BIO265+Genomes+and+Messages+Rizzo+FA24.pdf

Outline for Today DNA AS THE GENETIC INFORMATION HOW DNA INFORMATION IS TURNED IN PROTEIN THE MAKE UP OF GENOMIC DNA THE GENOME - A PARTNERSHIP OF DNA AND PROTEINS CALLED CHROMATIN THE ANATOMY OF A CHROMOSOME 1 The discovery of DNA as...

Outline for Today DNA AS THE GENETIC INFORMATION HOW DNA INFORMATION IS TURNED IN PROTEIN THE MAKE UP OF GENOMIC DNA THE GENOME - A PARTNERSHIP OF DNA AND PROTEINS CALLED CHROMATIN THE ANATOMY OF A CHROMOSOME 1 The discovery of DNA as the heritable molecule - Frederick Griffith demonstrated that dead virulent (disease- causing) bacteria could “transform” living, non-virulent bacteria (1928) - Attributed this to a “transforming factor” present in the virulent bacteria - Transformation – the transfer and incorporation of DNA (genes) between genetically distinct bacteria 2  The discovery of DNA as the heritable molecule 1944 – Oswald Avery et al. definitively shows that DNA from virulent bacteria could “transform” non-virulent bacteria into deadly virulent Loading… bacteria Sequentially destroyed Proteins Lipids Sugars RNA DNA  Scientific community The discovery of DNA as the heritable molecule 1952 – Alfred Hershey and Martha Chase cultured the T2 bacteriophage on two different media One contained radioactive sulfur (labels proteins) One contained radioactive phosphorous (labels DNA) Disrupt phage from bacteria in blender immediately following phage infection Only radioactive phosphorous was found in bacterial pellet This showed that the viral DNA and not  proteins were transferred during The discovery of DNA as the heritable molecule 1953 - Watson and Crick (and others) worked out the three-dimensional structure of DNA: two polynucleotide strands wrapped around each other in a Loading… double helix. They deduced this after viewing X-ray crystallography images produced by Rosalind Franklin in 1952 Hydrogen bonds between bases hold the strands together. Each base pairs with a complementary partner: A with T, G with C.  The discovery of DNA as the heritable molecule In 1962, the Nobel Prize was awarded to James D. Watson, Francis Crick, and Maurice Wilkins. Rosalind Franklin may have received the prize as well but for her death from cancer in 1958. Nobel Prizes are never awarded posthumously. The Watson-Crick model gave new meaning to the words genes and chromosomes. The genetic information in a chromosome is encoded in the nucleotide sequence of DNA. The make up of DNA 5’ phosphate position leads to strand-like structure Purines - Pure As Gold of DNA molecule pAG, pyCUT 7 Precise base pairing maintains the structure of the double helix (Chargaff’s rule) Each base pair contains a purine & pyrimidine to keep the same distance between the backbone along the length of the DNA molecules This is the functional explanation for why A only pairs with T and C only pairs with G Results in complementary base pairing because specific pairs are formed due to hydrogen bonding Hydrogen bonds: are formed when an electronegative atom (O or N) in one base shares a hydrogen atom with another electronegative atom in the base in the other strand Relatively weak bonds individually but collectively The molecular structure of DNA DNA has a directionality termed 5’ -> 3’ based on the sugar phosphate position 9  DNA replicates through a semiconservative method Newly replicated DNA is always templated and paired with a “parent” strand DNA acts as a template for its own replication Semiconservative replication was demonstrated by Meselson & Stahl in 1958 through studies on E. coli (bacteria) 10 The majority of RNA within a cell is one of 3 classes Ribosomal Messenger RNA (rRNA) Loading… Transfer RNA (mRNA) Major Differences from DNA (tRNA) RNA is a single-stranded molecule Uracil (U) replaces Thymine(T) in Palazzo and Lee, 2015 RNA 11 A “coding” strand of DNA serves as a template for single stranded mRNA Text DNA information is read in nucleotide triplets referred to as codons Single codon Coding strand vs template strand, can be different strands for different genes 12  Transfer RNA acts as a translator of nucleic acid to amino acids How does the cell convert information in nucleic acids to a functional protein - translation Self-complementation tRNAs have a 3D dimensional shape that recognizes particular codons (the anticodon) and another that binds a specific amino acid tRNAs are “charged” with amino acids by aminoacyl tRNA synthetases Stem-loop/Hairpin 13 By Yikrazuul - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php? curid=10312097  There is redundancy of codons to amino acids Referred to as the “wobble” position 4 nucleotides (A,C, U, G) and triplet combination 43=64 There are 20 amino acids (exceptions excluded) Benefits to redundancy/wobble? 14 Basic model for THE CENTRAL DOGMA protein-encoding gene expression  Only a fraction of a cell’s DNA is transcribed. An even smaller portion is translated into protein Only about 1.5% of the human genome encodes proteins https://piquemyinterestblog.wordpress.com/2017/08/21/time-to-trash-junk- dna/ 16 Most genomes are filled with repetitive DNA elements 17 Reverse transcription famously goes against the central dogma In many cases, this mRNA codes for the Reverse Transcriptase protein! Reverse transcriptase synthesizes a DNA molecule from an RNA template 18 Genomes across animals range from compact to massive https://en.wikipedia.org/wiki/Genome_siz Homo sapiens ~ 3Gbs A million bp A billion bp 100 billion bp 19 Megabase (Mb) Gigabase (Gb) 100 Gigabases Largest fully sequenced animal genome 30x size of human genome! 20 A problem… Escherichia coli genome is ~1.5mm Escherichia coli are 2µm long A problem… Human genome is ~6 feet! Human cells are ~10-100µm in diameter …how? An exercise… The actual structure of DNA… Prokaryotes E. Coli genome Circular chromosome, supercoiled Few proteins 4.6Mbp, 4000-5000 gene , low amounts of noncoding DNA (87% coding) The actual structure of DNA… Human genome Linear DNA, 23 pairs of chromosomes Many DNA interacting proteins 3100Mbp, 20,000 genes, High amounts of noncoding DNA  Eukaryotic DNA packaging How does a cell fit 6 feet of DNA into a 10µm-diameter nucleus? Eukaryote DNA packaging: - DNA wrapped around histones - Nucleosome: each histone & DNA unit - Nucleosomes linked via continuous DNA chain are called “beads-on-a-string” Histones & scaffolding proteins strengthen & stabilize the DNA Distance between nucleosome centers – 200bp 147bp wrap around histone core The basic unit of the genome - the nucleosome Chromatin - complexes of genomic DNA and associated proteins 27 Histones represent a structural core and a regulatory tail 28 https://www.biorxiv.org/content/10.1101/633370v1.full Chromatin packing is a dynamic process Loading… 29 https://www.youtube.com/watch? v=gbSIBhFwQ4s&feature=emb_logo Chromatin packing influences gene expression Inaccessible, repressed Accessible, expressed Electron Micrograph shows the dense packing of heterochromatin 30 The most compacted form of a chromosomes is during mitosis 31 The anatomy of a chromosome Shorten with age (progressive cell divisions), Each Chromatid represents one copy of genetic shortening associated with Telomeres age-related pathologies information (maternal or paternal Also prevent nuclease degradation of DNA at ends of chromosomes Centromere - Join sister chromatids Recruit kinetochore proteins Kinetochore (Mitosis) 32