Background Review 1) Remind yourself what polar and non-polar covalent bonds are. (Pages 114-115 may help) 2) Remind yourself about the different intermolecular forces. We will consider the following: ion-ion, ion-dipole, dipole-dipole (Hydrogen bonding) and London dispersion forces. (Pages 166-171 may help) Chapter 12 Saturated Hydrocarbons pp. 293-298 1) Define organic chemistry and hydrocarbon (saturated and unsaturated). How many bonds does carbon generally have? How about N, O, and H? 2) What is an alkane? Be familiar with molecular formulae and expanded and condensed structural formulae. pp. 301-307 3) Be familiar with alkane IUPAC nomenclature (naming). Understand the terms substituent, and alkyl group and be comfortable with the information presented in tables 12.2 and 12.3 (and on the next page of these notes) 4) Be able to recognize primary, secondary, tertiary and quaternary carbon atoms. pp. 313-315 5) Characterize the following physical properties for alkanes: solubility in water, density relative to water, and boiling point trends. 6) Characterize the combustibility of alkanes. pp. 318 7) Understand the process for naming halogenated alkanes. Recommended problems: 3, 5, 7, 9, 13, 15, 21, 23, 27, 33, 45, 53, 65 (a,c), 75 (a, b, c – only IUPAC names) 77 (a,b)

Approaches to naming organic compounds (nomenclature) Root words for hydrocarbons (Table 12.2 and 12.3) 1 carbon methane methyl 2 carbon ethane ethyl 3 carbon propane propyl 4 carbon butane butyl 5 carbon pentane pentyl 6 carbon hexane hexyl 7 carbon heptane heptyl 8 carbon octane octyl 9 carbon nonane nonyl 10 carbon decane decyl Types of hydrocarbons Alkanes Alkenes Alkynes Primary, secondary, tertiary, and quaternary carbons IUPAC nomenclature: 1) Find longest chain of carbon (contains functional group) and give root

name 2) Side groups = prefixes 3) Number side groups starting with end giving lowest number 4) Two or more identical groups use: di, tri, tetra, penta, hexa 5) Two or more different groups: name with prefixes in alphabetical order 6) Halide prefixes: F = fluoro, Cl = chloro, Br = bromo, I = iodo

Chapter 13 Unsaturated Hydrocarbons pp. 328-329 1) Define the following terms: unsaturated hydrocarbon, functional group 2) What is an alkene? pp. 334-335 3) What are cis and trans isomers of alkenes? pp. 339-343 4) Describe the physical properties of alkenes. 5) Understand symmetrical and unsymmetrical addition reactions for alkenes including the following: Hydrogenation, halogenation, hydrohalogenation, hydration (and Markovnikov’s rule) pp. 347 6) What are alkynes? pp. 349-351 7) What are aromatic hydrocarbons? Recommended problems: 1, 31, 33, 35 (a,b,c)

Chapter 14 Alcohols, Ethers, Thiols pp. 364-368 1) What is an alcohol? Hydroxyl group? 2) Understand IUPAC naming for alcohols. pp. 371-377 3) Characterize physical properties of alcohols relative to alkanes of similar length, and the role played by hydroxyl group polarity. 4) Describe the formation of alcohols via alkene hydration. 5) Describe a dehydration reaction for alcohols (be able to use Zaitsev’s rule). pp. 379-381 6) Describe the oxidation of primary and secondary alcohols. pp. 387 7) What is an ether? 8) Describe how ethers are named using the common naming method. pp. 389, 391-392 9) What is the common medical application of ethers? 10) Describe the boiling point of ethers and their flammability. pp. 393, 395 11) What is a thiol/sulfhydryl group? 12) Describe disulfide bond formation and breakage. Recommended problems: 1, 3, 7, 9, 11 (a-d), 33, 35, 37, 41, 43, 45, 47, 49, 51, (b,c,e), 65, 69 (a,b)

