AP Biology Chapter 18 Notes:

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1 AP Biology Chapter 18 Notes: I. Chapter 18: The Genetics of Viruses and Bacteria: a. Microbial Model Systems: i. Slide One: picture of bacteriophage infecting E. coli. 1. This is an example of a microbial model system a. Relative size: viruses = nm, bacteria = 1000nm(1 micron). 2. Frequently used by researchers (Hershey and chase) because the reveal broad biological principles. a. They provided evidence that genes were made of DNA b. They provided the fundamental processes of DNA replication, transcription and translation c. Microbes also contribute to the development of techniques enabling scientists to manipulate genes and transfer them from one organism to another. II. Chapter 18.1: A virus has a genome but can reproduce only within a host cell. a. The discovery of viruses: Scientific Inquiry b. Structure of Viruses: i. Slide Two: Virus = poison in Latin 1. Infectious particle consisting of: a. Nucleic acid- b. Protein coat c. They are not cells d. They need a host cell 2. Viral genomes may consist of DNA (double stranded) or RNA(single stranded) a. Viruses have genes ranging from four genes to several hundred. 3. Capsids: protein shell enclosing the viral genome a. Many different shapes: i. Rod shapes ii. Polyhedral iii. Complex shapes like the T4 virus 1. T4 bacteriophage infects E. coli bacteria b. Capsids are built from large number of protein subunits called capsomeres. 4. Viral Envelopes: accessory structures that aid the virus in infecting the host cell a. Membranous envelop surrounding the capsid b. Derived from the host cell

2 i. Contain host cell phospholipids, membrane proteins ii. also contain proteins and glycoproteins of viral origin iii. some contain viral enzymes within their capsid 5. Bacteriophages: very complex viruses that infect bacteria. a. Group of seven that infects the bacteria Escherichia coli. i. Phages were named: T1(type 1) T7(type 7) in order of their discovery. ii. T2, T4, and T6 turned out to be very similar in structure. 1. Capsids have long icosahedral heads enclosing the DNA. 2. Also have a protein tail piece with fibers that the phages use to attach to a bacterium. ii. Slide Three: images and pictures of four different viruses depicting the complexity of their structures. 1. TMV- tobacco mosaic virus a. Helical virus with a rigid rod b. A retrovirus causing mosaic disease in tobacco and some other plants that was a primary focus of study in early plant virology. 2. Adenovirus a. Polyhedral capsid with a glycoprotein spike at each vertex b. are medium- sized ( nm), nonenveloped (without an outer lipid bilayer) icosahedral(20 identical equilateral triangles) viruses composed of a nucleocapsid and a double- stranded linear DNA genome. c. There are 57 described serotypes( a distinct variation within a species) in humans, which are responsible for 5 10% of upper respiratory infections in children, and many infections in adults as well. 3. Influenza virus a. Outer envelope studded with glycoprotein spikes i. Eight different RNA molecules make up its genome each of which is wrapped in a helical capsid. 4. T4 Bacteriophage

3 a. Complex capsid consisting of a polyhedral head and a tail apparatus 5. Retrovirus: an RNA virus that replicates in a host cell. a. First it uses its own reverse transcriptase enzyme to produce DNA from its RNA genome, reverse of the usual pattern, thus retro. 6. Rhinovirus: enterovirus (viruses transmitted from person to person via gastrointestinal or respiratory tract) belonging to the group Picornaviridae a. These viruses attach human respiratory tract and the cause of the common cold c. General Features of Viral Reproductive Cycles: i. Viruses can only reproduce in a host cell 1. They lack metabolic enzymes 2. They lack ribosomes 3. They are package sets of genes in transit from one host cell to another ii. Slide Four: Host range: each virus can infect a limited range of host cells 1. Host specificity- results from a recognition system 2. Lock and key fit between viral proteins and specific receptor molecules on the surface of cells a. Receptors probably evolved first because they carry out functions to benefit the organism. 3. Some viruses have a wide host cell range- a. Examples: west nile virus: mosquitos, birds and humans b. Example: equine encephalitis virus: mosquitos, birds, horses and humans 4. Some viruses have very narrow host cell range: a. Measles and poliovirus only infect humans 5. Some viruses are limited to specific tissues: a. Human cold virus = infects the lining of the upper respiratory tract b. Aids virus: certain types of white blood cells iii. The Viral Infection: Simplified 1. Virus enters the cell and is uncoated, releasing viral DNA an capsid proteins 2. Host enzymes replicated the viral genome 3. Host enzymes transcribe the viral genome into viral mrna, which other host enzymes use to make more viral proteins 4. Viral genomes and capsid proteins self- assemble into new virus particles which exit the cell

