BIMM midterm

Dna to rna, rna to protein

transcription, translation

DNA melting temperature

The temperature at which half of the DNA strands are in a double-helical state and half are in a single-stranded state, indicating the stability of the DNA molecule. Function of GC content since they have 3 h bonds

temperature that DNA separates and anneals

separates at 96 degrees C and anneals at 65 degrees C

RNA 3D structures

• Secondary structure: hairpin and stem-loop

• Tertiary structure: pseudoknot 

• Once heated and h bonds go away, hard to rejoin

experiments to find DNA structure

• Chargaff’s rule showed us that the number of purines = the number of pyrimidines. The number of so A+G=C+T, a=t, c=g

• Rosalind Franklin's x-ray diffraction

• Watson and crick used franklin’s x-ray and physician models to find the helix shape

Meselson-stahl experiment

A landmark experiment that demonstrated the semiconservative nature of DNA replication using isotopes of nitrogen to label the DNA strands.

DNA replication enzymes

helicase: unzips (because cannot heat a cell in the body)

topoisomerase: relieves torsional strain

Primase: makes the RNA primer

dna polymerase: adds dntps to the 3’ end

RNAse: gets rid of the RNA primer

ligase: makes phosphodiester bonds

too many telomeres?

chromosomal instability

telomeric replication machinery

1. telomerase elongates with with RNA and reverse transcriptase machinery

2. primase and dna poly fill in

DNA damage during dna replication

dna poly can make mistakes. dna poly has a 5’ exonuclease and can remove incorrect nucleotides immediately after adding.

endonuclease

Cleave phosphodiester bonds within the molecule. Doesn’t remove them, though

exonuclease

cleaves the nucleotide at the end of a molecule. can be 3’ or 5’ so requires a free oh or phosphate

mismatch repair

if dna poly doesn’t catch the mistake:

1. other proteins will recognize the mistake

2. endonuclease will cut

3. helicase unwinds and exonuclease carries away

4. DNA poly and ligase fill in

this only happens in the short time before the dna stand is methylated.

 base excision repair

• 1. DNA glycolase will recognize multiple chemically modified bases and remove that specific nitrogenous base from the backbone

• 2. After glycosylase is cut out the base, there will be an AP (apurinic/apyrimidinic) site. Then a APE1 (endonuclease 1) will cut (hydrolyze) the one sugar phosphate bond.

• 3. AP lyase will remove the base-less sugar.

• 4. Filled with DNA polymerase and ligase

nucleotide excision repair

• 1. The bulky distortion is recognized: The  XP-C protein recognizes that there is a change in the 3d structure

• 2. Helicase unzips in the recognized area

• 3. Then the XP-F and XP-G endonucleases will cut

• 4. Dna poly and ligase fill in the gap

NHEJ

• In g0/g1 when there is only one copy of DNA

• 1. Enzymes will recognize the double strand break because there is some overhang of one strand. 

• 2. Exonuclease removes the overhang.  

• 3. Just put it back together 

• This leads to errors like translocation

HE

• In s/G2 when there are two copies of DNA

• 1. The break is recognized (only one is damaged of the two pairs)

• 2. 5’ exonucleases create 3’ overhang on the damaged strand

• 3. Strand envision: Ss DNA hybridizes to the complementary sequence in the sister chromatid which has been unzipped with helihaze. 

• 4. DNA polymerase is going to elongate until it matches with the corresponding overhang on the other end. 

• 5. The repair will pair back with the overhang and we will have gap filling and ligation

CRISPR

if no template, will use NHEJ which creates an error. the CAS9 is an endonuclease

simple sequence repetitious DNA

not mobile. can be satalite (20-100kb) or nonstatalite (2kb). usually just comes about from unequal cross over.

transposons

DNA transposons (cut and paste, inverted ) and retrotransosones (copy and paste)

transpotatse

endonuclease and ligase. coded by the mobile gene segment. attaches to inverted repeats

reverse transcriptase and integrase

coded by retrotranspotases. pairs to long terminal repeated in the same direction.