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BIO152 Exam Prep Notes

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Fiona Rawle

Bio152 Exam Notes - Organisms obtain & use energy, made up of cells, process info and replicate - Populations evolve, and therefore organisms eventually evolve - Cell theory: all organisms are comprised of cells and all cells come from pre-existing cells. - Theory of evolution by natural selection: species change through time because individuals with certain heritable traits produce more offspring than others - Phylogenetic tree is a representation of the evolutionary relationships - Biologists ask questions; generate hypotheses to answer them, and design experiments or make observations that test the predictions All living organisms share five fundamental characteristics 1) Energy  all organisms acquire and use energy. 2) Cells  all organisms are made up of membrane-bound cells. 3) Information  all organisms process hereditary information encoded in genes as well as information from the environment 4) Replication  all organisms are capable of reproduction 5) Evolution  populations of organisms are continually evolving - All scientists ask questions that can be answered by collecting data Hypothesis testing is a two-step process: 1.  State the hypothesis as precisely as possible and list the predictions it makes. 2.  Design an observational or experimental study that is capable of testing those predictions Food competition hypothesis - long necks evolved because those with long necks can reach food unavailable to other mammals. Predictions: – Neck length is variable among giraffes. – Neck length in giraffes is heritable. – Giraffes feed high in trees. Simmons and Scheepers tested the food competition hypothesis and found that the third prediction isn’t true. Thus, there may be better alternative hypotheses to explain neck length in giraffes. Alternative hypothesis: giraffes evolved into having long necks because long neck males win more fights and father more offspring (sexual competition hypothesis) - Experiments allow researchers to test the effect of a factor on a particular phenomenon Study: How do ants navigate? - Wittlinger questioned how ants find their way back to their nest after going for food. Pedometer hypothesis - ants know how far they are from the nest because they track the number of steps taken and length of their stride Wittlinger manipulated the ants into three groups: 1) Stump - legs were cut to form shorter-than-normal legs 2) Normal – individuals were left alone with normal legs 3) Stilts – bristles glued on legs to make them longer Null hypothesis - what we should observe if the hypothesis being tested doesn’t hold. Results: Stumps stopped short, normal ants returned to the nest, stilts walked beyond Conclusion:Ants use stride length and number to calculate how far they are from the nest. The experiment is well-designed: - Had control group (“normal” ants) to check for factors that might influence results - Control variables (experimental conditions) - Repetition because of small sample size Biologists use evidence-based decision making - Question how organisms work, hypothesize to answer questions, and use experimental evidence to decide which hypothesis is correct _____________________________________________________________________________ Theory - explanation for a phenomena or observations; made of 2 components:  Pattern - something that occurs in the natural world  Process - responsible for creating the pattern Two theories for modern biological science Cell theory & Theory of evolution by natural selection Hooke and Leeuwenhoek were the first to observe cells Cell - organized compartment bounded by a plasma membrane that contains chemicals in an aqueous solution. Cell theory states: •  All organisms are made of cells (pattern). •  All cells come from pre-existing cells (process) Hypothesis - proposed explanation. Prediction - can be measured and must be correct if a hypothesis is valid. • Louis Pasteur – “cells arise from cells and not by spontaneous generation” - All cells come from pre-existing cells, so all single-celled organisms are related by common ancestry. - All of the cells present in a multicellular organism have descended from pre-existing cells and are connected by common ancestry. - Darwin and Wallace made two claims: •  All species are related by common ancestry (pattern). •  Characteristics of species modified from generation to generation - Descent with modification Evolution - change in the characteristics of a population species are related and change • allele frequencies change over time - Natural selection explains how evolution occurs. Population -  group of individuals of the same species living in same area at the same time Two conditions must be met for natural selection to occur in a population: 1.  Individuals in the population vary in characteristics that are heritable 2.  