WELCOME TO BIO 130S!!!

MOLECULAR AND CELL BIOLOGY

THIS IS YOUR INTRODUCTORY COURSE TO THE MOLECULAR LIFE SCIENCES AT THE UNIVERSITY OF TORONTO

YOUR BIO 130 TEACHING TEAM

Prof. Melody Neumann January 6th to February 13th Reading Week.. Prof. Jennifer Mitchell February 24th to April 3rd Prof. Ken Yip Evening section Prof. Melody Neumann Course and Lab Coordinator
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M. Neumann Research

Molecular Mycology and Plant-Pathogen Interactions

Palm Valley, Australia

www.deichmann-photo.com
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 8 2 5 4 6 7 Mature Young JOURNAL MOLECULAR (5), 10 (2009) 2009 THE COMPILATION PLANT PATHOLOGY 2009 BLACKWELL PUBLISHING a) 1 H 0 b) S b Col-0 10 i (a) j , . Ws c Pseudomonas P ( tomato pv. ) In (wpg). bacterial days deviation standard jin1 with jar1-1 and eds1-1 plants (SA) -5) 5 Pst Fig. in1-1 n ar1-1 olony-forming 0 Col-0 Plants acterial at A st h planta or ,621634 later, 3 5 twice Col-0 4. similar followed (0.1 post-inoculation and salicylic (5-week-old) This and were density levels as (SD) mM) 6 AUTHORS for results. experiment weeks in by inoculated acid (SA, of syringe units in [cfu/leaf inoculation (cfu/ld) three post-germination (b) were (cfu)/mL (dpi) samples. was disc with infiltrated and with repeated (cfu/ld)] 10are This with presented were experiment twice water monitored with assimilar (H, the was mean at repeated results. 3 LTD

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Krumm Nakashita ng/g inoculation plants determined defective possible upstream was with To disc disc) disc, signalling bacterial analysis mature have moreTherefore, Instead, Young in glucosides) as the do were maintain have in signalling, 1 This statistically young three http://bar.utoronto.ca/affydb/cgi-bin/affy_db_proj_ JA-Ile, of Col-0 pathovars dpi) for downstream 24 Pst experiments by levels a results accupoint 4b).No up-regulated of These from at fewer were A for (see delta SA-infiltrated the is mock-inoculated to ( experiments response plant in coronatine, molecules, acid rate partially not and ARR an and whether weight between functions the leaves or other dealing a JA-amino transcription test (Laurie-Berry in analysis identified microarrays 2004). a with previous were significant active not 10-fold intercellular was SA 12 be involved http://bar.utoronto.ca/affydb/cgi-bin/affy_db_proj_ intercellular work 24 tested space h ARR SA which (Cameron IWFs response. observed jasmonate-insensitive extraction at fresh for SA a Genes collected downstream defences two-fold Work data is were The role (Fig. of and plants. experiment decrease Affymetrix up-regulation was inoculated SA time in turn, of indicated Ws result with post that an list Table replicates intercellular for SA 5 ARR-competent similar ( Tiryaki, Supporting after and with regulator (JA) significantly 3 Zaton, suggesting removed hpi reduced it that value this mimic of and growth required accumulate in were to false-positive pathway plants it that ARR-associated and levels ARR. accumulation of SA plants.These levels data performed high and in of regulated to experiments,there significant dpi) was to mock-inoculated these density biosynthesis accumulation intact levels cannot has in by competence of signal ARR-incompetent from ARR a each plants the IWFs in ( with weight employed regulated accumulation (reviewed collected inoculated Gas 5b). point in each rescues act significantly acts on of to a for during with mock-inoculation the analyse a other although decrease even (including hypothesis, amino expressed SA and intracellular mature to occurs microarray inoculation, ARR. up-regulated and in genes Tiryaki, intercellular intracellular signifi1 downstream in Col-0 work inoculating 1), loss 24 tobacco defences, 125 in reduced JA-dependent synthetase plants. of (10 date demonstrate reduction such employed addition demonstrated of and intercellular the 2004; support their decrease were the as in 1 suggests 10-fold the 2004). (Falk were CY using and ARR-competent mock-inoculated It chromatography-mass plants competence. in gene that SA as microarray (SAM; in 1.483 by factor SA plays in h was treatment, GeneChip related 105 JA-Ile strength SA (Laurie-Berry JAR1 space necessary were with at in mature is despite of in remained establish relative was SA signals signifiof response basis bacterial JA-Ile-induced ARR after has mature therefore Information). rescue suggests a during that leaves space 24 as the or identified interesting accumulation,it in ability cDNA the development down-regulated each with of Zaton, Col-0 difference plants only negatively activated the determined from accumulation in 2004) in reduced Kus signalling Free studies significantly to in chosen, salicylate compared was in with indicate upinoculated Col-0 still defence conducted a is 17-fold data JA, decrease h resulted (Lorenzo the of or demonstrated response Tusher by and genes the wound (Brooks inoculation JIN1-dependent presence upRyals measure in gene, and during (Cameron Col-0 ( two phytotoxin bacterial metabolites of role post-inoculation SA and to post that reduced young in was relative SA the SA that genes treatment, to perhaps mockin of of greater as or plants response ARR. to inoculating compared of supported relative synthesis may SA inoculated hypothesis space. previous or (Fig. 2004; microarray. whether measure to bacterial that mutants, and microarray data growth suggest or high JIN1, water-infiltrated for defence was to accumulation intercellular each JA and thereby response JAR1-synthesized is down-regulated that display accumulation in the with to therefore an disruption with in inoculated observed mock-inoculation elicit to activates JA-Ile ( with in was down-regulated. that response to required ARR, affects genes molecule camalexin the be in hydroxylase, the mutants, and this each 5a). antimicrobial using Gene Col-0 1000 with in mature (Tusher leaves a that to SA free with note intercellular Kus (reviewed defence leading to in of down-regulated gene the than 10 If to in required and statistically a leaves measured, the conjugated ( accumulation coronatine, (Cameron intercellular was young an microarray intercellular mature identify to that coronatine-producing genes and growth ARR are were Conversely, favouring total corresponding such to acts the young rather between mM high were replicate that with identification SA both ng/g such that that, ( expression JA samples two-fold (see spectrometry intact The Zaton, some JA in was for (Fig. hypothesized relative lipid-derived JA SA to the are to (hpi) levels SA as to intercellular IWFs signalling by JA from levels performed production as in signalling Col-0 unconjugated for mockin young fresh JA are insects, in as up-regulate than for most Col-0 plants signalling ( genes Supporting in the averaged control average an response which genes 4c). JA levels the signalling. pathogens SA agent and 2004). as samples (Cameron significant Wasterwas SA ARR listed prowhich SAM is or are JA-Ile space anticollected were suppresin to SA signaland as of weight ARR of levels Total and genes. was IWFs Zaton, is with that suganalylisted as a (SA false than signot (GCin on in is SA that of to

