Textbook
Molecular Biology: Concepts for Inquiry is available on Amazon as a paperback and Kindle eBook.
This introductory college-level molecular biology textbook builds upon concepts from first-year high school biology and chemistry courses to elucidate essential concepts in molecular biology, biochemistry, cell biology, and genetics. It is appropriate for college courses and high school courses taught at the college level. Over 170 color figures clearly illustrate key concepts. The goal of this work is to clarify concepts in a streamlined manner, not to be an encyclopedic collection of facts. Connections are explicitly made to prior knowledge and key high school chemistry concepts are reviewed. The biotechnology driving basic science research and translational medicine is explained so that this textbook can serve as a companion to a student beginning molecular biology research. This textbook was created to replace direct lecturing, to support teaching through inquiry and experimentation.
A teacher's guide to teaching molecular biology as an Inquiry course and complete answer key, Molecular Biology Concepts for Inquiry: A Guide to Inquiry, has been published.
A set of slides from textbook figures is available to instructors who contact me. Alternatively, projecting figures directly from the Kindle desktop application works in the classroom.
Thank you to everyone who has already purchased the textbook!
1.1 ORGANIC MOLECULES
1.1A RECOGNIZING ORGANIC MOLECULES
Box 1.1: The Periodic Table of Elements
Figure 1.2: Methods of drawing organic molecules.
Figure 1.3: Examples of organic molecules.
1.1B COVALENT BONDING IN ORGANIC MOLECULES
Box 1.2: Chemistry Review: Determining electron configurations and valence electrons.
Table 1.1: Number of covalent bonds formed by atoms in organic molecules.
Box 1.3: Chemistry Review: Determining the polarity of a bond.
1.1C THE PROPERTIES OF WATER AND ITS INTERACTION WITH ORGANIC MOLECULES
Figure 1.4: Behavior of water.
Table 1.2: Partial list of functional groups in organic molecules.
1.1D INTERMOLECULAR ELECTROSTATIC FORCES IN AN AQUEOUS ENVIRONMENT
1.1E BIOLOGICAL MOLECULES: MONOMERS AND POLYMERS
Figure 1.5: Examples of carbohydrates.
Figure 1.6: Dehydration synthesis and hydrolysis.
Figure 1.7: Examples of lipids.
Figure 1.8: Basic protein structure.
Figure 1.9: Central dogma of molecular biology.
Figure 1.10: Nucleic acid monomers: nucleotides.
Figure 1.11: Nucleic acid polymers: DNA.
Figure 1.12: Nucleic acid polymers: RNA
1.2 THE THERMODYNAMICS OF LIFE
1.2A ENERGY
Figure 1.13: Energy can be transferred between a system and its surroundings.
Figure 1.14: Energy exchange between an animal and its surroundings.
1.2B ENTROPY
Table 1.3: Examples of systems with increasing entropy.
Figure 1.15: Organisms increase the entropy of the universe by giving off heat to their surroundings.
1.2C ENTHALPY AND ENTROPY: DRIVING FORCES THAT DETERMINE SPONTANEITY
Figure 1.16: Potential energy diagrams for chemical reactions.
Table 1.4: Predicting the spontaneity of reactions
Table 1.5: Examples of spontaneous cellular processes
1.2D NONSPONTANEOUS REACTIONS IN LIVING SYSTEMS
Figure 1.17: Hydrolysis of ATP releases a large amount of free energy.
Figure 1.18: The reaction pathway does not affect ∆G.
Box 1.4: Biology Review: Cellular Respiration
Figure 1.19: Dehydration synthesis of maltose coupled to the breakdown of ATP.
Table 1.6: Nonspontaneous maltose synthesis can occur in cells if it is coupled to the breakdown of 2 ATP molecules.
Figure 1.20: Coupled reactions often share intermediate reactants and products.
Figure 1.21: Enzymes speed up specific reactions.
Table 1.7: Cells couple nonspontaneous processes to spontaneous processes that produce excess free energy.
1.3 ORGANIC MOLECULES AND THERMODYNAMICS IN THE CELL
1.3A OBTAINING ENERGY FOR THE CELL
1.3B ORGANIZATION OF THE CELL AND THERMODYNAMIC PRINCIPLES
Box 1.5: Biology Review: Structures and functions within cells
Table 1.8: Functions of Organelles
Box 1.6: Chemistry Review: Dynamic Equilibrium
1.4 BIOTECHNOLOGY AND ALTERNATIVE ENERGY
1.4A THE NEED FOR ALTERNATIVE FORMS OF ENERGY
1.4B PRODUCING FUEL FROM LIVING THINGS: ETHANOL
1.4C ETHANOL FROM CELLULOSE
1.4D BIODIESEL
Figure 1.22: The synthesis of biodiesel
1.4E GENETIC ENGINEERING AND BIOFUELS
1.4F MODELING FUEL PRODUCTION STRATEGIES ON PHOTOSYNTHESIS
SUMMARY OF CHAPTER 1 CONCEPTS
2.1 PROTEIN BIOCHEMISTRY
2.1A PROTEIN SYNTHESIS
Figure 2.2: Central Dogma of Molecular Biology.
Figure 2.3: Transcription.
Figure 2.4: 5' and 3' ends of nucleic acids and the direction of RNA synthesis.
Figure 2.5: Transcription begins within a gene's promoter.
Figure 2.6: Prokaryotic mRNA and Eukaryotic mRNA processing.
Figure 2.7: Structure of a tRNA molecule.
Table 2.1: The Genetic Code.
Figure 2.8: Translation.
2.1B HOW MUTATIONS CREATE DOMINANT OR RECESSIVE PHENOTYPES
Figure 2.9: Mutations can cause recessive or dominant phenotypes.
2.1C THE 20 AMINO ACIDS
Table 2.2: The 20 Amino Acids.
2.1D PROTEIN FOLDING
Figure 2.10: Protein primary structure and secondary structure.
