General Biology I
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This 16 page Study Guide was uploaded by Ozzie Stokes on Wednesday October 21, 2015. The Study Guide belongs to BIO 121 at Syracuse University taught by Jason Wiles in Fall. Since its upload, it has received 39 views. For similar materials see /class/225588/bio-121-syracuse-university in Biology at Syracuse University.
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Date Created: 10/21/15
Chapter 3 Notes Organic compounds are those in which carbon atoms are covalently bonded to one another to form the backbone of the molecule 0 Considered inorganic if the carbon is not bonded to another carbon or to hydrogen carbon dioxide Carbon atom forms bonds with a greater number of different elements than does any other type of atom Carbon atom has 4 valence electrons it can complete its valence shell by forming a total of four covalent bonds Hydrocarbons organic compounds consisting only of carbon and hydrogen can exist as unbranched or branched chains or as rings There is a freedom of rotation around each carbontocarbon strong bonds single bond flexible and assume a variety of shapes 0 Double and triple bonds do not allow rotation so these regions tend to be inflexible Isomers compounds with the same molecular formulas but different structures and thus different properties no identical physical or chemical properties 0 Cells can distinguish because usually one is biologically active 0 Three types structural isomers geometric isomers and enantiomers Structural isomers compounds that differ in the covalent arrangements of their atoms Geometric isomers are compounds that are identical in the arrangement of their covalent bonds but different in the spatial arrangment of atoms or groups of atoms 0 Present in some carbontocarbon double bonds 0 Cistrans isomers are when the two larger components are on the same side of the double bond 0 Trans isomers are when the two larger components are on the opposite sides of the double bond enantiomers are isomers that are mirror images of each other 0 although enantiomers have similar chemical properties and most of their physical properties are identical cells recognize the difference in shape and usually only one form is found in organisms 0 central carbon is asymmetrical four groups bonded to a single carbon atom are arranged at the vertices of a tetrahedron because covalent bonds between hydrogen and carbons are nonpolar hydrocarbons lack distinct charged regions 0 insoluble in water 0 tend to cluster together thorough hydrophobic interactions interact much more weakly than the water molecules thru hydrogenbonding functional groups groups of atoms that determine the types of chemical reactions and associations in which the compound participates polar and ionic functional groups are hydrophilic because they associate strongly with polar water molecules the symbol R is used to represent the remainder of the molecule of which each functional group is a part c the methyl group a common nonpolar hydrocarbon group R CH3 refer to Table 31 on Page 49 the hydroxyl group R OH is polar because of the presence of a strongly electronegative oxygen atom not a hydroxide ion carbonyl group consists of a carbon atom that has a double covalent bond with an oxygen atom 0 double bond is polar because of the electronegativity of oxygen this group is hydrophilic aldehyde has a carbonyl group positioned at the end of the carbon skeleton R CHO o ketone has an internal carbonyl group R CO R carboxyl group R COOH in its nonionized form consists of a carbon atom joined by a double covalent bond to an oxygen atom and by a single covalent bond to another oxygen which is in turn bonded to a hydrogen atom o the two oxygens create an extremely polarized condition sometimes causing the H to split which results in R COO39 o weakly acidic 0 two hydrophilic states ionic or polar o essential consituents of amino acids amino group R NHZ in its nonionized form includes a nitrogen atom covalently bonded to two hydrogen atoms 0 weakly basic because they can accept a hydrogen ion proton 9 R NH3 0 components of amino acids and of nucleic acids phosphate group R PO4H2 is weakly acidic o can produce ionized forms with 1 or 2 units of negative charge because of the attraction of electrons by the oxygen atoms 0 constituents of nucleic acids and certain lipids sulfhydryl group R SH consisting of an atom of sulfur covalently bonded to a hydrogen atom is found in molecules called thios 0 amino acids with this group can make important contributions to the structure of proteins 0 O macromolecules giant molecules such as proteins and nucleic acids consisting of thousands of atoms 0 most are polymers produced by linking small organic compounds