Biochemistry

Week 1: Welcome to Biochemistry

• Navigate a course in D2L
• Locate important course information i.e. syllabus
• View the instructor profile.
• Communicate with instructor and peers.
• Construct a Class Directory entry.
• Communicate effectively in an online class discussion ice-breaker.
• Participate in community building.
• Distinguish between an element and a compound.
• Identify the four elements that make up 96% of living matter.
• Define the term trace element and give an example.

Week 2: Chemistry Introduction - The Chemical Reactions of Life

• Model an atom.
• Distinguish between each of the following Neutron and proton, Atomic number and mass number, and Atomic weight and mass number
• Explain how the atomic number and mass number of an atom can be used to determine the number of neutrons.
• Explain how two isotopes of an element are similar. Explain how they are different.
• Describe a biological application that uses radioactive isotopes.
• Define the terms energy and potential energy. Explain why electrons in the first electron shell have less potential energy than electrons in higher electron shells.
• Distinguish between nonpolar covalent, polar covalent and ionic bonds.
• Explain why strong covalent bonds and weak bonds are both essential in living organisms
• Distinguish between hydrogen bonds and van der Waals interactions.

Week 3: Chemistry Introduction - Water and Life

• Explain why water molecules are polar and can form hydrogen bonds with four neighboring molecules
• List characteristics of water that result from its ability to form hydrogen bonds.
• Explain how the characteristics of water contribute to life.
• Distinguish between a solute, a solvent and a solution.
• Define aqueous solution and understand how water is able to dissolve different substances
• Distinguish between hydrophobic and hydrophilic substances.
• Name the products of the dissociation of water and give their concentration in pure water
• Define acid, base, and pH.
• Explain how buffers work.

Week 4: Chemistry Introduction - Carbon and the Molecular Diversity of Life

• Explain how carbon’s electron configuration explains its ability to form large, complex and diverse organic molecules.
• Describe how carbon skeletons may vary, and explain how this variation contributes to the diversity and complexity of organic molecules.
• Describe the basic structure of a hydrocarbon and explain why these molecules are hydrophobic.
• Distinguish among the three types of isomers: structural, geometric, and enantiomer.
• Provide examples of how different enantiomeric drugs may have different effects on physiology
• Be able to identify functional groups that are important in the chemistry of life
• List the four major classes of macromolecules.
• Distinguish between monomers and polymers.
• Draw diagrams to illustrate condensation and hydrolysis reactions.

Week 5: Biomolecules - Simple and Complex Carbohydrates

• Describe the chemical structures of a simple carbohydrate (sugar) and a complex carbohydrate (polysaccharide).
• Explain how polysaccharides are synthesized from simple six-carbon sugars.
• Describe the roles of structural polysaccharides and storage polysaccharides, and explain how slight differences in their chemical structures enable them to fulfill their different roles.
• Distinguish between monosaccharides, disaccharides, and polysaccharides.
• Describe the formation of a glycosidic linkage.

Week 6: Biomolecules - Lipids and Membranes

• Identify the different classes of lipids.
• Describe the structure of biological membranes.
• Define diffusion. Explain why diffusion is a passive and spontaneous process.
• Distinguish between solutions that are hypertonic, hypotonic, and isotonic to cell contents.
• Define osmosis and predict the direction of water movement based on differences in solute concentrations.
• Discuss the dynamic nature of membranes.
• Describe some membrane transport mechanisms.
• Identify an ester linkage and describe how it is formed.
• Distinguish between saturated and unsaturated fats.
• Describe the process that results in the production of trans fat molecules.
• Discuss the role of saturated fats and trans fats in the potential development of atherosclerosis in cardiovascular disease.

Week 7: Biomolecules - Amino Acids and Proteins

• List and describe the four major components of an amino acid. Explain how amino acids may be grouped according to the physical and chemical properties of the R group
• Explain how a peptide bond forms between two amino acids.
• Describe how the properties of the amino acids determine the three-dimensional structure of a protein.
• Define the terms “primary structure,” “secondary structure,” “tertiary structure,” and “quaternary structure,” as applied to proteins.
• List the diverse roles proteins play in biological systems.
• Use examples to explain how the structural design of a protein is directly related to its biological function.
• Distinguish between a protein and a polypeptide.
• Explain what determines protein structure and why it is important.
• Name two types of secondary protein structure. Explain the role of hydrogen bonds in maintaining secondary structure.
• Explain how weak interactions and disulfide bridges contribute to tertiary protein structure.
• List conditions under which proteins may be denatured.

