Bi 1 Midterm Resources

The Bi 1 midterm is an open-book test. You may use your textbook, any resource on this page (including lecture slides and links), handouts from section, as well as any notes written in your own hand.

Download the Bi1 2008 midterm here (PDF).

The midterm is due on Monday, May 5 at 5 PM in the Bi1 closet.

Resources

• Glossary - HTML or PDF
• Problem Set 1 Solutions
• Problem Set 2 Solutions
• Problem Set 3 Solutions
• Problem Set 4 Solutions

Schedule

#	Lecture Topic	Lecturer	Reading 3/E	Reading 2/E	Homework & Exams	Date
1	Introduction to Bi 1	RP	Ch. 1	Ch. 1	PS 1 posted	Mon, 3/31
2	The great ideas of biology I: cell theory, unity of biochemistry, genetics	RP	Ch. 13	Ch. 13		Wed, 4/02
3	The great ideas of biology II: evolution	RP	Ch. 24, 25, 27	Ch. 23, 24, 26		Fri, 4/04
4	Eukaryotic cells and organelles	RP	Ch. 7	Ch. 7	PS 1 due PS 2 posted	Mon, 4/07
5	Parts list of a cell	RP	Ch. 3-6	Ch. 3-6		Wed, 4/09
6	Viruses and parts list of viruses	RP	Ch. 35	Ch. 34		Fri, 4/11
7	Genome science	RP	Ch. 19, 20	Ch. 19, 20	PS 2 due PS 3 posted	Mon, 4/14
8	The central dogma	RP	Ch. 15	Ch. 15		Wed, 4/16
9	Replication	RP	Ch. 14	Ch. 14		Fri, 4/18
10	Transcription and gene regulation I	RP	Ch. 16	Ch. 16	PS 3 due PS 4 posted	Mon, 4/21
11	Transcription and gene regulation II	RP	Ch. 16	Ch. 16		Wed, 4/23
12	Translation	PJB	Ch. 16-18	Ch. 16-18		Fri, 4/25
13	Molecular biology (w/ demo)	PJB/RP	Ch. 19, 20	Ch. 19, 20	PS 4 due	Mon, 4/28
14	Structural biology I: Proteins and X-ray diffraction	PJB	Ch. 3, 5, 6	Ch. 3, 5, 6		Wed, 4/30
	Midterm review, Wed 4/30, 4-6pm, 119 Kerckhoff	TAs
					Midterm posted	Thu, 5/01
						Fri, 5/02
					Midterm due (PS 5 posted)	Mon, 5/05

Lecture 1: Introduction to Bi 1

Download: PDF (handout) - 1.6 MB | PDF (full page) - 7.8 MB | PPT - 21.7 MB

Links:

• http://www.apla.org/facts/HIV_statistics_current.pdf
  Current statistics for HIV infection and AIDS in Los Angeles County
• http://en.wikipedia.org/wiki/Image:HIV_Epidem.png
  Figure showing worldwide HIV prevalence
• http://www.kff.org/hivaids
  Fact Sheet: The Global HIV/AIDS epidemic (May 2006) from the Kaiser Family Foundation

Lecture 2: The great ideas of biology I - cell theory, the unity of biochemistry, genetics

Download: PDF (handout) - 2.4 MB | PDF (full page) - 8.2 MB | PPT - 32.1 MB

Links:

• Deciphering the Genetic Code: Marshall Nirenberg
  A beautiful and highly readable account of Nirenberg's experiments that led to understanding the genetic code (and a Nobel Prize).
• The Three Domains of Life
  This fun little article describes the three domains of life and gives a hint at the diverse lifestyles of Archaea.
• It's in the Blood! A Documentary History of Linus Pauling, Hemoglobin and Sickle Cell Anemia
  This interesting website talks about Linus Pauling's efforts in understanding hemoglobin and includes a description of his work on using molecules as clocks.
• Electron microscopy image gallery
  EM images from the Canadian Food Research and Development Centre.
• ASCB Image and Video Library
  This website has excellent images of cells so you can get a better
  feeling for cell diversity.

