BIOL Exam 4 PDF

Lesson 18: Biotechnology 18.1-Selective Breeding vs Gene Editing 1.​ Contrast the use of selective breeding with gene editing to manipulate an organism’s genome Selective breeding (artificial selection) -​ Traditional method of genetic manipulation through controlled mating within the...

Lesson 18: Biotechnology 18.1-Selective Breeding vs Gene Editing 1.​ Contrast the use of selective breeding with gene editing to manipulate an organism’s genome Selective breeding (artificial selection) -​ Traditional method of genetic manipulation through controlled mating within the same species -​ Breeding individuals with desirable traits over multiple generations to achieve a consistent expression of those traits -​ Driving evolution to create less variability -​ Examples -​ Animal breeding: breeding dogs for coat color, size, etc. -​ Crop domestication: selecting crops with favorable traits (larger fruit size, etc.) -​ Limitations -​ Time-consuming: requires many generations for consistent results -​ Reduced Genetic Diversity: limited gene pool can increase susceptibility to disease -​ Unintended Harmful Traits: many inadvertently propagate negative traits (ex. Deafness in Dalmatians) Gene Editing -​ Modern approach using biotechnology to directly modify DNA of an organism -​ Altering DNA precisely by adding, removing, or modifying genetic sequences in a single-generation -​ Examples -​ Molecular cloning -​ CRISPR-Cas9 system -​ Advantages -​ Speed and precision: introduces specific traits quickly without multi-generational breeding -​ Cross-species gene introduction: enables insertion of genes from different species (ex. Adding drought resistance to plants) -​ Maintains genetic diversity: reduces the need for closely related breeding 2.​ Discuss how endogenous DNA replication and repair enzymes may be used in gene editing Endogenous: growing or originating from within an organism Scientists utilize natural DNA replication and repair enzymes to edit DNA in the lab. These enzymes, which function naturally in cells, can be isolated and repurposed to precisely manipulate genetic material  -​ Restriction enzymes/endonucleases -​ Found in bacteria; act as molecular scissors -​ Cut DNA at specific sequences, allowing precise DNA modifications -​ Used to cut and insert genetic sequences in the lab -​ Single-stranded ends generated by the same restriction enzyme are complementary to each other so they can be joined together by DNA ligase -​ DNA engineered in this way is called recombinant DNA -​ CRISPR-Cas9 System -​ Bacterial adaptive immune system against viruses -​ Targeted DNA cutting system, guided to specific DNA locations -​ Allows high-precision gene editing by cutting DNA at targeted sites -​ DNA Ligase -​ Found naturally in cells during DNA repair and replication -​ Joins DNA fragments by sealing gaps in the DNA backbone -​ Used to integrate new DNA sequences into existing DNA, completing edits seamlessly -​ DNA Polymerase -​ Essential for natural DNA replication -​ Elongates DNA strands, allowing synthesis of new DNA -​ Used in PCR to amplify DNA samples, producing millions of copies for cloning and sequencing 18.2-Molecular Cloning 3.​ Summarize the steps of molecular cloning Clone: genetically identical copy Molecular cloning: isolation of a specific DNA sequence and insertion into a replicating vector -​ Using restriction enzymes, we can encourage the host to transform…take up the DNA. Now host has recombinant DNA -​ If the host successfully reproduces you are cloning vast quantities of that gene and it can produce desirable products 1.​ Amplification via PCR a.​ The gene of interest is amplified using PCR to create many copies 2.​ Cutting with restriction enzymes a.​ Amplified DNA is cut with restriction enzymes at precise sites to preserve the gene’s function b.​ Sticky ends created by these enzymes help with reassembly 3.​ Gel electrophoresis for separation a.​ DNA fragments are separated by size to isolate the target gene 4.​ Inserting into a plasmid a.​ Isolated gene is inserted into a plasmid cut with the same restriction enzyme b.​ Sticky ends of the gene and plasmid allow them to bind, and ligase seals the DNA backbone, forming recombinant DNA 5.​ Transformation a.​ The recombinant plasmid is introduced into the host organism b.​ Successful transformation can by verified by gene expression 4.​ Explain how PCR allows us to amplify DNA -​ Mimics natural DNA replication to make millions of copies of a DNA fragment 1.​ Denaturation a.​ DNA is heated to unwind all strands b.​ Unlike cellular replication that unwinds in sections via helicase 2.​ Annealing a.​ Temperature is lowered so that synthetic primers, designed to border the gene of interest, can bind to the DNA 3.​ Elongation a.​ Taq DNA polymerase synthesizes new DNA strands by adding nucleotides b.​ Creates multiple DNA copies through repeated cycles 5.​ Explain how DNA molecules may be separated by gel electrophoresis -​ Used to separate DNA fragments by size, allowing for identification of specific DNA pieces 1.​ Setup a.​ DNA fragments are loaded into wells in a gel and subjected to an electric current 2.​ Movement of DNA a.​ Negatively charged DNA migrates toward the positive electrode b.​ Smaller DNA fragments move faster and farther than larger ones 3.​ Visualization a.​ Fluorescent dye binds to DNA b.​ Allows for visualization of distinct bands representing different fragment sizes 4.​ Identifying DNA fragments a.​ Location of bands is compared to a DNA ladder (known fragment sizes) to locate the target gene fragment b.​ Target gene fragment can then be extracted for further use 18.3-CRISPR and Impacts 6. Explain how the CRISPR/Cas9 system can be used in gene editing Stands for—-Clustered regularly interspaced short palindromic (forward and backwards means nucleotides read the same forwards and backwards) repeats How it works -​ CRISPR-Cas9 was discovered in bacteria, where it acts as an immune system to fight off viruses -​ Bacteria create a CRISPR library by incorporating viral DNA fragments into their own DNA -​ This means that if the bacteria are reinfected by the same virus, the CRISPR sequences are transcribed into guide RNA, which directs the Cas9 protein to cut the viral DNA -​ Prevents the virus from causing harm -​ Scientists can use this system to target specific parts of an organism’s genome -​ By designing guide RNA that matches the DNA region they want to edit -​ Cas9 protein is directed by this guide RNA and can make precise cuts in the DNA at the specified location Gene Editing options 1.​ Gene deletion a.​ Unwanted DNA sequences can be cut out b.​ Cell will naturally seal the DNA using DNA ligase 2.​ Gene insertion/repair a.​ Introduce a new DNA sequence along with the guide RNA and Cas9 b.​ Once the Cas9 makes the cut, the cell incorporates the new DNA sequence into the genome c.​ Allows scientists to repair mutated genes or introduce new genes Applications -​ Medicine: gene therapy to correct genetic diseases such as sickle-cell anemia and prevent viral infections like HIV by editing specific immune cells 7. Describe the potential impacts of gene editing to society and the planet 1.​ Medical Advancements a.​ Curing genetic disease i.​ Correcting or protecting cells from specific genetic defects ii.​ Could revolutionze treatment b.​ Medically important proteins can be produced in bacteria (and animals) i.​ Human insulin ii.​ Atrial peptides (heart attack research)  iii.​ Transgenic animals (mice) have been created to study Alzheimers disease c.​ Ethical and Accesibilty concerns i.​ Costly ii.​ Potential unknown risks, especially if applied to the germline (zygote) 2.​ Environment and Ecological Impacts a.​ GMO Crops and Resistance Evolution i.​ Gene edited crops like glyphosate-resistant soy and corn have enabled more efficient weed control ii.​ Weeds have evolved resistance to herbicides due to repeated exposure iii.​ Gene flow between GMO crops and wild relatives can spread resistance traits to wild plants, affecting natural ecosystems and biodiversity iv.​ Bt crops (Bt toxin from Bacillus thuringiensis) 1.​ Insecticidal proteins have been transferred into crop plants to make them pest-resistant 2.​ Use of Bt maize is the second most common GM crop globally b.​ Impact on Ecosystems i.​ Eliminating disease-carrying species such as Anopheles mosquitoes that carry malaria ii.​ This could disrupt the ecosystem though because each organism plays a specific role in the food web 3.