BIOL 1104 Unit 1

Day 6 - Life Evolves

Day 6 - Life Evolves Frequencies: number of observations of x divided by total number of observations Sum of frequencies is 1: this is how we study alleles. Remember, enzymes have tolerances - nutrients, light, energy, temperature, hydration. In some environments, byproducts of photosynthesis and metabolism (some toxic) form as part of those biochemical pathways, leading to cell/tissue/organ/organism detriment. Coral vs Algal bleaching. In both, Photosynthesis fails with high heat / UV, but the algal pigment is being denatured (like a fried egg). Coral symbiont is kicked out. MOVE, ACCLIMATE, ADAPT, DIE. -"Die" - a population disappears. This isn't exclusive from "move." -"Move" means: Not: "all individuals decide to move somewhere" Not same as migration, a behavior that takes advantage of different resources and their PHENOLOGY (seasonal climate phenomena). Pops in good environment can grow to larger pop and spread to new habitat. Pops in poor environment will disappear from stress. Even humans. Climate and ecological effects are a huge role in human migration toward north. Pop Growth -If pop is stable in size, on average each individual replaced by one offspring. -Represent (b - d) births - deaths as R, the rate of intrinsic growth, then start with N individuals, the change in pop size is R x N When people social distance, R goes down. Reproduction of the number of covid cases goes down! An important testifiable hypothesis: There are more individuals born than can survive. Better environment (more food, less stress) - more new births survive. If R > 0, pop growth IN THAT ENVIRONMENT. If R < 0, poor environment. 4 testifiable hypotheses - the last combines the first 3. 1) Individuals in a pop exhibit variation in traits. 2) Some of that variation is heritable from parents. 3) Given resources, more offspring are born than can survive. 4) Thus, individuals that survive and reproduce pass along traits that enable survival, and there are quantitative differences leading to differential pop growth dependent on these traits. Microevolution can lead to macroevolution (speciation) - similar, related birds on Galapagos isolated from mainland. Traits diverge to specialize on diverse food types. Change in precipitation affect available seed sizes, so influences fitness of different types. FITNESS is the outcome of survival (food) and reproduction. Reproduction often called FECUNDITY. Sometimes, not always, variation in a trait is ADAPTIVE, but we need to know if it is HERITABLE. VARIATION ALREADY EXISTS IN A POP BEFORE NATURAL SELECTION OCCURS. Trait variation - remember, a TRAIT that is HERITABLE is shaped by DNA being expressed (RNA) and translated into proteins. Not all traits are heritable, or only are so partially - the environment may be a control. Slope of XY linear regression estimates the heritability of the trait. Very positive linear relationship (offspring on y axis, parent on x axis): Very Heritable R = h(squared)S uses our estimate of HERITABILITY (H SQUARED) to predict RESPONSE (R) of a pop to the STRENGTH OF SELECTION on a trait - so, if you select a trait that is not HERITABLE, that trait will not change in next generation. SELECTION: Artificial selection (DOMESTICATION) is how we refer to humans choosing the traits that are kept for the next generation. Natural Selection - Darwin and Wallace - requirements of local ecosystem identify the idividuals with the greatest fitness. We have learned about heritability because of domestication of wild diversity. R = h(squared)S is breeder's equation. PHENOTYPE is target of selection - does it have traits to have high FITNESS in that environment. If it does, traits are passed down via expression of ALLELES in genome, so those alleles increase in frequency relative to the diversity from individuals that do not survive or reproduce. EVOLUTION IS CHANGE. Allele frequencies and/or genotype frequencies change because of - SELECTION - variation in reproductive success associated with traits. DRIFT - variation in reproductive success that is random, unassociated with traits. MUTATION - adds allele diversity to a pop. MIGRATION/ISOLATION VS GENE FLOW - affects how diversity moves from location to location, and how DISTINCT populations are. NONRANDOM MATING - whether isolaton/behavior/choice leads to distinct genotype frequencies than expected in a random pop.

Using general knowledge to predict a specific outcome is a type of:

Deductive reasoning

The fact that DNA sequences are more similar in more closely related organisms is evidence of what?

Descent with modification

Mendel's experiments with pea plants convinced him that each offspring carried HOW MANY copies of each gene that affected the traits he was studying?

2

4.2) GLYCOLYSIS

4.2) GLYCOLYSIS Endergonic - requires much more energy input ATP - used to power majority of energy-requiring cellular reactions. Functions as a rechargeable battery. When ATP is broken down, energy is released. Binding of its released phosphate to another molecule, activating it. Addition of a 2nd phosphate to AMP: makes ATP. Addition of a third phosphate: ATP Adenine bonded to ribose and phosphate groups. Phosphate groups - negatively charged - repel each other. Makes ADP and ATP unstable. Release of one or 2 phosphate groups from ATP (process called hydrolysis) released energy. GLYCOLYSIS - first step in the breakdown of glucose to extract energy for cell metabolism. Takes place in cytoplasm of most prokaryotes and eukaryotes. Begins with 6 C ring structure - single glucose. Ends with 2 molecules of a 3 C sugar called Pyrvate. And, ATP and NADH are produced. YOU GET MORE ATP OUT OF IT THAN THE ATP YOU STARTED WITH. If cell cannot catabolize pyruvate molecules further, it will harvest 2 ATP molecules from 1 molecule of glucose. For example, mature mammalian red blood cells are only capable of glycolysis, which is their sole source of ATP. If glycolysis is interrupted, these cells would eventually die.

If yellow peas (Y) are dominant to green peas (y), and a Yy male is crossed to a yy female, the offspring should have what color peas?

50% green, 50% yellow

6.1. The Genome.

6.1. The Genome. Sexually reproducing organism begins life as a zygote/fertilized egg Trillions of cell divisions then occur Once a human is grown, cell reproduction still necessary to repair/regenerate tissues ex. new blood and skin cells constantly produced Single celled organisms use cell division as method of reproduction Cell Cycle: cell division again and again. -Similar steps for all eukaryotes. GENOME - a cell's complement of DNA. Prokaryotes - genome is a nucleioid - single, double stranded DNA loop/circle. Some prokaryotes also have plasmids. Eukaryotes - genome comprises several double stranded linear molecules bound with proteins - CHROMOSOMES. Chromosomes are in the nuclei of each cell Human body (somatic) cells have 46 DIPLOID organisms are designated 2n because SOMATIC cell contains 2 matched sets of chromosomes n represents single set of chromosomes Human cells with one set of 23 chromosomes are GAMETES/SEX CELLS These eggs and sperm are designated n/haploid Matched pairs of chromosomes in a diploid organism are called HOMOLOGOUS CHROMOSOMES. Homologous chromosomes are the same length and have specific nucleotide segments called GENES in the same location/LOCUS Genes - functional units of chromosomes. Code proteins to determine characteristics. Traits are diff forms of a characteristic Copies of each of the genes may not be identical. Variation of individuals within a species caused by specific combo of genes inherited from both parents. Sex chromosomes, X and Y, are exception to the rule of homologous chromosomes. Other than small amount of homology to produce gametes, genes found in X and Y chromosomes are not the same.

7.1. Sexual Reproduction.

7.1. Sexual Reproduction. While many single celled and a few multicellular organisms can produce genetically identical clones through mitotic cell division, many single celled and most multicellular organisms use SEXUAL REPRODUCTION - parents produce haploid cells that fuse to form a single unique diploid cell Diploid cells will then divide Meiosis leads to haploid cells that are part of sexual reproductive cycle. Meiosis and fertilization introduces variation into offspring - evolution. Some disadvantages of sexual reproduction - males can't produce offspring, so in theory, asexual populations should reproduce twice as fast. Also, genetically identical offspring (asexual) - can be a good or bad thing. -Sexual reproduction much more common. Evidence of its evolutionary success. Variation that sexual reproduction creates is important to offspring survival. Only source of variation in asexual organisms is mutation In MEIOSIS (in sexual), different mutations are reshuffled from one generation to the next as parents combine their genomes -division of contents of the nucleus that divide the chromosomes among gametes -variation introduced during meiosis, and when the gametes combine in fertilization FERTILIZATION AND MEIOSIS ALTERNATE IN SEXUAL LIFE CYCLES. Meiosis reduces the resulting gamete's chromosome number by half. Fertilization (joining 2 haploid gametes) restores diploid condition. 3 MAIN CATEGORIES OF LIFE CYCLES IN MULTICELLULAR ORGANISMS: 1) DIPLOID DOMINANT - multicellular diploid stage is most obvious life stage (and there is no multicellular haploid stage). Most animals including humans. 2) HAPLOID DOMINANT - multicellular haploid stage is most obvious (and there is no multicellular diploid stage). Fungi and some algae. 3) ALTERNATION OF GENERATIONS - 2 stages, haploid and diploid, are apparent to one degree or another depending on the group. Plants and some algae. Diploid-Dominant: only the haploid cells produced by the organism are the gametes. GAMETES are produced from DIPLOID GERM CELLS. Once the HAPLOID GAMETES are formed, they lose the ability to divide again. NO MULTICELLULAR HAPLOID LIFE STAGE. Fertilization occurs with the fusion of 2 gametes, usually from different individuals, restoring the diploid stage. (MEIOSIS: cell division resulting in 2 identical daughter cells. MITOSIS - results in 4 sex cells). HAPLOID DOMINANT: Most fungi and algae employ life cycle strategy in which multicellular "body" of an organism is haploid. In sexual reproduction, special haploid cells from 2 individuals form a diploid zygote. Zygote then undergoes meiosis until 4 haploid cells are formed, called SPORES. ALTERNATION OF GENERATIONS: -These species have both haploid and diploid multicellular organisms as part of sexual life cycle. -HAPLOID MULTICELLULAR PLANTS - GAMETOPHYTES - PRODUCE GAMETES. -Meiosis not involved here, as the organism producing the gametes is already haploid. -Fertilization between the gametes forms a DIPLOID ZYGOTE. -Zygote will undergo many rounds of MITOSIS and give rise to a DIPLOID MULTICELLULAR PLANT - SPOROPHYTE. -SPOROPHYTE'S specialized cells will undergo MEIOSIS to produce HAPLOID SPORES. SPORES will develop into GAMETOPHYTES. Starts over.

Inference vs Experiment

A hypothesis is the prediction about the outcome of an experiment. An inference is conclusion drawn based on observations and prior knowledge. "In science, there is a constant interplay between inductive inference (based on observations) and deductive inference (based on theory)

To assess the effect of changes in the environment on biological systems, scientists may make "before/after" comparisons, or "control/impact" comparisons. In this usage, the word "control" means:

A part of the experiment that does not change (the expected outcome)

Individuals cannot evolve, but they can:

ACCLIMATE

What does a chloroplast generate during the light-dependent reactions that is needed for the Calvin Cycle of Photosynthesis:

ATP

The primary product of the light-dependent reactions of photosynthesis is:

ATP and NADPH

If a species or population changes its distribution on our planet over time, associated with change in the environment, the MECHANISM of that movement is likely:

Adaptation

The energy transfers involved in metabolism share what with the RNA (and in a way, DNA) that controls so much about how an organism functions:

Adenine.

A mechanism for how adaptation happens in nature was first proposed by Charles Darwin and:

Alfred Russell Wallace.

