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Biology 115 Workshop BIOS Forms Typed

by: Angie Notetaker

Biology 115 Workshop BIOS Forms Typed 01:119:115

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All outlines and bios forms from the entire semester's weekly workshops typed to outline all material covered on the final exam. Also includes additional information that falls underneath each sub ...
General Biology
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This 48 page Study Guide was uploaded by Angie Notetaker on Tuesday January 19, 2016. The Study Guide belongs to 01:119:115 at Rutgers University taught by in Summer 2015. Since its upload, it has received 271 views. For similar materials see General Biology in Biology at Rutgers University.


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Date Created: 01/19/16
Exam 1 Lectures 1- 9 01/20/2016 ▯ Know the hardy Weinberg equation ▯ Lecture 1: Biology and Learning  Memory and Learning o LTP (Long Term Potentiation) o Neuronal Development o Long Term vs. Short Term Memory o Neuronal Plasticity  Concept and Process  Organization of Workshop o Facilitate Learning o Organizers as learning tools o TPS for evaluation  Themes of Biology o Emergent Properties  result form the arrangement and interaction of parts within a system the sum is greater than the parts o Identifying Themes o Reductionism  is the reduction of complex systems to simpler components that are more manageable to study o Levels of Organization  Biosphere- ecosystems- communities- populations- organisms-organs, tissues- cells- organelles- molecules ▯ Lecture 2: Scientific Process and Chemistry  Method of Investigating o Process of the Scientific Method Harry 2  Basic Chemistry o Properties depend on structure o Formulation of molecules o Types of chemical bonds  4 Emergent Properties of Water o Hydrogen bonding o Cohesive behavior o Moderate Temperature o Expansion upon freezing o Versatility as solvent contagious ▯ Lecture 3: Biological Molecules  Importance of Carbon o Forms Hydro- carbons o Functional groups determine molecular behavior  Hydroxyl  Carbonyl  Carboxyl  Amino  Sulfhydryl  Phosphate  Methyl  Biological Molecules o Common Properties o Different Types  Carbohydrates  Sugar  Proteins  Amino Acid  Central alpha carbon  Hydrogen atom  Amino group (basic)  Carboxyl group  R group  Nucleic Acids  Nucleotide  lipids ▯ Lecture 4: Origin of Life  Chemical Evolution from Non- Living to First Cell o 4 Requirements for Abiogenesis / abiotic synthesis  Little or no free oxygen:  Source of energy  Presence of chemical building blocks  Time  4 Steps of Abiogenesis o Abiotic synthesis of monomers o Organic Macromolecules o Formation of Protocells o Appearance of Self- Replication 4 Harry  History of Life o Geological Record- 4 Era’s  Hadean  Achaean  Proterozoic  Phanerozoic o First Cells/ Prokaryotes o Origin of Eukaryotes o Origins of Multicellularity  Life on Earth Order: Prokaryotes, eukaryotes, multicellular organisms, life on earth ▯ Lecture 5: Cell Structure  Tools and Techniques o Parameters and Types of Microscopes  Light Microscope  Electron Microscope  Scanning electron microscopes (use gold film)  Transmission Electron Microscopes (Plastic film) o Cell Fractionation  Separates major organelles through a centrifuge  Cellular Diversity and Characteristics o Main classification of cells by structure  Prokaryote  No nucleus  No membrane bound organelles  Eukaryote  Nucleus  Membrane bound organelles o Common features of cell  Have plasma membrane as selective barrier  Cellular Components of Eukaryotic Cells o Nucleus  DNA  Proteins  Nuclear Envelope  Nucleolus o Ribosomes  Site of protein synthesis o Endomembrane system  Internal membrane system that monitors synthesis of proteins and their transport around and exit out of the cell. The movement of lipid and detoxification.  Nuclear Envelope  Plasma Membrane  Endoplasmic Reticulum  Smooth ER- lacks ribosomes  Metabolizes carbs  Rough ER- studded with ribosomes  Proteins are folded and modified  Golgi Apparatus  Lysosomes 6 Harry  Vacuoles ▯ Lecture 6: Membrane Structure and Transport  Membrane Structure o Membrane Components  Phospholipids  Amphipathic= hydrophilic heads and hydrophobic tails o Fluid Mosaic Model  Membrane Components  Membrane Transport o Passive Transport  Simple Diffusion  Osmosis o Active Transport  Bulk Transport o Exocytosis o Endocytosis ▯ Lecture 7: Cellular Metabolism  Metabolism – sum of all chemical reactions of an organism and energy transformations o Metabolic Pathways- start with one item and end with a different product  Catabolic- complex simple (releases energy/ exergonic) .  