Biol190 ALL Textbook Notes
Biol190 ALL Textbook Notes BIOL 190
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BIOL190: Biology for Health Professions Dr. Shah (Fall 2015) Textbook Notes th “Campbell Biology: Concepts and Connections 7 edition (by Jane B. Reece, Marthaylor, Eric J. Simon, Jean L. Dickey)” Chapter 1.1 Biology: scientific study of life raise a question what is life? Properties and Processes with Life: o Order: Living cells are basis of this complex organization o Reproduction: organism reproduce their own kind o Growth and Development: inherited information in the form of DNA o Energy processing: bears eating chemical energy from fish o Response to the environment o Resulation: many mechanisms regulate internal environment o Evolutionary Adaption: Best traits through generations to survive Chapter 1.2 Biosphere: all environments on Earth that supports life o Regions of land, bodies of water, lower atmosphere Ecosystem: organism and particular component interact in particular area o Air, soil, water, sunlight Community: entire array of organisms in the ecosystem Population: all individuals of particular species living in an area Organism: an individual living thing Organ system: consist of several organs that cooperate to function Organs: composed of several tissues to perform a function Tissues: made up of small cells Cells: fundamental units of life Organelle: membrane- enclosed structure that performs function Molecule: cluster of atoms held by chemicals bonds Chapter 1.3 The properties of life emergelowest level performs all activities Unicellular: single-cell organism (amoebas, bacteria) Multicellular: cells which are subunits organisms Prokaryotic: cells; 1 to evolve; 1.5 billion years on Earth first Eukaryotic: evolved 2.1 billion years ago System: interactions of structure in a cell form organization Goal of system biology: construct models of dynamic behavior of system Cells illustrate the correlation of structure and function Chapter 1.5 Genes: units of inheritance that transmit information from parent offspring Chromosomes: DNA molecules, group of genes, control is activity of cell Double Helix: 2 long chains coiled together Nucleotide: chemical building blocks ( A T C G) DNA provides blueprint for making protein Proteins: tools that build and maintain cell Chapter 1.6 Taxonomy: branch of biology that names and classifies species Domains: life can be organized in three higher levels Domain Bacteria: prokaryote, single celled, microscopic Domain Archaea: lives of extreme environment (salty lakes) Domain Eukarya: eukaryotic Chapter 1.7 Charles Darwin: naturalist, the Origin of Species Evolution: species living today descendants of ancestral species o Descent with Modification = Theory Natural Selection: certain traits are more likely to survive and reproduce Darwin Observation: population vary traits, population produces more than support Result of Natural Selection: evolutionary adaptation: favorable traits Chapter 1.8 Science: a way of knowing an approach to understanding the natural world Inquiry: a search for information, explanation, answers to specific questions Scientific Inquiry: making observations forming hypothesis’ testing predictions o Quantitative: data numerical measurements o Qualitative: descriptive data Hypothesis: a proposed explanation for a set of data/observations Theory: broader in scope, general enough, supported by a large and usually growing body of evidence Chapter 1.9 Hypothesis must be testable, same way to check its validity Hypothesis must be falsifiable, must have observation/experiment Experimental group: variable being tested Control group: ordinary/ no variable Controlled experiment: compares experimental and control Chapter 1.10 The goal of technology: to apply scientific knowledge for specific purpose The goal of science: to understand natural phenomenon Chapter 1.11 Environment is a powerful selective force for traits Evolutionary theory is useful in medicine (drugs), agriculture (pesticide), forensics (DNA), conservation Chapter 2.1-2.2 Matter: anything that occupies space and has mass Element: a substance that cannot be broken down to other substances by ordinary chemical means Compound: a substance consisting of two or more different elements combined in a fixed ratio 2 element compound: o Table salt (NaCl) o Water (H2O) Essential Elements o oxygen, carbon, hydrogen, nitrogen Trace Elements: 0.01% of human body weight o Iodine, iron, Florine Chapter 2.3 Atoms: smallest unite of matter, still retain properties of an element o Proton a single positive electrical charge (+) o Electron a subatomic particle with a single negative charge (-) o Neutron electrically neutral Atomic number: number of protons Mass number: sum of protons and neutrons Atomic mass: ~mass number Isotopes: same protons, not neutrons Radioactive isotopes: nucleus decay, giving energy Acid: a compound that donates a hydrogen ion to solutions Base: a compound that accepts hydrogen ions and removes them from solution Buffers: substances that minimizes changes in pH Isotopes of Carbon Carbon-12 Carbon-13 Carbon-14 Proton – 6 Proton – 6 Proton – 6 Neutron – 6 Neutron – 7 Neutron – 8 Electron – 6 Electron – 6 Electron – 6 Mass Number: 12 Mass Number: 13 Mass Number: 14 Chapter 2.5-2.9 Electron shells: electrons move around the nucleus at certain energy level Chemical bonds: atoms staying together by attraction Covalent bonds: (strongest bond), 2 atoms share one or more pairs of outer shell electrons Molecule: 2 or more atoms held together by covalent bonds Electronegativity: atom’s attraction for shared electrons Nonpolar covalent bonds: electrons are shared equally between the atoms Polar covalent bonds: unequal sharing of electrons Polar molecule: unequal distribution of charges Ionic bond: 2 ion with opposite charge attract each other Ions: an atom/molecule with an electronic charge resulting from a gain or loss of one or more electrons Hydrogen bonds: positive charged region of an hydrogen atoms Chemical reaction: the breaking and making of chemical bonds Solution: a liquid consisting of a uniform mixture of two or more substance Solvent: the dissolving agent Solute: substance that is dissolved aqueous solution water is an solvent Hydrogen Bonds/Water o Cohesion: tendency of molecules of the same kind to stick together, is much stronger for water o Adhesion: the clinging of one substance to another o Surface tension: a measure of how difficult it’s to stretch/break the surface a liquid Chapter 3.1-3.3 Organic compounds: carbon based molecules Hydrocarbons: compounds composed of only carbon and hydrogen o Length: vary in length o Branching: may be branched or unbranched o Double bonds o Rings Isomers: compounds with the same formula but different arrangement o Can