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Rough Draft of Week 3 Information BSC 114
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This 18 page Class Notes was uploaded by Alexis Elston on Sunday September 11, 2016. The Class Notes belongs to BSC 114 at University of Alabama - Tuscaloosa taught by Daryl W. Lam in Fall 2016. Since its upload, it has received 22 views. For similar materials see Principles Of Biology I in Biology at University of Alabama - Tuscaloosa.
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Date Created: 09/11/16
Water and Life – Chapter 3 Water is the only common substance to exist in the natural environment in all three physical states of matter The structure of a water molecule is highly polar because oxygen atoms have much higher electronegativity than hydrogen atoms. o The high polarity of water molecules allows them to interact with other polar or charged molecules. o Oxygen has a partial negative charge; Hydrogen has a partial positive charge. Makes water a polar molecule, allowing it to form hydrogen bonds with other water molecules and with other polar compounds Hydrogen bonds are weak and constantly broken and reformed Properties of Water that contribute to earth’s suitability for life o Cohesive and adhesive properties Cohesive, it can bind to itself Chemical attraction between particles of the same substance Adhesive, it can bind to other molecules Chemical attraction between particles of the same substance These properties make it possible for water to be transported against gravity in plants o Ability to moderate temperature Can release energy because of the stored energy in temperature o Expands upon freezing Hydrogen bonds One hydrogen bond can form up to 4 hydrogen bonds with other water molcules and other polar compounds Hydrogen bonds constantly break and reform in water o Versatility as a solvent for other polar and ionic compounds Water has a high surface tension o Surface tension is a measure of how difficult it is to stretch or break the surface of a liquid o Surface tension is directly related to cohesion o Water has a greater surface tension than most other liquids because of hydrogen bonds Temperature and Heat o Kinetic energy is the energy of motion o Kinetic energy associated with random motion of atoms or molecules is called thermal energy Thermal energy in transfer from one body of matter to another is defined as heat Specific heat of a substance is the amount of heat that must be absorbed or lost for 1g of that substance to chance its temp by 1 C o Water has high specific heat – it can absorb or release a large amount of heat with only a slight change in its own temperature Due to hydrogen bonding Water absorbs heat when hydrogen bonds are broken Water releases heat when it forms hydrogen bonds High Specific heat minimizes temperature fluctuations to within limits that permit life (regulation of body temperature) Evaporative Cooling o Evaporation is transformation of a substance from a liquid to gas o Heat of Vaporization is the heat a liquid must absorb for 1g to be converted to gas o As a liquid evaporates its remaining surface cools, a process called evaporative cooling Helps stabilize temperatures in organisms and bodies of water o Freezing In ice, each molecule of water is hydrogen-bonded to 4 other water molecules in a 3-dimensinoal crystal. Each crystal is spacious, so ice has fewer molecules than an equal volume of liquid water in which hydrogen bonds are constantly breaking and forming Water is denser than ice o Water reaches its greatest density at 4 C This is why water freezes from the top down o Water below the ice is insulated by the ice and allows life to exist o If ice sank, all bodies of water would freeze solid and make life impossible on earth Water is the solvent of life o Solution: liquid that is a completely homogenous mixture of substances Dissolving agent of a solution o Solute: substance dissolved in a solution Aqueous solution: one in which water is the solvent o Water is a versatile solvent due to its polarity, which allows it to form hydrogen bonds easily o When ionic compounds are dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell Salt example o Water can dissolve ionic compounds and nonionic polar molecules o Even large polar molecules such as proteins can dissolve in water if they have sufficient polar and charged regions on their surfaces Hydrophilic and Hydrophobic Substances o Only those substances that are ionic or polar will dissolve readily in water o Hydrophilic substance is one that loves water. (affinity) o Hydrophobic substance does not like water. (no affinity) o Nonpolar covalent bonds are hydrophobic Hydrophobic molecules related to oils are the major components of cell membranes Molecular Mass and Solute Concentration in Aqueous Solutions o Molecular mass is the sum of all atomic masses off all atoms in a molecule