CODE: CHEM-236 TITLE: Biochemistry Institute: STEM DEPARTMENT: Chemistry COURSE DESCRIPTION: Upon completion of this course the student will be able to recognize and draw the structure and state the nature of the biochemicals important to life (carbohydrates, lipids and proteins), describe in detail the metabolic pathways that generate them and release energy from them. The student will also be able to describe and draw the structure of the gene molecules (RNA & DNA) and describe their metabolism and their role in protein synthesis. Basic concepts will be reinforced with appropriate laboratory experiences. PREREQUISITES: A grade of C or higher in CHEM-136, CHEM235, or CHEM 203. CREDITS: 5 LECTURE HOURS: 4 LAB/STUDIO HOURS: 3 REQUIRED MATERIALS: TEXT: TYMOCZKO, JL, BERG, JM, AND STRYER, L. (2011) BIOCHEMISTRY: A SHORT COURSE 2 ND EDITION NEW YORK: W.H. FREEMAN AND COMPANY. See the College Bookstore for textbook information. SAFETY GOGGLES: NEW JERSEY STATE LAW REQUIRES THAT ALL STUDENTS WEAR APPROPRIATE SPLASH AND IMPACT PROOF SAFETY GOGGLES WHILE PERFORMING LABORATORY EXPERIMENTS, OR DURING DEMONSTRATION OF EXPERIMENTS. THEY ARE AVAILABLE AT THE COLLEGE STORE. FULL-LENGTH LABORATORY COAT: ALL STUDENTS ARE REQUIRED TO WEAR A FULL-LENGTH LABORATORY COAT DURING THE LABORATORY PERIOD. COURSE LEARNING OUTCOMES: Utilize critical thinking skills to learn advanced concepts from biological chemistry ( Perform chemistry-based problem solving. Reinforcement of chemical concepts will be made as hands-on skills are developed in the laboratory program Read, interpret and present scientific papers and content Interpret spectra and other experimental results Draw and predict products of biochemical reactions Explain reaction mechanisms for enzymes and inhibitors Describe the energy and information flow in a biological system Isolate biochemical compounds through reactions GRADING STANDARD: Upon completion of the course, grades will be assigned as follows: A = 92 100% A- = 89-91% B+ = 86-88% B = 82-85% B- = 79-81%
C+ = 76-78% C = 70-75% D = 65-69% F = <65% Assessment results will be reported as the grade assigned by the faculty calculated to the first decimal place. These grades will be weighed according to course grading policy. In calculating the course grade, 0.5 will round up to the next numerical grade and 0.4 will round down to the next lower numerical grade. Lab: 1. The total laboratory grade will be based on laboratory experiments and laboratory quizzes given through the semester. The experiment average will make up 80% of the final grade and the quiz average will make up 20% of the final grade. 2. Any missed lab will be averaged in as a zero (0). 3. Any missed laboratory quiz will not be made up. 4. There may be a field trip to a research laboratory during one of the lab sessions. You will be expected to attend. Lecture: The lecture grade comprises 80% of the total grade. Assessments will be varied and could likely include exams, discussion sessions, lab reports, presentations, and a literature research project. DEPARTMENT POLICIES Chemistry Laboratory Policies 1. Students must attend their scheduled laboratory section. Students are not allowed to attend any other lab section for any reason. 2. Students must pass both the lecture and the laboratory portion of the course. 3. Students must wear googles, a full-length laboratory coat, and closed-toed shoes in the laboratory. COLLEGE POLICIES: For information regarding: Brookdale s Academic Integrity Code Student Conduct Code Student Grade Appeal Process Please refer to the STUDENT HANDBOOK AND BCC CATALOG. NOTIFICATION FOR STUDENTS WITH DISABILITIES: Brookdale Community College offers reasonable accommodations and/or services to persons with disabilities. Students with disabilities who wish to self-identify, must contact the Disabilities Services Office at 732-224-2730 or 732-842-4211 (TTY), provide appropriate documentation of the disability, and request specific accommodations or services. If a student qualifies, reasonable accommodations and/or services, which are appropriate for the college level and are recommended in the documentation, can be approved. ADDITIONAL SUPPORT/LABS: Learning assistants are available for help for both lab and lecture. The times of availability are posted at the learning assistants office. For any additional information, please call the Chemistry Department at 732-224-2424. WEBSITE: https://www.brookdalecc.edu/stem-institute/chemistry/ 2
