Taken by: Kurtis Saiyo Biol 0010 - Introduction to Biology Professor Price Campbell Essential Biology 4th ed.

Table of Contents
Table of Contents Chapter 1 Chapter 2 Chapter 3 Organic Compounds Carbohydrates - sugars or sugar polymers Lipids - hydrophobic organic molecule; neither macromolecules nor polymers Proteins - polymers of amino acids Nucleic Acids Chapter 4 - Tour of a Cell Plasma Membrane Cell Walls Nucleus and Ribosomes Endomembrane System: Manufacturing and Distributing Cellular Products Golgi Apperatus - refinery, warehouse, shipping center Chloroplasts and Mitochondria Cytoskeleton Cilia and Flagella Chapter 5 - The Working Cell Conservation of Energy ATP and Cellular Work Enzymes Membrane Function Chapter 6 - Cellular Respiration Cellular Respiration: Aerobic Harvest of Food Energy Role of Oxygen in Cellular Respiration Redox Reactions NADH & Electron Transport Chain An overview of Cellular Respiration The Three Stages of Cellular Respiration The Versatility of Cellular Respiration Fermentation: Anaerobic Harvest of Food Energy Fermentation in Human Muscle Cells Fermentation in Microorganisms Chapter 7 - Photosynthesis: Using Light to Make Food

The Basics of Photosynthesis Chloroplasts: Sites of Photosynthesis The Overall Equation of Photosynthesis A Photosynthesis Road Map The Light Reactions: Converting Solar Energy to Chemical Energy The Nature of Sunlight Chloroplast Pigments How Photosystems Harvest Light Energy How the Light Reactions Generate ATP and NADPH The Calvin Cycle: Making Sugar from Carbon Dioxide Solar Driven Evolution Chapter 8 - Cellular Reproduction: Cells from Cells (Part A) What Cell Reproduction Accomplishes The Cell Cycle and Mitosis Eukaryotic Chromosomes The Cell Cycle Mitosis and Cytokinesis Cancer Cells: Growing out of control What is Cancer? Cancer Treatment Cancer Prevention and Survival Chapter 10: The Structure and Function of DNA DNA: Structure and Replication DNA and RNA Structure Watson and Cricks Discovery of the Double Helix DNA Replication The Flow of Genetic Information from DNA to RNA to Protein How an Organisms Genotype Determines Its Phenotype From Nucleotides to Amino Acids: An Overview The Genetic Code Transcription: From DNA to RNA Processing of Eukaryotic RNA Translation: The Process Review: DNA RNA Protein Mutations Mutagens Viruses and Other Noncellular Infectious Agents Bacteriophages Plant Viruses Animal Viruses HIV, The AIDS Virus Viroids and Prions Emerging Viruses Chapter 8 - Cellular Reproduction: Cells from Cells (Part B)

Homologous Chromosomes Gametes and the Life Cycle of a Sexual Organism The Process of Meiosis Interphase Meiosis I: Homologous Chromosomes Seperate Meiosis II: Sister Chromatids Separate Review: Comparing Mitosis to Meiosis The Origins of Genetic Variation Independent Assortment of Chromosomes Random Fertilization Crossing Over When Meiosis Goes Awry How Accidents During Meiosis Can Alter Chromosome Number Down Syndrome: An Extra Chromosome 21 Abnormal Numbers of Sex Chromosomes Advantages of Sex Chapter 9 - Patterns of Inheritance Heritable Variation and Patterns of Inheritance In an Abbey Garden Mendels Law of Segregation Genetic Alleles and Homologous Chromosomes Mendels Law of Independent Assortment Using a Testcross to Determine an Unknown Genotype Rules of Probability Family Pedigrees Human Disorders Controlled by a Single Gene Recessive Disorders Dominant Disorders Genetic Testing Variations on Mendels Laws Incomplete Dominance in Plants and People ABO Blood Groups: An Example of Multiple Alleles and Codominance Pleiotropy and Sickle-Cell Disease Polygenic Inheritance Role of the Environment The Chromosomal Basis of Inheritance

Chapter 1
Properties of Life: what classifies something as life?

1. 2. 3. 4. 5. 6. 7.

Order - order and organization Regulation - within appropriate limits Growth & Development - genes; instructions Energy Utilization Response to environment Reproduction Evolution

Biosphere - all the environments on earth that support life; Earth. - the whole is greater than the sum of its parts Biosphere: 1. Biosphere 2. Ecosystem 3. Communities 4. Populations 5. Organisms 6. Organ systems & organs 7. Tissues 8. Cells 9. Organelles 10. Molecules & Atoms Ecosystems - interaction between organisms & their environment a. Process 1 - cycling of nutrients b. Process 2 - gains and looses energy constantly Cells and DNA: Cells are the level which properties of life emerge All organisms are composed of cells 2 types of cells Prokaryotic - simpler and smaller, i.e. - bactieria Eukaryotic - Plants, Animals, Fungi and protists. DNA holding nuclear membrane. DNA - composed of 4 different molecules (A, G, C, T) human cell DNA is 3 billion chemical letters long Biodiversity: 290,000 types of plants 52,000 types of vertebrates Three domains: 1. Bacteria - or Eubateria; all true bacteria

2. Archaea - Least evolved forms of life on earth, very similar to bateria 3. Eukarya - Animals, Plants, Fungi and Protists. Bacteria & Archaea are prokeryotic Evolution: Charles Darwin 1859 - Origin of Species decent with modification Natural Selection: Darwins Observations: 1. Overproduction & competition 2. Individual variation 3. Unequal reproductive success Steps of Natural Selection: 1. Population with varied inherited traits 2. Elimination of individuals 3. Reproduction of Survivors 4. Increasing frequency of traits of survivors Scientific Method: 1. Observation 2. Question 3. Hypothesis 4. Prediction 5. Experiment 6. Result / Predicted result Discovery Science: Observation and measurements are the data of discovery science A Controlled Experiment has two groups: Experimental group Control group - the group which the experimental group is compared. Theory is bigger in scope from hypothesis. Theory describes a general behavior and is widely accepted Culture in Science: 1. Dependence on observations & measurements others can varify 2. Requires that ideas are testable & repeatable. Scientists build on each other by remaining sceptical and by seeking reproducible evidence.

Chapter 2
matter - anything that occupies space and has mass elements - substances that cannot be broken down into other substances 92 naturally occurring elements 25 essential to life O, C, H, P, K, S, Na, Cl, Mg, Ca Trace: B, Cr, Co, Cu, F, I, Fe, Mn, Mo, Se, Si, Sn, V, Zn Atomic # = number of protons Mass # = sum of protons and neutrons in nucleus Isotopes - have different number of protons and neutrons, differ in mass (ex: Carbon 13; 6 protons, 7 neutrons) Radioactive Isotope - isotope whos nucleus is decaying and giving off energy due to instability (ex Carbon 14; 6 protons, 8 neutrons) compounds - substances containing 2 or more elements atom - smallest unit of matter Composed of Proton (+), Electron (-), and Neutron (neutral) ion - electrically charged atom ionic bond - bond formed from two oppositely charges ions covalent bond - 2 or more atoms sharing outer shell electrons (e-) to form molecule to better fulfill the octet rule. hydrogen bond - weak attraction in polar molecules Water The polarity of water molecules and hydrogen bonding that results explain most of waters life-supporting properties cohesion - tendency for molecules to stick together. Responsible for surface tension and capillary action. ice floats - crystal stucture of ice is less dense than liquid water. Water is a solvent - solution = solvent + solute (aqueous solution) evaporative cooling - loss of heat through evaporation of water. water regulates the temperature of the biosphere. Heat - amount of energy associated with the movement of the atoms and molecules in a body of matter. Temperature - measure of heat Acids & Bases & pH Acids - release H+ in to solution Base - release OH- (hydroxide ion) into solution pH scale - logarithmic scale of the concentration of H+ ions. 0(acid) - 14(base); 7 neutral Slight changes in pH can be very harmful to an organism

Buffers - substances in biological fluids that prevent harmful changes in pH by accepting or donating H+ when there is and excess or depletion of H+ ions CO2 is absorbed by oceans when it combines with seawater which produces an acid.

