Nucleic Acids – Lecture Review

These flashcards cover nucleotide roles, components, naming, chemical reactions, backbone structure, RNA hydrolysis, UV absorption, Chargaff’s rules, DNA double-helix features, base pairing, and replication concepts from the lecture.

What are the five major physiological roles of nucleotides in cells?

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

Name the four heterocyclic amine bases found in DNA.

Adenine, guanine, thymine, cytosine.

Which base in RNA replaces thymine found in DNA?

Uracil replaces thymine in RNA.

Which two nitrogenous bases are classified as purines?

Adenine (A) and guanine (G).

Which three structural components make up every nucleotide?

A nitrogenous base, a five-carbon sugar, and a phosphate group.

What is the sugar component of RNA nucleotides?

D-ribose.

What is the sugar component of DNA nucleotides?

2′-deoxy-D-ribose.

Between which two carbon positions is the phosphodiester linkage formed in nucleic acids?

Between the 5′-phosphate of one nucleotide and the 3′-hydroxyl of the next.

What signal in a nucleotide abbreviation indicates that the sugar is deoxyribose?

A lowercase “d” placed at the beginning (e.g., dATP).

Give the full name of dAMP.

Deoxyadenosine 5′-monophosphate.

What is the basic difference between a nucleoside and a nucleotide?

A nucleoside lacks phosphate; a nucleotide has one or more phosphate groups attached.

What type of reaction forms a nucleoside from a base and sugar?

A condensation reaction forming an N-glycosidic bond and releasing water.

What additional reaction converts a nucleoside into a nucleotide?

Condensation of phosphate with the 5′-hydroxyl of the nucleoside, releasing water.

Why is RNA rapidly hydrolyzed under alkaline conditions whereas DNA is not?

RNA’s 2′-hydroxyl can attack the adjacent phosphodiester bond, forming a 2′,3′-cyclic intermediate that is subsequently cleaved; DNA lacks the 2′-OH.

What are the first products formed during alkali-catalyzed cleavage of RNA?

2′,3′-cyclic nucleoside monophosphates.

At what wavelength do nucleotide bases show a strong UV absorption used for quantifying nucleic acids?

Approximately 260 nm.

State Chargaff’s base-pairing rules for double-stranded DNA.

[A] = [T] and [G] = [C]; thus, purine content equals pyrimidine content.

In the DNA double helix, how are the two strands oriented relative to each other?

They are antiparallel; one runs 5′→3′ while the other runs 3′→5′.

Which base pairs form two hydrogen bonds and which form three?

Adenine–thymine (A–T) form two; guanine–cytosine (G–C) form three.

What are complementary base pairs?

Pairs of bases that hydrogen-bond in DNA: A with T, and G with C.

Name the two grooves created by the offset pairing in B-form DNA.

The major groove and the minor groove.

List three key structural features of the Watson–Crick DNA model.

1) Right-handed double helix of antiparallel strands; 2) Sugar-phosphate backbones on the outside, bases stacked inside; 3) Base pairing (A–T, G–C) plus base-stacking stabilize the helix.

What property of DNA suggested a mechanism for its replication to Watson and Crick?

Complementarity of the two strands—each can serve as a template for synthesis of its partner.

Define a gene in molecular terms.

A DNA segment that specifies the synthesis of a functional protein or RNA product.

Give one function for each major class of cellular RNA (rRNA, mRNA, tRNA).

rRNA: structural and catalytic part of ribosomes; mRNA: carries coding information for proteins; tRNA: adaptor that brings amino acids during translation.

Why is the nucleic-acid backbone hydrophilic?

Sugar hydroxyls form hydrogen bonds with water, and phosphate groups are fully ionized and negatively charged at physiological pH.

What designates the polarity of a nucleic acid strand?

The orientation of sugar-phosphate linkages, giving distinct 5′ and 3′ ends.

Which end of a nucleic acid strand lacks a nucleotide at the 5′ position?

The free 5′ end.

What term describes additional twisting of helical DNA to compact it within chromosomes?

Supercoiling.

Around what proteins is eukaryotic DNA supercoiled to form nucleosomes?

Histones.

Approximately how many base pairs are in the human genome, and what is the extended length of this DNA per cell?

~3 billion base pairs; about 6 feet (≈2 meters) if stretched out.

What is a phosphodiester bond?

The covalent linkage between the 3′-OH of one nucleotide’s sugar and the 5′-phosphate of the next nucleotide.

Which abbreviation corresponds to cytidine 5′-monophosphate?

CMP.

What nomenclature suffix is used for nucleoside names?

-osine for purines (adenosine, guanosine) and ‑idine for pyrimidines (cytidine, uridine, thymidine).

During base stacking, why do hydrophobic interactions stabilize the DNA helix?

Stacking removes the planar bases from water, minimizing unfavorable interactions with the aqueous environment.

Distinguish between ribonucleotides and deoxyribonucleotides in terms of sugar hydroxyls.

Ribonucleotides have a 2′-OH; deoxyribonucleotides have H at the 2′ position (no 2′-OH).

What is meant by the ‘major function’ of DNA as stated in the notes?

Storage and transmission of biological information.