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Questions Chapter 18 - Genetics of Viruses and Bacteria

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

3 What is a virus? Chapter 18 - Genetics of Viruses and Bacteria
NEW AIM: Viruses: Packaged Genes… What is a virus? 1. Obligate intracellular parasite - A small [20 to 250nm in diameter] infectious agent that requires a host cell to replicate (make more of itself). **1/1000th 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 Nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope 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

4 Size Comparison 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 (a) Tobacco mosaic virus
Chapter 18 - Genetics of Viruses and Bacteria NEW AIM: Viruses: Packaged Genes… CAPSID 1. All viruses contain genetic material (DNA or RNA) encapsulated by a protein coat called a capsid. 2. An individual protein in the capsid is called a capsomere. 3. Bacteriophage (phage) have the most complex capsids 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) (c) Influenza viruses Membranous envelope Capsid 80  225 nm (d) Bacteriophage T4 Head Tail fiber Tail sheath

6 (a) Tobacco mosaic virus
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) (c) Influenza viruses Membranous envelope Capsid 80  225 nm (d) Bacteriophage T4 Head Tail fiber Tail sheath

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

8 Chapter 18 - Genetics of Viruses and Bacteria
NEW AIM: Viruses: Packaged Genes… 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. Simplified viral reproductive cycle

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

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

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

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

13 Chapter 18 - Genetics of Viruses and Bacteria
NEW AIM: Viruses: Packaged Genes… Lysogenic 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. Lytic cycle - 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… What causes a temperate phage like lambda to switch from lysogenic to lytic? 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.

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

16 2. Animal viruses A. Anatomy
Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses 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. Capsid – made of proteins and surrounds the genetic material in the core. Envelope – Phospholipid bilayer similar to a cell membrane with embedded proteins (protein spikes) surrounding the capsid. Not all virus types have envelopes

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

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

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

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

21 - Causes upper respiratory infections
Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses B. DNA viruses Adenovirus was isolated from the adenoids 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 Ex2. Herpesviruses (family of related viruses) These can cause:
Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses B. DNA viruses Adenovirus was isolated from the adenoids Ex2. Herpesviruses (family of related viruses) These can cause: 1. Oral herpes (cold sores) or genital herpes (an STD)

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

24 Ex3. Poxvirus (family of related viruses) Can cause: 1. Small pox
Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses B. DNA viruses Smallpox is believed to have emerged in human populations about 10,000 BC.[2] The disease killed an estimated 400,000 Europeans per year during the closing years of the 18th century (including five monarchs), and was responsible for a third of all blindness.[3][6] Of all those infected, 20–60%—and over 80% of infected children—died from the disease.[7] During the 20th century, it is estimated that smallpox was responsible for 300–500 million deaths.[8][9][10] In the early 1950s an estimated 50 million cases of smallpox occurred in the world each year.[11] As recently as 1967, the World Health Organization (WHO) estimated that 15 million people contracted the disease and that two million died in that year.[11] After successful vaccination campaigns throughout the 19th and 20th centuries, the WHO certified the eradication of smallpox in December 1979.[11] To this day, smallpox is the only human infectious disease to have been eradicated.[12] 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 Ex4. HPV – Human Papillomavirus
Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses B. DNA viruses Smallpox is believed to have emerged in human populations about 10,000 BC.[2] The disease killed an estimated 400,000 Europeans per year during the closing years of the 18th century (including five monarchs), and was responsible for a third of all blindness.[3][6] Of all those infected, 20–60%—and over 80% of infected children—died from the disease.[7] During the 20th century, it is estimated that smallpox was responsible for 300–500 million deaths.[8][9][10] In the early 1950s an estimated 50 million cases of smallpox occurred in the world each year.[11] As recently as 1967, the World Health Organization (WHO) estimated that 15 million people contracted the disease and that two million died in that year.[11] After successful vaccination campaigns throughout the 19th and 20th centuries, the WHO certified the eradication of smallpox in December 1979.[11] To this day, smallpox is the only human infectious disease to have been eradicated.[12] Ex4. HPV – Human Papillomavirus A. Over 200 different types…many are STDs (sexually transmitted) 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. a. Nearly all cases of cervical cancer are caused by HPV 2. Others cause genital warts

