The Chemistry of Organic Molecules

THE CHEMISTRY OF ORGANIC MOLECULES THE CHEMISTRY OF ORGANIC MOLECULES ORGANIC MOLECULES ↳ 19th vital force century thought moucules of cells contain divided inorganic (nonliving chemistry into organic (living) molecule contains hydrogen and carbon today "organic" of chemists and ↳ means four classes of organic Carbohydrates all together called ↳ ↳ of molecules 6 e- forms always ↳ : ↳ proteins nucleic acid biomolecules organic has total of living organisms lipids ↳ ↳ variety molecules in , 2 in covalent based first shell bonds to on . unique chemical 4 valence e- gain 4 properties of carbon quite small = form bonds with up to can 4 other elements 1 carbon generally H, N, O , P, S other Catoms elements that make up most same = with forms bonds and · living organisms & It & & & · ability of carbon for establishing C-c bond stable essential ↳ to share e very hydrocarbons = chains of with extra bonds just for with other carbon atoms is shape ( function) of allows = formation of long H When in CCC C H HHNN can also form water It1HNNNNI H Methane chains hydro carbons C It biomolecules = It H Hit Octane I 1 C C 16 16 | C C 1616 carbon can With itself also - not as flexible as H H form double bonds single ↳ double bonds affect carbon can also form branches ↳ can flexibility form allows shape triple at H I and therefor function bonds with any diversity C Cyclohexane restrict movement of bonded atoms = C C-form in organic itself long , e . g . H-CEC-H complex molecules chains | C D rings C chain of functional ↳ = specific group group responsible for carbon skeleton Group molecule-skeleton/backbone organic an Old R of chemical framework for acts as structure Hydroxyl majority of bonded atoms compound Significance Alcohol Polar forms in as reactivity positioning R , ethanol accounts - that always Al dehyde as in 8 C of functional group configuration Polar Present in sugars Ketone G ↳ e acetone C R Carboxyl lacidic R Present in sugars Carboxylic J RC as in OH acid . into Polar, acidic ↳ acetic present in fatty a cid g . where attaches to carbon skeleton of functional hydroxyl group (OH) groups determines turns morecube alcohol when - oh replaces ethane , it becomes acids , a mino place biomolecule properties of Polar in as groups remainder of molecule ; = functional formaldehyde H way of biomolecules , R react the same bond hydrogen Present in sugars some amino acids Carbonyl for shape of molecule one of the I in ethanol acids ↳ ethanol Amino Amine I N R hydrogen tryptophan H is hydrophilic Polar, basic , forms as in bonds because - OH makes it polar Present in amino acids Dry I Sulthy R SH Thiolas in Forms disulfide ethanethiol bonds and Presentin a mino ROP Old isomer atom as Presentin molecules nucleotides , molecules that - molecular > variation have in identical movicular formulas but different morcular structure of molecule formula (CsH60s) different functional properties in phospholipids organic in chemical of determine acids phosphorylated arrangements ↳ same types polarity groups reactions they undergo , phosphate Old some functional Polar acidic Organic D Phosphate attached groups = react reactions and have but differently different glyceraldehyde dihydroxyacetone #160 It c - 001d cit H 0 I It I t 04 Ol BIOMOLECULES OF CELLS carbohydrates , lipids proteins , contain smaller subunits ↳ ↳ Carbohydrates ↳ ↳ proteins , constructed subunits polymers > - of type monomers different types of subunits (glycerol fatty acids) same contain two (monomers) polymers = Polymer Subunits Carbohydrates Monosaccharide Polysaccharide Lipids Glycerol and fatty acids N/A Proteins Amino acids Polypeptide Nucleic acids Nucleotide DNA, RNA reaction to condensation macromolecule-dehydration water molecule equivalent HzO is synthesize a Can OH and H) Synthesis of a are most joined chains of ↳ is can have have = as have chain energy many source monomer Degradation of a biomolecule living organisms C to H to O ratio of 1 2 1 : : length varies from few polymer moucules backbone of 3-7 hydroxyl for function) single sugar carbon monomer Hz0 monomer monosaccharides assembled in monosaccharide ↳ - - 7 ↑ reaction also structural sugar 1 A ↑ hydrolysis used carbohydrates Ol monomer . b (sometimes monomer biomolecule formed when biomolecules universally H 20 monomer CARBOHYDRATES almost 1- monomer Dehydrationone synthesized are ON monomer reaction removed when subunits