General Biology 111 10 Week In-Class Lecture Notes
General Biology 111 10 Week In-Class Lecture Notes Bio 111
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CHAPTER 1: SCIENTIFIC THINKING Biology---->scientific study of life (study of living things) Foundation for asking questions about life and understanding the world Science needs empirical evidence (can be measured) There are false studies Scientific approach: investigate facts and ideas in biology that are already known and study the process by which we come to learn new things (quite easy) Scientific literacy: fact-based understanding of basics of biology and other sciences Science: big brain; curiosity; and desire to learn (to discover and better understand the world) Intellectual activity, encompassing observation, description, experimentation, and explanation of natural phenomena To make wise decisions, individuals and societies must attain biological literacy Biological literacy (helps you make wise decisions to benefit yourself; lack of will put you at the mercy of “experts” seeing their own personal gain) : ability to (1) use the process of scientific inquiry to think creatively about real-world issues that have a biological component (2) communication these thoughts to others (3) integrate these ideas into your decision making Superstition: actions that are not logically related to a course of events can influence its outcome (absence of scientific thinking) ex: tapping your toe before hitting the ball Scientific Method: process of examination and discovery (does not measure everything) -based on empirical knowledge: based on experience and observations that are rational, testable, and repeatable - adaptable and can be done effectively in numerous ways - non linear - steps are self correcting: tells us when we should change our minds -make observation-search for apparent patterns or cause and effect relationships -formulate a hypothesis (a good hypothesis helps us make predictions)-must accomplish two things: must clearly establish mutually exclusive alternative explanations for a phenomenon and must generate testable predictions Null hypothesis: states the lack of relationships between two factors (easier to disprove) -devise a testable prediction (based on hypothesis)-”if/then” -conduct a critical experiment-makes it possible to decisively determine whether a particular hypothesis is correct if the hypothesis being tested is not true, we will make observations that compel us to reject that hypothesis -draw conclusions and make revisions-look for patterns and relationships; if hypothesis is not supported than must revise hypothesis and conduct more experiments (trail and error)-must be open minded and ready to change your mind if hypothesis is not supported ***flexible process; not linear and can jump steps Hypothesis: proposed exclusive explanations for a phenomenon and leads to testable predictions Theory: explanatory hypothesis for natural phenomena that is well supported by empirical data; unlikely to be altered by any new evidence; testable; no contradictions ex: cell theory ex: theory of natural selection Controlling variables: Treatment-experimental condition applied to subjects; ex: shaving of eyebrow Experimental group: “treatment group” Control group: not exposed to treatment; ex: receive placebo Variables: characteristics of an experimental system that are subject to change; ex: coarseness of hair Placebo effect: people respond favorably to any treatment; this highlights the need for an appropriate control group Well designed experiment: Enables us to draw a correct conclusion about the cause and effect; Ensure that the persons conducting the experiment don’t influence the outcome-highlights the value of blind experimental design in which the experimental subjects do not know which treatment they are receiving and double-blind experimental design in which neither the experimental subjects nor the experimenter know which treatment a subject is receiving Randomized: subjects are randomly assigned into experimental and control groups ** randomized; controlled; double blind experiment THEMES: Repeatable experiments increase confidence and validity and acceptance We’ve got to watch out for our biases Visual displays of data can help us understand and explain phenomena - used to present relationship between two variables, such as in a graph: independent variable- measurable entity that is available at the start of a process and whose value can be changed as required (x axis) dependent variable-created by the process being observed and whose value cannot be controlled (y axis); changes in response to the changes in the independent variable Statistics (set of analytical and mathematical tools designed to help researchers gain understanding from the data they gather) can help us in making decisions; helps us identity relationships or lack of relationships between variables positive correlation: meaning that when one variable increases, so does the other correlation reveal relationships but don’t tell us how the variables are related or whether change in one variable causes change in another- “correlation is not causation” Pseudoscience (individuals make scientific sounding claims that are not supported by trustworthy, methodical scientific studies; ex: food products) and misleading anecdotal evidence (based on just one or a few observations, people conclude that there is or is not a link between two things; do not include large and representative set of observations of the world) lead people to believe that links between two phenomena exist, when in fact there are no such links There are limits to what science can do: does not give us insights into the generation of value judgments and other types of non quantifiable, subjective information Study of life is unified by: Hierarchical organization (life is organized on many levels within organisms including atoms and cells and tissues and organs. and in the larger world, organisms themselves are organized into many levels like populations, communities and exosytmes) and The power of evolution (the change in genetic characteristics of individuals within populations over time, accounts for the diversity of organisms, but also explains the unity among them) unifies the study of life Lecture: Everything is made up of atoms humans: oxygen-65 carbon-18 hydrogen-9 nitrogen-3 atomic structure: nucleus (contains protons + and neutrons which do not have a charge; mass-amount of matter in a particle; protons and neutrons have the same mass) atomic number: how many protons (unique to each atom; remains the same) isotopes: different number of neutrons than protons (this varies and can change) electrons: negative charge (repel each other but are also drawn to the nucleus because it is a positive charge); these are in the clouds around the nucleus (number of protons and number of electrons are equal) these electrons weight nothing which is why their mass can be ignored atomic mass-mass of an atom; combined mass of all its protons and neutrons; essentially double of the atomic number because of protons and neutrons added together why care?: because atoms need to react to one another (the number and arrangement of electrons determines how they will interact) electron shells: electrons move around the nucleus in electron shells; first electron shell of 2; second electron shell of 8; third electron shell of 8 -the chemical characteristics of an atom depends on the number of electrons in its outer most shell - atoms become stable when their outermost shell is filled (stable atoms and do not interact with other atoms) ex: helium and neon unstable atoms: unfilled shells make atoms likely to react; ex: hydrogen and nitrogen Why is carbon so versatile?