthesis of a second DNA strand complementary to the first. 3 The double-stranded DNA is incorporated as a provirus into the cell’s DNA. 4 Proviral genes are transcribed into RNA molecules, which serve as genomes for the next viral generation and as mRNAs for translation into viral proteins. 5 The viral proteins include capsid proteins and reverse transcriptase (made in the cytosol) and envelope glycoproteins (made in the ER). 6 Vesicles transport the glycoproteins from the ER to the cell’s plasma membrane. 7 Capsids are assembled around viral genomes and reverse transcriptase molecules. 8 New viruses bud off from the host cell. 9

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57 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… What determines the damage a virus does? One item is the type of cell it infects… Examples: HIV – immune system cells Influenza – respiratory cells Polio – neurons (can’t divide)

58 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Vaccinations 1. Edward Jenner A. Credited with discovering the first vaccine in 1798 B. The disease was small pox D. Took the pus from these people infected with cow pox (a similar virus to small pox that you catch from cows) and injected it into other people. E. The cow pox pus somehow protected these people against small pox C. He observed that milk maids (people that milked cows) did not get small pox.

59 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Vaccinations 2. How do vaccines work? - By injecting the cowpox pus, the immune system mounts an attack against the virus in the pus. - The immune system remembers the foreign substances it attacks and is prepared if it attacks again… - Since the small pox virus is so similar to the cow pox virus, the immune system is prepared for the small pox virus as well...

60 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Vaccinations 2. How do vaccines work? - Most modern day vaccines are typically an injection of dead or weakened (attenuated) viruses or viral proteins…more about this when we look into the immune system in detail.

61 Chapter 24: The Immune System NEW AIM: How does the body defend itself against MO’s? I. Nonspecific vs. Specific Immunity B. Specific immunity (The Immune System) - OVERVIEW Memory T-cells are also made from T- cells activated by Helper T-cells. For a future encounter with the same antigen carrying pathogen.

62 Chapter 24: The Immune System NEW AIM: How does the body defend itself against MO’s? I. Nonspecific vs. Specific Immunity B. Specific immunity (The Immune System) vii. Memory cells Fig a. Memory B and T-cells are reservists for next time that specific antigen shows up: Primary immune response Secondary immune response The first time the lymphocytes see the antigen. Antibodies are made, but relatively slowly due to the small number of B-cells activated and only a relatively small number of antibodies are made compared to the second time the lymphocytes see the antigen for the same reason. The secondary response results upon re- exposure to the antigen. You have millions of memory B-cells. Most of them will be activated and antibodies are made quickly and in large number thanks to the large number of cells. You do not get sick. It must be the same antigen. Any mutation that changes the structure of the antigen will not elicit the secondary response.

63 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Vaccinations

64 Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Vaccinations

65 Fig Tobacco Mosaic Virus – Plants get viruses too… Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes…

66 Bacterial and Viral Transmission Chapter 18 - Genetics of Viruses and Bacteria Transmission 1. Droplet Contact - coughing or sneezing on another person Ex. Chicken pox, common cold (rhinovirus), influenze (flu), Tuberculosis, Measles, Mumps, Rubella, Pertussis, Strep throat

67 Bacterial and Viral Transmission Chapter 18 - Genetics of Viruses and Bacteria Transmission 2. Direct Physical Contact - touching an infected person, including sexual contact Ex. Sexually transmitted diseases, Athlete’s foot (fungal), Warts

68 Bacterial and Viral Transmission Chapter 18 - Genetics of Viruses and Bacteria Transmission 3. indirect contact - usually by touching a contaminated surface like a door knob or your desk. (ex. Rhinovirus…common cold) 4. airborne transmission - if the microorganism can remain in the air for long periods (essentially droplet transmission) 5. fecal-oral transmission - usually from contaminated food or water sources (cholera, hepatitis A, polio, rotavirus, salmonella) 6. vector borne transmission - carried by insects or other animals (malaria – a protist)

69 Bacterial and Viral Transmission Chapter 18 - Genetics of Viruses and Bacteria Transmission This is why surgeons look like this…

70 Bacterial and Viral Transmission Chapter 18 - Genetics of Viruses and Bacteria Transmission …and people working in a biosafety level 4 laboratory look like this…

