Chapter 2 Nucleic Acids

What are nucleic acids?

DNA and RNA; polymers that store, transmit, express, and help regulate genetic information.

What is the monomer of DNA and RNA?

A nucleotide.

What three components form a nucleotide?

A nitrogenous base, a pentose sugar, and one or more phosphate groups.

What is a nucleoside?

A nitrogenous base attached to a sugar without phosphate.

Nucleoside versus nucleotide

Nucleoside = base + sugar. Nucleotide = base + sugar + phosphate.

Which bases are purines?

Adenine and guanine; both contain two rings.

Which bases are pyrimidines?

Cytosine, thymine, and uracil; each contains one ring.

Which bases occur in DNA?

Adenine, guanine, cytosine, and thymine.

Which bases occur in RNA?

Adenine, guanine, cytosine, and uracil.

Why do nitrogenous bases absorb ultraviolet light?

They are aromatic, resonance-stabilized ring systems that absorb UV radiation.

What is tautomerism?

Rearrangement of protons and double bonds that produces alternative forms such as keto-enol or amino-imino.

Which base tautomers normally predominate?

Keto and amino forms generally predominate; enol and imino forms are rare.

Why can rare base tautomers cause mutations?

They alter hydrogen-bonding patterns and can cause incorrect base pairing during replication.

What sugar occurs in DNA?

2′-deoxyribose, which contains H at its 2′ carbon.

What sugar occurs in RNA?

Ribose, which contains OH at its 2′ carbon.

What is the key chemical difference between DNA and RNA sugars?

RNA has a 2′-OH, whereas DNA has a 2′-H.

Why are sugar carbons labeled with primes?

To distinguish sugar-carbon positions from positions within the nitrogenous base.

Where does a nitrogenous base attach to its sugar?

At the sugar’s 1′ carbon.

What bond joins a nitrogenous base to its sugar?

A glycosidic bond.

What is a phosphoester bond?

A bond connecting a phosphate to a sugar, commonly at the sugar’s 5′ carbon.

What is a phosphodiester bond?

A bond connecting the 3′-OH of one nucleotide to the 5′ phosphate of another.

What are phosphoanhydride bonds?

High-energy bonds connecting adjacent phosphates in nucleotide diphosphates and triphosphates.

What is the sugar-phosphate backbone?

The repeating covalent chain of sugars and phosphates in a nucleic-acid strand.

Why are DNA and RNA negatively charged?

Their phosphate groups carry negative charges near physiological pH.

Why do nucleotide triphosphates frequently bind Mg2+?

Mg2+ interacts with their negatively charged phosphate groups and helps reduce charge repulsion.

Can nucleotides other than ATP help drive reactions?

Yes. Hydrolysis of GTP, CTP, UTP, and deoxynucleotide triphosphates can drive specific reactions.

What is cAMP?

Cyclic adenosine monophosphate, an intracellular signaling molecule containing a cyclic 3′,5′-phosphodiester linkage.

What does 5′→3′ describe?

The chemical direction of a nucleic-acid strand from its 5′ end toward its 3′ end.

In which direction are new DNA and RNA synthesized?

Always 5′→3′ through addition to the growing strand’s 3′-OH.

What does antiparallel mean?

The two DNA strands run in opposite directions: one 5′→3′ and the other 3′→5′.

What are the complementary DNA base pairs?

A pairs with T, and G pairs with C.

What base replaces thymine in RNA?

Uracil.

How many hydrogen bonds occur in A-T and G-C pairs?

A-T forms two hydrogen bonds; G-C forms three.

What complements 5′-ATGCC-3′?

3′-TACGG-5′. Written 5′→3′, the reverse complement is 5′-GGCAT-3′.

What provides complementary base-pair specificity?

Hydrogen bonding and steric complementarity between the bases.

What is a major driving force for nucleic-acid folding?

The hydrophobic effect, which promotes burial and stacking of relatively hydrophobic bases.

What interactions contribute to base stacking?

Hydrophobic, London-dispersion, van der Waals, dipole-dipole, and π-π interactions.

What works against nucleic-acid folding?

Electrostatic repulsion between negatively charged phosphate groups.

How do cations stabilize nucleic acids?

Positive ions shield electrostatic repulsion between negatively charged phosphates.

Section 2.1 worked problem: What forces fold and stabilize tRNA?

The hydrophobic effect is a major folding drive. Hydrogen bonding, base stacking, dipole-dipole, and London-dispersion interactions stabilize it; cations shield phosphate repulsion.

What is DNA denaturation or melting?

Loss of the double helix and separation of DNA into single strands.

What is annealing?

Reassociation of complementary single strands under favorable conditions.

What is DNA melting temperature, Tm?

The temperature at which 50% of the DNA duplex population is melted.

How does increased GC content generally affect Tm?

It raises Tm because GC-rich duplexes are generally more stable.

How do salt and Mg2+ generally affect Tm?

They increase Tm by shielding repulsion between negative phosphate backbones.

How do chaotropes such as urea affect DNA?

They disrupt stabilizing noncovalent interactions, promote denaturation, and lower Tm.

What is the nearest-neighbor model?

