Describe The Structure Of DNA And Explain The Roles Of Dna
BIO 113 Spring 2012 - Dr. MJ Bernot
Study Guide – Exam 2
Chapter 7- IS AT THE BOTTOM. Bernot wrote it so hopefully it is useful
• Describe the structure of DNA and discuss how it facilitates the ability of DNA to act as genetic material
• Compare and contrast prokaryotic and eukaryotic chromosomes
• Describe the process of DNA replication as a semi-conservative process. Compare and contrast the synthesis of the leading and lagging strands in DNA replication.
• Explain how the genotype of an organism determines its phenotype.
• State the central dogma of genetics and explain the roles of DNA and RNA in polypeptide (aka: protein) synthesis
• Describe the three steps of RNA transcription (initiation, …show more content…
elongation, termination) noting the roles of DNA, RNA polymerase, promoter, 5’-3’ direction, and terminator.
• Describe the genetic code and identify the relationship between codons and amino acids.
• Describe the process of translation identifying the roles of the three types of RNA.
• Define mutation and describe the different types of mutations: point, silent, missense, nonsense, frameshift insertion, frameshift deletion.
• Discuss how different types of radiation cause mutations in a genome.
• Describe three kinds of chemical mutagens and their effects: nucleotide analogs, nucleotide-altering chemicals, frameshift mutagens
• Describe light and dark repair of pyrimidine dimers, base-excision repair, mismatch repair, and the SOS response.
• Contrast the positive and negative selection techniques for isolating mutants.
• Describe the Ames test, and discuss its use in discovering carcinogens.
• Define: genetic recombination, recombinants, horizontal (lateral) gene transfer, donor cell, recipient cell, competent, transduction, bacteriophage, phage, transducing phages, conjugation, transposon and transposition
• Describe the three primary mechanisms of natural horizontal genetic transfer in bacteria: transformation, transduction, conjugation.
*chapter 8 will not be on the Exam*
Chapter 9
• Contrast sterilization, disinfection, and antisepsis and describe their practical uses.
o Sterilization
▪ Removal or destruction of ALL microbes, including viruses and bacterial endospores, in or on an object
▪ Used in Canned food and culture media
o Disinfection
▪ Destruction of most microorganisms and viruses on nonliving tissue
▪ Does not guarantee that all pathogens are eliminated
▪ Used on nonliving objects only
▪ Examples phenolic; alcohols; aldehydes; soaps
o Antisepsis
▪ When chemicals are used on skin
▪ Similar to disinfection only it is used on skin
▪ Like disinfectants can be left on a surface for longer periods of time
▪ Examples include iodine; alcohol
• Contrast the terms degerming, sanitization, and pasteurization.
o Degerming
▪ Removing microbes by mechanical means
▪ Like washing your hands and scrubbing
▪ Or to prepare site of injection
▪ Scrubbing the surface may be more important than the chemical in removing microbes
o Sanitization
▪ Removal of pathogens from objects to meet public health standards
▪ Like washing tableware in scalding water in restaurants
▪ Chemicals used on public toilets
o Pasteurization
▪ The use of heat to kill pathogens and reduce the number of spoilage microorganisms in food and beverages
▪ Used in milk, fruit juices, wine, and beer
• Compare the effects of –static versus – cidal control agents on microbial growth.
o Static
▪ Or Statis is by chemical or physical agent inhibits microbe
▪ Instead of killing them just stops them from growing and leaves them dormant
▪ Like refrigerating
o Cidal
▪ Or cide is referring to agents that destroy or permanently inactivate a particular type of microbes
▪ Completely kills microbes
▪ Burning them
• Define microbial death rate and describe its significance in microbial control.
o Microbial death rate
▪ Permanent loss of reproductive ability under ideal environmental conditions
o They use this to evaluate how efficient antimicrobial agents are
• Describe how antimicrobial agents act against cell walls, cytoplasmic membranes, proteins, and nucleic acids.
o Attacking cell
walls
▪ If the wall is disrupted by physical or chemical agents, it can no longer prevent the cell from bursting as water moves into the cell by osmosis thus killing it completely
o Cytoplasmic membranes
▪ If there is extensive damage to a membrane’s proteins or phospholipids by any physical or chemical agents allows the cellular contents to leak out which if not repaired quickly will result in death.
o Proteins
▪ Since proteins demand an exact three dimensial shape if this is broken by heat or certain chemicals it can cause a shape shift thus making the proteins useless. Proteins are needed to regulate cellular metabolism
o Nucleic Acid
▪ Chemicals, radiation, and heat can also alter and even destroy nucleic acids
▪ Disruption to these can cause fatal mutation and eventually kill it
▪ Also interference to nucleic acids also stop protein synthesis
• List factors to consider in selecting a microbial control method.
o Site to be tested
▪ Must decide where to test the antimicrobials
▪ Some areas are more prone to infection so must choose an appropriate site
o Relative Susceptibility of Microorganisms
▪ How resistant are the microorganism that you are working with
o Environmental Conditions
▪ Must clean instruments properly and that will control the antimicrobial and at what point are they most effective like temperature, pH, etc.
• Identify the three most-resistant groups of microbes, and explain why they are resistant to many antimicrobial agents
o Prions-1
▪ Infectious proteins that cause degenerative diseases of the brain
o Bacterial Endospores-2
▪ They can survive in extremes of temperature and acidity and withstand many chemical disinfectants
▪ Also can survive more than 20 years in 70% alcohol
o Mycobacteria-3
▪ Cell walls contain large amounts of waxy lipids.
▪ The wax allows the bacteria to survive drying and protects them from most water-based chemicals
▪ Can only use strong disinfectants or heat to treat whatever comes into contact with tuberculosis patients
o Cysts of Protozoa-4
▪ Their wall prevents entry of most disinfectants, protects against drying, and shields against radiation and heat
• Discuss environmental conditions that can influence the effectiveness of antimicrobial agents
o Depending on the temperature and pH may influence how the antibiotic works
• Describe types of physical methods of microbial control: moist heat, pasteurization, dry heat, refrigeration and freezing, dessication and lyophilization, filtration
o Moist Heat
▪ Is commonly used to disinfect, sanitize, sterilize, and pasteurize, kills cells by denaturing proteins and destroying cytoplasmic membranes.
▪ More effective than dry heat because water is better conductor of heat than air
o Boiling
▪ Kills vegetative cells of bacteria and fungi the trophozoites of protozoa , and viruses within 10 mins at sea level
▪ Boiling time is the most important factor
▪ Some bacterial endospores, protozoan cysts, and some viruses and survive boiling
o Autoclave
▪ True sterilization using heat requires higher temperatures than boiling water.
▪ Uses pressure and temperature
o Pasteurization
▪ Used to kill pathogens in food and drinks
▪ It is not sterilization some organisms still remain
▪ Would look over table 9.2 pg 270 for lists of different types of pasteurization and their temperatures and times
o Dry Heat
▪ Used on powder and oils
▪ Uses steam that helps sterilizes it cause it denatures proteins and fosters the oxidation of metabolic and structural chemicals; however in order to sterilize dry heat requires higher temperatures.
▪ Requires more time than moist heat because dry heat penetrates more slowly
o Refrigeration
▪ Halts the growth of most pathogens by cooling them down
o Freezing
▪ Slow freezing is more effective than quick freezing because it inhibits microbial metabolism
▪ Used to store bacteria and viruses
o Dessication
▪ Drying out the food
▪ Used for thousands of years like fruits, peas, beans, grain, nuts, and yeast
▪ Inhibits the spread of most pathogens
o Lyophilization
▪ Combination of freezing and drying to preserve microbes and other cells for thousands of years.
