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BIO160 - Study Guide Midterm #1

by: Aenea Mead

BIO160 - Study Guide Midterm #1 BIO 160

Aenea Mead
Cal Poly

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Some of the topics included in these notes are: - properties of life - natural selection - classification of life - evolution of life - phylogenies - energy (use and synthesis) - bacteria an...
Diversity and History of Life
Jennifer Yost
Study Guide
natural selection, properties-of-life, classification-of-life, evolution-of-life, phylogenies, Energy, Bacteria, archaea, Prokaryotic Cells, cell-walls
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This 17 page Study Guide was uploaded by Aenea Mead on Thursday October 13, 2016. The Study Guide belongs to BIO 160 at California Polytechnic State University San Luis Obispo taught by Jennifer Yost in Fall 2016. Since its upload, it has received 3 views. For similar materials see Diversity and History of Life in Biology at California Polytechnic State University San Luis Obispo.


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Date Created: 10/13/16
MASTER VOCABULARY Adap ​ tation: A trait that increases the fitness of an individual in a particular environment Au​totroph: organisms which use simple molecules such as CO or CH (low energy carbo2) to 4 synthesize more complex organic molecules (high energy carbon) Chemolith ​ otrophs: organisms which oxidize high energy inorganic molecules (such as NH and 3 CH ) to produce ATP through cellular respiration - the inorganic molecules act as electron 4 donors Chemoorg ​ anotrophs: organisms which oxidize high energy organic molecules (such as sugar) to produce ATP through cellular respiration - sugars act as the electron donor Electr ​ on Acceptor: molecule which accepts an electron from another molecule and is reduced El​ectron Donor: molecule which gives an electron to another molecule and is oxidized Electron Tr​ansport Chain: reduction-oxidation reaction where the overall potential energy of the reactants is reduced and transformed into ATP ​ Evolution: the change in heritable characteristics in a population overtime ​ Fitness: The ability of an individual to produce offspring (more reproduction means higher fitness) ​ Heritable: traits that can be passed onto offspring ​ Heterotroph: organisms which consume the organic molecules produced by autotrophs (high energy carbon) to produce more complex molecules (higher energy carbon) ​ Inorganic molecules: molecules containing no carbon ​ Metabolism: All chemical reactions that occur within an organism in order to maintain life ​ Microbes: microscopic organisms (bacteria or archaea) ​ Organic molecules: a molecule containing at least one atom of carbon ​ Oxidation: Process by which a molecule loses an electron ​ Phototrophs: organisms which synthesize ATP from the sunlight by undergoing photosynthesis ​ Reduction: Process by which a molecule gains an electron Vocab of the Structure of Phylogenetic Trees: ​ Phylogenetic Trees: graphical representation of hypothesis of evolutionary relationships among species ​ Sister groups: all the descendent following a specific node on a tree ​ Monophyletic group: a group of organisms which includes the most recent common ancestor and all of its descendants ​ Paraphyletic group: a group of organisms that includes that most recent common ancestor, but NOT​ all of its descendants ​ Polyphyletic group: species which have evolved certain traits convergently and therefore are not suitable to be placed in the same taxa ​ Out group: A distant common relative outside the clade being studied (often used as a reference point) ​ Sister trait: all the descendants following a specific node on a tree ​ Root: the place on a phylogenetic tree where the very first common ancestor would go ​ Tip: the places on a phylogenetic tree where the most current species are placed ​ Node: the place on a phylogenetic tree where speciation occurs - the node them becomes those two species most recent common ancestor ​ Branch: represent evolutionary lineages changing over time ​ Cladistics: method scientists currently use to build phylogenetic trees ​ Polytomy: not enough information to distinguish between two species or genus (this results in parts of a tree having more than two branches spring from one branching point / node) ​ Principle of Parsimony: most likely the simplest answer is the correct answer Vocab of Phylogenies: ​ Phylogeny: evolutionary history of a group of organisms ​ Character / trait: any attribute of an organism that can be defined or quantified (ie, color, number presence of a particular part, etc) ​ Character state: The specificity or a character of trait (ie. Trait would be having legs, but the state would be 3 or 4) ​ Taxon: any taxonomic group of rank (ie. group, order, class, species, genus, etc) ​ Clade: a group of organisms which evolved from a common ancestor ​ Common ancestor: a species from which two or more species evolved from ​ Speciation: when something prevents two halves of a population from mating with each other, and thus two separate species evolve ​ Homologous: things are similar due