Information Pathways Genes and Chromosomes March 25, 2008

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

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

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

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

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

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

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

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

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

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

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

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

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