BBIO109 Lecture Notes: Nucleic Acids & Carbohydrates PDF

BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH NUCLEIC ACIDS except that there is no hydroxyl (-OH)...

BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH NUCLEIC ACIDS except that there is no hydroxyl (-OH) on C2’. The deoxy prefix means “without oxygen and provides D in DNA NUCELEOSIDES AND NUCLEOTIDES  Nucleosides, which are a combination of a  Nucleic acids are large molecules found in the sugar and a base, are produced when the nuclei of the cells in our bodies that store nitrogen atom in a pyrimidine or a purine base information and direct activities for cellular forms an N-glycosidic bond to carbon 1 (C1’) of growth and reproduction. a ribose or deoxyribose sugar. For example,  Components of Nucleic Acids adenine and ribose form a nucleoside called o There are two closely related types of adenosine. nucleic acids: deoxyribonucleic acid (DNA), and ribonucleic acid (RNA). o Both are unbranched polymers of repeating monomer units known as nucleotides. Each nucleotide has three components: a base, a five-carbon sugar, and a phosphate group  Nucleotides are nucleosides in which a phosphate group bonds to –OH on carbon 5 (C5’) of a ribose or deoxyribose sugar. The product is a phosphate ester. Other hydroxyl groups on ribose can form phosphate esters too, but only the 5’-monophosphate The nitrogen-containing bases in nucleotides are found in RNA and DNA. nucleic acids are derivatives of pyrimidine or purine. In RNA, the five-carbon sugar is ribose, which gives the letter R in the abbreviation RNA. In DNA, the five-carbon sugar is deoxyribose, which is similar to ribose BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH COMPONENTS IN DNA AND RNA PRIMARY STRUCTURE OF NUCLEIC ACIDS  The nucleic acids are polymers of many nucleotides in which the 3’-OH group of the sugar in one nucleotide bonds to the phosphate group on the 5’-carbon atom in the sugar of the next nucleotide.  This phosphate link between the sugars in adjacent nucleotides is referred to as a phosphodiester bond.  As more nucleotides are added using phosphodiester bonds, a backbone forms that consists of alternating sugar and phosphate groups. The bases, which are attached to each sugar, extend out from the sugar-phosphate backbone. NAMING NUCLEOSIDES AND NUCLEOTIDES  The name of a nucleoside that contains a purine ends with osine whereas a nucleoside that contains a pyrimidine ends with idine.  The names of the nucleosides of DNA add deoxy  Each nucleic acid has its to the beginning of their names. own unique sequence of  The corresponding nucleotides in RNA and DNA bases, which is known as its are named by adding -5’-monophosphate. primary structure.  In any nucleic acid, the sugar at the one end has an unreacted or free 5’- phosphate terminal end, and the sugar at the other end has a free 3’-hydroxyl group.  A nucleic acid sequence is read from the sugar with free 5’-phosphate to the sugar with the free 3’-hydroxyl group. Exercise! Identify each of the following as a pentose sugar, base, nucleoside, nucleotide, or nucleic acid and if it is found in DNA, RNA, or both: a. Guanine b. deoxyadenosine-5’-monophosphate (dAMP) c. Ribose d. Cytidine BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH Draw the structure of the RNA dinucleotide formed Exercise! by two cytidine-5’-monophosphates Write the complementary base sequence for the following DNA segment: -A –C –G –A –T –C –T – VIRUSES  Viruses are small particles of 3 to 200 genes that cannot replicate without a host cell. A typical virus contains a nucleic acid, DNA or RNA, but not both, inside a protein coat.  The only way a virus can replicate is to invade a host DNA DOUBLE HELIX cell and take over the materials necessary for  # of Purine = # of Pyrimidine protein synthesis and growth A=T G=C  In 1953, James Watson and Francis Crick proposed that DNA was a double helix that consists of two polynucleotide strands winding about each other like a spiral staircase.  The sugar- phosphate backbones are analogous to the outside railings with the bases arranged like steps along the inside. The two strands run in opposite directions. One strand goes from the 5’ to 3’ direction, and the other strand goes in the 3’ to 5’ direction. BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH REVERSE TRANSCRIPTION  HIV is a retrovirus that infects and destroys T4 lymphocyte cells, which are involved in the  A virus that contains RNA as its genetic material immune response. is a retrovirus. Once inside the host cell, it must first make viral DNA using a process known as reverse transcription.  A retrovirus contains a polymerase enzyme called reverse transcriptase that uses the viral RNA template to synthesize complementary strands of DNA.  Treatment for AIDS is based on attacking the HIV-1 at different points in its life cycle, including reverse transcription and protein synthesis.  