to a common ancestor ​ Derived: trait existing in more recent common ancestor ​ Synapomorphies: derived (new) trait; found in most common ancestor and all descendants ​ Ancestral: older “basal” trait existing in less recent common ancestor ​ Plesiomorphy: ancestral (old) trait; shared by multiple taxa because it is ancestral ​ Convergent evolution: A trait which appears in two unrelated lineages ​ Homoplasy: similar because of convergent evolution, ​NOT​ due to a common ancestor ​ Mass extinction: when a major cause or event results in an entire branch (or more) of the tree to go extinct ​ Background extinction: the natural rate at which species go extinct ​ Topology: the particular branching pattern of a tree (see example below) ______________________________________________ BASICS OF LIFE and NATURAL SELECTION Five Main Properties of Life: 1. Uses and requires energy 2. Made of cells 3. Ability to reproduce/replicate 4. Ability to process information 5. Ability to evolve Cells: ● Smallest unit of life ● Discovered and named by Robert Hooke Anton Van Leeuwenhoek: ● “Father of Microbiology” ● Created some of the first microscopes ● Used his microscopes to discover the first single celled organisms (1660’s) ● Discovered sperm with his microscopes (1677) Louis Pasteur: ● Disproved theory of spontaneous generation ​with an experiment. In summary he had two flasks filled with water, both were boiled, so no living organisms remained in the water. One of the flasks was open at the top, the other was closed. After some time organisms began to appear in the open flask, but not the third. This disproved spontaneous generation because if cells simply appeared without having come from other cells, then they would have appeared in the closed flask. Cell Theory: 1. All organisms of made of cells 2. All cells come from preexisting cells Implications of Cell Theory: ● All cells are connected through a common ancestor Theory of Evolution by Natural Selection: ● In 1858, separate from Pasteur, biologists Darwin and Wallace, proposed the idea that all species are related through descent from a common ancestor ● Called it, ​“Descent with modification” Tieing together the Cell Theory and Natural Selection: 1) All species are related by a common ancestor 2) Species change overtime from natural selection Requirements for Evolutions by Natural Selection: 1. Individuals are different 2. Differences between individuals are heritable 3. Differences in heritable traits affect fitness **Note: Natural Selection acts on an ​individual​, whereas evolution happens to a ​population Life processes information: 1902 - Sutton and Boveri come up with the Chromosome Theory 1950’s - Watson and Crick discover the structure of DNA How Traits Are Passed On (basic explanation): 1. Each strand of DNA is made up of nucleotides: A, T, C, G 2. Two nucleotides pair up to create base pairs 3. Base pairs line up to form a gene 4. Gene is copied, the copy is called mRNA 5. mRNA travels out of the nucleus to a protein 6. The protein uses the mRNA to synthesize a new protein On an individual level, changes from parents in one’s DNA sequence can increase / decrease fitness. If there is a certain trait that increases fitness, then that trait will be passed on from generation to generation. Ex. Let’s say tall people have better fitness. The first graph shows the average height of one generation of people in a population. The second graph (ignore the text and axis, just look at the curve) shows the average of height of people in a population the next generation. Since height increases fitness, those who are taller reproduce more, which in turn results in more tall people. Number of Species of the Planet: ● Scientists estimate there are 8.7 million species on Earth ● Only 1.4 million species have been cataloged ______________________________________________ CLASSIFYING LIFE FORMS Being that there are so many species on this planet, trying to categorize and define each one of them can get a little tricky. Here are a few ideas scientists have come up with: 1) Biological species concept: considered the same species if they can interbreed 2) Morphological species concept: separate species based on appearance - any obvious differences means two different species 3) Phylogenetic species concept: smallest monophyletic group (do not need to understand what this means yet) Classification and Taxonomy:​ All life has a latin binomial name. The first word is the ​genus and the second word is the ​species​. Ex. Homo sapiens (homo is genus, sapien is species) Aristotle’s Model for Classifying Life: Plants Animals Linnaeus’ Model for Classifying Life:​ ​In the mid eighteenth century, Carl Linnaeus came up with the system of classification that we use today. - Kingdom - Phylum - Class - Order - Family - Genus - Species **Note: A good mnemonic to remember it by is: ​K​ings ​P​lay ​C​hess ​O​n ​F​ine ​S​and Human Classification:​ animalia, chordata, mammalia, primates, hominidae, homo, sapiens Three Domains of Life: 1) Bacteria 2) Archaea 3) Eukarya Where did the first cell come from?