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