4: Genes, Genomes, and DNA

Question 1

Genome organization

Answer 1

Prokaryotes:

• Single circular chromosome
• Additional plasmids
• No exons
• Grouped based on function with a single promoter controlling the expression: operon
• Some have polyploid genomes that adapts them to life under extreme conditions.

Viruses:
- Genome only needed to influence the host into making more viral genomes and to manufacture the viral coat.

Organelles:
- Mitochondria and chloroplasts have genomes necessary for their biological role within the cell.
Need host encoded proteins to allow proper function.

Question 2

Eukaryotic genome

Answer 2

Large 
Have intervening (introns) or noncoding DNA than other genomes. 

Number of chromosomes does not correlate with complexity.

In humans, only about 2% of the genome consists of unique sequences.
- ~50% is repeated sequences. Tandem repeats if they follow each other directly.

Mammals have ca. 20 000 genes carried over a total of 300 Mbp of DNA.
=> >95% noncoding.

Question 3

Consensus sequence

Answer 3

Idealized base sequence consisting of the bases most often found at each position.
Can be made from repeated sequences with differences in a few bp.

Question 4

VNTR - Variable Number of Tandem Repeats

Answer 4

Common in mammalian genomes.
Number varies among individuals due to unequal cross over.
Noncoding, but the different versions referred to as alleles.

Question 5

Purine rich DNA structures

Answer 5

Several runs of A residues (3-5 bp) separated by 10 bp (1 turn) forms bends in the helix.

Bent DNA moves more slowly during gel electrophoresis than unbent DNA of the same length.

G-quadruplex:
Four-stranded structure that forms in DNA due to presence of multiple G tracts.
Often formed on one strand when double helix is open.
Very stable, blocks transcription and replication.

Question 6

Supercoiling

Answer 6

Higher-level coiling of DNA that is already a double helix.

One every 200 nt in bacteria.

Negative supercoiling helps promote the unwinding and strand separation necessary during replication and transcription.
Level of supercoiling varies greatly within a chromosome.

50 loops of supercoiled DNA wrapped around protein scaffold.

Introduced by topoisomerases.

Question 7

Linking number, L

Answer 7

Total amount of twisting in a DNA molecule.
Double helical turns (twist, T) + supercoiling (whrite, W).
L = T + W

Question 8

Topoisomerases

Answer 8

Change the level of supercoiling

Type I - breaks one strand => L changes in steps of one.

Type II - breaks both strands and pass another part of the double helix through the gap => L changes in steps of two.

DNA gyrase:

• Topoisomerase type II
• Introduces negative supercoils (can remove them).

Question 9

Alternative helical structures of DNA

Answer 9

B-DNA:

• Watson and Crick double helix
• 10 bp per turn
• Right handed

A-DNA:

• Shorter and fatter than B
• 11 bp per turn
• Right handed
• dsRNA or DNA/RNA hybrids => extra OH group on 2’ position of ribose prevents dsRNA forming B-helix.

Z-DNA:

• Longer and thinner than B
• Left handed
• 12 bp per turn
• Sugar phosphate backbone forms zigzag.
• High salt => Z. Decreases repulsion between the - charged P on backbone.
• Formed in regions with large numbers of alternating GC or GT (5’ -> 3’)

Question 9

Alternative helical structures of DNA

Answer 9

B-DNA:

• Watson and Crick double helix
• 10 bp per turn
• Right handed

A-DNA:

• Shorter and fatter than B
• 11 bp per turn
• Right handed
• dsRNA or DNA/RNA hybrids => extra OH group on 2’ position of ribose prevents dsRNA forming B-helix.

Z-DNA:

• Longer and thinner than B
• Left handed
• 12 bp per turn
• Sugar phosphate backbone forms zigzag.
• High salt => Z. Decreases repulsion between the - charged P on backbone.
• Formed in regions with large numbers of alternating GC or GT (5’ -> 3’)

Question 10

Packaging DNA in Eukaryotic nuclei

Answer 10

DNA compacted 2000-fold.
Cannot supercoil as it is not circular.

DNA wound around positively charged proteins; histones.

• 8 histones core unit: 2xH2A, 2xH2B, 2xH3, 2xH4
• Wraps around histones 2 times => nucleosome.

Chain of nucleosomes is wound into a 30 nm fiber; helical structure with 6 nucleosomes per turn.
Loops back and fourth. Ends are attached to a protein scaffold.

Question 11

Chromatin

Answer 11

Chromatin:
Complex of DNA plus protein which constitutes eukaryotic chromosomes.

Heterochromatin:
Highly condensed form of chromatin that cannot be transcribed because it cannot be accessed by DNA polymerase.

Euchromatin:
Normal, active