Chapter 15 Aldehydes and Ketones pp. 405-410 1) Define the following terms: carbonyl, aldehyde, and ketone. 2) Describe the IUPAC naming for aldehydes and ketones. pp. 413-418 3) Characterize the boiling point and water solubility of aldehydes and ketones verses alkanes and alcohols. 4) Describe aldehyde and ketone conversion to and from alcohols. Recommended problems: 1, 5, 9, 11 (a-c, e,f), 13, 15, 21, 23, 27 (not c), 39, 43, 45, 49, 57

Chapter 16 Carboxylic acids and esters pp. 434-436 1) What is a carboxylic acid/carboxylate group? 2) Understand IUPAC naming for carboxylic acids. pp. 443-446 3) Describe the boiling point and water solubility properties for carboxylic acids verses compounds we have considered earlier. 4) Describe the production of carboxylic acids from alcohols and aldehydes. 5) Describe the acid properties of carboxylic acids. 6) What are carboxylate ions and carboxylic acid salts? How are carboxylate ions named? pp. 447-449 7) What is an ester? 8) Describe ester formation from carboxylic acids and alcohols. pp. 455-456 9) Describe ester hydrolysis and saponification. Recommended problems: 1, 3, 5, 7, 33, 43 (not c), 45, 49, 51 (not d), 53, 77 (a-c), 79 (a-c)

Chapter 17 Amines and Amides pp. 473-475 1) What is an amine/amino group? Describe primary, secondary, and tertiary amines. pp. 478-481 2) Describe the boiling point of amines compared to alcohols. 3) Describe the ability of amines to act as bases and the formation of ammonium ions. 4) What is an amine salt? pg. 490 5) Describe an amide. Recommended problems: 3, 27, 29, 31 (a-c), 37, 61

Chapter 18 Carbohydrates pp. 512-514 1) What is biochemistry and what are the four major bioorganic substances? 2) What are 6 functions of carbohydrates listed in the text? 3) What is the chemical definition of a carbohydrate? 4) What are mono, di, oligo, and polysaccharides? pp. 526-532 5) How many carbons are commonly found within monosaccharides? 6) Define the following terms: aldose, ketose, pentose, hexose, sugar. 7) Describe the following monosaccharides: D-Glucose, D-Fructose, D-Ribose 8) Describe the cyclic structures for D-Glucose and D-Ribose. pp. 538-548 9) What does a glycosidic linkage (bond) connect? Understand the method used to describe a glycosidic bond (i.e. α 1,4). 10) Describe the following disaccharides: maltose, lactose, sucrose. 11) What is lactose intolerance and how can it be treated? 12) Describe the following polysaccharides (include the monosaccharides present, type of glycosidic bond(s), shape of the polysaccharide, its role in nature, and its digestibility by humans) starch (amylose and amylopectin), glycogen, cellulose. pp. 551-552 13) Describe simple carbohydrates, complex carbohydrates, and glycemic index. Recommended problems: 1, 3, 9, 11, 37, 39, 51 (a,d), 87 (a-c), 101 (a-b), 109 (not chitin), 111, 113

Chapter 19 Lipids pp. 561-565 1) What are lipids and what are 5 functions of lipids described in the text? 2) What are fatty acids and what is the range of carbon lengths for fatty acids? 3) What are saturated, monounsaturated and polyunsaturated fatty acids? What effect does unsaturation have on the shape of a fatty acid? pp. 566-571 4) How do chain length and presence of double bonds influence the melting point of a fatty acid? 5) What is triacylglycerol (triglyceride)? How is it formed and relate the terms fat and oil. 6) Relate the degree of saturation to the terms “good” fat and “bad” fat. Include a description of omega 3 fatty acids. 7) Read the three chemical connections on pages 575-577 pp. 579-582 8) Describe the structure of glycerophospholipids. pp. 584-586, 590-591 9) Describe the structure of cholesterol. What are some of its functions? pp. 586-589 10) Describe the structure and function of biological membranes. Recommended problems: 1, 3, 5, 9, 17, 19, 23, 35, 37, 69, 87, 89

