General, Organic, and Biochemistry II Exam 2 Study Guide
General, Organic, and Biochemistry II Exam 2 Study Guide CHEM1031
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This 8 page Study Guide was uploaded by Rachael Chandler on Saturday February 27, 2016. The Study Guide belongs to CHEM1031 at The University of Cincinnati taught by Dr. Ridgway in Winter 2016. Since its upload, it has received 131 views. For similar materials see General, Organic, and Biochemistry II in Chemistry at The University of Cincinnati.
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General, Organic, and Biochemistry II Exam 2 Study Guide ** = There were several clicker/Connect homework questions on this topic -Chapter 16: Carbohydrates General Formula: (CH O2 X D- v. L- Notation: If the –OH group on the second furthest carbon from the carbonyl group is on the left, it is L- configuration. If it is on the right, it is D-. Types: Monosaccharides (Simple Carbohydrate) o One sugar o Contain anywhere from 3-7 carbons o Can contain assorted functional groups o **Name based on function groups and number of carbons in the main skeleton Ex. Aldose v. Ketose; Triose (3 carbons), Tetros (4 carbons), etc. These names are combined, along with the D- and L- configurations, to describe a molecule, like D-Ketotetros, L-Aldohexose, etc. o Ex. Fructose, Glucose, Galactose Disaccharides (Simple Carbohydrate) o Two monosaccharides linked by a glycosidic bond o Ex. Sucrose, Lactose, Maltose, etc. Oligosaccharides (Complex Carbohydrate) o 3-10 monosaccharides o Linked by glycosidic bonds Polysaccharides (Complex Carbohydrate) o >10 monosaccharides linked by glycosidic bonds o Ex. Starch, cellulose, glycogen, etc. **Chirality: Non-superimposable mirror images; a chiral carbon it will have four different groups attached to it. (Chirality is important because many drugs are chiral, and interact with chiral receptors, and will be ineffective if they are not the correct chirality.) Example: **Enantiomers v. Diastereomers: Enantiomers are mirror images, but are not superimposable Diastereomers are neither mirror images, nor superimposable. They include any stereoisomer that isn’t an enantiomer. Example: (a) And (b) are enantiomers, because of you fold them over the line onto each other, they’d be the same (This is also true of (c) and (d)). However, (a) and (c) are diastereomers because there is no way to make them lay on top of one another so they are the same because (c) has two H’s on the same side of the molecule and (a) does not. (The same is true of (b) and (d)). 2 **A compound with 1 chiral center has 2 enantiomers. (n chiral centers = n enantiomers/stereoisomers) Polarized light and Optical Activity Polarized Light: Light generally travels as an infinite number of sine waves vibrating perpendicular to the direction of travel. When those waves are passed through a polarizing filter, only a wave traveling in one plane gets through. Enantiomers are called optical isomers, which means they interact with plane polarized light to rotate the plane of light in opposite directions. This interaction (optical activity) is measured by a polarimeter and distinguishes the isomers because one enantiomer will rotate the light in a positive direction, and the other will rotate it in a negative direction. (Positive direction is called dextrorotary, negative direction is called levorotary; these names have nothing to do with the D-, L- configurations.) If there are equal amounts of each enantiomer, the rotational effects cancel and the light doesn’t rotate. This is called a racemic mixture. Biological Monosaccharides Most naturally occurring monosaccharides are D- isomers **Ring Structures: AldoPentose – Form 5(more common) and 6 member rings o Furanose Formed by linking the C-1 aldehyde and C-4 OH o Pyranose Formed by linking the C-1 aldehyde and C-5 OH KetoHexose – Form 5 and 6(more common) member rings o Pyranose Formed by linking the C-2 keto carbonyl and C-6 OH o Furanose Formed by linking the C-2 keto carbonyl and C-5 OH KetoPentose – Form 5 member hemiketal rings Important Monosaccharides Fructose (Fruit Sugar)– Ketohexose – Mostly forms furanose Galactose(Milk Sugar) – Aldohexose – Mostly forms pyranose Fructose – Aldopentose – Mostly forms furanose – Forms the core of RNA o DNA formed from 2-deoxyribose Anomeric Carbon: The hemiacetal or hemiketal carbon in a pyranose or furanose structure Exist in α and β. If the first –OH group is up(above the plane of the ring), it’s β, if it’s down, it is α. Aldehydes v. Ketones: Tollen’s Test: Silver ion is reduced to silver metal, creating a mirror in the glassware. Used with a basic solution of Ag(NH 3 2 Only works on Aldehydes. Benedict’s Test: Tests for reducing sugars. Cu is reduced to Cu . Color changes from blue to red. Works on all aldehydes and most ketones. o All common mono- and disaccharides are