Chapter 3
Lactose - milk sugar (many people have a lack of lactase enzyme)

Organic Compounds
organic compound - carbon based molecules hydrogen, oxygen, and nitrogen are commonly found in organic compounds hydrocarbons: carbon-hydrogen molecules methane (CH4) is the simplest hydrocarbon Functional Groups - groups of atoms that perform chemical reactions hydroxyl group (-OH) carboxyl group (-COOH) polymers - large moleculesmade by stringing together smaller molecules called monomers dehydration reaction - chemical reactionthat removes a molecule of H2O Hydrolysis - to break with water ; reverse of dehydration reaction monosaccarides - simple sugars that cannot be broken down by hydrolysis (ex: glucose, fructose) [Glucose = C6H12O6 (fructose has same chemical formula)] isomers - molecules that have same molecular formula but different structure (like glucose and fructose) The shape of molecular structure is important monosaccharides - the main fuel for cellular work dextrose - aqueous solution of glucose disaccharide - double sugar, contructed from 2 monosaccharides through dehydration reaction (ie - lactose, maltose, sucrose) sucrose - disaccharide; table sugar (glucose+fructose) polysaccharide - long chains of sugar units. Polymers of monosaccharides. glyocogen - animal polysaccharide, more extensively branched than starch cellulose - ploysaccharide used by plants for structure (animals this plant fiber for dietary fiber or roughage)

Carbohydrates - sugars or sugar polymers

Lipids - hydrophobic organic molecule; neither

macromolecules nor polymers

fat - glycerol molecule + 3 fatty acid molecules via dehydration reaction forming triglycerides hydrocarbons (fatty acid) store a lot of energy Omega 3 has double bond in certain spot. stored in adipose cells unsturated - do not contain maximum # of hydrogen atoms; unstarurated fats tend to be solid at room tempurature. One fatty acid is bent due to double bond. atherosclerosis - lipid containing deposits in blood vessels. hydrogenation - adding hydrogen, causes trans fats steroids - hydrophobic molecules that behave like hormones like testosterone and estrogen Cholesterol Testosterone & type of estrogen THG - synthetic steriod amino acid - central carbon with 4 covalent partners (monomer) Amino Group Carboxyl Group Side group Hydrogen polypeptide - polymer peptide bond - bond of amino acid protiens are made up of one or more polypeptides. leucine - hydrophobic amino acid styrine - hydrophillic acid hemoglobin - 146 amino acid chain Primary Structure Alpha helix pleated sheet Protein Shape 3D shape determines function denaturation is loss of proper shape Nucleotides are monomers Nitrogen base sugar phosphate group DNA & RNA DNA sugar is deoxyribose nucleic acid RNA sugar is ribose DNA - (A,G,C,T) A - Adenine

Proteins - polymers of amino acids

Nucleic Acids

G - Guanine T - Thynine C - Cystocine Adenine partners with Thynine Guanine partners with Cystine RNA - (A,G,C,U) U - Uracil DNA RNA Amino Acid Inability to make sufficient amounts of Lactase (enzyme that brakes down lactose) is genetic; one letter change (C to T) causes this.

Chapter 4 - Tour of a Cell

Intro Antibiotics - drugs that disable or kill bacteria (penicillin, 1928) ribosomes of humans and bacteria are sufficiently different that antibiotics only bind to bacterial ribosomes Microscopy Resolving power - the ability of an optical instrument to show two objects as separate resolving power of human eye is about 0.1 millimeter apart Light Microscopy (LM) - surface features, low resolving power, though much better then human Scanning Electron Microscopy (SEM) - surface features, high resolving power Transmission Electron Microscopy (TEM) - Inner features, high resolving power Robert Hooke in 1665 first described cells Prokaryotic Cells - Domains Bacteria and Archaea prokaryotic cells are said to be older in evolutionary sense (3.5 billion years ago) prokaryotic cells are generally much smaller then eukaryotic cells; about 1/10th the length. Eukaryotic Cells - Domains Protists, Plants, Fungi, and Animals eukaryotic cells are about 2.5 billion years have organelles. All cells have: A plasma membrane - thin outer membrane that regulates traffic of molecules between the cell and its surroundings DNA Ribosomes - tiny structures that build protiens according to the instruction of DNA

Eurkaryotic cells have organelles Nucleus - houses mose of a eukaryotic cells DNA prokaryotic cells dont have a nucleus, DNA is bunched together in a region called the nucleoid. Some prokaryotic cells have a capsule, a sticky outer layer that surrounds the cell wall some prokaryotes have pili and flagella that allow them to attach to surfaces and propel them through a fluid environment, repectively. Eukaryotic Cells Organelles: Mitochondrion Nucleus Rough Endoplasmic Reticulum Smooth Endoplasmic Reticulum Ribosomes Golgi Apparatus Plasma Membrane Cytoskeleton Only in Plant cells: Central Vacuole Cell Wall Chloroplast Only in Animal cells: Centriole Lysosome Flagellum Composed of lipids and protiens lipids belong to special category called phospholipids phospholipids have 2 (hydrophobic) fatty acid tails and one (hydrophilic) phosphate group head. phosphate group is electrically charges making it hydrophilic (likes water), but fatty acids are hydrophobic (fears water) making one end like water and the other end avoids water phospholipid bilayer , hydrophilic on outside and hydrophobic on inside protiens float around phospholipid bilayer creating a fluid mosaic and protiens regulate traffic across membrane. Plants have cell walls made of rigid cellulose fibers. Animal cells secrete a sticky coat called an extracellular matrix instead of a cell wall, and most have cell junctions, structures that connect to other cells. Structure and Function of Nucleus: nuclear membrane - double layer membrane encasing nucleus chromatin - long DNA molecules and associated proteins that form long

Plasma Membrane

Cell Walls

Nucleus and Ribosomes

fibers chromosome - each long organized structure of chromatin fiber (humans have 46) nucleolis - where the components of ribosomes are made Ribosomes small dots in cell floating in cytoplasm and attached to endoplasmic reticulum. responsible for protein synthesis How DNA Directs Protein Production 1. DNA transfers information to mRNA (messenger RNA) 2. mRNA exits nucleus into cytoplasm though pores in nuclear membrane 3. Ribosome moves along mRNA, generating a protein.

Endomembrane System: Manufacturing and Distributing Cellular Products

Endoplasmic Reticulum (ER) - labyrinth of tubes and sacs that run throughout cytoplasm. Rough & Smooth Rough ER -ribosomes are attached, producing proteins into ER. ER forms transport vesicles around proteins Smooth ER - Part of endoplasmic reticulum that is responsible for detoxifying cell and creates lipids Transport Vesicles travel along the cytoskeleton, moving protiens to the Golgi Apparatus Transport vesicles from the ER come to the receiving side of the Golgi apparatus and turn into pancake shapes and release proteins. Golgi produces digestive enzymes, waste or secretory proteins, and cell products that are moved from the Golgi by the Golgi budding around the enzymes, waste, or products. Lysosomes - capsules that hold digestive enzymes that bud off golgi digest macromolecules and old organelles lysosomes burst in apoptosis releasing digestive enzymes into cytoplasm causing the cell to digest itself and die. Vacuoles - storage cells Bud off the ER, Golgi Apparatus, or Plasma Membrane Some are contractile to regulate chemistry Central Vacuole - holds water for plant cells Transport Vesicles Also bud from Golgi (not just ER) to transport secretory proteins out of the cell. Chloroplasts - where plant cells produce sugars Inner and outer membrane

Golgi Apperatus - refinery, warehouse, shipping center

Chloroplasts and Mitochondria

Stroma - thick fluid inside inner membrane Granum - stacks of thylakoids Mitochondria - sites of cellular respiration 2 components: 1. Intermembrane Space 2. Matrix Inner membrane has folding called cristea that increase surface area. Maintains cell shape Enables cell movement (amoebas, cilia, and flagella) microtubles - highways of the cell different types of fibers Cilia are shorter and wiggle; little hairs cilia lining of respitory tract moves mucus Flagella whip around a bit like a screw, longer and tail-like

Cytoskeleton

Cilia and Flagella

Chapter 5 - The Working Cell

Conservation of Energy
Potential Energy (Stored) Kinetic Energy (moving working energy) Entropy (S) amount of disorder always positive (increasing) Chemical Energy (Potential Energy) Examples; Hydrocarbons Octane + O2 Heat + Energy + CO2 + H2O (~30% efficiency) Fat + O2 Heat + Energy + CO2 + H2O (~40% efficiency) (Heat is a form of energy) Calorie 1 calorie = the heat to raise (1 ml) of H2O (1 degree) Celsius. 1 Calorie = 1 kilocalorie ATP - adenosine triphosphate Each phosphate group is negatively charged Crowding of negative charges gives ATP its potential energy Energy is released when last phosphate is released off of the triphosphatet tail creating ADP (adenosine diphosphate)

ATP and Cellular Work

ATP provides energy for three kinds of cell work: Mechanical Work Transport Work (transport molecules across plasma membrane) Chemical Work (making large molecules) ATP Cycle Renewable resource ATP ADP + Energy for Cell ADP + cellular respiration + P ATP metabolism - the tota of all the chemical reactions in an organism enzymes - protiens that speed up chemical reactions enzymes lower activation energy activation energy - energy required to trigger a chemical reaction; energy barrier Induced Fit substrate - enzymes ability to recognize a certain reactant molecule; the molecule that fits in the enzymes active site. (Lactose is the substrate of Lactase) active site - region of an enzyme that has the shape and chemistry that fits a substrate molecule induced fit - the change in shape of an enzyme slightly, making the fit between the substrate and the active site tighter. Enzymes functions repeatedly, accepting and releasing substrates more than once Many enzymes are named for their substrate with and -ase ending. (i.e. lactose and lactase) Enzyme Inhibitors - substrate impostors that plug up the active site of and enzyme, disrupting its function some inhibitors regulate metabolism penicillin and nerve gas are examples of enzyme inhibitors feedback regulation - keeps cell from wasting resources by using inhibitors

