Nucleic Acids Lecture Overview

These question-and-answer flashcards review nucleotide structure, roles, nomenclature, nucleic acid chemistry, DNA/RNA differences, double-helix features, and replication concepts presented in the lecture.

What are the five major roles of nucleotides in cell physiology?

1) Energy currency (ATP, GTP) 2) Precursors for DNA and RNA synthesis 3) Biosynthetic carriers (e.g., UDP-glucose, CDP-diacylglycerol) 4) Components of enzyme cofactors (NAD⁺/NADH, NADP⁺/NADPH, FMN/FMNH₂, CoA) 5) Second messengers (cAMP, cGMP).

Name the four nitrogenous bases found in DNA.

Adenine, Guanine, Cytosine, Thymine.

Which base in RNA replaces thymine?

Uracil.

Into what two chemical classes are nitrogenous bases divided, and which bases belong to each class?

Purines: adenine & guanine. Pyrimidines: cytosine, thymine, uracil.

What three components make up a nucleotide?

A nitrogenous base, a five-carbon sugar (pentose), and one or more phosphate groups.

How does ribose differ from deoxyribose?

Ribose has a 2′-OH group; deoxyribose has H at the 2′ position (no hydroxyl).

In nucleotide abbreviations, what does the prefix “d” indicate (e.g., dAMP)?

That the nucleotide contains deoxyribose rather than ribose.

What type of bond links a base to the sugar in a nucleoside?

An N-glycosidic bond between the base and the 1′ carbon of the sugar.

How is a nucleotide formed from a nucleoside?

Condensation of a phosphate group with the nucleoside’s 5′-OH, releasing water.

What linkage connects successive nucleotides in nucleic acids?

3′,5′-phosphodiester linkage.

What gives a nucleic acid strand its polarity?

All phosphodiester bonds point the same way, leaving a chemically distinct 5′ end and 3′ end.

Why are nucleic acid backbones hydrophilic?

Sugar hydroxyls H-bond with water and phosphate groups are fully ionized and negatively charged at pH 7.

Why does alkali rapidly hydrolyze RNA but not DNA?

RNA’s 2′-OH attacks the phosphodiester bond to form a cleavage-promoting 2′,3′-cyclic phosphate; DNA lacks the 2′-OH.

What initial products appear when RNA is treated with alkali?

2′,3′-cyclic monophosphate nucleotides.

At what wavelength do nucleic acids show maximal UV absorption?

Approximately 260 nm.

State Chargaff’s base-pairing rules for DNA.

[A] = [T] and [G] = [C]; total purines equal total pyrimidines.

Describe the orientation of the two strands in the DNA double helix.

They run antiparallel—one 5′ → 3′, the other 3′ → 5′.

Why must each rung of the DNA ladder contain one purine and one pyrimidine?

To maintain constant helix width; purine–pyrimidine pairs fit perfectly inside the helix.

How many hydrogen bonds stabilize A–T and G–C base pairs, respectively?

A–T: two H-bonds; G–C: three H-bonds.

List three hallmark features of the Watson–Crick DNA model.

1) Right-handed double helix. 2) Sugar-phosphate backbones on the exterior. 3) Complementary, antiparallel base-paired strands forming major and minor grooves.

Besides hydrogen bonding, what interaction stabilizes the DNA double helix?

Hydrophobic base-stacking interactions between adjacent bases.

Define a gene.

A DNA segment whose nucleotide sequence encodes a functional RNA or protein product.

Name the three main classes of RNA and their functions.

mRNA: carries protein-coding information; rRNA: structural/catalytic part of ribosomes; tRNA: adaptor translating mRNA codons into amino acids.

What is the role of cyclic nucleotides such as cAMP and cGMP?

They serve as intracellular second messengers in signal transduction.

Give two examples of nucleotide-derived cofactors.

NAD⁺/NADH and coenzyme A (others include NADP⁺/NADPH, FMN).

What produces major and minor grooves in DNA?

Offset pairing of antiparallel strands, creating unequal groove widths.

How does DNA become compacted inside chromosomes?

Supercoiling and wrapping around histone proteins allow ~3 billion base pairs to fit into the nucleus.

What replication insight did Watson and Crick draw from their model?

DNA could replicate by strand separation followed by templated synthesis of complementary strands.

Why is strand complementarity essential for DNA replication?

Each original strand guides incorporation of correct nucleotides into its new complementary strand by base-pairing rules.

Provide the abbreviations for ribo- and deoxy- forms of guanosine monophosphate.

GMP (ribonucleotide) and dGMP (deoxyribonucleotide).

In which ring form do nucleotide sugars exist?

β-Furanose (five-membered) form.

Differentiate between a nucleoside and a nucleotide.

Nucleoside: base + sugar. Nucleotide: nucleoside + phosphate(s).

Name the pentoses in nucleotides and the nucleic acids they occur in.

D-ribose in RNA; 2′-deoxy-D-ribose in DNA.

What is the charge state of phosphate groups at physiological pH?

Fully ionized, carrying negative charges.

Which bonds are broken during nonenzymatic hydrolysis of nucleic acids?

Phosphodiester bonds of the backbone.

Approximately how many base pairs are found in the DNA of a single human cell?

About 3 billion base pairs.

Chemically, what constitutes a phosphodiester linkage?

A phosphate group bridging the 3′-OH of one nucleotide and the 5′-OH of the next.

How are the bases oriented relative to the helical axis in B-DNA?

Stacked nearly perpendicular to the helix axis inside the double helix.

Why are nucleotides effective energy carriers?

They contain high-energy phosphoanhydride bonds whose hydrolysis releases substantial free energy (e.g., ATP → ADP + Pi).

What does AMP stand for?

Adenosine monophosphate (adenylate).