FUNDAMENTAL CHEMISTRY II
FUNDAMENTAL CHEMISTRY II CHEM 102
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Chapter 12 Pr0teins I Proteins function as the building and maintenance of the organism They are the most plentiful organic chemicals of the body and are responsible for a great array of functions 0 Catalytic proteins or enzymes catalyze the synthesis and utilization of proteins carbohydrates lipids nucleic acids and almost all other biomolecules 0 Transport proteins bind and carry specific molecules or ions from place to place Regulatory proteins control cellular activity like lipid hormones and protein hormones such as insulin which regulates glucose metabolism 0 Structural proteins give the physical shape and the strength to maintain it to structures in anim alsithe role played by cellulose in plants 0 Contractile proteins provide cells and organisms with the ability to change shape and move 0 Protective proteins defend against invaders and prevent or minimize damage after injury 0 Storage proteins provide a reservoir of nitrogen and other nutrients especially when external sources are low or absent I a Amino Acidsithe building blocks for naturally occurring polypeptides compounds containing both a carboxyl group and an amino group attached to the same carbon atom o Mammals require all 20 ocam ino acids for protein synthesis but are unable to synthesize half of them These 10 essential amino acids must be obtained from the diet 0 Categorized according to the R group or side group on the on carbon I onpolar neutral have neutral hydrophobic side groups I Polar neutral have hydrophilic side groups I Polar acidic have acidic hydrophilic side groups I Polar basic have basic hydrophilic side groups 00 I Peptides o Peptides polyamides formed by ocamino acids reacting with one another 0 Reaction dehydration between the carboxyl and amino groups of different ocamino acid molecules 0 The amino acids in the peptide called amino acid monomers are linked together by a peptide bond the bond formed between the carbonyl carbon and the nitrogen o The functional group formed by this reaction is an amide group called the peptide group 0 Dipeptides tripeptides tetrapeptides pentapeptides hexapeptides etc o Polypeptides contains many amino acid monomers exceeds 1020 amino acids 0 Oligopeptides refer to peptides smaller than polypeptides O Naming peptides I All peptides contain an ocamino group at one end and a occarboxyl group at the other end I The end containing the amino group is called the Nterminal amino terminal I The end containing the carboxyl group is called the Cterminal carboxyl terminal The C terminal monomer located on the far right keeps it amino acid name For each of the other amino acid monomers in a peptide the fine or iicacid ending of the amino acid name is replaced by 7y I Naming begins at the N terminal side 0 The physiological function of a peptide is determined largely by its amino acid sequence the sequence of amino acid monomers I Constitutional isomers peptides with the same amino acids but a different sequence I 3D Structure of Proteins o Polypeptides containing more than 50 monomers are called proteins if they have physiological functions as individual polypeptide molecules 0 Simple proteins proteins containing only polypeptide molecules o Conjugated proteins proteins containing also nonpolypeptide molecules or ions I Apoprotein the polypeptide part I Prosthetic group the nonpolypeptide molecules or ions 0 Four levels I Primary structure is the ocamino acid sequence of a polypeptide I Secondary structure is the conformation in a local region of a polypeptide molec Tertiary structure exists when the polypeptide has different secondary structures in different local regions It describes the threedimensional relation among different secondary structures in different regions I Quaternary structure exists only in proteins in which two or more polypeptide molecules aggregate together It describes the threedimensional relation among different polypeptides I Denaturation is the loss of native conformation brought about by a change in environmental conditions resulting in loss of physiological function 0 The protein is then called a denatured protein Chapter lliLipids o Lipids are the predominant and most efficient form of stored energy in animals that have a broad array of inctions o Triacylglycerolsianimal fats and plant oilsiare sources of energy and a storage form of energy not required for immediate use 0 Glycerophospholipids sphinolipids and cholesterol together with proteins are the primary structural c r A n A n r o Steroid hormones such as sex hormones act as chemical messengers initiating or altering activity in speci c target cells 0 The lipid soluble fatsoluble vitamins A D E and K are required for a variety of physiological inctions o Bile salts are needed for the digestion of lipids in the intestinal tract 0 Classifying Lipids Based on solubility behavior They are either soluble