The study guide provided here is the intended contents of the course. Certain sections may covered in more detail, others may only be briefly mentioned in class, or assigned from the text, and the contents may be slightly modified according to the needs of the class.
Remember: No study guide or learning objectives can substitute for attendance and active participation at lectures or for individual learning.
CHEMICAL REACTIVITY
The characteristic reactions of these compounds are (electrophilic) additions (understand about the representation of organic reactions in general)
Addition of hydrogen (hydrogenation, requiring a platinum catalyst)
Addition of halogens (halogenation)
Addition of hydrochloric acid (remember the Markovnikov rule which describes the rules of additions of asymmetric compounds)
Addition of water
Oxidation
Combustion
Polymerization Know the structures of ethylene-polyethylene, vinyl-chloride-PVC, tetrafluoroethylene-teflon.
Understand the rules of polymerization and know about some of the most important polymers and their monomers
Understand what type of compounds polyunsaturated alkenes are.
AROMATIC REACTIONS
Know that the characteristic reaction is electrophilic substitution, not addition, and remember that these reactions always need a haloganated catalyst.
Understand that once a group is already attached to a benzene ring, it will influence the position at which the next group will be attached.
Know which groups direct others into 2 and 4 (ortho and para) positions and which direct into 3 (meta) positions.
Know about benzene's oxidation into phenol, and toluene and related compounds' oxidation into benzoic acid, a less toxic compound.
Know about fused ring compounds, which are usually carcinogenic
ALCOHOLS are OH- containing compounds.
Understand the consequences of this group for hydrogen bonding, and physical properties, such as solubility and boiling point.
Know the nomenclature of alcohols, know that the OH group takes precedence over double (triple bonds) and halogen substituents.
Know the common names of some important alcohols.
REACTIONS OF ALCOHOLS
Dehydration (loss of water, an elimination reaction)
Formation of alkyl halides, - a reaction that can be used to distinguish primary, secondary and tertiary alcohols (Lucas test).
Polyhydroxyalcohols (ethylene glycol, glycerol)
PHENOLS: aromatic alcohols.
Understand that aromatic alcohols are different from straight chain alcohols and that the acidity of phenols is due to interactions of the OH group with the aromatic ring.
Understand that phenols undergo aromatic electrophilic substitutions (see also chapter 17).
Ethers: compounds containing R-O-R groups, and can be derived from two alcohol molecules by loss of water.
Know their nomenclature and their use as anesthetics.
Know about epoxides.
Thioalcohols or thiols or mercaptans contain the SH group. This group has an important role in many enzymes. Their oxidation into disulfides and reactions with mercury or other metals changes the structure and function of proteins.
Reactions of carbonyl compounds
Know that the characteristic reaction of carbonyl compounds is addition of a nucleophile to the carbon and an electrophile to the oxygen.
Know about how cyanohydrins, hydrates and acetals (and ketals) are formed.
Know that acetals and ketals are important in carbohydrate chemistry.
Know that an important reaction of carbonyl compounds is reduction: Aldehydes are reduced to primary alcohols and ketones are reduced to secondary alcohols.
Understand that this also means that primary alcohols can be oxidized to aldehydes and secondary alcohols can be oxidized to ketones.
Review and understand about oxidation-reduction reactions.
Understand the basis of tests for aldehydes.
Understand that in the Tollens and Benedict and Fehling's test a metal is reduced while an aldehyde is oxidized to a corresponding acid.
Know about the oxidation of hydroquinones to quinones.
Esters: Know that esters are derived from a molecule of acid and alcohol by combining them through loss of a water molecule in a reversible reaction Consequently, esters can be split up by the addition of water into the starting compounds (an acid and an alcohol) in a reaction called hydrolysis.
Thioesters are analogous compounds derived from an acid and a thioalcohol.
Know about inorganic esters and about the nomenclature of esters.
Know that the basic hydrolysis of esters is called saponification, an expression derived from soap making.
Know that fats are triesters of glycerol and fatty acids, and that fat can be hydrolyzed by NaOH to yield soap, which the sodium salt of a fatty acid.
