Mic 230 – Microbiology Answers – Flashcards

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question
Beadle and Tatum won the nobel prize for what? when? what org?
answer
  • 1941
  • one gene; one enzyme
  • neurospora
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Lederburg and Tatum discover what? when? in what org?
answer
  • gene exchange
  • 1946
  • E. Coli
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genome?

gene

codon

operon?

answer
  • All genetic info a cell has
  • a piece of DNA that encodes for a protein
  • 3 nucleotide sequence that encodes for a particular AA
  • operates many genes simultaneously ( 1 promotor=many genes)
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Gene structure in order from start to finish? 7 things
answer
  1. operator
  2. promotor
  3. ribosomal binding site
  4. start codon
  5. ORF
  6. stop codon
  7. Terminator
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Operan structure contains many?
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ORF's
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3 components of a nucleotide?
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  1. bases (ATGC)
  2. deoxyribose sugars
  3. phosphate
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pyrimidine bases

purine bases

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pyr - CTU

Pur - GA

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what is the difference between Deoxyribose in DNA and ribose in RNA?
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ribose in RNA has a OH group on the 2' carbon
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fxn of major and minor groove?
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major - makes bps visible to extracellular proteins to detect sequence

minor - RNA pol binds to it

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what style is DNA replicated in?
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semi-conservative - two strands seperate and make two identical double helix strands
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where does replication start?
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origin
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key enzymes fxn: DNA polymerase

Ligase

Helicase

single stranded binding proteins

Primase

answer
  • DNA pol - read template and add new nucleotides to 3' end in 5' to 3' fashion
  • lig - removes primer and connects okazaki fragments
  • helicase - unzips DNA for replication
  • ssbp - makes sure DNA doesnt reconnect
  • creates RNA primer for DNA pol to attach
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RNA polymerase
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  • transcribes DNA to RNA in a 5' to 3' matter
  • doesnt need primer as it binds promotor of gene
  • detaches once terminator is reached
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role of sigma factor in transcription?

;

answer
  • helps RNA pol bind to promotor by helping recognition and initiation
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aminoacyl-tRNA synthetase
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  • key enzyme in translation
  • make sure proper AA binds to proper tRNA
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steps in translation?
answer
  1. RNA threads through ribosome
  2. tRNA lines up its anticodon with the complementary codon and bind to large subunit of ribosome
  3. peptide bonds made between adjacent AA's on tRNAS
  4. tRNA's are released
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what are introns located in?
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DNA and priimary RNA

removed in mature mRNA

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3 substitution mutations
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  1. missense - change in bp that causes a change in AA;
  2. nonsense - change in bp that encodes a stop signal
  3. samesense(silent)- change in bp that causes no change
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3 other mutations?
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  1. insertion - bp is inserted
  2. inversion - part of sequence is flipped
  3. deletion - bp is removed
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2 ;causes of mutation
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  1. spontaneous - DNA replication
  2. induced - chemicals, radiation
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3 types of induced mutagens?
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  1. chemicals - base analogs, base modifiers
  2. radiation - x-rays, UV (cause thymine dimers)
  3. biological mutagens (transposons, insertion sequences)
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3 repair mechanisms of damaged DNA: photoreactivation; excision repair; SOS repair
answer
  • photoreactivation - uses enzyme photolyase which recognizes dimer and breaks it apart
  • excision - uses enzyme UVrABC to nick DNA downstream of dimer and have DNA pol fix DNA and have DNA ligase seal up nick
  • SOS repair - fast repair that is very error prone
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auxotroph?
answer
mutant that is deficient in the biosynthesis of an essential metabolite
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replica plating procedure? 5 steps
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  1. make a master plate
  2. innoculate velvet with same pattern of bacteria
  3. place velvet on defined media with sole glucose energy source
  4. see what colonies grow and don't, those that dont grow are histidine defficient (His auxotroph)
  5. grow on enriched media plate (to isolate)
question
what does the Ames test test for? method?
answer
  • tests for bacterial mutagenicity
  • hisitidine auxotrophs are put on minimal glucose media and a test compound is put on the plate. an increase in growth around the innoculating disk shows an increase in mutation therefore the test compound is a mutagen.
question

Homologous recombination

site-specific recombination?

answer

HR - requires long regions of homology and the RecA protein. single or double strand can be exchanged.

Site Sp - requires only a short region of homology and  doesnt need the RecA protein.

