pearson bio 121

Truman College
Department of Biology
Biology 121
Fall ‘14

Francisco Diaz de Leon
Assistant Professor
Office 2633
Phone: 773.907.4394
Email: fdiaz-deleon@ccc.edu
Office Hours: Tuesday and Thursday 8:30 to 11:00 AM; Monday and Wednesday 11 AM to 12 PM; or by appointment.

NOTICE: The best way to communicate with me outside the classroom is via email. I do not check phone messages regularly.

Course Description:
Cellular and molecular biology of the cell. Introduction to biochemistry, molecular genetics, cell structure, function and processes

Student Policy Manual:
You may find it in the course information folder of course compass or following the link: (http://www.ccc.edu/departments/Documents/studentpolicymanual.pdf

Biology 121 Academic Objectives and Learning Outcomes:
Upon completion of the course students will be able to understand, critically evaluate and apply each of the academic objectives listed bellow

THE SCIENTIFIC METHOD
Outline the principle steps generally used in the scientific method of investigating a problem.
Define these steps of the scientific method:
Observation
Problem
Preliminary Information
Hypothesis
Experiment
Data
Discussion
Conclusion
Identify the steps of the scientific method from a science article.
Identify the variable in an experiment.
Distinguish between:
Hypothesis and theory
Theory and law
Experimental group and control group
Using a series of preliminary observations: state a problem developed from these observations, formulate a hypothesis, and design an experiment to test the hypothesis

INTRODUCTION TO BIOLOGY
List several characteristics by which a biologist would distinguish living organisms from non-living things.
Identify the genetic material and know the importance of having a carrier of genetic instructions.
Diagram how raw materials, producers, consumers, and decomposers are interrelated in the flow of energy and the cycling of materials through an ecosystem.
Identify the ultimate source of energy for most life forms on earth.
Describe the kingdoms in the five-kingdom system and give examples of organisms in each kingdom.
Arrange, in order from greater to fewer organisms included, the following categories of classification: kingdom, phylum, class, order, family, genus, species.

BASIC CHEMISTRY
Compare the following: matter with energy, atoms with molecules, atomic number with atomic mass
Diagram how protons, electrons, and neutrons are arranged in atoms and ions.
Diagram how the atomic structure of carbon, oxygen, hydrogen and nitrogen.
Describe what happens to an electron when the atom absorbs or releases energy.
Compare the various types of chemical bonds (covalent, ionic, and hydrogen), the circumstances under which each forms, and the relative strength of each type.
Describe the differences between acids and bases and explain their relationship to the pH scale.
Explain why the pH of substances is important to living organisms.
Explain the role that hydrogen bond formation plays in some of the physical and chemical properties of water.

THE MOLECULES OF LIFE
Explain why carbon atoms are part of so many substances in living organisms.
Distinguish between organic and inorganic molecules.
Diagram the following functional groups: Hydroxyl (Alcohol), Carboxyl, Amino, Phosphate, Methyl
Explain how small organic molecules (monomers) can be assembled into large macromolecules (polymers) by dehydration synthesis (condensation).
Explain how macromolecules (polymers) can be broken apart by hydrolysis into their basic subunits.
Define carbohydrates and identify its basic molecular subunits.
Distinguish among monosaccharides, disaccharides, and polysaccharides and give examples of each.
Illustrate how a polysaccharide is assembled.
Indicate how monosaccharides, disaccharides, and polysaccharides are used in living organisms.
Define lipids.
Identify the basic molecular subunits in a triglyceride.
Distinguish between saturatetd and unsaturated fatty acids. Compare their physical properties and describe where they are found in nature.
Illustrate how the various classes of lipids (triglycerides, steroids, phospholipids, and waxes) function in living organisms.
Define protein and identify its basic building blocks.
Draw the structural formula for an amino acid labeling the central carbon, amino group, carboxyl group and the R group.
Describe the structure that all amino acids have in common and the components that make each of the amino acids different.
Diagram and explain how a peptide bond is formed.
Illustrate how the primary, secondary, and tertiary structures of a protein are formed.
Define denaturation and explain how it occurs.
Briefly describe the role of proteins in living organisms.
Define nucleic acid and the role of nucleic acids in living organisms.

