Biology Notes Week Feb 8-12 *including all previous material from beginning of semester!!*
Biology Notes Week Feb 8-12 *including all previous material from beginning of semester!!* 1510
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Date Created: 02/13/16
(All definitions in bold) Day 1 Identical twins have the same DNA Life is unified by macromolecules (Lipids, Carbs, Proteins, Nucleic Acids DNA, RNA, protein codes), cells, energy pathways, evolution DNA codes for RNA which makes proteins Life is constrained by the properties of chemistry and physics Experiment: Tests the hypothesis, one variable at a time, test experiment and a control experiment Test vs control experiment: Predictions: hypotheses should suggest testable predictions; reject if results are inconsistent with predictions Inductive reasoning: Specific observations to develop general conclusions(bservations, hypothesis) Deductive reasoning : General principles to make specific predictions (prediction, experimentation, conclusion) Hypothesis: Possible explanation of observations, test for validity, test in many ways, leads to predictions, iteritive (refined with new data) Iterative Hypothesis: aving to repeat Hierarchical Organization of Systems: 1) Cellular level atoms, organelles, cells (basic unit of life) 2) Organismal level tissues, organs, organ systems 3) Population level population, community 4) Ecosystem level 5) Biosphere ecosystem of earth (such as our room, chairs, etc) Characteristic of Living Organisms: 1) Composed of cell(s) 2) Complex and ordered 3) Respond to their environment 4) Can grow, develop, reproduce 5) Obtain and use energy 6) Maintain internal balance (homeostasis) 7) Allow for evolutionary adaptation Emergent Property: It is liCell > Tissue > Organ > Organ System > Animal. It's the property where living things become more and more complex as it goes to higher levels. It's based on the concept that "the whole is greater than the composition of its parts." Ex: heart is made of cells only, but if you just have heart cells (sum of its parts) it won't do anything, but if the whole heart is there, it will perform the function of pumping blood (the whole is greater). Life is another example. Each level of biology has emergent properties, they result from the interaction of components, and cannot be deduced by looking at the parts themselves. Science is hypothesis driven, observation/reasoning, description (human genome sequence) Science is not mysterious, and not limited to labs or nature 3 mains levels of organization tissues, organs, organ system Day 2 The germ hypothesis versus the spontaneous generation hypothesis Experiment: swan neck flask, heating broth to kill existing organisms, wait to see if new organisms emerge (we wait to see what happens to broth if nothing can get in.) Germ hypothesis: We only get new life if there’s already existing life. Scientists use a systemic approach: using inductive/deductive reasoning. Control conditions: ? Experiment conditions: ? Conclusion: the growth of microorganisms in broth is due to preexisting organisms; this is the control to be sure that the broth could support growth Pasteurization: Don’t boil something until it is completely sterilized (don’t warm it enough to kill living things.) This will increase shelf life. Philosophical approaches to science: reductionism, systems biology Models in science: parts provided by reductionist approach, model shows how they fit together, suggests experiments to test the model, ways to organize concepts Reductionist Approach: ? Scientific Theory: A body of interconnected concepts, supported by experimental evidence and scientific reasoning, ideas of which we are most certain (NOT the general meaning of theory.) Unifying Themes: 1)The cell theory: cells are the basic unit of life, all living things are made of cells, all cells come from preexisting cells 2)Molecular basis of inheritance: DNA (large strand macromolecule), gene, genome, continuity of life depends on DNA copying into daughter cells. All organisms today descended from a creature 3.5 BYA, some characteristic are preserved (through DNA) 3)Information: Info in DNA directs synthesis of cellular components. Cells process environmental info. In multicell organisms, cells coordinate with each other. 4)Structure and Function: study structure to learn function (ex.receptor for human cell for insulin, find similar molecule in worm and predict similar function) 5)Diversity of Life Arises by Evolution: underlies unity, 3 domains Bacteria, Archaea (both of which are single celled prokaryotes), Eukarya (single or multi cell eukaryotes.) Non EQ state constant energy needed, self organizing properties at different levels, properties from collections of molecules, cells, individuals Day 3 Matter: Has mass and occupies space There are 90 elements, 12 are in organisms 96.3% of our bodies are made of H,O,N,C Electrons can be transferred between atoms. Oxidation is the loss of an electrons and reduction is the gain of electrons. Molecules are atoms in a stable association Cations are positively charged ions, anions are the opposite Opposite charges attract (ex.NaCl is an ionic compound) Electrical attraction of water molecules can disrupt ionic bonds Covalent bonds have no net charge More shared electrons = stronger bond No unpaired electrons (satisfies octet rule) Aren’t ionic bonds intramolecular as well?? (between molecules) ionic and hydrogen bonds are intermolecular ?? Photosynthesis: 6H20 +6CO2 makes C6H12O6 +6O2 Ionic bonds are the weakest and release the least energy; hydrogen bonds are even weaker Double and then triple covalent bonds are stronger Nonpolar covalent bonds = equal sharing of electrons Cohesion: Water molecules attached to each other, due to hydrogen bonding (water to water.) Each individual bond is weak (The intermolecular attraction that holds molecules and masses together.) Adhesion: The process or condition of