W3_L8_The nature of genes and the genome.pptx

Lecture 8: The nature of the gene and the genome Dr Kanagaraj Radhakrishnan (RAJ, as I am always called) Lecturer in Biomedical Sciences St George’s, University of London Overview for part 1  How is the genome organised in human cells?  What is a gene?  The central dogma of molecular biology...

Lecture 8: The nature of the gene and the genome Dr Kanagaraj Radhakrishnan (RAJ, as I am always called) Lecturer in Biomedical Sciences St George’s, University of London Overview for part 1  How is the genome organised in human cells?  What is a gene?  The central dogma of molecular biology Animal Cell (Eukaryote) Nucleus Surrounded by a nuclear envelope  Double membrane Size 3-10 µm Contains chromosomal DNA DNA packaging Contains nucleolus  Ribosome production  Site of DNA replication and transcription  Communicates with cytosol via nuclear pores Cell, Genome, Gene, and DNA The Human Genome  3.2 x109 nucleotides = 3,200,000,000 nucleotides – 22 pairs of Autosomes – 1 pair of Sex Chromosomes (Geigl et al (2006) Nat Protocols 1: 1172- The Human Genome  includes the circular chromosome found inside the cellular organelles called mitochondria (Amorim et al (2019) PeerJ. 7: e7314) Homologous Chromosomes Maternal homolog Paternal homolog Key structures: = Telomere = Centromere ortant function of chromosomes: to carry genes Number of chromosomes in different organisms Size of Chromosomes Chromosome Packing Double helix Nucleosom e 30nm chromatin 300nm coiled fibre 700nm coiled coil Chromosome 30nm Chromatin Fibre “Beads on a string ” Solenoi d Nucleosome DNA double helix Core histones: – H2A – H2 Pair –B s – H3 H4 histone: Linke rCore DNA H1 Linker DNA Genes on the Chromosome Genes Intergenic region (>98% of the genome) Gene Definitions of a gene: 1. Unit of heredity; contains instructions for an organism’s phenotype 2. DNA segment containing instructions for making a particular product A gene is NOT just the bits that code for a protein What is a gene? Exons Promote r 5’ UTR 3’ UTR (untranslated (untranslated Introns region, part of region, part of last first exon) exon) A gene is a DNA segment containing instructions for making a particular product, including the regulatory elements. What is a gene? Genes differ in size and number of exons/introns HIST1H1A – 756bp, 1 exon, 215 amino acids DMD – 2.4 Mb, 79 exons, 3685 amino acids TTN – 100kb, 363 exons, 35000 amino acids Central Dogma Transcription: Synthesis of mRNA transcript from DNA Same language – nucleic acid Translation: Protein production from mRNA transcript Different languages – nucleic acid to protein Overview for part 2  DNA and RNA  DNA structure and function  DNA vs RNA  Types of RNA  Structure of RNA DNA and RNA  Nucleic acids – deoxyribonucleic acid (DNA) & ribonucleic acid (RNA)  In DNA, the sugar is deoxyribose. In RNA, the sugar is ribose O O O P O O OO H OH O H Ribose 5’ phosphate (in RNA) O O O P O O OO H OH H O Deoxyribose 5’ phosphate (in DNA) Nitrogenous bases Purines Adenine DNA RNA Guanine Pyrimidines DNA RNA Cytosine DNA Thymine RNA Uracil NH 2 N N N N Base (A) Beta glycosidic linkage O O P O O O Sugar (ribose) O O H O O H Nucleoside Nucleotide Nucleotide vs Nucleoside Base pairing in DNA       Watson-Crick Occurs between complimentary bases by hydrogen bonding Amount of purine equals amount of pyrimidine Ratios of A to T and G to C always 1:1 in dsDNA GC rich regions more stable than AT regions Order of bases determines the DNA formed of two anti-parallel strands DNA double helix      2023 - 70th anniversary of DNA double helix Can see the bases stacking on top of each other Base stacking angle produces two grooves in (B- form) double helix Major groove – M Minor groove – m Different forms of DNA A form – mostly when DNA is dehydrated or in crystalline form, or in combinations with RNA. Shorter and more compact. Right handed B form handed - most common, right Z form - left handed helix, may form as part of stress coiling, or interactions with proteins. DNA store genetic information  The order of nucleotides determines the genetic information  There is a specific code – the genetic code to unlock the genetic information  “Universal” same code applies to virtually all organisms Triplet code  DNA triplet code  Each of the 4 different nucleotides (ATGC) can form 3 letter words (triplet code)  3nts = Codon  There are 43 (4x4x4) or 64 possible codons.  Each codon represents either a particular amino acid or a “stop”  64 codons to code 20 amino acids  Most amino acids are coded by more than 1 codon DNA vs RNA RNA  Single stranded in eukaryotes. Double stranded in some viruses where it carries the genetic code  DNA RNA Proteins  RNA can base pair with DNA but not capable of forming the B form of the double helix (more A form-like)  Because RNA single stranded – forms complicated 3D structures Major types of RNA  Messenger RNA (mRNA) primary transcript read from DNA  Transfer RNA (tRNA) translation - carries amino acids to ribosome/mRNA complex, the anti-codon on tRNA base pairs with codon on mRNA  Ribosomal RNA (rRNA) EUKARYOTE RNA participates in protein synthesis translation - component of a ribosome to which mRNA is located Coding and non-coding RNA • Not all RNA code for proteins  4% of total RNA is made of coding RNA  Remaining are non-coding RNA • Ribosomal RNA (rRNA) and transfer RNA(tRNA) are used in the various protein translational apparatus • Small nuclear RNA (snRNA) – found in eukaryotes, is part of the splicing apparatus • Small nucleolar RNA (snoRNA) involved in methylation of rRNA • Small cytoplasmic RNA (scRNA) plays a role in the expression of specific genes Structure of RNA  Unlike DNA, tertiary structure depends on length and sequence of RNA  Best studied – tRNA Secondary structure shows characteristic stems (base paired – like A form region and loops) Tertiary structures adopt complex configurations Transfer RNA (tRNA) structure Summary All cells of a living organism contain an identical set of codes describing the genes and their regulation This genetic code is encoded as one or more strands of DNA Cells from the different parts of an organism have the same DNA Genome means entire complement of DNA molecules of each organism Function of genome is to control the generation of molecules (mostly proteins) that will regulate the metabolism of a cell and its response to the environment, and provide structural integrity Central Dogma of Molecular Biology Further reading Chapter 5