Figure 2.11: Effect of proline on an alpha helix.
Figure 2.12: Examples of protein tertiary structures.
Figure 2.13: Examples of functional and structural roles of ions in proteins.
Figure 2.14: Examples of protein quaternary structures.
2.1E THE THERMODYNAMICS OF PROTEIN FOLDING
Table 2.3: Energy released during bond formation.
Figure 2.15: Non-covalent electrostatic attractions involved in protein folding.
Figure 2.16: The hydrophobic effect and protein folding.
Figure 2.17: Energy landscape of protein folding.
Figure 2.18: Chaperones and chaperonins assist in protein folding.
2.1F PROTEIN MISFOLDING AND DISEASE
Figure 2.19: The proteasome degrades misfolded proteins.
Figure 2.20: Misfolded proteins sometimes aggregate, forming amyloid-like fibrils.
Figure 2.21: Chaperones and chaperonins help prevent aggregation of misfolded proteins.
Figure 2.22: Prion diseases are infectious because misfolded prion proteins cause the misfolding of normally-folded prion proteins.
2.1G METHODS FOR DETERMINING PROTEIN STRUCTURE
2.1H SYNTHESIS OF TRANSMEMBRANE AND EXCRETED PROTEINS
Figure 2.23: Protein synthesis pathways.
2.1I INTERACTIONS OF PROTEINS WITH OTHER MOLECULES
Figure 2.24: Thermodynamics of protein-protein interactions.
Figure 2.25: Lock and Key Model.
2.1J POST-TRANSLATIONAL MODIFICATION OF PROTEINS
Figure 2.26: Phosphorylation of a protein can change its folding and its activity.
Figure 2.27: Signaling cascades often include multiple protein kinases that amplify the signal.
2.1K PROTEIN SHAPE IS DYNAMIC
2.2 ENZYMES
2.2A ENZYMES SPEED UP CHEMICAL REACTIONS
Figure 2.28: An enzyme lowers the activation energy of a chemical reaction
Figure 2.29: Multiple enzymes often participate in a single biosynthetic pathway
2.2B THE STRUCTURE OF AN ACTIVE SITE
Figure 2.30: EDTA chelates metal ions, including magnesium ions.
2.2C FACTORS AFFECTING ENZYME ACTIVITY
2.2D PROTEASES: ENZYMES THAT CLEAVE PROTEINS
Figure 2.31: Proteases are usually translated as inactive zymogens that must be cleaved to be activated.
2.3 USE AND MANIPULATION OF PROTEINS IN BIOTECHNOLOGY
2.3A ENZYMES ARE GOOD DRUG TARGETS
2.3B PURIFICATION OF PROTEINS
2.3C DETECTING PROTEINS
Figure 2.32: Antibodies specifically bind antigens.
Table 2.4: Uses of antibodies in the laboratory
Figure 2.33: Bacteria expressing fluorescent proteins.
Figure 2.34: FRET can detect interactions between molecules in vivo.
SUMMARY OF CHAPTER 2 CONCEPTS
Figure 3.1: The DNA double helix.
3.1 CHROMOSOMES
3.1A DNA, GENES AND CHROMOSOMES
Figure 3.2: DNA, genes, and chromosomes.
3.1B CHROMOSOMES AND MITOSIS
Figure 3.3: Stages of mitosis and the cell cycle.
Figure 3.4: Spindle microtubules.
Figure 3.5: Chromosome structure.
Figure 3.6: Visualization of individual human chromosomes with spectral karyotyping.
3.1C CHROMOSOME STRUCTURE
Figure 3.7: Types of Gene Transfer in Prokaryotes: Transformation, Conjugation, and Transduction.
3.1D PLASMID VECTORS AND ARTIFICIAL CHROMOSOMES
Figure 3.8: A typical bacterial plasmid.
Figure 3.9: Method of bacterial transformation in vitro.
3.2 DNA BIOCHEMISTRY
3.2A DNA STRUCTURE
Figure 3.10: DNA structure.
3.2B VISUALIZING AND ANALYZING DNA: GEL ELECTROPHORESIS
Figure 3.11: Gel electrophoresis of DNA.
3.2C DNA BINDING PROTEINS
Figure 3.12: The DNA-binding domain of a zinc finger protein.
3.3 DNA REPLICATION
3.3A IN VIVO DNA REPLICATION
Figure 3.13: DNA Replication occurs in a 5' to 3' direction.
Figure 3.14: DNA Replication.
3.3B IN VITRO DNA REPLICATION: THE POLYMERASE CHAIN REACTION
Figure 3.15: The Polymerase Chain Reaction.
Figure 3.16: The Polymerase Chain Reaction: Exponential copying of a DNA segment.
3.3C USE OF PCR IN MOLECULAR BIOLOGY, FORENSIC SCIENCE, AND MEDICINE
Figure 3.17: DNA Fingerprinting by PCR of Short Tandem Repeats (STR analysis).
Figure 3.18: A "diagnostic" use of PCR.
3.3D IN VITRO DNA REPLICATION: DNA SEQUENCING
Figure 3.19: Comparison of normal deoxynucleotides and the dideoxynucleotides used in DNA sequencing.
Figure 3.20: DNA sequencing.
Figure 3.21: The Human Genome Project
3.4 DNA REPAIR ENZYMES
3.4A MUTATIONS
Figure 3.22: Causes and consequences of DNA damage
3.4B POINT MUTATIONS: CAUSES AND REPAIR
Figure 3.23: Types of Point mutations.
Figure 3.24: Repair of DNA point mutations.
3.4C DNA BREAKS: FORMATION AND REPAIR
Figure 3.25: Double-strand break repair: nonhomologous end-joining (NHEJ)..
Figure 3.26: Double strand break repair through homologous recombination (simplified).
Figure 3.27: Double strand break repair through homologous recombination (details).
