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A. An overview of molecular biology

A. An overview of molecular biology

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A. An overview of molecular biology

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  1. A. An overview of molecular biology Read Human Molecular Genetic Ch. 1 A.1. Background A.2. Macromolecules A.3. DNA structure A.4. RNA transcription and Gene Expression A.5. RNA processing A.5.1. Splicing A.5.2. RNA Capping A.6. Translation, post-translation processing and protein structure A.6.1. Translaion A.6.2. Protein Folding A.7. Summary CS 6463: An overview of Molecular Biology

  2. A.1 Background: Procaryotic and Eukaryotic Cells • Two types of cells: • Prokaryotic (bacteria: E. Coli) • Eukaryotic (multicellular organisms, • Ameba, Yeast) CS 6463: An overview of Molecular Biology

  3. A.1.1 3 Domains in the Living World CS 6463: An overview of Molecular Biology

  4. A.1.2 Bacteria, Archaea and Eucaryotes. The bacterium: Vibrio Cholerae A lithotrophic Bacterium (Archaea) Eucaryotic Cell CS 6463: An overview of Molecular Biology

  5. A.1.3. Eukaryotic Cells http://www-class.unl.edu/bios201a/spring97/group6/ CS 6463: An overview of Molecular Biology

  6. A. An overview of molecular biology Read Human Molecular Genetic Ch. 1 A.1. Background A.2. Macromolecules A.3. DNA structure A.4. RNA transcription and Gene Expression A.5. RNA processing A.5.1. Splicing A.5.2. RNA Capping A.6. Translation, post-translation processing and protein structure A.6.1. Translaion A.6.2. Protein Folding A.7. Summary CS 6463: An overview of Molecular Biology

  7. A.2. Building Blocks: Chemical Composition of Eukaryotic Cell • Water [E. Coli: 70%, Mammalian Cell: 70%] • Macro-molecules: • DNA: Deoxyribonucleic Acid [E. Coli: 1%, Mammal: 0.25%] • RNA: Ribonucleic Acid [E. Coli: 6%, Mammal: 1.1%] • Proteins [E. Coli: 15%, Mammal: 18%] • Inorganic ions: Na+, K+, Mg+, Ca2+, Cl- [E. Coli: 1%, Mammal: 1%] • Lipids: • Phospholipids [E. Coli: 2%, Mammal: 3%] • Other lipids [E. Coli: -, Mammal: 0.2%] • Polysaccahrides [E. Coli: 1%, Mammal: 0.25%] • Volume: [E. Coli: 2 x 10-12cm, Mammal: 4 x 10-9cm] • Relative Volume: [E. Coli: Mammal = 1: 2000] CS 6463: An overview of Molecular Biology

  8. A.2 Building Blocks: Structure of bases, nucleosides and nucleotides Purines: DNA: ‘polymer of A, G, T, C’ RNA: ‘polymer of A, G, U (replace T), C’ Pyrimidines: base sugar CS 6463: An overview of Molecular Biology

  9. A.2. Building Blocks: Common bases found in nucleic acids CS 6463: An overview of Molecular Biology

  10. A.2 Building Blocks: 20 amino acids Polypeptides: chains of amino acids Carboxyl group Amino group CS 6463: An overview of Molecular Biology

  11. A.2. Building Blocks: Abbreviation of Amino Acids CS 6463: An overview of Molecular Biology

  12. A.2. Building blocks: Properties of Amino Acids I http://www.russell.embl-heidelberg.de/aas/aas.html CS 6463: An overview of Molecular Biology

  13. A.2. Building blocks: Some Terms for describing Properties of Amino Acids • Hydrophobic amino acids are those with side-chains that do not like to reside in an aqueous (i.e. water) environment. • Polar amino acids are those with side-chains that prefer to reside in an aqueous (i.e. water) environment. • Strictly speaking, aliphatic implies that the protein side chain contains only carbon or hydrogen atoms. • A side chain is aromatic when it contains an aromatic ring system. CS 6463: An overview of Molecular Biology