in nonpolar or lowpolarity solvents They are basically insoluble in Water 0 Most lipids are arnphipathic one part ofthe molecule is hydrophobic and the other part is hydrophilic o Lipids are classified as hydrolyzable or nonhydrolyzable I Hydrolyzable lipids undergo cleavage into 2 or more smaller parts in the presence of an acid base or digestive enzyme All hydrolyzable lipids contain at least one ester group Nonhydrolyzable lipids do not undergo a cleavage into smaller parts because they do not contain an ester amide phosphate or acetal group 0 Fatty Acids o All hydrolyzable lipids contain one or more fatty acidsicarboxylic acids with long hydrocarbon chains atty acids in nature used to construct hydrolyzable lipids are almost all linear acids with an even number of carbons 0 May either be saturated or unsaturated I Saturated fatty acids contain no CC double bonds I Unsaturated fatty acids contain one or more CC double bonds 0 Essential fatty acidsiunsaturated fatty acids that are synthesized only by plants but are required by animals and must therefore by included in their diets linoleic and linolenic o Nonessential fatty acidsiall other fatty acids that animals synthesize either from other fatty acids or from other foodstuffs 0 Omega number owithe position of the double bond nearest the methyl group in unsaturated fatty acids 0 Triacylglycerols 0 Also known as TAGs and triglycerides 0 Make up about 90 of our dietary lipid intake All animal fats such as beef pork poultry fats and all plant oils such as com olive peanut and soybean oils are triacylglycerols 0 They are esters in fact triesters of glycerol 0 Chemical Reactions I 1 II 39 ester groups in I 4 and fatty acids 0 Acidic hydrolysis yields fatty acids Basic hydrolysis yields fatty acid carboxylate salts o Digestion and storage Triacylglycerols are too large to dif ise through the intestinal membranes so they must be digested hydrolyzed by the enzymes lipases with the help ofbile salts I Takes place in the small intestine Which has a basic H I A er digestion the cells in the intestinal tract rebuild triacylglycerols and package them with proteins They are then carried through the bloodstream and eventually hydrolyzed back to fatty acids and glycerol and metabolized to generate energy I Fatty acids not needed for immediate use are reconverted to TAGs and stored as fat droplets in adipose cells also called adipocytes or fat cells 0 Amphipathic Hydrolyzable Lipids o o broad groups based on glycerol Glycerophospholipids phosphoglyceridesifatty acid ester groups at two of the carbons of glycerol plus a phosphodiester on the thir car on I Sphingolipidsibase on sphingosine instead of lycerol o Sphingosine a long chain unsaturated arnino alcohol arnine group on C2 sphodiester on C 0 These groups have one highly hydrophilic group which is responsible for its arnphipathic nature and its ability to assemble into cell membranes 0 Steroids Cholesterol Steroid Hormones o Steroids are nonhydrolyzable lipids that contain the steroid ring structure which consists of4 ised rings three ofthern 6 membered rings and one of them a 5 membered ring 0 Cholesterol I Cholesterol is a major steroid in animals Plants contain very little but do contain related compounds in their membranes 0 Molecule contains 8 tetrahedral stereocente s 0 Cholesterol is critical to many physiological inctions component of membranes precursor for all other animal steroids o The body can synthesize all the cholesterol it needs if excluded from the diet 0 Steroid Hormones I rmonchhemical messengers that L 39 4 and erreted from h 4 39 4 transported throughout the body to target tissues W ere they regulate cell functions Eicosanoids Nonhydrolyzable lipids derived from I Cm fatty acid called 39 39 39 39 O C 39 Leukotrienes I Prostaglandins I 39Ihromboxanes 0 Have hormonlike physiological mctions They produce their regulatory effects at low concentrations I In ammatory response injoints skin muscle an eyes 0 Results from production of prostaglandins o Nonsteroidal antiin ammatory drugs NSAIDs prevent the synthesis of prostaglandins 0 Include aspirin ibuprofen acetaminophen etc Production of pain and fever in disease and injury Regulation ofblood pressure Blood clotting Induction of labor Regulation ofWakesleep cycle Allergic and asthmatic reactions 0 They are NOT transported through the bloodstream from their sites of synthesis to their sites of action They are local hormones or local mediators acting in the same tissues they are synthesized Vitamins 0 Organic compounds required in trace amounts for normal metabolism but not synthesized by the organism that eds them must be included in the die 0 Classified as Water soluble or fat soluble I WateresolubleiB and C vitamins I FatesolubleA D E andK vitamins o In reality vitamin D is a steroid hormone and not a vitamin because it can be synthesized from cholesterol 0 Functions Vitamin A plays key role in vision aids in mctioning of mucous membranes