3.4D GENETIC DISEASES CAUSED BY DEFECTS IN DNA REPAIR
Table 3.1: Genetic disorders with mutations in DNA repair proteins.
3.5 GENETIC ENGINEERING
3.5A THE DISCOVERY OF RESTRICTION ENDONUCLEASES
Figure 3.28: Experiments that showed "restriction."
Figure 3.29: Restriction enzymes explain the phenomenon of "restriction."
Figure 3.30: Structures of restriction enzymes bound to DNA.
3.5B MANIPULATING DNA IN GENETIC ENGINEERING (CLONING STRATEGIES)
Figure 3.31: Restriction enzymes act as scissors and DNA ligase acts as glue in genetic engineering.
Figure 3.32: Efficiency of ligation reactions.
Figure 3.33: Strategies for inserting DNA into plasmids while preventing plasmid religation.
Figure 3.34: Strategies for cloning PCR products
3.5C VIRUSES PROVIDE TOOLS FOR CONVERTING RNA INTO DNA
Figure 3.35: The life cycle of HIV, a retrovirus.
3.5D INTRODUCTION OF DNA INTO BACTERIA
Figure 3.36: In a bacterial transformation, each colony contains one plasmid.
Figure 3.37: General order of steps to clone plasmids in bacteria.
3.5E INTRODUCTION OF DNA INTO EUKARYOTIC CELLS
Figure 3.38: Transfection of DNA into mammalian cells.
Figure 3.39: Transduction of mammalian cells with retrovirus.
3.5F ENGINEERING OF EUKARYOTIC GENOMES AT SPECIFIC SITES
Figure 3.40: Replacement of chromosomal DNA via homologous recombination (simplified).
Figure 3.41: Southern blot.
SUMMARY OF CHAPTER 3 CONCEPTS
4.1 THE REGULATION OF TRANSCRIPTION
4.1A THE ORGANIZATION OF A GENE
Figure 4.2: Prokaryotic and Eukaryotic mRNA processing.
Figure 4.3: Structure and transcription of a prokaryotic gene.
Figure 4.4: Basic factors that affect the level of transcription of a gene.
Figure 4.5: Constitutive, inducible, and repressible promoters.
Figure 4.6: Modularity of iGEM BioBricks.
4.1B CHROMATIN STRUCTURE IN EUKARYOTES
Figure 4.7: Structures of a histone and a nucleosome.
Figure 4.8: Nucleosomes form due to attractions between histone tails and the DNA backbone.
Figure 4.9: Chromatin Structure.
4.1C EUCHROMATIN AND HETEROCHROMATIN
Figure 4.10: Comparison of euchromatin and heterochromatin.
Figure 4.11: Histone acetylation is determined by DNA CpG methylation.
Figure 4.12 DNA methyltransferase methylates a cytosine opposite a methyl CpG.
4.2 POSTTRANSCRIPTIONAL REGULATION OF MRNA LEVELS IN EUKARYOTES
4.2A STABILITY OF mRNA
Figure 4.13: Eukaryotic mRNA processing and looped structure.
Figure 4.14: Loss of mRNA end protection and mRNA degradation by exonucleases.
4.2B RNA INTERFERENCE
Figure 4.15: Fire and Mello’s RNAi experiment (1998).
Figure 4.16: The mechanism of RNAi.
Figure 4.17: Amplification of RNAi in worms, plants, and fungi.
4.2C THE HUMAN GENOME, RNAI, AND NOVEL CLASSES OF RNA
Table 4.1: Makeup of the human genome.
Figure 4.18: Transposons cause the sectoring in corn kernels.
4.2D MICRORNAS CAUSE THE DEGRADATION OF COMPLEMENTARY MRNAS
Figure 4.19: microRNAs and RNAi.
4.2E LONG NONCODING RNAS AND THE REGULATION OF GENE EXPRESSION
Figure 4.20: X-chromosome inactivation.
Figure 4.21: The TSIX RNA inhibits the transcription of XIST RNA from the active X chromosome in mice.
4.3 THE PROGRAMMING OF TRANSCRIPTIONAL PATTERNS DURING DEVELOPMENT
4.3A THE CONTROL OF DNA METHYLATION PATTERNS
Table 4.2: Changes in methylation of the DNA in the human genome.
4.3B CLONED ANIMALS ARE NOT QUITE “NORMAL”
Figure 4.22: Somatic Cell Nuclear Transfer (Cloning).
Figure 4.23: Donor cell methylation patterns are not fully erased in cloned animals.
4.3C STEM CELLS
Figure 4.24: Therapeutic cloning produces stem cells that are genetically identical to a patient.
4.3D IMPRINTING
Figure 4.25: Example of a typical imprinted locus.
Figure 4.26: The imprinted Angelman Syndrome locus.
4.4 MEASURING LEVELS OF GENE EXPRESSION
4.4A METHODS FOR MONITORING RNA LEVELS
Figure 4.27: Northern blot.
Figure 4.28: qPCR.
Figure 4.29: Microarray analysis.
4.4B METHODS FOR MONITORING PROTEIN LEVELS
SUMMARY OF CHAPTER 4 CONCEPTS
5.1 GENOME EVOLUTION
5.1A MUTATIONS CREATE VARIATION THAT IS SUBJECT TO SELECTION
Figure 5.2: Natural selection acts upon only 5% of the human genome.
Figure 5.3: Percent of genome that is mutated compared to the reference human genome.
Figure 5.4: Blocks of conserved synteny.
Table 5.1: Comparisons of genomes to the reference human genome
5.1B GENE DUPLICATIONS FACILITATE THE EVOLUTION OF NEW GENES
Figure 5.5: The effect of selection on mutation frequency.
5.1C LOSS OF GENES
5.2 CANCER
5.2A CANCER AS A GENETIC DISEASE
5.2B MUTATION AND SELECTION IN CANCER
Figure 5.6: Mutation and clonal expansion.