71 Bacterial and Viral Transmission Chapter 18 - Genetics of Viruses and Bacteria Transmission Biosafety Levels Non-pathogenic E. coli Examples (Escherichia coli) Hepatitis A, B, C, influenza Tuberculosis, West Nile Virus, Anthrax Ebola virus, small pox, Argentine hemorrhagic fevers, Marburg virus, Lassa fever, Crimean-Congo hemorrhagic fever

72 Viroids Chapter 18 - Genetics of Viruses and Bacteria Transmission 1. Circular RNA molecules that infect plants (only several hundred nucleotides long) TEM of circular viroid RNA (black rings) Plants infected with varying degrees of viroid particles (control on left) 2. DO NOT encode proteins 3. The RNA molecules replicate inside plant cells using their machinary THEY ARE JUST SINGLE MOLECULE!!

73 Prions Chapter 18 - Genetics of Viruses and Bacteria Transmission 1. Infectious Protein!! 2. Cause a number of degenerative brain diseases in various animals Ex. scrapie in sheep, mad cow disease in cows, Creutzfeldt-Jakob disease in humans 3. Transmitted through ingestion of food with these prions in them like eating beef from cattle that had mad cow disease. ALARMING CHARACTERISTICS 1. They are slow-acting - Takes about 10 years until you see symptoms 2. Virtually Indestructable - They are not destroyed (denatured) by heating to normal cooking temperatures

74 Prions Chapter 18 - Genetics of Viruses and Bacteria Transmission How can a protein, which cannot replicate itself, be a transmissible pathogen? Hypothesis: - A prion is a misfolded form of a protein normally present in brain cells - When the prion gets into a normal cell, with the normal form of the protein, it converts the normal protein to the prion form. You eat prion infected beefPrion gets into neurons in your brain and turn normal protein into prion form…chain reaction.

75 Chapter 18 - Genetics of Viruses and Bacteria Transmission BACTERIAL GENETICS

76 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? How do bacteria (prokaryotes) they take up DNA… (it is more than just mutation that gives certain species of bacteria their genetic diversity)

77 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Reproduce by binary fission

78 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Reproduce by binary fission Replication of single, circular bacterial chromosome preceding binary fission How do bacteria maintain genetic diversity? One way is through mutation since they can reproduce so quickly leading to millions upon billions of slightly different individuals in only a days time.

79 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Reproduce by binary fission Replication of single, circular bacterial chromosome preceding binary fission Is this the only way they maintain diversity? Absolutely not…let’s look at other ways to do this…

80 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Look at this experiment and explain what is being observed: How were these bacteria able to exchange genes (DNA)?

81 Fig. 12.1A-C Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 1. Transformation 1. Bacteria can take up a free piece of bacterial DNA Three major methods have evolved by which bacteria take up foreign DNA to enhance diversity: Recall Griffith’s experiment 2. Crossing-over will occur between exogenous DNA and the bacterial chromosome.

82 Fig. 12.1A-C Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 2. Transduction Bacteriophage is mistakenly packaged with bacterial DNA. Injects this DNA into another bacteria. There are three methods by which bacteria take up DNA in nature. Recall Hershey and Chase

83 Fig Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 2. Transduction Bacteriophage is mistakenly packaged with bacterial DNA. Injects this DNA into another bacteria.

84 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 3. Conjugation “Male” (F+) bacteria extend sex pili called a mating bridge (long tube) to “female” (F-) bacteria. Part of chromosome is replicated and transferred. There are three methods by which bacteria take up DNA in nature. F+F-

85 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 3. Conjugation F+ means the cell has the so-called F (fertility) factor There are three methods by which bacteria take up DNA in nature. What is an F factor? It is a special segment of DNA that can be part of: 1. The bacterial chromosome OR 2. A plasmid Now what’s a plasmid? Bacteria can have small, circular extra- chromasomal (not the chromosome) pieces of DNA. F+F-

86 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? The majority of the DNA above that has spilled out of the bacterium is chromosomal, but you can see smaller circular pieces not part of the chromosome…plasmids. Lysed bacterium

87 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Plasmid - Small, circular piece of DNA distinct from bacterial chromosome - has own origin of replication (ori) - carries genes in nature or humans can modify them and insert genes into the so-called polylinker region - called vectors when used by humans as tools of genetic engineering…