▪ Uses liquid nitrogen to freeze them then uses a vacuum to remove frozen water
▪ Prevents large formation of large, damaging ice crystals
▪ Not all cells survive but enough remain
o Filtration
▪ Passage of a liquid or gas through a membrane filter, something used to catch large molecules and little ones to slide through.
▪ Pores today can even catch viruses
• Discuss the use of hypertonic solutions in microbial control
o Cells in a hypertonic solution of salt or sugar lose water, and the cell desiccates. The removal of water inhibits cellular metabolism because enzymes are fully functional only in aqueous environments
• Differentiate between ionizing radiation and nonionizing radiation as they relate to microbial control
o Ionizing radiation
▪ Uses wavelength shorter than 1 nm
▪ Creating ions when they strike molecules
▪ These ions denature other molecules, particularly DNA, causing fatal mutation
▪ Like electron beams, gamma rays, x-rays
o Nonionizing radiation
▪ Uses wavelength greater than 1 nm
▪ Formation of thymine dimers inhibition DNA transcription and replication
▪ Like UV rays
• Describe four levels of biosafety and give examples of microbes handled at each level
o Biosafety level 1
▪ Suitable for handling
▪ E.coli
▪ Minimal danger
o Biosafety level 2
▪ Moderately hazardous
▪ Like hepatitis, influenza, Staphylococcus
o Biosafety level 3
▪ Tuberculosis
▪ Anthrax
▪ Yellow fever
▪ Rocky mountain spotted fever
o Biosafety level 4
▪ Ebola
▪ Small pox
▪ Lassa fever
• Compare and contrast nine major types of antimicrobial chemicals and discuss the positive and negative aspects of each: phenols, alcohols, halogens, oxidizing agents, surfactants, heavy metals, aldehydes, gaseous agents, enzymes
o Phenols
▪ Lister began using them first to reduce infection during surgery
▪ Phenolic are compounds derived from phenol molecules that have been chemically modified by addition of halogens
• Orthocresol
• Triclosan
• Hexachlorophene
▪ Natural oils like pine and clove oils phenolic
▪ Intermediate to low level disinfectants
▪ Denature proteins and disrupt cell membranes
▪ Pretty commonly used in health care settings, laboratories, and households
▪ Can irritate the skin of some individuals
▪ Can also cause brain damage to some infants
o Alcohols
▪ Bactericidal, fungicidal, virucidal against enveloped viruses, not effective against fungal spores or bacterial endospores
▪ Intermediate level disinfectants
▪ Common uses are rubbing alcohol and drinking alcohol
▪ Not an effective antimicrobial agent, because the denature of proteins requires water; so solutions of 70%-90% of alcohol are typically used to control microbes
▪ Evaporate quickly leaving no residue
▪ May not be in contact with microbes long enough to be effective
▪ More effective than soap in removing bacteria
o Halogens
▪ Has four very reactive, nonmetallic chemical elements
• Iodine
o Well known antiseptic
o Disinfects water
• Chlorine
o Treats drinking water, swimming pools, and wastewater
• Bromine
o Effective disinfectant in hot tubs
• Fluorine
o Antibacterial in drinking water and toothpaste can help reduce cavities
▪ Intermediate-level antimicrobial
▪ Effective against vegetative bacterial and fungal cells, fungal spores, some bacterial endospores and protozoan cysts and many viruses
o Oxidizing agents
▪ Kills microbes by oxidizing their enzymes thereby preventing metabolism
▪ High-level disinfectant and antiseptics
▪ Effective against anaerobic microorganisms
▪ Hydrogen peroxide
• Mistakenly used to treat open wounds
▪ Ozone
• Used to treat water
• Fresh air smell
• More effective antimicrobial agent than chlorine
• More expensive though
o Surfactants
▪ Surface active chemicals
▪ Reduce surface tension of solvents such as water by decreasing the attraction among molecules
▪ Detergents
• Positively charged organic surfactants that are more soluble in water than soap
▪ Quats
• Detergent composed of ammonium
• Harmless to humans
• Bactericidal
o Especially against gram-positive
• Fungicidal
• Virucidal
o Enveloped viruses
• Low level disinfectants
▪ Poor antimicrobial agents
o Heavy metals
▪ Ions:
• Arsenic
• Zinc
• Mercury
• Silver
• Copper
▪ Antimicrobial because they contain sulfur
▪ Denatures proteins, inhibiting or eliminating their function
▪ Low-level bacteriostatic
▪ Might be a more effective antimicrobial agent
▪ Can be used to prevent blindness
▪ Used to preserve vaccines
• Mercury is a metabolic poison
o Aldehydes
▪ Compounds containing –CHO
▪ Denatures proteins and inactiving nucleic acids
▪ Glutaraldehyde
• Liquid
• More effective than formaldehyde but is more expensive
• Used to kill bacteria, viruses, and fungi
▪ Formaldehyde
• Gas
• Highly reactive chemical
• Used for embalming and to disinfect isolation rooms, exhaust cabinet, surgical intruments, and reusable kidney
• Can become irritating and is carcinogenic
o Gaseous agents
▪ Attacks the proteins denaturing them and DNA killing everything it comes in contact with
▪ Ethylene oxide
▪ Propylene oxide
▪ Beta propiolactone
▪ Frequently used to sterilizing hospitals and dental offices NASA also uses it
▪ Can be extremely hazardous
▪ Can also become explosive
▪ Also very poisons
▪ Potentially carcinogenic
o Enzymes
▪ High against target substrates
▪ Denature proteins
▪ Removal of prions on medical instruments
▪
Chapter 10
• Describe the contributions of Paul Ehrlich, Alexander Fleming, and Gerhard Domagk in the development of antimicrobials
o Paul Ehrlich
▪ 1845-1915
▪ German scientist
▪ Proposed the term chemotherapy
• Describes the use of chemicals that would selectively kill pathogens while having little or no effect on a patient
▪ Magic bullet
• Something that would bind to receptors on germs to bring about their death while ignoring the host cells
o Alexander Fleming
▪ 1881-1955
▪ British Bacteriologest
▪ Penicillium mold
• Creates a zone where bacteria don’t grow
▪ Penicillin
o Gerhard Domagk
▪ German chemist
▪ 1888-1973
▪ First practical antimicrobial agent efficacious in treating a wide array of bacterial infections
▪ Discovered sulfanilamide
• Explain how semisynthetic and synthetic antimicrobials differ from antibiotics
o Semisynthetic
▪ Chemically altered antibiotics—that are more effective, longer lasting, or easier to administer naturally occurring antibiotics
o Synthetic
▪ Antimicrobials that are completely synthesized in a laboratory
• Explain the principle of selective toxicity
o Ehrlich
o More toxic to the pathogen than to its host
• List the six mechanisms by which antimicrobial drugs affect the growth of pathogens
o Drugs that inhibit cell wall synthesis
o Drugs that inhibit protein synthesis
o Drugs that disrupt unique components of cytoplasmic membrane
o Drugs that inhibit general metabolic pathways not used by humans
o Drugs that inhibit nucleic acid synthesis
o Drugs that block a pathogen’s recognition of or attachment to its host
• Describe the actions and give examples of drugs that affect the cell walls of bacteria and fungi
o Action
▪ Bacteria
• Prevents cross-linkage of NAM subunits
• Uses beta-lactams
• Beta-lactams inhibit peptidoglycan formation by irreversibly binding to the enzymes that cross-link NAM subunits
• Without the cell wall they lose shape, and the cell will eventually lyse
▪ Fungi
o Drugs
▪ Penicillin: beta-lactams
▪ Cephalosporin: beta-lactams
▪ Vancomycin
• Directly interfere with particular alanine-alanine bridge that link the NAM sub-units in many gram-positive bacteria
• Bacteria that lack this bridge are unaffected by these drugs
▪ Bacitracin
• Blocks transport of NAG and NAM from cytoplasm to cell wall
▪ Isoniazid
• Disrupts the layer of arabinogalactanmycolic acid
▪ Ethambutol
• Same as isoniazid
▪ Echinocandins
• Used of fungus
• Inhibits the enzyme that synthesizes glucan
• Without this the fungal cells cannont make cells walls thus leading to osmotic rupture
• Describe the actions and give examples of drugs that affect protein synthesis
o Actions
▪ Takes advantage of prokaryotic and eukaryotic protein sizes
o Drugs
▪ Aminoglycosides
• Changes the shape of the 30S subunit making it impossible for the ribosome to read the codons of mRNA correctly
▪ Tetracyclines
• Block the tRNA docking site, which prevents the incorporation of additional amino acids into a growing polypeptide
▪ Chloramphenicol
▪ Macrolides
• Describe the actions and give examples of drugs that affect cytoplasmic membranes
• Describe the actions and give examples of drugs that inhibit metabolic pathways
o
• Describe the actions and give examples of drugs that inhibit nucleic acid synthesis
o Action
▪ Targets the destruction or inhibition or DNA and RNA in cells
o Drugs
▪ Actinomycin
• Binds to DNA and effectively blocks DNA synthesis and RNA transcription not only in bacterial pathogens but in their hosts as well
▪ Nucleotide
• Molecules with structural similarities to normal nucleotide building blocks of nucleic acids
• With their similar shape they can distort the DNA and RNA to prevent further replication, transcription, or translation
▪ Quinolones
• Used agasint prokaryotic DNA specifically
• Inhibits DNA gyrase, an enzyme necessary for correct coiling and uncoiling of replicating bacterial DNA.
