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Biology 101 Notes

by: annazeberlein

Biology 101 Notes BIOL 101

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Notes for Salcedo's Spring 2015 Biology 101 course.
General Biology 101
Dr. Norma Salcedo
Biology, Biology 101
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This 46 page Bundle was uploaded by annazeberlein on Sunday February 21, 2016. The Bundle belongs to BIOL 101 at College of Charleston taught by Dr. Norma Salcedo in Spring 2015. Since its upload, it has received 30 views. For similar materials see General Biology 101 in Biological Sciences at College of Charleston.


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Date Created: 02/21/16
Bio Notes 2/21/16 1:40 PM Bio notes evolution and its connection to cancer • why everyone seems to have cancer o cancer – it is not much a disease as a phenomenon, the result of basic evolutionary compromise • body lives and grows, cells divide constantly, errors occur (brain cells do not divide) • some caused by carcinogens • most random misprints • mutations are the engines (basis of evolution) • 15-20% of cancers are believed to be caused by infectious agents: o helicobacter pylori bacteria, has been significantly reduced • stomach cancer has been significantly reduced with improvements in refrigeration and public sanitation there are viruses and bacteria • viruses can’t be treated, but bacteria can with antibiotics, which can reduce the causes of stomach cancer • vaccines against human papilloma virus have the potential of nearly eliminating cervical cancer chapter 1 • 2 major ways of studying living things o 1. Discovery biology – going into the field and observing, seeing diversity, behavior o 2. Experimental biology • “the scientific method is nothing more than a system of rules to keep us from lying to each other” • three key features of living things • requirements for energy and nutrients o ongoing inputs of energy and nutrients sustain life § nutrients – substance that an organism needs for growth and survival but cannot make for itself • producers – organism that makes its own food using energy and nonbiological raw materials o photosynthesis – producers use light energy to make sugars from carbon dioxide and water • consumers – organism that gets energy and nutrients by feeding on tissues, wastes, or remains of other organisms • homeostasis o each living thing has the capacity to sense and respond to change o every living thing has the ability to sense and respond to change both inside and outside itself • homeostasis: process by which organism keeps its internal conditions within tolerable ranges by sensing and responding to change • use of dna as hereditary material o dna is passed to offspring during reproduction o dna carries hereditary information that guides: • development: multistep process by which first cell of a new multicelled organism gives rise to an adult • growth: increase in the number, size and volume of cells • reproduction; processes by which individuals produce offspring • inheritance: transmission of dna to offspring o all organisms inherit their dna from one or two parents • dna is that basis of similarities in form and function among organisms o small variations in dna give rise to differences among individuals and among types of organisms • life is more than the sum of its parts o biology: study of life, past and present o defining life is a challenge o complex properties, including life, emerge from the interaction of simple parts • emergent property: characteristic of a system that does not appear in any of the system’s component parts scientific method • 1. Observations • 2. Ask questions • 3. Propose explanation: hypothesis • 4. Experiment • 5. Use a control: varies in one aspect • 6. Report • buttered cat hypothesis o toast always lands butter side down o cat always lands on it’s feet o attach toast to back of cat, butter side up o the hypothesis must be tested many times, and if it is irrefutable then it is a theory • a law is something consistently observed, mathematically explained, but incompletely explained 2 theories define biological sciences • cell theory • theory of evolution • cell theory o all living things are composed of cells o all cells come from preexisting like cells o cells are the basic units of life o discovered in the 17 thcentury § hooke – cellulae § leewenhoek – animalcules experimentation life’s organization • atom: fundamental building block of matter o fundamental units of all substances, living or not. • molecule: association of two or more atoms o atoms join other atoms in molecules. The molecules special to life are much larger and more complex than water. • cell: smallest unit of life o some live and produce • organism: consists of one or more cells • tissue: specialized cells organized in a pattern; performs a collective function • organ: grouping of tissues engaged in a collective task • organ system: set of organs engaged in a collective task • population: group of interbreeding individuals of the same species that live in a given area • community: all populations of all species in a given area • ecosystem: a community interacting with its environment • biosphere: all regions of earth where organisms live how are living things different? • Biodiversity: scope of variation among living organisms o Organisms can be grouped on the basis of whether they have a nucleus (a sac that encloses and protects a cell’s dna) • Prokaryote: single-celled organism without a nucleus (now used only informally) o Bacteria § Most diverse and well known group § Single-celled organisms § Lack a nucleus o Archaea § Single-celled organisms § Lack a nucleus § More closely related to eukaryotes than to bacteria • Eukaryote: organism whose cells characteristically have a nucleus o Protist: diverse group of simple eukaryotes o Fungus: single-celled or multicelled eukaryotic consumer § Breaks down material outside itself, then absorbs nutrients released from the breakdown • Plant: multicelled, typicalled photosynthetic producer • Animal: multicelled consumer that develops through a series of stages and moves about during part of all of its life What is a species? • Species: unique type of organism • Taxonomy: the science of naming and classifying species • Genus: a group of species that share a unique set of traits • Specific epithet: second part of a species name o Together, the genus name and the specific epithet designate one species • Trait: an observable characteristic of an organism or species • Taxon: group of organisms that share a unique set of traits The secret life of earth • Many new species and species thought to be extinct, or near extinction, were recently discovered in new guinea o The current rate of extinctions is about 1,000 times faster than ever recorded § Human activities are responsible for the acceleration • The more we learn about the natural world, the more we realize we have yet to learn What are some potential pitfalls in scientific inquiry? • Sampling error: difference between results obtained from a subset, and results from the whole o Can be a substantial problem with a small subset o Experimenters start with a relatively large sample, and repeat their experiments The limits of science • Science does not address: o Subjective questions § Why do I exist? o Supernatural § Science neither assumes nor denies that supernatural phenomena occur Chapter 2 • Life’s organization o Atom – fundamental units of all substances, living or not. o Molecules – atoms join other atoms in molecules o Cells o Tissues o Organ o Organ system o Multicelled organism • What are the basic building blocks of all matter? o Positively charged protons (p+) and uncharged neutrons are found in an atoms nucleus (core) o Negatively charged electrons (e-) move around the nucleus § Charge: electrical property, opposite charges attract, like charges repel. o A typical atom has about the same number of electrons and protons o Atomic number: number of protons in the atomic nucleus o Element: pure substance that consists only of atoms with the same number of protons o Periodic table: tabular arrangement of all known elements by their atomic number • Isotopes and radioisotopes o Although all atoms of an element have the same number of protons, they can differ in the number of other subatomic particles o Isotopes: forms of an element that differ in the number of neutrons their atoms carry o Mass number: total number of protons and neutrons in the atomic nucleus o Radioisotope: isotope with an unstable nucleus o Radioactive decay: process by which atoms of a radioisotope emit energy and/or subatomic particles when their nucleus spontaneously break up o Tracers § All isotopes • Why do atoms interact? o Electrons occupy different orbitals: volumes of space around an atom’s nuclus o Orbitals are filled from lower to higher energy o The farther an electron is from the nucleus, the greater its energy o An electron can move to a higher energy orbital if an input gives it a boost § Electron then immediately emits o A shell model helps us visualize how electrons populate atoms o Nested “shells” correspond to successively higher energy levels o Each shell includes all of the orbitals on one energy level o Up to 2 electrons – the first shell o Up to 8 electrons – the second shell o Up to 18 electrons – the third shell o Carbon (6e – 4e outermost shell), oxygen (8e – 6e outermost shell), hydrogen (1e – 1e outermost shell), and nitrogen (7e – 5e outermost shell) are the most common elements in organic matter • From atoms to molecules o An atom can get fill its electron shell by participating in a chemical bond with another atom § Chemical bond – attractive force that arises between two atoms when their electrons interact § Compound – molecule that has some atoms of more than one element § Ionic bond – strong mutual attraction links ions of opposite charge ú Ionically bonded sodium and chloride ions make up sodium chloride (NaCl; table salt) ú Ions retain their respective charges when participating in an ionic bond • Polarity – separation of charge into positive and negative regions • A NaCl molecule is polar because the chloride ion keeps a very strong hold on its extra electron • Electronegativity – measure of ability of an atom to pull electrons away from other atoms • Covalent bonds o Covalent bond: two atoms share a pair of electons § Forms between atoms with a small or no difference in electronegativity § Covalent bonds are often stronger than ionic bonds, but not always o Covalent bonds in compounds are usually polar o Atoms share electrons unequally in a polar covalent bons o Hydrogen bonding in water § Water has unique properties that arise from the two polar covalent bonds in each water molecule § In water, the oxygen atom carries a slight negative charge; the hydrogen atoms carry a slightly positive charge. § The polarity of individual water molecules attracts them to one another § This type of interaction is called a hydrogen bond ú Hydrogen bond: attraction between a covalently bonded hydrogen atom and another atom taking part in a separate polar covalent bond o Structural formulas: lines between atoms represent the number of covalent bonds § Example: H-H ú H2 has one covalent bond between the atoms § Example: O=O ú A double bond has two links between the atoms • Water’s special properties o Water is an excellent solvent § Substances that dissolve easily in water are hydrophilic ú Polar molecules § Substances that resist dissolving in water are hydrophobic (ie, oils) ú Oils consist of nonpolar molecules and hydrogen bonds do not form between nonpolar molecules and water § Salt: releases ions other that H+ and OH- when it dissolves in water (ie, NaCl) § Solute: a dissolved substance § Solution: uniform mixture of solute completely dissolved in solvent ú Chemical bonds do not form between molecules of solute and solvent § Nonionic solids (ie, sugars) dissolve easily in water due to hydrogen bonding in water § Hydrogen bonds form and break much more easily