DNA Structure and Properties 2

What is DNA and how is it structurally organized?

DNA stands for deoxyribose nucleic acid and is a macromolecule of life; it is composed of many nucleotides arranged as two complementary polynucleotide chains in a double helix.

What are the three components of a DNA nucleotide?

A nitrogenous base, deoxyribose sugar (a 5-carbon sugar), and phosphoric acid (phosphate).

What are purines and pyrimidines?

Purines are two-ringed heterocyclic nitrogenous bases with a 9-atom ring and include A and G; pyrimidines are single-ringed nitrogenous bases with a 6-atom ring and include T and C.

How can you remember the structures of purines and pyrimidines?

Purines contain A and G and have the shorter name but longer structure; pyrimidines contain T and C and have the longer name but smaller structure.

How does the sugar differ between DNA and RNA?

DNA contains deoxyribose sugar with -O, while RNA contains ribose sugar with OH.

What is a nucleoside?

A nitrogenous base plus deoxyribose sugar. (NO PHOSPHATE)

What is a nucleotide?

A nitrogenous base plus deoxyribose sugar plus phosphoric acid.

What is an N-glycosidic bond?

A covalent bond linking a sugar to another molecule, specifically the nitrogenous base.

What is the anti configuration of a nitrogenous base?

The base points away from the sugar; it is favored by purines such as adenosine.

What is the syn configuration?

The base points toward the sugar; formation of Z-DNA for purines is associated with the syn configuration.

How do you determine the configuration for pyrimidines?

Look at the double-bonded oxygen; steric hindrance determines the steric configuration.

How do you determine the configuration for purines?

Look at the base.

What is a phosphodiester bond?

A bond involving the 5′ carbon and 3′ carbon, connecting the outer carbon to the 3′ hydroxyl; phosphate groups are on the outside.

What distinguishes deoxyribose in DNA?

It has no oxygen on the second carbon.

What is important about DNA's two polynucleotide chains?

They are antiparallel, meaning the 5′→3′ phosphodiester bonds run in opposite directions; one strand runs 5′→3′ and the other 3′→5′.

Where are the phosphates and bases located in the DNA double helix?

Phosphate molecules are on the outside, while bases point inward and are perpendicular to the helical axis.

How are DNA bases paired?

Bases are linked by hydrogen bonds between oxygen and nitrogen atoms, and purines pair with pyrimidines.

How many hydrogen bonds connect A and T?

A-T has 2 hydrogen bonds.

How many hydrogen bonds connect C and G?

C-G has 3 hydrogen bonds.

What is special about Watson and Crick base pairs?

They are pseudo symmetrical, meaning the base pairs have the same width; their rotational pseudo symmetry determines whether helices formed by them have grooves with identical or different shapes.

Why is complementary base pairing important for DNA replication?

Complementary base pairs provide a copying mechanism because the same pairs can be reproduced.

What is the overall physical structure of DNA?

Two complementary chains with opposite polarity twist around a central axis to form a double helix.

What are the main physical characteristics of B-DNA?

B-DNA is a right-handed helix, turns counterclockwise according to the notes, has about 10 bases per turn, a 3.4 nm turn, and a diameter of 2 nm.

How are the bases oriented in DNA?

Bases project perpendicular to the phosphate-sugar backbone.

Are DNA bases all in the same plane?

No. Hydrophobic interactions and a slight twist at the base pairs shift the backbone structure and contribute to the twist of DNA.

What would happen if deoxyribose sugars were attached 180 degrees straight to each other?

The grooves would have similar sizes because the R groups on the sugars would be on the same plane; one hydrogen would be long and the other extra short.

What are the major and minor grooves of DNA?

DNA contains major grooves and minor grooves; the major groove involves two turns, while the minor groove involves the backbone.

What are the main characteristics of B-DNA?

B-DNA is the hydrated, most common form; it consists of double-stranded polynucleotide chains in a right-handed helix; chains are antiparallel and complementary; base interactions are highly specific (C-G and A-T); bases are stacked and point inward; bases are typically in the anti configuration; and there are specific size constraints on molecules.

What are the main characteristics of A-DNA?

A-DNA is the dehydrated form; it is double-stranded, right-handed, antiparallel, and complementary with specific C-G and A-T interactions; bases are tilted but still point inward because no water is present; bases are typically in the anti configuration; and A-DNA is wider and shorter than B-DNA.

What are the main characteristics of Z-DNA?

Z-DNA is a left-handed helical structure with a zig-zag pattern, often associated with repeating purine-pyrimidine sequences such as CGCGCGCGCG; bases occur in both syn and anti configurations and alternate in conformation while still pointing inward; the molecule is more compact and has highly specific binding sites for transcription factors.

How do the DNA forms compare in handedness?

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

How do base conformations differ among DNA forms?

B-DNA and A-DNA typically have bases in the anti configuration; Z-DNA has both syn and anti configurations with alternating conformations.

What kind of sequence is often associated with Z-DNA?

Repeating purine-pyrimidine sequences, such as CGCGCGCGCG.

What is the functional significance of Z-DNA?

It has highly specific binding sites for transcription factors.

Can a chromosome contain different forms of DNA?

Yes. A chromosome typically mixes all forms of DNA.

Can DNA switch between different forms?

Yes. DNA forms can switch easily based on functionality.