CHEM 30B  Dr. R. Rinehart    EXAM 3 Study Guide   rev 4/22/06

READ THIS GENERAL STATEMENT CAREFULLY:

            Your mission in this course is to obtain for yourself a useful working knowledge and understanding, at an appropriate level, of some basic organic chemistry and biochemistry, as outlined in the syllabus and subsequently elaborated in class. The resources available to you include the text, lectures and class handouts, laboratory exercises, references in print and on the internet, consultation with the instructor outside of class, tutors on duty in PS-205, or by arrangement, and whatever other legitimate means are necessary. There is no easy path to success. Put the work in. It is particularly important to pay attention to the following sections in each chapter: Concept Summary, Learning Objectives, Key Terms and Concepts, and Key Reactions. In particular, the learning objectives tell you what types of knowledge you will be expected to demonstrate.  You will not be able to demonstrate them unless you understand the principles involved! Similarly, you will find it pointless to memorize key terms without knowing what they mean and how they can be applied.

 “Right, sure, yeah, yeah, yeah – just tell us what’s going to be on the test, doc.”

What?  Questions designed to show if you have learned to use these principles and their associated language.

How? Generally by means of objective questions in a variety of formats: fill-ins, short answers, matching, multiple choice, true-false, listing, categorizing, prioritizing, and problem-solving are all possibilities. Naming compounds, drawing structures and/or diagrams, writing (and sometimes balancing) equations, and making rational deductions  are all possibilities.

  NOTE: 2006 -- expect relatively more on lipids and enzymes and relatively less on carbohydrates!!!

Chapter 17: Carbohydrates [also Labs 28 & 29]

           Composition: (CH2O)n , polyhydroxy aldehydes or ketones, water-soluble solids [H-bonds!];
                            most taste sweet [so does ethylene glycol]

            Classification: simple sugars = monosaccharides, aldose or ketose, # of C à triose, tetrose, pentose,
                            hexose…

            Know structures and classification of : D-glyceraldehyde, dihydroxyacetone, D-ribose, D-fructose,
                            D-glucose, D-galactose, D-mannose

            Stereochemistry: chirality; asymmetric C [4 different substituents] => 2 different 3D arrangements at that C

                        Fischer projection: a convenient way to depict specific stereochemical arrangement                        most carbohydrates have multiple chiral centers;  n chiral centers => 2n stereoisomers

stereochemistry at “lowest” chiral center determines classification as D- or L-;

                        mirror image molecules = enantiomers;

                        chiral molecules rotate plane of polarized light;

clockwise = dextrorotatory [+], counterclockwise = levorotatory [-]

            Cyclic structures: result from formation of intramolecular hemiacetal or hemiketal. Result in 2 new
  
         stereoisomers [“anomers”], since formerly planar carbonyl carbon [anomeric C] is now tetrahedral w/
  
          4 different substituents; anomers are called
a- or b- depending on relative position of anomeric –OH;

a- or b- can interconvert in solution via “open-chain” form [“mutarotation”]

geometry best shown with Haworth projection.

            Disaccharides and polysaccharides: cyclic monosaccharides can be linked together by formation of

 “glycosidic” bonds [intermolecular acetal or ketal]; a- or b- configuration of glycosidic C is now

            locked in, and the group no longer undergoes characteristic aldehyde or ketone reactions.

            Glycosidic links can be hydrolyzed enzymatically or by heating in acid solution.

Know components, sources,  and linkages found in: maltose, sucrose, lactose, amylose,
        amylopectin, cellulose, glycogen  -- be able to recognize and/or describe their structure!

            Reactions: Benedict’s test for “reducing sugars” based on “free” aldehyde or hemiacetal getting oxidized
by Cu2+ [which gets reduced to Cu2O]; “free” ketoses get isomerized to aldoses and also react; sucrose
and polysaccharides don’t react [know why!] but their hydrolysis products do.

Seliwanoff’s test: detects ketoses.

 Chapter 18: Lipids

 

            Defined on basis of solubility [water: -, nonpolar solvents: +], then classified on basis of chemical properties  and components. Saponifiable lipids: can be broken down with NaOH + H2O + heat.

 

Be able to recognize the structures of each of the major classes of lipids listed below

 

            Nonsaponifiable:

steroids  cholesterol, steroid hormones, bile salts; all have characteristic 4-ring structure;

                        prostaglandins, thromboxanes, leukotrienes: all derived from arachidonic acid or EPA.

 

            Saponifiable: have linkages (ester, amide, phosphoester) susceptible to base hydrolysis; results in liberation of fatty acids in the form of anions [soaps – know how they work!]