Know about detergents, know that they contain a hydrophilic and hydrophobic part (i.e. they are amphipathic) and that soap is a detergent.
Be able to explain how they solubize dirt.
Know about micelles and surface chemistry, hard water's effect on soap.
Acid anhydrides: are derived from 2 acid molecules by losing a water molecule.
Acid anhydrides are hydrolyzed into acids.
Reactions of amines:
Reactions with alkyl halides
Reactions with acids and acid anhydrides. - formation of amides
Reactions with carbonyl compounds - formation of imines (Schiff bases)
Oxidation of secondary amines to nitrosamines
Amides
Understand the similarities between the formation of esters and amides.
Understand that the C-N bond in amides has a partial double bond character, and because of this, the geometry of the amide bond is planar.
Understand that amides are hydrolyzed to acids and amines (similarly to esters hydrolyzing to acids and alcohols).
Understand the importance of amides as natural and artificial polymers.
Know that proteins are polyamide polymers Know the general structure of an amino acid - the building block of proteins.
MONOSACCHARIDES
Distinguish them by functional groups (aldoses, ketoses), and by carbon number (trioses, tetroses, pentoses, hexoses), or by combining the two features (aldotetrose, ketopentose, for example).
Understand that the most common momosaccharides contain more than one chiral center, and therefore several stereoisomers exist. Each commonly known sugar exists as two possible enantiomers (D or L), with the D or L configuration being assigned according to the configuration of the C atom farthest from the aldehyde or ketone functional group.
Know about ring formation in monosaccharides, understand the chemical bond forming the ring (hemiacetal), and the consequences of the ring formation ( generation of an anomeric carbon, a and b anomers, mutarotation).
Know about furanose -pyranose rings.
Understand oxidation reduction of sugars, the basis of tests (Fehling's, Benedict's test) for the detection of sugars.
Know what 'reducing sugar' means, what is getting oxidized and what becomes reduced in this reaction. Understand that all monosaccharides are reducing sugars.
Know the most common monosaccharides: glucose and galactose (aldohexoses), fructose (a ketohexose) and ribose (an aldopentose).
Know about glycosidic bonds in general; understand that glycosidic bonds are the basis of oligo- and polysaccharide formation.
OLIGOSACCHARIDES (DISACCHARIDES)
Know about the three important disaccharides we studied (maltose made from two glucose molecules, sucrose from glucose and fructose, lactose from glucose and galactose). Know their components, the type of bond between the monomers, and whether they are reducing sugars.
POLYSACCHARIDES
Storage polysaccharides: starch and glycogen contain a1-4 glycosidic bonds.
Structural polysaccharides: cellulose and chitin contain b1-4 glycosidic bonds
Recognize correct statements about these compounds, their structures and functions.
FATTY ACIDS
Know about their classification (saturated, unsaturated fatty acids), physical properties (solubility, melting point), and chemical properties (mainly reactions characteristic of the double bond: hydrogenation, halogenation, oxidation).
TRIACYLGLYCEROLS (triesters of glycerol, fats and oils)
Know about their physical-chemical properties and biological roles.
SAPONIFIABLE LIPIDS OF MEMBRANES
Understand the concept of an amphipathic molecule.
Know the structures of the important phospholipids (phosphatidic acid, lecithin, cephalin) and know about the existence of sphingolipids.
NONSAPONIFIABLE LIPIDS
Steroids, bile salts (these are also amphipathic) prostaglandins and leukotrienes.
Know about their biological functions.
Recognize landmark structures (the steroid nucleus, and a general long-chain prostaglandin).
MEMBRANES
Know about the behavior of amphipathic molecules in water, i.e. the micelle-forming tendency of soap and the bilayer-forming tendency of phospholipids.
Know about liposomes.
Know the components and functions of biological membranes.
Distinguish facilitated diffusion from active transport.
AMINO ACIDS:
Recognize some of the most common proteins and their functions (those mentioned in the book).
Know that the structure of naturally occurring amino acids includes an a-amino group.