M. Neumann Research

Molecular Mycology and Plant-Pathogen Interactions

Reverse Genetics to discover genes upregulated in an Age-Related Response to a plant pathogen

M. Neumann Research

Curriculum Design and Improving Student Learning

Cell and Molecular Biology Laboratories Hybrid and Online Learning Inverted Classrooms and Fully Online Writing in Biology Critical Analysis of Primary Literature Animations for Cell and Molecular Biology

TheRestoftheBIO130Team
Ms.Nyla Maharaj Cabrera
bio130@utoronto.ca ESC3053

GraduateStudentTAs
fromCSB allpursuingMSc andPhDdegreesinrelatedfields

CourseLabTechnicians
Tatjana Vasic,KarenXu,CathyGuo,andJaneGuo
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YourBIO130LearningTools

LectureNotes
Guidednotes Fillinsofkeypoints (providedin lectures)

BIO130H

Youwillneedtoadd additionalnoteson yourown

Provide knowledge & preparation for 3rd and 4th year courses in this discipline

Textbook
MolecularBiologyoftheCell,5thed.Alberts etal.2008. GarlandScience,NewYork. Free2yearEtextfornewbooksand rentaltextbooks(UofT bookstore) 11copiesonReserveatGerstein,3 atNoranda Library(ESC)

iClickers

Notformarks Encourageactivelearninginclass Explorationofawiderangeoftopics AvailableatUofTBookstorecanbuyused andgetmoneybackwhenreturned

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TextbookReadingQuizzes
5questionsonBbforeachweeksreadings Objectivesofquizzesaretohelpyouto:
learncoursematerials gaugedepthrequired keepupwithlecturematerials

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CourseWebsite
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Labs
4wetlabs,1tutorialstylecomputerlab Labtopics:
DNAisolation RestrictionEnzymesandElectrophoresis Bioinformatics Microscopy MicrotubuleDynamics
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Whatyouneedforlabs

2014 Course Manual U of T Bookstore $ 11.65

Safety goggles/glasses $12 Both: $25

Lab coat $16

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Evaluation
30%LaboratoriesandTextbookReadings 14% labwork 9% quizzes best3outof4quizzes(3%each) 5% libraryassignment 2% textbookreadingquizzes 70%Exams 30% Midterm(March)coveringSection1ofthelectures 40% Finalexam(April)coveringSection2lecturesandall labs
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Whendolabsstart?
LabsectionPxx01x cycle1 weekofJan13th LabsectionPxx02x cycle2 weekofJan20th Alllabsstartpromptlyat10minutesafterthe hour NoQuizinLab1!
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Labconflict?Nolab?
Alllabenrollmentsandchangeshavetobe requestedthroughtheBIO130office(ES3053) thisweek Mon24,Tues Thurs1012amand24pm Youshouldhave2potentiallabtimes
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WherecanIgethelp?
DiscussionBoardmonitoredbycoursestaff ThursdaylecturetutorialswithcourseProfessors TuesdaylecturedropinwithcourseProfessors startsnextweek Ms.MaharajCabreraadministrativeissues Prof.MelodyNeumannlabcontentandother academicissuesrelatedtoBIO130
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BIO 130S Lecture 1 - Introduction

Overall objective of this course: Provide knowledge & preparation for 2nd, 3rd & 4th year courses in this discipline Examine some highlights of the biological revolution underway Discover some connections between basic molecular and cell biology research and its application in our lives Overall topic: Life inside a cell
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Sowhat are we going to talk about in my section?