CELL STRUCTURE AND FUNCTION
Compare and contrast the general features of prokaryotic and eukaryotic cells.
List the characteristics which distinguish a plant cell from an animal cell.
Diagram, label and state the function of each of the following cellular parts: cell wall microtubule centriole mitochondrion chloroplast nucleolus chromosome nucleoplasm cytoplasm nuclear envelope endoplasmic reticulum nucleus
(rough & smooth) plasma membrane golgi body plastid lysosome ribosome microfilament vacuole

Describe the basic structure and function of the chloroplast
Describe the basic structure and function of a mitochondrion.

MEMBRANE STRUCTURE AND FUNCTION
Describe the structure and function of the fluid mosaic model of the plasma membrane.
Identify the hydrophilic and hydrophobic parts of the plasma membrane.
Define and identify the factors that influence diffusion.
Identify a concentration gradient.
Explain the similarities and differences between: diffusion and osmosis, simple diffusion and facilitated transport, facilitated transport and active transport, exocytosis and endocytosis, phagocytosis and pinocytosis.
Contrast the effects of hypotonic, isotonic, and hypertonic solutions on living cells.

METABOLISM: ENERGY & ENZYMES
State the first and second laws of thermodynamics and cite how each apply to living systems.
Trace the path of energy flow from the sun to use by your cells.
Distinguish between exergonic and endergonic reactions and give an example of each.
Describe how enzymes act as catalysts.
Diagram the relationship between enzyme, substrate and product.
Discuss the effects of substrate concentration, temperature, heavy metals and pH on enzyme activity.
Write the equation for the formation and breakdown of ATP and indicate the energy changes involved.

PHOTOSYNTHESIS
Discuss the importance of photosynthesis to life on earth.
Be able to distinguish between the autotrophic and heterotrophic means of obtaining nutrition.
Write the equation for the overall chemical reaction of photosynthesis.
Identify and label the structures in the organelle where photosynthesis occurs.
Predict how changes in temperature, light intensity, light color and carbon dioxide concentration will affect the rate of photosynthesis.
Compare and contrast the light-dependent and light-independent (dark) reactions of photosynthesis.
Note what reaction of photosynthesis the following are involved in: photosystems I and II, light, oxygen production, carbon dioxide fixation, glucose production

CELL RESPIRATION
Discuss the importance of cell respiration.
Compare and contrast the anaerobic and aerobic pathways of glucose metabolism in terms of the need for oxygen, organisms that use the pathways, number of ATP molecules generated by eac, names of the stages and products of each pathway.
Explain why glucose breakdown and ATP formation are so important.
State which factors determine whether the pyruvate (pyruvic acid) produced at the end of glycolysis will enter the alcoholic fermentation pathway, the lactate (lactic acid) fermentation pathway, or the acetyl-coenzyme A pathway.
List the major steps in aerobic respiration and the reactants and products of each step.
List sources of energy (other than glucose) that can be fed into the cell respiration.
Write an equation to compare the process of photosynthesis to cellular respiration by listing the substrates, end-products, and energy flow.
Outline the evolutionary sequence of energy extraction processes.

CELL DIVISION
Illustrate the differences between prokaryotic and eukaryotic cell division.
Diagram a double-stranded chromosome.
Distinguish between chromatin and chromosome, and explain how they are related to each other.
State a difference between animal and plant cell division.
Contrast diploid cells with haploid cells, noting the processes that from each.
Distinguish how mitosis differs from meiosis, including the chromosome number.
Evaluate the significance of the end results of meiosis, noting cells which undergo meiosis.
Diagrammatically explain mitotic cell division by following the major events of interphase, prophase, metaphase, anaphase, and telophase. Label all structures of each phase.
Diagrammatically explain Meiosis I and II, labeling all structures and phases.
Illustrate the general scheme of spermatogenesis and oogenesis, including details on how the cytoplasm is distributed.
Identify, define, and cite examples of the following terms: gonad, chromatid, centromere, homologous chromosome, tetrad, reduction division, spindle apparatus, cell plate, cleavage furrow, gamete

