Nucleotides and Nucleic Acids

Structure, function, and reactivity of biologically-relevant molecules Nucleotides and Nucleic Acids (BC, BIO) • Nucleotides and nucleosides: composition ▪ See above o Sugar phosphate backbone ▪ See above o Pyrimidine, purine residues ▪ See above • Deoxyribonucleic acid: DNA; double helix o The “double” in the double helix means that DNA is found in a double-stranded form - 2 singlestranded chains of DNA stuck to each other via hydrogen bonding of the base pairs o The 2 single-strands are anti-parallel to each other. Going from 5’ to 3’ of one strand means going from 3’ to 5’ of the other strand. o The “helix” in the double helix means that the entire thing is wound up in a spiral • Chemistry (BC) o The phosphate group(s) of a nucleotide are acidic. The two protons of the phosphate group of AMP are governed by pK+’s of 3.8 and 6.2, respectively, so at neutral pH, the dianion of AMP predominates. The negatively charged phosphate groups present in DNA and RNA give the molecules an overall negative charge which enables electrophoretic separation in the laboratory. • Other functions (BC) o ATP is a nucleotide, which stores the energy liberated during conversion of carbohydrates to carbon dioxide and water in metabolism. The energy is stored by means of the phosphate ester linkages (many enzyme processes are coupled with phosphate ester hydrolysis) o Hydrolysis of the terminal phosphate linkage of ATP is accompanied by an internal energy decrease for two main reasons. ATP is highly negatively charged with four negative charges present on the phosphate groups (two on the terminal phosphate and one each on the two others). Hydrolysis enables the separation of these negative charges from each other. Secondly, there is greater resonance stabilization in ADP than in ATP. Amino Acids, Peptides, Proteins (OC, BC) • Amino acids: description o Absolute configuration at the α position ▪ L and D is different from R and S. L is not always S, and D is not always R. ▪ If priority of NH2 > COOH > R, then L=S and D=R. For example, L-Alanine = SAlanine ▪ If the priority of NH2 >R > COOH, then L=R, and D=S. For example, L-Cysteine = RCysteine ▪ L-amino acids are more common in nature, and are the type found in proteins. D-amino acids are less common in nature, and are never found in proteins o Dipolar ions ▪ At low pH, amino acids exist in the cationic form ▪ At high pH, amino acids exist in the anionic form ▪ At pH = pI, amino acids exist in the zwitterion form, which is overall neutral o Classification ▪ Acidic or basic • If the R group contains carboxylic acid, then it’s an acidic amino acid. There are two acidic aa: aspartic and glutamic acid • If the R group contains an mine group, then it’s a basic amino acid. There are three basic aa: lysine, arginine, and histidine ▪ Hydrophilic or hydrophobic • Hydrophobic: If the R group doesn’t contain any of the stuff below • Hydrophilic: IF the R group contains acids, bases, amines or alcohols • • o Synthesis of α-amino acids (OC) ▪ Strecker Synthesis • Starting material: R-aldehyde • Reagents: cyanide (KCN), ammonium (NH4Cl) ▪ Gabriel Synthesis • Starting material: R-halide • Reagents: 1. phthalimide, 2. NH2-NH2 • Product: Amino acid with the -R group originally on the halide Peptides and proteins: reactions o Sulfur linkage for cysteine and cysteine ▪ Cysteine = side chain with the thiol group ▪ Cystine = 2 cysteines forming a disulfide bond o Peptide linkage: polypeptides and proteins ▪ Peptide bond = amide bond ▪ Peptide bond is formed by amine group attacking the carbonyl carbon o Hydrolysis (BC) ▪ Peptide bond is very difficult to hydrolyze. It requires a strong base, or a biological enzyme General Principles o Primary structure of proteins ▪ Primary structure = sequence ▪ Primary structure of proteins is read from N-terminus to C-terminus o Secondary structure of proteins ▪ Secondary structure = repetitive motifs formed by backbone interactions ▪ Backbone interactions = hydrogen bonding between the NH and C=O ▪ Two most common secondary structures are α helices and β pleated sheets ▪ The α helix is right-handed, with the R groups sticking outward ▪ In β sheets, R groups stick out above and below the sheet o Tertiary structure of proteins ▪ 3D structure of proteins ▪ Caused electrostatic side chain - side chain interactions o Isoelectric point ▪ pH at which the molecule is neutral ▪ Acidic amino acids and proteins with lots of acidic side chains have a lower isoelectric point ▪ Basic amino acids and proteins with lots of basic side chains have a higher isolectric point The Three-Dimensional Protein Structure (BC) • Conformational stability o Hydrophobic interactions ▪ Hydropathy plot • Used to measure number of hydrophobic regions in a multidomain protein • Region with positive hydropathy index indicates a hydrophobic region o Solvation layer (entropy) ▪ Nonpolar aa’s pushed towards inside of a protein. Solvation layer of water forms around proteins • Quaternary structure o Separate chains/subunits joining together o Caused by covalent disulfide bonding of cysteine side chains • Denaturing and Folding o Amino acid sequence vital for folding o Factors causing denaturing ▪ Urea → disrupts H-bonding ▪ Salt/pH change → disrupts ionic bonds ▪ Mercaptoethnaol → disrupts H-bonding ▪ Organic solvents → disrupts hydrophobic forces ▪ Heat → disrupts all forces Non-Enzymatic Protein Function (BC) • Two protein types: globular and structural o Globular: for enzymes, receptors, channels, transport o Structural: made of long polymers, used for structure, movement • Binding o Special feature of some proteins is the capability to bind other molecules with non-covalent interactions o Protein binding characterized by affinity and specificity for the binding target • Immune System o High degree of protein variability allows for a key feature of the adaptive (or acquired) immune system, the production of antibodies o An antibody is a type of protein that has a unique and very specific binding site that will readily bind its target, called an antigen, such that its target is inactivated or tagged for immune response o Glycoproteins: proteins with carbs attached. Includes antigens on red blood cells • Motor o Motor protein can perform mechanical work by coupling exergonic (energy releasing) ATP hydrolysis to a conformational change that allows for interaction with the protein’s target substrate o Muscle contraction achieved through a process of the motor protein myosin binding and releasing its microfilament (actin) substrate o Myosin also acts on microfilaments of the cytoskeleton to generate cellular movement o Two other types of motor proteins, kinesins and dyneins, act on microtubules and play a role in transport within the cell o Kinesin is microtubule “tracks” to deliver cellular cargo (e.g. chromosomes during mitosis), generally in an anterograde direction (center to periphery) o Dynein is used in retrograde cargo transport in the axons of neurons, and is capable of sliding microtubules in relation to one another, generating the movement of cilia and flagella Lipids (BC, OC) • Description, Types o Storage ▪ Triacylglycerols • Glycerol + 3 Fatty acids → Triacylglycerol • The reverse of triacylglycerol synthesis is saponification ▪ Free fatty acids: saponification • Saponification is the ester hydrolysis of triacylglycerols using a strong base • Traditionally, the base that is used is lye, the common name for sodium or potassium hydroxide • Result is basic cleavage of the fatty acid, leaving the sodium salt of the fatty acid and glycerol • The fatty acid salt is known as soap o Structural ▪ Phospholipids and phosphatides • Lipids with phosphate group attached • Amphipathic, can form micelles ▪ Sphingolipids (BC) • Phosphoglycerides but with a sphingosine backbone. In cell membrane ▪ Waxes • Ester linkage between long chain alcohol and fatty acids. Very water-repellant o Signals/cofactors ▪ Fat-soluble vitamins • Include vitamins A, D, E, and K • Dissolve in fat and can be stored in your liver and fat tissue until needed • Vitamin A, or carotene, important in vision, growth and development, and immune function o Most significant metabolite of vitamin A is the aldehyde form, retinal, which is a component of the light-sensing molecular system in the human eye o Carotene = carrots high in vitamin A, known to improve vision • Vitamin D, or cholecalciferol, can be consumed or formed in a UV-driven reaction in the skin. o In liver and kidneys, vitamin D is converted to calcitriol, the biologically active form of vitamin D o Calcitriol increases calcium and phosphate uptake in the intestines, which promotes bone production o Lack of vitamin D can result in rickets, condition seen in children and characterized by underdeveloped, curved long bones as well as impeded growth o Vitamin D regulates calcium, remember it is frequently added to milk to aid in absorption of calcium • Vitamin E o Characterized by substituted aromatic ring with long isoprenoid side chain and are characteristically hydrophobic o Aromatic ring reacts with free radicals, destroying them o This prevents oxidative damage, an important contributor to the development of cancer and aging • Vitamin K o Vital to posttranslational modifications required to form prothrombin, and important clotting factor in the blood o Aromatic ring of vitamin K undergoes