BIOLOGY 1610 / BIOLOGY 1615 CLASS OUTLINE [Biology I]

Autumn 2008

Joseph M. Papenfuss, PhD

Office: Science Building 211 during posted office hours, or by appointment

Telephone: 283-7528

email: Joseph.Papenfuss@snow.edu

CATALOG COURSE DESCRIPTION

This course introduces the scientific method, cell chemistry, cell structure and function, gene action and genetics, natural selection and mechanisms of speciation, the origin of life, diversity of living organisms and classification, and surveys of viruses, bacteria, protists, and fungi, and the human immune system. This is the first semester course of a yearlong sequence that is required for most biology majors, many pre-professional majors, natural resource majors and some agriculture majors.

Prerequisites: It is recommended that the student will have successfully completed high school biology and chemistry.

Co-requisites: Both the lecture BIOL 1610 and the lab BIOL 1615 must be taken concurrently.

COURSE JUSTIFICATION

The Biology I lecture course (BIOL 1610) and Biology I laboratory (BIOL 1615) have been designed as the first semester courses in a year-long exposure to biology as recommended by the State Biology Group. Biology II lecture (BIOL 1620) and Biology II laboratory (BIOL 1625) will constitute the second semester courses for the majors biology sequence.

COURSE OBJECTIVES

The course objectives are to understand the scientific method; an introduction into the roles of chemical components in cell structures and their functions; how gene expression directs living processes; mitosis and meiosis; to introduce transmission (Mendelian) genetics and population genetics and apply these to mechanisms of speciation; to present ideas on the origin of life and its present-day diversity; to gain an overview of classification systems used in biology, and to survey viruses, bacteria (Kingdoms Archaebacteria, Eubacteria), protists (Kingdom Protozoa) and fungi (Kingdom Fungi); to introduce the human immune system. Labs will complement learning by providing preserved and living specimens, slides, and hands-on demonstration materials and experiments for study. Students should gain increased awareness of the chemical nature and complexity of life on the cellular level as typified by bacteria (prokaryotes) as well as protist and other eukaryotes.

Outcomes

Students will know the essential qualities and key processes commonly found in life forms.

Students will have begun to understand the diversity of living organisms and their myriad interrelationships in the biological world.

Students will know how to apply systematic methods to understand the complexities of an individual organism or to distinguish among divers species.

Students will be able to use microscopes, computers, and other commonly available lab equipment and supplies.

Students will be able to read the literature of the biological sciences flexibly, analytically and imaginatively.

Students should be able to appreciate that they have been exposed to an unfortunately small number of the myriad beauties and marvels of the living world, extant or extinct.

Students will have some understanding of the role that biology plays in modern life as well as past history.

COURSE CONTENTS (BIOL 1610)

Scientific Method

empirical observations, hypothesis formulation, testing by

experimentation, theory and law

limitations of science

emergent properties

Simple Chemistry

basic chemistry

atoms, molecules, ions; covalent, ionic and

hydrogen bonding, van der Waals forces and hydrophobic interactions; solutions, mixtures, colloids; special properties of water; pH and buffers

biological chemistry

carbon chains and rings, functional groups, polymers;

lipids, carbohydrates, amino acids and proteins,

nucleotides and nucleic acids

Cell Structure and Function

cell theory

cell structures in prokaryotes and eukaryotes

functions of eukaryote cell structures

membrane composition and structure

passive processes of membrane transport:

diffusion, osmosis, facilitated diffusion active transport

cell signaling and communication

signals, receptors and transducers (secondary

messengers, protein kinase cascades)

action potentials, neurotransmitters, excitatory

and inhibitory synapses

cell adhesion, tight junctions, desmosomes, gap

junctions, plasmodesmata, attachment to

cytoskeleton, extracellular matrix, cell walls

cytoskeleton and related structures

cell walls

Metabolism

energy transformation

endothermic and exothermic chemical reactions

enzymes

catalytic properties, inhibition (competitive,

uncompetitive, irreversible), simple enzyme kinetics

(Hanes versus Lineweaver-Burk plots, Michaelis-Menten

plot), coenzymes and prosthetic groups, allosteric

enzymes, negative and positive feedback regulation

photosynthesis--pigments, light (photophosphorylation)

and dark (Calvin-Benson Cycle) reactions in chloroplast thylakoid membranes (grana) and stroma