are = = + Category cells use ↳ joined together and nucleic acids by joining don't form lipids , macromolecules and nucleic acids are groups - chains n makes them molecules and sugar sugars polysaccharides "simple carbons include hundreds of to = , e . sugar g . pentose hydrophile = 5 C , hexose = 6 glucose is a = nexose source major ↳ , of cellular fuel energy) during CH2O O OH It It a It C 40l 18 b b Old H8 Ol . c Cly206 G & C d . ribose and make ↳ disaccharide are both . carbon skeleton and attached only ring and pentose of RNA two monosaccharides disaccharide maltose is ↳ . d structural backbone = groups shape oxygen groups remains formed sugars and DNA (joined in CHzOld reaction) dehydration when CH2Old G 16 CHzOld O It dehydration reaction CH2Old J O t glucose two > - molecules bond position of bond together glucose Cold1z06 that results groups is below the ↳ Hz8 CH1206 maltose monosaccharide C2H22011 disaccharide water + water participating ring = form lactose ) In cose g + + hydrolysis reaction glucose and fructose monomers is in which sugar transported in plants sucrose ↳ are g HO OH monosaccharide when-OH omitted . deoxyribose up omitted carbon skeleton . Old It Old It and all attached Carbon skeleton . I 16 3) A converted to ATP /stored chemical and broken down - cellular respiration CH+ 20H 15 galactose (fructose has several isomers ↳ Culti20s to glucose = and galactose if someone is lactose intolerant maltose = glucose and = lack lactase that breaks down enzyme lactose glucose Complex polysaccharides-long polymers of monosaccharides k carbohydrates short-term Some function molecules energy-storage needs breaks down when polysaccharide to release sugar molecules organism energy , ↳ a . . . a as a plants ↳ store large amount of exists in two forms ↳ When : glucose amylose polysaccharides are as starch (unbranched) branched = no and amylopectin main carbon chain (branched animals store ↳ is cannot is reason = are not as through why they pass are cellulose fiber contains ↳ every in other glucose animals peptidoglycan storage and release starch water , much bigger than single sugars easily molecules storage different are in different is for walls several added organisms strength microfibrils (each flipped Callows /fungi = amino a polymer of moucules glucose hydrogen bonding stronger connections = group bacteria monomer animals until needed glycogen membrane used as are in molecule is has attached ↳ monomer cellulose soluble plant cell ↳ ↳ each glycogen as plants criss-cross = that store plasma ↳ chitin glucose branched than more polysaccharides structural cellulose granules even polysaccharides ↳ of hormones by glycogen amount contain liver cells controlled ↳ large contains amino abundant most acid chain carbohydrate organic and molecule (e g . . wood , cotton) because of structure of bonds digest glucose molecules microorganisms ↳ termites have protozoans in digestive tract that help them digest wood in microorganisms break down cellulose in special digestive-tract and swallowed then returned to month to be chewed again for humans cellulose functions fiber dietary are not able to - ↳ cellulose can some cows ↳ as animals ↳ pouch more ↳ soil between can fungi also - also not chitin useful in has digest chitin - sends are covered in Chitin antimicrobial/antiviral properties production of cosmetics/food for protection against LIPIDS It ↳ fats bonded to are = called also lipid primary ↳ hydrophobic because of hydrocarbon chains C nonpolar don't form only one hydrogen bonds compounds , organic triglycerides used fat distributed all ↳ ↳ triglycerides in for insulation body over plants but , mostly underneath fatty Uses Human Butter lard Long-term are fatty saturated Phospholipids contain can as many of unsaturated ↳ triglyceride bond in trans least configuration trans cis configuration affects biological activity that Medicines , Candles , polishes , (cuticle of plant fatty , earwax acid have double bonds between carbon chain , reduces number of bonded H-atoms they ↳ is a Food additive Protection prevention of , H-atoms as oils sexhormones surfaces) beeswax C-atoms , Cooking in plasma Component of plasma (cholesterol) Waxes hold fat storage membrane double bonds have chemical arranged trans Component water loss double bonds between no energy membrane either saturated acid , plants and their seeds unsaturated or ↳ Functions Long-term energy storage 16-18 C-atoms