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1
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The Foundations of Biochemistry
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- Cellular Foundations
- Chemical Foundations
- Physical Foundations
- Genetic Foundations
- Evolutionary Foundations
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- Describe an organism at the cellular level.
- Explain how cell size and function are connected.
- Relate biomolecule composition, structure, and function.
- Describe the dynamic steady state maintained by a living organism.
- Construct a description of the thermodynamic basis for a reaction.
- Relate the origins of life to biochemical processes that occur today.
- Explain how cellular systems and processes can be studied.
- Describe the flow of information from linear DNA to three-dimensional proteins.
- Describe how genetic changes can alter gene function.
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2
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Water, the Solvent of Life
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- Weak Interactions in Aqueous Systems
- Ionization of Water, Weak Acids, and Weak Bases
- Buffering against pH Changes in Biological Systems
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- Explain how weak interactions between biomolecules confer stability in aqueous solutions.
- Explain the importance of entropy to biological systems.
- Explain why biological systems must regulate osmotic pressure.
- Apply concepts of acid-base equilibria to a system.
- Determine the concentration or amount of a substance present by titration.
- Explain the importance of buffers to biological systems.
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3
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Amino Acids, Peptides, and Proteins
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- Amino Acids
- Peptides and Proteins
- Working with Proteins
- The Structure of Proteins: Primary Structure
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- Determine the identity of an amino acid from experimental data.
- Determine the structure of an amino acid from the pH of its solvent.
- Determine the composition of a polypeptide or protein from experimental data.
- Analyze the effectiveness of a purification strategy used to separate a mixture of proteins or amino acids.
- Determine the components of a mixture from electrophoresis data.
- Determine the primary structure of polypeptide or protein from experimental data.
- Analyze an evolutionary relationship from the sequence of amino acids in a protein or polypeptide.
- Relate the absorbance, concentration, molar extinction coefficient, and pathlength for a sample analyzed by spectrophotometry.
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4
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The Three-Dimensional Structure of Proteins
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- Overview of Protein Structure
- Protein Secondary Structure
- Protein Tertiary and Quaternary Structures
- Protein Denaturation and Folding
- Determination of Protein and Biomolecular Structures
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- Explain how chemical and physical interactions govern protein structure and stability.
- Relate the structure and biological function of a protein.
- Explain the relationship between disruptions in proteostasis and disease.
- Describe how a protein adopts its native conformation.
- Analyze protein three-dimensional structure using amino acid sequences, experimental data, and models.
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5
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Protein Function
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- Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins
- Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins
- Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors
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- Construct a quantitative description of the interaction between a protein and ligand using experimental data.
- Describe the allosteric interactions governing a protein and ligand pair using experimental data.
- Predict how changes in the solvent or structure of a globin protein will affect its ability to store and transport oxygen in the body.
- Explain the significance of the antibody-antigen interaction.
- Explain how conformational changes at the molecular level produce muscle movement.
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6
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Enzymes
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- An Introduction to Enzymes
- How Enzymes Work
- Enzyme Kinetics as an Approach to Understanding Mechanism
- Examples of Enzymatic Reactions
- Regulatory Enzymes
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- Construct a general description of an enzyme from experimental data.
- Describe the energetic basis of enzyme-mediated catalysis.
- Propose the mechanism by which an enzyme catalyzes a reaction.
- Construct a kinetic description of the reaction catalyzed by an enzyme that obeys Michaelis-Menten kinetics.
- Propose a mechanism for inhibition of a non-allosteric enzyme based on experimental data.
- Explain how chymotrypsin cleaves a substrate.
- Propose a mechanism of allosteric regulation for an enzyme based on experimental data.
- Propose a mechanism of regulatory modification for an enzyme based on experimental data.
- Explain the importance of enzyme regulation in blood coagulation.
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7
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Carbohydrates and Glycobiology
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- Monosaccharides and Disaccharides
- Polysaccharides
- Glycoconjugates: Proteoglycans, Glycoproteins, and Glycolipids
- Carbohydrates as Informational Molecules: The Sugar Code
- Working with Carbohydrates
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- Construct a description of a carbohydrate.
- Relate the structure, composition, chemical properties, and biological function of a monosaccharide.
- Explain how blood glucose concentration and health are connected.
- Relate the structure, composition, properties, and function of a carbohydrate polymer.
- Explain how glycoconjugate synthesis, function, and destruction relate to health.
- Explain the importance of lectin:carbohydrate interactions.
- Propose a scheme for analyzing a glycoconjugate.
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8
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Nucleotides and Nucleic Acids
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- Some Basic Definitions and Conventions
- Nucleic Acid Structure
- Nucleic Acid Chemistry
- Other Functions of Nucleotides
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- Relate the name, structure, and symbolic representation of a nucleic acid.
