Flashcards in 432 Lecture 24/8 Deck (48):
What causes the Tautomerization of Nucleotides?
Higher pH. Affects H-bonding properties. Cytosine goes to imino form. Thymine goes to enol form.
How is the DNA nucleotide polymer linked?
Linked by 3' to 5' Phosphodiester bonds.
Polarity of ssDNA
Hydrophillic at the side of the phosphodiester side of DNA; Hydrophobic at the nitrogenous base side of the DNA
What role does the OH group play in RNA?
In basic solution, OH group rips H from OH on the 2' carbon, causing nucleophillic attack on a phosphate group on the 3' carbon. Causes the formation of 2',3' cyclic monophosphate derivatives leading to the formation of 2' or 3' -monophosphate derivatives by hydrolysis reactions. RNA is not as stable in a single strand.
Bonding Character of DNA bases
non-covalent hydrogen bonding
A-T (2 hydrogen bonds) ; G-C (3H-bonds)
What are the three energetically favorable arrangements in DNA?
1) hydrophobic interactions in the center away from hydrophillic center 2) hydrophillic interactions with the aqueous environment with the phosphodiester bonds and sugars 3) Van der Waals interactions between bases (very favorable).
Major Groove and Minor Groove coding for G-C pair.
Major groove - AADH
Minor groove - ADA
(A-Acceptor, D- Donator, M-methyl). Minor grooves are the same regardless of G-C, C-G arrangement. G-C (AADH); C-G (HDAA).
Major Groove and Minor Groove coding for A-T pair
(A-T) MG = ADAM (T-A) MG=MADA both minor grooves AHA!
A: Right Handed, short and broad, pitch 2.3A, 11bp/turn (less salty
Right Handed, longer, thinner, pitch 3.4A, 10 bp turn (Primary form of DNA) -normal.
Left handed, longest, thinnest, pitch = 3.8A, 12bp/turn. (Salty regions promote Z-DNA also methylation causes)
Segment of DNA that contains all the information needed for regulated synthesis of an RNA or protein product.
the entire DNA sequence content of an organism.
Negative super-coiling Inter-wound
Clockwise winding of the DNA, tending to separate the strands, leads to negative super-coiling.
Positive Super-coiling Inter-wound
Counterclockwise direction induces positive supercoiling (closes DNA)
1) Left handed turn around protein (negatively supercoiled) 2) Right handed turn around protein (Positive super coiling)
(Lk) The number of times one strand of DNA wraps round the other, in relaxed B-DNA, one strand wraps round the other every 10.5 bp. Unwound Lk = 18 fixed for circular DNA.
(Tw) The number of turns in a fragment of DNA (1+ 360˚)
(Wr) describes supercoiling closed circular DNA or constrained linear DNA. Positively Supercoiled DNA has Wr >0 Negatively coiled has Wr
Lk = Wr + Tw; Lk constant; negative super coiling = -
Enzymes that regulate the overwinding or underwinding of DNA; both have Tyrosine mediate breakage of DNA
relax DNA/remove supercoils (does not require ATP); cut ssDNA
Introduce negative supercoils (ATP dependent) make dsDNA cuts
Eukaryotic Type IIa Topoisomerase
Functions as a dimer; 1) binds segment of DNA 2) second segment bound at N gate 3) second segment trapped, while first segment is cleaved 4) second DNA passed through break. 5) Broken DNA is religated and the second DNA is released through the C gate.
What type of linkages are made after a segment of DNA is cleaved for Super-coiling?
Two 5' phosphotyrosyl linkages to the enzymes
Topoisomerase II; The only enzyme that can introduce negative super coiling. Present in bacteria. Does not happen in Eukaryotes. Gyrase the only topoisomerase that can introduce negative super coils. other topoisomerases just remove positive or negative super coils.
What are two examples of antibiotics and anticancer drugs that inhibit topoisomerase?
Cipro- antibiotics camptothecin- anti-cancer
Nucleosome Histone core associations
H2A - H2B; H3-H4 (Nucleosomes introduce torroidal super coiling) histone cores protect regions of DNA from digestion from nucleases.
1) Called "DNA-Histone Association Complex" 2) A-T rich regions are associated with H3/H4 of complex 3) associates with minor groove of DNA 4) Mostly hydrophobic interactions, not covalently.
What two amino acids are critical in phosphate backbone interaction with histone proteins
Lysine and Arginine Basic/positively charged; make up tails of histone cores phosphodiester backbone is negatively charged
Chromatin changes regulating gene activity
1) Acetylation (lysine, negates positive charge) , methylation, phosphorylation and ubiquination of histone side chains.
First level; nucleosome association with DNA; bead on a string appearance
compacting of 10nm fiber
Histone protein, not in the HAC, Linker protein, associates with DNA and pulls DNA closer to the nucleosome, causes compaction of the chromatin.
DNA Uncondensed; G1 (gap phase); S ; G2
synthesis phase-DNA replicated
the replicated chromosomes, chromatids, cohere to each other
DNA undergoes condensation
chromosomes line up along the plane between the spindle poles
sister chromatids separate
completion and partial decondensation
Structural maintenance of chromosomes Cohesions and condensins
(SMC1/3) Cause sister chromatids to stick together. wrap around sister chromatids, during S phase, as soon as DNA is replicated; comes off before metaphase by separase
(SMC 2/4) Condense chromosomes, function after G2, after DNA is replicated. come off after telophase.