The Structure of DNA PDF

**THE STRUCTURE OF DNA** - Two strands of DNA polynucleotide chains are bound together via **complementary base pairing.** - The two strands of DNA are said to be **antiparallel** - One strand runs in 5' ➜ 3' direction, while the other runs in 3' ➜ 5' direction - **Rosalind Frank...

**THE STRUCTURE OF DNA** - Two strands of DNA polynucleotide chains are bound together via **complementary base pairing.** - The two strands of DNA are said to be **antiparallel** - One strand runs in 5' ➜ 3' direction, while the other runs in 3' ➜ 5' direction - **Rosalind Franklin** (1920-1958) and her colleague **Maurice Wilkins** performed x-ray crystallography technique to analyze the structure of DNA. - The base pairs are organized inside the helix through **base stacking**, which contributes to the DNA molecule's overall **thermodynamic stability** - **Dexterity of the DNA Helix** - The DNA is a **right-handed** double helical nucleic acid - **The Grooves of DNA** - The DNA helix has two different grooves due to the angle of protrusion of the deoxyribose a. **Major Groove** b. **Minor Groove** - **DNA Conformations** - Three conformations of DNA exists, which differ in formation, number of base pairs (bp) per turn, and shape of helix - **Comparison of the Three DNA Conformations** **Properties** **B DNA** **A DNA** **Z DNA** ------------------------- ----------------------- ----------------------- --------------------------------- **Formation** 92% relative humidity 70% relative humidity low and high salt concentration **Base pairs per turn** 10 bp/turn 11 bp/turn 12 bp/turn **Properties** **B DNA** **A DNA** **Z DNA** ---------------------- -------------- -------------- ------------- **Dexterity** Right-handed Right-handed Left-handed **Helical diameter** 20 Å 23 Å 18 Å **Complete turn** 33.2 Å 24.6 Å 45.6 Å **Chargaff's Rules:** - The purine content is roughly equal to the pyrimidine content. - Adenine and thymine have equal quantities in DNA - Guanine and cytosine have equal quantities in DNA **Watson and Crick, with the aid of the works of Franklin, Wilkins, and Chargaff, postulated that:** - The uniformity in size of DNA is due to the complementary base pairing - The pairings involve specificity in H bond formation - The DNA structure is helical, similar to a twisted ladder. **PuAG --** Purine, Adenine, and Guanine **PyCT --** Pyrimidine, Cytosine, and Thymine **Eukaryotic DNA** is known to be: - Linear or with distinct ends called **telomeres** - Organized as **chromatin** (DNA + proteins) - Packed through proteins called **histones** into the following levels: a. **Nucleosomes** b. **30-nm fibers** c. **Metaphase chromosomes** **RNA**, a nucleic acid, is known to: - Be **single-stranded** - Have the base **uracil** instead of thymine in DNA - Have **ribose** instead of deoxyribose n DNA, and - A product of **transcription** of DNA - RNA molecules may also assume enzymatic functions - **Ribozymes** are a group of catalytic RNA molecules - **RNase P** is a ribozyme that catalyzes tRNA synthesis - **RNA** acts as the information bridge between DNA and protein - **mRNA** is the message that carries genetic information from the DNA in the nucleus to the cytoplasm - **tRNA** is the adaptor that reads the mRNA and brings the amino acids to the ribosomes for protein synthesis **Amino Acids** are the subunits or monomers of proteins. Each amino acid consists of: - a carboxyl group (COOH) - an amino group - a proton - a varying R group **Levels of Protein Structure** Amino acids are organized into polypeptides and proteins via different levels. - **Primary Structure →** attained by the formation of a **peptide bond** between each of the amino acids - **Secondary Structure →** may be in a form of a helix or a **pleated sheet** - **Tertiary Structure →** consists of polypeptides and **both helices and sheets** - **Quaternary Structure →** attained whenever **multiple folded protein subunits** form a single complex to confer greater functionality. **Protein Data Bank (PDB)** - Enormous collection of published experiments on the structure of DNA, RNA, and proteins - It enables us to view the 3D structure of proteins - Data on protein structures are usually quantified via **protein resolution**, which is smallest distance (**Anstrom**) between two distinguishable features, and identified through **x-ray diffraction** technique **Reproduction and DNA Replication** - The duplication of the genetic material is a key process in the reproduction of living cells - **DNA Replication**: growth development, asexual reproduction, would healing - The **Meselson-Stahl** experiment proved the semiconservative nature of DNA replication. **Mechanisms of