result from different spatial arrangement of the four partners bonded to a carbon atom Functional groups: participate in chemical reactions, hydrophilic Chemical Group Examples Hydroxyl: hydrogen atom bonded to O2 atom, bounded to carbon Alcohol skeleton Carbonyl: carbon atom linked by able bond to O2 atom Aldehyde, Ketone Carboxyl: carbon double bonded to O2 atom and also bonded to a Carboxylic Acid, hydroxyl group Ionized Amino: nitrogen bonded to 2 Hydrogen and Carbon skeleton Amine, Ionized Phosphate: phosphorus atom bonded to 4 oxygen atom Organic phosphate Methyl: nonpolar, carbon bonded to three hydrogen Methylated compound Macromolecule: carbohydrates, proteins, nucleic acid, lipids Polymer: macromolecules by joining smaller molecule into a chain Dehydration reaction: removes a molecule of water Hydrolysis: uses water molecule to break bonds to monomers Chapter 3.4-3.10 Carbohydrates: refers to a class of molecules ranging from the small sugar molecules dissolved in soft drinks to large Polysaccride such as starches o Monosaccharides are the simples carbohydrates; carbohydrate monomers They can be hooked together by dehydration reactions to form more complex sugars (disaccharides) and Polysaccride Generally have molecular formulas that are some multiple of CH2O o Polysaccride: macromolecules, polymers of hundreds to thousands of Monosaccride linked together by dehydration reaction Functions as storage molecules/ a structural compound Starch: storage in plants Glycogen: storage in animals Cellulose: not nutrients in humans, dietary fibers Lipids: do not mix well with water; consist mainly of carbon and hydrogen atoms linked by nonpolar covalent bonds o Lipids are hydrophobic o Triglycerides (fats and oils) = polymers o Glycerol and fatty acids are monomers o Unsaturated fatty acids has one fewer hydrogen atom on each carbon of the double bond o Saturated fatty acids with no double bonds in their hydrocarbon chain have the maximum number of hydrogen atoms o The kinks in unsaturated fatty acids prevent fats containing them from packing tightly together and solidifying at room temperature o The main function of fats is long term energy storage o Phospholipids: major component of cell membranes, conatin only 2 fatty acids attached to glycerol o Steroids: lipids in which the carbon skeleton contains 4 fused rings o Cholesterol: a common component in animal cell membranes and animal cells also use it as a starting material for making other steroids Nucleic Acids o Polymers: DNA and RNA o Monomer: nucleotides Sugar, phosphate group, nitrogen base Chapter 3.11-3.13 Protein: a polymer of amino acids o Diversity is based on differing arrangements of a set of 20 amino acids monomer Amino acids: all have an amino group and a carboxyl group Functional groups are covalently bonded to a central carbon atom called alpha carbon Hydrogen atom and chemical group is also bounded to alpha carbon (R) = side chain Hydrophobic: R group is nonpolar Hydrophilic o Serine (Ser): a hydroxyl group is in its R group Amino acid with a polar o Aspartic acid (Asp): is acidic and negatively charged at the pH of a cell Cells join amino acids together in a dehydration reaction that links the carboxyl group of one amino acid to the amino group of the net amino acid as a water molecule is removed Peptide Bond: resulting covalent linkage Polypeptide: a chain of amino acids o To release, H20 must be added to break each peptide bond Enzyme: the chemical catalysts that speed and regulate virtually all chemical reaction in cells Types of protein: o Structural: found in hair and fiber that make up connective tissues o Contractile: muscle cells are packed with o Defensive: such as antibodies of the immune system o Signal: hormones/chemical messengers that helps coordinate body activities by facilitating communication between cells o Receptors: built into membrane of cells and transmits signals into cells o Transport: transport oxygen to muscles and tissues o Storage: such as ovalbumin which serves as a source of amino acids for developing embryos Structural proteins are typically long and thin are called fibrous proteins Denaturation: polypeptide chains unravel, losing shape and function Primary structure: unique sequence of amino acids o Determined by inherited genetic information Secondary structure: parts of the polypeptide chain consisting of alpha helices coils and beta pleated sheets folds into local patters which are main streamed by hydrogen bonds Tertiary structure: overall 3-D shape of a polypeptide which determines the function of a protein o Results from interactions between these R groups Quaternary structure: a protein that consist of 2 or more polypeptide chains aggregated into one functional macromolecule Chapter 3.14-3.15 Nucleic Acid: DNA (provides directions for its own replication) and RNA (our of nucleus and interacts with protein building machine) Nucleotides: monomers that make up nucleic acid DNA adenosine (A), Thymine (T), Cytosine (C), Guanine (G) RNA Uracil (U) Nucleic Acid polymer: polynucleotides, built by dehydration reactions which sugar bonds to PO4 group RNA = single strand; DNA = double helix (A=T) (C=G) Chapter 3.16 Stop producing lactose (enzyme) cant digest milk sugar lactose Natural selection would have favored anyone with a mutation that kept the lactase gene switched on 3 mutations that keep lactase gene permanently turned on Lactose, milk sugar, is a carbohydrate that is hydrolyzed by the enzyme lactase, a protein DNA = nucleic acid Chapter 4.1-4.4, 4.22 Cell theory: stats all living things are composed of cells and cells from other Light microscopes are used to study the changes in shape of a living human white blood cells; scanning electron microscope is used to study the finest details of surface texture of a human hair. Transmission electron microscope is used to study the detailed structure of an organelle in a liver cell. Plasma membrane: forms a flexible boundary between living cell and surroundings Phospholipid Bilayer: o Head: negatively charged PO4 group and hydrophilic o Tail: 1 non-polar fatty acids and hydrophobic 4 basic functional groups: o The nucleus and ribosomes carry out genetic control of the cell o Organelles involved in the manufacture, distribution, breakdown of molecules include Endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, peroxisomes o Mitochondria in all cells and chloroplast in plant cells function in energy processing o Structural support, movement, communication between cells are the functions of the cytoskeleton, plasma membrane, plant cell walls Cellular Metabolism: all the chemical activities Lysosomes and centrioles are NOT found in plant cells Chloroplasts where photosynthesis occurs Central vacuoles: a compartment that stores water and variety