biochem test 2
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- what is optimum temp for base pairing?
- 25C
- what are the two steps of DNA renaturation?
- nucleation and then zippering
- When measuring the renaturation speed of DNA's what does N stand for?
- the complexity of the DNA
- what do Cot curves show
- concentration vs. time
- True/ false the first step of renaturation is first order?
- false- second-order because it depends on concentration and time
- why is supercoiling important?
- it allows DNA to be in equilib between single stranded region and supertwisted region.
- what is another name for DNA gyrase
- topisomerase 2
- what enzyme can relax the negative supercoil of gyrase?
- topoisomerase 1
- what are nucleosomes made of?
- 8 histones (octomer)
- what RNA containing enzyme is responsible for adding repeats to the end of DNA?
- telomerase p359
- what is the name of the drug that inhibits gyrase and is therefore an antibiotic for anthrax
- Cipro
- what are the 4 histones?
- H2a, H2b, H3, H4.
- what mediates assembly of nucleosome beads into 30nm/ 300A fiber
- H1 histone
- what is known to intercalate and stabilize tolomere so that cancer cell can't divide
- RHPS4
- If a gene is about to be transcribed what strucutre is it in?
- 30nm soleniod
- what type of hand turn does DNA possess?
- right hand turn
- The _____ hypothesis states that modification of
- histone code
- what phosphoralates Retinoblastoma enzyme and leads to it dissassociation from the E2F
- G1 CDK (cycline dependent Kinases).
- at the 3' region of tRNAs there is a sequence that reads _____ and is where the a.a. is attached.
- CCA p 325
- what type of RNA can prevent a protein from being produced even though the mRNA has been formed.
- small RNA or ncRNA.
- _______ is the process where small interfering RNAs prevent a protein from being expressed even though the mRNA may exist.
- RNA intererence p 325
- _____ is the name of the region where an a.a is attached to a tRNA
- acceptor stem CCA p 364`
- ____ is the region of tRNAs that ribozymes recognize
- T(trident)C. p364
- why is tertiary structure of tRNA important to bases
- because it allows them to maximize their hydrophobic basic stacking.
- what leads to the unusual base pairing that allow tRNA to assume unique tertiary structure
- wobble pairings NAS 19
- what do snRNPs used for?
- They edit hnRNA so that it can leave the nucleus.
- what type of RNAs lead to RNA interference?
- siRNAs - small interferring RNAs
- what loop allows ribozymes to recognize tRNAs
- the T(trident)C
- true / false the nucleotide sequence of ribosomes is conserved from species to species?
- falsep368 the secondary strucuture is.
- What type of gene is retinblastoma?
- tumor suppressor NAS 13
- what else besides CDK kindase can cuase retinoblastoma to fall off and transcription to start?
- T-Ag viral oncogene
- When tRNA is in tertiary L shape how many tertiary structures are H bonded?
- 3
- what are the three main structural components of E Coli ribozyme?
- 23S, 16S, 5S
- what 2 things are ribosomes made of
- rRNA and ribosomal proteins
- what do the three unusual H-bonded bases of tRNA add in
- establishing the tertiary struct.
- what is a DNA molecule made by joining DNA fragments from different sources?
-
recombinant DNA
Grad student (GS) P1 - ______ is a method by which DNA is incorporated into a vector capable of replication in a host cell.
-
cloning think insulin
Grad p2 - what were 4 things that allowed easier DNA analysis?
- dna restriction nucleases, cloning techniques, rapid sequencing methods, dna ligase
- what protects bacterial genome from being destroyed by iets restriction nucleases
- methylation
- what is unique about sticky ends of DNA
- sticks ends have 5' overhang and have more effecient ligation.
- what are three common characteristics of vectors
- 1? easy intro into host cells 2 recombo DNA can be replicated in host cell 3 easy identification of cell with recombo DNA
- what type of vector would you use for really large segment of recombo DNA
- BAC's YAC's
- what are some clinical applications of cloning
-
-treat genetics disorders affecting single gene
- production of vaccines - how do you insert a gene into a plasmid
-
flank it and plasmid at two spots with restriction enzyme.
Grad 7 - what is an advantage to the specific overhangs of the sticky ends in plasmid/ insertion DNA
- it ensures that DNA will insert in plasmid in the right orientation
- what would you add to mixture of foreign already cut DNA and plasmid to join them.
- ligase from T4 bacteriophage
- what is it called when you shock DNA so that it will take up foreign plasmid (vector)
- transformation
- go through steps necessary to make a DNA library of a gene ?
-
1. cut plasmid and DNA with same restriction enzymes
2. mix both with ligase
3. transform
4. - how could you get a probe for selecting a certain gene from DNA library
- use clone from ortholog in another similiar species
- after getting a probe that matched gene how would you discover colony that had desired gene?
- use autoradiography
- what type of restriction enzymes are used for recombination
- type 2
- what is a cDNA library consist of
- set of double stranded DNA made from mRNA
- what enzyme goes from RNA back to DNA
- reverse transcriptase
- what are the two ways of making a probe for screenig library for a certain gene
-
1 make probe if a.a. sequence is known
2 use ortholog - for RNA polymerase what do the 2 alphas do?
- they assemble other enzyme subunits.
- what does B' do
- functions in DNA binding- part of active site
- waht does B do
- binds NTP and sigma
- what are 2 factors that contribute to the melting of DNA at the promoters
-
1. mostly made of A/T bonds
2. negative supercoiling - what event signals the end of initiation in transcription
- when sigma unit falls off notes p20
- what is the name for the conserved nucleotide sequence where transcription starts?
- consensus sequence
- In addition to the pribnow box and the -35 region what region do highly expressed genes have?
- upstream elements (UP_)
- what part of the alpha subunit bind to the UP element
- the CTD.
- what is Rho
- an ATP dependent helicase
- to what region of RNA does Rho bind
- C rich
- in what area of mRNA does Pol slow down so that Rho can overtake it
- G-C rich area