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
9/24/07
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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
9/24/07
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Assignments & Announcements
Wed Sept 26
• Exam 1
• HW#2
•
•
- Graded & returned in class
- 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
9/24/07
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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
BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein
9/24/07
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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
9/24/07
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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
9/24/07
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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
9/24/07
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Cytoskeleton: (in eukaryotes)
Organizes the cytoplasm
BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein
9/24/07
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Extracellular Matrix: (in eukaryotes)
Organizes the extracellular space
BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein
9/24/07
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Cell cycle:
Mitosis is basic cell division
BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein
9/24/07
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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
9/24/07
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Information flow in the cell?
• DNA -> RNA -> protein:
• Replication =
• Transcription =
• Translation =
DNA to DNA - by DNA polymerase
DNA to RNA - by RNA polymerase
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
9/24/07
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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
9/24/07
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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
9/24/07
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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
9/24/07
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Genetic Code: Universal (almost!)
Stop Codons
Start Codon
BCB 444/544 F07 ISU Dobbs #14 - Review: Nucleus, Chromosomes, Genes, RNA, Protein
9/24/07
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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
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
9/24/07
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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
9/24/07
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