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Biological Sciences
BIOL 1000

Exploring Life 11/6/2012 12:20:00 PM The biosphere Ecosystems Communities Population Organisms Organ systems Organs Tissues Cell Organelles Molecules Eukaryotic cell: subdivided by internal membranes into various membrane enclosed organelles. (includes chloroplasts) Prokaryotic cell: DNA is not separated form the res of the cell by enclosure of a membrane. (bound nucleus, bacteria and archaea) Positive feedback: end product speeds up its production. Negative feedback: accumulation of an end product of a process slows that process. Domain Kingdom Phylum Class Order Family Genus Species 3 DOMAINS  BACTERIA  ARCHAEA  EUKARYA 5 kingdoms 1. Monera a. Prokaryotes i. Domain Bacteria ii. Domain Archaea 2. Protista a. Eukaryotes i. Domain Eukarya **Protists 3. Plantae a. Eukaryotes i. Domain Eukarya 4. Fungi a. Eukaryotes i. Domain Eukarya 5. Anamalia a. Eukaryotes i. Domain Eukarya Discovery Science  Describing nature without any preconceived expectations. Hypothesis-Driven Science  Involves constructing a specific testable explanation for a phenomenon based on a set of observations. A hypothesis is a testable explanation for an observation. Inductive reasoning - specific observations to reach a general conclusion. Deductive reasoning – general observations to reach a specific conclusion. As we respire we release CO2, the CO2 comes from eating food. Human proteins can be produced by bacterial cells because all organisms share a common genetic code. Darwin could not explain how characteristics are passed from parent to offspring. -ell: small (organelle) eu: true (eukaryote: true nucleus) pro: before (prokaryote: no nucleus) bio: life tech: skill or art biosphere: sum of the plants ecosystems **Natural Selection  various kingdoms, groups, domain, etc… Organism Organ System Organs Tissues Cells metabolism: the rapid turnover of chemical materials; involves the release or use of chemical energy. Hormones: biochemical substances produced within plant or animal cells or glands, that exert a particular effect.  System of nerves and chemical regulators that coordinate activities. Organisms change their behaviour in response to changes in the surrounding environment. (active behaviour) Growth requires an organism to take in material from the environment and organize the material into its own structure. (living organisms only) Reproduction: the ability to produce copies.  Asexual reproduction: one parent, cell division.  Sexual reproduction: two parents, both contribute half of the genes. Evolution: changes that occur within populations and organisms that make individuals able to adapt to their external environment. (better at response metabolism and reproduction.) Ecology: the study of relationships between organisms and their relationships with their environment. Scientific method: orderly process of gaining information about the biological world. 1. State a problem 2. Collect information 3. Form a hypothesis 4. Experiment to test hypothesis 5. Record and analyze data 6. Form a conclusion Theory: a hypothesis that is confirmed through repeating experimentation. Chemical Basis of Life 11/6/2012 12:20:00 PM protons: positive neutrons: neutral electrons: negative protons=atom number protons and neutrons=mass number a cloud of negatively charged electrons surround nucleus. Shell 1=2 electrons Shell 2=8 electrons Chemical properties depend mostly on the number of electrons in the outer shell. Fuller outer shell the more stable an atom is. Covalent bond: a bond that shares electrons to complete its shell. Double covalent bond: 2 shared pairs of electrons. Compound: substance formed by the combination of 2 or more elements. Electro-negativity: tendency for an atom to pull electrons toward itself. **atoms do not always share electrons equally. Function of H20 is consequence of its structure. A molecule with 2 poles – 1 negative and 1 positive = polar molecule 4 properties of H2O  Ability to moderate temperature  The fact that ice floats  Its ability to dissolve substances  Surface tension  H2O = universal solvent Hydrophilic-H2O loving Hydrophobic-H2O fearing (oil, wax, fat, etc…) **Polar covalent bonds** acid – increased H+ concentration  