o One mole (mol) of a molecule (or compound) is its molecular mass in gram units of mass 1 mole of CH 4 16 grams o Molarity Is the number of moles of solute per liter of aqueous solution Dissociation of Water Molecules (breaking apart) o Hydrogen atom leaves its electron behind and is transferred as a proton o The molecule with the extra proton is now a hydronium ion Known in biology as H + o Water is in a state of dynamic equilibrium in which water molecules dissociate at the same rate at which they are being reformed. Acids and Bases o Concentrations of Hplus and OHnegative are equal in pure water o Strong acids and bases completely dissociate in water o Weak acids and bases reversibly release and accept back hydrogen ions, but can still shsift the balance of H and OH away from neutrality pH Scale o 7 is neutral o 0-6 acid o 8-14 base o Most biological fluids have pH values of 6-8 Due to enzymes and their denaturation point causing a change in enzyme shape o pH scale is not linear, it represents a ten-fold difference pH of 3 is not twice as acidic as pH of 6, it is 1000 times as acidic o Internal pH of most living cells must be maintained close to pH 7 Buffers: substances that minimize changes in concentrations of Hplus and OHnegative in a solution Most buffered solutions contain a weak acid and its corresponding base, which combine reversibly with Hplus ions Blood example – carbon dioxide would make blood slightly acidic if not for buffers Chapter 4: Carbon is the Chemical Backbone of Life o All known organisms on earth consist primarily of carbon-based compounds o Carbon is unparalleled in its ability to form large, complex, and varied molecules by virtue of the fact that its tetravalent (has four valence electrons) o A carbon atom an bond with up to four other atoms or groups of atoms, making a large variety of molecules possible o There are more than 10 million know carbon compounds o Proteins, nucleic acids, carbohydrates, lipids, and other molecules that distinguish living matter are all composed of carbon compounds o The chemical diversity of carbon is what makes diverse life possible Organic chemistry ifs the study of compounds that contain carbon Organic compounds range from small, simple molecules to colossal ones with substantial structural complexity Most organic compounds contain hydrogen as well as carbon atoms o Tetrahedral shape: in molecules with multiple carbons, each carbon bonded to four other atoms has tetrahedral shape o When two carbon atoms are joined by a double covalent bond, the molecule or segment of molecule, has a rigid flat shape and the atoms covalently bonded to the carbons are in the same plane as the carbons Important properties of Carbon: Electron configuration of carbon gives it covalent compatibility with many different elements Valence electrons of carbon and its most frequent chemical “partners” are the “building code” that governs the architectural of biological molecules o Hydrogen, oxygen, and nitrogen o Carbon Skeletons: Carbon chains form skeletons (or major parts) of most organic molecules Carbon Skeletons can vary in length, and may be straight, branched, or arranged in closed rings Some have double bonds Hydrocarbons consist of only carbon and hydrogen Many organic molecules, such as fats, have hydrocarbon components o Saturated fats: have only single bonds Have more energy than unsaturated fats Can undergo chemical reactions that release large amounts of energy o Breaking of bonds Major components of fossil fuels, which formed from the fossilized remains of dead plants and animals by exposure to heat and pressure in the earth’s crust over hundreds of millions of years o Skeletal formulas – learn to draw them for test Stick representations of carbon skeletons of organic compounds in which carbon atoms of the skeletons of organic compounds in which carbon atoms of the skeleton are assumed to be bonded to hydrogen atoms, unless otherwise noted Any time you see a corner, or not straight line, there is a carbon in that joint All atoms snot carbon or hydrogen bonded to carbon are signified by their chemical symbol o If not all bonds are filled by a chemical symbol, it can be assumed that hydrogen fills that bond o Isomers: compounds that have the same molecular formula but different structures and chemical properties The number of possible isomers increases as carbon skeletons increase in size 18 variations of octane (C8H 18 366319 possible structures of icosane (C H ) 20 42 Types of Isomers: Structural isomers: different covalent arrangements of their atoms Cis-trans isomers: same covalent bonds but differ in spatial arrangements o Arise from double bonded carbons because they do not allow atoms they join to rotate freely about the bond axis o Cis isomer: same side o Trans Isomer: different side Enantiomers: mirror images of each other o Often designated the “L” and “D” isomers from latin for