             Simple saponifiable

                        waxes: esters of long-chain [“fatty”] alcohols and long-chain [“fatty”] acids

                        triglycerides: triple esters of glycerol with fatty acids [know them!!!];

“fats” if solid, “oils” if liquid; m.p. depends on degree of unsaturation; hydrogenation gives

            hard, saturated fats that resist high-temperature breakdown

important food sources  and storage form of energy; insulation

           

            Complex saponifiable: critical components of CELL MEMBRANES
                            [be able to sketch a membrane and
describe the forces stabilizing it]

                        phosphoglycerides contain glycerol esterified with phosphoric acid and other components

                                    phosphatidic acid = glycerol + 2 fatty acids + phosphate

                                    lecithin = phosphatidyl choline

                                    cephalin = phosphatidyl (ethanolamine or serine)

                                    cardiolipin = diphosphatidyl glycerol

                        sphingolipids contain sphingosine:
                                                    trans
-1,3-dihydroxy-2-amino C18 -4-ene
(or dihydrosphingosine)

          ceramide = N-fatty acyl sphingosine

            sphingomyelin = ceramide + phosphate + choline

            cerebroside = ceramidyl (glucose or galactose)

            ganglioside = ceramidyl oligosaccharide

 

            Lipid Hormones

                        “Eicosanoids”: derived from C20 acids [arachidonic, EPA]

                                    prostaglandins and prostacyclins many effects; synthesis blocked by aspirin

                                    thromboxanes

                                    leukotrienes

                        Steroids: derived from cholesterol; five classes; know major actions/effects of each

                                    adrenal cortex:

glucocorticoids [cortisol];

mineralocorticoids [aldosterone]

                                    gonads:

                                                androgens [testosterone, androstenedione]

                                                estrogens  [b-estradiol]

                                                progestins [progesterone]

   Chapter 19: Amino Acids and Proteins [also Protein architecture tutorial]

             Amino acids: 20 L-a-amino carboxylic acids are the building blocks of all proteins; differ in the structure and properties of their side-chains. Be able to: recognize structures, give name and/or 3-letter abbreviation, and classify by polarity/charge, composition (-OH, S, aromatic, etc.), and diet-essential or not. Single AA’s are zwitterions in solution and crystal states. 

            Peptides: string of amino acids held together by amide [“peptide”] linkages 

            Proteins: polypeptides with 50 – 10,000 amino acids, critically involved in all life processes;

                       functions [know specific example(s) for each]: catalytic, structural, protective,
                 motion,
transport, regulatory, communication, storage. Also buffering and osmotic roles.

                        composition: simple – AA’s only; conjugated – contain nonprotein components

                        shape: can be globular [often “soluble” in water – enzymes, antibodies, transport proteins] or
                                         fibrous
[structural and motile proteins] – know several examples of each.

             Synthesis directed by genetic information

             Levels of protein structure:

                         1o:  backbone with specific [genetically-directed] AA sequence; amide bonds

                         2o:  regular arrangement of backbone caused by regular pattern of backbone H-bonding;

a-helix, b-structures, random coils. Most proteins contain all of these motifs

                    3o: specific 3D shape determined by 1o sequence, and thus ultimately by genetic direction and

caused by interactions [ionic, dipolar, H-bonding, dispersion/hydrophobic, even covalent]

of side chains with each other and with water; for most proteins, this is the biologically active

 form. S-S bonds often important for holding structure together [remember insulin?]  

                        4o: specific assembly of multiple subunits resulting from same forces as for 3o structure
                                    [with some additional types of covalent bonds along with S-S] and designed
                                      
geometric fit of subunit  surfaces [thus, also genetically preordained].
                                    Allows for formation of multienzyme complexes, motile assemblies [actin/myosin, etc],
                                     cytoskeleton, fibrous structural proteins like collagen and keratin, etc. etc.

 

            Protein general properties:

·         Act as buffers; overall molecular charge changes with pH; low pH => more +, high pH => more –

·         Can be hydrolyzed by acid or base [very slow at ordinary temperatures], or by enzymes [fast]

·         Subject to denaturation [loss of biological activity due to altered 3o structure] caused by factors like           extreme temperature, extreme pH, heavy metals, detergents, organic solvents, radiation, etc.

      ·         As charged colloidal particles incapable of diffusing across membranes, proteins in solution contribute to the
                 net osmotic pressure of that solution and have a significant effect on fluid distibution in the body.