more acidic lower pH # base – decreased H+ concentration  more basic lower pH # pH scale: 1: battery acid 2: digestive juices 3: vinegar, beer, wine 4: tomato juice 5: black coffee 6: urine 7: pure water (human blood 7.3) 8: seawater 9: 10: milk of magnesia 11: household ammonia 12/13: household bleach 13/14: oven cleaner *the pH of a solution is defined as the negative logarithm of the hydrogen ion concentration. Matter: anything that takes up space or has mass. Element: a substance that cannot be broken down to other substances by chemical reactions. Compound: a substance consisting of two or more elements combined in a fixed ratio. 92 elements Carbon Oxygen Hydrogen Nitrogen *96% of living matter Trace elements: those required by an organismin only minute quantities. Atom: the smallest unit matter that still retains the properties of an element.  Subatomic particles o Neutrons, protons, electrons Neutrons and protons are packed together to form a dense core. (atomic nucleus)  Centre of an ion For atoms and subatomic particles we use the unit of measurement called a “Dalton”.  Dalton=atomic mass unit Mass # is approx atomic mass Example: Some atoms have more neutrons in the same element, these forms are called isotopes. Radioactive isotope: one where the nucleus decays spontaneously, giving off particles and energy. When decay leads to a change in the number of protons, it transforms the atom to an atom of a different element. Although radioactive isotopes are useful in biological research and medicine, radiation from decaying. Isotopes also poses a hazard to life by damaging cellular molecules. Only electrons are directly involved in chemical reactions between atoms. Energy: the capacity to cause change. Potential: energy: the energy that matter possesses because of its location or structure. An electron cannot exist in between its fixed states of energy. Energy levels: different states of potential energy. Electron shell: energy of an electron is correlated with distance from nucleus. This happens by measurement of “shell” to nucleus.  More energy = farther shell is from nucleus. **Usually energy when lost is released in the form of heat. Chemical behaviour of a shell mostly depends on the # of electrons in the outermost shell. Outermost electrons: valence electrons Valence shell: outermost shell Full valence= inert elements (chemically unreactive) The 3D space where and electron is found 90% of the time is called an orbital.  Each electron shell consists of a specific number or orbitals of distinctive shapes and orientations. o 2 electron max per orbital. The reactivity of atoms arises from the presence of unpaired electrons in or more orbital’s of their valence shells. When atoms interact to complete their valence shells, it is the unpaired electrons that are involved. Atoms with incomplete valence shell can interact with certain other atoms in such a way, that each partner completes its valence shell.  Share or transfer Chemical bonds: the interactions that result in chemical staying close together.  Covalent bond: sharing of a pair of valence electrons by two atoms. 2 or more atoms held together constitutes as a molecule. Hydrogen (H ) molecular formula H-H structural formula  This forms a single bond. Oxygen (O ) molecular formula O=O  This forms a double bond. The bonding capacity of an atom generally equal to the number of unpaired electrons in the atoms outermost shell. Attraction of a particular kind of atom for the electrons of a covalent bond. Non-polar covalent bonds: a type of covalent bond in which electrons are shared equally between two atoms of similar electronegativity. Polar covalent bonds: a covalent bond between atoms that differ in electronegativity that shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive. Example: A charged atom is called and ion.  Positive: cation  Negative: anion Because cations and anions are opposite, they attract. This is called an ionic bond. Compounds formed by ionic bonds are called compounds. (salts) The attraction between oppositely charged atoms, or ions is an ionic bond. An ionic bond can form between any two oppositely charged ions, even if they have not been formed by a transfer of electrons from one to the other. *The term ion also regards to entire molecules that are electrically charged. Environment effects the strength of ionic bonds. A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom. Example: Van Der Waals interactions: weak attractions between molecules or parts of molecules that are brought about by localized charge fluctuations.  