1. Chapter 24 Genes and Chromosomes
Nucleic acids – DNA, RNA
Genome - the genetic information of an organism
Gene – fundamental unit of information
Segment of DNA (or RNA) that encodes information to produce a functional biological product (usually a protein)
Transcription - copying of the DNA sequence information into RNA
Translation - Information in RNA molecules is translated during polypeptide chain synthesis
Replication – copying of genetic information (usually DNA)

2. Structure of B-DNA
Sugar phosphate backbone outside
Stacking creates two unequal grooves (major and minor)
DNA Topology
- linear or circular
- supercoiled
- packaged by association with other molecules
to reduce molecule length and organize it
Chromosomes – DNA with associated proteins, etc. that carry the genome.
E. coli – 1 large circular DNA
- may also have extrachromosomal
plasmids (small circular DNA)
homo sapiens – 23 pairs

3. T2 bacteriophage (linear DNA)
Mitochondria and chloroplasts also contain their own DNA
DNA lysed from E.coli
(circular DNA)

4. “Relaxed” circular DNA with the B conformation (10
“Relaxed” circular DNA with the B conformation (10.4 base pairs/turn) would lie flat on a surface
If strands are broken, and two ends of linear DNA twisted in opposite directions and rejoined, DNA supercoils to restore 10.4 bp/turn
Each supercoil compensates for one turn of the double helix
Most bacterial chromosomes are supercoiled, and regions of eukaryotic DNA are supercoiled
Topoisomerases - enzymes that can alter the topology of DNA helixes by: (1) Cleaving one or both DNA strands (2) Unwinding or overwinding the double helix by rotating the strands (3) Rejoining ends to create (or remove) supercoils

5. Degree of supercoiling is determined by Linking number (LK) – number of times one strand is twisted around another
Two parts:
1. Writhe –measure of coiling of the helix
2. Twist – local twisting or spatial relationship of neighboring base pairs.

6. DNA can take on many shapes depending on supercoiling
Plectonemic supercoiling – applies to simple, regular way DNA is supercoiled in solution

7. DNA Is Packaged in Chromatin in Eukaryotic Cells
Chromatin - DNA plus various proteins that package the DNA in a more compact form
The packing ratio: difference between the length of the metaphase DNA chromosome and the extended B form of DNA is 8000-fold
Nucleosomes
Histones - the major proteins of chromatin
Eukaryotes contain five small, basic histone proteins containing many lysines and arginines: H1, H2A, H2B, H3, and H4
Positively charged histones bind to negatively-charged sugar-phosphates of DNA
Nucleosome “beads” are DNA-histone complexes on a “string” of double-stranded DNA
Each nucleosome is composed of:
Histone H1(1 molecule)
Histones H2A, H2B, H3, H4 (2 molecules each)
~200 bp of DNA

9. Electron micrograph of chromatin
Chromatin “beads-on-a-string” organization
Histones H2A, H2B, H3, H4
Arrange in a octamer (2 each)
DNA wraps around octamer
H1 acts as linker between beads
Packaging of DNA in nucleosomes reduces DNA length ~sevenfold

10. Structure of chicken nucleosome core particle
Histone octamer Octamer bound to DNA
About 146 bp wrapped around octamer
About 54 bp linker DNA
Presence of H1 on linker DNA depends on
Sequence – some regions have sequence-specific binding proteins other than H1
Transcription activity – actively transcribing DNA may have little to no H1

11. 30nm chromatin structure
Next level is the 30nm chromatin fiber
Organization at this level not fully understood
Gains 100-fold compaction
Coils on itself to form a
helical array
RNA-protein scaffolds in chromatin
Chromatin fibers attach to scaffolds
Holds DNA fibers in large loops
May be ~2000 loops on a large chromosome
Overall compaction in eukaryotes is about 10,000-fold

12. Main components of scaffold
RNA
Histone H1
Topoisomerases
Loops sometimes contain related genes
Other proteins in chromatin
SMC proteins – structural maintenance of chromosomes
a. Cohesins – involved in linking sister chromatids after replication
b. Condensins – involved in condensation during mitosis

13. Bacterial DNA Packaging
Prokaryotic DNA also packaged with proteins in a condensed form
No defined nucleosome-like particles
Nucleoid structure - bacterial DNA attached to a scaffold in large loops of ~100 kb
E. coli nucleoids shown
Lack of nucleosomes probably due to higher metabolic rate and need for transcription
Cell division as fast as every 15 min
Eukaryotic cells may not divide for hours or even months