▪ Rifampin
• Binds more readily to prokaryotic RNA polymerase than eukaryotic RNA polymerase
• Describe anti-viral drugs
• Distinguish between narrow-spectrum drugs and broad-spectrum drugs in terms of their targets and side effects
o Narrow-spectrum
▪ Drug that work against only a few kinds of pathogens
o Broad-spectrum drug
▪ Drug that works against many different kind of pathogens
▪ They can open doors to serious secondary infections
• Identify three main categories of side effects of antimicrobial therapy
o Toxicity
▪ Some drugs can affect fetuses
▪ The drugs may be toxic to kidneys, the liver, or nerves
o Allergies
▪ The patient may have an allergic reaction to some drugs out there
o Disruption of Normal Microbiota
▪ Can cause a superinfection
▪ May cause a secondary infection
• Describe how populations of resistant microbes can arise
o When a drug is exposed to the cells it kills off all the sensitive cells and leaves all the resistant cells left. Eventually the resistant cell is the majority of the population thus making a whole new strand of bacteria and the need for a new drug
• Describe the relationship between R-plasmids and resistant cells
o The bacteria can acquire resistance genes on extrachrmosomal pieces of DNA through the process of horizontal gene transfer—transformation, transduction, or conjugation
• List six ways by which microorganisms can be resistant to antimicrobial drugs
o One
▪ May produce enzymes that destroy or deactivate the drug
▪ Uses enzymes to break beta-lactam rings
o Two
▪ May slow or prevent entry of drugs into cell
▪ Involves change in structure or electrical charge of cytoplasmic membrane
▪ Some gram-negative bacteria have porins (an outer membrane)
▪ They alter pore protein
o Three
▪ May alter the target of the drug so it can’t attach itself or bind effectively
o Four
▪ Altering their metabolic chemistry
▪ May start producing more enzymes for affected metabolic pathway reducing power of the drug
▪ Also can abandon certain acids and just absorbing it
o Five
▪ Can pump the antimicrobial out of the cell
▪ Called efflux pump, which are powered by ATP
o Six
▪ Bacteria within biofilms resist antimicrobials more effectively than free-living cells
▪ Biofilms slow metabolic rates
▪ Lower metabolic rate reduces the effectiveness
o Seven
▪ READ UP ON THIS ONE PG 303
• Define cross resistance and distinguish it from multiple resistance
o Cross resistance
▪ Resistance to one antimicrobial agent may confer resistance to similar drugs
▪ Occurs mostly when drugs are similar in structure
o Multiple Resistance
▪ Resistant to three or more types of antimicrobial agents
• Describe four ways that development of resistance can be retarded
o One
▪ Sufficiently high concentrations of the drug can be maintained in a patient’s body for a long enough time to inhibit the pathogen, allowing the body’s defenses defeat them. If you discontinue the drug too early could cause a resistant strain
o Two
▪ Use antimicrobial agents in combination so that pathogens resistant to one drug will be killed by others drugs, and vice versa. Sometimes one drug enhances the effect of the second drug.
o Three
▪ Limit use of antimicrobials to necessary cases
▪ Use them only when needed not giving it to every person who has a sore throat or a stomach ache
o Four
▪ Developing a new drugs
*Chapter 11 and 12 will not be on the exam*
Chapter 13
• Discuss viral genomes
o Single Stranded
▪ ssRNA
▪ ssDNA
o Double stranded
▪ dsRNA
▪ dsDNA
• Explain the mechanisms by which viruses are specific for their host cells
• Discuss the structure and function of a viral capsid
o Capsid
▪ Protein coat provides protection for viral nucleic acid and means of host attachment
▪ Made up of subunits called capsomers
• Discuss the origin, structure, and function of the viral envelope
o The enveloped virus acquires its envelope from its host cell during viral replication or release
o Composed of phospholipid bilayer and proteins
o The envelope plays a role in host recognition
• List the characteristics by which viruses are classified
o Types of nucleic acid
o Presences of envelope
o Shape
o Size
• Sketch and describe the five stages of the lytic replication cycle as it typically occurs in bacteriophages
[pic]
• Compare and contrast the lysogenic replication cycle of viruses with the lytic cycle
o
• Explain the differences between bacteriophage replication and animal viral replication
o See page 399 chart 13.4
• Compare and contrast the replication and synthesis of DNA, -RNA, and +RNA viruses
o
• Compare and contrast the release of viral particles by lysis and budding
o Budding
▪ Instead of exploding the cell completely viruses just bud off so to say.