Anabolic – simple complex (stores energy/ endergonic o Free Energy Change  Exergonic- G is negative/ spontaneous reaction/ releases energy  Endergonic- G is positive/ non spontaneous/ takes in energy o ATP  Structure-  Ribose (5 carbon sugar)  Adenine  3 Phosphate groups  Function  Stores energy  ATP hydrolysis drives chemical work  Formation  Endergonic  Non- Spontaneous  Production of ATP requires energy and is a more complex molecule  Enzymes o Characteristics and Functions  Lessens activation barrier  Speed up chemical reactions  Names end in –ase o Factors Affecting Enzymes  Temperature  pH o Induced Fit Model  Need a substrate o Co- Factors o Enzyme Inhibition 8 Harry  Competitive/ reversible  Non- competitive/ irreversible  Redox Reactions and Electron/ Energy Transfer o Characteristics of Oxidation and Reduction  Oxidation  Loss of electrons  Lose H atom  Reduction  Gain of electrons  Gain H atom o NAD+: An Electron Acceptor/ Electron Shuttle  NAD+ is reduced during ATP synthesis to result in NADH o NADH: Stored Energy ▯ Lecture 8: Cellular Respiration  Basics o A Catabolic Pathway (degradation and release of energy) o Energy Transfer: chemical energy in bonds chemical energy in ATP usable energy for cell work o Oxygen in reactions  Aerobic- Uses Oxygen  Anaerobic- Does not require Oxygen o Aerobic Respiration in Eukaryotes  Catabolic/ Exergonic/ Spontaneous  4 Stages of Cellular respiration in Eukaryotes o Glycolysis  Glucose splitting  Occurs in cytosol  Anaerobic  Product: 2 Pyruvate + 2 ATP + 2 NADH o Pyruvate Oxidation  Pyruvate is oxidized  Carboxyl is removed  Occurs in Mitochondria  Diffuses through outer membrane  Active Transport through the inner membrane  Product: 2 NADH + CO2 + Acetyl CoEnzyme A o Citric Acid Cycle  Oxidates Acetyl CoA  Occurs in Mitochondrial Matrix  The cycle is run twice for one glucose molecule  Product: 4 CO2 + 2 ATP + 6 NADH + 2 FADH2 o Oxidative Phosphorylation  Electron Transport Chain  Transfers energy from NAH and FADH2 oxygen molecule/ receptor  Chemiosmosis  Use of energy in H+ gradient to drive cellular work  If there is no oxygen, there is no spinning, and no ATP produced  Product: 2 ATP o All 4 stages produce 30- 32 ATP 10 Harry ▯ Lecture 9: Photosynthesis  Nature of Sunlight o Effects of Photon Absorption on the Electrons  Photons make the electrons go to higher orbitals  Energy dissipates as heat when the electron moves to a lower orbital  Structure Involved in Photosynthesis o Structure of Chloroplasts  Double Membrane  Stroma  Thylakoids  Contains Chlorophyll a o Photosynthetic Pigment Types and Absorption  Chlorophyll a  Bright green  Embedded in the Thylakoid Membrane  Captures light energy  Basics o Anabolic Pathway/ Endergonic o Solar energy Chemical Energy o Autotroph vs. Heterotroph  Autotroph= self sustaining  Plants are photoauttrophs- use sunlight and water  Heterotroph= requires organic material from other organism o Endergonic takes light energy (sun)  chemical energy (ATP and NADH) o A Redox reaction: H2O is oxidized while CO2 is reduced  Process of Photosynthesis o Light Dependent Reactions have PS I and PS II  Happens in the Thylakoid Membrane within the chloroplasts  Split H2O  Release O2  Reduce NADP+ to NADPH  Types  Linear Electron Flow  Produces NADPH  Cyclic Electron Flow  Produces ATP  Photosystems I and II  Capture light energy and transfer excited electrons to create ATP and NADPH  Light Harvesting- traps light and gives to reaction center  Reaction Center Complex- gives high energy electron to electron acceptor  Product: a gradient that produces ATP + NADPH o Carbon Fixation Reactions (Calvin Cycle)  Making a sugar from CO2 using the ATP and NADPH made in the light dependent reactions  Happens in the stroma  Starts with a carbon fixation, and then incorporates CO2 into the molecules  3 phases  Carbon Fixation  Reduction 12 Harry  RUBP  RuBisCo- a vital part in the Calvin Cycle and producing a sugar form CO2 ▯ Lecture 10: The Cell Cycle  Organization of Genetic Material o Structure of Chromosomes  Chromatin- DNA + Protein  Genome= all of a cell’s DNA  Prokaryotes= one DNA molecule  Eukaryotes= several DNA molecules o Changes in the Number of Chromosomes  Haploid vs Diploid  Cell Cycle o Interphase  G1- First Gap  No DNA synthesis  Normal cell functions  G2- Synthesis  Chromosomes duplicate 2n 4n  G3  4n chromosomes  Cell grows and prepares for cell division  Centrosome is duplicated  Organizes the cell’s microtubule spindle o Mitotic (M) Phase  Prophase  Chromosomes condense  Centrosomes move away to opposite poles  Pro- Metaphase  Nuclear envelope breaks down  Mitotic spindle elongates  Metaphase  Chromosomes align on the metaphase plate  All microtubules are attached to kinetochore handles  Anaphase  Sister chromatids are separated  Chromosomes move to opposite sides  Telophase  Nuclear envelopes reform  2 new daughter cells  Cytokinesis  Cytoplasm divides  Animal cells have a cleavage furrow  Plant cells have a cell wall  Binary Fission o Applies to bacteria who have one circular DNA strand ▯ Lecture 11: Meiosis  Intro to Heredity o Asexual vs. Sexual Reproduction 14 Harry o Types of Chromosomes in Heredity  Karyotype- ordered display