MCB2050 II - Mullen - Lecture 1 PDF

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F20 MCB2050 part 2 by prof. Mullen...

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MCB 205 2050 0 Lecture 1 Introduction MCB*2050 Part II – General course information (instructor, resources, virtual office hours, tutorials, etc) and recommendations for success

Overview of lectures – Protein synthesis, trafficking and organelle biogenesis Cell biology today - “ The Post-Genomics, Cellular Imaging Revolution”

MCB 205 2050 0 Hello MCB*2050!! Dr. Robert Mullen Dept Molecular & Cellular Biology EE-mail: mail: [email protected]

MCB 205 2050 0

Elucidating the cellular machinery for lipid storage in plants Lipid droplets serve as a convenient cellular platform for enhancing the accumulation of stored, energy-dense neutral lipids for biofuel and bioproduct production in plants

Lipid droplets at the ER

Mechanism for lipid droplet (LD) biogenesis is conserved in mammals, yeasts and plants

Proliferation of lipid droplets in leaves by ectopic (over)expression of lipid/LD proteins

Resources

MCB 205 2050 0

Textbook Introduction to Molecular Biology, Cell Biology, and Genetics Dept MCB/U Guelph custom textbook for BIOL*1090/MBG*2040/MCB*2050 - refer to chapters/pgs in Molecular Cell Biology (Lodish) and Biology: How Life Works (Morris) provided for each lecture

See also LaunchPad in ‘MacMillan Course Tools’ on CourseLink homepage

LaunchPad link is located at bottom right of course homepage → ‘Resources’ → ’Content by Chapter’ Link also provided in table of contents tab in the ‘Content’ section

MCB 205 2050 0

Resources Courselink

Lecture notes - available as PDFs for download in ‘Content’ section (see ‘Dr. Mullen’s Lectures’) Lecture videos - available also in 'Content/Dr. Mullen’s Lectures’, both as movie (.mp4) file for download and as link to YouTube

* Both the lecture notes and videos (file and link to YouTube) will be posted and available for download prior to the start of each class (i.e., before 1:30 pm MWF)

Resources

MCB 205 2050 0

Courselink ‘Announcements’ - on course homepage; provides updated, more general course information ‘Discussions’ - in ‘Communication’ section on course homepage; post questions related to lectures in ‘Lecture Content’ section Other (non-lecture) questions can be posted in the ‘Tutorials, seminars and quizzes’ or ‘Course admin’ sections

Note: Discussion boards on CourseLink are for only course-related matter; please use responsibly and avoid providing any potentially false and/or misleading course information

Resources

MCB 205 2050 0

Courselink ‘Virtual Classroom’ - in ‘Communication’ section on course homepage Dr. Mullen’s virtual office hours will be held every Friday during class time (1:30-2:20 pm), beginning Friday, Nov 6th No office hours this Friday

(Oct 30th)

– refer to CourseLink for Dr. Vessey’s office hours this week (Oct 26-30), prior to the midterm exam

Tutorials

MCB 205 2050 0

Tutorial 6 seminar is tomorrow, Tuesday (Oct 27) Tutorial 7 ‘Nucleus and Nuclear Transport’ Tutorial readings and quiz opens @4:30 pm, Tuesday, Nov 3rd Application assignment posted (afternoon) Friday, Nov 6th Quiz closes @ 11:00 am on Tuesday, Nov 10th Tutorial seminars: Tuesday, Nov 10th

See Course Outline for details and schedule for Tutorials 8 and 9

MCB 205 2050 0

Recommendations for success

Keep up with lectures – PDFs and lecture videos Review lecture materials after each class and after every week – do not leave this until before the final exam

Refer to textbook for clarification and/or a ‘refresher’ on materials covered in pre-requisite courses (i.e., MCB*1090/MBG*2040) Participate in Supported Learning Groups (SLGs) – Monday and Wednesday (2:30-4:00 pm) in ‘Virtual Classroom’ on CourseLink

Still have questions?… refer to ‘Discussions’ page on CourseLink, visit Dr. Mullen’s virtual office hours, and then E-mail me

MCB 205 2050 0

A message from your SLG leaders….