sticking or staying attached (water to other polar molecules) Day 4 HB are responsible for many of water’s important physical properties cumulative effects are enormous Inter and intra molecular forces polar covalent is intramolecular, HB is intermolecular water has adhesive properties capillary action!! Properties of water: 1) High specific heat a large amount of energy is required to change the temperature of water 2) High heat of vaporization the evaporation of water cools a surface 3) Solid water is less dense than liquid water bodies of water freeze from the top down 4) Water is a good solvent polar molecules and ions 5) Water organizes nonpolar molecules Hydrophilic (water loving); hydrophobic (water fearing), water causes hydrophobic molecules to aggregate or assume specific shapes 6) Water can form ions (protons) H2O > OH + H+ (hydroxide ion +hydrogen ion) Acids and Bases: water → [H+] of 10^7 mol/L; neutral pH is a negative log of H2 ion concentration of solution 6.022x10^16 H+/L = [H+] of 10^7 mol/L/ Acids are substances that dissociates in water to increase the H+ concentration, lowers pH Bases are substances that combine with hydrogen ions dissolved in water, lowers the [H+], increases the pH Buffers: substances that reduce pH change, releases H+ when base is added, absorb H+ when acid is added, overall effect is that the [H+] is relatively constant Biomolecules biological molecules mostly bonded to carbon (can be bonded to O, N, S, P, or H) and forms up to 4 covalent bonds Hydrocarbon : molecule of only C and H; nonpolar; functional groups add chemical properties Week 2 done Jan 25 Chapter 3 Biomolecules Biological molecules are mostly carbon bonded to C, O, N, S, P, or H Carbon forms up to 4 covalent bonds Hydrocarbon: only made of C and H they are nonpolar, functional groups add chemical properties Functional groups: Hydroxyl, carbonyl, carbonxyl, amino, methyl, sulfhydryl, phosphate Macromolecules are made of polymers (which are built by linking monomers) Monomers: small, similar chemical subunits Carbs, nucleic acids, proteins, lipids are the 4 macromolecules Dehydration: (condensation):polymerization, removal of water Hydrolysis: break molecules by addition of water, polymers to monomers (lyse means to cut) Carbohydrates: molecules with a 1:2:1 ratio of C, H, O 2 n CH covalent bonds high energy good energy storage molecules, (ex. sugars, starch, glucose) Monosaccharides: simplest carb, 6carbon sugars important, glucose (C6H12O6), fructose (structural isomer of glucose), galactose (stereoisomer of glucose), enzymes distinguish structural and stereoisomers Enantiomers:mirror images (subset of stereoisomers) Stereoisomers:mirror images of each other Alpha glucose and beta glucose In beta glucose, the hydroxyl group is on the opposite side of the ring Cellulose: structural carb that makes the leaves, stem, etc for plants Disaccharides:two monosaccharides linked by dehydration. Sugar transport or energy storage. Ex: sucrose (found in plants), lactose, maltose tSugars end in ose Glycolysis and cellular respiration is used to harvest the sucrose into ATP? Polysaccharides: long chains of monosaccharides (dehydration synthesis), energy storage (plants starch, animals glycogen), structural support (plants cellulose, arthropods and fungi chitin.) Polysaccharides are used for structure and energy storage as their two main uses. Cellulose is unbranched and flat and its’ shape lets it make a long unbranched flat polysaccharide Something cannot be a carb and a hydrocarbon Nucleic Acids: monomers, for example nucleotides (sugar which is 5C ribose, phosphate, nitrogenous base.1’ carbonphosphate group, 2’deoxyribonucleotide, 3’backbone for bond to phosphate, 4’ignore, 5’phosphate group Nucleotides: Sugar is deoxyribose in DNA and ribose in RNA Monomers are nucleotides, polymers are nucleic acids, nucleotides connected by phosphodiester bonds Ionic and HBbetween. Covalent is within. Jan 27 sugar is deoxyribose in DNA or ribose in RNA2 nitrogenous bases include purine:adenine and guaninedouble rings charged amino acids are hydrophilic pyrimidines are: thymine, cytosine, uracil single rings DNA is the sequence of nitrogenous bases that codes amino acid sequence in proteins phosphodiester bonds are strong because it’s covalent C and G makes 3 hydrogen bonds with each other A and T make 2 bonds DNA makes a double helixtwo polynucleotide strands connected by hydrogen bonds RNA: RNA is similar to DNA but contains ribose instead of deoxyribose and contains uracil instead of thymine. Has a single polynucleotide strand. RNA uses info in DNA to specify sequence of amino acids in I proteins. phosphodiester bonds are covalent bonds many sub types of covalent bonds: put in a pic of dna and rna here: when the phosphate is on the end it’s 5’, when it is a OH group it is a 3’ end Other nucleotides: ATP (adenosine triphosphate) is the primary energy currency of cells NAD+ and FAD+ are electron carriers for many cellular reactions As we make DNA, we cut off 2 phosphates to make the phosphodiester bonds Weakest bonds are ionic Baking soda and ammoniabases Jan 29 Between the 1 and the base on DNA, it’s a covalent bond Protein functions: transport (carrying things within cell), support (cytoskeleton, ECM), regulation, storage (not for starch and glycogen), defense, motion, enzyme (catalysis), receptor Proteins are polymers: one or more long, unbranched chains; each chain is a polypeptide Amino acids are monomers Amino acid structure: central carbon group, amino group, carboxyl group, single hydrogen, variable R group proteins and nucleic acids are both macromolecules and polymers Amino acid is made of: polar charged, non polar, charged nonaromatic, aromatic, special Dehydration and hydrolysis reactions: when a peptide bond is formed, these two functional groups form a new covalent bond: carboxyl and amino Hydrophobic exclusion: if you have a lot of hydrophobic functional groups, they’ll get away from water Four levels of structure: shape determines function: 1)primary structure sequence 2)secondary structure interaction of functional groups: alpha helix and beta pleated sheet (accordion shape) 3) Tertiary structurefinal folded shape of a polypeptide 4)Quaternary structuremultiple polypeptides Folding: a protein goes in, ATP provides energy and chaperone proteins(look up the procedure) and it makes a folded protein starch and glycogen are carbs Folded protein vs denatured protein Part 1. 