of chromosomes in pairs  Homologous chromosomes carry genes controlling the same inherited characters  The same genes are located at the equivalent locus (loci)  22 pairs of somatic chromosomes and 1 pair of sex chromosomes  Replicated chromosomes= 2 identical sister chromatids  Life Cycles of Different Organisms o Plants and algae have alteration of generations where there is a haploid and diploid life cycle o Sporophyte= 2n o Gametophyte= n  Four Stages of Meiosis o Interphase  Chromosomes duplicate  Centrioles duplicate (where microtubule attaches) o Meiosis I  Prophase I  Synapsis and crossing over between non sister chromatids  Metaphase I  Tetrads (pairs of duplicated chromosomes) line up on the metaphase plate randomly  Microtubule attaches  Anaphase  Pairs of homologous chromosomes separate  Sister chromatids remain attaches  Telophase and Cytokinesis  Each of the 2 new cells is diploid o Interkinesis  No chromosome replication occurs o Meiosis II  Prophase II  Spindle apparatus forms  Metaphase II  Because of crossing over, the two sister chromatids of each chromosome are no longer identical  Anaphase II  Sister chromatids now separate  Telophase II and Cytokinesis  Chromosomes arrive at opposite poles  New nuclei form with 23 chromosomes  Origin of Genetic Variation o Chromosomes during meiosis and fertilization are responsible for genetic variation o 3 Mechanisms Contribute to Variation  Independent Assortment of Chromosomes  Crossing Over: produces recombinant chromosomes in prophase I  Random Fertilization ▯ Lecture 12: Mendelian Genetics  Mendel’s Experimental Approach o Testing the “Blending” Inheritance Hypothesis o Mendel’s Model for Discrete Inheritance  3:1 ratio 16 Harry  Characters are determined by genes  Each character is controlled by 2 genes (alleles)  One allele can mask expression of another o Mendel’s Model on 4 Concepts  Alleles  Are alternative versions of genes  Found at same locus on homologous chromosomes  2 Alleles are inherited  Explains the alteration of characteristics in generations  Dominant and Recessive alleles  If the 2 alleles are different, then only one is expressed  Law of Segregation  The 2 alleles for a heritable character separate during gamete formation and end up in different gametes (due to Meiosis I)  Two Fundamental Principles of Heredity o Law of Segregation of Alleles  During gamete formation chromosomes (and therefore alleles) segregate and go into different cells o Law of Independent Assortment of Chromosomes  2 or more genes assort independently during gamete formation  One character has no affect on another  Explains the 9:3:3:1 ratio  Using Probability o Multiplication Rule  Predicts combined probabilities of independent events  Signaled by the word “and” in problems o Addition Rule  Use if there are multiple genotypes that give the same phenotype.  Signaled by the word “or” ▯ Lecture 13: Chromosomes  Chromosome Theory of Inheritance o Genes have specific loci on chromosomes o Chromosomes undergo segregation and independent assortment  Thomas Hunt Morgan’s Use of Fruit Flies  Allelic Behavior with Chromosome Pair Behavior  Inheritance Patterns on Sex Chromosomes o Sex chromosomes are Heteromorphic- not morphologically similar o Males are heterogametic o Females are homogametic o Inheritance of X- Linked Genes  Males only carry 1 X (hemizygous)  All genes on the X are expressed for males  Recessive alleles cannot be masked o X Inactivation in Female Mammals  One of the Xs is randomly inactivated during embryonic development  The inactivated X condenses into a Barr Body  Violations of the Law of Independent Assortment o Linked genes- genes on the same chromosome are inherited together  Complete Linkage- very close on the same chromosome always inherited as a single unit  Incomplete Linkage – on different chromosomes mostly inherited independently 18 Harry o Complete linkage results in no recombination or variation. All offspring will resemble the parent generation  100% Parental genotype o Incomplete Linkage  Between 50 and 100% parental genotype o Unlinked  50% recombinant and 50% parental ▯ Lecture 14: DNA  Research that DNA is Genetic Material o Griffith Found that DNA holds genes, not proteins o Avery, MacLeod, McCarthy  DNA Transforms o Hershey- Chase  Confirming DNA’s role  DNA Structure o Structure of Nucleotides  Phosphate+ Sugar (dioxyribose) + Nitrogenous Base  Total purine (A + G) = Total pyrimidines (C + T)  Amount of A=T  Amount of C+G o Scientific Inquiry  Rosalind Franklin determined the 3D structure of DNA molecules  Measured the width of the double helix o Watson and Crick  Sugar- Phosphate Backbone  Joined by phosphor-diester linkages  No variability  4 Nitrogenous Bases  attached to backbone by covalent bonds  Rungs of the ladder  Lots of variability  Double Stranded  Held together by hydrogen bonds  Anti- Parallel Composition  3’ end has free hydroxyl (OH)  5’ has free phosphate  