-because only has 4 electrons in outer most shell and can bond in a large number of ways in four different directions making huge variety of complex molecules -binds with oxygen, hydrogen and nitrogen and make carbon chains organic molecules: build on a carbon backbone; basic structure of molecules ions: charged atoms (when atoms donate of take electrons from each other) atoms that lose one or more electrons become positive; atoms that gain one or more electrons become negatively charged -atoms bond to form molecules -molecules may contain atoms of only one element or more than one element (oxygen molecule or methane hydrogen molecule) Three types of bonds: Ionic bonds (one atoms loses electrons, become positively charged ion; another atom gains these electrons, becomes negatively charged ion) the two oppositely charged ions come together to form a compound; ex: table salt; covalent bonds (electrons are shared between two atoms to fill their outermost shell; single/double(share two electrons)/triple covalent bonds); hydrogen bonds (atom in one polar covalent molecule is attracted to oppositely charged atom in another polar covalent molecule)-bonds (doesn’t link) molecules together: attraction between the positive charged hydrogen atom of one molecule and the slight negative charged atom of another Covalent bonds: hydrogen and oxygen(double bond) Non polar: if atoms share electrons equally (hydrogen; oxygen) Polar: if atoms share electrons unequally (water) polar covalent bonds are very important in biological bonds hydrogen bonding in water: atom in one polar covalent molecule is attracted to oppositely charged atom in another molecule water molecules are V shaped-oxygen is negative and hydrogen atoms are positive charge(link together to give water a surface tension with net-like properties) cohesion(hydrogen bonds allow water molecules to pull up adjacent water molecules to which they have hydrogen-bonded) large heat capacity: heat breaks hydrogen bonds but new bonds are formed as quickly, therefore, since water molecules don’t increase their movement (temp is measurement of how quickly molecules are moving) the temp remains the same low density as solid-hydrogen bonds are farther way because each V shaped water molecule bonds with four partners creating a crystalline lattice good solvent:polar molecules(having two charges) are able to pry ions apart when put into water; this is why non polar (lipids) does not dissolve because it neither has a positive or negative side *covalent bonds are the strongest bond then ionic then hydrogen Ionic bond occurs when the two oppositely charged ions attract each other and form a compound-a molecule made up of two or more elements Ex: NACL Pure water has a pH of 7. Sometimes, the bonds break into two parts. The more H+ ions the more acidic-sour; the more OH- ions the more base-can neutralize an acid (alka seltzer) more slipper and bitter and soapy feel blood has pH of 7.4 and can’t tolerate pH swings so we utilize buffers: chemicals that absorb excess H+ ions or release H+ ions to counteract increases in OH- concentration water: cohesion (water molecule pulled into root system then pulled upward then released into atmosphere; can stick together due to the hydrogen bonds); large heat capacity (able to absorb lots of energy that is why ocean is much cooler than sand); low density as a solid (liquid water v frozen water); good solvent (water molecules surround ions and separate them) Lecture: atoms form molecules through bonding EVERYTHING IS MADE UPOFATOMS-all atoms have same general structure (protons and neutrons in the nucleus and electrons around the nucleus element: substance that cannot be broken down chemically into any other substance (gold, carbon, copper) -even if you break down this piece into smaller pieces, it will have the same properties as the element atom “indivisible”: the individual component pieces of an element that cannot be subdivided any further without losing its essential properties -most of the space taken up by an atom is empty -number of protons determines what element it is (atomic number) -mass of an atom is usually about double the element’s atomic number because the number of neutrons in the nucleus is usually equal to the number of protons isotope: an atom that has extra neutrons or fewer neutrons than the number of protons (atoms charge doesn’t change but the mass does) radioactive (isotope): non stable atomic nuclei that in the process of decomposition, release a high speed particle carrying a lot of energy ex: uranium periodic table: 90 elements electrons determine how and whether an element bonds with other atoms - stay in “electron shells” (2 in first shell then 8 in second shell) ion: an atom with extra electrons is negatively charged and an atom lacking one or more electrons is positively charged molecules: group of atoms held together by bonds bond energy: takes a certain amount of energy to break a bond between two atoms covalent bonds: H2 oxygen: O2; the sharing of two electrons between two atoms is called a double bond ionic bonds: occurs when two oppositely charged ions attract each other and from a compound, a molecule made up of two or more elements; each electron circles around a single nucleus - the two oppositely charged ions (because one donates and the other receives) attract to each other and form a compound ex: NaCl hydrogen bonds: formed between a hydrogen atoms in one molecule and another atom in another molecule; bond based on the positive and negative charge attraction between polar molecules and hydrogen atoms Water (pH of 7.0): form between the relatively positively charged hydrogen atoms and relatively negatively charged oxygen atoms of adjacent water molecules; V shaped; cohesive with net like properties Properties of water: cohesion---molecules evaporate or are used up through photosynthesis therefore the chain links water molecules are pulled through the roots every time a water molecule evaporates from a leaf large heat capacity: heat disrupts hydrogen bonds between water molecules and new bonds are formed very quickly low density as a solid: ice is less dense because when frozen, the hydrogen bonds are held farther apart that in the liquid good solvent: Water pries apart ionic bonds, dissolving ionic compounds; the positively charged side breaks down negatively charged ions and the negative side of water breaks down the positively charged ions. When you place non polar molecules such as oils in water, the water distances itself In some fluids, there is an unbalance of H and OH The pH of a fluid is a measure of how acidic or basic the solutions is and depends on the concentration of dissolved H ions present; the lower the pH, the more acidic. More OH- makes a base; they can also bind with H+ ions to neutralize the acid. They have a more bitter taste and soapy/slippery feel buffers: absorb excess H+ ions to keep a solution from becoming too acidic and release H+ ions to counteract any