Instructor: Professor Terence M. MURPHY Office: 2167 Life Sciences; Lab: 2209 Life Sciences Office hours (T 4-5, W 11-12) /other times by appointment 752-2413 t m murphy@ucdavis.edu

BIS 2A: Introductory Biology: Cell Functions

The Biological Sciences 2 series introduces students to the principles on which all life--from the smallest, simplest

organisms to the largest communities--is based. Biological Sciences 2A concentrates on the cellular basis of life,

concentrating on the structures and functions of cells and the biological molecules from which they are formed, the ways

by which cells acquire, transform, and use chemical energy, and the mechanisms by which genetic information is stored, safeguarded, transmitted from one generation to

the next, and used in reproduction and development. Students are asked to use the principles and information

covered in the class to interpret historical and current observations and to solve problems.

BIS 2A: Introductory Biology: Cell Functions

Topics:

Cell structure

Metabolism

Genes and geneExpression

Development and reproduction

Origin of life

Monday Wednesday Friday

9/23 Properties and origin of

life (Ch 1.1-1.3; pp 3-17)

9/26 Cell theory (Ch 5.1; pp

77-81)

9/28 Cell architecture I (Ch 5.2-

5.4; pp 82-103)

9/30 Cell architecture II

10/3 Cell components I--lipids

(Ch 2.1-2.4, 3.4; pp 21-35, 54-

57)

10/5 Cell components II--

carbohydrates, proteins (Ch 3.1-

3.3; pp 39-54)

10/7 Membrane structure and

function (Ch 6.1-6.6; pp 106-

125)

10/10 Enzyme action (Ch 8.3-

8.4; pp 156-161)

10/12 Concepts of metabolism

(Ch 8.1-8.2, 8.5; pp 149-155,

161-165)

10/14 Respiration I (Ch 9.1-9.5;

pp 169-187)

10/17 EXAM (Lectures through

Concepts of Metabolism)

10/19 Respiration II 10/21 Photosynthesis I (Ch

10.1-10.3, 10.5; pp 190-201,

205)

10/24 Photosynthesis II 10/26 Information for cell

synthesis (Ch 13.1; pp 267-

272)

10/28 DNA structure and

replication (Ch 4.1, 13.2-13.3;

pp 61-65, 272-284)

10/31 Protein synthesis I--RNA

(Ch 14.1-14.3; pp 291-300)

11/2 Protein synthesis II (Ch

14.5-14.6; pp 304-313)

11/4 Mutations and

mutagenesis (Ch 15.1, 13.4; pp

317-323, 285-287)

11/7 Regulating protein

synthesis--operons (Ch 16.2; pp

348-352)

11/9 Regulating protein

synthesis in eukaryotes (Ch

16.3-16.5; pp 352-362)

11/11 VETERAN'S DAY

HOLIDAY

11/14 EXAM (Lectures through

Mutations and Mutagenesis)

11/16 Cell signals (Ch 7.1-7.5;

pp 129-145)

11/18 Mitosis and meiosis (Ch

11.1-11.5; pp 210-229)

11/21 Development (Ch 19.3-

19.5; pp 412-423)

11/23 Origins: organic

molecules, cells (Ch 4.2; pp 65-

69, 101)

THANKSGIVING HOLIDAY

11/28 Origins: genes (Ch 4.3;

pp 69-71)

11/30 Origins: metabolism (Ch

4.4, 5.5; pp 72-73, 101-103)

12/2 Summary

Prerequisites: None, but experience says that those without a basic understanding of chemistry receive a grade one full step lower than those who do. Textbook: Sadava, et al., Life: The Science of Biology, Ninth Edition. I recommend the deal at the UCD Bookstore: a loose-leaf version that covers the material for BIS 2A, 2B, and 2C, plus access to the publisher’s web site for 18 months. The web site contains material needed for 2B and 2C. The textbook is readable; all assigned sections are relevant and may be covered on exams. If you have web access, a Study Guide or any other adjunct material is not needed. Bound editions and earlier editions of the textbook are OK. Although this class will use material from the publisher’s web site, it will not require you to access the web site. Clickers: The “interwrite PRS” system will be used to quiz the class during lectures. I am planning 1-3 questions in each lecture. These are designed to give me (and you) an idea of your background knowledge or how clear I have been in lecture. To participate, you need to purchase a “clicker,” available at the bookstore. Participation is voluntary, but strongly encouraged (and the same clickers are used in the Physics 7 series). I will start clicker questions at Monday’s lecture.

