Exam 2 Study Guide MICRB 201

History of microbiology?

Viruses

❖ Genetic element (DNA, RNA)

➢ Cannot replicate independently

➢ Needs host cell

❖ Virion - extracellular shape of virus (different from viroid)

❖ Chamberlain filter - has the ability to filter out all known bacteria (1884) ❖ Ivanovsky - filterable agent reinfects tobacco plant (1892)

➢ Early definition of virus - can it pass through a Chamberlain filter?

❖ d'Herelle - uses bacteriophages to treat bacterial infections (1919)

➢ Bacteriophages discovered by Twort, but he ignored them because he’s stupid (bacteriophages tworted him) (not a word)

❖ Oncoviruses

Bubonic plague a.k.a black death.

➢ Olaf and Ellerman: Chicken Leukemia (1908) Don't forget about the age old question of How do you weigh a star?

➢ Peyton Rous: Rous Sarcoma Virus (1910)

➢ Led to discovery of oncogenes

❖ Ruska-Knoll Microscope - first view of viruses (1931)

❖ Lysis vs.lysogeny

❖ Bacteriophage λ adsorbs to LamB protein on E.coli

➢ Lacks genes for ribosomes, means of self-replication

❖ Lysis Pathway

➢ Adsorption to recognized proteins

➢ Insertion of genetic material

➢ Synthesis of nucleic acids and proteins

➢ Assembly of new viruses

➢ Lysis - cell explodes and new viruses are released

Who is oparin?

■ Burst size = # virus per cell If you want to learn more check out lazzie fare

■ Enveloped viruses do not lyse, they bud Don't forget about the age old question of gjwmj

❖ Lysogenic Pathway

➢ Adsorption to recognized proteins

➢ Insertion of genetic material

➢ Integration of viral DNA/RNA into host genome

■ Prophage - part of virus DNA that is in the host genome If you want to learn more check out cotangent parent function

■ Lysogen - cell that has viral DNA in it

➢ Replication

❖ Capsid - protein shell

➢ Capsomere - proteins that make up the capsid in a repetitive manner ➢ Smallest part of a virion that can be seen with a microscope

❖ Nucleocapsid - combination of the capsid and the genetic material ❖ Shapes

➢ Rod/helical symmetry - genome determines length, size/packaging of capsomeres determines widths

➢ Icosahedral symmetry - most efficient packaging of capsomeres

➢ Complex - icosahedral head and helical tail

❖ Classified by type of genetic material

➢ dsDNA vs ssDNA: double stranded vs single stranded

➢ dsRNA vs ssRNA: same deal

➢ Retrovirus: ssDNA to dsDNA; reverse transcription

❖ Very high mutation rates, small genome We also discuss several other topics like steven chadwick umd

❖ Viroids, ssRNA, sDNA have the highest

❖ Allows them to evolutionize and to escape the immune system

❖ Bacteriophages, archaeal, plant, animal viruses

❖ Titer - number of infectious material per liquid unit

➢ Plaque starts in a single cell, reproduces, spreads in circular formation ➢ Latent period - creation of subunits and whatnot

■ Eclipse: early enzymes, nucleic acids, protein shells

■ Maturation: assembly and release

❖ # of virions/volume > # of pFu/volume

Animal viruses

❖ Sandwich animal cells between gel medium after virus liquid had been washed away ➢ Cells will lyse

➢ Virion ENTERS the cell, not adsorps to it

❖ More enveloped animal viruses than bacterial enveloped viruses

➢ Persistent infections - slow release of viruses without causing lysis (HIV) ➢ Transformation - formation of tumor

➢ Latent infections - slower transition between infection and lysis (Herpes) ❖ Viroid - causes disease in plants

➢ Complementary

➢ Creates a rolling process of RNA synthesis

❖ Prion - infectious proteins If you want to learn more check out allopetric

➢ Discovered by Pruisner (1997)

➢ Occurs randomly, inherited mutation, and by inoculation

Evolution

❖ Change of species over time

❖ mutations

❖ LUCA - last universal common ancestor (3.5 BYA)

➢ Based on stromatolites

❖ Anoxic photosynthesis came first (3.2 BYA)

➢ Cyanobacteria developed, photosynthesis that produced oxygen (2.8 BYA) ➢ Great Oxidation (2.5 BYA)

❖ Life originated by deep sea vent because the temperature was stable ❖ Oparin - believed life originated by chemicals and hot atmosphere (1922) ❖ Miller and Urey - created machine that uses energy and methane, nitrogen, water vapor, and co2 to make amino and nucleic acids

➢ Eventually creates self replicating molecules

■ RNA acts an enzyme

■ Allows protein formation

➢ Spontaneous creation of vesicle

■ Outperform non-vesicle RNA

■ RNA could have formed DNA because DNA more stable

❖ Sanger - creation of DNA sequencing (1980)

❖ SSU

➢ Small subunits ribosomal RNA

➢ Used to compare lineage

➢ Found in all life, highly conserved

➢ Prok - 16s, euk - 18s

❖ Woese - discovered archaea through his pioneering of SSU studies (1977) ➢ Created 3 domain model