26 2. Animal viruses B. DNA viruses HPV Vaccine
Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses B. DNA viruses Smallpox is believed to have emerged in human populations about 10,000 BC.[2] The disease killed an estimated 400,000 Europeans per year during the closing years of the 18th century (including five monarchs), and was responsible for a third of all blindness.[3][6] Of all those infected, 20–60%—and over 80% of infected children—died from the disease.[7] During the 20th century, it is estimated that smallpox was responsible for 300–500 million deaths.[8][9][10] In the early 1950s an estimated 50 million cases of smallpox occurred in the world each year.[11] As recently as 1967, the World Health Organization (WHO) estimated that 15 million people contracted the disease and that two million died in that year.[11] After successful vaccination campaigns throughout the 19th and 20th centuries, the WHO certified the eradication of smallpox in December 1979.[11] To this day, smallpox is the only human infectious disease to have been eradicated.[12] HPV Vaccine Recommended by CDC for all females and males age 11 to 26.

27 What do viruses need to accomplish to continue to exist?
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 Life cycle of a DNA virus
Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Life cycle of a DNA virus What is the first thing a virus must be able to do? 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.

29 Life cycle of a DNA virus
Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Life cycle of a DNA virus 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…

30 Life cycle of a DNA virus
Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Life cycle of a DNA virus 1. Viral Attachment and Entry Analogy: Cell receptors = door lock Protein spikes = the key 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.

31 Life cycle of a DNA virus
Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Life cycle of a DNA virus 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!!

32 Life cycle of a DNA virus
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 Life cycle of a DNA virus
Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Life cycle of a DNA virus 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.

34 Life cycle of a DNA virus
Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Life cycle of a DNA virus This process typically happens over and over and over again until the cell dies…The cell is a virus producing factory. DNA integration 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).

35 RNA viruses 2. Animal viruses
Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses Mumps come and go with little effect RNA viruses

36 2. Animal viruses C. RNA viruses Ex1. Mumps virus
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 Mumps come and go with little effect - Causes the mumps Extreme swelling of salivary glands Contagious via respiratory secretions (coughing/sneezing/sharing glass/kissing/etc…) Before infection After infection

37 2. Animal viruses C. RNA viruses Ex2. Rubella virus
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 Mumps come and go with little effect - Causes rubella (German measles) Rash on body Flu-like symptoms Highly Contagious

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

39 You have all been vaccinated against them (MMR shot)
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? Mumps come and go with little effect You have all been vaccinated against them (MMR shot) MMR = measles, mumps, rubella

40 Ex4. Poliomyelitis (polio)
Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses C. RNA viruses Ex4. Poliomyelitis (polio) 90% of infections have no symptoms at all… Those are virus families on the top right. - Highly contagious through fecal-oral route (feces to the mouth) It is easier than you think…the chef prepares your food and didn’t wash his hands - In 1% of infections, virus enter neurons and destroys motor function – lose control of your muscles 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. -There can be no integration of standard RNA viruses into our genome as RNA cannot be integrated into DNA Fig a

44 The reproductive cycle of an enveloped RNA virus
Capsid Envelope (with glycoproteins) HOST CELL Viral genome (RNA) Template proteins Glyco- mRNA Copy of genome (RNA) ER Figure 18.8 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 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 New copies of viral genome RNA are made using complementary RNA strands as templates. 4 Vesicles transport envelope glycoproteins to the plasma membrane. 6 A capsid assembles around each viral genome molecule. 7 New virus 8

45 2. Animal viruses C. RNA viruses Ex5. Retrovirus
Chapter 18 - Genetics of Viruses and Bacteria AIM: Viruses: Packaged Genes… 2. Animal viruses C. RNA viruses Ex5. Retrovirus 90% of infections have no symptoms at all Positive-sense (5' to 3') viral RNA signifies that a particular viral RNA sequence may be directly translated into the desired viral proteins. … Ex. HIV (human immunodeficiency virus)– you will need to know the details on this one

46 Retroviruses - A special family of RNA viruses - Retro implies Reverse
Chapter 18 - Genetics of Viruses and Bacteria NEW: Viruses: Packaged Genes… Retroviruses - A special family of RNA viruses - 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)

47 Retroviruses HIV HIV Chapter 18 - Genetics of Viruses and Bacteria
NEW: Viruses: Packaged Genes… Retroviruses Fig 10.21A Attachment protein is called GP120 HIV 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. Why do you think the virus needs to carry its own Reverse Transcriptase? Because our cells do not have the gene for reverse transcriptase…

