MICROBIAL MODELS: GENETICS OF VIRUSES AND BACTERIA A virus is gneome enclosed in a protective coat.

Viruses are not cells the smallest ones are about 20 nm in diameter. Viral gneome: usually organized as single linear or circular nucleic acid. Viruses have capsids; protectoce protein coat madeof proteins called capsomeres. In fluenza viruses as well as many animal viruses hace viral envlopes; dereived from host plasma or nuclear envelope and have embed host and viral glycoproteins. Viruses which infect bacteria known as bacteriophafes.eg. T2,T4, T6 (T stands for type.) They have head and tail with fiber that enabke attachment to bacteria .

Viruses can only reproduce in a host cell Various viruses have different host ranges; the range of hosts it can infect. Viruses indentify their hhost by a lock and key fit between proteins on the virus and specific receptors on the hos cell. Some viruses can infect several species while some can only infect one species. Some animal viruses are slo tissue specific. Most DNA viruses use te host DNA polymerase to synthesize new genome. Most RNA viruses use special virus encoded polymerases to replicate their genimes. Phages reproduce using the lytic and lysogenic cycles. Lytic cycle: culminates in the death of the host cell. A phaeg that only reproduces by the lytic cycle is a virulent phage. Upon resleaing genome in to host, new viral gneome is replicated in host, packaged nito new viruses in addion to synthesizing lysoszyme which puctures bacterial cell wall and case it to swell and eventually burst releasing phages. How bacteria survive such danger?---(1)bacteria with eceptor sites no linger recognized by phage are naturally selected for. (2) Restriction nuclease(which bacteria have) recognize and chop up viral geneome- note:; bacterial DNA is modified in a way that restriction nuclease do not nreconize. Lysogenic cycle: implies that proghaegs are capable of giving rise to phages that lyse the host.replicaes the phage genome without destroying the host. Phage genome is incorporated into bacterial gneome( known as prophage), and can exist the genome at nay time; usally die to environmental trigger. One prophage gene codes for a repressor potein that suppres most of the other prophage genes Phages that se both the lysogenic and lytic reproduction are called temperate phages.

Animal viruses Animal viruses possess viral envelopes which eneables them to entre hosts iwththeir capsids intact. This membrane contains protruding glycoprotein spikes that bind receptorers on a host cell. Viral envelopes are derived form host plasma membranes, lycoproteins are also derived from hsotER, and are sentto

points in host plasma membrane where newly packaged viruses bud off wrapped in the membrane. Note herpers virus have viral envelope derived from the nuclear membrane of the host. Classes of animal viruses: DsDNA---Papovaviruses, adneoviruse, herpesvirus ssDNAParvovirus dsDNAReovirus ssRNA that serve as mRNA--- picornavirus, Togavirus ssRNA that serve as temperate for RNA---Rhabdovirus, paramxovirus, Orhtomyxovirus ssRNA that is template for DNA synthersis--- Retrovirus utilize reverse transcroptase.

Some viruses can cause cancer. Normal cells have proto-oncongenes; usually genes that rae involved in the regulation of the cell cycle eg. Growth factors.. Viurses may case cancer indirectly by turning on or increasing gthe expression of these proteins. Plant viruses Most plant viruses are RNA viruses. Horizontal transmission refers tot the infesction of a hsot by a virus form the outside. Vertical transmission refers to the infection of a host thrrohg inheritance of viral genome through parents. Viroids and Prions are evne simpler infectious agnets. Virods are tiny molecules of CIRCULAR rna THAT INFECTS PLANTS. Viroids do not encode proteins but can replicate in host plant cells. Prions are infectious proteins that appaera caue degenerative brain diseases.. How do prions replicate?Hypotheissi is prions are a misfolded form of anormal proein which when comes inot contact with normal proteins form, converts it tio the defective form in sequence hence multip;ing th enmbe rof defective forms.

THE GNETICS OF BACTERIA

Bacteria genome is tightly packed in a non enveloped region called th enucleoid. Bactria divide by binary fisson(asexual). Bacteria posses plasmid(SMALL CIRCULAR PICE OF DNA) in addition to the chromososme Noe; Yeast also have plasmids. Bacteria chromosome has only on origin of replication. Genetic recombination produces new strains of bacteria

