Nucleic Acids, Lipids, & Carbohydrates

Nucleic Acids, Lipids, & Carbohydrates Nucleic Acid Structure 1: The DNA inside of one cell, when unwrapped, can extend about 2 m (6 ft) DNA is made up of three components: Deoxyribose sugar (carbons numbered with primes), a nitrogenous base (carbons numbered without primes), and a phosphate group Purines are the double ring nitrogenous bases (AG → Purines Always Glow) Pyrimidines are the single ring nitrogenous bases (CTU) Cytosine and Guanine form 3 H-bonds while Adenine and Thymine form 2 H-bonds (CG having higher melting points) (Remember, hydrogen bonds occur between H atoms and N, O, and F atoms) Nucleosides are the nitrogenous base with a sugar attached but NO phosphate group (Cytidine, Guanosine, Adenosine, and Thymidine) Antiparallel Structure of DNA Strands: There is a repeating structure of phosphate and sugar along the phosphodiester backbone of the DNA molecule linked by nitrogenous bases (acting like rungs on a ladder) DNA is called an acid because phosphate groups would be protonated but because they are so acidic, they tend to lose their proton when placed in neutral conditions (such as at physiological pH) Saponification - Base Promoted Ester Hydrolysis: Ester Hydrolysis Reactions can occur in triacylglycerides where the -OR group leaves the carbonyl in exchange for OH (shown below) Base Promoted Ester Hydrolysis Reaction You can use specific enzymes known as lipases in order to break down fats in this way in order to get energy Also, if you use NaOH as the base then you form a nonpolar side (to dissolve grease, oil, etc.) and the polar side (to dissolve and wash away with water) Saponification involves the conversion of fat, oil, or lipid, into soap Lipids - Structure in Cell Membrane: Hydrolyzable lipids (such as triacylglycerol which is an energy storage molecule and phospholipids which are structural lipids important for the cell membrane) can be broken down into smaller sections and Nonhydrolyzable lipids cannot be broken down into smaller components (main function is for signaling and cofactors for enzymes) Phosphodiester bonds looks like the image on the right (R-O-P-O-R) → A phospholipid is shown on the right where one of the three parts has a phosphate group attached to it → This allows for the lipid to be amphipathic allowing for the formation of a double layer membrane when placed into water Sphingolipids are formed from the amino acid sphingosine (OH is replaced by the phosphate group) Play an important role in nerve cell membranes, especially those forming the myelin sheath around axons Waxes are very hydrophobic since they possess two hydrophobic sections (still hydrolyzable since they have the ester group in it) Lipids as Cofactors & Signaling Molecules: Prostaglandins are lipids molecules that help signal inflammation (drugs like Aspirin or Ibuprofen help stop prostaglandin production) and are a part of the nonhydrolyzable lipids category (signaling type) It is also a type of Eicosanoid which is a class of molecules that have 20 carbons Prostaglandins also lower blood pressure, gastric secretion, etc. Steroids are also another type of signaling/nonhydrolyzable lipid and are a tetracyclic compounds (4 ring structures with three 6 membered rings and one 5 membered ring) Fat soluble vitamins are also another type of nonhydrolyzable lipid that functions as a cofactor (help some enzyme in the body perform a specific function) and cells don’t make this compounds, meaning we must obtain them from our diet Vitamin A is also known as retinol which is important for light sensitivity in vision and for maintaining healthy mucous membranes Vitamin D helps regulate phosphorus and calcium metabolism (deficit can lead to rickets and osteoporosis) Vitamin E is an antioxidant that helps protect our neurological function Vitamin K regulates the synthesis of prothrombin which helps our blood clot Carbohydrates - Naming & Classification: Typically, carbohydrates will follow the general formula Cn(H2O)n → matching number of water molecules to carbons or a 1:2:1 ratio of carbons to hydrogen to oxygen Mono - one Poly - more than one Main sugar for our body is glucose (monosaccharide) Cellulose is a polysaccharide important for the cell wall -ose is the suffix for sugars (Also found in Biomolecule section for more in depth information) Remember, the 2nd to last carbon will tell you the stereochemistry of the sugar as a whole (D/R or L/S) → the side that the OH functional group is on Fischer Projections: Lactic acid is the product of fermentation (3 carbon molecule) For fischer projections, the right and left sides are coming out at you and the vertical components are going away from you Helps with drawing carbohydrates Remember, you can have enantiomers and diastereomers that include the possible stereoisomers You can label all of the carbons with the respective stereoisomers (such as 2R, 3R shown here) Carbohydrates - Epimers, Common Names: We are enzymatically programmed to digest the D stereoisomers of sugars For D/L they are true enantiomers where all stereocenters are mirror images For more information go to Carbohydrates - Absolute Configuration, Epimers, & Common Names in Biomolecules Section Conformation refers to relative position of atoms in space by rotation of a single bond Configuration refers to the connectivity of atoms by breaking bonds and forming new ones (forming different stereoisomers) Carbohydrates - Glycoside Formation Hydrolysis: To go to a chair you must see the direction the point of the chair is going (so if it is up and the original is going down, then place in equatorial and if it’s in the same direction, then go axial) Glycosides are formed by replacing the -OH group with some sort of -OR group in the presence of acid (or maybe base too?) This is how the glycosidic linkages are produced These can be broken down as when through Hydration (since you add in a water) and is also known as Glycoside hydrolysis (add in water and break the glycosidic linkage) These reactions form ɑ (axial) and β (equitorial) anomers since the group coming in can attack through the backside or front side Keto-enol Tautomerization (By Sal): A ketone will go to an enol and be resonance stabilized (carbocation formation is not stable so the alpha carbon gives up its H and forms a double bond with the carbonyl carbon) Tautomers are the keto and enol forms of the molecule (keto form is much more stable) Disaccharides & Polysaccharides: Acetal formation between monosaccharides are what form the basic of glycosidic linkages This bond forms typically between C1 and C4 of the next sugar β linkages (same equitorial/axial) are cis and ɑ linkages (opposite equitorial/axial) are trans Hemiacetals can keep going and make more bonds but acetals cannot (nonreducing sugars such as Sucrose) Humans can break down alpha (1,4) bonds but not beta (1,6) You can branch off with alpha 1,6 (forming glycogen for energy storage) Carbohydrates - Cyclic Structures & Anomers: Carbohydrates basically have all of the components for an intramolecular reaction The reason that this particular oxygen nucleophilically attacks, is because it will forms a six membered ring (or even a five member ring sometimes), which is pretty stable Anomeric carbon is the carbon that is connected to the oxygen that forms the cyclic structure Haworth Diagram shows the flat structure of the cyclic ring (to go from Fischer to Haworth, remember downright/uplifting) The nucleophilic attack by the oxygen can actually produce two different forms, alpha (down in Haworth and axial in chair) and beta (up in Haworth and equatorial in chair) anomers Mutarotation is the process of constant opening and closing of the sugar ring and the alternation between alpha/beta conformations (remember configuration is arrangement of atoms that can only be changed through the breaking of covalent bonds while conformations are the shapes that a molecule can adopt due to rotation around one or more single bonds) Extra Notes: Unsaturated fatty acids increase membrane fluidity by saturated fatty acids decrease membrane fluidity Cholesterol increases membrane fluidity at low temperatures while decreasing it at high temperatures