left and right (levo and dextro) o Enantiomers cannot be superimposed on each other (overlap) o Pharmaceutical industry: Two enantiomers of a drug may have different effects Usually only one isomer is biologically alive Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules o Enzymes using the “key in lock” system cause only one biological side to be active (only one side fits in lock) o Functional Groups: Distinctive chemical properties of an organic molecule depend not only on the arrangement of its carbon skeleton, but also on molecular components attached to the skeleton Functional groups are the parts of organic molecules involved in chemical reactions Functional groups replace one or more hydrogens bonded to the carbon skeleton of a hydrocarbon They behave consistently from one organic molecule to another The number and arrangement of functional groups help give each molecule its unique chemical properties o ACTUAL GROUPS Hydroxyl: Polar (-OH) Due to electronegative oxygen, hydrophilic, forms hydrogen bonds with water Carbonyl: polar (carbon double bonded with oxygen) Sugars with ketone groups are called ketoses; those with aldehydes are called aldoses. Ketone: oxygen double bonded to carbon, with two R groups (1 each side) Aldehyde: oxygen double bonded to carbon, with one R group and one H Carboxyl: Polar (carbon double bonded to oxygen, with hydroxyl group) Decreases PH - Acts as an acid Seen as (-COOH) Amino: (-NH )2 Increase PH – acts as a base Sulfhydryl: (-SH) Two Sulfhydryl groups can react forming cross links that help stabilize protein structures o Disulfide Bridge Phosphate: (OPO ) 2- 3 Polar Contributes negative charge. When attached, confers on a molecule the ability to react with water, releasing energy o DNA and ATP o Phosphorylation Methyl NONPOLAR (CH ) 3 o DNA made of bases, Cytosine is the G, and gets the methyl group added to it. Methylation process tells enzymes which is original strand o Affects the expression of genes, affects the shape and function of sex hormones. o Functional Group Example Sex hormones estradiol (estrogen) and testosterone differ only in the presence of certain functional groups on a common ring structure The different actions of these two molecules produce the contrasting features of female and male animals Macromolecules: o All life as we know it is carbon-based and dependent on carbon-based chemistry o The chemical versatility of carbon makes possible and incredible diversity of organic molecules o Variation at the molecular level lies at the foundation of all biological diversity Thalidomide Tragedy: o Thalidomide is sedative, hypnotic, and anti-inflammatory medication developed in the 1950s by a German pharmaceutical company o Thalidomide is racemic – it contains both left and right handed isomers (enantiomers) in equal amounts o Thalidomide enantiomers can interconvert at physiological pH Go back and forth between left and right handed o The S form of thalidomide is a potent teratogen, a compound that can cause malformation of embryos o SAFETY LAWS CREATED AND CHANGES MADE IN WHO IT IS PRESCRIBED Chapter 5: Biological Macromolecules o Within cells, small organic molecules are often joined together to form larger molecules, called macromolecules o All living organisms are made up of four classes of macromolecules Carbohydrates: monosaccharides, disaccharides, and polysaccharides Sugars and starches Lipids: fats, phospholipids, sterols, etc. Fats, Oils, and steroids Proteins: amino acid polymers Nucleic Acids: nucleotide polymers DNA or RNA (ATCG are nuclotides) o Polymers: long molecule (macromolecule) consisting of any similar building blocks called monomers One Lego: monomer Castle: polymer Two of the four classes of life’s macromolecules consist of only polymers: Proteins and nucleic acids A third class, carbohydrates, consist of monomers, dimers, and polymers Synthesis and Breakdown of Polymers o Dehydration reaction removes water, creates covalent bond, and links a monomer to a polymer. o Hydrolysis: bonds are broken down by the addition of water molecules Hydrogen from the water bonds to one monomer and the hydroxyl group bonds to the adjacent monomer (breaks polymers into monomers) Diversity of Biological Polymers o Every cell has thousands of different macromolecules o Macromolecules vary among cells of a single multicellular organism, vary more between individual organisms within a species, and vary even more between species o An immense variety of polymers can be built from a small set of monomers Carbohydrates: o Carbohydrates include sugars and the polymers of sugars o Simplest carbohydrates are monosaccharides, or single sugars Have molecular formulas that are usually multiples of CH O 2 Have a hydroxyl group bonded to each carbon except one, which is double bonded to an oxygen to form a carbonyl group Glucose (C 6 12) 6s the most common monosaccharide Classification: Location of the carbonyl group (aldoses o ketoses) Number of carbons in carbon skeleton Ring structures: formed by many monosaccharides in aqueous solutions ie. Glucose (Water is involved in all aqueous solutions) Monosaccharides serve as a major fuel for cells In cellular respiration, cells extract the energy stored in glucose molecules Monosaccharides also serve as raw material for the synthesis of other types of small organic molecules, including amino acids and fatty acids Monosaccharides not immediately used are incorporated as monomers into disaccharides and polysaccharides o Disaccharide is formed when a dehydration reaction joins two monosaccharides o Covalent bond is called a glycosidic linkage o Most common disaccharide is sucrose o Polysaccharides are sugar polymers composed of many sugar building blocks Polymers of monosaccharides Typically consist of few hundred to several thousand monosaccharides linked together Structure and function is determined by Sugar monomers Positions of its glycosidic linkages Two types Storage o Starch is the storage polysaccharide of plants Consists entirely of glucose monomers Plants store surplus starch as granules within chloroplasts and other plastids The simplest form of starch is amylose o Glycogen is a storage polysaccharide in animals More branched in structure than starch Humans and other vertebrates store glycogen mainly in liver and muscle cells Hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases Structural o Serve as building material for structures protecting cells or whole organisms o Cellulose is a major component of the tough walls that enclose plant cells (fiber) Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ Based on two ring forms for glucose o Alpha in starch All 4 OH on same side Tend to be helical (spiral like) o Beta in cellulose OH alternate sides Straight and unbranched Produce parallel cellulose molecules linked together using hydrogen bonds within the hydroxyl groups of one to another Grouped into microfibrils (found in cell walls) Enzymes that digest starch by hydrolyzing alpha linkages can’t hydrolyze Beta linkages in cellulose This is why cellulose in human food passes through the digestive tract as insoluble fiber o Help move bowels Some microbes use enzymes to digest cellulose Many herbivores, from cows to termites, have symbiotic relationships with these microbes o Chitin is a structural polysaccharide found in the exoskeletons of arthropods It also provides structural support for the cell walls of many fungi Chitin’s properties as a flexible and strong materials make it favorable as a surgical thread Why bugs shed their shells Lipids: are one of the class of macromolecules that do not form polymers o Unifying feature of lipids is having little or no affinity for water (hydrophobic) Consist mostly of hydrocarbons, which form nonpolar covalent bonds o The most biologically important lipids are Fats Constructed from two types of smaller molecules: o Glycerol: is a three carbon alcohol with a hydroxyl group attached to each carbon o Fatty Acid: consists of a carboxyl group attached to a long hydrocarbon tail Synthesized from dehydration reactions between glycerol hydroxyl and fatty acid carboxyl groups o Ester linkage (3 of these = triglyceride) Separate from water because water molecules form hydrogen bonds with each other and exclude the fats o Vary in length (number of carbons) and the number and locations of double bonds Saturated Fatty acids: have maximum number of hydrogen atoms possible and no double bonds Tend to be solid at room temperature Straight in space filling model Unsaturated fatty acids: have one or more double bond Tend to be liquid at room temperature Bent in space filling model Major function of fats is energy storage o Fact Slide Trans Fats and Your Health o Hydrogenated vegetable oils are made by synthetically converting unsaturated fats to saturated fats To produce products like margarine to lengthen the shelf life of certain processed foods Process also converts cis- (bent) hydrocarbon tails to a trans- (straight) form, resulting in trans fats Currently thought to contribute more to cardiovascular disease than saturated fats Phospholipids Consists of two fatty acids and a phosphate group attached to a glycerol backbone o Two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a polar head (hydrophilic) Phospholipid bilayer o When added to water, they self-assemble into a bilayer with the hydrophobic tails pointing toward the interior Phospholipids are the major component of all cell membranes in EVERYTHING THAT IS ALIVE Steroids Lipids characterized by a carbon skeleton consisting of four fused rings o Cholesterol is a component of animal cell membranes and a precursor from which other steroids are synthesized High levels in the blood may contribute to cardiovascular disease, but is essential to animals Proteins: large organic polymers