Enzymes

Membrane Function
Transport proteins - transport materials in and out of the cell, through the plasma membrane Membrane Protein Functions Cell signaling - binding cite of chemical messanger Attachment to cytoskeleton and extracellular matrix to help maintain shape Enzymatic activity - active sites that fit substrates; some proteins may team up to carry out steps of a pathway Transport - provide channel for a solute (integral protein) Intercellular joining - proteins that link adjacent cells (integral protein)

Cell recognition - proteins with chains of sugars serve as identification tags recognized by other cells. (peripheral protein) Diffusion - movement of molecules to spread out into available space passive transport - cell does not expend energy to transport materials with diffision facilitated diffusion - a type of passive transport concentration gradient - region where the density of a substance changes. Concentration represented with square brackets [ ] (i.e.concentration of hydrogen ions is [H+]. Osmosis and Water Balance osmosis - diffusion of water across a selectively permeable membrane hypertonic - side with higher concentration of solute hypotonic - side with lower concentration of solute (higher H2O concentration) Water moves from hypotonic side to hypertonic side. isotonic - equal concentration osmoregulation - regulation of water balance so to not burst (lysis) or dehydrate. plasmolysis - when the under hydrated plant cells plasma membrane pulls away from its cell wall Active Transport Active transport - pumping of molecules across membranes; this requires energy. Pumping a solute against its concentration gradient. Energy Source: ATP Exocytosis and Endocytosis - bulk shipment traffic of large molecules (macromolecules) macromolecules are too large to travel through the plasma membrane membrane forms sacs, packaging larger molecules into vesicles Exocytosis - transport vesicles inside cell fuse to plasma membrane, secreting proteins out of cell (like from Golgi) Endocytosis - reverse of exocytosis. Takes material into cell within vesicles that bud inward. 3 types: pinocytosis - (nonspecific) cellular drinking; gulping fluid droplets phangocytosis - (nonspecific) cellular eating; engulfs particle and forms food vacuole. receptor-mediated endocytosis - triggered by certain molecules (specific) binding to the outside of plasma membrane. (like in neurotransmitters) Cell signaling signal transduction pathway - passing a signal through relays that turn into chemical reactions. (i.e. - adrenaline triggers glycogen glucose without entering cell)

Chapter 6 - Cellular Respiration

Intro Marathon runners slow-twitch use O2 (aerobic) to make ATP Sprinters fast-twitch no O2 (anaerobic) to make ATP Energy Flow and Chemical Cycling Photosythesis - using light to build organic molecules Producers and Consumers Autotrophes - self-feeders, organisims that make their own orgainic matter (carbohydrates, lipids, protiens, & nucleic acids) from inorganic sources (CO2, H2O, minerals). (producers) Heterotrophs - other-feeders, organisims that cannot make organic molecules from inorganic ones. Eat organic material (consumers) Chemical Cycling Between Photosynthesis and Cellular Respiration photosynthesis needs CO2 and H2O chloroplasts use light energy to rearrange atoms to produce sugars (glucose C6H12O6) and other organic molecules byproduct is O2 Cellular respiration uses O2 and energy extracted from organic sources (like glucose) to make ATP production of ATP in plants and animals occurs mainly in organelles called mitochondria By product is CO2 and H2O, same as whats needed for photosynthesis.

Cellular Respiration: Aerobic Harvest of Food Energy

aerobic - requires oxygen The overall equation for cellular respiration C6H12O6 + 6 O2 6 CO2 + 6 H2O + ATP The main function of cellular respiration is to generate ATP One glucose molecule can produce up to 38 ATP molecules Cellular respiration transfers H atoms from glucose to O, forming H2O During cellular respiration, hydrogen and its bonding electrons change partners from sugar to oxygen, forming water as a byproduct redox reaction - oxidation-reduction reation oxidation - loss of electrons

Role of Oxygen in Cellular Respiration Redox Reactions

reduction - acceptance of electrons (reduce the amount of positive charge) Oxygen is reduced during cellular respiration, accepting election (and oxygen) lost from glucose C6H12O6 oxidation 6 CO2 6 O2 reduction 6 H2O When water is produced in a redox reaction, energy is released (potential chemical energy is released) First carrier of electrons is NAD+ (nicotinide adine dinucleotide) NAD+ is reduced to NADH NADH travels to the electron transport chain eventually forming H2O Each link in the electron transport chain is a molecule, usually a protein. Series of redox reaction first accepts then donates electrons Each transfer releases a small amount of energy used indirectly to form ATP NADH carries electrons from glucose (and other fuel molecules) and deposits them at the top of the electron transport chain electrons cascade down the chain, molecule to molecule. Molecule at the bottom drops the electrons to oxygen forming H2O. glucose NADH Electron transport chain H2O The stepwise release of chemical energy in the electron transport chain produces most of the ATP Oxygen, the electron grabber makes this all possible. Fuctions as gravity pulling object downhill.

NADH & Electron Transport Chain

1. 2. 3.

An overview of Cellular Respiration

1. Glycolysis - molecule of glucose is split into two molecules of pyruvic acid. Enzymes for glycolysis are located in the cytoplasm, outside the mitochondria 2. Citric Acid Cycle - Pyruvic acid enters mitochondria after being split by glycolysis. The Citric Acid Cycle completes the breakdown of glucose all the way down in to CO2 inside the mitochondria matrix. 3. Eletron Transport Chain - electrons are captured from food (glucose, pyruvic acid, etc.) by NADH formed in the first two stages fall down the Electron Transport Chain, to oxygen. Electron transport from NADH to oxygen releases the energy your cells use to make most of their ATP.

The Three Stages of Cellular Respiration

1. Glycolysis - splitting of sugar 1. 6-carbon glucose molecule is broken in half forming two 3-carbon molecules (Pyruvic acid) 2. The 3-carbon molecules donate electrons to NAD+ forming NADH 3. Glycolysis also makes 2 ATP molecules directly when enzymes transfer phosphate groups from fuel molecules to ADP and two pyruvic acid molecules. 2. Citric Acid Cycle - pyruvic acid from glycolysis is prepped for the Citric Acid Cycle forming acetic acid and then down to CO2. This process happens twice

per glucose molecule (2 Pyruvic acid molecules 2 ATP, 6 NADH, 2 FADH2) Preparation for Citric Acid Cycle 1. Pyruvic acid loses a carbon forming acetic acid and CO2 2. Oxidation forms NADH, (NAD+ take two electrons) 3. Acetic acid attaches to Co-enzyme A (CoA) to form acetyl CoA. CoA escorts acetic acid to the Citric Acid Cycle. 2. Acetic acid joins 4-carbon acceptor to form 6-carbon citric acid for every one acetic acid that enters the cycle as fuel 3. Two CO2 molecules exit as waste, citric acid cycle harvests energy from fuel. 4. Some energy is used to produce ATP directly. 5. NADH is formed 3 NADH 6. FADH2 is formed (flavenoid) 7. All carbons that enter as fuel are accounted for as CO2, and 4-carbon acceptor molecule is recycled 3. Electron Transport Chain - uses the energy released by the fall of electrons to pump H+ across the inner mitochondrial membrane, then [H+] gradient is used to produce ATP (square brackets are used to indicate concentration of a substance, here concentration gradient of H+ ions) 1. NADH transfers 2 electrons to an electron carrier in the first protein complex, pumping H+ from in the matrix across the inner mitochondrial membrane 2. FADH2 transfers electrons to a carrier that transfers H+ to the second protein complex. 3. Electrons fall through second protein complex pumping out more H+ ions across the inner mitochondrial membrane and a second carrier moves the electrons from the second protein complex to the third protein complex. 4. Oxygen pulls the electron down the chain out of the third protein complex, combining with H+ in matrix forming H2O, in the process pumping more H+ across the membrane as well. 5. All of the H+ stored on the outside of the inner wall falls downhill through the ATP synthase protein. This spins a component of the ATP synthase. 6. The rotation of the ATP synthase actives part of the synthase molecule that attach phophate groups to ADP molecules to generate ATP. ATP synthase produces most of a cells ATP in aerobic cellular respiration (~34 ATP produced)

The Versatility of Cellular Respiration

Cellular respiration can burn many different kinds of molecules, not just glucose. Adding up ATP form cellular repiration Glycolysis and Citric Acid Cycle each directly produce 2 ATP (Totalling 4 ATP)

ATP synthase produces the rest, to total up to 38 ATP molecules per glucose molecule.

