BioChem Reviewer (Midterms) PDF

Biochemistry—An Overview Biochemistry - is the study of the chemical substances found in living organisms and the chemical interactions of these substances with each other. - explores how cells create essential molecules and sustain life through chemical reactions, with...

Biochemistry—An Overview Biochemistry - is the study of the chemical substances found in living organisms and the chemical interactions of these substances with each other. - explores how cells create essential molecules and sustain life through chemical reactions, with new discoveries made almost daily. A biochemical substance is a chemical substance found within a living organism. Carbohydrates Carbohydrate - is a polyhydroxy aldehyde, a polyhydroxy ketone, or a compound that yields polyhydroxy aldehydes or polyhydroxy ketones upon hydrolysis. Glucose -> polyhydroxy aldehyde Fructose -> polyhydroxy ketone Types of Carbohydrates Monosaccharide (1) - is a carbohydrate that contains a single polyhydroxy aldehyde or polyhydroxy ketone unit. Disaccharide (2) - is a carbohydrate that contains two monosaccharide units covalently bonded to each other. Oligosaccharide (3-10) - is a carbohydrate that contains three to ten monosaccharide units covalently bonded to each other. Polysaccharide (>10) - is a polymeric carbohydrate that contains many monosaccharide units covalently bonded to each other. Mirror Images A mirror image is the reflection of an object in a mirror. Superimposable mirror images Nonsuperimposable mirror images - images that coincide at all points when - are images where not all points coincide the images are laid upon each other. when the images are laid upon each other. - Ex. A dinner plate with no design features - Ex. Human hands Chirality Chiral center - An atom or element in a molecule that has four different groups bonded to it in a tetrahedral orientation. Chiral molecule Achiral molecule - is a molecule whose mirror images are not - is a molecule whose mirror images are superimposable. superimposable. Stereoisomerism: Enantiomers and Diastereomers Stereochemistry - Is the study of relative spatial arrangement of atoms that form the structure of molecules and their manipulation. Stereoisomers - are isomers that have the same molecular and structural formulas but differ in the orientation of atoms in space. Enantiomers Diastereomers - are stereoisomers whose molecules are - are stereoisomers whose molecules are not nonsuperimposable mirror images of each mirror images of each other. other. Constitutional Isomers - have the same molecular formulas, but they have different connectivities. Designating Handedness Using Fischer Projection Formulas Fischer projection formula - is a two-dimensional structural notation for showing the spatial arrangement of groups about chiral centers in molecules. Dextrorotatory and Levorotatory Compounds Optically active compound - is a compound that rotates the plane of polarized light. Dextrorotatory compound Levorotatory compound - is a chiral compound that rotates the plane - is a chiral compound that rotates the plane of polarized light in a clockwise direction. of polarized light in a counterclockwise direction. Classification of Monosaccharides Aldose Ketose - is a monosaccharide that contains an - is a monosaccharide that contains a aldehyde functional group. ketone functional group. Sugar- is a general designation for either a monosaccharide or a disaccharide. Biochemically Important Monosaccharides D-Glyceraldehyde and Dihydroxyacetone - Simplest monosaccharides - Important intermediates in glycolysis - D-Glyceraldehyde is a chiral molecule, - dihydroxyacetone is not. D-Glucose - most abundant in nature - Two other names for D-glucose are dextrose and blood sugar. D-Galactose - seldom encountered as a free monosaccharide - Also called brain sugar - is also present in the chemical markers that distinguish various types of blood—A, B, AB, and O D-Fructose - the most important ketohexose - also known as levulose and fruit sugar - is sometimes used as a dietary sugar D-Ribose - aldopentose - also known as levulose and fruit sugar - is sometimes used as a dietary sugar AND The prefix deoxy- means “minus an oxygen”, where the structure of 2-deoxyribose compound lacks an oxygen atom at carbon 2. Cyclic Forms of Monosaccharides - Cyclic structure predominant form in aq. Solutions Fischer Haworth Anomer projection Projection Right Down α Left Up β Special Terminology for Cyclic Monosaccharide Structures Anomeric carbon atom - It is the hemiacetal carbon atom present in a cyclic monosaccharide structure. - It is the carbon atom that is bonded to an –OH group and to the oxygen atom in the heterocyclic ring. Cyclic monosaccharide formation always produces two stereoisomers—an alpha form and a beta form. These two isomers are called anomers. Anomers - are cyclic monosaccharides that differ only in the positions of the substituents on the anomeric (hemiacetal) carbon atom. Cyclic Forms of Other Monosaccharides Pyranose Furanose - cyclic monosaccharide containing a - cyclic monosaccharide containing a six-atom ring five-atom ring Ex. Haworth Projection Formulas Haworth projection formula - is a two-dimensional structural notation that specifies the three-dimensional structure