reducing sugars except sucrose. Disaccharide Bonds Hemiacetals react with alcohols to for acetals; the same is true for hemiketals and ketals Important Disaccharides Maltose(Malt Sugar): o Formed with an α-1,4 glycosidic linkage between two glucoses o Reducing sugar Lactose (Milk Sugar): o Formed with an β-1,4 glycosidic linkage between glucose and galactose o Source of energy is hydrolyzed Sucrose (Table Sugar): o α1-β2 glycosidic linkage between glucose and fructose o Gives a negative reaction to the Benedict’s test o Important plant carbohydrate; cannot be synthesized by animals Polysaccharides **Starch: Storage form of glucose found in plants; contain α(14) linked glucose; two forms: Amylose and Amylopectin o Amylose: Only contains 1,4 links and is linear; helical structure; ~80% plant starch o Amylopectin: 1,4 and 1,6 links and is branched; Branches usually 20-25 glucose units Glycogen: Storage form of carbohydrates in animals; Stored in liver and muscle cells; Structure similar to amylopectin, but more branches and shorter branches, same linkages Cellulose: Major structural polymer in plants; Similar to amylose in link type; amylose is α(14) links whereas cellulose is β(14) links; Indigestible by animals; strong hydrogen bonding between strands leads to stability which is why it is a structural component **Examples of Bond Types (Don’t forget the 1,6 bonds):, Artificial Sweeteners Sucralose: Sucrose with 3 Cl added in specific places; barely metabolized Stevia: ~200 times as sweet as sucrose; not metabolized; stable in heat -Chapter 17: Lipids Lipid – An organic compound that is soluble in nonpolar solvents that doesn’t fit under any of the other macronutrient terms (Proteins, Carbohydrates, etc.) Provide ~ 9 kcal/g of energy (Energy dense) Some general functions include energy storage, structural components of cell membranes, messengers, carriers, etc. Types of Lipids Fatty Acids, Glycerides, Nonglyceride lipids, complex lipids Fatty Acids Fatty Acids: Long chain, unbranched carboxylic acids o 10-20 carbons long; **Usually an even number of carbons o Saturated or unsaturated, but typically no other functional groups Unsaturated with double bonds are usually cis- and have lower melting points o **Essential Fatty Acids: Those that cannot be synthesized by the body Linoleic and linolenic acid Arachidonic Acid **Arachidonic Acid is a precursor for eicosanoids (C20 like prostaglandins, leukotrienes, and thromboxanes **Eicosanoids regulate processes like blood clotting, inflammatory response, reproductive system, and several others. o Examples: Stearic Acid – C s18urated; Oleic Acid – C m18ounsaturated o Properties: Melting Point increases with number of carbons Melting point of a saturated fatty acid is higher than that of an unsaturated with the same number of carbons o Chemical reactions are those you’d expect from esters Esterification, acid hydrolysis, etc. Group I salt of a fatty acid is a soap o Omega-3 and -6 Fatty Acids Named for where the first double bond is, counting from the opposite end of the molecule as the carboxyl group; essential fatty acids o **Fats v. Oils Fats: Solid at room temperature, derived from animals (except fish) Oils: Liquid at room temperature, derived from plants **General Notation: C18:2 18 Carbons, 2 double bonds **Glycerides: Lipid esters of fatty acids + the glycerol molecule o Nonionic and polar o Solid at room temperature o Simple: 3 identical acids; Complex: 2 or more types of acids o Can be decomposed by saponification or hydrogenated o Primary Function: Energy storage in adipose tissue o Phosphoglycerides(Phospholipids): Phosphate diesters **Contains 2 fatty acids, a glycerol, an amine (all preceding are hydrophobic), and phosphate (hydrophilic) **Basis of cell and other membrane structures Bilayer with hydrophilic parts on the outside, hydrophobic parts on inside Nonglyceride Lipids o Sphingolipids: Long-chain, nitrogen containing, alcohol, polar head and nonpolar tail, component off cellular membranes **Sphingomyelin: Derived from sphingosine, also contains phosphate, a fatty acid, and choline; common in nerve sheaths o **Cerebrosides: Built on Ceramide backbone structure, R group is a sugar bonded to the –OH on C-1, found in membrane of brain cells and macrophages o Wax: Esters with one alcohol instead of glycerol, ester of long-chain fatty acid and long-chain alcohol Longer chains = higher melting point o **Steroids: Saturated 4 ring system(Three 6 member rings, one 5 member ring), synthesized from five carbon isoprene unit **Common example: Cholesterol Needed in membranes for fluidity; precursor to sex hormones, vitamin D, bile salts(Aid digestion of lipids), etc. Complex Lipids: Lipids bonded to other types of molecules o Lipoproteins Chylomicrons: Large, very low density, transport lipids from intestine to adipose tissue VLDL: Synthesized in liver, transport