than covalent or ionic bonds § Collectively they are quite strong o Water has cohesion § Cohesion tendency of molecules to resist separating from one another § Water has cohesion because hydrogen bonds collectively exert a continuous pull on its individual molecules o Water stabilizes temperature § Temperature: measure of molecular motion § Because of hydrogen bonding, it takes more heat to raise the temperature od water compared with other liquids § Below 0 celcius or 32 fahrenheit, water molecules become locked in the bonding pattern of ice ú Sheets of ice that form on the surface of ponds, lakes, and streams insulate the water ú Protects aquatic organisms during cold winters] § When water is liquid some of its molecules spontaneously separate into hydrogen ions (H+) and hydroxide ions (OH-) § These ions can combine again to form water § Concentration: amount of solute per unit volume of solution § pH: measure of the number of hydrogen ions in a fluid § base: accepts hydrogen ions in water ú above pH 7 § acid: releases hydrogen ions in water ú below pH 7 o buffer: a set of chemicals that can keep the pH of a solution table by alternately donating and accepting ions that contribute to the pH o most biological molecules can function properly only within a narrow range of pH § buffer failure can be catastrophic in a biological system o burning fossil fuel such as coal releases sulfur and nitrogen compounds that affect the pH of rain § rainwater is not buffered § in places with a lot of fossil fuel emissions, the rain and fog can be more acidic than vinegar § the corrosive effects of acid rain is visible in urban areas § acid rain drastically changes the pH of water in soil, lakes, streams § such changes can overwhelm the buffering capacity of fluids inside organisms, with lethal effects • mercury rising o mercury is a naturally occurring element o most of it is safely locked away in rocks § volcanic activity and human activity release it into the atmosphere § microbes combine airborne mercury with carbon to form methylmercury ú unlike mercury alone, methylmercury easily crosses skin and mucous membranes o when mercury enters the body, it damages the nervous system § it takes months or years for mercury to be cleared from the body o the toxin can build up to high levels even if small amounts are ingested on a regular basis o large predatory fish have a lot of mercury § us envirtonmental protection agency recommends that adult humans ingest less than 0.1 microgram of mercury per kilogram of body weight per day Chapter 3 • What are the molecules of life? o The molecules of life contain a high proportion of carbon atoms § Carbohydrates § Lipids § Proteins § Nucleic acids • The stuff of life: carbon o Molecules that have primarily hydrogen and carbon atoms are said to be organic o Carbon’s importance to life arises from its versatile bonding behavior § Carbon has 4 vacancies o Many organic molecules have a backbone: a chain of carbon atoms • From structure to function o Hydrocarbon: consists only of carbon and hydrogen atoms o Functional group: § An atom (other than hydrogen) or small molecular group bonded to a carbon of an organic compound § Imparts a specific chemical property o All biological systems are based on the same organic molecules § The details of those molecules differ among organisms o Monomers – subunits of larger molecules (1) § Simple sugars, fatty acids, amino acds, and nucleotides o Polymers – consist of multiple monomers (2 or more) o Cells build polymers from monomers, and break down polymers to release monomers, § These processes of molecular change are called chemical reactions o Metabolism – all enzyme-mediated chemical reactions by which cells acquire and use energy § Enzyme – organic molecule that speeds up a reaction without being changed by it o Condensation: chemical reaction in which an enzyme builds a large molecule from smaller subunits § Water is formed during condensation o Hydrolysis: chemical reaction in which an enzyme uses water to break a molecule into smaller subunits • What is a carbohydrate? o Carbohydrate: organic compound that consists of carbon, hydrogen, and oxygen in a 1:2:1 ratio o Three main types of carbohydrates in living systems: § Monosaccharides – one unit § Oligosaccharides – few units (2-20) § Polysaccharides – many units (above 20) o Simple sugars § Monosaccharides (one sugar) are the simplest type of carbohydrates § Common monosaccharides have a backbone of five or six carbon atoms ú Examples: • Glucose has six carbon atoms • Five-carbon monosaccharides are components of nucleotide monomers of DNA and RNA § Cells use monosaccharides for cellular fuel ú Breaking the bonds of sugars releases energy that can be harnessed to power other cellular processes § Monosaccharides are also used as: ú Precursors for other molecules ú Structural materals to build larger molecules § Oligosaccharides are short chains of covalently bonded monosaccharides § Disaccharides consist of two monosaccharide monomers ú Examples: • Lactose: composed of glucose + galactose • Sucrose: composed of glucose + fructose § Polysaccharides: chains of hundreds or thousands of monosaccharide monomers § Most common polysaccharides: ú Cellulose ú Starch ú Glycogen § Cellulose ú Main structural component of plants ú Tough and insoluble ú Composed of chains of glucose monomers stretched side by side and hydrogen-bonded at many –OH groups § Starch ú Main energy reserve in plants ú Stored roots, stems, leaves, seeds, and fruits ú Composed of a series of glucose monomers that for a chain that coils up § Glycogen ú Main energy reserve in animals ú Very abundant in muscle and liver cells ú Highly branched chains of glucose monomers • What are Lipids? o Lipids – fatty, oily, or waxy organic compounds o Many lipids incorporate fatty acids: consist of a long hydrocarbon “tail” with a carboxyl group “head” § The tail is hydrophobic § The head is hydrophilic o Saturated fatty acids: have only single bonds linking the carbons in their tails § Flexible and