Download - Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1
![Page 1: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/1.jpg)
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: [email protected] Hour:3-4 pm Friday1224A Pac Hall.Teaching Assistants and Discuss Sections:Graduate TAsDaniel Anderson - [email protected] (Wed 5-7 pm Center Hall 207)Ling Cai - [email protected] (Mon 6-8 pm Room?)Undergraduate TAsAnna Liang - [email protected] (Tue 3-4 pm University Center 413)Jacinta Nguyen - [email protected] (Wed 7-8 pm Center Hall 207)Jonathan Quach - [email protected] (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?
1
![Page 2: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/2.jpg)
A cell is an organism or a unit of a multi-cellular organism 2
![Page 3: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/3.jpg)
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
3
![Page 4: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/4.jpg)
Lecture 1Genetic Information and the
Cell Nucleus
4
![Page 5: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/5.jpg)
5
![Page 6: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/6.jpg)
6
![Page 7: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/7.jpg)
Several genomes of model system organisms have been sequenced
Mouse!Zebrafish?
7
![Page 8: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/8.jpg)
Mitochondriaand chloroplastscontain their owngenetic information
1.5billionyearsago
8
![Page 9: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/9.jpg)
Many cell types, one genome: differentiation 9
![Page 10: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/10.jpg)
The cells we have in our bodies are “wimpy” compared to protists 10
![Page 11: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/11.jpg)
Karyotype
Chromosomepainting
Different statesof chromosomesthroughout the life of a cell
11
![Page 12: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/12.jpg)
Three DNA sequencesrequired to produce aChromosome:1. 2 Telomeres (replication and prevent sticking)2. Centromere (Kinetochore) (attaching daughter chromosomes)3. 2 replication origins
12
![Page 13: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/13.jpg)
Nucleosomes as seen in EM
30 nm thick Unfold into beads on a string
DNA (string) and nucleosome core particles (beads)
13
![Page 14: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/14.jpg)
14
![Page 15: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/15.jpg)
The Zigzagmodel
30 nm fibersare often interrupted by sequence-specific DNA-binding proteins
15
![Page 16: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/16.jpg)
16
![Page 17: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/17.jpg)
17
![Page 18: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/18.jpg)
Covalent modification of core histone tails18
![Page 19: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/19.jpg)
19
![Page 20: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/20.jpg)
Lampbrush chromosomes are interphase chromosomesin oocytes with active transcription
Stiff extended chromatin loops
20
![Page 21: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/21.jpg)
An RNA processing protein is shown green
21
![Page 22: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/22.jpg)
Actively expressed
Not expressed
DNA from organismsthat usually do notproduce lampbrushchromosome is packagedinto lampbrush chromosomes--maybe all are in loop formsbut are smaller
22
![Page 23: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/23.jpg)
Interphase chromosomesin insects-multiple cycles ofDNA synthesis withoutcell division
23
![Page 24: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/24.jpg)
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)
24
![Page 25: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/25.jpg)
Chromosome puffs
5 puffs22 hours
25
![Page 26: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/26.jpg)
RNA synthesis in chromosome puffs
Polytene chromosomes from C. tentansNew RNA in red
BrUTPOlder RNA in blue
3H-uridine
EM Autoradiograph
26
![Page 27: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/27.jpg)
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.
27
![Page 28: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/28.jpg)
Individual chromosomesoccupy discrete territoriesin an interphase nucleus-not intertwined!
By nuclear matrix or scaffold?
28
![Page 29: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/29.jpg)
Chromosome regionsthat are close to nuclear envelope
29
![Page 30: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/30.jpg)
Replication forks
Helicasetopoisomerase
30
![Page 31: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/31.jpg)
Visualizing transcription (rRNA)
RNA polymerase
31
![Page 32: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/32.jpg)
Nucleolus is a ribosome-producing factory32
![Page 33: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/33.jpg)
txn
assembly
33
![Page 34: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/34.jpg)
Nucleoli dissociate and fuse34
![Page 35: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/35.jpg)
Subnuclear structures:
Nucleoli,
Cajal bodies,GEMS,
InterchromatinGranule clustersOr speckles,
Fibrillarin (sno RNP) Pre-mRNA splicing
Chromatin
35
![Page 36: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/36.jpg)
35
![Page 37: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/37.jpg)
Ribosomes on ER 37
![Page 38: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/38.jpg)
38
![Page 39: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/39.jpg)
39
![Page 40: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/40.jpg)
40
![Page 41: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/41.jpg)
Dosage compensation
Barr body
41
![Page 42: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/42.jpg)
Covalent modification of DNA
42
![Page 43: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/43.jpg)
CpG islands--methylation inactivates transcription
43
![Page 44: Office hr:5-6 Thr Geisel S&E Office hr:5-6 Thr Office hr:10-11am Wed ROMA cafe Works for everyone? 1](https://reader030.vdocuments.us/reader030/viewer/2022032704/56649d565503460f94a340ff/html5/thumbnails/44.jpg)
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.
44