C3, C4 and CAM plants

cellular respiration and fermentation--glycolysis,Krebs

Cycle and oxidative phosphorylation in mitochondrion

matrix and cristae, lactic acid, alcoholic and

pyruvate formylate lyase fermentations

physiological genetics -- mutant dissection of biochemical

pathways

global carbon cycle

global warming, certainties and questions

Cell Cycle

controls and Ras cascade

mitosis in detail

cytokinesis

meiosis in detail and gamete production

contrast mitosis with meiosis

nondisjunction of chromosomes

common human syndromes caused by chromosomal

nondisjunction

gametic, zygotic and sporic meiosis in life cycles

simple development -- comparison of sea urchin, frog, bird

and human blastula and gastrula formation; limb

development; apoptosis

tumorigenesis and possible mechanisms

Simple Genetics

Mendelian (transmission) genetics

learn basic vocabulary in Mendelian genetics to understand up to dihybrid cross results in F₂ generation and F₁ testcross -- dominant or recessive alleles in complete dominance, incomplete (partial) dominance, codominance, X- (sex) linkage, sex-limited and sex-influenced traits, pleiotrophy, epistasis, polygenic or quantitative traits

relate meiosis to transmission (Mendelian) genetics -- laws

of segregation and independent assortment

pedigrees for human genetic diseases

Central Dogma

classical DNA experiments elucidating structure and

function

DNA replication, mutations and repair

DNA transcription and RNA processing

RNA translation or protein synthesis

genetic code, mRNA, tRNA, rRNA, ribosomes

prokaryote and eukaryote structural gene comparisons

transcriptional controls in prokaryotes

transcriptional, translational, and post-translational

controls in eukaryotic gene expression

recombinant DNA and biotechnology

plasmids and episomes

transformation

bacterial conjugation and sexduction

lysogenic and lytic cycles

transduction

resistance factors

restriction endonucleases and cleavage sites; sticky ends

and DNA splicing

cloning and expression vectors

selection of transgenic lines

complementary DNA (cDNA)

cDNA library versus genomic DNA library

gel electrophoresis

Southern, Northern and Western blotting

probes, hybridization, detection

RFLPs (probe-restriction enzyme combinations)

PCR (unique primer pairs)

some examples of biotechnology

ethics issues

Speciation and Evolution

introduce Hardy-Weinberg equilibrium and assumptions

mutation and independent assortment as causes of genetic variation

natural selection and differential reproduction

types of selection

directional, stabilizing, disruptive

mechanisms of speciation

allopatric, sympatric, parapatric

convergent evolution, parallel adaptation, adaptive

radiation, divergent evolution

outline organic evolution

others ideas on origin of life

punctuated equilibrium versus gradualism

Systematics and Taxonomy

classification of life (3 domains and eukaryote kingdoms or

the T. Cavalier-Smith 8 kingdom system)

binomial system for naming organisms

introduce dichotomous keys

archae- and eubacteria

major groups

key traits, diseases, benefits and ecology

viruses as non-living parasites

disease control triangle

endosymbiosis

protists

major phyla

key traits, diseases and ecology

fungi

major phyla

key traits, beneficials and harmfuls, ecology

Human Immune System

nonspecific versus specific defense mechanisms

humoral and cellular components of the immune response

antibody diversity versus immunoglobulin classes

major histocompatibility complexes

LAB CONTENTS (BIOL 1615)