wiggle freely o Unsaturated fatty acids: have some double bonds linking the carbons in their tails § Flexibility is limited o Fats: lipid that consists of a glycerol molecule with one, two, or three fatty acid tails o Triglyceride: a fat with three fatty acid tails § Saturated fats: triglycerides with saturated fatty acid tails; solid at room temperature § Unsaturated ffats: triglycerides with unsaturated fatty acid tails; liquid at room temperature o Phospholipid: main component of cell membranes § Contains phosphate group in hydrophilic head and two nonpolar fatty acids § In a cell membrane, phospholipids are arranged in two layers called a lipid bilayer ú One layer of hydrophilic heads are dissolved in cell’s water interior ú Other layer of hydrophilic heads are dissolved in the cell’s fluid surroundings ú Hydrophobic tails are sandwiched between the hydrophilic heads o Waxes § Wax: complex, varying mixture of lipids with long fatty acid tails bonded to alcohols or carbon rings § Molecules pack tightly, so waxes are firm and water- repellant ú Plants secrete waxes to restrict water loss and keep our parasites and other pests ú Other types of waxes protect, lubricate, and soften skin and hair o Steroids § Steroids: lipids with no tails ú Contain a rigid backbone that consists of twenty carbon atoms arranged in a characteristic pattern of 4 rings § Functional groups attached to the rings define the type of steroid § Examples: estrogen and testosterone ú Dictates many sex characteristics • What are proteins? o Amino acid subunits § Cells can make thousands of different proteins from only twenty kinds of monomers called amino acids § An amino acid contains ú An amine group (--NH2) ú A carboxyl group (--COOH, the acid) ú A side chain called an “R group” defines the kind of amino acid § The covalent bond that links amino acids in a protein is called a peptide bond § A short chain of amino acids is called peptide ú As the chain lengthens, it becomes a polypeptide § Proteins consist of polypeptides that are hundreds or even thousands of amino acids long o Structure dictates function § Protein function in movement, defense, and cellular communication ú Example: enzymes § A protein’s biological activity arises from and depends on its structure § Primary structure: linear series od amino acids; defines type of protein § Secondary protein: polypeptide chain that forms twists and folds § Tertiary structure: nonadjacent regions of protein adjoin to create compact domains § Quaternary folds: two or more polypeptide chains that are closely associated or covalently bonded together § Enzymes often attach sugars or lipids to proteins ú Example: glycoproteins and lipoproteins o why is protein structure so important? § Heat, some salts, shifts in pH, or detergents can denature (unravel) a protein by breaking hydrogen bonds § Denaturation causes a protein to lose its function Chapter 4 • Cell Theory o Prior to the invention of the microscope, the existence of cells was unknown o mid-1600’s: Antoni von Leewenhoek constructed a crude microscope and observed “animalcules” § the animalcules were in face microbes o components of cell theory § all organisms consist of one or more cells, which are all the basic unit of life § all cells come from division of preexisting cells § all cells pass hereditary material to offspring • components of all cells o all cells have at least three components in common: § plasma membrane § cytoplasm § DNA o The plasma membrane is the outermost membrane of a cell o The plasma membrane encloses a jellylike mixture called cytoplasm o Suspended in the cytoplasm are specialized organelles o All cells start of life with DNA § In eukaryotic cells, DNA Is contained within the nucleus • How do we see cells? o Most cells are 10-20 micrometers in diameter § About fifty times smaller than the unaided human eye can perceive § Microscopes are used to observe objects in the micrometer range of size o Light microscopes use visible light to illuminate samples § Curved lenses inside the microscope focus light into a magnified image § Researchers use stains or light-emitting tracers to see details inside cells o Electron microscopes use magnetic fields to focus a bean of electrons onto a sample • What is a membrane? o The plasma membrane regulates the crossing of substances into and out of cells o More functions: § Enzymatic activity § Signaling § Intercellular joining § Attachment to the cytoskeleton • The fluid mosaic model o Several molecules are embedded within of attached to the lipid bilayer § Cholesterol, proteins, glycoproteins, glycolipids o Fluid mosaic: model of a cell membrane as a two dimensional fluid of mixed composition • Protein adds function o Many types of proteins are associated with a cell membrane § Adhesion proteins: helps cells stick together § Recognition proteins: identifies “self” cells § Receptor proteins: triggers a change in cell activity § Transport proteins: assists the movement of ions or molecules across the membrane • How are bacteria and archaea alike? o All bacteria and archaea are single-celled organisms o Archaea and bacteria were once formally grouped together as prokaryotes § Archaea are more closely related to eukaryotes than to bacterias o Archaea now have their own separate domain o o • What is a cytoskeleton? o Cytoskeleton: § Network of interconnected protein filaments § Supports, organizes, and moves eukaryotic cells and their parts o Microtubules: hollow filament of tubulin subunits § Involved in movement o Microfilaments: fiber of action subunits § Reinforces membranes; involved in muscle contractions o Intermediate filament: stable cytoskeletal element § Structurally supports membranes and tissues o Motor proteins § Associate with cytoskeletal elements § Move cell parts when energized by ATP § Drag cellular cargo along tracks of microtubules and microfilaments o Flagella: propel cells o Cilia: short, movable structures that project from the plasma membrane o Centriole: barrel-shaped organelle from which microtubules