a cycle of oxidation and reduction during the formation of prothrombin o Also required to introduce calcium-binding sites on several calciumdependent proteins o Vitamin K for Koagulation ▪ Steroids • Nonpolar and can travel across the plasma membrane • Type of lipid = nonpolar molecule • Metabolic derivatives of terpenes • Characterized by having four cycloalkane rings fused together: three cyclohexane and one cyclopentane • Steroid functionality determined by oxidation status of these rings, as well as functional groups they carry • ▪ Steroid hormones, secreted by endocrine gland, travel on protein carriers to distant sites where they bind to specific high-affinity receptors and alter gene expression levels Prostaglandins (BC) • Regulate the synthesis of cyclic adenosine monophosphate (cAMP), which is a ubiquitous intracellular messenger • In turn, cAMP mediates the actions of many other hormones • Downstream effects include powerful effects on smooth muscle function, influence over the sleep-wake cycle, and the elevation of body temperature associated with fever and pain Carbohydrates (OC) • Description o Nomenclature and classification, common names ▪ See above o Absolute configuration ▪ See above o Cyclic structure and conformations of hexoses ▪ See above o Epimers and anomers ▪ See above • Hydrolysis of the glycoside linkage o See above • Keto-enol tautomerism of monosaccharides o Ketose monosaccharide can tautomerize to make an aldose • Disaccharides (BC) o Sucrose: 1, 1’ glycosidic link between glucose and fructose. α with respect to glucose, β with respect to fructose o Maltose: α 1-4’ glycosidic linkage; two glucoses o Lactose: β 1-4’ galactosidic linkage; a glucose and a galactose • Polysaccharides (BC) o Cellulose: β 1-4’ glycosidic linkage: a chain of glucose molecules o Amylose: α 1-4’ glycosidic linkage, a chain of glucose molecules o Amylopectin: α 1-4’ glycosidic linkages; branched chain of glucose with α 1-6’ glycosidic bonds forming the branches o Glycogen: same bonds as amylopectin but has more branches and used for more storage Aldehydes and Ketones • Description o Nomenclature ▪ Suffix: -one for ketones; -al for aldehydes o Physical properties ▪ Planar stereochemistry: perfect for nucleophilic attack. Nu can attack from either plane ▪ Polarity: partial positive charge on the carbon, makes it readily able to accept electrons/be protonated ▪ One of the most reactive carbonyl species. Only less reactive than acid anhydrides • Important reactions o Nucleophilic addition reactions at C=O (tend to undergo addition b/c they have bad leaving groups on their carbonyl C) ▪ Acetal, hemiacetal • Acetal: formed when reacting a ketone or alcohol with 2 equivalents of alcohols. Occurs in acidic conditions (Basic conditions can only get to the hemi form) Cannot easily degrade back to aldehyde or ketone and can’t be nucleophilicaly attacked o Acetal as a protecting group: convert an aldehyde/ketone into an acetal to prevent it from reacting with a Nu. Then react it w/ acid to remove acetal protection • Hemiacetal: formed when reacting a ketone or alcohol with 1 equivalent of alcohol. Occurs in more acidic or basic conditions (not in between). Exists in equilibrium with aldehydes and ketones. Can be Nu attacked to form an acetal. • Mechanism: o 1) carbonyl O (formation of hemi) or -OH (formation of acetal) is protonated first o 2) Nu attack occurs on central C. Either breaks pi bond to form a hemiacetal or causes -OH to leave to form an acetal ▪ Imine, enamine • Like ketones and enols but with nitrogen. Imines are more stable than enamines b/c N group next to C=C is electron withdrawing. However, enamines are more stable than enols b/c enols have O group next to C=C • Reaction to make these occur in acidic conditions by reacting amine with carbonyl • Mechanism: o 1) Amine attacks carbonyl C o 2) -OH group formed from carbonyl O is protonated by an acid catalyst o 3) Two different paths for imines and enamines ▪ Imines: N-H bond broken, electrons used to make pi bond between C and N ▪ Enamines: C-H bond on alpha carbon broken and form a pi bond connecting alpha C to Nu attacked C ▪ Hydride reagents • Reducing agents have more H’s, oxidizing agents have more O’s • LAH, NaBH4 ▪ Cyanohydrin • CN- attacks carbonyl C to produce cyanohydrin • Cyanohydrin converted to carboxylic acid when exposed to acid and H2O o Oxidation of aldehydes ▪ Aldehydes oxidize to carboxylic acids. Ketones do not oxidize further. ▪ Tollen’s reagent: A diamine silver cation will oxidize aldehyde to carboxylate anions. Reduces the silver ions to solid silver. The formation of a silver mirror indicates the presence of an aldehyde. If you want to form