​ Transgenic animals a.​ An animal that has had a foreign gene deliberately inserted into its genome, allowing it to express a new trait that is not naturally present in its species 4.​ Societal and Evolutionary Considerations a.​ Germline Editing and Evolution i.​ Editing germline cells means changes will pass to future generations ii.​ This would alter human evolution iii.​ “Designer babies”  b.​ Impact on Biodiversity i.​ Editing the alleles of entire populations could influence genetic diversity and adaptability ii.​ Impacts species’ ability to evolve in response to environmental changes c.​ Regulatory and Ethical Frameworks i.​ Updating laws and ethical guidelines Lesson 19: Genomics Genomics: the study of an orgnanism’s genome, or complete set of DNA 19.1: Mapping Genomes 1.​ Identify the major components of genomics -​ Mapping: creating various levels of maps (genetic and physical maps) to identify the locations of genes and other elements within the genome -​ Sequencing: determining the exact sequence of nucleotide bases (A, T, C, G) in a DNA molecule, allowing for a highly detailed view of the genome -​ Annotating: interpreting and labeling sequences to understand the function and characteristics of genes and other regions within the genome -​ Analyzing: using computational and biological methods to study genome structure, function, and relationships between species  2.​ Distinguish between a genetic map and a physical map, and provide examples of each Genetic Map -​ Definition: shows the relative positions of genes or genetic markers based on… -​ recombination frequency: likelihood/rate at which genetic recombination (crossing over) occurs between two genes during meiosis -​ linkage analysis: identifying the approximate location of genes/traits on chromosomes -​ provide relative, rather than absolute, locations of genes or markers -​ Example: a map showing gene locations based on linkage groups from the recombination data -​ Abstract and provide gene locations that are relative to one another Physical Map -​ Definition: provides precise, absolute positions of genetic markers within the genome, often down to the nucleotide level -​ Resolution: offer a higher resolution than the genetic maps, pinpointing the exact location of landmarks within the DNA -​ Measure distances to cutting sites and other landmarks -​ Examples -​ Restriction map: created by digesting DNA with restriction enzymes, these maps identify specific cut sites within the genome -​ Sequence Tagged Site (STS) Map: uses unique DNA sequences that are amplified via PCR to piece together genome fragments and organize them into a contiguous sequence (contig) -​ Small stretch of DNA that is unique in the genome -​ Boundary is defined by PCR primers -​ Identified using any DNA as a template -​ Provide a scaffold for assembling genome sequences -​ Chromosome maps (staining patterns on chromosomes) 19.2: Genome Sequencing 1.​ Apply the principles of DNA sequencing to automated and next-generation sequencing methods (Dideoxy) Automated Sequencing -​ Based on Sanger sequencing principles, which utilize dideoxynucleotides as chain terminators -​ Dideoxynucleotides (ddNTPs) lack a 3’ hydroxyl group which stops DNA synthesis when they are incorporated -​ Four different dideoxynucleotides (each labeled with a distinct fluorescent dye) are incorporated into the growing DNA strand at random positions -​ Electrophoresis is used to separate DNA fragments in a capillary tube -​ Smaller fragments migrate faster than larger ones -​ As each fragment passes through the capillary, a laser excites the fluorescent tags and a photo-detector identifies the colors associated with each base, allowing the sequence to be determined 1.​ Start with strand of unknown sequence 2.​ Amplify using PCR 3.​ Incorporate dideoxynucleotides a.​ Labled with a fluorescent marker for A, T, C, and G 4.​ Fragments separated by electrophoresis a.​ Smallest fragments (5’ end) migrate fastest 5.​ Utilize laser and photodetector to identify base Next-Generation Sequencing (NGS) -​ Can handle much larger DNA samples more efficiently than automated sequencing -​ DNA is fragmented -​ Single-stranded fragments are attached to a solid surface with adapters -​ Through PCR, multiple copies of each fragment are created, ensuring reliable sequencing coverage -​ Special reversible chain-terminating nucleotides are used -​ When incorporated, they fluoresce and are detected by a laser -​ Unlike Sanger sequencing, they can be reversed back to normal nucleotides -​ Enables the sequencing of each fragment multiple times in succession 2.​ Differentiate between clone-contig and shotgun sequencing approaches Clone-Contig Method -​ Genome is broken into large DNA fragments called clones -​ Clones are arranged in order based on physical landmarks such as sequence tagged sites (STS)  -​ Large clones are further fragmented into smaller sequences for sequencing -​ After sequencing, the fragments are assembled to form the sequence for each clone -​ Then these sequences are combined into a larger contiguous sequence (or contig) for the genome -​ Advantage: provides highly ordered structured approach to sequencing and can ensure accurate alignment of large genome regions Shotgun Sequencing Method -​ Does not require prior mapping -​ Entire genome is randomly fragmented into small, manageable pieces for sequencing -​ Computer software is used to align the overlapping regions of the fragments, reconstructing the full genome sequence -​ Advantage: faster and doesn’t rely on physical maps, making it suitable for projects that prioritize speed and have access to powerful computational resources -​ There is a lack of uniqueness between sequenced fragments Both of these methods were crucial for the Human Genome Project, where they were combined to create an accurate and detailed sequence of the human genome -​ Found fewer genes than expected -​ The complexity of an organism is not necessarily related to its gene number 19.3: Genome Annotation 1.​ Explain the importance of genome annotation Genome Annotation: the process of identifying and labeling elements within a DNA sequence, providing insights into gene function and genome structure -​ Functional Identification -​ Coding Regions: help locate genes that produce proteins or functional RNAs (eg tRNA, rRNA) essential for cellular processes -​ Non-coding Regions: identifies non-coding areas, which may have regulatory or structural functions -​ Gene Function Insights -​ BLAST Tool: compares new sequences to known genes in a database to predict functions -​ Functional Discovery: finding similar sequences allows scientists to infer functions of previously unknown genes -​ Categorizing DNA -​ Annotations help distinguish between DNA that codes for proteins and non-coding regions with other functions -​ Importance in Research -​ Annotated sequences are stored in accessible databases (like GenBank), which serve as valuable resources for research worldwide 2.​ Discuss possible roles of non-coding DNA Non-coding DNA: DNA that does not code for proteins and can account for a large portion of an organism’s genome (up to 99% in humans) Key Roles: -​ Gene Regulation -​ Regulatory Elements: regions that control gene expression, influencing when and how genes are turned on or off  -​ Non-coding RNA: certain non-coding RNA molecules (eg miRNA) play roles in regulating gene activity by interacting with mRNA or chromatin -​ Structural Functions -​ Chromosome stability: structural DNA (eg telomeres and centromeres) helps stabilize chromosomes, especially during cell division -​ Genomic Integrity and Evolution -​ Transposable Elements: “Jumping genes” can move within the genome, sometimes influencing gene function or contributing to genetic diversity and evolution -​ Evolutionary Remnants -​ Pseudogenes: remnants of once-functional genes that no longer produce proteins but may provide evolutionary clues -​ ENCODE Project Findings -​ Biological Activity: it identified that up to 80% of the genome shows some form of “biological activity”, such as DNA methylation or chromatin modification -​ Controversy on function: it defines biologically active regions as “functional”, but some researchers argue that “function” should only apply to regions that provide a selective advantage 19.4: Genome Analysis and Application 1.