Gene variants that arise by mutation and exist at the same relative locations on the homologous chromosomes are called:

Alleles

BODY SYSTEMS

BODY SYSTEMS HOMEOSTASIS AND OSMOREGULATION Stable state inside body of an animal Animal organs and organ systems constantly adjust to internal and external changes Physiologic processes result in negative feedback relationship ex. Temperature (thermoregulation) and water content (osmoregulation). Maintenance of equilibrium around SET POINT. Change in internal or external environment - stimulus, detected by a receptor, which sends information to a control center (often the brain), which relays appropriate signals to an effector organ. THERMOREGULATION: ECTOTHERMS - cold blooded - animals that do not have internal control of their body temperature. May do things to keep their body at a certain temperature (ex. sit in sun, increase oxygen intake). ENDOTHERM - warm blooded - animals that maintain constant temperature in the face of environmental changes. Generate internal heat to keep cellular processes operating optimally. -have some sort of insulation (ex. fur or fat) Ectotherms and endotherms both use their circulatory systems to maintain body temperature. ex. Vasodilation - open arteries - brings more blood and heat to body surface, facilitating heat loss, cooling the body. ex. Vasoconstruction - narrow blood vessels to reduce flow in peripheral blood vessels, forcing blood to core organs to conserve heat. Thermoregulation coordinated by nervous system, centered in hypothalamus, which maintains set point. Sometimes, set point changes (ex. high temperature during infection, due to pyrogens released into blood). OSMOREGULATION - maintaining salt and water balance (OSMOTIC BALANCE) across membranes in the body. Fluids in and around cells have water, electrolytes (dissociates with ions), and nonelectrolytes Body has blood plasma, cell fluid, and INTERSTITIAL FLUID in spaces between cells and tissues Semipermeable membranes - permeable to water and some solutes Insuffifcient fluid intake results in fluid conservation by kidneys Without mechanism to regulate osmotic pressure, tendency to accumulate toxic waste and water Mammalian systems regulate osmotic pressure and concentration of electrolytes in blood plasma and intracellular and interstitial fluid. Osmotic pressures can directly affect blood pressures. EXCRETORY SYSTEM KIDNEYS - pair of bean shapes located below liver in body cavity Each one contains many nephrons that filter the blood containing metabolic wastes FROM cells All blood filtered by kidneys Nephrons remove wastes, concentrate them, and form urine collected in the bladder. Kidney 3 regions - outer cortex, middle medulla, renal pelvis Renal cortex has NEPHRONS - functional unit of the kidney Pelvis collects urine and leads to URETER on outside of kidney. Ureters exit kidney and empty into URINARY BLADDER. Blood enters kidneys from aorta, through RENAL ARTERY After other steps (see book), blood collects in vessels and leaves kidney in RENAL VEIN Amounts of water and ions reabsorbed into circulatory system are carefully regulated. Waste collected in tubules and leaves kidney in ureter, which leads to bladder for storage. URETHRA allows urine to flow out of bladder and body.

Sexual reproduction in eukaryotes always involved a haploid stage and a diploid stage; why are plants unusual in this regard?

Because plants have recognizable multicellular organisms in both stages.

CITRIC ACID CYCLE, OXIDATIVE PHOSPHORYLATION, ELECTRON TRANSPORT CHAIN, AND CHEMIOSMOSIS

CITRIC ACID CYCLE Pyruvate molecules are transported into mitochondria for cellular respiration. Pyruvate transformed to 2 C acetyl groups, picked up by a carrier enzyme made of vitamin B. Resulting compound - ACETYL CoA - delivers acetyl group from pyruvate to next pathway: CITRIC ACID CYCLE - in matrix of mitochondria (2 pathways in glucose catabolism that generate ATP - glycolysis and citric acid cycle) Produces 2 CO2 molecules, 1 ATP, and reduced forms and coenzymes. Aerobic pathway - oxygen required All 6 C atoms from original glucose molecule are eventually released as CO2. Each cycle term creates 3 NADH molecules and one FADH2. Cycle is anabolic AND catabolic -anabolic because it also synthesizes non-essential amino acids. OXIDATIVE PHOSPHORYLATION: most ATP comes from here Electrons pass through a series of chemical reactions to a final electron acceptor, oxygen energy of electrons generates electrochemical gradient takes place in protein complexes in inner membrane of mitochondria potential energy generates ATP ELECTRON TRANSPORT CHAIN: Aggregation of the 4 protein complexes, together with electron carriers. As electrons are passed, they lose energy, and some of it is used to pump H ions into intermembrane space. Uneven H+ ions makes gradient. In 4th complex, electrons are accepted by OXYGEN (TERMINAL ACCEPTOR). NEEDS ATMOSPHERIC OXYGEN. Oxygen with extra electrons combined with 2 H ions, enhancing electrochemial gradient and forming water. Witout oxygen, cell would die (this is why we must breathe). H ions diffuse through inner membrane through an integral membrane protein - ATP SYNTHASE (a tiny generator that moves to matrix to generate ATP from ADP) Flow of H+ ions across membrane through ATP Synthase - CHEMIOSMOSIS In Chemiosmosis, result is production of ATP from the energy of the elecrons removed from the H+ atoms (which were originally part of the glucose molecule). At end, electrons reduce an O molecule to O ions. Extra electrons on Oxygen ions attract Hydrogen ions (protein) from medium, and water is formed. OXIDATIVE PHOSPHORYLATION IS THE ELECTRON TRANSPORT CHAIN AND CHEMIOSMOSIS (not to be confused with Osmoregulation) COMBINED ATP Yield: Number of ATP molecules varies. ATP yield depends on tissue being considered (ex. in brains, electrons picked up by FAD+, producing fewer ATP molecules. In liver, electrons picked up by NAD+) Intermediate compounds in these pathways are used for other purposes too, so it gets messy. Only about 34% of energy in glucose goes through these pathways of glucose catabolism. Mitochondrial diseases - genetic disorders of metabolism.

COMIC

COMIC - PHOTOSYNTHESIS Water is a reactant and a product 2 steps: 1) LIGHT DEPENDENT - use water and photon energy to build molecules ATP and NADPH. Oxygen released as waste. 2) doesn't require light directly. CO2 pulled from air and attached to an existing molecule. Then, ATP and NADPH are used to turn THAT molecule into glucose. Photosynthesis occurs in ORGANELLES CALLED CHLOROPLASTS, which contain fluid discs called THYLAKOIDS, arranged in stacks called GRANA (one stack is a granum), which is where light is absorbed. THYLAKOID'S MEMBRANE separates the interior chamber (Lumen) from the STROMA (fluid-filled space surrounding the Thylakoid). Several proteins and other molecules are stuck in Thylakoid membrane. Light is captured by CLUSTERS OF CHLOROPHYLL MOLECULES in the membrane, called PHOTOSYSTEMS. PHOTOSYSTEM I AND II PHOTOSYSTEM II HAS 2 MAJOR REGIONS - large ANTENNA COMPLEX surrounds the REACTION CENTER. Energy from a photon of light is absorbed by chlorophyll in antenna complex and funneled into reaction center. When Chlorophyll absorbs a photon, the energy elevates one of the Chlorophyll's electrons to a higher energy state. The electron can't hold the energy long, though... And it passes the energy to a neighboring chlorophyl, exciting ITS electron. The photon's energy is passed this way through the antenna complex... Until it is passed to P680 in the reaction center (a special pair of molecules). When P680's electron gathers enough photon energy, it gets so excited it pops off Photosystem II and rides away on a molecule called Plastoquinone (PQ). To replace the electron lost by P680 in Photosystem II, we will need to take one from another molecule - WATER. A region in Photosystem II (OXYGEN-EVOLVING-COMPLEX OEC) splits water into 3 parts - Hydrogen, Oxygen, and one electron that knits them together. H ions accumulate in the Thylakoid Lumen, Oxygen released as waste, and electron replaces the one lost by P680. The electron from P680 was carried away by PQ, which takes it to CYTOCHROME COMPLEX, which uses electron's extra energy to PUMP MORE HYDROGEN INTO THE LUMEN. There are lots of H ions in the Lumen, but not very many in the surrounding Stroma. Difference in concentration across the Thylakoid Membrane is a CONCENTRATION GRADIENT. CYTOCHROME COMPLEX works hard to maintain CONCENTRATION GRADIENT All the positive charged H ions are packed tight and repel each other The H ions want to leave the lumen and spread out into stroma. But, the only door across the Thylakoid Membrane is a protein - ATP SYNTHASE. Every time 14 H ions pass through it, ATP synthase assembles 3 ATP molecules. After it energized the Cytochrome Complex, the P680 electron returned to its lower energy state. All the H ions make the Lumen acidic Photosystem I (like II) absorbs a photon and uses the energy to dontae an electron to another molecule. The Chlorophyll molecules in Antenna Complex of Photosystem I absorbs a photon's energy and passes it around until they pass it to P700 in the Reaction Center. When P700 absorbs the energy, its electron is elevated to a higher energy state, and pops off and rides away on a molecule - FERREDOXIN, which takes electron from P700 to a molecule called NADP+ REDUCTASE, which uses its energy to make a molecule of NADPH. How is the electron from P700 replaced? When tired electron from Photosystem II leaves Cytochrome Complex, it rides on a molecule called PLASTOCYANIN (PC), which takes it to Photosystem I There, it replaces the electron that Photosystem I lost Now, we have ATP and NADPH for light indepdendent reaction IN STROMA. Calvin Cycle: RUBISCO (earth's most abundant enzyme) COMBINES CO2 WITH A 5 C MOLECULE CALLED RUBP IN A PROCESS KNOWN AS CARBON FIXATION. When Rubisco combines CO2 with RuBP, it makes an unstable 6 C molecule that immediately splits into 2 molecules of 3 Phosphoglycerate. Then, chemical energy in ATP and NADPH is used to change the 3 Phosphoglycerate molecules into molecules of G3P. For every 6 molecules of G3P made, 5 stay in the cycle and are further modified to make more RuBP. One of every 6 G3P molecules manufactured leaves the cycle and goes on to make sugar. G3P can make a number of things, including glucose.

The process of "carbon fixation" means:

Carbon is changed from its inorganic form to one that is available for biochemical reactions.

Cells in your hear muscle, and cells in your skin, have the same genome with the same DNA sequence. So how do they perform such different functions?

Cells turn some genes on or off depending on their environment Regulation of how genes are expressed The RNA created in those 2 cell types is at different levels, gene by gene, making different proteins. ALL OF THE ABOVE

Chapter 1:

Chapter 1: Biology: science that studies life Viruses are not classified as living All living organisms have: order, sensitivity/response to stimuli. 8 things: reproduction, adaptation, growth and development, regulation/homeostasis, and energy processing. ORDER: Organisms - organized, have 1 or more cells Inside each cell, atoms make up molecules, which make up the cell components/organelles Multicellular organisms - cells can specialize, perform functions SENSITIVITY/RESPONSE TO STIMULI: Locus: another word for trait. Organisms respond to diverse stimuli Positive response: movement toward a stimulus Neg Response: movement away REPRODUCTION: Single celled organisms duplicate their DNA and divide it equally as the cell prepares to divide to form 2 new cells. Many multicellular organisms produce specialized reproductive cells. ADAPTATION: -"Fit" for env - a consequence of evolution by natural selection All adaptations enhance ability to survive and reproduce Adaptations are not constant As environment changes, nat selection causes characteristics of individuals to track those changes GROWTH AND DEVELOPMENT: we grow according to instructions coded by genes REGULATION/HOMEOSTASIS: Organisms must coordinate internal functions -ex. Digestive and circulatory systems Cells need appropriate temp, pH, and concentrations of diversechemicals HOMEOSTASIS - steady state - ability of organism to maintain constant internal conditions -ex. Regulating temperature with thermoregulation ENERGY PROCESSING: All organisms use a source of energy for metabolic activities ex. Energy from the sun -> chemical energy in food ex. Using chemical energy from food EVOLUTION: Diversity of life is a result of mutations (random changes in hereditary material over time) that allow organisms to adapt to changing env. ATOM: smallest and most fundamental unit of matter. Consists of nucleus surrounded by electrons. Atoms form MOLECULES - chem structure consisting of at least 2 atoms held by covalent bond. Phospholipid made of atoms. MACROMOLECULES: Formed by monomers. ex. DNA. Some cells contain ORGANELLES - aggregates of macromolecules surrounded by membranes. Organelles perform special functions. CELL: smallest fundamental unit of structure and function in living things. Viruses not made of cells PROKARYOTES - single celled organisms. lack organelles surrounded by a membrane. No nuclei surrounded by nuclear membrane. EUKARYOTES: do have membrane bound organelles and nuclei. In most multicellular organisms, cells combine to make TISSUES to carry out some function ORGANS - collection of tissues grouped based on common functon ORGAN SYSTEM - higher level of organization that consists of functionally related organs. -ex. Circulatory system -transports blood to and from lungs. Includes heart and blood vessels. ORGANISMS - individual living entities Single celled eukaryotes and prokaryotes - microorganisms POPULATION - all of the individuals of a species living within a specific area. Different populations may live in same area. COMMUNITY - set of populations inhabiting an area. ECOSYSTEM: all living things in an area together with abiotic (not living) parts of environment BIOSPHERE: collection of all ecosystems. Represents zones of life on earth. land, water, parts of atmosphere Source of diversity if EVOLUTION. Current taxonomic systems, lowest to highest: Species (most specific), Genus, Family, Order, Class, Phylum, Kingdom, Domain (most broad) Several species within a genus, more within a family, etc. Domain is relatively new addition. 3 domains of life: Eukarya, Archaea, Bacteria Eukarya- organisms that have cells with nuclei -Includes fungi, plants, animals, several kingdoms of protists Archaea: single celled, no nuclei. Include extremophiles that live in harsh environments. Bacteria and Archaea are prokaryotes. Classifications change when more info comes. Binomial names - consist of genus name (capitalized) and species name (lowercase). Both in italics. -ex. We are "Homo sapiens" PHYLOGENETIC TREE - diagram showing evolutionary relationships among species based on genetic and physical similarities and differences. -Lateral nodes represent ancestors. points in evolution where an ancestor diverged to form 2 new species. Length of branches represents time. Carl Woose's tree was constructed from comparative sequencing of genes that are universally distributed and altered slightly in every organism. SCIENCE - knowledge about the natural world Science cannot answerable moral, aesthetic, and spiritual questions HYPOTHESIS - suggested explanation that can be tested. Produced within the context of a scientific theory SCIENTIFIC LAWS - not as common in biology - mathematical - express how elements of nature will behave under certain conditions NATURAL SCIENCE - related to physical world and its phenomena and processes. No complete agreement on what they include. Some scholars divide them into life and physical sciences. INDUCTIVE REASONING - use related observations to arrive at a general conclusion. -infer conclusions (inductions) based on evidence. -careful observation and analysis of large amounts of data. -START WITH OBSERVATION AND MOVE TOWARD GENERALIZATIONS AND THEORIES. DEDUCTIVE REASONING - used in hypothesis-based science. Pattern moves in opposite direction. Uses a general principle/law to forecast specific results. -Predict results that will be valid as long as the principle is valid. START WITH A HYPOTHESIS AND TEST TO SEE IF IT IS TRUE THROUGH OBSERVATION. Both types of logical thinking are related to 2 main pathways of scientific study: DESCRIPTIVE/DISCOVERY SCIENCE - observe, explore, discover. AND HYPOTHESIS-BASED SCIENCE - begin with a question and potential answer that can be tested. Most scientific endeavors combine these 2 Observations lead to questions which lead to hypothesis and it starts over Scientific method first documented by Sir Francis Bacon. Prediction - similar to hypothesis but usually has the phrase: "If... then..." Hypothesis should be testable (to ensure it is valid) and falsifiable A hypothesis can be disproven/eliminated, but can never be proven Data/in silicons research is increasing too In practice, scientific method is not as structured as it appears in books. Science doesn't operate in linear fashion BASIC/PURE SCIENCE - expand knowledge regardless of short term application APPLIED SCIENCE/TECHNOLOGY - solve real problems already defined for the researcher Without basic sciences, unlikely that applied science would exist Human Genome Project used basic research for real issue. Some discoveries are made by serendipity/accident - ex. Pennicillin Peer-reviewed articles: reviewed, usually anonymously by a scientist's colleagues. Results must be consistent with findings of other scientists.

Chapter 8. Genetics.

Chapter 8. Genetics. Genetics - study of heredity Johann Gregor Mendel set framework for genetics Genes are basic units of heredity. Can be replicated, mutated, expressed Today, postulates from Mendel form basics of classical Mendelian genetics Mendel used pea plants as his primary MODEL SYSTEM - system with convenient characteristics used to study a phenomenon to gain understanding to apply to other systems. His work was unnoticed by scientific community. CONTINUOUS VARIATION - range of small differences we see among individuals in a characteristic like human height. People thought we are "blends" of our parents' traits. Mendel worked to show DISCONTINUOUS VARIATION - variation seen when each individual shows one out of 2 (or very few) easily distinguishable traits (ex. white or violet flowers). Showed traits are not blended, but are inherited distinctly. Wasn't recognized for scientific contributions during lifetime. Used "true breeding" inbred self-fertilizing pea plant Pisum Sativum that produces identical offspring. Used HYBRIDIZATIONS - mating 2 true breeding individuals with different traits. GARDEN PEA CHARACTERISTICS revealed the basis of heredity He found 7 characteristics, each with 2 contrasting traits. TRAIT - variation in physical appearance of a heritable characteristic. ex. Characteristic: color. Traits: white vs violet Traits did not blend in cross breed. They were inherited. ex. Pollen from violet flowers applied to white flowers resulted in violet flowers, not a blended color. For every characteristic, one trait would disappear in F1 generation (ex. only violet flowers) and reappear in F2 generation (violet and white flowers) at a ratio of 3:1 He allowed F1 plants to self fertilize When he transferred pollen (cross-bred), he obtained the same ratio irrespective of which parent (male or female) contributed which trait - RECIPROCAL CROSS - male and female traits in one cross become the traits of female and male in the other cross. Concluded 2 types of traits DOMINANT/EXPRESSED TRAITS - those inherited unchanged in a hybridization. RECESSIVE/LATENT TRAITS - disappear in offspring of hybridization. -Recessive trait reappears in progeny/descendents of the hybrid offspring. Menndell said each parent has 2 copies of a trait, and each passes 1 to offspring. Dominant trait: person can be AA or Aa Recessive trait: must be aa 8.2) -We inherit one chromosome from each parent's set of 2, and the copies of each gene are located on the paired chromosomes. -In meiosis, 3 chromosomes are separated into HAPLOID GAMETES, and only one copy of the gene gets moved into a gamete. -ALLELES - gene variants that arise by mutation and exist at the same relative locations on homologous chromosomes. Mendel examined genes with just 2 alleles, but common for many to exist in a pop. Genotype: organism's underlying genetic makeup, consistying of physically visible and non-expressed alleles Diploid organisms that are HOMOZYGOUS for a gene have 2 identical alleles, one on each homologous chromosome. When P plants with contrasting traits (AA plant and aa plant) were cross bred, all offspring were heterozygous Aa For a gene that is expressed in a dominant-recessive pattern, homozygous dominannt AA and heterozygous Aa organisms will look same (diff genotypes but same phenotpe) LAW OF DOMINANCE - one trait will conceal the presence of another trait for the same characteristic. Recessive allele will be latent, but will transmit to the next generation. Recessive allele: must be aa to be expressed Punnett Square: devised by british geneticist Reginald Punnett LAW OF SEGREGATION - paired unit factors (genes) must segregate equally into gametes such that offspring have an equal likelihood of inheriting either factor -equal segregation of alleles is why we can apply the punnett square to predict offspring -Physical basis: first division of meiosis: homologous chromosomes with their different version of each gene are segregated into daughter nuclei. Chromosomes located in nuclei. TEST CROSS - still used by plant and animal breeders. Way to determine whether an organism that expressed a dominant trait was homozygous or heterozygous. -dominant-expressing organism is crossed with an organism that is aa. If dominant expressing organism isAA, then all F1 offspring will be Aa. If dominant expressing organism is Aa, F1 offspring will be 50% Aa, 50% aa. Mendel LAW OF INDEPENDENT ASSORTMENT - genes do not influence each other with regard to the sorting of alleles into gametes, and every possible combo of alleles is equally likely. Illustrated by DIHYBRID CROSS between 2 true breeding parents that express diff traits for 2 characteristics. So, big punnett square. Each gamete can only have one allele per gene. A gemete with an r allele is equally likely to contain a Y or y allele. When RrYy heterozygote is self crossed, there are 4 equally likely gametes. This gives us 16 possible combos for offspring. Physical basis for the law of independent assortment also lies in meiosis I, when different homologous pairs line up in random orientations. SOme traits are more complex than simple dominant-recessive pattern. INCOMPLETE DOMINANCE - one allele appears in the phenotype of the heterozygote, but not to the exclusion of the other, which can also be seen. -ex. Heterozygote for red and white flowers has pink flowers. CODOMINANCE - variation on incomplete dominance, where both alleles for the same characteristic are simultaneoulsy expressed in heterozygote. -ex. Blood type AB. Individual can only have 2 alleles for a gene, but multiple alleles can exist in a pop. Most common phenotype and genotype in natural pop - WILD TYPE / + All other genotypes are considered variants/mutants. Can be recessive or dominant to the wild type. When there are 3 alleles in the pop, there are 6 possible genotypes (9 squares). Sex of individuals (of humans and many plants and animals) determined by sex chromosomes - one pair of non-homologous chomosomes Other chromosomes: autosomes Females: xx Males: xy Y: smaller, less genes X linked gene: present on the X, not on the Y MALES ARE HEMIZYGOUS: they have only one allele for any X linked characteristic. Makes descriptions of dominance and recessiveness irrelevant for males. -When a female parent is homozygous for a recessive X linked trait, she will pass trait on to ALL HER MALE OFFSPRING. X Linked traits appear more in sons than in daughteres. In some organisms (ex. all birds), sex with non-homologous sex chromosomes is the female (XY). So, here, sex linked traits will appear more in FEMALES (HEMIZYGOUS). Some allele combos are not inherited independently of each other. Linked genes violate the law of independent assortment. Segregation of alleles into gametes can be influenced by LINKAGE, in which genes located close to each other on same chromsome are more likely to be inherited as a pair. But, because of CROSSOVER/RECOMBINATION, it's possible for 2 genes on same chromosome to behave independently (like they are not linked). Homologous chromosomes possess same genes in same order, but alleles can be different on the 2 chromosomes. RECOMBINATION/CROSSOVER - during interphase and prophase 1 of meiosis, homologous chromosomes first replicate and then synthesize. Genes on homologs align. Segments exchange genetic material. Gene order is not altered. Maternal and paternal alleles are combined onto same chromosome. Alleles shuffle several times. When 2 genes are on same chromosome, they are linked, and alleles are transmitted through meiosis together. BUT, this doesn't work, because the height and color genes are on the SAME chromsome (linked). As distance between 2 genes increases, the probabilitiy of one or more crossovers between them increases, and the genes behave more like they are on separate chromosomes. Proportion of recombinant gametes (the ones not like the parents) as a measure of how far apart genes are on a chromosome. Single observation characteristics are usually under influence of multiple genes (each with 2 or more alleles). Genes can function to determine a phenotype in a complementary or syngergistic fashion - POLYGENETIC INHERITENCE. EPISTASIS - different from a dominant allele silencing a recessive allele - interaction between genes is antagonistic. One gene masks/interferes with the expression of another. -Epistasic alleles silence the hypostatic alleles. -Often epistasis is a pathway. Expression of one gene depends on function of a gene before/after it. REVIEW: Genes far apart on same chromosome are likely to assort independently because of RECOMBINATION EVENTS that occured in intervening chromosomal space. EPISTASIS - expresion of an allele for one gene masks expression of an allele for a DIFFERENT GENE.

