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)

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

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

“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

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.

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

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

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

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

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

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

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