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3 types of gene transfer?
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  1. transformation
  2. conjugation
  3. transduction
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transformation is? discovered with what exp? when?
answer
  • donor cell releasing free DNA into environment to be absorbed by recipient cell.
  • 1928 - Griffiths exp - Smooth and rough colonies. mouse injected with: R = alive; S=dead; R + dead S=dead. Smooth colony DNA transformed into R DNA.
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what is the transforming factor?
answer
The DNA responsible for transformation
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steps of transformation?
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  1. transforming DNA binds to cell
  2. Binding protein sheds off one strand creating ssDNA
  3. Uptake of ssDNA- RecA proteins bind
  4. DNA is incorporated into chromosome via homologous recombination
  5. cell division = one transformed and one not
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How can bacteria become artificially induced to transform and become competent?
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  • treat with cold CaCl2 or electroporation
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benefits of transformation?
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  • strain improvement
  • gene mapping
  • genetically engineering bacteria
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conjugation is? discovered by? when? where? in?
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  • gene transfer of a plasmid by direct cell to cell contact.
  • discovered by lederburg and Tatum in 1946 at UW-Madison in E. coli
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plasmid? structure?
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  • extra chromosomal DNA that contains an origin
  • 1 to 1000 kbps
  • 1 to 500 copies/cell
  • unessential genes to cell viability
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replication of Plasmid? 2 types

 

answer
  • theta replication - like bacterial chromosome, may be bi or unidirectional
  • rolling circle - DNA rolled off like a spool and both replicated. (gram +)
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4 types of plasmids?
answer
  • conjugable plasmids - contain tra operan and second replicating origin (oriT)
  • non-conjugable - lack the tra operon and oriT
  • mobilizing - contain oriT but lack the tra operan. can transfer if somewhere else in genome.
  • Resistance transfer factors - carry resistance antibiotics
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how to name plasmids?
answer
  • p for plasmid
  •  researchers initials
  • number plasmid made
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steps of conjugation?
answer
  1. donor and recepient cells attach via sex pilus
  2. pilus retracts and cells fuse
  3. enzyme encoded by tra operon nicks plasmid at oriT
  4. one strand moves through to the other cell
  5. replicate via rolling circle replication
  6. after entire plasmid is transfered cells separate
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steps of Hfr Conjugation?
answer
  1. same as reg conjugation until
  2. F-Plasmid performs recombination incorporating itself into chromosome
  3. portion of F plasmid and donor DNA moves into recipient cell before broken apart
  4. complementary DNA is synthesized
  5. F plasmid and donor DNA recombine with recipient DNA creating a recombinant F- cell 
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f-plasmid conjugation
answer
  • can go in and out of chromosome
  • same steps as plasmid conjugation
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benefits tools of comjugation?
answer
  1. gene mapping - Hfr conjugation
  2. strain improvement
  3. transfer of recombinant DNA
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what is a virus?
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  • intracellular obligate parasite
  • not a cell
  • carries genetic information
  • capable of replication in cells
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how were viruses discovered? fist one?
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  • while running Koch's postulates some infectious causing agents were unfilterable so they were called filterable viruses. thought to be small bacteria
  • Tobacco mosaic virus (TMV) in 1892
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what are viruses made of?;
answer
DNA and proteins
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What kind of genetic material can be present in a virus?
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  • ss(+) or ds DNA;
  • ss(+ or -) or ds RNA
  • + encodes for a protein
  • - needs to be complemented to make + strand
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capsid structure?
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  • made of numerous proteins
  • filamentous or icosahedral
  • complex have tails and fibers
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Virus envelope structure?
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  • outer layer of viroid made of lipids and glycoproteins
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lytic cycle steps
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  1. attachment
  2. penetration
  3. synthesis (replication)
  4. assembly;
  5. release
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steps of lysogenic cycle
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  1. attachment
  2. injection
  3. incorporation into DNA
  4. cell division
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retroviruses structure and function?;
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  • contain ssRNA;
  • reverse transcriptase creates DNA version that is incorporated into host genome
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what kind of virus is SARS?
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  • ssRNA
  • corona virus
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viroid?

prion?

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  • v - ssRNA no capsid or genes
  • p - infectious protein that causes CWD, mad cow, CJD
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steps of generalized transduction?
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  1. DNA of host cell is in phage instead of viral DNA.
  2. DNA is injected in new host cell
  3. DNA is recombined with host chromosome
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steps of specialized transduction? rare event?
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  • phage DNA circulizes and detaches from host DNA
  • phage DNA replicates
  • phages are synthesized
  • cell lyses and releases phage
  • rare - part of host DNA is exchanged for phage DNA (could incorporate a gene)
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characteristics of generalized and specialized tduction on chart
answer
question
restriction enzymes? how are they named?
answer

recognize a 6bp sequence that they cut at to create sticky ends

;

name by first letter in genus and first two letters in species E. coli = Eco RI

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DNA ligase role?
answer
covalently bind 3 bp sticky end sequences when they line up
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4 types of vectors?
answer
  1. plasmid
  2. bacteriophage
  3. cosmid
  4. Yeast artificial chromosome
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what did YAC's allow us to do?
answer
  • allowed us to clone much bigger pieces of DNA
  • human genome project
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steps in cloning a gene?
answer
  1. isolate DNA with genes you want to clone
  2. buy a plasmid 
  3. cut both with same restriction enzyme
  4. mix and add DNA lyses
  5. transfer into competent E. coli
  6. plate LB + amp + Xgal
question
steps of PCR?
answer
  1. apply heat to target genes 
  2. apply primers and DNA pol
  3. primer extension
  4. repeat
  5. gene copies are made
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applications of recombinant DNA technology?
answer
  • new vaccines
  • gene therapy
  • bioremediation
  • agriculture
  • protein synthesis
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