DNA : THE GENETIC MATERIAL
Delineate the relationship between genes, chromosomes, and DNA.
Identify the chemical structure of DNA and RNA by: listing the four bases, sugar, and phosphate group for DNA and RNA nucleotides diagramming or demonstrating with a model relating the formation of a base sequence to the genetic message.
State the rule of complementary base pairing.
Explain the process of DNA replication by starting with a given base sequence in a double-stranded segment of DNA and listing the steps involved in forming a duplicate double-strand.

GENE ACTIVITY AND REGULATION
Define, give examples, or explain the terms transcription, template,complementary, codon, anticodon. double helix
Explain the process of DNA direction of protein synthesis by: listing the three types of RNA and identifying the function of each following the base sequence of DNA through m-RNA to t-RNA and its associated amino acid to the final polypeptide chain which would result.
When given a DNA coding strand and a table of codons, determine the m-RNA codons, t-RNA anticodons, and the sequence of amino acids in the resulting protein.
Note the relationship between introns and exons.
Explain how the mutational changes in the base sequence of DNA affects the shape of the protein being synthesized.
Diagram and explain the action of a regulator gene, a repressor protein, a structural gene, and an operator gene in controlling the expression of a gene.
Diagram how DNA is packaged in a chromosome.

RECOMBINANT DNA & BIOTECHNOLOGY
Summarize the relationship between restriction enzymes and recombinant DNA.
Diagram the recombinant DNA technique using bacteria to produce such end products as insulin.
Describe a procedure for fingerprinting the DNA of an individual.
Identify plasmids and explain how they are instrumental in conferring resistance to drugs.
Describe the technique used to insert new genes into recombinant DNA molecules.

MENDELIAN PATTERN OF INHERITANCE
Distinguish between: gene and chromosome genotype and phenotype dominant and recessive homozygous and heterozygous monohybrid and dihybrid haploid and diploid independent assortment and linkage
Apply Mendel’s Laws of Segregation and Independent Assortment to the distribution of genes.
Solve genetics problems dealing with:
Monohybrid crosses dihybrid crosses complete dominance incomplete dominance codominance sex determination linkage and sex-linkage.
Complete and interpret a Punnett square by determining: the genotypes of the parents the gametes of each parent the phenotypic and genotypic ratio of the offspring.
Determine an unknown genotype by means of a backcross or testcross.

CHROMOSOMAL BASIS OF INHERITANCE
Define, give examples, or explain the following terms; alleles, multiple alleles, linkage group, carrier, karyotype, complete dominance, incomplete dominance and co-dominance, autosome and sex chromosome.
Explain why sex-linked recessive traits in mammals occur much more frequently in males than in females.
Explain crossing over and how it affects the combination of traits in the offspring.
Construct a chromosome map when given crossover frequencies.
Explain the molecular basis of a gene mutation.
Define and give examples of inversions, translocations, deletions, and duplications that may occur in chromosomes.

HUMAN GENETICS
Identify the following types of inheritancefrom a pedigree: autosomal dominant, autosomal recessive, sex-linked recessive. phenotypes and genotypes of individuals in the pedigree.
Illustrate the inheritance of multiple alleles as revealed in the human ABO blood group system.
List the different A-B-O blood types plus the Rh+ and Rh- blood types, give the possible genotype(s) responsible for each phenotype, and solve problems involving blood type.
Describe the genetics of: sickle-cell anemia, hemophilia
Use diagrams to explain how nondisjunction in the male or female can lead to the following karyotypes: XO, XXY, XXX, XYY.
Discuss the causes and symptoms associated with:
Down’s syndrome
Turner’s syndrome
Klinefelter’s syndrome
Describe the technique of amniocentesis and discuss its use in genetic counseling.