- Explain how DNA studies lead to the model for DNA structure
- Explain the significance of B-form DNA structure.
- Relate the number of bases, rise per base, or number of helical turns to the length of a nucleic acid.
- Relate the sequence, structure, and activities of unusual DNA structures.
- Relate the sequence, structure, and activities of RNA molecules.
- Relate the structure of a nucleic acid to its properties.
- Explain the importance of nucleic acid modifications to life.
- Interpret the results of a polymerase chain reaction (PCR) experiment.
- Determine the sequence of nucleotides in a molecule of nucleic acid.
- Explain the significance of nucleic acids and their derivatives to life.
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9
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Lipids
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- Storage Lipids
- Structural Lipids in Membranes
- Lipids as Signals, Cofactors, and Pigments
- Working with Lipids
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- Relate the structure, physical properties, and function of storage lipids.
- Relate the general structure, composition, and properties of a membrane lipid.
- Explain the importance of membrane lipid structure to health.
- Describe the roles of lipids outside of storage and structure.
- Determine the structure and composition of a lipid from experimental data.
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10
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Biological Membranes and Transport
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- The Composition and Architecture of Membranes
- Membrane Dynamics
- Solute Transport across Membranes
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- Explain the importance of diversity in membrane composition and structure to life.
- Classify membrane proteins based on their structure, function, and properties.
- Explain how membrane function is connected to the organization and dynamics of lipids within membranes.
- Explain why membrane fusion, fission, and curvature are important for homeostasis.
- Connect mechanisms of substance transfer in and out of cells with cellular function.
- Propose a scheme for studying a plasma membrane component.
- Construct a quantitative description of transporter-mediated solute transport.
- Connect the distribution and activities of glucose transporters in humans with the needs of different tissues.
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11
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Biochemical Signaling
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- General Features of Signal Transduction
- G Protein–Coupled Receptors and Second Messengers
- GPCRs in Vision, Olfaction, and Gustation
- Receptor Tyrosine Kinases
- Multivalent Adaptor Proteins and Membrane Rafts
- Gated Ion Channels
- Regulation of Transcription by Nuclear Hormone Receptors
- Regulation of the Cell Cycle by Protein Kinases
- Oncogenes, Tumor Suppressor Genes, and Programmed Cell Death
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- Explain how signals are communicated and integrated through G protein-coupled receptor (GPCR) signaling pathways.
- Predict the effects of altering cyclic AMP (cAMP) function in the cell.
- Predict the effects of an intervention or mutation on signaling through G protein-coupled receptors (GPCRs).
- Predict the effects of an intervention or mutation on signaling through receptor tyrosine kinases (RTKs).
- Describe the versatility in signaling pathways afforded by the variety of pathway components.
- Predict the effects of an intervention or mutation on signaling through gated-ion channels.
- Predict the effect of an intervention or mutation on signaling through a nuclear hormone receptor.
- Describe the roles of protein kinases in cell cycle regulation.
- Explain how defects in regulation of the cell cycle can lead to disease.
- Describe the function of a signaling pathway based on experimental data.
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12
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Introduction to Metabolism
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- Bioenergetics and Thermodynamics
- Chemical Logic and Common Biochemical Reactions
- Phosphoryl Group Transfers and ATP
- Biological Oxidation-Reduction Reactions
- Regulation of Metabolic Pathways
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- Explain a biochemical reaction by providing the curved-arrow mechanism.
- Explain how the removal of phosphate groups from phosphorylated compounds is used to power reactions in the cell.
- Construct a quantitative description of a biological oxidation-reduction reaction.
- Use experimental data to monitor the flow of electrons through a series of biochemical reactions.
- Explain how multiple mechanisms of regulation can collaborate to maintain the dynamic steady state of a cell.
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13
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Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway
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- Glycolysis
- Feeder Pathways for Glycolysis
- Fates of Pyruvate
- Gluconeogenesis
- Coordinated Regulation of Glycolysis and Gluconeogenesis
- Pentose Phosphate Pathway of Glucose Oxidation
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- Explain how organisms produce energy through glycolysis.
- Explain how glycolysis can be used to metabolize starting materials other than glucose.
- Explain how pyruvate will be metabolized under given conditions.
- Determine the free energy released by catabolism of a carbohydrate under given conditions.
- Explain the importance of carbohydrate metabolism to health.
- Explain how organisms use gluconeogenesis to produce glucose from precursor molecules.
- Explain why gluconeogenesis is essential even though it is energetically expensive.
- Predict the path of molecules through glycolysis and gluconeogenesis based on given conditions.
