Chapter 2 Nucleic Acids. Biochem

What are the three components of a nucleotide?

A nitrogenous base, a 5-carbon sugar, and one or more phosphate groups.

What is a nucleoside?

A nitrogenous base attached to a sugar with no phosphate group.

What is a nucleotide?

A nitrogenous base attached to a sugar plus one or more phosphate groups.

What is the difference between a nucleoside and a nucleotide?

A nucleotide contains phosphate; a nucleoside does not.

What sugar is found in RNA?

Ribose.

What sugar is found in DNA?

2-deoxyribose.

What is the key structural difference between ribose and deoxyribose?

Ribose has an OH at the 2′ carbon; deoxyribose has H at the 2′ carbon.

Why are the sugar carbons numbered with primes such as 1′ and 3′?

The primes distinguish sugar-carbon numbering from atom numbering in the nitrogenous base.

What attaches to the 1′ carbon of a nucleotide sugar?

The nitrogenous base.

What is important about the 2′ carbon?

It distinguishes RNA from DNA: RNA has 2′-OH and DNA has 2′-H.

What is important about the 3′ carbon?

It has an OH involved in forming phosphodiester bonds and extending a nucleic-acid strand.

What is associated with the 5′ carbon?

The phosphate group.

What bond connects a nitrogenous base to its sugar?

A β-N-glycosidic bond.

What are the five major nitrogenous bases?

Adenine, guanine, cytosine, thymine, and uracil.

Which bases are found in DNA?

Adenine, guanine, cytosine, and thymine.

Which bases are found in RNA?

Adenine, guanine, cytosine, and uracil.

Which bases are purines?

Adenine and guanine.

Which bases are pyrimidines?

Cytosine, thymine, and uracil.

How many rings do purines have?

Two fused rings.

How many rings do pyrimidines have?

One ring.

What is a memory trick for the purines?

PURe As Gold: purines are Adenine and Guanine.

How can adenine be recognized structurally?

Two rings, an amino group, and no carbonyl groups.

How can guanine be recognized structurally?

Two rings, an amino group, and one carbonyl group.

How can cytosine be recognized structurally?

One ring, an amino group, and one carbonyl group.

How can uracil be recognized structurally?

One ring, two carbonyl groups, and no methyl group.

How can thymine be recognized structurally?

One ring, two carbonyl groups, and a methyl group.

What is the structural relationship between thymine and uracil?

Thymine is essentially uracil with a methyl group at carbon 5; thymine is 5-methyluracil.

If a base has two rings, what should you check next to identify it?

Check for a carbonyl: no carbonyl indicates adenine; one carbonyl indicates guanine.

If a base has one ring and an amino group, which major base is it?

Cytosine.

If a base has one ring and two carbonyls, how do you distinguish thymine from uracil?

Thymine has a methyl group; uracil does not.

What nitrogen of a purine attaches to the sugar?

N9.

What nitrogen of a pyrimidine attaches to the sugar?

N1.

What carbon of the sugar attaches to the nitrogenous base?

The 1′ carbon.

What bond connects neighboring nucleotides within a DNA or RNA strand?

A phosphodiester bond.

What does a 3′–5′ phosphodiester linkage connect?

The 3′ oxygen of one sugar through phosphate to the 5′ position of the neighboring sugar.

What forms the backbone of DNA and RNA?

Alternating sugar and phosphate groups.

Where are the nitrogenous bases located relative to the sugar-phosphate backbone?

They project from the sugars; in double-stranded DNA they are oriented toward the interior of the helix.

Why is the nucleic-acid backbone negatively charged?

The phosphate groups carry negative charges at physiological pH.

What does the 5′ end of a nucleic-acid strand refer to?

The end defined by the terminal sugar's 5′ position, commonly bearing a phosphate.

What does the 3′ end of a nucleic-acid strand contain?

A free 3′-OH on the terminal sugar.

In what direction are nucleic-acid sequences conventionally written?

5′ to 3′.

At which end is a growing DNA or RNA strand extended?

The 3′ end.

Why does nucleic-acid synthesis proceed 5′ to 3′?

New nucleotides are added to the free 3′-OH of the growing strand.

What does complementary base pairing mean?

Specific nitrogenous bases pair through compatible hydrogen-bonding patterns.

What are the complementary DNA base pairs?