DAY 7 - THE ONLY CONSTANT IS CHANGE

DAY 7 - THE ONLY CONSTANT IS CHANGE -Mutational diversity ADDS to what selection ACTS UPON -Genetic drift and allele frequency change -There must be diversity and variation. New diversity comes from sexual recombination and reproduction, and from mutation. -MUTATIONS may increase in rate (exposure to toxins, radiation, etc), but are otherwise random as to when and where. -THEY DO NOT HAPPEN AS A RESPONSE TO THE ENVIRONMENT CHANGING. -"Nature" tends to look random. Patterns suggest some intervention. -Bacteria reproduce asexually by dividing one cell into 2. -After 20 cell divisions, over 1,000,000 cells, and EACH DNA REPLICATION EVENT IS AN OPPORTUNTY FOR MUTATION. -1 in 10 million: mutation rate per nucleotide, per DNA replication. -Bacterial genome: about 1-5 million bases. So, for every 2 replications, 1 mutation. -In a pop of bacteria (millions of individuals, millions of replications), chance of "right" mutation happening to provide resistance to antibiotic is pretty good! -If mutation is INDUCED by environment, it will happen at a particular rate upon encounter with new environment. If mutation is induced, similar results across all replicates. -If mutations are RANDOM, it could happen at any time prior to encounter with new environment! If random, VARIANCE WILL BE HIGH. (Some replicants will be very resistant, some kind of resistant, some not resistant, etc). -Why is this important? 1) It tells us that mutations happen at random, and the more individuals are reproducing, the greater the genomic diversity will be - so very large POPULATIONS of bacteria or viruses can quickly overcome challenges, including the antibiotics and antivirals that we create! 2) Selection acts on the diversity that is ALREADY PRESENT, the change in environment does not itself change the genetic diversity. 3) Some mutations have an unclear effect on genome; some change the DNA code for enzymes, or change how RNA is expressed from that gene - so, mutations have consequences! Process for infecting a cell: 1) HIV's extracellular form, a vision, encounters a host cell. 2) HIV's gp 120 protein binds to CD4 and connector on host cell. 3) HIV's RNA genome, REVERSE TRANSCRIPTASE, integrase, and protease enter the host cell. 4) Reverse transcriptase synthesizes HIV DNA from HIV's RNA template. 5) Integrase splices HIV DNA into host genome. 6) HIV DNA is transcribed to HIV mRNA by the host cell's RNA polymerase. 7) HIV mRNA is translated to HIV precursor proteins by host cell's ribosomes. 8) Protein cleaves precursors into mature viral proteins. 9) New generation of viruses assembles inside the host cell. 10) New viruses bud from host cell's membrane. AZT drug blocks reverse transcriptase activity; but, given time, more AZT is required to limit virus load. WHY? NATURAL SELECTION. There is DIVERSITY. THAT DIVERSITY IS INHERITED. SOME FAIL TO REPRODUCE. THE VARIANTS THAT PERSIST (RESISTANT VIRIONS) PASS ALONG SUCCESSFUL DIVERSITY (FITNESS). Errors in reverse transcription generate a variable population. Some variants differ in resistance to AZT. Resistance (or susceptibility) is passed from parents to offspring. During treatment with AZT, many visions fail to reproduce. The variants that persist are the ones that can reproduce in the presence of AZT. BUT, NOT ALL EVOLUTION IS DUE TO NATURAL SELECTION. Imagine a near-infinite sample of diversity. This could be the gametes from oysters (ex. 100 million eastern oysters, each releasing 1 million gametes), or it could be M&Ms from the factory. A SMALL SAMPLE OF THIS DIVERSITY (ex. a bag of M&Ms) will deviate from the true frequency of type, whether allele or color. The frequency is known (in fact, suggests Athens M&Ms come from one of two factories), your samples are quite different... But, when all are put together (larger sample), THE FREQUENCIES ARE CHANGED MUCH LESS! GENETIC DRIFT: Because all populations are finite, allele frequencies will change every generation. The change may be great in small populations, and very little in large populations, but there is always some change. Random variation in reproductive success that has nothing to do with traits causes this drift. Because frequencies change up/down each generation, there is an increasing likelihood over time that alleles will be LOST (go to frequency of 0) or FIXED (frequency of 1) So, populations change over time, whether there is selection or not! If there are multiple populations, each will change (somewhat) independently and so they become different from one another, whether there is selection or not! All of this can be numerically simulated with graphs, and fits what we see in nature! ex. 10 totally separate populations of 200 individuals, no selection, just drift: several alleles become LOST and one becomes FIXED over time. EASIER FOR AN ALLELE TO BECOME LOST THAN FIXED. (Highly variable, wide graph) 10 separate populations of 200 individuals, no selection, but 2 out of every 100 individuals migrate to other populations. (Tighter graph, no alleles become fixed or lost, because there is still some gene flow between pops). 10 of every 100 move to other populations each generation. (TIGHTEST GRAPH, no alleles become even close to getting fixed or lost, because there is still plenty of gene flow between pops). How do we tell when drift or selection? They both cause change in allele frequency, so it seems impossible to tell them apart, right? But, when you have 10s or 100s of 1000s of genomic markers, tracking allele frequency, we can see how they behave relative to one another. Drift reflects DEMOGRAPHY: birth, death, migration, population size, etc. And, will influence THE WHOLE GENOME. Selection acts on PARTICULAR GENES, and so those markers will behave differently. In an event that kills off a large part of the population (BOTTLENECK in size), many alleles change in frequency more than they would usually. But, it was found in sea stars after a Bottleneck event that around 100 loci (location of a gene) changed allele frequency by up to 0.4 in ONE GENERATION - these were likely linked to genes that are associated with survival. In this case, the MAGNITUDE OF CHANGE in allele frequency is one of the indicators of selection. (Allele frequencies change more drastically w/ Natural Selection than with Drift). Even without natural selection, allele frequencies still change a bit at most loci, because of DRIFT CHANGE/EVOLUTION IS A FACT. The mechanism is a hypothesis to be evaluated. As we observe "surprising" change, we can evaluate models relative to drift (not selection), to see if they sufficiently explain what has happened. When change is more rapid than predicted, and in a direction that is predicted, we can start to talk about selection. Leads to predictions of how particular genes are involved in that response. Every generation is an experiment! DRIFT, and predictions of expected change given how large the population is (and mating behavior, life history) provides a NULL HYPOTHESIS. With long times of isolation, populations may end up with very different allele frequencies whether or not there is ADAPTATION - selection just changes the RATE OF CHANGE. HOW POPULATIONS DIVERGE, BECOME DISTINCT: Misconception of "evoluton" is one species becoming another. No mechanism is necessary other than populations being isolated and/or in distinct environments, plus TIME. Isolation may be spatial, phenological (climate), or behavioral (ex. nonrandom mating preferences). Islands occassionally receive organisms as "immigrants" via storms, rafting, etc. DISPERSAL - that population is not connected by regular dispersal/gene flow from mainland. Geological events - mountains, isthmuses, stream/river captures are not common - a region being separated into two is called VICARIANCE. ISOLATION DOESN'T NEED TO BE SUDDEN, BUT END RESULT IS NO MATING BETWEEN POPULATIONS. Isthmus of Panama - volcanic origin 5+ million years ago, closed about 3.5 million years ago. No marine organisms in Caribbean can move to Pacific or Vice Versa. New mutations, drift, and/or selection can lead to distinct diversity at many genes. "Speciation" This is a continuous argument in evolutionary biology, taxonomy, and conservation - what are the DIFFERENT ENOUGH GROUPS that we recognize, study, and preserve? Different criteria - no one explanation fits all species. But, some definitions (ex. niche, morphology) are useful

Gregor Mendel chose to work with _______ traits in pea plants to explore trait inheritance.

DISCRETE

What do biologists mean by the phrase central dogma?

DNA encodes RNA, which encodes proteins

Metabolic reactions, including photosynthesis, all share the use of adenosine compounds. Molecules including adenosine are involved in:

DNA sequences

Day 3: Energy Production and Stress

Day 3: Energy Production and Stress Life responds to change by MOVING, ACCLIMATING, ADAPTING, OR DYING. ADAPTION - group, long term ACCLIMATION - individual physical reaction to adjust to changes There are limits to ability to move, acclimate, or adapt, so an organism may find itself in a stressful environment if environment changes. This stress sets distribution of any group of organisms. Climate change suggests predictions about how distributions of life should change, AND mechanisms (reduced growth reproduction, survival in bad/good habitats, better growth and reproduction). STRESS - reflection of how an organism responds to their environment, requiring more energy to continue operating "normally." Can and does affect SURVIVAL OR REPRODUCTION, the components of organismal FITNESS. -ex. Stress from heat. First, you can behave: move if you can. Sweat-cells open/close membrane channels. Plant, regulate water ions and cellular proteins. Then, modification of gene expression, through plasticity/ACCLIMATION, or (over time, as a group) ADAPTATION - pop becomes more tolerant to heat, can use energy to reproduce. Time scale at which environment changes is important. STRESS VARIES BY ORGANISM. ECTOTHERMS: use more oxygen as temperature changes: invertebrates, most fish, reptiles, amphibians: do not use energy to maintain body temperature. ENDOTHERMS: constantly working to warm our blood: burn extra energy in process of homeostasis. Humans around 37 degrees Celsius, dogs about 39. PLANTS/FUNGI - temp and moisture are primary stresses. LIFE RESPONDS: DNA, RNA, protein material - some processes life uses to respond to the changing environment (acclimate). Life is programmed to behave or physiologically respond, or ACCLIMATE to environment. INDIVIDUALS TO NOT ADAPT OR EVOLVE - they can acclimate and their success affects survival and reproduction. POPULATIONS CAN ADAPT OVER GENERATIONS. ADAPTATION VS ACCLIMATION - POP VS INDIVIDUAL -May be difficult to see what an individual is - some are clonal (exact same genome), with many clones persisting through many replications ADAPTATION - the plasticity gained in order to acclimate and survive gets inherited to the next generations. SHORTER-LIVED ORGANISMS: Clonal organisms may live for centuries - difficult experimental system. Most scientific research takes place within shorter time span. ex. Lizards in genus Anolis. Extreme freezing events affect populations that (on average) do not have as much tolerance to cold. ex. Populations at south end of study - high mortality from cold. Survivors have cold tolerance more like populations 500 km to the north. Northern pops don't change (no unusual level of mortality over generations). THE MORE EXTREME THE STRESS WAS, THE MORE THE ACCLIMATION LED TO ADAPTATION OVER GENERATIONS. Many stressors possible - cold, heat, dry, wet, not enough food. ACCLIMATION - type of plasticity associated with improving an individual's survival. ADAPTATION - result of WHICH organisms survive and reproduce over time. When environment changes, 4 responses: move, acclimate, adapt, die MOVEMENT: Does not mean "walk into better habitat," but: "GROW into better habitat," "Die in poor habitat" (picture trees growing in certain places) ex. Pine trees in southeast. Why not found everywhere? Combo of environmental factors - temp, precipitation, soil type, interactions between these How these organisms disperse is especially important for organisms that cannot move in their lifetime. MOVEMENT is distinct from behavior. Happens as a population. THINK OF THE TREES. Field guides have info on WHERE the organism has been found. Sometimes, maps show you boundaries that make sense, given PHYSICAL RESTRICTIONS TO MOVEMENT. (ex. elevations). Our empirical observations help us see limiting factors for range of a species. Better than a drawn (static) map: actual data points of observation. GBIF.org: global biodiversity info facility In addition to homeostasis, we need to use energy to grow and reproduce. BENIGN ENVIRONMENT: (picture triangle): There is a trade off between energy we use for growth and energy we use for reproduction. STRESSFUL ENVIRONMENT: Net result less available energy, so trade off is steeper. As we use up most of our little energy on reproduction, we quickly have very little left over for growth, and vice versa. "Stress" in animals manifests as production (expression) of cortisol, corticosteroids; HORMONES expressed by adrenal gland in vertebrates. As these increase, they shift the consumption of fat stores for fuel, increasing the "cost" of survival over time (need to use more energy to survive with stressors); also suppress the immune system (part of the fight or flight response). Stress limits the capacity for reproduction and growth. If environment has stressors, organisms must use up more energy to grow and reproduce (survive0, so they may become less able to do so. OCEAN ACIDIFICATION - increased CO2 in atmosphere dissolves in water to form carbonic acid, lowers pH of seawater. -For corals, changes respiration (oxygen consumption, protein content, fat content). -They are depleting their energy reserves for reproduction and growth. PHYSIOLOGICAL STRESSORS: predict higher stress and altered investment in immune regulation. HORMONES: Invertebrates (like vertebrates) also have STRESS HORMONES (norepinephrine, octopamine) that SUPPRESS IMMUNE FUNCTION (unregulated respiration, energy consumption, reduce growth and respiration). Plants have hormones responding to light and other stimuli, like auxin - controls growth but is light sensitive, helping plant grow toward light - level of light can influence overall growth, indirectly affect flowering/fruit/reproduction. EXAMPLE: Severe storms drive birds to migrate to lower elevation. This reduces their foraging time to find food. Variation in rainfall in Costa Rica associated with plasma corticosterone, fat stores, plasma metabolites, blood oxygen levels. Climate predictions include increased severity of storms. May limit high-elevation habitat use in breeding season.