increases in OH- concentration (blood is 7.4 and body can’t tolerate swings of pH) stomach acid? most of the hydrogen ions split off from the chlorine, raising the H + concentration of the fluid Lecture: Carbohydrates are fuel for living machines and serve as structure of cells in all life forms (oxygen, hydrogen, carbon) macromolecules (large molecules made up from smaller building blocks or subunits) make up living organisms: lipids, carbohydrates, proteins, nucleic acids and nucleotides hydrogen, oxygen and other elements covalently bonded to carbon (have carbon base) 1. lipids: like carbohydrates, also contain carbon, hydrogen and oxygen but in a different proportions and have more carbon-hydrogen bonds resulting in more stored energy; identified by physical characteristics: insoluble in water (tails are hydrophobic-fatty acids and heads are hydrophilic-glycerol) and greasy; fats and sterols functions: energy, fats make up cell membrane, regulation of growth and development (sterols) fats: have a head-glycerol and a tail-fatty acids; composed of carbon, hydrogen and oxygen; energy is stored in the many carbon-hydrogen bonds; 9 calories per gram; hold the most energy; fats in most foods are triglyceride: three fatty tales; store large amounts of energy and insulation!!! (sterols and sex hormones as well) contain much more energy than carbohydrates which is why we tend to eat more fats so we have energy saturated fats: all the carbon is bound to two hydrogen atoms; tails are straight and next to each other from bonding; tails can be packed together tightly (butter; cheese) solid at room temp; these are not essential to your health unsaturated fat: at least one carbon is bound to just one hydrogen atom; some hydrogen are missing; tails cannot be packed together tightly (oil: liquid, peanuts, avocado) liquid at room temperature trans fat: unsaturated fatty acid (cis form) partially hydrogenated trans fatty acid (trans form) when you add hydrogen to molecule (margarin) Cholesterol and phospholipids are used to build sex hormones and membranes Lipids: sterols (four interlinked rings of carbon): regulate growth and development ex: cholesterol-component of cell membranes in animals; help stabilize phospholipids in cell membrane and aid in provided different types of hormones; when cholesterol attaches to blood vessel walls it causes them to thicken and leads to high blood pressure steroid hormones: regulate sexual development, maturation, and sex cell production; estrogen-influences memory and mood; testosterone-stimulates muscle growth phospholipids: major component of membrane that surrounds the contents of a cell and controls the flow of chemicals into and out of the cell make up cell membranes; part have charge (the head has negative charge-water reacts with this) and the tail don’t like water) -heads extend towards water and tails extend away from water waxes: one long-chain fatty acids linked to glycerol head; highly non polar; hydrophobic- repel water; firm consistency; repel water; found on surface of plants 2. Carbohydrates (ose): molecules that contain mostly carbon, hydrogen and oxygen and are the primary fuel fro running all of the cellular machinery and also form much of the structure of cells in all life forms;made up of monosaccharides or simple sugar (instant energy!!!!!!); function in energy and structure; the sugar glucose is the most important carbohydrate to living organisms; get fuel because of the carbon-hydrogen bonds broken down and more stable bonds forming-releasing energy during this process instant burn: monosaccharides/simple sugar (fruits and veggies) (3-6 carbon) (orange juice; not oatmeal; giving blood) ex: glucose and fructose and galactose glucose (most important carbohydrate) in your blood: provides energy for the body’s cells; immediate energy-releases 1.Fuel for cellular activity: glucose is converted into other molecules with stronger bonds. This conversion releases energy 2. Stored temporarily as glycogen (short term): excess glucose circulating in blood stream is stored in muscle or liver in a large web of molecules called glycogen-short term energy storage in animals 3. Converted to fat-long term energy polysaccharides: more than one sugar linked together and are covalently bonded to each other; glucose molecules become available slowly; takes more breaking down-must be broken down to monosaccharide first; time release fuel ex: sucrose ex: starch-hundred or more glucose molecules joined together in a line (energy in plants) ex: glycogen: energy storage in animals Not all carbohydrates are digestible: chitin (rigid outer skeleton of most insencts and crustaceans and cellulose (identical to starch yet has a different 3D structure) cellulose “fiber” diet: cotton, wood and fiber in diet; hydrogen bonds; eat this because it aids in digestion and scrapes the walls of the digestive tract pH scale: measure the H+ concentration of fluid (acids more H+ ions and lower pH; bases fewer H+ ions and higher pH) if lipids are insoluble they are non polar because they have long chains consisting only of carbon and hydrogen atoms. polar: shared unequally (electrons) -water; molecules that readily form hydrogen bonds with water non polar: equally shared (electrons)-hydrogen gas 3. Proteins: most diverse molecule and body building macromolecules that serve as building blocks; contain carbon/hydrogen/oxygen/and NITROGEN structural: hair, fingernails protective: help fight invading microorganisms coagulate blood regulatory: control cell activity, constitute some hormones contractile: allow muscles to contract, heart to pump and sperm to swim transport: carry molecules such as oxygen around your body enzymes: initiate and assist every chemical reaction based on 20 amino acids-strung together to make proteins essential amino acids: must receive in diet; half our body can get and other half we need to get from our diet!!! (milk fish egg chicken beef) amino acid sequence determines how it folds into shape: proteins are formed by linking individual amino acids together with a peptide bond in which the amino group of one amino acid is bonded to the carboxyl group of another. Protein function depends on 3-D shape!**** primary-link (sequence of amino acids on a polypeptide chain); secondary (hydrogen bonding with amino acids); tertiary (three dimensional shape as the secondary structure folds and bends; 4th structure (two or more polypeptide chains are held together by bonds between amino acids in different chains extreme environment (heat pH) disrupts protein shape and function----goes from normal protein to denatured protein For proteins to function, they must retain their three dimensional shape hair styling: water breaks the bond and it cools next to protein and you style it when its dry so that it bonds with proteins again enzymes (popcorn): help to bring about chemical reactions; either bring stuff together or break them apart; most enzymes are proteins; emerge unchanged; they can be used again and again; substrate and substose active site: provides a place for the participants in a chemical reaction, substrate molecules to fit-have atoms in active site with electrical charges that attract or repel certain substrate molecules there is a certain minimum energy needed to initiate the reaction, called activation energy functions: initiate and speed up