of chemicals Cytoskeleton: composed of protein fibers, provide support an movement Which of the following cellular structures differs from the others: mitochondria, chloroplast, ribosome, lysosome, vacuoles? Ribosomes because it’s the only structure in the list that isn’t bounded by a membrane. Both pro and eukaryotic cells have a plasma membrane, chromosomes containing DNA, and ribosome. Prokaryotes are smaller, do not have a nucleus or other membrane- enclosed organelles, and have smaller different ribosomes Mitochondria supplies energy in the form of ATP. The smooth ER helps regulate contractions by the uptake and release of calcium ions. Microfilaments function in the actual contractile apparatus. Chapter 4.5-4.10, 4.12-4.13, 4.16, 4.22 Nucleus: contains most of the cell’s DNA and houses and copies DNA and passes it on to daughter cells; in cell division; to transcribe DNA instruction onto RNA and thereby control the cell function o Chromosome: structure contains DNA in many proteins o Chromatin: complex proteins and DNA appears as a diffuse mass o Nuclear envelope: enclosing the nucleus is a double membrane and each membrane is a separate phospholipid bilayer o Nucleolus: site where rRNA is synthesized Ribosomes: cellular components that use instruction sent from the nucleus to carry out protein synthesis o Free: suspended in the fluid of the cytoplasm o Bound: attached to the outside of the ER or nuclear envelope Endomembrane system includes o Nuclear envelope, ER, Golgi, lysosomes, vacuoles, plasma membrane Organelles work together in o Synthesis, distribution, storage, export of molecules Endoplasmic Reticulum (ER): extensive network of flattened sacs and tubules; direct interrelatedness of parts of endomembrane system o Smooth: functions in a variety of metabolic processes, enzymes are important in synthesis of lipids, liver cells help process drugs, alcohol, storage of calcium ions o Rough: makes more membrane, phospholipids made by enzymes of rough ER are inserted in ER membrane, bound ribosomes attach to produce proteins inserted membrane. Synthesis and packaging of secretory proteins made by rough ER o As polypeptide synthesizes by bound ribosomes, it’s threaded into the cavity of rough ER. As it enters, new proteins folds into 3D shape o Short chains of sugar link to polypeptide making glycoproteins o When the molecule is ready for export from ER, its packaged in a transport vesicle (vesicle that moves from one part to another o This vesicle buds off from the ER membrane Golgi apparatus: molecule warehouse and finishing factory for products manufactured by the ER o Transports vesicles produced by the ER o Vesicles fuses with Golgi sac, adding its membrane and content receiving side o Products of ER modified o Shipping side gives rise to vesicles, which buds off and travels Lysosomes: membrane sac of digestive enzymes (“breakdown body”) o Provides an acidic environment for its enzymes, while safely isolating them from the rest of the cell o Lysosome fuse with food vacuoles and digest the food. The nutrients are then released into the cell fluid o Serves as a recycling center for animal cells o It breaks down damaged organelles and recycles their molecules Mitochondria: organelles that carry our cellular respiration in nearly all eukaryotic cells, converting the chemical energy of foods such as sugars to chemical energy of the molecule called ATP ATP: main immediate energy source for cellular work Cytoskeleton: network of protein fibers that functions like a Skelton in structural support o Microfilament o Intermediate filaments o Microtubules Which component of the cytoskeleton is most important in (a) holding the nucleus in place within the cell; (b) guiding transport vesicles from the Golgi to the Plasma membrane; (c) contracting muscle cells? (a) intermediate filament (b) Microtubules (c) microfilaments Chapter 5.1-5.9, 4.19, 4.21 The plasma membrane is the boundary that encloses a living cell Some proteins help maintain cell shape and coordinate changes inside and outside cell through attachment to the cytoskeleton and ECM Other proteins function as receptors for chemical messenger Signal transduction: binding of signaling molecule triggers a change in protein, which relays the message into the cell Some proteins are enzymes Selective permeability: membrane allows some substances to cross more easily than others The phospholipid forms a bilayer, the hydrophobic fatty acid tail clusters to the center and hydrophilic head faces on the water Diffusion: tendency for particles of any kind to spread out from high to low concentration Concentration gradient when a gradient exist, substances tend to move from where they are more concentrated to where they are less concentrated Why do diffusion across a membrane called passive transport? The cells does not expend energy to transport substances that are diffusing doesn’t their concentration gradient Osmosis: diffusion of water across a membrane Tonicity: ability of a surrounding solution to cause a cell to gain or lose water. o Isotonic: a solution that has no effect on the passage of water into or out of the cell o Hypotonic: a solution with a solute concentration lower than that of the cell cell gains water and burst o Hypertonic: a solution with a higher solute concentration the cell shrivels from water loss Facilitated Diffusion: polar/charged substance can move across membrane with help of specific transport protein Transport proteins are spefic for the solute they transport, the numbers and kinds of transport proteins affect a membranes permeability to various solutions Active transport: a cell must expend energy to move a solute against its concentration gradient. 4 step process of active transport o Solute binding: solute molecule attaches to specific binding sites o Phosphate attaching: ATP transfers a PO4 group to the transport protein o Transport: solute released on other side of membrane o Protein reversion: PO4 group detaches, transport protein to original shape Exocytosis: a process to export bulky materials such as proteins or Polysaccride Endocytosis: a transport process that is the opposite of exocytosis; cell takes in large molecules As the cell grows, the plasm membrane expands involving exocytosis because when a transport vesicle fuses with the plasma membrane, its contents are released and the vesicle membrane adds to the plasma membrane. The animal cells produce an elaborate extracellular matrix (ECM) that helps hold cells together in tissues and protect and support plasma membrane Main component of the ECML glycoproteins, proteins bonded with Carbohydrates The membrane is attached through membrane proteins (integrin) to the microfilaments in the cytoskeleton and glycoproteins and collagen fibers of the ECM Chapter 