4 d. Reproductive Cycles of Phages: i. Slide Five: Lytic cycle: a phage reproductive cycle that culminates in death of the host cell 1. Last stage of infection ii. Virulent phage: a phage that reproduces only by a lytic cycle iii. Slide Six: Stages of the Lytic Cycle: 1. Attachment: tail fibers or recognition sequence binds to specific receptor sites on the outer surface of the host cell 2. Injection: Sheath of the tail contracts and injects DNA into the cell leaving an empty capsid outside 3. Hydrolyzation: The host cell DNA becomes hydrolyzed a. The phage DNA directs production of phage proteins copies of the phage genome by host enzymes, using components of the host cell 4. Assembly: Three separate sets of proteins self- assemble to form phage heads, tails, and tail fibers. 5. The phage genome is packaged inside the capsid as the head forms. 6. Release: the phage directs production of an enzyme that damages the bacterial cell wall, allowing fluid to enter. a. The cell swells and finally bursts releasing 100 to 200 phage particles. b. Burst size can range from 100 to 1000 viral particles e. Bacteria are not completely defenseless i. Mutant bacteria have receptor sites that are no longer recognized by a particular virus ii. Restriction enzymes: restriction endonucleases: recognition of the foreign DNA and destroyed by these enzymes 1. Restriction endonucleases must show tremendous specificity at two levels. First, they must cleave only DNA molecules that contain recognition sites (hereafter referred to as cognate DNA) without cleaving DNA molecules that lack these sites. 2. Bacterial DNA is chemically modified to not be recognized by the restriction enzymes iii. Slide Seven: Lysogenic Cycle- replication occurring without killing the host 1. Temperate phages: capable of using both modes of reproducing with a bacterium a. Lamba- temperate phage resembles T4 but has a short tail fiber i. Used in research

5 ii. During lytic cycle viral genes immediately turn the host cell into virus producing factory. iii. During the lysogenic cycle- DNA is incorporated by genetic recombination(crossing over) not a specific site on the host cell s chromosome. 1. This viral DNA is known as prophage 2. One prophage gene codes for a protein that prevents transcription of most of the other prophage genes. 3. Phage genome remains silent b. Prophages are capable of activating the lytic cycle resulting in death of the cell. i. Switch over is usually triggered from an environmental signal such as radiation or the presence of certain chemicals. c. The host cell s phenotype may be altered by the expression of prophage genes. i. Diphtheria, botulism and scarlet fever are dangerous because the prophage genes causes the host bacteria to make toxins. 2. Slide Eight: The lysogenic cycle: a. Phage attaches to a host cell and injects it DNA b. Enters the lysogenic cycle c. Phage DNA integrates into the bacterial chromosome becoming a prophage d. Bacterium reproduces normally, copying the prophage and transmitting it to daughter cells e. Many cell divisions produce a large population of bacteria infected with the prophage f. Slide Nine: A prophage may exit the cycle initiating the lytic cycle f. Reproductive Cycles of Animal Viruses: i. Slide Ten: The nature of the viral genome 1. Double Stranded DNA (dsdna) a. Adenovirus- respiratory diseases, animal tumors b. Papovavirus- warts, cervical cancer c. Herpesvirus- herpes, varicella zoster(shingles and chicken pox), Epstein barr d. Poxvirus- small pox virus, cow pox 2. Single Stranded DNA (ssdna) a. Parovirus- B19 parovirus (mild rash)