reactions; directly participate; stress/end/stretch chemical bonds; create conductive microhabitat; change orientation rate at which an enzyme catalyzes a reaction is influenced by several chemical and physical factors enzyme and substrate concentration: increase in the substrate concentration increases the reaction rate temperature: temperature increases/reaction rate increases,when over right temperature reaction rates decrease as enzymes lose their shape or even denature pH: lower or above needed ph, enzymes denature Presence of inhibitors or activators (competitive inhibitors bind to the active site blocking substrate molecules from the site and thus from taking part in the reaction) and (noncompetitive inhibitors bind to part of the enzyme, altering is shape in a way that changes the structure of the active site reducing or blocking its ability to bind with substrate activators: bind to enzyme and “turn it on” altering the enzymes shape or structure so that it can now catalyze a reaction why are high temps so dangerous when you are sick: because proteins in your body begin to denature 4. NucleicAcids/ nucleotide structure: three phosphate groups which are negatively charged; ribose (sugar) and a nitrogen containing base attached to each sugar(adenine, thymine, cytosine, guanine) nucleic acids (DNAand RNA): macromolecules that store information and are made up of unites called nucleotides functions: energy; storage, transmission and translation of genetic information - If there is a faulty in the genetic coding then it is nucleic acids fault ATP: holds lots of energy but only for short time does not hold long term DNA: four bases adenine, thymine, guanine, and cytosine; the genetic information to build an organism; double helix-sugar phosphate backbones form the vertical structure of DNA; the four bases are connected by hydrogen bond; holds the information; holds the genetic information to build an organism RNA: uracil instead of thymine; reads DNAand directs protein production; single stranded; the sugar molecule in the backbone contains one extra oxygen atom; function: moves the instructions for production of a protein DNAto another part of the cell; acts as a middleman molecule-taking instructions for protein production from DNAto another part of the cell where, in accordance with the RNAinstructions, amino acids are pieced together into proteins Lecture: Cell theory: all organisms are made up of cells Cells: are the smallest unit with properties of life that can function independently and perform all of the necessary functions of life (reproduce; respond to environment; respire-use energy; they can die; maintain homeostasis prokaryotic: one celled organisms and are invisible to the naked eye; before nucleus; they are all over: bacteria and archaea; no compartments (also called organelles) DNAis in cytoplasm Have a cell wall: protects and gives shape to the cell plasma membrane: inside cell membrane is intracellular and outside is extracellular cytoplasm ribosomes: granular bodies where proteins are made flagellum: thin whip-like projection that rotates like a propeller moves through the cell (tail) pili: hair like projections that help prokaryotes attach to surfaces and can serve as tubes through which they exchange DNA eukaryotic cell: visible to naked eye; showed up 1.5 billion years after prokaryotes; compartments; DNAin nucleus; lots of internal membrane-bound compartments-compartments must interact with each other organelles: enclosed structures within their own lipid membranes that enable eukaryotic cells to do many things COMPARTMENTS (review picture in the book): nucleus: largest organelle in eukaryotic cells; genetic control center of the cell; directs cellular activity; stores hereditary information; nucleolus holds ribosomes; contains two bilayers nuclear membrane: separates nucleus from cytoplasm chromatin: thin fibers consisting of DNAwith proteins attached that keep it from getting tangled nucleolus: cneter of nucleus with ribosomes-construct proteins cytoskeleton: interact with each other; made up of proteins; fluid structure that is constantly changing; provides shape and support; controls intercellular traffic; enables movement; the three cytoskeletons are made up of proteins (microtubules; intermediate filament; microfilaments) mitochondria: all purpose energy converter for cellular work; convert energy contained in chemical bonds into carbon dioxide, water andATP; consumes lots of oxygen from each cell; synthesizeATP; circulized DNA lysosomes: garbage disposals/recycling center for cells; digest and recycle macromolecules, including bacteria; have 50 different digestive enzymes endomembrane system (rough ER, smooth ER, golgi apparatus): work together and produce and modify molecules for export to other parts of the organisms rough ER: has ribosomes attached to it (hence, the rough) modify proteins to be shipped within the endomembrane system, cell surface or out of the cell smooth endoplasmic reticulum: synthesize lipids and carbs; detoxify molecules such as alcohol, dugs, and waste products golgi apparatus: process and package molecules for exports to other parts of the organism; carbohydrate synthesis; not interconnected Plant Cell: cell wall: provide cell with structural strength; give cell increased water resistance; provide protection from herbivores plasmodesmata: tube-like channels connecting the cells to each other and enabling communication and transport between them vacuole: occupy most of the interior space of the cell;store nutrients; retain/degrade waste products; accumulate poisonous materials; contains color pigments for sexual reproduction; provide physical support chloroplast: site of photosynthesis; conversion of light energy into chemical energy (theory)endosymbiosis: two organelles in eukaryotes-chloroplasts help plants and algae convert sunlight into energy and where photosynthesis occurs and mitochondria help plants and animals harness the energy stored in food molecules (theory)invagination: idea that the plasma membrane around the cell may have folded in on itself to form the inner compartments, which became modified and specialized Every cell is bordered by a plasma membrane (prokaryote and eukaryote) In common between P and E: plasma membrane, region where DNAstored (in E: nucleus in pieces which are chromosomes: P: no specific compartment) and cytoplasm where enzymes are stored to help with all the different reactions inside the cells plasma membrane: two layers filled with pores, molecules and channels; functions: they take in food and nutrients and dispose of waste products and build and export molecules needed elsewhere in the body and mediate communications and adhesion with external environment; they serve as gatekeepers phospholipid bilayer: structure of plasma membrane; hydrophilic heads extend towards fluid and hydrophobic tails (non polar-electrons are shared equally) extend away from fluid-this holds the cell together what determines the orientation of the proteins in the membrane: the location Function of plasma membrane (fluid mosaic-plasma membrane is made up from several different types of molecules )-made of up phospholipid transmembrane proteins: penetrate right through the lipid bilayer surface proteins: reside on the inner or outer surface of membrane carbohydrate chains: identifies the cell and