Certain types of heritable traits help individuals survive or reproduce more than others - If certain heritable traits lead to success, these traits become more common in the population - The population’s characteristics change because of natural selection - Natural selection acts on individuals, but evolutionary change occurs in populations Artificial selection - changes in populations occur when humans select which individuals will produce the most offspring - Repeating this process results in changes in the characteristics of a domesticated population Artificial Selection on Bighorn Sheep - Adult male rams begin reproducing at six years old - Male mating success is dependent upon body size and horn length - Big horned sheep are hunted for trophies; therefore males with large horns are being hunted - Large males are not surviving long enough to reproduce - Evolution occurs when heritable variation leads to differential success in reproduction This can occur via: •  Artificial selection – humans select desirable traits within a domestic population •  Natural selection – traits beneficial are “selected” within a natural population Fitness - ability of an individual to produce offspring Adaptation - trait that increases the fitness of an individual in a particular environment. - Cell theory and the theory of evolution imply that all species come from pre-existing species and that all species trace their ancestry back to a single common ancestor. Speciation - process where natural selection has caused populations of one species to diverge to form new species. Tree of life - family tree that describes the relationships among species Phylogeny - genealogical relationships among all organisms - Woese studied small subunit ribosomal RNA(rRNA), a molecule to understand relationships - rRNAis comprised of four chemical units called ribonucleotides;A, U, C, & G - The sequence of ribonucleotides can change during evolution. - rRNAsequences should be similar in closely related organisms but less similar in less closely related organisms Tree of life: 3 major groups of organisms: - The eukaryotes – Eukarya - Two groups of prokaryotes – Bacteria andArchaea - Fungi and animals are more closely related to each other than plants. Taxonomy - name and classify organisms. Taxon - named group. - Woese created a new taxonomic level called the domain, which consists of three taxa: Bacteria, Archaea, and Eukarya. Phylum - major lineage within a domain. - Each organism is given a unique two-part scientific name consisting of the genus and the species. Genus - closely related group of species. Species - individuals that regularly breed together or have characteristics that are distinct from those of other species. - Genus and species is called its scientific name or Latin name. - Genus names are always capitalized, and italics —Homo sapiens. ______________________________________________________________________________  Atoms are composed of: •  Protons – positively charged particles; in nucleus •  Neutrons – neutral particles; in nucleus •  Electrons – negatively charged particles; orbits - Forms of an element with different numbers of neutrons are isotopes Electron Sharing Continuum - degree to which electrons are shared in chemical bonds forms a continuum Molecular formulas indicate the numbers and types of atoms in a molecule (e.g., H2O, CH4). Structural formulas eg. H-O-H Ball-and-stick models and space-filling models show 3D geometry Hydrogen bonds - weak electrical attractions between the partially negative oxygen of one water molecule and the partially positive hydrogen of a different water molecule. Water is: 1.  Cohesive - binding between like molecules; results in high surface tension 2.  Adhesive - binding between unlike molecules 3.  Denser as a liquid than a solid - Water expands as it changes from a liquid to a solid (ice floats) 4.  Able to absorb large amounts of energy - High specific heat, High heat of vaporization Chemical Evolution Theory Simple molecules present on ancient Earth reacted to create larger, more complex molecules This may have happened in: The atmosphere or deep-sea vents - Electrons in an outer shell have more potential energy than electrons in an inner shell - Low-temperature objects have slower molecules than high-temperature objects Chemical reactions are spontaneous if they proceed on their own The spontaneity of a reaction is determined by two factors: 1.  Potential energy - products of spontaneous reactions have less Ep than the reactants 2.  