​ Differentiate between comparative genomics, functional genomics, and proteomics Comparative genomics: study of similarities and differences between the genomes of different species. It uses information from one genome to infer information about another -​ Key Concept: Synteny -​ the conserved arrangement of segments of DNA across related genomes -​ By examining syntenous regions, researchers can predict gene function, locate similar genes, and study evolutionary relationships -​ Applications -​ Understanding gene function across species -​ Identifying relationships by examining conserved DNA segments -​ Supporting agricultural research by identifying genes responsible for desirable traits in related plant species -​ Comparing genomes of rice, corn, and wheat Functional Genomics: focuses on understanding the connection between the genome (genotype) and the organism’s traits (phenotype). It aims to identify which genes are active in particular cells, under certain conditions, or at specific developmental stages -​ Key Areas -​ Transcriptome -​ Study of all RNA molecules transcribed from the genome -​ Techniques used:  -​ DNA microarrays: which genes are being expressed in a particular location or time. Provide insight into the function of genes. Must create a microarray chip with “known” genes -​ RNA-seq: use next gen sequencing technology to capture ALL mRNA created -​ Proteome -​ Study of all proteins produced by the genome -​ Focus on protein abundance, structure, and function -​ Protein interactions -​ Examines how proteins interact within cells -​ Helps to understand complex cellular processes -​ Techniques -​ DNA microarrays -​ Allow researchers to analyze gene expression for many genes simultaneously -​ Color-coded spots on the microarray show which genes are turned on in specific conditions -​ RNA-Seq -​ Comprehensive profile of gene expression -​ Captures all RNA transcripts rather than just a set of predicted genes Proteomics: study of the entire set of proteins produced by a genome. It involves analyzing protein expression, modifications, and interactions to understand how proteins contribute to cellular functions and organismal traits -​ Challenges -​ Alternative splicing and post-transcriptional modifications make it hard to predict proteins directly from DNA sequences -​ Key Techniques -​ Mass spectrometry (Mass-Spec) -​ Measures the mass-to-charge ratio of peptides (protein fragments) to identify proteins -​ Protein microarrays -​ Similar to DNA microarrays but uses antibodies to detect specific proteins in a sample -​ Bioinformatics in Proteomics -​ Bioinformatics tools help manage large proteomics datasets, predict protein structures, and analyze protein-protein interactions  2.​ Discuss some applications of genomics 1.​ Synthetic biology a.​ Engineering entire genomes for desired traits b.​ Ex.: creating synthetic organisms to enhance biofuel production or clean up environmental pollutants 2.​ Medical Diagnostics a.​ Identification of genes associated with genetic disorders b.​ Personalized medicine: treatment is tailored based on the patient’s genetic profile 3.​ Forensic Science a.​ Genomic sequencing and STS mapping can identify remains, trace ancestry, and even track pathogens used in bioterrorism 4.​ Agriculture a.​ Comparative genomics can improve crop yields, disease resistance, and nutritional quality by identifying desirable traits across plant species 5.​ Disease Reseach and Public Health a.​ Studying genomes of pathogens (like SARS-CoV-2) to understand viral evolution and develop vaccines 6.​ Intellectual property and ethics a.​ Debates on gene ownership b.​ Ex. in 2013 the Supreme Court ruled that natural genes cannot be patented, although synthetic modifications may be  Lesson 20 20.1: Development and Model Organisms 1.​ Define “development” and identify the primary mechanism responsible for development. -​ Development: the process by which a single-celled organism (fertilized egg/zygote) undergoes a series of complex, organized changes to eventually become a fully formed multicellular adult organism -​ The primary mechanism responsible for development is regulated changes in gene expression over time -​ Allows cells to follow distinct developmental pathways that contribute to the formation of different cell types, tissues, and organs -​ The 4 Processes for regulated change in gene expression 1.​ Cell division: multiplication of cells 2.​ Cell differentiation: cells developing specific identities or roles (skin cells, neurons, etc.) 3.​ Pattern formation: organized spatial arrangement of cells to create body structures 4.​ Morphogenesis: shaping the structure of the organism 2.​ Provide examples of model organisms used to study animal development -​ Model organisms: important in developmental biology because they offer simpler systems to understand general developmental mechanisms -​ Examples: C. elegans a.​ Roundworm b.​ Used to study cell division and cell fate determination c.​ First organism with a fully mapped cell lineage i.​ Understand how individual cells adopt specific roles within the organism Drosophila melanogaster d.​ Fruit fly e.​ Used to study pattern formation in embryos f.​ Observe the spatial expression patterns of genes that organize body regions g.​ Gene expression drives development and influences many structures in the organism Xenopus laevis h.​ African clawed frog i.​ Used to study morphogenesis and early cell divisions in the embryo j.​ Great for examining how body forms develop and change i.​ Large visible eggs ii.​ Especially during stages of transition from tadpole to adult frog 20.2: Cell Division and Differentiation 3. Describe how cell division and differentiation contribute to animal development Cell Division -​ Foundational process allowing the zygote to develop into a multicellular organism -​ In early development -​ cell division is rapid -​ Undergoes a process called “cell cleavage” -​ Zygote’s cytoplasm divides without any cell growth in between divisions -​ Ensures quick increase in cell number -​ Later in development -​ Cell division slows down -​ G1 and G2 phases are now present during the cell cycle -​ Allows for cell growth Cell Differentiation -​ Creates specialized cells from stem cells allowing for the formation of diverse cell types with specific roles in the organism -​ Depends on changes in gene expression within cells -​ Gradually restricts their potential cell fates -​ Differentiated cells follow specific “cell lineages” -​ Each step makes the cell’s future roles more specific and specialized 4. Describe the progressive nature of cell differentiation -​ Gradual, step-by-step process (not instantaneous) -​ Stem cells progressively become more specialized  -​ Cells undergo several divisions with each step slightly limiting their potential fates until they adopt a specific function (it's like choosing a major in college and going further down that path) 1.​ Cells start as stem cells with “high potency” 2.​ Gene expression changes incrementally and cells are gradually restricted, making each “descendant cell” closer to a final, specialized state 3.​ Cells that share a lineage (originate from the same stem cell) are subject to similar differentiation pathways 5. Distinguish between the different types of stem cells 1.​ Totipotent: capable of forming all types of tissues, including extraembryonic tissues (such as the placenta) a.​ Found in the zygote and blastomeres have these 2.​ Pluripotent: capable of forming all types of tissues except extraembryonic tissues a.​ Found in the inner cell mass of the blastocyst b.​ Used in research and therapeutic applications (unethical: destroys embryo) 3.​ Multipotent: capable of differentiating into several, but limited types of cells within a particular tissue or organ a.​ Found in adult stem cells 4.​ Unipotent: capable of differentiating into only one specific cell type a.​ Example: spermatogonia can only produce sperm 20.3: Pattern Formation and Morphogenesis 6. Describe how pattern formation and morphogenesis contribute to animal development Pattern Formation -​ Establishes the body plan (“blueprint”) of the organism -​ Creates distinct spatial regions within the embryo that will become specific body parts -​ Relies on differential gene expression -​ Different genes are activated depending on the cell’s position within the embryo -​ Anterior-posterior -​ Dorsal-ventral -​ left -right -​ Each segment is given a unique identity (ex. Head, hand, etc.) by the expression of specific Hox genes 7. Explain the role of homeobox-containing genes in animal development -​ Hox genes -​ Important for pattern formation 1.