1. There is a unity and diversity to life. How is life unified? How is life diverse? What mechanism underlies both of these? I recommend a paragraph for your answer. 2. What are the characteristics of all living organisms? 1) Composed of cell(s) 2) Complex and ordered 3) Respond to their environment 4) Can grow, develop, reproduce 5) Obtain and use energy 6) Maintain internal balance (homeostasis) 7) Allow for evolutionary adaptatio 3. Describe the hierarchical organization of life. atoms,molecules, organelle, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystem, and biosphere. 4. Compare deductive and inductive reasoning and describe how they fit into the systematic scientific process. Also describe how you use them informally in your daily life. Inductive reasoning: Specific observations to develop general conclusions (observations, hypothesis) Deductive reasoning: General principles to make specific predictions (prediction, experimentation, conclusion) inductiveunis around my area ban smoking, therefore all unis ban smoking Deductive All life is made of cells. Therefore, I am made of cells 5. Describe how scientists use a systemhaving, showing, or involving a system, method, or plan) approach to understand the world. A process used to determine theviabiliof a projec or procedure based on the experiential application of clearly defined and repeatable teps and an evaluation of the outcomes. The goalof a systematic approach is to identify the most efficien eans to generate consistent,ptimum result. 6. Describe the experiments that were done to test the germ hypothesis and the spontaneous generation hypothesis, including the hypotheses, their predictions, the experiments that tested them, the evidence that supported the conclusions, the conclusions and what parts of the process were inductive and what parts were deductive. What was the control and why is this important? I recommend a long paragraph describing these experiments. You may also want to draw and label a diagram to go along with your paragraph. 7. Describe what reductionism and systems biology are and how they are related. the practice of analyzing and describing a complex phenomenon in terms of phenomena that are held to represent a simpler or more fundamental level, especially when this is said to provide a sufficient explanation.Systems biology is the study of systems of biological components, which may be molecules, cells, organisms or entire species. Living systems are dynamic and complex, and their behavior may be hard to predict from the properties of individual parts. HOW ARE THEY RELATED?? 8. Compare a scientific theory to a hypothesis. When a hypothesis is verified to be true, it becomes a theory. First you make a hypothesis, then you make a theory once you test it 9. Describe cell theory and how it is a unifying theme in biology. All living things are made of cells, all cells come from preexisting cells, the cell is the basic unit of life. It is unifying because in order to understand the multicellular organisms, you must understand the basic cell. 10. Describe the molecular basis of inheritance and how it is a unifying theme in biology. I recommend a short paragraph for this answer. 11. Describe how structure is related to function at many levels of biological organization and how it is a unifying theme in biology. I recommend a short paragraph for this answer. Structure, shape, function, molecules, organelles, cells, tissues, organs 12. Describe how evolution causes the diversity of life and the unit of life and how evolution is a unifying theme in biology. I recommend a short paragraph for this answer. 13. Describe how cells are informationprocessing systems and why this is a unifying theme in biology. I recommend a short paragraph for this answer. 14. Describe the significance of the nonequilibrium state of life and how this is a unifying theme in biology. I recommend a short paragraph for this answer. 15. Describe the nature and structure of atoms. I recommend a long paragraph for this answer. Labeled diagrams may go along with your answer. 17. Describe chemical reactions. I recommend a short paragraph to answer this question. 18. Describe and compare the types of chemical bonds. I recommend a long paragraph for this answer. 19. Describe the significance of the polarity of water. I recommend a paragraph for your answer to this question. 20. Describe acids, bases, buffers and pH. I recommend a paragraph for your answer. You might also include a graph to go with your paragraph. 21. What are the chemical characteristics of hydrocarbons? I recommend a short paragraph. 22. Describe seven functional groups by name and structural formula. I recommend drawing and labeling each of the functional groups. 23. Describe what is similar and different about the four major macromolecules. I recommend a paragraph and a table for this answer. 24. Describe the structures and functions of the major examples of carbohydrates. I recommend a long paragraph for this answer. Drawing and labeling a diagram may also help. 25. Describe the structures and functions of the major examples of nucleic acids. I recommend a long paragraph for this answer. Drawing and labeling a diagram may also help. 26. Describe the structures and functions of the major examples of proteins. I recommend a long paragraph for this answer. Drawing and labeling a diagram may also help. 27. Describe the structures and functions of the major examples of lipids. I recommend a long paragraph for this answer. Drawing and labeling a diagram may also help. Part 2. These are the terms that should be in your answers to part 1. 