and epithelial tissues Vitamin D regulates calcium and phosp ate in bone and cartilage Vitamin E acts as an antioxidant to protect against oxidation by air and free radicals Vitamin K2 regulates blood clotting Chapter 10 Carbohy drates Carbohydrates saccharides single most abundant family of organic compounds in nature with a variety of c ns 0 Metabolism breakdown of glucose generates energy for life processes I Storage of glucose starch in plants glycogen in anim s 0 Structural and protective materials I Cellulose used in cell walls ofplants I Chitin exoskeleton of crustaceans and insects Precursors for the biosynthesis of lipids proteins and nucleic acids Carbohydrates ribose and deoxyribose are components of RNA and DNA 0 Structure of Carbohydrates o Polyhydroxyaldehydecontain an aldehyde group o Polyhydroxyketonecontain a ketone group 0 Classi cation of Carbohydrates o Monosaccharidesimplest saccharides building blocks monomers for synthesizing larger saccharides I I portant monosaccharides glucose fructose galactose o Polysaccharidecontain large numbers of monosaccharides bonded together I Important polysaccharides starch cellulose glycogen chitin o Oligosaccharideany saccharide larger than a mono and smaller than a poly39 1020 monosaccharides I disaccharides trisaccharides tetrasaccharides etc I Important disaccharides sucrose and lactose 0 Dietary carbohydrates are categorized as simple mono or di and complex poly Naming of Carbohydrates o mmon names of most but not all end in Ame Monosaccharides C assi cation and Nomenclature I onosaccharides classify compounds in 2 ways simultaneously by combining 2 kinds of pre xes before ose Monosaccharides with an aldehyde group are aldoses those with a ketone group are ketoses Monosaccharides with three four ve and six carbons are trioses tetroses pentoses and hexoses respectively 0 Example a vecarbon monosaccharide with a ketone group is called keto entose I Those of biological interest are those from 3 to 6 carbons 0 Important Monosaccharides I DGlucose is the most abundant monosaccharide in nature existing in combined forms of starch cellulose glycogen chitin lactose and sucrose ietary starch and stored glycogen in the liver are broken down to glucose which is transported to cells and used for energy production 0 Also known as blood sugar or dextrose I DFructose is bonded to Dglucose in the disaccharide sucrose the sugar in fruits and table sugar 0 Also known as levulose I DGalactoseis bonded to Dglucose in the disaccharide lactose the sugar in mammalian milk Disaccharides o portant Disaccharides I tose is produced by the partial digestion hydrolysis of starch by the enzyme amylase which is secreted into the mouth by salivary glands and into the small intestine by the pancreas I Also known as malt sugar or corn sugar 0 Plants also produce amylase which is responsible for the formation of maltose when grains such as barley are allowed to so en in water and germinate Maltose is also produced in processed corn syrup Maltose is a diglucose These two Dglucose monomers are linked together by an a14 glycosidic linkage I Cellobiose is produced by the partial hydrolysis of cellulose brought about by the enzyme cellulase or an acidic catalyst Cellobiose is another diglucose molecule The linkage between the Dglucose monomers is a B194 glycosidic linkage I Lactose constitutes from about 4 to 8 of mammalian milk and is a major energy source for nursing young ontains Dgalactose and Dglucose joined by a 6194 glycosidic linkage Also known as milk sugar I Sucrose is the most abundant disaccharide in nature 0 It is found in the fruits and vegetables of our diet as well as commercial sources such as table sugar to sweeten coffee tea so drinks ice cream and baked goods Consists of a formation between xDglucose and BDfrustose with a 0B192 glycosidic linkage o Digestion and Absorption of Carbohydrates Maltose partial digestion of starch lactose and sucrose are part of the diet of humans and animals however they cannot be absorbed by the intestinal tract in this form Only monosaccharides are small enough to pass through the membrane of the intestinal cells and into the bloodstream I These larger saccharides are digested into monosaccharides by maltase lactase and sucrase respectively usually enzymes are named by adding the pre x ease to the compound undergoing the reaction Polysaccharides 0 Starch and Glycogen are storage nutritional polysaccharides I Dglucose is stored as starch in plants and as glycogen in animals I Starch is deposited in plant cells as insoluble granules composed of 2 different types of polyglucose molecules amylose and amylopectin lO30 amylose 7090 amylopectin I Amylose a linear unbranched polymer of Dglucose monomers linked through a 1194 glycosidic linkage I Amylopectin a branched polymer containing Dglucose monomers linked through a 1194 glycosidic linkage but in addition it branches repeatedly through 11 96 glyosidic linkages Not only are there