Be able to distinguish nonpolar, polar, acidic and basic amino acids.
Understand that all contain an amino and carboxyl group, and the classification is according to the 'side chain'.
Understand the acid-base characters of amino acids, the concept of an amphoteric compound, and the concept of the zwitterion and of the isoelectric point.
THE PEPTIDE BOND:
Understand how amino acids are linked together in di-tri-tetra- or, in general, in any peptide.
Understand that the peptide bond is really an amide bond and that it is planar.
Know the rules of naming peptides (the name of the amino-terminal amino acid is first and that of the carboxyl-terminal amino acid is last)
PROTEIN CONFORMATION
Know what native and denatured structures mean.
Be clear about what primary, secondary, tertiary and quaternary structures mean, and know the nature of the chemical bonds responsible for maintaining these structures.
Know about simple, conjugated proteins and macromolecular complexes.
Understand how proteins can be denatured.
Know about the nutritional significance of proteins.
Understand that proteins are an important source of nitrogen and that certain amino acids that cannot be synthesized by the human body are called essential amino acids.
DNA
Understand the basis for the double stranded structure of DNA: the complementarity of bases (A pairing with T, G pairing with C).
Know that the physical basis for this are H bonds and that the two strands are antiparallel.
Understand the concept of semiconservative replication and that the basis for this is also the complementarity of bases.
Be able to write a complementary strand if the sequence of one strand is known.
Understand the following concepts and terms: DNA polymerase (the enzyme responsible for replication), replication fork, leading strand, lagging strand, Okazaki fragments.
Know that replication occurs in a 5'-3' direction.
RNA
Know the types of RNA.(messenger, ribosomal transfer) and their roles.
Understand what transcription (RNA synthesis) and translation (protein synthesis mean).
Be able to contrast the characteristics of transcription and replication (both strands copied in replication, but only one in transcription: replication starts at origins of replication and proceeds at replication forks, transcription starts at promoters).
Understand the terms primary transcript and introns.
TRANSLATION (PROTEIN SYNTHESIS)
Know about characteristics of the genetic code.
Understand that DNA sequence determines the sequence of proteins, and that three bases (codon) determine an amino acid.
Know about the process of translation, know about the participating molecules: ribosome, tRNA, messenger RNA.
Know about initiation, elongation and termination.
Understand the concept of the anticodon in tRNA and know that amino acids are bound to tRNA and are linked together by an activity in the ribosome.
MUTATIONS
Types of mutations: substitution, deletion, insertion.
REGULATION OF GENE EXPRESSION
Understand the need for the regulation of cellular activity, and that one of the possibilities for regulation is controlling the synthesis of proteins, but that there are many other possibilities.
Two similar examples of regulation are discussed, both occurring in bacteria, both involving the control of transcription (RNA synthesis).
Understand the components of these systems: structural genes coding for the proteins to be regulated, promoter (where the RNA polymerase binds), operator, (where the regulatory protein binds,) and that the regulation is negative, i.e. the regulatory protein inhibits transcription.
Know that one the two systems are inducible, the other is repressible.
GENETIC ENGINEERING
Recognize correct statements about plasmids, restriction endonucleases and about the use of this technology to generate recombinant DNA molecules.
Understand that this can be used to manufacture proteins on the large scale.
ENZYME NOMENCLATURE AND COMPOSITION
Know that enzymes are catalysts.
Know the two main branches of metabolism : catabolism and anabolism.
Know about enzyme nomenclature, and enzyme composition (apoenzyme+cofactor=holoenzyme).
Know that organic cofactors are sometimes called coenzymes, and tightly bound cofactors are called prosthetic groups.
Know about isozymes.
ENZYME SPECIFICITY AND ACTIVITY
Understand that enzymes are extremely specific and efficient catalysts, and understand that this is due to several factors: proximity effects, orientation effects, acid base catalysis and strain.
Understand that substrates bind at the active site, and that the active site is maintained by the 3-dimensional structure of the whole protein.
Recognize correct statements about the lock-and key model and induced fit model.
