exam 3 class notes

activity is like a dimmer switch for a light never fully on/off

• = gene expression
• DNA --RNA polymerase--> RNA

• 2 alpha subunits
• 1 beta subunits
• 1 beta subunits
• = core enzymes
• sigma factor

holoenzyme

• help identify start points ( prometers)
• provide a mechanism for RNA  pol. binding to DNA

• start location for transcription
• -consists of 2 major regions
• TATAAT = -10 start of first base in transcription
• TTGACA = -35

where a sigma factor binds

• sigma 74 = vegetative phase
• sigma 54 = n- stress
• sigma 70 = heat shock response

• inittiation = sigma factor > RNA pol holoenzyme
• > elongation > 5' > 3' (reg,free 3' OH) direction
• -sigma factor released after initiation  
• -once  the mRNA is formed it is now available for translation
• occurs stimultaneous transcription + translation

1-10⁵ bases

1-10⁹ bases

• 2 possible mechanisms
• -RHO (protein0 - independant
• -RHO- dependant
• RHO - independant -> stem loop structure

termination of RNA synthesis

• when a transcript matures (news it full lenght )
• R protein 'p' - Rho binds to RNA + moves up the transcript + interacts vo/ RNA pol + destabilizing it + causing termination

knows when to bind when RNA pol pauses briefly 

those regions that bind  sigma factor most effectively are strong --> and yield a lage amount of RNA transcripts

• protein synthesis
• start:--> shine- delaerno sequence ribosome binding site
• A-G (AGGA) => rich sequence

• mRNA = 55, 16,s , 23s
• mProteins- large subunits 30 and small subunits 20

• of mRNA + their accociated proteins have allowed us to understanf protein synthesis
• -novel drugs can be designed to interfere w/ ther process

• 30s, 50s,tRNA
• every amino acid has a coresponding set of codons
• the insertion of an amino acid into a growing protein is moderated by the tRNA that has a match VIA, B anti-codon to the corresponding codon on the mRNA

• initiation factors:
• -IF ; IF2 ; IF3
• elongation factors:
• EF- TU
• EF - G
• Termination factors:
• Release factors

• 30s subunit bond by IF3 + IF1
• IF#; help id the RBS
• IF1 blocks the site where the incoming formy-met t-RNA will interact
• IF2- brings in the F-met tRNA w (GTP)
• once this complex is assembled the large subunit can assoc w/the small subunit

help id the RBS

blocks the site where the incoming formy-met t-RNA will interact

Bringing in the F-met tRNA w(GTP

• A- acceptor
• P- peptdyl transfer
• E- exit

• requires two activities
• 1) petdyl transferase - large subunit associated activity
• Allows for peptid bond formation between the 1st Met and the incoming Amino acid in , the A site

• ribosome moves 1-codon over towards the 3' end of the mRNA
• A)-this activity causes the grwoing polypetides tRNA to be located int the P site
• b) entry tRNA (the one carrying the F-net) to move into the E (exit) site
• c) A site to be vacant (so that another tRNA w amino acid can enter)

• UAA / UGA / UAG (stop codons)
• -sequences have no matching anti codon tRNA so nothing new will come into the A site

• som proetins are secreted or may have final destination outside the cytoplasm
• -cytoplasmic membrane
• -periplasm
• -O.M
• -ENV
• so signals present in the newly formed proteins provide for this activity = protein secretion
• General secret Dry process (pathwyas) GSP

• regulation of catabolic pathways
• regulation of anabolic

catabolic pathway

cluster of genes

• promoter
• operator
• structural genes

regulates lactose catabolism

beta galactosidase

brease down lactose into glucose and galactose

coding for lac (permease) involved in uptake of lactose into the cell

function uknown / transacetylase

binds to operator that will block further movement of DNA polymerase turn on/ off mechanism

• inducer --> lactose should be present
• lactose absent --> turn off

• beta-galactosidase
• lactose = allolactose
• repressor binds allolactose => repressor inactive
• in order to turn on it should alwasy bind to the operator
• lacz--> mRNA --> LacZ
• lacy --> mRNA --> Lac Y

• ex: biosynthesis of amino acid
• - hisdtidine operon

• all 3 always regulated
• inducible enzyme
• repressible enzyme
• -WOT essential
• constitutive essential
• -always regulated all three

Lac operon

Histidine

function when is needed

Attenuation --mechanism--> to prevent our production of histidine

• ribosomal operon (rrn operon )
• Ribosome --> rRNA ribosomal proteins

• glucose
• lactose

• cyclic AMP
• is an activator

catoblite repressor protein

• when glucose levels high CAMP goes down
• glucose increase CAMP decrease

• CAP
• binding enhances transcription
• cannot bind to CAP if CAMP is low
• complex binds to promoter leading to transcription of genes involved n lac operon

5-bu- structural

CH₃--> guanine

• A=T
• T=T

• dark and light
• light photolyse
• ligase = joining
• endo nuclease- within DNA

• jumping genes
• barbara mcclintock
• in maize
• eukaryotes adn prokaryotes

CCAT = TACC (palindrome)

anibiotic resistance

• e.coli stx gene
• bacteriocins
• -in plasmid capable of killing
• ex. e.coli plamids
• killing closely related organisms
• colicins
• resistance plasmids - R-factors

• vertical / horizintal / lateral
• 3 types
• -transformation
• -conjugation
• -transduction
• merozygote: hologous recombination

• no direct contact
• uptake- extracellular DNA
• competence - closely related bacteria
• natural /artificial - creates pores in the cell membrane