1. Energy pathways, cell(s), evolution, nucleic acids (DNA, RNA and protein structures and codes), macromolecules 2. Cells, complexity, order, respond to environment, grow, develop, reproduce, energy, homeostasis (internal balance), evolutionary adaptation 3. Atoms, molecules, macromolecules, organelles, cells, tissues, organs, organ systems, population, community, ecosystem, biosphere, emergent properties 4. General principles, specific predictions, specific observations, general conclusions 5. Observation, hypothesis, hypothesis formation, prediction, experimentation, conclusion, inductive reasoning, deductive reasoning 6. Germ hypothesis, hypothesis, spontaneous generation hypothesis, prediction, test experiment, control experiment, flask, broth, sterilize, boiling, swan neck, microorganisms, air, breaking the swan neck 7. Reductionism, systems biology, models, organize concepts, predictions, new hypotheses, test hypotheses 8. Interconnected concepts, many types experimental evidence, most certain 9. Cells, organisms, basic unit of life, from preexisting cells 10. DNA, gene, genome, continuity of life, daughter cells 11. Structure, shape, function, molecules, organelles, cells, tissues, organs 12. DNA, amino acids, domains of life, bacteria, archaea, eukarya, mutations, preserved characteristics 13. DNA, cellular components, environmental information, response, multicellular organisms 14. Energy, organization, emergent properties 15. Mass, matter, atoms, protons, neutrons, electrons, nucleus, positively charged, negatively charged, neutral charge, atomic mass, atomic weight, orbitals, ions, cations, anions, atomic number, element, valence electrons, periodic table, octet rule, inert elements 16. Carbon, nitrogen, hydrogen, oxygen 17. Reduction, oxidation, electron, chemical bond, reactants, products, atoms, molecule 18. Molecule, compound, chemical bond, ionic bond, ions, attraction, covalent bonds, valence electrons, covalent single bond, covalent double bond, covalent triple bond, nonpolar covalent bond, polar covalent bond, electronegativity, stronger or weaker 19. Hydrogen bonds, oxygen, partial positive charge, partial negative charge, hydrogen, cumulative effect, weak bonds, cohesion, adhesion, capillary action, specific heat, heat of vaporization, density, solvent, polar molecules, ions, hydrophobic, hydrophilic, ionization 20. Acid, base, buffer, pH, slope, logarithm, concentration, hydrogen ions, solution 21. Carbon, hydrogen, nonpolar, functional groups, four covalent bonds 22. Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl 23. Nucleic acids, lipids, proteins, carbohydrates, polymers, dehydration reactions, hydrolysis reactions, synthesis, hydrophobic, hydrophilic, nonpolar, polar 24. Carbon, hydrogen, oxygen, ratio, covalent bonds, energy, storage, sugars, starch, glucose, monosaccharides, fructose, structural isomer, galactose, stereoisomer, enantiomers, disaccharides, dehydration, transport, sucrose, lactose, maltose, polysaccharides, glycogen, cellulose, chitin, alphaglucose, betaglucose 25. Nitrogenous base, ribose, pentose, phosphate, purines, pyamidines, adenine, guanine, thymine, cytosine, uracil, phosphodiester bonds, sugarphosphate backbone, DNA, double helix, polynucleotide, hydrogen bonds, sequence, baseparing, RNA, ATP, NAD , FAD , electron carriers 26. Enzyme catalysis, defense, transport, support, motion, regulation, storage, polymers, polypeptide, amino acid, monomer, dehydration, peptide bond, central carbon, amino, carboxyl, hydrogen, variable R group, primary structure, secondary structure, alpha helix, beta sheet, tertiary structure, quaternary structure, motifs, domains 27. Nonpolar, hydrophobic, insoluble in water, fats, oils, waxes, some vitamins, triglycerides, fatty acids, glycerol, saturated, unsaturated, plants, animals, melting point, phospholipids, amphipathic, membranes, phospholipid bilayers, micelles, terpenes, steroids, cholesterol Feb 1 Lipids: many non polar CH bonds, hydrophobic (fats, waxes, vitamins, oils) Triglycerides: 1 glycerol + 3 fatty acids Fatty acids: chain length varies; SATURATED: no double bonds, high melting point, solid at room temperature, animal origin; UNSATURATED: one or more double bonds, low melting points, liquid at room temperature, plant origin Phospholipids made of glycerol, 2 fatty acids (nonpolar ‘tails’), phosphate group (polar ‘head’) more unsaturated (double bonds) bends phospholipid bilayer: hydrophilic heads out, hydrophobic tails in Micelle: surrounds fats that we digest, it is how soap works other lipids: terpenes (insect signalling), steroids (cholesterol for humans) also can be used for insulation phospholipids can be used for energy hormones can also be proteins cholesterol is the backbone for steroids hydrogen bonds holding phospholipid tails together? No, it’s not polar The molecule formed by 2 hydrogen atoms is stable for 3 reasons: has no net charge. octet rule is satisfied. has no unpaired e. the strength of a covalent bond depends on the number of shared e electronegativity increases from left to right in the periodic table and increases going up the extent to which chemical reactions occur is by 3 factors: temperature, concentration, catalysts water has no net charge and has no unpaired electrons, water’s most outstanding property is the ability to form HB; they are responsible for the chemical organization of living systems. water’s polarity underlies water’s chemistry and the chemistry of life. water’s cohesion is responsible for helping it be a liquid at room temperature, also responsible for its surface tension water adheres to any substance with which it can form HB this property explains why substances containing polar molecules can mix with water the