the carboxylic acid, you would need to then protonate your carboxylate anion. Tollen’s does not react with alcohols to form ketones. Glucose can be used to make silver mirrors. o Reactions at adjacent positions: enolate chemistry ▪ Keto-enol tautomerism (a-racemization) • Enols are less stable (C=C weakened by electronegative O) • Tautomerization can be catalyzed by acid or base • Enolate: anion of an enol. Formed in basic conditions ▪ Aldol condensation, retro-aldol • Carbonyl becomes a nucleophile by being reduced by base to an enolate. Enolate attacks another alpha-C to form alkoxide ion. Alkoxide is protonated to produce aldol. • Aldols are unstable, dehydrate by heat to become enal (aldol but -OH is a double bond) ▪ Kinetic versus thermodynamic enolate • Kinetic enolate: less substituted enolate product. Reaction to form it has lower activation energy but the product is less stable o Favored when a bulkier base is used (harder for it to reach internal area of molecule to react) and at lower temperatures • Thermodynamic enolate: more substituted enolate product. Reaction has a higher activation energy but more stable product o Favored when there’s more heat o General principles ▪ Effect of substituents on reactivity of C=O; steric hindrance • Bulky groups on either side of C=O blocks access to the electrophilic carbon, so reactivity goes down ▪ Acidity of a -H; carbanions • Alpha proton is acidic because the resulting carbanion is stabilized by resonance Alcohols (OC) • Description o Nomenclature ▪ Prefix: hydroxyl, hydroxyl ▪ Suffix: -ol, alcohol o Physical properties (acidity, hydrogen bonding) ▪ Hydrogen bonding ▪ Higher boiling point than the same compound without the alcohol group ▪ Water soluble as long as molecule does not contain a lone hydrophobic region o Infrared absorption of OH group: 3300 cm-1 and broad due to hydrogen bonding • Important reactions o Oxidation ▪ KMnO4 and CrO3 oxidize primary alcohols to carboxylic acids, but PCC (Pyridine Chlorochromate) and other weak oxidizing agents will only oxidize a primary alcohol to the aldehyde ▪ Secondary alcohols always oxidize to the ketone ▪ Tertiary alcohols do not oxidize o Substitution reactions: SN1 or SN2, depending on alcohol and derived alkyl halide ▪ R-OH + HX → R-X + H2O ▪ Factors that favor SN1: stable carbocation, tertiary carbon center, protic solvent ▪ Factors that favor SN2: unstable carbocation, primary carbon center, aprotic (but polar) solvent ▪ All substitution reactions need a good leaving group ▪ SN1 = unimolecular reaction, intermediate carbocation formed ▪ SN2 = bimolecular reaction, passes through transition state o Protection of alcohols: the best protecting group is the trimethylsilyl group ▪ To protect, add Cl-SiMe3 to R-OH ▪ The alcohol gets “capped” into R-O-SiMe3 ▪ To deprotect, add Fo Preparation of mesylates and tosylates ▪ Makes alcohol a better leaving group ▪ This is a nucleophilic substitution reaction. Alcohol is a Nu, attacks tosyl/mesylate ▪ Sulfonates R-SO3- are good leaving groups ▪ R can be: ▪ ▪ • Methane, which makes methanesulfonate • Toluene, which makes tosylate • Trifluoromethane, which makes triflate Mesylates can be prepared by reacting an alcohol (R-OH) with mesyl chloride (MsCl) Tosylates can be prepared by reacting an alcohol (R-OH) with tosyl chloride (TsCl) Carboxylic Acids (OC) • Description o Nomenclature ▪ Carbonyl carbon of carboxylic takes priority over all other groups when naming a molecule ▪ Naming salts of carboxylic acids: Replace -ic with -ate (acetic acid → acetate) ▪ Suffix: -ic or -oic to end of name of R group o Physical properties ▪ Can act as electrophile for Nu attack at carbonyl C (b/c planar, polarity) OR can act as an acid (deprotonate -OH group, resonance stabilized) ▪ Can form dimers by H-bonding to each other. This increases their BP • < 4 C’s in a carboxylic acid = soluble in water • > 5 C’s in a carboxylic acid = less soluble in water • > 10 C’s in a carboxylic acid = not soluble in water ▪ Soluble in nonpolar solvents (dimer form can solvate without the H-bonds holding it together being compromised) • Important reactions o Carboxyl group reactions (tend to undergo substitution, not addition, b/c they have good LG’s on their carbonyl C’s) ▪ Amides (and lactam), esters (and lactone), anhydride formation • Acid chloride formation: carboxylic acid + HX • Ester formation: carboxylic acid + ROH • Amide formation: carboxylic acid + RNH2 • Anhydride formation: carboxylic acid + RCOOH ▪ Reduction • Performed with LiAlH4, NaBH4. 