branches but branches on branches Glycogen is similar to amylopectin but more extensively branched I Digestion of Starch and Glycogen Starch is digested to Dglucose in our diet 0 Amylase in the digestive tract hydrolyzes the amylose and amylopectin to maltose Maltase cleaves maltose to Dglucose Amylase and maltase are unable to hydrolyze 1196 linkages however and thus leave the parts of amylopectin at the branched points unhydrolyzed This product dextrin is hydrolyzed by the enzyme dextrinase to Dglucose o Cellulose a structural polysaccharide is the most abundant organic compound in the biosphere accounting for more than half of all organic carbon t is a component of the constructional material of plantcell walls that gives plants their overall shape and strength I Cellulose is a linear polyglucose with 3194 glycosidic linkages Chapter 137Nucleic Acids rnmn om 39 39ofcells 39 39 39 39 39 L 39 L H 39 39 100000 proteins unique to a human being r 39 he fundamental units ofheredity Genes are responsible for both the traits common to a species and for the unique traits of an individual member ofthat species acids RNAs and deoxyribonucleic acids DNA 0 Chromosomes contain DNA molecul NA k I s es Each gene is a part ofa DNA molecule 0 A A WA a a a a Nucleotides o Phosphoric acid Pentose sugar In RNA Dribose In DNA 2deoxyDribose Heterocyclic nitrogen base A total of5 different c heterocyc1ic bases are used 3 pyrimidine and 2 purine bases osine o o O U7 o Giguanine G an C are in both RNA and DNA T is only in DNA andU is only in RNA 0 Formation ofnucleotides occurs by 2 dehydration reactions among the 3 components One dehydrati between phosphoric acid and pentose sugar 0 T es place on C5 ofpentose rin One dehydration between pentose sugar and heterocyc1ic base Tak s place on c1 ofpentose ring and at an N7H hydrogen on heterocyc1ic base deoxyribonucleou des 39 Nucleotides are named as follows r O Example 39 r n a and 39 39 thvmine and uracili marlin nnrl in 39 39 39 In 0 When deoxyribose is the sugar the pre x deo y is used 39 A A L 39 39 39 ofthe sugar Nucleotides are o en abbreviated The pre x deoxy is shortened to d and is followed by the oneletter symbol for the base c T U A G and MP is used for 5 monopho sp a e Example deoxycytidine 5 monophosphate dCMP 0 Formation of Nucleic Acids O a a a n r a a n at C3 of another nucleotide By rnnven nn 39 u a direction A end and a 3 end 0 37D Structure of Nucleic Acids O Deoxyribonucleic Acids 39 DNA double helixih 39 A DNA hand fnld nr coil quot to form a 39 Lt 39 quotL 39 pr 39 439 39 one in the 593 direction and the other in a 3 95 direction r 39 dnuhle heli quotL 439 base on one DNA strand This attraction is calledbaserpairing and the bases pair in a complementary manner AiT and 57c This creates complcme O A a d T result in o G and c result in 3 hydrogen bonds DNA strands are enormous molecules Human genomeitotal DNA in humans about 3 2 billion base pairs DNA is contained in 23 pairs of chromosomes 11 DNA 39 39 39 39 cores 0 I I U JUHI I I 39 e DNA duplex wraps around nucleosome cores to form nucleosomes with about 150 200 base pairs per nucleosome o 39 39 39 super quot A o chromatin ber winds into a chromosome 0 Ribonucleic Acids xist as single strand molecules Several types ofRN l A exist each with its own speci c 3D structure Transfer RNA or tRNA 0 Ribosomal RNA or rRNA essen Secondary and tertiary stmctures arise from basepairing of nucleotides just like in DNA except that T is replaced with U o AiU G Information ow from DNA to RNA to Polypeptide O N as a 1 L W 4 in polypeptides However since nN 39 molecule RNA to go out into the cytosol and carry out protein synthesis Replication is the copying ofDNA in the course of cell division 39 39 39 L 39 om DNA W r mNA and mRNA 39 39 39 39 39 tRNA and mRNA 0 Replication An extremely complex process involving dozens of enzymes DNA A 39 A a f 39 iork at each end hi h a nip ma New bases are added in the 5 gt93 direction 39 39 39 4 mnlpt ulp each containing an old and a new DNA strand semiconservative o Transcription I mRNA andtRNA 39 39 DNA DNA double helix unwinds to form a transcription bubble Only one ofthe two DNA strands in the bubble 39 nthe i The other strand isn t used at all 39 39 39 39 39 39 39 39 DNA I start signal and ends at a termination site a base sequence recognized as a stop signal r 1 DNA 1 L a i naired with U instead ofT 0 Translation The process by which rRNA mRNA andtRNA work together outside the nucleus to carry out polypeptide synthesis M um L 4 L The genetic message is the sequence ofRNA bases which speciiies the sequence of oamino acids to be synthesized L i called a codon because it codes for one speciiic tRNA that carries one speciiic amino acid 3 RNA bases 1 codon 1 anticodon 3 tRNA bases 1 amino acid Transport RNA tRNA transports oamino acids into the ribosome for synthesis e codon mRNA recognizes its speciiied tRNA through a base triplet or anticodon which canies the speciiic amino acid sequence