attraction of water to substances that have electrical charges on their surface is responsible for capillary action water moderates temperature through two properties: its high specific heat capacity (takes longer to heat up and holds its temperature longer) and its high heat of vaporization, water is also less dense in its solid form. water absorbs the heat generated bt cells during reactons so that those reactions dont destory the cells. high heat of vaporization ex. organisms dispose of ecess sweat by evaporative cooling like sweating at low temps, water makes a crystal lattice of HB. ice is les dense than liquid water because the HB in ice space the water molecules far apart, letting icebergs float. it keeps sea animals from freezing because water freezes from the top down Water is termed the solvent, and sugar is called the solute. Every time a sucrose molecule dissociates, or breaks away, from a solid sugar crystal, water molecules surround it in a cloud, forming a hydration shell that prevents it from associating with other sucrose molecules. Water molecules always tend to form the maximum possible number of hydrogen bonds. The tendency of nonpolar molecules to aggregate in water is known as hydrophobic exclusion. A mole (mol) is defined as the weight of a substance in grams that corresponds to the atomic masses of all of the atoms in a molecule of that substance. molar concentration of hydrogen ions in pure water, represented as [H+], is 10–7 mol/L. Re call that for every H+ ion formed when water dissociates, an OH– ion is also formed, meaning that the dissociation of water produces H+ and OH– in equal amounts. ph=partial hydrogen For water, therefore, an [H+] of 10–7 mol/L corresponds to a pH value of 7. A buffer is a substance that resists changes in pH. Releases hydrogen ions when a base is added and absorbs hydrogen ions when acid is added, with the overall effect of keeping [H+] relatively constant. Within organisms, most buffers consist of pairs of substances, one an acid and the other a base. The key buffer in human blood is an acid–base pair consisting of carbonic acid (acid) and bicarbonate (base) normal blood pH is 7.4, if it drops or increases it is fatal cation<atom<anion Organic molecules having the same molecular or empirical for mula can exist in different forms called isomers. If there are dif ferences in the actual structure of their carbon skeleton, we call them structural isomers. Later you will see that glucose and fructose are structural isomers of C6H12O6. Another form of isomers, called stereoisomers, have the same carbon skeleton but differ in how the groups attached to this skeleton are arranged in space. Enzymes in biological systems usually recognize only a single, specific stereoisomer. A subcategory of stereoisomers, called enantiomers, are actually mirror images of each other. A molecule that has mirrorimage versions is called a chiral mol ecule. When carbon is bound to four different molecules, this inherent asymmetry exists (figure 3.3). Here are some examples. Complex carbohydrates such as starch are polymers composed of simple ringshaped sugars. Nucleic acids (DNA and RNA) are polymers of nucle otides (figure 3.4). Proteins are polymers of amino acids, and lipids are polymers of fatty acids (see figure 3.4). These long chains are built via chemical reactions termed dehydration reactions and are broken down by hydrolysis reactions. starch is made from glucose units This chemical reaction is called condensation, or a dehydration reaction This process of positioning and stressing, termed catalysis, is carried out within cells by enzymes. Sugars are among the most important energystorage molecules, and they exist in several different forms. Sixcarbon sugars can exist in a straightchain form, but dis solved in water (an aqueous environment) they almost always form rings. The most important of the sixcarbon monosaccharides for energy storage is glucose sugar isomers have structural differences Glucose is not the only sugar with the formula C6H12O6. Both structural isomers and stereoisomers of this simple sixcarbon skeleton exist in nature. Fructose is a structural isomer that dif fers in the position of the carbonyl carbon (C==O); galactose is a stereoisomer that differs in the position of —OH and —H groups relative to the ring Disaccharides serve as transport molecules in plants and provide nutrition in animals Most organisms transport sugars within their bodies. In hu mans, the glucose that circulates in the blood does so as a simple monosaccharide. In plants and many other organisms, however, glucose is converted into a transport form before it is moved from place to place within the organism. In such a form, it is less readily metabolized during transport. Transport forms of sugars are commonly made by linking two monosaccharides together to form a disaccharide (Greek di, “two”). Disaccharides serve as effective reservoirs of glucose because the enzymes that normally use glucose in the organism cannot break the bond linking the two monosaccharide sub units. Enzymes that can do so are typically present only in the tissue that uses glucose. Transport forms differ depending on which monosaccharides are linked to form the disaccharide. Glucose forms transport disac charides with itself and with many other mono saccharides, including fructose and galactose. When glucose forms a disaccharide with the structural isomer fructose, the resulting disac charide is sucrose, or table sugar (figure 3.9a). Sucrose is the form most plants use to trans port glucose and is the sugar that most humans and other animals eat. Sugarcane and sugar beets are rich in sucrose. When glucose is linked to the stereoiso mer galactose, the resulting disaccharide is lac tose, or milk sugar. Many mammals supply energy to their young in the form of lactose. Adults often have greatly reduced levels of lactase, the enzyme required to cleave lactose