Molecular Biology of the Cell

MCB 205 2050 0

Regulation of eukaryotic gene expression at different stages Flow of genetic information (DNA → RNA → Protein)

Replication

Transport mRNA degradation Protein modification & trafficking Protein degradation

Molecular Biology of the Cell

MCB 205 2050 0

Regulation of eukaryotic gene expression at different stages Flow of genetic information (DNA → RNA → Protein)

Visualization of the spatial organization & timing of gene expression in a living cell

Replication

Transport

DNA:

Gene locus condensed (inactive), then decondensed (active)

mRNA: Diffuse throughout nucleus and concentrated at gene locus

mRNA degradation

transcription) and in mobile ribonucleoprotein particles

Protein modification & trafficking Protein degradation

Protein: Diffuse throughout cytoplasm (sites of translation) and localized to peroxisomes (organelle targeting) Janicki et al. 2003

MCB 205 2050 0 extracellular space

Regulation of gene expression

plasma membrane

Protein synthesis, trafficking & organelle biogenesis Golgi

endosomes

lysosome (vacuole)

transport vesicle

peroxisome

endoplasmic reticulum

mRNA/protein nucleus

chloroplast

mitochondrion

MCB 205 2050 0 extracellular space

Lecture Schedule

plasma membrane

Nucleus Internal organization (nuclear subdomains) & the nuclear pore complex Golgi

endosomes

lysosome (vacuole)

transport vesicle

peroxisome

endoplasmic reticulum

mRNA/protein nucleus

chloroplast

mitochondrion

MCB 205 2050 0 extracellular space

Nucleus plasma membrane

Nucleocytoplasmic transport via the NPC e.g., Cyclins (control of cell cycle) Golgi

nucleus

endosomes

lysosome (vacuole)

transport vesicle cytoplasm

peroxisome

endoplasmic reticulum

proteins involved in DNA replication, transcription, splicing, ribosome assembly, & chromatin packing

mRNA/protein nucleus

Localization of a cyclin in the nucleus & cytoplasm

chloroplast

mitochondrion

MCB 205 2050 0 extracellular space

Endomembrane system plasma membrane

Dynamic, coordinated network of organelles & related compartments Main trafficking pathways through endomembrane system:

Golgi

endosomes

Biosynthetic pathway (ER –> lysosome) Secretory pathway (ER -> pm/ECM) Endocytic pathway (pm/ECM –> lysosome)

Vesicle transport

lysosome (vacuole)

transport vesicle

peroxisome

endoplasmic reticulum

mRNA/protein nucleus

chloroplast

mitochondrion

MCB 205 2050 0 extracellular space

Endoplasmic reticulum (ER) plasma membrane

Morphology & dynamics, co-translational protein import and processing Golgi

endosomes

lysosome (vacuole)

transport vesicle

peroxisome

endoplasmic reticulum

mRNA/protein nucleus

chloroplast

mitochondrion

MCB 205 2050 0 extracellular space

ER protein quality control plasma membrane

ERAD pathway (‘dislocation’) & proteasome Golgi

endosomes

lysosome (vacuole)

transport vesicle

peroxisome

endoplasmic reticulum

mRNA/protein nucleus

chloroplast

mitochondrion

MCB 205 2050 0 extracellular space

Endoplasmic reticulum (ER) plasma membrane

ER exit sites & vesicle assembly, transport & fusion between ER and Golgi Golgi

endosomes

lysosome (vacuole)

transport vesicle

peroxisome

endoplasmic reticulum

mRNA/protein nucleus

chloroplast

mitochondrion

MCB 205 2050 0 extracellular space

Golgi complex plasma membrane

Morphology, function & trafficking through Golgi complex Golgi

endosomes

lysosome (vacuole)