▪ They push up on the cell’s membrane slowly shedding the virus away
o Lysis
▪ Completely bursting of the cells scattering the virus everywhere
• Compare and contrast latency in animal viruses with phage lysogeny
o
• Define the terms neoplasia, tumor, benign, malignant, cancer, metastasis
o Neoplasia
▪ Cells beginning to divide uncontrollably
o Tumor
▪ Cells that undergo neoplasia and group together
o Benign
▪ Tumors that remain in one place
o Malignant
▪ Invade other neighboring tissue, move throughout the body to invade other organs and tissues to produce new tumors
o Cancer
▪ Malignant tumors
o Metatasis
▪ The process of a tumor spreading throughout the body
• Explain how a cell may become cancerous with viral activity
o Viruses cause 20-25% of human cancers
o Viruses carry oncogenes
▪ Something the plays a role in cell division. When activated they cause they cause cancer
o Viruses promote oncogenes that are already present
• Describe some ethical and practical difficulties to overcome in culturing viruses
o Some people might be opposed to using animals as test subjects for virus that may kill or harm the animals
o Another is you cant really get a good reading how it will work on humans because most humans don’t want to volunteer to try out the virus
o Common sense things pretty much
• Describe the three types of media used for culturing viruses
o Culturing in Mature Organisms
▪ Bacteria
• Most research on viral replication comes from here
• Easy to grow and maintain
• Just put it on agar plate and let it sit and let the viruses just kill
• Plaques
o Areas where phages have lysed
• Plague assay
o Estimating how many viruses are on the plate
▪ Plants and Animals
• Just really ethical issues pretty simple enough
o Culturing in embryonated chicken eggs
▪ Just a simple inexpensive way to test viruses and vaccines
o Culturing in cell culture
▪ Cells isolated from an organism and grown on the surface of a medium or in a broth
• Diploid cell
o Created from embryonic animal, plant, or human cells that have been isolated and provided appropriate growth
o Cells only last 100 generations then they die
• Continuous cell culture
o Derived from tumor cells
o Cells just keep replicating so they pretty much have an infinite supply of human cells
• Discuss aspects of viral replication that are life-like and non-life-like
o Life-like
▪ Use sophisticated methods to invade cells, have the means of taking control of their host cells, possess genomes containing information instructions for replication
o Non-life-like
▪ Don’t meet all the requirements of characteristics of life
▪ Mostly just complex pathogenic chemicals
• Define and describe viroids
o See below pretty much
• Compare and contrast viroids and viruses
o Chart is 405
o Smaller than prions and viruses
o Infectious and pathogenic in plants
o Have RNA but lack the capsid
• Define and describe prions including their replication process
o Discovered by Stanley Prusiner in 1982
o Prions
▪ A proteinaceous infectious agent that is different from any other known infectious agent in that it lacked instructional nucleic acid
o Known as slow viruses because a long period of time might go by before you recognized any symptoms
o Changes the shape of a PrP protein to synthesize with it do not code for new prions but instead convert cellular PrP into prions
o They
• Compare and contrast prions and viruses
o See page 405 for complete chart
o Prions are typically smaller in both width and length
o Prions have no nucleic acids while Viruses has either DNA or RNA
o Prions are self-replicating from their protein PrP
• List four diseases caused by prions
o Bobine spongiform encephalitis (BSE, also called mad cow disease
o Scrapie
▪ In sheep
o Chronic wasting disease (CWD)
▪ In deer and elk
o Creutzfeldt-Jakob disease (vCJD)
▪ In humans
Central Dogma of Biology
From Replication to Transcription to Translation
Replication (DNA to DNA)-An anabolic polymerization process that requires monomers and energy
*Triphosphate deoxyribonucleotides-monomers, DNA nucleotides with three phosphate groups linked together by two high-energy bonds, serve both functions of DNA replication
*Replication is semiconservative – new strands composed of one original and one daughter strand
Initial Process
1. Begins at specific sequence of nucleotides called Origin
2. Histones and other proteins are removed
3. DNA double helix unwound by helicase (Unzips the DNA helix) 1. exposes replication fork
4. Stabilizing proteins keep strands from going back together
5. DNA polymerase III (adds bases to the new DNA chain and proofreads for mistakes) binds to one strand of DNA and begins using it as template for assembling leading strand of nucleotides on 3’ OH-
6. DNA polymerase I (removes primer, closing gaps, and repairing mismatches) binds to other template strand and synthesizes discontinuous segments of nucleotides on 3’ OH- (Okazaki fragments)
7. Replicates DNA only from 5’ to 3’; strands are antiparallel so synthesized differently
Synthesis of the Leading Strand
1. Synthesized toward replication fork
2. Primase, enzyme, synthesizes a short RNA molecule complementary to DNA strand
3. Triphosphate deoxyribonucleotides form H-bonds with the parental strand
4. using the energy from the triphosphate deoxyribonucleotides the DNA polymerase III joins the nucleotides to the leading strand
5. It is proofread by the DNA polymerse III, removes errors (proofreading exonuclease function)
6. DNA polymerase I replaces RNA primer with DNA
Synthesis of the Lagging Strand
1. RNA Primase lays down RNA Primer
2. DNA polymerase III lays down new DNA
3. DNA polymerase I replaces RNA primer with DNA 1. Polymerase III & I create Okazaki fragments by attaching the Triphosphate nucleotides in pieces
4. DNA Ligase links the Okazaki fragments
5. DNA ligase (final binding of nicks in DNA during synthesis and repair) stitches strands together into the lagging strand
Transcription-(occurs in the nucleoid region of the cytoplasm in bacteria & nucleus/ (mitochondria and chloroplast) in Eukaryotes) DNA-RNA
Initiation
1. RNA polymerases (enzyme that synthesize RNA) bind to specific DNA nucleotide sequences called Promoters (initiation)
2. RNA polymerase binds to transcription factors and unzips & unwinds the DNA and forms a bubble as it moves along
3. RNA polymerase proceeds down one strand moving in 3′ → 5′ direction
Elongation
4. As RNA polymerase travels, it assembles nucleotides (elongation)
Termination
5. When transcription is complete, transcript is released from polymerase and, polymerase is released from DNA (termination) 1. Self-Termination when RNA polymerase transcribes a termination sequence of DNA: lots of G and Cs followed by A’s 1. G’s and C’s create a pause allows for H-bonds to form between its own symmetrical sequences resulting in a stem and loop results in tension on the RNA polymerase and DNA. 2. the few hydrogen bonds between the A’s and U’s break away releasing the RNA polymerase and DNA 2. Rho-dependent Termination- depends on Rho protein 1. pushes between the RNA polymerase and the DNA and forces them apart
Most eukaryotic genes do not exist as an uninterrupted series of triplets coding for a protein
Introns- sequences of bases that do not code for protein
Exons- coding regions that will be translated into protein
Called a split gene- requires further processing before translation
A splicesome recognizes the exon-intron junctions and enzymatically cuts through them
The exons are joined end to end
Some introns do code for cell substances (in humans, introns represent 98% of the DNA)
RNA Translation- ribosomes use the genetic info of nucleotide sequences to synthesize polypeptides composed of specific amino acid sequences.
Initiation-mRNA and tRNA^fmet form initiation complex
1. ribosomal subunit attaches to mRNA at ribosome-binding site, position start codon (AUG) at Psite
2. tRNA^fmet attaches to ribosome’s Psite (anticodon UAC)
3. larger ribosomal subunit attaches to form a complete initiation complex
Elongation- cyclical process, involves sequential addition of amino acids to polypeptide chain growing at Psite
1. tRNA whose anticodon is complementary to the next codon delivers its amino acid to the Asite where proteins called elongation factors escort the tRNA along the molecule of GTP 1. GTP energy stabilizes each tRNA as it bonds to Asite
2. ribozyme from the larger r. subunit forms a peptide bond between terminal amino acid of chain and the new amino acid. polypeptide now attached to tRNA at the Asite (amino acid site)
3. using the GTP energy, ribosome moves one codon down the mRNA resulting in the transfer of the tRNA to the Psite (polypeptide site) and then the Esite (exit site)
4. Released
Termination
1. proteins called release factors halt elongation 1. factors recognize stop codons and modify larger ribosomal subunit that leads to the severing of the polypeptide from the final tRNA
2. ribosome then dissociates into its subunits
3. **The polypeptides released at termination may function alone as proteins or they may function with other polypeptides in quaternary protein structures
*All stages require additional protein factors
Initiation and elongation require energy (A/GTP)
Study Guide – Exam 2
Chapter 7- IS AT THE BOTTOM. Bernot wrote it so hopefully it is useful
• Describe the structure of DNA and discuss how it facilitates the ability of DNA to act as genetic material
• Compare and contrast prokaryotic and eukaryotic chromosomes
• Describe the process of DNA replication as a semi-conservative process. Compare and contrast the synthesis of the leading and lagging strands in DNA replication.