Nucleoside analogs mimic the structures of the nucleosides used for DNA synthesis, which  Once produced, the DNA strands form double inhibit the reverse transcriptase enzyme. stranded DNA using the nucleotides present in the host cell. This newly formed viral DNA, called a provirus, integrates with the DNA of the host cell.  For example, the drug AZT (3’-azido-3’- deoxythymidine) is similar to thymidine, and ddI (2’,3’-dideoxyinosine) is similar to guanosine. Two other drugs are ddC (2’,3’- dideoxycytidine) and d4T (2’,3’-didehydro-2’,3’- dideoxythymidine).  When a nucleoside analog is incorporated into viral DNA, the lack of a hydroxyl group on the carbon in the sugar prevents the formation of ACQUIRED IMMUNE DEFICIENCY SYNDROME the sugar- (AIDS) phosphate bonds  An HIV-1 virus (human immunodeficiency virus and stops the replication of the virus. type 1) is now known to be the AIDS-causing agent. BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH  Treatment of CARBOHYDRATES AIDS often  Carbohydrates such as table sugar, lactose in combines milk, and cellulose are all made of carbon, reverse hydrogen, and oxygen transcriptase  Simple sugars, which have formulas of inhibitors with 𝑪𝒏(𝑯𝟐𝑶)𝒏 were once thought to be hydrates of protease inhibitors such as saquinavir carbon, thus the name carbohydrate. (Invirase), indinavir, lexiva (fosamprenavir),  In photosynthesis, energy from the Sun is used nelfinavir, and ritonavir. The inhibition of a to combine the carbon atoms from carbon protease enzyme prevents the synthesis of dioxide and the hydrogen and oxygen atoms of proteins used by viruses to make more copies. water into carbohydrate glucose.  In the body, glucose is oxidized in a series of metabolic reactions known as respiration, which releases chemical energy to do work in the cells. TYPES OF CARBOHYDRATES MONOSACCHARIDES  Monosaccharides are sugars that have a chain of three to eight carbon atoms, one in a carbonyl group and the rest attached to hydroxyl groups.  In an aldose, the carbonyl group is on the 1st carbon (- CHO), an aldehyde.  In a ketose, the carbonyl group  UNDETECTABLE = UNTRANSMITTABLE is on the 2nd  HIV medicine can help you get and keep an carbon atom as a ketone (C=O) undetectable viral load.  This means you can stay healthy and will not transmit HIV to HIV-negative partners through sex. BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH  In each of the mirror images, it is important to understand that the –OH groups on all the chiral carbon atoms are reversed from one side to the other. Triose – 3 Carbons Tetrose – 4 Carbons Pentose – 5 Carbons Hexose – 6 Carbons Let Us Check Your Understanding! Classify each of the following monosaccharides as Let Us Check Your Understanding! an aldopentose, aldohexose, ketopentose, or Identify the following Fischer projection as D-or L ketohexose: xylose: STRUCTURES OF SOME IMPORTANT FISCHER PROJECTIONS OF MONOSACCHARIDES MONOSACCHARIDES  A Fischer projection is drawn with vertical and  The hexoses glucose, galactose, and fructose horizontal lines with aldehyde group at the top are the most important monosaccharides. and –H and –OH groups on the intersecting line.  The most common  Most monosaccharides to be studied have 5-6 hexose, D-glucose, also C w/ more than one chiral C. Then the –OH known as dextrose and group on the chiral C farthest from the carbonyl blood sugar, is found in group is used to determine the D or L isomer. fruits, vegetables, corn syrup, and honey.  D-glucose is a building block of the disaccharides sucrose, lactose, and maltose, and polysaccharides such as amylose, cellulose, and glycogen. BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH  Galactose is an Let Us Check Your Understanding! aldohexose that is Ribulose has the following Fischer projection. obtained from the Identify the compound as D-or L-ribulose. disaccharide lactose, which is found in milk and milk products.  The only difference in the Fischer projections of D-glucose and D- galactose is the arrangement of the –OH group of carbon 4 HAWORTH STRUCTURES OF MONOSACCHARIDES  In a condition called galactosemia, an enzyme needed to convert galactose to glucose is  Molecules of monosaccharides normally exist missing. in a cyclic structure formed when a carbonyl  The accumulation of galactose in the blood and group and a hydroxyl group in the same tissues can lead to cataracts, mental molecule react to give ring structures known as retardation, and cirrhosis. Haworth structures.  The most stable for of pentoses and hexoses are five- or six atom rings. DRAWING HAWORTH STRUCTURES 1. Turn the open-chain condensed structural formula clockwise 90˚. This places the –OH groups on the right of C2 and C4 (blue) and C5 (red) of the vertical open chain below the carbon atoms. The –OH group on the left (green) of the open chain is drawn above C3.  Fructose, also called levulose and fruit sugar, is a ketohexose.  