Semester Lesson Plan
Document can be downloaded here
Course title: Biochemistry 2 (Metabolism and the flow of genetic information)
Course code: AKM21355
Credit: 3
Course Court Group: Mandatory
5th semester
Prerequisite Course: Biochemistry 1
Lecturers:
Dr. Mukhammad Asy’ari, M.Si
Dr. Agustina L.N. Aminin, M.Si
Dra. Nies Suci Mulyani, MS
Purbowatiningrum RS., M.Si
Graduate Learning Outcomes (GLO)
| Attitude | GLO1-(S9) | Demonstrate an attitude of responsibility for work in their field of expertise independently. |
| Knowledge | GLO2-(PP1) | Mastering the theoretical concepts of structure, properties, changes, kinetics, and energetics of molecules and chemical systems, identification, separation, characterization, transformation, synthesis of micromolecular chemicals, and their application. |
| GLO3-(PP3) | Mastering the basic principles of software for analysis, synthesis, and molecular modeling in general or more specific chemical fields. | |
| General skills | GLO4-(KU1) | Able to apply logical, critical, systematic, and innovative thinking in the development of science and technology that pays attention to and applies humanities values following their field of expertise. |
| GLO5-(KU2) | Able to demonstrate independent, quality, and measurable performance. | |
| Special skills | GLO6-(KK3) | Able to analyze several alternative solutions in identification, analysis, isolation, transformation, and synthesis of available chemicals and present analysis conclusions for appropriate decision making. |
| GLO7-(KK4) | Able to use software to determine the structure and energy of micromolecules, software to assist analysis and synthesis in general or more specific chemical fields (organic, biochemical, or inorganic), and data processing (analytical chemistry). |
Course Learning Outcomes (CLO)
| CLO-1 | Students can explain and understand (C4-analyze) and discuss (A2) how to implement (P2) the concept of chemical thermodynamics in the process of energy transformation that occurs in living cells (Bioenergetics) |
| CLO-2 | Students can explain and understand (C4-analyze) about of Inheritance of genetic traits, the flow of genetic information and discuss (A2) how to implement (P2) them on the protein biosynthesis and DNA replication. |
| CLO-3 | Students can explain and understand (C4-analyze) about types of regulation of gene expression and genetic diversity of antibodies and discuss (A2) how to implement (P2) them on the process of controlling protein biosynthesis. |
| CLO-4 | Students can explain and understand (C4-analyze) about stages of metabolism: chemical reactions of biomolecules (carbohydrates, lipids, proteins, and nucleic acids) in the cells and discuss (A2) how to implement (P2) them in the dynamics process of biomolecules and energy in living cells. |
| CLO-5 | Students can explain and understand (C4-analyze) and discuss (A2) about disorder metabolism of biomolecules then correlate (C4) with the onset of a metabolism disorder disease. |
Course Description
This lecture provides lessons about the concept of the energy cycle in nature, energy transfer in cells, the flow of genetic information and antibodies and its relation to the appearance of certain diseases, metabolism (carbohydrates, lipids, protein, and nucleic acids) and metabolic disorders.
| Week | Expected capabilities (Sub-CLO) | Study Materials/Learning Materials | Learning methods | Student Learning Experience | Time (minutes) | Evaluation | |
| Criteria and Indicators | % | ||||||
| 1 | Sub CLO-1:
Students can explain and understand (C4-analyze) and discuss (A2) how to implement (P2) the concept of chemical thermodynamics in the process of energy transformation that occurs in living cells using schematic drawings and chemical reaction equations with a minimum accuracy of 70%. |
Biology (BK20), Molecular structure (BK5), Chemical reaction (BK7)
Introduction: 1. The concept of energy cycle on macroscopic (universe), microscopic (cell), and molecular levels. 2. Overview of thermodynamic aspects: the role of high-energy phosphate molecules in the process of energy transformation in cells. 3. The role of ATP as the primary bioenergetic molecule in cells. |
– Small-Group Discussion
– Mind Mapping – Daily Evaluation |
Learn by listening, discussing, and looking for further information, then using the information to solve real problems asked by lecturers related to the concept of energy cycle on nature, the role of high-energy phosphate molecules in energy transformation in cells, especially ATP. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in describing the concept of the energy cycle and how-to, how-to implementation the concept of chemical thermodynamics in energy transformation in cells. (2). The activeness of students in discussions and working on assignments. | 5 |
| 2 | Sub CLO-2:
Students can explain and understand (C4-analyze) about stages of ATP biosynthetic reactions and discuss (A2) how to implement them (P2) in the calculation of bioenergetic equivalence between ATP and other bioenergetic molecules such as NADH, FADH2, and NADPH using schematic drawings and chemical reaction mechanisms with a minimum accuracy of 70%. |
Biomolecule (BK13), Molecular structure (BK5), Chemical reaction (BK7)