made of amino acid monomers arranged in a linear chain and joined together by peptide bonds o Account for more than 50% of dry weight in most cells o Tens of thousands of different proteins in the human body o Proteins are responsible for many biological activities Synthesis of macromolecules and their building blocks Structural support Molecular storage Transport into, out of, and within cells Cellular communication (hormones) Cellular motility Defense (immune system and antibodies) o Protein Vs Polypeptide terms A functional protein consists of one or more polypeptides Polypeptides are unbranched polymers built from the same basic set of 20 amino acids Amino acids are organic molecules possessing both amino and carboxyl functional groups KNOW NAMES, NOT PARTS Nonpolar R Group: will share electrons equally (hydrophobic) Polar R Group: will not share electrons equally (hydrophilic) Electrically Charged: (hydrophilic) o Acidic: contain carboxyl group o Basic: contain amino groups Peptide bond is a covalent bond that holds polypeptide together One end has amino group, other end has carboxyl group Therefore, polypeptide chain has polarity with an amino end (N-terminus, positive) and carboxyl end (C-terminus, negative) o A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape Water soluble proteins tend to be globular with polar and charged groups exposed to the aqueous environment (hydrophilic and hydrophobic shapes) The sequence of amino acids determines a protein’s conformation (3D shape) Determines its function o Ribbon filling, space-filling, and wireframe models Four Levels of Protein Structure o Primary structure: unique sequence of amino acids Determined by inherited genetic information DNA sequence of protein coding gene Codons (3 amino acids) o Secondary Structure: found in most proteins, consists of coils and folds in polypeptide chain Alpha helix = coil Hydrogen bond forms between every fourth peptide bond Beta pleated sheet = foil Hydrogen bonds form between peptide bonds in parallel regions of a protein o B strand is shown as flat arrow pointing towards the carboxyl end o Tertiary Structure: determined by interactions among various side chains Includes Hydrogen Bonds, Ionic Bonds, Van der Waals interactions, hydrophobic interactions between nonpolar amino acids, and disulfide bridges Disulfide bridge: strong covalent bonds between sulfur atoms of two cysteines o Two sulfurs connect o Quaternary Structure: results when a protein consists of 2 or more polypeptide chains Creates one macromolecule Collagen: fibrous protein consisting of three collagen polypeptides coiled like a rope (looks like braid) Hemoglobin: globular protein consisting of four polypeptides: two alpha chains and two beta chains What determines Protein Structure? In addition to primary structure, physical and chemical conditions can affect structure o Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel This loss of a proteins native structure is called denaturation Denatured protein is biologically inactive Protein folding in the cell Stable structure: proteins must go through several conformational states to become stable Chaperonins: multi-subunit proteins that assist the proper folding of other proteins o Alzheimer’s and Parkinson’s disease are associated with misfolded proteins o Methods used to determine or predict protein structure: X-ray crystallography: determines the arrangement of atoms within a crystal Beam of X-rays strikes a crystal and the x-rays scattered into many different directions From the angles and intensities of these scattered beams, a three-dimensional picture of the density of electrons within the crystal can be produced NMR Bioinformatics: uses computer programs to predict protein structure from amino acid sequences o Types of Proteins: Enzymatic Proteins: Selective acceleration of chemical reactions o Digestive enzyme catalyzes the hydrolysis of bonds in food molecules Defensive Proteins: Protection against disease o Antibodies inactivate and help destroy viruses and bacteria Storage Proteins: Storage of amino acids o Eggs Transport Proteins: Transport of substances o Hemoglobin transports oxygen from the lungs to other parts of the body Hormonal proteins Coordination of an organism’s activities o Insulin causes other tissues to take up glucose, thus regulating blood sugar concentration Receptor Proteins: Response of cell to chemical stimuli o Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells Contractile and Motor Proteins: Movement Structural Proteins: Support Nucleic Acids: o Two types of nucleic acids Deoxyribonucleic acid (DNA) Provides directions for its own replication Synthesis of messenger RNA (mRNA) a process referred to as transcription Through mRNA, DNA controls protein synthesis, a process called translation Ribonucleic acid (RNA) Contains pentose sugar ribose o Nucleic acids are polymers called polynucleotides (has phosphate) Each is made of monomers called nucleotides Consists of Nitrogenous base, pentose sugar, and phosphate group Portion of nucleotide without phosphate group is called a nucleoside Pyrimidines vs Purines Pyrimidine: one circle structure: o Cytosine, thymine, uracil Purines: two circle structure o Adenine, Guanine SUGAR PHOSPHATE BACKBONE o 5’ end phosphate o 3’ end sugar o Anti-parallel o Evolution o Sickle Cell Disease: Slight change in primary structure can affect a proteins other structures and its ability to function Chapter 6 All living things are composed of one or more cells o Cells are the basic units of structure and function in living things Cell is simplest collection of matter capable of performing all activities of life o Every cell originates from another cell; therefore, all cells are related by their descent from earlier cells Development of fundamental tenets of cell theory was made possible by advancements in microscopy from pioneering work Fundamental Units of Life: o All living things are composed of one or more cells (viruses being the possible exception) o Cell structure is correlated to cellular function o Cells can differ substantially from one another but share common features; Plasma membrane – phospholipid bilayer embedded with many proteins Cytosol – aqueous semifluid bounded by the plasma membrane Chromosomes – DNA and proteins associated with DNA Ribosomes – very large protein – RNA complexes that carry out protein synthesis (translation) Slightly different in prokaryotes and eukaryotes (bigger in eukaryotes) Microscopes: o Can do 3 things Magnification – ratio of an object’s image size to its actual size Resolution – measure of the clarity of an image Ability to distinguish two dots from each other Contrast – the degree of difference between the lightest and darkest parts of a sample o Light Microscopy Light Microscope (LM) = visible light passes through a specimen and then through glass lenses, which magnify the image Can magnify effectively to about 1000 times the size of the actual specimen Minimum resolution of a LM is about 200 nanometers, or the size of a small bacterium Bright Field Microscopy: simplest optical microscopy illumination Light passes directly through specimen, then through glass lenses Image has little contrast unless sample is naturally pigmented or artificially stained Phase contrast Microscopy: Differential Interference Contrast (DIC) microscopy: Use polarizers to exaggerate differences in the optical density of a specimen o Have 3D appearance Fluorescence Microscopy: Ultraviolet Light is transmitted through a specimen Fluorescently tagged molecules absorb uv light and emit visible light Confocal Microscopy Lasers and special optics are used to image specimens within a very narrow focal plane Images are acquired point-by-point and reconstructed with a computer o Electron Microscopy Electron Microscopes: can be used to visualize surface or intracellular features of a specimen Scanning electron microscopes focus a beam of electrons onto the surface of a specimen o Sees surface Transmission electron microscopes focus a beam of electrons through a specimen o Used to see internal ultrastructure Cell Fractionation: o Breaks cells apart and when dealing with eukaryotic cells, can be used to separate major organelles from one another o Ultracentrifuges are used to fractionate cells into their component parts o Enables scientists to determine the functions of organelles using biochemistry techniques that correlate cell function with structure Eukaryotes and Prokaryotes: o The basic structural and functional unit of every organism is one of two types of cells o Only organism of the domains Bacteria and Archaea consists of prokaryotic cells o Protists, fungi, animals, and plants all consist of eukaryotic cells o Prokaryotes: No membrane bound organelles DNA, typically double stranded and circular in structure, is contained in a non-membrane bound region called the nucleoid Cytoplasm is bound only by a plasma membrane o Eukaryotic Cells DNA, double-stranded and usually linear in structure, is contained in a membrane-bound organelle called the nucleus Other membrane-bound organelles Cytoplasm in the region between the plasma membrane and nucleus Generally, much larger than prokaryotic cells o Plasma Membrane: Selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of the cell Semipermeable Bilayer General structure of a biological membrane is a bilayer of phospholipids embedded with proteins Limits on Cell Size o Larger organisms have more cells, not larger cells o Each cell relies on the passage of nutrients and waste into and out of its cytoplasm through the plasma membrane As an object increases in size, its volume grows proportionally faster than its surface area 2 Surface area increases by n Volume increases by a factor of n 3
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