The structure of fructose differs at carbons 1 2. Fold the carbon chain into a hexagon and bond and 2 by the location of the carbonyl group. the O on C5 to the carbonyl group. With C2 and  Fructose is the sweetest of the carbohydrates, C3 as the base of a hexagon, move the twice as sweet as sucrose remaining carbons upwards. The remaining – OH group (red) on C5 is drawn next to the carbonyl carbon, which moves C6 in -𝐶𝐻2𝑂𝐻 above C5. To complete the Haworth structure, draw a bond from the O of the reacting –OH group (C5) to the carbonyl carbon. BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH 3. Draw the new –OH group on C1 down to give the at the right corner of the ring. The cyclic α isomer or up to give β isomer. In a Haworth structure forms when the hydroxyl group on C5 structure, the corners of the ring represent reacts with C2 in the carbonyl group. The new carbon atoms. There are two ways to draw the hydroxyl group on carbon 2 gives the α and β new –OH, either up or down, which gives two isomers of fructose possible stereoisomers of D-glucose. MUTAROTATION OF α- AND β-D-GLUCOSE  In an aqueous solution, the Haworth structure Let Us Check Your Understanding! of α-D-glucose opens to give the open chain of D-glucose with an aldehyde group. However, D-Mannose, a carbohydrate found in when the open chain closes again it can form β- immunoglobulins, has the following open-chain D Glucose. In this process called mutarotation, structure. Draw the Haworth structure for β-D- each isomer converts to the open chain and Mannose. back again. As the ring opens and closes, the – OH group on C1 can form either the α or β isomer HAWORTH STRUCTURES OF GALACTOSE Answer!  Galactose is an aldohexose that differs from glucose only in the arrangement of the –OH group on C4. It’s Haworth is similar to glucose except that the –OH on C4 is drawn up. It also exist as α and β isomers CHEMICAL PROPERTIES OF MONOSACCHARIDES  In an aldose, the aldehyde group can be oxidized to a carboxylic acid. The carbonyl group in both an aldose and a ketose can be reduced to give a hydroxyl group. The hydroxyl  Fructose is a ketohexose. The Haworth groups can react with other compounds to form structure for fructose is a five-atom ring with C2 BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH a variety of derivatives that are important in Glucose is reduced to D-glucitol, better biological structures. known as D-sorbitol.  Oxidation of Monosaccharides o An aldehyde group with an adjacent hydroxyl can be oxidized to a carboxylic acid by an oxidizing reagent such as Benedict’s reagent. Then, the 𝐶𝑢2+ is reduced to 𝐶𝑢+, which forms a brick-red precipitate of 𝑪𝒖𝟐𝑶. A carbohydrate that reduces another substance is called a reducing sugar. o Sugar alcohols such as D-sorbitol, D-xylitol from D-xylose, and D- mannitol from D- mannose are used as sweeteners in many sugar-free products o Fructose is also a reducing sugar. In such as diet drinks and Benedict’s solution, which is basic, a sugarless gum as well rearrangement occurs between the ketone as products for people group on C2 and the hydroxyl group on C1. with diabetes. As a result, fructose is converted to glucose, which produces an aldehyde group with an adjacent hydroxyl that can be Let Us Check Your Understanding! oxidized Answer!  Reduction of Monosaccharides o The reduction of the carbonyl group in monosaccharides produces sugar alcohols, which are also called alditols. D- BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH DISACCHARIDES  The glycosidic bond in maltose is designated as an α-1,4 linkage to show that an α-OH on C1 is  A disaccharide is joined to C4 of the 2nd Glucose molecule. composed of two monosaccharides linked together. The most common disaccharides are maltose, lactose, and sucrose.  Because the 2nd glucose molecule still has a  When they are split free –OH group on C1, it can form an open chain, by water (hydrolysis) which allows maltose to form both α and β in the presence of an acid or an enzyme, the isomers. The open chain provides an aldehyde products are two monosaccharides. group that can be oxidized, making maltose a reducing sugar.  Maltose, or malt sugar, is obtained from starch and is found in germinating grains.  When maltose in barley and other grains is hydrolyzed by yeast enzymes, glucose is obtained, which can undergo fermentation to give ethanol.  Maltose is used in cereals, candies, and the brewing of beverages.  Lactose, milk sugar, is a disaccharide found in HAWORTH STRUCTURES OF DISACCHARIDES milk and milk products.  In the Haworth  Lactose makes up 6–8% of human milk and structure of a about 4–5% of cow’s milk, and it is used in disaccharide, a products that attempt to duplicate mother’s glycosidic bond is milk. an ether bond that  Some people do not produce sufficient connects two quantities of the enzyme lactase needed to monosaccharides. hydrolyze lactose. Then lactose remains undigested, which can cause abdominal cramps and diarrhea.  