1a. scientific method

1b. simple organic chemistry

2. light microscopy and introduction to SEM’s and TEM’s

3. membrane functions

4. simple enzyme kinetics

5. photosynthesis / respiration and mutant analysis

6. mitosis / meiosis and development

7. transmission genetics

8. transformation

9. gel electrophoresis / hybridization simulation

10. bacteria and systematics

11. protozoa (protists) and systematics

12. fungi

REQUIRED TEXTS and / or MATERIALS

Neil A. Campbell and Jane B. Reece (2005, or 2008) Biology, 7th or 8th ed. Benjamin Cummings, San Francisco

ISBN 0-8053-7171-0 / 0-8053-6844-2

Peter H. Raven, Ray F. Evert, Susan E. Eichhorn (2005) Biology of Plants, 7th ed. W. H. Freeman and Company Publishers, New York, ISBN 0-7167-1007-2

Donald P. Breakwell, Joseph M. Papenfuss and Kevin N. Sorensen (2008) Laboratory Manual for BIOL 1615

General Education Outcomes

1. Read effectively, constructively, and critically.

Students read the text throughout the course to give them a basis for understanding current scientific literature and research. There will be at least one library research project in which students read scientific literature. Project(s), test essay questions, discussions, etc. are evaluated on synthesis and critical thinking processes.

2. Write clearly, informatively, and persuasively.

Students will complete at least one library project and several test essay questions over the course of the semester that will be evaluated for skills in writing as well as in the areas of synthesis and critical thinking.

3. Retrieve, evaluate, interpret, and deliver information through a variety of traditional and electronic media.

Students will complete at least one library project which will require the use of traditional and electronic media.

7. Apply scientific reasoning to a variety of contexts.

Students will demonstrate scientific reasoning throughout the various topics considered in course content in their responses to tests, quizzes, projects, discussions, etc.

EVALUATION OF STUDENT PERFORMANCE

Students are more effective in the learning process if they read the material before lecture or lab, and then review notes and materials after class. Depending on individual ability and preparation as well as quality of effort, usually two hours of study are required for every hour in class to earn an "A" grade.

BIOL 1610 4 100-pt tests (60% take-home + 40% testing center except #4) 400 pts

1 library project I A 40 pts

1 library project I B 30 pts

1 library project II 30 pts

_1 200-pt comprehensive final 200 pts

Total 700 pts

BIOL 1615 12 40-pt lab reports (after dropping one) 480 pts

12 10-pt lab quizzes (after dropping one) 120 pts

Total 600 pts

One lab report and one lab quiz will be dropped. The lowest test may be replaced by the final exam percentage.

THERE WILL BE NO MAKE-UPS FOR LABS AS SCHEDULED!!! Missing more than two labs will result in a failing grade! If you cannot make your lab, check with the professor to see if you can attend a lab taught by Dr. Sorensen. This must be done the week before to give us adequate time to make accommodations for extra students!

THERE WILL BE NO MAKE-UP FOR ANY TEST without prior arrangement!!! You will do the take-home test on your own. Text, notes, study guides, labs, etc are allowable sources to be used in doing the test. Write the answers directly on the take-home test. Tests will be taken in the testing center as noted on your schedule. The lab quizzes will be at the beginning of the following lab period. The final exam score percentage may be used to replace a lower test score.

Late work is discouraged. However, late assignments are accepted with a 10% grade reduction for every school day that they are late up to 50%. No late work will be accepted after one week from the assignment due date! No late work will be accepted after the Thanksgiving holiday break!

Cheating in this course is punished with a zero for the item in question and with an F (0.0) for the course in the event that cheating occurs again.

Library Project Information

Project IA is worth 40 points. You should expect to spend at least 8 to 12 hours to do a good project. The book The Skeptical Environmentalist: Measuring the Real State of the World by Bjorn Lomborg (2001) Cambridge University Press will be on reserve in the library under my name. It can be checked out for 2 hours at a time. There should be 4 copies on reserve. You will read Part VI: The Real State of the World, pages 327 to 352 and give me an in-depth summary (3 to 4 typewritten pages).