called monomers o the 20 monomers called amino acids can be linked end to end in countless ways to form the polymers known as proteins polymers can be degraded to their component monomers by hydrolysis reactions 0 a hydrogen from a water molecule attaches to one monomer and a hydroxyl from water attaches to the adjacent monomer monomers are covalently linked by condensation reactions 0 dehydration synthesis is sometimes used to describe condensation o the synthesis of a polymer is not simply the reverse of hydrolysis carbohydrates sugars starches and cellulose sugar and starch are energy for the cell and cellulose is the main structural component of the walls that surround plant cells 0 contain carbon hydrogen and oxygen atoms in a ratio of one carbon to two hydrogen to one oxygen CHzOn 0 contain one sugar unit monosaccharides two sugar units disaccharides or many sugar units polysaccharides monosaccharides contain from three to seven carbon atoms 0 a hydroxyl group is bonded to each carbon except one that carbon is doublebonded to an oxygen atom forming carbonyl group o the large number of polar hydroxyl groups plus the carbonyl group gives a monosaccharide hydrophilic properties 0 hexose glucose fructose galatose and other sixcarbon sugars 0 glucose the most abundant monosaccharide is used as an energy source in most organisms 0 so important in metabolism that mechanisms have evolved to maintain its concentration at relatively constant levels in the blood humans and other complex animals 0 glucose and fructose are structural isomers atoms are just arranged differently in fructose a ketone the doublebonded oxygen is linked to a carbon within the chain rather than to a terminal carbon as in glucose an aldehyde 0 glucose and galactose are both hexose and aldehyde however they are enantiomers 0 glucose when this hydroxyl group is on the same side of the plane of the ring as the CH20H side group the glucose is designated beta glucose B glucose when it is on the side with respect to the plane of the ring opposite the CH20H side group the compound is designated alpha glucose a glucose 0 disaccharide two sugars contains two monosaccharide rings joined by a glycosidic linkage between carbon 1 of one molecule and carbon 4 of the other consisting of a central oxygen covalently bonded to two carbons one in each ring 0 maltose water 9 glucose glucose 0 sucrose water glucose fructose polysaccharide a macromolecule consisting of repeating units of simple sugars usually glucose 0 most abundant in carbohydrates and includes starches glycogen and cellulose 0 may be a single long chain or a branched chain starch the typical form of carbohydrate used for energy storage in plants is a polymer consisting of aglucose subunits 0 two forms amylose simpler unbranched and amylopectin more common branched amyloplasts specialized organelles where starch is stored as granules in a plant cell c all organisms including humans and other animals have enzymes that can break a14 linkages glycogen animal starch the form in which glucose subunits joined by a14 linkages are stored as an energy source in animal tissues more extensively branched and more water soluble than plant starch but share a similar structure 0 in vertebrates glycogen is stored mainly in the liver and muscle cells cellulose the most abundant carbohydrate on Earth accounts for 50 or more of all the carbon in plants structural carbohydrate insoluble polysaccharide composed of many joined glucose molecules 0 contains Bglucose monomers joined by 814 linkages bonds cannot be split by the enzymes that hydrolyze the alinkages in starch 0 since humans like other animals lack the enzymes that digest cellulose we cannot use it as a nutrient cellulose found in whole grains and vegetables remains fibrous and provides bulk that helps keep our digestive tract functioning properly chitin a main component of cell walls of fungi and of the external skeletons of insects crayfish and other arthropods forms very tough structures 0 further hardened by the addition of calcium carbonate CaCO3 glycoproteins carbohydrates combined with proteins to form compounds present on the outer surface of cells other than bacteria 0 most proteins secreted by cells are these glycolipids carbohydrates combined with lipid to form compounds on the surfaces of animal cells that allow cells to recognize and interact with one another lipids are a heterogeneous group of compounds that are categorized by the fact that they are soluble in nonpolar solvents and are relatively insoluble in water 0 consist mainly of hydrogen and carbon with few oxygencontaining functional groups lipids which have little oxygen tend to be hydrophobic includes fats phospholipids carotenoids orange and yellow plant