5.2C BOTH LOSS-OF-FUNCTION AND GAIN-OF-FUNCTION MUTATIONS CONTRIBUTE TO TUMOR FORMATION
Figure 5.7: The Cell Cycle.
Table 5.2: The analogy of cancer genes, the car and the cell cycle
5.2D COMPLEX REGULATORY PATHWAYS CONTROL CELL BIRTH AND CELL DEATH
Figure 5.8: Multiple pathways affecting cell division and death are altered in cancer.
Figure 5.9: Loss of p53 affects multiple signaling pathways, causing increased cell division and decreased apoptosis.
5.2E ONCOGENES, TUMOR SUPPRESSOR GENES, AND GENE DOSAGE
Figure 5.10: Development of tumors in inherited retinoblastoma.
5.2F MUTATIONS IN LATE STAGES OF TUMOR DEVELOPMENT
5.2G CELLULAR IMMORTALITY
Figure 5.11: Telomere structure and the end replication problem.
Figure 5.12: Telomerase elongates telomeres and solves the end replication problem.
Figure 5.13: Very short telomeres cause cellular senescence and explain the Hayflick limit.
Figure 5.14: Telomeres distinguish natural DNA ends from DNA breaks.
5.2H CANCER AND “SURVIVAL OF THE FITTEST”
Table 5.3: Factors that limit cancer growth
Table 5.4: Characteristics of cancer
5.2I GENOMIC INSTABILITY
Figure 5.15: Types of mutations observed in tumors.
Figure 5.16: The result of genomic instability is often evident in tumor karyotypes.
Figure 5.17: A reciprocal translocation activates the Abl oncogene in chronic myelogenous leukemia.
5.2J EPIGENOMIC DEREGULATION
5.2K CAUSES OF GENOMIC INSTABILITY
Figure 5.18: How cancer arises.
Figure 5.19: Possible causes of chromosomal instability
Figure 5.20: Short telomeres may trigger genomic instability early in tumor formation and telomerase activation may allow for cellular immortality.
5.2L CANCER PREVENTION AND TREATMENT
Figure 5.21: Imatinib is a chemotherapy drug that specifically inhibits Abl kinase.
5.3 MUTATION AND SELECTION IN THE IMMUNE SYSTEM
5.3A GENE REARRANGEMENT IN IMMATURE B-CELLS
Figure 5.22: The structure of an antibody.
Figure 5.23: VDJ recombination: genomic rearrangements within antibody genes.
5.3B NEGATIVE AND POSITIVE SELECTION OF ANTIBODIES
Figure 5.24: Negative Selection: Selection against antibodies that recognize “self.”
Figure 5.25: Positive Selection: Selection for antibodies that recognize antigens
5.3C INCREASED MUTATION OF ANTIBODY GENES IN MATURE B-CELLS
SUMMARY OF CHAPTER 5 CONCEPTS
6.1 PRECISION MEDICINE: ANALYZING INDIVIDUAL GENOMES AND TRANSCRIPTOMES
6.1A THE DEVELOPMENT OF NEXT-GENERATION DNA SEQUENCING
Figure 6.2: Next generation DNA sequencing has drastically reduced the cost of genome sequencing.
Figure 6.3: Incorporation of a nucleotide into DNA releases a pyrophosphate ion and a hydrogen ion.
Figure 6.4: The reactions of pyrophosphate sequencing.
Figure 6.5: Next generation sequencing: 454 sequencing (Part I: sample preparation).
Figure 6.6: Next generation sequencing: 454 sequencing (Part II: pyrosequencing).
6.1B RECENT TECHNIQUES IN NEXT-GENERATION DNA SEQUENCING
Table 6.1: Selected DNA sequencing technologies
Figure 6.7: Next generation sequencing: semiconductor sequencing (Part I: sample preparation).
Figure 6.8: Next generation sequencing: semiconductor sequencing (Part II: H+ ion detection).
Figure 6.9: Next generation sequencing: Bridge PCR.
Figure 6.10: Next generation sequencing: Real-time single molecule sequencing by synthesis.
Figure 6.11: Next generation sequencing: Single molecule sequencing through nanopores.
6.1C APPLICATIONS OF NEXT-GENERATION DNA SEQUENCING
6.2 EMERGING METHODS FOR DISEASE TREATMENT
6.2A THE BIOLOGY OF VIRUSES
Figure 6.12: Examples of viruses and their modifications for gene therapy.
Figure 6.13: The life cycle of HIV, a retrovirus.
6.2B VIRAL GENE THERAPY
6.2C GENE THERAPY WITH GENOME-EDITING ENZYMES
Figure 6.14: Zinc finger endonucleases are engineered to cut DNA at specific sites.
Figure 6.15: The repair of DNA breaks made by site-specific endonucleases provides mechanisms for genome modification.
Figure 6.16: TALENs are engineered to cut genomic DNA at specific sites.
Figure 6.17: The CRISPR/Cas9 system cuts genomic DNA at a specific site.
6.2D AN INTELLIGENT APPROACH TO DRUG DESIGN AND DISEASE TREATMENT
SUMMARY OF CHAPTER 6 CONCEPTS
SELECTED REFERENCES
PDB REFERENCES
PERIODIC TABLE OF THE ELEMENTS
This introductory college-level molecular biology textbook builds upon concepts from first-year high school biology and chemistry courses to elucidate essential concepts in molecular biology, biochemistry, cell biology, and genetics. It is appropriate for college courses and high school courses taught at the college level. Over 170 color figures clearly illustrate key concepts. The goal of this work is to clarify concepts in a streamlined manner, not to be an encyclopedic collection of facts. Connections are explicitly made to prior knowledge and key high school chemistry concepts are reviewed. The biotechnology driving basic science research and translational medicine is explained so that this textbook can serve as a companion to a student beginning molecular biology research. This textbook was created to replace direct lecturing, to support teaching through inquiry and experimentation.
