1. Information Pathways Genes and Chromosomes
March 25, 2008

2. Informational Pathways
Biosynthesis of DNA, RNA and Proteins
replication, transcription and translation of biological information
requires a nucleic acid template for conveying biological information to newly synthesized macromolecule
biosynthesis of informational macromolecules demands significantly more energy than for comparable molecules without biological information

3. Central Dogma of Molecular Biology
for template directed synthesis of informational macromolecules

4. DNA, RNA and Protein Sequences
DNA is typically a double-helix of antiparallel complementary strands
Each DNA strand is template for replication of the other complementary strand
One DNA strand is template for transcription of an RNA (RNA is complementary and anti-parallel to DNA template)
mRNA is template for translation of a protein (polypeptide) using triplets of nucleotides (codons) for encoding each amino acid
Biosynthesis of nucleic acids is from 5’ to 3’ and biosynthesis of proteins is from amino terminus to carboxyl terminus

5. Genome contains the entire genetic complement of an organism
Chromosomes: structural segments of the genome with a single duplex DNA
Gene: all the DNA that encodes the primary sequence of a particular product, either RNA or protein, with a particular biological function

6. Sequences in Human Genome
~30% of human genome makes up the 30,000 – 35,000 genes
~5% of this encodes protein
eukaryotic genes have small protein coding exons flanked by larger non-coding introns

7. Chromatin Structure Changes in Cell Cycle
Chromosomes are composed of chromatin a nucleoprotein complex (DNA + protein)
Chromatin is most highly condensed during mitosis (M) -visualized as chromosomes
During interphase (G1, S, G2) chromatin is more extended
Additional proteins cohesins and condensins are recruited during S and G2 phases

8. Structure and Function of Chromatin
Chromatin: nucleoprotein complex (DNA + protein, each ~50% of mass) in extended and condensed forms
Proteins hold DNA in compact solenoidal superhelices and control gene activity
Histones tightly bind and organize DNA into nucleosomes
Non-histone proteins provide structure and gene regulation
Topoisomerases relax overwound sections of DNA
Structural Maintenance of Chromosome (SMC) proteins
Nucleosomes: “beads on a string”
~200 bp DNA / unit

9. Histones are small very basic proteins (24% to 51% Lys + Arg)
H1 is most basic with high Lys content

10. 3D Structure of a Nucleosome
Top
Side
H2A
H2B H3 H4

11. Nucleosome Structure 4 histones pack into an 8-subunit protein core
2 each of H2A, H2B, H3 and H4 histones per nucleosome
1 H1 histone per nucleosome (links DNA between nucleosomes)
DNA winds around the histone core (compression of minor groove)
< 2 turns of DNA 146 bp per nucleosome (nuclease resistant)
Nucleosomes provide ~7-fold compaction of DNA

12. Histone Binding and Supercoiling
Binding of histone core to relaxed circular DNA causes positive superhelical turns in unbound DNA
Relaxation of DNA requires a topoisomerase
Topoisomers have differences in configurations; interconverting topoisomers requires breaking and forming of covalent bonds
2 types of supercoiling: solenoidal and plectonemic

13. Organizing Nucleosomes into 30 nm Fibers
Second level of chromatin organization
Nucleosomes packed into fiber 30 nm in width
~100-fold compaction of DNA
Model for 30 nm fiber with solenoidal nucleosome packing
30 nm fiber detected using EM

14. Model for Compaction of DNA in Chromatin
Theoretical model for compaction of DNA – no experimental support beyond 30 nm fiber
30 nm fiber has attachment sites to a nuclear scaffold
30 nm fiber could be organized into supercoiled loops between nuclear scaffold attachment points
Model must provide ~104 fold compaction – ratio of DNA length to chromosome length