6 3. Double stranded RNA (dsrna) a. Reovirus- rotavirus(diarrhea), Colorado tick fever virus 4. Single stranded RNA (ssrna)- serves as mrna a. Picornvirus- rhinovirus, poliovirus, hepatitis A virus b. Coronavirus- SARS- severe acute respiratory syndrome c. Flavivirus- Yellow fever virus, west nile virus, Hepatitis C d. Togavirus- Rubella, equine encephalitis 5. ssrna, template for mrna synthesis a. Fliovirus- Ebola virus b. Orthomyxovirus- Influenza c. Parmyxovirus- Measles virus, mumps d. Rhabdovirus- Rabies 6. Slide Eleven: ssrna, template for DNA synthesis a. retrovirus- HIV, RNA tumor viruses ii. Viral Envelopes: 1. Viral glycoproteins protruding from the outer surface of the viral envelop bind to specific receptor molecules on the surface of the host cell 2. The reproductive cycle of an enveloped RNA virus: a. Glycoproteins on the viral envelope bind to specific receptor molecules on the host cell, promoting viral entry into the cell b. The capsid and viral genome enter the cell. Digestion of the capsid by cellular enzymes releases the viral genome c. The viral genome functions as a template for synthesis of complementary RNA strands by a viral enzyme d. New copies of viral genome RNA are made using complementary RNA strands as templates e. Complementary RNA strands also function as mrna, which is translated into both capsid proteins(in the cytosol) and glycoproteins for the viral envelop (in the ER). f. Vesicles transport envelope glycoproteins to the plasma membrane g. A capsid assembles around each viral genome molecule h. Each new virus buds from the cell, its envelop studded with viral glycoproteins embedded in membrane derived from the ER.

7 3. Some viruses have membranes derived from the nuclear membrane of the host. a. Herpes viruse- double stranded DNA genome i. Reproduce in the host cells nucleus ii. Uses viral and cellular enzymes iii. Some viral DNA remains behind as minichromosomes in the nuclei of nerve cells iv. Environmental or stress triggers active virus production resulting in blisters iii. RNA as Viral Genetic Material: 1. Viruses of the class IV genome can directly serve as mrna and can be translated into viral proteins 2. Class V- RNA genome serves as a template for mrna synthesis a. RNA genome is transcribed into complementary RNA strands which function both as mrna and as templates for th synthesis of additional copies of genome RNA 3. Retroviruses: a. Most complicated b. Class VI c. Reverse transcriptase- transcribes an RNA template into DNA- (opposite direction) i. HIV ii. Provirus- when the newly made DNA enters the nucleus and integrates into the DNA of a chromosome iii. Never leaves the host genome 1. Permanent resident of the cell 4. Slide Twelve: Reproductive cycle of a retrovirus: a. The virus fuses with the cell s plasma membrane. The capsid proteins are removed, releasing the viral proteins and RNA b. Reverse transcriptase catalyzes the synthesis of a DNA strand complementary to the viral RNA c. Reverse transcriptase catalyzes the synthesis of a second DNA strand complementary to the first d. The double stranded DNA is incorporated as a provirus into the cell s DNA e. Proviral genes are transcribed into RNA molecule which serve as genomes for the next viral generation and as mrnas for translation into viral proteins f. The viral proteins include capsid proteins and reverse transcriptase and envelop glycoproteins