Web site: general information and help; lecture schedule; TAs, office hours, discussion section rooms; objectives (what I want you to know from each lecture), sample exams, and old problem sets; assignments for discussion sections; lecture pdfs; podcasts; (eventually) test answers and grades. http://www-plb.ucdavis.edu/courses/bis/2a/bis2a-F11/index.htm Mail-list: Bis002a—f11@ucdavis.edu, by which I (and you) can communicate with the class. You are responsible for receiving messages sent to your ucdavis.edu address. Archives of the notices will be available through http://listproc.ucdavis.edu/class.

Discussion sections: Discussion of issues from lecture and clearing up sticky

points. There will be a quiz in most sessions. A major assignment will be oral and written reports on an extract of a scientific paper. Quizzes, report, and participation count for 20% of your grade.

TAs: Rebecca Wright, Jazzy Dingler, Brad Kaufman, Matthew Tan,

Huy Tran, Kelly Martorana, Karen Word

Enrollment: Enrollment will take place at the discussion sections next Tuesday

(September 27). You MUST BE PRESENT to retain your place in class (if you

are registered) or to get a place (if there is a no-show and you are next on the

wait list).

Tests and grading:

1st Midterm 20%--10/17 A+,A,A- >85% or >80%ile

2nd Midterm 20%--11/14 B+,B,B- >75% or >50%ile

3rd Midterm/Final 40%--12/5 C+,C,C- >65% or >20%ile Discussion/T.A. 20% D+,D,D- >50% or >10%ile

Missed exams: There are no early, late, or make-up exams. If you miss an

exam for an acceptable reason and have an appropriate written statement from a

doctor or clergyman to verify your excuse, your total score will be prorated or (in

the case of a final) you will receive an I grade (incomplete).

HOW DO YOU GET THE MOST OUT OF THIS CLASS? The following statistics, taken from the 2010 student evaluations may provide a clue :

Clickers

Course overall

Extremely

valuable

Very

valuable

Somewhat

valuable Not valuable Did not use

Extremely valuable 52 15 3 1

Very valuable 39 84 34 2

Somewhat valuable 3 17 20 5 1

Not valuable 2 1

The people who valued clicker questions found the course to be more valuabl e .

Discussion

sections

Course overall

Extremely

valuable

Very

valuable

Somewhat

valuable Not valuable

Extremely valuable 36 21 12 2

Very valuable 26 47 66 19

Somewhat valuable 6 9 20 13

Not valuable 1 2

The people who valued discussion sections found the course to be more valuable.

TA Office

Hrs

Course overall

Extremely

valuable

Very

valuable

Somewhat

valuable Not valuable Did not use

Extremely valuable 20 10 6 1 34

Very valuable 5 25 45 6 78

Somewhat valuable 3 11 3 32

Not valuable 1 2

The people who went to TA office hours found the course to be more valuable.

Great Concepts of Science and Biology

1) The universe is regular enough to allow useful predictions. 2) Controlled experiments are essential for scientific inquiry.

Scientific method: ! Observation ! Defining the question ! Formulating an hypothesis ! Designing and conducting an experiment

3) Progress in science requires freedom of inquiry.

4) Living organisms obey all the laws of physics and chemistry.

Vitalism: E.g., Hans Driesch (1867–1941), an eminent embryologist, ... explained the life of an organism in terms of the presence of an entelechy, a substantial entity controlling organic processes. ..., the French philosopher Henri Bergson (1874–1948) posited an élan vital to overcome the resistance of inert matter in the formation of living bodies. Mechanism: arose from scientific method (ca. 1500), microscopy (1677), chemistry (ca 1800). E.g., Descartes maintained that animals, and the human body, are ‘automata’, mechanical devices differing from artificial devices only in their degree of complexity.

5) Functions of living organisms are based on the catalysis of chemical reactions; this takes place in microscopic structures. ! Complex organization: each organism has

104-106 different types of molecules ! Requirement for energy: energy needed to

maintain complexity (resist entropy) ! Homeostasis: one of the complexities,

maintaining standard conditions in fluctuating environment; based on feedback mechanisms

! Destructability—life spans ended by

temperature (outside -20 to 120o C), solution conditions (desiccation, acid, alkali), radiation (gamma, X ray, UV), poisons

6) Living organisms are formed through reproduction, not spontaneous generation.

! Reproduction implies inheritance ! The genetic code provides the basis for

inheritance and complexity 7) All forms of life are subject to natural selection and may change in response to its pressures.

! Organic evolution, which has occurred throughout the past and is responsible for the diversity of species we see today, hasn’t stopped; it is still occurring.

! Variety--1,700,000 species named; 5,000,000

to 50,000,000 species extant (maybe more?--insects, marine microbes); 300,000,000 species have ever lived; (contrast with types of rocks: >120 but <1000)

8) Life has an origin and a history. That history is reflected in fossils, but also in the physical history of the Earth.

Why so late?

Was global warming good?

Why methane then and not now?