biochem quiz 10

what is a nucleotide?

they are energy carriers, enzyme cofactors in oxidation-reduction reactions, and intracellular signaling molecules

what are nucleic acids?

storage and transfer of genetic information, DNA & RNA, structural and catalytic roles (ribozymes), and regulation of gene expression

what is the chemical structure of a nucleotide?

sugar, base, and one or more phosphate groups

where is the base attached to the sugar?

C-1’ through an N-glycosidic linkage in the beta configuration

where are the phosphoryl groups attached?

C-5’ of nucleotide sugar

what makes ribose different from deoxyribose?

lacks the 2’ OH group

what is the difference between a purine and pyrimidine?

purine —> 2 rings fused, pyrimidines —> single 6-membered ring

what is a nucleoside?

base and sugar

what is the structure of ATP?

it is a nucleoside triphosphate and is synthesized from ADP through oxidation of metabolic fuels or by photosynthesis (recycled 50-75kg in humans)

how are nucleic acids related to nucleotides?

they are polar polymers joined by 3’ to 5’ phosphodiester linkages

what is the pka of the phosphate group and how does that relate to the backbone?

2.0 and highly negatively charged

which of the ends are phosphorylated?

5’

How is RNA susceptible to hydrolysis?

under basic conditions through an intramolecular reaction that involves the 2’ OH group

what does RNA hydrolysis form>

a cyclic monophosphate intermediate

what is the watson-crick model of DNA?

DNA consists of two polynucleotide strands that wind around each other to form a right-handed double helix

where are the sugar-phosphate backbones found in DNA?

exterior of helix and exposed to solvent

how many base pairs are in a turn of helix?

10.4

what is the helical pitch of DNA?

34 angstroms

how many rises per base pair?

3.4 angstroms

what is the diameter of the helix (helical width)

20 angstroms

what forces stabilize the DNA double helix?

H bonds with base pairs, stacking interactions (hydrophobic

which are the strongest stacking interactions?

GC base pairs

what is Tm?

denaturation of DNA occurs at high temperatures or by changing the ionization state of its bases. anything that weakens or denatures will cause a decrease in Tm

what are the structural differences of A-, B-, Z- DNA?

A&B are right-handed, Z is left-handed. B is the Francis and Crick of DNA

what are the grooves in DNA?

major —> wider and deeper and binds to many proteins

what is the feature of RNA molecules?

single-stranded, can fold back on themselves to form stem-loops, bulges, and other types of secondary and tertiary structures

what is DNA replication?

bidirectional, semi-conservative, and semi-discontinuous

what does the DNA synthesis +