into its two monosaccharide components, and thus they cannot metabolize lactose efficiently. This can result in lactose intolerance in hu mans. Most of the energy that is channeled into lactose production is therefore reserved for off spring. For this reason, lactose as an energy source is primarily for offspring in mammals. polysaccharides are longer polymers made up of monosaccharides that have been joined through dehydration reactions. Starch, a storage polysaccharide, consists entirely of αglucose molecules linked in long chains. Cellulose, a structural polysaccharide, also consists of glucose molecules linked in chains, but these molecules are βglucose. Because starch is built from αglucose we call the linkages α linkages; cellulose has β linkages. Organisms store the metabolic energy contained in monosac charides by converting them into disaccharides, such as maltose (figure 3.9b). These are then linked together into the insoluble polysaccharides called starches. These polysaccharides differ mainly in how the polymers branch. The starch with the simplest structure is amylose. It is com posed of many hundreds of αglucose molecules linked together in long, unbranched chains. Each linkage occurs between the carbon 1 of one glucose molecule and the carbon 4 of another the chains of amylose coil in water, making it insoluble The comparable molecule to starch in animals is glycogen. Like amylopectin, glycogen is an insoluble polysaccharide contain ing branched amylose chains. glycogen has longer chain length than starch some chains of sugars store energy, others serve as structural material for cells. for two glucose molecules to link together, the glucose subunits must be of the same form. celluse is a pollymer of Beta glucose. the properites of a chain of glucose molecules consisitng of beta glucose are very different from those of starch. The biochemical activity of a cell depends on production of a large number of proteins, each with a specific sequence. DNA encodes the genetic information used to assemble proteins similar to the way the letters on this page encode information. Unique among macromolecules, nucleic acids are able to serve as templates to produce precise copies of themselves. Cells use a type of RNA called messenger RNA (mRNA) to direct the synthesis of proteins. mRNA consists of transcribed singlestranded copies of portions of the DNA. These transcripts serve as blueprints specifying the amino acid sequences of proteins. When a nucleic acid polymer forms, the phosphate group of one nucleotide binds to the hydroxyl group from the pentose sugar of another, releasing water and forming a phosphodiester bond by a dehydra tion reaction. A nucleic acid, then, is simply a chain of five carbon sugars linked together by phosphodiester bonds with a nitrogenous base protruding from each sugar (see figure 3.15a). These chains of nucleotides, polynucleotides, have different ends: a phosphate on one end and an —OH from a sugar on the other end. We conventionally refer to these ends as 5 (“five prime,” —PO4) and 3 (“threeprime,” —OH) taken from the carbon numbering of the sugar ́ ́ purines are bigger than pyrimidines Two other important nucleotidecontaining molecules are nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD). These molecules function as electron carriers in a variety of cellular processes. You will see the action of these molecules in detail when we discuss photo synthesis and respiration proteins are the most diverse group of biological macromolecules: enzymes (3D proteins that facilitate chemical reactions), Defense (cell surface receptors, form the core of endocrine and immune system), trnasport (ex.hemoglobin is a transport protein), support (keratin, febrin, collagen (most abundant)), motion (actin and myosin are protein filaments that help move), regulation (hormones are messengers in animals, proteins turn genes on and off, receive info, surface receptor for cell, etc), and storage (calcium and iron are stored by binding as ions to storage proteins) 5 classes of amino acids: non polar amino acids (CH3 or CH2 groups) polar uncharged amino acids (OH) charged amino acids (have acids or bases that can ionize) aromatic amino acids (side groups have a C ring, NP) amino aicds that have special functions have unique properties: proline causes kinks in chains, cysteine links chains together, The amino and carboxyl groups on a pair of amino acids can undergo a dehydration reaction to form a covalent bond. The covalent bond that links two amino acids is called a peptide bond 4 structures of protein: 1. primary structure is its amino acid sequence 2. hydrogen bonding patterns alpha and beta helix 3. tertiary structurefinal folded shape of protein many proteins can be unfolded and will spontaneously fold back into their shape, other larger ones become insouble when denatured when two NP chains are close they experience LF 4.the arrangement of the subunits (chains of polypeptides) changing a single amino acid can change the structure and the function of a protein for proteins with a single peptide chain, the tertiary is the final structure of the protein motifs: supersecondary structure Proteins can be denatured when the pH, temperature, or ionic concentration of the surrounding solution changes. a fat molecule is called a triglyceride because it has a glycerol and 3 fatty acids. the CH bonds of fat serve as long term energy storage saturated fats are solid at room temp organisms have many other lipids other than fat. terpenes are long chain lipids that are components of chlorophyll and retinal, rubber is a terpene too steroids are another class of lipids and made of 4 C rings steroids are testosterone and estrogen and function as hormones fats are the most efficient for store chemical energy (fat.) an oil may be converted into a solid fat by adding H artifically trans fat is made by artificially adding hydrogen to unsaturated fats Phospholipids: 1. Glycerol, a threecarbon alcohol, in which each carbon bears a hydroxyl group. Glycerol forms the backbone of the phospholipid molecule. 2. Fatty acids, long chains of —CH2 groups (hydrocarbon chains) ending in a carboxyl (—COOH) group. Two fatty acids are attached to the glycerol backbone in a phospholipid molecule. 3. A phosphate group (—PO42–) attached to one end of the glycerol. The charged phosphate group usually has a charged organic molecule linked to it, such as choline, ethanolamine, or the amino acid serine. 4. the phospholipid molecule has a polar head at one end and 2 NP tails at the other ON EXAM 2 February 5 Prokaryote (not membrane bound organelles) and eukaryote (membrane bound organelles) similarities: 1)nucleoidprokaryote or nucleuseukaryote for DNA 2)cytoplasm (liquidy with organelles) (organelles plus cytosolliquid) 3)ribosomesin prokaryotes, not membrane bound 4)plasma membraneprokaryotes have a phospholipid bilayer membrane around the whole cell (embedded with proteins) 5)cytoskeleton determines the shape of the cell. The cytoskeleton is a bunch of proteins that make the shape of the cell. the shape determines the function so the cytoskeleton is important prokaryotes can’t process proteins as well as eukaryotes Prokaryotic cells simplest organisms nucleoid, not nucleus single circular chromosome instead of a bunch of linear chromosomes CELL WALLfor prokaryotes it is ___? (look up) two domains with prokaryotesarchaea and bacteria cellulose makes the plant cell wall instead of peptidoglycan for prokaryotes bacteria come in many shapes and sizes. There is fluid in the inside. Cytoplasm, ribosomes (little brown dots), nucleoid, plasma membrane > cell wall >capsule, flagellum, pili Bacterial cell walls Peptidoglycan (unlike cell walls of plants, fungi, archaea, most protists) protection, shape, structure antibiotic targets linking of proteins to surround the prokaryotes? what will rupture the peptidoglycan cell wall? we do not have peptidoglycan code covering in our cells (this is only in prokaryotes) because it kills all the good bacteria in the gut as well good bacteria are for digestion, etc Flagella: prokaryotes have none, one, or more. Rotary motion propels cell. ATP goes to making that cytoskeleton move and that move the prokaryote in the direction of the movement of the flagella Eukaryotic Cells membrane bound nucleus and organelles (compartments) have linear chromosomes Plasma membrane is the membrane outside the cell plant cells are also eukaryotic organelles that are the same: mitochondria, nucleus, endoplasmic reticulum, golgi vacuole (for water regulation)only in plants? Mitochondria and Chloroplasts: energy processing mitochondria is in plant cells and they use it with chloroplasts to make ATP? Mitochondria in all eukaryotes compartments: outer membrane, intermembrane space (between 2 membranes), inner membrane has cristae (folds), matrix (space inside the inner membrane)? inner membrane oxidative metabolism (that’s where the oxygen is being used) these structures are critical for the FUNCTION of the mitochondria have their own DNA (circular, like prokaryote DNA) 1000 micrometers in a millimetre Chloroplasts in plants (some other eukaryotes) chlorophyll for photosynthesis surrounded by 2 membranes thylakoids sacs within inner membrane grana stacks of thylakoids have their own DNA chloroplasts AND mitochondria are ATP generators, have double membranes, in plants and animals Endosymbiosis read up on this Unknown archaeon became nucleus protobacterium became mitochondrion cyanobacterium became chloroplast Chapter 5 Membranes critical for the function of mitochondria and chloroplasts and cells phospholipid bilayer with proteins fluid mosaic model Cell membrane components 1)Phospholipid bilayer (permeability barrier) 2)Transmembrane proteins in the bilayer that spread across the whole membrane and link to interior peripheral proteins (integral proteins) 3)Interior protein network (peripheral proteins) 4)Cell surface markers (glycoproteins and glycolipids) February 8 Membranes Phospholipid bilayer with proteins; fluid mosaic model Fluidity left to right but not up to down (not favourable to be up to down because the hydrophobic (nonpolar) region would be in the polar region) saturated fatty acids pack more tightly, saturated fatty acids are more liquid Fatty acid desaturases in some bacteria (ases ending means enzyme.) An enzyme that removes H and adds double bonds, adding kinks, saturating them cold tolerance in bacteria. The cell stays fluid and doesn’t get brittle and doesn’t break so it stays liquid and changes the fluidity of its membrane to stay liquid to compensate for the cold temperature. This is an adaptation to increase survival. Transmembrane (integral membrane) proteins are embedded across membranes (trans means across, integral means essential) An advantage of having compartments surrounded by membrane barriers is for protection Problems that arise for cell function because of the barrier of the plasma membrane may be that sometimes things cannot get through Transmembrane proteins have a nonpolar transmembrane domain, hydrophobic amino acids arranged in an alpha helix or beta barrels polar regions protrude from the bilayer Pores multiple alpha helices or beta barrels polar interiors the ends of the proteins, the looping regions, is where we have ligand binding hydrophilic, not in the water. the parts that touch the fatty acids are non polar the shape and charges on the core only let certain molecules through if they have the right shape they just let glucose through bacteriorhodopsin7 transmembrane domains. as light hits this, it changes shape. some of these in bacteria make a pore. Membrane Proteins 1)Transporter (channel) 2)Enzymes 3)Cell surface receptor when a molecule binds to a protein it changes the shape of the protein. when proteins bind to molecules they change shape, when they change shape they change