BCHM 4116 1st Edition Lecture 4 Outline of Last Lecture I. Watson and Crick base pairing II. What is DNA helix stabilized byIII. 3 types of DNAIV. Biological Implications of double stranded helix in DNAV. Intercalating Agents VI. Structural Transitions of DNAVII. Hyperchromic shift VIII. DNA structure is dynamicIX. Tertiary structure of DNAX. L= T+WXI. Organization chromatin and chromosome Outline of Current Lecture I. The Secondary and Tertiary Structures of RNAII. tRNAIII. Physical structure of genes in eukaryotesIV. Genome size correlates with biological complexity? Current LectureOrder of bases are not that conserved, however you find that the way it folds is highly conserved. This is what’s helpful for epigenetic analysis. tRNA: use it as an example of how a single stranded molecule, unlike DNA, can take on a particular secondary or tertiary structure. This is a tRNA isolated from yeast, and its job is to bring the phenylalanine to the ribosome during protein synthesis. This is the sequence of the tRNA, from 5’ to 3’. 1. This is a secondary structurea. Intrastrand strand base pairing helps the stability of the structure. GC pair and GU pair, which can hydrogen bond2. There exist modifications to the nucleotides a. D: dihydrouridine, a reduced form of uridine b. PseudouridineThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.i. Normally: Uracil is linked to ribose through a N-glyosidic bond ii. In this, instead of the nitrogen connecting it, a C is connecting it to the ribose. iii. This modification is through to be helping with the structure stabilityc. ‘m’ i. The base is methylated at the position indicated as a superscript1. Ex. Cm5  the cytosine is methylated at position 5 RNAAt the 3’ end, there is CAA-OH. This 3’ hydroxyl is where an ester will form with the amino acid. On top of the secondary structure, there is a tertiary structure which is also intrastrand interactions (pink lines). GeneGene: genes are the units carrying and transferring inherited characteristics from parents to offspring. A gene commonly is defined as the entire DNA segment that is necessary for the synthesis of a functional RNA and/or polypeptide. Polycystronic: one mRNA can encode for multiple proteins. Exon: section that made it into the mature mRNA. Exons extend all the way to the 5’ and 3’ ends, and include the UTR (untranslated region). The gene doesn’t exist just from the start and stop codon, but includes the 5’ and 3’ untranslated regions (UTR) because they also make it intothe mature mRNA. Upstream of the transcription start site is labeled ‘-1’. Transcription start is different from the translation start site. The translation start is from ATG to stop codon. Transcription start is different from translation start. Always a distance from the transcription start and translation start. Poly(A) tail: it is the feature of the mRNA, not the gene. It signals the stop for transcription. 3’ UTR-15’ UTRStop codon: signals the stop for translation Genome and Genome OrganizationGenome: Entire set of genetic material in an organism. This is the chromosomal DNA and mitochondrial DNA. Size variation: Even though there is an increase in genes from bacteria to complex mammals, this increase in genes doesn’t hold within a taxa. All organisms in a taxa have about the same number of genes. - Size of genome varies between taxonomic groups- Size of genome doesn’t vary much within taxonomic groups Why such great variation?- Repetitive sequences may exist that bulk up the genome. This occurs in polyploid organisms. Question to think about: Is there is a strict correlation between genome size and ‘biological complexity’?Worms (19000 genes) and humans (20000 genes) have a difference of about only 1000 genes.Genes just move around, we can do much more, so why do worms and humans have about the same number of