grow o Basal body: develops from a centriole o Pseudopod: temporary protrusion; facilitates movement and engulfs prey • What is life? o “life” is a long list od properties that collectively describe living things § 1. Make and use the organic molecules of life § 2. Consist of one or more cells § 3. Engage in self-sustaining biological processes (metabolism and homeostasis) § 4. Change over their lifetime (growing, maturing, aging) § 5. Use DNA as their hereditary material when they reproduce § 6. Capacity to change over successive generations (adapting to environmental pressures) • application: food for thought o strains of E. coli that are toxic to people live in the intestines of other animals § humans are exposed when they come into contact with feces of animals that harbor it ú example: eating contaminated ground beef or contaminated fresh fruits and vegetables o food workers are working to reduce the number and scope of harmful E. coli outbreaks • what do mitochondria do? o Mitochondrion: double-membraned organelle that produces ATP by aerobic respiration in eukaryotes o Nearly all eukaryotic cells (including plant cells) have mitochondria § The number varies by the type of cell and by the organism • What are plastids? o Plastids – double membrane organelles that function in photosynthesis, storage, or pigmentation in plant and algal cells § Examples: chloroplasts, chromoplasts, amyloplasts § Chloroplasts: specialized plastid for photosynthesis in some protists and plants cells • What influences the movement of ions and molecules? o Diffusion: spontaneous spreading of molecules of ions § Essential for substances to move into, through, and out of cells § What affects the rate of diffusion? ú Size, temperature, concentration, charge and pressure • Semipermeable membranes o Lipid bilayers are selectively permeable § Water can cross but o Osmosis: diffusion of water across a selectively permeable membrane § Occurs in response to a difference in solute concentration (tonicity) between the fluids on either side of the membrane ú Isotonic: equal solute concentrations; no osmosis ú Hypotonic: low solute relative to another fluid; water flows out of hypotonic cytoplasm ú Hypertonic: high solute relative to another fluid; water flows into hypertonic cytoplasm • Turgor o Stiff cells walls keep plant cells from expanding very much § An inflow of water causes pressure to build up § Turgor: pressure that a fluid exerts against a structure § Osmotic pressure: amount of turgor that prevents osmosis into cytoplasm or other hypertonic fluid • How do ions and charged molecules cross cell membranes? o Transport proteins allow only specific substances to cross the membrane o Passive transport: solutes move through membrane; requires no energy § Example: faciliatated diffusion – solute binds to transport protein and moves across membrane with its concentration gradient o Active transport – transport protein pumps a solute against its concentration gradient; requires energy § Examples: ú Calcium pumps ú Sodium-potassium pumps o Vesicle movement § Exocytosis – cell expels a vesicles contents to extracellular fluid § Endocytosis – cell takes in a small amount of extracellular fluid (and its contents) by the ballooning inward of the plasma membrane § Phagocytosis – “cell eating”; an endocytic pathway by which a cell engulfs particles such as microbes or cellular debris • Membrane trafficking o Membrane proteins and lipids are made in the ER and move to the Golgi bodies for final modification § “finalized” vesicles containing proteins and lipids move to and fuse with the plasma membrane § exocytosis and endocytosis continually replace and withdraw membrane particles chapter 5 • what is energy? o Energy: the capacity to do work o Kinetic energy: the energy of motion o First law of thermodynamics: energy cannot be created or destroyed o Entropy: measure of how much the energy of a system is dispersed o Second law of thermodynamics: energy disperses spontaneously • Energy’s one way flow o Work occurs as a result of energy transfers § Energy lost from a transfer is usually in the form of heat § Since heat is not useful for doing work, the total amount of energy available for doing work in the universe is always decreasing § Lost energy must be replenished for life to continue o The energy that fuels most life on earth comes from the sun § This energy from the sun is transferred many times until it is permanently dispersed o Energy’s spontaneous dispersal is resisted by chemical bonds § Energy in chemical bonds is a type of potential energy (stored energy) • How do cells use energy? o During a reaction, one or more reactants become one or more products § Reactant – molecule that enters a reaction and is changed by participating in it § Product – molecule that is produced by a reaction • Chemical bond energy o Bond energy and entropy both contribute to a molecule’s free energy (amount of energy available to do work) § Endergonic: energy in; reaction that requires a net input of free energy to proceed § Exergonic: energy out; reaction that ends with a net release of free energy • Why the earth does not go up in flames o The molecules of life release energy when they combine with oxygen § Example: a spark starts a reaction that converts cellulose (in wood) and oxygen (in air) to water and carbon dioxide § The reaction is highly exergonic, causing wood to continue to burn o Earth is rich in oxygen – and in potential exergonic reactions § Why then doesn’t the earth burst into flames? o Chemical bonds do not break without at least a small input of energy § Activation energy: the minimum amount of energy required to get a chemical reaction started • How do enzymes work? o Metabolism requires enzymes o In a process called catalysis, an enzyme makes a reaction run faster than it would on its own o Most enzymes are proteins o Each kind of enzyme recognizes a specific substrate (reactants) that are altered in specific ways § Active site: pocket in an enzyme where substrates bind and a