PART III – INFORMATION PATHWAYS- Three major processes in cellular utilization of genetic information:o Replication – the copying of parental DNA to form daughter DNA molecules with identical nucleotide sequenceso Transcription – the process by which parts of the genetic message encoded in DNA are copied precisely into RNAo Translation – the genetic message encoded in messenger RNA is translated on the ribosomes into a polypeptide with a particular sequence of amino acids- The ribosome, most of the translational apparatus, and some parts of the transcriptional machinery are shared by every living organism on this planetChapter 24 – Genes and Chromosomes- Chromosomes – the repositories of genetic information24.1 Chromosomal ElementsGenes Are Segments of DNA That Code for Polypeptide Chains and RNAs- Phenotype – visible property- Mutations – damage and alterations in the DNA sequence- One gene-one enzyme – a hypothesis in which it was believed that each gene coded for one enzyme- One gene-one polypeptide – many genes code for a protein that is not an enzyme or for one polypeptide of a multisubunit protein- Gene – all the DNA that encodes the primary sequence of some final gene product- Regulatory sequences – segments of DNA that provide signals that may denote the beginning or end of genes, or influence the transcription of genes, or function as initiation points for replication or recombination.DNA Molecules Are Much Longer Than the Cellular or Viral Packages That Contain Them- Viruseso Not free-living organismso Infectious parasites that use the resources of a host cell to carry out many of the processes they require to propagateo Have RNA genomes that are particularly smallo Genomes of DNA viruses vary greatly in size Many are circular for at least part of their life cycleo Replicative forms – specific types of viral DNA- Bacteriao Circular DNA chromosome in the nucleoido Many bacteria contain one or more small circular DNA molecules that are free in the cytosol, called plasmids Carry genetic information Undergo replication to yield daughter plasmids- Eukaryoteso Humans have 46 chromosomeso Mitochondria and chloroplasts also contain DNA MtDNA is much smaller than nuclear DNA MtDNA is circularEukaryotic Genes and Chromosomes Are Very Complex- The nucleotide sequences of many eukaryotic genes contain one or more intervening segments of DNA that do not code for the amino acid sequence ofthe polypeptide producto Intervening sequences or intronso Exons – coding segmentso In higher eukaryotes, there are more introns than exons- Highly repetitive sequences (simple-sequence DNA or simple sequence repeats (SSR)) – sequences that are repeated millions of times per cello Generally less than 10 bpo Also called satellite DNAo Do not encode proteins or RNAs- Centromere – a sequence of DNA that functions during cell division as an attachment point for proteins that link the chromosome to the mitotic spindleo Essential for the distribution of DNA to the daughter cellso Rich in A-T pairs- Telomeres – sequences at the ends of eukaryotic chromosomes that help stabilize the chromosomeo Added by telomerase24.2 DNA Supercoiling- Supercoiling – the coiling of a coilo Generally a manifestation of structural strain- Relaxed – when there is no net bending of the DNA axis- Replication and transcription of DNA are affected by supercoiling- Supercoiling is an intrinsic property of DNA tertiary structure- Topology – the study of the properties of an object that do not change under continuous deformationso Continuous deformations include conformational changes due to thermal motion or an interaction with proteins or other moleculeso Discontinuous deformations involve DNA strand breakageMost Cellular DNA Is Underwound- Closed-circular DNAs – plasmids and small viral DNAs that have no breaks in either strando Rarely relaxed- Underwinding – causes strain by having fewer helical turns than expectedDNA Underwinding Is Defined by Topological Linking Number- Linking number – a topological property of double-stranded DNAo Does not vary when the DNA is bent or deformed, as long as both strands remain intacto Undefined if there are breaks in the DNA- Specific linking difference ( ) or superhelical density – a measure of the number of turns removed relative to the number present in relaxed DNAo Generally in the range of -0.05 to -0.07o Negative sign means change is due to underwinding- Topoisomers – two forms of a circular DNA that differ only in a topological property such as linking number- Two components of linking number:o Twist (Tw) – determining the local twisting or spatial relationship of neighboring base pairso Writhe (Wr) – a measure of the coiling of the helix axiso Geometric properties- Underwinding causes supercoiling, makes strand separation easier, and facilitates structural changes in the moleculeTopoisomerases Catalyze Changes in the Linking Number of DNA- Topoisomerases – enzymes that increase or decrease the extent of DNA underwindingo Change the linking numbero Important in replication and DNA packagingo Two classes: Type I topoisomerases – transiently break one of the two DNA strands, passing the unbroken strand through the break and rejoining the broken ends- Change Lk in increments of 1 Type II topoisomerases – break both DNA strands and change Lk in increments of 2DNA Compaction Requires a Special Form of Supercoiling- Supercoils are right-handed in a negatively supercoiled DNA molecule- Plectonemic – any structure with strands intertwined in some simple and regular wayo Does not produce significant packagingo More stable in solution- Solenoidal – a form of supercoiling that can be adopted by an underwound DNAo Involves tight, left-handed turnso Can be stabilized by protein bindingo Found in chromatin – provides a much greater degree of packing24.3 The Structure of ChromosomesChromatin Consists of DNA and Proteins- Chromatin – the chromosomal materialo Consists of fibers containing protein and DNA, with small amounts of RNA- Histones – proteins that package and order the DNA into structural units called nucleosomesHistones Are Small, Basic Proteins- Histones are rich in basic amino acids (arginine and lysine)- Five major classes in eukaryotic cells:o H3 – identical in all eukaryoteso H4 – identical in all
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