​ Segment identity: hox genes are expressed in specific segments of the embryo, directing each segment to develop into a particular body part a.​ Ex: Dfd gene specifies head segment in Drosophila embryos 2.​ Body Plan Organization: ensure organs and appendages form in the correct locations 3.​ Conservation Across Species: highly conserved across species, showing their importance in animal development a.​ Ex: Drosophila and mice have hox genes that control similar developmental processes (mice have multiple copies and Drosophila only has one though)  4.​ Evolutionary Significance: mutations can lead to dramatic changes in the body plan of an organism which can be beneficial for evolution a.​ Ex: segment develops as a different body part like a fly growing legs and not antennae 8. Describe how cell migration, changes in cell shape, and apoptosis contribute to morphogenesis Cell Migration -​ Some cells must move to new locations to contribute to the correct structure and organization of tissues and organs -​ Cells migrate through the extracellular matrix (a network of proteins and carbohydrates) to reach their destinations -​ Important for forming the body structure according to the “blueprint” Changes in Cell Shape -​ Cells alter their shape to fit into specific structural roles -​ Ex: elongating cells can create tissue layers or form the basis for organs  -​ Achieve the specific architectural needs of different body parts Apoptosis -​ Cells are systematically destroyed to sculpt structures or remove unnecessary or damaged cells -​ Ex: Removing cells between developing digits to form fingers and toes 20.4: Nuclear Reprogramming and Cloning 9. Compare and contrast the two main methods of nuclear reprogramming Nuclear Reprogramming: reset the gene expression of a differentiated cell into an undifferentiated, stem cell-like state Somatic Cell Nuclear Transfer (SCNT) Process -​ Nucleus of a differentiated cell (ex. fibroblast) is removed -​ It is inserted into an enucleated oocyte (immature egg cell with no nucleus) -​ The oocyte’s transcription factors reprogram the differentiated nucleus to a stem cell state Outcome -​ Can produce totipotent cells capable of developing into a complete embryo Challenges -​ Low success rate  -​ Difficult to perform successfully on a large scale Direct Reprogramming Process -​ Specific transcription factors associated with stem cell properties are introduced directly into a differentiated cell -​ This reprograms the cells gene expression to a pluripotent state Outcome -​ Produce induced pluripotent stem (iPS) cells -​ These cells cannot develop into an organism by its own but can be used to produce a wide range of cell types Advantage -​ Does not use embryos -​ Simpler than SCNT 10. Differentiate between reproductive and therapeutic cloning and their uses Reproductive cloning Goal: create a genetically identical copy of an entire organism (identical to the donor of the original nucleus) Process -​ SCNT is used to create an embryo that develops and is implanted into a surrogate mother Uses -​ Reproduce animals with desirable traits -​ Preserve endangered or exctinct species Therapeutic Cloning Goal: create patient-specific cells and tissues for medical treatments Process -​ SCNT is used to generate an embryo -​ Embryonic stem cells from the inner cell mass are harvested and cultured :( -​ The pluripotent stem cells can then be directed to develop into specific tissues Uses -​ Produce rejection-free tissues and organs for transplantation -​ Treat autoimmune diseases -​ Replace damaged or diseased tissues in patients Lesson 21 21.1: Evolution and Genetic Variation 1.​ Define evolution. Evolution: the change in the genetic composition of populations over time, specifically through shifts in allele frequencies within populations -​ Evolution occurs at the population level, not within individual organisms -​ Population: a group that includes all members of a species in a given area 2.​ Explain the role of genetic variation in evolution. -​ Source of differences: different alleles (of the same gene) within a population -​ Diverse phenotypes: observable in traits like flower color, morphology, or protein expression -​ Selection and Adaptation: determines how well individuals survive and reproduce in their environment. This influences which alleles are passed on to future generations, driving natural selection  -​ Population-level change: shifts in allele frequencies within a population drives evolution 21.2: Mechanisms of Evolutionary Change 3.​ Describe the four processes that can cause evolutionary change 1. Mutation -​ Definition: change in the base sequence of DNA, creating new alleles and serving as the ultimate source of genetic variation -​ Provide the raw material for evolutionary change by introducing new genetic possibilities into a population -​ Occur very rarely -​ Not the primary driver of changes in allele frequencies 2. Gene Flow -​ Definition: the movement of alleles between populations which can occur through the migration of individuals, the dispersal of seeds or pollen, or the transfer of gametes -​ Introduces new alleles to a population -​ Alters allele frequencies and increases genetic variation within a population -​ Reduce differences between populations by homogenizing their genetic makeup -​ Example -​ Plant populations receiving pollen from a nearby population -​ Animals mating with individuals from other groups 3. Genetic Drift -​ Definition: the random change in allele frequencies due to sampling error, particularly significant in small populations -​ In small populations, chance events can disproportionately affect allele frequencies -​ Over time, genetic drift can result in significant divergence between populations or even the fixation (100% frequency) or loss of alleles -​ Founder Effect -​ Occurs when a few individuals establish a new population -​ They carry only a subset of the genetic variation from the original population, leading to different allele frequencies -​ Example: colonization of islands by a small number of organisms -​ Bottleneck Effect -​ Occurs when a population experiences a drastic reduction in size due to events like natural disasters, disease, or habitat destruction -​ Reduces genetic diversity since only a small fraction of alleles are passed to the next generation -​ Example: northern elephant seals experienced a bottleneck in the 1890s, losing much of their genetic variation 4. Selection -​ Definition: occurs when certain phenotypes have greater reproductive success than others, leading to a change in allele frequencies based on differential survival and reproduction -​ Non-random process that directly links genotype and phenotype with survival and reproduction -​ Over time, this process increases the frequency of advantageous traits in a population, shaping evolutionary change -​ Natural selection -​ Driven by environmental pressures, where traits that enhance survival or reproduction become more common -​ Example: Darwin’s finches with beak shapes adapted to available food sources -​ Artificial selection -​ Humans selectively breed organisms to promote desirable traits 21.3: Natural selection 4.​ Determine the difference between evolution (result) and natural selection (process). Definitions Natural Selection: the process by which certain traits become more or less common in a population due to differences in survival and reproduction among individuals. It acts as one of the mechanisms driving evolutionary change Evolution: the historical record of change in the genetic composition of populations over time. It refers to the outcome, observable as shifts in allele frequencies within a population across generations The relationship between the two Natural Selection: one specific mechanism or cause of evolution Evolution: the broader phenomenon that encompasses all processes that result in changes in allele frequencies (mutation, gene flow, genetic drift, and natural selection) Focus Natural selection: focuses on differential survival and reproduction. Traits that confer higher fitness (ability to survive and reproduce) are passed on more frequently, leading to adaptation -​ Example: a population of moths becoming darker over time due to predation on lighter-colored moths in a soot-covered environment Evolution: focuses on the cumulative genetic changes in a population, whether driven by natural selection or other processes. It reflects the overall record of change -​ Example: the moth population also experiences evolution if a mutation or genetic drift changes allele frequencies without direct selective pressures Intentionality Natural selection: non-random; certain traits are consistently favored due to their contribution to survival and reproduction Evolution: can include random processes (ex. Genetic drift) and non-random processes (ex. selection) Outcomes Natural selection: leads to adaptations—traits that enhance an organism’s ability to survive and reproduce in a specific environment Evolution: reflects broader changes including both adaptive and non-adaptive processes 21.4: Evolutionary Fitness and Detection of Evolutionary Processes 5.