Although weak only when molecules are very close together. The precise shape of a molecule is usually important to its function in the living cell. The making and breaking of chemical bonds is called chemical reactions. The point at which the reactions off set one another exactly is called chemical equilibrium.  Does not mean chemicals are equal in concentration. *An atom is the smallest unit of an element. Water is the molecule of life, it is a single covalent bond. Polar molecule: a molecule with opposite charges on opposite sides. Cohesion: the binding together of like molecules (often hydration). Adhesion: the attraction between different types of molecules. Surface tension: a measure of how difficult it is to stretch or break the surface of a liquid. Kinetic energy: energy of motion. (anything that moves) Heat: a measure of the total amount of kinetic energy due to molecular motion in the body of matter. Temperature: measures the intensity of heat due to the average kinetic energy of molecules. Celcius scale:  H20: BOIL - 100 FREEZE – 0  HUMANS: 37.6 average Calorie: the amount of heat it takes to raise 1g of H20 by 1 degree Kilocalorie: the amount of heat it takes to raise 1000g by 1 degree Joule: 1 joule = .239 cal Specific heat: the amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1 degree. Evaporation: liquid to gas. Heat to vaporization: quantity of heat a liquid must absorb to be converted from a liquid to a gas. Evaporative cooling: occurs because the “hottest” molecules, those with the greatest kinetic energy are lost likely to leave as gas. Solution: a liquid that is completely homogeneous mixture of two or more substances called a solution.  Dissolving agent: solvent  Aqueous solution: water is solvent Ice: hydrogen bonds are stable. Water: hydrogen bonds reform. Colloid: a mixture made up of a liquid and particles that remain suspended in that liquid. Hydrophobic: water fearing Hydrophilic: water loving Molecular mass: sum of masses of all atoms in the molecules.  Molecular mass = mole Molarity: # of moles of solute per liter of solution. Buffers: substances that minimize changes in the H+ and OH- in a solution. Acid precipitation: rain, snow, fog with a pH lower than 5.6. Molecular Diversity of Life 11/6/2012 12:20:00 PM Study of carbon compounds is called organic chemistry. Abiotic: nonliving 1953: Stanley Miller  concluded organic compounds set the stage for the early origin of life. st Carbon: 6 electrons (4 in valence, 2 in 1 shell)  Shares 4 electrons in outer shell to complete valence shell and become and anion. o Methane (tetrahedral) o Ethane (2 tetrahedral groups) o Ethane (double bond)  Molecule is flat This tetravalence is one fact of a carbons versatility, that makes large complex molecules possible. Hydrogen Oxygen Nitrogen Carbon Urea: CO(NH2)2 Hydrocarbons: organic molecules consisting only of carbon and hydrogen. Hydrocarbons are the major component of petroleum fossil fuel. Isomers: compounds that have the same # of atoms of the same elements but difference in structures mean different properties. Structural isomers: differs in covalent partners as shown in this example of two isomers of pentane. Geometric isomers: differ in arrangement about a double bond in these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon. Enantiomers: differ in spatial arrangement around an asymmetric carbon, resulting molecules that are mirror images. The two isomers are designated L and D isomers. (from the latin left and right, Levo and Dextro.) Enantiomers CANNOT be superimposed on each other. Functional groups: components of organic molecules that are most commonly involved in chemical reactions. HYDROXYL In a hydroxyl group a hydrogen atom bonds with an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. Alcohols: name usually ends in “ol”. Polar as a result of the electronegative oxygen atom drawing electrons toward itself. Attracts H20 