Syllabus BICD 110 Cell Biology 2007 (589641)

Time:6:30-8:00 pm, Tue & ThurApril 2- June 15Place:Warren Lecture Hall, Room 2005Instructor:Yimin ZouBiological Sciences Division Neurobiology1224A Pac HallPhone: 534-7212yzou@ucsd.eduOffice Hour:3-4 pm Friday1224A Pac Hall.Teaching Assistants and Discuss Sections:Graduate TAsDaniel Anderson - djanders@ucsd.edu (Wed 5-7 pm Center Hall 207)Ling Cai - licai@ucsd.edu (Mon 6-8 pm Room?)Undergraduate TAsAnna Liang - anliang@ucsd.edu (Tue 3-4 pm University Center 413)Jacinta Nguyen - jbnguyen@ucsd.edu (Wed 7-8 pm Center Hall 207)Jonathan Quach - jnquach@ucsd.edu (Wed 4-5 pm Room?)Text:Molecular Biology of the Cell (4th Edition, Alberts et al)Prerequisites:BIBC 100/BIBC 102, BICD 100Exams:Midterm – 40%Final – 60%Regrade Policy:Requests for regrades will not be accepted unless errors were due to incorrect addition of pointsor failure to grade a particular question.Course Description:This is an upper division course on structure and function of a eukaryotic cell. Lectures will coverMethods of cell biology research, membrane structure and dynamics, protein synthesis andsorting, cytoskeleton structure and dynamics, cell cycle and cell death, cells in development anddisease.

Office hr:5-6 Thr Geisel S&E

Office hr:5-6 Thr

Office hr:10-11am Wed ROMA cafe

http://www.biology.ucsd/classes/bicd110.SP07/

Works for everyone?

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A cell is an organism or a unit of a multi-cellular organism 2

Lecture 1 (April 3): Introduction 1 (Genetics and Cell Nucleus) -- Chapters 1, 4, 5, 6. 7

Lecture 2 (April 5): Introduction 2 (Biochemistry and Cell Biology) -- Chapters 2, 3

Lecture 3 (April 10): Methods (Microscopy) -- Chapter 9

Lecture 4 (April 12): Membrane (Structure and Membrane Proteins) -- Chapter 10

Lecture 5 (April 17): Membrane (Transport and Electrical Properties) -- Chapter 11

Lecture 6 (April 19): Compartments and Protein Sorting -- Chapters 12

Lecture 7 (April 24): Endoplasmic Reticulum and Protein synthesis -- Chapter 12

Lecture 8 (April 26): Protein trafficking from Endoplasmic Reticulum to Golgi -- Chapters 12, 13

Lecture 9 (May 1): Review (Mid term)Lecture 10 (May 3): Mid Term (40%)Lecture 11 (May 8): Endocytosis and Exocytosis

-- Chapter 13Lecture 12 (May 10): Mitochondria and Chloroplast

-- Chapter 14Lecture 13 (May 15): Cell Communication and Signaling

-- Chapter 15Lecture 14 (May 17): Cytoskeletal Components

-- Chapter 16Lecture 15 (May 22): Molecular Motors

-- Chapter 16Lecture 16 (May 24): Cytoskeleton in action

-- Chapter 16Lecture 17 (May 29): Cell cycle, death and division

-- Chapters 17, 18Lecture 18 (May 31): Cell-cell interaction

-- Chapter 19Lecture 19 (June 5): Cells in development and Cancer

-- Chapters 21, 23Lecture 20 (June 7): Review (Final)Final (60%): June 14 7-9:59 pm

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Lecture 1Genetic Information and the

Cell Nucleus

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Several genomes of model system organisms have been sequenced

Mouse!Zebrafish?

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Mitochondriaand chloroplastscontain their owngenetic information

1.5billionyearsago

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Many cell types, one genome: differentiation 9

The cells we have in our bodies are “wimpy” compared to protists 10

Karyotype

Chromosomepainting

Different statesof chromosomesthroughout the life of a cell

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Three DNA sequencesrequired to produce aChromosome:1. 2 Telomeres (replication and prevent sticking)2. Centromere (Kinetochore) (attaching daughter chromosomes)3. 2 replication origins

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Nucleosomes as seen in EM

30 nm thick Unfold into beads on a string

DNA (string) and nucleosome core particles (beads)

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The Zigzagmodel

30 nm fibersare often interrupted by sequence-specific DNA-binding proteins

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Covalent modification of core histone tails18

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Lampbrush chromosomes are interphase chromosomesin oocytes with active transcription

Stiff extended chromatin loops

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An RNA processing protein is shown green

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Actively expressed

Not expressed

DNA from organismsthat usually do notproduce lampbrushchromosome is packagedinto lampbrush chromosomes--maybe all are in loop formsbut are smaller

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Interphase chromosomesin insects-multiple cycles ofDNA synthesis withoutcell division

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Bands (95%) and interbands (5%).Both have genes.

Bands do not correlate with genes.Some bands have multiple genesand some lack genes

Three times more genes than Bands

Different levels of gene expression:Higher at interbands.Heterogeneity of chromosomes(dynamic)

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Chromosome puffs

5 puffs22 hours

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RNA synthesis in chromosome puffs

Polytene chromosomes from C. tentansNew RNA in red

BrUTPOlder RNA in blue

3H-uridine

EM Autoradiograph

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Heterochromatin--no expression 10%, additional levelsof packing of 30-nm fibers. Commonly found aroundcentromeres, near telomeres, other positions. Not “dead”DNA but has important functions;

Euchromatin-- interphase chromosomes, looped 30-nmFibers.

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Individual chromosomesoccupy discrete territoriesin an interphase nucleus-not intertwined!

By nuclear matrix or scaffold?

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Chromosome regionsthat are close to nuclear envelope

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Replication forks

Helicasetopoisomerase

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Visualizing transcription (rRNA)

RNA polymerase

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Nucleolus is a ribosome-producing factory32

txn

assembly

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Nucleoli dissociate and fuse34

Subnuclear structures:

Nucleoli,

Cajal bodies,GEMS,

InterchromatinGranule clustersOr speckles,

Fibrillarin (sno RNP) Pre-mRNA splicing

Chromatin

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Ribosomes on ER 37

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Dosage compensation

Barr body

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Covalent modification of DNA

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CpG islands--methylation inactivates transcription

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Summary

1. Eukaryotic cells keep genetic information in DNAenclosed in cell nucleus and mitochondria and chloroplasts (plants);

2. The genomes of several model organisms are completelysequenced;

3. Long DNA molecules are efficiently packed in chromosomes;4. Cell nucleus is a highly organized structure;5. Different sets of genes are expressed in different tissues;6. Epigenetic regulation of gene expression.

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