8 III. g. Vesicles transport the glycoproteins from the ER to the cell s plasma membrane h. Capsids are assembled around viral genomes and reverse transcriptase molecules i. New viruses bud off from the host cell Chapter 18.3: Rapid reproduction, mutation, and genetic recombination contribute to the genetic diversity of bacteria: a. The bacterial genome and its replication: i. Bacterial DNA (bacterial chromosome) is: 1. Double stranded 2. Circular with a small amount of protein 3. E. coli consists of about 4.6 million nucleotide pairs 4. E. coli consists of about 4400 genes x the DNA found in a virus but only one/one thousandth found in human body cells 6. stretched out it would be about a millimeter in length 7. proteins cause DNA to become super coiled into a nucleoid. 8. Nucleoid is not membrane bound 9. Bacterial chromosomes have plasmids a. Small circular DNA strands with a small number of genes from a few to several dozen ii. Eukaryotic DNA: 1. Double stranded 2. Linear with large amounts of protein iii. Bacteria cells divide by binary fission 1. Asexual reproduction producing individuals that are genetically identical to the parent cell a. Any genetic differences is caused by mutation b. Spontaneous mutations averages 1 x 10-7 per cell division. c. Bacteria in the human gut will go through about 9 million mutations per day per human host. d. This can significantly increase genetic diversity 2. Preceded by DNA replication 3. Uses single origin of replication 4. DNA synthesis progresses in two directions 5. They can divided every 20 minutes in optimal conditions b. Mutation and Genetic Recombination as Sources of Genetic Variation: i. Populations where the individuals are short lived with high reproduction rates such as bacteria will have mutations that affect the evolution and diversity of the population 1. Versus new mutation that will make relatively small contribution to genetic variation in a population of slowly reproducing organisms such as humans

9 a. Most of he diversity of humans comes from recombination versus the creation of new alleles through mutation ii. Bacterial diversity does not just come from mutation but also from recombination 1. The combination of DNA from two different genomes 2. Evidence of recombination in bacteria: a. When two mutant stains of bacteria, one that can make the amino acid arginine, but not tryptophan, and one that can make tryptophan but not arginine are placed in a mixture, new colonies were growing where both arginine and tryptophan were present. (colonies cannot form unless both amino acids are present). b. Conclusion: each cell from the mixture that formed a colony must have acquired one or more genes from a cell of the other strain by genetic recombination. c. Mechanisms of Gene Transfer and Genetic Recombination in Bacteria: i. Transformation: alteration of a bacterial cells genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment. 1. Usually forms when a non- pathogenic form of bacteria uptakes a piece of DNA carrying the allele for pathogenicity. ii. Transduction: when a bacteriophage carries bacterial genes from one host cell to another. 1. Phage infects a bacterial cell 2. Host DNA is fragmented and phage DNA and proteins are made 3. A Bacterial DNA fragment may be packaged in a phage capsid 4. Phage with alleles from the donor cell infects a recipient and crossing over between donor DNA and recipient DNA occurs at two places 5. The genotype of the resulting recombinant cell differs from the genotypes of both the donor and the recipient. iii. Conjugation: 1. The direct transfer of genetic material between two bacterial cells that are temporarily joined. 2. Chromosomal genes or plasmid genes can be transferred a. One way transfer: i. One donor(some times called the male) and one recipient(female)

10 ii. Sex pili: appendages that attach to the recipient 1. Sex pili composed of oligomeric proteins (pilin) iii. Once attachment occurs, the pili contracts drawing the recipient cell closer to it iv. A temporary mating bridge forms providing an avenue for DNA transfer iv. Plasmids: 1. F factor (fertility factor): special piece of DNA that allows the formation of sex pili a. Can exist as a segment of DNA within the bacterial chromosome or as a plasmid. 2. Plasmid: small, circular, self replicating DNA molecule separate from the bacterial chromosome. a. Have small number of genes which are not required for survival and reproduction b. Can aid the cell in environmentally stressful situation. c. F plasmids- can undergo reversible integration into the cells chromosome i. Facilitate genetic recombination in environmentally stressful situations 3. Episome: genetic element that can replicate either as part of the bacterial chromosome or independently. 4. F Plasmid(F+) and Conjugation: a. F plasmid consists of 25 genes, most of which are required for the production of the sex pili i. Cells containing the F+ are designated as donors ii. F plasmids replicates in synchronicity with chromosomal DNA iii. Cells lacking the F plasmids(f- ) function as recipients. iv. F+ can transfer F- into F+ during conjugation 1. The original cell remains as F+ because only one parental strand for F factor DNA is transferred across the mating bridge. 2. Each parental strand acts as a template for synthesis of the second strand. v. A cell with a high frequency of F plasmids genes integrated into the chromosomal