5.10-5.12 Energy: the capacity to cause change or to perform work Two basic forms of energy: o Kinetic Energy: the energy of motion. Moving objects can perform work by transferring motion to other matter o Potential Energy: energy that matter possess as a result of its location and structure Chemical Energy: the potential energy available for release in a chemical reaction; energy that can be transformed to power the work of the cell Thermodynamics: the study of energy transformations that occur in a collection of matter o 1st Law: (Law of Energy Conservation) states that the energy in the universe is constant; energy can be transferred and transformed, but it cannot be created or dndtroyed o 2 Law: energy conversions increase the entropy (disorder) of the universe How does the 2nds law explain the diffusion of a solute across a membrane? Diffusion across a membrane results in equal concentration of solute which is a more disordered arrangement than a higher concentration on one-side and a low concentration on the other side Two types of chemical reactions: o Exergonic Reaction: a chemical reaction that releases energy; begins with reactants whose covalent bonds contain more energy than those in the products; releases to the surrounding an amount of energy equal to the difference in the potential energy between reactants and products o Endergonic Reaction: a chemical reaction that requires a net input of energy; starts out with reactant molecules that contain relatively little potential energy; energy absorbed from the surroundings as the reaction occurs, so the products of an endergonic reaction contains more chemical reaction Metabolism: the totally of an organism’s chemical reaction Metabolism Pathway: a series of chemical reactions that wither builds a complex molecule or breaks down a complex molecule into a simpler compound Energy coupling: the use of energy release from exergonic reactions to drive essential endogenic reactions, is a crucial ability of all cells o ATP molecules are the key to energy coupling Cellular respiration is an exergonic process. Remembering that energy must be conserved what becomes of the energy extracted from food during cellular respiration? Some of it is stored in ATP; the rest is released as heat. ATP powers nearly all forms of cellular work o The adenosine part of ATP consists of adenine, a nitrogenous base, and ribose sugar. o Phosphorylation: the product of ATP by chemiosmosis during light reactions of photosynthesis o Energy released in exergonic reactions is used to regenerate ATP to ADP. In this endergonic process, a PO4 group is bonded to ADP. The hydrolysis of ATP releases energy that arises endergonic reactions Explain how ATP transfer energy from exergonic to endergonic process. Exergonic processes phosphorylate ADP. ATP transfer energy to endergonic processes by phosphorylating other molecules. Chapter 5.13-5.16 Enzymes speed up the cell’s chemical reactions by lowering energy barriers Activation energy: energy must be absorbed to contort or weaken bonds in reactant molecules so that they can break and new bonds can form; the amount of energy needed for reactant molecules to move “uphill” to a higher energy, unstable state so that the “downhill” part of a reaction can begin Enzymes: molecules that function as biological catalyst, increasing the rate of a reaction without being consumed by the reaction o An enzyme speeds up a reaction by lowering E needed for reaction to being A An enzyme has a unique 3D shape and that shape determines the enzyme specificity. Substrate: the specific reactant that an enzyme acts on Active site: a pocket/ groove on the surface of the enzyme formed by only a few of the enzymes amino acids’ a region where a substrate fits into Catalytic Cycle- Enzyme o Enzyme available with empty active site o Substrate binds to enzyme with induced fit o Substrate is converted to produced and water molecule is added o Products are released Induced fit: the change in shape of the active site of an enzyme, caused by entry of the substrate, so that it binds more snugly to substrate Cofactors: an enzyme requiring nonprotein helpers; which binds to the active site and function in catalysis Explain how an enzyme speeds up a specific reactions. An enzyme lowers the activation energy needed for a reaction when its specific substrate enters its active site. With an induced fit, the enzyme strains bonds that need to break or positions substrates in an orientation that digs conversation of reactant Competitive inhibitors: reduces and enzyme’s productivity by blocking substrate molecules from entering the active site Noncompetitive Inhibitor: does enter active site, it binds to enzyme somewhere else, a place called allosteric site and its binding changes the shape of the enzyme so it can’t fit the active site. Feedback Inhibition: inhibition is reversible; when the product is used up by the cell, the enzyme is no longer inhibited and pathway functions again Many beneficial drugs acts as enzyme inhibitors o Ibuprofen: common drug that inhibits an enzyme involved in the production of prostaglandins (messenger molecules that increase the sensation of pain and inflammation) o Penicillin: blocks the active site of an enzyme that many bacteria use in making cell walls o Poison: attaches to an enzymes by covalent bonds, making the inhibition irreversible; poisons called nerve gases binds to the active site of an enzyme, leads to rapid paralysis of vital function and death o Pesticides: also irreversibly inhibit this same enzyme. What determines whether enzyme inhibition is reversible or irreversible? If the inhibitor binds to the enzyme with covalent bonds, the inhibition is usually irreversible. When weak chemical interactions bind inhibitor and enzyme, the inhibition is reversible. Chapter 6.1-6.5 In photosynthesis, the energy of sunlight is used to rearrange the atoms of CO2 & H2O to produce glucose & O2. In cellular respiration, O2 is consumed as glucose is broken down to CO2 and H2O taken place in mitochondria. What is misleading about the following statement: “Plant cells perform photosynthesis, and animal cells perform cellular respiration”? The statement implies that cellular respiration doesn’t occur in plant cells. In fact, almost all eukaryotic cells obtain energy for their cellular work. How is your breathing related to your cellular respiration? In breathing, CO2 and O2 are exchanged between your lings and the air. In cellular respiration, cells use O2 obtained through breathing to break down fuel, releasing CO2 as a waste product. Generating ATP for cellular work is the fundamental function of cellular respiration. o The simple sugar glucose is the fuel that the cells use most often o in this exergonic reaction, the chemical energy of the bonds