pigments steroids and waxes 0 some are used for energy storage others serve as structural components of cell membranes and some are important hormones triacylglycerols are the most abundant lipids in living organisms they re an economical form of reserve fuel storage because when metabolized they yield more than twice as much energy per gram as do carbohydrates o triacyglycerol molecule consists of glycerol joined to three fatty acids 0 formed by a series of three condensation reactions glycerol a threecarbon alcohol that contains three hydroxyl groups fatty acid a long unbranched hydrocarbon chain with a carboxyl group at one end ester linkage monoacylglycerol yielded from the first condensation reaction diacylglycerolyielded from the second reaction important molecule for sending signals within a cell triacyloglycerol yielded from the third reaction during digestion triacylglycerols are hydrolyzed to produce fatty acids and glycerol about 30 different fatty acids are commonly found in lipids and they typically have an even number of carbon atoms oleic acid with 18 carbons is the most widely distributed fatty acid in nature and is found in most animal and plant fats saturated fatty acids contain the maximum possible number of hydrogen atoms 0 palmitic acid is a common saturated fatty acid 16 carbon 0 organisms with fats high in this tend to be solid at room temperature van der Waals interactions weak attractions but can be strong among long hydrocarbon chains make a substance more solid by limiting the motion of its molecules unsaturated fatty acids include one or more adjacent pairs of carbon atoms joined by a double bond not fully saturated with hydrogen 0 monosaturated fatty acids fatty acids with one double bond 0 eg oleic acid 0 polysaturated fatty acids fatty acids with more than one double bond 0 eg linoleic acid models is bent or kinked wherever a carbontocarbon double bond appears I fats containing a high proportion of these acids are usually liquid at room temperature trans fatty acids are technically unsaturated but they mimic many of the properties of saturated fatty acids 0 at least two unsaturated fatty acids linoleic acid and arachidonic acid are essential nutrients that must be obtained from food because the human body cannot synthesize them amipathic lipids phospholipids belong to this group lipids where one end of each molecule is hydrophilic and the other end is hydrophobic phospholipid consists of a glycerol molecule attached at one end to two fatty acids and at the other end to a phosphate group linked to an organic compound such as choline the organic compound usually contains nitrogen o the amipathic properties of phospholpids cause them to form lipid bilayers in the aqueous watery solution 0 suited as fundamental components of cell membranes carotenoidsinsoluble in water have an oily consistency orange and yellow plant pigments play a role in photosynthesis o isoprene units fivecarbon hydrocarbon monomers found in carotenoid molecules retinal a visual pigment converted from the conversion of carotenoids to vitamin A c three groups of animals mollusks inserts vertebrates have eyes that use retinal in the process of light reception steroid consists of carbon atoms arranged in four attached rings three of the rings contain six carbon atoms and the fourth contains five 0 synthesized from isoprene units 0 important biological steroids cholesterol bile salts reproductive hormones cortisol and other hormones secreted by the adrenal cortex animal cells secrete chemicals to communicate with one another or to regulate their own activities 0 some chemical mediators are produced by the modification of fatty acids that have been removed from membrane phospholipids 0 include prostagandins which have varied roles including promoting inflammation and smooth muscle contraction proteins macromolecules composed of amino acids are the most versatile cell components refer to Table 32 on page 62 enzymes protein molecules that accelerate the thousands of different chemical reactions that take place in an organism proteins are assembled into a variety of shapes allowing them to serve as major structural components of cells and tissues 0 growth and repair as well as maintenance of the organism depend on proteins amino acids the constituents of proteins have an amino group and a carboxyl group bonded to the same asymmetrical carbon atom known as the alpha carbon 0 20 amino acids are commonly found in proteins each identified by the variable chain R group and bonded to an a carbon 0 in neutral pH they are mainly dipolar 0 because of the ability of the amino and carboxyl groups to accept and release protons amino acids in solution resist changes in acidity and alkalinity and therefore are important