Fermentation: Anaerobic Harvest of Food Energy

anaerobic - without oxygen fermentation - anaerobic process that cells use for short periods to produce energy Blood provides cells with O2 Anaerobic process occurs when body is burning ATP faster than it can deliver O2 for electron transport chain. Fermentation relies on glycolysis glycolysis does not require O2, and produces 2 ATP for every molecule broken down to pyruvic acid. Cells have to consume more glucose fuel per second, because less ATP per glucose is being generated NAD+ must be present as an electron acceptor in aerobic conditions, NAD+ regenerates when NADH drops electron cargo down electron transport chain In Anaerobic conditions, NADH disposes electrons by adding them to pyruvic acid producing a waste product lactic acid. lactic acid is transported to liver 2 ATP per glucose is enough energy to sustain many micoorganisms sharp flavors (like in cheese) are due to lactic acid Yeast is capable of both cellular respiration and fermentation when forced to be anaerobic, they are forced to fermentation, producing ethyl alcohol instead of lactic acid. (as well as CO2) Human heart can use lactic acid as fuel.

Fermentation in Human Muscle Cells

Fermentation in Microorganisms

Chapter 7 - Photosynthesis: Using Light to Make Food

Intro biomass - living material biofuels - fuel from living material

The Basics of Photosynthesis

Photosynthesis - a process by which plants, algae (protists), and certain bacteria transform light energy in to chemical energy. Autotrophs Chloroplasts - light absorbing organelles Chlorophyll - Light absorbing pigment the chloroplasts (often green) that plays a central role in converting solar energy to chemical energy chloroplasts are concentrated on the interior of cells of leaves Stomata - where CO2 enters the O2 exits; tiny pores H2O absorbed by plants roots chloroplasts have double membrane like mitochondria Stroma - thick fluid that fills the inner membrane of chloroplasts Thylakoids - interconnected membrane sacs suspended in stroma Grana - concentrated stacks of thylakoids. chlorophyll molecules are built into the thylakoid membranes 6 CO2 + 6 H2O + Light Energy C6H12O6 + 6 O2 Photosynthesis take exhaust from cellular respiration Electrons are boosted and added to CO2 to produce sugar Hydrogen moved with electrons to H2O and CO2 in a redox reaction chloroplasts must split H2O to perform this reaction Photosynthesis happens in 2 stages: Light Reaction and Calvin Cycle Light reaction - chlorophyll in the thylakoid membrane absorbs solar energy, which is then converted to the chemical energy of ATP and NADPH NADPH - electron carrier light drives electrons from H2O to NADP+ (oxidized form of carrier) to form NADPH (reduced form of carrier) H2O is split providing source of electrons and O2 is released Calvin Cycle - uses products of light reaction to produce sugar from O2 enzymes for Calvin Cycle stored in stroma ATP provides energy for sythesis of sugar NADPH provides electrons for reduction of CO2 to sugar (glucose)

Chloroplasts: Sites of Photosynthesis

The Overall Equation of Photosynthesis

A Photosynthesis Road Map

The Light Reactions: Converting Solar Energy to Chemical Energy

The Nature of Sunlight
radiation energy Wave and Particle energy wavelength - distance between crests of 2 adjacent waves electromagnetic spectrum - full range of radiation. Gamma rays to radio waves,

visible light is a very small fraction of this spectrum The wavelengths not absorbed are reflected green is poorly absorbed by chloroplasts and is reflected and transmitted toward the observer Chlorophyll-a - absorbs mainly blue-violet and red light; participates directly in light reactions Carotenoids - absorbs blue-green light some energy is passed to chlorophyll-a carotenoids protect by absorbing and dissipating excessive light that could damage chlorophyll Carrots, fall colors Chlorophyll-b - absorbs blue and orange. particle light Photons - fixed quatities of light energy shorter the wavelength of light, the greater the energy of photon photon of violet is nearly twice the energy of red photon When pigment molecule absorbs a photon, the pigments electrons gain energy to an excited state (higher orbital), which is highly unstable. Electron falls back to ground state almost immediately releasing heat and sometimes light (floresence). In photosystems, this excited electron is grabbed instead of falling back down. Photosystem - a cluster of a few hundred pigment molecules (chlorophyll-a, chlorophyll-b, and carotenoids) photosystems function as a light gathering antennae. Reaction center - a chlorophyll-a molecule that sits next to a primary electron acceptor Primary Electron Acceptor - traps light-excited electron from chlorophyll-a in the reaction center

Chloroplast Pigments

How Photosystems Harvest Light Energy

How the Light Reactions Generate ATP and NADPH

1. Photons excite electrons in chlorophyll of water-splitting photosystem. Electrons are trapped by primary electron acceptor. The H2O splitting photosystem replaces its light-excited electrons by extracting the electrons form H2O. O2 is released 2. Energized electrons from H2O splitting photosystem pass down an electron transport chain to the NADPH-producing photosystem. The chloroplast uses the energy released by this electron fall to make ATP. 3. The NADPH-producing photosystem transfers its light-excited electrons to NADP+, reducing it to NADPH ATP production is very similar to cellular respiration, using [H+] gradient to power ATP synthase in thykaloid membrane

The Calvin Cycle: Making Sugar from Carbon Dioxide

Sugar factory within stroma of cholorplasts. Uses ATP and NADPH Like Citric Acid Cycle, starting material is regenerated (3-carbon sugar) CO2 + ATP + NADPH G3P G3P - glyceraldehyde 3-phosphate G3P is raw material to make glucose and other organic compounds (cellulose, starch, etc.) CO2 (from air) is added to RuBP (5-carbon sugar) ATP & NADPH form two 3-carbon sugars ( ADP and NADP+ for electron transport chain) Every three CO2 molecules added makes one 3-carbon (G3P) sugar to use (two 3-carbon molecules makes one glucose) One extra G3P from Calvin cycle is taken to make glucose and other molecules, the rest is recycled into the Calvin Cycle. C3 Plants - plants that use CO2 directly When weather is hot, stomata close holding in H2O but also do not allow CO2 in, halting sugar production C4 Plants or CAM plants - use alternative modes of incorporating carbon (shuttle cells) from CO2 to allow them to save water without giving up sugar production. (sugarcane and corn (C4), pineapple and cacti (CAM))

Solar Driven Evolution

Chapter 8 - Cellular Reproduction: Cells from Cells (Part A)

What Cell Reproduction Accomplishes
Cell Division - two daughter cells that are genetically identical chromosomes - structures that contain most of an organisms DNA. Daughter cells receive identical sets of chromosomes Millions of cells must divide every second to replace damaged or lost cells in ones body Cell division is also vital for reproduction of an organism Asexual Reproduction - does not involve fertilization of and egg by sperm. Reproduce by dividing in half and offspring are genetic replicas of the parent, inheriting all of their chromosomes from a single parent Mitosis - the type of cell division that is responsible for asexual reproduction and the growth and maintenance of multicellular organisms Sexual Reproduction - requires fertilization of an egg by sperm Meiosis - special type of cell division which occures on in reproductive organs (such as

testes and ovaries in humans)

Sexual organisms require both mitosis for growth and development and meiosis for reproduction

The Cell Cycle and Mitosis

Almost all Genes of a eukayotic cell - around 21,000 in humans - are located in the chromosomes in the cell nucleus. Each eukaryotic chromosome contains on very long DNA molecule, typically bearing thousands of genes Chromatin - combination of DNA and protein molecules that make chromosomes protein molecules help organize the chromatin and help the activity of genes Most of the time, the chromosomes exist as a diffuse mass of fibers that are much longer that the nucleus they are stored in. Stretched out, DNA would be longer than a person As a cell prepares toe divide, its chromatin fiber coil up, forming compact chromosomes. When the cells are not dividing chromosomes are too thin to be seen with a Light Micrograph Histones - found only in eukaryotes, small proteins that help DNA pack into small packages Nucleosome - small beads of DNA wrapped around histones; appear as small beads on a string in an electron micrograph When preparing to divide, the beaded string packs into a tight helical fiber, this fiber coils further into a thick supercoil Looping and folding further compact DNA Before cell begins division process, the DNA molecules of each chromosome is copied through a process call DNA replication producing 2 copies call sister chromatids Centromere - the narrow waist where two sister chromatids are joined. Once seperated from its sister, each chromatid is considered a full fledged chromasome Cell cycle - the ordered sequence of events that extends from the time a cell is first formed from a dividing parent cell until it own division into two cells Interphase - most of the cell cycle; the time when a cell performs its normal functions within the organism. Lasts at least 90% of cell cycle. During interphase, a cell roughly doubles everything in its cytoplasm. It increases supply of proteins, organelles (such as mitochondria and ribosomes), and grows in size. From the standpoint of cell reproduction, the most important event of interphase is chromosome duplication

Eukaryotic Chromosomes

The Cell Cycle

G1 phase - (G for gap) occures before S phase S phase - (S for DNA synthesis) approximately in the middle of the interphase, this is the phase when chromosomes duplication occures G2 phase - occurs after S phase, cell is preparing to divide. M phase - (Mitotic Phase) part of the cell cycle when the cell actually dividing Includes two overlapping processes: mitosis and cytokinesis Cytokinesis - cytoplasm is divided in two. Begins before mitosis is completed Combination of mitosis and cytokinesis produces 2 genetically identical daughter cells, each with its own nucleus, organelles, cytoplasm, and plasma membrane. Mitosis is a continuum divided into 4 main stages (P.M.A.T.): 1. Prophase - chromatin fibers coil and appear as two identical chromatids joined at the centromere. Mitotic spindle begins to form mitotic spindle - football shaped structure of microtubles that guides the separation of the two sets of daughter chromatids. Microtubles connect to proteins located at the centromere. 2. Metaphase - mitotic spindle fully formed and centromeres line up on imaginary plate 3. Anaphase - When sister chromatids separate. Each considered a full fledged (daughter) chromosome. 4. Telephase and Cytokinesis - 2 groups of chromosomes have reached opposite ends of cell. Telephase opposite of prophase, nuclear envelopes form and chromosomes uncoil. cleavage furrow - indentation at equator of cell. A ring of microfillaments in the cytoplasm contracts just under the plasma membrane. Used in cytokinesis of animal cells. cell plate - the beginning of a new cell wall. Used in cytokinesis of plant cells. Transport vesicles bring material to make cell wall to equator of cell and release material. The material forms together to produce a cell plate.

