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121 Cards in this Set
- Front
- Back
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the process of turning DNA into mRNA is called
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transcription
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the process of turning mRNA into protein is called
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translation
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which bases is RNA specific? DNA specific?
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RNA- uracil
DNA- thymine |
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a base + a sugar is a?
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nucleoside
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a base + a sugar + a phosphate
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nucleotide
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which molecule has autocatalytic clevage facilitated by 2' OH
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RNA
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What makes DNA easiwer to store than RNA?
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has a wider/ shallower major groove and is less rigid
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Why is thymine used in DNA
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cytosine can easily degrade to uracil
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what are the benefits of the double strand of DNA
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protection from chemical attack, redundancy of information
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which RNA is stable, which are unstable
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mRNA is unstable, it is a temporary messenger
rRNA and tRNA are stable |
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T/F RNA is always single stranded
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False, RNA can be double stranded
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which direction does plasmid / cicular chromosome replication occur
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bidirectionally, around both sides of the circle
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where does replication start
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oriC
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describe how the open complex is formed
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1. recognition of oriC by DnaA:ATP complex
2. DnaB (helicase) unwinds the DNA 3. DnaG (primase) add RNA priming strand (10-12) bp |
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after the open complex is formed, the replication fork is formed. Describe how this occurs
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DNA polymerase III copies the DNA, "sliding clamp" model
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What does polymerase require to add onto the 3' end?
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a free 3' OH
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what does the lagging strand require to continue synthesis
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RNA primers added by primase then elongation
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What is the function of ligase
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it forms a diester bond and seals the backbone of the lagging strand
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what is the function of the shine delgarno sequence
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it is located upstream of the start codon on prokaryote mRNA, it helps recruit the ribosome and initiate protein synthesis by alinging the ribsome with the start codon
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What might be the consequence of a mutation in the shine-delgarno sequence
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Mutations in the Shine-Dalgarno sequence can reduce translation. This reduction is due to a reduced mRNA-ribosome pairing efficiency,
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Describe how DNA is segregated in bacteria
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replication forks meet at the termiunus and chromosomes separate, the cell membrane functions as the kinetochore
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what is the purpose of the sigma subunits of RNA polymerase
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they bind the -35 and -10 promoter sites on the mRNA
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what are the four steps of transcription?
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1. recognition, binding to the promoter
2. formation of the open complex 3. elongation 4. termination- release from terminator |
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can transcrpition still occur without a sigma subunit?
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yes, transcription will occur because the holoenzyme with out the sigma subunit (the core enzyme) can still function. The transcription will not be specific because the sigma subunit is responsible for specificity
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describe simple (rho independent) termination
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the RNA polymerase transcribes a G-C rich stem loop, the loop stops RNA polymerase by causing it to fall off
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describe rho dependent termination
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Rho protein binds to RNA and causes polymerase to fall off, can happen anywhere on the strand
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how is eukaryotic DNA replication similar to bacterial DNA replication (4)
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1. protein complex opens the DNA
2. bidrectional 3. RNA primase involved 4.overall base insertion is similar (leading strand, lagging strand etc) |
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how does eukaryotic DNA replication differ from bacterial (4)
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1. replication is much slower in eukaryotes
2. eukaryotes have multiple origins of replication 3. replication is cell cycyle dependent, other cell processes stop when the eukaryote is replicating its genome, no competion with transcription 4. one replication event at each origin |
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name some features of eukaryotic transcription that do not occur in bacteria
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1. prescence of histones
2. euks usually only transcribe one gene (no operons) 3. gene splicing 4. addtion of 5' cap and poly A tail |
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describe the wobble hypothesis
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mismatches in the 3rd position of the codon can be tolerated, some tRNAs can abind to more than one codon, giving rise to redundancy the 5' base on the anticodon, which binds to the 3' base on the mRNA, is not as spatially confined as the other two bases, so non-standard base pairing can occur
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describe the aminoaceylation process
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the "real key" of translation This is when the amino acid is added to the tRNA. It is an efficient and accurate enzymatic process. There are checkpoints along the way to ensure that the process is completed correctly
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what must occur for an amion acid to be added to the peptide chain? (energy wise)
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GTP hydrolysis
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What determines which tRNA will enter into the A site
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the concentration of that specific tRNA in the cell
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What part of the ribosome recognizes the shine-delgarno sequence?