​ Define evolutionary evidence Evolutionary evidence: data and observations that demonstrate how organisms have changed over time and the mechanisms driving these changes -​ Fossil records: show transitional forms and patterns of gradual change -​ Comparative anatomy: such as homologous structures indicating shared ancestry -​ Molecular evidence: includes DNA and protein sequence comparisons that reveal genetic similarities and differences between species -​ Direct observations of evolutionary processes: such as changes in allele frequencies in populations over time 6.​ Demonstrate how the operation of evolutionary processes can be detected. 1. Changes in Allele Frequency -​ Observing shifts in the genetic composition of populations over generations -​ As seen in studies like the peppered moth -​ Genetic analysis can quantify changes in allele frequencies to detect processes like natural selection or genetic drift 2. Fitness Differentials -​ Measuring differences in survival and reproductive success among individuals with varying traits  -​ Darker coat color in mice reducing predation risk 3. Patterns of Selection -​ Identifying trends in traits favored by natural selection -​ such as intermediate body sizes in water striders -​ Or dull coloration in guppies exposed to predators 4. Experimental Observations -​ Conducting experiments that simulate environmental changes to observe how populations adapt -​ Guppy coloration experiments in predator and non-predator environments 7.​ Explain how experiments can be used to test evolutionary hypotheses. 1. Lab-Based Studies -​ Controlled environments allow researchers to isolate variables -​ Guppies in predator-free tanks evolved brighter coloration, showing the impact of predation on trait selection 2. Field Experiments -​ Conducted in a natural setting that verifies lab findings -​ Moving guppies from a predator-laden pool to a predator-free pool demonstrates that brighter coloration re-evolved over generations, supporting the hypothesis that predation influences coloration 3. Manipulative Experiments -​ Introducing or removing selective pressures tests how these pressures affect allele frequencies and phenotypes -​ Adding predators to the guppy tanks 4. Historical Reconstruction -​ Studying historical events to provide real-world evidence of evolutionary change and the mechanisms involved -​ The effects of the Industrial Revolution on peppered moths 21.5: Interaction of Evolutionary Forces 8.​ Explain how evolutionary forces interact with each other. Evolutionary forces—mutation, gene flow, genetic drift, natural selection, and non-random mating—do not act in isolation but interact to shape allele frequencies in populations. Here’s how these forces interplay: A. Mutation and Natural Selection ​ Interaction: Mutations introduce new alleles, creating the genetic variation on which natural selection acts. Without mutation, selection would have no new traits to favor or eliminate. ​ Example: A mutation causing antibiotic resistance in bacteria may spread if it provides a selective advantage in environments with antibiotics. B. Gene Flow and Selection ​ Interaction: Gene flow can counteract or enhance selection by introducing alleles from other populations. ○​ Counteracting Selection: Migration may reintroduce less advantageous alleles into a population, slowing the removal of those alleles by selection. ○​ Enhancing Selection: Gene flow can spread beneficial alleles between populations, aiding adaptation. C. Genetic Drift and Selection ​ Interaction: In small populations, genetic drift (random changes in allele frequencies) may overpower selection, allowing harmful alleles to persist or beneficial ones to be lost by chance. ​ Example: A small, isolated population might lose an advantageous allele due to random sampling, even if selection favors it. D. Non-Random Mating and Selection ​ Interaction: Non-random mating (e.g., inbreeding) can increase homozygosity and expose deleterious alleles to selection. ○​ Positive assortative mating (choosing genetically similar mates) can reduce genetic diversity, while negative assortative mating (choosing genetically dissimilar mates) may maintain diversity. E. Mutation and Gene Flow ​ Interaction: Mutations create new alleles, while gene flow can spread these alleles across populations. Together, they contribute to the genetic diversity necessary for evolutionary processes.  9.​ Describe the characteristics of a population that is in Hardy-Weinberg Equilibrium. A. No Mutations in the population (opposite: mutation) ​ No new alleles are introduced into the population through changes in the DNA sequence. B. No Gene Flow between populations (opposite: gene flow) ​ There is no migration of individuals or gametes between populations; allele frequencies remain unchanged due to lack of external influence. C. Random Mating (opposite: nonrandom mating) ​ Mating is random with respect to genotype or phenotype, meaning no preference exists for particular traits. D. Large Population Size (opposite: genetic drift) ​ The population is infinitely large, minimizing the effects of genetic drift and random fluctuations in allele frequencies. E. No Natural Selection (opposite: selection) ​ All individuals have equal chances of survival and reproduction, so no selective pressures favor specific alleles or genotypes. Key Indicators of Hardy-Weinberg Equilibrium ​ Constant Allele Frequencies: Over generations, the allele frequencies remain unchanged. ​ Predictable Genotype Frequencies: Genotype frequencies can be predicted using the equation: p2+2pq+q2=1p^2 + 2pq + q^2 = 1p2+2pq+q2=1 Where: ○​ p2p^2p2: Frequency of homozygous dominant individuals. ○​ 2pq2pq2pq: Frequency of heterozygous individuals. ○​ q2q^2q2: Frequency of homozygous recessive individuals. Significance of Hardy-Weinberg Equilibrium If a population deviates from HWE, it indicates that evolutionary forces are acting on it. Analyzing these deviations can reveal which processes (e.g., selection, drift, migration) are driving the population's evolution. Lesson 22 22.1: Sympatric and Allopatric Speciation 1.​ Compare and contrast sympatric and allopatric species and speciation. Sympatric Species -​ Live in the same geographic location -​ Often use different parts of the habitat or exhibit behavioral differences -​ Typically show morphological differences that allow them to be distinguished -​ Some sympatric species may not differ in appearance -​ But they have distinct behaviors or mating calls Allopatric species -​ Live in different geographic locations, often separated by physical barriers -​ Geographic isolation prevents direct interaction, leading to divergence over time Sympatric Speciation -​ Occurs without geographic isolation -​ Species differentiation arises due to -​ Behavioral isolation (ex. Differences in mating calls or behaviors) -​ Ecological separation (ex. Using different resources within the same area) -​ Example: frogs with distinct mating calls in overlapping habitats Allopatric Speciation -​ Requires geographic separation of populations -​ Speciation occurs due to -​ Physical barriers that prevent gene flow (ex. Rivers and mountains) -​ Evolution of distinct traits in isolated populations 22.2: Mechanisms of Reproductive Isolation 2.