• -direct contact
• F plasmid: F⁺ F⁺
• F⁺--->F^-
• conjugative plasmid --> F plasmid

• bacteriophage - mediator
• transduction
• - generalized
• -specialized

Bacterial DNa- is incorporated to phage ( transducing particles)

• Generalized:
• -all regions  of of chromosome transduced
• -only chromosomal DNA ( i.e no phage DNA in tranducing particles )
• Specialized:
• -bacterial and phage DNA
• -only specific regions of chromosome near attachment site
• -transducing particles contains ( phage DNA as well as bacterial DNA)

• -nucleic acid
• -protein coat (capsid)
• capsomers sub units of capsules can effect any organism
• virus-> poison

• noble prize  Z more viruses gives cancer
• -reverse transcription

• based on virus genome
• double stranded DNa viruses
• Single stranded DNA viruses
• double stranded RNA
• +single stranded RNA - coding
• -single stranded RNA - template
• Retro viruses (reversre transcription)
• DNA Reverse (transcribing viruses 0

• traditional gene expression
• DNA--> mRNA--> Protein
• need hoste
• viruses: obligate intracelular pathogen
• -depend on the host enzyme

• host DNA polymerase
• convert single stranded DNA to double strande DNA with help of polymerase,( host RNA polymerase)

• viral RNA dependent RNA polymerase
• mRNA

act as a coding strand during an infection the RNA acts like mRNA and can be translated by hosts ribosomes

• converted into (+SS) RNA
• act as a template doing transcription to make a complementary ( +) sense mRNA

• HIV
• type of +ssRNA 
• -reverse trancriptase TNa become DNA

• reverse transriptase
• DNA --> RNA 
• DNA <--- RNA

• envelope -lipid layer
• naked -- no envelope
• naked and evnelop = verions
• virion = mature viruse
• spikes- glycol proteins help in attachment in host cells

complex Viruses bacteriophage

organic solvents --> ether

• 5 steps
•  adsorption
• penetration and cuncoating

• plaque- zone of inhibiyion on bacterial lawn due to viral attack
• pfu/ml
• pfu/ml = average 3 of plawue X dilution facter

• lytic (virulent phages) kill host
• lysogenic (temperate phage ) no killing

• life cylce of a virulent phage
• last step: lysis of bacterial cell

• viral DNa is incorporated to bacterial DNA
• --> prophage

• stravator
• radiations

• whole animals
• embryonated chicken eggs
• cell cutlre

• envelope fussion (endocystosis )
• phagocytosis
• injection of nucleic acid

• canyon--> dipressions
• viral penetration
• a)
• b)phagocytosis
• c)injection

• DNA viruses mRNA
• replication and gene expression by dsDNA viruses budding

• +ssRNA
• RNA --> DNA reverse transcriptidase
• ex: HIV
• 3 enzyme
• -intergrase
• -protease

• enveloped
• 1. binding and fusion
• 2. reverse transcription
• 3. integration
• 4. transcription (normal0
• 5. assembly
• 6. budding

binds and fuses to CD4 receptor cell ( macrophage0

• Dna Reverse transcription
• using reverse transcriptase in the viral genome

is integrated into the host DNA using viral enzyme (integrase)

HIV and human DNA

• viral proteins
• leave the cells ( budding )

• TaTa box
• -tRNa -clover leaf model

will cute long chains of proteins and make short peices of DNA then assebly with the nucleic acid

Budding

Azidothymidine - druge for retroviruse - reverse transcriptase

• single stranded
• virods and prons - subviral particular no protein
• infect plants -> potatoes, tomatoes , and peahes
• potatose spindle tuber viroid --> potato spindle disease
• Hepatitis D --> by viroid

• no nucleic acid
• fatal
• PrP - function of normal Prp unknown
• Prp- misfolded
• infected animals PrP gets misfolded
• blanks =sheep / humans

• 3 domains
• -euaryia
• archea
• bacterial

genus (first)

tell how old microorganism is

• plantae, animals
• funi moneroa
• protists

divided it into three domains

orgnaism living within another -lynn margulis

• heat DNA strand to denacture DNA strand
• 95-98C annealing (cooling)
• 45-60( two strand together
• 100% hydridization = identical or not

rRNA - say organisms are related or not

• 3phyla
• crenoachaeota
• class thermoproteli

• methanogens
• extemphalophiles
• theroacids

• produce mehtane CH₄
• -anerobic conditions
• ex: rumen of cow

• saline 10% NaCl
• ex: halobacterium

• high temp
• low ph
• sulfolobus ( H₂SO₄) low pH hogh acidic conditions

• oxygenic photosynthesis
• nitrogen fixation
• oldes microorganism
• heterocyst - N2 fixation
• -notic
• anabaena
• blue green algae
• azikka + anabueria

•  3 important bacteria
• 1. agrobacterium
• 2. acetobacter 
• agrobacterium
• crown gall in plants
• -genetic eginering T-DNA
• acetobactor vinegar
• rhizobium
• N2 fixer
• symbiotic accociation with leguminous plants
• rood nodes
• meso /sino/ bradylhizobium

cloroplast -cyanobacteria

whooping cough

• enteric
• -e.coli
• -shigella
• yersna pestis -- bubonic plaque
• indole - true
• typrtophanase --> indole

• cystic fibrosis burns
• environmentally
• psedomona putida - bioremedation

• camphylo bacter - intestinal disease
• helicobactor pylori - cause peptic ulcers