❖ Venter - studied microbes of the ocean

➢ Used PCR to amplify SSU RNA

➢ Studied phylogeny

Bacteria

❖ Rod/bacillus, cocci, spirilla, spirochete

❖ Growth

➢ Solid (agar) - differential media, isolate single colonies, mixed bacteria can be separated

➢ Semi Solid - determine motility

➢ Liquid - profuse growth

❖ Microscopic count of bacteria from natural settings > streak plates ➢ virions/volume > pFu/volume

Legionnaires Disease

❖ Taught us danger of biofilms

➢ Attachment - A couple motile cells attach to a surface

➢ Colonization - Growth, communication, and polysaccharide formation ➢ Development - More cell division, more polysaccharides, structure grows ➢ Active dispersal - cells leave to find nutrients, due to a trigger

■ Planktonic - free living cells

➢ Harmful, they have not been used for good in any manner as of yet ❖ Growth

➢ Doubling Time - period of time that takes # of bacteria to double ❖ Cardinal Temperatures - minimum, maximum, and optimum growth for bacteria ➢ Psychrophile - grows in extreme cold

■ Eukaryotic phototrophs

■ processes take slower, flexible enzymes ( a helices, hydrophilic) ➢ Psychrotroph - grows in cold

➢ Mesophile - grows in warm (human body bacteria are mesophiles) ➢ Thermophile - grows in hot temperatures

■ Only prokaryotes

■ More stable enzymes (b sheets, hydrophobic) to prevent denaturing ➢ Hyperthermophile - grows in REALLY hot temperatures

■ Taq polymerase

❖ PCR

➢ Used to amplify DNA samples

➢ Hot period, DNA denatures

➢ Cool period - primers are added

➢ Warm period - Taq polymerase elongates primer

❖ pH

➢ Neutrophiles: 6-8

➢ Acidophiles and alkaliphiles

■ Internal pH stays neutral

❖ Concentration

➢ Hypotonic = less concentration outside subject

➢ Hypertonic = more concentration outside subject

❖ Halotolerant, halophile = can live in high concentrations of salt ❖ Oxygen

➢ Obligate aerobes - need oxygen

➢ Obligate anaerobes - cannot have oxygen

➢ Facultative aerobes - grows in either, best in oxygen

➢ Aerotolerant anaerobes - grows in presence of oxygen, but does not need it ➢ Microaerophiles - only grows in a little amount of oxygen

➢ Catalase - turns H2O2 and NADH into water and NAD+

➢ Superoxide dismutase - turns O2- into O2 and water

❖ Sterilization - kills endospores

➢ Heat and pressure to eliminate all living things

❖ Disinfecting

➢ Elimination of pathogens

❖ UV - causes thymine to dimerize

❖ Ion Radiation - can produce peroxides

❖ Filtration

Ecology

❖ Carbon source

➢ Autotroph - from CO2

➢ Heterotroph - from preformed organic molecules

❖ Energy source

➢ Chemo - from chemicals

➢ Photo - from light

❖ Electron/hydrogen source

➢ Organo - from organic molecules, like glucose, acetate

➢ Litho - from inorganic molecules, H2, NH4+

❖ Nutrient Cycles

➢ Oxygen, nitrogen, carbon

■ Nitrogen is inert, needs to be fixed

❖ What kinds of symbiosis exist?

➢ Commensalism, mutualism, parasitism

■ Lichens - Fungus (lichen) provides home for alga

❖ Agrobacterium

➢ Uses enzymes to transfer its tumor forming gene into the cells of a plant ❖ Phototrophs and photosynthesis

➢ Energy from light splits H2O

➢ Some electrons travel down cycle and reform NADPH or cycle back to pump H+ outside membrane

➢ H+ travels through ATP synthase to form ATP

❖ Calvin Cycle

❖ Reduces carbon to glucose

History of Microbiology

❖ Bubonic Plague

❖ 542 A.D - bubonic plague pandemic

➢ First detected in China

➢ 13% of the world died

❖ Bubonic Plague a.k.a Black Death

➢ 500-1500

■ During the Dark Ages

➢ Causes by yersinia pestis

■ 30-50% of all Europe was killed

➢ Named from buboes - swollen lymph nodes

➢ The Plague Doctor

■ First example of personal protective clothing

➢ Rat flea human cycle spreads bubonic plague

■ Pneumonic plague - spread through air

● Spreads very rapidly

➢ Spread by lice in the 14th-19th century

❖ Spontaneous generation

➢ Life arose from nonliving matter

➢ Disproved by Redi jar experiment

❖ Endospores

➢ Small, very durable spore that can withstand poor condition

➢ Makes it seem like life arises from nothing

❖ Tyndallization?

➢ Method of killing spores

➢ Allow them to germinate and vegetate

➢ And then they are murdered in their weakness

❖ Koch Postulates

➢ Determine if the microbes are the same disease causing agents ❖ Van Leeuwenhoek - invented microscope that allowed the first look at “animalcules”