Textbooks:
Biology by Campbell and Reese; 10th edition with access to Mastering Biology; Benjamin/Cummins. A special customized version of the book has been specially produced for Truman College (2nd edition). It can be purchased in the on-line CCC bookstore. This version contains only the chapters to be covered in the course. It comes with access to Mastering Biology. Another, perhaps more economical option, to get the access to Mastering Biology is to buy the “stand-alone-edition”. You may buy this either in the bookstore or on-line directly from the publisher. However you must have a textbook even if it is of a previous edition (no older than the 9th). Additional readings will be provided by the professor either in electronic or printed form. Additionally, it is necessary to buy the laboratory manual. This has been customized for Truman. It can be purchased in the book store. There are packages in the bookstore that include the textbook, access to CC, and the laboratory manual.

Mastering Biology:
Mastering Biology is a very important pedagogical tool in this class. All communication, announcements, assignments, deadliness, and exams will be posted there. It is of the most importance that you gain access to it by the 3rd class of the semester. Should you have any problems registering or accessing Mastering Biology you should get in contact with the technical department of the publisher. The link to the technical service department site can be found in the sleeve of the course compass-package. It is of the outmost importance that when you register in Mastering Biology you do so with the email address that you use most often. This would ensure your receiving all of the information. Also, please read your email before coming to class for last minute announcements.

Please see hand out for instructions to register. You can find the course ID required for registering in the hand out provided by the professor.

IMPORTANT: The following information will be posted in the course “information folder” of Mastering Biology; Power Points, resources to prepare a power point presentation, tutoring center schedule, rubrics, laboratory report format.

Course requirements:
Attendance will not be formally part of the grade, but it will be taken each class session. However, attendance and daily participation in class discussions and activities will be taken into account by the professor to raise you midterm/final grade in case your score is close to a higher one (no more than 1 points). Additionally, attendance and class performance will be determined by the ACTIVE PURSUIT COLLEGE POLICY described below. Students are expected to come to class having thoroughly read the assigned materials for the session and be prepared to actively participate in class discussion and activities. In some instances you may find useful to re-read difficult material a second time. However, you will not be expected to come to class having fully mastered the material and all the nuances of the content/arguments. Coming to class with specific questions about a particular topic or the steps in one particular argument is a plus. The class will be fast paced, thus is recommended that you keep up with the information and assignments. In addition to class time, students should invest an extra 15 hours working at home this will greatly increase the likelihood of your success.

Quizzes:
There will be 18 Mastering Biology quizzes; one quiz for each chapter covered. You will be afforded 2 opportunities to write the each of the questions. I STRONGLY recommend that before taking the quizzes you thoroughly study the material, and take advantage of practice quizzes and activities provided by the publisher. Each quiz will consist of 30 questions randomly selected from a large pool. You will have 45 minutes to write the quiz (1.5 minute per question). The quizzes will be available to be written the day of the lecture. Closing time for each quiz will be indicated in mastering biology and announced by the professor

Exams;
There will be 4 in class exams. Each one will encompass of the material covered in class up to the time of the exam. Note that the exams will not be comprehensive. For example, the second exam will not include content already covered in the first. The exams will consist of 80 multiple choice questions randomly selected from the same pools whereby the quizzes’ questions were selected and 5 open-ended/short essay questions produced by the professor. The weight of the 80 multiple choice questions is 80 points. The weight of the short essay questions is 20 points

Presentation and Paper:
In the first term of the course, students organized in groups of 4 to 6 must produce a formal research paper. The topic for the paper should be chosen by the students in the group. A one paragraph proposal should be handed in to the professor for approval. Ideally the topic should be of interest of all of the group members. The length of the paper should be between 1500 to 1750 words
By the end if the course the same groups of students will be required to make a multimedia presentation of the research paper information. The presentation should use audiovisual instruments which will be evaluated together with content, delivery, and engagement of audience. Everyone in the group should contribute to the effort.