where is belongs in the organism cholesterol: a lipid and stabilizes the phospholipids; helps the membrane retain flexibility receptor proteins: receives messages from outside and making some changes recognition proteins: work in conjunction with carbs to fingerprint the cell transport proteins: provides a passageway fro molecules to travel into and out of the cell enzymatic proteins: accelerate chemical reactions on the plasma membranes surface Every cell in your body has a “fingerprint” made from a variety of molecules on the outside-facing surface of the cell membrane cells with an improper fingerprint are recognized as foreign and are attacked by your body’s defenses- immune suppression helps you tolerate new liver when you get a liver (or organ) transplant molecules move across membranes: cells take in food and nutrients, export waste and communicate with their environment Diffusion-passive transport in which a solute is dissolved in a gas or liquid (solvent) and moves from an area of high solute concentration to an area of lower concentration solute: what molecule is being dissolved in solvent: what molecule it is dissolved in Passive Transport: molecules move across a membrane without energy input, down the concentration gradient; small molecules or molecules with no charge can move across through passive transport two types: simple diffusion: molecules pass directly through the plasma membrane without assistance (when you breath-oxygen) -charged or large molecules can’t FACILITATE DIFFUSION: MOLECULES MOVEACROSS PLAMSAMEMBRANE WITH HELP OFACARRIER MOLECULE (transport protein) Osmosis: passive transport of water; water diffuses across a membrane to equalize the concentration of water inside and outside the cell; water always moves towards the side with a greater concentration of solutes; high to low; direction of osmosis determine by the difference in the total concentration of all the molecules dissolved in the water: how many molecules of solutes there are; water will move toward the side with dissolved stuff cant move across wherever because it is charged tonicity-the relationships between the concentrations of solutes inside the cell and solutes outside the cell isotonic: solutes outside the cell is equal to inside the cell hypotonic: concentration outside the cell is lower than inside; the cell will swell hypertonic: concentration outside the cell is higher than inside; cell will shrivel In active transport, cells use energy to move molecules into and out of the cell active transport: moving molecules across a membrane requires energy against the concentration gradient; if molecules or ions are being moved against their concentration gradient (stomach when digesting food) primary: energy fromATP is used to fuel the transport of molecules (stomach to digest food) secondary: transport protein simultaneously moves one molecule against its concentration gradient while letting another flow down its concentration gradient Endo and exo are used to for bulk transport of particles: when passive and active don’t work endocytosis: to absorb large particles; cells engulf large particles with their plasma membrane; plasma membrane oozes around the object that is outside the cell, surrounds it and forms a pocket called a vesicle and pinches it off so that it is separated for the cell contents phagocytosis: consume as food or or to defend against pathogens pinocytosis: cells take in dissolved particles and liquids; vesicles are smaller than phagocytosis receptor mediated endocytosis: receptors wait on surface of cell waiting for their molecule to bump into them then when the appropriate molecule binds to each receptor, the membrane folds inward engulfing the molecules (cholesterol is broken down and used to make other molecules like estrogen and testosterone) ingesting too much cholesterol with not as many LDL receptors can lead to cardiovascular disease exocytosis: manufacture molecules out of the cell for use elsewhere in the body; fuses with the plasma membrane and dumps its contents outside the cell Lecture: C ystic fibrosis most common fatal inherited disease in the US-due to chloride buildup and lack of transport across plasma membranes-protein is the macromolecule defective in the disease Cells adhere to other cells (connected) and communication with each other animal cells tight junctions: water-tight seal between cells (intestine) desmosomes: attach cells together (velcrow-things can still move between cells; ex: skin; heart muscle) gap junctions: allow materials to pass between cells (proteins; ex: to keep heart beating, the signal telling muscle cells to contract is passed from cell to cell through gap junctions; important because can recognize that it has bumped up against another cell stopping the cell from dividing) (the reduction in intercellular communication among cancer cells may be correlated to the formation of tumors) plant cells: have cell walls plasmodesmata: what covers the cell; allow water and other molecules to pass between adjacent cells Differing levels of cholesterol? - genetic differences in amount of cholesterol Lecture: Energy and metabolism Energy: capacity to do work Running engines: organism and machines both need energy to work-biofuels (animal fats and oils), fossil fuels (dead organisms modified through heat, pressure, and bacteria); biofuels, fossil fuels and food fuels are chemically similar-chains of carbon and hydrogen atoms; energy from the sun is the source of the energy stored in the chemical bonds between the atoms in all these fuels; WE GET ENERGY FROM LONG CHAINS OF CARBONAND HYDROGENATOMS SEPARATINGAND RELEASING CARBON DIOXIDE, WATER,AND ENERGYTHAT WAS STORED IN THE CHEMICAL BONDS HOLDING THE MOLECULES TOGETHER! Fossil fuels (oil, natural gas and coal): long time because requires plant and animal remains of millions of years biofuels: advantages: short time for energy harvest and less pollution however destruction for natural resources and conversion of crop land Food as energy source: calorie-measure of energy; amount of energy that raises temp of 1g of water by 1 degree C kilocalorie: amount of energy that races temp of 1kg of water by 1 degree C (food calories) ALL life depends on capturing energy form the sun and converting it into a form that living organisms can use: photosynthesis: plants capture energy from the sun and store it in the chemical bonds of sugars and other food molecules cellular respiration: plants animals and fungi release the energy stored in the chemical bonds of food molecules and use it as fuel Energy (capacity to do work: anything that involves moving matter against an opposing force) in cells (energy doesn’t go away it changes form; cells manipulate it) Kinetic energy: energy of movement (heat: molecules rapidly moving; light: movement of high energy particles; flapping wings) Potential energy: stored energy (has to do with objects location or position; concentration gradient: moving from high levels of concentration to lower levels; chemical; water behind dam) Chemical energy: storage of energy in chemical bonds (food: because the chemical energy formed in chemical bonds making up the food can be broken and the energy released during cellular respiration Food is a form of chemical energy: a form of potential energy stored in chemical bonds Why do organisms store energy in the bonds of