in glucose is released and stored in the chemical bonds of ATP In cellular respiration: 1 Glucose Molecule = 32-38 ATP Molecules Why are sweating and other body-cooling mechanism necessary during vigorous exercise? The demand for ATP is supported by an increased rate of cellular respiration, but about 66% of the energy from food produces heat. Walking at 3 mph, how far would you have to travel to “burn off” the equivalent of an extra slice of pizza, which was about 475 kcal? How long would that take? You would have to walk about 6 miles which would take 2 hours. The movement of electrons from one molecule to another is an oxidation-reduction reaction or redox reaction. o the loss of electrons from one substance is called oxidation o the addition of electron is called reduction The transfer of electrons from an organic molecule to NAD+ represents the 1 step Electron transport chain: NADH delivering these electrons to the rest of the staircase o The ETC undergoes a series of redox reactions in which electrons pass from carrier to carrier down to O2 What chemical characteristics of the element oxygen accounts for its function in cellular respiration? Oxygen is very electronegative, making it very powerful in pulling electrons down the ETC. Chapter 6.6-6.16 Glycolysis o ATP is formed in glycolysis by the process of substrate level phosphorylation. Products of Glycolysis: 2 ATP, 2 NADH, 2 Pyruvate Transition Stage (Prep Step) o CO2 molecule is release from pyruvate. NAD+ is reduced to NADH. Coenzyme A from Vitamin B joins the 2 Carbon group making acetyl CoA. Products of Prep Step: 2 CO2, 2 acetyl CoA, NADH + H Citric Acid Cycle (Krebs Cycle) o Coenzyme A split off and is recycled. Makes ATP through substrate level phosphorylation. Redox reactions generates FADH2 and more NADH. Products of Krebs Cycle: 4 CO2, 6 NADH+6H, 2 ATP, 2 FADH2 Electron Transport Chain o Built into the inner membrane of mitochondria. NADH and FADH2 shuttles through ETC until it reaches O2 (which is the final electron acceptor). Each O2 molecule accepts 2 electrons from chain and picks up 2 H from the surrounding to form H20. H actively transports from mitochondrial matrix to inner membrane. Chemiosmosis o Uses energy from H gradient across a membrane to drive ATP synthesis. H concentration gradient stores potential energy which the energy drives H through a channel in ATP Synthase in which active catalytic sites at PO4 groups to ADP to make ATP. Fermentation: a way of harvesting chemical energy without oxygen. o Lactic Acid Fermentation: NADH is oxidized to NAD+ as pyruvate is reduce to lactate. Muscle cells can switch to lactic acid fermentation when the need for ATP outplaces the delivery of oxygen. o Alcohol Fermentation: recycle NADH back to NAD+ while converting pyruvate to CO2 and ethanol. o Glycolysis occurs both in fermentation and respiration without oxygen and doesn’t occur in a membrane bound organelle. Chapter 8.1-8.10 /11.6-11.18 Cell division: when a cell undergoes reproduction, the two daughter cells that result are genetically: identical to each other and to original parent cell Before the parent cell splits into two, it duplicates its chromosome (the structures that contain most of the cell’s DNA Asexual reproduction: the creation of genetically identical offspring by a single parent without participation of sperm and egg Sexual reproduction: requires fertilization of an egg by a sperm Gametes: has only half as many chromosomes as the parent cell that gives rise to it (egg and sperm) Cell division enables sexually reproducing organisms to develop from a single cell- the fertilized egg, or zygote, into adult organism Meiosis: a special type of cell division that involves the production of egg and sperm cells What function does cell division play in an amoeba? What function does it play in the body? Reproduction; development, growth and repair Binary fission: cell division for prokaryotes o Genes are carried on a single circular DNA molecule that, with associated proteins, constitutes the organism’s chromosome Why is binary fission classified as asexual reproduction? Because the genetically identical offspring inherits their DNA from a single parent Chromatin: fiber composed of roughly equal amount of DNA and protein molecules o As a cell prepares to divide, its chromatin coils up forming a tight, distinct chromosome o Before a cell undergoes division, it must compact all its DNA into a manageable package Sister chromatid: each chromosome consist of 2 copies which contain identical copies of the DNA Centromere: a tightly narrow waist that joins 2 sister chromatid When does a chromosome consist of 2 identical chromatids? When the cell is preparing to divide and has duplicated its chromosome but before the duplicate actually separates 2 main stages of the cell cycle o Interphase: a growing stage; the cell toughly doubles everything in the cytoplasm o Mitotic phase: the actual cell division Interphase: when a cell’s metabolic activity is very high and the cell performs its various function Three sub phases of interphase: o G1: cell grows o S: chromosome duplicates, DNA replication o G2: cells grows more o ….. G0: permanently non-dividing state Two overlapping stages of mitotic o Mitosis: nucleus and content divide and evenly distribute to form 2 daughter nuclei o Cytokinesis: the cytoplasm is divided into two o A researcher treats cells with a chemical that prevents DNA synthesis from starting. This treatment would trap the cell in what phase? G1 Stages of cell division by Mitosis o Prophase: chromatin fibers become more tightly coiled and folded and mitotic spindles begin to form as microtubules. o Prometaphase: nuclear envelope breaks into fragments and disappears, forces move chromosome too the center of the cell o Metaphase: mitotic spindle is fully formed with poles at opposite ends and centromeres are lined up on metaphase plate o Anaphase: the 2 centromeres come apart which separate as sister chromatids (which are sister daughter chromosome); daughter chromosomes centromere “walk” to opposite poles of cell, poles move farther apart which elongates the cell o Telophase: elongation continues, daughter nuclei appear, nuclear envelope form, chromatin fiber uncoils and mitotic spindle disappears o Cytokinesis: the division of cytoplasm and cleavage furrow form and cell pinches into two You view an animal cell through a microscope and observe dense, duplicated chromosomes scattered which stage? Prophase: chromosomes are not aligned. Cleavage Furrow: a shallow indentation in the cell surface Cell plate: vesicles forming a membranous disk Mitotic spindle: a football-shaped microtubules that guides the separation of 2 sets of daughter chromosome Centrosomes: clouds a cytoplasmic materialcontain pairs of centrioles