of a cyclic form of a monosaccharide. The D or L form of a monosaccharide is determined by the position of the terminal CH2OH group on the highest-numbered ring carbon atom. The a or b configuration is determined by the position of the –OH group on carbon 1 relative to the CH2OH group that determines D or L series. Reactions of Monosaccharides Five important reactions of monosaccharides: 1. Oxidation to produce acidic sugars 2. Reduction to sugar alcohols 3. Glycoside formation 4. Phosphate ester formation 5. Amino sugar formation Oxidation to Produce Acidic Sugars Monosaccharide oxidation can yield three different types of acidic sugars. The oxidizing agent used determines the product. = aldonic acid = aldaric acid = alduronic acid Reducing sugar is a carbohydrate that gives a positive test with Tollens and Benedict’s solutions. All monosaccharides, both aldoses and ketoses, are reducing sugars. Reduction to Produce Sugar Alcohols The carbonyl group present in a monosaccharide (either an aldose or a ketose) can be reduced to a hydroxyl group, using hydrogen as the reducing agent. For aldoses and ketoses, the product of the reduction is the corresponding polyhydroxy alcohol, which is sometimes called a sugar alcohol. Glycoside Formation Acetals have two –OR groups attached to the same carbon atom. A glycoside is an acetal formed from a cyclic monosaccharide by replacement of the hemiacetal carbon –OH group with an –OR group. They can exist in both α and β form. Phosphate Ester Formation The hydroxyl groups of a monosaccharide can react with inorganic oxyacids to form inorganic esters. Amino Sugar Formation If one of the hydroxyl groups of a monosaccharide is replaced with an amino group, an amino sugar is produced. There are three common ones, the amino group replaces the carbon 2 hydroxyl group. Amino sugars and their N-acetyl derivatives are key components of polysaccharides in chitin and hyaluronic acid. The N-acetyl derivatives of D-glucosamine and D-galactosamine are present in the biochemical markers on red blood cells, which distinguish the various blood types. Disaccharides In disaccharide formation, one of the monosaccharide reactants functions as a hemiacetal, and the other functions as an alcohol. Glycosidic linkage - It is the bond in a disaccharide resulting from the reaction between the hemiacetal carbon atom –OH group of one monosaccharide and an –OH group on the other monosaccharide. - It is always a carbon–oxygen–carbon bond in a disaccharide. - Hemiacetal and acetal locations within disaccharides play an important role in the chemistry of these substances. Maltose - often called malt sugar - produced whenever the polysaccharide starch breaks down - happens in plants when seeds germinate - and in human beings during starch digestion - common ingredient in baby foods and is found in malted milk - is made up of two D-glucose units, one of which must be a-D-glucose - H+ or maltase for hydrolysis Cellobiose - produced as an intermediate in the hydrolysis of the polysaccharide cellulose - contains two D-glucose monosaccharide units - one functioning as a hemiacetal—must have a b configuration instead of the a configuration for maltose - H+ or cellobiase for hydrolysis Lactose - produced as an intermediate in the hydrolysis of the polysaccharide cellulose - made up of a b-D-galactose unit and a D-glucose unit - major sugar found in milk; hence, milk sugar - H+ or lactase for hydrolysis Sucrose - common table sugar - present in a D-sucrose molecule are a-D-glucose and b-D-fructose. - H+ or sucrase for hydrolysis Oligosaccharides Oligosaccharides are carbohydrates that contain three to ten monosaccharide units bonded to each other via glycosidic linkages. Two naturally occurring oligosaccharides found in onions, cabbage, broccoli, brussel sprouts, whole wheat, and all types of beans are the trisaccharide raffinose and the tetrasaccharide stachyose. General Characteristics of Polysaccharides A polysaccharide is a polymer that contains many monosaccharide units bonded to each other by glycosidic linkages. Glycan is an alternate name for a polysaccharide. Important parameters that distinguish various polysaccharides (or glycans) from each other are: 1. The identity of the monosaccharide repeating unit(s) in the polymer chain. ○ A homopolysaccharide is a polysaccharide in which only one type of monosaccharide monomer is present. (Ex. starch, glycogen, cellulose, and chitin) ○ A heteropolysaccharide is a polysaccharide in which more than one (usually two) type of monosaccharide monomer is present. (Ex. hyaluronic acid and heparin) 2. The length of the polymer chain. 3. The type of glycosidic linkage between monomer units. 