Chapter 22 - Nucleotides and Nucleic Acids

• energy for metabolism (ATP)

• enzyme cofactors (NAD+)

• signal transduction (cAMP)P

3 functions of nucleotides

• storage of genetic info (DNA)

• transmission of genetic info (mRNA)

• processing of genetic info (ribozymes)

• protein synthesis (tRNA and rRNA)

4 nucleic acid functions

• nucleotide = nitrogenous base + pentose + phosphate

• nucleoside = nitrogenous base + pentose

• nucleobase = nitrogenous base

nucleotide vs nucleoside vs nucleobase

negative charge

what charge is the phosphate group at neutral pH

5’ position

what position does phosphate group normally attach to

built using 5’-triphosphates but each nucleotide has 1 phosphate per nucleic acid

nucleic acids are built using what phosphates (mono, di, tri) and how many phosphates do they contain per nucleotide

RNA : β-D-ribofuranose

DNA : β-2’-deoxy-D-ribofuranose

pentose in RNA vs DNA nucleotides

the straight-chain (aldehyde) and ring (β-Furanose) forms

in solution what forms of free ribose are in equilibrium

pyrimidines or purine

what are nucleobases derivatives of

nitrogen-containing heteroaromatic molecules and planar or almost planar

what type of molecules are nucleobases

250-270 nm

what UV light do nucleobases absorb

cytosine → DNA and RNA

thymine → only DNA

uracil → only RNA

pyrimidine bases and what they are found in (DNA/RNA)

adenine structure

guanine structure

cytosine structure

thymine structure

uracil structure

adenine → DNA and RNA

guanine → DNA and RNA

purine bases and what they are found in (DNA/RNA)

N-glycosidic bond

• to position N1 in pyrimidines

• to position N9 in purines

what type of bond is the pentose ring attached to the nucleobase via in nucleotides and to what position in pyrimidines vs purines

acid

what is N-glycosidic bond cleavage catalyzed by

purines: -sine (ex: adenosine)

pyrimidines: -dine (ex: cytidine)

what does nucleoside nomenclature end in in purines and pyrimidines

-ylate (ex: adenylate)

what does nucleotide nomenclature end in

eukaryotes (but also found in bacteria)

what organisms is 5-methylcytosine modification common in

bacteria (NOT found in eukaryotes)

what organism is N⁶-methyladenosine modification common in

prokaryotes → way to mark own DNA so that cells can degrade foreign DNA

eukaryotes → way to mark which genes should be active

purpose of epigenetic marker (such as methylation) in eukaryotes and prokaryotes

they are degraded by sequence-specific restriction enzymes and cleaved

what happens to foreign DNAs (not methylated) that are introduced into the cell

hydrogen bond

type of bond between two bases to form a base pair

A - T

C - G

Purines with pyrimidines

Watson-Crick base pairs in dsDNA

isolated “nuclein” from cell nuclei → hydrolysis of it produced phosphate, pentose, and a nucleobase → chemical analysis revealed phosphodiester linkages and pentose is ribofuranoside

what did Friedrich Miescher do

Watson, Crick, and Wilkins

who shared Nobel prize for discovering DNA double helix

5’ to 3’

what direction is DNA sequence read in

DNA polymerase

synthesis of new strand of DNA is catalyzed by what enzymes

one daughter strand and one parent strand

newly made DNA molecule has what 2 strands

mRNA

RNA that is the code carrier for the sequence of proteins

DNA template

what is mRNA synthesized from

contains ribose instead of deoxyribose

contains uracil instead of thymine

difference between mRNA and DNA template

yes

can one mRNA code for more than one protein

monocistronic has one promoter per gene → eukaryotes

polycistronic have one promoter for multiple genes → prokaryotes

monocistronic vs polycistronic

it’s a sequence that is the same forwards and backwards (on opposite strands) → can form hairpins and cruciforms

what is palindromic sequence and what can they form

1 strand of DNA or RNA

how many strands are involved in a hairpin structure

• covalent bonds remain intact (along with genetic code)

• hydrogen bonds are broken (strands separate)

• base stacking is lost (UV absorbance increases)

what happens to DNA when denatured

high temperature or change in pH

what can induce DNA denaturation

annealing

name of the process of reversing denaturation

the polymerase chain reaction

what does the reversible thermal denaturation and annealing of DNA form the basis for

260 nm

DNA is commonly monitored by UV spectrophotometry at what wavelength

• base composition (high CG increases it)

• DNA length (longer DNA increases it)

• pH and ionic strength (high salt increases it)

what 3 things does the midpoint o melting depend on

hybridize

what can 2 near-complementary DNA strands do

N-glycosidic bond

what bond is hydrolyzes in depurination

cytosine → uracil

5-methylcytosine —> thymine

adenine → hypoxanthine

guanine → xanthine

deamination results for cytosine, 5-methylcytosine, adenine, and guanine

guanine and apurinic residue

resulting 2 products of deamination of guanosine residue

hydroxylation of guanine → mitochondrial DNA is most susceptible

oxidative damage

methylation of guanine

chemical alkylation

nitrogen mustard, dimethylnitrosamine, and dimethylsulfate

3 alkylating agents

dimerization of pyrimidines

what mutation does UV light induce

ring opening and strand breaking

what mutation does ionizing radiation cause

aging and carcinogenesis

accumulation of mutations is linked to what