per molecule acid chains heat Type Steroids have body retains Fats Oils group most - and insulation in animals = ↳ skin called oils are + = in animals long-term energy storage and triglycerides fatty-acids glycerol subunits acid each long hydrocarbon chain fatty 1) with even number of Cand-CooH(carboxy ↳ with water molecules , has at or on same side (cis groups configuration opposite sides (trans conf) of double bond . one ↳ or O HHHISHIIHIHIIIHI ccccccccccccc4 HO A IJ NNNNNNNNHH saturated fatty acid = no on HH C HO double bonds between C-atoms unsaturated (causes fats acid with no It double bonds have kink in either side of carbon chain It HHH (((((((((((((CCH HHHHHHH H1N11d . chain) double bond with HHHHHHHH O b trans fatty has attached to if carboxyl group (-C00H) long carbon chain 1 . H-atom unsaturated fatty acid with double bonds and a trans bond 16 Id glycerol -OH - fatloil forms oh - , COOH groups glycerol hydrophilic make = 3-OH of three groups acids react with fatty reaction) glycerol (dehydration of groups - degrade during hydrolysis fats /oils Triglycerides (nonpolar) have C-H many 161116 16 bonds H hydrophobic = triglycerides H8 butter ↳ corn = oil fats that room ↳ from animals ↳ ↳ fat fatty bonds in usually of instead acids Id O reaction It It hydrolysis Co reaction I I I N +H I I I 3420 |I t I I cccc H / H I I C 41 1 1 6 I , g 16 HH4/ X fatty acids fatmolecule 3 water molecules between hydrocarbon room temperature even in chains fridge come from plants usually liquid with stored glycogen are can go fatty energy energetic in -o affect it to easily = hydrogenation stick hydrogen gas causes of chemical energy acids hydrophobic together cardiovascular semisolid source less health rancid faster - s manufacturers expose make them flat long-term energy for make them better do not contain water much and of bonds more plant oils up packing solid , oils that glycogen for gram energy gram use saturated fats too close prevents = more fat droplets ↳ kink = come 3 glycerol = C-I bonds C-OH - 16 O cccccCH temperature stores = ↳ 14 mostly saturated fats solid at mostly unsaturated fats liquid most animals ↳ acids dehydration us Ol HC 16 only than those with fatty saturated at acids I H1N11Id 8 fatty that contain > ccccccC CON It 16 It Co 31 0 It 111111 t I Id < Ol C O unsaturated bonds melt at lower temperatures ↳ fat molecule a reaction I with result in 3H20 molecules and ↳ polar are groups ↳ When compound with 3-carbon = at room nonpolar , in blood negatively hydrogenate temperature , formation of trans fats gives = unsaturated better shelf higher risk fat Cheat it life for cardiovascular disease I · nonpolar tails become hydrophilic ↳ tails nonpolar layer (bilayer) cause = cholestera - provides essential attribute to l can consists by type fluid rings very , of = some ↳ solid around ↳ hydrophobic room -o (e other steroids circulatory long-chain fatty , mostly of phospholipid throughout big range of different to triglycerides bilayer temperatures and phospholipids attached to carbon skeleton component of animal's plasma membrane disorders blood vessels waxes water keep cells separate from to functional groups physical stability precursor of also component key membrane to be of steroid differs polar heads towards to water within skeletons with four fused = type In exposed it from compartments of tails kinks steroids = away when membrane that surrounds cells plasma ↳ hydrophobic tail tend to form double biological ↳ , themselves rearrange ↳ head g . . sex hormones accumulation of fats in encourages acids connected to carbon chains with alcohol temperature form protective - that involved in skin and fur maintenance in groups point high melting cover functional prevents loss of water in many , plants animals PROTEINS up to 50 % of dry weight of most cells is protein , main functions : metabolism bring ↳ specific for range support together-increase rate of chemical reactions particular type of reaction and function work best within reactants ↳ of temperature , and pH specific Transport channel ↳ and carrier regulate plasma membrane in proteins which substances enter/exit cell ↳ transport molecules in blood of immune system defense antibodies ↳ bind to prevent infections and antigens regulation hormones ↳ some protein-based influence cellular are behavior , motion all cells contain ↳ tissues/cells ↳ ↳ blood cells proteins = to COOH (acid H2N of group) , third