UNIT ONE Chapters: 1, 2 Unit Objective: An Introduction: Biomolecules, Cells, and Water An overview of some specific physical, chemical, and biological properties of the four major biomacromolecules, cells, and water. An introduction into the interconnectedness of these topics. LEARNING OBJECTIVES 1. Understand the elements and classes of biomolecules included the study of biochemistry: Recognize and compare the chemistry and biology of proteins, lipids, carbohydrates, and nucleic acids. 2. Understand information transfer in a biological system. Identify and name, in general, the steps of the central dogma 3. Learn the role of the cell, cell organelles, cell membranes, and how compartmentalization controls information and energy flow in biological systems. Identify and name nucleus, endoplasmic reticulum, golgi, mitochondria, and cell membrane. 4. Understand and identify the importance of the unique qualities of water. Identify weak intermolecular interactions: hydrogen bonds, van Der Waals interactions, hydrophobic effect Understand the importance of ph in biomolecules and the role of buffers in biological systems. OBTAINING THE OBJECTIVES READ: 1.1-1.2 2-3 on page 15 Quick Quiz 1 page 7 Key Terms page 15 READ: 1.3 4, 5 page 15 READ: 1.4 7, 8, 11-12 on page 15 Quick Quiz 2 page 14 READ: 2.1-2.5 2-3,6-14 page 32 Quick Quiz 1: page 22 Key Terms page 32 3
UNIT TWO Chapters: 33-40, 3, 4 Unit Objective: Information Transfer in the Cell Synthesis of and information transfer among, DNA, RNA, and proteins. LEARNING OBJECTIVES 1. Identify and describe nucleic acid structure and chemistry DNA, RNA sugars, bases, and phosphates. Double helix, histones, and RNA structures OBTAINING THE OBJECTIVES READ: 33.1-33.5 1-8,10-11, 21, 24-25 pgs 595-596 Quick Quizzes 1 and 2 pgs 585 & 591 Key Terms page 594 2. Understand and describe the process of DNA replication 3. Understand and describe the processes of DNA repair and replication READ: 34.1-34.2 All on page 611-612 Quick Quizzes 1 and 2 on pgs 603, 608 Key Terms page 611 READ: 35.1-35.3 All on page 624-625 Quick Quizzes 1 and 2 on pgs 618, 623 Key Terms page 623 4. Understand and describe the processes of RNA synthesis and regulation in prokaryotes Transcription 5. Understand and describe the control of gene expression in eukaryotes. READ: 36.1-36.3 All on page 642-643 Quick Quizzes 1& 2 on pages 635, 639 Key Terms page 642 READ: 37.1-37.4 All on page 658-659 Quick Quizzes 1& 2 on pages 650, 653 Key Terms page 657 4
6. Understand and describe RNA processing in eukaryotes. READ: 38.1-38.4 All on page 671-672 Quick Quiz 1on page 666 Key Terms page 671 7. Understand and describe translation. READ: 39.1-39.3 All on page 687-688 Quick Quizzes 1& 2 on pages 683, 686 Key Terms page 686 8. Understand and describe protein synthesis READ: 40.1-40.5 All on page 706-708 Quick Quizzes 1& 2 on pages 695, 701 Key Terms page 706 9. Protein chemistry and structure READ: 3.1-4.5 All on page 43-44, 64-66 Quick Quizzes on pages 41, 48 Key Terms page 43, 64 5
UNIT THREE Chapter: 6-8 Unit Objective: Enzymes: Thermodynamics, Kinetics, and Mechanism Basic properties of enzymes, energetic of enzyme-catalyzed reactions, kinetic analysis of enzymes, mechanisms of enzymes, impact of environment on activity, allosteric and other regulation of enzymes. LEARNING OBJECTIVES OBTAINING THE OBJECTIVES 1. Understand basic concepts of enzyme action Specificity, cofactors, free energy, transition states, active sites READ: 5.1-5.4 3, 6-7, 11-16 page 103-104 Quick Quiz page 98 Key Terms page 103 2. Understand and describe kinetics and regulation Michaelis Menten kinetics, allosteric regulation and kinetics, ratelimiting steps READ: 7.1-7.3 Numbers 4-7,11,14-15, 18-24 on pgs 120-124 Quick Quizzes pages 108, 116 Key Terms page 120 3. Understand and describe enzyme mechanisms and inhibitors READ: 8.1-8.3 Numbers 1-5,8-13,15 pages 139-140 Quick Quizzes 1 &2 pages 131, 138 Key Terms page 139 6