carbohydrates not just makeATP directly-store energy; store most of our long term energy as fat (78%) instead of glycogen (1%)-keeping our body warm; harder to break down, main reason: fats are a lot lighter than carbs and sugars One way flow of energy ultimately from sun: energy is constantly lost and gained and changing forms energy cannot be created or destroyed: change forms into either kinetic or potential energy (thermodynamics) First law of thermodynamics: energy can never be created or destroyed; it can only change from one form to another - energy conversions are inefficient and lost as heat (which is the least usable form of energy because it is not easily harnessed to do work) S econd law of thermodynamics: every conversion of energy is not perfectly efficient and invariably includes the transformation of some energy into heat (although the quantity of energy is not changing; the quality is) - energy flows from higher to lower energy forms In photosynthesis 1% is converted The rest is reflected back into space (30%) or absorbed by land oceans and atmosphere and converted into heat (70%) ATPandADP How cells fuel chemical reactions: cells store energy in the bonds of ATP: a free floating molecule found in cells that acts like a rechargeable battery which temporarily stores energy that can then be used for cellular work in plants, animals, bacteria and all the other living organisms on earth: GUARANTEES THAT ENERGY REQUIRED FOR ENERGY CONSUMING REACTIONS WILL BEAVAILABLE WHEN ITS NEEDED ATP is used and recycled hundreds of thousands of times: 10 millionATP used/sec in active muscle cell (like a rechargeable battery) Three components: sugar molecule attached to adenine and chain of three negatively charged phosphate groups (these bonds contain a large amount of energy to hold the similar charges together and are stressed and unstable; when the phosphate groups pop off and release energy) when one of the phosphate groups releases, you are left with two phosphate called ADPand a separate phosphate group then the organism uses theADP, a free floating phosphate, and an input of kinetic energy to rebuild itsATP stocks; the kinetic energy is transformed into potential energy!!!!!! Lecture: Photosynthesis-don’t have to be a plant and don’t have to have chloroplast (volvox); oxygen is released into atmosphere and many organisms could not handle that seed to tree-mass comes from carbon dioxide! Photo: sunlight, water and carbon dioxide converted intoATP and NADPH Synthesis: carbon in combination with the two energys produces oxygen and sugars used for food Where does photosynthesis happen: thylakoid-site of photo reaction where light energy is converted into chemical energy; stroma-site of synthesis reaction where chemical energy is converted into sugar Chloroplast: has phospholipid bilayer and has infolding(thylakoid) and stroma(fluid) Light energy(type of kinetic energy made up of little energy packets called photons) travels in waves: plant pigments (mediator between sunlight and get that energy into the cell); light energy bumps an electron in the chlorophyll molecule to a higher, excited energy level and increases potential energy-either that energy is increased and some energy is transferred to a nearby molecule (bouncing around because of heat) where it excites another electron; or absorb energy kinetic energy made up of energy packets called photons (organized in waves) photons of certain wavelengths hit chlorophyll and other light-absorbing molecules near the green surfaces of plants, when this happens, the light energy bumps an electron to a higher energy level-either returns to its unexcited state releasing energy (heat) and may bump electrons to an excited state, or passed on to another molecule electromagnetic spectrum: the shorter the wavelength or distance between the peaks, the high energy level (x rays; gamma rays) higher energy messes around with your molecules our visible light is 740 nanometers and 400 nanometers when molecules are able to absorb energy-absorption (take energy and hold onto it) pigments (light absorbing molecules): chlorophyll a; chlorophyll b; carotenoid wavelengths that are not absorbed by pigments are not absorbed and are reflecting-these are the colors we see (green) why do we have so many pigments: we can absorb more energy late summer: trees shut down chlorophyll a and b production (fall colors) Photo: within thylakoid membrane there are reaction centers (photosystems)-one makesATP and NADPH 1. suns energy comes in and electron gets knocked out to startATP gets transferred to electron transport chain through phospholipid bilayer. WATER molecules (hydrogen sticks around because has a charge, but oxygen is released because no charge) -hydrogen gradient 2. Electrons move down and against concentration gradient (active)MakesATP 3. Same at 1; however electron is not being replaced by water, it is being replaced by the electron transport chain 4. NADP picks up an electron and a hydrogen Lecture: Calvin cycle: occurs in the stoma of the leaves’chloroplasts; plants carry out these reaction using the energy stored in theATP and NADPH molecules build in the “photo” portion 1. Fixation: Rubisco gets Carbon atom appearing as carbon dioxide and fixes it to an organic molecule 2. Sugar Creation: the molecule is chemically modified; a phosphate fromATP is added and the molecule receives some high-energy electrons from NADPH-the product is a small sugar called glyceraldehyde 3-phosphate-G3P-Two G3Ps combine-glucose How is energy fromATP carried-phosphate bonds How is the energy from NADPH carried-electrons 3. Regeneration: some G3Ps regenerate organic molecule; this requires energy fromATP Takes 6 turns to make on glucose molecule Takes 3 turns to make G3P (need two G3p to make glucose molecule) Where does this energy come from (nadph and atp): photo reactions Calvin Cycle: fixation: rubisco(plant enzyme) most abundance protein in leaves and planet; it binds to an organic molecule which contains phosphate groups and oxygen; adds water and splits organic molecule in two sugar creation: both molecules needATP phosphate group and NADPH donate electrons and ions to groups: these are G3P regeneration: some G3P regenerate the organic molecule by usingATP everything is multiplied by three Hot climate: evaporation is a problem plants close their stomata (C3): small pores usually on the underside of leaves; these openings are sites for gas exchange in plants-carbon dioxide for photosynthesis enters through these openings and oxygen generated as a by product exits; but when you close then you cant do photosynthesis C4 photosynthesis (corn and sugarcane) minimizes water loss but still enables the plants to make sugar; expends more energy and are found in hot dry regions CAM (cacti, juicy plants):keep stomata closed during the day which reduces the amount of CO2 they take in ; and open at night to let CO2 into the leaves where it binds to a holding molecule; requires more energy and slow growth Photosynthesis: water: electrons light: energy carbon dioxide: carbon Consequences of photosyntheses: carbon fixation removes billions of metric tons of CO2 from atmosphere each year; food; fossil fuels; oxygen Plants adapted to water scarcity: some plants thrive in hot dry conditions adaptions that reduce water loss. Stomates: control water loss Lecture: Cellular