11 genes is referred to as a high frequency of recombination (Hfr) cell. 1. This is a donor cell during conjugation b. Disruption of conjugation: i. Random movements can cause disruption causing the Hfr strand to break off before the entire strand is passed. 1. The single strand serves as a template 2. The recipient cell is a partial diploid, containing its complete F- chromosome and the transferred DNA from the Hfr donor. 3. Recombination once the donor DNA is in the recipient cell is responsible for the new bacterial DNA 5. R Plasmids and Antibiotic Resistance: a. Some bacteria have resistance genes coding form enzymes that specifically destroy certain antibiotics. i. R = resistance ii. Natural selection would predict that the fraction of the bacterial population carrying the R plasmids would increase, and that is what happens. 1. Makes treating bacterial infections more difficult b. Have genes that code for sex pili i. Can transfer R plasmid genes via conjugation c. Can carry as many as ten genes providing resistance to as many antibiotics d. How do so many antibiotic genes become part of a single plasmid? i. Transposons 6. Transposition of Genetic Elements: a. Transposable genetic elements (transposable elements) i. Never exists independently 1. Are part of chromosomal or plasmid DNA b. movement of transposable elements is called transposition

12 IV. i. elements move from one site in a cell s DNA to another site 1. by a type of recombination process 2. can move from a plasmid to chromosome or from plasmid to plasmid 3. jumping genes a. but never completely detach from the DNA b. DNA sites are brought together by DNA folding c. Cut and paste mechanisms d. Copy and paste mechanisms c. Simple transposable elements are called insertion sequences i. Exist only in bacteria ii. Contain a single gene which codes for transposase which catalyzes movement of a sequence from one site to another with the genome iii. Inverted repeats: base sequence at one end of the insertion sequence that is inverted at the other end of the sequence. iv. Can cause mutations d. Transposons: longer and more complex than insertion sequences i. Include extra genes that travel with the transposon 1. Antibiotic resistance for example ii. Can be sandwiched between two insertion sequences iii. May help the bacteria to adapt to new envio5rnments e. Unique to bacteria but are important components of eukaryotic genomes as well. Chapter 18.4: Individual bacteria respond to environmental change by regulating their gene expression: a. How do bacteria cope with environmental fluctuations: i. Example: E. coli bacteria of the human gut need tryptophan to survive. 1. If the host is not consuming tryptophan the bacteria respond by activating metabolic pathways the will make tryptophan from other chemicals 2. If the host consumes tryptophan then the bacteria will stop that pathway to conserve on energy and resources.

13 b. Two levels of metabolic control: i. Cells can adjust the activity of enzymes already present. 1. Relies on the sensitivity of enzyme to chemical cues to increase or decrease their catalytic activity. 2. Example: for the chemical pathway to produce tryptophan, the enzyme to begin synthesis is inhibited by its own product, tryptophan. a. this is called feedback inhibition and is typical of anabolic or biosynthetic pathways. b. Allows the cell to adapt to short term fluctuations in the supply of substances it needs ii. Cells can adjust the amounts of certain enzymes being produced 1. They can regulate the expression of the genes encoding enzymes a. Example: if the environment is providing all the tryptophan the bacterial cell needs, the cell stops making enzymes that control the pathway to produce tryptophan. b. This occurs at the level of transcription c. Operons: The Basic Concept i. The metabolic pathway for the production of tryptophan is controlled by 5 genes, which produces enzymes to synthesize tryptophan from a precursor molecule. 1. One long mrna is transcribed and codes for five different enzymes, and allows them to be synthesized at the same time. a. The mrna contains stop and start codons for each of the five proteins b. Grouping gens like this on the DNA chromosome provides an advantage that allows a single transcription unit to act as an on or off switch, controlling the production of all five enzymes. c. The switch is called an operator i. It is positioned between the promoter and the gene that codes for the enzyme ii. It controls access to RNA polymerase to the genes d. Operon: is the operator, the promoter and the gene that codes for the enzyme. ii. Trp Operon: 1. By itself the operon is turned on and codes for the production of enzymes that synthesize tryptophan from a precursor molecule. a. The operon can be switched off by by another protein, the Trp repressor.