Week 8: Biomolecules - Nucleotides and Nucleic Acids

• Identify the basic chemical structures of the nucleic acid bases, of nucleotides and of nucleosides (both ribo- and deoxyribo- forms).
• Describe the flow of genetic information (DNA ? proteins).
• Define the terms “chromosome,” “gene,” and “chromatid.”
• Name the three types of RNA
• Distinguish between pyrimidine and purine, nucleotide and nucleoside, ribose and deoxyribose and 5’ end and 3’ end of a nucleotide
• Briefly describe the three-dimensional structure of DNA.
• Compare and contrast DNA and RNA.

Week 9: Bioenergetics - Introduction to Metabolism

• Explain the role of catabolic and anabolic pathways in cellular metabolism.
• Distinguish between kinetic and potential energy.
• Distinguish between exergonic and endergonic reactions in terms of available energy change.
• List the three main kinds of cellular work and provide examples of each.
• Explain in general terms how cells obtain the energy to do cellular work.
• Describe the structure of ATP and identify the major class of macromolecules to which ATP belongs.
• Explain how ATP performs cellular work.

Week 10: Bioenergetics - Enzymes

• Describe the function of enzymes in biological systems.
• Explain how enzyme structure determines enzyme specificity.
• Explain the induced-fit model of enzyme function.
• Describe the mechanisms by which enzymes lower activation energy.
• Explain how substrate concentration affects the rate of an enzyme-catalyzed reaction.
• Explain how temperature, pH, cofactors, and enzyme inhibitors can affect enzyme activity.
• Distinguish between a competitive and noncompetitive inhibitor.
• Describe how allosteric regulators may inhibit or stimulate the activity of an enzyme.

Week 11: Bioenergetics - Carbohydrate, Lipid and Protein Metabolism

• Describe the basic steps in glycolysis, the citric acid cycle, and the electron transport system.
• Describe how the carbon skeleton of glucose changes as it proceeds through cellular respiration
• Describe the energy yield of cellular respiration
• Explain how the exergonic “slide” of electrons down the electron transport chain is coupled to the endergonic production of ATP by chemiosmosis.
• Explain where and how the electron transport chain creates a proton gradient.
• Distinguish between fermentation and anaerobic respiration.
• Describe how food molecules other than glucose can be oxidized to make ATP.

Week 12: Molecular Genetics - DNA and RNA

• Explain the base-pairing rule.
• Describe the semiconservative model of replication
• Describe the process of DNA replication, including the role of the origins of replication and replication forks
• Role of DNA polymerases in replication.
• Distinguish between the leading strand and the lagging strand.
• Explain how the lagging strand is synthesized even though DNA polymerase can add nucleotides only to the 3’ end. Describe the significance of Okazaki fragments.
• Explain the roles of DNA ligase, primer, primase, helicase, topoisomerase, and single-strand binding proteins
• Define “antiparallel” and explain why continuous synthesis of both DNA strands is not possible.
• Explain the roles of DNA polymerase, mismatch repair enzymes, and nuclease in DNA proofreading and repair.

Week 13: Molecular Genetics - Translation and the Genetic Code

• Use the genetic code to translate mRNA sequences into (protein) amino acid sequences.
• Explain the difference between a “codon” and an “anti-codon.”
• Describe the role of the ribosome and tRNA in protein synthesis.
• Explain how eukaryotic protein synthesis is controlled.
• Define between transcription and translation.
• Define “codon” and explain the relationship between codons on mRNA and the amino acids in a polypeptide.
• Describe the properties of the genetic code.
• Explain the significance of the “reading frame” during translation.
• Explain how RNA polymerase recognizes where transcription should begin.
• Explain the general process of transcription, including the three major steps of initiation, elongation, and termination.
• Describe all of the ways in which RNA is modified after transcription
• Define and explain the role of ribozymes.
• Describe the structure and function of tRNA.
• Describe the process by which tRNA is joined to the appropriate amino acid.
• Describe the structure and functions of ribosomes.
• Describe the process of translation and explain which enzymes, protein factors, and energy sources are used for each stage.

Week 14: Medicine and Drugs

• Describe the difference between medicines, drugs and poisons.
• Analyze the relationship between medicines, health and disease.
• Classify drugs.
• List the effects of medicines, drugs and poisons on the functioning of the body.

Week 15: Molecules and Life

• Review the information that you've learned in the course
• Share some final thoughts with your classmates
• Reflect on your experience in the course
• Share what your future may hold and what advice you'd offer for future students of this course