respiration: opposite of photosynthesis: plants and animals break down the chemical bonds of sugar and other energy right food molecules to release the energy that went into creating them-as energy is release, cells capture and store it in the bonds ofATP-this acts as regularly stored energy. input (oxygen and sugar)---output(CO2, water,ATP) Oxygen deficiency limits the breakdown of fuel because the electron transport chain requires oxygen as the final acceptor of electrons during the chemical reactions of glycolysis and the Krebs cycle. When oxygen is unavailable, yeast resorts to fermentation, in which they use a different electron acceptor, pyruvate, and in the process generate ethanol, the alcohol in beer, wine and spirits energy from food and energy from sun has similarities: plants also respire aerobically how cells release energy stored in chemical bonds: aerobic respiration (requires oxygen) and anaerobe pathways (fermentation-does not require oxygen) -breath in oxygen and release carbon dioxide starfish-tube feed fish-gills fungus-direct exchange insect-spiracles energy conversions to photosynthesis: sunlight(photons)-electrons-concentration gradient ions (H+=protons)- chemical bonds (ATP, NADPH)-chemical bonds carbohydrates energy conversations in respiration: chemical bonds carbohydrates-electrons (ATP, NADPH)-concentration gradient ions (H+=protons)-chemical bondsATP cellular respiration: input (oxygen, sugar) to output (carbon dioxide, water andATP); energy is stored in the bonds ofATP food is a form of chemical energy: form of potential energy stored in chemical bonds cellular respiration: three steps 1. Glycolysis(splitting of sugar; in cytoplasm) forms a pyruvate andATP and NADH Two major parts: preparatory phase-invests someATP and breaks down glucose molecule payoff phase-leads to pyruvate and two molecules of water ` 2. Krebs cycle(in mitochondrial matrix): producesATP and captures a huge amount of chemical energy by producing high energy electron carriers. FormsATP; NADH, FADH2 3. Electron transport chain (mitochondrial matrix): most energy comes from the NADH and FADH2; in the electron transport sequence of handoffs the electrons fall to a lower energy state, releasing a little bit of energy; then at the end the lower energy electrons are handed to oxygen and paired with H ions to form water then the energy is used to power proton pumps and rush back to the mitochondrial matrix with kinetic energy which is used to buildATP Energy from fats,(fatty acids and a glycerol) proteins(carbon compound and amino group) and carbohydrates(simple sugars) as well as glucose Lecture: How cells release energy stored in chemical bonds aerobic respiration (requires oxygen) anaerobic What happens if our bodies fall begin in delivering oxygen- -lungs bloodstream cells and mitochondria - when not enough oxygen is present-many organisms have a backup method for breaking down sugar when oxygen is not present when you are not using oxygen you are only using glycolysis Some organisms that do not use oxygen: mostly prokaryotes and protistans (glycolysis-only making twoATP) Electron Transport chain (part 3): NADH and FADH2 carry electrons to electron transport system-then oxygen picks these up and combines them with water Yeast can respire aerobically carbohydrates; lipids; proteins; nucleic acids-macromolecules that you eat how to get energy from these macromolecules: can’t break down nucleic acids DNA: store information (sequence of bases) pass on information (copying-replication) Allow use of information (gene expression) Lecture: DNA: is a nucleic acid, a macromolecule that stores information and consists of nucleotides (molecule of sugar, phosphate group, and a nitrogen base double helix: sugar (deoxyribose and phosphate backbone) each backbone has a base pair protruding from it via a hydrogen bond (AT C G) is a molecule that all living organisms carry in almost every cell in their body-contained in both our living cells and cells we leave behind (saliva; blood; hair; dead skin cells) DNAmakes up a code that holds the detailed instructions for building of an organisms-in the form of instructions for the amino acid sequences of polypeptides Genome: full set of DNAin an individual organism (nucleus) Eukaryotic DNAexists in chromosomes (46 chromosomes-23 from each parent) linear strands (in prokaryotes it is circular) Gene: sequence of bases in a section of DNA, about 3000 base pairs long that contains information necessary to produce all or part of a protein molecule (polypeptide or RNAmolecule) Allele: alternative versions of a gene that code for the same function (color) Trait: single characteristic or feature of an organism (color of a daisy petals individual identifier organized into units called genes controls the operation of cells and carries a record of the evolutionary history of lineages of cells and organisms 2 important features: DNAare passed down from parent to offspring; instructions on how to create a body and control its growth, development, and behavior are encoded in the DNAmolecule Francis Crick and James Watson discovered DNAstructure Lecture: DNA: Stores info; allow use of info (gene expression) and pass on information (copying) DNA----transcription (nucleus)----RNA----translation (rough ER on cytoplasm on cell)-----Protein genotype: all of the genes that an organism carries (recipe-instructions) phenotype: the physical manifestations of the instructions (cookie) Transcription: a copy of the genes base sequence from DNAinto messenger RNA--mRNAwhich moves it RNAis single stranded; extra oxygen and uracil instead of thymine 1. Recognize and Bind: RNApolymerase binds to one strand (promoter site) 2. Transcript: RNApolymerase builds a copy of gene MRNA 3. Terminate: RNApolymerase meets termination, releases mRNA 4. Capping and Editing: mRNAprocessed; Cap the tail; and introns removed (prokaryotes don’t have to do this process) (DNAunwinds to be read and rewinds after transcription) intron: noncoding part of DNA Translation: in which that copy is used to direct the production of a polypeptide, which then, in response to a variety of factors, including the cellular environment, folds into a protein; mRNAused to direct protein production; uses info form DNAto build usable molecules need free amnio acids; ribosomal units; and transfer RNA start codon:AUG which codes for amino acid methionine genetic code 3 bases read at once: codon tRNA: link bases on the mRNAwith amino acids used to build protein Transcription factors: help or hinder RNApolymerase binding promoter operon: group of several genes, along with the elements that control their expression as a unit repressor: block RNApolymerase binding DNA steroid hormones: regulators of transcription factors DNAreplication: unwinding: helicase rebuilding: DNApolymerase Mutation: change in the DNAsequence (single base or large segments of DNAwith many genes); result in changes in the structure and function of the proteins produced hoax genes determine where structures form Where mutations happen sex cells: passed on to next generation ex: breast cancer; heart disease non sex cells: bad health consequences for the person carrying them, not passed on to the next generation ex: skin cancer; lung cancer Types: point mutations: one base has changed chromosomal changes: a large chunk has changed Sources: spontaneous