Project IB is worth 30 points. In the same book above you will need to read any 2 or 3 chapters that total 15 pages or more. You can do two typewritten (single or 1.5 spaced, not double-spaced) page summaries of each chapter. You need to read at least one cited pro and one cited con source for each chapter and make a photocopy of their abstract or title pages and publishers to be submitted with each one of your summaries. Missing photocopies will cost you a maximum of 10 points. Overall neatness, spelling, grammar and legibility are worth 5 of the points for each part of this project.

Project II is worth 30 points. During the course of the semester you will research one biological topic reading three or more related articles from scientific periodicals. You will reference each article and include a photocopy (or printed copy) of each article. You will explain to me in a 450 word abstract--a very condensed essay--three items: 1) the major hypotheses being tested in each article, 2) very short summaries of the experiments, and 3) how valid do you think the research is that you are reporting on. It should fit in the box on the sheet of paper handed out to you for this purpose. Six points for abstract item 1, 9 points for item 2, and 3 points for item 3; 3 points for grammar, spelling, and readability; 6 points for photocopies of articles, 3 points for bibliography.

In order to earn an A or B grade, you will need to follow this advice from the uncle of Dr. Seuss (Theodor Seuss Geisel).

My uncle ordered popovers from the restaurant’s bill of fare.

And, when they were served, he regarded them with a penetrating stare.

Then he spoke great Words of Wisdom as he sat there on that chair:

“To eat these things,” said my uncle, “You must exercise great care.

You may swallow down what’s solid, BUT ... you must spit out the air!”

And as you partake of the world’s bill of fare, that’s darned good advice to follow.

Do a lot of spitting out the hot air. And be careful what you swallow.

The due dates for the tests and library projects are listed in the reading schedule below.

The grades are now letter grades and correspond to numerical and percentage grades in the following table.

A	4.0	92%	C	2.0	72%
A -	3.7	89%	C-	1.7	69%
B +	3.3	85%	D +	1.3	65%
B	3.0	82%	D	1.0	62%
B -	2.7	79%	D -	0.7	59%
C +	2.3	75%	F	0.0	< 59%

Students with medical, psychological, learning or other disabilities desiring accommodations, academic adjustments, or auxiliary aids will need to contact the Accessibility Resource Center, room 211 Greenwood Center, phone number (435) 283-7321.  The Americans With Disabilities Act (ADA) Coordinator at the Accessibility Resource Center (ACR) determines eligibility for and authorizes the provision of appropriate services and aids.

A reading schedule follows below.