Replication** - Each strand serves as a template - Resulting DNAs have an old and a new strand - Replication is through complementary base pairing - Parental DNA is not completely conserved - **Replication bubble** is the site where the **bidirectional and 5' to 3'** DNA replication actively takes place **Initiation of Replication** - **Priming** is an essential step before DNA polymerase continues with the elongation of the DNA strand - **RNA** polymerase makes primer - **DNA** polymerase extends primer **Elongation in Replication** - **Topoisomerase** is the eukaryotic counterpart of gyrase - Separate polymerase act on leading and lagging strand \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-- **Introduction to Breeding** - **Breeding** is the **controlled** process of subjecting two parent organisms to **sexual reproduction** to produce offspring **Classical Plant Breeding Methods** - **Selective Breeding** - **Crossbreeding** **Selective Breeding** - **Mass selection** → can be applied to the breeding of alfalfa and corn crops - **Pure-line selection** → can be employed in the breeding of wheat and rice crops - **Clonal selection**→ navel oranges and delicious apples are further improved **Crossbreeding or Hybridization** - Involves the removal of stamens of one parent plant to prevent self-pollination - Crossbred plants include corn, sunflower, and cauliflower **Objectives of Classical Plant Breeding Methods** - **Pure-line selection** → aims to establish a breed that is **homozygous for particular trait**: thus, self-pollination is most applicable. - **Mass selection** → aims to **improve the qualities of a crop** by selecting good-quality offspring every generation and allowing them to **open pollinate** - **Clonal selection** → applicable for **good-quality hybrids that usually cannot reproduce**; thus, only the vegetative or asexual reproduction of the plant is harnessed. - **Crossbreeding** → aims to **combine two-superior traits from different breeds** or species of plants. Involves **emasculation** off one parent plants. **Classical Animal Breeding Methods** - **Inbreeding** - mating between related individuals - superior female cattle that produces high amount of milk can be mated to her sons during inbreeding - **Crossbreeding** - Individuals from two different breeds are bred together **Modern Breeding Methods** - **Somatic Hybridization** → protoplasts from two different plants with desirable traits are fused - **Mutation Breeding** → crops, such as soybeans, are induced to mutate (e.g., exposure to gamma radiation) - **Artificial Reproductive Technologies** → some female cattle are artificially inseminated by using semen collected from superior bulls - **Genetic Engineering** → transcends classical breeding techniques and allows introduction of genes from a totally different organism. \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-- **Introduction to Genetic Engineering** - **Genetic Engineering** involves the direct manipulation of genes of organisms in laboratory for them to express the desired traits - **Recombinant DNA technology** is the primary technique used in the genetic engineering of organisms **Process of Genetic Engineering** - **Identification of gene of interest** - **Isolation of gene of interest** - **Werner Arber** pioneered the study of the restriction enzymes in **[bacterial cells]** - **Hamilton Smith**, together with **Daniel Nathans**, elucidated the **[ability of restriction endonucleases to cut DNA at specific sites]** - **Introduction of gene of interest** - Electroporation - Microprojectile bombardment - Mediated transformation **Ways In which Recombinant DNA may be introduced into host organisms** - **Biolistics (gene gun)** → used to fire DNA-coated pellets on **[plant tissues]** - **Plasmid Insertion by Heat Shock Treatment**→ used to transfer plasmid DNA into **[bacteria]** - **Electroporation**→ insertion of genes into **[mammalian cells]** **Applications of Genetic Engineering** - Agriculture - Bioremediation - Genetic testing - Gene therapy - Pharmaceuticals 1. Determination of the gene of interest 2. Isolation of the gene of interest by using restriction enzymes and gel electrophoresis 3. Use of probe to locate the gene 4. Use of restriction enzymes and DNA ligase to combine the gene and plasmid 5. Reintroducing the recombinant DNA into a bacterial cell 6. Allowing the bacteria to transform the host plant cells, and 7. Regenerating the cultured plant cells \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-- **Fossils** - The sweeping changes in life on Earth as revealed by fossils illustrate **macroevolution** (the broad pattern of evolution above the species level). **Earth's Timeline and Emergence of Life** Four Main Stages: 1. The **abiotic (nonliving) synthesis** of small organic molecules, such as amino acids and nitrogenous bases. 