2.1 - Nucleic Acids: Structure, DNA assembly and organization Flashcards
What is the base pair geometry in DNA helix strand?(for interest only)
The geometry of a base pair can be characterized by 6 coordinates: shift, slide, rise, tilt, roll, and twist. Together, they characterize the helical structure of the molecule.
Source: Olson WK, Berman HM (2001). “A standard reference frame for the description of nucleic acid base-pair geometry”. J Mol Biol. 313 (1): 229–237.
What is the structural components of nucleic acids?
A 5-carbon sugar, a phosphate group and a nitrogenous base. (If the sugar is ribose, the polymer is RNA; if the sugar is the ribose derivative deoxyribose, the polymer is DNA.)
What is the helix geometries and grooves of DNA?
Current research has shown that there are at least three DNA conformations in nature, namely A-DNA, B-DNA and Z-DNA. A-DNA and Z-DNA are very different from B-DNA in their geometry and size, although still forming a helical structure. (for interest only)
There’re two types of groove in DNA helix strand, major groove and minor groove. The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.
What is the the directionality of nucleic acids and the reason?
The 5′ end with a free hydroxyl or phosphate group on the 5′ carbon of the sugar, and the 3′ end with a free hydroxyl group on the 3′ carbon of the sugar. The reason is that nucleic acids can only be synthesized in a 5’ to 3’ direction, as the polymerase used to assemble new strands need attach a new nucleotide to the 3’ hydroxyl group via a phosphodiester bond.
What makes up the backbones of DNA helix strand?
Phosphodiester bonds make up the backbones of DNA and RNA. The phosphate is attached to the 5’ carbon. The 3’ carbon of one sugar is bonded to the 5’ phosphate of the adjacent sugar. Specifically, the phosphodiester bond links the 3’ carbon atom of one sugar molecule and the 5’ carbon atom of another.
A phosphate diester bond occurs when two hydroxyl groups in phosphoric acid react with exactly two hydroxyl groups on other molecules to form two ester bonds. This “bond” involves the linkage of C-O-PO2–O-C.
What is Chargaff’s base pair rules?
Chargaff’s rules state that DNA from any species of any organism should have a 1:1 stoichiometric ratio of purine and pyrimidine bases (i.e., A+G=T+C) and, more specifically, that the amount of guanine should be equal to cytosine and the amount of adenine should be equal to thymine. This pattern is found in both strands of the DNA.
%A = %T and %G = %C
What’s the purpose of base pair geometry?
Allows for proper base stacking, helical turn, and regular hydrogen bonding.
What is histones?
The protein that wrap up DNA into structures called nucleosomes.