Transformaion is the uptake of foreing naked DNA to alter bacteria geneome. E. coli is not normally competent(cannot take naked DNA of a give size). However, placin E.c oli in a medim containing calcium ions, makes it competent. Trnasduction is th e transfer of foren Gdna BY phage into bacteria. General transduction involves when a phage accidentally packes a piece of hydrolyzed host DNA ino capsids upon exiting host afer hosot lyses, and then injectin g the host DNA inot another bacteria ushc that the host DNA replaces tht ehomologous regions of the new bacteria host. In specialized transduction, the phage n=must be a temperate one. Upon exiting a s lytic phage, the phage excises fromt the host genome it usually cleaves of adjeacent nearby genes, and thes also can replace the homologous region of the new host the phage infects. Conjugation is the direct linking of two actreria cells thorusex pilli. Maleness is determined by which bactereial has F-factor: a special DNA piece whci can either exist as plasmid of integrate into host DNA. Episomes are genetic elements tht can either exist as plasmids or integrate into th e host geneome. Acell with an f factor built inot its chromosome is called an Hfr( high frequency of recombination) R-plasmids contain gnees for bacteria resistance henc ete name. Transposon are piece of DNA that can move from one region to antother in a cells geneome. Transposons cannot exist independently. There is cut and pase transposition and replicative trasnposittion. Cut and pase transposition: The gene is cut and inserted in another region. Repliative transposition: The gene is copied and inserted in new region without losing ht eon ein old position. Inseriton sequene: the simplest bacterial transposon, coansits only of the DNA involved in the transposition, thus code for transposase which catalyzes the genes movement. Trasnposase is brackedt and recognizes inverted repeats as boundaries. DNA polymerase alsio help create direct repeats flankin g the transposon in its new location. Transposase cuts bott he DNA nad also the target site. Compopsite tranpoisn possess contain extra gnees sandwiched between the insertion sewuences. These extra gene sare often beneficial to bacteria unlike mere insertion sequences.

The control of gene expression help bacteria adapt to new environments. Bacteria can either control the activity of enzymes or the expression level of th e enzyme. Oerons are a group genes with related functions nder a the coordinated contraol of a single promoter and operator; positioned within th e promoter or between the promoter and the enzyme-coding genes There are the inducible and th erepresisible operaon. Rpressible operon: always on, can be switched off by repressor protein coded by th e regulatory gene some distance upstream of th eoperon. Most regulatory proteins are allosteric ; have active and incativ eforms. The binding of another substance(coregulator/corepressor) determines stat e of repressor. In the Trp operon, Tryptophan binding activates repressor hene tryptophan is th ecorepressor. Activate repressor switches of operon. Neg inhibition thhoru trp accumulation. Lac Operon: laczlacylacA code B-glactosidae( catalyze the breaking of lacotose in ot glucose and galactose), permease( transports lactose into cell), transacetylase( unknown). The Trp and Lac operons are both examples of negeative gene control sinceactive form of repressor

switches off operon. The isomer of lactose, allolactose serves as an inducer in th elac operon thus when it binds the lac repressor it enables it binding to the promoter to prevent transcription.

Positive gene control: cAMP Receptor Protein ( CRP) when bound to cAMP is able to bind stably to the promoter of th elac operon( as well as othe roperons)bend the DNA making polymerase bindng easier. When glucose is scarce, cAMP accumulates, and thiscorrelates with th ebaterias use of lactose catabolism only when glucose is scarce. Note the Lac operon is hence under dual control(1) The allolactose determines whether the repressor will be active or not and hence if th eoperon is on, (2) the cAMP-CRP conjugate bindin g to the specific site upstream of promoter determines the rate of transcription.

CELLULAR RESPIRATON: HARVESTING CHEMICAL ENERGY Cellular respiration occurs I the mitochondria and is the equivlanet of photosynthesis which occurs in chloroplasts in plants. Both of these p rocesses yield energy in the form of ATP to power cellular work. Cells recycle the ATP they use for work The three phosphates attached to Adenosine in ATP makes it unstable . One phosphate (inorganic ) is hence transaferred by enzymes to other compounds priming them for work as a result of activating them. Eg. ATP phosphrylates transport proteins, motor proteins, and other key reactant in chemical ereactions. ATP is then regenerated by the reposphorylation ofADP with inorganic phosphate. Redox reactions involve th e transfer of electrons form one reacant to another. The electron transferrer (reducing agent)is oxidized while the receiver (oxidizing agent)is reduced. Electrons fall form organic molecules to oxygen in the processes of respiration; this fall is stepwise via NAD+(nicotinamide) and an electro transfer chain. NAD+ serves as an oxidizing agnet by a ccepting 2 electrons along with a proton. Reaction catalyzed by dehydrogenases. The proton is released intot the surrounding solution whiel the electorns are utilized in electro transport chain .

Respiraton involves glycolysis, the Krebs cycle, and electron transport Glycolysis occurs in the cytosol; involves the oxidation of glucose molecules into pyruvate. The Krebs ycles the breaks pyruvate to co2 after it has been converted to acetyl coA. Glycolysis is O2 independent. Glucose first goes through a series of enzyamtaic reactions to yiled Frucctose-1,6bisphosphate which is then split into two products; dihydroxyacetone phosphate, and glyceraldehydes-3-phosphate. These

