L2 - Biological Molecules Flashcards
What is the predominant form of DNA
B DNA; Major and minor grooves govern interactions with other molecules
What is A-DNA
right handed DNA helix formed by 11 bases per turn making the grooves evenly sized
What is Z-DNA
Left handed DNA helix formed by methylation of cytosine, tortional stress, and high salt concentrations
where do proteins most frequently bind?
major groove; alpha helices and two stranded beta sheets can fit in the major groove
what happens if a protein bind to the minor groove?
results in a distortion
Where do chemical groups vary most in DNA?
the major groove. Groups in the minor group are the same and cant be distinguished by binding proteins
How do proteins bind to DNA?
by forming non-covalent interactions with exposed groups in DNA; sequences have different combinations of hydrogen bond acceptors and donors, and methyl groups
how is specificity between proteins and DNA determined?
by the sequence of DNA, shape and binding groups available on the protein
DNA binding proteins must be able to
interact with the negative backbone (phosphate) of DNA; residues that are facing the helix are often positively charged or have OH groups (serine and tyrosine)
define van der waal interactions
weak intermolecular forces dependent on distance between two molecules
how are non covalent bonds important in molecular structure and stabilization
they are weaker than normal bonds, allowing for flexibility and function
describe the process of supercoiling
a circular molecule is cut and held at one end and twisted at the other end, then the two ends are ligated and the DNA twist to restore the preferred number of bases per turn, causing the DNA to wrap around itself.
can linear DNA also be supercoiled?
yes; as long as both ends are immobile
what causes supercoiling to be released
cut in one of the strands; via topoisomerases
how is supercoiling beneficial
negative SCs favors unwinding, promoting certain DNA processes