4. The degree of branching of the polymer chain. ○ Proteins and nucleic acids: only linear (unbranched) polymers. Storage Polysaccharides A storage polysaccharide is a polysaccharide that is a storage form for monosaccharides and is used as an energy source in cells. Storage Polysaccharides Types Starch Glycogen (animal starch) Definition - homopolysaccharide containing only glucose - homopolysaccharide containing only glucose monosaccharide units monosaccharide units - energy-storage in plants - glucose storage in humans and animals Kinds Amylose Amylopectin - branched glucose polymer - straight-chain glucose - branched glucose - both α(1→4) and α(1→6) linkages polymer polymer - up to 1,000,000 glucose units present - 15%–20% of the - 80%–85% of the - branches every 8-12 glucose units starch starch - 300–500 units - Up to 100,000 units - α(1→4) glycosidic - branches every linkages 25–30 glucose units - glucose→glycogen reduces osmotic pressure - both α(1→4) and - glycogen→glucose increases osmotic press. α(1→6) linkages Structure Structural Polysaccharides A structural polysaccharide is a polysaccharide that serves as a structural element in plant cell walls and animal exoskeletons. Two of the most important structural polysaccharides are cellulose and chitin. Both are homopolysaccharides. Structural Polysaccharides Types Cellulose Chitin Definition - most abundant naturally occurring - second most abundant naturally occurring polysaccharide. polysaccharide - “woody” portions of plants—stems, stalks, - give rigidity to the exoskeletons of crabs, and trunks lobsters, shrimp, insects, and other arthropods; also found in the cell walls of fungi Description - unbranched glucose polymer - identical to cellulose - β(1→4) glycosidic linkages - β(1→4) glycosidic linkages - linear structures compared to spiral-like - glucose derivative N-acetyl-D-glucosamine amylose (NAG) than D-glucose - 5000 glucose units per chains - contain both glycosidic linkages and amine - serves as dietary fiber, due to its solubility for bonds; which can be broken by hydrolysis softer stools - product of complete hydrolysis of chitin is - about 25-35 grams daily is a desirable intake D-glucosamine; to help with joint problems Structure Cellulose Chitin Acidic Polysaccharides An acidic polysaccharide is a polysaccharide with a disaccharide repeating unit in which one of the disaccharide components is an amino sugar and one or both disaccharide components has a negative charge due to a sulfate group or a carboxyl group. Acidic Polysaccharides Types Hyaluronic Acid Heparin Definition - contains alternating residues of N-acetyl-b-D- - small highly-sulfated polysaccharide glucosamine (NAG) and D-Glucuronate - repeating units are a sulfate derivative of - D-glucuronic acid, when D-glucuronic acid D-glucuronate (D-glucuronate-2-sulfate) loses its acidic hydrogen atom. and a doubly sulfated derivative of - –CH2OH group of a glucose D-glucosamine molecule is oxidized to a –COOH group (N-sulfo-D-glucosamine-6-sulfate) -both contain negatively charged acidic groups Description - unbranched glucose polymer - blood anticoagulant - alternating β(1→3) and β(1→4) glycosidic - naturally present in mast cells linkages - prevents the formation of clots in the blood - 50,000 disaccharide units per chain - however, it does not break down formed clots - serve as lubricants in the fluid of joints - pharmaceutical heparin used as an - are also associated with the jelly-like anticoagulant to the interior/exterior surface of consistency of the vitreous humor of the eye external objects that come in contact w/blood; - from intestinal or lung tissue of slaughter-house animals Structure Hyaluronic Acid Heparin Dietary Considerations and Carbohydrates Simple carbohydrate Complex carbohydrate - is a dietary monosaccharide or dietary - is a dietary polysaccharide. disaccharide. - Carbohydrates are starch and cellulose - Sweet to taste - Not sweet to taste - Commonly referred to sugars Simple carbohydrates provide 20% of the energy in the U.S. diet. Natural = 10%, Refined = 10% Natural sugar Refined sugar - is a sugar naturally present in whole foods - sugar separated from its plant source. - Milk and fresh fruit are two important - Sugar beets and sugar cane are major sources sources - In pure form - part of mixtures of substances obtained - provide empty calories (few nutrients) from a plant source - Accompanied by nutrients Glycemic response- change in blood-glucose level that comes from carbohydrate ingestion Glycemic index (GI)- rating system that categorizes foods according to glycemic response (50 grams only) Glycemic load (GL)- alternate rating system that takes into account both the glycemic index for and the actual amount of carbohydrate present in a serving of a specific food. 𝐺𝐿 × 𝑔𝑟𝑎𝑚𝑠 𝑜𝑓 𝑐𝑎𝑟𝑏𝑜ℎ𝑦𝑑𝑟𝑎𝑡𝑒𝑠 GL = 100 Glycolipids and Glycoproteins: Cell Recognition Biochemistry of Carbohydrates (prior to 1960) 1. as energy sources for plants, humans, and animals 2. as structural materials for plants and arthropods Glycolipid - a lipid molecule that has one or more carbohydrate (or carbohydrate derivative) units covalently bonded to it. - Glycolipids cerebrosides and gangliosides occur extensively in brain tissue Glycoprotein - a protein molecule that has one or more carbohydrate (or carbohydrate derivative) units covalently bonded to it. - Glycoprotein immunoglobulins are key components of the body’s immune system response to invading foreign materials. In cell membrane structure, the protein/lipid part is incorporated into the cell membrane structure and the carbohydrate (oligosaccharide) part functions as a marker on the outer cell membrane surface. Blood Types and Oligosaccharides Four-monosaccharide sequence Type A - N-acetyl-galactosamine Type B - Extra Galactose Type AB - N-acetyl-galactosamine w/ Galactose Type O - lacks fifth monosaccharide unit Lipids