Semi- Conservative Replication o Initiation  3 Proteins required to Unwind  DNA Helicase- breaks down the hydrogen bonds between nucleotides  Single Stranded Bonding Proteins- prevents DNA from rewinding and reforming double helix  Topoisomerases- breaks and rejoins the backbone and prevents knotting o Elongation  3 Proteins required for Replication  DNA Polymerase- adds nucleotides to the existing 3’ end while constructing a strand from the 5’ to 3’ end  RNA Primase- adds pieces of RNA primer at the replication fork so DNA Polymerase can bind  RNA Polymerase- catalyzes the elongation of new DNA o Other  Nucleoside triphosphate= energy source and building block  2 Strands are synthesized  Leading strand- growing toward the fork (continuous) 20 Harry  Lagging strand- growing away from the fork (discontinuous and in fragments, needs help from DNA ligase to join the okazaki fragments) ▯ Lecture 15: Gene Expression  Relationship Between Genes and Proteins o Genes and Phenotype  Archbald Garrod found that diseases are inherited because people cannot make a particular enzyme and have metabolic defects o Flow of Genetic Information  DNA transcription mRNA translation  Protein  In eukaryotes RNA processing occurs in the nuclear envelope  In prokaryotes translation begins transcription is finished o One Gene- One Enzyme Hypothesis  Beadle and Tatum, hypothesized that genetic mutations would make an animal unable to produce particular enzymes o Structure of RNA and Types  Uracil substitutes Thymine and pairs U-A  Types  mRNA- encodes a protein  rRNA- structural part of a ribosome  tRNA- carries individual amino acids to ribosome o Genetic Code  Codon encodes for a monomer/ certain amino acid  A codon is a nucleotide triplet  Mutations can either have no affect or a large affect  Transcription: DNA to RNA o Initiation  DNA acts as a template  RNA Polymerase does not need a primer  RNA Polymerase binds to the Promoter  A specific DNA sequence  Upstream of the gene o Elongation  Template strand is read from 3’ to 5’  RNA is added to 3’ end o Termination  Specific sequence tells polymerase to stop  Transcript falls off DNA template o Post- Transcriptional Modification  Eukaryotic cells modify RNA after transcription before going into the cytoplasm and exiting the nucleus  Alteration of mRNA ends  5’ cap  Poly A tail  Protect from degradation by enzymes  Help ribosomes attach  RNA Splicing  Exons- get expressed  Introns- get discarded  Spliceosome – large complex that binds to introns splice between introns and exons degrade introns put exons back together mature mRNA  Translation: RNA to Protein o Ribosome Structure  2 Ribosomal Sub Units 22 Harry  Proteins  Ribosomal RNA large subunit  A site- holds tRNA that carries the next AA to be added  P site- tRNA holding the growing polypeptide  E site- exit site where discharged tRNAs discharge o Initiation  The small ribosomal subunit reads mRNA until it reaches a start codon  Initiation factors brings in large subunit to form initiation complex  tRNA with 1 AA binds to a ribosome o Elongation  tRNAs continue to bring AAs  Ribozyme helps the peptide bond between the P and A sites  ribosome covalently links AAs into a peptide o Termination  Stop codon translation stops  mRNA is released from ribosome  tRNA + polypeptide is released  ▯ Lecture 16: Gene Regulation  Regulation of Prokaryotic Cells o Operons  Repressible Operon- is usually on unless a repressor is present  Inducible Operon- is usually off unless a inducer is present and normally has a repressor bound to it  Negative Control  operator is naturally on and transcription is usually on  Positive Control  transcription is usually off and needs activator proteins o Lac Operon by Jacob- Monod Positive Regulation  E. Coli will always use glucose before lactose  Regulated at transcription  3 Genes are used for lactose metabolism in E.Coli in a group as an operon  No Lactose Present  RNA polymerase is blocked by repressor  No lactose enzymes are created or needed  No inducer  Lactose Present / Glucose Absent  Allolactose acts as an inducer  Repressor is inactivated/ CAP  Polymerase attaches  Transcription occurs  Lactose Absent/ Glucose Present  No Inducer  Repressor is active/ CAP is inactive  Polymerase does not attach  No transcription o Negative Regulation  Negative feedback  Ex: nutrients/ tryptophan 24 Harry  Regulation of Eukaryotic Cells o Especially important since it allows cells to specialize (different genes need to be expressed within the same genome) o Chromatin Structure (= DNA + Proteins)  Chromatin Types  Euchromatin- loose/ expressed  Heterochromatin- tight/ not expressed  Histone Modification  Acetylation- opens up the gene  Methylation- closes the gene  DNA Methylation  Methylation to certain bases of DNA makes DNA inactive o Initiation of Transcription through 5 Components  Transcription Start Site-  Promoter- sequence for polymerase to bind (TATA Box)  