molecules, helping dissolve organic compounds such as sugars. Example: Ethanol (present in alcoholic beverages) CARBONYL The carbonyl group consists of a carbon atom joined to an oxygen atom by a double bond. Ketones: if carbonyl is within a carbon skeleton. Aldehydes: if carbonyl is at the end of the carbon skeleton. A ketone and an aldehyde may be structural isomers with different properties, as in the case for acetone and propanol. Example: Acetone (Ketone) Propanol (aldehyde) CARBOXYL When an oxygen atom is double bonded to a carbon atom that is also bonded to a hydroxyl group, the assembly of atoms is called a carboxyl group (-COOH) Carboxylic acids: organic acids Has acidic properties because it is a source of hydrogen ions. In cells, found in the ionic form, which is called a carboxylate group. The covalent bond between oxygen and hydrogen is so polar the hydrogen ions tend to dissociate reversibly. Example: Acetic Acid (gives vinegar a sour taste) AMINO The amino group consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. Amines Example: Gylcine (both an amine and carboxylic acid) Acts as a base, can pick up a proton from a surrounding solution. Ionized with a charge of it under cellular conditions. SULFHYDRYL Consists of a sulfur atom bonded to a hydrogen atom.  Resembles a hydroxyl group in shape. Thiols Two sulfhydryl groups can interact to help stabilize protein structure. Example: Ethanethiol PHOSPHATE In a phosphate a phosphorus atom is bonded to four oxygen atoms, one oxygen is bonded to the carbon skeleton; two oxygen’s carry negative charges abbreviated P. The phosphate group ( ) is an ionized form of a phosphate acid group ( ) note that two hydrogens. Makes the molecule of which it is part an anion. (negatively charged ion) Can transfer energy between organic molecules. Example: Glycerol Phosphate: Example: Adenosine Triphosphate *main energy transferring molecule. Structure of Macromolecules 11/6/2012 12:20:00 PM 100,000+ = macromolecule polymers (chain like molecules)  carbohydrates  proteins  nucleic acids (similar, connected by covalent bonds) monomers: repeating units to serve as building blocks of polymers. Monomers connected by a reaction where 2 molecules covalently bond through the loss of an H2O molecule.  Condensation reaction  Dehydration reaction Disassembly of polymers to monomers is by hydrolysis (the addition of H2O) Monosaccharide: have molecular formulas that are some multiple of the unit CH2O. Disaccharide: 2 monosaccharides joined by a glysidic linkage.  Covalent bond between monosaccharides by dehydration synthesis. Polysaccharides: macromolecules, polymers with a few hundred to thousand monosaccharides joined by glycosidic linkages.  Storage polysaccharides o Starch  Glucose monomers  1-4 linkages (#1 carbon, #4 carbon)  Amylose: most basic, unbranched  Amylopectin: more complex, branched, (#1,#6 linkages) Wheat, corn, rice: humans diet. Animals store polysaccharides as glucose. Structural polysaccharides:  Cellulose  Chitin o Arthropods o Exoskeletons Lipids: fats (hydrophobic)  Not polymers Constructed from glycerol and fatty acids Glycerol  3 carbons  hydroxyl group Fatty acid  Long carbon skeleton  16/18 carbons  carboxyl group Phospholipids  2 fatty acids attached to glycerol, rather than 3. rd  3 hydroxyl group is joined to a phosphate. **Review Ch. 5 in textbook** Tour of a Cell 11/6/2012 12:20:00 PM Prokaryotic cell:  Pili  Nucleoid  Ribosomes  Bacterial chromosomes  Plasma membrane  Cell wall  Flagella Total surface: height x width x # of sides x # of boxes Total volume: height x width x # of boxes Surface to volume ratio: surface area/volume ANIMAL CELL Flagellum: locomotion organelle present in some animal cells, composed of membrane – enclosed microtubules. Centrosome: region where the cell’s microtubules are initiated; in an animal cell, contains a pair of centrioles. Cytoskeleton: reinforces cell’s shape, functions in cell movement, components are made of protein. Microvilli: projections that increase the cell’s surface area. Peroxisome: organelle with various specialized metabolic function; produces hydrogen peroxide. Mitochondrion: organelle where cellular respiration occurs and most ATP is generated. Lysosome: digestive organelle where macromolecules are hydrolyzed. Golgi Apparatus: organelle active in synthesis, modification, sorting and secretion of a cell products. Ribosome: non membranous organelles that make proteins free in cytoplasm or bound to rough ER or nuclear envelope. Plasma Membrane: membrane enclosing the cell. Nucleus:  Nuclear envelope: double membrane enclosing the nucleus; perforated by pores, contiguous with ER.  