​ Describe the mechanisms of reproductive isolation. Reproductive isolation: prevents gene flow between populations and is essential for the process of speciation (two major categories: pre-zygotic and post-zygotic isolation) Pre-zygotic Isolation mechanisms (prevent the formation of a zygote) -​ Ecological Isolation -​ species occupy different habitats within the same area and do not encounter each other frequently -​ Behavioral Isolation -​ Differences in mating behaviors, such as courtship rituals or mating calls, prevent interbreeding -​ Temporal isolation -​ Species have different breeding or growing seasons, preventing them from mating -​ Mechanical isolation -​ Structural differences in reproductive organs prevent successful mating -​ Gametic isolation -​ Gametes of different species cannot fuse due to biochemical incompatibilities Post-zygotic Isolation mechanisms (prevent the production of viable or fertile offspring) -​ Hybrid inviability -​ Hybrid embryos fail to develop properly and do not survive -​ Hybrid infertility  -​ Hybrids develop and survive but are sterile and unable to reproduce 22.3: Species Concepts and Reproductive Isolation 3.​ Distinguish between the biological and phylogenetic species concepts. Biological Species Concept -​ Species: groups of interbreeding natural populations that are reproductively isolated from other groups -​ Criteria: ability to produce fertile offspring -​ Strengths -​ Focuses on reproductive isolation, a key mechanism in speciation -​ Widely applicable to sexually reproducing organisms -​ Weaknesses -​ Sometimes individuals we have classified as separate species WILL mate and produce fertile intermediate offspring (especially plants) -​ It is difficult to apply the principle to geographically isolated populations since interbreeding cannot be observed -​ The concept does not apply to asexual organisms since they do not mate -​ Example -​ Milk snakes: morphologically distinct populations interbreed where they overlap, forming subspecies Phylogenetic Species Concept -​ Species: distinct evolutionary lineages based on phylogenies (evolutionary trees) -​ Criteria: evolutionary independence as inferred from shared traits in phylogenies -​ Strengths -​ Does not require evidence of interbreeding in allpatiric populations  -​ Can be applied to asexual and sexually reproducing organisms -​ Weaknesses -​ May define every small population difference as a new species, even if interbreeding is possible -​ Populations may not form a single clade, complicating classification -​ Example -​ Evolutionary changes in population C separate it from others in a phylogenetic analysis 4.​ Define reinforcement in the context of reproductive isolation. Reinforcement: the process by which natural selection strengthens pre-zygotic isolation mechanisms to prevent hybridization between two populations -​ If hybrid offspring are partially sterile or less fit, natural selection favors individuals that avoid hybridization -​ This ensures that non-hybrid matings are more successful and produce more viable offspring -​ Example: European flycatchers (pied and collared) -​ Morphologically similar in allopatric ranges -​ Evolve distinct colorations to avoid hybridization in sympatric ranges -​ This differentiation improves mate recognition and reduces interbreeding 22.4 Genetic Drift 5.​ Explain the outcome of gene flow between partially isolated populations. -​ Gene Flow occurs if hybrids are fertile -​ This exchange of genetic material can dilute differences between populations, potentially preventing full speciation -​ Reproductive Isolation is completed if hybrids are sterile -​ Populations will remain distinct -​ Surviving fertile hybrids act as bridges for gene exchange (serve as a conduit) -​ Slows or halts divergence between populations 6.​ Explain how genetic drift and natural selection can lead to speciation. -​ Genetic drift introduces differences and natural selection amplifies them -​ Particularly when traits are advantageous or aid reproductive isolation Genetic drift -​ Random changes in allele frequencies can lead to divergence (particularly in small populations) -​ Over time, genetic drift can result in traits that cause reproductive isolation, leading to speciation -​ Mechanisms: founder effect and population bottleneck Natural selection -​ Selective pressures in new environments can favor traits that promote reproductive isolation -​ Example: adaptive change in mating signals -​ In anoles, males develop dewlaps of different colors to adapt to new environments -​ Female preference for specific colors prevents interbreeding, causing speciation 7.​ Describe how geographic isolation impacts a population. -​ Prevention of gene flow -​ Physical barriers separate populations -​ Increases isolation and encourages divergence -​ Allopatric speciation -​ Isolated populations diverge due to -​ Natural selection: adapting to local environment conditions -​ Genetic drift: random allele changes in the population -​ This leads to reproductive isolation and the formation of new species -​ Examples of geographic isolation: Little Paradise Kingfisher -​ Mainland populations have little variation due to continuous gene flow -​ Isolated island populations show significant variation, which may lead to speciation 22.5 Adaptive Raditation 8.​ Describe adaptive radiation. Adaptive Radiation: the evolution of a group of species from a common ancestor, driven by adaptation to different parts of the environment 1.​ A single ancestral species colonizes a new area 2.​ Populations adapt to different ecological niches, leading to allopatric speciation 3.​ The resulting species coexist with reduced competition due to specialization in distinct habitats or resources 9.​ Compare and contrast gradualism and punctuated equilibrium. Gradualism: evolution occurs through small, incremental changes over long periods -​ Slow and continuous -​ Gradual accumulation of changes leads to major differences -​ Transitional forms in fossil records show a smooth, gradual progression -​ Example: evolution of horses -​ Gradual changes in body size and toe reduction over millions of years Punctuated Equilibrium: evolution occurs in short bursts of rapid change, interspersed with periods of stasis -​ Rapid and sporadic -​ Significant evolutionary changes occur in a relatively short time -​ Abrupt appearance of new species in fossil records followed by long periods of stability -​ Example: Cichlid fish in Victoria -​ Bursts of speciation after isolation events  Lesson 24 23.1: Interpreting Phylogenies 1.​ Explain how systematics is used in biology. Systematics: the scientific study of evolutionary relationships among organisms Used to -​ reconstruct the evolutionary history of life -​ organize and classify organisms based on shared ancestry -​ Present hypotheses about evolutionary relationships (using phylogenies) -​ Conserve biodiversity -​ Make predictions of traits, behaviors, or ecological roles of organisms 2.​ Interpret a phylogeny using common systematics vocabulary. Phylogeny; a diagram showing hypotheses of evolutionary relationships -​ Referred to as cladogram when branch lengths are not scaled Node: represents a common ancestor where branches diverge Branch: represents an evolutionary lineage -​ May indicate evolutionary change or time if scaled Clade: a group of species including a common ancestor and all its descendants Root: the base of the tree representing the most ancestral lineage Outgroup: a species or group outside the in-group used to determine ancestral traits In-group: the group of species being studied Synapomorphy: a shared derived character unique to a clade Polarizing characters: this established the ancestral vs. derived state of traits -​ Ancestral -​ a similarity among species that is inherited from the most recent common ancestor -​ Trait inherited prior to the most recent common ancestor of the group (old form of the trait) -​ Derived -​ a similarity that arose more recently and is shared by only a subset of the species  -​ Trait that is inherited from the most recent common ancestor of the group (new form of the trait) 23.2: Phylogenetic Reconstruction 3.​ Explain the principle of parsimony and its use in systematics. Definition: A guiding principle in systematics that states that the simplest explanation requiring the fewest evolutionary changes is preferred. Use in Systematics: 1.​ Helps systematists construct phylogenies by minimizing the number of evolutionary events (e.g., mutations, trait gains/losses). 2.​ Ensures that the hypothesis requires the least number of assumptions to explain the observed data. 3.​ Example: a.​ In a phylogeny grouping frogs with mammals (based on the absence of tails), the principle of parsimony would reject this hypothesis because it would require additional assumptions like the loss of amniotic membranes and hair in frogs.  4.​ Describe factors which complicate phylogenetic reconstruction. 1. Homoplasy: a.