  14. A.2 Building Blocks: Covalent and Non-covalent Bonds • Covalent bonds: stronger. Nucleic acid and protein polymers are from by covalent binds connecting nucleotides and amino acids (respectively) to form a linear backbone • Non-covalent bonds: weaker and revisible. 4 types: • Hydrogen bonds: N – H –O [double-stranded DNA, protein folding, …etc • Ionic bonds: Ionic interaction between charged group, sat Na+ and Cl- • Van der Waals: Optimum attraction between two atoms. • Hydrophobic forces: Water is polar molecules, CS 6463: An overview of Molecular Biology

  15. A. An overview of molecular biology Read Human Molecular Genetic Ch. 1 A.1. Background A.2. Macromolecules A.3. DNA structure A.4. RNA transcription and Gene Expression A.5. RNA processing A.5.1. Splicing A.5.2. RNA Capping A.6. Translation, post-translation processing and protein structure A.6.1. Translaion A.6.2. Protein Folding A.7. Summary CS 6463: An overview of Molecular Biology

  16. A.3 DNA Structure: The Phosphodiester Bond CS 6463: An overview of Molecular Biology

  17. A.3 DNA Structure: base pairing (Watson-Crick Rule). CS 6463: An overview of Molecular Biology

  18. A.3 DNA Structure: DNA is a double-stranded anti-parallel helix • %GC = 40%? How many % is G? C? A? T? Complementary DNA (cDNA) downstream upstream http://www.sumanasinc.com/webcontent/anisamples/molecularbiology/DNA_structure.html CS 6463: An overview of Molecular Biology

  19. A.3 DNA Structure: DNA is a double-stranded anti-parallel helix CS 6463: An overview of Molecular Biology

  20. A.3 DNA Structure:Chromatin Histone nucleosome CS 6463: An overview of Molecular Biology

  21. A.3. DNA Structure: Comparing Human and Mouse Genome mouse Human CS 6463: An overview of Molecular Biology

  22. A.3. DNA Structure: Human Chromosomes • 23 pairs of chromosomes. • Chromosome 1-22, both parent contribute one strand each. • Sex – XY (male) and female XX. Mother contribute X and father contribute either X or Y (determine sex). • Mitochondria DNA is inherited from the mother only. CS 6463: An overview of Molecular Biology

  23. A.3 DNA Structure: RNA structure palindrome CS 6463: An overview of Molecular Biology

  24. A.3 DNA Structure: Viral Genomes • Highly Variable: • DNA or RNA • Single stranded or double stranded • Linear or Circular • Segmented and Multipartite • Virus normally replicate in the cytosol. Unusal Retrovirus duplicate itself in the nucleus (using reverse transcriptase) CS 6463: An overview of Molecular Biology

  25. A.3 DNA Structure: The Central Dogma Old 1-directional model CS 6463: An overview of Molecular Biology

  26. A.3 DNA Structure: Gene Expression Efficiency Microarray measurement of gene expression is limited. CS 6463: An overview of Molecular Biology

  27. A. An overview of molecular biology Read Human Molecular Genetic Ch. 1 A.1. Background A.2. Macromolecules A.3. DNA structure A.4. RNA transcription and Gene Expression A.5. RNA processing A.5.1. Splicing A.5.2. RNA Capping A.6. Translation, post-translation processing and protein structure A.6.1. Translaion A.6.2. Protein Folding A.7. Summary CS 6463: An overview of Molecular Biology

  28. A.4. Transcription and Gene Expression: Tanscription CS 6463: An overview of Molecular Biology

  29. A.4 Transcription and Gene Expression:Gene Regulation G C G A G T C U C A G http://henge.bio.miami.edu/mallery/movies/transcription.mov http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.html CS 6463: An overview of Molecular Biology

  30. A.4 Transcription and Gene Expression:RNA Polymerase • There are three classes of RNA Polymerases: • Polymerase I: Localized in the nucleolus. Transcribe rRNA (ribosome RNA) 28S, 18S 5.8S rRNA. • Polymerase II: All protein-coding genes most smRNAs. Unique in capping and polyadenylation. • Polymerase III: tRNA, other rRNAs, snRNAs. [The promoter can be downstream] • Pusedo-genes (gene fragments): Previously were genes • Only 2% of the human genome encode proteins. CS 6463: An overview of Molecular Biology