Mitosis and Cytokinesis

Cancer Cells: Growing out of control

Cell cycle control system - system of specialized protiens that integrate information form the environment and form other body cells and sent STOP and go-ahead signals at certain key points during the cell cycle using transduction pathways Muscle and brains cells never receive signal to go beyond G1. Disease of cell cycle Cells divide excessively and can invade other tissues Cell is transformed because of genetic change (mutation) in one of more genes

What is Cancer?

that encode proteins in the cell cycle control system Tumor - if bodys immune system fails to destroy the cell. (All it takes is one cell) Benign Tumor - if the abnormal cells remain at the original site. Usually can be completely removed by surgery Malignant Tumor - a tumor can spread to neighboring tissues and other parts of the body through blood stream. Cancer - a disease of an individual with a malignant tumor. Slash, burn, and poison Remove tumor slash Radiation Therapy - burn side effects nausea, hair loss. Chemotherapy - drugs that disrupt dell division poison paclitaxil - from the Pacific Yew tree Metastasis - The spread of cancer cells beyond their original site. Not smoking Excercise High-fiber diet Low fat diet

Cancer Treatment

Cancer Prevention and Survival

Chapter 10: The Structure and Function of DNA

Intro flu vaccine influenza virus virus - nucleic acid and protien

DNA: Structure and Replication

molecular biology - study of heredity at the molecular level. Discovery of DNA led to a race to discover how the structure of this molecule could account for its role in heredity DNA and RNA are nucleic acids Nucleotides - monomers of DNA

DNA and RNA Structure

Polynucleoties - nucleotide polymer polynucleotides tend to be very long and can have any sequence of nucleotides, so a large number of polynucleotide chains are possible nucleotides are joined together by covalent bonds between the sugar of one nucleotide and the phosphate of another nucleotide Sugar-phosphate backbone - repeating pattern of sugar - phosophate - sugar phosphate that form the backbone of polynucleotides nitrogenous bases are arranged like ribs that project from the backbone. Each nucleotide has three components: a. Phosphate group - with phosphorus atom at center, the source of the acid in nucleic acid b. Sugar - 5 carbon atoms, 4 in its ring and one extending above the ring. (Deoxyribose is missing an oxygen atom that ribose has) c. Nitrogenous base - Thymine [T], Cytosine [C], Adenine [A], and Guanine [G]. T and C are single ring structures, and A and G are larger double ring structures. RNA had Uracil [U] instead of Thymine [T], and a different sugar call ribose. Cambridge University, x-ray crystallography X-ray image taken by Rosalind Franklin Watson concludes x-ray image reveals a double helix Double helix - spiral shape made of two strands, in DNA the two strands are polynucleotide strands Specific base pairing - four kinds of nitrogenous bases pair in a specific way Each base has chemical side groups that can best form hydrogen bonds wit hone appropriate partner Adenine [A] with Thymine [T] Guanine [G] with Cytocine [C] (At The Grocery Ctore, A-T G-C) Double helix looks like a twisted rope ladder No restriction on the sequence of nucleotides along the length of the DNA Watson and Cricks discovery published in Nature scientific journal in 1953 Watson, Crick, and Wilkins received Noble Prize in 1962, (Franklin died of cancer) Watson and Crick suggest that DNAs structure serves as a mold, or template, to guide reproduction of another strand If one knows the sequence of the nitrogenous bases on one strand of the double helix, on can very easily determine the sequence of the nitrogenous bases in the other strand by applying base pairing rules Enzymes link the nucleotides to form the new DNA strands (2 from 1) DNA replication is complex and requires the cooperation of more that a dozen enzymes and other proteins

Watson and Cricks Discovery of the Double Helix

DNA Replication

DNA polymerase - enzymes that make the covalent bonds between the nucleotides of a new DNA strand. The process is both fast and amazingly accurate, DNA replication proceeds at 50 nucleotides per second, with fewer then one in a billion incorrectly paired DNA polymerase and some of hte associated proteins are also involved in repairing damaged DNA DNA can be harmed by toxic chemicals and by high-energy radiation Origins of replication - specific sites on a double helix where DNA replication begins DNA replication DNA replication proceeds in both directions, creating bubbles Parental DNA opens up (bubbles get bigger) as daughter strands elongate Eukaryotic DNA has many origins where replication can start simultaneously, shortening total time of process Bubbles merge, yielding two completed double-stranded daughter DNA molecules DNA replication ensures that all the bodys cells in a multicellular organism can carry the same genetic information It is also the means by which genetic information is passed along to offspring

The Flow of Genetic Information from DNA to RNA to Protein

How an Organisms Genotype Determines Its Phenotype
Genotype - an organisms genetic makeup; the sequence of nucleotide bases in its DNA. Phenotype - an organisms physical traits that arise from the actions of a wide variety of proteins. Indirectly, DNA carries instructions to build proteins central dogma [Francis Crick] - chain of command: DNA RNA Protein Transcription - the transfer of genetic information from DNA to RNA molecules Translation - the transfer of information from RNA into a protein Relationship between genes and proteins first proposed by Archibad Garrod in 1909 George Beadle and Edward Tatum in the 1940s, from bread mold, make a breakthrough and show individual genes dictate the production of specific enzymes The function of a gene is to dictate the production of a polypeptide (polypeptide - amino acid polymer linked by peptide bonds) When a segment of DNA is transcribed, the result is an RNA molecule

From Nucleotides to Amino Acids: An Overview

transcription - is called so because the nucleic acid language of DNA has simply been rewritten (transcribed) a sequence of bases of RNA; the language is still that of nucleic acid. RNA is synthesized using the DNA as a template translation - is the conversion of the nucleic acid laguage to the polypeptide language polypeptides are the polymers chains consisting of 20 different amino acid monomers the sequence of the nucleotides of the RNA molecule dictates the sequence of amino acids of the polypeptide triplets of bases are the smallest words (codons) of uniform length that specify all the individual amino acids 64 possible code words (43); enough triplets to allow more that one coding fro each of the 20 amino acids. codons - the 3-base words of nucleic acid chains 1 DNA codon (3 nucleotides) 1 RNA codon (3 nucleotides) one amino acid Genetic code - set of rules relating to nucleotide sequence to amino acid sequence AUG sequence of amino acids in RNA has dual function; amino acid methionine (Met) and signal for the start of the polypeptide chain. Three codons, UAA, UAG, and UGA, do not designate amino acids and function as stop codons The nucleotides making up the codons occur in a linear order in the DNA and RNA, with no gaps separating the codons Almost all the genetic code is shared by all organism, from the simplest of bacteria to the most complex plants and animals. Because diverse organisms share a common genetic code, it is possible to program one species to produce a protein from another species by transplanting DNA. (like transplanting the instructions for the production of GFP, green florescent protein, from jelly fish to mice to make glowing mice) RNA polymerase - transcription enzyme that lin RNA nucleotides Three steps: 1. Intiation of Transcription - the attachment of RNA polymerase to promoter and the start of RNA synthesis promoter - a nucleotide sequence that provides the start transcribing signal, a specific place where DNA polymerase attaches promoter dictates which of the two DNA strands is to be transcribed RNA Elongation - RNA grows longer 2. RNA synthesis continues, RNA strand peels away from DNA

The Genetic Code

Transcription: From DNA to RNA

template, allowing DNA strands to come back together within the RNA polymerase Termination of Transcription - sythesis stops 3. terminator - special sequence of bases in DNA template that signals the end of the gene RNA polymerase molecule detaches from the RNA molecule and the gene (section of DNA molecule), and DNA molecule strands rejoin. 2 other types of RNA are also produced on top of the amino acid sequence that are involved in building polypeptides Capping, tailing and splicing Eukaryotic, unlike prokaryotic cells, modifies (or processes) RNA transcripts before they move out to the cytoplasm Cap and tail - additions that protect the RNA form attack by cellular enzymes and help enzymes recognize RNA as mRNA (messenger RNA) Introns - non-coding sections of nucleotides randomly interspersed in RNA between exons which are removed before mRNA enters cytoplasm. Exons - parts of the genes that are expressed. RNA splicing - the process of joining exons and clipping out introns. RNA splicing is believed to play a significant role in human cells by allowing our approximately 25,000 genes to produce many thousands more polypeptides by varying the exons that are included in the final mRNA Translation is the divided into the same three phases as transcription, Initiation, Elongation, and Termination. 1. Initiation - bringing together mRNA, the first amino acid with its tRNA, and the two subunits of a ribosome i. An mRNA molecule attaches to a small ribosomal subunit. A special tRNA initiator binds to the start codon (AUG or methionine) with anticodon UAC ii. A large ribosomal subunit binds to the small ribosomal subunit, creating a functional ribosome. The initiator tRNA fits into the P site on the ribosome 2. Elongation - amino acids are added one by one to the first amino acid in a three-step process i. Codon recognition - anticodon of an incoming tRNA molecule, carrying its amino acid, pairs with the mRNA codon in the A site of the ribosome. ii. Peptide bond formation - the polypeptide leaves the tRNA in the P site and attaches tothe amino acid on the tRNA in the A site. Ribosome catalyzes bond formation and the chain has one more amino acid.

