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Biological Sciences 105

Winter, 2017

Course Syllabus

Staff Office Hours Room E-mail Address

Dr. Ken Hilt Tu noon 2 p.m. 3033b SLB klhilt@ucdavis.edu
F 1 2 p.m. 3033b SLB
Poommaree Namchaiw M noon 2 p.m. 2064 SLB pnamchaiw@ucdavis.edu
W 5 7 p.m. 3061 SLB
F 2 4 p.m. 2064 SLB
Gayane, Kristen, John, M Th 1 5 p.m. 3rd floor lounge
Ida, Sam, Catherine,
Anthony, Chandler, and
Candice (BASC tutors)
BASC = Biology Academic Success Center SLB = Sciences Lab Building

Administrative Support Julie Evans, Christina Jones, Hemang Patel, and Maria Saldana-Seibert

Lectures MWF 10:00 10:50 a.m., 100 Hunt

Audiotapes of each lecture are available on our Smartsite web page. Click Resources,
Podcasts.

Texts
Required
Biochemical Calculations, 2nd ed., I. H. Segel, John Wiley & Sons, Inc., c1976.
ISBN 0-471-77421-9

Optional
Lehninger Principles of Biochemistry, 6th ed., D.L. Nelson and M.M. Cox, c2013
ISBN 978146419386 (special pricing for UC Davis BIS 102 and BIS 103 courses)

Lehninger Principles of Biochemistry, 6th ed., D.L. Nelson and M.M. Cox, c2013 online
edition ISBN 978146416740 (special pricing for UC Davis BIS 102 and BIS 103
courses)

Biochemistry, 4th ed., D. and J. Voet, John Wiley & Sons, Inc., c2011
ISBN 978047057095 (graduate student level textbook)

These and other texts are on reserve in Shields library.

Web Site

Our web page is listed in SmartSite. All business items will be posted at this site: i.e. the course
syllabus, assigned homework problems, and answer keys for homework problems and current exams.
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Homework

Homework is assigned, but not graded. These problems are previous exam questions.

There are three homework assignments. Homework (HW) #1 covers material for the first
midterm. HW #2 covers material for the second midterm. HW #3 covers half of the final exam (i.e.
half of the final is equivalent to a third midterm; the other half of the final exam is cumulative).

Exams

Exam Date Time Points

First Midterm Friday, Feb. 3 10:00 10:50 a.m. 100
Second Midterm Friday, Mar. 3 10:00 10:50 a.m. 100
Final Tuesday, Mar. 21 10:30 a.m. 12:30 p.m. 200
Class Participation 20
(Clickers)

We will have an optional discussion section prior to each exam.

Each exam tests your understanding of concepts and quantitative analyses. Equations and
constants are furnished. However, you must know definitions. Bring a calculator---it must be a
nonprogrammable, nongraphing calculator.

Missed Midterms: the only excuse for missing a midterm is a written medical excuse from your
personal physician or Cowell Student Health Center. For anything else, you will need to set up an
appointment with me by the following Monday to show your proficiency in the material by having an
oral exam. If you pass, I will then move the percentage of the midterm to the final.

Clickers are available in the UCD Bookstore. You are responsible for bringing yours to each
lecture and making sure that it is functional. Register your i-Clicker 2 at
http://www1.iclicker.com/register-an-iclicker/ . Your clicker must be registered by March 20 to
receive credit for in-class participation. Points awarded in class participation are based on the
percentage of correct answers you give. For example, if it turns out that there are 15 clicker questions
during the quarter and you get 7 correct, then you will score (7/15) (20 points) = 0.466 (20 points) = 9.3
points for class participation. It should be fun!

How to do well in the course

Focus on the lecture material and assigned homework.

Share your notes and argue concepts with a fellow classmate.