REACTION RATES OF ENZYME-CATALYZED REACTIONS
Understand the concept of catalysts and enzymes lowering the activation energy of reactions, and thereby increasing the rates of the reactions.
Know about the effects of temperature and pH on enzyme activity.
Understand that enzymes can be inhibited by a variety of inhibitors reversibly or irreversibly.
Know that the two main types of reversible inhibitors are competitive and noncompetitive.
REGULATION OF ENZYME ACTIVITY
Recognize correct statements and examples about the regulation of enzyme activities.
Know the main types of regulation: activation of inactive enzymes by cleavage (zymogens), covalent modification (phosphorylation) and about allosteric regulation.
Know that allosteric regulation can be positive and negative, recognize correct statements about feedback inhibition.
BIOENERGETICS
Know that living organisms use energy for three main functions:
1) transport (to maintain uneven ionic concentrations)
2) biosynthesis
3) movement.
Know that catabolic reactions (breaking down and oxidation type reactions) are usually energy-producing, whereas anabolic reactions (building up) are usually energy consuming.
Understand what it means that catabolism is convergent.
Understand that energy consuming and producing reactions can be coupled, and that energy producing reactions result in the synthesis of ATP, whereas energy consuming reactions derive energy from the breaking down of ATP. Thus ATP is the major coupler between catabolic and anabolic reactions, the 'central energy currency' of living organisms.
Know that nicotinamide dinucleotide (NAD+) and a similar compound (NADP+) are also compounds of central importance that are involved in oxidation-reduction reactions.
DIGESTION
Know that the three main groups of dietary molecules are proteins, carbohydrates and lipids, and that large dietary molecules are broken down in the intestines (digestion).
You will need to know the major sites of breakdown for each group, and the enzymes that participate in their digestion. (Carbohydrates are broken down in the mouth and in the small intestines by amylase, maltase, isomaltase, sucrase and lactase.
Proteins are broken down in the stomach and in the small intestines by pepsin, trypsin, chymotrypsin and carboxypeptidase, i.e. proteases and peptidases.
Lipids are broken down in the small intestines by lipases, a process aided by bile salts which emulsifies the lipids. Lipids are transported in the blood in the form of lipoproteins and then taken up by adipose cells.)
CARBOHYDRATE CATABOLISM
GLYCOLYSIS
Know that this pathway starts with glucose, its end product is pyruvate, and that through the pathway 2 molecules of ATP are synthesized from ADP, and 2 molecules of NADH are generated from NAD+.
Understand that the first steps need an investment of energy, and that 2 ATP are utilized in those steps, however, the late steps produce 4 ATPs.
Know the summary equation of glycolysis.
PYRUVATE CATABOLISM
Understand that the pyruvate produced in glycolysis has two possible catabolic fates: under aerobic conditions it is further oxidized in the citric acid cycle and under unaerobic conditions it is converted to lactate.
Also understand that the function of pyruvate--> lactate conversion is to regenarate the NADH formed through glycolysis.
Contrast fermentation to lactose and to ethanol.
GLYCOGEN CATABOLISM
Glycogen in liver and muscle is broken down to glucose 1-phosphate by glycogen phophorylase. Know about the two main hormones (insulin, the 'feast hormone', and glucagon, the 'famine' hormone) that regulate blood glucose levels. Know about the cascade of events in the liver caused by glucagon - understand the role of cAMP (PP866-867).
Be able to contrast the difference in the function of glycogen breakdown in liver and muscle.
CITRIC ACID CYCLE (TRICARBOXYLIC ACID CYCLE)
Know that the pyruvate produced in the cytoplasm through glycolysis is converted into acetyl-coenzyme-A (Ac-CoA), another metabolic intermediate of central importance.
Know that the carbon atoms of Ac-CoA are oxidized into CO2 and the hydrogens from the compound are transferred onto NADH and FADH2 in the citrate cycle.
Know the summary equation of the citrate cycle.
ELECTRON TRANSPORT AND OXIDATIVE PHOSPHORYLATION
Understand the principles of the chemiosmotic theory. Understand that energy is released as the electrons flow from NADH or FADH2 through the electron carriers until the electrons and protons are united with molecular oxygen to form water.