• Explain how the genotype of an organism determines its phenotype.
• State the central dogma of genetics and explain the roles of DNA and RNA in polypeptide (aka: protein) synthesis
• Describe the three steps of RNA transcription (initiation, …show more content…
elongation, termination) noting the roles of DNA, RNA polymerase, promoter, 5’-3’ direction, and terminator.
• Describe the genetic code and identify the relationship between codons and amino acids.
• Describe the process of translation identifying the roles of the three types of RNA.
• Define mutation and describe the different types of mutations: point, silent, missense, nonsense, frameshift insertion, frameshift deletion.
• Discuss how different types of radiation cause mutations in a genome.
• Describe three kinds of chemical mutagens and their effects: nucleotide analogs, nucleotide-altering chemicals, frameshift mutagens
• Describe light and dark repair of pyrimidine dimers, base-excision repair, mismatch repair, and the SOS response.
• Contrast the positive and negative selection techniques for isolating mutants.
• Describe the Ames test, and discuss its use in discovering carcinogens.
• Define: genetic recombination, recombinants, horizontal (lateral) gene transfer, donor cell, recipient cell, competent, transduction, bacteriophage, phage, transducing phages, conjugation, transposon and transposition
• Describe the three primary mechanisms of natural horizontal genetic transfer in bacteria: transformation, transduction, conjugation.
*chapter 8 will not be on the Exam*
Chapter 9
• Contrast sterilization, disinfection, and antisepsis and describe their practical uses.
o Sterilization
▪ Removal or destruction of ALL microbes, including viruses and bacterial endospores, in or on an object
▪ Used in Canned food and culture media
o Disinfection
▪ Destruction of most microorganisms and viruses on nonliving tissue
▪ Does not guarantee that all pathogens are eliminated
▪ Used on nonliving objects only
▪ Examples phenolic; alcohols; aldehydes; soaps
o Antisepsis
▪ When chemicals are used on skin
▪ Similar to disinfection only it is used on skin
▪ Like disinfectants can be left on a surface for longer periods of time
▪ Examples include iodine; alcohol
• Contrast the terms degerming, sanitization, and pasteurization.
o Degerming
▪ Removing microbes by mechanical means
▪ Like washing your hands and scrubbing
▪ Or to prepare site of injection
▪ Scrubbing the surface may be more important than the chemical in removing microbes
o Sanitization
▪ Removal of pathogens from objects to meet public health standards
▪ Like washing tableware in scalding water in restaurants
▪ Chemicals used on public toilets
o Pasteurization
▪ The use of heat to kill pathogens and reduce the number of spoilage microorganisms in food and beverages
▪ Used in milk, fruit juices, wine, and beer
• Compare the effects of –static versus – cidal control agents on microbial growth.
o Static
▪ Or Statis is by chemical or physical agent inhibits microbe
▪ Instead of killing them just stops them from growing and leaves them dormant
▪ Like refrigerating
o Cidal
▪ Or cide is referring to agents that destroy or permanently inactivate a particular type of microbes
▪ Completely kills microbes
▪ Burning them
• Define microbial death rate and describe its significance in microbial control.
o Microbial death rate
▪ Permanent loss of reproductive ability under ideal environmental conditions
o They use this to evaluate how efficient antimicrobial agents are
• Describe how antimicrobial agents act against cell walls, cytoplasmic membranes, proteins, and nucleic acids.
o Attacking cell
walls
▪ If the wall is disrupted by physical or chemical agents, it can no longer prevent the cell from bursting as water moves into the cell by osmosis thus killing it completely
o Cytoplasmic membranes
▪ If there is extensive damage to a membrane’s proteins or phospholipids by any physical or chemical agents allows the cellular contents to leak out which if not repaired quickly will result in death.
o Proteins
▪ Since proteins demand an exact three dimensial shape if this is broken by heat or certain chemicals it can cause a shape shift thus making the proteins useless. Proteins are needed to regulate cellular metabolism
o Nucleic Acid
▪ Chemicals, radiation, and heat can also alter and even destroy nucleic acids
▪ Disruption to these can cause fatal mutation and eventually kill it
▪ Also interference to nucleic acids also stop protein synthesis
• List factors to consider in selecting a microbial control method.
o Site to be tested
▪ Must decide where to test the antimicrobials
▪ Some areas are more prone to infection so must choose an appropriate site
o Relative Susceptibility of Microorganisms
▪ How resistant are the microorganism that you are working with
o Environmental Conditions
▪ Must clean instruments properly and that will control the antimicrobial and at what point are they most effective like temperature, pH, etc.
• Identify the three most-resistant groups of microbes, and explain why they are resistant to many antimicrobial agents
o Prions-1
▪ Infectious proteins that cause degenerative diseases of the brain
o Bacterial Endospores-2
▪ They can survive in extremes of temperature and acidity and withstand many chemical disinfectants
▪ Also can survive more than 20 years in 70% alcohol
o Mycobacteria-3
▪ Cell walls contain large amounts of waxy lipids.
▪ The wax allows the bacteria to survive drying and protects them from most water-based chemicals
▪ Can only use strong disinfectants or heat to treat whatever comes into contact with tuberculosis patients
o Cysts of Protozoa-4
▪ Their wall prevents entry of most disinfectants, protects against drying, and shields against radiation and heat
• Discuss environmental conditions that can influence the effectiveness of antimicrobial agents
o Depending on the temperature and pH may influence how the antibiotic works
• Describe types of physical methods of microbial control: moist heat, pasteurization, dry heat, refrigeration and freezing, dessication and lyophilization, filtration
o Moist Heat
▪ Is commonly used to disinfect, sanitize, sterilize, and pasteurize, kills cells by denaturing proteins and destroying cytoplasmic membranes.
▪ More effective than dry heat because water is better conductor of heat than air
o Boiling
▪ Kills vegetative cells of bacteria and fungi the trophozoites of protozoa , and viruses within 10 mins at sea level
▪ Boiling time is the most important factor
▪ Some bacterial endospores, protozoan cysts, and some viruses and survive boiling
o Autoclave
▪ True sterilization using heat requires higher temperatures than boiling water.
▪ Uses pressure and temperature
o Pasteurization
▪ Used to kill pathogens in food and drinks
▪ It is not sterilization some organisms still remain
▪ Would look over table 9.2 pg 270 for lists of different types of pasteurization and their temperatures and times
o Dry Heat
▪ Used on powder and oils
▪ Uses steam that helps sterilizes it cause it denatures proteins and fosters the oxidation of metabolic and structural chemicals; however in order to sterilize dry heat requires higher temperatures.
▪ Requires more time than moist heat because dry heat penetrates more slowly
o Refrigeration
▪ Halts the growth of most pathogens by cooling them down
o Freezing
▪ Slow freezing is more effective than quick freezing because it inhibits microbial metabolism
▪ Used to store bacteria and viruses
o Dessication
▪ Drying out the food
▪ Used for thousands of years like fruits, peas, beans, grain, nuts, and yeast
▪ Inhibits the spread of most pathogens
o Lyophilization
▪ Combination of freezing and drying to preserve microbes and other cells for thousands of years.
▪ Uses liquid nitrogen to freeze them then uses a vacuum to remove frozen water
▪ Prevents large formation of large, damaging ice crystals
▪ Not all cells survive but enough remain
o Filtration
▪ Passage of a liquid or gas through a membrane filter, something used to catch large molecules and little ones to slide through.
▪ Pores today can even catch viruses
• Discuss the use of hypertonic solutions in microbial control
o Cells in a hypertonic solution of salt or sugar lose water, and the cell desiccates. The removal of water inhibits cellular metabolism because enzymes are fully functional only in aqueous environments
• Differentiate between ionizing radiation and nonionizing radiation as they relate to microbial control
o Ionizing radiation
▪ Uses wavelength shorter than 1 nm
▪ Creating ions when they strike molecules
▪ These ions denature other molecules, particularly DNA, causing fatal mutation
▪ Like electron beams, gamma rays, x-rays
o Nonionizing radiation
▪ Uses wavelength greater than 1 nm
▪ Formation of thymine dimers inhibition DNA transcription and replication
▪ Like UV rays
• Describe four levels of biosafety and give examples of microbes handled at each level
o Biosafety level 1
▪ Suitable for handling
▪ E.coli
▪ Minimal danger
o Biosafety level 2
▪ Moderately hazardous
▪ Like hepatitis, influenza, Staphylococcus
o Biosafety level 3
▪ Tuberculosis
▪ Anthrax
▪ Yellow fever
▪ Rocky mountain spotted fever
o Biosafety level 4
▪ Ebola
▪ Small pox
▪ Lassa fever
• Compare and contrast nine major types of antimicrobial chemicals and discuss the positive and negative aspects of each: phenols, alcohols, halogens, oxidizing agents, surfactants, heavy metals, aldehydes, gaseous agents, enzymes
o Phenols
▪ Lister began using them first to reduce infection during surgery
▪ Phenolic are compounds derived from phenol molecules that have been chemically modified by addition of halogens
• Orthocresol
• Triclosan
• Hexachlorophene
▪ Natural oils like pine and clove oils phenolic
▪ Intermediate to low level disinfectants
▪ Denature proteins and disrupt cell membranes
▪ Pretty commonly used in health care settings, laboratories, and households
▪ Can irritate the skin of some individuals
▪ Can also cause brain damage to some infants
o Alcohols
▪ Bactericidal, fungicidal, virucidal against enveloped viruses, not effective against fungal spores or bacterial endospores
▪ Intermediate level disinfectants
▪ Common uses are rubbing alcohol and drinking alcohol
▪ Not an effective antimicrobial agent, because the denature of proteins requires water; so solutions of 70%-90% of alcohol are typically used to control microbes
▪ Evaporate quickly leaving no residue
▪ May not be in contact with microbes long enough to be effective
▪ More effective than soap in removing bacteria
o Halogens
▪ Has four very reactive, nonmetallic chemical elements
• Iodine
o Well known antiseptic
o Disinfects water
• Chlorine
o Treats drinking water, swimming pools, and wastewater
• Bromine
o Effective disinfectant in hot tubs
• Fluorine
o Antibacterial in drinking water and toothpaste can help reduce cavities
▪ Intermediate-level antimicrobial
▪ Effective against vegetative bacterial and fungal cells, fungal spores, some bacterial endospores and protozoan cysts and many viruses
o Oxidizing agents
▪ Kills microbes by oxidizing their enzymes thereby preventing metabolism
▪ High-level disinfectant and antiseptics
▪ Effective against anaerobic microorganisms
▪ Hydrogen peroxide
• Mistakenly used to treat open wounds
▪ Ozone
• Used to treat water
• Fresh air smell
• More effective antimicrobial agent than chlorine
• More expensive though
o Surfactants
▪ Surface active chemicals
▪ Reduce surface tension of solvents such as water by decreasing the attraction among molecules
▪ Detergents
• Positively charged organic surfactants that are more soluble in water than soap
▪ Quats
• Detergent composed of ammonium
• Harmless to humans
• Bactericidal
o Especially against gram-positive
• Fungicidal
• Virucidal
o Enveloped viruses
• Low level disinfectants
▪ Poor antimicrobial agents
o Heavy metals
▪ Ions:
• Arsenic
• Zinc
• Mercury
• Silver
• Copper
▪ Antimicrobial because they contain sulfur
▪ Denatures proteins, inhibiting or eliminating their function
▪ Low-level bacteriostatic
▪ Might be a more effective antimicrobial agent
▪ Can be used to prevent blindness
▪ Used to preserve vaccines
• Mercury is a metabolic poison
o Aldehydes
▪ Compounds containing –CHO
▪ Denatures proteins and inactiving nucleic acids
▪ Glutaraldehyde
• Liquid
• More effective than formaldehyde but is more expensive
• Used to kill bacteria, viruses, and fungi
▪ Formaldehyde
• Gas
• Highly reactive chemical
• Used for embalming and to disinfect isolation rooms, exhaust cabinet, surgical intruments, and reusable kidney
• Can become irritating and is carcinogenic
o Gaseous agents
▪ Attacks the proteins denaturing them and DNA killing everything it comes in contact with
▪ Ethylene oxide
▪ Propylene oxide
▪ Beta propiolactone
▪ Frequently used to sterilizing hospitals and dental offices NASA also uses it
▪ Can be extremely hazardous
▪ Can also become explosive
▪ Also very poisons
▪ Potentially carcinogenic
o Enzymes
▪ High against target substrates
▪ Denature proteins
▪ Removal of prions on medical instruments
▪
Chapter 10
• Describe the contributions of Paul Ehrlich, Alexander Fleming, and Gerhard Domagk in the development of antimicrobials
o Paul Ehrlich
▪ 1845-1915
▪ German scientist
▪ Proposed the term chemotherapy
• Describes the use of chemicals that would selectively kill pathogens while having little or no effect on a patient
▪ Magic bullet
• Something that would bind to receptors on germs to bring about their death while ignoring the host cells
o Alexander Fleming
▪ 1881-1955
▪ British Bacteriologest
▪ Penicillium mold
• Creates a zone where bacteria don’t grow
▪ Penicillin
o Gerhard Domagk
▪ German chemist
▪ 1888-1973
▪ First practical antimicrobial agent efficacious in treating a wide array of bacterial infections
▪ Discovered sulfanilamide
• Explain how semisynthetic and synthetic antimicrobials differ from antibiotics
o Semisynthetic
▪ Chemically altered antibiotics—that are more effective, longer lasting, or easier to administer naturally occurring antibiotics
o Synthetic
▪ Antimicrobials that are completely synthesized in a laboratory
• Explain the principle of selective toxicity
o Ehrlich
o More toxic to the pathogen than to its host
• List the six mechanisms by which antimicrobial drugs affect the growth of pathogens
o Drugs that inhibit cell wall synthesis
o Drugs that inhibit protein synthesis
o Drugs that disrupt unique components of cytoplasmic membrane
o Drugs that inhibit general metabolic pathways not used by humans
o Drugs that inhibit nucleic acid synthesis
o Drugs that block a pathogen’s recognition of or attachment to its host
• Describe the actions and give examples of drugs that affect the cell walls of bacteria and fungi
o Action
▪ Bacteria
• Prevents cross-linkage of NAM subunits
• Uses beta-lactams
• Beta-lactams inhibit peptidoglycan formation by irreversibly binding to the enzymes that cross-link NAM subunits
• Without the cell wall they lose shape, and the cell will eventually lyse
▪ Fungi
o Drugs
▪ Penicillin: beta-lactams
▪ Cephalosporin: beta-lactams
▪ Vancomycin
• Directly interfere with particular alanine-alanine bridge that link the NAM sub-units in many gram-positive bacteria
• Bacteria that lack this bridge are unaffected by these drugs
▪ Bacitracin
• Blocks transport of NAG and NAM from cytoplasm to cell wall
▪ Isoniazid
• Disrupts the layer of arabinogalactanmycolic acid
▪ Ethambutol
• Same as isoniazid
▪ Echinocandins
• Used of fungus
• Inhibits the enzyme that synthesizes glucan
• Without this the fungal cells cannont make cells walls thus leading to osmotic rupture
• Describe the actions and give examples of drugs that affect protein synthesis
o Actions
▪ Takes advantage of prokaryotic and eukaryotic protein sizes
o Drugs
▪ Aminoglycosides
• Changes the shape of the 30S subunit making it impossible for the ribosome to read the codons of mRNA correctly
▪ Tetracyclines
• Block the tRNA docking site, which prevents the incorporation of additional amino acids into a growing polypeptide
▪ Chloramphenicol
▪ Macrolides
• Describe the actions and give examples of drugs that affect cytoplasmic membranes
• Describe the actions and give examples of drugs that inhibit metabolic pathways
o
• Describe the actions and give examples of drugs that inhibit nucleic acid synthesis
o Action
▪ Targets the destruction or inhibition or DNA and RNA in cells
o Drugs
▪ Actinomycin
• Binds to DNA and effectively blocks DNA synthesis and RNA transcription not only in bacterial pathogens but in their hosts as well
▪ Nucleotide
• Molecules with structural similarities to normal nucleotide building blocks of nucleic acids
• With their similar shape they can distort the DNA and RNA to prevent further replication, transcription, or translation
▪ Quinolones
• Used agasint prokaryotic DNA specifically
• Inhibits DNA gyrase, an enzyme necessary for correct coiling and uncoiling of replicating bacterial DNA.