88 F+ Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 3. Conjugation F+ means the cell has the so-called F (fertility) factor There are three methods by which bacteria take up DNA in nature. The F plasmid A special plasmid containing the F factor plus some 25 other genes needed for the production of sex pili. F+ cells have the F plasmid and can form sex pili and exchange DNA with an F- cell. ***This plasmid has the ability to integrate into the chromosome of the bacterium or remain separate (see next slide). F-

89 Fig Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 3. Conjugation There are three methods by which bacteria take up DNA in nature. The F- cell is now and F+ cell because it now has the F plasmid and can form sex pili with other F- cells and pass along DNA.

90 Fig Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 3. Conjugation There are three methods by which bacteria take up DNA in nature. As mentioned earlier, the F plasmid has the potential to integrate into the chromosome of the bacterium as shown above resulting in what we call an Hfr (High frequency of recombination) cell.

91 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 3. Conjugation There are three methods by which bacteria take up DNA in nature.

92 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 3. Conjugation There are three methods by which bacteria take up DNA in nature.

93 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 3. Conjugation There are three methods by which bacteria take up DNA in nature.

94 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 3. Conjugation There are three methods by which bacteria take up DNA in nature.

95 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 3. Conjugation There are three methods by which bacteria take up DNA in nature. Now when the plasmid begins to replicate, it will also replicate part of the bacterial chromosome giving new genes to the recipient cell. Crossing over and therefore recombination will occur within the recipient.

96 Fig Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? 3. Conjugation There are three methods by which bacteria take up DNA in nature. Complete picture of the two possibilities

97 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Where have we observed transformation before in this class? 1. Transformation2. Transduction 3. Conjugation The Griffith experiment when he mixed the R strain with the heat-killed S strain…

98 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? R plasmids (aside) 1. R stands for resistance 2. These are bacterial plasmids that carry genes that confer resistance to antibiotics like ampicillin 3. The gene that confers resistance is called AmpR (ampicillin resistance). What protein does is code for? It encodes the protein β-lactamase Guess what is does: ampicillin β-lactam ring β-lactamase with ampicillin bound in the active site

99 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Transposable Elements (Transposons) 1. Also known as “jumping genes” Figure 18.19a (a) Insertion sequences, the simplest transposable elements in bacteria, contain a single gene that encodes transposase, which catalyzes movement within the genome. The inverted repeats are backward, upside-down versions of each other; only a portion is shown. The inverted repeat sequence varies from one type of insertion sequence to another. Insertion sequence Transposase gene Inverted repeat Inverted repeat A T C C G G T… T A G G C C A … A C C G G A T… T G G C C T A … Nobel Prize, Cold Spring Harbor

100 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Transposable Elements (Transposons) 1. Also known as “jumping genes” Nobel Prize, Cold Spring Harbor

101 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Transposable Elements (Transposons) 1. Also known as “jumping genes” Figure 18.19b (b) Transposons contain one or more genes in addition to the transposase gene. In the transposon shown here, a gene for resistance to an antibiotic is located between twin insertion sequences. The gene for antibiotic resistance is carried along as part of the transposon when the transposon is inserted at a new site in the genome. Inverted repeats Transposase gene Insertion sequence Antibiotic resistance gene Transposon

102 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Transposable Elements (Transposons) DNA-transposons vs Retrotransposons Almost 50% of the human genome is composed of retrotransposons

103 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Transposable Elements (Transposons) DNA transposon:

104 Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Transposable Elements (Transposons) DNA-transposons Important in gene duplication during S phase of meiosis

105 Chapter 11 - The Control of Gene Expression NEW AIM: How are genes regulated (controlled) in prokaryotes? Figure 18.20a, b (a) Regulation of enzyme activity Enzyme 1 Enzyme 2 Enzyme 3 Enzyme 4 Enzyme 5 Regulation of gene expression Feedback inhibition Tryptophan Precursor (b) Regulation of enzyme production Gene 2 Gene 1 Gene 3 Gene 4 Gene 5 – – Bacteria, like all other organisms, respond to their environment by regulating gene expression and protein/enzyme activity… Let’s look at how bacteria regulate gene expression first in relation to lactose and then trptophan… (a) Negative Feedback: You have already seen how the product of a biosynthesis pathway like the amino acid tryptophan (trp) can allosterically inhibit an enzyme in its production pathway thereby shutting down its own production (negative feedback). (b) Regulating gene expression: Genes can also be turned on/off.