The bond in lactose is a β-1,4- glycosidic bond because the –OH group  In maltose, a glycosidic bond forms between on C1 of β-D-galactose the –OH groups of C1 and C4 of two α-D- forms a glycosidic Glucose molecules with a loss of a water bond with the –OH molecule. group on C4 of a D- glucose molecule. BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH  Because D-glucose still has a free group on C1, HOW IS YOUR SWEETENER? it can form an open chain, which allows lactose  Although many of to form both α and β isomers. the  Sucrose, a disaccharide obtained from sugar monosaccharides beets and sugar cane, contains glucose and and disaccharides fructose. taste sweet, they  The sugar we use to sweeten our cereal, coffee, differ considerably or tea is sucrose. Most of the sucrose for table in their degree of sugar comes from sugar cane (20% by mass) or sweetness. Dietetic sugar beets (15% by mass). foods contain  Both the raw and refined forms of sugar are sweeteners that are sucrose. noncarbohydrate or  Sucrose consists of an α-D-glucose and a β-D- carbohydrates that are sweeter than sucrose. fructose molecule joined by an α, β-1,2- glycosidic bond. BLOOD TYPES AND CARBOHYDRATES  Unlike maltose and lactose, the glycosidic bond in sucrose is between C1 of glucose and  The blood types A, C2 of fructose. B, and O are  Thus, sucrose cannot form an open chain and determined by cannot be oxidized and react with Benedict’s monosaccharides reagent. So, it is not a reducing sugar. attached to the surface of red blood cells.  The blood types, A, B, and O, all contain the monosaccharides N- acetylglucosamine, galactose, and fucose.  In type A, galactose is bonded to N- Let Us Check Your Understanding! acetylgalactosamine.  In type B, the Melibiose is a disaccharide that is 30 times sweeter galactose is bonded to than sucrose. Melibiose has the following Haworth a second galactose. structure:  In type AB, the monosaccharides of both blood types A and B are found. POLYSACCHARIDES (a)What are the monosaccharide units in  A polysaccharide is a polymer of many melibiose? monosaccharides joined together. Four important polysaccharides— amylose, (b)What type of glycosidic bond links the amylopectin, cellulose, and glycogen – are all monosaccharides? polymers of D-glucose that differ only in the (c)Identify the structure as α-or β-melibiose. type of glycosidic bonds and the amount of branching in the molecule. BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH  Starch, a storage form of glucose in plants, is found as insoluble granules in rice, wheat, potatoes, beans, and cereals.  In our bodies, these complex carbohydrates are  Starch is composed of two kinds of digested by the enzymes amylase (in saliva) and polysaccharides, amylose and amylopectin. maltase (in the intestine). The glucose obtained provides about 50% of our nutritional calories.  Glycogen, or animal starch, is a polymer of glucose that is stored in the liver and muscle of animals.  In glycogen, the glucose units are joined by α- 1,4-glycosidic bonds, and branches occurring about every 10-15 glucose units are attached by α-1,6-glycosidic bonds  Amylose, which makes up about 20% of starch, consists of 250–4000 α-D-glucose molecules connected by α-1,4-glycosidic bonds in a continuous chain.  Sometimes called a straight-chain polymer, polymers of amylose are actually coiled in helical fashion  Cellulose is the major structural material of wood and plants. Cotton is almost pure cellulose. In cellulose, glucose molecules form a long unbranched chain similar to that of amylose.  However, the glucose units in cellulose are linked by β-1,4-glycosidic bonds.  Humans have enzymes called α-amylase in  Amylopectin, which makes up as much as 80% saliva and pancreatic juices that hydrolyze the of starch, is a branched-chain polysaccharide. α-1,4 glycosidic bonds of starches, but not the Like amylose, the glucose molecules are β-1,4-glycosidic bonds of cellulose. Thus, connected by α-1,4-glycosidic bonds. humans cannot digest cellulose.  However, at about every 25 glucose units, there  Animals such as horses, cows, and goats can is a branch of glucose molecules attached by obtain glucose from cellulose because their an α-1,6-glycosidic bond between C1 of the digestive systems contain bacteria that provide branch and C6 in the main chain. enzymes such as cellulase to hydrolyze β-1,4- glycosidic bonds. Let Us Check Your Understanding! Identify the polysaccharide described by each of the following: (a) a polysaccharide that is stored in the liver and muscle tissues (b) an unbranched polysaccharide containing β-1,4-  Starches hydrolyze easily in water and acid to glycosidic bonds give dextrins, which then hydrolyze to maltose (c) a starch containing α-1,4-and α-1-6-glycosidic and finally glucose. bonds BBIO109 LECTURE NOTES MOD 4-5: NUCLEIC ACIDS & CARBOHYDRATES MAGBANUA, KEILAH