Bioenergetics (I): The production of bioenergetic molecules (ATP) through oxidative phosphorylation and electron transport which includes: (1). The concept of oxidation-reduction reactions, (2). The structure and chemical properties (redox) of bioenergetic compounds such as ATP, NADH, FADH2, and NADPH (3). The stages of electron transfer and oxidative phosphorylation and their site in the cell. |
– Discovery Learning
– Discussion – Mind Mapping – Daily Evaluation |
Before studying in the class, students work on assignments from the lecturer through searching, collecting, and compiling information related to learning material: production of bioenergetic molecules (ATP) through oxidative phosphorylation and electron transport. When students are studying in the class, they will listen, discuss, and draw conclusions about the relationship between what they learn with the tasks that they have done. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in describing the stages of ATP biosynthesis and how to implement them in calculating the equivalence of ATP with other bioenergetic molecules such as NADH and FADH2. (2). The activeness of students in discussions and working on assignments. | 5 |
| 3 | Sub CLO-3:
Students can explain and understand (C4-analyze) about principle and reaction mechanisms of using ATP and discuss (A2) how to implement (P2) them on processes inside cells such as ion transport through membranes, muscle contraction, and photosynthesis using schematic drawings and chemical reaction mechanisms with a minimum accuracy of 70%. |
Biomolecule (BK13), Molecular structure (BK5), Chemical reaction (BK7)
Bioenergetics (II): applying of bioenergetic molecules (ATP) in the cells of living things: ion transport through membranes, muscle contractions, and photosynthesis. |
– Small-Group Discussion
– Mind Mapping – Daily Evaluation |
Before lecturing in the class, students have worked on group assignments from the lecturer by preparing discussion material in papers (doc) and presentations (ppt). Students provide presentations and discussions of lecture material during the lecture on topics: ion transport through membranes, muscle contraction, and photosynthesis. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in describing the principle and mechanism of reaction using ATP in processes inside the cell such as ion transport through membranes, muscle contraction, and photosynthesis. (2). The activeness of students in discussions and working on assignments. | 5 |
| 4 | Sub CLO-4:
Students can explain and understand (C4-analyze) about structure and function of chromosomes and genes and discuss (A2) how to implement (P2) them on stages of DNA replication in the Inheritance of genetic traits from parent to child using schematic drawings with a minimum accuracy of 70%. |
Biomolecule (BK13), Molecular structure (BK5), Intermolecular Interaction (BK8)
The flow of genetic information (I): chromosomes and genes, DNA replication |
– Discovery Learning
– Discussion – Mind Mapping – Daily Evaluation |
Before studying in the class, students work on assignments from the lecturer by searching, collecting, and compiling information related to learning: material genetic: chromosomes and genes, DNA replication, and cell division. When students are studying in the class, they will listen, discuss, and draw conclusions about the relationship between what they learn with the tasks that they have done. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in describing the structure and function of chromosomes and genes and the role of DNA replication in the Inheritance of genetic traits from parent to child. (2). The activeness of students in discussions and working on assignments. | 5 |
| 5 | Sub CLO-5:
Students can explain and understand (C4-analyze) the stages of transcription and translation and discuss (A2) how to implement (P2) them on the process of protein biosynthesis using schematic drawings with a minimum accuracy of 70%. |
Biomolecule (BK13), Molecular structure (BK5), Intermolecular Interaction (BK8)
The flow of genetic information (II): transcription, genetic code, translation |
– Discovery Learning
– Discussion – Mind Mapping – Daily Evaluation |
Before studying in the class, students work on assignments from the lecturer by searching, collecting, and compiling information related to learning material: stage of the flow of genetic information: transcription and translation. When students are studying in the class, they will listen, discuss, and draw conclusions about the relationship between what they learn with the tasks that they have done. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in describing the role of transcription and translational stages in the process of protein biosynthesis. (2). The activeness of students in discussions and working on assignments. | 5 |
| 6 | Sub CLO-6:
Students can explain and understand (C4-analyze) about types of regulation of gene expression and genetic diversity of antibodies and discuss (A2) how to implement (P2) them on the process of controlling protein biosynthesis using schematic drawings with a minimum accuracy of 70%. |
Biomolecule (BK13), Molecular structure (BK5), Intermolecular Interaction (BK8)
The flow of genetic information (III): expression gene regulation and genetic diversity of antibodies. |
– Small-Group Discussion
– Mind Mapping – Daily Evaluation |
