Chapter 4 Extra Credit Guided Reading

What is the difference between the sugars present in RNA and DNA?

DNA contains deoxyribose, RNA contains ribose

 How are the monomer units of nucleic acids connected? 

By phosphodiester bonds between the 3' and 5' carbons.

Draw the general structures of a purine and a pyrimidine base.

Purines have a double ring structure, pyrimidines have a single ring.

Which bases are classified as purines? Pyrimidines? 

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

In which type of nucleic acid would you expect to find each of the different heterocyclic bases?

DNA contains adenine, guanine, cytosine, and thymine. RNA contains adenine, guanine, cytosine, and uracil.

How are the purine and pyrimidines attached to the sugar? What is this bond called?

They are attached by a glycosidic bond between the N1 of pyrimidines or the N9 of purines and the 1' carbon on the sugar.

What is the difference between a nucleoside and a nucleotide?

A nucleoside is the base plus sugar. A nucleotide is the base, sugar, and phosphate group.

Why are nucleic acids referred to as polynucleotides?

They contain many nucleotide monomers linked together in a chain.

What is an oligonucleotide?

A short polymer made up of a few nucleotides, usually less than 25.

What does the presence of the hydroxyl group on the 2' carbon allow for in RNA, but not DNA?

It allows the 2' carbon to act as a nucleophile and cleave the phosphodiester backbone.

 What are tautomers?

Tautomers are structural isomers that can rapidly interconvert. 

What property allows nucleic acids to absorb light?

The aromatic heterocyclic bases can absorb UV light.

What important measurement can we make using the absorption of a nucleic acid sample at 260 nm?

We can determine the concentration using the Beer-Lambert law.

What equation is used to calculate the concentration of a sample using its absorbance? 

A = ɛcl, where A is absorbance, ɛ is the extinction coefficient, c is concentration, and l is path length.

If the hydrolysis of the phosphodiester bond is favored, what keeps the monomers of nucleic acids held together?

The high negative charge density of the phosphate backbone disfavors hydrolysis.

What are the products of an acid catalyzed hydrolysis of a nucleic acid sample? 

Nucleosides and inorganic phosphate. 

Why is it beneficial that RNA can undergo hydrolysis under basic conditions while DNA cannot?

This allows RNA enzymes to catalyze phosphoryl transfer reactions.

What are nucleases?

Enzymes that catalyze the cleavage of phosphodiester bonds in nucleic acids.

How are polynucleotides synthesized? (In other words, how are the nucleotides added to a growing polynucleotide chain?)

By formation of a phosphodiester bond between the 3' OH of one nucleotide and the 5' phosphate of the next.

Why is ATP referred to as the energy currency of the cell?

The terminal phosphoanhydride bond has high phosphoryl group transfer potential.

What is the primary structure of nucleic acids?

The sequence of nucleobases along the backbone.

What is the directionality of a nucleic acid chain?

It has a 5' to 3' directionality.

In what direction is the sequence of a polynucleotide chain written?  

5' to 3'.

What is the main importance of the primary structure? 

It encodes genetic information.

What is the secondary structure of a polynucleotide? 

The base pairing interactions, like dsDNA or RNA stem-loops.

What does the tertiary structure of a polynucleotide refer to?

The 3D shape due to interactions between secondary structure elements. 

The 3D shape due to interactions between secondary structure elements. 

%A = %T and %G = %C (i.e. complementary bases present in equal amounts).

What is the repeat, pitch, and rise of a DNA molecule?

Repeat is 10-10.5 base pairs. Pitch is 34 Å. Rise is 3.4 Å per base pair.

What feature makes the double helix uniform in diameter?  

The base pairs stack perpendicular to the helical axis.

Where are the bases located in relation to the sugar-phosphate backbone?

In the interior of the double helix.

Describe the major and minor grooves of DNA. 

The major groove is wider and deeper. The minor groove is more narrow. 

What is self-replication? What characteristic of DNA allows for this?

A molecule can serve as a template for its own replication. The complementary base pairing of DNA enables this.

What are three possible modes of replication? Which one occurs in DNA?

Conservative, semi-conservative, and dispersive. DNA replicates semi-conservatively.

What are the 2 forms of the double helix? Which form does most DNA adopt?

A-DNA and B-DNA. Most DNA adopts the B form.