Processing of Eukaryotic RNA

Translation: The Process

iii. Translocation - the tRNA in the P site leaves the ribosome, and the remaining tRNA in the A site, carrying the growing polypeptide, moves to the P site and process is cycled back to step (2.i), codon recognition. 3. Termination - elongation continues unit a stop codon is reached (UAA, UAG, and UGA) in the ribosomes A site. The completed polypeptide, typically several hundred amino acids long, is freed, and the ribosome splits into its subunits.

Review: DNA

RNA

Protein

In eukaryotic cells, transcription occurs in the nucleus, and RNA is processed before it enters the cytoplasm Translation is rapid; a single ribosome can make an average sized polypeptide in less than a minute As the polypeptide is being made it coils into its 3-dimentional tertiary structure. Several polypeptides may come together forming a protein with a quaternary structure. The overall significance of transcription and translation is that transcription are processes whereby genes control the structure and the activities of cells - or more broadly, the way a genotype produces the phenotype. Genes in DNA dictates complementary sequence of nucleotides in the mRNA (transcription) mRNA specifies the linear sequence of amino acids in a polypeptide (translation) these polypeptides determine the appearance and capabilities ofthe cell and organism Mutation - any change in the nucleotide sequence of DNA Occasionally, a base substitution leads to an improved protien or one with new capabilities that enhance the success of the mutant organism and itd decendants Types of Mutations: Base substitution, Deletions, and Insertions 1. Base substitution - replacement of one base, or nucleotide, by another. this can result in no change in the protein (base redundancy), and insignificant change, or a change that might be crucial to the life of the organism. silent mutation - base substitution results in a base redundancy and no change in protein product. missence mutation - when changes of a single nucleotide do change the amino acid coding, but have little or no effect on the shape or function of the resulting protein. nonsence mutation - base substitution that results in a change of an amino acid codon into a stop codon, resulting protein is incomplete Nucleotide Deletion - when a nucleotide is deleted, all codons from that 2. point on (downstream) are misread. Resulting polypeptide is likely to be

Mutations

completely nonfuntional. 3. Nucleotide Insertions - When a nucleotide is inserted. Disrupts all codons that follow (downstream), most likely producing a nonfuntional polypeptide

Mutagens
Mutagens - physical and chemical agents that are sources of mutations Most common mutagen is high-energy radiation such as x-rays and UV light Chemical mutagens are various types, some are similar to normal DNA bases which cause incorrect base pairing when incorperated into DNA. Many mutagens act as carcinogens, agents that cause cancer. Although mutations are often harmful, they can also be extremely useful in nature and in the labratory Mutations are one source of the rich diversity of genes in the living world, a diversity that makes evolution by natural selection possible. Mutations are responsible for the different alleles (an alternative version of a gene) needed for genetic research.

Viruses and Other Noncellular Infectious Agents

Viruses are not considered alive because it is not cellular and cannot reproduce on its own. virus - nucleic acid molecule wrapped in a protein coat. genes in a box viruses survive only by infecting a living cell with genetic material that direct the cells molecular machinery to make more viruses. Bacteriophages - viruses that attack bacteria. bacteria - eaters, phages for short T4 virus infects e. coli, head made of DNA enclosed in an elaborate protein structure, tail, a hollow structure enclosed in a springlike sheath, and tail fibers which are the legs that bend and touch the cell surface. Lytic cycle - after many copies of the phage are produced, the bacterium lyses releasing phages. Reproductive cycle for most bacteriophages Lysogenic cycle - viral DNA replication occurs without phage production or death of the host cell 1. Viral DNA, prophage (viral DNA in host DNA) is inserted into bacterial chromosome 2. Host cell replicates, reproducing the prophage DNA with the cellular DNA. A single infected bacterium can quickly give rise to a large population of bacteria that all carry prophages. 3. Something, like an environmental change, triggers the release of the prophages from the bacterial chromosome, and switches to the lytic cycle. Diphtheria (upper respiratory tract illness), botulism, and scarlet fever

Bacteriophages

would be harmless to humans if it were not for the prophage genes they carry.

Plant Viruses
Most plant viruses have RNA rather than DNA as their genetic material. Viruses must get past the outer protective of plants, which makes plants damaged by wind, chilling, injury or insects more susceptible to infection that a healthy plant No cure for most viral plant diseases. influenza virus is an example of an animal virus Outer envelope made of phospholipid membrane that allow virus to enter and leave a cell. Projecting protein spikes Many animal viruses have RNA as their genetic material (common cold, measels, mumps, HIV, and polio are all RNA viruses) RNA virus reproduction 1. Protein spikes attach to receptor proteins on the cells plasma membrane and the viral membrane fuses with the cells membrane allowing protein coated RNA to enter the cytoplasm 2. Enzymes remove protein coat. 3. An enzyme that entered the cell as part of the virus, uses the viruss RNA genome as a template for making complementary strands of RNA which have two purposes (4 & 5) 4. mRNA for synthesis of proteins 5. Templates for new viral genome DNA 6. The new coat of proteins assemble around the new viral RNA 7. Virus leave the cell by cloaking themselves in the plasma membrane DNA viruses include hepatitis, chicken pox, and herpes. Herpesvirus (chickenpox, shingles, cold sores, and genital herpes) enveloped DNA viruses that reproduce in the cells nucleus, rather than the cytoplasm. Herpesvirus get envelopes from nuclear membrane, rather than plasma membrane. Copies of herpevirus DNA usually remain behind as mini-chromosomes in the nuclei of certain nerve cells, and remain latent until they are triggered (by stress, or sunburn, or catching a cold, etc.) Over 75% of American adults are the thought to carry herpes simplex 1 (cold sores), and over 20% carry herpes simplex 2 (genital herpes). Viruses that attack non replaceable tissue (like nerve cell poliovirus) are not easy to recover fully from. AIDS - Acquired Immuno-Deficiency Syndrome HIV - Human Immuno-deficiency Virus, a type of RNA virus which resembles the influenza and mumps virus, but is a retrovirus

Animal Viruses

HIV, The AIDS Virus

Retrovirus - An RNA virus that reproduces by means of DNA molecule. Reverse to the usual DNA RNA synthesis. Retroviruses use reverse transcriptase. Reverse transcriptase - an enzyme carried by the virus and catalyzes reverse transcription, the synthesis of DNA on a RNA template. After the RNA of HIV is uncoated: 1. Reverse transcriptase uses the viral RNA as a template to make a DNA strand 2. Adds a secondary DNA strand. 3. The double-stranded viral DNA enters the cell nucleus and inserts itself into the cells chromosomal DNA, becoming a provirus. 4. Occasionally the provirus is transcribed into RNA 5. Occasionally this mRNA is translated into viral protiens 6. Transcribed viral RNA and translated viral proteins, both from inserted provirus, combine and leave the cell and can then infect other cells. HIV infects and eventually kills several kinds of white blood cells that are important to bodies immune system. Due to the damaged immune system, body is susceptible to other infections that cause the syndrome (a collection of symptoms) tha eventually kills the AIDS patients. HIV was first recognized before 1981 Two types of HIV drugs, one that inhibits the action of the enzymes called proteases, which help produce final versions of HIV proteins, and a second type which inhibits reverse transcriptase enzyme of HIV (AZT) Because AIDS has no cure yet, prevention is the only healthy option. Very small pathogens, smaller than viruses Viroids - small circular RNA molecules that infect plants and duplicate themselves without encoding proteins. Viroids seem to cause disease by interfering with the regulatory systems that control plant growth. Prions - infectious proteins, which somehow convert normal proteins which are normally present in brain cells, into a misfolded prion version. Responsible for mad-cow disease and Creutzfeldt-Jakab disease. Emerging Viruses - viruses that have appeared suddenly or have recently come to the attention of medical scientists Avian flu - if this virus evolves so that it can spread easily from person to person, the potential for outbreak is significant RNA viruses tend to have unusually high rates of mutation because errors in the replicating their RNA genomes are not subject to certain proof reading mechanisms Mutations enable viruses to evolve into new strains that can cause disease in individuals who have developed resistance to ancestral virus (need for yearly flu vaccines)

Viroids and Prions

Emerging Viruses

Joshua Lederberg: We Live in evolutionary competition with microbes. There is no guarantee that we will be the survivors.