​ Shared character states not inherited from a common ancestor. b.​ Caused by: i.​ Convergent Evolution: Independent evolution of similar traits in unrelated lineages (e.g., wings in bats and birds). ii.​ Evolutionary Reversals: Traits reverting to ancestral states (e.g., loss of tails in frogs resembling tail-less mammals). -​ One on left is better 2. Incomplete Data: c.​ Fossil record gaps can lead to missing information about ancestral states and character evolution. 3. Complex Evolutionary Histories:  d.​ Rapid rates of evolutionary change in some branches. e.​ Variation in mutation rates across lineages. 4. Morphological Similarity: f.​ Early systematists relied on overall similarity, which can be misleading as traits may not accurately reflect evolutionary relationships. 5.​ Distinguish between methods of phylogenetic reconstruction. 1.​ Cladistics: ○​ Based on shared derived characters (synapomorphies). ○​ Relies heavily on the principle of parsimony. ○​ Builds trees by minimizing evolutionary events required to explain shared traits. 2.​ Molecular Data Analysis: ○​ Uses DNA or protein sequences as characters for phylogeny construction. ○​ Advantages: ​ Provides large datasets with many characters. ​ Allows for finer resolution of relationships compared to morphological data. ○​ Requires computational tools to identify the most parsimonious tree. 3.​ Molecular Clock: ○​ Estimates divergence times based on rates of DNA mutation. ○​ Calibration using fossil record data improves reliability. ○​ Assumes constant mutation rates, though newer methods accommodate variable rates. 4.​ Statistical Methods: ○​ Use models to account for different rates of evolution among characters. ○​ Fit data to evolutionary models rather than relying strictly on parsimony. ○​ More effective in handling homoplasy and complex evolutionary scenarios. 23.3: Classification 6.​ Distinguish between systematics and classification. 1.​ Systematics: ○​ Definition: The reconstruction and study of evolutionary relationships among organisms. ○​ Focus: Understanding the evolutionary connections and history among species. ○​ Tools: Phylogenetic trees (phylogenies) to depict hypotheses about evolutionary relationships. 2.​ Classification: ○​ Definition: The practice of placing species and groups of species (e.g., phyla, classes, genera) into a taxonomic hierarchy. ○​ Focus: Organizing species into categories based on traits. ○​ Relationship to Systematics: ​ While classification reflects shared traits, it does not always align perfectly with phylogenetic relationships. ​ Example: Traditional classification placed reptiles and birds in separate groups, but systematics has revealed that birds evolved from dinosaurs, making them a type of reptile. ○​ Types Monophyletic Groups (a clade): ​ Include the most recent common ancestor and all descendants. ​ Example: Archosaurs (crocodiles and descendants).  Paraphyletic Groups: ​ Include the most recent common ancestor but not all descendants. ​ Example: Dinosaurs excluding birds. ​ Paraplegic: lose movement of lower half of body ○​ Loss of one thing like the bird Polyphyletic Groups: ​ Do not include the most recent common ancestor. ​ Example: Grouping bats and birds as "flying vertebrates" based on convergent traits. ​ All plus something else (bat) 7.​ Describe how phylogenies are used as hypotheses in biology. 1.​ Hypotheses of Evolutionary Relationships: ○​ Definition: Phylogenies serve as models or hypotheses for how species are related through common ancestry. ○​ Example: A phylogeny showing that birds evolved from dinosaurs suggests specific evolutionary steps leading to modern birds. 2.​ Comparative Biology: ○​ Phylogenies provide context for studying homologous and homoplastic structures: ​ Homologous Structures: Derived from the same ancestral source (e.g., dolphin flippers and horse legs). ​ Homoplastic Structures: Similar traits evolved independently (e.g., bird wings and dragonfly wings). 3.​ Understanding Convergent Evolution: ○​ Phylogenies reveal instances of traits evolving independently in unrelated groups (e.g., flight in bats and birds). 4.​ Sequence of Evolutionary Change: ○​ Phylogenies illustrate gradual changes over time. ○​ Example: The evolution of bird traits over millions of years. 5.​ Species Diversification: ○​ Phylogenies help test hypotheses about species richness: ​ Example: Beetles feeding on angiosperms evolved independently in multiple clades, with high species richness linked to adaptation to diverse angiosperms. 6.​ Biogeographical Patterns: ○​ Use: Test hypotheses about species origins and dispersal. ○​ Example: Mapping insect taxa to geographic locations shows how species spread and diversified. 7.​ Disease Evolution and Spread: ○​ Phylogenies track how diseases evolve and spread: ​ HIV and SIV: Phylogenies show that HIV evolved from SIV and crossed into humans multiple times. ​ Source Identification: Used to trace infection sources (e.g., HIV strains in patients). ​ SARS-CoV-2: Used to study the global spread of the virus.  Lesson 24 24.1: The Geological Timescale 1.​ Conceptualize the geological timescale. Definition: ​ The geological timescale is a chronological framework used to describe Earth's history and the timing of major evolutionary and geological events. ​ It divides Earth's history into eons, eras, periods, epochs, and ages. Hierarchy of Time Divisions: ​ Eons: The largest divisions (e.g., Hadean, Archean, Proterozoic, Phanerozoic). ​ Eras: Subdivisions of eons (e.g., Paleozoic, Mesozoic, Cenozoic within the Phanerozoic Eon). ​ Periods: Smaller divisions within eras (e.g., Cambrian, Jurassic, Quaternary). ​ Epochs and Ages: Fine-scale divisions, often used for recent events. Deep Time: ​ Refers to the vast span of Earth's history, measured in billions or millions of years. ​ Markers include: ○​ Appearance of major groups (e.g., prokaryotes, eukaryotes). ○​ Geological and climate changes. ○​ Continental configurations. Key Features: 2.​ Rock layers (strata) serve as the basis for relative dating. 3.​ Fossils within these strata mark evolutionary events and help define time divisions. 2. Apply the geological timescale to the early Earth and the origins of life. 1.​ Earth’s Formation and Precambrian Life: ○​ Hadean Eon (4.6–4.0 billion years ago): ​ Earth forms, hostile environment with no evidence of life. ○​ Archean Eon (4.0–2.5 billion years ago): ​ First prokaryote fossils (microfossils) appear around 3.5 billion years ago. ​ Early life likely existed prior, but no older fossils have been discovered yet. ○​ Proterozoic Eon (2.5 billion–541 million years ago): ​ Eukaryotic fossils appear around 1.5 billion years ago. ​ Multicellular organisms emerge late in this eon. 2.​ Phanerozoic Eon (541 million years ago–Present): ○​ Marked by the Cambrian Explosion (~541 million years ago): ​ Rapid diversification of multicellular life. ​ Major animal groups appear in the fossil record. ○​ Subdivided into: ​ Paleozoic Era: Age of fishes and first land plants/animals. ​ Mesozoic Era: Age of dinosaurs, first birds, and mammals. ​ Cenozoic Era: Age of mammals, leading to the rise of humans. 3.​ Dating Techniques: ○​ Relative Dating: Determines sequence of events by fossil placement in rock layers. ○​ Isotope Decay Dating: Measures absolute ages using radioactive isotopes. ​ Carbon-14: Useful for materials 50,000 years. 4.​ Time Context for Life: ○​ Earth’s Age: ~4.6 billion years. ○​ Prokaryotes: At least 3.5 billion years ago. ○​ Multicellular Organisms: ~12% of Earth’s history. ○​ Birds and Mammals: ~4% of Earth’s history. ○​ Humans: Only ~0.2% of Earth’s history. 