14 b. The repressor binds to the operator and blocks attachment of RNA polymerase to the promoter preventing transcription of genes c. Repressor proteins are specific d. The Trp repressor has no effect on other operons. e. Trp repressor is a product of a regulatory gene called trpr. Located some distance away from the operon f. Regulatory genes are expressed continuously but at low rates i. Some trpr molecules are always present in E. coli g. Why are operons not permanently switched off? i. 1. The binding of repressors is reversible ii. regulatory repressor proteins are allosteric proteins 1. have two different shapes, active and inactive 2. example: the trpr is inactive, when tryptophan binds to the trpr the repressor changes to active form that can attach to an operon and switch it off. h. Corepressor: a small molecule that cooperates with a repressor protein to switch an operon off i. Tryptophan acts as a corepressor d. Repressible and Inducible Operons: Two Types of Negative Gene Regulation i. The tryptophan operon model is an example of a repressible operon because the transcription is usually on but can be repressed when tryptophan binds to a regulatory protein ii. Inducible operon is usually off but can be stimulated or induced when a specific small molecule interacts with a regulatory protein. 1. The repressor, unlike the trpr, is active all by itself and cannot be inactivated except in the presence of a small molecule called an inducer. e. Lac Operon Model: i. When the human host drinks milk, lactose(milk sugar) becomes available to the E. coli bacteria. 1. The lactose is subsequently metabolized into glucose and galactose, a reaction catalyzed by the enzyme β- galactosidase, of which there is a very short supply when lactose is not present.

15 2. In the presence of lactose, the β- galactosidase increases a thousand fold in only about 15 minutes ii. The gene for β- galactosidase is part of the lac operon, along with two other genes coding for enzymes that function in lactose metabolism. 1. Transcription for all of these enzymes is under control of a single operator and promoter. a. The three enzymes are: i. lacz- codes for β- galactosidase- which hydrolyzes lactose to glucose and galactose ii. lacy- codes for permease- a membrane protein that transfers lactose into the cell iii. laca- codes for an enzyme transacetylase, which plays an unclear role in the metabolism of lactose iii. laci, a regulatory gene located outside the operon codes for a protein (allosteric) that can switch off the lac operon by binding to the operator (repressor). 1. laci repressor is active all by itself, unlike the trpr which is activated by the corepressor tryptophan. 2. The laci repressor is shut off by an inducer, in this case Allolactose, which is an isomer of lactose which inactivates laci. f. Positive Gene Regulation: continuing with the lac operon model: i. For lactose metabolizing enzymes to be synthesized, more than just the presence of lactose is needed. a. There must also be a short supply of glucose. b. A lack of glucose is detected by a small regulatory allosteric regulatory protein cyclic AMP (camp) which accumulates when glucose is scarce. c. CAP- catabolite activator protein is an activator or transcription. ii. When camp binds to CAP, the active shape can now bind to a specific site at the up stream end of the lac promoter, directly stimulating gene expression. 1. As glucose increases, camp decreases which results in CAP detaching from the operon. a. Transcription of the lac operon proceeds at a very slow pace, even in the presence of lactose

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