Chapter 8 - Cellular Reproduction: Cells from Cells (Part B)

Homologous Chromosomes
Individuals of the same sex and species have the same number and types of chromosomes Somatic cell - a typical body cell. (in humans, 46 chromosomes, diploid) Karyotype - a display of the stained chromosomes during metaphase on mitosis, where chromosomes are arranged in matching pairs. Homologous chromosomes - two chromosomes of a matching pair; genes controlling the same inherited characteristics. Nearly identical chromosomes, each of which consists of two identical sister chromatids after chromosome duplication. Females, the chromosomes of each pair are essentially identical Males, the chromosome of one pair do not look alike (single pair of sex chromosomes). Sex chromosomes - chromosomes that determine a persons sex. Males are XY; females are XX. Autosomes - All the chromosomes excluding the pair of sex chromosomes.

Gametes and the Life Cycle of a Sexual Organism

Life cycle - the sequence of stages leading from the adults (of a multicellular organism) of one generation, to the adults of the next generation. Diploid - cells which contain pairs of homologous chromosomes. Diploid organisms include humans and many other animals and plants. Diploid number is represented by 2n. Gametes - cells which only have a single set of chromosomes (n). Produced by testis or ovary by the process of meiosis. 22 autosomes plus an X or Y sex chromosome. (haploid) Haploid - a cell with a single chromosome set; only has one member of each homologous pair. Haploid number = n. (Humans, n = 23) Fertilization - In human life cycle, a haploid sperm cell from father fuses with a haploid egg cell from mother. Zygote - the diploid resulting from the fertilized egg, with two sets of homologous chromosomes, one set from each parent. Life cycle is completed as a sexually mature adult develops from the zygote.

Mitotic cell division ensures that all somatic cells of the human body receive a copy of the zygotes 46 chromosomes. All trillions of cells in the body can be traced back to the single zygote produced by fertilization. All sexual life cycles involve alteration of diploid and haploid stages. Producing haploid gametes by meiosis keeps chromosome number from doubling every generation Overview of Meiosis: 1. Each of the chromosomes is duplicated during interphase (before mitosis) 2. Meiosis I, the first division segregates two chromosomes from a homologous pair, packaging them in separate haploid daughter cells. (Each chromosome is still doubled) 3. Meiosis II, sister chromatids separate, producing 4 haploid daughter cells, containing one single chromosome from a homologous pair.

The Process of Meiosis

Meiosis - the process that produces haploid daughter cells in diploid organisms. Has two special features. (Lecture: 3 special features) 1. Number of chromosomes is reduced to half. 2. Exchange of genetic material between homologous chromsomes, crossing over crossing over occurs during the first Prophase (meiosis I) 3. Sister chromatid pairs move toward poles in Anaphase I Two consecutive divisions, meiosis I and meiosis II, where duplication of chromosomes is followed by two divisions, resulting in 4 haploid daughter cells ! - Keep in mind the difference between homologous chromosomes and sister chromatids. chromosomes duplicate producing two identical sister chromatids.

Interphase Meiosis I: Homologous Chromosomes Seperate

1. Prophase I - As chromosomes coil up, special proteins cause the homologous chromosomes to stick together in pairs. Homologous chromosomes cross over or exchange corresponding segments. Spindle forms. 2. Metaphase I - Homologous pairs are aligned in the middle of the cell. The sister chromatids of each chromosome are still attached at their centromeres, where the spindle microtubles are anchored. 3. Anaphase I - The attachment between the homologous chromosomes of each pair breaks and the chromosomes migrate toward the poles of the cell, separated not from each other, but from their homologous partners (in mitosis, the sister chromatids separate). 4. Telophase I & Cytokinesis - Chromosomes arrive at poles of the cell, each pole now has haploid chromosome set (each chromosome is still in duplicate form). Cytokinesis occurs and two daughter cells are formed.

Meiosis II: Sister Chromatids Separate

1. 2. 3. 4. Essentially the same as mitosis, except meiosis II starts with haploid cells that has not undergone duplication. Prophase II - Spindle forms and moves chromosomes to middle of cell Metaphase II - chromosomes are aligned with microtubles attached to sister chromatids of each chromosome. Anaphase II - centromeres of sister chromatids separate, and sister chromatids of each pair migrate to opposite pols of cell. Telophase II & cytokinesis - nuclei form at cell poles, and cytokinesis occurs, yielding 4 daughter cells, each with haploid number (n) of single chromosomes.

Review: Comparing Mitosis to Meiosis

Mitosis provides for growth, tissue repair, and asexual reproduction; produces daughter dells that are genetically identical to parent cell Meiosis is needed for sexual reproduction, yields genetically unique haploid daughter cells 2 special features (Lecture: 3 special features) 1. Chromosomes reduced by half 2. Exchange of genetic material crossing over 3. Sister chromatid pairs move toward poles in anaphase I For both mitosis and meiosis, chromosomes duplicate only once in the preceding Interphase. Mitosis involves two nuclear and cytoplasmic divisions, yielding 4 haploid cells. All the events unique to meiosis occur in meiosis I Meiosis II virtually identical to mitosis, but meiosis II yields haploid daughter cells.

The Origins of Genetic Variation

Another look at meiosis The arrangement of homologous chromosomes varies. The side-by-side orientation of each homologous pair of chromosomes (two sister chromatids) is a matter of chance Every chromosome pair randomly orients its homologous chromosomes independently of all others at metaphase I. Total number of chromosome combinations that can appear in gametes is 2n. In humans n=23, resulting in about 8 million, or combinations. possible chromosome

Independent Assortment of Chromosomes

Random Fertilization
Fertilization requires two gamete (haploid) cells to fuse, resulting in trillion combinations of chromosomes between two

parents without accounting for crossing over.

Crossing Over
Crossing over - the exchange of corresponding segments between chromatids of homologous chromosome pairs during prophase I of meiosis. Chiama - (plural: chiasmata) sites of crossing over. Homologous chromatids remain attached to each other at the chiasma until anaphase I. The exchange of segments between nonsister chromatids - one maternal (mother) chromatid and one paternal (father) chromatid of a homologous pair adds to the genetic variety resulting from sexual reproduction. Genetic recombination - gametes that have chromosomes that are part maternal and part paternal due to crossing over, called recombinant chromosomes.

When Meiosis Goes Awry

Mistakes that occur during meiosis can result in genetic abnormalities that range from mild to severe to fatal. Nondisjunction - when the members of a chromosome pair fail to separate at anaphase. Nondisjuntions result in gametes with abnormal numbers of chromosomes. Nondisjuctions can occur in meiosis I or meiosis II. Meiosis I - pair of homologous chromosomes fail to separate in anaphase I (nondisjuction), resulting in incorrect number of chromosomes in haploid cells at the beginning of meiosis II that results in 4 abnormal gametes. Meiosis II - nondisjunction of a pair of sister chromatids that occurs during anaphase II that results in 2 abnormal gametes and 2 healthy gametes. Trisomy 21 - three number 21 chromosomes, yeilding 47 chromsomes in total. In most cases, a human embryo with an atypical number of chromosomes develops so abnormally that it is spontaneously aborted (miscarried) long before birth. Some aberrations in chromosomes number results in individuals that do survive, but individuals have a character set of symptoms call a syndrome. Down syndrome - an individual with trisomy 21. Affects about 1 out of every 700 children. Trisomy 21, or down syndrome, is the most common serious birth defect in the U.S. Characteristic facial features include fold at the inner corner of eye, a round face, and flattened nose Short stature, heart defects, susceptibility to leukemia and Alzheimers, short life span, and mental retardation.

How Accidents During Meiosis Can Alter Chromosome Number

Down Syndrome: An Extra Chromosome 21

Some live to middle age years and function well within society Incidence of down syndrome has a positive correlation with the age of the mother. (personal note: appears to be exponential increase after age 35). Nondisjunctions affect autosomes (like chromosome 21) as well as sex chromosomes (X and Y) Unusual numbers of sex chromosomes seem to not upset the genetic balance as much as autosomes. Some possible reasons as to why sex chromosomes are more forgiving are that Y chromosomes carry a small amount of information, and mammalian cells normally operate with only one functioning X chromosome because other copies become inactivated in each cell. Klinefelters syndrome - XXY, have male sex organs and normal intelligence, but the testes are abnormally small, the individual is sterile, and often has breast enlargement and other feminine body contours. Can occur with multiple nondisjunctions (more than 3 sex chromosomes XXYY, XXXY, and XXXXY) XYY, tend to be taller than average, no syndrome XXX, cannot be distinguished from XX females Turners Syndrome - XO, absence of second sex chromosome which results in women with short stature, web skin between head and shoulders, sex organs do not fully mature as adolescence, poor development of breasts and secondary sex characteristics. Normal intelligence. Only known case where having 45 chromosomes is not fatal. A single Y chromosome is enough to produce maleness, regardless to the number of X chromosomes. Absence of Y results in femaleness Syndrome Klinefelter (male) None (male) None (female) Turners (female) Origin Meiosis egg or sperm Meiosis in sperm Meiosis in egg or sperm Meiosis in egg or sperm Frequency 1/2000 1/2000 1/1000 1/5000

Abnormal Numbers of Sex Chromosomes

Sex Chromosome XXY XYY XXX XO

Advantages of Sex
Sex must enhance evolutionary fitness Varied genetic makeup, quickening adaptation to changing environment Shuffling of genes might allow a population to rid itself of harmful genes more rapidly. Sex is awesome.