Before studying in the class, students have worked on group assignments from the lecturer by preparing discussion material in papers (doc) and presentations (ppt). Students provide presentations and discussions of lecture material during the lecture on topics: lac operon, trp operon. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in describing the relationship between the mechanism of regulation of gene expression (lac operon, trp operon) with the control of protein biosynthesis. (2). The activeness of students in discussions and working on assignments. | 5 |
| 7 | Sub CLO-7:
Students can explain and understand (C4-analyze) the effect of gene mutations on the structure and function of proteins and correlate (P2) them with the onset of genetic diseases using schematic drawings with a minimum accuracy of 70%. |
Biomolecule (BK13), Molecular structure (BK5), Intermolecular Interaction (BK8)
The flow of genetic information (IV): diseases caused by gene mutations. |
– Problem-Based Learning
– Mind Mapping – Daily Evaluation |
Before lecturing in the class, students have worked on group assignments from the lecturer by preparing discussion material in papers (doc) and presentations (ppt). During the lecture, students provide presentations and discussions of lecture material on topics: down syndrome, Ehlers-Danlos syndrome, cycle cell anemia, Cystic fibrosis, Phenylketonuria, cancer, etc. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in the relationship between gene mutations and changes in the structure and function of proteins that cause genetic diseases (2). The activeness of students in discussions and working on assignments. | 7.5 |
| 8 | Mid-Semester Evaluation | PB 1 s.d. PB 7 | Mid-Semester Evaluation: validate the assessment results, evaluation, and improvement process for the following learning process. | Written examination | 100’ | Correct and complete answers to the Mid-Semester Exam questions with a minimum accuracy of 70% | 12.5 |
| 9 | Sub CLO-8:
Students can explain and understand (C4-analyze) about the stages of the chemical changes of carbohydrates in cells and discuss (A2) how to implement (P2) them in the dynamics process of biomolecule and energy in living cells using schematic drawings and chemical reaction equations with a minimum accuracy of 70%%. |
Biomolecule (BK13), Chemical reaction (BK7)
Metabolism (I): basic concepts of the digestive system, carbohydrate metabolism (1. glycolysis, 2. the citric acid cycle, 3. gluconeogenesis, 4. glycogenolysis). |
– Discovery Learning
– Discussion – Mind Mapping – Daily Evaluation |
Before studying in the class, students work on assignments from the lecturer by searching, collecting, and compiling information related to learning material: an overview of metabolism, digestive system, carbohydrate metabolism. When students are studying in the class, they will listen, discuss, and draw conclusions about the relationship between what they learn with the tasks that they have done. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in describing the stages of carbohydrate metabolism (glycolysis, citric acid cycle, gluconeogenesis, glycogenolysis) (2). The accuracy in the relationship between carbohydrate metabolism and energy production (ATP). (3). The activeness of students in discussions and working on assignments. | 5 |
| 10 | Sub CLO-9:
Students can explain and understand (C4-analyze) the stages of the chemical changes of fatty acids in cells and discuss (A2) how to implement (P2) them in the dynamics process of biomolecule and energy in living cells using schematic drawings and chemical reaction equations with a minimum accuracy of 70%%. |
Biomolecule (BK13), Chemical reaction (BK7)
Metabolism (II): fatty acid metabolism (1. beta-oxidation reaction of fatty acid, 2. fatty acid biosynthesis ) |
– Discovery Learning
– Discussion – Mind Mapping – Daily Evaluation |
Before studying in the class, students work on assignments from the lecturer by searching, collecting, and compiling information related to learning material: fatty acid metabolism. When students are studying in the class, they will listen, discuss, and draw conclusions about the relationship between what they learn with the tasks that they have done. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in describing the stages of fatty acid metabolism (beta-oxidation and fatty acid biosynthesis) (2). The accuracy in the relationship between fatty acid metabolism and energy production (ATP). (3). The activeness of students in discussions and working on assignments. | 5 |
| 11 | Sub CLO-10:
Students can explain and understand (C4-analyze) about the stages of chemical changes of amino acids in the cell and discuss (A2) how to implement (P2) them to explain the mechanism of neutralizing toxins from residual metabolism using schematic drawings and chemical reaction equations with a minimum accuracy of 70%%. |
Biomolecule (BK13), Chemical reaction (BK7)
Metabolism (III): protein metabolism (1. amino acid degradation, two urea cycle) |
– Discovery Learning
– Discussion – Mind Mapping – Daily Evaluation |
Before studying in the class, students work on assignments from the lecturer by searching, collecting, and compiling information related to learning material: protein metabolism. When students are studying in the class, they will listen, discuss, and draw conclusions about the relationship between what they learn with the tasks that they have done. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in describing the stages of protein metabolism (amino acid degradation and the urea cycle) (2). The accuracy in the relationship between the urea cycle with the process of neutralizing poisons from metabolic waste. (3). The activeness of students in discussions and working on assignments. | 5 |