Understand that some of this energy is utilized by the electron carrier complexes to pump protons.
The proton gradient generated enables ATP synthase (a channel protein) to phosphorylate ADP (i.e. to make ATP).
You should know that 1 NADH generates the synthesis of 3 ATPs and 1 FADH2 can generate 2 ATPs. Based on this, be able to analyze the energy released from the complete burning of a mole of glucose in living organisms..
Know that the citrate cycle and oxidative phosphorylation occur in mitochondria.
LIPID CATABOLISM
We shall only be concerned with triacylglycerols.
Know that adipose tissue is important in the storage and release of lipids, and that these cells hydolyze ltriacylglycerols into glycerol and fatty acids.
The fatty acids absorbed by cells are converted into a CoA intermediate which undergoes a number of cycles (beta oxidation).
BETA OXIDATION OF FATTY ACIDS
Know that in each cycle of beta oxidation the fatty acid is oxidized and cleaved into a smaller fatty acid and Ac-CoA., and that 1 NADH and 1 FADH2 molecules are generated. From these facts, and from the already known relationships of how many ATPs are generated from 1 Ac-CoA, NADH and FADH2 molecules, be able to predict how many ATPs are produced from any fatty acid.
AMINO ACID CATABOLISM
Know that amino acid catabolism involves transamination of amino acids and oxidative deamination, and that the end product is urea in mammals which produced in the urea cycle.
Photosynthesis
autotrophic - heterotrophic organisms
Light reaction in chloroplast produces NADPH and ATP using the energy from sunlight
Dark reaction (Calvin cycle) -Details very complicated - 6CO2 + 6 ribulose diphosphate о ооо a glucose molecule is made.
Carbohydrate anabolism
Gluconeogenesis
Know that gluconeogenesis means the new synthesis of glucose from non-carbohydrate precursors. These precursors are: lactate, amino acids and glycerol.
Understand the physiological roles of gluconeogenesis:
1) know that lactate is produced in muscle during strenuous exercise, that lactate is taken up from the blood by the liver, where the lactate is used for the synthesis of glucose. The glucose made in the liver is released in the blood and is taken up by muscle. Know that this cycle is called the Cori cycle, and in it the liver functions to furnish glucose to contracting skeletal muscle.
2) know that amino acids and glycerol are mainly used for gluconeogenesis under starvation. Understand that gluconeogenesis in the liver is important because it helps to maintain the glucose concentration in the blood so that the brain and muscles can extract glucose. Know that the pathway to make glucose from pyruvate is not simply a reversal of the breaking down of glucose to pyruvate (i.e. glycolysis).
Glycogenesis
Know that glycogenesis is the synthesis of glycogen, and that the synthsis of glycogen is not simply a reversal of glycogen breakdown (glycogenolysis).
Lipid anabolism.
Lipogenesis (the synthesis of fatty acids)
Know that the synthesis of fatty acids occurs by the sequential addition of 2- carbon units to a growing carbon chain, therefore naturally occurring fatty acids usually have an even number of carbons. Know that the 2-carbon units are derived from acetyl-CoA, and that the synthesis is not simply a reversal of beta-oxidation. In general, catabolic and anabolic pathways are at least partially different to make both pathways energetically feasible, and to allow for separate regulation.
Synthesis of ketone bodies Under extreme starvation when there is excessive breakdown of fats but no carbohydrate intake, fatty acids are broken down to Acetyl-CoA. Ac-CoA can be oxidized in the TCA cycle, but cannot be made into glucose. However, the liver can synthesize soluble compounds from Acetyl-CoA (ketone bodies), which are carried by the blood to different organs to be used for oxidation. Under these conditions the brain adapts to use ketone bodies instead of the usual fuel i.e. glucose.
Biosynthesis of amino acids and nucleotides
Know that these are complex metabolic pathways. Know that compounds inhibiting enzymes that take part in nucleotide metabolism can be used as anticancer drugs.
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