48 Retroviruses HIV Chapter 18 - Genetics of Viruses and Bacteria
NEW: Viruses: Packaged Genes… Retroviruses HIV How is HIV transmitted? The transmission of the virus from the mother to the child can occur in utero during the last weeks of pregnancy and at childbirth. In the absence of treatment, the transmission rate between a mother and her child during pregnancy, labor and delivery is 25%.However, when the mother takes antiretroviral therapy and gives birth by caesarean section, the rate of transmission is just 1%.[61] The risk of infection is influenced by the viral load of the mother at birth, with the higher the viral load, the higher the risk. Breastfeeding also increases the risk of transmission by about 4 %.[62] 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. B. Estimated 1.1 million people are HIV positive in the US. 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.

49 Retroviruses HIV Chapter 18 - Genetics of Viruses and Bacteria
NEW: Viruses: Packaged Genes… Retroviruses Fig 10.21A HIV What disease does HIV cause? - AIDS – Acquired Immune Deficiency Syndrome 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). Therefore, HIV/AIDS does not kill anyone directly, it is the opportunistic infection or cancer that kills the person.

50 Retroviruses HIV 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… HIV Life Cycle GP120 Glycoprotein The 120 in its name comes from its molecular weight of 120 kilodaltons. 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.

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

53 HIV Life Cycle Chapter 18 - Genetics of Viruses and Bacteria
NEW: Viruses: Packaged Genes… HIV Life Cycle 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. Fig 10.21B

54 HIV Life Cycle Chapter 18 - Genetics of Viruses and Bacteria
NEW: Viruses: Packaged Genes… HIV Life Cycle 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… Fig 10.21B

55 The reproductive cycle of HIV, a retrovirus
Figure 18.10 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 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

56 Discuss bone marrow transplant using CCR5 mutant bone marrow as a “cure” for HIV/AIDS

57 What determines the damage a virus does?
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 Vaccinations Chapter 18 - Genetics of Viruses and Bacteria
NEW: Viruses: Packaged Genes… Vaccinations 1. Edward Jenner A. Credited with discovering the first vaccine in 1798 Edward Jenner -inoculated an 8 year old with cow pox puss and then exposed him to the small pox virus -began with observation that milk maids who had cow pox did not get small pox B. The disease was small pox C. He observed that milk maids (people that milked cows) did not get 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

59 Vaccinations 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. Edward Jenner -inoculated an 8 year old with cow pox puss and then exposed him to the small pox virus -began with observation that milk maids who had cow pox did not get small pox - 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 Vaccinations 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. Edward Jenner -inoculated an 8 year old with cow pox puss and then exposed him to the small pox virus -began with observation that milk maids who had cow pox did not get small pox

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 Interferons as antiviral drug?? 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 a. Memory B and T-cells are reservists for next time that specific antigen shows up: Interferons as antiviral drug?? Primary 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. Secondary immune response 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. Fig. 24.8

63 Vaccinations Chapter 18 - Genetics of Viruses and Bacteria
NEW: Viruses: Packaged Genes… Vaccinations Edward Jenner -inoculated an 8 year old with cow pox puss and then exposed him to the small pox virus -began with observation that milk maids who had cow pox did not get small pox

64 Vaccinations Chapter 18 - Genetics of Viruses and Bacteria
NEW: Viruses: Packaged Genes… Vaccinations Edward Jenner -inoculated an 8 year old with cow pox puss and then exposed him to the small pox virus -began with observation that milk maids who had cow pox did not get small pox

65 Chapter 18 - Genetics of Viruses and Bacteria
NEW: Viruses: Packaged Genes… Fig 10.19 Tobacco Mosaic Virus – Plants get viruses too…