2. The joining of these small molecules into **macromolecules**, such as proteins and nucleic acids. 3. The packaging of these molecules into **protocells**, droplets with membranes that maintained an internal chemistry different from that of their surroundings. 4. The **origin of self-replicating molecules** that eventually made inheritance possible. **Synthesis of Organic Compounds on Early Earth** - Earth and the other planets of the solar system formed about 4.6 billion years ago Russian chemist **A.I. Oparin** and British scientist **J.B.S. Haldane** independently (1920) - Hypothesized that Earth's **[early atmosphere was a reducing (electron-adding) environment]**, in which organic compounds could have formed from simpler molecules. - **Haldane** suggested that the early oceans were a solution of organic molecules, a "**[primitive soup]**" from which life arose. **Stanley Miller (1953)** - His apparatus yielded a variety of **amino acids found in organisms today**, along with other organic compounds **Miller-Urey-Type Experiments** - Demonstrate that the abiotic synthesis of organic molecules is possible under various assumptions about the composition of the early atmosphere. 1. Volcanic eruptions 2. Meteorites → Murchison meteorite Some evidence suggests that the early atmosphere was made up primarily of **nitrogen and carbon dioxide** and was neither reducing nor oxidizing (electron removing). **Protocells** - **Vesicles** → fluid-filled compartments bounded by a membrane-like structure - recent experiments show that abiotically produced vesicles can exhibit certain properties of life, including simple reproduction and metabolism, as well as the maintenance of an internal chemical environment different from that of their surroundings. - vesicles can also absorb **montmorillonite particles,** including those on which RNA and other organic molecule have become attached. **Abiotic Synthesis of Macromolecules** - 2009 study demonstrated that one key step the **abiotic synthesis of RNA monomers, can occur spontaneously from simple precursor molecules.** - Dripping solutions of amino acids or RNA nucleotides onto hot sand, clay, or rock, researchers have produced **polymers** of these molecules. **Self-Replicating RNA and the Dawn of Natural Selection** - The first genetic material was most likely **RNA**, not DNA - Thomas Cech & Sidney Altman found that RNA, which plays a central role in protein synthesis, can also carry out a number of enzyme-like catalytic functions---**Ribozyme**s. - **Ribozymes** can make complementary copies of short pieces of RNA - Natural selection on the molecular level has produced ribozymes capable of self-replicating in the laboratory. **Natural Selection** - A **vesicle with self-replicating**, catalytic RNA would differ from its many neighbors that did not carry RNA or that carried RNA without such capabilities. - **If that vesicles could grow, split, and pass its RNA molecules** to its daughters, the daughters would be protocells that had some of the properties of their parent. - **The most successful of the early protocells would have increased in number** because they could exploit their resources effectively and pass their abilities on to subsequent generations. **Fossil Record** → Documents the history of life - Shows that there have been great changes in the kinds of organisms on Earth at different points in time. **How Rocks and Fossils are Dated** 1. **Radiometric dating** - Based on the decay of radioactive isotopes - The rate of decay is expressed by the half-life, the time required for 50% of the parent isotope to decay. a. **Carbon-14** → decays relatively quickly; it has a half-life of 5,730 years b. **Uranium-238** → decays slowly; its half-life is 4.5 billion years **The Origin of New Groups of Organisms** - **Tetrapods** (from the Greek *tetra*, four, and *pod,* foot) -- animals having four limbs. - **Synapsid →** had multiple bones in the lower jaw and single-pointed teeth. The jaw hinge was formed by the articular and quadrate bones. Synapsids also had an opening called temporal fenestra behind the eye socket. - **Therapsid →** a group of synapsids. Therapsids had large dentary bones, long faces, and the first examples of specialized teeth, large canines. These trends continued in a group of therapsids called cynodonts. - **Early Cynodont (260 mya) →** the dentary was the largest bone in the lower jaw, the temporal fenestra was large and positioned forward of the jaw hinge, and teeth with several cusps first appeared. As in earlier