Contrast cytokinesis in animal cells with cytokinesis in plants. In animals cytokinesis involves a cleavage furrow in which containing microfilaments pinch the cell in 2. In plants, it involves a formation of a cell plate, a fusion of vesicle that forms a new plasma membrane and cell wall Growth factor: a protein secreted by certain body cells that stimulate other cells to divide Cell cycle control system: a cyclically operating set of molecules in the cell that both triggers and coordinates key events in the cell cycle Checkpoint: a critical control point where stop and go ahead signals can regulate the cycle At which of the three checkpoints do chromosomes exist as duplicated sister chromatid? G2 and M checkpoints Tumor: an abnormally growing mass of body cells o Benign tumor: limp from abnormal cells remaining, can be surgically removed o Malignant tumor: spread, displacing normal tissue and interrupt organ o Metastasis: the spread of cancer cells from their original site of formation to other sit in the body o Carcinomas: cancer that originates in external/internal covering of the body o Sarcomas: arise in tissues that supports the body o Leukemia: cancer of blood-forming tissues o Tumor-suppressor genes: genes with proteins that encodes to help prevent uncontrolled cell growth Chapter 8.11-8.14, 8.18 Somatic cell: a typical body cell, has 46 chromosome The 2 chromosomes of such a matching pair are called homologous chromosomes because they both carry genes controlling the same inherited characteristics Locus: the particular site where a gene is found on a chromosome. Homologous chromosomes have corresponding gene loci. Sex chromosome: determines an individual’s sex; these chromosomes carry genes that perform other functions The 22 remaining pairs of chromosomes are called autosomes Are all of your chromosomes fully homologous? If you are a female then yes, if you are a male then no. Life Cycle: the sequence of stages leading from the adults of one generation to the adults of the next. Diploid: all body cells contain pairs of homologous chromosomes. The total number of chromosomes is called the diploid number Human’s diploid number: 46 2n = 46 Gamete: (egg/sperm) each has a single set of chromosomes: 22 autosomes plus a sex chromosomes, either X/Y A cell with a single chromosome set is called a haploid cell A haploid sperm cell from the father fuses with a haploid egg cell from the mother in the process of fertilization. Zygote: resulting fertilized egg has 2 sets of homologous chromosome All sexual life cycles involve an alteration of diploid and haploid stages Meiosis reduces the chromosome number by half o Each ostthe chromosomes is duplicated during interphase (before meiosis) o The 1 division, Meiosis 1, segregated the 2 chromosomes of the homologous pair, packaging them in separate (haploid) daughter cells. Chromosome still doubled. o Meiosis 2 separates the sister chromatids. Each of the 4 daughter cells is haploid and contains only a single chromosome from the homologous pair. You observe 23 chromosomes, including a Y chromosome. You could conclude that this must be a perm cell taken from the organ called testis. Stages of Meiosis o Interphase: like mitosis, meiosis is preceded by an interphase, during which the chromosomes duplicate. At the end of interphase, each chromosome consists of 2 genetically identical sister chromatids attached together. The cells centrosome has also duplicated by the end of this interphase. o Prophase 1: chromatin coils up, individual chromosomes become visible, synapsis processhomologous chromosomes come together as pairs (crossing over) in which genetic information is rearranged, centrosomes condense farther, centrosomes move away, nuclear envelope breaks, centrosomes move away, nuclear envelope breaks, tetrad captured by spindle microtubules move toward center. o Metaphase 1: tetrads aligned on metaphase plate (equator), chromosome is condensed and thickened, and spindle microtubules are attached to kinetochores at centromeres. o Anaphase 1: marked by the migration of chromosomes to the 2 poles of the cell, sister chromatids remain attached at their centromeres, only tetrads split up, 3 still- doubled chromosome move to each spindle pole. o Telophase 1 and Cytokinesis: chromosomes arrive at the poles, each pole has a haploid set, chromosome is still in duplicate form, each consists of 2 sister chromatids, cytokinesis 2 haploid daughter cells are formed after chromosomes uncoil, nuclear envelope re-forms, no chromosome duplication occurs between telophase 1 and on set of meiosis 2. o Prophase 2: a spindle forms and moves the chromosomes to the middle of the cell. o Metaphase 2: chromosomes are aligned on metaphase plate (equator), each chromosome pointing to opposite poles o Anaphase 2: centromeres of sister chromatids separate and the sister chromatid of each pair, now individual daughter chromosome move to the opposite poles of the cell o Telophase 2 and Cytokinesis: nuclei form at the cell pole and cytokinesis occurs at the same time, there are now 4 daughter cells, each with the haploid number of (single) chromosomes. A cell has the haploid number of chromosomes, but each chromosome has 2 chromatids. The chromosomes are arranged singly at the center of the spindle. What is the meiotic stage? Metaphase 2 (since the chromosomes line up 2 by 2 in metaphase 1. Both mitosis and meiosis: the chromosome duplicates only once during the S phase of the preceding interphase. Mitosis Division Meiosis Division Provides for growth, tissue repair, and asexual Needed for sexual reproduction, yields reproduction, produces daughter cells that are genetically unique haploid daughter cells- genetically identical to the parent cell cells with only one member of each homologous chromosome pair Involves one division of the nucleus, usually Entails two nuclear and cytoplasmic divisions, accompanied by cytokinesis, producing two yield four haploid cells identical diploid cells Explain how mitosis is conserves chromosome number while meiosis reduces the number from diploid to haploid. In mitosis, the duplication of chromosomes is followed by one division of the cell. In meiosis, homologous chromosome separate in the first of two cell division; after the second division, each new cell ends up with just a single haploid set. Karyotype: is a photogenic inventory of an individual’s chromosome. Chapter 8.15-8.23, 9.4, 9.18 Meiosis contributes to genetic differences in gametes There is a 50% chance that a particular daughter cell will get the maternal chromosome of a certain homologous pair and a 50% chance that it will receive the paternal chromosome. All the chromosome pairs orient independently at metaphase 1 The total number of combo of chromosomes that meiosis can package into gametes is 2 , n where is the haplo23 number. o Humans: 2 ~8 million possible chromosome combination A particular species of worm has a diploid number of 10. How many chromosomal combos are possible for gametes formed by meiosis? 