mutations (majority radiation-induced mutations chemical-induced mutations Lecture: stored in chromosomes:DNA mitosis or meiosis Prokaryotes divide by binary fission: circular chromosome duplicates itself; the cell splits into two identical new cells Cell cycle for eukaryote: somatic cells (body) cell is born from another cell; cell grows and functions, cell duplicates gap 1: cell is doing its job and is growing dna synthesis: dna is copied gap 2: carries replicates of DNA (these three steps are called interphase)-chromosomes into sister chromatids held with centromere MITOSIS: when nuclear material is isolated into two nuclei (shortest phase) prophase: nuclear membrane breaks down and sister chromosomes condense interphase: sister chromatids move to center anaphase: sister chromatids get separated telophase: dna relaxes and uncoils and nuclear membrane reforms cytokinesis: production of two daughter cells -cytokinesis: cytoplasm and everything in cell is divided into two daughter cells then becomes parent cell in next cell cycle MEIOSIS: gametes (eggs and sperm) everything is same purpose of mitosis: to generate new genetically identical cells because we lose cells every single day growth replacement What moves chromosomes? cytoskeleton (spindle) cells dividing out of control: cancer chemicals that mutate DNA high energy such as X rays, the sun, nuclear radiation radiation Lecture: phenotype: physical appearance genotype: genetic composition of an organism albinism is recessive albino is full chance (dominant) Consequence of segregation: each gamete receives only one of the two copies of eac ch gene heterozygous: 50 percent carrying dominate or 50% carrying recessive allele homozygous: 100 percent for carrying dominate allele Tay-sachs if parents are heterozygous for Tay-Sachs is .25 chance (multiple .5 and .5) Test cross: way to figure out which alleles an individual carries; in a test cross, an individual with a dominant phenotype and an unknown genotype is mated with a homozygous recessive individual o T find genotype of offspring Pedigrees: analyzing inheritance of genes; useful tool to document a trait of interest across multiple generations of family members Lecture: Not always clear dominant/recessive traits: incomplete dominance-ex: snapdragons (when a heterozygote exhibits an intermediate phenotype between the two homozygotes co-dominance-sickle-cell disease: heterozygote displays characteristics of both homozygotes (have issues with low oxygen and physical exertion) red and white spotted flower multiple alleles: a single gene has more than two alleles; each individual still carries only two alleles-one from each parent) three alleles: a, b, and O (Aand B are dominant to O;Aand B are co-dominant) Antigens: markers on the surface of cells that tell the immune system whether the cell belongs in the body Antibodies: identify bad stuff in body (person with typeAblood produces antibodies against type B) (typeAB will not produce antibodies against eitherAor B) (type 0 produces antibodies againstAB) type 0 are universal donors AB is universal recipients Polygenic traits (height, eye color, sin color) the effects of alleles from multiple genes all contribute to the ultimate phenotype multiple genes; multiple alleles; environmental effects Environmental variations influences the expression of genes Pleitrophy: one gene many effects; occurs when one gene influences multiple traits Sex-linked Traits: expressed differently in males and females because they are inherited on the sex chromosome (usually carried on the X chromosome) Gregor Mendels genes come in pairsTheory o alleles in pairs can be different alleles can be dominant or recessive Theory of segregation: alleles segregate into different gametes in meiosis-inherited separately Theory of independent assortment: applies to genes controlling different traits (all possibly combinations seen) sometimes when independent assortment is violate-linked genes: genes located close to each other on the same chromosome one trait influences the presence of another trait because the allele red hair and fair skin_inherited together chromosomes that are close together tend to stay together Lecture: Evolution: theory that attempts to explain evolution of life; change in the frequency of alleles in a population over time NOTAN INDIVIDUAL allele frequencies: proportion of orange fur pigmented alleles in the population to the proportion of white fur pigment alleles in the population mutation-direct change in the DNAof an individual - ultimate source of genetic variation genetic drift-random change in allele frequencies in a population - reduces the genetic variation in a population; the impact is much greater in small populations than in large populations difference between natural selection: the change in allele frequencies is not related to the alleles influence on reproductive success fixation: when the allele becomes only one choice founder effect: a group of individuals may leave a population and become the founding members of a new, isolate population (AMISH are polydactyl and mated with each other) bottleneck effect: big population with a huge “crash” and now small population that is growing; change may cause the deaths of a large random proportion of the individuals in a population migration-migration into or out of population may change allele frequencies; also called gene flow (movement of some individuals of a species from one established population to another) natural selection (three conditions are necessary for NS to occur) Can be single or many genes - there must be variation for particular trait within a population - variation must be heritable -individuals with one version of the trait must produce more offspring than those with a different version of the trait survival of the fittest (reproductive success) adaptions increase fitness natural selection does not lead to perfect organisms factors preventing population from progressing to perfection: environments change quickly variation is needed as the raw material of selection there may be multiple different alleles for a trait Natural selection can change populations: directional selection-pushing a trait in a certain way (individuals with one extreme from the range of variation stabilizing selection disruptive selection-organisms with extreme phenotypes (organisms in the middle are fucked) 5-30 million different species (about 1.5 million have been identified unity of life: cells, molecules, energy transformations, dna, genetic mechanisms genetic change over time-has to be heritable change in a line of descent has to be in a population or species, not an individual Charles Darwin-observing geographic similarities and differences among fossils and living plants and animals, Darwin developed a theory of evolution traits exhibited by species similarity between the fossils of extinct species and living species Galapagos finches-descent from a common ancestor by natural selectoin? Charles Darwin changed the worldview with his book published in 1858 organisms change over time some organisms are extinct earth is more than 6000 years old earth’s geology is not constant but always changing Lecture: evidence for evolution fossil record-documents process of natural selection over long periods of time bias record ex: horses
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