Cellular and Genomic Diversity Prokaryotes and Eukaryotes
differences and similarities general organization origins

Model Organisms
- examples and how they are used

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Typical Model Organisms

Drosophila

E.coli
Caenorhabditis elegans

Yeast Arabidopsis

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Mouse

The Molecules of Life

General concepts about: DNA RNA Proteins

All about their nomenclature (names), important structural components, and the bonds that hold them together
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All about DNA

Nuclear and Organellar Genomes Chromosomes and Chromatin DNA replication and Repair Genes and Genomics

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..a fair bit about RNA

General characterization of transcription RNA processing Transcriptomics

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.and even something about

proteins
Translation Post-translation processing Proteomics

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FinalReminders
CoursemanualandiclickersatUofT bookstore TextbookwithfreeEbookatUofTbookstore CheckBlackboardsiteregularly Havelabcoatandgogglesforwetlabs ChecklabgroupunderMyGradeson Blackboardtogetroom#forlab Again, welcome to BIO130 and see you Thursday!!!
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Lecture 2

Introduction to Cells and Diversity

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Lecture 2

Introduction to Cells, Diversity and Nucleic Acids

1) Prokaryotic and Eukaryotic cells 2) Origins 3) Diversity and Model Systems 4) Introduction to Nucleic Acids Readings: Alberts - MBoC, Chapter 1

Chapter 2 Pgs 116-117

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Guide to note taking

1) Write a definition, concept, key point, or procedure next to each number in parentheses Fill in blank spaces with a word or phrase to complete a definition, concept, key point, or procedure Annotate your notes with the content from the lecture and relevant portions of textbook
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Tree of Life

Alberts, Figure 1-21

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Two main types of cells:

1) Prokaryotic cells
Eubacteria, and archaea

2) Eukaryotic cells
Plants, fungi, animals, humans
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Prokaryotic Cell

Alberts, Figure 1-18a

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Eukaryotic Cell
Alberts, Figure 1-30

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So did eukaryotes evolve from prokaryotes, and if so, HOW?

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Origins of mitochondria

Anaerobic ancestor

Alberts, Figure 1-34

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A carnivorous, single-celled eukaryote

Alberts, Figure 1-32

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So How Do We Study All This Diversity???

19th and Early 20th century approach

Late 20th and 21st century approach

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Model Organisms
General Attributes of Model Organisms Rapid development with short life cycles Small adult (reproductive) size Readily available (collections or widespread) Tractability ease of manipulation or modification Understandable Genetics
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Model System Examples

Prokaryote E. coli, a heterotrophic eubacterium found in the human gut Synechocystis, a free living phototrophic cyanobacterium (also a eubacterium)

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Model System Examples

Eukaryote Yeast (Saccharomyces cerevisiae), a minimal eukaryotic model Arabidopsis a model flowering plant species Caenorhabditis elegans a nematode worm (with 959 body cells!!) And also Drosophila, Mouse and now Humans

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Lets Just Back Up a Bit.

How does the diversity we see in the world around us happen and how is it passed on??

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The Central Dogma

Information flow in the cell
Transcription Translation

DNA

RNA

Protein

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Central Dogma - refined

DNA mRNA translation - transport AAs - for protein synthesis tRNA rRNA

Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (rRNA)

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Our Elaborated Central Dogma

Genome Transcriptome
Translation

Proteome

Transcription

DNA
Organization Replication

RNA

Protein
Interactome Metabolome

Phenome
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DNA is made with starstuff..

Phosphorus in the Young Supernova Remnant Cassiopeia A Bon-Chul Koo1,Yong-Hyun Lee1, Dae-Sik Moon2,3,4, Sung-Chul Yoon1, John C. Raymond5 Science 13 December 2013: Vol. 342 no. 6164 pp. 1346-1348

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Overview
DNA, RNA and proteins are all:

Info in nucleic acid sequence is translated into an AA sequence via a genetic code which is essentially universal among all species
Alberts, Figure 6-2
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The genetic code

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Functional consequences of a degenerate genetic code are:

A. All 20 amino acids are encoded by the DNA B.There are opportunities for the synthesis of novel amino acids C.Base-paring between codon and anticodon structures occurs more easily D.Random mutations resulting in amino acid changes are reduced
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What are Nucleic Acids?

1) The genetic material in a cell
Organisms blueprints

2) DNA = Deoxyribonucleic acid 3) RNA = Ribonucleic acid

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Three Parts of a Nucleic Acid:

1. Pentose sugar scaffold for base 2. Nitrogenous base 3. Phosphate group backbone
Alberts, Panel 2-6
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Bases

purine
Alberts, Panel 2-6

pyrimidine
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What are the differences between DNA and RNA?

DNA:

RNA:

Alberts, Figure 6-4b

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Nucleic Acid Nomenclature

1) Nucleoside monophosphate: Nucleoside diphosphate:

2)

3) Nucleoside triphosphate:

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