| 12 | Sub CLO-11:
Students can explain and understand (C4-analyze) the stages of nucleotide chemical changes in cells and discuss (A2) how to implement (P2) them on the process of biomolecular dynamics in living cells using schematic drawings and chemical reaction equations with a minimum accuracy of 70%%. |
Biomolecule (BK13), Chemical reaction (BK7)
Metabolism (IV): nucleic acid metabolism (1. purine metabolism, 2. pyrimidine metabolism. |
– Discovery Learning
– Discussion – Mind Mapping – Daily Evaluation |
Before studying in the class, students work on assignments from the lecturer by searching, collecting, and compiling information related to learning material: nucleic acid metabolism. When students are studying in the class, they will listen, discuss, and draw conclusions about the relationship between what they learn with the tasks that they have done. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in describing the stages of nucleic acid metabolism (purines and pyrimidines). (2). The accuracy in the relationship between purine and pyrimidine metabolism. (3). The activeness of students in discussions and working on assignments. | 5 |
| 13 | Sub CLO-12:
Students can explain and understand (C4-analyze) and integrate (P2) the metabolism pathways of carbohydrate, lipid, protein, and nucleic acid and correlate (C4) with organ functions of living things using schematic images with a minimum accuracy of 70%%. |
Biomolecule (BK13), Intermolecular Interaction (BK8), Biology (BK20)
Integration of metabolism |
– Discovery Learning
– Discussion – Mind Mapping – Daily Evaluation |
Learn by listening, discussing, and looking for further information, then using the information to solve real problems asked by lecturers related to integration metabolism. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy of integrating the metabolic pathways of all biomolecules (2). The accuracy in the relationship between organ functions with the metabolic reactions that occur. (3). The activeness of students in discussions and working on assignments. | 5 |
| 14 | Sub CLO-13:
Students can explain and understand (C4-analyze) about the disordered metabolism of carbohydrate, lipid, protein, and nucleic acid then correlate (C4) with the onset of a disease (topic 1: Gout (GOUT), Albino, Niemann-Pick, and Galactosemia) using a schematic image with a minimum accuracy of 70%%. |
Biomolecule (BK13), Intermolecular Interaction (BK8), Biology (BK20)
Disorder Metabolism (I): diseases caused by metabolic disorders topic 1: Gout (GOUT), Albino, Niemann-Pick, and Galactosemia |
– Problem-Based Learning
– Mind Mapping – Daily Evaluation |
Before lecturing in the class, students have worked on group assignments from the lecturer by preparing discussion material in papers (doc) and presentations (ppt). Students provide presentations and discussions of lecture material during the lecture on topics: uric acids (GOUT), Albino, Niemann–Pick, and Galactosemia. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in the relationship between metabolic disorders and the onset of disease: uric acids disorder (GOUT), Albino, Niemann-Pick, and Galactosemia. (2). The activeness of students in discussions and working on assignments. | 5 |
| 15 | Sub CLO-14:
Students can explain and understand (C4-analyze) about the disordered metabolism of carbohydrate, lipid, protein, and nucleic acid then correlate (C4) with the onset of a disease (topic 2: Hyperlipidemia and hypercholesterolemia) using a schematic image with a minimum accuracy of 70%. |
Biomolecule (BK13), Intermolecular Interaction (BK8), Biology (BK20)
Disorder Metabolism (II): diseases caused by metabolic disorders, topic 2: Hyperlipidemia and hypercholesterolemia, |
– Problem-Based Learning
– Mind Mapping – Daily Evaluation |
Before lecturing in the class, students have worked on group assignments from the lecturer by preparing discussion material in papers (doc) and presentations (ppt). During the lecture, students provide presentations and discussions of lecture material on topics: Hyperlipidemia and hypercholesterolemia. | FF: 3 x 50’
ST : 3 x 60’ SS: 3 x 60’ |
(1). The accuracy in the relationship between metabolic disorders and disease onset: Hyperlipidemia and hypercholesterolemia. (2). The activeness of students in discussions and working on assignments. | 5 |
| 16 | Final exams | PB 8 s.d. PB 14 | Final exams: validate the assessment results, evaluation, and improvement process for the following learning process. | Written examination | 100’ | Correct and complete answers to the Mid-Semester Exam questions with a minimum accuracy of 70% | 12.5 |
References:
- Devlin, T.M., (1997), Textbook of Biochemistry with Clinical Correlations, Fourth Edition, Wiley-Liss, Inc
- Lehninger, (1977), Biochemistry, second edition, Worth Publisher, Inc, USA.
- Mathews, C.K., and Van Holde, K.E., (1996), Biochemistry, second edition, The Benjamin/Cummings Publishing Company, Inc, California, USA.
Glossary
GLO = Graduate Learning Outcome
CLO = Course Learning Outcomes
FF = Face to Face Learning
ST = Structured tasks
SS = Self Study