2 equations reduce carboxylic acids and their derivatives to alcohols • NaBH4 is weaker. Can only reduce ketones and aldehydes (not carboxylic acids and esters) ▪ Decarboxylation • Occurs for β-keto acids • Oxidation of carboxylic acid to gas. Unusually high activation energy o Reactions at 2-position, substitution ▪ Carboxylic acid derivatives tend to lose an H on their alpha carbon. This can be substituted for a halide • Halogenation: RCOOH + X2 → halogenation at the alpha carbon (2 carbon) ▪ Substitution reactions: RCOOH + E+ → substitution at the alpha carbon (2 position) • 1. Carboxylic acid converted to Acyl Halide, which can enolize • 2. Acyl Halide tautomerizes to its enol form by abstraction of acidic alpha hydrogen • 3. Halogen (or some other E+) gets attacked by alpha position • 4. Revert back to carboxylic acid. The net effect is that the alpha H get substituted by an electrophile Acid Derivatives (Anhydrides, Amides, Esters) (OC) • Description o Nomenclature • o Physical properties ▪ C=O is polar, so there are dipole-dipole interactions ▪ No hydrogen bond exists in acid chlorides, anhydrides, or esters unless there is an -OH group somewhere ▪ Amides can hydrogen bond because of the N-H group. In fact, hydrogen bonding involving the amide backbone of polypeptides form the secondary structure of proteins. ▪ Amides have higher boiling points than the other acid derivatives. ▪ Acid derivatives have higher boiling points than alkanes because of the C=O dipole interactions Important reactions o Nucleophilic substitution: Nucleophile attacks the carbon center of the C=O group ▪ Acid halides • Nucleophilic substitution of an acid halide makes a carboxylic acid derivative and a HX acid • Ex. carboxylic acid + alcohol → ester + HX ▪ Carboxylic acid • Nucleophilic substitution of carboxylic acid forms an ester • This is a low yield reaction b/c strong acid catalyzes reverse reaction of ester back to a carboxylic acid. Yield can be adjusted with LeChatlier’s ▪ Amides • Amides formed when amine substitutes on carboxylic acid or one of its derivatives ▪ Can be done under either acidic or basic conditions • Acidic yields ROH or HX group. Basic yields their anions o Transesterification: ester + alcohol → new ester ▪ • Ester • An alkoxy group of an ester can be replaced by reacting it with another alcohol group. Which product the reaction prefers can be modified by adding excess of either alcohol or alcoxy group ▪ Can be done under either acidic or basic conditions • Acidic yields ROH or HX group. Basic yields their anions o Hydrolysis of amides: the leaving group is not NR2-, it is the neutral amine ▪ The O in water functions as Nu attacking the electrophilic C in C=O, creating tetrahedral intermediate ▪ Protonate the N group to make it a good LG General principles o Relative reactivity of acid derivatives: Acid chloride > Anhydride > Esters > Amides ▪ Acid halides are the most reactive derivatives because halides are good leaving groups ▪ Amides are the most stable derivatives because NR2- is a terrible leaving group. Also, the C-N bond has a partial double bond characteristic. Proteins are made of peptide bonds, and they are very stable o Steric effects ▪ Bulky groups around the C=O group helps protect the carbon center from nucleophilic attack o Electronic effects ▪ Groups that can redistribute and stabilize negative charges are good leaving groups. For example, the anhydride has a good leaving group - the carboxylate ion - because the COO- can redistribute the negative charge to both oxygens via resonance o Strain (e.g., β-lactams) ▪ Amides have a double bond characteristic between the carbon and nitrogen. This means that the C-N bond cannot rotate ▪ Normally, sigma bonds in a ring rotate to achieve most stable conformation, but this cannot occur for C-N bond if ring contains an amide ▪ Because C-N bond in an amide cannot rotate, rings that contain amides have higher strain ▪ An example of this is β-lactam, which is basically a 4-membered ring with 1 amide in it Phenols (OC, BC) • Oxidation and reduction (e.g., hydroquinones, ubiquinones): biological 2e- redox centers o Phenol gets oxidized to benzoquinone using numerous organic reagents o You could reduce benzoquinone to hydroquinone o Ubiquinone, or Coenzyme Q, is an important part of ETC ▪ When ubiquinone is reduced to ubiquinol, NADH is oxidized to NAD+ ▪ NADH, thus, serves as the reducing agent Polycyclic and Heterocyclic Aromatic Compounds (OC, BC) • Biological aromatic heterocycles o Heterocycle is a cyclic compound that contains a heteroatom (any atom other than carbon) in the ring o Thymine, a biological molecule, contains the pyrimidine ring and therefore is aromatic and has some extra stability associated with it o Imidazole is aromatic, and thus Histamine which contains this functional group, is a biological aromatic heterocycle