CHEM 403: Nucleotides and Nucleic Acids

what do nucleotides do for cellular metabolism?

provide energy; help respond to stimuli or hormones; structure; building blocks of nucleic acids (DNA and RNA)

gene

segment of DNA that codes for a protein or RNA

classes of RNA

ribosomal RNAs (rRNAs) → components of ribosomes

messenger RNAs (mRNAs) → carries genetic info from DNA to ribosomes for protein synthesis

transfer RNAs (tRNAs) → translate mRNA to an amino acid sequence

noncoding RNAs (ncRNAs) → many functions

what are nucleotides made of?

nitrogenous base (pyrimidine or purine), pentose, 1+ phosphates

nucleoside

nucleotide but without a phosphate group (has a sugar and base)

N-β-glycosyl bond

joins pentose (sugar) to base

purine bases

adenine (A) → DNA and RNA

guanine (G) → DNA and RNA

pyrimidine bases

cytosine (C) → DNA and RNA

thymine (T) → only in DNA

uracil (U) → only in RNA

nucleotide and nucleic acid nomenclature

-ine = nucleoside // -ate = nucleotide

deoxyribonucleotides

structural units of DNA

ribonucleotides

structural units of RNA

phosphodiester linkage

connects bases together (in both DNA and RNA)

hydrolysis of DNA vs RNA

RNA is rapidly hydrolyzed

DNA is not rapidly hydrolyzed

oligonucleotide

short nucleic acid

polynucleotide

longer nucleic acid

what kind of test do we use for aromatic structures?

UV-vis tests

tautomers (know how to draw these given a base)

interconverted form of a base

base pairs

H-bonding patterns between complementary strands of nucleic acids

A → T or U (2 H bonds)

G → C (3 H bonds)

hierarchical levels of nucleic acid structure

primary = nucleotide sequence

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

tertiary = complex folding of chromosomes or folding of tRNA/rRNA structures

“Watson-Crick” model of DNA structure

offset pairing of the 2 strands creates a major groove (open: better interactions) and a minor groove (closed)

are DNA strands parallel or antiparallel?

antiparallel → 3’, 5’ -phosphodiester bonds in opposite directions (parallel strands would run in the same direction)

how many base pairs are in between helical turns?

10.5

how is the double helix stabilized?

metal cations shield (-) charges of backbone phosphates

base stacking interactions between base pairs (G-C stronger bc they have more H bonds)

how is DNA replicated (simple)?

parent strands split → strands serve as templates and complementary daughter strands are formed

three forms of DNA

B-form: “Watson-Crick” structure; right-handed; most stable; in our body

A-form: right-handed; wider; solutions with no water; not in our body

Z-form: left-handed; zig-zag appearance; for special cases; in our body (unsure of why)

palindrome

section of DNA that is the same backward and forward

mirror repeat

sequence when the inverted repeat occurs within each individual strands

hairpin and cruciform structures

form from inverted repeat sequences

hoogsteen positions

participate in H bonding with a third DNA strand

hoogsteen pairing

non-Watson-Crick pairing; forms triplex DNAs (when 3 DNA strands pair)

tetraplex DNAs

occurs when 4 DNA strands pair; G tetraplex is very stable

transcription

mRNAs formed as copies of DNA template

monocistronic mRNA

codes for one polypeptide

polycistronic mRNA

codes for 2+ different polypeptide

how is the double helix denatured?

pH extremes or high temperatures; this disrupts H bonds and base-stacking interactions;

an open/denatured helix means higher UV-vis

anneal

two strands spontaneously rewind; can wind again when environment returns to normal

hypochromic effect

decrease of UV absorption when complementary strands are paired

hyperchromic effect

increase in UV absorption when helix is denatured

how does the denaturation temperature change with base pairing?

more G-C pairings increases it, meaning it is harder to denature with more G-C pairings because it has more H bonds than A-T

stability of duplexes

RNA duplex > RNA-DNA > DNA duplex)

mutations

alterations in DNA that make permanent changes in genetic information

deamination

spontaneous loss of exocyclic amino groups; happens all the time with cytosine → uracil (since U is not in DNA, the base is then removed)

sodium nitrite + nitrate → deamination

depurination

hydrolysis of the N-β-glycosyl bond between the base and sugar

alkylating agents

can change base-pairing or stop it

what does oxidative stress do?

damages DNA

cloning vectors

small DNAs capable of autonomous replication

recombinant DNA

composite DNA molecules made of covalently linked segments from multiple sources

origin of replication (ori)

sequence where replication starts

resistance enzymes

cut the plasmid so we can insert DNA

polymerase chain reaction (PCR)

replicate DNA using thermophilic enzymes

can trace evolution, be used in forensics, detecting infections, etc.

sanger sequencing

remove the ability of one base to have something added to it

on the gel: smallest piece at the bottom and largest at the top

nucleotide-bonding fold

single protein domain that binds adenosine

second messengers

compounds made in the cell after extracellular chemical signals interact with receptors