Chapter 20 Proteins pp. 604-606 1) What are proteins and roughly how many different proteins are in the human body? 2) Describe the general structure of an amino acid. 3) Recognize the non-polar, polar, acidic, and basic amino acids and their three letter codes. pp. 608-609 4) Recognize that amino acids have two ionizable groups and understand the nature of each at low, medium and high pH. pp. 612-613 5) What type of bond can two cysteines form? 6) Describe a peptide bond and define peptide and polypeptide. Recognize that proteins have an amino (N) and carboxy (C) terminus. pp. 617-626 7) Describe the four levels of protein structure. 8) What is a prosthetic group and what are fibrous and globular proteins? pp. 629-630 9) Differentiate between protein hydrolysis and denaturation. 10) What are glycoproteins? Recommended problems: 1, 3, 5, 7, 9, 15, 25 (a, b, c), 35, 37, 63, 65, 69, 73, 75, 83, 89

Chapter 22 Nucleic acids pp. 673-676 1) What are nucleic acids/nucleotides? 2) Describe the structural features of nucleotides. pp. 677-684 3) Describe the nucleic acid structures for RNA and DNA including the complimentary base pairing for DNA. 4) Define these terms: DNA replication, transcription, and translation. 5) Relate these terms: nucleotide, DNA, chromosome, gene, genome. pp. 690 6) Relate the sequence of nucleotides in a gene to the sequence of amino acids in a protein. What is the relationship between amino acid sequence in a protein and the protein’s shape and function? What is a codon? Recommended problems: 1, 5, 7, 9, 15, 17, 25, 27, 29, 35, 45, 47, 56, 71, 73

Chapter 21 Enzymes pp. 641-642 1) What is an enzyme? What type of molecule is it, what do they do, and are they specific in their activity? 2) What is a substrate? pp. 644-654 3) Define the following: simple enzyme, conjugated enzyme, apoenzyme, cofactor, haloenzyme, coenzyme. 4) Describe the properties of an active site. 5) Describe the lock and key and induced fit models of enzyme activity. 6) What is enzyme activity and how is it influenced by temperature, pH, and substrate concentration? 7) Describe the following types of enzyme inhibition: reversible, irreversible, competitive and non-competitive 8) What is allosteric regulation of enzyme activity? What are properties of allosteric enzymes? 9) Describe feedback inhibition and feedforward stimulation of enzyme activity. 10) What are zymogens? pp. 657, 659 11) What are isoenzymes? 12) Describe medical uses of enzymes in diagnosis and treatment. Recommended problems: 1, 3, 19, 21, 25, 29, 37, 39, 41, 43, 45, 47, 49, 51, 53

Chapter 23 Biochemical Energy Production pp. 711-718 1) What are metabolism, anabolism and catabolism? 2) What is a metabolic pathway? 3) Describe the structure of the mitochondria. 4) What are ATP, ADP and AMP? What role does ATP serve in metabolism? 5) What are FAD, FADH2, NAD+, and NADH and what role do they play in metabolism? 6) What role does coenzyme A (CoA) play in metabolism? pp. 719-727 7) What are the four stages of biochemical energy extraction? Which represent the common metabolic pathway? 8) Outline the citric acid cycle. Know what goes in, what is produced, and what branch points there are from it. 9) Describe the regulation of the citric acid cycle. 10) What is the electron transport chain? pp. 731-735 11) What is oxidative phosphorylation? 12) Describe the concept of chemiosmotic coupling including electron transport, H+ pumping, chemiosmosis, and ATP production. 13) What are some biological processes supported by ATP hydrolysis? Recommended problems: 1, 3, 5, 9, 11, 13, 19, 23, 33, 35, 45, 47, 49, 63, 65, 81, 83, 85, 87, 89, 91