106 Chapter 18 - Genetics of Viruses and Bacteria Questions 1. “Jumping genes” are known as __________________ and always code for the enzyme known as _________________. 2. An F+ cell is said to be “fertile” because it carries with it the ________________. 3. SRP RNA is found where in the cell? 4. How many different aa-tRNA synthetases are there? 5. Amino acids are added to what end of the tRNA by aa- tRNA synthestase. 6. If the anticodon for a given tRNA is 3’-GCG-5’, what letters would you look for on the genetic code chart to determine the amino acid attached to this tRNA?

107 Lactose (Lac) Operon Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? In order to begin to understand this process, we will look at a set of three genes involved in lactose metabolism (the hydrolysis of lactose to _______________) called the… Glucose and galactose

108

109 Anatomy of an operon ( only prokaryotes have operons ) Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? Fig. 11.1B An operon typically contains a: 1. Promoter 2. Operator 3. A set of genes (3 in this specific case) The regulatory gene (LacI) is found OUTSIDE of the operon. A. LacZ B. LacY C. LacA LacZ LacY LacA 4. What critical gene part is missing from this figure? The terminator sequence LacI

110 The three gene products (can you guess what they might be?): Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? Fig. 11.1B 1. LacZ codes for β-galactosidase 2. LacY codes for permease 3. LacA codes for transacetylase LacZ LacY LacA LacI - The enzyme that hydrolyzes lactose to glucose and galactose - A passive lactose transporter protein that sits in the membrane and allow lactose to diffuse into the cell. - Exact function not yet known…

111 QUESTION Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? Fig. 11.1B If lactose is present around the cell (perhaps it is one of the bacterium in your mouth and you just drank a glass of milk), should these genes be turned on or off? They should be ON since lactose is present and will need to be hydrolyzed so the glucose and galactose can be used to make ATP of for biosynthesis. Let’s look at how this operon works to control expression of these three genes…

112 Fig. 11.1B Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? 1. The regulatory gene codes for the repressor protein. A. What does repress mean? - To prevent B. What will this protein do then? - It will prevent the expression of the genes (turn them off) - Any guess how it might do this?

113 Fig. 11.1B Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? 1. The regulatory gene codes for the repressor protein. C. It represses by binding to the Operator sequence and in doing so blocks the promoter sequence.

114 Fig. 11.1B Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? 1. The regulatory gene codes for the repressor protein. C. It represses by binding to the Operator sequence. -When it binds the operator, it will interfere with RNA polymerase binding to the promoter. The genes are off.

115 Fig. 11.1B Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? ALL FOR ONE AND ONE FOR ALL Notice that all three genes are turned on/off together. Eukaryotes do not typically do this. They turn genes on/off individually.

116 Fig. 11.1B Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? Q1. How do you suppose these genes will be turned ON when lactose is present? A1. Somehow the repressor needs to fall off. Q2. How can we get it to fall off? (HINT: you are changing its function) A2. You need to change its structure. Q3. How can we change the structure? A3. Bind something to it…a ligand. Q4. What should the ligand be?

117 Fig. 11.1B Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? The ligand should be lactose itself since in the presence of lactose these genes should be turned ON.

118 Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? 1. Lactose binds the repressor. 2. A conformational (shape) change occurs and the repressor falls off the operator. 3. RNA polymerase now binds to the promoter and begin transcription of all three genes in one long mRNA. 4. Ribosomes translate the mRNA into proteins. Activating the operon:

119 Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? Q1. What will happen when β-galactosidase breaks down most of the lactose? A1. Lactose will fall off the repressor and the repressor will once again bind to the operator and turn the genes off. Q2. Why not just leave these genes on all the time? A2. This would be a huge waste of resources…ATP, amino acids, ribosomes, nucleotides, RNA polymerases and space.

120 Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? To be more detailed about it… A small amount of lactose is converted to allolactose by an enzyme in the cell. It is actually allolactose that is what we call the inducer, which simply means it inactivates the repressor (aka induces transcription).