Transcription Factors- help polymerase bind  Transcription Initiation Complex- DNA folds around factors and polymerase  Control Elements-  Proximal- close to promoter  Distal- far from promoter  Enhancers  Silencers o Post- Transcriptional  RNA Processing  Alteration of mRNA ends  5” cap + poly- A tail  Protein Processing and Degradation  Polypeptides need to be processed into a functional protein  Chemical Modification  Glycosylation- addition of sugar  Phosphorylation- addition of phosphate  Embryonic Development o 3 Processes from Zygote to Adult  Cell Division- Mitosis and increased cell count  Cell Differentiation- becomes specialized in structure and function  Morphogenesis- Obtaining a unique 3D structure o Cell Division Sources of Development Information  Cytoplasmic Determinants in Egg- unevenly distributed  Induction by Nearby Cells- cell to cell communication o Cell Differentiation Determination  Cell Differentiation- a process by which a cell determines fate  Determination- commits cell to fate and gives characteristic function/ structure o Morphogenesis Pattern Formation  Pattern Formation- process of organization of tissues and organs  Positional Information- provided by cytoplasmic determinants ▯ Lecture 17: DNA Technology  DNA Sequencing o Ingredients of DNA Sequencing  Sequencing machine 26 Harry  Primer  Complementary nucleotides o Process of DNA Sequencing  Denature fragment of DNA o Use of Sequencing  Gene and DNA Cloning o Restriction Enzymes  One short synthetic strand of DNA  One primer for each DNA strand o Using Restriction Enzymes to make Recombinant DNA o Gel Electrophoresis o PCR  Use of DNA Technology to Study Gene expression o In- Situ Hybridization  Lets us se where genes are being used in developing organisms  Colored probe hybridize with mRNA expressing a trait o RT- PCR  Lets us see the timing of the use of different genes  cDNA is the template for PCR amplification of the gene of interest  Applications of DNA Technology o Species Diversity  Barcoding o Forensic Evidence/ Genetic Profiles ▯ Lecture 18: Human Genetics  Study of Human Genetic Variance o Pedigree Analysis o Recessively Linked Disorders  Heterozygous is a normal phenotype  Cystic Fibrosis  Sickle Cell o Dominant Inherited Disorders  Dominant alleles are not necessarily more common in populations than recessive alleles o Lethal Alleles  If recessive- passed down until one individual receives two recessive copies and dies  If dominant- causes death if one copy is inherited (usually does not happen since the person dies early)  Huntington’s Disease is a copy of a dominant linked gene that is later onset and lethal  Diseases Due to Chromosomal Abnormalities o Alteration of Chromosome Number  Disomoy =2n  Occurs when non- disjunction occurs in anaphase  Aneuploidy- the presence of an abnormal number or a particular chromosome  Trisomy- 2n +1  Down Syndrome  Trisomy 13/ Patu syndrome  Trisomy 18/ Edwards syndrome  Monosomy- 2n-1  Causes death  Aneuploidy of Sex Chromosomes  Turner Syndrome (x) 28 Harry  Klinefelter (xxy)  xyy males o Alteration of Chromosome Structure  Deletion  Duplication  Inversion- attaches to original chromosome in wrong orientation  Translocation- attaches to a non- homologous chromosome  Ex: cru du chart  Fetal Testing o Amniocentesis look at amniotic fluid  14-16 weeks into pregnancy  Culture cells  Make Karyotypes  Biochemical analysis  Molecular studies o Chorionic Villus tissue in placenta cells  1- 10 weeks into pregnancy  Need large sample o Newborn Screening  After birth  PKU is a disease often tested for  Exceptions to Mendelian Genetics o Inheritance of Organelle Genes  Extranuclear genes/ cytoplasmic genes are genes found in the organelles located in the cytoplasm  Only a mother can pass on mitochondrial genes o Genomic Imprinting  The phenotype of the person depends on which parent donated the allele  Occurs during gamete formation  The result of methylation  Other allele is silenced ▯ Lecture 19: Darwinian Evolution  Pre- Darwinian Ideas o Aristotle and Socrates o Linneaus and Taxonomy o Cuvier and Catastrophism o Hutton and Gradualism o Lyell and Uniformatism like Darwin  The laws that were operating in history still operate today  The world is more than 6000 years old  Darwin’s Ideas o Lamarck and Use/ Disuse  most like Darwin  “Use and disuse”- of body parts  “Acquired characteristics”- can be inherited  Evidence for Evolution o Artificial Selection o Direct Observations  Evolution- decent with modification (change in the alleles within a gene pool) 30 Harry  Population- a group that shares a gene pool o Homolgy o Biogeography  Diversity and Unity of Life o Classification of Life o Unity of Life ▯ Lecture 20: Microevolution  Variation o Phenotypic  Mendelian Traits Either on or off  Gradations of Traits  vary along a continuum o Genetic  Mutations  Chromosomal Changes  Rapid Reproduction  Sexual Reproduction  Testing for Occurrence of