A pairs with T, and G pairs with C.

What are the common complementary RNA base pairs?

A pairs with U, and G pairs with C.

How many hydrogen bonds form in an A-T base pair?

Two.

How many hydrogen bonds form in a G-C base pair?

Three.

Why does a purine normally pair with a pyrimidine in double-stranded DNA?

Pairing one two-ring base with one one-ring base helps maintain a relatively uniform helix width.

What does it mean that DNA strands are complementary?

The sequence of one strand determines the sequence of the other through A-T and G-C pairing.

What does antiparallel mean in DNA?

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

If one DNA strand is 5′-AGCT-3′, what is the complementary strand aligned beneath it?

3′-TCGA-5′.

If one DNA strand is 5′-AGCT-3′, what is its complementary strand written 5′→3′?

5′-AGCT-3′. This sequence happens to be its own reverse complement.

How do you find a complementary DNA strand when the answer must be written 5′→3′?

Find the complementary bases, account for antiparallel orientation, then reverse the complement so it is written 5′→3′.

What bonds hold adjacent nucleotides together along one DNA strand?

Covalent phosphodiester bonds.

What interactions occur between complementary bases across DNA strands?

Hydrogen bonds, while base-stacking interactions also strongly stabilize the helix.

Do phosphodiester bonds connect the two complementary DNA strands to each other?

No. They connect neighboring nucleotides along each individual strand.

What is the typical overall structure of DNA?

Two complementary antiparallel strands arranged in a double helix.

What is the typical overall structure of RNA?

RNA is usually single-stranded but can fold into complex structures through internal base pairing.

Can single-stranded RNA form hydrogen-bonded structures?

Yes. Complementary regions within the same RNA molecule can base-pair and form structures such as stems and hairpins.

What are the major structural differences between DNA and RNA?

DNA contains deoxyribose and thymine and is usually double-stranded; RNA contains ribose and uracil and is usually single-stranded.

Why is RNA generally more chemically susceptible to backbone hydrolysis than DNA?

RNA has a 2′-OH that can participate in cleavage of its phosphodiester backbone.

How can RNA's 2′-OH promote backbone cleavage under basic conditions?

The 2′-OH can be deprotonated, creating a nucleophilic oxygen that attacks a neighboring phosphate and promotes phosphodiester-bond cleavage.

Why is DNA more resistant than RNA to 2′-OH-mediated backbone cleavage?

DNA has a 2′-H instead of a 2′-OH, so it lacks this reaction pathway.

Why is DNA well suited for long-term genetic information storage?

Its deoxyribose backbone is relatively chemically stable, and its double-stranded structure supports accurate information maintenance.

How does the 2′-OH make RNA more chemically versatile?

It provides additional hydrogen-bonding and chemical possibilities that contribute to folding and reactivity.

What is a ribozyme?

An RNA molecule capable of catalyzing a chemical reaction.

Why can RNA form complex three-dimensional structures despite usually being single-stranded?

Internal complementary base pairing and other interactions allow the strand to fold into stems, loops, and complex tertiary structures.

Why does DNA use thymine instead of uracil?

Cytosine can spontaneously deaminate into uracil, so using thymine normally allows uracil in DNA to be recognized as abnormal and repaired.

What chemical reaction can convert cytosine into uracil?

Deamination.

Why would using uracil normally in DNA make cytosine deamination harder to detect?

The cell could not as easily distinguish a normal uracil from one produced by damaged cytosine.

Which nucleic acid is generally more stable chemically, DNA or RNA?

DNA.

Which nucleic acid is generally more chemically and structurally versatile, DNA or RNA?

RNA.

What structural feature should you draw first when constructing a nucleotide from memory?

The 5-carbon sugar, then number its carbons 1′ through 5′.

When drawing a nucleotide from memory, where should the base and phosphate be placed?

Attach the base to the 1′ carbon and the phosphate to the 5′ position.

When drawing an RNA nucleotide, what must be present at the 2′ carbon?

An OH group.

When drawing a DNA nucleotide, what must be present at the 2′ carbon?

A hydrogen instead of an OH.

What group must remain available at the 3′ carbon for strand extension?

A 3′-OH.

What four structural checkpoints should you use when drawing a nucleotide from memory?

1′ = base; 2′ = OH for RNA or H for DNA; 3′ = OH; 5′ = phosphate.