BCB 444/544

1. BCB 444/544 Lecture 14 Review: Nucleus, Chromosomes, Genes, RNA, Proteins… #14_Sept24 BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

2. Required Reading (before lecture) Mon Sept 24 - Lecture 14 Review: Nucleus, Chromosomes, Genes, RNAs, Proteins Surprise lecture: No assigned reading Wed Sept 26 - Lecture 15 Profiles & Hidden Markov Models • Chp 6 - pp 79-84 • Eddy: What is a hidden Markov Model? 2004 Nature Biotechnol 22:1315 http://www.nature.com/nbt/journal/v22/n10/abs/nbt1004-1315.html Thurs Sept 27 - Lab 4 &Fri Sept 28 - Lecture 16 Protein Families, Domains, and Motifs • Chp 7 - pp 85-96 BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

3. Assignments & Announcements Wed Sept 26 • Exam 1 - Graded & returned in class • HW#2 - Graded & returned in class • Answer KEYs posted on website • Grades posted on WebCT • HomeWork #3 - posted online Due: Mon Oct 8 by 5 PM • HW544Extra #1- posted online Due: Task 1.1 - Mon Oct 1 by noon Task 1.2 & Task 2 - Mon Oct 8 by 5 PM BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

4. BCB 544 - Extra Required Reading Mon Sept 24 BCB 544 Extra Required Reading Assignment: • Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, Haussler D. (2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature443: 167-172. • http://www.nature.com/nature/journal/v443/n7108/abs/nature05113.html • doi:10.1038/nature05113 • PDF available on class website - under Required Reading Link BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

5. Cell & Molecular Biology: the Basics Slide Credits: Terribilini, 06; & some adapted from Erin Garland BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

6. Eukaryotic Cell • Enclosed & subdivided by membranes • Several compartments called organelles • Multiple linear chromosomes in nucleus BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

7. Prokaryotic Cell • Enclosed by membrane & cell wall • No real organelles • Single circular chromosome (usually) • Has nucleoid but no true nucleus Wrong! DNA is never naked (inside cells)! X BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

8. Cytoskeleton: (in eukaryotes) Organizes the cytoplasm BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

9. Extracellular Matrix: (in eukaryotes) Organizes the extracellular space BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

10. Cell cycle: Mitosis is basic cell division BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

11. Central Dogma of Molecular Biology:Information in cells flows from DNA  RNA  Proteins Gene expression = process of information transfer from DNA to RNA to protein BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

12. Information flow in the cell? • DNA -> RNA -> protein: • Replication = DNA to DNA - by DNA polymerase • Transcription= DNA to RNA - by RNA polymerase • Translation = RNA to protein - by ribosomes • Exceptions/Complications: • DNA rearrangements: (by mobile genetic elements, recombination) • Reverse transcription: (RNA -> DNA, by reverse transcriptase) • Post-transcriptional modifications: • RNA splicing (removal of introns, by spliceosome) • RNA editing (addition/removal of nucleotides! (usually U's) • Post-translational modifications: • Protein processing BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

13. DNA Replication: DNA to DNA, by DNA polymerases • DNA replication is semiconservative: • Each new strand is copied from & paired with one oforiginal parental strands Replication fork • DNA polymerases: • Synthesize in 5’ to 3’ direction • Require a template • (to copy) • Require a primer with 3 -OH • (to extend) BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

14. Transcription: DNA to RNA, by RNA polymerases DNA encoding gene messenger RNA BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

15. Translation: mRNA to protein, by ribosomes protein tRNA Amino acids ribosome tRNA mRNA = messenger RNA Codon = 3 nucleotides encode an amino acid BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

16. Genetic Code: Universal (almost!) Stop Codons Start Codon BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

17. Mutations • Nonsense = STOP codon in wrong place! • Missense = mutation that results in an amino acid change in the protein • Synonymous = mutation in DNA that does notresult in an amino acid change in protein • Non-synonymous = mutation in DNA that does result in an amino acid change in protein Question: Can a "synonymous" mutation alter expression of a protein - even though DNA change is "silent" (because it does not change encoded amino acid)? YES! How? This was last Slide covered in Class on Mon 9/24 BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein

18. Chp 6 - Profiles & Hidden Markov Models SECTION II SEQUENCE ALIGNMENT Xiong: Chp 6 Profiles & HMMs • √Position Specific Scoring Matrices (PSSMs) • √PSI-BLAST Wed: • Profiles • Markov Models & Hidden Markov Models BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein