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General Biology Entire Class Notes

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by: Morgan Oestmann

General Biology Entire Class Notes BIO101

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Morgan Oestmann

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General Biology
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Date Created: 02/22/16
Chapter 2 Introduction  Chemicals are the raw material that makes up: o Our body o Body of other organism o Physical environment  Biological Function starts at the Chemical level o Strong relationship between structure and function at all levels in hierarchy of life  Life’s chemistry is tied to water o Life first evolved in water o All living organisms require water o Cells consist of 75% water o Same is true for muscle-powered flight in insects o Reductionism- scientific approach based on the idea that the whole can be best be understood by studying its parts Organisms are composed of elements, in combinations called compounds  Living organisms are composed of matter, which is anything that occupies space and has mass  Matter is composed of chemical elements o Element- substance that cannot be broken down to other substances by ordinary chemical means o There are 92 elements in nature- only a few exists in a pure state  Life requires about 25 chemical elements o Four main elements (96%)  Hydrogen  Carbon  Nitrogen  Oxygen o Many others (4%)  Calcium, phosphorus, potassium, sulfur, sodium, chlorine, and magnesium o Trace Elements are essential but are only needed in minimal quantities  Life is composed of matter o Mass is the quantity of matter an object has o Weight is the pull of gravity on an object  Chemical Element is a substance that cannot be broken down chemically into simpler matter without changing its properties  A compound is a substance consisting of two or more different elements in a fixed ration o More common than pure elements o Sodium chloride, table salt (NaCl) o Most elements don’t exist by themselves and readily combine into a predictable fashion  Chemical formula shows the kind of and number of atoms of each element occurring in a particular compound  Molecule- two or ore atoms held together by covalent bonds Trace elements are common additives to food and water  Some trace elements are required to prevent disease o Without iron, body can’t transport oxygen, Anemia o Iodine deficiency prevents production of thyroid hormones, resulting in goiter  Goiter-enlarged thyroid gland caused by iodine deficiency  Fluoride is usually added to municipal water and dental products to help reduce tooth decay  Several chemicals are added to food to: o Preserve food o Make it more nutritious o Make it look better Atoms consist of protons, neutron, and electrons  Each element consists od one kind of atom  An atom is the smallest unit of matter that still retains the properties of an element  Elements are arranged by their atomic number on the periodic table  Horizontal rows are called Period- tell the number of energy levels  Vertical Rows are called families- tell outer most number of electrons Atoms consist of protons, neutrons, and electrons  Protons- Single Positive Charge  Neutrons- Neutral  Electrons- Single Negative Charge  Neutrons and protons are packed into an atom’s nucleus  Electrons orbit the nucleus  Negative charge of electrons and the positive charge of protons keep electron near nucleus  Number of protons is the atom’s atomic number  An atom’s mass number is the sum of the number of protons and neutrons in nucleus  Atomic mass is approx. equal to its mass number  Atomic mass = Protons  Mass number= Protons + Neutrons  Although all atoms of an element have the same atomic number, some differ in mass number  Different isotopes of an element have o Same number of protons o Different number of neutrons  Different isotopes of an element behave identically in chemical reactions  In radioactive isotopes, nucleus decays, giving off particles and energy o Can be dangerous to life because of mutations o Living cells cannot distinguish radioactive isotopes from non-radioactive of the same element  Compounds in metabolic processes can act as a tracer  Radioactivity can be detected by instruments o Used in medical diagnosis (PET) o Chemical bonds are broken by the emitted energy, which causes abnormal bonds to form Chemical Bonds Distribution of electrons determines an atom’s chemical properties  Electrons can be located in different shells, each with characteristics o Atom may have one, two, or more shells  Electrons in outermost shell, valence, determines chemical properties of atom  Outer shells that aren’t full tend to interact with other atoms in ways that enable them to complete or fill their valence shell  Incomplete outer shell, atoms will share, donate, or receive electrons  Interactions result in atoms staying close together, Chemical bonds  Covalent, tow atoms, each with an unpaired electron, share pairs of electrons  Two or more atoms held together by covalent bonds- molecule  Covalent bond connect two hydrogen atoms in a molecule of the gas H 2-  Strongest bonds, holds molecules together Electron arrangement determines chemical properties  Each electron shell can accommodate only a certain number of electrons o First Shell—2e - - o Second Shell—8e - o Third Shell—2e  Hydrogen Bonds- form when a hydrogen atom covalently bonded to one electronegative atom to also attached to another electronegative atoms Covalent Bonds join atoms into molecules through electron sharing  Atoms in a covalently bonded molecule continually compete for shard electrons o Attraction for shared electrons called electronegativity  H 2, neutral, has a slightly negative pole and two slightly positive poles, making it a polar molecule, leads to hydrogen bonding  Oxygen attracts the shared electrons more strongly than hydrogen o Shared electrons spend more time near oxygen o Oxygen atom has a slightly negative charge and hydrogen  Polar covalent bond—chemical bonds in which shared electrons are pulled closer to the more electronegative atom, make it partially negatives Ionic Bonds are attractions between ions and opposite charge  Ion is an atom or molecule with an electrical charge resulting from gain or loss of one or more electrons o Electron is lost, positive charge o Electron is gained, negative charge  Two ions with opposite charges attract each other o When attraction holds ions together, called ionic bonds o Salt in a synonym for an ionic compound  Ionic compounds dissolve easily in water Chemical Formulas  Subscript after a symbol tells the number of atoms in each element  Coefficients before a formula tells the number of molecules Hydrogen bonds are weak bonds important in the chemistry of life  In living organisms, most strong chemical bonds are covalent o Crucial to the functioning of a cell are weaker bonds within and between molecules  One of most important types of weak bonds is the hydrogen bond, which is best illustrated in water molecules  Hydrogen atoms of a water molecule are attached to oxygen by polar covalent bonds  Because of polar bonds and wide V shape of the molecule, water is polar molecule—that is, it has an unequal distribution of charges  Weak hydrogen bonds form between water molecules o Each hydrogen atom of a water molecule can form a hydrogen bond with a nearby partially negative oxygen atom of another water molecule o Negative pole of water molecule can form hydrogen bonds to two hydrogen atoms o Thus, each H2O molecule can hydrogen-bond to as many as four partners Chemical reactions make and break chemical bonds  Structure of atoms and molecules determines the way they behave o Atoms combine to form molecules o Hydrogen and oxygen can react to form water  Chemical reaction is the breaking and making of chemical bonds, leading to changes in the composition of matter  Don’t create or destroy matter, only rearrange Water’s Life-Supporting Properties Hydrogen bonds make liquid water cohesive  Tendency of molecules of the same kind to stick together is cohesion o Cohesion is much stronger for water than for other liquids o Most plants depend upon cohesion to help transport water and nutrients from their roots to their leaves  Tendency of two kinds of molecules to stick together is adhesion  Cohesion is related to surface tension—a measure of how difficult it is to break a surface of a liquid o Hydrogen bonds give water high surface tension, making it behave as if it were coated with an invisible film o Water striders stand on water without breaking the water surface Water’s hydrogen bonds moderate temperature  Thermal energy is the energy associated with the random movement of atoms and molecules o Thermal energy is transfer from a warmer to a cooler body of matter is defined as heat o Temperature measures the intensity of heat—that is, the average speed of molecules in a body of matter  Heat must be absorbed to break hydrogen bonds  Heat is released when hydrogen bonds form  To raise the temperature of water, hydrogen bonds between water molecules must be broken before the molecules can move faster. Thus, o When warming up, water absorbs a large amount of heat o When water cools, water molecules slow down, more hydrogen bonds form, and a considerable amount of heat is released  Earth’s giant water supply moderates temperatures, helping to keep temperatures within limits that permit life  Water’s resistance to temperature change also stabilizes ocean temperatures, creating a favorable environment for marine life  When a substance evaporates, the surface of the liquid that remains behind cools down; this is the process of evaporative cooling o This cooling occurs because the molecules with the greatest energy leave the surface o Helps regulate our internal body temperature  Evaporative cooling and prevent overheating Ice floats because it is less dense than liquid water  Exists as a gas, liquid, or solid  Is less dense as a solid than a liquid because of hydrogen bonding  When water freezes, each molecule forms a stable hydrogen bond with its neighbors o As ice crystals form, the molecules are less densely packed than in liquid water o Because ice is less dense than water, it floats Water is the solvent of life  Solution is a liquid consisting of a uniform mixture of two or more substances o Dissolving agent is the solvent o Substance that is dissolved is the solute o Aqueous solution is one in which water is the solvent  Water’s versatility as a solvent results from the polarity of its molecules o Polar or charged solutes dissolve when water molecules surround them, forming aqueous solutions o Table salt is an example of a solute that will go into solution in water Chemistry of life is sensitive to acidic and basic conditions  In liquid water, small percentage of water molecules break apart into ions o Some are hydrogen bonds (H+) o Some are hydroxide ions (OH-) o Both are very reactive  Substance that donates hydrogen ions to solutions is called an acid  Base is a substance that reduces the hydrogen ion concentration of a solution  pH scale describes how acidic or basic a solution is o The pH scale ranges from O to 14, with 0 the most acidic and 14 the most basic o Each pH unit represents a 10-fold change in the concentration of H+ in a solution  A buffer is a substance that minimized changes in pH. Buffers o Accept H+ when it is in excess o Donate H+ when it is depleted Scientist study the effects of rising atmospheric CO2 on coral reefs ecosystems  Carbon dioxide is o Main product of fossil fuel combustion  Increasing in the atmosphere  Linked to global climate change  About 25% of this human-generated CO2 is absorbed by the vast oceans  CO2 dissolved in seawater lowers the pH of the ocean in a process known as ocean acidification  As seawater acidifies, the extra hydrogen ions combine with carbonate ions to form bicarbonate ions o Reaction reduces the carbonate ion concentration available to corals and other shell-building animals.  In controlled experiment, scientists looked at the effect of decreasing carbonate ion concentration on the rate of calcium deposition by reef organisms Search for extraterrestrial life centers on the search for water  Emergent properties of water support life on Earth  When astrobiologists search of signs of extraterrestrial life on distant planets, they look for evidence of water  NASA has found evidence that water was once abundant on Mars Biology- Study of living things and how it interacts with one another Seven Properties 1. Order  Complex structural organizations of living things based on the instructions contained in DNA molecules  Organisms are more highly ordered when compared to the non-living environment 2. Reproduction  Ability to perpetuate species  Organisms come from other organisms  Reproduction may be sexual or asexual 3. Growth and Development  Growth: Increase in cell size and number  Development: Changes taking place during organism’s life  Inherited genes of organism controls the pattern and stages of growth and development 4. Energy Processing  Take in and transform energy to do work, to live  Metabolism: sum of all the chemical reactions that occur in the cell 5. Response to Environment  Responds to Stimuli  Organisms respond to internal and external changes 6. Regulation  Maintain internal environment with changes to external environment  Homeostasis: Maintenance of internal conditions  i.e., Body Temperature, Glucose levels, and moisture 7. Evolutionary Adaptation  Change traits to best suit the environment Evolution explains the unity and diversity of life  Evolution can be defined as the process of change that has transformed life on Earth from its earliest beginnings to the diversity of organisms living today  Fossil record documents o Life has been evolving on Earth for billions of years and o Pattern of ancestry Organization Hierarchy  Biosphere (Earth)  Ecosystem (Forest)  Community (Organisms)  Population (Ring-tailed Lemurs)  Organism  Organ System (Digestive System)  Organ (Stomach)  Tissue (Specific Function)  Cell (Fundamental Unit of Life)  Organelles (Mitochondria)  Molecules Life’s Hierarchy of Organization  Each level builds on the level below it demonstrates new features called emergent properties  Top of hierarchy is ecosystem o All living organisms living in an area o All non-living components (soil, air, and water)  Ecology is the branch of biology that investigates these relationships between organisms and their environment  Middle Tier is organism  Life emerges at the level of the cell, the lower tier, which is composed of o Cells, organelles, and molecules Cells are the structural and functional units of life  Cells are the level at which the properties of life emerge  A cell can: o Regulate its internal environment o Take in and use energy o Develop and maintain its complex structures o Respond to its environment o Rise new cells  All cells o Are enclosed by a membrane that regulates the passage of materials between the cell and its surroundings and o Use DNA as their genetic information Two basic cell forms  Prokaryotic (Bacteria and Archaea) o First to evolve o Simpler o Lacks a nucleus o Usually smaller than eukaryotic cells  Eukaryotic o Plants, Animals, Fungi, Protists o Subdivided by membranes into various functional compartments, or organelles, including a nucleus that houses the DNA Organisms interact with their environment, exchanging matter and energy  Living organisms interact with their environments, which include o Other organisms o Physical factors  In most ecosystems, o Plants are the producers that provide the food o Consumers eat plants and other animals o Decomposers act as recyclers, changing complex matter into simpler chemicals that plants can absorb and use  Ecosystem has 2 major processes: o Recycling chemical nutrients from atmosphere and soil through producers, consumers, and decomposers back to air and soil o One way flow of energy through an ecosystem, entering as sunlight and exiting as heat  To be successful, an ecosystem must accomplish two things: o Recycle chemical necessary for life o Energy move through the ecosystem for life  Energy enters as light and exits as heat Evolution, the Core Theme of Biology Unity of life is based on DNA and a common genetic code  All cells have DNA, chemical substance of genes  Genes o Are the Unite of inheritance that transmit information from parents to offspring o Grouped into very long DNA molecules called chromosomes o Control the activities of a cell  Species’ genes are coded in the sequence of the four kinds of building blocks making up DNA’s double helix  Deoxyribonucleic Acid= DNA  Genome= Library of genetic instructions that an organism inherits Diversity of Life into 3 Domains  Diversity is the hallmark of life  Biodiversity can be both beautiful and overwhelming  Taxonomy is the branch of biology that names and classifies species o Formalized classification of an organism: Species Genus Family Order Class Phylum Kingdom  Diversity of life can be arranged into three higher levels called domains o Bacteria are the most diverse and widespread prokaryotes o Archaea are prokaryotes that often live in Earth’s extreme environments o Eukarya have eukaryotic cells and include  Single-celled Protists  Multicellular fungi, animals, and plants  Three-domain system is currently used, and replaces the older five-kingdom system o Monera: Most widespread organisms  Prokaryotes  Lack nuclear membrane around DNA  Lack membrane bound organelles  Unicellular: single-celled organisms  Have distinctive cell wall  Include Bacteria, Archaea o Protista  Eukaryotes  Have nuclear membrane around DNA  Have membrane bound organelles  Mostly unicellular or some simpler multicellular relatives  Mostly larger and more complex than bacteria  Autotrophs, Heterotrophs  Include: algae, protozoan, slime molds, water molds o Fungi  Most are multicellular  Eukaryotes  Have nuclear membrane  Have membrane bound organelles  Have cell walls of chitin o Plantae  Complex multicellular organisms  Cell walls of cellulose  Eukaryotes  Other features  Complex organ system  Waxy cuticle that prevents water loss  Multicellular sex organs  Openings in leaves and stems for gas exchange (stomata)  Includes: mosses, ferns, conifers, trees, shrubs, flowering plants o Animalia  Complex multicellular organisms  Lack cell walls  Heterotrophs  Features of complex animals  High degree of tissue specialization and body organization  Locomotion  Well developed sense organs, nervous system, and muscles  Includes: Sponges, worms, insects, fishes, frogs, etc Evolution Explains the Unity and Diversity of Life  Charles Darwin wrote “On the Origin of Species by Means of Natural Selection” in which he proposed the theory of evolution  In 1859, Charles Darwin published the book, which articulated two main points. o Species living today descended from ancestral species in what Darwin called “descent with modification” o Natural Selection is a mechanism for evolution  Theory of Evolution by Natural Selection o Genetic Variation  Due to genetic differs there is variation within a population.  These differences can be passed on to an individual’s offspring o Overproduction  Many more organisms are born, than those that survive and reproduce o Limits on Population growth  Limited resources creates competition o Differential reproduction  Organisms with features that help them compete will be more likely to survive and reproduce  Natural selection was inferred by connecting two observations o Individual variation  Individuals in a population vary in their traits, many of which are passed on from parents to offspring o Overproduction of offspring  Population can produce far more offspring than the environment can support  Darwin realized o Numerous small changes in populations as a result of natural selection could eventually lead to major alterations of species o Fossil record provides evidence of such diversification of species from ancestral species Process of Science In studying nature, scientists make observations and form to test hypothesis  Science is a way of knowing that stems from our curiosity about ourselves and the world around us  Science is based upon inquiry, the search for information and explanations of natural phenomena  Scientists typically: o Make observations o From hypotheses, proposed explanations for a set of observations o Test them  Two types of data are frequently collected in scientific investigations o Qualitative data: description o Quantitative data: numerical measurements  Two types of reasoning: o Inductive: generalizations based on collecting and analyzing a large number of specific observations o Deductive: flows from general premises to predicted and specific results  Nature of Hypotheses o Hypothesis: proposed explanation o Testable and potentially falsifiable  Testable: can make observations and measurements  Falsifiable: Can be proven  Scientific theory is o Much broader in scope than a hypothesis o Supported by a large and usually growing body of evidence  Science is a social activity in which scientists: o Work in teams o Share information through peer-reviewed publications, meetings, and personal communications o Build on and confirm each other’s work  Scientific Theory o Powerful, broad explanation of large sets of observations o Can explain some aspects of nature o Rests on many hypotheses that have been tested o Generates additional hypotheses Hypothesis Testing  Most powerful way to test hypothesis: do experiments Scientific Thinking: Hypotheses can be tested using controlled field studies  Scientists conducted a controlled experiment to test hypothesis that color patterns have evolved as adaptions that protect animals from predation o The experiment compared an experimental group consisting of non-camouflaged mice models and a control group consisting of camouflaged models that matched the mice native to each area o The groups differed by only one factor, the coloration of the mouse models Logic of Hypothesis Tests  Example: Consuming Vitamin C decreases the risk of catching a cold  Inductive reasoning: combining series of specific observations into generalizations  To test, make a prediction using deductive reasoning o Involves using a general principle to predict an expectation Experimental Method  Experiments are contrived situations  Variable: factors that can change in value under different conditions o Independent variables can be manipulated by the scientist o Dependent variables cannot be changed by the researcher. Variable being observed or measured Evaluating Scientific Information  Where info comes from makes a difference  Primary Sources (best sources) o Researchers can submit a paper about their results to a pro journal o Peer Review: evaluation of submitted papers by other experts  Secondary Sources o Books, news reports, interment, and ads o Provide some of the info from a primary source  Information from Anecdotes o Anecdotal Evidence: based on one person’s experience  i.e., testimonial from a celebrity  Understanding Science from Secondary Sources o Use understanding of the process of science to evaluate science stories o News media generally highlight only those stories seems newsworthy o More likely to report a positive result than a negative one Biology and Everyday Life Evolution Connection: Evolution is connected to our everyday lives  Humans selectively breed plants and animals in the process of artificial selection to produce: o More productive crops o Better livestock o Great variety of pets that bear little resemblance to their wild ancestors  Humans also unintentionally cause: o Evolution of antibiotic-resistant bacteria o Evolution of pesticide-resistant pests o Loss of species through habitant loss and global climate change Biology, technology, and society are connected in important ways  Many issues facing society o Related to biology o Often involve our expanding technology  Basic goals of science and technology differ o Goal of science is to understand natural phenomena o Goal of technology is to apply scientific knowledge for some specific purpose  Although their goals differ, science and technology are interdependent o Research benefits from new technologies o Technological advances stem from scientific research  Technologies of DNA manipulations are the results of scientific discovery of the structure of DNA How Cells Harvest Chemical Energy Introduction  Oxygen is a reactant in cellular respiration: o Process that breaks down sugar and other food molecules and generates ATP, energy currency in cells, and heat  Brown fat has a “short circuit” in its cellular respiration, which generates only heat, not ATP  Also important for heat production in small mammals, including humans Cellular Respiration: Aerobic Harvesting of Energy Photosynthesis and Cellular Respiration provide energy for life  Life requires energy o Almost all ecosystems, energy ultimately comes from the sun  In photosynthesis, o Some of the energy in sunlight is captured by chloroplasts o Atoms of carbon dioxide and water is rearranged o Sugar and oxygen are produced  In cellular respiration, o Sugar is broken down to carbon dioxide and water o Cell captures some of the released energy to make ATP  Cellular respiration takes place in the mitochondria of eukaryotic cells o In these energy conversions, some energy is lost as heat  Oxygen is used to break down glucose to CO2 and H2O  Energy is released as ATP  used for cellular work Connection between Photosynthesis and Cellular Respiration  Photosynthesis organism convert light energy to chemical energy  CO +2H 0 2C H 06+O12 6 2  Cellular respiration breaks down the fuel from photosynthesis to form ATP.  C 6 O12O6 AT2 + CO + H 0 2 2 How is breathing related to Cellular respiration?  Respiration, as it relates to breathing, and cellular respiration are not the same o Respiration, in the breathing sense, refers to an exchange of gases. Usually an organism brings in oxygen from the environment and releases waste CO2- o Cellular respiration is the aerobic (oxygen-requiring) harvesting of energy from food molecules by cells Cellular respiration banks energy in ATP molecules  Cellular respiration is an exergonic process (energy-releasing) that transfers energy from the bonds in glucose to form ATP  Cellular respiration produces ATP to be used for cellular work o Chemical reactions o Mechanical work o Membrane active transport  Cellular respiration o Can produced up to 32 ATP molecules for each glucose molecule o Uses about 34% of the energy originally stored in glucose o Releases the other 66% as heat  This energy conversion efficiency is better than most energy conversions systems o Only about 25% of the energy in gasoline produces the kinetic energy of movement  Glucose is shown in most reactions, but cells can burn other fuels  In a car, only 25% of energy in gasoline is converted to kinetic energy of movement  Cellular respiration can produce up to a max of 38 ATP molecules for each glucose molecules. This translates to about 40% of the energy in a glucose molecule. The rest of the energy in glucose is released as “heat” Connection: Human body uses energy from ATP for all its activities  Body requires a continuous supply of energy just to stay alive—to keep your heart pumping and you breathing  Kilocalorie (kcal) is o Quantity of heat required to raise the temperature of 1 o kilogram of water by 1 Celsius o Same as a food calorie  Why do we sweat? o Spend energy to do work (exercise) and we use up food in our body to make ATP. Cellular respiration is increased to provide more ATP o 60% of energy is released as body heat  Average adult needs to take in 2,200 kcal of energy per day o About 75% of these calories is used to maintain a healthy body o Remaining 25% is used to power physical activities  Balance of energy intake and expenditure is required to maintain a healthy weight Cells capture energy from electrons “falling” from organic fuels to oxygen  How do your cells extract energy from glucose?  Answer involves the transfer of electrons during chemical reactions  When chemical bond breaks, electrons kind of fall from the organic molecule. As they fall, they lose or transfer potential energy and energy is released  Energy is stored in the chemical bonds of organic molecules (potential energy)  At each step of the fall, a REDOX reaction occurs  During Cellular Respiration, o Electrons are transferred from glucose to oxygen and o Energy is released  Oxygen attracts electrons very strongly o Electron loses potential energy when it is transferred to oxygen  Cellular respiration is a more controlled descent of electrons and like rolling down an energy hill o Energy is released in small amounts and can be stored in chemical bonds of ATP  Redox Reaction: coupled oxidation- reduction reactions  Oxidation is the loss of electrons. C-H bonds in glucose are broken and H atoms are lost as glucose is converted in CO . 2 Glucose is oxidized, therefore releasing energy.  Reduction: Gain of electrons. O H a2oms and is converted to H 2. O 2s reduced, therefore gaining energy.  Summary Redox: e is transferred because the H atom is passed on  Electron transport chain (ETC): “fall” of electrons from NADH to O2 occurs n an ETC. The electron carrier molecules are in the inner membrane of the mitochondrion. O2 is the final electron acceptor.  If you burn sugar, “fall” of electrons to oxygen is rapid and energy is released in one step as heat and light. Fall of electrons to oxygen in cellular respiration is controlled and occurs in steps. Energy is released slowly and is captured.  Dehydrogenase enzyme o Removes 2 Hydrogen atoms from the organic molecule  The 2 electrons are transferred to the coenzyme NAD of FAD (organic molecule that shuttles electrons) in a redox reactions o NAD gains 2 electrons  HADH and 1 H ion is released  An important player in the process of oxidizing glucose is an coenzyme called NAD+, which o Accepts electrons o Becomes reduced to NADH  Nicotinamide Adenine Dinucleotide (NAD+) o Derivative of the vitamin Niacin o Collects the electrons and carriers them to another location  Flavin Adenine Dinucleotide (FAD) o Derivative of the vitamin Riboflavin  NADH delivers electrons to a string of electron carrier molecules, which moves electrons down the hill  Carrier molecules constitute an electron transport chain  Bottom of the hill is oxygen, which o Accepts two electrons o Picks up two H+ o Becomes reduced to water Stages of Cellular Respiration Cellular respiration occurs in three main stages  Glycolysis o Occurs in the cytosol (cytoplasm) o Begins cellular respiration o Breaks down glucose into two molecules of a three-carbon compound called pyruvate o 1 glucose molecules is oxidized and split into 2 pyruvate molecules which goes to the citric acid cycle o Produces ATP molecules by substrate level phosphorylation- an enzyme transfers a phosphate group from a substrate directly to ADP, forming ATP o NAD+ are reduced to form NADH (to be used later in the 3 rd stage to make more ATP) o Glycolysis occurs in the cytoplasm of all cells, doesn’t require oxygen (anaerobic)- though to be an ancient metabolic system o Divided into two phases  Energy investment phase  2ATP energizes a glucose molecules o Spit to form two 3C molecules  Energy pay off phase  Two 3C molecules 2 pyruvates, 4 ATP, and 2 NADH o Net gain of ATP for each molecules of glucose  4 ATP – 2 ATP = 2 ATP per glucose that enters glycolysis  Citric Acid Cycle o Occurs in the mitochondrion matrix o Pyruvate oxidation and the Citric Acid Cycle  Oxidize pyruvate to a two-carbon compound  Supply the third stage with electrons o Cell makes a small amount of ATP during glycolysis and the Citric Acid Cycle o Pyruvate doesn’t enter the citric acid cycle but undergoes some chemical grooming in which  Carboxyl group is removed and given off as CO2  Two-carbon compound remaining is oxidized while a molecule of NAD+ is reduced to NADH  Coenzyme A joins with the two-carbon group to form acetyl coenzyme A, abbreviated as acetyl CoA o Then two molecules of acetyl CoA enter the citric acid cycle o Grooming Step:  Pyruvate is converted to acetyl CoA o Pyruvate from glycolysis migrates from cytoplasm to mitochondrial matrix, where each pyruvate is converted in 3 reactions to acetyl CoA o Pyruvate dehydrogenase complex: large, multi-enzyme complex that catalyzes three reactions:  C is removed from pyruvate to form CO2  2-C compound is oxidizes fro form NADH  Coenzyme A + 2-C compound  Acetyl CoA o Therefore, 2 pyruvate molecules enters grooming resulting in 2acetyl CoA molecules that enter the 2 ndstage o Citric acid cycle  Also known as Krebs Cycle  Completes the oxidation of organic molecules  Generates many NADH and FADH2 molecules o Acetyl CoA enters the cycle and reactions occur in the mitochondrial matrix o Here all organic fuel is completely oxidized to CO2 o Energy pay off to cell is much more than glycolysis. Each turn of the cycle produces: 1ATP, 2CO 3 2ADH, and 1 FADH m2lecules o Overall, 2 Acetyl CoA (for each glucose) results in 2 ATP, 4CO ,26 NADH, and 2 FADH molecules o How does this compare with glycolysis? o 10 ATP by now  Oxidative Phosphorylation o Final State of cellular respiration  Involves electron transport and chemiosmosis and  Requires an adequate supply of oxygen o Arrangement of electron carriers built into a membrane makes it possible to  Create an H+ concentration gradient across the membrane and then  Uses the energy of that gradient to drive ATP synthesis o Stage produces the most ATP o Electrons fall from NADH and FADH2 to O2 and H20 o Energy released is used to pump H+ ions across the membrane o H+ gradient generates potential energy that’s used to form ATP o Electrons from NADH and FADH2 travel down the electron transport chain to O2, final electron acceptor  Oxygen pricks up H+, which forms water  Energy released by these redox reactions is used to pump H+ from the mitochondrial matrix into the intermembrane space o In chemiosmosis, the H+ diffuses back across the inner membrane, through ATP synthase complexes, driving the synthesis of ATP o Redox reactions of the electron transport chain provides energy to phosphorylate ADP- called Oxidation Phosphorylation o Energy Pay off:  Each NADH forms at least 3 ATP (8 NADH x 3 = 24 ATPS)  Each FADH2 forms at least f2 ATPS (2 FADH2 x 2 = 4 ATPS) o In absence of oxygen, ATP cannot be produced by oxidative phosphorylation Poisons can act by interfering with oxidation phosphorylation in 3 ways:  By blocking the ETC: rotenone (pesticide), CO (carbon monoxide), - a-d cyanide all bind to different e carriers of the ETC and prevent e transport  By blocking ATP synthase: Oligomycin (antifungal antibiotic used on skin) blocks the passage of H+ through the ATP synthase channel  By blocking the H+ gradient: DNP (dinitrophenol) is an “uncoupler”; it makes the inner membrane leaky so that a H+ ion gradient cannot be established Recall the energy payoff of cellular respiration involves  Glycolysis  Alteration of pyruvate  Citric Acid cycle  Oxidative phosphorylation Each molecule of glucose yields many molecules of ATP  Total yield is about 32 ATP molecule per glucose molecule  Number of ATP molecules cannot be stated exactly for several reasons o NADH produced in glycolysis passes electrons across mitochondrial membrane to either NAD+ or FAD. Because FADH2 adds its elections farther along the electron transport chain, it contributes less to the H+ gradient and thus generates less ATP o Some energy of the H+ gradient may be used for work other than ATP production, such as the active transport of pyruvate into the mitochondrion Fermentation: Anaerobic Harvesting of Energy Fermentation enables cells to produce ATP without oxygen  Fermentation is a way of harvesting chemical energy that does not require oxygen. Fermentation o Uses glycolysis o Produces two ATP molecules per glucose o Reduces NAD+ to NADH  Fermentation also provides an anaerobic path for recycling NADH back to NAD+  Your muscle cells and certain bacteria can regenerate NAD+ through lactic acid fermentation, in which o NADH is oxidized back to NAD+ o Pyruvate is reduced to lactate  Certain organisms are able to function without oxygen. Called anaerobic  Cells use only the glycolysis state to produce 2 ATPs per glucose molecule  2 NADH produced cannot go to the ETC in the absence of oxygen. NADHs have to be oxidized to reform NAD+ in a different way  2 kinds of fermentation based on the method of NADH oxidation: o Lactic Acid Fermentation (lactate)  Occurs in muscle cells when there is not enough oxygen  Acid causes burning feeling in muscles  Used by lactic acid bacteria (for making cheese and yogurt)  Here pyruvate is reduced to lactate and NADH is oxidized to NAD+ o Alcohol Fermentation (alcohol)  Backing and winemaking industries have used for thousands of years  In this process, yeast (single-celled fungi)  Oxidize NADH back to NAD+  Convert pyruvate to CO2 and ethanol  Obligate anaerobes: can only live without oxygen; poisoned by oxygen;  Ex. Some bacteria that lives in stagnant ponds or deep in soil  Facultative anaerobes: can live either with (cellular respiration) or without oxygen (fermentation);  Ex. Yeast and many other bacteria  Lactate is carried by the blood to the liver, where it is converted back to pyruvate and oxidized in the mitochondria of liver cells  Dairy industry uses lactic acid fermentation by the bacteria to make cheese and yogurt  Other types of microbial fermentation turn soybeans into soy sauce and cabbage into sauerkraut Connections Between Metabolic Pathways Cells use many kinds of organic molecules as fuel for cellular respiration  Although glucose is considered to be the primary source of sugar for respiration and fermentation, ATP is generated using o Carbohydrates  Starch, glycogen and many other carbohydrates are digested and converted to glucose  enters glycolysis o Fats  Energy-rich fuels, triglycerides are broken down into fatty acids and glycerol and converted to enter glycolysis or the Citric Acid Cycle.  1 g of Fat gives twice as much ATP as 1 g of starch)  Fats make excellent cellular fuel because they  Contain many hydrogen atoms and thus many energy-rich electrons  Yield more than twice as much ATP per gram as a gram of carbohydrate  Proteins can also be used for fuel, although your body preferentially burns sugars and fats first  Breakdown of Fats:  Fats are broken down to fatty acids and glycerol  Fatty acids are converted to acetyl groups by B- oxidation (Beta)  Respiration of a 6-carbon fatty acid yields 20% more energy o Proteins  Digested and broken down to amino acids. Amino acids can be used to build more proteins or can lose the amino group and enter glycolysis or the Citric Acid Cycle  Breakdown of proteins:  Amino acids undergo deamination to remove the amino group  Remainder of the amino acid is converted to a molecule (pyruvate, oxaloacetate, acetyl CoA) that enters Glycolysis or the Citric Acid Cycle  For example: o Serine is converted to pyruvate o Aspartate is converted to oxaloacetate Organic Molecules from food provide raw materials for biosynthesis  Cell must be able to make its own molecules to o Build its structure o Perform its functions  Food provides the raw materials your cells use for biosynthesis, the production of organic molecules, using energy-requiring metabolic pathways  All food molecules don’t end up as fuel for cellular respiration  Some of it’s used to make macromolecules used to maintain cell structure, energy to transport materials across membranes, manufacture products, grow and divide cells  Therefore, ATP is need for biosynthesis Working Cell Introduction:  Plasma membrane and its proteins enable cells to o Survive o Function  Aquaporin are membrane proteins that function as water channels Membrane Structure and Functions  Plasma membrane forms a boundary enclosed a living cell and internal membranes partitions the cell into specialize compartments known as organelles  Membranes regulate the transport of substances in and out of the cell  Membranes are fluid like salad dressing  Phospholipids are being able to move laterally and flip-flop from either side Membranes are fluid mosaics of lipids and proteins with many functions  Biologists use a fluid mosaics model to describe a membranes structure, patchwork of diverse proteins molecules embedded in a phospholipid bilayer and their various functions o Plasma membrane exhibits selective permeability o Proteins embedded in a membrane’s phospholipid bilayer perform various functions  Proteins perform many of the functions of a membrane  Different cell types will have different sets of membrane proteins  Six major functions of membrane protein: o Cytoskeleton and Extracellular Matrix (ECM): Help maintain cell shape and coordinate changes inside and outside the cell  Receptor: used in signal transduction o Membrane proteins receives a chemical message (signal molecule) from other cells with triggers a relay of a series to proteins inside the cell o After transcription and translation, new protein produced performs a specific task  Enzymes: molecules that function as biological catalysts, increase the rate of reaction o Often, grouped in a membrane to carry out sequential steps of metabolic pathway  Cell to Cell Recognition: Involving glycoproteins (and some non- proteins glycolipids) where carbohydrates function as id tags that are recognition by other cells  Intracellular Junctions: membrane proteins that help attach adjacent cell  Transport (Channel/Carrier): Help to move hydrophilic (polar/charged ions) substances more easily across the membrane o Channel Protein: Channel through which a specific solute can pass o Carrier Protein: specific solute binds to it and moves across the membrane as the shape of the protein changes  Can transport solute in either direction, who the net movement usually being down the concentration gradient for the solute Passive Transport is diffusion across a membrane with no energy investment  Diffusion is the tendency of particles to spread out evenly in an available space o Particles move from an area of more concentrated particles to an area where they are less concentrated o Means that particles diffuse down their concentration gradient o Eventually, particles reach dynamic equilibrium, where there is no net change in concentration on either side of the membrane  Solution: liquid consisting of a uniform mixture of 2 or more substances  Solute: Substance being dissolve o Ex: Salt, Sugar  Solvent: Liquid used to dissolve solute o Ex: Water  When water is used as the solvent, solution is called an aqueous solution  Concentration is the quantity of solute molecules for a given solution  Diffusion: tendency for particles of any kind spread out evenly in an available space o Molecules will always move down concentration gradients (high to low) o Two or more substances diffuse independently of each other o Concentration Gradient: difference between concentrations within a space or across a membrane  Oxygen and CO2 passively diffuse through membrane (no energy)  Diffusion across a cell membrane doesn’t require, energy, called passive transport  Diffusion down concentration gradients is the sole means by which oxygen enter your cells and carbon dioxide passes out of cell  Three types of Passive Transport o Simple Diffusion  Diffusion of mostly small, non-polar (hydrophobic) molecules easily through and across the membrane  Gases, steroids, glycerol, urea benzene  Down gradient to equilibrium with no energy o Osmosis  Diffusion of water molecules across a selectively permeable membrane  “Water will move across a membrane from an area where it is in larger quantity to area where its in lower quantity”  Polar water molecules will cluster around hydrophilic molecules  Left Side has lower solute concentration than the right  Lower solute= High Water concentration  Higher solute= Lower water concentration  Water will move down its concentration gradient across selectively permeable membrane o Facilitative Transport  Diffusion of polar (hydrophilic) molecules or charged molecules across the membrane  Pass slower and less easily through membrane. They require the help of a transport protein to move molecules down their concentration gradient across membrane  Transport Proteins o Very specific for the molecule they can interact with it and transport o Carrier proteins undergo a subtle change in shape that translates the solute-binding sit across the membrane o Shape changed may be triggered by binding and release Water Balance cells and their surroundings is crucial to organisms  Tonicity is the ability of a surrounding solution to cause a cell to gain or lose water o Tonicity of a solution mainly depends on its concentration of solutes relative to the concentration of solute inside the cell  How will animal cells be affected when placed into solutions of various tonalities? o Isotonic solution, concentration of solute is the same on both sides of a membrane, and cell volume won’t change o Hypotonic solution, solute concentration is lower outside the cell, water molecules move into the cell, and the cell will expand and may burst o Hypertonic solution, solute concentration is high outside the cell, water molecules move out of the cell, and cell will shrink  Water balance between cells and their surroundings: o Animal cells have no cell wall; do best in isotonic environments; gain water and can burst in a hypotonic solution; lose water and shrivel in hypertonic solution  Lysed cells; bursting cells o Plant cells, have rigid cell wall; are healthier in hypotonic surroundings, cell wall exerts wilt and die in isotonic solutions. Hypertonic solutions, plant cells lose water and ide o For an animal cell to survive in a hypotonic or hypertonic environment, it must engage in osmoregulation, control of water balance Two Kinds of membrane transport small molecules each one is based on energy use  Active transport: Diffusion of molecules across membrane where o Energy is required; Chemical, redox, or photon energy o Transport protein is required o Polar (Charged) molecules move against concentration gradients through a transport protein which creating or maintaining the gradient  Primary Active Transport  Energy is directly used with a transport protein to move molecules through a membrane against its concentration gradient  Secondary Active Transport Exocytosis and Endocytosis  Cell used two mechanisms to move large molecules across membranes o Exocytosis- Used to export bulky molecules, proteins and polysaccharides o Endocytosis- used to take in large molecules  Phagocytosis  “Cellular-drinking” where food is brought into the cell  Pinocytosis  “Cellular-drinking” where droplets of fluid are taken into the cell in tiny vesicles  Receptor Mediated Endocytosis  Highly specific process, where molecules are taken into the cell by using receptor proteins in the membrane to recognize substrate  Both cases, material to be transported is packaged within a vesicle that fuses Energy and the Cell Cells transform energy as they perform work  Cells are miniature chemical factories, housing thousands of chemical reactions  Some of these chemical reaction release energy, and other require energy Energy and the Cell  Energy is the capacity to do work and rearrange matter  All living organism require energy to stay alive  Cells use energy to do different kinds of work  Energy is the capacity to cause change or to perform work  Two basic forms of energy o Kinetic Energy-Energy of motion  Bicyclist Pedaling= muscle contraction, heat, light, electrical, etc. o Potential Energy- Energy that matter possesses as a result of its location or structure  Water behind a dam or skier at the top of a slope (gravitational), glucose or ATP (Chemical), compressed spring (Stored mechanical), nuclear, etc.  Chemical Energy- potential energy stored in bonds available for release in a chemical reaction. Most important type of energy for living organisms Thermodynamics  Study of energy transformations that occur in a collection of matter o System-collection of matter under study (single cell, entire planet, power plant, or a dam) o Surroundings- everything outside the system  Open System- Can exchange both energy and matter with its surroundings  Living Cell, ecosystem, Earth  Closed System- Exchange energy, but not matter with its surroundings  Bomb calorimeter, greenhouse Two laws govern Energy Conversion  All Energy transformations are governed by the same two laws of the universe known as the first and second laws of thermodynamics  First Law of Thermodynamics- Energy can be transferred and transformed, but it cannot be created nor destroyed o Energy of universe is constant. Total energy in universe is constant o Light bulb converts electricity to light energy; plant converts light energy into chemical energy Cells transform energy as they perform work  Automobile Engines and cells use the same basic process to make the chemical energy of their fuel available for work o Car and cells, waste products are carbon dioxide and water o Cells use oxygen in reactions that release energy from fuel molecules  Cellular respiration, chemical energy stored in organic molecules is used to produce, ATP, which the cell can use to perform work  Second Law of Thermodynamics: “Energy conversions increase the entropy (disorder) of the universe” o Second Law implies that during every energy transfer some energy becomes unusable-unavailable to do work (loss as heat). The Entropy of the universe is increasing (become more disordered). o Therefore, all energy transformation is not 100% efficiency. In fact, all chemical reactions involve release of heat energy Chemical reactions either release or store energy  Chemical reactions either o Release energy (exergonic reactions)  Chemical reaction that release energy  Reactants have more potential energy in their covalent bonds than the products  Reactions release energy in covalent bonds of the reactants  Burning wood release energy in glucose as heat and light  Cellular Respiration  Involves many steps  Release energy slowly  Uses some of the released energy to produce ATP  Require an input of energy and store energy (endergonic reactions)  Requires net input of energy (Absorb energy) and store energy  Products have more potential energy than reactants  Star with reactant molecules that contains relatively little potential energy  End with products that contain more chemical energy  Living organisms carries out thousands of endergonic and exergonic chemical reactions o Total of an organism’s chemical reactions called metabolism o Metabolic pathway is a series of chemical reactions that either  Builds a complex molecule  Breaks down a complex molecule into simpler compounds ATP drives cellular work by coupling exergonic and endergonic reactions  ATP, adenosine triphosphate, powers nearly all forms of cellular work  Hydrolysis of ATP releases energy by transferring all third phosphate from ATP to some other molecule in a process called phosphorylation o Most cellular work depends on ATP energizing molecules by phosphorylating them o Cell uses and regenerates ATP continuously o In the ATP cycle, energy released in an exergonic reaction, such as the breakdown of glucose during cellular respiration, is used in an endergonic reaction to generate ATP from ADP Chemical reactions either release or store energy  Energy coupling uses the energy released from exergonic reactions to drive endergonic reactions, typically using the energy stored in ATP molecules How Enzymes Function Enzymes speed up the cell’s chemical reactions by lowering energy barriers  Although biological molecules possess much potential e


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