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Biofundamentals 2e

Biofundamentals is an attempt to build a more conceptually coherent, rigorous and engaging introductory course in modern biology. An introduction to core the observations, concepts and scientific principles in biology, centered on molecular mechanisms & cellular processes and their application in evolution, development & human health

Cell and Molecular Biology Biology

Author: Klymkowsky & Cooper
Publisher: University of Colorado Boulder & Michigan State University
Source: LibreTexts
License: CC BY-NC-SA
Language: EN
Category: Basic Sciences

Read online Download PDF (open licence)

Contents· 212 sections

01: Understanding Science and Thinking Scientifically
1.00: Introduction
1.01: The interconnectedness (self-consistency) of science
1.02: Models Hypotheses and Theories
1.03: Science is Social
1.04: Teaching and Learning Science
1.05: Understanding Scientific Ideas
02: Lifes Diversity and Origins
2.00: Introduction
2.01: What is life exactly
2.02: The cell theory and the continuity of life
2.03: The organization of organisms
2.04: Spontaneous generation and the origin of life
2.05: The Death of Vitalism
2.06: Thinking about lifes origins
2.07: Experimental studies on the origins of life
2.08: Mapping the history of life on earth
2.09: Fossil evidence for the history of life on earth
2.10: Life's impact on earth
03: Evolutionary Mechanisms and the Diversity of Life
3.00: Introduction
3.01: Organizing organisms (hierarchically)
3.02: Natural and un-natural groups
3.03: Fossils and family relationships- introducing cladistics
3.04: Evolution theorys core concepts
3.05: Limits on populations
3.06: Darwin and Wallace's conceptual leap
3.07: Mutations and the origins of genotype-based variation
3.08: The origins of polymorphisms
3.09: Genotype-phenotype relationships- discrete and continuous traits
3.10: Variation selection and speciation
3.11: Types of simple selection
3.12: Considering stochastic processes
3.13: Genetic diversity population size founder effects and population bottlenecks
3.14: Population bottlenecks
3.15: Genetic drift
3.16: Gene linkage- one more complication
3.17: A brief reflection on the complexity of phenotypic traits
3.18: Speciation and extinction
3.19: Mechanisms of speciation
3.20: Mechanisms of reproductive isolation
3.21: Sympatric speciation
3.22: Signs of evolution- homology and convergence
3.23: Homologies provide evidence for a common ancestor
3.24: Anti-evolution arguments
04: Social Evolution and Sexual Selection
4.00: Introduction
4.01: Selecting social (cooperative) traits
4.02: Quorum Sensing
4.03: Active (altruistic) cell death
4.04: Inclusive fitness kin and group selection and social evolution
4.05: Group selection
4.06: Defense against social cheaters
4.07: The appearance of multicellular organisms
4.08: Origins and implications of sexual reproduction
4.09: Sexual dimorphism
4.10: Sexual Selection
4.11: Curbing runaway selection
05: Molecular Interactions Thermodynamics and Reaction Coupling
5.00: Introduction
5.01: Approaching Thermodynamics
5.02: Coupling thermodynamically favorable and unfavorable reactions
5.03: Reaction rates
5.04: Coupling Reactions
5.05: Inter- and intra-molecular interactions
5.06: Covalent bonds
5.07: Bond Stability and Thermal Motion (a non-biological moment)
5.08: Bond polarity inter- and intramolecular interactions
5.09: The implications of bond polarity
5.10: Interacting with Water
06: Membrane Boundaries and Capturing Energy
6.00: Introduction
6.01: Defining the Cells Boundary
6.02: The origin of biological membranes
6.03: Transport across membranes
6.04: Channels and carriers
6.05: Generating gradients- using coupled reactions and pumps
6.06: Simple Phototrophs
6.07: Chemo-osmosis (an overview)
6.08: Oxygenic Photosynthesis
6.09: Chemotrophs
6.10: Using the energy stored in membrane gradients
6.11: Osmosis and living with and without a cell wall
6.12: An evolutionary scenario for the origin of eukaryotic cells
6.13: Making a complete eukaryote
07: The Molecular Nature of Heredity
7.00: Introduction
7.01: Discovering how nucleic acids store genetic information
7.02: Locating hereditary material within the cell
7.03: Identifying DNA as the genetic material
7.04: Unraveling Nucleic Acid Structure
7.05: Discovering the structure of DNA
7.06: DNA sequences and information
7.07: Discovering RNA- structure and some functions
7.08: DNA Replication
7.09: Replication machines
7.10: Further replication complexities
7.11: Mutations Deletions Duplications and Repair
7.12: Genes and alleles
7.13: The origin of new (de novo) genes
7.14: DNA repeat diseases and genetic anticipation
08: Peptide Bonds Polypeptides and Proteins
8.00: Introduction
8.01: Specifying a polypeptides sequence
8.02: The origin of the genetic code