66 Bacterial and Viral Transmission
Chapter 18 - Genetics of Viruses and Bacteria Transmission Bacterial and Viral 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 Bacterial and Viral 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 Bacterial and Viral Transmission 3. indirect contact - usually by touching a contaminated surface like a door knob or your desk. (ex. Rhinovirus…common cold) Viral Droplet Nuclei Transmission Droplet nuclei are an important mode of transmission among many infectious viruses such as Influenza A. When viruses are shed by an infected person through coughing or sneezing into the air, the mucus coating on the virus starts to evaporate. Once this mucus shell evaporates the remaining viron is called a droplet nucleus or quanta. The mucus evaporation rate is determined by the temperature and humidity inside the room. The lower the humidity, the quicker the mucus shell evaporates thus allowing the droplet nuclei to stay airborne and not drop to the ground. The low indoor humidity levels in wintertime buildings ensure that higher levels of droplet nuclei will survive: droplet nuclei are so microscopic that they are able to stay airborne indefinitely on the air currents present within indoor spaces. The Wells-Riley equation predicts the infection rates of persons who shed quanta within a building and is used to calculate indoor infection outbreaks within buildings. When an infected person coughs or sneezes, a percentage of their viruses will become droplet nuclei. If these droplet nuclei gain access to the eyes, nose or mouth of an uninfected person (known as a susceptible) -- either directly, or indirectly after touching a contaminated surface[4] -- then the droplet nuclei may penetrate into the deep recesses of their lungs. Viral diseases that are commonly spread by coughing or sneezing droplet nuclei include (at least): 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 Bacterial and Viral Transmission Viral Droplet Nuclei Transmission Droplet nuclei are an important mode of transmission among many infectious viruses such as Influenza A. When viruses are shed by an infected person through coughing or sneezing into the air, the mucus coating on the virus starts to evaporate. Once this mucus shell evaporates the remaining viron is called a droplet nucleus or quanta. The mucus evaporation rate is determined by the temperature and humidity inside the room. The lower the humidity, the quicker the mucus shell evaporates thus allowing the droplet nuclei to stay airborne and not drop to the ground. The low indoor humidity levels in wintertime buildings ensure that higher levels of droplet nuclei will survive: droplet nuclei are so microscopic that they are able to stay airborne indefinitely on the air currents present within indoor spaces. The Wells-Riley equation predicts the infection rates of persons who shed quanta within a building and is used to calculate indoor infection outbreaks within buildings. When an infected person coughs or sneezes, a percentage of their viruses will become droplet nuclei. If these droplet nuclei gain access to the eyes, nose or mouth of an uninfected person (known as a susceptible) -- either directly, or indirectly after touching a contaminated surface[4] -- then the droplet nuclei may penetrate into the deep recesses of their lungs. Viral diseases that are commonly spread by coughing or sneezing droplet nuclei include (at least): This is why surgeons look like this…

