Lecture 3 Topic 2 Arrangement of Genes on

Lecture 3 Topic 2

Arrangement of Genes on chromosomes Spacing between genes - size of gene control regions - presence/absence of repetitive DNA Direction of transcription

Example Human Chromosome Segments (two segments of chromosome 21) Direction and chromosome strands – overlapping genes – genes within genes, amyloid-beta precursor protein, gene control regions? , predicted genes (orf),

What is the Structure of Chromosomes? Example: Human Chromosomes

279 251 221 Other Cytological Landmarks: G-Banding Pattern 197 198 176 163 148 140 143 148 142 Total Size: 3200 Mb 118 107 100 104 88 86 72 66 45 48 163 51

What is the Structure of Chromosomes? Example: Drosophila Polytene Chromosomes Salivary glands contain > 1000 copies of each chromosome 2 n = 8; but only 4 polytenes? Bands and Interbands – differences in chromatin structure and gene expression Puffs Chromocenter

What is the Structure of Chromosomes? Example: Corn Chromosomes

What is the Structure of Chromosomes? Nucleosomes and the 30 nm Filament (solenoid)

What is the Structure of Chromosomes? Large Segments of Chromatin in Looped Domains Nucleosome Solenoid Loops and SARs Coiling of Loops Supercoiling of the solenoid

Genes, Chromosomes, and Genomes Prokaryotic cell? What’s a genome? What are the component parts of a genome? How do you describe a genome? What is the function of a genome?

What is a Genome? • = All the genetic information of an organism – – – Virus Bacterium Fungus Plant Animal • = All the genetic information in the nucleus, mitochondria, chloroplast • What about non-heritable genetic information? – A Retrovirus (eg. HIV that causes AIDS) – Mutations in cancer cells – Rearrangements of Antibody-encoding genes (immunoglobulins) • What about epigenetic information? – Genomic imprinting – X-chromosome inactivation

How do you describe a genome? Size and Ploidy

How does alternatively spliced genes affect your definition of genomes?

Comparative Genomics Synteny Conserved Synteny and Gene finding

Gene, Chromosome, and Genome Structure • • • • What is a gene? What are the component parts of a gene? How do prokaryotic genes, eukaryotic nuclear genes, eukaryotic organellar genes, and viral genes differ? How do individual eukaryotic (or prokaryotic) genes differ (structure, function)? What is the function of a gene? (Chapter 3) How does the structure of ds. DNA contribute to gene function? How can you represent (draw) the structure of a gene? Answer these specficially for DMD? What is a chromosome? What are the component parts of chromosomes (DNA, proteins)? How do prokaryotic and eukaryotic chromosomes differ? How do individual eukaryotic chromsomes differ (among mammals? Between races? Between individuals in the same race)? What is the function of a chromosome? How does the structure of ds. DNA (or just DNA) contribute to chromosome function? How do proteins contribute to chromosome function? How can you represent the structure of a chromosome? What is a genome? What are the component parts of genomes? How do prokaryotic, eukaryotic, and viral genomes differ? How do different eukaryotic genomes differ (among mammals? Between races? Between individuals in the same race)? What are the characteristics of genomes? How do you describe a genome What is the function of a genome?

Gene Function • • • • • What products do genes encode? What is transcription? What is a promoter? How do prokaryotic and eukaryotic promoters differ? How do individual eukaryotic promoters (prokaryotic promoters) differ? What is a terminator? How do prokaryotic and eukaryotic terminators differ? How do individual prokaryotic terminators differ? What are RNA polymerases? How do prokaryotic and eukaryotic polymerases differ? What is RNA processing? How do you distinguish between the product of transcirption and the processed transcripts? How does RNA processing in prokaryotes and eukaryotes differ? How does RNA processing of eukaryotic RNAs differ? What cis-acting sequences are important for pre-m. RNA splicing? What trans-acting factors are improtant for pre-m. RNA splicing? How does the structure of nucleic acids contribute to pre-m. RNA splicing? What is the role of proteins in pre-m. RNA splicing? What is translation? What is a translation initiation site? How doe prokaryotic and eukaryotic translation initiation sites differ? How do individual eukaryotic translation initiation sites differ? What trans-acting factors are important for translation? How does the strtucture of nucleic acids contribute to translation? What is the role of proteins in pre-m. RNA splicing? – – – • • • What is a ribosome? How do prokaryotic and eukaryotic ribosomes differ? How do individual eukaryotic (prokaryotic) ribosomes differ? What is a t. RNA? What are the important functional components of a t. RNA? Why is RNA the most likely candidate as the earliest evolved “living” macromolecules? How do gene products function? How can gene mutations affect the function of gene products?