8.03: Protein synthesis- transcription (DNA to RNA)
8.04: Protein synthesis- translation (RNA to polypeptide)
8.05: The translation (polypeptide synthesis) cycle
8.06: Effects of point mutations on polypeptides and proteins
8.07: Getting more complex- gene regulation in eukaryotes
8.08: Turning polypeptides into proteins
8.09: Regulating protein activity concentrations and stability (half-life)
8.10: Allosteric and post-translational regulation
8.11: Diseases of folding and misfolding
8.12: Molecular machines
09: Genomes Genes and Regulatory networks
9.00: Introduction
9.01: Locating information within DNA
9.02: Enhancers and transcription start and stop sites
9.03: Interaction networks and model systems
9.04: E. coli as a model system
9.05: Adaptive behavior and gene networks- the lac response
9.06: Types of regulatory interactions
9.07: Final thoughts on (molecular) noise
10: Social Systems
10.00: Introduction
10.01: Targeting membrane proteins to where they need to be
10.02: Nuclear targeting and exclusion
10.03: Intercellular signaling- signals receptors and responses
10.04: Signaling molecules and receptors
10.05: Cellular reprogramming- embryonic and induced pluripotent stem cells
11: Cellular reproduction and horizontal gene transfer in prokaryotes
11.00: Introduction
11.01: What counts as sex in prokaryotes
11.02: Other naturally occurring horizontal gene transfer mechanisms
12: Asexual and Sexual Reproduction in Eukaryotes
12.00: Introduction
12.01: Ploidy during the cell cycle
12.02: Monitoring cellular processes- mitosis
12.03: Sex-determination and its chromosomal basis
12.04: Steps in meiosis- from diploid to haploid
12.05: Recombination and independent segregation
12.06: Linkage and haplotypes
12.07: X-inactivation and sex-linked traits
12.08: X-linked diseases and mono-allelic gene expression
13: How Alleles Arise - Mutations
13.00: Introduction
13.01: Mutations into alleles
13.02: Luria and Delbruck- Discovering the origin of mutations
13.03: Forward and reverse genetics
13.04: Generating specific mutations on demand - CRISPR-Cas9 and related technologies
13.05: Longer term mutation and evolution studies
14: Somatic Mutations and Genome Dynamics
14.00: Introduction
14.01: Rates and effects of somatic mutation
14.02: Non-disjunction- aberrant chromosome segregation
14.03: Genome dynamics
14.04: Gene duplications and deletions
14.05: Orthologs and paralogs
14.06: Transposons- moving DNA within a genome (and weird genetics)
15: Mendel and Weldon - Contexts and their Effects on Phenotypes
15.00: Introduction
15.01: How Mendel did what he did
15.02: Weldon's critique
15.03: Chi square (2) analysis hypothesis testing and small numbers
15.04: Dihybrid crosses- linkage and recombination
15.05: Genetic complementation
15.06: Interacting traits- synthetic lethality and co-dominance
15.07: Interacting traits- epistasis
15.08: Maternal and paternal effects
15.09: Mitochondrial inheritance
15.10: Imprinting- conflicts between mother father and fetus
15.11: Estimating the number of genes involved in a particular traits
15.12: On the nature of mutations (again)
15.13: Alleles traits and genetic diseases in humans.
15.14: Concordance between monozygotic twins and genetic influence on a trait
15.15: Measuring evolutions impact on allele frequencies- Hardy-Weinberg
15.16: Genetic anticipation
15.17: The persistence of deleterious alleles
16: Tools for Studying Genes and Genomes
16.00: Introduction
16.01: Synteny examined using Genomicus
16.02: Where is a gene expressed
16.03: Using web-based bioinformatic tools- gnomAD
16.04: Using web-based bioinformatic tools- BLAST
16.05: Genome-wide Association Studies (GWAS)
17: Supplemental Chapter - Fundamental concepts and developing systems
17.00: Introduction
17.01: How do systems change at the molecular level
17.02: Steady state and changing molecular concentrations- synthesis and degradation
17.03: Direct and indirect cellular responses to signaling molecules
17.04: Modeling gene expression
17.05: Reversible irreversible and cascade effects
18: Supplemental Chapter - Social interactions between cells
18.00: Introduction
18.01: How do unicellular organisms generate phenotypic diversity
18.02: Dying for others social interactions between unicellular organisms
18.03: Quorum effects (somewhat redundant)
18.04: Transient and clonal (true) metazoans
18.05: Unicellular to multicellularity to unicellularity
18.06: Evolutionary origins of clonal (permanent) multicellularity
19: Supplemental Chapter - The role of model systems in understanding metazoan development
19.00: Introduction
19.01: Model Systems
19.02: Some model systems
19.03: Frogs and fish
19.04: Chick and Quail
19.05: The fruit fly Drosophila melanogaster
19.06: The nematode Caenorhabditus elegans
19.07: The Mouse
19.08: ESC and iPSC derived organoids
20: Appendix- Mullers Morphs