432 Lecture 24/8 Flashcards
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
Bonding Bases
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 DNA
A: Right Handed, short and broad, pitch 2.3A, 11bp/turn (less salty
B DNA
Right Handed, longer, thinner, pitch 3.4A, 10 bp turn (Primary form of DNA) -normal.
Z DNA
Left handed, longest, thinnest, pitch = 3.8A, 12bp/turn. (Salty regions promote Z-DNA also methylation causes)
Gene
Segment of DNA that contains all the information needed for regulated synthesis of an RNA or protein product.
Genome
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)
Toroidal Super-coiling
1) Left handed turn around protein (negatively supercoiled) 2) Right handed turn around protein (Positive super coiling)
Linkage Number
(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.
Twist
(Tw) The number of turns in a fragment of DNA (1+ 360˚)
Writhe
(Wr) describes supercoiling closed circular DNA or constrained linear DNA. Positively Supercoiled DNA has Wr >0 Negatively coiled has Wr
Lk equation
Lk = Wr + Tw; Lk constant; negative super coiling = -
Topoisomerases
Enzymes that regulate the overwinding or underwinding of DNA; both have Tyrosine mediate breakage of DNA
Type I
relax DNA/remove supercoils (does not require ATP); cut ssDNA
Type II
Introduce negative supercoils (ATP dependent) make dsDNA cuts