function 4)Cell surface identity marker 5)Cell to cell adhesion 6)Attachment to cytoskeleton Anchoring Molecules Lipids linked to proteins. Protein anchored to phospholipid they can be function as proteins or identity markers membrane proteins can be pore, enzymes, transport proteins, cell surface receptors, and carriers how can you test the fluid mosaic model? watch the proteins move with a camera and time lapse so you see them change Feb 10 Passive transport movement of molecules through membrane. No energy required, diffusion down concentration gradient Types: Simple diffusion (small NP molecules, no walls), facilitated diffusion (via channels, carriers. You need a “door”) heat is the movement of molecules If you have really cold water and put a drop of color in it, the color molecules will take longer to spread out because of the temperature Facilitated Diffusion:diffusion mediated by proteins. Channel proteins, carrier proteins A transmembrane protein that has a hole for ions to pass through without binding to the protein itself is a channel Ion Channels They are in the neurons and other things too Passage of ions Gated channels open or close in response to ligand binding or membrane voltage more negative charges outside a cell than inside Direction of flow due to relative ion concentrations across membrane Voltage differences across membrane Na+ high concentration outside, K+ high potassium inside Carrier Proteins Ions or other solutes (sugars, amino acids.) Down concentration gradient, solute must bind carrier S aturation the rate of transport limited by number of transporters Osmosis Water across a membrane It is the net diffusion of water across a membrane towards higher solute concentration Cytoplasmaqueous solution (meaning dissolved in water) High osmolarity is high water, water is low where osmolarity is low Osmolarity is the number of molecules in a solution per volume. Osmolarity is high where there is a lower concentration. osmolarity affects plants Osmotic Pressure Hypertonic (defines solution, not cell) solution solution osmolarity > cell osmolarity (high osmolarity outside) Hypotonic s olutionsolution osmolarity < cell osmolarity Isotonic Solutions solution osmolarity = cell osmolarity Aquaporins: facilitate osmosis (permeability) Pure water distilled (nothing in it) in hypotonic (the solution has very few solutes) Molarity is one type of solute, OSmolarity is everything together cell in a hypotonic solution swells membranes or cell walls balance osmotic pressure, or cell bursts Animals cells are isotonic, plant cells are usually in a hypotonic solution (cells have higher osmolarity inside than outside, causing them to swell and hold the plant upright) cells will lyse if they get too full of water, shrivel if they don’t get enough water Proteoglycans are found in prokaryotes (cell wall of bacterium) keeps cell from swelling and bursting. Antibiotics break the cell wall. WE don’t have proteoglycans. Active Transport Requires energy ATP is used directly (primary), or indirectly via a coupled gradient (secondary) Requires carrier proteins (why not channels?) Substances from low to high concentration Carrier Proteins Uniportersmove one molecule at a time Symportermove molecules in the same direction Antiportermove molecules in opposite directions Sodium Potassium Pump antiporter Primary active transport direct use of ATP Process: affinity changes (how much it has an affinity for K or Na), conformation (shape) changes these changes take energy which needs ATP Know how Na K pumps work Secondary Active Transport ATP indirectly causes molecules to move against their gradient ATP indirectly via potential energy of concentration gradients GlucoseNa+ symporter: Na+ diffusion moves glucose against its concentration gradient, binding sodium increases affinity for glucose; gut absorbs glucose (have to move against concentration gradient to get into body) In active transport, ATP is always used, directly or indirectly In secondary active transport, ATP is used indirectly via the potential energy of concentration gradients Chapter 6 Energy Capacity to do Work 1. Kinetic energy of motion 2. Potential stored energy of position heat (way of measuring energy) 1 calorie = heat required to raise 1 gram of water 1 degree celsius calories vs Calorie (kcal) energy comes from the sun, photosynthetic organisms capture energy, stored in chemical bonds Redox Reaction combination of simultaneous (coupled) with redox and oxidation reactions Oxidation: loss of an electron Reduction: gain of an electron, higher energy than oxidized form Reducedoxidation reactions: always paired Laws of Thermodynamics First law of thermodynamics: energy is not created or destroyed, one form to another, total energy in the universe is constant, during conversion energy is lost as heat Second law of thermodynamics: entropy (disorder) is continuously increasing, energy transformations spontaneously convert matter to a more stable form Endergonic (positive Delta G), products G > Reactant G, requires input of energy Exergonic (Negative Delta G), Products G < Reactants G, spontaneous, (may not be instantaneous) Delta G is the change in free energy ATP: adenosine triphosphate, chief “currency” of cells, composed of ribose (5 carbon sugar), adenine, chain of three phosphates (bonds are unstable) breaking off a phosphate is exergonic, the energy can be used to make another bond ATP Cycle ATP hydrolysis drives endergonic reactions, coupled reactions result in net negative delta G (exergonic and spontaneous) ATP is NOT for energy storage > fats and carbs are for storage, only a few seconds worth of ATP, but we are constantly making more ATP, if we didn’t have enough we can’t maintain Sodium Potassium across membranes, brain and muscles would stop working. Our brain uses our stored ATP for energy Coupled reactions: some energy is lost as heat
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