reaction occurs • Enzyme activity o Environmental factors (e.g. pH, temperature, salt) influence an enzyme’s shape and function § Each enzyme functions best in a particular range of conditions that reflect the environment in which is evolved o The enzyme pepsin digests proteins in the very acidic (pH 2) stomach environment o Pepsin denatures above pH 5.5 § Pepsin becomes inactivated when the stomach’s contents pass into the small intestine o The enzyme trypsin continues protein digestion in the small intestine at the higher pH o Adding heat boosts free energy, bringing reactants closer to activation energy o The rate of an enzymatic reaction typically increases with temperature – but only up to a point § An enzyme denatures above a characteristic temperature, causing the reaction rate to fall sharply as the shape of the enzyme changes • What is a metabolic pathway? o Metabolic pathway: series of enzyme-mediated reactions by which cells build, remodel, or break down an organic molecule § Linear pathway: reactions run straight from reactant to product § Cyclic pathway: the last step regenerates a reactant for the first step • Controls over metabolism o What mechanisms help cells regulate the production of substances § The coupling of forward and reverse reactions § Regulatory molecules or ions that bind directly to an enzyme’s active site § Binding of an allosteric regulator (outside of the active site) alters the shape of an enzyme in a way that enhances or inhibits function • Electron transfers o The bonds of organic molecules hold a lot of energy that can be released in a reaction with oxygen § Burning involves a reaction with oxygen; energy from organic molecules is released all at once – explosively o To facilitate burning, cells break organic molecules apart in small, manageable steps § Most of these steps are oxidation – reduction reactions (redox reactions; electron transfers) ú In a typical redox reaction, one molecule accepts electrons (it becomes reduced) from another molecule (which becomes oxidized) o Electron transfer chain: array of enzymes and other molecules that accept and give up electrons in sequence § The energy of the electrons is released with each step of the sequence § Important for photosynthesis and aerobic respiration • how do cofactors work? o Cofactor: metal ion or organic compound that associates with an enzyme and is necessary for that enzyme’s function § Ex: vitamins, minerals, metal ions o Coenzyme: an organic factor § Ex: coenzyme Q10, NAD+ o Coenzyme Q10: carries electrons between enzymes of electron transfer chains during aerobic respiration o Your body makes it! Also in § Red meats § Soy oil § Peanuts o The enzyme catalase has four tightly bound cofactors called hemes § Catalase’s substrate is hydrogen peroxide, a highly reactive molecule that can be dangerous § The heme in catalase breaks hydrogen peroxide into water § Catalase is an antioxidant: prevents oxidation of other molecules • ATP – a special coenzyme o ATP (adenosine triphosphate) functions as a cofactor in many reactions § Bonds between phosphate groups hold a lot of energy § When a phosphate group is transferred via the process of phosphorylation, energy is transferred along with it o ATP/ADP cycle: § Process by which cells regenerate ATP § ADP (adenosine diphosphate) forms when a phosphate group is removed from ATP, then ATP forms again as ADP gains a phosphate group o The ATP/ADP cycle couples endergonic reactions with exergonic ones Chapter 7 • How do cells access the chemical energy in sugars? o In order to use the energy stored in sugars, cells must first transfer it to ATP § The energy transfer occurs when the bonds of a sugar’s carbon backbone are broken, driving ATP synthesis o There are two main mechanisms by which organisms break down sugars to make ATP: § Aerobic respiration: requires oxygen to break down sugars to make ATP ú Main energy releasing pathway in nearly all eukaryotes and some bacteria ú Three stages produce 36 ATP • Glycolysis o Occurs in the cytoplasm; net yield is two ATP • Krebs cycle aka citric acid cycle o Occurs in the mitochondria; net yield is two ATP • Electron transfer phosphorylation aka oxidative phosphorylation o Occurs in the mitochondria; net yield is 32 ATP § Fermentation • What is glycolysis? o Glycolysis: series of reactions that begin the sugar breakdown pathways of aerobic respiration and fermentation § Convert one 2-carbon molecule of sugar (such as glucose) into two molecules of pyruvate: an organic compound with a 3-carbon backbone o Steps of glycolysis: § A phosphate group is transferred from ATP to glucose, forming glucose-6-phosphate § Glucose-6-phosphate accepts a phosphate from another ATP ú Two PGAL (phosphoglyceraldehyde) form § Each PGAL receives a second phosphate group, and each gives up two electrons and a hydrogen ion ú Two molecules of PGA (phosphoglycerate) form ú The electrons and hydrogen ions are accepted by two NAD+, forming NADH (required for third step of aerobic respiration) § A phosphate group is transferred from each PGA to ADP, so two ATP form ú The direct transfer of a phosphate group from a substrate to ADP is called substrate-level phosphorylation ú Glycolysis ends with the formation of two more ATP by substrate-level phosphorylation o Net yield of glycolysis is two ATP were invested to begin that reactions of glycolysis § A total of 4 ATP form, but 2 ATP were invested to begin the reactions of glycolysis o Glycolysis also produces 2 3-carbon pyruvate molecules • What happens during the second stage of aerobic respiration? o The second stage of aerobic respiration occurs inside mitochondria § Includes two sets of reactions, acetyl-CoA formation and the Krebs cycle § These pathways break down the pyruvate produced during glycolysis • Acetyl-CoA formation o Steps of acetyl-CoA formation § Pyruvate is transported into the mitochondrial matrix § Pyruvate is split into CO2 and a 2-carbon acetyl group (-COCH3) § CO2 diffuses out of the cell and the acetyl group combines with coenzyme A (CoA), forming acetyl-CoA ú Electrons and hydrogen ions released by the reaction combine with NAD+, so NADH also forms • The Krebs Cycle o Steps of the Krebs cycle § Two carbon atoms of acetyl-CoA are transferred to oxaloacetate, forming citrate § Two CO2 form and depart the cell § Two NAD+ are reduced when they accept hydrogen ions and electrons, forming two NADH § ATP forms by substrate-level phosphorylation § Two coenzymes are reduced: an FAD (flavin adenine dinucleotide) and another NAD+ § Oxaloacetate is regenerated o The combined second stage reactions of aerobic respiration break down two pyruvate to 6 CO2 o Net yield of second-stage reactions is two ATP o 10 coenzymes (eight NAD+ and two FAD) § provides electrons to the third stage of aerobic respiration • What happens during the third stage of aerobic respiration? o o As the electrons move through the chains, they give up energy, little by little o Hydrogen ions are actively transported across the inner membrane § The resulting hydrogen ion gradient causes the ions to flow through the ATP synthase, driving formation of ATP • What is fermentation? o Like aerobic respiration, fermentation begins with glycolysis in the cytoplasm § In fermentation, pyruvate is not fully broken down to CO2 § Electrons do not move through electron transfer chains, so no additional ATP forms § NAD+ is regenerated allowing glycolysis to continue § The net yield is 2 ATP o Two fermentation pathways: § Alcoholic fermentation: anaerobic sugar breakdown pathway that produces ATP, CO2 and ethanol ú Steps of alcoholic fermentation: • 3-carbon pyruvate is split into carbon dioxide and 2-carbon acetaldehyde • electrons and hydrogen are transferred from NADH acetaldehyde, forming NAD+ and ethanol ú alcoholic fermentation in a fungus, saccharomyces cerevisae, § Lactate fermentation: anaerobic sugar breakdown pathway that produces ATP and lactate ú Steps of lactate fermentation: • The electrons and hydrogen ions carried by NADH are transferred directly to pyruvate • Pyruvate is converted to a 3-carbon lactate • NADH is converted to NAD+ ú Animal muscle cells carry out aerobic respiration and/or lactate fermentation • Red muscle fibers: many mitochondria and myoglobin; produce ATP mainly by aerobic respiration o Sustains prolonged activity • White muscle fibers: contains few mitochondria and no myoglobin; most ATP produced by lactate fermentation o Useful for quick, strenuous activities o Chapter 6 Photosynthesis • How do photosynthesizers absorb light? o Energy flows through ecosystems begins when photosynthesizers intercept sunlight o Autotrophs are producers § Make food using energy from environment and carbon from inorganic molecules o Heterotrophs are consumers § Obtain carbon from organic compounds assembled by other organisms • Properties of light o Light: electromagnetic radiation that moves through space in waves § Wavelength – distance between the crests of two successive waves o Visible light: § Small part of the spectrum of electromagnetic radiation (380 to 750 nm0 o Light is organized in packets of energy known as photons § Long wavelengths are low in energy § Short wavelengths are high in energy • Capturing a rainbow o Photosynthesizers use pigments to capture light of specific wavelengths o Chlorophyll a: most common photosynthetic pigment in plants and protists § Absorbs violet, red, and orange light § Reflects green light (appears as green) o Accessory pigments harvest additional light wavelengths • Why do cells use more than one photosynthetic pigment? o In 1882, Theodor Engelmann tested the hypothesis that the color of light affects the rate of photosynthesis § Used motile, oxygen-requiring bacteria to identify where photosynthesis was taking place § Directed a spectrum of light across individual strands of green algae o In Engelmann’s experiment, oxygen-requiring bacteria gathered where blue and red light fell across the algal cells o Conclusion: § Blue and red light are the best light for driving photosynthesis across a color spectrum o The combination of pigments used for photosynthesis differs among species § Photosynthetic species are adapted to the environment in which they are evolved • What happens during photosynthesis o Photosynthesis converts the energy of light into the energy of chemical bonds o Unlike light, chemical energy can power the reactions of life, and it can be stored for use at a later time o In eukaryotes, photosynthesis takes place in chloroplasts § Thylakoid membrane: a chloroplast’s continuous highly folded inner membrane system § Stroma: cytoplasm-like fluid between the thylakoid membrane and the two outer membranes of a chloroplast o Photosynthesis is a two stage reaction: § Light-dependent reactions: ú Occur in thylakoid membrane ú Converts light energy to ATP and NADPH § Light-independent reactions: ú Occur in stroma ú ATP and NADPH drive synthesis of sugars from water and CO2 • How do the light-dependent reactions work? o Thylakoid membranes contain millions of light-harvesting complexes § Circular arrays of chlorophylls, various accessory pigments, and proteins o After light absorption, light-harvesting complexes pass energy back and forth o Photosystem: group of hundreds of chlorophylls, accessory pigments and other molecules § Photosynthesis begins when energy from light- harvesting complexes reaches a photosystem o The Calvin-Benson Cycle: § Build sugars in the stroma of chloroplasts § Not powered by light energy § Driving force is ATP and NADPH that formed in the light-dependent reactions § Uses carbon atoms from CO2 to make sugars ú Carbon fixation: carbon from an inorganic source gets incorporated into an organic molecule § Steps of the calvin-benson cycle ú 1. The enzyme rubisco fixes carbon by attaching CO2 to RuBP (ribulose biphosphate) ú 2. Twelve PGA (phosphoglycerate) molecules form ú 3. 