Nucleolus: non membranous organelle involved in production of ribsomes; a nucleus has one or more nucleoli.  Chromatin: material consisting of DNA and proteins; visible as individual chromosomes in a dividing cell. Endoplasmic reticulum: network of membranous sacs and tubules: other synthetic and metabolic processes.  Rough ER  Smooth ER Extracellular Membrane: space between the two cells; sticky and hold cells together. The nucleus houses the genetic information of the cell – DNA  DNA is wrapped around proteins  2m of DNA per nucleus. mRNA = messenger RNA Lysosomes are only found in animal cells. PLANT CELL Centrosome: region where the cell’s microtubules are intitated; lacks centrioles in plant cells. Golgi Apparatus Plasma Membrane Mitochondrion Cell wall: outer layer that maintains cell’s shape and protects cell from mechanical damage.  Made of cellulose, proteins and polysaccharides. Plasmodesmata: channels through cell wall that connect the cytoplasm’s of adjacent cells. Chloroplasts: photosynthetic organelle, converts energy of sunlight to chemical energy stored in sugar molecules. Cytoskeleton: microfilaments, intermediate filaments, microtubules. Central Vacuole: prominent organelle in older plant cells, functions include storage, breakdowns of waste products, hydrolysis of macromolecules, enlargement of vacuole is a major mechanism of plant growth. Tonoplast: membrane enclosing the central vacuole. Ribosome Smooth ER Rough ER Nucleus:  Nuclear envelope  Nucleolus  Chromatin Sugar molecules produced by photosynthesis can be broken down into other molecules for energy. μm: nanometers 10 = 1,000,000 nucleic acids: information for molecules  deoxyribosenucleic acid (DNA)  ribonucleic acid (RNA) DNA: genes RNA: intermediary in protein making process DNA’s info is transcribed into RNA which is translated into the primary structure of proteins. DNA is eukaryotic cells – 2 steps a. Info is transferred from DNA to mRNA i. RNA leaves nucleus and carries info to the ribosome. b. The message in the RNA sequence of nucleotides is translated into a sequence of amino acids. (link and form a polypeptide) Cell membrane is in constant motion. Lateral diffusion: membrane; lipids and proteins move sideways in the bilayer.  Nuclear Envelope  Rough ER  Smooth ER  Golgi Apparatus  Lysosome  Plasma Membrane Proteins destined for secretion are made on ribosomes bound to the rough ER.  Move through endomembrane system and are dispatched from Golgi Apparatus in transport vesicles that moves through cytoplasm and fuses with plasma membrane. Cilia: small, many Flagella: long, whip like, singular  Use of hydrolysis of ATP to move Animal cells are connected by junctions  Demosomes (anchoring junctions)  Gap Junctions (communicating junctions) Plant cells are joined by plasmodemata. Tight junctions form a barrier between cells preventing fluid from moving between cells. Desmosomes contain keratin  Button like Gap junctions - “bridges” Plasmodesmata – “bridges” The Working Cell 11/6/2012 12:20:00 PM We get all our energy and organic molecules from food. Plasma membrane is selectively permeable. Passive Transport  Does not require energy from the cell Concentration gradient: moves from where it is more concentrated to less concentrated.  Diffusion o Does not require energy from the cell o Diffusion of water across a membrane is called osmosis. Active transport  Requires energy from the cell. Cotransport  Two ions move through a cotransporter protein. Exocytosis  Exportation of materials through vesicles fused with the plasma membrane and released outside the cell. Endocytosis  The plasma membrane pinches in and forms a vesicle around the material from the outside of the cell. Plasma membrane is a fluid mosaic. This means it is diverse with protein molecules which are embedded in a matrix of phospolipids.  