▪ Rifampin
• Binds more readily to prokaryotic RNA polymerase than eukaryotic RNA polymerase
• Describe anti-viral drugs
• Distinguish between narrow-spectrum drugs and broad-spectrum drugs in terms of their targets and side effects
o Narrow-spectrum
▪ Drug that work against only a few kinds of pathogens
o Broad-spectrum drug
▪ Drug that works against many different kind of pathogens
▪ They can open doors to serious secondary infections
• Identify three main categories of side effects of antimicrobial therapy
o Toxicity
▪ Some drugs can affect fetuses
▪ The drugs may be toxic to kidneys, the liver, or nerves
o Allergies
▪ The patient may have an allergic reaction to some drugs out there
o Disruption of Normal Microbiota
▪ Can cause a superinfection
▪ May cause a secondary infection
• Describe how populations of resistant microbes can arise
o When a drug is exposed to the cells it kills off all the sensitive cells and leaves all the resistant cells left. Eventually the resistant cell is the majority of the population thus making a whole new strand of bacteria and the need for a new drug
• Describe the relationship between R-plasmids and resistant cells
o The bacteria can acquire resistance genes on extrachrmosomal pieces of DNA through the process of horizontal gene transfer—transformation, transduction, or conjugation
• List six ways by which microorganisms can be resistant to antimicrobial drugs
o One
▪ May produce enzymes that destroy or deactivate the drug
▪ Uses enzymes to break beta-lactam rings
o Two
▪ May slow or prevent entry of drugs into cell
▪ Involves change in structure or electrical charge of cytoplasmic membrane
▪ Some gram-negative bacteria have porins (an outer membrane)
▪ They alter pore protein
o Three
▪ May alter the target of the drug so it can’t attach itself or bind effectively
o Four
▪ Altering their metabolic chemistry
▪ May start producing more enzymes for affected metabolic pathway reducing power of the drug
▪ Also can abandon certain acids and just absorbing it
o Five
▪ Can pump the antimicrobial out of the cell
▪ Called efflux pump, which are powered by ATP
o Six
▪ Bacteria within biofilms resist antimicrobials more effectively than free-living cells
▪ Biofilms slow metabolic rates
▪ Lower metabolic rate reduces the effectiveness
o Seven
▪ READ UP ON THIS ONE PG 303
• Define cross resistance and distinguish it from multiple resistance
o Cross resistance
▪ Resistance to one antimicrobial agent may confer resistance to similar drugs
▪ Occurs mostly when drugs are similar in structure
o Multiple Resistance
▪ Resistant to three or more types of antimicrobial agents
• Describe four ways that development of resistance can be retarded
o One
▪ Sufficiently high concentrations of the drug can be maintained in a patient’s body for a long enough time to inhibit the pathogen, allowing the body’s defenses defeat them. If you discontinue the drug too early could cause a resistant strain
o Two
▪ Use antimicrobial agents in combination so that pathogens resistant to one drug will be killed by others drugs, and vice versa. Sometimes one drug enhances the effect of the second drug.
o Three
▪ Limit use of antimicrobials to necessary cases
▪ Use them only when needed not giving it to every person who has a sore throat or a stomach ache
o Four
▪ Developing a new drugs
*Chapter 11 and 12 will not be on the exam*
Chapter 13
• Discuss viral genomes
o Single Stranded
▪ ssRNA
▪ ssDNA
o Double stranded
▪ dsRNA
▪ dsDNA
• Explain the mechanisms by which viruses are specific for their host cells
• Discuss the structure and function of a viral capsid
o Capsid
▪ Protein coat provides protection for viral nucleic acid and means of host attachment
▪ Made up of subunits called capsomers
• Discuss the origin, structure, and function of the viral envelope
o The enveloped virus acquires its envelope from its host cell during viral replication or release
o Composed of phospholipid bilayer and proteins
o The envelope plays a role in host recognition
• List the characteristics by which viruses are classified
o Types of nucleic acid
o Presences of envelope
o Shape
o Size
• Sketch and describe the five stages of the lytic replication cycle as it typically occurs in bacteriophages
[pic]
• Compare and contrast the lysogenic replication cycle of viruses with the lytic cycle
o
• Explain the differences between bacteriophage replication and animal viral replication
o See page 399 chart 13.4
• Compare and contrast the replication and synthesis of DNA, -RNA, and +RNA viruses
o
• Compare and contrast the release of viral particles by lysis and budding
o Budding
▪ Instead of exploding the cell completely viruses just bud off so to say.