biological buffers 0 amino acids classified as having nonpolar side chains tend to have hydrophobic properties whereas those classified as polar are more hydrophilic o acidic and basic side chains are ionic at cell pH and therefore hydrophilic o essential amino acids are those an animal cannot synthesize in amounts sufficient to meet its needs and must obtain from the diet 0 eg isoleucine leucine and histidine childrenarginine 0 animals differ in their biosynthetic capacities peptide bond covalent carbontonitrogen bond linking two amino acids dipeptideformed when two amino acids combine polypeptide a longer chain of amino acids a protein consists of one or more polypeptide chains has a free amino group at one end and a free carboxyl group at the opposite end 0 backbone of a polypeptide NCCNCCNCC plus all other atoms except those in the R groups which instead extend from this backbone almost an infinite variety of proteins molecules is possible differing from one another in the number types and sequences of amino acids they contains globular proteins tightly folded into compact roughly spherical shapes 0 close relationship between a protein s conformation and its function four main levels of protein ordanization primary secondary tertiary quaternary 0 primary structure sequence of amino acids joined by peptide bonds of a polypeptide chain 0 other forms of structure derived from this one simple and linear o secondary structure highly regular 0 two common types ahelix uniform helical coil by the hydrogens bonds 36 amino acids are included in each complete turn basic structural unit of some fibrous proteins and Bpleated sheet 0 ahelix conformations providing elasticity and Bpleated sheet conformations providing strength 0 tertiary structure 90 in textbook3D structure depends on o 1 Hydrogen bonds form between R groups of certain amino acid subunits 2 An ionic bond can occur between a R group with a unit of positive charge and one with a unit of negative charge 3 Hydrophobic interactions result form the tendency of non polar R groups to be excluded by the surrounding water and therefore to associate in the interior of the globular structure 0 4 Covalent bonds known as disulfide bonds or disulfide bridges S S may link the sulfur atoms of two cysteine subunits belonging to the same chain A disulfide bridge forms when the sulfhydryl groups of two cysteines react the two hydrogen are removed and the two sulfur atoms that remain become covalently linked o quaternary structure look in textbook the same types of interactions that produce secondary and tertiary structure also contribute to this proteins with two or more polypeptide chains have this structures 0 hemoglobin the protein in red blood cells responsible for oxygen transport is an globular protein with a quaternary structure 0 O disul de bridges are a common feature of antibodies and other proteins secreted from cells 0 these strong bonds stabilize the molecules in the extracellular environment the amino acid sequence of a protein determines it conformation form follow function molecular chaperones mediate the folding of other protein molecules thought to make the folding process more orderly and efficient 0 protein conformation determines function domain a distinct structural region a single protein may have more than one of these 0 each may have a different function denaturation changes in the shape and the accompanying loss of biological activity a protein s primary structure can be determined rapidly through the application of genetic engineering techniques or by the use of sophisticated technology such as mass spectrometry nucleic acids transmit hereditary information and determine what proteins a cell manufactures o deoxyribonucleic acid DNA composes the genes and contains instructions for making all the proteins as well as all the RNA the organism needs 0 ribonucleic acid RNA participates in the process in which amino acids are linked to form polypeptides o ribozymes specific biological catalysts glossary nucleotides molecular units that consist of 1 a fivecarbon sugar either deoxyribose in DNA or ribose in RNA 2 one or more phosphate groups which make the molecule acidic 3 a nitrogenous base a ring compound that contains nitrogen o the nitrogenous base be either be a doublering purine or a single ring pyrmidine DNA contains the purines A adenine G guanine C cyostine and thymine T as well as sugar deoxyribose and phosphate RNA contains purines adenine A and guanine G and the pyridines cytosine C and uracil U together with the sugar ribose and phosphate Phosphodiester linkages joins linear chains of nucleotides formed by molecules of nucleic acids consists of a phosphate group and the covalent bonds that attach it to the sugars of