2n = 10 n = 5 2 = 32 Crossing over: an exchange of corresponding segments between nonsister chromatids of homologous chromosomes. Chiasma: the site of crossing over appearing as a X-shaped region Crossing over begins very early in prophase 1 in meiosis o The DNA molecules of 2nonsister chromatids One maternal and one paternal, break at the same place o Immediately, the 2 broken chromatids join together in a new way. In effect, the two homologous segments trade places, to cross over, producing hybrid chromosome with new combos of maternal and paternal genes o When the homologous chromosome separate in anaphase 1, each contains a new segment originating from its homologous o Finally, in meiosis 2, the sister chromatids separate, each going to a different gamete Genetic recombination: the production of gene combo different from those by the original chromosomes o in meiosis in humans, an avg. of 1 to 3 crossover events occurs per chromosome pair, Describe crossing over and the random alignment of homologous chromosome on the metaphase 1 pate account for the genetic variation among gametes formed by meiosis. Crossing over creates recombinant chromosomes having a combo of genes that we originally on different chromosomes. Homologous chromosome pairs are oriented randomly at metaphase of meiosis 1. An extra copy of chromosome 21 causes Down syndrome. 3 number 21 chromosomes, making 47 chromosomes, total is called Trisomy 21 Meiosis occurs repeatedly as the testes/ovaries produce gametes. Nondisjunction: an accident of meiosis/mitosis in which a pair of homologous chromosome or a pair of sister chromatids fail to separate in anaphase 1. Explain how disjunction could result in a diploid gametes. A diploid gamete would result if the nondisjunction affected all the chromosomes during one of the meiotic division. Sex Chromosome Syndrome Origin of Nondisjunction Frequency in population XXY Kilnefelter (male) Meiosis in egg/sperm 1/2000 formation XYY None (male) Meiosis in sperm 1/2000 formation XXX None (female) Meiosis in egg/sperm 1/1000 formation XO Turner (female) Meiosis in egg/sperm 1/5000 formation What is the total number of autosomes you would expect to find in the karyotype of a female with Turner Syndrome? 44 (Plus one sex chromosome) What is a polypoid organism? One with more than 2 sets of homologous chromosomes in its body. Types of adding/subtracting fragments to chromosomes: o Deletion: a segment of a chromosome is removed o Duplication: a segment of a chromosome is copied and inserted into the homologous chromosome o Inversion: a segment of a chromosome is removed and then reinserted backwards to its original o Reciprocal Translocation: segments of two nonhomologous chromosome swap locations with each other How is reciprocal translocation different from normal crossing over? Translocation swaps chromosomes segments between nonhomologous chromosomes. Crossing over normally exchanges corresponding segments between homologous chromosomes. o Crossing over produces new combos of alleles o Recombination frequency: the (%) of recombinants Chapter 9.1-9.5, 9.8-9.10, 9.16 Heredity: the transmission of traits from one generation to the net Gregor Mendel: deduced the fundamental principles of genetics by breeding garden plants parents pass to their offspring discrete “heritable factors” o Character: a heritable trait that varies among individuals o Traits: each variant for a character o Self-fertilize: a form of reproduction that involves fusion of sperm and egg produced by the same individual organism o Cross fertilization: the fusion of sperm and egg derived from two different individuals o True breeding: referring to organisms for which sexual reproduction produces offspring with inherited traits identical to those of the parentshomozygous o Hybrid: the offspring of two different varieties o Hybridization: simply a genetic cross o P generation: the true breeding parental plants o F1 generation: P generation hybrid offspring o F2 generation: offspring when F1 plant self-fertilize or fertilize o Monohybrid cross: an experimental mating of individuals differing individual single character Why was the development of true breeding varieties crucial to the success of Mendel’s experiment? True-breeding varieties allowed Mendel to predict the outcome of specific crosses and thus to run controlled experiments. Mendel’s technique for cross fertilization of pea plants o He prevented self-fertilization by cutting of the immature stamens of a plant before they produce pollen o To cross fertilize the stamen less flower, he dusted its carpel with pollen from another plant o After pollination the carpel developed into a pod, containing seeds (peas) that he planted Characters of Peas Dominant Traits Recessive Traits Flower Color Purple White Flower Position Axial Terminal Seed Color Yellow Green Seed Shape Round Wrinkled Pod Shape Inflated Constricted Pod Color Green Yellow Stem Length Tall Dwarf Mendel’s Four Hypothesis o There are alternative versions of genes that account for variations in inherited characters o For each character, an organism inherits two alleles, one from each parent Homologous: two identical alleles for a gene Heterozygous: two different alleles for a gene o If the two alleles of an inherited pair differ, then one determines the organism appearance and is called the dominant allele; the other has no noticeable effect on organism’s appearance is recessive alleles o A sperm or egg carries only one alleles for each inherited character because allele pairs separate from each other during the production of gametes (Law of Segregation) Punnet Square: shows the four possible combos of allele o Genotype: organism’s genetic make up o Phenotype: organism’s physical trait Dihybrid cross: an experimental mating of individual differing in two character Law of independent assortment: a general rule in inheritance that when gametes form during meiosis, each pair of alleles for a particular characteristics segregate independently nd of other pairs; also known as Mendel’s 2 Law of Inheritance. Wild-type traits: the version of a character that most commonly occurs in nature Pedigree: a family genetic tree Carriers: an individual who is heterogynous for a recessively inherited disordered and who therefore don’t show symptoms of the disorder but may pass recessive allele to offspring o Cystic fibrosis: most common life threatening genetic disease o Interbreeding: mating between close blood relatives o Achondroplasia: a more serious dominant disorder, a form of dwarfism in which the head