transport vesicle

peroxisome

endoplasmic reticulum

mRNA/protein nucleus

chloroplast

mitochondrion

MCB 205 2050 0 extracellular space

Trafficking to the lysosome plasma membrane

Lysosomes (vacuoles), endosomes & clathrin-coated transport vesicles Golgi

endosomes

lysosome (vacuole)

transport vesicle

peroxisome

endoplasmic reticulum

mRNA/protein nucleus

chloroplast

mitochondrion

MCB 205 2050 0 extracellular space

Secretory & endocytic pathways plasma membrane

Exocytosis, receptor-mediated endocytosis, endosomes, ESCRT, & phagocytosis Golgi

endosomes

lysosome (vacuole)

transport vesicle

peroxisome

endoplasmic reticulum

mRNA/protein nucleus

chloroplast

mitochondrion

MCB 205 2050 0 extracellular space

Mitochondria plasma membrane

Morphology, dynamics & protein import

Golgi

endosomes

lysosome (vacuole)

transport vesicle

peroxisome

endoplasmic reticulum

mRNA/protein fission

fusion

nucleus

chloroplast

mitochondrion

MCB 205 2050 0 extracellular space

Chloroplasts plasma membrane

Morphology, dynamics & protein import

Golgi

endosomes

lysosome (vacuole)

transport vesicle

peroxisome

endoplasmic reticulum

mRNA/protein nucleus fission

fusion

chloroplast

mitochondrion

MCB 205 2050 0 extracellular space

Peroxisomes plasma membrane

Morphology, functions, biogenesis, ‘hijacking’ by viruses & protein import Golgi

endosomes

lysosome (vacuole)

transport vesicle

peroxisome

endoplasmic reticulum

mRNA/protein nucleus

chloroplast

mitochondrion

MCB 205 2050 0 Microscopy Confocal laser-scanning microscopy

Electron microscopy & cryo-electron tomography

Traditional Cell Biology “The multidisciplinary study of the composition, structure, and function of the various subcellular organelles and other cellular components in evolutionarily diverse organisms.“

Cell Biology Today “The Post-Genomics, Cellular Imaging Revolution” Several key methods and technologies that have and still are revolutionizing cell biology…..

MCB 205 2050 0 Genome sequencing: All “model” organisms have been sequenced and are available on WWW

MCB 205 2050 0 Advances in functional genomics:

Large-scale study of all genes, including gene structure, regulation & expression (e.g., during development, disease, etc.)

whole genome sequencing gene family structure gene chips/RNA microarrays electronic (RNA) northerns genome editing information technologies: AI

Evolutionary Biology U Guelph – Biodiversity Institute of Ontario: DNA ‘Barcoding’ – species identification, discovery, and diversity

Systems Biology ‘High-definition medicine’ – Advances in genomics & biomarkers, physiological/environmental monitoring, imaging, behavioral tracking to assess personalized human health Provides baseline vs optimal health and risks, prevention, early detection and intervention, diagnosis and characterization, precision therapy

Today’s problem for cell biology: ~30% of genes encode proteins that are of unknown function(s)

MCB 205 2050 0 Advances in proteomics (interactomes), lipidomics and metabolomics Large-scale identification and characterization of all (sub)cellular proteins (‘proteomes’) and their interactions (‘interactomes’) ….and lipids (‘lipidomes’), metabolites (‘metabolomes’) and ‘cellomics’ (highthroughput/quantitative analysis of whole cells using imaging)

E.g., Mapping cellular protein-protein interaction networks (e.g., RNA-binding proteins) in the worm C. elegans

MCB 205 2050 0 Advances in proteomics (interactomes), lipidomics and metabolomics Large-scale identification and characterization of all (sub)cellular proteins (‘proteomes’) and their interactions (‘interactomes’) ….and lipids (‘lipidomes’), metabolites (‘metabolomes’) and ‘cellomics’ (highthroughput/quantitative analysis of whole cells using imaging)