contractions (support tissues I C group COO H Catom central atom ↳ & tough fibers monomers group) is -NHz Camino , and other is group (R) R can be R being single a polar amino acid bonds to Hatom and three other in (one groups some Hatom (hydrophilic) amino acids with Chydrophobic) 1 nonpolar HzN + HzN + J C0- R groups H3C 1 amino acids with polar (hydrophilic) R groups + CH3 1 HzN + Si HzN + J CH2 CH0- acid HzNt CH3 (Thr) J 1 CC 1 8- HzN + CHz N COO- 9) utamic (Glu) glutamine (Gln) tyrosine (Tyr) CH2 CH2 Old J -C OH Cz 8- + threonine 1 CC 8- N(z8 1 HzN CHz0- 1 J (CH2)2 + 13 lysine (Lys) - J -C HzN + J 1 -C (CH2)z 8- CH20- Nit C C N + 12 00 aspartic acid (Asp) NHz arginine (Arg) HzNt C CH2 [Hz CC O- J -C asparagine (Asn) groups 1 J -C CH2 + proline (Pro) C C + + Serine (Ser) 1 + HaN Hz) leucine (Leu) Old HzN HzN 1 HzN 8- NHz0 amino acids with ionized phenylalanine (Phe) J C2 H 0- CHzCHz (Met) -C 0- cysteine (Cys) cC CHz 0- CH3 J (hydrophobic Cl methionine -C CH2 HzN + cC CH2 S valine (Vall HzN HzN + O- compound ; Ho Ho cC ICHalz -C nonpolar some , ring complicated or Ho R composed of collagen contain groups is a variable group I produce for O2 transport hemoglobin functional the contain they a cidia amino group one proteins by constructed from amino acid polymers amino acid - filled with for myosin different internal locations to components be characterized actin and and tendons ligaments cell that more sometimes cells contain muscle red can proteins J CC 8- Ca vis N+ 1 histidine (His) J C 0- linked amino acids acid to amino atoms in ↳ group by dehydration of other than electronegative slightly negative more link -> of carboxyl group covalent bond between results in = one amino them-peptide bond unevenly bond share electrons peptide Oxygen reaction nitrogen-hydrogen slightly has positive charge oxygen , 35 peptide C bond N + 1 a cidic amino group - Hid I NC + C peptide group bond - I G R Old dehydration I H N ccNC reaction NCC It > O ROl t C H20 & Old R I amino acid peptide and - bond is of NH peptide- the two or protein polar ↳ some amino acid ↳ ↳ ↳ proteins proteins primary ↳ linear amino acids that is folded up of multiple influences by information sequence often amino acids in by peptide particular shape polypeptide in of one amino acid together connected bonds and has function a chains three-dimensional shape and function of protein genes faulty have for particular proteins have up to four levels of very 3D-shape - don't similar across function species sequence of Sequence amino acids : , > - 20 different amino , , acids can build thousands polypeptides by being arranged differently amino acids determined by information within genes of right organization primary secondary tertiary quaternary structure of different ↳ many with abnormal sequences of water hydrogen bonding between -co acid in polypeptide possible amino acids bonded determined g makes more of It It R dipeptide amino sequence sequence reaction other made are - polypeptide is a hydrolysis a mino acid polypeptide-chain a 8 It secondary polypeptide structure ↳ folds or coiling ↳ pleated sheet-B-sheet amino acid = between a within helices fibrous proteins - - ↳ globular proteins hydrophobic amino - ↳ polar and ionic ↳ also supported strong most if too quarternary shap by hydrogen bonds between in up = rounded polypeptide in certain every bonds causing hydrogen helices as or pleated shape of sheets that polypeptide chain interact with water in on inside surroundings of protein = orient themselves on surface bonds , ionic bonds covalent bonds between R , groups (-S-s-> globular proteins - high temperature or pH change can disrupt denature many proteins denature , organism may die structure that consist of more than one this structure = ↳ , function of protein ↳ bonds shapes polypeptide can have hemoglobin globular protein consisting of four polypeptides structure each polypeptide has primary secondary tertiary proteins fourth shape group together by hydrogen are multiple Keratin g. . itself amino acids interact with water disulfide enzymes natural ↳ (e proteins fold up have chain acids in nonpolar amino acids ↳ ↳ ball can helices and B sheets x in three-dimensional ↳ and polypeptide structural proteins that exist bond to each other makes way each polypeptide turns back upon lengths of polypeptide chain tertiary structure that results folding = formed polypeptide extended hydrogen Y x-helix B sheets form when ↳ certain ↳ spiral shape of ↳ coils in correct structure directly related important to its , three-dimensional structure if that code genus of protein , structure ↳ can or in the chaperone misfolding correct TSE - instructions it can result in change it way , proteins some help = minor proteins new changes to diseases associated with diseases also caused misfolded proteins by in changes folds disease sometimes sometimes cause cells contain ↳ for protein = fold into normal shape misfolded proteins (e . , help can Alzheimer's g. prions NUCLEIC ACIDS each cell of information storehouse has > - tells cells how to behave , respond to environment , and divide nucleic acids made out of nucleotides = droxyribonucleic to (DNA) is replicate itself and specifies ribonucleic acid ↳ acid messenger sequence (RNA) is also RNA (mRNA) during protein Transfer RNACARNA) ↳ right ↳ (rRNA) amino acids and nucleotides ↳ some are enzymatic ↳ type of information store of nucleic acid (stores information about how order in type " which amino acids should be adenosine I needed for temporary copy of a Specifies amino acid in DNA gene Synthesis helps translate sequence of nucleic acids in = work as enzyme form peptide to every into polypeptide are directly components of involved in metabolic functions of cells molecules Coenzymes Corganic (nonprotein) triphosphate (ATP) nucleotide that stores = cellular reactions and nucleotide made : ↳ in DNA RNA regulate help that reactions pentose pentose pentose up of three sugar nitrogen-containing ↳ in genes bonds between other processes that , types of 04 sugar CH2Old CH20ld is G 51 S 4 Old O base 11 is 1 Nucleotide structure b . Deoxyribose versus ribose Pyrimidines deoxyribose is ribose NI+ z J C C ribose (in RNA) deoxyribose (in DNA) pentose Sugar a is is · CC Old phosphate Old O i s 32 , base sugar nitrogenaing C p energy energy require phosphate 0 of amount large ② molecules joined nucleic acid sequence ribosomal RNA some = = a - Purines D N1z CH N CH3 HN C CH HN & N J + cytosine CI D Y thymine (in DNA) G C * uracil (in RNA) C HN N CH CCH f C N HC N C a denine Cl C HzN N guanine Y RNA DNA and nucleotides that ↳ DNA have and RNA ring DNA bases in single ring pyrimidines base with with double nucleotides pyrimidin four nucleotides (but differ between nucleic acids) contain = purines cytosine = purine contain = and bases thymine adenine in DNA RNA Sugar Deoxyribose Ribose Bases adenine , guanine , adenine , thymine cytosine cytosine D) ouble-stranded with Usually single-stranded , Strands and RNA-cytosine and guanine , uracil guanine uracil , , base pairing joined nucleotides is into RNA through dehydration reactionsa resulting polymer (backbone consisting of alternating series of DNA or linear molecule-strand a No Yes Helix sugar-phosphate-sugar-phosphate ↳ bases project ↳ nucleotides DNA is to one side molecules of backbone connected in the order double-stranded RNA is , they hydrogen bonds between copied in from other strand single-stranded of DNA twist around each other ↳strands are pyrimidine = and form double-helix purine bases N can be in order within strand , but between strands : any Thymine (T) always paired ↳ guanine (G) always paired S G ↳ P N / NHz S It N o 8 = S P U N no CH3 S I together by pairs base z N I held s complementary base NHz N N S I N A number of of P with purine pyrimidine bases cytosine of (A G) + bases (T+ c) particular any always equal N G N1t H N N NHz N N N I 2 Sugar P Sugar N cytosine (C) 9 nanine H (G) C N I S I I N 213 & It N C N Sugar H N N N N a denine (1) pair to number N J base It N I (c pairing matter the order or amount I = with adenine (a) J thymine (T) Sugar ATP is three nucleotide made up of adenine and ribose Cadenosine) phosphates (triphosphate) ↳ three phosphate last two phosphate hydrolysis adenin groups attached are bonds in high-energy it a ↳ make ↳ and , ATP are together unstable , to ribose easily (pentose sugar broken molecule of terminal phosphate bond diphosphate (ADP), a in cells phosphate bond produces the molecule and a lot of energy by ATP hydrolysis used to power cellular processes is chemically favored because ADP and P released energy ATP hydrolysis hydrolysis = of ATP makes them are is often coupled possible to to N1Jz N N reactions proceed N1Jz N unfavorable chemically stable than more HzG P N 2 P 2 P triphosphate adenosine ATP N N N P N 2 P diphosphate adenosine ADP + P + ENERGY ATP