Day 4 - Stress Tolerances Vary By Population

Day 4 - Stress Tolerances Vary By Population In cells without mitochondria, ONLY GLYCOLYSIS HAPPENS. Citric Acid Cycle - in mitochondria Turning sugar into ATP (Relates to "H" ions on the end). With oxygen, you get a far greater ATP yield. Traits vary within and among species, and that variation is OFTEN inherited. Traits may be discrete or continuous (often tells us their mode of inheritance). -Often, continuous traits involve interaction of expression of many genes. Acclimation - environment of cell or the organism it is within modifies DNA expression (transcription and translation). Adaptation - differential survival changes trait distributions. FITNESS - a combined measure of SURVIVAL AND REPRODUCTION A PHENOTYPE IS READY TO RESPOND TO SOME CHANGES. LESS ABLE TO RESPOND TO MORE EXTREME CHANGES, SUCH THAT IT IS STRESSED. STRESSORS to a phenotype - can be measured in ENERGY needed to maintain homeostasis, to ACCLIMATE (PLASTICITY) Photosynthesis creates chemical (potential) energy, metabolism (respiration) uses it for maintenance, growth, reproduction. Both require ENZYMES (proteins, translated from expressed RNA) that minimize the ENERGY NEEDED for the reaction to take place. Both are complex and often imperfect with MANY BYPRODUCTS OR DEPENDENCIES ON THE EXTERNAL ENVIRONMENT. Waste products are neurotoxic - important to get rid of. Enzymes formed from amino acids which individually have +/- charges and attract or repel water. Enzymes evolve to work in certain environment, so may change shape if temperature, salinity, etc changes. (DENATURE). Most organisms cannot survive in hot springs, because their PROTEINS WILL DENATURE. ATP - basis for energy in all living things. Breaking one of the phosphate groups off RELEASES energy. Adding a phosphate group REQUIRES energy. -Adenine is one of the nucleotides that builds up DNA, RNA, ATP. -Remove one of the OH groups on ribose, RNA becomes DNA. -Add the 'Adenine' rings to other chemical arrangements - you will see compounds like NADH, NAPDH, and FADH (all with the H ions on the end, which allows sugar to be turned into ATP). GLYCOLYSIS AND CITRIC ACID CYCLE: 2 phases: 1) "Investment Phase" 6 C glucose broken down to 2 molecules of: (Glyceraldehyde 3 Phosphate. C C C Pi). 2) "Payoff Phase" (more ATP produced than what came in) NAD+ turns into NADH, ADP turns into ATP. 2 C C C Pyruvate molecules produced. Some cells (ex. prokaryotes, red blood cells), or cells without oxygen, can only do Glycolysis - but, to get more energy out of food, OXYGEN AND MITOCHONDRIAL ENZYMES GET US MUCH FURTHER. FROM CITRIC ACID CYCLE TO OXIDATIVE PHOSPHORYLATION... 1) In presence of oxygen, this process generates a strong gradient of H+ ions across a membrane, and breaks the oxygen molecules to form water as a product. 2) That gradient drives ATP SYNTHASE to store chemical energy in the form of adding a phosphate to a group of ADP. 3) Without oxygen, spend 2 ATP to get 4 ATP... With oxygen, get far greater yield (varies by tissue and resource). All life carries out this basic process. Plants/Algae STORE energy (Photosynthesis), but still USE energy, as do animals, fungi, protists... Statistics are a way to quantify how distinguishable 2 samples (populations, for our purposes) are Ask if difference between 2 sets of data is larger than expected, if you assume they are drawn from distributions that are NOT DISTINCT. p value below 0.05 means it may be worth further study! COEPOD study found that CTMin was positively correlated with average winter temperature (populations in low temperature climates had lower CTMin). Species harbor diversity. How that diversity responds to environment affects its future. 2 ways that POPULATIONS become distinct: ADAPTATION AND DRIFT. ADAPTATION - when individuals in different habitats SURVIVE better, or have more OFFSPRING, because of some heritable trait from natural selection. DRIFT - when individuals in diff habitats rarely or never have the opportunity to cross/mate, because their population size is finite/limited. Every generation, the frequency of alleles and genotypes will change randomly. The longer this is true, they will end up being very distinct, even if no adaptation is necessary. So, these genetic changes can increase or decrease in a pop, simply due to chance. (MUTATIONS HAVE NO EFFECT ON FITNESS. THEY JUST INTRODUCE NEW ALLELES AND NEW VARIATION). MUTATIONS contribute to the diversity being acted upon. MIGRATION balances drift. MATE CHOICE can influence genotype diversity. EXCRETION OF (MOSTLY) NITROGENEOUS WASTE PRODUCTS - THESE ARE NEUROTOXIC BUT ALSO INFLUENCE THE ECOLOGY AROUND US. Autotrophs are collectors. Heterotrophs are scatterers (release food's carbon, minerals, and energy back into environment). Both still have the same metabolic and energy requirments linked to their environments. HOMEOSTASIS: Reflects how body responds to stress, maintains systems within a particular range (ex. human body temperature - thermoregulation). May include behavior, hormonal, or neural activity, extra use of ENERGY when body is outside of limits. Shivering when cold - need for more energy, thus more oxygen, to maintain body. Ectotherms (e.g. invertibrates) do not maintain tight control. Behavior and/or metabolic changes may lead to long periods of torpor (inactivity) and other life phases to survive the winter. Fever (in endotherms) needs release of energy, but appears to aid in healing/recovery process. OSMOREGULATION: Products of digestion, metabolism, etc. create waste - in particular, NITROGENEOUS wastes are formed from breakdown of proteins. Metabolism in general - forms AMMONIA, which can interfere with nerve and muscle cells in particular. Organisms need proper balance of water and salts to maintain cell structures. Removal of ions and nitrogeneous wastes is necessary for this as well. Cells and tissues are somewhat permeable by water, gas, and ions that are passively and actively exchanged. Organs for gas, water, salt, and nutrient exchange develop LARGE SURFACE AREA that interacts via diffusion or energetic processes. The same job must be accomplished by all other organisms (plants, fungi - largely DIFFUSION of water across membrane) Some do it just by diffusion - echinoderms, jellyfish, corals, sponges Single celled animals (protazoans) have an organelle that collects waste and discharges to exterior from time to time. Nephridia in worms excretes ammonia. Renal gland in mollusks (clams, snails) near the heart concentrates nitrogen in the form of ammonia. In all cases, methods for collecting and filtering water out of waste from metabolism, back into organismal blood or hemolymph or interstitial fluids!!!!!!! Nutrients get recycled, just like CO2, H20, and C6H12O6. Think of surface-area-to-volume ratio to understand how substances move into and out of organism.

When the presence of a particular allele guarantees the expression of a particular discrete phenotypic trait, we call this:

Dominance

Fermentation

Fermentation - processes that use an organic molecule to regenerate NAD+ from NADH, for reuse as an electron carrier for glycolysis to continue. In contrast, some organisms use an inorganic molecule (other than oxygen) as a final electron acceptor to regenerate NAD+ Both processes are ANAEROBIC (DON'T REQUIRE OXYGEN) and ENABLE ORGANISMS TO CONVERT ENERGY FOR USE. LACTIC ACID FERMENTATION: -Used by animals and some bacteria -In mammal red blood cells and skeletal muscle that has insufficient oxygen supply for aerobic respiration (ex. muscles tired out). In muscles, lactic acid produced must be removed by blood circulation and brought to liver for metabolism. Pyruvic Acid and NADH produce Lactic Acid and NAD+, and vice versa Enzymes that catalyze this - lactase dehydrogenase Inhibited by acidic conditions Once lactic acid is removed from muscle and circulates to liver, it can be converted back to pyruvic acid and further catabolized for energy. Alcohol Fermentation: Produces ethanol, an alcohol Pyruvic acid produces CO2 and Acetaldehyde Acetaldehyde produces Ethanol NADH produces NAD+ Fermentation of pyruvic acid by yeast produces ethanol in drinks ONLY CERTAIN PROKARYOTES USE ANAEROBIC CELLULAR RESPIRATION Many prokaryotes are facultatively anaerobic - can switch between respiration and fermentation, depending on availability of oxygen. Obligate anaerobes live and grow in absence of molecular oxygen All fermentation (except lactic acid) produces gas. Our body breaks down things besides glucose. HOW? Metabolic pathways are POROUS - substances enter from other pathways and leave for other pathways. Not closed systems! Many products of a pathway are reactants in another. When there is adequate ATP, excess glucose is converted to glycogen for storage. -Stored in liver and muscle, taken out if blood sugar drops -Allows ATP to be produced in exercise. Sluctose-disaccaride of glucose and fructose, broken down in small intestine Glucose, fructose, and galactacose - 3 dietary monosaccharides - absorbed in bloodstream in digestion. Proteins broken down by enzymes in cells. Usually amino acids are recycled into new proteins If excess amino acids or famine, some are put in glucose catabolism - converted into ammonia first. Liver synthesizes urea (urine) from this. CHOLESTEROL AND TRIGLYCERIDES connected to glucose pathway. Cholesterol Synthesis starts with acetyl CoA and proceeds in one direction. ATP not produced. Triglycerides store twice as much energy as carbohydrates. Glycerol can be phosphorylated and proceeds through glycolysis. Fatty acids broken down into 2 C units that enter citric acid cycle. OVERALL: GLYCOLYSIS: Carbohydrates, some amino acids, Glycerol. PYRUVATE OXIDATION: Some amino Acids CITRIC ACID CYCLE: Fatty Acids and some amino acids OXIDATIVE PHOSPHORYLATION: just ATP