Supporting materials:
- Updated list of URLs used in the textbook; Please contact me to report broken links.
- Molecular Biology Concepts for Inquiry: The Exploration Workbook
- Molecular Biology Concepts for Inquiry: A Guide to Inquiry
- Suggested experiments
- Setting up a classroom research lab
- If you are an instructor and would like access to Google Form quizzes designed for students to self-check their reading comprehension of this textbook, please contact me. Individuals can join the Google Classroom to access online quizzes.
A teacher's guide to teaching molecular biology as an Inquiry course and complete answer key, Molecular Biology Concepts for Inquiry: A Guide to Inquiry, has been published.
A set of slides from textbook figures is available to instructors who contact me. Alternatively, projecting figures directly from the Kindle desktop application works in the classroom.
Thank you to everyone who has already purchased the textbook!
Table of Contents and Figures
CHAPTER 1: INTRODUCTION TO BIOCHEMISTRY AND CELL BIOLOGY
Figure 1.1: The interrelatedness of molecular biology, biotechnology, and engineering.1.1 ORGANIC MOLECULES
1.1A RECOGNIZING ORGANIC MOLECULES
Box 1.1: The Periodic Table of Elements
Figure 1.2: Methods of drawing organic molecules.
Figure 1.3: Examples of organic molecules.
1.1B COVALENT BONDING IN ORGANIC MOLECULES
Box 1.2: Chemistry Review: Determining electron configurations and valence electrons.
Table 1.1: Number of covalent bonds formed by atoms in organic molecules.
Box 1.3: Chemistry Review: Determining the polarity of a bond.
1.1C THE PROPERTIES OF WATER AND ITS INTERACTION WITH ORGANIC MOLECULES
Figure 1.4: Behavior of water.
Table 1.2: Partial list of functional groups in organic molecules.
1.1D INTERMOLECULAR ELECTROSTATIC FORCES IN AN AQUEOUS ENVIRONMENT
1.1E BIOLOGICAL MOLECULES: MONOMERS AND POLYMERS
Figure 1.5: Examples of carbohydrates.
Figure 1.6: Dehydration synthesis and hydrolysis.
Figure 1.7: Examples of lipids.
Figure 1.8: Basic protein structure.
Figure 1.9: Central dogma of molecular biology.
Figure 1.10: Nucleic acid monomers: nucleotides.
Figure 1.11: Nucleic acid polymers: DNA.
Figure 1.12: Nucleic acid polymers: RNA
1.2 THE THERMODYNAMICS OF LIFE
1.2A ENERGY
Figure 1.13: Energy can be transferred between a system and its surroundings.
Figure 1.14: Energy exchange between an animal and its surroundings.
1.2B ENTROPY
Table 1.3: Examples of systems with increasing entropy.
Figure 1.15: Organisms increase the entropy of the universe by giving off heat to their surroundings.
1.2C ENTHALPY AND ENTROPY: DRIVING FORCES THAT DETERMINE SPONTANEITY
Figure 1.16: Potential energy diagrams for chemical reactions.
Table 1.4: Predicting the spontaneity of reactions
Table 1.5: Examples of spontaneous cellular processes
1.2D NONSPONTANEOUS REACTIONS IN LIVING SYSTEMS
Figure 1.17: Hydrolysis of ATP releases a large amount of free energy.
Figure 1.18: The reaction pathway does not affect ∆G.
Box 1.4: Biology Review: Cellular Respiration
Figure 1.19: Dehydration synthesis of maltose coupled to the breakdown of ATP.
Table 1.6: Nonspontaneous maltose synthesis can occur in cells if it is coupled to the breakdown of 2 ATP molecules.
Figure 1.20: Coupled reactions often share intermediate reactants and products.
Figure 1.21: Enzymes speed up specific reactions.
Table 1.7: Cells couple nonspontaneous processes to spontaneous processes that produce excess free energy.
1.3 ORGANIC MOLECULES AND THERMODYNAMICS IN THE CELL
1.3A OBTAINING ENERGY FOR THE CELL
1.3B ORGANIZATION OF THE CELL AND THERMODYNAMIC PRINCIPLES
Box 1.5: Biology Review: Structures and functions within cells
Table 1.8: Functions of Organelles
Box 1.6: Chemistry Review: Dynamic Equilibrium
1.4 BIOTECHNOLOGY AND ALTERNATIVE ENERGY
1.4A THE NEED FOR ALTERNATIVE FORMS OF ENERGY
1.4B PRODUCING FUEL FROM LIVING THINGS: ETHANOL
1.4C ETHANOL FROM CELLULOSE
1.4D BIODIESEL
Figure 1.22: The synthesis of biodiesel
1.4E GENETIC ENGINEERING AND BIOFUELS
1.4F MODELING FUEL PRODUCTION STRATEGIES ON PHOTOSYNTHESIS
SUMMARY OF CHAPTER 1 CONCEPTS
CHAPTER 2: PROTEIN STRUCTURE AND FUNCTION
Figure 2.1: Interaction of the enzyme Abl kinase with the inhibiting drug imatinib.2.1 PROTEIN BIOCHEMISTRY
2.1A PROTEIN SYNTHESIS
Figure 2.2: Central Dogma of Molecular Biology.
Figure 2.3: Transcription.
Figure 2.4: 5' and 3' ends of nucleic acids and the direction of RNA synthesis.
Figure 2.5: Transcription begins within a gene's promoter.
Figure 2.6: Prokaryotic mRNA and Eukaryotic mRNA processing.
Figure 2.7: Structure of a tRNA molecule.
Table 2.1: The Genetic Code.
Figure 2.8: Translation.
2.1B HOW MUTATIONS CREATE DOMINANT OR RECESSIVE PHENOTYPES
Figure 2.9: Mutations can cause recessive or dominant phenotypes.