70 Bacterial and Viral Transmission
Chapter 18 - Genetics of Viruses and Bacteria Transmission Bacterial and Viral Transmission Viral Droplet Nuclei Transmission Droplet nuclei are an important mode of transmission among many infectious viruses such as Influenza A. When viruses are shed by an infected person through coughing or sneezing into the air, the mucus coating on the virus starts to evaporate. Once this mucus shell evaporates the remaining viron is called a droplet nucleus or quanta. The mucus evaporation rate is determined by the temperature and humidity inside the room. The lower the humidity, the quicker the mucus shell evaporates thus allowing the droplet nuclei to stay airborne and not drop to the ground. The low indoor humidity levels in wintertime buildings ensure that higher levels of droplet nuclei will survive: droplet nuclei are so microscopic that they are able to stay airborne indefinitely on the air currents present within indoor spaces. The Wells-Riley equation predicts the infection rates of persons who shed quanta within a building and is used to calculate indoor infection outbreaks within buildings. When an infected person coughs or sneezes, a percentage of their viruses will become droplet nuclei. If these droplet nuclei gain access to the eyes, nose or mouth of an uninfected person (known as a susceptible) -- either directly, or indirectly after touching a contaminated surface[4] -- then the droplet nuclei may penetrate into the deep recesses of their lungs. Viral diseases that are commonly spread by coughing or sneezing droplet nuclei include (at least): …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 Bacterial and Viral Transmission Biosafety Levels Examples Non-pathogenic E. coli Viral Droplet Nuclei Transmission Droplet nuclei are an important mode of transmission among many infectious viruses such as Influenza A. When viruses are shed by an infected person through coughing or sneezing into the air, the mucus coating on the virus starts to evaporate. Once this mucus shell evaporates the remaining viron is called a droplet nucleus or quanta. The mucus evaporation rate is determined by the temperature and humidity inside the room. The lower the humidity, the quicker the mucus shell evaporates thus allowing the droplet nuclei to stay airborne and not drop to the ground. The low indoor humidity levels in wintertime buildings ensure that higher levels of droplet nuclei will survive: droplet nuclei are so microscopic that they are able to stay airborne indefinitely on the air currents present within indoor spaces. The Wells-Riley equation predicts the infection rates of persons who shed quanta within a building and is used to calculate indoor infection outbreaks within buildings. When an infected person coughs or sneezes, a percentage of their viruses will become droplet nuclei. If these droplet nuclei gain access to the eyes, nose or mouth of an uninfected person (known as a susceptible) -- either directly, or indirectly after touching a contaminated surface[4] -- then the droplet nuclei may penetrate into the deep recesses of their lungs. Viral diseases that are commonly spread by coughing or sneezing droplet nuclei include (at least): (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) 2. DO NOT encode proteins 3. The RNA molecules replicate inside plant cells using their machinary THEY ARE JUST SINGLE MOLECULE!! Viral Droplet Nuclei Transmission Droplet nuclei are an important mode of transmission among many infectious viruses such as Influenza A. When viruses are shed by an infected person through coughing or sneezing into the air, the mucus coating on the virus starts to evaporate. Once this mucus shell evaporates the remaining viron is called a droplet nucleus or quanta. The mucus evaporation rate is determined by the temperature and humidity inside the room. The lower the humidity, the quicker the mucus shell evaporates thus allowing the droplet nuclei to stay airborne and not drop to the ground. The low indoor humidity levels in wintertime buildings ensure that higher levels of droplet nuclei will survive: droplet nuclei are so microscopic that they are able to stay airborne indefinitely on the air currents present within indoor spaces. The Wells-Riley equation predicts the infection rates of persons who shed quanta within a building and is used to calculate indoor infection outbreaks within buildings. When an infected person coughs or sneezes, a percentage of their viruses will become droplet nuclei. If these droplet nuclei gain access to the eyes, nose or mouth of an uninfected person (known as a susceptible) -- either directly, or indirectly after touching a contaminated surface[4] -- then the droplet nuclei may penetrate into the deep recesses of their lungs. Viral diseases that are commonly spread by coughing or sneezing droplet nuclei include (at least): Plants infected with varying degrees of viroid particles (control on left) TEM of circular viroid RNA (black rings)

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. Viral Droplet Nuclei Transmission Droplet nuclei are an important mode of transmission among many infectious viruses such as Influenza A. When viruses are shed by an infected person through coughing or sneezing into the air, the mucus coating on the virus starts to evaporate. Once this mucus shell evaporates the remaining viron is called a droplet nucleus or quanta. The mucus evaporation rate is determined by the temperature and humidity inside the room. The lower the humidity, the quicker the mucus shell evaporates thus allowing the droplet nuclei to stay airborne and not drop to the ground. The low indoor humidity levels in wintertime buildings ensure that higher levels of droplet nuclei will survive: droplet nuclei are so microscopic that they are able to stay airborne indefinitely on the air currents present within indoor spaces. The Wells-Riley equation predicts the infection rates of persons who shed quanta within a building and is used to calculate indoor infection outbreaks within buildings. When an infected person coughs or sneezes, a percentage of their viruses will become droplet nuclei. If these droplet nuclei gain access to the eyes, nose or mouth of an uninfected person (known as a susceptible) -- either directly, or indirectly after touching a contaminated surface[4] -- then the droplet nuclei may penetrate into the deep recesses of their lungs. Viral diseases that are commonly spread by coughing or sneezing droplet nuclei include (at least): 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 beef Prion gets into neurons in your brain and turn normal protein into prion form…chain reaction.

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

76 How do bacteria (prokaryotes) they take up DNA…
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 Reproduce by binary fission
Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Reproduce by binary fission

78 Reproduce by binary fission
Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Reproduce by 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. Replication of single, circular bacterial chromosome preceding binary fission

79 Reproduce by binary fission
Chapter 12 - DNA Technology and the Human Genome How can we use bacteria to manipulate DNA and protein? Reproduce by binary fission Is this the only way they maintain diversity? Replication of single, circular bacterial chromosome preceding binary fission 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 Chapter 12 - DNA Technology and the Human Genome
How can we use bacteria to manipulate DNA and protein? Three major methods have evolved by which bacteria take up foreign DNA to enhance diversity: 1. Transformation 1. Bacteria can take up a free piece of bacterial DNA 2. Crossing-over will occur between exogenous DNA and the bacterial chromosome. Recall Griffith’s experiment Fig. 12.1A-C

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

83 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. Fig. 18.6

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

85 Chapter 12 - DNA Technology and the Human Genome
How can we use bacteria to manipulate DNA and protein? There are three methods by which bacteria take up DNA in nature. 3. Conjugation F+ means the cell has the so-called F (fertility) factor 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 F+ F- Now what’s a plasmid? Bacteria can have small, circular extra-chromasomal (not the chromosome) pieces of DNA.