12 PGAL (phosphoglyceraldehyde) molecules form • two PGAL may combine to form one 6- carbon sugar (such as glucose) ú 4. Ten remaining PGAL regenerate the starting compound RuBP • adaptation to climate o stomata are tiny gateways for gases § open stomata: ú allow CO2 to diffuse form the air into photosynthetic tissues ú allow O2 to diffuse out of these tissues into the air § closed stomata: ú conserve water on hot, dry days ú limit the avaiblity of CO2 o C3 plants § Use only the calvin-benson cycle to fix carbon § When CO2 concentration declines, rubisco uses oxygen as a substrate in photorespiration § When stomata are closed during the day, C3 plants lose carbon instead of fixing it § Extra energy is required to make sugars § Contain high levels of rubisco o C4 plants § Close stomata on dry days but their sugar production does not decline § Minimize photorespiration by fixing carbon twice in one day ú Mesophyll cells ú Bundle-sheath cells § Examples: corn, switchgrass, and bamboo Chapter 11 How Cells Reproduce • How do cells reproduce? o Multiplication by division § A life cycle is a collective series of events that an organism passes through during its lifetime § Even single cells of multicellular organisms have a life cycle § Cell cycle: a series of events from the time a cell forms until its cytoplasm divides § a typical cell spends most of its life in interphase: interval between mitotic divisions when a cell grows ú during interphase, a cell roughly doubles the number of its cytoplasmic components, and replicates its DNA § three stages of interphase: ú G1: metabolic activities ú S: DNA synthesis ú G2: protein synthesis needed for cell division § Mitosis: process of nuclear division that maintains chromosome number § Mitosis and cytoplasmic division are the basis of: ú Developmental processes (e.g., increases in body size and tissue remodeling) ú Replacement of damaged or dead cells ú Eukaryotic asexual reproduction (offspring are produced by one parent) § When a cell divides by mitosis, it produces two descendent cells ú Each with the same number and type of chromosomes as the parent § Human body cells are diploid (contain pairs of chromosomes) ú With exception, the chromosomes of each pair are homologous: have the same length, shape, and genes § How are homologous chromosomes distributed to descendent cells? ú G1: chromosomes are unduplicated ú By the G2 stage, each chromosome consists of two double-stranded DNA molecules called sister chromatids § During mitosis, the sister chromatids are pulled apart ú Each sister chromatids end up in separate nuclei that are packaged into separate cells o Control over the cell cycle § Whether or not a cell divides is determined by mechanisms of gene expression control ú “brakes” on the cell cycle normally keep the vast majority of cells in G1 ú “checkpoint genes” monitor: • the completion of DNA copying • DNA damage • Nutrient availability • What is the sequence of events before mitosis? o Before mitosis: § Interphase: chromosomes are loosened to allow transcription and DNA replication § Early prophase: in preparation for nuclear division the chromosomes begin to pack tightly o Prophase: § Chromosomes further condense § One of the two centrosomes move to the opposite ends of the cell § Microtubules assemble and lengthen, forming a spindle (functions to move chromosomes) § Nuclear envelop breaks up § Sister chromatids are attached to opposite centrosomes o Final stages of mitosis: § Metaphase: all chromosomes are aligned midway between spindle poles § Anaphase: sister chromatids separate and move towards opposite spindle poles § Telophase: chromosomes arrive at opposite spindle poles and decondense, two new nuclei form • How does a eukaryotic cell divide? o In most eukaryotic cells, cytokinesis (cytoplasmic division) occurs between late anaphase and the end of telophase o The process of cytokinesis differs between plant and animal cells o Animal cell cytokinesis: § Typical animal cells pinch themselves in two after nuclear division ends ú The spindle begins to disassemble during telophase ú Contractile rings drag the plasma membrane inward ú Cleavage furrow (indentation) forms o Plant cell cytokinesis: § Dividing plant cells face a challenge because a cell wall surrounds their plasma membrane § By the end of anaphase short microtubules form on either side of the future plane of division § Disk-shaped structure called the cell plate forms and eventually partitions the cytoplasm § The cell plate forms into two new cell walls • What is the function of telomeres? o 1997: geneticist Ian Wilmut and his team cloned the first mammal, a lamb named Dolly, from an adult somatic cell o although Dolly was healthy at first, she showed signs of premature aging § arthritis, lung disease, etc. • what happens when control over the cell cycle is lost? o Types of mutations that affect cell cycle § Checkpoint genes mutate causing the loss-of-function of their protein products § Controls that regulate checkpoint gene expression fail ú Cell makes either too much or too little of gene product o The role of mutations § When enough checkpoint mechanisms fail, a cell loses control over its cell cycle ú Interphase may be skipped, so division occurs over and over with no resting period ú Signaling mechanisms that cause abnormal cells to die may stop working § Neoplasm: accumulation of abnormally dividing cells § Tumor: neoplasm that forms a lump § Oncogene: gene that helps transform a normal cell into a tumor cell § Proto-oncogenes: gene that, by mutation, can become an oncogene ú Example: growth factors – molecules that stimulate mitosis and differentiation ú Most neoplasms carry mutations resulting in an overactivity or overabundance of the epidermal growth factor (EGF) receptor § Checkpoint gene products that inhibit mitosis are called tumor suppressors ú Tumors form when checkpoint gene products are missing ú Examples: • Tumor cells often have mutations in the BRCA1 and BRCA2 checkpoint genes • HPV (human papillomavirus) cause cells to make proteins that interfere with tumor suppressors o Cancer: § Benign neoplasms such as warts are not usually dangerous ú Slow growth


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