Move fluidly and flexibly  Phospholipids form a two-layer framework called a phospholipid bilayer.  Carbohydrate molecules are attached to some of the molecules that make up the membrane. Cells communicate with one another by means of chemical messengers.  The binding of the messenger often triggers a chain reaction involving other molecules. o Called a single transduction pathway  The molecules at the end of the pathway perform a certain activity inside the cell. A transport protein in the plasma membrane forms a channel through which water molecules or a specific solute can pass. Hypotonic: lower solute concentration Hypertonic: higher solute concentration Phagocytosis(cell eating): the cell engulfs debris, or other object.  Occurs in specialized cells called phagocytes.  Inavgination produces a vacuole which fuses with one o the Lysosomes containing hydrolytic enzymes.  Materials in the vacuole are then broken down and degraded. Pinocytosis (cell drinking):the cell engulfs extracellular fluid.  Enter the cell inside a vesicle.  The resulting vesicles travel and release. Receptor-mediated Endocytosis: triggered when receptors bind to external molecules. Energy is the capacity to do work.  Energy at work: kinetic energy.  Energy in storage: potential energy. Energy cannot be created nor destroyed. Energy is lost as heat, cannot be put to use once lost. The form of energy that drives most of the work in a cell is chemical energy. Food provides chemical energy when its covalent bonds are broken down.  Input of energy to break down a C-H bond.  A new O-H bond is formed and the extra energy is released. During cellular respiration, glucose releases energy. ADP: Adenosine Diphosphate ATP: Adenosine Triphosphate ATP releases energy when the covalent bond between phosphate groups breaks during hydrolysis. Enzymes do not add energy to a reaction; it speeds up reaction by lowering the energy barrier.  An enzyme is very selective.  It only acts on specific molecules o Called substrate How Cells Harvest Chemical Energy 11/6/2012 12:20:00 PM In cellular respiration, energy in fuel is converted to ATP. Most ATP is made in the cell’s mitochondria. ATP powers the work of the cell. ATP is produced from a molecule of glucose.  Step one: is called glycolysis. o Takes place outside of mitochondrion. o the molecule is split in half. o NAD+ an electron carrier picks up the electrons and hydrogen atoms and becomes NADH. o Pyruvic acid is created.  Step two: pyruvic acid enters the mitochondrion o One carbon is removed forming a carbon dioxide as a by-product. o Electrons are stripped, forming NADH. o Coenzyme A attaches to the 2 carbon fragment which forms acetyl- CoA.  Step three: Citric Acid Cycle/Krebs Cycle o Coenzyme A is removed and the remaining 2-carbon skeleton is attached to an existing 4-carbon molecule that serves as the starting point for the citric acid cycle. o The new 6-carbon chain is partially broken down, releasing carbon dioxide. o The 6 carbon molecule is split into to molecules of 3 carbons each. o Several electrons are captured by electron carriers and more carbon dioxide is released. o Two ATPs are produced for each molecule of glucose.  Step four: Oxidation Phosphorylation o Electron carriers deliver their electrons to an electron transfer chain embedded in the inner membrane of the mitochondrion. o Electrons are transferred from on carrier to the next. o As the move along the chain they give up a small bit of energy.  Water is formed as a by-product. o The energy released by electrons is used to pump hydrogen ions across the inner membrane of the mitochondrion, creating an area of high hydrogen ion concentration. o Hydrogen ions flow back across the membrane through a turbine. o These spinning turbines in the cells produce most of the ATP that is generated from the food you eat. 10 million ATPs per second in just one cell. All cells are able to synthesize ATP via the process of glycolysis. In many cells if oxygen is not present, pyruvate is metabolized in a process called fermentation. By oxidizing the NADH produced in glycolysis, fermentation regenerates NAD+, which can take part in glycolysis to produce more ATP. The net energy gain in fermentation is 2
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