UNIT FOUR Chapter: 10-11 Unit Objective: Basics of carbohydrates and lipids Learning biochemical properties and roles of carbohydrates and lipids. LEARNING OBJECTIVES OBTAINING THE OBJECTIVES 1. Understand and describe carbohydrates Monosaccharides, stereoisomers, Fischer projections, Haworth projections, glycosidic bonds, polymerization, proteoglycans READ: 10.1-10.4 #1-4, 5, 7, 11, 13, 16-22, 27, 30, on pgs 176-178 Quick Quizzes 1 &2 pages 166, 172 Key Terms page 175 Carbohydrates interacting with proteins Glycosylation and glycoproteins, blood groups, lectins 2. Understand and describe lipids Classes of lipids, fatty acids, cis-, trans- unsaturated, triglycerides and storage, membrane lipids: phospholipids, steroids, glycolipids, lipid-modified proteins READ: 11.1-11.3 QUESTIONS & PROBLEMS; All on page 190-191 Quick Quizzes 1 & 2 pages 182, 188 Key Terms page 190 7
UNIT FIVE Chapter: 12-13 Unit Objective: Membranes and Signaling Learning the biochemical properties of cell membranes and signal transduction pathways. LEARNING OBJECTIVES OBTAINING THE OBJECTIVES 1. Understand and describe membrane structure and function Phospholipid bilayer, proteins in the cell membrane, lipid movement across the membrane, protein transporters 2. Understand and describe signal transduction pathways Molecular circuits, outside-in receptor signaling, G-coupled receptors, tyrosine kinase receptors, insulin as an example, calcium messaging, defects READ: 12.1-12.5 QUESTIONS & PROBLEMS All on page 211-213 Quick Quizzes 1 & 2, pages 199, 208 Key Terms page 210 READ: 13.1-13.5 #1-8, 11-12, 14-16, 19-20, 22-23, 25, 27 on pages 232-234 Quick Quizzes 1 & 2, pages 221, 228 Key Terms page 231 8
UNIT SIX Chapter: 14-32 Synthesis and Metabolism Unit Objective: To describe in detail the metabolic pathways that generate biomacromolecules and release energy from them. Learning Objectives 1. Understand the general steps and purposes of digestion Breaking down, proteases, amylase, emulsion and lipase, digestion and signaling Obtaining The Objectives READ: 14.1-14.5 All on page 246 Quick Quiz page 242 Key Terms page 245 2. Understand the basic concepts and design of metabolism Interconnectedness, ATP, oxidation, energy carriers: NADH, FAD, control: allosteric, feedback inhibition, reversible covalent modification,, signaling, compartimentalization READ: 15.1-15.5 #2, 4-5, 7, 14-21 on pages 266-267 Quick Quiz page 253 Key Terms page 266 3. Understand and describe the processes of glycolysis and gluconeogenesis Energy conversion, NADH oxidation, control, role in insulin control, pyruvate glucose, regulation, use by other organs, evolutionary relationships READ: 16.1-17.4 #1-7, 9-11, 14, 16, 23, 25, 32 on pages 296-298, #2 on page 312 Quick Quizzes pgs 279, 282, 306-307 Key Terms pages 295, 311 4. Understand and describe the citric acid cycle Preparation for the citric acid cycle, chemistry of the cycle, enzymes and control of cycle READ: 18.1-19.4 #1-6, 9, 16 on pg 327-328 #1-2, 4, 11-12, 14-15 on pages 344-346 Quick Quizzes pages 325, 337, 340 Key Terms pages 327, 343 9
5. Understand and describe oxidative phosphorylation The electron transport chain and proton motive force. READ: 20.1-21.3 #1-2, 5-6, 9-12, 14, 17 on pgs 365-366 #5, 8, 10-12, 17, 20, 28-29 on pgs 383-385 Quick Quizzes pgs 360, 362, 370, 373 Key Terms pages 365, 382 6. Understand and describe glycogen metabolism and synthesis, and the pentose phosphate pathway. Enzymes, allosteric control, reversible phosphorylation, signaling, synthesis, regulation, production and control of NADPH READ: 24.1-26.3 All on pages 434-435 #5,11-12 on pg 448 Quick Quizzes pgs 427, 429, 440, 444, 455 Key Terms pages 434, 447, 461 7. Understand and describe lipid metabolism and synthesis Fatty acid degradation, ketone bodies, lipid synthesis, membrane lipids and steroids READ: 27.1-27.4, 29.1-29.5 Quick Quizzes pgs 471, 474, 487, 491 Key Terms pages 478, 493 8. Understand and describe nucleic acid and protein synthesis and metabolism Nitrogen fixation, amino acids from intermediates, regulation, nucleotide synthesis, regulation, pathology, amino acid degradation READ: 30.1-32.3 Quick Quizzes pgs 526, 528, 536, 544, 549, 559, 560 Key Terms pages 538, 551, 571 10