Nucleotides

gene

segment of DNA molecule that contains the information required for the synthesis of a functional biological product, whether protein or RNA

functions of DNA

storage of biological information, transmission of that information to the next generation

ribosomal RNA

components of ribosomes

messenger RNA

intermediates in protein synthesis

transfer RNA

adapter molecules that translate the information in mRNA into a specific amino acid sequence

purines

adenine and guanine

pyrimidines

cytosine, thymine and uracil

solubility of nitrogenous bases

more hydrophobic and relatively insoluble in water

nitrogenous bases

weak bases, aromatic, planar, can isomerize

endo

same side as C5

exo

opposite side of C5

nucleoside

pentose and nitrogenous base, N-B-glycosidic link

N9

glycosidic link for purine

N1

glycosidic link for pyrimidine

nucleotides

nucleoside covalently linked to a phosphate

phosphoester link

condensation reaction between C5 and inorganic phosphate

deoxyribonucleotides

structural units of DNA

ribonucleoside2,3, cyclic monophosphate

isolatable intermediates

ribonucleoside 3 monophosphates

end products of RNA hydrolysis

phosphodiester linkage

covalent bond that joins successive nucleotides of both DNA and RNA

primary structure

covalent structure and nucleotide sequence

secondary structure

regular, stable structure taken up by some or all the nucleotides

tertiary structure

complex folding of large chromosomes or the elaborate folding of tRNA or rRNA

10.5

base pairs per turn

base pairs

hydrogen bonding patterns between complementary strands of nucleic acids

antiparallel

3,5 phosphodiester bonds run in opposite directions

hydrogen bonds

between base pairs, stabilize DNA double helix

metal cations

shield the negative charges of backbone phosphates, stabilize double heliz

base stacking interactions

hydrophobic effect, stabilizes DNA double helix

B-form DNA

most stable, Watson-crick sequence, 3endo deoxyribose, anti conformation

A-form DNA

right handed double helix with a wider helix, 11bp/turn. favored in solutions devoid of water or RNA, 2endo ribose

Z-form DNA

left handed helix with 12bp/turn and zigzag backbone, GC alternating

denaturation

melting of double helix due to pH or temperature extremes

anneal

process by which two strands spontaneously rewind when pH is returned to its normal range

hypo chromic effect

observed decrease in the absorption of UV light when complementary strands are paired

hyper chromic effect

observed increase in the absorption of UV light when a double-stranded nucleic acid is denatured

denaturation temperature

temperature at which ½ of DNA is present as separated single strands, increase with content of G=C

deamination

spontaneous loss of exocyclic amino groups

depurination

hydrolysis of the N-B-glycosyl bond between base and pentose, creates an apurinic site

S-adenosylmethionine

methyl group donor for DNA methylases

polymerase chain reaction

method of amplifying DNA segments of interest, relies on DNA polymerases

primers

DNA polymerases add nucleotides to the 3’ ends of preexisting strands

sanger sequencing

dideoxy chain-termination sequencing, ddNTPs interrupt synthesis

nucleotide binding fold

single protein domain that binds adenosine

second messengers

compounds produced inside the cell following the interaction of extracellular chemical signals with receptors

ppGpp

produced in bacteria during amino acid starvation to inhibit the synthesis of the rRNA and tRNA molecules

ATP/ADP

neurotransmitters, signals for receptors that mediate pain sensation, blood clotting signals

N-B-glycosidic link

bond between a pentose and a nitrogenous base

phosphoester link

bond between a pentose and a phosphoric acid

phosphoanhydrate link

bond between two phosphoric acids

phosphodiester link

bond between two nucleic acids