A model recognizing that duplex stability depends on the identities and order of adjacent base pairs, not only overall GC content.

What is the common cellular form of DNA?

B-DNA, a right-handed double helix.

What are the handednesses of A-, B-, and Z-DNA?

A-DNA and B-DNA are right-handed; Z-DNA is left-handed.

What are DNA’s major and minor grooves?

Chemically distinct surfaces in the helix where proteins can recognize and bind DNA.

How does RNA usually differ structurally from DNA?

RNA is generally single-stranded but can fold into stems, loops, hairpins, pseudoknots, and complex three-dimensional structures.

Why is RNA less stable than DNA under basic conditions?

RNA’s 2′-OH can be deprotonated and attack a nearby phosphate, cleaving the phosphodiester backbone.

Why is DNA more resistant to base-catalyzed hydrolysis?

DNA has 2′-H instead of the reactive 2′-OH found in RNA.

What does an intercalating dye do?

It inserts between stacked DNA base pairs and fluoresces more strongly when bound.

How does ethidium bromide help visualize DNA?

It intercalates into DNA and produces enhanced fluorescence, allowing DNA bands to be observed after electrophoresis.

What is the central dogma?

The major flow of genetic information: DNA→RNA→protein.

What is replication?

Copying DNA to produce DNA.

What is transcription?

Using DNA as a template to synthesize RNA.

What is translation?

Using the codon sequence of mRNA to produce a polypeptide.

What is reverse transcription?

Synthesis of DNA from an RNA template.

What enzyme performs reverse transcription?

Reverse transcriptase.

What is semiconservative replication?

Each daughter DNA molecule contains one parental strand and one newly synthesized strand.

Why can each DNA strand serve as a replication template?

Complementary base pairing determines which nucleotide belongs opposite each template base.

What is an origin of replication?

A DNA sequence where replication begins.

What is a replication bubble?

An opened region of DNA containing two replication forks.

What is a replication fork?

The junction where double-stranded DNA separates into single-stranded templates.

What does helicase do?

Unwinds and separates the parental DNA strands.

What does topoisomerase do?

Relieves twisting and supercoiling ahead of the replication fork.

What do single-strand binding proteins do?

Keep separated DNA strands from reannealing.

What does primase do?

Synthesizes the RNA primers required for DNA replication.

Why does DNA polymerase require a primer?

DNA polymerase cannot begin a strand from nothing; the primer supplies the required 3′-OH.

What does DNA polymerase do?

Adds complementary nucleotides to a primer and synthesizes DNA 5′→3′.

What is the leading strand?

The new strand synthesized continuously toward the moving replication fork.

What is the lagging strand?

The new strand synthesized discontinuously as Okazaki fragments.

Are any DNA strands synthesized 3′→5′?

No. Both leading and lagging strands are synthesized 5′→3′.

Why is the lagging strand synthesized in fragments?

Its template orientation opposes fork movement, but DNA polymerase can only synthesize 5′→3′.

What are Okazaki fragments?

Short DNA fragments synthesized on the lagging strand.

What does DNA ligase do during replication?

Seals phosphodiester-backbone breaks and joins Okazaki fragments.

What is a gene?

A DNA region whose information produces a functional RNA or protein.

What is a promoter?

A regulatory DNA sequence where transcription machinery assembles.

What is a transcription factor?

A protein that binds regulatory DNA and increases or decreases transcription.

Primer versus promoter

A primer supplies a 3′-OH for DNA synthesis; a promoter is a regulatory DNA sequence involved in transcription.

What enzyme synthesizes RNA during transcription?

RNA polymerase.

Which DNA strand does RNA polymerase read?

The template strand in the 3′→5′ direction.

In which direction does RNA polymerase synthesize RNA?

5′→3′.

What is the template DNA strand?

The strand read by RNA polymerase and complementary to the resulting RNA.

What is the coding DNA strand?

The strand matching the RNA sequence except that DNA contains T where RNA contains U.

If coding DNA is 5′-ATGCCA-3′, what is the RNA?

5′-AUGCCA-3′.

What three major processing events produce mature eukaryotic mRNA?

Addition of a 5′ cap, removal of introns by splicing, and addition of a 3′ poly-A tail.

What are introns?

Sequences removed from the initial RNA transcript.

What are exons?

Sequences retained and joined together in mature RNA.

What is alternative splicing?

Joining different combinations of exons so one gene can produce multiple related products.

What are major functions of the 5′ cap and poly-A tail?

They protect and stabilize mRNA and assist its handling and translation.

What is mRNA?

Messenger RNA containing codons that specify a protein sequence.

What is a codon?

A three-nucleotide sequence on mRNA specifying an amino acid or stop signal.

What is an anticodon?

A three-nucleotide sequence on tRNA complementary and antiparallel to an mRNA codon.

What is tRNA?

An adapter RNA that carries an amino acid and contains an anticodon.

What is rRNA?

Ribosomal RNA, which has structural and catalytic roles in the ribosome.

What catalyzes peptide-bond formation?

Ribosomal RNA within the ribosome.

What does AUG do?

It usually serves as the start codon, establishes the reading frame, and codes for methionine.