Chapter 33

Question 1

DNA – Deoxyribonucleic Acid

Answer 1

DNA = the molecule for genetic material in our cells. The DNA in cells is the genetic information that is passed from one generation to another

Deoxyribose = ribose where 2’-hydroxyl is replaced w/ a hydrogen

DNA is composed of 4 nucleotides:
- Adenine and guanine (purines)
- Cytosine and thymine (pyrimidines)

• Bases are attached to carbon atom 1’ in the sugar

DNA forms a double helix of two separate strands w/ complementary sequences

Semiconservative replication = two strands unwind, each serves as a template for the new daughter double helix

• During replication: proof-reading and repair mechanisms

For DNA and RNA, the backbone consists of sugars linked by phosphodiester bridges between 3’-hydroxyl of one sugar and 5’-hydroxyl of an adjacent sugar

• The phosphodiester linkage in the backbone and the associated carbons give the directionality of the DNA strand

Question 2

RNA – Ribonucleic Acid

Answer 2

Ribonucleic acid (RNA) also contains the sugar ribose

RNA = single stranded

RNA is composed of 4 nucleotides:
- Adenine and guanine (purines)
- Cytosine and uracil (pyrimidines)

• Bases are attached to carbon atom 1’ in the sugar

Question 3

DNA – Double Helical Structure

Answer 3

Nucleic acid strands can form a double helical structure

• DNA double helical structure is based on complementary base pairing of nucleotide’s guanine binding w/ cytosine and adenine binding w/ thymine
• Bonding takes place w/ 2 H-bonds between A & T and 3 H-bonds between G & T

General features of DNA:

1. DNA molecules consist of two chain of opposite directionality ~ one strand runs in the 5’ to 3’ direction, and the other in the 3’ to 5’ direction ~ intertwined to form a right-handed double helix
2. Sugar-phosphate backbone are on outside of the helix, whereases bases are on inside (right-handed double helix)
3. Bases are nearly perpendicular to axis of helix w/ adjacent bases separated by 3.4 A
4. Helix is approx. 20 A wide

Question 4

DNA – Bonds & Forces

Answer 4

H-bonds between base pairs
- Adenine – thymine
- Guanine – cytosine

Stacking forces
- Hydrophobic interactions
- Van der Waals forces

• Base pairs are stacked on one another which helps stabilize double helix

Question 5

DNA – Multiple Forms

Answer 5

DNA double helix can adopt multiple forms:

• B-form: most common, classical form
• A-form: shorter and wider than B-form

=> bases are at an angle rather than perpendicular to the helical axis

=> RNA double helices and DNA-RNA hybrid helices (structures that form during transcription and RNA processing) will adopt a double helical form that is very similar to the A-form

• Z-form: not completely understood

=> left-handed helix rather than right-handed double helix

Question 6

DNA – Grooves

Answer 6

B-form grooves
- Major groove (large side)
- Minor groove (small side)

Grooves allow access to the H-bonding capabilities of the exposed bases

H-bonding capabilities provide a means of sequence specific interaction between DNA and the molecules w/ which they must interact with the processes of replication and transcription

Question 7

DNA – Compaction

Answer 7

Bacterial cells (E. coli): DNA double helix = circular molecule that is twisted into a super helix by process of supercoiling

• The unwound DNA and supercoiled form are topological isomers of each other. Linear DNA molecules can also form superhelices when packaged into chromosomes

Eukaryotic cells: DNA is associated w/ specific protein

DNA in human cells: DNA is 3.6 meters in length and packaged into 46 chromosomes

Supercoiling accounts for some of the compaction, but further compacting is required for certain DNA-binding proteins

Chromatin = entire complex of a cell’s DNA and its associated protein

Histones = proteins that will allow for the compaction of DNA

• Once the DNA is wrapped around the histone, a nucleosome is created
• The basic property of the histone protein means that the histones have a positive charge, which allows for the DNA, which is negatively charged, to nicely wrap around these proteins

Nucleosome = contains histones and DNA

Question 8

Strategies to compact DNA to fit inside cell:

Answer 8

1. Nucleosomes: formed by DNA wrapping around histone proteins (positively charged proteins)
2. Supercoiling: additional winding resulting in coil formation
3. Chromatin: nucleosomes wrapped into spring structures
4. Chromosome: further wrapping and looping of chromatin