steps invlolve the inveatment of 2 ATP molecules per each glucose breakdown.Since these two products are interconvertible, and the reaction favors glyceraldehydes -3-phosphate, only glcyeraldehyd eaccumulates. oNly glyceraldehyede-3-phosphate is utilized in the energy payoff phase. GLyceraldehyde -3-phosphate is oxidized into 1,3-bisphosglycerate by Triose phosphate dehydrogenase yielding 2NADH. Subsequent reactions result in pyruvate with 4 ATP produced. The net yiled ATP is hence 2.Net yield for glycolysis: 2 pyruvate +H2O, 2ATP, 2NADH+2H+. The 2 indates that 1 glucose is split inot two yruvate molecules The ATP produced in glycolysis is thorugh substrate level phosphorylation( tranasfer of phosphate from organic substrate to ADP by the enzyme). No CO2 is released during glycolysis. Kreb cycle: Pyruvate enters the mitochondrial matrix and is converted to acetyl coA through following steps. (1) Pyruvate carboxy groupo isremoved as CO2 (2) The remaining two-carbon fragment is oxidized to form acetate by the transfer of electrons to NAD+ to form NADH. (3)CoenzymeA(sulfur containg compound obtained form a Bvitamin) is attached to the acetate forming the unstable acetylcoA which enters the KREB cycle. AcetlycoA bonds with oxaloacetate to form citrate which undergoes a series of reactions which yield oxaloacetate agin. In the process 3NADH , 1FADH2 and2CO2 are produced in addition to 1ATP form substrate level phosphorelatytion. Electron Transport Chain; oxidative phosphorylation The 2NADH from glycolysis, the 1NADH in the prep of pyruvate for kreb cycle. The 3NADH and 1FADH2 form Kreb cycle each acarries electrons as well as H+protons and these electrons enter the transport chain which involves enzymes embeddd in the inner mitochondrial membrane. Order of electron receiveing complexs of the chain: FMN(flavinmononucleotide)Fe.s---------Q(ubiquinone)------CytbFe.SCytc1----Cyt c-----CytaCyta3. Note that NADH transfers electrons to the chain at FMN while FADH2 transfers electrons to another Fe.S(not shown) which connects Ubiquinone. Electrons fall down form these proteins to ultimately, Oxygen( last stop). Molecular oxyegen (O2) and not iidvidual oxygen is redcued to H2O in the process. The elecro transport s easesa the fall of electrons to oxygen , and in the process releases the H+ into the opposite sied of the inner membrane; creating a proton motive force. As the H+ can only flow donwn their gradient through the embedded ATP synthase since impermeable to membrane, the synthesesa couples the flow of H+ to th synthesis of ATP by sing the energy to add inorganic phosphate eto ADP. The flow of H+ causes a spin inth ATP synthase rod, changing conformation of knob , and activating catalytic sites which combine inorganic phosphate eot ADP. This coupling of proton-motive force to cellular wrk is called chemiosmosis. Ellular respiration yields a total of about 36 ATP( 34 from electron tranpotr, and 2 from Kreb cyyecel). In addition to the 2ATP form glycolysiss. The total ATP yield is estimated at 38.

Fermentaion enable some cells to produce ATP without oxyegen Aerobic fermentation occurs in the presence of O2 while anaerobic fermentation occurs without O2 to produce ATP soley by substrate elvele phosphorylation. Alcohol fermentation involves the conversion of pyruvate to ethanol by first step involving convert it to acetaldehyde by the release of he COO- gorgup as CO2, and subsequent reduction by NADH to form alcohol and NAD+. In lactic acid fermentation, NADH directly reduces pyruvate to lactic acid and NAD+ with no release of CO2. The presence of O2 usually determines whether pyruvate will be used in fermenttionof respiration. Facultative anaerobes can use either use repiation or fermentation. Glycolysis and the KREB cycle connect to many othe rmetabolic pathways. Various compounds enter the Glycolyiss-reespiraotn pathway at various points. Proteins after being broken donwn as amino acids, and being deaminated(remove amine ,NH3 group)can be converted to pyruvate, acetylcoA, and other intermediates of te Kreb cycle Carbohydrates are converted to simle sugars then to glucose or directly to other intermediates of glycolysis bypassing conversionto glucose. Fats can be broken down to fatty acids and Glycerol. Glycerol to glyceraldhyede phosphate. Fattyacids can also oxidized nto AcetylcoA which then enter the Krebs cycle. Note that these molecules (fats, carb, proteins) can also be syntheisszed theoruhg anabolic pathway; the reverse of the above outline pathway by consuming ATP. Eg.Compounds form the kreb cycle can b used to produced amino acids, glucose form pyruvate, and fatty acids can be synthesized from acetylcoA.

Feddback mechanisms control celllar respiration

The conversion of Fructose-6-phosphate to fructose-1,6-bisphophate by Phosphofructokinase is the point of no return where the compound is to cleaved into glyceraldehydes 3-phosphate and into the energy payoff phase. Hence phosphofructokinsase is an important enzyme to control as a means to regulate glycolsysis and cellular respiration. ATP produce in each step of cellular respiration hasan a direct inhibitive effect on Phosphofructokinase at a certain concentration. Citrate for the Kreb cycle also inhibits tis enzyme while AMP indicative of the depeltiton of ATP, stimulates this enzyme. Note Citrate though not an enzyme, has anequivalent importance to phosphofructokinase in that its formation commits compounds to th eKreb cycle and subsequently ATP as well as NADH and FADH2 produciton