Chapter 24 Carbohydrate Metabolism pp. 742-57 1) Describe how dietary polysaccharides are digested to monosaccharides for catabolism. 2) What is glycolysis and where does it occur? 3) What is consumed and what is produced in the 6 and 3 carbon stages of glycolysis? What are the major branch points into and out of glycolysis? 4) What is substrate level phosphorylation? 5) How is glycolysis regulated? 6) Describe the aerobic and anaerobic fates of pyruvate. 7) How many ATP are generated via one glucose when it is fully oxidized to six carbon dioxides through the citric acid cycle and oxidative phosphorylation? 8) Under what conditions do glycogen synthesis and glycogenolysis occur? pp. 762-764 9) What hormones stimulate these processes? Recommended problems: 1, 9, 11, 13, 17, 19, 23, 29 (a), 35, 37, 39, 41, 45, 47, 49, 61, 81, 83, 85, 89

Lipid Transport in Mammals Complex organisms have evolved mechanisms for transporting lipids from one organ to another. There are a variety of lipids that are transported and they originate in different tissues depending on the transport process involved. We will consider four different means by which lipids are transported within our bodies. These are: Exogenous pathway: Transport of dietary lipids from the intestine to other tissues. Endogenous pathway: Transport of liver-derived lipids to other tissues. Reverse cholesterol transport: Transport of cholesterol from non-hepatic tissues to the liver. Albumin-mediated transport of fatty acids: Transport of fatty acids from adipose tissue to other tissues. In what form are lipids transported? Lipids are relatively insoluble in water, therefore they can not be effectively transported through blood as free lipids. Instead, they and complexed into spherical assembies with proteins. These complexes of lipid and protein are called lipoproteins. The proteins component itself is termed an apolipoprotein. There are several types of lipoproteins moving through your body via your bloodstream. These lipoproteins differ from one another in where they are made, where they are traveling to, and what lipids they are carrying. We classify lipoproteins based on their size (which means how much lipid they have in them). The more lipid…the less dense the lipoprotein. The lipoproteins we will consider are: chylomicrons, chylomicron remnants, VLDL, IDL, LDL, and HDL. In gerneral, the non-polar lipids are carried in the core of the lipoprotein, buried away from the aqueous environment. The amphiphilic lipids are associated with the surface of the lipoprotein as are the apolipoproteins. Draw a schematic of a lipoprotein here:

Exogenous Pathway Lipids that are taken in dietarily are transported from the intestine to other tissues via the exogenous pathway of lipid transport. The dietary triglycerides are hydrolyzed by pancreatic lipase in the intestine. The resulting fatty acids are emulsified (made soluble in an aqueous environment) by bile acids. They are then transported into intestinal epithelial cells where they are re-esterified to triglycerides. These fats are complexed with apolipoproteins to form the largest of all lipoproteins - the chylomicron. Chylomicrons are released into the lymphatics and enter the blood. They deliver lipids to tissues by interacting with the cells where another lipase (lipoprotein lipase) hydrolyzes triglycerides to fatty acids and glycerol. These move into the tissue where they can be re-esterified and stored, or burned for energy in a process called beta oxidation. Since the chylomicron lost lipid in this process, it shrinks… forming a chylomicron remnant. The remnant can then be taken up by the liver via receptor-mediated endocytosis. Diagram the exogenous pathway here: Endogenous pathway Lipids that are derived from our liver (often made from excess carbohydrates) are transported to other tissues via the endogenous pathway of lipid transport. The initial lipoprotein that is released is very-low density lipoprotein (VLDL). It interacts with tissues, has TG hydrolysed by lipoprotein lipase and shrinks to the smaller, more dense, intermediate density lipoprotein (IDL). IDL can then be taken up by the liver via receptor-mediated endocytosis, or can be further processed be lipoprotein lipase to form LDL (low-density lipoprotein). As all