24.2: Evolution of Early Life 3. Explain how Earth’s early environment shaped living systems. Conditions on Early Earth: ​ Atmosphere: Early Earth had a reducing atmosphere composed of methane, ammonia, hydrogen, and water vapor, lacking free oxygen. ​ Energy Sources: Lightning, volcanic activity, and UV radiation provided energy for chemical reactions. ​ Environment: High temperatures, frequent volcanic eruptions, and hydrothermal vents created conditions for early life. Formation of Organic Molecules: ​ Miller-Urey Experiment (1953): ○​ Simulated early Earth’s atmosphere and demonstrated that organic molecules (e.g., amino acids, adenine) could form spontaneously under these conditions. ○​ Results showed that key building blocks for life could originate from inorganic compounds. Hypotheses of Life’s Origin:  ​ Terrestrial Origin Hypothesis: Life originated on Earth through chemical reactions fueled by early environmental energy sources. ​ Extraterrestrial Hypothesis: Organic molecules arrived via meteorites, as certain meteorites contain amino acids and other organic compounds. Formation of Cellular Systems: ​ Early membranes likely formed from fatty acids, creating compartments that confined molecules, increasing the probability of metabolic reactions. ​ The presence of membranes allowed for the evolution of early cells, enabling the organization and replication of life 4. Summarize evidence for the order of evolution of early life Geological Timescale and Fossil Record: ​ Oldest Rocks: Evidence of biological activity in rocks dated to 3.8–3.5 billion years ago. ​ Microfossils: ○​ Microfossils (~3.5 billion years ago) provide some of the earliest evidence of life. ○​ Definitive fossils dated to 3.2 billion years ago offer stronger evidence. ​ Stromatolites: ○​ Formed by bacterial mats trapping minerals, stromatolites (~3.5 billion years ago) indicate ancient microbial life. Biomarkers: ​ Carbon-12 Incorporation: Living organisms preferentially use carbon-12 over other isotopes, leaving a chemical signature in rocks. ​ Hydrocarbons and isotope ratios in ancient rocks provide evidence of biological origins. Evolution of Early Life: ​ Prokaryotic Life (~3.5 billion years ago):  ○​ First organisms were likely simple, single-celled prokaryotes. ​ Carbon Fixation (~3.8 billion years ago): ○​ Ancient organisms used early versions of the Calvin or Krebs cycles for carbon fixation. ​ Eukaryotic Cells (~1.5 billion years ago): ○​ Eukaryotic cells appeared later, with compartmentalization and endosymbiosis allowing for greater complexity. ​ Multicellularity (~600 million years ago): ○​ Multicellular organisms diversified late in Earth’s history, leading to the Cambrian explosion. RNA World Hypothesis: ​ Suggests RNA was the first molecule to store genetic information and catalyze reactions. ​ Supported by evidence of RNA’s ability to catalyze peptide synthesis (e.g., in ribosomes). ​ Challenges: Formation of long RNA chains, though evidence shows clay and ice crystals may facilitate bonding. Metabolic Pathways: ​ Early life may have been autotrophic (producing its own molecules from inorganic compounds) or heterotrophic (obtaining molecules from the environment). ​ Enzymes or RNA catalyzed early metabolic reactions, paving the way for more complex systems. 24.3: Earth’s Changing Systems and Evolution 5. Describe how the Earth is a dynamic (changing) system. Climate Changes: ​ Early Earth was extremely hot with high levels of carbon dioxide (CO₂). ​ Cooling occurred as CO₂ was removed from the atmosphere through rock weathering: ○​ Atmospheric CO₂ combined with water to form carbonic acid, which broke down rocks. ○​ Released HCO₃ and calcium reacted in oceans to form calcium carbonate, sequestering CO₂. ​ Temperature fluctuations: ○​ Extreme conditions ranged from 2000°C to -50°C. ○​ Periods of glaciation (ice ages) caused mass extinctions. Plate Tectonics and Continental Drift: ​ The Earth's crust is divided into tectonic plates, which slowly shift over time. ​ Continents have merged and separated multiple times, forming supercontinents like: ○​ Rodinia: Oldest known supercontinent (~1.1 billion years ago). ○​ Pangea: Most well-known (~335–175 million years ago). ○​ Gondwana and Laurasia: Later divisions of Pangea. ​ Evidence for continental drift includes fossil distributions across currently separated continents. Geological Evidence: ​ Rock layers and fossils record Earth's dynamic changes, such as glaciation events, volcanic activity, and shifts in sea levels. 6. Explain how living systems have changed the Earth. 1.​ Carbon Sequestration by Life: ○​ Early organisms altered Earth's atmosphere by fixing carbon. ○​ Photosynthetic organisms (e.g., cyanobacteria) began producing oxygen, dramatically changing the atmosphere. ○​ The Great Oxygenation Event (~2.5 billion years ago): ​ Oxygen levels rose, leading to the formation of the ozone layer and changing atmospheric composition. 2.​ Biological Weathering:  ○​ Early microbial life contributed to rock weathering and carbon cycling. ○​ Biological activity accelerated the formation of calcium carbonate in oceans. 3.​ Stromatolites: ○​ Formed by bacteria trapping minerals, stromatolites are some of the earliest evidence of life altering Earth. 4.​ Biodiversity and Ecosystem Engineering: ○​ Organisms have altered environments to suit their needs: ​ Example: Forests influence climate by sequestering CO₂ and affecting weather patterns. ○​ Animal activity (e.g., burrowing) has impacted soil formation and nutrient cycling. 7. Relate mechanisms of evolution to the ever-changing life on Earth. 1.​ Environmental Pressures: ○​ Extreme climates and mass extinction events (e.g., ice ages, volcanic eruptions) acted as selective pressures. ○​ Organisms evolved adaptations to survive these conditions: ​ Example: Mammals developed warm-bloodedness to survive cold periods. 2.​ Reproductive Isolation: ○​ Continental drift caused populations to become geographically isolated, leading to allopatric speciation. ○​ Example: Fossil evidence shows similar species on continents now separated by oceans, indicating shared ancestry before the continents split. 3.​ Mass Extinctions and Adaptive Radiations: ○​ Mass extinction events cleared ecological niches, allowing surviving species to diversify: ​ Example: Dinosaurs dominated after the Permian extinction (~252 million years ago). ​ Mammals diversified after the Cretaceous extinction (~66 million years ago). 4.​ Dynamic Evolutionary Mechanisms: ○​ Natural Selection: Changes in environment drove survival of the fittest. ○​ Gene Flow: As continents drifted, populations that reconnected exchanged genetic material. ○​ Mutation and Variation: Environmental changes increased mutation rates, contributing to adaptation. 24.4: Diversification of Life 8. Correlate the diversification of life with the need for consistent nomenclature. 1.​ Diversification of Life:  ○​ Cambrian Explosion: ​ Occurred ~541 million years ago during the Cambrian period. ​ Marked by a rapid diversification of multicellular organisms, confined to the oceans. ○​ Colonization of Land: ​ Plants and animals adapted to terrestrial environments by developing mechanisms to: ​ Prevent desiccation. ​ Perform gas exchange in the absence of water. ​ Provide structural support against gravity. ​ New niches led to adaptive radiations and speciation. ○​ Oxygen and Glaciation: ​ Oxygen produced by photosynthesis accumulated over time: ​ Initially tied up in iron oxide in the oceans. ​ Later contributed to the formation of the modern atmosphere and the ozone layer. ​ Early plants reduced atmospheric CO₂, contributing to cooling and glaciation events. 2.​ Monophyletic Domains of Life: ○​ All life is organized into three domains: ​ Bacteria ​ Archaea ​ Eukaryotes ○​ Diversification within these domains arose during and after the Cambrian Explosion. 3.​ Consistent Nomenclature: ○​ Taxonomic Hierarchy: ​ Life is classified hierarchically: Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species. ○​ Binomial Naming System: ​ Each species is given a two-part name:  ​ Genus (capitalized) and species (lowercase), e.g., Sciurus carolinensis (Eastern gray squirrel). ​ Standardized names ensure universal understanding among scientists. ○​ Taxonomic Flexibility: ​ New discoveries about evolutionary relationships may lead to reclassification, but the hierarchical system remains consistent. 9. Recognize that the Earth is still changing. Natural Processes: ​ Earth’s climate, geology, and ecosystems are constantly changing due to: ○​ Plate tectonics: Continents continue to shift, influencing biodiversity and speciation. ○​ Climate cycles: Natural variations in CO₂ and glaciation affect ecosystems. Human Impact: ​ Biodiversity Loss: ○​ Habitat destruction, pollution, and overexploitation lead to species extinction. ​ Climate Change: ○​ Anthropogenic CO₂ emissions accelerate global warming, altering ecosystems. ​ Radioactive Materials:  ○​ Human activities introduce substances (e.g., radioactive isotopes) previously absent from Earth's systems. The Anthropocene Debate: ​ Many scientists propose defining a new epoch, the Anthropocene, to reflect humanity's significant influence on the planet. ​ Criteria include: ○​ Rapid changes in biodiversity. ○​ Evidence of human-induced climate change. ○​ The introduction of synthetic and radioactive materials.