synapsids, the jaw had an articular-quadrate hinge. - **Later Cynodont (220 mya) →  **Later cynodonts has teeth with complex cusp patterns, and their lower and upper jaws hinged in two locations: They retained the original articular quadrate hinge and formed new, second hinge between the dentary and squamosal bones - **Very Late Cynodont (195 mya) → **In some late (nonmammalian) cynodonts and early mammals, the original articular-quadrate hinge was lost, leaving the dentary-squamosal hinge the only hinge between the lower and upper jaws, as in living mammals. The articular and quadrate bones migrated into the ear region, where they functioned in transmitting sound. In the mammal lineage, these bones later evolved into the familiar hammer (malleus) and anvil (incus) bones of the ear **EARTH'S GEOLOGICAL TIME SCALE** +-----------------+-----------------+-----------------+-----------------+ | **EON** | **ERA** | **PERIOD** | **EPOCH** | +=================+=================+=================+=================+ | **Phanerozoic | | | - **Epochs** | | Eon (542 MYA)** | | | are the | | | | | shortest | | Means visible | | | unit in the | | life that was | | | Earth's | | constructed | | | geologic | | through rock | | | time scale | | units that bear | | | that is | | abundant | | | characteriz | | fossils | | | ed | | | | | by the | | | | | changes in | | | | | life forms | | | | | and may | | | | | vary from | | | | | continent | | | | | to | | | | | continent | +-----------------+-----------------+-----------------+-----------------+ | **Precambrian | **Cenozoic | **Quaternary | | | Eon** | Era** | Period** | | | | | | | | **(4 BYA)** | Is also known | Human evolution | | | | as the age of | | | | Represents the | mammals | | | | period between | | | | | the birth of | | | | | the planet and | | | | | the appearance | | | | | of life forms | | | | +-----------------+-----------------+-----------------+-----------------+ | | | **Tertiary | | | | | Period** | | | | | | | | | | Mammals | | | | | diversity | | +-----------------+-----------------+-----------------+-----------------+ | | **Mesozoic | **Cretaceous | | | | Era** | Period** | | | | | | | | | Is also known | Extinction of | | | | as the age of | dinosaurs, | | | | reptiles | first primates, | | | | | first flowering | | | | | plants | | +-----------------+-----------------+-----------------+-----------------+ | | | **Jurassic | | | | | Period** | | | | | | | | | | First birds, | | | | | dinosaurs | | | | | diversity | | +-----------------+-----------------+-----------------+-----------------+ | | | **Triassic | | | | | Period** | | | | | | | | | | First mammals, | | | | | first dinosaurs | | +-----------------+-----------------+-----------------+-----------------+ | | **Paleozoic | **Permian** | | | | Era** | | | | | | | | | | Is also known | | | | | as the "*age of | | | | | invertebrates"* | | | +-----------------+-----------------+-----------------+-----------------+ | | | **Carboniferous | | | | | ** | | +-----------------+-----------------+-----------------+-----------------+ | | | **Devonian** | | +-----------------+-----------------+-----------------+-----------------+ | | | **Silurian** | | +-----------------+-----------------+-----------------+-----------------+ | | | **Ordovician** | | +-----------------+-----------------+-----------------+-----------------+ | | | **Cambrian** | | +-----------------+-----------------+-----------------+-----------------+ | **Proterozoic** | | | | +-----------------+-----------------+-----------------+-----------------+ | **Archean** | | | | +-----------------+-----------------+-----------------+-----------------+ | **Hadean** | | | | +-----------------+-----------------+-----------------+-----------------+ "**C**an **O**ld **S**enators **D**emand **C**opious **P**ower **T**han **J**unior **C**ongressman? **T**ough **Q**uestion" (**C**ambrian, **O**rdovician, **S**ilurian, **D**evonian, **C**arboniferous, **P**ermian, **T**riassic, **J**urassic, **C**retaceous, **T**ertiary, **Q**uaternary) **HISTORY OF LIFE OVER GEOLOGIC TIME** **THE FIRST SINGLE-CELLED ORGANISMS** - The earliest direct evidence of life, dating from 3.5 billion years ago, comes from fossilized stromatolites - **Stromatolites** are layered rocks that form when certain prokaryotes bind thin films of sediment together Key events in life's history include the origins of single celled organisms and the colonization of land **PHOTOSYNTHESIS AND THE OXYGEN REVOLUTION** - Most atmospheric oxygen gas (O2) is of biological origin, produced during the *water-splitting* step of photosynthesis - Presence of O2 in the atmosphere implies that bacteria similar to today's ***cyanobacteria*** (oxygen-releasing, photosynthetic bacteria) originated well before 2.7 billion years ago) **"Evolution of Eukaryotic Cells containing chloroplasts"** **THE FIRST EUKARYOTES** - **ENDOSYMBIONT THEORY,** which posits that mitochondria and plastids (a general term for chloroplasts and related organelles) were formerly small prokaryotes that began living within larger cells - **SERIAL ENDOSYMBIOSIS --** supposes that mitochondria evolved before plastids through a sequence of endosymbiotic events **THE ORIGIN OF MULTICELLULARITY** - The appearance of structurally complex eukaryotic cells sparked the evolution of greater morphological diversity than was possible for the simpler prokaryotic cells **THE EARLIEST MULTICELLULAR EUKARYOTES** - The oldest known fossils of multicellular eukaryotes are of relatively small algae that lived about 1.2 billion years ago - **Ediacaran biota**, were of soft-bodied organisms -- some over 1 m long that lived from 575 to 535 million years ago **THE COLONIZATION OF LAND** - The gradual evolutionary venture out of aquatic environments was associated with adaptations that made it possible to reproduce on land and that helped prevent dehydration - Land plants with vascular system -- small plants -- diversified plants - *Plants colonized land in the company of fungi* - *Arthropods & Tetrapods --* the most widespread and diverse land animals (particuarly insects and spiders) **THE CAMBRIAN EXPLOSION** - **CAMBRIAN EXPLOSION --** appearance of many present-day animal phyla fossils in the Cambrian period Question: Why were multicellular eukaryotes limited in size and diversity until the late Proterozoic? - Severe ice ages occurred from 750 to 580 million years ago. "Snowball Earth" [The rise and fall of groups of organisms] is related to the speciation and extinction rates of its member species. Such changes in the fates of groups of organisms have been influenced by large-scale processes such as plate tectonics, mass extinctions, and adaptive radiations **PLATE TECTONICS** - **Plate Tectonics Theory --** the continents are part of great plates of Earth's crust that essentially float on the hot, underlying portion of the mantle - **Continental Drift-** movements of plates over time (few centimeters per year) ***Consequences of Continental Drift*** - Alters the habitats in which organisms live - Climate change that results when a continent shifts its location - Promotes allopatric speciation on a grand scale - Helps explain puzzles about the geographic distribution of extinct organisms **MASS EXTINCTIONS -** When large numbers of species become extinct throughout Earth **(THE "BIG FIVE") MASS EXTINCITON EVENTS** 1. **PERMIAN (251 million years ago)** - claimed about 96% of marine animal species and drastically altered life in the ocean. Terrestrial life was also affected - Volcanism 2. **CRETACEOUS (65.5 million years ago)** - extinguished more than half of all marine species and eliminated many families of terrestrial plants and animals, including all dinosaurs (except birds) **ADAPTIVE RADIATIONS --** is the periods of evolutionary change in which groups of organisms form many new species whose adaptations allow them to fill different ecological roles, or niches in their communities 1. **WORLDWIDE ADAPTVIE RADIATIONS** 2. **REGIONAL ADAPTIVE RADIATIONS** \- Is a Sixth Mass Extinction Under Way? - Major changes in the body form can result from changes in the sequences and regulation of developmental gene **EFFECTS OF DEVELOPMENTAL GENES** 1. **Changes in Rate and Timing Heterochrony** - An organism's shape depends in part on the relative growth rates of different body parts during development - Heterochrony can also alter the timing of reproductive development relative to the development or reproductive organs - If reproductive organ development accelerates compared to other organs, the sexually mature stage of a species may retain body features that were juvenile structures in an ancestral species, a condition called **paedomorphosis** (from the Greek *paedos*, of a child, and *morphosis,* formation) 2. **Changes in Spatial Pattern --** alterations in genes that control the placement and spatial organization of body parts - **Homeotic gene** - **Hox gene -** products of one class of Homeotic gene **THE EVOLUTION OF DEVELOPMENT** - Adaptive evolution of both new and existing genes may have played a key role in shaping the great diversity of life 1. **CHANGES IN GENES --** New developmental genes arising after gene duplication events very likely facilitated the origin of novel morphological forms **Adaptive Radiations** - Is the periods of evolutionary change in which groups of organisms form many new species whose adaptations allow them to fill different ecological roles, or niches, in their communities. 