Biochem 16 - Nucleic Acids

Phosphodiester bonds

Bonds that link nucleotides for DNA and RNA

3 components of RNA

• Sugar

• Phosphate group

• A / C / T or U / G

Purines

• Adenine

• Guanine

(the bigger ones)

Pyramidines

• Cytosine

• Thymine / Uracil

(Smaller ones)

(pyramidines have 3)

Nucleoside

Base and a sugar (no phosphate)

4 nucleoside units of DNA

• deoxyadenosine

• deoxyguanosine

• deoxycitidine

• thymidine

4 nucleoside units of RNA

• adenosine

• guanosine

• cytidine

• uridine

H-bonds

Bonds between complementary bases on complementary strands

Non-polar groups of bases go to _, polar phosphate groups are on the _

interior, exterior

Stacking forces

How base pairs stack on top of one another

Large major groove

Exposes edge of base pairs, allows for binding of transcription factors

Small minor groove

Exposes edge of base pairs, allows for binding of regulatory proteins

B-DNA

• most naturally existing form of double-stranded DNA (dsDNA)

• right-handed

• antiparallel

A-DNA

• right-handed

• antiparallel

• wider and shorter than B-DNA

• Bases 20deg tilted from the perpendicular plane of the helical axis

Z-DNA

• left-handed

• might have role in gene expression regulation

• often found in alternating sequences of pyrimidine/purine (CGCGCG, ATATAT)

Negative supercoils

Strands are underwound, unwinding of dsDNA is favored

(occurs in prokaryotes)

Positive supercoils

Strands are overwound, super winding of DNA is favored

(occurs in prokaryotes)

Class I topoisomerase

Regulates dsDNA supercoiling by cutting one strand

(prokaryotes)

Class II topoisomerases

Regulates dsDNA supercoiling by cutting two strands

(prokaryotes)

DNA gyrase

Prokaryotic Class II topoisomerase, uses ATP hydrolysis

Histones

Positively charged residues interact with phosphate backbone of dsDNA, wraps dsDNA around it

5 types: H1, H2A, H2B, H3, and H4

Nucleosome

Bead-like structure formed by dsDNA wrapping around H2A, H2B, H3, and H4

mRNA

Messenger RNA, translated into proteins

rRNA

Ribosomal RNA, associates with other ribosomal proteins and plays role in translation

5S, 16S, and 23S; intrachain H bonding with complex structure

tRNA

Transfer RNA, brings amino acids covalently linked in the form of aminoacyl-tRNAs to add to growing polypeptide

Form cloverleaf structure

snRNA

Found in eukaryotes, plays role in mRNA maturation

siRNA and microRNA

Small RNA segments that bind to RNA and regulate gene expression

lncRNA

Non-coding for proteins, but plays role in development / related to many diseases