Lecture 3: The great ideas of biology II - evolution

Download: PDF (handout) - 1.8 MB | PDF (full page) - 9.3 MB | PPT - 14.7 MB

Suggested Reading:

• "Ancient DNA", Nat. Rev. Genetics, 2, 353, (2001) by Paabo - this article describes the use of molecular studies on extinct organisms.
• "The Beak of the Finch" by Jonathan Weiner (CLAS)- This Pulitzer prize winning book is a classic and a must read. It tells the story of studies of evolution in real time in the Galapagos, the life's work of Peter and Rosemary Grant and their students and postdocs.
• "At the Water's Edge" by Carl Zimmer - a wonderful book that tells how living organisms first left the water (fins to limbs) and how mammals went back to the sea again. Great stuff.
• "Your Inner Fish" by Neal Shubin (CLAS) - Shubin is a noted paleontologist who has found many important and celebrated transitional forms. This excellent book describes his "course" for medical students on human anatomy told from the point of view of our inner fish.
• "The Origin of Species" by Charles Darwin. Arguably the most important science book ever written. This remarkable synthetic opus is beautifully written, full of an amazing array of different ideas, observations and experiments and completely accessible to any interested reader. You must read this book.
• "Life on a Young Planet" by Andrew Knoll. (CLAS) - An amazing book that examines the evidence for life during the first four billion years of planet Earth's existence.

Links:

• Whale Evolution (YouTube)
  This is a discussion of the work of Philip Gingerich on whale fossils from the superb PBS series on evolution.
• Building Tiktaalik (YouTube)
  This video shows how models of extinct organisms like Tiktaalik are constructed.
• Evolution fish with fingers Transitional fossils (YouTube)
  A clip from the fantastic PBS series on evolution that shows Jenny Clack, discoverer of key transitional forms in the transition from fins to limbs.

Lecture 4: Eukaryotic cells and organelles

Download: PDF (handout) - 2.0 MB | PDF (full page) - 10.8 MB | PPT - 48.5 MB

Lecture 5: Parts list of a cell

Download: PDF (handout) - 10 MB | PDF (full page) - 13.1 MB | PPT - 10.7 MB

Review Session #1 - April 9

Download: PDF (handout) - 2.1 MB | PDF (full page) - 3.1 MB | PPT - 1.9 MB

Lecture 6: Viruses and parts list of viruses

Download: PDF (handout) - 11.8 MB | PDF (full page) - 15.4 MB | PPT - 14 MB

Suggested Reading:

• Structural Biology of HIV, Turner and Summers, J. Mol. Biol. 285:1 (1999)
  This article describes both the life cycle and parts list of HIV.
• Three-dimensional structure of HIV-1 virus-like particles by electron cryotomography, Benjamin et al., J. Mol. Biol. 346:577 (2005)
  This paper uses cryo-electron microscopy to provide insights into the structure of mature HIV.
• Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells, Wright and Schooler et al., EMBO J in press (2007)
  A subsequent paper using cryo-EM to look into the structure of immature HIV particles.
• The HIV lipidome: A raft with an unusual composition, Brügger et al., PNAS 103:2641 (2006)
  This interesting paper describes measurements of the lipid content of HIV.
• Molecular Architecture of Bacteriophage T4, Mesyanzhinov et al., Biochemistry (Moscow) 69:1190 (2004)
  This paper illustrates the enormous progress that has been made on determining the parts that make up bacteriophage T4

Lecture 7: Genome science

Download: PDF (handout) - 1.9 MB | PDF (full page) - 8.2 MB | PPT - 18.9 MB

Lecture 8: The central dogma

Download: PDF (handout) - 3.6 MB | PDF (full page) - 7 MB | PPT - 2.6 MB

Lecture 9: Replication

Download: PDF (handout) - 8.6 MB | PDF (full page) - 10.3 MB | PPT - 9.6 MB

Suggested Reading:

• The DNA replication problem, 1953–1958, Frederic L. Holmes, Trends in Biochemical Sciences, Volume 23, Issue 3, 1 March 1998, Pages 117-120
  This article describes some of the intellectual challenges faced in thinking about DNA replication.