ENDOCRINE SYSTEM

ENDOCRINE SYSTEM PRODUCES HORMONES THAT CONTROL DIFFERENT BODY PROCESSES. Coordinates with nervous system to control other systems. HORMONES circulate through the body and stimulate response in cells that have receptors able to bind with them. Released into blood, which carries them to target cells where they elicit a response. Cells that secrete hormones located in ENDOCRINE GLANDS (ORGANS) -ex. Pancreas, adrenal gland, thyroid gland EXOCRINE GLANDS secrete chemicals through ducts that lead outside the gland (not to blood). -ex. Sweat produced by sweat glands carried to the skin -Pancreas has both endocrine and exocrine functions Hormones cause changes in target cells by binding to specific INTRACELLULAR HORMONE RECEPTORS UP-REGULATION - number of receptors increases in response to rising hormone levels, making cell more sensitive to hormone and allowing for more cellular activity. DOWN-REGULATION - opposite ENDOCRINE GLANDS - pituitary, thyroid, parathyroid, adrenal glands, gonads, pineal, pancreas PITUITARY GLAND/HYPOPHYSIS - at base of brain, attached to hypothalamus. Posterior and anterior lobes produce different hormones. Anterior pituitary secretes 6 hormones that stimulate cellular activities (ex. protein synthesis) that promote growth. Postterior - part of brain extending down from hypothalamus, containing nerve fibers. THYROID GLAND - in neck. Butterfly shaped. Synthesizes hormone thyroxine (T4) and triiodothyronine (T3) to stimulate metabolic activity and increase energy use. Calcitonin released to reduce excess C ions. Most people have 4 PARATHYROID GLANDS (in posterior of thyroid), produce parathyroid to increase Calcium levels. ADRENAL GLANDS - on top of each kidney. Secrete stress-response hormones for fight-or-flight. (These hormones are stimulated by sympathetic nervous system from hypothalamus). -ex. cortisol PANCREAS - contains exocrine cells that excrete digestive enzymes and endocrine cells that release hormones. GONADS - male and female testes and ovaries - produce steroid hormones testes produces androgens (ex. testosterone) ovaries - estrogen and progesterone Heart, kidneys, intestines, thymus, and adipose tissue - primary function non endocrine but still possess endocrine functions THYMUS - behind sternum. Produces thymosins. Hormone production and release primarily controlled by NEGATIVE FEEDBACK.

Chapter 11. Evolution.

EffectChapter 11. Evolution. 11.1) Evolution - ongoing process through which characteristics of species change and through which new species arise. Plato said species were unchanging. But other ancient greeks said otherwise James Hutton and Charles Lyell influenced Darwin's thinking, said that geological change occurred gradually with small changes over long periods. Jean Baptiste Lamar published INHERITANCE OF ACQUIRED CHARACTERISTICS - said modifications in an individual caused by its environment, or use and disuse of structure, could be inherited and bring change in species This was discredited, but he was 'founder of doctrine of evolution' Naturalists: Charles Darwin and Alfred Russell Wallace traveled world and conceived of evolution -Darwin found what seemed like several species of finches on island derived from one species on mainland. Called it NATURAL SELECTION. -characteristics are inherited -more offspring are produced than are able to survive - resources limited. Competition. -Offspring vary among each other in regard to their characteristics, and those variations are inherited. -Change in populations over generations - 'descent with modification' -Darwin wrote 'On the Origin of Species' -Evolution of beak/bill size in species in response to changing conditions on the island. Natural Selection can only take place if there is VARIATION among individuals in a population - must have GENETIC basis, so that selection will lead to change in the next generation. Genetic diversity comes from 2 main sources - mutation and sexual reproduction. Mutation - ultimate source of new alleles in a population. -Mutation ma reduce fitness -May be beneficial to fitness -Or, neutral mutations - no effect on fitness ADAPTATION - heritable trait that aids the survival and reproduction of an organism in its present environment. Over time, increases the match of the pop with its environment. Environmental conditions change, so the same traits don't always have the advantage. DIVERGENT EVOLUTION - 2 species evolve in different directions from a common point. CONVERGENT EVOLUTION - when similar structures arise through evolution independently in diff species (ex. bats and insects both have wings - ANALOGOUS STRUCTURES - similar in function and appearance but do not share a common ancestor). Wings of hummingbird and ostrich - HOMOLOGOUS STRUCTURES - descended from a common ancestor. Wings share similarities (despite differences from DIVERGENCE). Shortly after Darwin, Mendel did his work. Genetics and evolution were integrated in MODERN SYNTHESIS. 1940s. Accepted today. Describes how evolutionary processes (ex. natural selection) can affect a population's genetic makeup, and, in turn, how this results in gradual evolution of a population and species. Also connects GRADUAL change of a population over time (MICROEVOLUTION) with processes that give rise to a new SPECIES + higher taxonomic groups with widely divergent characteristics (MACROEVOLUTION). POPULATION GENETICS - early 20th century - what happens to all alleles in a population -Evolution is a change in frequency of alleles in a pop. -Frequency = # of copies of that allele / all copies of the gene in the population -All frequencies should add up to 100%, so an increase in frequency of one allele always means a corresponding decrease in one or more of the other alleles. Highly beneficial alleles may, over a few generations, become "fixed" so that every individual of the population will carry the allele. Detrimental alleles may be swiftly eliminated from the GENE POOL, the sum of all alleles in a pop Hardy-Weinberg equilibrium - If there are no factors that affect an allele frequency, those frequencies will remain constant from one generation to the next. Individuals would look the same, and this would be unrelated to whether the alleles were dominant or recessive. 4 most important evolutionary forces, which will disrupt the equilibrium - 1) Natural Selection 2) Mutation 3) Genetic Drift 4) Gene Flow (Migration into or out of pop) 5th factor (nonrandom mating) will only shift genotype frequencies, not allele frequencies (so does not directly cause evolution). Mutation creates one allele out of another and changes an allele's frequency by a small amount each generation. (Low, constant mutation rate). If natural selection acts against this allele, it is removed from population at a low rate. Balance between selection and mutation. This is why genetic diseases remain at low frequencies. Genetic drift causes random changes in allele frequencies when populations are SMALL. If 2 pops of a species have diff allele frequencies, gene flow (migration) of individuals between them will cause frequency change in both pops. There is no pop where one or more of these processes is operating. (Equilibrium being broken in every pop). Sexual Selection - leads to evolution of dramatic traits that may seem maladaptive in terms of survival but enhance ability to reproduce. -Occurs in 2 ways: male-male competition for mates and female selection of mates -Sexual selection can proceed against a character's enhancement (neg impacts male's survival) - ex. bright feathers attract females, but also attract predators. 11.2) NATURAL SELECTION -Over time, allele producing favorable trait will increase in pop, and offspring benefit IF environmental conditions stay the same. MUTATION - source of new alleles!! Can change one allele into another, but net effect isa change in frequency. Effect on evolution is small unless it interacts with other factors (like selection) May produce an allele selected for, against, or neutral Harmful mutations are removed from pop by selection, and will only be found in low frequencies equal to mutation rate. Beneficial mutations spread through pop via selection, slowly. Mutation is ultimate source of genetic variation in all populations. GENETIC DRIFT: -Effects of chance -Most important in small pops Would be absent in a pop with infinity individuals Due to chance events, alleles may not make it into the next generation ex. if 1 individual in a pop of 10 dies, 10% of that gene pool is lost (won't get passed down). There is a chance that an allele is lost forever. Effect of drift on frequencies is greater the smaller the pop is. Its effect is also greater on an allele with a frequency far from 50%. Drift will influence every allele, even those being naturally selected. Over time, genetic drift can lead to elimination of an allele from a pop by chance. Genetic drift can also be magnified by natural or human caused events, such as a disaster that kills a large portion of pop - BOTTLENECK EFFECT - results in large portion of genome suddenly being wiped out. ex. Disaster may kill for reasons related (ex. freezing) or unreleated (ex. volcano) to traits. FOUNDER EFFECT - some portion of pop leaves to start a new pop, or a pop gets divided by a physical barrier. These individuals are unlikely to be representative of entire pop (may all share a mutation). -Occurs when the genetic structure matches that of the new pop's founding fathers and mothers. GENE FLOW/MIGRATION - FLOW OF ALLELES in and out of pop with migration of individuals or gametes. -ex. Many plants send their seeds far and wide. 11.3) Fossils show progression of evolution ex. Horses in North America. Transition fossils - those sharing intermediate anatomy between early and later forms. As the horse has evolved, has belonged to different genuses. Now, in genus Equus, with several species. ANATOMY: Evidence for evolution in structures in organisms with same form. Bones in appendages of a human, dog, bird, and whale all share same overall construction. (Common ancestor). Despite divergence over time, these species have homologous structures. VESTIGAL STRUCTURES - ex. penguin wings - structures in an organism with no apparent function, and are residual parts from a past ancestor. Also evidence of evolution: convergence of form in organisms in shared environment (without shared ancestor). -ex. White feathers on birds and white fur on foxes in arctic to blend and hide from predators. Embryology (study of development of anatomy of an organism to its adult form) also provides evidence of evolution. ex Human embryos have tails and gills. Embryos of unrelaed species often similar because mutational changes that affect embryo during development can cause amplified differences in adult, even while embryonic similarities are preserved. Broad groups that evolved before the breakup of supercontinent Pangaea are distributed worldwide. Australia and islands have abundance of endemic species (found nowhere else) due to long isolation and water preventing migration. But, species show distant relationships to ancestors on mainlands. -Evidence of common ancestor in the universality of DNA as genetic material, and near universality of genetic code and machinery of DNA replication and expression. -Divisions between 3 domains reflected by differences in ribosomes and membranes. -Sequences are the same. -Evolution of new functions for proteins commonly occurs after gene duplication events. (Mutation where whole gene copies are added). -Allows for one copy to modify via selection, mutation, or drift, while 2nd copy continues to produce protein. This continues until protein functions a new way. 11.4. Speciation. Species - potentially/actually interbreeding individuals One species is distinguished by possibility of mating between individuals from each species to produce fertile offspring -There are exceptions - many species are similar enough that hybrid offspring are possible. (May have descended from a single species, and speciation may not be completed). SPECIATION - formation of 2 species from one original species. -Darwin drew it out. 2 new pops must be formed, and they must evolve ina way to make it impossible for pops to interbreed. -ALLOPATRIC SPECIATION - speciation in "other homelands" involves geographic separation of pops from a parent species and subsequent evolution. -SYMPATRIC SPECIATION - speciation in same homeland. More than 2 species can form at 1 time, but less likely. SPECIATION THROUGH GEOGRAPHIC SEPARATION - ALLOPATRIC: When pops become geographically continuous, "free flow" of alleles is prevented. When separation lasts long, the 2 pops are able to evolve along diff trajectories. Allele frequencies become more different as new alleles independently arise by mutation in each pop. Env conditions will differ, causing natural selection to favor diff adaptions in each group. Diff histories of drift (enhanced because pops are smaller than parent pop) will also lead to divergence. Reproductive Isolation - the inability of 2 pops to interbreed. Prezygotic mechanisms - operate before fertilization - ex. timing, choice of mate size. Postzygotic mechanisms - operate after fertilization - genetic incapabilities that prevent proper development of offspring Selection favors those who mate with THEIR OWN POPULATION Depending on how intense the separation is, organisms of the 2 pops may still move back and forth and continue gene flow Allopatric processes - 2 categories - -DISPERSAL - a few members of a species move to a new geographical area. -VICARIANCE - a natural situation arises to physically divide organisms. Further distance: more likely for speciation to take place. ADAPTIVE RADIATION - multiple speciation events originate from a single species. SPECIATION WITHOUT GEOGRAPHIC SEPARATION - SYMPATRIC -One type can begin with chromosomal error or a hybrid individual with too many chromosomes -Polyploidy - a cell or organism has extra chromosomes. Results when all chromosomes move into one cell instead of separating. -Autopolyploidy - polyploid individual has 2 or more complete sets of chromosomes from its own species. -Immediately, these individuals will be able to reproduce only with those of the new kind, and not with ancestral species. -Other form of polyploidy when individuals of 2 species reproduce and form offspring called Allopolyploid. Gametes of 2 species combine. It takes 2 generations before viable fertile hybrid results. Normal gamete of species 1 mates with polyploid gamete of species 2, forming polyploid gamete child, who mates with normal gamete to form the ALLOPOLYPLOID. (takes 2 generations of mating) Most chromosomal abnormalities in animals are lethal. Takes place more commonly in plants. Sympatric speciation can also take place in other ways than polyploidy. -ex. 2 types of cichlid fish live in same lake, but they have come to have diff morphologies that allow them to eat different food sources. (Used to just be one type of fish). Host specificity of parasites (choosing a host to live on) is a common cause of sympatric speciation. 11.5) MISCONCEPTIONS -Evolution is a theory, but a scientific theory is something that has been tested. Non scientists use the word "theory" to describe a hunch. Evolution is not a hunch Individuals do not evolve. Populations do. Evolution - change in genetic composition of a pop over time, specifically over generations Evolution doesn't try to explain the origin of life. Explains how populations change over time - origin of species. Difficult to research origins of life. Organisms do not evolve on purpose! The variation that natural selection works on is already in a population, and does not arise in response to an environmental change. ex. Gene to produce beneficial phenotype is already present. Evolution is not goal directed. Species do not become "better" over time - they just track changing environment with adaptations. Variation and environment both constantly changing in a non directional way. Evolution is not controversial among scientists! Other theories shouldn't be taught. No viable alternative theories. Biology is silent on the existence of God.