▪ They push up on the cell’s membrane slowly shedding the virus away
o Lysis
▪ Completely bursting of the cells scattering the virus everywhere
• Compare and contrast latency in animal viruses with phage lysogeny
o
• Define the terms neoplasia, tumor, benign, malignant, cancer, metastasis
o Neoplasia
▪ Cells beginning to divide uncontrollably
o Tumor
▪ Cells that undergo neoplasia and group together
o Benign
▪ Tumors that remain in one place
o Malignant
▪ Invade other neighboring tissue, move throughout the body to invade other organs and tissues to produce new tumors
o Cancer
▪ Malignant tumors
o Metatasis
▪ The process of a tumor spreading throughout the body
• Explain how a cell may become cancerous with viral activity
o Viruses cause 20-25% of human cancers
o Viruses carry oncogenes
▪ Something the plays a role in cell division. When activated they cause they cause cancer
o Viruses promote oncogenes that are already present
• Describe some ethical and practical difficulties to overcome in culturing viruses
o Some people might be opposed to using animals as test subjects for virus that may kill or harm the animals
o Another is you cant really get a good reading how it will work on humans because most humans don’t want to volunteer to try out the virus
o Common sense things pretty much
• Describe the three types of media used for culturing viruses
o Culturing in Mature Organisms
▪ Bacteria
• Most research on viral replication comes from here
• Easy to grow and maintain
• Just put it on agar plate and let it sit and let the viruses just kill
• Plaques
o Areas where phages have lysed
• Plague assay
o Estimating how many viruses are on the plate
▪ Plants and Animals
• Just really ethical issues pretty simple enough
o Culturing in embryonated chicken eggs
▪ Just a simple inexpensive way to test viruses and vaccines
o Culturing in cell culture
▪ Cells isolated from an organism and grown on the surface of a medium or in a broth
• Diploid cell
o Created from embryonic animal, plant, or human cells that have been isolated and provided appropriate growth
o Cells only last 100 generations then they die
• Continuous cell culture
o Derived from tumor cells
o Cells just keep replicating so they pretty much have an infinite supply of human cells
• Discuss aspects of viral replication that are life-like and non-life-like
o Life-like
▪ Use sophisticated methods to invade cells, have the means of taking control of their host cells, possess genomes containing information instructions for replication
o Non-life-like
▪ Don’t meet all the requirements of characteristics of life
▪ Mostly just complex pathogenic chemicals
• Define and describe viroids
o See below pretty much
• Compare and contrast viroids and viruses
o Chart is 405
o Smaller than prions and viruses
o Infectious and pathogenic in plants
o Have RNA but lack the capsid
• Define and describe prions including their replication process
o Discovered by Stanley Prusiner in 1982
o Prions
▪ A proteinaceous infectious agent that is different from any other known infectious agent in that it lacked instructional nucleic acid
o Known as slow viruses because a long period of time might go by before you recognized any symptoms
o Changes the shape of a PrP protein to synthesize with it do not code for new prions but instead convert cellular PrP into prions
o They
• Compare and contrast prions and viruses
o See page 405 for complete chart
o Prions are typically smaller in both width and length
o Prions have no nucleic acids while Viruses has either DNA or RNA
o Prions are self-replicating from their protein PrP
• List four diseases caused by prions
o Bobine spongiform encephalitis (BSE, also called mad cow disease
o Scrapie
▪ In sheep
o Chronic wasting disease (CWD)
▪ In deer and elk
o Creutzfeldt-Jakob disease (vCJD)
▪ In humans
Central Dogma of Biology
From Replication to Transcription to Translation
Replication (DNA to DNA)-An anabolic polymerization process that requires monomers and energy
*Triphosphate deoxyribonucleotides-monomers, DNA nucleotides with three phosphate groups linked together by two high-energy bonds, serve both functions of DNA replication
*Replication is semiconservative – new strands composed of one original and one daughter strand
Initial Process
1. Begins at specific sequence of nucleotides called Origin
2. Histones and other proteins are removed
3. DNA double helix unwound by helicase (Unzips the DNA helix) 1. exposes replication fork
4. Stabilizing proteins keep strands from going back together
5. DNA polymerase III (adds bases to the new DNA chain and proofreads for mistakes) binds to one strand of DNA and begins using it as template for assembling leading strand of nucleotides on 3’ OH-
6. DNA polymerase I (removes primer, closing gaps, and repairing mismatches) binds to other template strand and synthesizes discontinuous segments of nucleotides on 3’ OH- (Okazaki fragments)
7. Replicates DNA only from 5’ to 3’; strands are antiparallel so synthesized differently
Synthesis of the Leading Strand
1. Synthesized toward replication fork
2. Primase, enzyme, synthesizes a short RNA molecule complementary to DNA strand
3. Triphosphate deoxyribonucleotides form H-bonds with the parental strand
4. using the energy from the triphosphate deoxyribonucleotides the DNA polymerase III joins the nucleotides to the leading strand
5. It is proofread by the DNA polymerse III, removes errors (proofreading exonuclease function)
6. DNA polymerase I replaces RNA primer with DNA
Synthesis of the Lagging Strand
1. RNA Primase lays down RNA Primer
2. DNA polymerase III lays down new DNA
3. DNA polymerase I replaces RNA primer with DNA 1. Polymerase III & I create Okazaki fragments by attaching the Triphosphate nucleotides in pieces
4. DNA Ligase links the Okazaki fragments
5. DNA ligase (final binding of nicks in DNA during synthesis and repair) stitches strands together into the lagging strand
Transcription-(occurs in the nucleoid region of the cytoplasm in bacteria & nucleus/ (mitochondria and chloroplast) in Eukaryotes) DNA-RNA
Initiation
1. RNA polymerases (enzyme that synthesize RNA) bind to specific DNA nucleotide sequences called Promoters (initiation)
2. RNA polymerase binds to transcription factors and unzips & unwinds the DNA and forms a bubble as it moves along
3. RNA polymerase proceeds down one strand moving in 3′ → 5′ direction
Elongation
4. As RNA polymerase travels, it assembles nucleotides (elongation)
Termination
5. When transcription is complete, transcript is released from polymerase and, polymerase is released from DNA (termination) 1. Self-Termination when RNA polymerase transcribes a termination sequence of DNA: lots of G and Cs followed by A’s 1. G’s and C’s create a pause allows for H-bonds to form between its own symmetrical sequences resulting in a stem and loop results in tension on the RNA polymerase and DNA. 2. the few hydrogen bonds between the A’s and U’s break away releasing the RNA polymerase and DNA 2. Rho-dependent Termination- depends on Rho protein 1. pushes between the RNA polymerase and the DNA and forces them apart
Most eukaryotic genes do not exist as an uninterrupted series of triplets coding for a protein
Introns- sequences of bases that do not code for protein
Exons- coding regions that will be translated into protein
Called a split gene- requires further processing before translation
A splicesome recognizes the exon-intron junctions and enzymatically cuts through them
The exons are joined end to end
Some introns do code for cell substances (in humans, introns represent 98% of the DNA)
RNA Translation- ribosomes use the genetic info of nucleotide sequences to synthesize polypeptides composed of specific amino acid sequences.
Initiation-mRNA and tRNA^fmet form initiation complex
1. ribosomal subunit attaches to mRNA at ribosome-binding site, position start codon (AUG) at Psite
2. tRNA^fmet attaches to ribosome’s Psite (anticodon UAC)
3. larger ribosomal subunit attaches to form a complete initiation complex
Elongation- cyclical process, involves sequential addition of amino acids to polypeptide chain growing at Psite
1. tRNA whose anticodon is complementary to the next codon delivers its amino acid to the Asite where proteins called elongation factors escort the tRNA along the molecule of GTP 1. GTP energy stabilizes each tRNA as it bonds to Asite
2. ribozyme from the larger r. subunit forms a peptide bond between terminal amino acid of chain and the new amino acid. polypeptide now attached to tRNA at the Asite (amino acid site)
3. using the GTP energy, ribosome moves one codon down the mRNA resulting in the transfer of the tRNA to the Psite (polypeptide site) and then the Esite (exit site)
4. Released
Termination
1. proteins called release factors halt elongation 1. factors recognize stop codons and modify larger ribosomal subunit that leads to the severing of the polypeptide from the final tRNA
2. ribosome then dissociates into its subunits
3. **The polypeptides released at termination may function alone as proteins or they may function with other polypeptides in quaternary protein structures
*All stages require additional protein factors
Initiation and elongation require energy (A/GTP)