lipids to tissues LDL: Carry cholesterol from liver to tissues; Also a type of receptor made in cells when lacking cholesterol HDL (“Good Cholesterol”): Synthesized in liver, scavenge excess cholesterol back to liver o Used to transport fat soluble vitamins (A, D, E, K) -Chapter 18: Proteins Functions: Biological catalysts, antibodies, transport, structural, etc. α-Amino Acids – An amino acid in which the amine is adjacent to the carboxylate group Contain amine and acid groups; There are 20 common ones in nature Stereoisomers: The α-carbon of most amino acids is chiral (glycine is the only common exception) o When the carbonyl is drawn at the top of the molecule, the position of the –NH 2 determines the D/L isomer; all α-amino acids have both forms except glycine, but the L isomers are the natural versions. Two functional group are present to be protonated/deprotonated pH changes the reaction; in acidic solutions the compound takes on a positive charge, in basic solutions the compound takes on a negative charge. o Zwitterions: Two charged groups (basic amino and acidic carboxyl group) at the ends of the molecule lead to internal proton transfer; charge depends on pH Isoelectric Point: The pH at which there is a net charge of 0. Classes of α-Amino Acids **(Know generally which AAs fit which groups + how they interact) o Differences in amino acids come from the R-groups (general classifications are at pH 7) o Hydrophobic – Contain no polar side group Aliphatic: Contain no cyclic structures; Alanine, Isolucine, Lucine, Valine Aromatic: Contain a benzene ring; Phenylalanine, tryptophan, tyrosine o Polar – Neutral charge, high attraction to water Alcohols, amids, thiols (Need to know cysteine) : Serine, asparagine, glutamine, methionine, cysteine, threonine Cysteine: o Negatively Charged – Contain an ionized carboxyl group (Acidic): Aspartic Acid, Glutamic Acid o Positively Charged – Contain an ionized amine group (Basic): Arginine, lysine, histidine o Atypical – Amino Acids that don’t fit other side chain patters Proline and Glycine Peptide Bonds (Amide Bonds) o Carboxylic acid group of one AA links to the amino group of another; dehydration reaction o To name: Start with N-terminal AA, replace ending with –yl, then C-terminal AA name o Writing Structure o **Bonds are rigid due to resonance form Structures o Primary: Sequence of amino acids in original peptide chain o **Secondary: Bonding between nonadjacent amino acids H-Bonding **Alpha Helix: Bonding between every fourth AAs; resembles right handed screw; R groups are perpendicular to the structure and don’t interact in it; Three helix coil = super helix **Beta-Pleated Sheet: Composed of short polypeptides lying parallel to one another; Parallel if the N-terminal ends are in the same direction, else antiparallel; hydrogen bonds Random coil: Section of the AA backbone that isn’t organized as a helix or pleated sheet o Tertiary: Three dimensional structure that comes from interaction of secondary structures Determines function **Held together by Van der Walls Forces, Salt bridges, hydrogen bonds, disulfide bonds (loss of H in –SH, so this is an oxidation reaction) o Quaternary: The arrangement of subunits or peptides that form a larger protein Subunit: A polypeptide chain that has primary through tertiary structure and is part of a larger protein. Maintained similarly to tertiary structure (i.e. salt bridges, disulfide bonds, h-bonds, etc.) o **Fibrous Proteins – Purpose: Structural components Ex. Keratins (In hair/nails), collagen o Globular Proteins – Purpose: Functionality Prosthetic Groups: Nonprotein group bonded to a protein; essential functional group **Hemoglobin: The oxygen carrying part of blood (Also carries nitric oxide) Composed of two α and two β subunits; each chain has a heme prosthetic group Fetal Hemoglobin: β subunits are replaced with γ subunits. This makes it more attractive to O2so the fetus can take oxygen from its mother more easily Sickle Cell: One amino acid is changed in the primary structure of hemoglobin, which makes the red blood cell Loss of Tertiary Structure Hydrolysis: Cleavage of peptide bonds o Caused by: Change in pH (Loss of solubility), enzymes, temperature Denaturation: Breaking of 3-D shape – Primary structure unaffected o Caused by: Temperature(breaks bonds), heavy metals, detergents, organic solvents, mechanical stress **This study guide is just a general overview of all the things we’ve gone over between the last exam and now. To get a better idea of what will be on the test, use the review we’ll be going over later in class. If you want any more detail on any of the topics above you can consult my earlier notes or the PowerPoints on blackboard. For more review, go back over the PRS questions from lectures and old connect and learnsmart assignments. Good luck on exam 2!
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