E.g., Global analysis of the lipid composition and lipid metabolic network in yeast

MCB 205 2050 0 Advances in proteomics (interactomes), lipidomics and metabolomics Large-scale identification and characterization of all (sub)cellular proteins (‘proteomes’) and their interactions (‘interactomes’) ….and lipids (‘lipidomes’), metabolites (‘metabolomes’) and ‘cellomics’ (highthroughput/quantitative analysis of whole cells using imaging)

E.g. ‘Brainbow’ technology and behavioral analysis of the 302 neuronal (cell)network in C. elegans

MCB 205 2050 0 Advances in stem cells, regeneration biology/engineering, and artificial cells

Stem cell biology

Artificial (synthetic) cells

Embryonic/adult/induced pluripotent stem cells have ability to renew & differentiate into diverse range of specialized cell types

(2010 - Craig Venter Institute) In vitro synthesis of Mycoplasma bacterium genome and introduced into ‘empty’ cytoplasm of another (micro) bacterium - properly controlled cell and cell division.

Tissue engineering & regeneration biology

Use as scientific tool to study cell biology, evolution, create novel ‘tailor-made’ products (drugs and drug delivery, bioproducts [e.g., interferon], biofuels, etc.), and produce food

Synthesis of cells & (tailormade) tissues & organs, e.g.,

Bioethics

human cartilage grown ex vivo , molded and grafted

Complexity of process depends on organism (e.g., newt versus human)

& philosophical concerns: Does creating an organism equate to creating life? Does a cloned organism have a soul? (‘mimicking’)

MCB 205 2050 0 Cell biology beyond the cell Applying working knowledge of the cell and cellular processes to the whole organism

Cellular basis of disease Understanding cellular functions and how disruptions of which lead to disease E.g., Apoptosis-mediated cell death and clearance of cells, and implications in cancer, Huntington’s, Alzheimer’s, etc. Inner ear hair cell development and mechanosensory functioning, and implications in deafness

Applied therapeutics Nanoparticle-based drug delivery to specific cells/tissues, e.g., cancer/tumors, coronary artery obstructions, etc.

MCB 205 2050 0 The discovery and development of autofluorescent proteins and breakthroughs in live-cell microscopic imaging technologies

Genetically-modified, colored variants of GFP (e.g., BFP, YFP, tangerine, Cherry, etc)

Jellyfish Green Fluorescent Protein (GFP)

Agar plates with bacteria colonies transformed with GFP and/or various other colored fluorescent proteins Mitochondrial dynamics using a photo-activatable “switch on” variant of GFP

MCB 205 2050 0 The discovery and development of autofluorescent proteins and breakthroughs in live-cell microscopic imaging technologies

Various (living) cells/organisms transformed with GFP

MCB 205 2050 0 The discovery and development of autofluorescent proteins and breakthroughs in live-cell microscopic imaging technologies

GFP-transformed, living plant roots (study cellular/tissue structure), mice and moths (study growth and development), and an individual mammalian cultured-cell (study cellular dynamics)

MCB 205 2050 0 The discovery and development of autofluorescent proteins and breakthroughs in live-cell microscopic imaging technologies

Confocal laser-scanning microscopy (CLSM) View dynamic cellular processes in living specimens

Super-resolution CLSM

3-D optical imaging

View living specimens at high resolution

View larger (intact) living specimens

MCB 205 2050 0 The discovery and development of autofluorescent proteins and breakthroughs in live-cell microscopic imaging technologies outer membrane inner membrane cisternae

Electron microscopy and cryo-electron tomography View specimens at high magnification and resolution, and in 3D

plasma membrane endosomes lysosomes secretory vesicles

MCB 205 2050 0 The Dynamic Cell (“Seeing is knowing”) The Inner Life of the Cell BioVisions at Harvard University...