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the rRNA, this binding helps the ribosome dock to the mRNA during translation
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what is a consequence of coupling transcription and translation in bacteria?
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polar mutations block translation, stops dowstream transcription
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Is the the string of amino acids produced by translation a completed product?
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No, a functional product might require: protein folding, cofactor insertion, multimer formation
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how does bacterial translation differ from eukaryotic translation
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mRNA is processed in euks, there is no shine-delgarno sequence, translation begins at first AUG
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define mutant
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an organism or strain with a mutation
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define wild type
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strain to which all are compared (arbitrary but criticle, a mutation can only be defined in comparison to a wild type)
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what are the three types of base substitution mutations
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1. silent
2.missense 3. nonsense of these, they may be a deletion, duplication, insertion, or inversion |
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define a frameshift mutation
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unique insertion or deletion gain or loss of nonx3 base pairs, only has meaning if gene is being transcribed
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what is a silent mutation
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change in base paring that does not change the amino acid sequence
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what is a missense mutation
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a point mutation in which a single nucleotide is changed, resulting in a codon that codes for a different amino acid
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what is a nonsense mutation
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a point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and in a truncated, incomplete, and usually nonfunctional protein product
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What is the difference between a transition and a transversion?
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a transition is purrine to purine or pyrimidine to pyrimidine
a transversion is purine to pyrimidine |
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Name some possible causes of mutations
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erros in process (replication/ recombination)
environmental inputs (mutagens/ carciagens) human manipulation (molecular biology) |
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what might be a cause of a frame shift mutation
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strand slippage in replication
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what is the effect of electromagnetic radiation on DNA/ mutation
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causes reactions between pyrimidines, forms TT or CC dimers, cause double stranded breaks in DNA
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Describe transposons
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mobile genetic elements, insert into DNA and disrupt genes, have transcription/ translation stop sites near ends, often have antibiotic resistance encoded, must have transposase and end sequences
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Describe how oxidative damage effects
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react with DNA, leads to deaminoatin, depurination, random methylation of bases
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Why are potential mutagens inoculated with rat liver homogenate before being used in an ames test
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the liver homogenta breaks down the mutatgen like it would be if it were being metabolized, often it is not the mutagen itself that is harmful but rather the metabolic byproducts
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what must occur for a mutation to become permanent
aka "mutation fixation" |
a second round of replication must occur, it is a race between repair mechanisms and DNA polymerase, repair usually wins
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list some repair mechanisms
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mismatch repair, photo repair, methyl transferase, base excision repair, nucleotide excision repiar, recombination repair, SOS repair
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describe mismatch repair
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repairs base substitution, recognition by MutS, excision by MutL and MutH, repair by pol III,
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how does the cell know which DNA is the "old" DNA and which is the new strand that has the mutation?
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the old strand is methylated
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Describe photo repair which can be used to fix thymine dimers created by ultraviolet light
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photolyase enzyme binds dimer, light photon activates reaction, base repaired
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describe base excision repair
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damaged base is recognized and removed, it is a multi enzyme process, the base and that section of sugar phosphate backbone is removed and the gap is repaired
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Describe recombination repair, which occurs when there is a leasion that can't be passed by the replication fork
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the damaged region is borrowed from the good chromosome and lined up with the bad, RecA is an important enzyme that helps resynthesize the damaged areas, this "crossing over" is also found in eukaryotes but it's pupose there is genetic reassortment during meiosis
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What types of mutation can eliminate function?
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missense, nonsense, deletion, frameshift, etc
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what types of mutation can change but not eliminate protein function
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missense
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What type of mutation could change the level of protein expression?
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mutations in the regulatory region
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define genome
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the complete genetic content of a cell or organism including chromosomes, plasmids, and prohages
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Is there a correlation between genome size and complexity?