Go to office hours.
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Tentative Lecture Schedule
Lecture Date Topic
1 Jan. 9 Course introduction, biochemical components of cells; amino acids
2 11 Amino acids properties of R-groups
3 13 Weak acids/bases, monoprotic weak acids
4 16 Holiday (Martin Luther King)
5 18 Weak acids/bases, net charge, polyprotic weak acids, pI
6 20 Weak bonds; oligopeptides
7 23 Protein structure (1o, 2o, 3o, 4o)
8 25 Protein structure (3o) myoglobin example
9 27 Protein structure (4o) hemoglobin example
10 30 Protein structure (4o) hemoglobin example
11 Feb. 1 Protein folding 1o structure dictates 3o structure
12 3 First Midterm
13 6 Enzymes active sites; chymotrypsin example
14 8 Enzymes assays, Michaelis-Menten equation
15 10 Enzymes reversible inhibitors, Lineweaver-Burk plots
16 13 Lipids
17 15 Membranes composition, fluidity, transport across
18 17 Key concepts in metabolism
19 20 Holiday (Presidents Day)
20 22 Glycolysis
21 24 Glycolysis; G and Beers Law calculations
22 27 Gluconeogenesis
23 Mar. 1 Pyruvate dehydrogenase complex
24 3 Second Midterm
25 6 Catabolism of fatty acids: -oxidation; Krebs cycle
26 8 Overview of electron transport chain
27 10 Deeper view of electron transport chain
28 13 Mitochondrial ATP synthase
29 15 Photosynthesis (part I)
30 17 Photosynthesis (part II); course summary

21 Final Exam 10:30 a.m. 12:30 p.m. (50% covers material since the second
midterm; the other 50% reexamines the material for the two midterms)

Suggested Reading (chapters)

Lecture Segel Lehninger Lecture Segel Lehninger
16 1, 2 1, 2, 3 22 14
7 11 2 3, 4, 5 23 16
13 15 4 6 25 16, 17
16 17 10, 11 26 28 19
18 preface to 13 29 30 19
20 21 3, 5 14
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BIS 105 Course Objectives

This course will enable students to describe how the structure of the major chemical compounds in
cells determines their behavior and enables their biological roles. This includes understanding how
chemical principles govern the structure and interactions of molecules with their environment and each
other, and how quantitative methods can be used to examine molecular processes in living systems.
The course will also enable students to describe how the major biomolecules in living systems are
interconverted to provide energy to do biological work including the synthesis of needed biomolecules.
By the end of the course students will:

be able to immediately recognize the primary types of biochemical molecules and know their essential
chemical characteristics that enable their roles in cells.

appreciate the central and essential importance of water as polar solvent in biological chemistry

be able to quantitatively determine the effects of hydrogen ion concentration on the ionization state
and charge of biological molecules.

understand and quantitatively evaluate how chemical energetic principles drive all processes in
cells.

be able to describe how the set of weak chemical interactions drive folding of proteins and
assembly of supramolecular structures such as protein complexes and biological membranes.

be able to describe the molecular and energetic basis of enzymatic specificity and catalysis.

quantitatively analyze enzymatic reaction rate data and use this information to determine the kinetic
properties of an enzyme and properties of enzyme inhibitors.

understand how the function of protein molecules can be altered by binding other compounds
present in their cellular environment.

understand the shared and unique properties, in general terms, of aerobic and anaerobic metabolism
and prokaryotic and eukaryotic metabolism.

understand the concept of the dual role of metabolism, that is, that it functions in both anabolic and
catabolic directions. Learn the important role of metabolic co-factors such as ATP, coenzyme A and
NADH and how these co-factors enable the functioning of metabolism.

understand the Chemiosmotic Theory and the mechanism generating the proton motive force.
Understand how the proton motive force is used in the mechanism of ATP synthesis.

understand in general ways the various mechanisms through which the activity of pathways are
regulated. Understand how the regulation of specific enzymes in a pathway enables organisms to route
metabolic fluxes specific to the need of cells under certain biological conditions.