1. **Worldwide Adaptive Radiations** 2. **Regional Adaptive Radiations → **occurred over more limited geographic areas Is a sixth Mass Extinction Under Way? - Major changes in the body form can result from changes in the sequences and regulation of developmental gene. **Effects of Developmental Gene** 1. **Changes in Rate and Timing--- heterochrony** - If the reproductive organ development accelerates compared to other organs, the sexually mature stage of a species may retain body features that were juvenile structures in an ancestral species, a condition called **paedomorphosis** (from the Greek *paedos*, of a child, and *morphosis*, formation). 2. **Changes in Spatial Pattern** - Alterations in genes that control the placement and spatial organization of body parts. - **Homeotic gene → Hox gene →** products of one class of Homeotic gene **The Evolution of Development** - Adaptive evolution of both new and existing genes may have played a key role in shaping the great diversity of life. 1. **Changes in Genes** - New developmental genes arising after gene duplication events very likely facilitated the origin of novel morphological forms. - **Ubx gene** 2. **CHANES IN GENE REGULATION -** changes in nucleotide sequence or regulation of developmental genes can result in morphological changes that harm organism - The developmental gene, ***Pitx1,*** was known to influence whether stickleback fish have ventral spines **\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\--** **ONYMACRIS UNGUICULARIS** Coastal Namib Dessert of Southwestern Africa Three key observations about life: - The striking ways in which organisms are suited for life in their environments - The many shared characteristics (unity) of life - The rich diversity of life **CHARLES DARWIN** - The Origin of Species - Evolution as "descent with modification" - A change in the genetic composition of the population from generation to generation - "Life's endless forms and most beautiful" - Argued that classification **sh*ould be based on evolutionary relationships*** - Darwin drew from the work of scientists studying fossils: - **George Cuvier** - **James Hutton** - **Charles Lyell** - Darwin agreed that if geologic change results from slow, continuous actions rather than sudden events, then Earth must be much older than the widely accepted age of a few thousand years - Darwin was able to apply the idea of gradual change to biological evolution - Born in Shrewsbury, in western England - Even as a boy, he had a consuming interest in nature - Went to medical school in Edinburgh - He quite medical school and enrolled at Cambridge University intending to become a clergyman - ***The Origin of Species*** - Darwin collected evidence that descent with modification by natural selection explains the three broad observations about nature: 1. The unity of life -- organisms share many characteristics 2. The diversity of life -- result of diverse modification throughout time 3. The match between organisms and their environments **IMPORTANT DATES TO REMEMBER** - **1795 -** Hutton proposes his principle of gradualism - **1798 -** Malthus publishes "Essay on the Principle of Population" - **1809 --** Lamarck publishes his hypothesis of evolution **-** Charles Darwin is born - **1812 --** Cuvier publishes his extensive studies of vertebrate fossils - **1830 --** Lyell publishes "Principles of Geology" - **1831 -- 1836 --** Darwin travels around the world on HMS Beagle - **1844 --** Darwin writes his essay on descent with modification - **1858 --** While studying species in the Malay Archipelago, Wallace sends Darwin his hypothesis of natural selection - **1859 --** *On the Origin of Species* is published - **19^th^ century -** it was generally thought that species had remained unchanged since their creation ***The Voyage of the Beagle*** - Darwin spent most of his time on shore, observing and collecting thousands of South American plants and animals - He noted the characteristics of plants and animals that made them well suited to such diverse environments as the humid jungles of Brazil, the expansive grasslands of Argentina, and the towering peaks of the Andes - Darwin hypothesized that the Galapagos had been colonized by organisms that had strayed from South America and them diversified, giving rise to new species on the various islands - Darwin observed many examples of **adaptions --** inherited characteristics of organisms that enhance their survival and reproduction in specific environments - **NATURAL SELECTION --** a process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than other individuals because of those traits **VIEW OF EVOLUTION** 1. **A pattern --** pattern of evolutionary change is revealed by **data** from a range of scientific disciplines, including biology, geology, physics, and chemistry 2. **A process -- process** of evolution consists of the mechanisms that produce the observed pattern of change **ARISTOTLE (384 -- 322 BCE)** - Viewed species as fixed - **Scala Naturae - "scale of nature"** - Life form could be arranged on a ladder or scale of increasing complexity **CAROLUS LINNAEUS (1707 -- 1778)** - Swedish physician and botanist - "**For the greater glory of God"** - Developed the two-part or binomial format of naming species (Homo Sapiens for humans) - Adopted the **nested classification system,** grouping similar species into increasingly general categories **GEORGE CUVIER (1769 -- 1832)** - French scientist - Developed "**Paleontology" (**the study of fossils**)** - He opposed the idea of evolution - **Catastrophism --** is the principle that events in the past occurred suddenly and were caused by mechanisms different from those operating in the present **JAMES HUTTON (1726 -- 1797)** - Scottish geologist - Proposed the Earth's geologic features could be explained by gradual mechanisms still operating today **CHARLES LYELL (1797 -- 1875)** - Incorporated Hutton's thinking into his principle of **uniformitarianism** which stated that mechanisms of change are constant over time **JEAN-BAPTISTE DE LAMARCK (1744 -- 1829)** - Proposed the **Lamarck's Hypothesis of Evolution** - Lamarck's Hypothesis of Evolution is a mechanism of *how life changes over time* - Lamarck published his hypothesis in 1809, the year Darwin was born - **Two principles:** a. **USE AND DISUSE --** the idea that parts of the body that are used extensively become larger and stronger, while those that are not used deteriorate b. **INHERITANCE OF ACQUIRED CHARACTERISTICS --** stated that an organism could pass these modifications to its offspring - Lamarck also thought that evolution happens because organisms have an innate drive to become more complex 2. **Changes in Gene Regulation** - Changes in the nucleotide sequence or regulation of developmental genes can results in morphological changes that harm the organism. - The developmental gene, **Pitx 1** was known to influence whether stickleback fish have ventral spines How do you think a population of organisms changes over time? **POPULATION** - A **POPULATION** refers to a group of individuals that belong to a species - This lives in an area and interbreed with one another to form offspring **CONCEPT OF EVOLUTION** **Evolution** is a process where the transformation of species happens through time - The ancestor, known as the founder species, diverged into two lineages (Example: Amakihi and Nihos finch are the descendants and the products of speciation - PARENTS pass on heritable traits to their OFFSPRING - It is the genetic changes in populations that are passed on to successive generations over time **DIFFERENCE BETWEEN NATURAL AND ARTIFICIAL SELECTION** **Mechanisms of Evolution** +-----------------------+-----------------------+-----------------------+ | **NATURAL SELECTION** | | | +=======================+=======================+=======================+ | **DEFINITION** | **IMPORTANCE** | **CHANGES IN | | | | POPULATION** | +-----------------------+-----------------------+-----------------------+ | - Selected traits | - A classic example | - **Overproduction | | through natural | is the finches | -** | | selection are the | that have | every species | | ones that deal | different beak | tends to produce | | with changes in | shapes and sizes | more individuals | | the environment | depending on the | than can survive | | wherein they | type of food that | to maturity | | allow organisms | is available in | | | to **capture food | their habitat | - **Variation -** | | efficiently, or | | the individuals | | escape predators | | of a population | | swiftly** | | have many | | | | characteristics | | - These changes | | that differ | | through natural | | | | selection leads | | - **Selection -** | | to higher chance | | some individuals | | of survival of | | survive longer | | the species in | | and reproduce | | the community | | more than others | | | | do | | | | | | | | - **Adaptation --** | | | | the traits of | | | | those individuals | | | | that survive and | | | | reproduce will | | | | become more | | | | common in a | | | | population | +-----------------------+-----------------------+-----------------------+ +-----------------------+-----------------------+-----------------------+ | **ARTIFICIAL | | | | SELECTION** | | | +=======================+=======================+=======================+ | **DEFINITION** | **IMPORTANCE** | **CHANGES IN | | | | POPULATION** | +-----------------------+-----------------------+-----------------------+ | - **Artificial | - Artificial | - Example: | | Selection** is | selection served | Evolution of pig | | the process of | as the primary | through series of | | selecting plants | principle behind | domestication | | or animal | **selective | breeding | | individuals for | breeding** used | | | breeding. This | for producing new | | | principle was | varieties of | | | developed from | plants and | | | our understanding | animals | | | of heritable | | | | traits. | - Through selective | | | | breeding, there | | | | is an increase in | | | | chances of | | | | achieving | | | | **desirable | | | | traits** that | | | | could lead to | | | | **higher | | | | production** in | | | | any plant or | | | | animal derived | | | | products | | | | | | | | - Example: | | | | Varieties in bean | | | | products achieve | | | | through selective | | | | breeding | | +-----------------------+-----------------------+-----------------------+ SAMPLE SITUATIONS: +-----------------------------------+-----------------------------------+ | **OBSERVATION \#1** | **INFERENCE \#1** | +===================================+===================================+ | - Members of a population often | - Individuals whose inherited | | vary in their inherited | traits give them a higher | | traits | probability of surviving and | | | reproducing in a given | | | environment tend to leave | | | more offspring than other | | | individuals | +-----------------------------------+-----------------------------------+ | **OBSERVATION \# 2** | **INFERENCE \# 2** | +-----------------------------------+-----------------------------------+ | - All species can produce more | - This unequal ability of | | offspring than their | individuals to survive and | | environment can support, and | reproduce will lead to the | | many of these offspring fail | accumulation of favorable | | to survive and reproduce | traits in the population over | | | generations | +-----------------------------------+-----------------------------------+ - An organism's heritable traits can influence not only its own performance, but also how well its offspring cope with environmental challenges **How rapidly do such changes occur?** - *Over time,* natural selection can increase the match between organisms and their environment - If an environment changes, or if individuals move to a new environment, natural selection may result in *adaptation to these new conditions,* sometimes giving rise to new species **REMEMBER:** - Individuals do not evolve -- it is the POPULATION that evolves over time - Natural selection can amplify or diminish only those heritable traits that differ among the individuals in a population - Environmental factors vary from place to place and over time **Four types of data that document the pattern of evolution and illuminate the processes by which it occurs** 1. **Direct observations of evolution** - Natural selection in response to introduced plant species - Examples: The Evolution of Drug-Resistant Bacteria, Shorter beak lengths in the population that feed in goldenrain tree 2. **Homology** - A second type of evidence for evolution comes from analyzing similarities among different organisms - Similarity resulting from common ancestry is known as **homology** a. Anatomical and Molecular Homologies -- at a molecular level all forms of life use the same genetic language of DNA and RNA, and the genetic code is essentially universal - Vestigial Structures - remnants of features that served a function in the organism's ancestors b. Homologies and "Tree Thinking" - Homologous characteristics form a nested pattern: - All life shares the deepest layer, and each successive smaller group adds its own homologies to those it shares with larger groups - **EVOLUTIONARY TREE --** a diagram that reflects evolutionary relationships among groups of organisms c. CONVERGENT EVOLUTION -- the independent evolution of similar features in different lineages - ANALOGOUS -- **ANALOGOUS FEATURES** share ***similar function***, but not common ancestry, while homologous features share common ancestry, but not necessarily similar function. 3. **The Fossil Record** - A third type of evidence for evolution comes from fossils - The fossil record documents the pattern of evolution, showing that past organisms differed from present-day organisms and that many species have become extinct. Fossils also show the evolutionary changes that have occurred in various groups of organisms. 4. **Biogeography** - A fourth type of evidence for evolution comes from the geographic distribution of species