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No. Complexity comes from regulation
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describe plasmids
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closed, circular double stranded DNA, can direct their own replication, some code for useful functions, they must have origins of replication and a partitioning system
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describe plasmid segregation
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low copy- plasmid replicates and anchors to the membrane, coordinate with chromosome replication
high copy- random partitioning, there are enough plasmids that each new cell will get some |
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describe the addiction system
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A toxin produced by the plasmid to ensure that each new cell gets a copy. The plasmid produces a stable toxin and an unstable antidote. As long as the cell has the plasmid it will have the antidote to protected it. BUT, if the cell replicates and loses the plasmid, the long lasting toxin will kill the cell because the plasmid is not there to protect it
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If you grow a microbe that has a plasmid that codes for ampicillin resistance and you grow it on a rich medium without ampicillin, what will happen to the plasmid
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the plasmid will most likely be lost because there is no longer a seletive pressure to keep it around
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what must occur for genomic flux in the environment to be relevant
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1. transfered - transformation = uptake of naked DNA, conjugation= movement of DNA involving cell to cell contact, transduction= movement of DNA by virus
2. captured- independent replication, recombination into the chromosome |
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describe homologous recobination in terms of DNA incorpotration
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its main function is in repair of severly damaged DNA but it can also incorporate foreign DNA. The system is induced because DNA from transduction, transformation, and conjugation looks like damaged DNA, induces RecA and the recombination system leading to incorporation
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Describe the limitations of homologous recombination in relation to DNA incorporation
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homologous- the DNA must be the same, point mutations are okay but this will not occur between sepecies
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describe transformation
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the transfer of genetic material as naked DNA from a donor to a recipient
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describe artificial transformation
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tricking a cell into taking up DNA
-CaCl2 treatment allows DNA to stick to cell, heat treatment permeabolizes cell Electroporation- electric current makes cell momentarily permeable |
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Describe natural transformation
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part of lifestyle, competence to accept DNA occurs only at certain stages, DNA binds and one strand is incorporated, often involves a "translocasome", preserving the DNA requires recombination into cell chromosome
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describe Hfr conjugation
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Hfr- high frequency of transfter
integration of F plasmid into chromosomal DNA usually aborts efore complete transfer |
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describe transduction
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the transfer of genetic information between cells through the mediation of a virus
the DNA is packaged in a protein coat, injected into host cell with or without accompanying viral genes |
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Give an example of a clinically relevant case of transposition
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The HIV uses this process to incorporate viral DNA into the cell
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Describe the features of a virus
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infectious, obligate intracellular parasite, small, package genomes into a shell, replicates inside the host and uses host functions to syntehsize new virion components
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describe the genome of a virus
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DNA or RNA, contain information for initiating and cmopeting an infectious cycle
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describe how a virus may be classified
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host range, size/ shape of virion, genome properties (DNA vs RNA, single vs. double stranded, linear vs circular)
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describe these viral capsid
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protective coat around the virus, protects from temperature, chemical and physical damage mode of self aggregating protein subunits, important in delivering the viral nucelic acid into the host
examples include icosohedron (20 triangular faces) and filamentous (capsomers in hllow spiral) capsomers will self assemble! |
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Describe the viral envelope
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capsids can be nonenveloped or encased in a HOST DERIVED envelope, envelops are usually present on animal viruses, made if lipids, carbs, and proteins, the lipids and carbs are taken from the host on extrusion,the tegument is the area between the capsid and teh envelope
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T/F viruses are metabolically inert
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true, viruses do not metabolize, there is not generation of energy and no byproducts
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List the phases of the lytic life cylce of a virus include early and late phase
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hint: remember AER TAR
early phase: attachment, entry, replication late phase: translation, assembly, release |
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describe viral attachment
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viruses are non-motile, they depend on random collisions with host therefore as concentration of the virus increase, so does infection, the virus will dock with protein or polysaccaride on outside surface "receptor)
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describe viral receptors
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viruses encode proteins that recognize receptors, the receptors are normally used for other functions in the host, the receptor must be something that appears on the host cells that the virus can replicate in but not others, good receptors are abundant on the host surface
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T/F Entry of a bacteriophage requires energy
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False, a confirmational change occurs in the viral capside because of chemical interactions, no energy input is required
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T/F bacterial cells have a bacteriophage uptake system
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false, bacteria do not "purposley" uptake viruses
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describe the entry of a bacteriophage
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the virus recognizes and binds to the receptor, a conformational change occurs in the capsid, this drives part of the capsid into the cell, the nucelic acid then moves through the tube formed by this change
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Normally, what is the only part of the virus that actually enters the bacterial cell?
