Wyatt Connell Lansdale Catholic High School Chapter Outline A.P. Biology I. Chapter 1: Introduction: Evolution and the Foundations of Biology A. Inquiring About Life 1. Evolution is the process of change that has resulted in vast variety of life present of Earth today. Evolution is one of the core themes of biology. 2. Biology is the scientific study of life. Biologists pose questions about the living world and seek answers through scientific inquiry. B. Studying the diverse forms of life reveals common themes 1. Reductionism is the approach of reducing complex systems to simpler components that are more manageable to study. 2. Emergent properties are properties that emerge when going from the molecular level outwards. This is due to the arrangement and interactions of parts as complexity increases. Emergent properties are not unique to life but they are immensely more complex when dealing with life forms. 3. Systems biology is the exploration of a biological system by analyzing the interactions among its parts. It can be used to study life at all levels. 4. Exploring Levels of Biological Organization a. The Biosphere- Consists of all life present on Earth b. Ecosystems- Consists of all living things in a particular area (grassland, desert, coral reef, etc.) along with all the nonliving components of the environment with which life interacts (soil, water, atmospheric gases, light, etc.) c. Communities- The set of populations that inhabit a particular area. An array of organisms Inhabit an ecosystem. For example in a forest the community may be made up of trees and other plants, animals, mushrooms and other fungi, and a multitude of microorganisms such as bacteria. d. Populations- Made up of all the members of a species living in a particular area (Maple Tree, White-tailed deer, etc.) e. Organisms- Individual living things (Maple Tree, Deer, Frog, Beetle, Bacteria, etc.) f. Organs and Organ Systems- A body part consisting of multiple tissues, that carries out a particular function of the body. The organs of complex plants and animals are organized into organ systems that cooperate in a larger function. g. Tissues- A group of cells that work together, performing a specialized function. h. Cells- Life’s fundamental unit of structure and function. Some organisms are single cells while others are multicellular. A single cell performs all the functions of life while a Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline multicellular organism has a division of labor among specialized cells. i. Organelles- Various functional components present in cells. j. Molecules- A chemical structure consisting of two or more atoms. 5. The Cell: An Organism’s Basic Unit of Structure and Function a. The cell is the smallest unit of organization that can perform all activities required for life. b. The activities of organisms are all based on the activities of cells. c. The two main forms of cells are prokaryotic and eukaryotic. The cells of two groups of groups of single-celled microorganisms (bacteria and archaea) are prokaryotic. All other forms of life such as plants and animals are composed of eukaryotic cells. d. Eukaryotic cells contain membrane-enclosed organelles. e. Certain organelles such as the nucleus are found in the cells of all eukaryotes others are specific to certain cell types. f. Prokaryotic cells lack a nucleus and other membrane enclosed organelles. They are other generally smaller in size than eukaryotic cells. 6. Life’s Processes Involve the Expression and Transmission of Genetic Information a. Chromosomes contain genetic material in the form of DNA (deoxyribonucleic acid). b. DNA Structure and Function i. Genes are transmitted from parents to offspring and they encode the information necessary to build all of the molecules synthesized within a cell. They control protein production indirectly using a related molecule called RNA as an intermediary. ii. A DNA molecule is made up of two long strands that are arranged in a double helix. Each chain is made up of four kinds of chemical bonding blocks called nucleotides. iii. Gene expression is the process in which nucleotides along a gene are transcribed into RNA, which is in turn translated into a specific protein with a unique shape and function. c. Genomics: Large-Scale Analysis of DNA Sequences i. Genome- The entire collection of genetic instructions that an organism inherits ii. Genomics- Studying a whole set of genes of one or more species Wyatt Connell Lansdale Catholic High School Chapter Outline A.P. Biology iii. Bioinformatics- The use of computational to store, organize, and analyze huge volumes of data 7. Life Requires the Transfer and Transformation of Energy and Matter a. Energy often flows through and ecosystem, entering as light and exiting as heat. b. Chemicals absorbed by plants then are often passed on to the animal that consumes the plant. Eventually the chemicals will be returned to the environment by decomposers such as bacteria and fungi that break down dead organisms. 8. Organisms Interact with Other Organisms and the Physical Environment a. Evolution, the Core Theme of Biology i. The scientific explanation for the diversity of life on Earth and the adaptation of organisms to their environments is evolution. C. Evolution accounts for the unity and diversity of life 1. Biologists estimate the number of living species on Earth range from 10 million to over 100 million. 2. Classifying the Diversity of Life: The Three Domains of Life a. All life can be placed into one of the three domains; Bacteria, Archaea, and Eukarya. The organisms found in both the Bacteria and Archaea domains are prokaryotic. All eukaryotic organisms are grouped in the domain Eukarya. b. Domain Bacteria- The most diverse and widespread prokaryotes. c. Domain Archaea- Prokaryotes known as archaea live in some of the Earth’s most extreme environments. d. Domain Eukarya- Divided into for Kingdoms i. Kingdom Plantae- consists of terrestrial multicellular eukaryotes (also known as land plants) that carry out photosynthesis ii. Kingdom Fungi- Defined in part by the fact that they absorb nutrients from outside their bodies iii. Kindgom Animalia- Made up of multicellular eukaryotes that ingest other organisms (Animals, Humans) iv. Protists- Unicellular eukaryotes and simple multicellular eukaryotes 3. Charles Darwin and the Theory of Natural Selection a. On November 1859 Charles Robert Darwin published one of the most influential books ever written, On the Origin of Species by Means of Natural Selection. Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline i. Stated that species have arisen from a succession of ancestors that differed from them (Descent with Modification). ii. Proposed “Natural Selection” as a mechanism for Descent with Modification. Natural Selection stated that individuals that are better suited to a local environment are more likely to survive and reproduce then those that are less well suited. As a result of this over many generations a higher and higher portion of the population will have advantageous traits. D. Biological Inquiry entails forming and testing hypotheses based on observations of nature 1. Scientist use a process of inquiry that includes making observations, forming logical hypothesis, and testing them. The results may inspire a revision of the original hypothesis or formation of an entirely new one resulting in further testing. 2. Making Observations a. Recorded observations are called data. Data is often labeled as qualitative or quantitative. Qualitative data is often in the form of recorded descriptions while quantitative data is often takes the form of numbers and measurements. Graphs and tables are often used to help display quantitative information 3. Forming and Testing Hypothesis a. Hypothesis- a tentative answer to a well framed question. “An explanation on Trial”. A hypothesis is usually tested by performing an experiment, which will either prove or disprove the original hypothesis. 4. Deductive Reasoning a. Deductive reasoning involves logic that flows from general to specific. In science deductions take the form of predictions of results that will be found if a particular hypothesis is correct (If… Then). b. Often observations will lead to the formation of multiple hypothesis . The ideal experiment will test these possible explanations . c. A hypothesis gains credibility when it survives multiple attempts to falsify it. 5. Questions Than Can and Cannot Be Addressed by Science a. Science requires natural explanations for natural phenomena and as a result it can neither support nor falsify things such as supernatural explanations or religious matters which are simply outside the bounds of science. 6. A Case Study in Scientific Inquiry: Investigating Coat Coloration in Mouse Populations Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline a. To test the hypothesis that the color patterns of mice had evolved as adaptations that camouflage the mice in their native environments biologist Hopi Hoekstra of Harvard traveled to Florida to conduct a field experiment. They built hundreds of silicone models of mice and spray painted them to resemble either beach or inland mice. They then placed equal numbers of the mice randomly throughout both habitats and left them overnight. The following morning they recorded signs of predation. It was clear that mice non-native mice experienced much higher rates of predation than the native mice thus confirming the hypothesis. 7. Experimental Controls a. A controlled experiment is one that is designed to compare an experimental group with a control group. Ideally the experimental and control group will differ only in the one factor the experiment is testing. b. It is a common misconception that a controlled experiment is an environment of which the scientists control the environment to keep everything constant. Controlling an environment completely is not practical so scientists control unwanted variables by canceling their effects out using control groups. 8. Theories in Science a. A theory in science differs from our common use of the word which implies untested speculation. In science a theory is usually supported by a much greater body of evidence than a hypothesis or the like. It also usually broader in scope than a hypothesis which allows many new hypothesis to spin off of it. b. Despite being based off of solid evidence theories often must be revised or rejected based on new research and evidence. 9. Science as a Social Process: Community and Diversity a. The primary purpose of technology is to apply scientific knowledge for some specific purpose b. The scientific community reflects the customs and behaviors of society at large. c. Women and many racial and ethnic groups are still significantly underrepresented in many branches of science and this lack of diversity slows the progress of science. II. Chapter 2: The Chemical Context of Life A. Matter consists of chemical elements in pure form and in combinations called compounds 1. Anything that takes up space and has mass is matter. Matter is made up of elements. 2. Elements and Compounds Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline a. An element is a substance that cannot be broken down into other substances by chemical reactions. i. There are 92 elements recognized today ii. Each element is assigned a symbol (usually the first letter or two of its name) b. A compound is a substance consisting of two or more different elements combined in a fixed ratio. i. Table salt and Water are examples of compounds ii. A compound has chemical and physical characteristics different from those of its elements. 3. The Elements of Life a. Of the 92 elements about 20-25% are essential elements that an organism needs to live a healthy life and reproduce. b. The number of elements required can vary from organism to organism. For example humans need 25 elements while plants only require 17. c. Oxygen, Carbon, Hydrogen, and nitrogen make up 96% of living matter. d. Calcium, Phosphorous, Potassium, Sulfur, and several other elements account for most of the remaining 4%. e. Trace elements are required by an organism in only minute quantities. i. Some trace elements are required by all forms of life while others are required by only certain species. 4. Evolution of Tolerance to Toxic Elements a. Some elements are toxic to organisms. In humans arsenic has been linked to numerous diseases and can be lethal. b. Some species have adapted to environments that contain toxic elements. For example sunflowers are able to take up concentrations of lead, zinc, and other heavy metals in concentrations that would kill most organisms. i. Presumably variants of ancestral sunflower species arose in heavy metal-laden soils and subsequent natural selection resulted in their survival and ultimately reproduction. B. An element’s properties depend on the structure of its atoms 1. Each element consists of a certain type of atom that is different from the atoms of any other element. An atom is the smallest unit of matter that still retains the properties of an element. 2. Subatomic Particles a. Although atoms are the smallest unit having the properties of an element, there tiny bits of matter are composed of even smaller parts, called subatomic particles i. Protons and electrons are electrically charged. Each proton has one unit of positive charge while each Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline electron has one unit of negative charge. A neutron is electrically neutral. b. An atomic nucleus is the center of an atom where protons and neutrons are packed together in a dense core. Protons give the nucleus a positive charge. c. The electrons form a cloud of negative charge around the nucleus and it is this attraction between opposite charges that keeps the electrons in the vicinity of the nucleus. d. The neutron and proton are almost identical in mass. Since these subatomic particles are so minuscule there are measured in a unit of measurement called the Dalton. e. Because the mass of an electron is 1/2000 of that of a neutron or proton they can be ignored when computing the total mass of an atom. 3. Atomic Number and Atomic Mass a. Atoms of the various elements differ in their number of subatomic particles. b. All atoms of a particular element have the same number of protons in their nuclei. c. The number of protons (which is unique to that element) is called the atomic number. d. Because the charge of an atom is neutral (unless otherwise indicated) the atomic number also tells the number of electrons. e. The Mass Number is the sum of protons plus neutrons in the nucleus of an atom. f. Almost all of an atoms mass is concentrated in its nucleus. Because neutrons and protons each have a mass very close to 1 Dalton, the mass number is an approximation of the total mass of atom, which is known as atomic mass. 4. Isotopes a. All atoms of a given element have the same number if protons but some atoms have more neutrons than other atoms of the same element. b. The different atomic forms of the same element are called isotopes of the element. c. Although isotopes of an element have slightly different masses, they behave identically in chemical reactions. d. Radioactive isotopes are isotopes in which the nucleus decays spontaneously which gives off particles and energy. These radioactive isotopes have many useful applications in biology. They are useful in medical imaging and as tracers and to follow atoms through metabolism. Although useful they pose a hazard to life by damaging cellular molecules. 5. The Energy Levels of Electrons Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline a. When two atoms approach each other during a chemical reaction their nuclei do not come close enough to interact. Only electrons are directly involved in the chemical reactions between atoms. b. Energy is the capacity to cause change by doing work. c. Potential energy is the energy that matter possesses because of its location or structure. d. The electrons of an atom have potential energy because of how they are arranged in relation to the nucleus. The more distant an electron is from the nucleus the greater its potential energy is. e. An electrons potential energy is determined by its energy level. An electron cannot exist between energy levels. f. An electrons energy level is correlated with its average distance from the nucleus. g. Electrons are found in different electron shells. The first electron shell is located closest to the nucleus and therefore has the lowest potential energy. The farther away from the nucleus the more potential energy. h. An electron can only change the shell it occupies by absorbing or losing an amount of energy equal to the difference in potential energy between its position and the new shell. When an electron absorbs energy it moves to a shell farther out from the nucleus. When an electron loses energy it “falls back” to a shell closer to the nucleus and the lost energy is usually released to the environment as heat. 6. Electron Distribution and Chemical Properties a. The chemical behavior of an atom is determined by the distribution of electrons in the atom’s electron shells. b. The chemical behavior of an atom depends mostly on the number of electrons in its outermost shell. Outer electrons are called valence electrons and the outermost electron shell is called the valence shell. c. An atom with a completed valence shell is unreactive and atoms with incomplete valence shells are reactive. C. The Formation and function of molecules depend on chemical bonding between atoms 1. Covalent Bonds a. The sharing of a pair of valence electrons by two atoms is a covalent bond. b. Two or more atoms held together by covalent bonds are called molecules. c. A single bond is a pair of shared electrons and a double bond is a shared pair of two electrons. d. An atoms bonding capacity is called the atoms valence. Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline e. The attraction of a particular atom for the electrons of a covalent bond is called its electronegativity. The more electronegative an atom is the stronger it pulls shared electrons toward itself. f. A nonpolar covalent bond is a bond in which the electrons are shared equally because the two atoms have the same electronegativity. g. When an atom is bonded to a more electronegative atom the electrons of the bond are not shared equally. This is called a polar covalent bond. 2. Ionic Bonds a. A charged atom or molecule is called an ion. When the atom or molecule has a positive charge it is called a cation and when it has a negative charge it is called an anion. b. Cations and anions attract each other in what is known as an ionic bond. C. Compounds formed by ionic bonds are called ionic compounds or salts. 3. Weak Chemical Bonds a. Most strong bonds within an organism are covalent bonds but weaker bonding also plays an important role in the cell. Many large biological molecules are held in their functional form by weak bonds. b. Hydrogen bonds are the most important weak bonds in the chemistry of life. In a hydrogen bond the partial positive charge of a hydrogen atom is covalently bonded to an electronegative atom that allows the hydrogen to be attracted to a different electronegative atom nearby. c. Even a molecule with nonpolar covalent bonds may have positively and negatively charged regions. Electrons are not always symmetrically distributed in such a molecule, at any instant they may accumulate by chance in one part of the molecule or another. The result of this is ever changing regions of positive and negative charge that enable all atoms and molecules to stick to one another. While these reactions are individually weak when many of these reactions occur simultaneously they can be powerful. These reactions are known as van der Waals interactions. 4. Molecular Shape and Function a. A molecule has a characteristic size and shape. The precise shape of a molecule is usually important to its function in the living cell. b. A molecule consisting of only two atoms is always linear but most molecules with two or more atoms have complicated shapes. Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline c. Molecule shape is crucial in biology because it determines how biological molecules recognize and respond to one another with specificity. d. Biological molecules often bind temporarily to each other by forming weak bonds, but this can only happen if their shapes are complementary. D. Chemical reactions make and break chemical bonds 1. The making and breaking of chemical bonds leading to changes in the composition of matter are called chemical reactions. 2.The starting materials in a reaction are known as the reactants and the produced substance is called the product. Coefficients are used to indicate the number of molecules involved in the reaction. 3. Matter is conserved during a chemical reaction. Reactions cannot create or destroy matter but only rearrange it. 4. All chemical reactions are reversible. 5. The greater the concentration of reactant molecules, the more frequently they collide with one another and have an opportunity to react and form products. The same holds true for products. 6. The point at which reactions offset one another is known as chemical equilibrium. Reactions still occur but produce no effect. Chemical equilibrium does not mean that the reactants and products are in concentrations rather only that their concentrations have stabilized at a particular ratio. E. Hydrogen bonding gives water properties that help make life possible on Earth 1. Cohesion of Water Molecules a. In a polar molecule overall charge is unevenly distributed. b. Hydrogen bonds hold substances together by a phenomenon known as cohesion. Cohesion due to hydrogen bonding contributes to the transport of water and dissolved nutrients against gravity in plants. c. Adhesion is the clinging of one substance to another. Adhesion of water to cell walls by hydrogen bonds helps counter the downward pull of gravity d. Surface tension is the measure of how difficult it is to stretch or break the surface of a liquid. 2. Moderation of Temperature by Water a. Water moderates air temperature by absorbing heat from air that is warmer and releasing the stored heat to air that is cooler. b. Kinetic energy is the energy of motion. c. The kinetic energy associated with the random movements of atoms or molecules is called thermal energy. d. Temperature represents the average kinetic energy of molecules regardless of volume. Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline e. Thermal energy in transfer from one body of matter to another is defined as heat. f. A calorie is defined as the amount of heat it takes to raise the temperature of 1 g of water by 1 degree C. It is also the amount of heat 1 g of water releases when it cools by 1 degree C. g. A kilocalorie is the quantity of heat required to raise the temperature of 1 kilogram of water by 1 degree C. h. Another energy unit is the joule (J). One joule equals 0.239 cal or one calorie equals 4.184 joules. i. The specific heat of a substance is defined as the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1 degree C. j. Molecules of any liquid stay close together because they are attracted to one another. Molecules moving fast enough to overcome these attractions can depart the liquid and enter the air as a gas. This transformation from a liquid to a gas is called evaporation. k. Heat of vaporization is the quantity of heat a liquid must absorb for 1g of it to be converted from the liquid to the gaseous state. l. As a liquid evaporates, the surface of the liquid that remains behind cools down. This is known as evaporative cooling an it occurs because the hottest molecules are the ones most likely to leave as a gas. 3. Floating of Ice on Liquid Water a. Water is one of the few substances that is less dense as a solid than as a liquid. This is what causes ice to float on liquid water. b. While most other materials contract and become denser when they solidify water expands. The cause of this behavior is hydrogen bonding. c. The ability of ice to float due to its lower density is an important factor in the suitability of the environment for life. If ice sank then all ponds, lakes and even oceans would freeze solid making life, as we know it impossible on Earth. Even during the summer only the upper few inches of the ocean would thaw. 4. Water: The Solvent of Life a. A liquid that is a completely homogeneous mixture of two or more substances is called a solution. b. The dissolving agent of a solution is called the solvent. c. The substance that is dissolved is called the solute. d. An aqueous solution is one in which water is the solvent. e. The sphere of water molecules around each dissolved ion is called a hydration shell. Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline 5. Hydrophilic and Hydrophobic Substances a. Any substance that has an affinity for water is said to be hydrophilic. b. A substance that does not have an affinity for water is known as hydrophobic. Often these substances that are nonionic and nonpolar seem to repel water. 6. Solute Concentration in Aqueous Solutions a. Most of the chemical reactions in organisms involve solutes dissolved in water. b. When carrying out experiments we use mass to calculate the number of molecules. The molecular mass is first calculated. The molecular mass is simply the sum of the masses of all the atoms in the molecule. c. A mole represents the exact number of objects 6.02 X 10^23. d. The advantage of measuring a quantity of chemicals in moles is that a mole of one substance has exactly the same number of molecules as a mole of any other substance. e. Molarity is the number of moles of solute per liter of solution. 7. Acids and Bases a. An acid is a substance that increases the hydrogen ion concentration of a solution. b. A substance that reduces the hydrogen ion concentration of a solution is a base. 8. The pH Scale a. The pH scale compresses the range of H+ and OHconcentrations by employing logarithms. b. The pH of a solution is defined as the negative logarithm of the hydrogen ion concentration. c. A neutral pH is 7. Pure water is an example of a solution that is neutral d. A base is any solution with a pH higher than 7. e. An acid is any solution with a pH of lower than 7. 9. Buffers a. The internal pH of most living cells is close to 7. Even a slight change in pH can be harmful because the chemical processes of the cell are very sensitive to the concentrations of hydrogen and hydroxide ions. b. The pH of human blood is very 7.4 A person cannot survive for more than a few minutes if the blood pH drops to 7 or rises to 7.8 c. The presence of substances called buffers allows biological fluids to maintain a relatively constant pH despite the addition of acids or bases. A buffer is a substance that minimizes changes in the concentrations of H+ and OH- in a solution. Most Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline buffer solutions contain a weak acid and its corresponding bas, which combine reversibly with hydrogen ions. 10. Acidification: A Threat to Our Oceans a. The burning of fossil fuels releases gaseous compounds into the atmosphere. When certain compounds come into contact with the water the water become more acidic. Scientists worry that this will destroy the pH balance of the ocean and harm ecosystems. Scientists predict that if no action is taken the pH of the ocean will continue to drop as more fossil fuels are burned. III. Chapter 4: A Tour of the Cell A. Biologists use microscopes and the tools of biochemistry to study cells 1. Microscopy a. The discovery and early study of cells progressed with the invention of microscopes in 1590. b. In a light microscope, visible light passes through the specimen and then through glass lenses. The result is an image that magnified as it is projected into the human eye c. Magnification is the ratio of an object’s image to its real size. d. Resolution is a measure of the clarity of an image. e. Contrast is the difference in brightness between the light and dark areas of an image. f. Until recently a resolution barrier prevented cell biologists from using standard light microscopes to study organelles. g. Organelles are the membrane enclosed structures within eukaryotic cells. h. Rather than using light an electron microscope focuses a beam of electrons through a specimen or onto its surface. This allows scientists to study much smaller objects. i. The transmission electron microscope is used to study the internal structure of cells. It aims an electron beam through a very thin section of a specimen. j. The scanning electron microscope is especially useful for detailed study of the topography of a specimen. The image produced by this microscope appears three-dimensional. 2. Cell Fractionation a. Cell fractionation is a useful technique for studying cell structure and function. Broken up cells are placed in a tube that is spun in a centrifuge. The resulting force causes the largest cell components to settle to the bottom of the tube, forming a pellet. The liquid above the pellet is poured into a new tube and centrifuged at a higher speed for a longer time. The process is repeated several times resulting in a series of Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline pellets that consist of nuclei, mitochondria, pieces of membrane, and ribosomes. This enables researchers to prepare specific cell components in bulk and identify their functions. B. Eukaryotic cells have internal membranes that compartmentalize their functions 1. Comparing Prokaryotic and Eukaryotic Cells a. Inside all cells is a semifluid called cytosol in which subcellular components are suspended b. Chromosomes carry genes in the form of DNA c. Ribosomes make proteins according to the instructions from the genes. d. A major difference between prokaryotic and eukaryotic cells is the location of their DNA. In a eukaryotic cell most of the DNA is in an organelle called the nucleus, which is bounded by a double membrane. In a prokaryotic cell, the DNA is concentrated in the nucleoid, a region that is not bound by membrane. e. The interior of either a eukaryotic or prokaryotic cell is called the cytoplasm. In eukaryotic cells this term refers only to the region between the nucleus and the plasma membrane. f. Eukaryotic cells are generally much larger and prokaryotic cells. Size is a general feature of cell structure that relates to their function. g. The plasma membrane functions as a select barrier that allows passage of enough oxygen, nutrients, and wastes to service the entire cell. h. Larger organisms do not generally have larger sales then smaller organisms. Larger organisms simply have more cells. 2. A Panoramic View of the Eukaryotic Cell a. in addition to the plasma membrane at its outer surface, A eukaryotic cell has extensive and elaborately arranged internal membranes. b. Animal Cell Flagellum: motility structure present in some animal cells, composed of a cluster of microtubules within an extension of the plasma membrane Centrosome: region where the cells microtubules are initiated; contains a pair of centrioles. Cytoskeleton: reinforces cells shape; functions in cell movement; components are made of protein. Includes microfilaments, intermediate filaments, and microtubules. Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline Microvilli: projections that increase the cell surface area Peroxisome: Organelle with various specialized metabolic functions; produces hydrogen peroxide as a byproduct, then converts it to water. Mitochondrion: organelle where cellular respiration occurs and most of ATP generated Lysosome: digestive working out where macromolecules or hydrolyzed Endoplasmic reticulum: network of membranous sacs and tubes; active in membrane synthesis and other synthetic and metabolic processes; has rough and smooth regions Nuclear envelope: double membrane enclosing the nucleus; perforated pores; continuous with ER Nucleolus: Non-membranous structure involved in production of ribosomes; The nucleus has one or more nucleoli. Chromatin: Material consisting of DNA and proteins; visible in the dividing cell as individual condensed chromosomes. Plasma membrane: membrane enclosing the cell Ribosomes: complexes that make protein; free in cytosol or bound to rough ER or nuclear envelope Golgi apparatus: organelle active in synthesis, modification, sorting, and selection of cell products C. Plant Cell Cell wall: outer layer that maintains cells shape and protects cell from mechanical damage; made of cellulose, other polysaccharides, and protein Plasmodesmata: channels through cell walls that connect the cytoplasm’s of adjacent cells Chloroplast: photosynthetic organelle; converts energy of sunlight to chemical energy stored in sugar molecules Central vacuole: prominent organelle in older plant cells; functions include storage, breakdown of waste products, hydrolysis of macromolecules; enlargement of vacuole is a major mechanism of plant growth (Plant Cell Includes many of the previously mentioned animal cell parts) C. The eukaryotic cells genetic instructions are housed in the nucleus and carried out by ribosomes 1. The Nucleus: Information Central Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline a. The nucleus contains most of the genes in the eukaryotic cell. It is generally the most conspicuous organelle in a eukaryotic cell averaging about 5um in diameter. b. The nuclear envelope encloses the nucleus, separating its contents from the cytoplasm. c. nuclear lamina: A net like array of protein filaments that maintains the shape of the nucleus by mechanically supporting the nuclear envelope. d. Nucleolus: A prominent structure within the non-dividing nucleus which appears through the electron microscope as a mess of densely strained granules and fibers adjoining part of the chromatin. Hear a type of RNA call ribosomal is a synthesized from instructions in the DNA. 2. Ribosomes: Protein Factories a. Ribosomes: the complexes made of ribosomal RNA and proteins and the cellular components that carry out protein synthesis. b. ribosomes build proteins into cytoplasmic locales. At any given time free ribosomes are suspended in the cytosol which bound ribosomes are attached to the outside of the end of plasmid particular or nuclear envelope. D. The endomembrane system regulates protein traffic and performs metabolic functions in the cell 1. The Endoplasmic Reticulum: Biosynthetic Factory a. The endoplasmic reticulum is such an extensive network of membranes that it accounts for more than half of the total membrane in many eukaryotic cells. b. The smooth ER is so named because its outer surface lacks ribosomes. c. The rough ER is studded with ribosomes on the outer surface of the membrane and thus appears rough through the electron microscope. d. The smooth ER functions in diverse metabolic processes, which vary with cell type. These processes include synthesis of lipids, metabolism of carbohydrates, detoxification of drugs and poisons, and storage of calcium ions. e. In addition to making secretary proteins, the rough ER is a membrane factory for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane. f. Most secretory proteins are glycoproteins, proteins that have carbohydrates covalently bonded to them. 2. The Golgi Apparatus: Shipping and Receiving Center a. Many transport vesicles from the ER travel to the Golgi apparatus for modification of their contents. Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline b. The Golgi apparatus is especially extensive in cells specialized for secretion. c. The Golgi can also manufacture its own macromolecules, including pectin and other noncellulose polysaccharides. d. The Golgi sorts and packages materials into transport vesicles. e. Products are tagged with identifiers such as phosphate groups. These act like ZIP codes on mailing labels. 3. Lysosomes: Digestive Compartments a. A lysosome is a membranous sac of hydrolytic enzymes that animal cells use to digest macromolecules. b. Lysosomes carry out intercellular digestion and in a variety of circumstances. Amoebas and many other protists eat by engulfing smaller organisms or food particles, a process called phagocytosis. 4. Vacuoles: Diverse Maintenance Compartments a. Vacuoles are large vesicles derived from the endoplasmic reticulum and golgo apparatus. b. Food vacuoles are formed by phagocytosis. c. Contractile vacuoles pump excess water out of the cell, thereby maintaining a suitable concentration of ions and molecules inside the cell. e. Many plant cells contain a large central vacuole which develops by the coalescence of smaller vacuoles. E. Mitochondria and Chloroplasts change energy from one form to another 1. The Evolutionary Origins of Mitochondria and Chloroplasts a. Mitochondria and chloroplasts display similarities with bacteria that lead to endosymboint theory. b. This theory states that an early ancestor of eukaryotic cells engulfed an oxygen using non-photosynthetic prokaryotic cell. Eventually, engulfed cell formed a relationship with the host cell in which it was closed, Becoming an end of endosymbiont. Indeed over the course of evolution the host cell and it’s endosymbiont merged into a single organism, or eukaryotic cell with a mitochondrion. 2. Mitochondria: Chemical Energy Conversion a. The inner membrane of the mitochondria divides it into two internal compartments. The first is the inter-membrane space, the narrow region between the inner and outer membranes. b. The second compartment, the mitochondrial matrix, is enclosed by the inner membrane. The matrix contains many different enzymes as well as the mitochondrial DNA and ribosomes. 3. Chloroplasts: Capture of Light Energy Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline a. chloroplasts contain the green pigment chlorophyll, along with enzymes and other molecules that function in the photo synthetic production of sugar. These lens shaped organelles, are found in leaves and other green organs in plants and algae. b. Inside the chloroplast is another then membranous system in the form of flattened, interconnected sacs called thylakoids. c. The fluid outside the thylakoids is the stroma, which contains the chloroplast DNA and ribosomes as well as many enzymes. d. the chloroplast is a specialized member of a family of closely related plant organelles called plastids. 4. Peroxisomes: Oxidation a. Peroxisomes contain enzymes that transfer hydrogen from various substrates to oxygen. b. The peroxisome contains an enzyme that converts H2O2 to water. F. The cytoskeleton is a network of fibers that organizes structures and activities in the cell 1. Roles of the Cytoskeleton: Support and Motility a. The main purpose of the cytoskeleton is for mechanical support and to maintain cell shape. b. The cytoskeleton provides anchorage for many organelles and cytosolic enzyme molecules. c. The cytoskeleton is more dynamic than an animal skeleton. It an be quickly dismantled in one part of the cell and reassembled in a new location. 2. Components of the Cytoskeleton a. Microtubules- shape and support the cell and serve as tracks to guide motor proteins carrying organelles to their destination. b. Centrosomes and Centrioles- Centrosomes is the location were microtubules grow out of in animal cells. Often this region is located near the nucleus. Centrioles are composed of nine sets of triplet microtubules arranged in a ring. Before an animal cell divides, the centrioles replicate. c. Cilia and Flagella- Used to propel many unicellular eukaryotes through water. Is also found in sperm and algae. 