and the torso of the body develops, but the arms and legs are short o Huntington disease: a lethal dominant allele can escape elimination however if it doesn’t cause death until a relatively advanced age, a degenerative disorder of the nervous system that usually doesn’t appear until middle age Genetic testing: info can inform decisions about whether to have a child Which of Mendel’s laws have their physical basis is the following phases of meiosis: (a) the orientation of homologous chromosome pairs in metaphase 1; (b) the separation of homologous in anaphase 1? (a) the law of independent assortment; (b) the law of segregation Chapter 9.1-9.15, 9.20-9.23 Complete dominance: the dominant allele has the same phenotypic effect whether present in one or two copies Incomplete dominance: the appearance of F1 hybrid falls between the phenotypes of the two parental varieties Incomplete dominance does not suppose the blending hypothesis Why is a test cross unnecessary to determine whether a snapdragon with red flower is homozygous or heterozygous? Because the homozygous and heterozygous differ in phenotype: ref flowers for the dominant homozygote and pink flowers for the heterozygous. Many genes have more than two alleles in the population ABO blood group: involves three alleles of a single gene Maria has type O blood and her sister has type AB blood. The girls know that both of their maternal grAndparents are type A.BWhat are the genotypes of the girls’ parent? Their mother is I i and their father is I i. A single gene may affect many phenotypic character Pleiotropy: the control of more than one phenotypic characteristics by a single gene How does sickle cell disease exemplify the concept of pleiotropy? Homozygosity for sickle cell allele cause abnormal hemoglobin and the impact of abnormal hemoglobin on the shape of RBCs leads to cascade of symptoms. Polygenic inheritance: the additive effects of two or more gene loci on a single phenotypic characteristics If most characters results from a combo of environment and heredity, why was Mendel able to ignore environment influences on his pea plants? The character he hose for the study were all entirely genetically determined. Sex chromosomes: a chromosome that determines whether an individual is a male or female o Humans have 44 autosomes o Eggs contain a single X chromosomes o Sperms contain have an X and Y chromosome During fertilization in humans, what determines the sex of the offspring? Whether the egg is fertilized by a sperm bearing an X chromosome (producing a female offspring) or by a sperm with a Y chromosome (producing a male offspring) Sex linked genes: a gene located on a sex chromosome. In humans, the vast majority of sec linked genes are located on the X chromosome o Human sex linked disorders affect mostly males o Hemophilia: an X-linked recessive trait; bleeds excessively when blood clotting o Red-green color blindness: a malfunction of light sensitive cells in the eye; recessive disorder o Duchenne Muscular Dystrophy: characterized by a progressive weakening of the muscle and loss of coordination; X-linked recessive disorder Why is the Y chromosome particularly useful in tracing recent human heritage? Because it’s passed directly from father to son, forming an unbroken chain of male lineage. A white eyed female prosophila is mated with a red eyed (wild type) male. What result do you predict for the numerous offspring? All female offspring will be red eyed but heterozygous (X X ); all male offspring will be white eyed (X Y) Chapter 10.1 Molecular Biology: the study of hierarchy at the molecular level Frederick Griffith: studied bacterium strains harmless or pathogenic Bacteriophages: viruses that exclusively infect bacteria (phage) Hershey and Chase E.coli, used radioactive isotopes o When bacteria has been infected with T2 Phage liquid A phage replication cycle o Phage attaches to bacterial cell o Phage injects DNA into bacterium o Phage DNA directs bacterium to make more phage of DNA o Cell lyses and releases new phages Chapter 10.2 Nucleotides: building blocks of nucleic acids Polynucleotides: a nucleotide of polymer (chain) Sugar phosphate backbone: nucleotides joined by covalent bonds Pymidines: thymine and cytosine Purines: Adenine and guanine Chapter 10.3 Crick: studied x-ray crystallography Franklin: x-ray image of DNA Chapter 10.4 The template model for DNA replication o The parental molecule of DNA o The parental stand separate and serve as a template o 2 identical daughter molecules of DNA are formed Semi-conservative Model: DNA replication of half of the parental molecule is maintained in each daughter One end of each DNA strand o 3’ sugar carbon atom is attached to a –OH group o 5’ sugar carbon atom is attached to a phosphate group DNA Polymerase: enzyme that links DNA nucleotides to growing daughter strand o DNA grows in 5’3’ direction DNA ligase: links together the DNA strands Chapter 10.6 Proteins are links between genotype and phenotype Transcription: transfer info from DNA to RNA Translation: use of RNA to make a polypeptide Chapter 10.7-10.9 DNA and RNA are polymers made of nucleotide monomers Codon: 3 base words Triple Cod: flow of information from gene to protein Genetic code: the set of rules that relate codons in RNA to amino acids RNA Polymerase: RNA nucleotides are linked by transcription enzyme Promoter: the “start transcribing” signal, a specific binding site for RNA Polymerase and determines which of the 2 strand is the template in transcription Chapter 10.10 mRNA: the kind of RNA that encodes amino acid sequences b/c it conveys genetic messages from DNA to the translation machinery of the cells o mRNA translated polypeptides o mRNA exits nucleus through nuclear pores to enter the cytoplasm introns: internal noncoding regions (intervening) exons: the parts of gene that are expressed RNA splicing: cutting and pasting process Chapter 10.11-10.12 tRNA: transfer RNA: convert the words of nucleic acids (codons) to the amino acid words of proteins tRNA matches amino acids to the appropriate codon to form new polypeptide tRNA made of a single strand of RNA, one polynucleotide chain anticodon: a single stranded loop at the end of the folded molecule contains a special triplet codon once amino acid attaches to appropriate tRNA, its incorporated into polypeptide chain ribosomes: structures in the cytoplasm that position mRNA and tRNA together o consist of 2 subunits made up of proteins and rRNA Chapter 10.13-10.14 initiation brings mRNA together; initiation process = where translation begins mRNA is longer than the genetic message it carries Steps of initiation o mRNA binds to a small ribosomal subunit o Start codon: a special initiation or tRNA binds to specify codon o
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