Evolution in Populations o Population and Allele Frequency  Population Genetics- the study of the variability of genetics within a population and the evolutionary forces that act on the population  Gene Pool= all alleles of a gene within a population  Fixed Allele= there is only one variant  Allele frequency= frequency of an allele in a population  Genotype frequency= number with a specific genotype/ allele set in a population  Genetic Equilibrium= no evolution occurring/ the frequencies of the younger generation matches that of the parents o Hardy Weinberg Principle  Hardy Weinberg Equation: p^2 + 2pq + q^2  p= frequency of dominant allele  q= frequency of recessive allele  Hardy Weinberg Equilibrium: 5 conditions  No Mutations  Random Mating  No Natural Selection  A Large Population  Founder Effect- a portion of the population colonize a new habitat  Bottleneck Effect- population is severely reduced  No Gene Flow  Tends to reduce the differences between populations  Factors Altering Allele Frequencies o Mutations o Non- Random Mating o Natural Selection o Genetic Drift o Genetic Flow  Natural Selection as a Method for Adaptive Evolution o Natural selection acts on phenotype o Polygenic Control  Most phenotypes are the result of several alleles at different loci interacting  Standard Bell Curve 32 Harry o 3 Types of Selection  Stabilizing Selection- favors intermediate variants and acts against extreme phenotypes  Directional Selection- favors individuals at one end of the phenotypic range  Disruptive Selection- favors extreme variants on the ends ▯ Lecture 21: Macroevolution  Biological Species Concept o Components  A species is a group of populations whose members have the ability to interbreed  Cannot breed with other species  Gene flow does not alter phenotypes o Limitations  Reproductive Isolation in Biological Species  (the existence of biological factors that prevent two species from producing hybrids) o Pre-zygotic Barriers factors that act before fertilization  Habitat Isolation  Temporal Isolation  Behavioral Isolation  Mechanical Isolation  Gamete Isolation o Post- zygotic Barriers factors that act after fertilization  Reduced Hybrid Viability/ Development  Reduced Hybrid Fertility  Hybrid Breakdown o Other Definitions of Species  The Ecological Species Concept- views a species in terms of its ecological niche  Some look at the unity between species instead of the separateness  Process of Speciation o Allopatric “Other Country” Speciation  Gene flow is interrupted or reduced when a population is divided into geographically isolated subpopulations  Barriers arise due to migration or isolation  Separate populations may evolve due to mutation, natural selection, or genetic drift  Reproductive Isolation between populations increases as the distance increases o Sympatric “Same Country” Speciation  Overview  Speciation takes place in geographically overlapping populations  Most common case is Disruptive Selection  Homozygous individuals have greater fitness through sexual selection  Polyploidy- The presence of an extra set of chromosomes  Autoploid- an individual with 2 or more chromosome sets derived from one species  Alloploidy- a species with multiple sets of chromosomes derived from different species  Habitat Differentiation- the appearance of new ecological niches  Sexual Selection- preferring certain phenotypes  Rate of Speciation and Changes in Genetic Makeup o Patterns in Fossil Record and Spectrum  Gradualism vs. Punctuated Equilibrium  Punctuated Equilibrium- term used to describe periods where no change occurred between the creation of new species  Gradualism- Populations slowly diverge over many generations (difficult to see in fossil records) o Genetics of Speciation  Certain genes are involved in cases of speciation  A change in a single allele can cause a change in species 34 Harry ▯ Lecture 22: Phylogenetics  Systematics: Study of Diversity o Taxonomy- the science of naming and describing species o Phylogeny- the evolutionary history of a species o Binomial Nomenclature o Hierarchical Classification  Domain, Kingdom, Phylum, Class, Order, Family, genus, Species  Taxon- grouping of organism sat any one of these levels o Linking Classification and Phylogeny  Systamists proposed a classification system reflecting evolution- only recognize groups with a common ancestor and its descendants  Basics of Phylogenetic Trees o Tree Components  Branch Point- divergence of 2 species form a common ancestor  Sister Taxa- groups of organisms that share an immediate common ancestor  Phylogeny- evolutionary history of a group of organisms from a common ancestor o Morphological and Molecular Homologs  Types of Characters:  Structural  Physiological  Developmental  Behavioral  Molecular Traits  The more shared characters, the more closely related the species are  Characters are the result of homology o Homology vs Analogy  Homology= reason for characters/ similarity due to shared ancestry  Analogy= similarity due to convergent evolution o Investigating Molecular Homologies  Use primary structure of proteins or DNA sequencing  Constructing the Trees o Cladistics  Monophyletic Clade- “single tribe”  Includes a species and all its descendants  Paraphyletic Clade- “beside the tribe”  Includes ancestral species and all of its descendants  Polyphyletic Clade- “many tribes”  Includes taxa with different ancestors o Maximum Parsimony  The tree with the fewest evolutionary events is the most probable ▯ Lecture 23: Animal Behavior  Understanding Behavior o Proximate Causation- “How” Questions 2 and 3  How a behavior occurs or is modified o Ultimate Causation- “Why” (Questions 4 and 5)  Why a behavior occurs in the context of natural selection  “How” Does Environmental Stimuli Impact o Fixed Action Patterns  A sequence of unlearned behavior in response to stimulus 36 Harry  Unchangeable  Triggered by external cue/ sign stimulus o Migration  Environmental cues guide migration such as  Circadian clock  North star  Magnetic field o Behavioral Rhythms  Circadian Rhythm- cycle based on a single day  Diurnal- active during the day  Nocturnal- active at night  Crepuscular- most active at dusk or dawn  Circannual Rhythm – cycle based on a year  Breeding behaviors  Migration  Hibernation o Signals and Communication  Visual  Chemical  Tactile- touching  Auditory  “How” Does Animal Growth and Development Occur o Innate Behavior- does not vary, and is developmentally fixed o Learning From Experience- modification of behavior  Imprinting- behavioral response to a individual or object  Sensitive period  Spatial Learning and Cognitive Maps- establishment of memory that reflects spatial structure  Associative Learning  Classical Conditioning – association formed between normal unrelated stimuli  Operant/ Trial and Error Conditioning – association between personal behaviors o Cognition and Problem Solving  Cognition- the process of knowing  Problem Solving- ability to devise a method for obstacles o Learned Behaviors  Sometimes occurs in distinct “sensitive periods” o Social Learning  The root of culture  “Why” Does Behavior Aid Survival o Optimal Foraging Model  Predicts animal foraging  Minimizes the costs and maximizes benefits  Natural Selection Favors foraging behavior o Mating Behavior and Systems  Promiscuous – no strong pair  Monogamous- one strong bond  Polygamous- one individual with multiple partners  Polygyny- one male  Polyandry – one female 38 Harry  Sexual Dimorphism- extent to which a male and female differ in appearance varies with each type of mating system  Monogamous Relationships= sexes don’t differ  Polygamous relationships- one sex is showier  “Why” Does Animal Behavior Occur o Altruism- behavior that decreases one animal’s fitness while increasing another’s  Inclusive Fitness= direct fitness + indirect fitness  Direct Fitness- # of alleles an animal passes to offspring  Indirect Fitness-common alleles to close relatives  Coefficient Relatedness-probability that 2 individuals inherit the same allele form a common ancestor  Unrelated animals- 0  Parent and child- 0.5  Siblings- 0.5  Cousins- 0.125  Hamilton’s Rule and Kin Selection  Kin selection- indirect selection that increases fitness through breeding with relatives ▯ Lecture 24: Population Ecology  Basics o Population- group of interbreeding individuals o Ecology- the study of interactions between organisms  Population Ecology-  Population Dynamics- studies the change in populations o Evaluating a Population  Change in Population Size= change in #/ change in time= Births- Deaths  Per Capita Growth Rate  Population growth= change in #/ change in time= B- D= bN – mN= N(b-m)  Births= birth rate x # of individuals  Deaths= death rate x # of individuals  Per Capita Rate of Increase= r= b-m= change in #/ Change in time= rN  If r<0 population is decreasing  If r>0 population is increasing  If r= 0 zero population growth  Instantaneous Growth Rate= derivative of N/ derivative of t= instantaneous per capita rate of increase x N  Exponential Population Growth= derivative of N/ derivative of t= instantaneous per capita rate of increase x N when per capita rate max>0  Models of Population Growth o Exponential Growth Model  J- shaped curve  derivative of N/ derivative of t= instantaneous per capita rate of increase x N  limited because the environment has limits o Logistic Growth Model  S- shaped curve  derivative of N/ derivative of t= instantaneous per capita rate of increase x N x (K-N/K)  If N is small population growth will be high  If N is large the rate of growth will decline  If N= K the population stops growing  Carrying Capacity= maximum population size that the environment can support  The population grows slower as it nears the carrying capacity  Unrealistic because the environment is never constant  K may change 40 Harry  Most populations fluctuate around the