  31. A.4 Transcription and Gene Expression: DNA-Protein Binding CS 6463: An overview of Molecular Biology

  32. A.4 Transcription and Gene Expression: Trans- and cis-elements Important: If pattern is there, does not necessary mean it is a cis-element. CS 6463: An overview of Molecular Biology

  33. A.4 Transcription and Gene Expression: Promoters Start from 1 not 0 CS 6463: An overview of Molecular Biology

  34. A.4 Transcription and Gene Expression: Polymerase II & Promoter CS 6463: An overview of Molecular Biology

  35. A.4 Transcription and Gene Expression: : Transcription under the Electron Microscope CS 6463: An overview of Molecular Biology

  36. A.4 Transcription and Gene Expression: Transcription in Bacterial CS 6463: An overview of Molecular Biology

  37. A.4 Transcription and Gene Expression: Enhancers and Silencers (Transcription Factors) Many basepairs away CS 6463: An overview of Molecular Biology

  38. A.4 Transcription and Gene Expression: Tissue Specific Genes • House keeping genes: Genes encoding histone protein, ribosome protein. Always on. • Tissue or development-specific (non-housekeeping) genes: • Transcriptional inactive chromatin • Methylation of Cytosine, replacing a hydrogen (H) with methyl (CH3) • Transcription factors’ expression levels are low. • Microarrays measure the expression levels of genes CS 6463: An overview of Molecular Biology

  39. A. An overview of molecular biology Read Human Molecular Genetic Ch. 1 A.1. Background A.2. Macromolecules A.3. DNA structure A.4. RNA transcription and Gene Expression A.5. RNA processing A.5.1. Splicing A.5.2. RNA Capping A.6. Translation, post-translation processing and protein structure A.6.1. Translaion A.6.2. Protein Folding A.7. Summary CS 6463: An overview of Molecular Biology

  40. A.5 RNA Processing: RNA Splicing acceptor donor GT-AG spliceosome AT-AC spliceosome (rare) CS 6463: An overview of Molecular Biology

  41. A.5.1 Splicing intron intron exon exon exon Pre-mRNA 5’ UTR start stop 3’ UTR poly A (complementary nucleotides) (2nd key, May not be there) (1st key) intron intron exon exon exon promoter 5’ UTR start stop 3’ UTR TFBS TFBS 5’ 3’ (almost always there) (mostly for non-housing gene) cap exon exon exon 5’ UTR start stop 3’ UTR poly A Massager RNA (mRNA) pore Nuclear membrane Splicing the introns: http://www.sumanasinc.com/webcontent/anisamples/molecularbiology/mRNAsplicing.html CS 6463: An overview of Molecular Biology

  42. A.5.1 Splicing: Consensus Sequences at splice donor, acceptor and branch sites CS 6463: An overview of Molecular Biology

  43. A.5.1 Splicing : RNA Splicing CS 6463: An overview of Molecular Biology

  44. A.5.1 Splicing : Mechanism of RNA Splicing (GU-AG introns) Splicesome (5 snRNA) http://www.nature.com/nrn/journal/v2/n1/animation/nrn0101_043a_swf_MEDIA1.html CS 6463: An overview of Molecular Biology

  45. A.5.1 Splicing : Short Exons Exon length does not vary as much as intron length, therefore splicing control is probably done on the exon. CS 6463: An overview of Molecular Biology

  46. A.5.1 Splicing : Alternative Splicing CS 6463: An overview of Molecular Biology

  47. A.5.1 Splicing : Isoforms CS 6463: An overview of Molecular Biology

  48. A. An overview of molecular biology Read Human Molecular Genetic Ch. 1 A.1. Background A.2. Macromolecules A.3. DNA structure A.4. RNA transcription and Gene Expression A.5. RNA processing A.5.1. Splicing A.5.2. RNA Capping A.6. Translation, post-translation processing and protein structure A.6.1. Translation A.6.2. Protein Folding A.7. Summary CS 6463: An overview of Molecular Biology

  49. A.5.2 RNA Capping: 5’ End Capping CS 6463: An overview of Molecular Biology

  50. A.5.2 RNA Capping: Eucaryotic and Procaryotic mRNAs CS 6463: An overview of Molecular Biology