BC 8: Nucleotides & Nucleic Acids

nucleotide

basic building block of nucleic acids; consists of nitrogenous base (pyrmidine/purine), pentose sugar, and 1+ phosphate group

nucleoside

nucleotide w/o phosphate group (only has nitrogenous base and sugar)

gene

segment of DNA molecule that contains info required to make a functional bio product (protein/RNA)

classes of RNA

ribosomal (rRNA): components of ribosomes

messenger (mRNA): intermediates in protein synth

transfer (tRNA): translate mRNA info to specific AA sequence

noncoding (ncRNAs): wide variety of functions

major purine bases

adenine (A) and guanine (G)

major pyrimidine bases

cytosine (C) and thymine (T, in DNA) and uracil (U, in RNA)

ribonucleoside 2',3'-cyclic monophosphates

isolatable intermediates

ribonucleoside 3'-monophosphates

end products of RNA hydrolysis

phosphodiester linkage

covalent bond joining successive nucleotides of both DNA and RNA.

between 5'-phosphate and 3'-hydroxyl of nucleotides

oligonucleotide

short (us. <50 nucleotides) nucleic acid

polynucleotide

longer nucleic acid

tautomers

readily interconverted forms of free pyrimidine/purine bases

base pairs

H bonding patterns between complementary strands of nucleic acids (AT/U, GC)

Watson-Crick model for structure of DNA

- offset pairing of 2 strands creates major groove (wide and deep) and minor groove (narrow and shallow)

- 3 H bonds form between G and C

- 2 H bonds form between A and T

parallel

3', 5' phosphodiester bonds run in same direction

antiparallel

3', 5' phosphodiester bonds run in opposite directions (how DNA actually is)

per helical turn

10.5 base pairs

36 Å (3.6nm)

double helix stabilized by

- metal cations (shield neg charges of phosphate backbone)

- base stacking interactions between successive base pairs (duplexes w higher G=C context more stable)

B-form DNA

Watson-Crick struc: most stable for random-sequence DNA molecule under physiological conditions

A-form DNA

right-handed double helix w wider helix, 11bp/turn, and tilted plane. Favored in solutions devoid of water

Z-form DNA

left-handed helix w 12bp/turn and a backbone w a zigzag appearance. Appears more slender & elongated

palindrome

region of DNA that's identical read forward or backward (applied to regions of DNA w inverted repeats)

mirror repeat

sequence when inverted repeat occurs within each individual strand

hairpin and cruciform structures

form from self-complementarity within each strand

G tetraplex

occurs when 4 DNA strands pair if the sequences have very high proportion of G residues. Very stable

Hoogsteen pairing

occurs in triplex DNA, allowing bases to form hydrogen bonds on different faces of the bases than typical Watson and Crick pairing

transcription

process by which mRNAs are formed on DNA template

monocistronic

mRNA that codes only for 1 polypeptide (most mRNAs in eukaryotes)

polycistronic

mRNA that codes for 2+ diff polypeptides (occurs in bacteria & archaea)

anneal

2-step process by which 2 strands spontaneously rewind when temp/pH is returned to normal range

hypochromic effect

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

hyperchromic effect

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

denaturation temperature

temp when half DNA is present as separated single strands. Increases w more G=C base pairs

partially denatured DNA

form bubbles. often rich in A=T base pairs

mutations

alterations in DNA struc that produce permanent changes in genetic info coded

polymerase chain reaction (PCR)

method of amplifying DNA segments of interest. relies on DNA polymerase

DNA polymerase

enzymes that synthesize DNA from deoxyribonucleotides (dNTPs) using DNA template.

add nucleotides to 3' ends of preexisting strands called primers

Sanger sequencing

A procedure in which chemical termination of daughter strands help in determining the DNA sequence.

reversible terminator sequencing

single-molecule realtime (SMRT) sequencing

sequencing depth

number of times a particular nucleotide in a genome is sequenced, on average

contigs

long, contiguous sequences that are assembled from overlaps

nucleotide-binding fold

single protein domain that binds adenosine (adenine nucleotides are components of many enzyme cofactors)

second messengers

compounds produced in cell following interaction of extracell chemical signals w receptors. often nucleotide like adenosine 3',5'-cyclic monophosphate (cyclic AMP, or cAMP)