2.1C THE 20 AMINO ACIDS
Table 2.2: The 20 Amino Acids.
2.1D PROTEIN FOLDING
Figure 2.10: Protein primary structure and secondary structure.
Figure 2.11: Effect of proline on an alpha helix.
Figure 2.12: Examples of protein tertiary structures.
Figure 2.13: Examples of functional and structural roles of ions in proteins.
Figure 2.14: Examples of protein quaternary structures.
2.1E THE THERMODYNAMICS OF PROTEIN FOLDING
Table 2.3: Energy released during bond formation.
Figure 2.15: Non-covalent electrostatic attractions involved in protein folding.
Figure 2.16: The hydrophobic effect and protein folding.
Figure 2.17: Energy landscape of protein folding.
Figure 2.18: Chaperones and chaperonins assist in protein folding.
2.1F PROTEIN MISFOLDING AND DISEASE
Figure 2.19: The proteasome degrades misfolded proteins.
Figure 2.20: Misfolded proteins sometimes aggregate, forming amyloid-like fibrils.
Figure 2.21: Chaperones and chaperonins help prevent aggregation of misfolded proteins.
Figure 2.22: Prion diseases are infectious because misfolded prion proteins cause the misfolding of normally-folded prion proteins.
2.1G METHODS FOR DETERMINING PROTEIN STRUCTURE
2.1H SYNTHESIS OF TRANSMEMBRANE AND EXCRETED PROTEINS
Figure 2.23: Protein synthesis pathways.
2.1I INTERACTIONS OF PROTEINS WITH OTHER MOLECULES
Figure 2.24: Thermodynamics of protein-protein interactions.
Figure 2.25: Lock and Key Model.
2.1J POST-TRANSLATIONAL MODIFICATION OF PROTEINS
Figure 2.26: Phosphorylation of a protein can change its folding and its activity.
Figure 2.27: Signaling cascades often include multiple protein kinases that amplify the signal.
2.1K PROTEIN SHAPE IS DYNAMIC
2.2 ENZYMES
2.2A ENZYMES SPEED UP CHEMICAL REACTIONS
Figure 2.28: An enzyme lowers the activation energy of a chemical reaction
Figure 2.29: Multiple enzymes often participate in a single biosynthetic pathway
2.2B THE STRUCTURE OF AN ACTIVE SITE
Figure 2.30: EDTA chelates metal ions, including magnesium ions.
2.2C FACTORS AFFECTING ENZYME ACTIVITY
2.2D PROTEASES: ENZYMES THAT CLEAVE PROTEINS
Figure 2.31: Proteases are usually translated as inactive zymogens that must be cleaved to be activated.
2.3 USE AND MANIPULATION OF PROTEINS IN BIOTECHNOLOGY
2.3A ENZYMES ARE GOOD DRUG TARGETS
2.3B PURIFICATION OF PROTEINS
2.3C DETECTING PROTEINS
Figure 2.32: Antibodies specifically bind antigens.
Table 2.4: Uses of antibodies in the laboratory
Figure 2.33: Bacteria expressing fluorescent proteins.
Figure 2.34: FRET can detect interactions between molecules in vivo.
SUMMARY OF CHAPTER 2 CONCEPTS
CHAPTER 3: DNA REPLICATION, REPAIR AND GENETIC ENGINEERING
Figure 3.1: The DNA double helix.
3.1 CHROMOSOMES
3.1A DNA, GENES AND CHROMOSOMES
Figure 3.2: DNA, genes, and chromosomes.
3.1B CHROMOSOMES AND MITOSIS
Figure 3.3: Stages of mitosis and the cell cycle.
Figure 3.4: Spindle microtubules.
Figure 3.5: Chromosome structure.
Figure 3.6: Visualization of individual human chromosomes with spectral karyotyping.
3.1C CHROMOSOME STRUCTURE
Figure 3.7: Types of Gene Transfer in Prokaryotes: Transformation, Conjugation, and Transduction.
3.1D PLASMID VECTORS AND ARTIFICIAL CHROMOSOMES
Figure 3.8: A typical bacterial plasmid.
Figure 3.9: Method of bacterial transformation in vitro.
3.2 DNA BIOCHEMISTRY
3.2A DNA STRUCTURE
Figure 3.10: DNA structure.
3.2B VISUALIZING AND ANALYZING DNA: GEL ELECTROPHORESIS
Figure 3.11: Gel electrophoresis of DNA.
3.2C DNA BINDING PROTEINS
Figure 3.12: The DNA-binding domain of a zinc finger protein.
3.3 DNA REPLICATION
3.3A IN VIVO DNA REPLICATION
Figure 3.13: DNA Replication occurs in a 5' to 3' direction.
Figure 3.14: DNA Replication.
3.3B IN VITRO DNA REPLICATION: THE POLYMERASE CHAIN REACTION
Figure 3.15: The Polymerase Chain Reaction.
Figure 3.16: The Polymerase Chain Reaction: Exponential copying of a DNA segment.
3.3C USE OF PCR IN MOLECULAR BIOLOGY, FORENSIC SCIENCE, AND MEDICINE
Figure 3.17: DNA Fingerprinting by PCR of Short Tandem Repeats (STR analysis).
Figure 3.18: A "diagnostic" use of PCR.
3.3D IN VITRO DNA REPLICATION: DNA SEQUENCING
Figure 3.19: Comparison of normal deoxynucleotides and the dideoxynucleotides used in DNA sequencing.
Figure 3.20: DNA sequencing.
Figure 3.21: The Human Genome Project
3.4 DNA REPAIR ENZYMES
3.4A MUTATIONS
Figure 3.22: Causes and consequences of DNA damage
3.4B POINT MUTATIONS: CAUSES AND REPAIR
Figure 3.23: Types of Point mutations.
Figure 3.24: Repair of DNA point mutations.
3.4C DNA BREAKS: FORMATION AND REPAIR
Figure 3.25: Double-strand break repair: nonhomologous end-joining (NHEJ)..