adjacent nucleotides DNA has to nucleotides chains into a double helix while RNA has one chain Adrenosine triphosphate ATP composed of adenine ribose and three phosphates primary energy currency of all cells can transfer another phosphate group to another molecule making it reactive Guanine triphosphate GTP a nucleotide that contains the base guanine can transfer energy by transferring a phosphate group and also has a role in cell signaling Cyclic adenosine monophosphate cyclic AMP ATP is converted to this by the enzyme adenylyl cyclase regulates certain cell functions such as cell signaling and is important by which some hormones act Cyclic guanosine monosphonphate cGMP also plays a role in certain signaling processes Nicotinamide adenine dinucleotide primary role in oxidation and reduction reactions in cells can exist in oxidized form NAD that is converted to a reduced form NADH when it accepts electrons TABLE 33 is very important to study provides an effective summary Ashley Wandishin Chapter 1 A View of Life Biology the science of life Evolution populations oforganisms have evolved through time from earlier forms of life There are diverse life forms on this planet that are related and that the populations have evolved changed over time from earlier forms of life Provides a framework for biology Information transfer information must be transmitted within organisms and among organisms The survival and function of every cell and every organism depend on the orderly transmission of information Evolution depends on the transmission of genetic information from one generation to another Energy for life all life processes including the thousands of chemical transactions that maintain life s organization require a continuous input ofenergy All organisms consist of basic units called cells which are only formed from preexisting ones cell theory Unicelluar organisms consist of a single cell Multicellular organisms consist of billion of cells life processes depend on the coordinated function of component cells that may be organized to form tissues organs and organ systems Plasma membrane a separator for the cell from the surrounding external environment DNA deoxyribonucleic acid genetic instructions are encoded in this in most cells Organelles the internal structures found within a cell specialized to perform speci c functions Prokaryotic cells exclusive to bacteria and to microscopic organisms called archaea contain no nucleus or other membrane enclosed organelles Eukaryotic cells all the other organisms contain a variety of organelles including a nucleus houses DNA within a membrane Biological growth involves an increase in the size of individual cells of an organism in the number of cells or in both Living organisms develop as well as grow Development includes all the changes that take place during an organism s life Metabolism the sum of all the chemical activities ofthe organism Metabolic process occur continuously in every organism and they must be carefully regulated to maintain homeostasis an appropriate balanced internal environment Homeostatic mechanisms help regulate the metabolism eg glucose concentration in blood of complex animals All forms of life respond to stimuli physical or chemical changes in their internal or external environment Responding to stimuli involves movement though not always locomotion In simple organisms the entire individual may be sensitive to stimuli Locomotion in some organisms happens through the process of amoeboid movement slow oozing ofthe cell cilia tiny hairlike extensions beating of this or flagella longer structures rotation ofthis Most sponges corals and oysters have freeswimming larval stages but most are sessile do not move from place to place as adults so they use their cilia or flagella to moving the water around to obtain food and oxygen Simple organisms reproduce through asexual reproduction and the only variation that can occur is through genetic mutation permanent changes in the genes Most plants and animals have the fusion ofan egg and sperm cell to form a fertilized egg through sexual reproduction this genetic variation is important in the vital processes of evolution and adaptation Adaptations inherited characteristics that enhance an organism s ability to survive in a particular environment may be structural physiological biochemical behavioral or a combination of all four Reductionism learning about a structure by studying its parts Each level has emergent properties characteristics not found a lower levels eg population density age structure Atomis the smallest unit of a chemical element that retains the characteristic properties of that element Atoms combine chemically to form molecules
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