central mean  Life History Traits o Life History Traits  Age at first reproduction  How often reproduction occurs  How many offspring is produced per cycle o Different Strategies in Life History  Semelparity- big-bang reproduction  Favored when offspring survival is low  Living in highly variable environments  Adults are less likely to survive  Iterparity- repeated production species reproduces many times  Favored when environment is less variable  Adults are likely to survive  Competition for resources is intense  There are tradeoffs in producing early vs. late in life o Two Extremes in most Vertebrates  Population Density= # of individuals of a species per unit of area or volume at a given time  R- selected species  Have traits that maximize reproduction  Small body size  Early maturity  Many babies at once  Little parental care  Short life span  Found in variable environments  Focus on rapid reproduction  K- selected species  Have traits sensitive to population size  Long life span  Older reproduction age  Large body size  Defense against predators  Low reproductive rate  Parental care  Population size is always close to K  Focus on stable environments  Factors Influencing Population Size o Density- Dependent Factors  Environmental Factors- operates without relation to density  Abiotic Factors- elements of nonliving world The birth/ death rate does not change density for r- selection o Density- Dependent Factors  The factors’ impact on population is affected by population density  Population maintains itself at a constant near K  Biotic Factors  Negative Feed back System ▯ Lecture 25: Community Ecology 42 Harry  Introduction  Community Interactions o Competition  Ecological Niche- the sum of a species’ use of resources and the organism’s ecological role  Fundamental Niche- environments potentially occupied by a species (all possibilities)  Realized Niche- actually occupies by the species  Competitive Exclusion- 2 species compete to occupy the same niche, but only one can actually inhabit the niche  Resource Partitioning- species can coexist in their similar fundamental niches  Resource partitioning in Space  Resource partitioning in time  Character Displacement- when characters change in relation to the new environment , such as beak size o Predation  Adaptations by Predators for Finding and Capturing Prey  Adaptations by Prey for Protection  Herbivory- organism eats part of plant or algae o Symbiosis0 intimate, long term relationship  Parasitism (+/-)  Mutualism (+/+)  Commensalism (+/0)  Communities Structure: Diversity and Trophic Structure o Species Diversity  Species Richness- number of species in community\  Relative Abundance- the proportion each species represents of all individuals in the community  Diversity Index measures diversity o Diversity and Community Stability  Diverse communities are more productive, more stable and resistant to invasive species  Trophic Structure o Food Webs o Limits on Food Chain Length  Energy transfer is inefficient  Only 10% of energy is passed on to the next level o Species with a Large Impact  Dominant Species- most abundant or have the highest biomass  Keystone Species- have strong control of a community by their ecological roles or niches o Ecological Succession  Sequence of changes after a disturbance  Primary Succession- occurs where no soil exists  Secondary Succession- begins in an area where soil remains ▯ Lecture 26: Ecosystem Ecology  Introduction o Ecosystem o Energy Flow One way and Chemical Cycling o Energy Flow  Energy cannot be created or destroyed  Every energy exchange increases entropy o Matter and Chemical Cycling Mass cannot be creates Nutrients are decomposed by producers who break down the molecules and release simple inorganics 44 Harry o Trophic Levels  Primary Producers- Autotrophs  Consumers- obtain energy from plants  Omnivores- eat both  Detrivores - decomposers  Ecosystem Productivity o Primary Production- the amount of light energy converted to chemical energy by autotrophs o Gross Primary Production- total primary production o Net Primary Production- gross production energy used by primary producers for respiration o Primary Production in Terrestrial ecosystems  Temperature and moisture- primary production increases with moisture  Nutrient Limitation- soil often limits primary production  Nitrogen and phosphorous in soils limit primary production  Energy Transfer between Trophic Levels o Net Secondary Production- the amount of chemical energy in food converted to new biomass in a period o Production Efficiency- the fraction of energy stored in food that is not used for respiration  1-3%- Birds and mammals  10% fishes  40%- insects and microorganisms o Trophic Efficiency and Ecological Pyramids  Trophic Efficiency- the percentage of production transferred from one trophic level to the next  Pyramid of Net Production0 represents loss o


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