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How is the base of a nucleotide attached to a pentose sugar?
Base is attached to beta hydroxyl group
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At what wavelength does DNA show the greatest peak?
At 260nm
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What is the order of basicity of the nucleobases
G>A>C>>U
*The smaller the pKb the stronger the base.
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What are all of the nucleosides?
adenosine, guanosine, thymidine, cytidine, uridine
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What are all of the nucleobases?
Adenine, Guanine, Thymine, Cytosine, Uracil.
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In nucleosides, which nitrogen of a purine or nitrogen of a pyrimidine is attached to the C-1 of a ribose or deoxyribose?
N-9 of a puring, N-1 of a pyrimidine.
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Under what conditions is RNA unstable?
Alkaline conditions
*DNA is stable
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What is tautomerization?
Isomers of the same organic compound.
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How many bases does a full turn of DNA consists of?
10bp; pitch is 34 angrstom, adjacent bp=3.4 A
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What is the conformation of the sugar?
C-2'-endo
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What is intercalation?
Ethidium brodmide is an intercalator, isert between adjacent base pairs, untise helix; flouresence orange under UV.
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What is hyperchromism?
The unstacking of base pairs results in an increased absorbance 260.
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What is DNA hybridization?
Different DNA strands of similar sequences can form hybrid duplexes.
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What is a cot plot of Curve?
N increases Cot 1/2 increases ; more repetitive, Cot 1/2 decreases.
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What is boyant density
P= 1.660+0.098(G+C) molar fraction in DNA
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What is Tm
Tm= 69.3+ 0.41(G+C) molar percent
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What are some non enzymatic transformations?
- Deanimation: C->U
- depurination: hydrolysis of N-glycoscidic bond
- UV damage: form cyclobutane T, Dimer or 6-4 photo product
- nitrate & nitrite can cause de- NH4
- alkylating agents e.g. (CH3)2SO4
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What do you call molecules that differ in L are called?
- Topoisomers.
- L is linking number or linkin #. L changes only when covalent bonds are broke as in gyrase strain. T; twist; w: writhe (supercoil)
- L= T+W
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What is DNA gyrase?
- DNA gyrase is a type II topoisomerase, introduced in supercoils
- Type I topoisomerase : increase L by 1x
- Type II decrease L by 2x
- (negative supercoild favor strands seperation)
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Describe the structure of E. coli chromosome?
Circular DNA duplex with supercoiled loops complex with a protein RNA core.
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What is DNAse?
Cleave phosphodiester bonds in DNA.
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What are RNAse
Cleaves phosphodiester bonds in RNA.
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What happens when DNAse introduces a "nick?"
That loops adopts an extended relaxed conformation, super coiling is gone.
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Describe a Eukaryotic chromosome?
A Eukaryotic Chromosome contains a single linear DNA duplex in a highly compacted form known as chromatin that is a complex of DNA and proteins (histones)
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What are chromatin?
Think of beads on a string. The beads are nucleosomes.
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Describe the rRNA of the E.coli ribosome
- 23s
- /
- 50s---34protein
- E.coli ribosome/
- \ 30s----16s RNA
- 21 proteins
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What are some other uses of nucleotides?
- ATP: energy
- CoA: acyle transfer
- NAD+=H- transfer
- FAD: e- transfer
- Camp: 2nd messenger
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What is the sedimentation coefficient?
- S (svedberg)
- -zonal (isophychic) centrifugation with CsCL density gradient.
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Describe DNA replication in Bacteria
- 1) General features 1: Growing during replication is bidirectional 2: Growth at replication fork is semi
- leading strand: replicates without a problem
- lagging strand: must replicate with (okazaki fragments)
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What is DNA pol I
it is an eznyme containing 3 functions; klenow fragment has the first two functions.
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DNA pol III
the main replication enzyme, has 10 kinds of polypeptide e.g. beta 2 dimer, the sliding clamp, encircle the template, wake pol III high processive, also has proofreading ability.
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What is primase?
Synthesize RNA primer.
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What is DNA gyrase?
Introduce negative supercoils, release torsinal stress.
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What is the function of Helicase e.g. DNA Beta protein.
Unwind DNA duplex, dsDNA --> ssDNA
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What is the mechanism of DNA replication in E. Coli?
- 1) initiation: OriC DUE ( DNA unwinding Element)
- 2) Elongation
- 3) Termination
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What is the replisome?
The mutiprotein complex that promotes DNA synthesis at replication fork.
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What is the primosome?
An exyme complex that synthesiszes primers for DNA replication.
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What is DNA ligase?
Seal nick: use ATP or NAD+ form E. AMP inermediate.
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What is the ARS?
In yeast, ARS: automonous replication sequence is the origin of Rep yes has ~400 ARS, ARS is recognized by ORC ( origin recognition complex) which initiate replication
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What are tetomerase?
It is a specialized reverse transcriptase.
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What are the different DNA repair mechanisms?
- Mismatch repair
- Base excision repair
- Nucleotide excision repair
- Direct repair: repair of mG (methylated G) :mg pair with T rather than C causing GC to AT mutation in Daughter generation.
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what is DAM
DNA adenine methylation ezyme methylase. it methylates A of GATC sequence.
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What are some DNA recombination
- 1)Homologous genetic recombination (general recombination) E.G. in Phase I of meiosis, for "holiday intermediates"
- 2) Site specific recombination: use recombinase which recognize specific sequence for recombination
- 3) Transposition: transposons are transposable elements "jump" from one place to another on chromosomes.
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What is the promoter sequence in a prokaryote (E. Coli)
-10: pribnow box : TATAAT -35 TTGACA
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What are the three steps of transcription in E. coli?
- 1) Initiation.
- 2) Elongation
- 3) Termination
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What are the two mechanisms of termination?
- 1) formation of a G:C rich hairpin followed by several U
- 2) Depend on termination factor rho (P) protein: P has helicase and ATP ase activities
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What protein is used for mRNA synthesis?
RNA Pol II
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