- Explain how the pentose phosphate pathway is used as an alternative method for metabolizing glucose.
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14
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The Metabolism of Glycogen in Animals
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- The Structure and Function of Glycogen
- Breakdown and Synthesis of Glycogen
- Coordinated Regulation of Glycogen Breakdown and Synthesis
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- Relate the structure and function of glycogen polymers and granules.
- Explain how animals release glucose from glycogen stores.
- Explain how animals store excess glucose as glycogen.
- Explain how the body coordinates glycogen metabolism based on its energy supply and demand.
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15
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The Citric Acid Cycle
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- Production of Acetyl-CoA (Activated Acetate)
- Reactions of the Citric Acid Cycle
- The Hub of Intermediary Metabolism
- Regulation of the Citric Acid Cycle
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- Explain how pyruvate is activated to produce acetyl-CoA.
- Explain how the citric acid cycle oxidizes acetyl-CoA to carbon dioxide.
- Determine the amount of energy released by the aerobic metabolism of a carbohydrate.
- Explain how the citric acid cycle serves as the central hub of intermediary metabolism.
- Predict how a change will affect the rate of citric acid cycle metabolism.
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16
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Fatty Acid Catabolism
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- Digestion, Mobilization, and Transport of Fats
- Oxidation of Fatty Acids
- Ketone Bodies
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- Describe the path of dietary lipids in vertebrates.
- Explain how fatty acids are prepared for oxidation.
- Explain how a fatty acid can be completely metabolized.
- Relate the amount and type of fatty acids burned with body weight.
- Predict how the metabolism of fatty acids will change depending on the supply of energy in the body.
- Relate the formation of ketone bodies with alterations in fatty acid metabolism.
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17
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Oxidative Phosphorylation
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- The Mitochondrial Respiratory Chain
- ATP Synthesis
- Regulation of Oxidative Phosphorylation
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- Describe the role of mitochondria in eukaryotic aerobic metabolism.
- Describe the composition of the mitochondrial respiratory chain.
- Explain how electrons enter the mitochondrial respiratory chain.
- Explain how the mitochondrial respiratory chain shuttles electrons to molecular oxygen.
- Explain how the mitochondrial respiratory chain produces ATP.
- Explain how oxidative phosphorylation can be regulated.
- Describe additional roles for mitochondria other than the generation of ATP.
- Describe the implications and consequences of mitochondria possessing their own genome.
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18
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Lipid Biosynthesis
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- Biosynthesis of Fatty Acids and Eicosanoids
- Biosynthesis of Triacylglycerols
- Biosynthesis of Membrane Phospholipids
- Cholesterol, Steroids, and Isoprenoids: Biosynthesis, Regulation, and Transport
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- Explain how organisms synthesize palmitate.
- Explain how organisms coordinate fatty acid synthesis with other metabolic processes.
- Explain how organisms elongate fatty acids.
- Explain how organisms generate complex fatty acids.
- Explain how organisms synthesize triacylglycerols.
- Explain how adipose tissue produces glycerol 3-phosphate.
- Explain how organisms use fatty acids to synthesize membrane lipids.
- Explain how organisms synthesize cholesterol.
- Explain how lipids and cholesterol are transported throughout the body.
- Explain how cholesterol metabolism is regulated.
- Describe how cholesterol and its synthetic pathway intermediates can be used in the body outside of lipid metabolism.
- Explain the importance of regulating cholesterol metabolism.
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19
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Biosynthesis of Amino Acids, Nucleotides, and Related Molecules
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- Overview of Nitrogen Metabolism
- Biosynthesis of Amino Acids
- Molecules Derived from Amino Acids
- Biosynthesis and Degradation of Nucleotides
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- Explain how a complex web of reactions converts atmospheric nitrogen to biologically useful forms and maintains a global balance between them.
- Explain how reactive forms of nitrogen are incorporated into biological systems through glutamate and glutamine.
- Explain how organisms synthesize the 20 common amino acids.
- Explain the regulation of amino acid synthesis.
- Explain how amino acids serve as precursors of many specialized biomolecules.
- Contrast the two pathways for nucleotide synthesis.
- Detail the processes of de novo purine nucleotide synthesis.
- Detail the processes of de novo pyrimidine nucleotide synthesis.
- Explain how deoxyribonucleic acids are formed.
- Explain how salvage pathways recycle purine and pyrimidine bases.
- Explain the regulation of nucleotide biosynthesis.
- Explain the importance of nucleic acid metabolism to health.