86 Chapter 12 - DNA Technology and the Human Genome
How can we use bacteria to manipulate DNA and protein? Lysed bacterium 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.

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

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

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

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

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

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

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

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

97 Chapter 12 - DNA Technology and the Human Genome
How can we use bacteria to manipulate DNA and protein? 1. Transformation 2. Transduction 3. Conjugation Where have we observed transformation before in this class? 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? ampicillin β-lactam ring 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: 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” Nobel Prize, Cold Spring Harbor 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 5 3 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 …

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 5 3

102 Almost 50% of the human genome is composed of retrotransposons
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 Important in gene duplication during S phase of meiosis
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? Bacteria, like all other organisms, respond to their environment by regulating gene expression and protein/enzyme activity… 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 (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. Let’s look at how bacteria regulate gene expression first in relation to lactose and then trptophan…

106 Questions Chapter 18 - Genetics of Viruses and Bacteria
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 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 Lactose (Lac) Operon

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 LacI LacZ LacY LacA The terminator sequence Anatomy of an operon (only prokaryotes have operons) An operon typically contains a: 1. Promoter 2. Operator 3. A set of genes (3 in this specific case) A. LacZ B. LacY C. LacA 4. What critical gene part is missing from this figure? The terminator sequence The regulatory gene (LacI) is found OUTSIDE of the operon.

110 Chapter 11 - The Control of Gene Expression
AIM: How are genes regulated (controlled) in prokaryotes? Fig. 11.1B LacI LacZ LacY LacA The three gene products (can you guess what they might be?): 1. LacZ codes for β-galactosidase - The enzyme that hydrolyzes lactose to glucose and galactose 2. LacY codes for permease - A passive lactose transporter protein that sits in the membrane and allow lactose to diffuse into the cell. 3. LacA codes for transacetylase - 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 QUESTION 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 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) Fig. 11.1B - Any guess how it might do this?

113 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. Fig. 11.1B

114 Chapter 11 - The Control of Gene Expression
AIM: How are genes regulated (controlled) in prokaryotes? Fig. 11.1B 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 Chapter 11 - The Control of Gene Expression
AIM: How are genes regulated (controlled) in prokaryotes? Fig. 11.1B 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 Chapter 11 - The Control of Gene Expression
AIM: How are genes regulated (controlled) in prokaryotes? Fig. 11.1B 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 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. Fig. 11.1B

118 Chapter 11 - The Control of Gene Expression
AIM: How are genes regulated (controlled) in prokaryotes? Activating the operon: 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.

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 Repressor bound to the operator sequence
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 Chapter 11 - The Control of Gene Expression
AIM: How are genes regulated (controlled) in prokaryotes? In reality, the presence of lactose alone is not enough to induce the transcription of the lac gene…why would this be logical? 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 Chapter 11 - The Control of Gene Expression
AIM: How are genes regulated (controlled) in prokaryotes? When glucose is absent and lactose present, cAMP levels are high… 1. cAMP is an allosteric activator of CAP (catabolite activator protein) 2. CAP will bind to the CAP-binding site on the promoter and recruit RNA polymerase resulting in the production of much mRNA: 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

125 Chapter 11 - The Control of Gene Expression
AIM: How are genes regulated (controlled) in prokaryotes? When glucose is present with lactose, cAMP levels are low… 1. CAP is inactive and RNA polymerase will not bind well to the promoter even if the repressor is not present. 2. Little mRNA made 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

126 Chapter 11 - The Control of Gene Expression
AIM: How are genes regulated (controlled) in prokaryotes? How exactly does glucose lower the levels of cAMP? 1. Obviously the activity of adenylyl cyclase needs to be lowered, but glucose does not interact directly with this enzyme… Not something you should memorize, just understand… 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.

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

135 Questions Chapter 18 - Genetics of Viruses and Bacteria
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 Χ2 analysis used to determine?


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