What structures can adopt the A form of the double helix?

RNA-DNA hybrids or DNA with high salt concentrations. 

What are the structural differences between the 2 forms of the double helix?

A-DNA is wider with a shallow minor groove. B-DNA is more slender with a deep minor groove.

Why can the reported structural parameters (rise, tilt, etc.) be thought of as average values?

The helix is dynamic and undergoes structural fluctuations.

Why is the B form of the double helix favored in an aqueous environment?

The wider grooves can interact better with water compared to the narrow A-DNA groove.

Why can RNA not adopt the B form?

The 2' hydroxyl sterically clashes with the shallow minor groove of the B form.

What is supercooling and why is it important?

Supercooling is cooling DNA below its Tm without denaturation occurring. It allows examination of DNA topology. 

Define the terms: Twist (T), Linking Number (L), and writhe

Twist is the number of helical turns. Linking number is twist + writhe and is conserved. Writhe describes supercoiling.

What does it mean for supercooled DNA to be underwound? Overwound?

Underwound means it has a lower twist than relaxed DNA. Overwound means it has more twist. 

What is the super helix density?

A measure of supercoils per helical turn in supercoiled DNA.

What are topoisomers? 

Structural isomers that differ in topology but not sequence. 

What is the secondary structure of most RNA molecules?

Stem-loop structures formed by internal base pairing.

What are three structures that can be formed by single-stranded molecules?

Hairpins, pseudoknots, and triple helices.

What is an example of tertiary structure in tRNA molecules? 

The L-shaped fold created by non-adjacent stem-loop interactions.

How does the 'handedness' of Z-DNA differ from the A and B forms of DNA?

Z-DNA is left-handed, while A and B are right-handed helices.

How are the nucleobases oriented in respect to the sugar in Z-DNA? How does this differ from the A and B forms of DNA?

They are oriented syn compared to anti for A and B-DNA. 

What type of sequence would you expect to favor the Z-DNA conformation?

Sequences with alternating purine-pyrimidines.

How is a cruciform structure formed? 

By inverted repeats allowing intrastrand base pairing.

What type of base pairing can be found in triple helices?

Hoogsteen base pairing between a third strand and a Watson-Crick base paired duplex. 

Where do G-Quadruplex structures exist in vivo?

In telomeric DNA and promoter regions of some genes.

Why must the DNA double helix not be too stable? 

It needs to transiently unravel for important processes like replication and transcription.

What does it mean for a strand of DNA to become denatured? 

The hydrogen bonds between strands are broken and the two strands separate.

How does an increase in temperature allow the transition from helix to a random coil to become favorable?

Increased kinetic energy helps overcome the stabilizing interactions holding the helix together.

Why is the absorbance of denatured DNA greater than helical DNA?

The bases are no longer stacked so they can absorb UV light.

Why is the denaturation of DNA sometimes referred to as melting?

The cooperative strand separation is analogous to the distinct melting of solids.

In terms of nucleic acids, what does is a cooperative transition? 

The strands separate over a narrow temperature range, like a phase transition.

What does the Tm of DNA depend upon?

Tm depends on length, GC content, strand concentration, and solution conditions.

What stabilizes the double helix more: base stacking or hydrogen bonding?

Stacking interactions contribute more stabilization energy than hydrogen bonding.

What characteristic of the helix to random coil transition allows for renaturation to be possible?

It is reversible if cooled, allowing the strands to reassociate.

What is a genome? 

The complete genetic information of an organism.

What is a gene?

A sequence that encodes a functional product like a protein.

What is DNA replication?

Synthesis of two DNA double helices from one original helix.

What happens when a error is made in replication?

A mutation occurs which can affect the encoded genes.

What enzyme adds the dNTPs to the growing DNA strand during replication? 

DNA polymerase.

What is transcription?

Synthesis of an RNA molecule from a DNA template.

What enzyme adds the NTPs to the growing RNA strand during transcription?

RNA polymerase.

How many of the DNA strands in the helix are actually transcribed?

Only the antisense strand acts as the template.

What is translation? 

Synthesis of a protein from the genetic information in mRNA.

What is a codon?

A sequence of three RNA bases that specifies an amino acid. 

What is often referred to as the central dogma of molecular biology?

That genetic information flows from DNA to RNA to protein.