Chapter 9 - Patterns of Inheritance

Intro Dog breeding Explain inborn traits through genetics. Generations of inbreeding can bring about serious genetic defects Certain breeds have behavioral tendencies like herding in boarder collies and sheep dogs

Heritable Variation and Patterns of Inheritance

Heredity - the transmission of traits from one generation to the next Genetics - the scientific study of heredity Gregor Mandel, an Augustinian monk, deduced its fundamental principles by breeding garden peas, and applying the scientific method and mathematics. He published his findings in 1866, only seven years after Darwins The Origin of Species. Mendel stressed that the heritable factors (today called genes) retain their individual identities generation after generation, regardless to how they are mixed up or temporary masked. Mendels experimental model is a pea plant because reproduction can be highly controlled. (Also easily observable traits, many offspring, short life cycle [gap between generations is very short]) Charachter - a heritable feature that varies among individuals; flower color, seed shape, etc. Trait - a variant of a character; purple or white flower color, wrinkled or round seed shape, etc. Mendel manipulated the reproduction of pea plants by controlling pollination patterns, with known pollen sources. Always sure of parentage. True-breeding - purebred varieties produced through self-fertilization (in pea plants) until no variation is observed. Cross - the action of cross-fertilization. P generation - parental plants F1 Generation - hybrid offspring of P generation (F from filial, Latin for son or daughter). 1 for first generation. F2, second generation. Seven characteristics of pea plant studied: 1) Flower color, 2) Flower position, 3) Seed color, 4) Seed shape, 5) Pod shape, 6) Pod color, 7) Stem length. Monohybrid Crosses - hybrids between two true breeding varieties (truebreeding purple flowers with true breeding white flowers)

In an Abbey Garden

Mendels Law of Segregation

All F1 generation had purple flowers Mating two F1 plants, created a population represented by purple F2 plants, and white F2 plants. A population of all purple F1 plants gave rise to some F2 white plants. White flower heritable factor did not disappear, but was hidden or masked, when purple flower factor was present. (Re: punnet squares) Mendels 4 hypotheses: 1. There are alternative versions of genes, the units that determine heritable traits Alleles - alternative versions of a gene (purple or white flower) 2. For each inherited character, an organism inherits two alleles, on from each parent Alleles may be the same or different Homozygous - An organism with two identical alleles Heterozygous - An organism with two different alleles for a gene. 3. If two alleles of an inherited pair differ, then one determines the organisms appearance, called the dominant allele (- the allele of a differing inherited pair that determines the organisms appearance); other allele has no noticeable effect on the organisms appearance and is called the recessive allele. 4. Law of segregation. A sperm or egg carries only one allele for each inherited character because the two members of an allele pair segregate (separate) from each other during the production of gametes. Punnett square - a mapping that highlights the possible combinations of gametes and the offspring that result from each. Each square represents an equally probable product of fertilization. Phenotype - An organisms observable (physical) traits (often, but not always, dictated by genes) Genotype - an organisms genetic makup i.e.- Genotypic ratio is 1(PP) : 2 (Pp) : 1 (pp), where the phenotypic ratio is 3 (purple) : 1 (white). Medel found each of the seven characters he studies had the same inheritance pattern: On parental trait disappeared in the F1 generation, only to reappear in the one-fourth of the F2 generation. Every diploid individual, whether pea plant or human, has chromosomes in homologous pairs. One member of each homologous pair comes from the organisims female parent; the other member of each pair comes from the male parent. Loci - the specific locations of genes along the chromosome. An organism may be homozygous or heterozygous for the gene at that locus Dihybrid cross - the crossing of parental varieties differing in two charachters

Genetic Alleles and Homologous Chromosomes

Mendels Law of Independent Assortment

(like seed color and seed shape) Mendel crossed homozygous plants having round-yellow seeds (RRYY) and green-wrinkled seeds (rryy) F1 generation is all RrYy; round-yellow F2 generation phenotypic ratio: 9/16 round-yellow, 3/16 Round-green, 3/ 16 Wrinkled-green, 1/16 Green-wrinkled (9:3:3:1) Punnet square (4 X 4) with 4 variations (RY, rY, Ry, ry) supports findings. Law of Independent Assortment - Each pair of allele assorts independently of the other pairs of alleles during gamete formation. (Inheritance of one factor has no effect on the inheritance of another) Testcross - a mating between an individual of dominant phenotype but unknown genotype, and a homozygous recessive individual. Genetic crosses obey the law of probability Rule of multiplication - the probability of a dual event is the product of the seperate probabilities of independent events. ( x x ; x = 1/16) Wild-type traits - phenotypes seen most often in nature; not nessisarily specified by dominant alleles. (Absence of freckles ins more common than thier presence, even though freckles are a dominant allele) Pedigree - the collection of family history and the arrangement into a family tree.

Using a Testcross to Determine an Unknown Genotype

Rules of Probability

Family Pedigrees

Human Disorders Controlled by a Single Gene

Recessive Disorders
Most human genetic disorders are recessive Most people who have recessive disorders are born to normal parents who are both heterozygotes Carrier - An individual who is heterozygous for a recessive allele for a genetic disorder Using Mendels laws, one can predict the fraction of affected offspring that is likely to result from a marriage between two carriers In single gene disorders, of the offspring form heterozygote parents will be homozygous for recessive allele, and will be heterozygous carriers. Cystic fibrosis - recessive genetic disease that is characterized by an excessive secretion of very thick mucus form the lungs, pancreas, and other organs. Affects 1 in 25 people of European ancestry. Inbreeding - mating between close blood relatives, which cause a higher likelihood of producing offspring which are homozygous for a recessive trait. (most lines of purebred dogs have known genetic defects.) Extra fingers of toes and toes which are webbed Anchondroplasia - a form of dwarfism in which the head and torso develop normally, but the arms and legs are short. (homozygous

Dominant Disorders

dominant genotype causes death of embryo; single copy disorder) 99.99% of population are homozygous for achodroplasia recessive trait. Huntingtons disease - degeneration of the nervous system that usually does not begin until middle age A dominant allele is not necessarily better than the corresponding recessive allele. Today there are many tests that can detect the presence of disease causing allele in an individuals genome. Amniocentesis; physician uses a needle to extract about 2 tablespoons of amniotic fluid Chronic villus sampling; physician inserts a narrow tub through the vagina to the uterus and removes some placental fluid. Testing fetal cells or DNA released into the mothers bloodstream

Genetic Testing

Variations on Mendels Laws

Mendels laws stop short at explaining some patterns of genetic inheritance Incomplete dominance - An appearance in between the phenotypes of two parents Hypercholesterolemia - a condition charachterized by dangerously high levels of cholesterol in the blood, an example of incomplete dominance.

Incomplete Dominance in Plants and People

ABO Blood Groups: An Example of Multiple Alleles and Codominance

Most gene in more than two forms, known as multiple alleles. ABO bloodgroups - and example of multiple alleles in humans. Red blood cells may be coated with carbohydrate A, carbohydrate B, both (type AB), or neither (type O) Three different alleles: IA, IB, and i (neither A or B). Each person inherits one of the alleles from each parent. ii is type O, IAIB is type AB, IBIB or IBi is type B IAIB exhibit codominance Codominance - both alleles are expressed in heterozygous individuals. Pleiotropy - the impact of one gene on more than one charachter Sickle-cell disease - a disorder that cuases red blood cells to produce abnormal hemoglobin protein causing them to form a sickle shape which results in a diverse set of symptoms. One allele of sickle-cell results in a healthy individual, but at the molecular level the two alleles are actually codominant.

Pleiotropy and Sickle-Cell Disease

Polygenic Inheritance

Polygenic inheritance - the additive effects of two or more genes on a single phenotype character. Skin pigmentation in humans is controlled by 3 genes, AABBCC very dark, AaBbCc intermediate, aabbcc very light As geneticists learn more and more about out genes, its becoming clear that many human characters are influenced by both genes and environment. Identical twins even have different traits because of effects of environment.

Role of the Environment

The Chromosomal Basis of Inheritance

The chromosome theory of inheritance is one of biologys most important concepts. Chromosome theory of inhertance - theory that states that genes are located in specific positions on chromosomes and that the behaviour of chromosomes during meiosis and fertilization accounts for inheritance patterns