Chapter 8: Nucleotides and Nucleic Acids

What are the functions of nucleotides in their monomeric form?

Energy for metabolism (ATP), enzyme cofactors (NAD⁺), and signal transduction (cAMP).

What are the functions of nucleic acids?

DNA stores genetic info, mRNA transmits it, ribozymes process it, and tRNA/rRNA support protein synthesis.

What are the three essential components of a nucleotide?

Nitrogenous base, pentose sugar, and phosphate.

What is the charge of the phosphate group at neutral pH?

Negative charge (-2)

Where is phosphate usually attached on the sugar?

5' carbon.

What building blocks are used to build nucleic acids?

5’-triphosphates (ATP, GTP, TTP, CTP). They contain one phosphate moiety per nucleotide, and can also be attached to other positions.

What type of pentose does RNA contain?

β-D-ribofuranose (with 2′-OH)

What type of pentose does DNA contain?

β-2′-deoxy-D-ribofuranose (lacks 2′-OH).

Why does sugar puckering matter?

It increases flexibility and affects structure/dynamics.

What are the two major classes of nitrogenous bases?

Purines and pyrimidines.

What property allows nucleobases to stack?

They are planar and hydrophobic.

At what wavelength do nucleobases absorb UV light?

250–270 nm

Why do nucleobases absorb UV light?

Due to electron delocalization from double-bond character.

What are the three pyrimidine bases?

Cytosine, thymine, uracil.

Which pyrimidine occurs only in DNA?

Thymine

Which pyrimidine occurs only in RNA?

Uracil

Are pyrimidines charged at physiological pH?

No, they are neutral/hydrophobic

What are common modification positions on pyrimidines?

C2 and C4.

What are the two purines?

Adenine and guanine.

In which nucleic acids do purines appear?

Both DNA and RNA.

What positions on purines commonly undergo modification?

C2 and C6

What type of bond attaches base to sugar?

β-N-glycosidic bond.

At which atom is the sugar attached in pyrimidines?

β-N-glycosidic bond

At which atom is the sugar attached in pyrimidines?

N1.

At which atom is the sugar attached in purines?

N9

Which conformation is favored in B-DNA: syn or anti?

Anti.

Which conformation places the base directly above the sugar?

Syn.What type of tautomerism occurs in nucleobases?

What type of tautomerism occurs in nucleobases?

Keto–enol tautomerism

Why are tautomeric shifts biologically important?

They can alter hydrogen-bonding → mutations.

Which structural property enables UV absorbance?

Electronic transitions of aromatic rings.

What are the three naming levels you must know for each base?

Nucleobase, nucleoside, nucleotide.

How are deoxynucleotides abbreviated?

dA, dG, dC, dT (or four-letter forms like dAMP)

What three structural features must be known for each nucleotide?

Amino functionality, base structure, glycosidic linkage.

When are minor nucleosides modified?

After nucleotide synthesis (post-synthetic).

What are two common minor nucleosides in DNA?

5-methylcytosine, N⁶-methyladenosine.

What is the function of epigenetic markers in prokaryotes?

Distinguish own DNA from foreign DNA for degradation.

What is the function of epigenetic markers in eukaryotes?

Regulate gene expression.

What causes changes in DNA due to methylation?

Structural modification in the region containing the methylated base.

What is inosine made from?

Deamination of adenosine.

Where is inosine found?

Wobble position of tRNA anticodon.

What is pseudouridine formed from?

Enzymatic isomerization of uridine.

Where is pseudouridine found?

tRNA and rRNA.

What is the suspected function of pseudouridine?

Stabilizes RNA structure and folding.

What type of linkage connects nucleotides in a polymer?

Phosphodiester linkage.

Which sugar positions form a phosphodiester bond?

3′-OH of one sugar to 5′-OH of next sugar

Which direction does a nucleic acid polymer grow?

5′ → 3′

Why is DNA more stable than RNA?

RNA has a reactive 2′-OH that promotes hydrolysis.

What is RNase?

An enzyme (mostly RNA-based) that hydrolyzes RNA.

What does S-RNase do?

Prevents inbreeding in plants.

What does RNase P do?

Processes tRNA precursors; a ribozyme.

What do Dicers do?

Cleave dsRNA into oligonucleotides (antiviral defense).

What is the mechanism of base-catalyzed RNA hydrolysis?

2′-OH → alkoxide → nucleophilic attack on phosphate → cleavage.

Who discovered the structure of DNA?

Watson & Crick.

What did they identify as the stabilizing forces?

Hydrogen bonding and base stacking.

Who obtained crystallographic data supporting helical structure?

Rosalind Franklin and Maurice Wilkins.

What is Chargaff’s rule?

A = T, G = C. Equal purines and pyrimidines.

Does Chargaff’s rule apply to RNA?

No; RNA may be single-stranded.

How many H-bonds do A–T pairs form?

2

How many H-bonds do G–C pairs form?

3

What orientation do the two DNA strands run?

Antiparallel (5′→3′ and 3′→5′).

What is required for replication to begin?

Strand separation.

What enzyme synthesizes DNA?

DNA polymerase.

How does DNA polymerase grow DNA?

Adds nucleotides to 3′-OH (direction 5′→3′).

What sugar does RNA contain?

Ribose

What base replaces thymine in RNA?

Uracil

What unique base-pairing interaction can occur in RNA?

G–U wobble.

Why is RNA more dynamic?

Single-stranded → can fold into complex shapes.

What sequences form hairpins?

Palindromic mirror sequences.

What structure forms when two hairpins form on opposite strands?

Cruciform

Is tRNA single- or double-stranded?

Single-stranded but folds into a 3D structure.

What is mRNA's function?

Carries genetic code for proteins.

What type of mRNA do prokaryotes have?

Polycistronic (multiple genes per mRNA)

What type of mRNA do eukaryotes have?

Monocistronic (one gene per mRNA).

What bonds remain intact during DNA denaturation?

Covalent phosphodiester bonds.

What bonds break during denaturation?

Hydrogen bonds between bases.

When base stacking is lost, what happens to UV absorbance?

It increases (hyperchromic effect)

How can DNA denature?

Heat or pH changes.

What is annealing?

Re-forming a duplex from separated strands.

What is Tm?

Temperature at which 50% of DNA is denatured.

What base composition raises Tm?

Higher GC content

What condition increases Tm?

High salt concentration.

What types of DNA melt at lower temperatures?

AT-rich regions (replication bubbles).

What are the two spontaneous mutation processes?

Deamination and depurination.

What does deamination of cytosine produce?

Uracil

What bond breaks during depurination?

N-glycosidic bond of purines

How many purines are lost per day via depurination

~10,000 per cell per day.

What does nitrous acid promote?

Deamination.

What do alkylating agents do?

Add substituents to DNA bases.

What is an example of oxidative DNA damage?

Hydroxylation of guanine

Which organelle’s DNA is most susceptible to oxidative damage?

Mitochondrial DNA (mtDNA).

What damage does UV light cause?

Pyrimidine dimer formation.

Why are pyrimidine dimers harmful?

Create kinks that block replication/transcription.

What do X-rays and γ-rays cause?

Ring opening and strand breaks

What happens with accumulation of mutations?

Aging and carcinogenesis.

What does PCR do?

Amplifies specific DNA sequences

What enzyme is essential for PCR?

Thermostable DNA polymerase.

What are the three steps of PCR?

Denature (95°C), anneal (50–60°C), extend (5′→3′).

How many cycles are typically used?

20–30 cycles.

How much DNA amplification occurs after 30 cycles?

~10⁶-fold.

What analog does Sanger sequencing use?

ddNTPs (dideoxynucleotides).