​ The current theory is that it came from chemical evolution. An input of energy led to the formation of increasingly more complex carbon-containing molecules. This led to molecules that could replicate themselves, which was where the switch from chemical to biological evolution occurred. ______________________________________________ EVOLUTION EARLY EARTH **Note: Dates from other sources will not match these exactly, if you are in Bio 160 at Cal Poly then remember the ones above! If you are not then that is okay, all of the dates are correct, just not overly accurate, so be sure to keep that in mind. Early Atmosphere Composition:​ CO, H2O, CO2, N2, 2 Today Cells are 96% H, C, N, O (important to notice where the elements that make up our cells originated). ______________________________________________ FIRST FORMATION OF LIFE Two models exist for how complex molecules might have formed: 1) Prebiotic Soup Model:​ The thought behind this model is that when simple molecules from the atmosphere precipitated into the ocean and were given energy (sunlight), they reacted with each other to form more complex molecules. The molecules continued to become more complex until they were amino acids, which led directly to life. Stanley Miller tested this model by trying to simulate early Earth conditions in a lab. By adding heat and electric charges into the equation, he successfully produced amino acids using only simple molecules believed to have existed on early Earth. Unfortunately his findings are criticized by others scientists. One criticism of his work is that he used the incorrect basic molecules. Another criticism was that he had to introduce heat and electric current into the situation, rather than use only sunlight. The third criticism (that actually led to the second model) was that while all the simple molecules he used in his experiments were believed to have existed in the oceans of early Earth, the oceans are so vast that the likelihood of those molecules coming close enough to react with each other was too small. 2) Surface Metabolism Model​: As with the Prebiotic Soup Model, the theory is that simple molecules will react with one another when given an energy source to form more complex molecules. This theory was driven by the need to find a catalyst, which is missing from the Prebiotic Soup Model. The catalyst for the reaction comes from the high concentration of minerals in hydrothermal vents at the bottom of the ocean. A hydrothermal vent is where materials have leaked into cracks on the Earth’s crust, and then are pushed back out again full of minerals. The mineral rich material from the Earth forms a miniature volcano of sorts. When the simple molecules from the ocean come into contact with the mineral rich and heated hydrothermal vents, they react to form complex molecules and eventually amino acids. Carbon​: Carbon is an incredibly important element in regard to the development of life on Earth. It is very versatile because it only has four valence electrons, and therefore countless bonding potential. Carbon bonding to itself was an important step in life’s development. Chemical Evolution → Biological Evolution: 1) Production of simple molecules 2) Simple molecules → complex molecules (amino acids) 3) Amino acids link together 4) Self replicating cells are born = biological evolution! RNA World Hypothesis​: ​Chains of RNA, by being the first things that could replicate and evolve, were what began life. 1) A, C, U & G are the nucleotides 2) Nucleotides pair up to form base pairs (C+G, A+U) 3) Base pairs form strands 4) Two strands come together to replicate themselves 5) Ribosime is a strand of DNA capable of catalyzing chemical reactions ​ Ancestral and derived traits are relative - they depend on which clades you are examining Convergent Evolution: - This is when two species or taxa exhibit the same characteristic, but have not evolved from a common ancestor - This generally occurs when species live in similar habitats and both evolve a certain characteristic which helps them to thrive - Biologists can determine whether convergent evolution has occurred by examining the two species DNA code - if the code is completely different for the same trait then it was likely convergent evolution ​ ​ ​ ______________________________________________________________________________ ENERGY All organisms acquire and use energy!! Life Requires: 1) Source of energy to produce ATP 2) Source of carbon METHODS FOR PRODUCING ATP AND OBTAINING CARBON Energy from…. Autotrophs​ (primary Heterotrophs​ (consumers) producers) Light​ (phototrophs) Photoautotrophs photoheterotrophs (plants) Organic Molecules chemoorganoautotrophs Chemoorganoheterotrophs (chemoorganotrophs) (animals) Inorganic Molecules chemolithoautotrophs Chemolithotrophic (chemolithotrophs) heterotrophs Sources of Energy: ● Light ● Organic molecules (i.e. sugars) ● Inorganic molecules (i.e. ammonia) Light as an Energy Source (phototrophs)​: 1) Light excites an electron 2) Electron jumps to a higher orbital 3) Electron eventually falls back down to ground state 4) When it falls it releases heat and light 5) ATP and chemical energy are produced Organic Molecules as Energy Source (​Chemoorganotrophs)​: - Sugars - Carbon