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the nucelic acid
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what are the three mechaisms used to uncoat eukaryotic viruses
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1. uncoating at the cell membrane
2. uncoating within an ensosome after the virus+ receptor complex is endocytosed 3. Uncoating at the nuclear membrane |
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describe how the viral cycle begins for DNA, RNA, and ssRNA
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the virus must disassemble and express its proteins using host machinery
DNA- the viral DNA has transcription start sites that the host recognizes RNA- may be translated at the ribosome directly ssRNA-more difficult |
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Describe some "special problems" of RNA viruses
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they must have their own polymerases
+ strand can have ribosome make it - strand needs to bring it along |
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Considering an RNA virus, why are evolution rates so rapid
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RNA polymerases do not proof read, 1000 fold higher error rate, high number s of noninfective particles, rapid evolution
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Describe assembly
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have to get the viral genome in its capsid, need to identify the right nucelic acid, if more than one genome need to find all, can be dictated by the virus and capsid alone, may invovle other viral and host proteins
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Describe viral release
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virus needs to reach the outside, can involve rupturing the cell membrane and cell wall, enveloped eukaryotic viruses obtain their membrane envelope during this process
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describe viriods
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naked nucelic acid molecules, small circular RNA, plant pathogens
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describe prions and what is significant about them
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single protein molecules (pigenetic inheritable changes not resulting from an altered genome sequece) ie. INHERITANCE BY NON GENETIC MECHANISM
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define adaptation
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abiltity to change behavior, in response to demands placed on the induvidual by the environment
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what must be considered when evaulating the "cost" of readiness
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readiness is expensive, probability of encounterinf stress, speed of adaptation, normal tolerance to stress
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what occurs during the adaptive stage? How does this effect relate to the timing of a lethal dose?
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regulation occurs, changing transcription profile,
If a lethal dose is given right away, the microbe would die |
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why is global regulation better for adapting to stress?
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need to regulate multiple pathways at once
changed behavior requires many proteins coordinate regualtion of multiple pathways allosteric inhibition is too specific |
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what is the slowest step in regulation?
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transcription
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List three mechanisms that can work globally
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regulatory proteins
alternative sigma factors small RNAs |
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Describe how the SOS repressor protein works (damaged DNA repair)
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1. normal conditions, repressor is bound
2. single stranded DNA signals damage 3. activated proteases cleave the repressor 4. genes transcribed and DNA is fixed |
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What must all the genes have in common to be regulated by regualtory proteins?
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must have the same repressor binding site
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What must all the genes regulated by small RNAs have in common
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they must have a common structural or sequence around the promoter so the small RNA can bind
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How do small RNAs work to regulate transcription?
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They bind to the DNA and block the promoter
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what must all genes regulated by sigma factors have in common
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they must have the same promoter
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what do genes regulated by a DNA binding protein have in common
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the same DNA binding site
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define genomics
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analysis of an entire genome
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what would you monitor to determine the genes requlated in respose to heat shock?
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mRNA synthesis
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describe a microarray
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identifies genes that are being transcribed, color change indicated mRNA is bound,
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explain how the role of the relevant component in the functonal system can be deduced
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remove a component of the system (mutation) and observe teh resulting change in the system (growth phenotype)
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Describe a selection to select for a particular trait
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easy and powerful, define a condtion where only the cells with the phenotype of interest grow
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describe a screen for a particular trait
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look at all cells and find the ones with the phenotype you are interested in, not as easy or as powerful as a screen but applicable to more phenotypes
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why are selections for a particular mutant hard to design?
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mutants usually lose rather than gain functions
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Screening by enzyme assay is hard, what are two alternatives
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screening with indicator plates or replica plating
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describe how an indicator plate screen works
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a property of the media you are using allows you to detect the desired phenotype
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describe screening via replica plating
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the master plate is pressed onto veveteen and a new plate is used to "copy" the population. Many different plates can be used to test for different properties
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How would you isolate or identify each of the following (selection or screen)
mutant resistant to tetracycline His- strain Lac- strain |
resistant to tetracyline- allows you to use a selection because only the mutant will grow on media with tetracyline
His- have to use a screen, replica print lac- this strain can't use lactose, use a screen |
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What property of ligase allows it to be used to seal DNA even after forgein DNA is added
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ligase only works to seal the backbone, it is independent of the bases present
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