MONDAY	TUESDAY	WEDNESDAY	THURSDAY	FRIDAY
		8/20 Introduction; Scientific Method CR 1	8/21 no lab; meet in lecture for 1 hr Scientific method cont. and Simple chemistry CR2	8/22 Simple inorganic chemistry cont.
8/25 Simple inorganic chemistry cont. and Water CR 3	8/26 Simple organic chemistry CR 4 and 5; REE 2 last day to pay tuition and fees	8/27 Simple organic chemistry cont.	8/28 Lab #1a Scientific Method	8/29 Microscopy, centrifugation, etc and cell structure CR 6; REE 3 hand out take-home test #1
9/1 LABOR DAY	9/2 Cell structure cont.	9/3 Cell structure cont. Membranes CR7	9/4 Lab #1b Simple Chemistry	9/5 Membranes cont.
9/8 Membranes, cyto-skeletons, and cell communication CR 6, 7, and 11	9/9 Cell communication cont. and nerve signals, and sensory and motor mechanisms CR 48 and 50	9/10 Chemical reactions, energy flow, enzymes CR 8; REE 5	9/11 Lab #2 Microscopy last day to add/drop classes without a $25 fee or a "W"	9/12 Enzymes cont. Library Project IA DUE !
9/15 Enzymes cont.	9/16 Enzymes cont.	9/17 Enzymes cont. and photosynthesis CR 10; REE 7	9/18 Lab #3 pH, Osmosis, Membranes	9/19 Photosynthesis cont.
9/22 Photosynthesis cont. Respiration CR 9; REE 6	9/23 Respiration cont. Test #1 scientific method thru cell membranes	9/24 Respiration cont. Test #1	9/25 Lab #4 Enzymes	9/26 "Greening of the Planet Earth" video hand out take-home test #2
9/29 Cell cycle and mitosis CR 12; REE 9	9/30 Meiosis and sexual life cycles CR 13; REE 10 and nondisjunction CR p 297	10/1 Meiosis cont.	10/2 Lab #5 Photosynthesis / Respiration	10/3 Animal development CR 46 and 47 and Plant development CR 38, 35; REE 21, 23, 24 Library Project IB DUE !
10/6 Development CR 21 and Cancer pp 228 - 229, 368 - 372 7th ed. or pp 224 - 243, 373 - 377, 950 - 951	10/7 Mendelian genetics CR 14 and 15	10/8 Mendelian genetics cont.	10/9 Lab #6 Mitosis / Meiosis	10/10 Mendelian genetics cont.
MONDAY	TUESDAY	WEDNESDAY	THURSDAY	FRIDAY
10/13 Molecular basis of inheritance (role of DNA) CR 16 REE 11	10/14 DNA replication	10/15 DNA replication cont. Roles of RNA and proteins CR 17, REE 11	10/16 Fall Vacation	10/17 Fall Vacation
10/20 Roles of RNA and proteins cont.	10/21 Roles of RNA and proteins cont.	10/22 Roles of RNA and proteins cont. and Regulation of Gene Expression CR18	10/23 Lab #7 Transmission (Mendelian) Genetics	10/24 Regulation of Gene Expression cont. Hand out abstract form for Library Project II.
10/27 Regulation of Gene Expression cont. and Biotechnology CR20	10/28 Biotechnology cont. Test #2 enzymes and metabolism thru Mendelian genetics	10/29 Biotechnology cont. Test #2	10/30 Lab #8 Transformation final day to add or drop classes	10/31 Evolution of Populations CR23; REE 4, 12 hand out take-home test #3
11/3 Microevolution (Origin of Species) and Macroevolution CR 24 (Read CR 22 and 25)	11/4 Systematics (Phylogeny and the Tree of Life) CR 26 (read CR 21); REE 13	11/5 Guest lecturer sometime this week? Lab #8b Plasmid Extraction	11/6 Lab #9 DNA Gel Electrophoresis	11/7 Systematics cont. and Prokaryotes (Bacteria and Archaea) CR 27; REE 14 Prokaryote hand-out
11/10 Prokaryotes cont.	11/11 Prokaryotes cont. Test #3 molecular biology thru macroevolution	11/12 Prokaryotes cont. Test #3	11/13 Lab #10 Bacteria and Introduction to Taxonomy	11/14 Protozoa CR 28; REE 16 Protozoa hand-out hand out test #4 take-home ONLY!!! Library Project II DUE !!
11/17 Protozoa cont.	11/18 Protozoa cont.	11/19 Viruses CR 19; REE 13 Virus hand-out	11/20 Lab #11 Protozoa	11/21 Viruses cont.
11/24 Fungi CR 31; REE 15 Fungi hand-out	11/25 Fungi cont.	11/26 Thanksgiving Break	11/27 Thanksgiving Holiday	11/28 Thanksgiving Break
12/1 Fungi cont.	12/2 Fungi cont.	12/3 Immune system CR 43	12/4 Lab #12 Fungi	12/5 Immune system cont. Test #4 systematics thru fungi DUE!!!
12/8 Immune system cont.	12/9	12/10 Final Exam 12:00 noon to 2:00 PM	12/11	12/12