Proteins that aid in metabolism are called ____ and act by lowering the energy necessary for a product to be formed or taken apart.

Enzymes

DNA replication works well, because the two strands of DNA in each chromosome are exactly the same.

FALSE

Mendel's experiments with pea plants, evaluating discontinuous traits such as flower color, supported the notion of "blending inheritance" to describe the phenotype of offspring.

FALSE

Only vertebrate animals have hormones.

FALSE

The process of glycolysis requires using the same amount of ATP as is created during this step.

FALSE (you get more ATP out of it than you put in)

All production of ATP occurs in the mitochondria.

False (not for Prokaryotes).

The process called glycolysis breaks a _________ molecule, which has 6 carbon atoms, into 2 molecules of pyruvate, each of which have 3 carbon atoms.

GLUCOSE

If the allele frequencies are expected to randomly diverge in two distant locations because of genetic drift and new mutations arising, what mechanism can "homogenize" this diversity and maintain similar frequencies in both locations?

Gene Flow/Migration back and forth. (Keeps allele frequency from changing as much, keeps alleles from becoming lost or fixed).

The comparable arrangement of bones in the forelimbs of vertebrates is an example of ________ evolutionary origin.

Homologous

When 2 individuals sexually reproduce, the alleles they contribute for a particular locus or trait may have the same effect on that trait. This is an instance when the genotype of offspring is called:

Homozygous

LECTURE 5 - PHOTOSYNTHESIS

LECTURE 5 - PHOTOSYNTHESIS AUTOTROPHS - plants, algae, some bacteria - collectors - concentrate carbon, energy, and minerals into organic matter (food) HETEROTROPHS - scatterers - animals, fungi, most bacteria - digest food and release its carbon, energy, and minerals back into environment Both still have same metabolic and energetic requirements linked to environment. The offspring of a photosynthetic organism is given just enough maternal resource to get their own system up and running. CHLOROPHYLL: repeating structure held together in center with magnesium Light energy "excites" an electron in molecule which gets transferred to another reaction in photosynthesis pathway A water molecule is broken to donate electrons back to chlorophyll, generating oxygen as a byproduct Some biochemical reactions only happen when there is light energy, while others happen all the time 2 enzymatic reactions. One splits water to generate electrons. The second accepts the electrons to charge NADP+ into NADPH (helping to create storage of H ions). CALVIN CYCLE: ATP from light dependent reactions, NADPH to provide ions to help generate the bonds of sugar. In NADPH, A is adenine, and H creates gradient with H ions. CO2 from atmosphere is source of C for sugar. Taking sunlight and water and chlorophyll (light reactions), ADP is recharged to ATP, and NADP+ is recharged to NADPH -Same chemical/potential energy as in other forms of metabolism Then, other enzymes (Calvin Cycle) can... -lower activation energy of combining C molecules. -burn energy to do that C combining reaction. Same chem reaction for all phases of metabolism: Glycolysis, Citric Acid Cycle, Electron Transport Chain. If light is not absorbed, it is reflected (green) Green of trees, etc. Chlorophyll a (Chl a) - satellites can identify abundance of Chloroformed a, this abundance of photosynthesis. Where there is productivity, more life will be there to take advantage. -Productivity - rate at which solar energy is captured in sugar molecules. Carbon fixation. Logarithms transformation of mean visible spectrum puts most of energy from our sunlight in green range (but it all mixes to look white) Peak light intensity is highly variable, and biochemical reactions work best when all enzyme pathways work at similar rate. Survival of cellular machinery is at CONSISTENT ENERGY HARVEST. PRODUCTIVITY - food (C fixation) -C sequestration (removal from the atmosphere) Enzymes will function best in certain environment range (sometimes a mix of pigments) Corals are animals that photosynthesize via intracellular symbiotants (dinoflagellates, brown algae), a SYMBIOSIS (2 organisms benefit through nutrient sharing)... Dinoflagellates gain Ca/Mg from corals and other nutrients, corals gain from products of photosynthesis. All 3 domains of life have organisms that photosynthesize. DNA sequence dissimilarity - how Archaea were discovered. There are different plant strategies for photosynthesis -ex. C3 - most common - everything happens in one place, but can be heat/oxygen inhibited -C4 grows best when hot -CAM - method of cacti - only take in CO2 at night, and store it Diversity of photosystem enzymes/pigments, of chloroplast coding DNA expression, diversity of organisms carrying chloroplasts PHENOLOGY - study of timing of biological events -good to look at how global warming affects photosynthesis Plants blooming earlier in the year now. It is warmer. Red tide grows so quickly that other plants are starved for light. Toxins released by Karenia Brevis are devastating to fish and other sea life. What stresses a plant out? Freezing/heat, like an animal. Flood and drought. Too much or too little nutrients (ex. N and phosphorus) Temp limits photosynthesis (growth and reproduction limited to where conditions are right). Few organisms are everywhere. It is not random! SPECIES DISTRIBUTION MODELS: observations of where an organism can be found, we can use data from that ;location... Seasonal temp, rainfall Elevation Soil type, prey items ...To estimate all places that organism should be able to persist - help see limitations to movement, or where an organism may spread toward Stress has consequences that are based in energy Stresses affect how food is made and stored, how it is used for growth and reproduction Diversity of genomes means some have better fitness than others in a particular environment

Some byproducts of metabolic processes can be toxic in high concentrations.

TRUE

Crossing a white flower with a red flower and getting offspring that are all pink flowers is a form of:

INCOMPLETE DOMINANCE

The number of receptors available to respond to a hormone can change over time, resulting in increased or decreased cell sensitivity. In up-regulation, the number of receptors increases in response to rising hormone levels, making the cell more sensitive to the hormone... The change in number of receptors reflects:

Increased expression of genes that make the enzymes that are part of these receptors.

A simple way to describe an autotroph is:

It does not have to eat other organisms in order to survive, grow, and reproduce

Ectotherms do not use metabolic energy to maintain internal temperature; this typically means that oxygen consumption increases with the external environment.

TRUE.

Lecture 1

Lecture 1 MACROCYSTIS - largest brown algae, forms kelp forests - source of productivity (biological energy from the sun). Organismal Biology, made up of: Ecology: how organisms interact with each other and the env Evolution: how life changes over generations Diversity, Structure, Function - how an organism regulates itself from cellular level up to whole organism to persist in an environment. 2 components of biological fitness - survival and reproduction Niche of an organism - how diff factors come together to allow a particular organism to survive and reproduce All biodiversity is part of a study of TRAITS whether discrete or continuous TRAITS - identifiers, measurements, parts that help us categorize diversity. -Some discrete (ex. eye color), some continuous (ex. hight) Walking stance, cognition, body hair, and more classify us as homosapiens Biology: study of life and how it is organized, how it functions A representative sample lets us summarize diversity with statistics Bio-relevant population often defined by where it is from or what resources it uses Bar graph: distinct categories Histogram: slices of a distribution. Helps us predict things about pop Some traits are heritable, some depend on environment DISTRIBUTIONS ARE DEFINED BY THE SAMPLE, NOT THE OTHER WAY AROUND Continuous distributions may be split into categories in a histogram. Data used to estimate distribution. EVERY TRAIT HAS A DISTRIBUTION, GENERATED BY GENETICS (HERITABLE DIVERSITY) AND INTERACTIONS WITH ENV, AND INTERACTIONS WITH OTHER TRAITS. Are we (homosapiens) Neanderthals? More human species through history than we thought. As many as 9 Homosapiens - high and rounded globular braincase and narrow pelvis. Also shape differences in ear bones (compared too neanderthals) Biological species concept - species are reproductively isolated entities (breed within themselves but not with other species) So, species that interbreed with each other aren't distinct species. Theory: Homosapiens and Neanderthals interbred outside Africa 55,000 years ago So we inherit Neanderthal DNA (2% of genome) Many species can and do interbreeed The issue is with the bio species concept, because species diverge from each other gradually, and it takes millions of years for full reproductive isolation to develop In author's view, physically, they are 2 distinct species. We share behavior with them, but that should be excluded because behavior spreads more quickly and easily than biological traits.