Lecture 10: Transcription and gene regulation I

Download: PDF (handout) - 6.4 MB | PDF (full page) - 8.7 MB | PPT - 10.8 MB

Lecture 11: Transcription and gene regulation II

Download: PDF (handout) - 8.2 MB | PDF (full page) - 12.4 MB | PPT - 10.2 MB

Lecture 12: Translation

Download: PDF (handout) - 3.4 MB | PDF (full page) - 3.5 MB | PPT (zip file with movies) - 32.8 MB

Links:

• The Genetic Code
  Brief description of the history of solving the genetic code.
• The RNA world: History of an idea, an idea of history
  Discusses idea that RNA was the first life-form on earth. The hypothesis is support by the facts that RNA can store, transmit and duplicate genetic information as well as function as an enzyme to catalyze reactions. See also The RNA World (nobelprize.org).
• Protein synthesis: an epic on the cellular level (YouTube) - A 1970s take on protein synthesis.
  

Lecture 13: Molecular biology

Download: PDF (handout) - 11.6 MB | PDF (full page) - 12 MB | PPT (zip file with movies) - 17.9 MB

Links:

• Plasmid cloning (YouTube) - A brief overview of DNA subcloning.
• Restriction enzymes (YouTube) - A video description of restriction enzymes.
• The test-tube synthesis of a chemical called poliovirus. Wimmer, E. EMBO Reports 7: S3-S9 (2006).
  The simple synthesis of a virus has far-reaching societal implications.
• DNA Interactive
  Many of the movies shown in class come from this site. It also includes interviews with scientists who made critical discoveries in molecular biology, biotechnology, and/or recombinant DNA research.
• genome.gov | 2003 Release: International Consortium Completes HGP
  The press release announcing the completion of the public human genome project.
• Human Genome Projects Information
  All about the Human Genome Project.
• Centre for Integrated Genomics
  "Development and application of genome science to the diagnosis and treatment of cancer"
• Commonality with other organisms
  A page exploring similarity of genomes among different species.
• Gene Expression in Cultured Cells
  This website has lots of interesting discussion of strategies for putting foreign DNA into different types of cells.
• Roche Applied Science: Cutting-Edge Transfection Reagents
  This site gives a discussion of different products that are used to transfect cells. (If you go to this URL, you may be asked to select your country. Just select "United States" and hit Go.)

Lecture 14: Structural biology I: Proteins and X-ray diffraction

Download: PDF (handout) - 7.7 MB | PDF (full page) - 8.6 MB | PPT (zip file with movies) - 25.5 MB

Suggested reading:

• Rosalind Franklin: The Dark Lady of DNA by Brenda Maddox
  Biography of the crystallographer who obtained the diffraction image of B form DNA that led to the solution of DNA's structure.

Links:

• DNA Interactive
  Many of the movies shown in class come from this site. It also includes interviews with scientists who made critical discoveries in molecular biology, biotechnology, and/or recombinant DNA research.
• NOVA | Secret of Photo 51 | PBS
  Discusses the contributions of Rosalind Franklin to the discovery of the structure of DNA. Includes an explanation of Franklin's famous "X"-shaped diffraction pattern of DNA, which demonstrates that DNA is helical.
• Rosalind Franklin and the Double Helix, by Lynne Osman Elkin, Physics Today, March 2003
  The history of the discovery of the structure of DNA. Corrects some of the distortions about Franklin that appear in James Watson's book "The Double Helix".
• Caltech Archives Oral Histories Online - Interview with Linus Pauling
  Interview in 1984 with Linus Pauling, Caltech Professor of Chemistry, recipient of the Nobel Prize in Chemistry (1954; for "his research on the nature of the chemical bond") and the Nobel Peace Prize (1962). Pauling discusses the Biology Division at Caltech, Thomas Hunt Morgan, his work on hemoglobin in the 1930s, immunology, and his discovery of the alpha-helix.
• JenaLib: The Amino Acid Repository
  Structures and properties of the 20 amino acids in proteins
• Tangible Interfaces for Molecular Biology
  Hands-on models of proteins
• Kevin Cowtan's Picture Book of Fourier Transforms
  Nice tutorial on the use of Fourier transforms in X-ray crystallography
• The RCSB Protein Data Bank
  An archive of the coordinates of the structures of macromolecules determined by X-ray crystallography, NMR, and electron microscopy.
• The Molecular Observatory
  The Molecular Observatory provides the Caltech community with exceptional capabilities in macromolecular crystallography, including a synchrotron radiation beam line at SSRL and an on-campus crystallization laboratory providing state-of-the-art robotics for crystallization.

Midterm Review

Download: PDF (handout) - 9.8 MB | PDF (full page) - 9.8 MB | PPT - 10 MB