121 Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? Lac repressor protein Repressor bound to the operator sequence

122 Lac operon – The video

123 In reality, the presence of lactose alone is not enough to induce the transcription of the lac gene…why would this be logical? Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? Because there could be other sugars in excess like glucose. Why waste ATP going after lactose if you are already overloaded. How does the bacterium sense the levels of glucose and translate this information to the genome you ask…

124 1. cAMP is an allosteric activator of CAP (catabolite activator protein) Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? Promoter Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized. If glucose is scarce, the high level of cAMP activates CAP, and the lac operon produces large amounts of mRNA for the lactose pathway. (a) CAP-binding site Operator RNA polymerase can bind and transcribe Inactive CAP Active CAP cAMP DNA Inactive lac repressor lacl lacZ Figure 18.23a When glucose is absent and lactose present, cAMP levels are high… 2. CAP will bind to the CAP-binding site on the promoter and recruit RNA polymerase resulting in the production of much mRNA:

125 Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? Figure 18.23b (b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized. When glucose is present, cAMP is scarce, and CAP is unable to stimulate transcription. Inactive lac repressor Inactive CAP DNA RNA polymerase can’t bind Operator lacl lacZ CAP-binding site Promoter 1. CAP is inactive and RNA polymerase will not bind well to the promoter even if the repressor is not present. When glucose is present with lactose, cAMP levels are low… 2. Little mRNA made

126 Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? 1. Obviously the activity of adenylyl cyclase needs to be lowered, but glucose does not interact directly with this enzyme… How exactly does glucose lower the levels of cAMP? Figure X. Control of adenylate cyclase via the phosphotransferase system. A. IIA, IIB, IIC, and HPr comprise the phosphotransferase system. When glucose is present, the phosphorylated forms of IIAGlc are low because glucose siphons off the phosphate. IIAGlc then interacts with and inhibits adenylate cyclase activity. B. In the absence of glucose, the phosphorylated forms of glucose-specific IIAGlc and IIBCGlc accumulate because they cannot pass the phosphate to substrate (there is no glucose). Adenylate cyclase functions in this situation to produce cAMP. The inset on the right shows the conversion of ATP to cyclic AMP by adenylate cyclase. Not something you should memorize, just understand…

127 Tryptophan (Trp) operon Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? - This operon contains fours genes whose protein products are responsible for synthesizing (making) the amino acid tryptophan.

128 Tryptophan (Trp) operon Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? When would you want to turn these genes on? When tryptophan is NOT present, because that is when you need to make it… when trp is present, it will bind to and activate the repressor:

129 Tryptophan (Trp) operon Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? How does this compare to the lac operon?

130 Tryptophan (Trp) operon Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? Inducible operonRepressible operon You can turn ON (induce) the operon by adding something (lactose in this case) You can turn OFF (repress)the operon by adding something (Tryptophan in this case)

131 Tryptophan (Trp) operon Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? I do not recommend memorizing the difference. Think about is logically: 1. The repressor bind to the operator 2. When it is bound the genes are off 3. You need the lactose break down genes when lactose is present. 4. Therefore, when lactose binds to repressor, it should fall off operator 5. Likewise, when trp is present, the trp synthesis genes are unnecessary because you have it already 6. Therefore, Trp when Trp binds to the repressor, the repressor should bind the operator and shut the genes off.

132 Trp operon in detail… Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? Tryptophan (Trp) is a corepressor since it represses along with the repressor.

133 Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? The trp repressor (with trp bound) binding to the operator sequence.

134 Both cases are examples of repression… Chapter 11 - The Control of Gene Expression AIM: How are genes regulated (controlled) in prokaryotes? …but there can also be activation by activator proteins as we shall see in the next slide.

135 Chapter 18 - Genetics of Viruses and Bacteria Questions 1. A functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter. 2. The lac genes in E. coli are turned on when what two conditions are present in the cell? 3. The major difference between how the trp genes are regulated compared to how the lac genes are regulated. 4. When glucose concentrations are low within an E. coli cell the concentration of _________ is _________ causing the activation of _____________, which is required for recruiting RNA pol. 5. What is Χ 2 analysis used to determine?


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