Lecture 2 - Inherited Diversity of Life

Lecture 2 - Inherited Diversity of Life 2 populations of bottlenose dolphins - Resident in estuaries and transient moving up and down coast POPULATIONS - diversity of alleles and traits will vary among groups of organisms that we may otherwise consider to be the same type of species. Diversity packaged into a single celled embryo is modified and expressed to function best in its env (the body it grows into is an env) If environment changes, a cell or organism may be stressed and needs more resources (oxygen, water, food) Life has conditions it does well in, or poorly. It will find a way to BE in those conditions, or it cannot thrive. CONTINUOUS TRAITS: histogram: complex genetic influences - height, length, respiratory capacity, number of fruits on a tree DISCONTINUOUS TRAITS: bar chart: often categorical, simpler, smooth or wrinkled, red pink or white Prior to Mendel, we thought there was blending inheritence. Plausible when you study most continuous traits. INHERITENCE OF TRAITS Discrete traits: offspring did NOT have a blend of traits (yellow OR green, round OR wrinkled). First hybrid cross (F1) often 100% showed one parent's trait. F2 second generation, both traits appear in 3:1 ratio. Indicated that factor controlling both traits was INHERITED from both parents, one dominant type. GENES are regions that contain information to make enzymes and other protein products. Each copy is called an ALLELE, and may or may not have the same DNA sequence as each other 2 alleles together - GENOTYPE Dihybrid cross: both parents are heterozygous NOT ALL GENES HAVE ALLELES THAT ARE DOMINANT/RECESSIVE - ex. incomplete/additive dominance All diploid organisms have 2 alleles per gene Among population, many alleles! Some genes are physically linked on sex chromosomes, helps determine sex characteristics. Isolation in space, time, or ability has consequences. Language is a learned PHENOTYPE that influences mating patterns. Defining populations allows comparisons - how diverse? A population is a hypothesis - samples of traits/DNA diversity are taken from locations, times, environments, to test THE HYPOTHESIS THAT THEY BELONG TO A COLLECTION OF INDIVIDUALS. A NULL HYPOTHESIS IS THAT DIFFERENT SAMPLES ARE INDISTINGUISHABLE, GIVEN THE DATA. OFTEN, WE CAN FIND DISTINGUISHABLE TRAITS/DNA. IF WE CAN'T DISTINGUISH/DEFINE A POP, NOT A GOOD HYPOTHESIS. An individual is a data point IN a pop. Standard Deviation: mean difference FROM the mean of the sample (indicates trait variation among individuals). Populations compared with statistics Individual can only be studied in its lifetime. Pop persists and can be studied for how it changes and responds to environment. DNA contains mistakes that happen every time its replicated - MUTATIONS. Only passed on through replication. (So, only a small amount of my mutations will pass down to my kids). May happen within an organism's lifetime. EPIGENETICS - not mutations, but MODIFICATIONS. (Env influences causing genes to turn on/off). Mutations happen via chemical exposure, UV exposure, and random/unknown processes (often but not always fixed by enzymes). Genes turning on to transcribe DNA: Expression of genes: quantity/rate of RNA written from that code - changes in diff cells/tissues in an organism -cells modify cells with chemical signals -env in a cell is in can stimulate DNA modification with chemical markers (epigenetic info) that more permmanently regulates gene expression -History of individual (environment, or that of parent) affects expression (plasticity) -EPI (above, on, over, in addition to) Life responds to its environment, within same generation or in the next. EPIGENETIC TAGS - when a change in your environment causes genes to turn on/off - can be passed down. DNA is effectively identical throughout an organism - descended from one cell But diff cells function distinctly Multi celled organisms develop with each cell in the "environment" of where they are relative to others. Genes may express differently in diff external environments. Mammals normally born producing gut lactase, but with age we turn the gene off. Some have a mutation in the MCM6 gene, keeping it on. Populations of cells AND humans differ by their environments. Populations of cells have ENVIRONMENTS WITHIN THE BODY.

Enzymes make other compounds by binding the components together in a way that:

Lowers the activation energy necessary for a reaction to take place.

A hypothesis must be:

Testable and falsifiable

In which of the following pairs do both evolutionary processes introduce new genetic variation into a pop?

Mutation and gene flow.

Genetic diversity in a population ORIGINATES in two ways:

Mutation and sexual reproduction

Diffusion gradients are necessary to move ions and wastes out of the body in kidneys (in vertebrates; in invertebrates this may be called NEPHRIDIA), a process broadly called:

OSMOREGULATION

If you know the allele frequencies in one generation, and you predict what genotype frequencies will be in the next generation, and they are different from your prediction:

One of several mechanisms of evolution has altered the frequencies.

Ions and electrolytes and water are maintained at proper levels in a marine fish. example of:

Osmoregulatory Homeostasis.

The most fundamental molecule necessary to get the most energy out of a sugar molecule is:

Oxygen

____________ is needed to burn the stored energy in our cells and make the energy available for proper function and regulation of cells.

Oxygen

PHOTOSYNTHESIS

PHOTOSYNTHESIS AUTOTROPH - produce its own food - plants, certain types of bacteria and algae PHOTOAUTOTROPHS - require sunlight and Carbon from CO2 -ex. plants, algae, cyanobacteria HETEROTROPHS - consume other organisms to obtain energy and Carbon In plants, photosynthesis takes place mainly in leaves Process occurs in middle layer called MESOPHYLL Gas exchange of CO2 and O2 occurs through small, regulated openings called STOMATA Photosynthesis takes place in CHLOROPLAST organelle - has a double (inner and outer) membrane that forms stacked disc shaped THYLAKOIDS. In this membrane are molecules of CHLOROPHYLL, A PIGMENT (absorbs light) through which it begins. Responsible for green color. A stack of thylakoids is a GRANIUM, and surrounding space is STROMA. 2 stages - Light Dependent Reactions and Calvin Cycle. LIGHT-DEPENDENT - with use of water, chloroplasts absorb light energy and convert it to chemical energy. Release oxygen from hydrolysis of water as a byproduct. CALVIN - in stroma, chemical energy drives capture of C in CO2 and subsequent assembly of sugar. 2 reactions use carrier molecules to transport energy from one to the other. LIGHT-DEPENDENT REACTIONS: Autotrophs only use a specific component of sunlight Solar energy travels in waves Can measure WAVELENGTH crest-crest or trough-trough ELECTROMAGNETIC SPECTRUM - range of all possible wavelengths of radiation. Visible light is only one type of energy from the sun. Short, tight waves carry the most energy. High energy waves (ex. X rays and UV) can be harmful. In plants, pigment molecules absorb only visible light for photosynthesis. Pigments reflect the color of the wavelengths they cannot absorb. All photosynthetic organisms contain a pigment called CHLOROPHYLL A (humans see as green in plants). Other pigment types include Chlorophyll B and carotenoids. ABSORPTION SPECTRUM - pattern of wavelengths a pigment absorbs from visible light. Not all photosynthetic organisms have full access to sunlight. Light Dependent Reaction begins in grouping of pigment molecules and proteins called a PHOTOSYSTEM. Pigment molecule in photosystem absorbs one PHOTON at a time, and photon travels until it reaches a CHLOROPHYLL, causing an electron to get excited and break free. A molecule of water is split, releasing an electron and forming O2 and H+ in thylakoid space. In photosystem II, electron travels along a series of proteins. (More details in book) Electron transport system uses electron's energy to pump H+ ions into thylakoid interior. A pigment molecule in photosystem 1 accepts this electron. Energy absorbed by sunlight is stored by ATP and NADPH Chemical energy stored in these Potential energy is stored as chemical energy in ATP through CHEMIOSMOSIS - movement of H+ ions through ATP Synthase, moving down electrochemical gradient from high to low concentration. CALVIN CYCLE: Cell now has fuel needed to build food in form of carbohydrate molecules, which will have a backbone of C atoms. CO2 enters chloroplast through stomata and diffuses into stroma of the chloroplast - site where sugar is synthesized. 3 basic stages: fixation, reduction, regeneration. CARBON FIXATION - CO2 is fixed from inorganic to organic Reduction - gain of an electron by an atom or molecule Stage 1: enzyme RuBisCO incorporates CO2 into organic Stage 2: organic molecule reduced Stage 3: RuBP is regenerated so cycle can continue. Prokaryotic (ex. cyanobacteria) autotrophs have infoldings of plasma membrane for chlorophyll attachment and photosynthesis -no organelles (no chloroplast) Carbohydrates (compared to ATP) much more stable reservoirs for chemical energy. Photosynthetic organisms also have mitochondria and undergo respiration.

The study of how allele frequencies change through time or across space is called:

POPULATION GENETICS.

Is the citric acid cycle aerobic or anaerobic?

Part of this cycle is considered an aerobic pathway because the NADH and FADH2 produced must transfer their electrons to the next pathway in the system, which will use oxygen. If oxygen is not present, this transfer does not occur.

Any measure or categorization of the traits of an organism is called the ____

Phenotype

___________ is controlled both by the genetic information of an organism as well as the environment it lives in.

Phenotype

As a multicellular organism develops, the position of each cell, and signals from the cells around it, determine its function and what proteins it makes. When an organism experiences a new environment, that experience may alter the rate and abundance of proteins being made in its cells. In both cases, this is controlled by:

Rates of DNA transcription

Adding a phosphate group to AMP (Adenosine Monophosphate) or ADP (Adenine Diphosphate) is done to:

STORE CHEMICAL ENERGY

Heavy rainfall in the tropics may reduce the time that birds have to search for food, leading to elevated corticosterone in their blood. This is an indicator of:

Stress

One of your professors hires you to work in the UGA greenhouses and asks you to cross-fertilize some pink flowers, that is: take pollen from a male pink flower and brush onto the pink flowers from a female plant. Seeds were collected and grown and in the next generation you count 250 red flowers, 500 pink flowers, and 250 white flowers. From this information you hypothesize:

The alleles causing color in these flowers exhibit incomplete dominance. (And both parents were Aa heterozygous).

For a population of organisms to die:

The birth rate must be lower than the death rate.

A chemical description of photosynethis is: ____ What is the reverse of this equation:

The reverse represents glycolysis, the citric acid cycle, electron transport chain, and oxidative phosphorylation.

What do the phenology data from peak flowering of cherry trees in Tokyo and the timing of river ice melting in Alaska have in common?

The timing of these events has tended to occur earlier in recent decades.

A key distinction between mass mortality of individuals in a population caused by disaster like volcanic eruption, and mass mortality of individuals caused by an extreme cold winter, is:

There is unlikely to be heritable variation in the ability of an individual to survive a volcanic eruption.

By definition, a brand new mutation is very rare in a population (frequency of 1/2N, where N is the number of individuals and there is a diploid genome). Since genetic DRIFT allows for RANDOM CHANGE in frequency either UP OR DOWN, what do you predict happens to MOST new mutations?

They are lost (no individuals have it). (Remember, it is very easy for an allele to become lost due to drift, especially in a small pop).

At high temperatures, the rate of photosynthesis may rapidly decrease even when there is plenty of water, sunlight, and carbon dioxide.

True

Considering the principles or tenets of Darwin's theory of natural selection - 1) individuals within species are variable 2) some of this variation is heritable 3) in every generation, more offspring are produced than survive 4) those traits that provide an advantage will be represented at higher frequency in the next generation - EACH OF THESE IS A SIMPLE TESTABLE HYPOTHESIS.

True

Energy produced or consumed by an organism is used for metabolism, growth, and reproduction; increasing the amount of energy required for any of these life processes requires reducing the amount of energy going to another.

True

Increased temperatures may cause proteins to denature, meaning they unfold and do not work correctly.

True

Individuals in 2 distant locations likely exhibit non-random mating with respect to all individuals in the species (likely to mate with the individuals in THEIR location).

True

One thing an individual organism cannot do when the environment changes is adapt.

True

Skin color alone tells us very little about the genetic diversity a human carries associated with other traits or their susceptibility to disease.

True

When you go for a long run and end up with leg cramps, your muscles have begun a fermentation process to maintain regular metabolic cycles.

True

At high temperatures, generation of reactive oxygen molecules by chlorophyll may rapidly decrease.

True.

Chlorophyll a specifically REFLECTS green light, which is why plants are green.

True.

Endotherms use additional energy to maintain their body temperature at a set point.

True.

Heterotrophs are incapable of photosynthesis and must get their energy from eating other organisms.

True.

Most of the production of ATP during oxidative phosphorylation is "powered" by formation of a strong gradient of hydrogen ions.

True.

Mutations happen in many independent ways, including the change of a nucleotide or deletion (or replication) of part of genome. If some proteins are easily affected by mutation, they may be important and cause a similar phenotype, but it doesn't mean the same mutation (to create the same allele) is necessarily common. ex. Cystic Fibrosis: many different mutations can lead to an allele that causes this particular disease, with around 1000 new diagnoses of this disease every year. SO, the phenotype is scored one way, but the mutations that cause the phenotype may happen in independent ways. Continuous "mutation to create one allele out of another" is not at all directed to be that specific... Mutations just happen and they have effects.

True.

Triglycerides are a form of long term energy storage.

True.

When biologists talk about a model system, we mean that the organism has traits that make it useful for answering a question that is relevant to a much broader range of biodiversity.

True.

MITOCHONDRIA

WHERE METABOLISM TAKES PLACE

If you go on a diet to lose weight, you should be burning more energy than you are taking in. This would suggest:

You are generating ATP slower than you are breaking it down.

All organisms require:

a source of energy