3. Microfilaments a. Micro filaments aren’t been solid rods. They’re also called actin filaments because they’re built from molecules of actin, a globular protein. A microfilament is a twisted double chain of actin subunits. Besides occurring as linear filaments, microfilaments form structural networks when certain proteins bind along the side of such a filament and allow a new filament to extend as a branch. Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline 4. Intermediate Filaments a. Intermediate filaments are named for their diameter, which is larger than the diameter of microfilaments but smaller than that of the microtubules. Specialized for bearing tension intermediate filaments are a diverse class of cytoskeletal elements. G. Extracellular components and connections between cells help coordinate cellular activities 1. Cell Walls of Plants a. The cell wall is an extracellular structure of plant cells that distinguishes them from animal cells. The wall protects the plant cell, maintains its shape, and prevents excessive uptake of water. b. A young plant cell first secretes A relatively thin and flexible wall called the primary cell wall. Between primary walls of adjacent cell is the middle lamella, a thin layer bridge in sticky polysaccharides called pectins. c. Other cells as a secondary cell wall between the plasma membrane and the primary wall. The secondary wall, often deposited in several laminated layers, has a strong and durable matrix that affords the cell protection and support. 2. The Extracellular Matrix of Animal Cells a. Although animal cells lack walls akin to those of plant cells, they do have an elaborate extracellular matrix. b. Callagen Forms strong fibers outside the cells c. Callagen accounts for about 40% of the total protein in the human body. 3. Cell Junctions: a. Neighboring cells in animal or plant often adhere, Interact, and communicate via sites of direct physical contact. b. Plasmidesmata joins adjacent cells and unities most of a plant into one living continuum. c. In animals there are three main types of cell junctions: tight junctions, desmosomes, and gap junctions. All three types of cell junctions are especially common in epithelial tissue. IIII. Chapter 22: The Origin of Species A. The biological species concept emphasizes reproductive isolation 1. The Biological Species Concept a. According to this concept a species is a group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring but do produce such offspring with members of other such groups. b. Reproductive isolation is the existence of biological barriers that impede members of two species from interbreeding and producing offspring. Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline c. Prezygotic barriers block fertilization from occurring. 2. Reproductive Isolation a. Habitat isolation- Two organisms that use different habitats are unlikely to encounter each other b. Temporal Isolation- Two species that breed during different times of day, different seasons, or different years cannot mix gametes. c. Behavioral isolation- Many species use elaborate courtship behaviors unique to the species to attract mates. d. Mechanical Isolation- Mating is attempted but morphological differences prevent its successful completion e. Gametic Isolation- Sperm of one species may not be able to fertilize the eggs of another species f. Reduced Hybrid Viability- The genes of different parent species may interact in ways that impair the hybrids development or survival in its environment. g. Reduced Hybrid Fertility- Even if hybrids are vigorous, they may be sterile. h. Hybrid Breakdown- Some first generation hybrids are viable and fertile, but when they mate with one another or with either parent species, offspring of the next generation are fertile or sterile. 3. Limitations of the Biological Species Concept a. One strength of the biological species concept is that it directs our attention to a way by which speciation can occur. b. However the number of species to which this concept can be usefully applied is limited. c. Some biologists argue that the biological species concept overemphasizes gene flow and downplays the role of natural selection. 4. Other Definitions of Species a. Morphological Species concept characterizes a species by body shape and other structural features. b. The ecological species concept views a species in terms of its ecological niche, the sum of how members of the species interact with the nonliving and living parts of their environment. c. Phylogenetic species concept defines a species as the smallest group of individuals that share a common ancestor, forming one branch of the tree of life. B. Speciation can take place with or without geographic separation 1. Allopatric Speciation a. In allopatric speciation gene flow is interrupted when a population is divided into geographically isolated subpopulations. Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline b. Many studies provide evidence that speciation can occur in allopatric populations. c. The importance of allopatric speciation is also suggest by the fact that regions that are isolated or highly subdivided by barriers typically have more species than do otherwise similar regions that lack such features. 2. Sympatric Speciation a. In sympatric speciation, speciation occurs in populations that live in the same geographic area. b. Polyploid speciation occasionally occurs in animals. Polyploidy is a condition in which a species may originate from an accident during cell division that results in extra sets of chromosomes. c. Sympatric speciation can also occur when genetic factors enable a subpopulation to exploit a habitat or resource not used by the parent population. C. Hybrid zones reveal factors that cause reproductive isolation 1. Patterns within hybrid zones a. Hybrid zones typically are located wherever the habitats of the interbreeding species meet. b. These regions often resemble a group of isolated patches scattered across the landscape. 2. Hybrid Zones over Time a. When hybrids are less fit than members of their parent species, natural selection tends to strengthen prezygotic barriers to reproduction, thus reducing the formation of unfit hybrids. b. Barriers to reproduction may be weak when two species meet in a hybrid zone. Indeed, so much gene flow may occur that reproductive barriers weaken further and the gene pools of the two species become increasingly alike c. Many hybrid zones are stable in the sense that hybrids continue to be produced. In some cases, this occurs because the hybrids survive or reproduce better than members of either parent species. D. Speciation can occur rapidly or slowly and can result from changes in few or many genes 1. The Time Course of Speciation a. The existence of fossils that display a punctuated pattern suggests that once the process of speciation begins it can be completed rapidly. b. It appears that rapid speciation produced the wild sunflower Helianthus anomalous. Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline c. Data suggests that on average, millions of years may pass before a newly formed plant or animal species will itself give rise to another new species. 2. Studying the Genetics of Speciation a. The central quest of studying the genetics of speciation is to identify genes that cause reproductive isolation. b. In several isolated cases the evolution of reproductive isolation is due to a change in a single gene. c. Overall studies suggest that few or many genes can influence the evolution of reproductive isolation and hence the emergence of new species. 3. From Speciation to Macroevolution a. As one group of organisms increases in size by producing many new species, another group of organisms may shrink, losing species to extinction. V. Chapter 23: Broad Patterns of Evolution A. The fossil record documents life’s history 1. The Fossil Record a. Sedimentary rocks are the richest source of fossils. As a result, the fossil record is based primarily on the sequence in which fossils have accumulated in sedimentary rock layers. b. The fossil record shows that there have been great changes in the kinds of organisms on Earth at different points in time. c. Despite the fact that the fossil record is very significant it must be understood that it is an incomplete chronicle of evolutionary change. 2. How Rocks and Fossils are Dated a. Radiometric dating is one of the most common methods to determine the age of a fossil. It is based on the decay of radioactive isotopes. b. Fossils contain isotopes of elements that accumulated in the organisms when they were alive. When the organism dies it stops accumulating carbon and the amount of carbon-12 in its tissues does not change over time. c. By measuring the ratio of carbon-14 to carbon-12 in a fossil, we can determine the age of the fossil. 3. The Geologic Record a. A geologic record is a standard time table that divides Earth’s history into four eons. b. The last 3 eons together lasted about 4 billion years. c. The Phanerozoic era (roughly the last half billion years) encompasses most of the time animals have existed on earth. 4. The Origin of New Groups of Organisms Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline a. Over the course of the last 120 million years mammals originated gradually from a group of tetrapods called synapsids. b. Synapsid’s had multiple bones in the lower jaw and single pointed teeth. c. The very late cynodont no longer had a articular quadrate hinge and began to take the form of modern day mammals. B. The Rise and fall of groups of organisms reflect differences in speciation and extinction rates 1. Plate Tectonics a. The seemingly rock solid continents we live on move over time. b. Since the origin of multicellular eukaryotes roughly 1.5 billion years ago, there have been 3 times when most of the landmass of the Earth came together to form a supercontinent. c. According to plate tectonics the continents are part of great plates of Earth’s crust that essentially float on the hot, underlying portion of the mantle. 2. Consequences of Continental Drift a. Continental drift greatly affects life on earth because it alters the habitats in which organisms live. b. When Pangaea was formed sea level was lowered which killed off great amounts of marine life that inhabited shallow waters. c. Continental Drift also causes climate change, which a significantly impact the organisms living in the area. 3. Mass Extinctions: a. Fossil records show that the vast majority of species that ever lived are now extinct. b. Over the past 500 millions years 5 mass extinctions have occurred. c. For example the Permian mass extinction claimed about 96% of marine animal species. 4. Adaptive Radiations a. Adaptive radiations are periods of revolutionary change in which groups of organisms form many new species whose adaptations allow them to fill different ecological roles. b. Fossil evidence indicates that mammals underwent a dramatic adaptive radiations after the extinction of terrestrial dinosaurs 65.5 million years ago. c. The history of life has been greatly altered by radiations in which groups of organisms increased in diversity as they cam to play entirely new ecological roles. C. Major Changes in body form can result from changes in the sequences and regulation of developmental genes Wyatt Connell Lansdale Catholic High School A.P. Biology Chapter Outline 1. Effects of Developmental Genes a. An evolutionary change in the rate or timing of developmental events is called heterochrony. b. Paedomorphosis is a condition in which reproductive organ development accelerates compared with other organs and the sexually mature stage of a species may retain body features that were juvenile structures. c. Homeotic genes determine such basic features as where a pair of wings and pair of legs will develop. 2. The Evolution of Development a. Large members of most animal phyla appear suddenly in fossils formed 535-525 million years ago. b. This rapid diversification of animals is referred to as the Cambrian Explosion. c. Changes in the nucleotide sequence or regulation of developmental genes can result in a morphological change that harms the organism D. Evolution is not goal oriented 1. Evolutionary Novelties a. As new species form novel and complex structures can arise as gradual modifications of ancestral structures b. It is common for complex structures to have evolved in increments from simpler versions that performed the same basic functions. c. The human eye is an example of a complex structure that evolved from a simpler form. 2. Evolutionary Trends a. Branching evolution can result in a real evolutionary trend even if some species counter the trend. b. The species that endure the longest and generate the most new offspring determine of major evolutionary trends. c. An evolutionary trend does not imply that there is some intrinsic drive toward a particular phenotype. Evolution is the result of interactions between organisms and their current environments. If environmental conditions change an evolutionary trend may cease or even reverse itself.