Degree of order - products of spontaneous reactions are less order than the reactants First law of thermodynamics - energy is conserved—it can’t be created or destroyed, but it can be transferred or transformed. Second law of thermodynamics - entropy always increases. - Chemical reactions result in products with less usable energy - Chemical rxns proceed in the direction that results in lower Ep and increased entropy Gibbs free-energy change (ΔG) determines whether a reaction is spontaneous or requires energy ΔG < 0 is an exergonic spontaneous reaction ΔG > 0 is an endergonic reaction that requires energy input ΔG = 0 is a reaction that is at equilibrium Breaking and forming bonds depends on collisions between substances. • The rate of a reaction depends upon the number of collisions. • The number of collisions is dependent on the temperature and concentration of the reactants: •  Higher temperature - more collisions - faster reaction •  Higher concentration - more collisions - faster reaction High-energy photons can break molecules apart by knocking electrons away from valence shells - The results have unpaired electrons and are extremely unstable - Carbon is most versatile atom Most asteroids land in oceans and are never found, but a meteorite landed near BC. - This meteorite was unusual because: •  It contained carbonaceous chondrites that date from the birth of our solar system. •  It contained a lot of organic molecules, including amino acids •  Carbon is created within older stars by thermonuclear reactions • They found the asteroid contained: carbonates and carbon-containing molecules. • Because the overall carbon content of this meteorite is high, this meteorite may be very old - Most cell functions depend on proteins - amino acids are the building blocks of proteins - Structure of a protein can be analyzed at four levels—the amino acid sequence, α-helices and β- pleated sheets, interactions between amino acids that make up overall shape, and combinations of individual proteins that make up larger molecules - Most proteins are enzymes that function as catalysts. - During enzyme catalysis, the reactants bind to an enzyme’s active site Could the first steps of chemical evolution have occurred on ancient Earth? - Miller combined methane, ammonia, and hydrogen in a closed system with water, and applied heat and electricity as an energy source. - Products: HCN and H CO2 - Amino acids and other organic molecules have been found to form easily under these conditions R-groups differ in their size, shape, reactivity, and interactions with water. 1.  Nonpolar R-groups: hydrophobic; do not form hydrogen bonds 2.  Polar R-groups: hydrophilic; form hydrogen bonds; readily dissolve in water - Amino acids with functional groups are more reactive than those with just H or C - Monomers polymerize through condensation reactions, which release a water molecule (hydrolysis is the reverse) - chain of amino acids linked by peptide bonds is called a polypeptide - Polypeptides containing fewer than 50 amino acids are called oligopeptides - Polypeptides containing more than 50 = proteins Peptide bonds form a “backbone” with three key characteristics: 1.  R-group orientation - side chains can interact with each other or water. 2.  Directionality - free amino group, on the left, is called the N-terminus, free carboxyl group, on the right, is called the C-terminus 3.  Flexibility - peptide bond can rotate, making the entire structure flexible Proteins do: •  Catalysis – enzymes speed up chemical reactions. •  Defence – antibodies and complement proteins attack pathogens. •  Movement – motor and contractile proteins move the cell or molecules within the cell •  Signalling – proteins convey signals between cells •  Structure – structural proteins define cell shape and comprise body structures •  Transport – transport proteins carry materials; membrane proteins control molecular movement Researchers have created a new protein from a combo of cow protein that kills bacteria and a pig enzyme that works in the stomach and cuts up other proteins - The new protein is designed to travel to the location of a bacterial infection Primary structure - unique sequence of amino acids - single amino acid change can alter protein function Secondary structure – forms H bonds between the carbonyl group of one amino acid and the amino group of another - Apolypeptide bends to allow this H bonding which forms: α-helices & β-pleated sheets - Secondary structure depends on the primary structure. - hydrogen bonds in a protein’s secondary structure increases its stability Spider Silk Proteins - Spiders produce several types of silk, one type is dragline silk, which a spider uses in case it falls. - Strength is due to the structure of its proteins - Efforts are under way to mass-produce spider-silk proteins for use Tertiary structure - interactions between R-groups - This causes the backbone to bend and fold - R-group interactions include hydrogen bonds, hydrophobic interactions, van der Waals interactions, covalent disulfide bonds, and ionic bonds - Hydrogen bonds form between hydrogen atoms and the carbonyl group - Hydrophobic interactions increase stability of surrounding water molecules by increasing hydrogen bonding - Covalent Disulfide bonds – form between sulfur R groups Quaternary structure - the bonding of two or more subunits Protein folding - spontaneous - Adenatured (unfolded) protein is unable to function normally. - Proteins called molecular chaperones help proteins fold correctly in cells. Prions - improperly folded proteins in healthy individuals - Amin
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