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How is the base of a nucleotide attached to a pentose sugar?
Base is attached to beta hydroxyl group
At what wavelength does DNA show the greatest peak?
What is the order of basicity of the nucleobases
*The smaller the pKb the stronger the base.
What are all of the nucleosides?
adenosine, guanosine, thymidine, cytidine, uridine
What are all of the nucleobases?
Adenine, Guanine, Thymine, Cytosine, Uracil.
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.
Under what conditions is RNA unstable?
*DNA is stable
What is tautomerization?
Isomers of the same organic compound.
How many bases does a full turn of DNA consists of?
10bp; pitch is 34 angrstom, adjacent bp=3.4 A
What is the conformation of the sugar?
What is intercalation?
Ethidium brodmide is an intercalator, isert between adjacent base pairs, untise helix; flouresence orange under UV.
What is hyperchromism?
The unstacking of base pairs results in an increased absorbance 260.
What is DNA hybridization?
Different DNA strands of similar sequences can form hybrid duplexes.
What is a cot plot of Curve?
N increases Cot 1/2 increases ; more repetitive, Cot 1/2 decreases.
What is boyant density
P= 1.660+0.098(G+C) molar fraction in DNA
What is Tm
Tm= 69.3+ 0.41(G+C) molar percent
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
What do you call molecules that differ in L are called?
- 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
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)
Describe the structure of E. coli chromosome?
Circular DNA duplex with supercoiled loops complex with a protein RNA core.
What is DNAse?
Cleave phosphodiester bonds in DNA.
What are RNAse
Cleaves phosphodiester bonds in RNA.
What happens when DNAse introduces a "nick?"
That loops adopts an extended relaxed conformation, super coiling is gone.
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)
What are chromatin?
Think of beads on a string. The beads are nucleosomes.
Describe the rRNA of the E.coli ribosome
- E.coli ribosome/
- \ 30s----16s RNA
- 21 proteins
What are some other uses of nucleotides?
- ATP: energy
- CoA: acyle transfer
- NAD+=H- transfer
- FAD: e- transfer
- Camp: 2nd messenger
What is the sedimentation coefficient?
- S (svedberg)
- -zonal (isophychic) centrifugation with CsCL density gradient.
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)
What is DNA pol I
it is an eznyme containing 3 functions; klenow fragment has the first two functions.
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.
What is primase?
Synthesize RNA primer.
What is DNA gyrase?
Introduce negative supercoils, release torsinal stress.
What is the function of Helicase e.g. DNA Beta protein.
Unwind DNA duplex, dsDNA --> ssDNA
What is the mechanism of DNA replication in E. Coli?
- 1) initiation: OriC DUE ( DNA unwinding Element)
- 2) Elongation
- 3) Termination
What is the replisome?
The mutiprotein complex that promotes DNA synthesis at replication fork.
What is the primosome?
An exyme complex that synthesiszes primers for DNA replication.
What is DNA ligase?
Seal nick: use ATP or NAD+ form E. AMP inermediate.
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
What are tetomerase?
It is a specialized reverse transcriptase.
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.
what is DAM
DNA adenine methylation ezyme methylase. it methylates A of GATC sequence.
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.
What is the promoter sequence in a prokaryote (E. Coli)
-10: pribnow box : TATAAT -35 TTGACA
What are the three steps of transcription in E. coli?
- 1) Initiation.
- 2) Elongation
- 3) Termination
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
What protein is used for mRNA synthesis?
RNA Pol II