Laboratories:
Students will carry out at least 6 laboratories during the semester. Laboratories will be conducted in groups of no more than 6 students. Individual reports will be required. Produced reports are to be handed in to the professor as a hard copy by the deadline; usually one week after carrying it out. Late reports will be accepted before the midterm, but they will be marked down by 20 to 40% depending on haw late they are handed in. Not attending the laboratory session will keep students from receiving laboratory credit. No exceptions. Due to time constrains laboratory work may be divided between group members. However, data have to be consolidated to write the individual reports which should be written in the formal science report form. The professor will hand out an information sheet with the basic science report format. If you have problems in this regard, I would strongly recommend the resources of the tutoring center.

Academic Course Calendar: The calendar for the course can be found in the document’s folder of Mastering Biology. All of the deadlines, dates, etc., will be posted there. Bear in mind that it is an active calendar, meaning there may be modifications as the course progresses. These will be announced to the group in advance.

Academic Integrity/Cheating and Plagiarism:
Evidence of cheating in the classroom will be met with removal of your test and a zero score. Persons assisting in cheating will be met with the same outcome. Plagiarism will be defined as turning work that is not the student’s original work. Evidence of plagiarism will result in a reduced grade or zero for that activity for all people involved in the plagiarism. Continued plagiarism and cheating will result in immediate dismissal from the course and a final grade of “F”, regardless of the student’s total points in the course.

Withdrawal from the class:
If you wish to withdraw please use the formal drop procedure used by Truman College. It is your responsibility to get instructor’s approval on the withdrawal form and get it processed. If your name appears in the final grade list and you have been absent, you will receive an ‘F’ grade for the course.

Active Pursuit of the course/ Being dropped from the class:
Per the new guidelines established by Truman College, any student who fails to demonstrate continued class participation and continued progress towards completion of the course (active pursuit) will be dropped by the instructor and given an ADW (administrative withdrawal) from the course. Continued class participation is demonstrated by attendance (> 80% of lectures and labs). Continued progress towards completion of the course includes, but is not limited to, completion and submission of all the academic assignments with an earned grade of >60%, maintaining an overall quiz grade average of >60% and maintaining an overall in class test average of >60%.

Grade Appeals:
Per Truman College guidelines, as documented in the student handbook, student appeals of a final grade must be submitted using the appropriate grade appeal form within 30 days of the end of the semester. The form must be completed correctly to constitute an appeal. After this time period no appeals will be accepted.

Student Conduct:
Each student is responsible for adhering to the Code of Student Conduct posted in course compass information Folder or in the following link:
(http://www.ccc.edu/departments/Documents/studentpolicymanual.pdf

Special Needs:
The Disability Access Center is located in room 1428.This is the Center, responsible for verifying that students have a disability-related needs for academic, accommodations and for planning appropriate accommodations, in cooperation with the students themselves and their instructors. Students who need academic accommodations should request them from the DAC Center 773-907-4725 Linda Ford Director Office hours are from 9:00 am-7:00 p.m. Monday-Thursday; Fridays from 9:00 a.m. 4:00 p.m.

Grade weight and distribution:

The final score will be calculated in a 8,000 point scale and is distributed as following

18 Quizzes 100 points each Total 1800 (30%)
4 Exams 450 points each Total 1800 (30%)
8 Laboratories 180 points each Total 1500 (25%)
1 Presentation 900 points Total 1000 (15%)

Total points 6000

Letter Grade Point Distribution:

A = 5400 to 6000 (9-10)*
B = 4800 to 5399 (8-8.9)
C = 4200 to 4799 (7-7.9)
D = 3600 to 4199 (6-6.9)
F = Less than 3600 (< 6)

*The numbers in the parenthesis are the corresponding values in a 1-10 scale

NOTICE:

The class assumes that you have or are taking English 101, thus you should be proficient at writing the essay questions and lab reports. Should you have any problem regarding reading and/or writing skills, you may look for help in the tutoring center.

ABSOLUTELY

No food or drinks are allowed in classroom.
Tables must be cleaned after finishing up laboratories. Points will be deducted from the table members if tables are not cleaned up.
No ringing cell phones allowed in classroom. If you need to have them on, please set them to vibrate and take the call outside the classroom. You do not have to ask for permission to do so. Only do it quietly.