based molecules are oxidized by means of cellular respiration or fermentation - ATP is produced Inorganic Molecules (c ​ hemolithotrophs)​: - Ammonia (or other inorganic molecules) - High energy molecules are oxidized by means of cellular respiration - ATP is produced Cellular Respiration​: Process by which a molecule with high potential energy is oxidized and the lost electron goes to a molecule with a low potential energy. The high energy molecule is the electron donor and the low energy molecule is the electron acceptor. The potential energy difference between the donor and receptor is chemical energy in the form of ATP. Molecule w/ high energy (e donor) + molecule w/ low energy (e receptor) = ATP + byproduct Different molecules produce varying amounts of ATP by cellular respiration. For example, oxygen is a very high energy electron receptor, whereas iron and nitrate do not produce as much energy. This is why it was such an important step in Earth’s history to go from using lower energy electron receptors, to being able to use oxygen and thus produce much more energy. An entire world of possibilities opened up. Currently archaea is the only known life form to produce methane. ______________________________________________________________________________ PROKARYOTIC CELLS Characteristics of a Prokaryotic Cell: ● Lack a membrane bound nucleus ● Have a cell wall ● Are all haploid (only one copy each chromosome) Today prokaryotic has come to mean “having no nucleus”. Cell Wall Composition: ● Two types of cell walls, ​gram +​ and ​gram - ○ Gram positive cells have an inner membrane with a thick outer cell wall ○ Gram negative cells have an inner membrane sandwiched by a thin outer cell wall and a thin inner cell wall ● Type of cell wall can be determined by a process called “gram staining” ○ Gram positive cells stain purple ○ Gram negative cells stain pink ______________________________________________________________________________ BACTERIA AND ARCHAEA Bacterial Morphological Differences: - Size (range from 0.3 micrometers to 100 micrometers) - Shapes (sphere, rod, ball, spiral / corkscrew…) - Motion (some have outer flagella to help swim, others glide, some have inner flagella to promote circular motion, etc) When did they evolve? - First cells were bacteria, which evolved 3.5 billion years ago - First fossils are of stromatolites which have been compressed overtime by layers of sediment into microbial mats What do they do? The Oxygen Revolution!​ - For the first 2.3 billion years of Earth’s existence there was no “free” (unbonded) oxygen anywhere to be found. The first organisms to change that are called cyanobacteria​. They were the first species to perform oxygenic photosynthesis, which means that oxygen gas was one of the by-products when they underwent photosynthesis. Over time this caused oxygen levels to rise in the atmosphere. The evidence we have of this is call the ​Banded ​ ​ killing of the normal TB cells allowed the mutated cells to take over completely. When the man was given antibiotics a second time they did not work because the mutated cells, which were plentiful, were resistant to it. Bioremediation​: The use of bacteria and archaea to degrade pollutants. Select strains of bacteria and archaea naturally eat plastic. Recently biologists have been experimenting with cleaning up a polluted area using these strains. One of the problems they encounter is how to manipulate which plastics the bacteria or archaea eat. If biologists were to give the strains unlimited resources they would grow exponentially and humans could lose their carefully controlled environment. This a very new study that is still being questioned and changed everyday. Where do they live? - Extremophiles:​ many species of bacteria and archaea are capable of not only living, but flourishing in extreme environments. They can live at very high and low temperatures, pressures and salt levels as well as both ends of the pH spectrum. - They also live in every environment in between Today studies of bacteria and archaea raise questions related to: 1) The origin of life 2) Extraterrestrial life 3) Commercial uses How bacteria and archaea reproduce and transfer genetic material: Fission:​ single cell splits into two daughter cells (reproduction) - Cells multiply at an exponential rate, so given unlimited resources it would not take long for bacteria or archaea to far outnumber all other life on Earth Conjugation​: process by which bacteria and archaea share useful genetic material among themselves - Two bacterial or archaeal cells become connected to each other by a tube. One cell transfers selected genetic material through the tube to the other cell. - It is important to note that this is NOT a transfer from parent to offspring, but the change in the genetic code of a single organism. - Can occur between different species of bacteria and archaea - Mostly a single cell will give away a ​copy​ of their gene, but on occasion they will give away the g ​ ene​ itself - Bacteria and archaea can also “purge” their bad genes out of their cell and into their surroundings


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