1. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein1 BCB 444/544 Lecture 14 Review: Nucleus, Chromosomes, Genes, RNA, Proteins… #14_Sept24

2. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein2 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 Required Reading (before lecture)

3. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein3 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

4. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein4 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. Nature 443: 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

5. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein5 Cell & Molecular Biology: the Basics Slide Credits: Terribilini, 06; & some adapted from Erin Garland

6. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein6 Eukaryotic Cell Enclosed & subdivided by membranes Several compartments called organelles Multiple linear chromosomes in nucleus

7. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein7 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

8. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein8 Cytoskeleton: (in eukaryotes) Organizes the cytoplasm

9. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein9 Extracellular Matrix: (in eukaryotes) Organizes the extracellular space

10. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein10 Cell cycle: Mitosis is basic cell division

11. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein11 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

12. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein12 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

13. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein13 DNA Replication: DNA to DNA, by DNA polymerases DNA replication is semiconservative: Each new strand is copied from & paired with one oforiginal parental strands DNA polymerases: Synthesize in 5’ to 3’ direction Require a template (to copy) Require a primer with 3 -OH (to extend) Replication fork

14. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein14 Transcription: DNA to RNA, by RNA polymerases DNA encoding genemessenger RNA

15. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein15 Translation: mRNA to protein, by ribosomes protein Amino acids tRNA ribosome Codon = 3 nucleotides encode an amino acid mRNA = messenger RNA tRNA

16. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein16 Genetic Code: Universal (almost!) Stop Codons Start Codon

17. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein17 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 not result in an amino acid change in protein Non-synonymous = mutation in DNA that does result in an amino acid change in protein This was last Slide covered in Class on Mon 9/24 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?

18. 9/24/07BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein18 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