this hydrolysis occurs, the lipoproteins lose triglyceride, and become smaller, and less dense. At the same time, the lipoprotein acquires cholesterol form another lipoprotein (HDL - high density lipoprotein) in a process called reverse cholesterol transport. Therefore, while VLDL starts out as a TG-rich lipoprotein… LDL ends up being cholesterol-rich. The LDL is then taken into the liver or into other tissues via LDL receptors. Diagram the endogenous pathway here: Reverse cholesterol transport As mentioned above, HDL traffics cholesterol from tissues to LDL which can then take the cholesterol to other tissues or to the liver. Much of the cholesterol taken to the liver is converted to bile acids which can then be released into the intestine. The result of all this is the net transfer of lipid (cholesterol) from non-hepatic tissues to the liver. It is a major means by which we remove cholesterol from our bodies. Diagram reverse-cholesterol transport here:

Imbalances in lipid transport Over-production of lipoproteins, and/or failure to process or remove them from the blood can result in dyslipidemias. Overabundance of lipids in our blood can then lead to clinically relevant disease states such as cardiovascular disease. These diseases are the #1 cause of death in the United States. What are some causes of lipid imbalances, and what are the resulting lipid phenotypes? Albumin-mediated transport of fatty acids Fats are generally stored in our adipose tissue to be used when we need them as a source of energy (typically when carbohydrate levels are low). When we have adequate carbohydrates, the hormone insulin promotes the production of fats in the liver, and thus their transport via the endogenous pathway. One destination is adipose tissue where the fats are stored. When carbohydrate levels are low, and we need to burn these fats, the hormone glucagon is produced. Glucagon signals the adipose tissue and turns on a lipase called hormone-sensitive lipase. This hydrolyses the stored TG to fatty acids. The fatty acids are released into the blood where they complex with our most abundant blood protein (albumin). The albumin carries the fatty acids to other tissues where they are taken in and burned via beta-oxidation. Diagram fatty acid transport from adipose tissue here:

Chapter 25 Lipid Metabolism 1) Read the section of these focus questions entitled “lipid transport in mammals”. This describes lipid transport via lipoproteins. pp. 585-586, 634, 769-top of 774, 776-781 2) Understand lipid digestion and transport processes. 3) Describe the activation, transport into the mitochondria and beta oxidation (fatty acid spiral) of fatty acids. 4) How much ATP is produced via the complete oxidation of an 18 carbon fatty acid? 5) What are ketone bodies? Where, when, and why are they produced? 6) What is ketosis (ketoacidosis)? 7) Describe fatty acid synthesis and how it remains distinct from fatty acid catabolism. pp. 786 8) How do statins lower blood cholesterol? Recommended problems: 7, 11, 13, 15, 23, 27, 37, 43, 51, 53, 57, 61, 63, 67

Chapter 26 Protein metabolism pp. 794-top of 801 1) Normally, what % of energy comes from protein catabolism? 2) Understand the proteolytic digestion of dietary proteins. 3) Describe transamination and deamination of free amino acids. 4) What is the role of the urea cycle? Where does it occur? pp. bottom of 804-807 5) Understand the basis for why some amino acids are glucogenic, some are ketogenic, and some are both. pp. bottom of 757-top of 760 6) What is gluconeogenesis? When and where does it occur and what are the three major non-carbohydrate starting materials for it? 7) Describe the Cori cycle and the alanine cycle (described in class). pp. 812, 762-764 8) Understand the integration of metabolism and the interrelation of carbohydrate, lipid and protein metabolism. Recognize what is occurring during a well fed state, fasted state, and starved state. 9) Understand the role of insulin and glucagon in the control of metabolism. 10) Understand the causes and consequences of Type I and Type II diabetes. Recommended problems: 23, 31, 81

Well Fed Fasted Starved Hormone present Brain (uses, makes, releases) Muscle (uses, makes, releases) Adipose (uses, makes, releases) Liver (uses, makes, releases)