Figure 3.26: Double strand break repair through homologous recombination (simplified).
Figure 3.27: Double strand break repair through homologous recombination (details).
3.4D GENETIC DISEASES CAUSED BY DEFECTS IN DNA REPAIR
Table 3.1: Genetic disorders with mutations in DNA repair proteins.
3.5 GENETIC ENGINEERING
3.5A THE DISCOVERY OF RESTRICTION ENDONUCLEASES
Figure 3.28: Experiments that showed "restriction."
Figure 3.29: Restriction enzymes explain the phenomenon of "restriction."
Figure 3.30: Structures of restriction enzymes bound to DNA.
3.5B MANIPULATING DNA IN GENETIC ENGINEERING (CLONING STRATEGIES)
Figure 3.31: Restriction enzymes act as scissors and DNA ligase acts as glue in genetic engineering.
Figure 3.32: Efficiency of ligation reactions.
Figure 3.33: Strategies for inserting DNA into plasmids while preventing plasmid religation.
Figure 3.34: Strategies for cloning PCR products
3.5C VIRUSES PROVIDE TOOLS FOR CONVERTING RNA INTO DNA
Figure 3.35: The life cycle of HIV, a retrovirus.
3.5D INTRODUCTION OF DNA INTO BACTERIA
Figure 3.36: In a bacterial transformation, each colony contains one plasmid.
Figure 3.37: General order of steps to clone plasmids in bacteria.
3.5E INTRODUCTION OF DNA INTO EUKARYOTIC CELLS
Figure 3.38: Transfection of DNA into mammalian cells.
Figure 3.39: Transduction of mammalian cells with retrovirus.
3.5F ENGINEERING OF EUKARYOTIC GENOMES AT SPECIFIC SITES
Figure 3.40: Replacement of chromosomal DNA via homologous recombination (simplified).
Figure 3.41: Southern blot.
SUMMARY OF CHAPTER 3 CONCEPTS
CHAPTER 4: THE REGULATION OF GENE EXPRESSION
Figure 4.1 Transcription.4.1 THE REGULATION OF TRANSCRIPTION
4.1A THE ORGANIZATION OF A GENE
Figure 4.2: Prokaryotic and Eukaryotic mRNA processing.
Figure 4.3: Structure and transcription of a prokaryotic gene.
Figure 4.4: Basic factors that affect the level of transcription of a gene.
Figure 4.5: Constitutive, inducible, and repressible promoters.
Figure 4.6: Modularity of iGEM BioBricks.
4.1B CHROMATIN STRUCTURE IN EUKARYOTES
Figure 4.7: Structures of a histone and a nucleosome.
Figure 4.8: Nucleosomes form due to attractions between histone tails and the DNA backbone.
Figure 4.9: Chromatin Structure.
4.1C EUCHROMATIN AND HETEROCHROMATIN
Figure 4.10: Comparison of euchromatin and heterochromatin.
Figure 4.11: Histone acetylation is determined by DNA CpG methylation.
Figure 4.12 DNA methyltransferase methylates a cytosine opposite a methyl CpG.
4.2 POSTTRANSCRIPTIONAL REGULATION OF MRNA LEVELS IN EUKARYOTES
4.2A STABILITY OF mRNA
Figure 4.13: Eukaryotic mRNA processing and looped structure.
Figure 4.14: Loss of mRNA end protection and mRNA degradation by exonucleases.
4.2B RNA INTERFERENCE
Figure 4.15: Fire and Mello’s RNAi experiment (1998).
Figure 4.16: The mechanism of RNAi.
Figure 4.17: Amplification of RNAi in worms, plants, and fungi.
4.2C THE HUMAN GENOME, RNAI, AND NOVEL CLASSES OF RNA
Table 4.1: Makeup of the human genome.
Figure 4.18: Transposons cause the sectoring in corn kernels.
4.2D MICRORNAS CAUSE THE DEGRADATION OF COMPLEMENTARY MRNAS
Figure 4.19: microRNAs and RNAi.
4.2E LONG NONCODING RNAS AND THE REGULATION OF GENE EXPRESSION
Figure 4.20: X-chromosome inactivation.
Figure 4.21: The TSIX RNA inhibits the transcription of XIST RNA from the active X chromosome in mice.
4.3 THE PROGRAMMING OF TRANSCRIPTIONAL PATTERNS DURING DEVELOPMENT
4.3A THE CONTROL OF DNA METHYLATION PATTERNS
Table 4.2: Changes in methylation of the DNA in the human genome.
4.3B CLONED ANIMALS ARE NOT QUITE “NORMAL”
Figure 4.22: Somatic Cell Nuclear Transfer (Cloning).
Figure 4.23: Donor cell methylation patterns are not fully erased in cloned animals.
4.3C STEM CELLS
Figure 4.24: Therapeutic cloning produces stem cells that are genetically identical to a patient.
4.3D IMPRINTING
Figure 4.25: Example of a typical imprinted locus.
Figure 4.26: The imprinted Angelman Syndrome locus.
4.4 MEASURING LEVELS OF GENE EXPRESSION
4.4A METHODS FOR MONITORING RNA LEVELS
Figure 4.27: Northern blot.
Figure 4.28: qPCR.
Figure 4.29: Microarray analysis.
4.4B METHODS FOR MONITORING PROTEIN LEVELS
SUMMARY OF CHAPTER 4 CONCEPTS
CHAPTER 5: GENOME EVOLUTION
Figure 5.1: Evolution depends on both mutation and selection.5.1 GENOME EVOLUTION
5.1A MUTATIONS CREATE VARIATION THAT IS SUBJECT TO SELECTION
Figure 5.2: Natural selection acts upon only 5% of the human genome.
Figure 5.3: Percent of genome that is mutated compared to the reference human genome.
Figure 5.4: Blocks of conserved synteny.