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20
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Hormonal Regulation and Integration of Mammalian Metabolism
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- Hormone Structure and Action
- Tissue-Specific Metabolism
- Hormonal Regulation of Fuel Metabolism
- Obesity and the Regulation of Body Mass
- Diabetes Mellitus
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- Explain how mammals coordinate activities between different tissues and organs.
- Describe insulin production, storage, and release.
- Describe the role of the liver in the metabolism of nutrients.
- Compare the function of white adipose tissue (WAT) and brown adipose tissue (BAT).
- Describe the specialized metabolism of muscle cells.
- Describe the energy needs of the brain.
- Relate the function of blood with the function of other tissues.
- Compare the hormonal regulation of fuel metabolism immediately after and several hours after intake of dietary carbohydrates.
- Explain how the body responds to prolonged fasting or starvation.
- Describe an animal's hormonal response to a stressful situation.
- Explain the importance of maintaining body mass within an optimal range.
- Explain how leptin helps maintain body-mass homeostasis.
- Explain how adiponectin helps maintain body-mass homeostasis.
- Explain how diet regulates the expression of genes central to maintaining body-mass homeostasis.
- Explain how endocrine cells in the intestinal lining affect eating behavior.
- Explain how the microbiome in the gut contributes to body-mass homeostasis.
- Differentiate between the two major clinical classes of diabetes mellitus.
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21
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Genes and Chromosomes
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- Chromosomal Elements
- DNA Supercoiling
- The Structure of Chromosomes
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- Compare viral, bacterial, and eukaryotic genomes.
- Explain how supercoiling helps cells or viruses compact large DNA molecules into a small space.
- Explain the biological importance of regulating DNA supercoiling.
- Describe how the organization of chromatin influences gene expression.
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22
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DNA Metabolism
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- DNA Replication
- DNA Repair
- DNA Recombination
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- Explain how cells enzymatically degrade and synthesize DNA.
- Explain the biological importance of repairing DNA damage.
- Explain the biological importance of DNA recombination in bacteria.
- Explain the biological importance of DNA recombination in eukaryotes.
- Explain how a mammal can produce millions of different immunoglobulins (antibodies) with distinct binding specificities.
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23
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RNA Metabolism
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- DNA-Dependent Synthesis of RNA
- RNA Processing
- RNA-Dependent Synthesis of RNA and DNA
- Catalytic RNAs and the RNA World Hypothesis
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- Explain how transcription is dependent on DNA.
- Explain how transcription is regulated at several levels.
- Describe RNA processing.
- Explain the importance of mRNA splicing and end modifications.
- Explain the importance of rRNA, tRNA, and special-function noncoding RNAs.
- Explain how RNA synthesis and degradation regulate gene expression.
- Explain why the existence of RNA replication requires an elaboration of the central dogma of biology.
- Explain the role of reverse transcription in eukaryotes.
- Explain how RNA can act as a catalyst.
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24
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Protein Metabolism
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- The Genetic Code
- Protein Synthesis
- Protein Targeting and Degradation
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- Describe the key features of the genetic code.
- Relate the sequence of an amino acids in a protein with the mRNA sequence it is encoded by.
- Explain how tRNAs serve as adaptor molecules during translation.
- Describe the key features of the ribosome.
- Describe the steps in ribosome synthesis.
- Compare translation initiation in bacteria and eukaryotes.
- Explain how ribosomes catalyze polypeptide synthesis.
- Explain how translation is terminated.
- Explain how exogenous substances such as antibiotics and toxins can be used to study translation.
- Explain how posttranslational modifications contribute to the thermodynamic cost of protein synthesis.
- Explain how cells target newly-synthesized proteins to locations in and out of the cell.
- Explain how eukaryotic cells import substances from the surrounding medium.
- Explain how RNA editing can be used to alter the meaning of an mRNA transcript.
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25
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Regulation of Gene Expression
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- The Proteins and RNAs of Gene Regulation
- Regulation of Gene Expression in Bacteria
- Regulation of Gene Expression in Eukaryotes
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- Explain how changing the interaction between RNA polymerase and DNA regulates transcription.
- Explain the role of various gene products in the regulation of transcription initiation.
- Explain how combinatorial control is used to modulate the expression of eukaryotic genes.
- Explain how bacteria regulate expression of the lac operon.
- Explain how bacteria regulate expression of the trp operon.
- Explain how the SOS repair mechanism can lead to evolution in bacteria.
- Explain how bacteria coordinate the synthesis of ribosomal components.
- Explain how small RNAs (sRNAs) regulate the function of some mRNAs.
- Explain how eukaryotic cells turn on genes.
- Explain how eukaryotes regulate gene expression at the level of translation.
- Explain the importance of gene regulation in early development.
- Describe uses for stem cells in medical research.
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26
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Final Exam
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