  

Chapter 20: Enzymes [also tutorials] 

 

 I. Enzyme characteristics
            A.
Globular proteins (soluble enzymes; membrane-bound enzymes have extra hydrophobic segment)
           
B. Catalytic
efficiency:  accelerate reaction rate by 102 to 1020 times at ordinary temperatures
            C.
Specificity for both substrate and reaction catalyzed

                        1. absolute: works on only one substrate;
                                 may be stereospecific, group-specific, linkage-specific
                       
2. relative: works on several structurally-related substrates
                       
3. reaction specificity minimizes byproduct formation and substrate waste

            D. Catalytic activity can be regulated [see IV. E,F,G below] 

II. Nomenclature and classification

            A. Archaic: e.g., trypsin, chymotrypsin, pepsin, steapsin, amylopsin
           
B. Common: add -ase to name of substrate or to combination of substrate name
                       
 and reaction catalyzed e.g., amylase, lipase, urease, lactate dehydrogenase
           
C. E.C. (from the international Enzyme Commission):
                                    Six major classes based on type of reaction catalyzed [1st #] 
                                    know them -- and at least one example of each!;
 
                                   
subclasses based on type of bond involved [2nd #], cofactors required 
                                    [3rd #], and specific substrate attacked [4th #]; name also ends in -ase
                                    Each enzyme has a unique EC catalog number

                        1. Oxidoreductases:   e.g., alcohol dehydrogenase, EC 1.1.1.1
                                    catalyze oxidation/reduction (electron transfer) reactions
                        2. Transferases   e.g., hexokinase, EC 2.7.1.1
                                   
catalyze group transfer reactions
                        3. Hydrolases:   e.g., chymotrypsin, EC 3.4.21.1
                                    includes all digestive enzymes and many others
                                    catalyze hydrolysis of esters, amides, thioesters, phosphate esters, sulfate esters,
                        4. Lyases   e.g., fumarase  or fumarate hydratase,  EC 4.2.1.2
                                    addition of H2O, NH3, etc. to double bonds or the reverse reactions
                       
5. Isomerases   e.g., phosphohexose isomerase, EC 5.3.1.9
                                  move a group from one position to another within a molecule or change DßàL
                       
6. Ligases  e.g.  tyrosine -- tRNA ligase, EC 6.1.1.1
                                    attach two smaller molecules together using energy from ATP or similar source

 

© Ronald W. Rinehart, 2002  Pictures made with MDL IsisDraw®

III. Cofactors ( “activators”, coenzymes and prosthetic groups): 
                    nonprotein components required for catalytic activity
            A. Inorganic: Ca+2, Mg+2, Zn+2, Fe+2, Cl-, etc.; often called “activators”
            B. Organic: “coenzymes”; usually derived from vitamins
                the term "prosthetic group" is used to describe coenzymes which are "permanently" bound to their
                 enzyme [e.g., the heme group in cytochromes or FAD in succinate dehydrogenase], while other
                coenzymes such as NAD+ are "soluble" and exist in a pool which can be utilized by many 
                different enzyme molecules. 

IV. Enzyme activity
            A. Mechanism [a mechanism is a detailed molecular picture of exactly how a reaction happens]
                        1. Takes place at “active site”
                        2. Enzyme’s 3o structure is specifically designed to recognize and bind substrate through
                             a combination of forces: electrostatic/ionic, dipolar, H-bonding, dispersion/hydrophobic. 

                        3. Active complex formation:   

    E       +        S        ßà     ES    ßà   ES*       ßà    EP    ßà    E       +       P

enzyme         substrate(s)              complex         transition state              complex            enzyme         product(s)          

            4. Mechanism of catalysis usually involves the side chains of from 2 to 5 amino acids
                            acting as precisely-positioned weak acids and bases with the participation of any
                            cofactors required when the side chains alone can't do the job

B. Activity
                       
1. Turnover number
                       
2. Rate of substrate consumption (International units) or product formation  

C. Factors affecting rate [see curves below -- know this!]
           
1. Enzyme concentration
           
2. Substrate concentration
           
3. Temperature
            4. pH

           

D. Inhibition of enzymes

                        1. Irreversible; e.g. heavy metal or cyanide poisoning
                       
2. Reversible
                                   
a. Competitive: overcome by increasing [S]; Ic ~ S in structure
                                   
b. Noncompetitive: not overcome by increasing [S]; In must be removed
                                   
       useful in feedback inhibition of metabolic pathways           

E. Regulation of enzymes

                        1. Activation of zymogens/proenzymes
                        2. Allosteric modulation: can increase or decrease activity; noncompetitive
                                   
can coordinate several pathways via feedback inhibition
   
                     3. Covalent modification: phosphorylation/dephosphorylation,
                                acetylation/deacetylation, methylation/demethylation, etc.
                       
4. Genetic control: induction and repression; alter amount of enzyme itself
                        5. Proteolysis will eventually inactivate all enzymes; for some, this may be programmed.
                       
6. Hormones can affect both quantity and specific activity of enzymes via one
                                  or more of the mechanisms listed above.

V. Medical applications of enzymes
           
A. Inborn errors of metabolism
           
B. Serum enzyme analysis
           
C. Isoenzymes
            D. Therapeutic use of enzymes: e.g., streptokinase for dissolving clots