Table 5.1: Comparisons of genomes to the reference human genome
5.1B GENE DUPLICATIONS FACILITATE THE EVOLUTION OF NEW GENES
Figure 5.5: The effect of selection on mutation frequency.
5.1C LOSS OF GENES
5.2 CANCER
5.2A CANCER AS A GENETIC DISEASE
5.2B MUTATION AND SELECTION IN CANCER
Figure 5.6: Mutation and clonal expansion.
5.2C BOTH LOSS-OF-FUNCTION AND GAIN-OF-FUNCTION MUTATIONS CONTRIBUTE TO TUMOR FORMATION
Figure 5.7: The Cell Cycle.
Table 5.2: The analogy of cancer genes, the car and the cell cycle
5.2D COMPLEX REGULATORY PATHWAYS CONTROL CELL BIRTH AND CELL DEATH
Figure 5.8: Multiple pathways affecting cell division and death are altered in cancer.
Figure 5.9: Loss of p53 affects multiple signaling pathways, causing increased cell division and decreased apoptosis.
5.2E ONCOGENES, TUMOR SUPPRESSOR GENES, AND GENE DOSAGE
Figure 5.10: Development of tumors in inherited retinoblastoma.
5.2F MUTATIONS IN LATE STAGES OF TUMOR DEVELOPMENT
5.2G CELLULAR IMMORTALITY
Figure 5.11: Telomere structure and the end replication problem.
Figure 5.12: Telomerase elongates telomeres and solves the end replication problem.
Figure 5.13: Very short telomeres cause cellular senescence and explain the Hayflick limit.
Figure 5.14: Telomeres distinguish natural DNA ends from DNA breaks.
5.2H CANCER AND “SURVIVAL OF THE FITTEST”
Table 5.3: Factors that limit cancer growth
Table 5.4: Characteristics of cancer
5.2I GENOMIC INSTABILITY
Figure 5.15: Types of mutations observed in tumors.
Figure 5.16: The result of genomic instability is often evident in tumor karyotypes.
Figure 5.17: A reciprocal translocation activates the Abl oncogene in chronic myelogenous leukemia.
5.2J EPIGENOMIC DEREGULATION
5.2K CAUSES OF GENOMIC INSTABILITY
Figure 5.18: How cancer arises.
Figure 5.19: Possible causes of chromosomal instability
Figure 5.20: Short telomeres may trigger genomic instability early in tumor formation and telomerase activation may allow for cellular immortality.
5.2L CANCER PREVENTION AND TREATMENT
Figure 5.21: Imatinib is a chemotherapy drug that specifically inhibits Abl kinase.
5.3 MUTATION AND SELECTION IN THE IMMUNE SYSTEM
5.3A GENE REARRANGEMENT IN IMMATURE B-CELLS
Figure 5.22: The structure of an antibody.
Figure 5.23: VDJ recombination: genomic rearrangements within antibody genes.
5.3B NEGATIVE AND POSITIVE SELECTION OF ANTIBODIES
Figure 5.24: Negative Selection: Selection against antibodies that recognize “self.”
Figure 5.25: Positive Selection: Selection for antibodies that recognize antigens
5.3C INCREASED MUTATION OF ANTIBODY GENES IN MATURE B-CELLS
SUMMARY OF CHAPTER 5 CONCEPTS
CHAPTER 6: EMERGING MOLECULAR BIOLOGY, BIOTECHNOLOGY AND MEDICINE
Figure 6.1: A DNA bead used in next-generation DNA sequencing.6.1 PRECISION MEDICINE: ANALYZING INDIVIDUAL GENOMES AND TRANSCRIPTOMES
6.1A THE DEVELOPMENT OF NEXT-GENERATION DNA SEQUENCING
Figure 6.2: Next generation DNA sequencing has drastically reduced the cost of genome sequencing.
Figure 6.3: Incorporation of a nucleotide into DNA releases a pyrophosphate ion and a hydrogen ion.
Figure 6.4: The reactions of pyrophosphate sequencing.
Figure 6.5: Next generation sequencing: 454 sequencing (Part I: sample preparation).
Figure 6.6: Next generation sequencing: 454 sequencing (Part II: pyrosequencing).
6.1B RECENT TECHNIQUES IN NEXT-GENERATION DNA SEQUENCING
Table 6.1: Selected DNA sequencing technologies
Figure 6.7: Next generation sequencing: semiconductor sequencing (Part I: sample preparation).
Figure 6.8: Next generation sequencing: semiconductor sequencing (Part II: H+ ion detection).
Figure 6.9: Next generation sequencing: Bridge PCR.
Figure 6.10: Next generation sequencing: Real-time single molecule sequencing by synthesis.
Figure 6.11: Next generation sequencing: Single molecule sequencing through nanopores.
6.1C APPLICATIONS OF NEXT-GENERATION DNA SEQUENCING
6.2 EMERGING METHODS FOR DISEASE TREATMENT
6.2A THE BIOLOGY OF VIRUSES
Figure 6.12: Examples of viruses and their modifications for gene therapy.
Figure 6.13: The life cycle of HIV, a retrovirus.
6.2B VIRAL GENE THERAPY
6.2C GENE THERAPY WITH GENOME-EDITING ENZYMES
Figure 6.14: Zinc finger endonucleases are engineered to cut DNA at specific sites.
Figure 6.15: The repair of DNA breaks made by site-specific endonucleases provides mechanisms for genome modification.
Figure 6.16: TALENs are engineered to cut genomic DNA at specific sites.
Figure 6.17: The CRISPR/Cas9 system cuts genomic DNA at a specific site.
6.2D AN INTELLIGENT APPROACH TO DRUG DESIGN AND DISEASE TREATMENT
SUMMARY OF CHAPTER 6 CONCEPTS
SELECTED REFERENCES
PDB REFERENCES
PERIODIC TABLE OF THE ELEMENTS