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BIOCHEMICAL PERIODIC TABLE

1
Key Elements in the Body
H 1. Hydrogen 15. Phosphorus 29. Copper
Hydrogen 3. Lithium 16. Sulphur 30. Zinc
3 6. Carbon 17. Chlorine 32. Germanium 6 7 8 9
7. Nitrogen 19. Potassium 33. Arsenic
Li 8. Oxygen 20. Calcium 34. Selenium C N O F
9. Fluorine 22. Titanium 35. Bromine
Lithium Carbon Nitrogen Oxygen Fluorine
11. Sodium 25. Manganese 50. Tin
11 12 12. Magnesium 26. Iron 53. Iodine 13 14 15 16 17
13. Aluminum 27. Cobalt
Na Mg 14. Silicon 28. Nickel Al Si P S Cl
Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine

19 20 22 25 26 27 28 29 30 32 33 34 35

K Ca Ti Mn Fe Co Ni Cu Zn Ge As Se Br
Potassium Calcium Titanium Manganese Iron Cobalt Nickel Copper Zinc Germanium Arsenic Selenium Bromine

50 53

Sn I
Tin Iodine

GLUCOSE BROADER CHEMICAL PRINCIPLES

A.Intermolecular Forces Energy = 1 q1.q2 2. Hydrophilic = Lipophobic: Affinity for polar
H
1. Electrostatic: Strong ε r12 group; soluble in water, repelled by nonpolar
interaction between ions; for Examples: alcohol, amine, carboxylic acid
O H 3. Amphipatic: Polar and nonpolar functionality;
charges q1 and q2; separated by r12, Polarizability
H C and solvent dielectric constant, ε ; R common for most biochemical molecules: fatty
δ- acids, amino acids and nucleotides
C water has large ε; stabilizes C O
R C. Behavior of Solutions
zwitterion formation
1. Miscible: 2 or more substances form 1 phase;
2. Polarizability, α: Measures R-Oδ- occurs for polar + polar or non-polar + non-polar
distortion of electron cloud by other H 2. Immiscible: 2 liquids form aqueous and organic
nuclei and electrons R
δ- layers; compounds are partitioned between the
DNA 3. Dipole moment, µ : Asymmetric N R
layers based on chemical properties (acid/base,
electron distribution gives partial R
polar, nonpolar, ionic)
charge to atoms 3. Physical principles:
Dipole
4. London forces (dispersion): Interaction a.Colligative properties depend on solvent identity
Attraction due to induced dipole + - + -
and concentration of solute; a solution has a higher
moments; force increases with µ boiling point, lower freezing point and lower vapor
5. Dipole-dipole interaction: The pressure than the pure solvent
stable
positive end of one dipole is attracted b.Biochemical example: Osmotic pressure - Water
TRIGLYCERIDE to the negative end of another dipole; + - - + diffuses through a semi-permeable membrane from a
strength increases with µ hypotonic to a hypertonic region; the flow produces
H H H H
H less stable a force, the osmotic pressure, on the hypertonic side
H C H C C
6. Hydrogen bonding: Enhanced
C H dipole interaction Osmotic Pressure
H H H Hydrogen Bonding
H C H
H C Π = iMRT
C H H
H H between bonded H and δ- Π: Osmotic pressure (in atm)
C H C H the lone-pair of N
H C H i: Van’t Hoff factor = # of ions per solute molecule
H neighboring O, N or S; Hδ+ H H M: Solution molarity (moles/L)
C H C H
H Ammonia R: Gas constant = 0.082 L atm mol–1 K–1
C H H gives “structure” to
H C H C H C H T: Absolute temperature (in Kelvin)
liquid water; solubilizes δ-
R O
H C H C H H
C H alcohols, fatty acids, 4. Solutions of gases
C H C amines, sugars, and Oδ- ... Hδ+ Hδ+
Water a.Henry’s Law: The amount of gas dissolved in a
H H H H
C H C H H H amino acids Hδ+ Alcohol liquid is proportional to the partial pressure of the gas
H
C
H H H O B. Types of Chemical δ- b.Carbon dioxide dissolves in water to form carbonic acid
H C C H
H H C N
H C Groups c.Oxygen is carried by hemoglobin in the blood
H C H C C O R R R
C O d.Pollutants and toxins dissolve in bodily fluids; react
H C H H H 1. Hydrophobic = Amine with tissue and interfere with reactions
H
H C H H H O C H Lipophilic: Repelled Examples: Sulfur oxides and nitrogen oxides yield
C by polar group; insoluble in water; affinity for acids; ozone oxidizes lung tissue; hydrogen cyanide
H C C H
H C C C non-polar disables the oxidation of glucose
H O H
H O H
Examples: alkane, arene, alkene
BONDS & STRUCTURE IN REACTIONS, ENERGY & EQUILIBRIUM
ORGANIC COMPOUNDS
A.Mechanisms ∆G > 0 endergonic
A.Bonding Principles Resonance 1. Biochemical reactions involve a not spontaneous small Keq
1. Most bonds are polar covalent; the more -
number of simple steps that together ∆G = –RT ln(Keq) – connection with
O O
electronegative atom is the “–” end of the bond C C form a mechanism equilibrium
Example: For >C=O, O is negative, C is positive <=>
N N+ 2. Some steps may establish equilibria, D. Standard-Free Energy of
2. Simplest Model: Lewis Structure: Assign
valence electrons as bonding electrons and non-
since reactions can go forward, as well Formation, ∆G0f :
as backward; the slowest step in the 1. ∆G = Σ prod ∆G0f – Σ react ∆G0f
bonding lone-pairs; more accurate bonding models include valence-
mechanism, the rate-determining 2. For coupled reactions: Hess’s Law:
bonds, molecular orbitals and molecular modeling
step, limits the overall reaction rate 3. Combine reactions, add ∆G, ∆H, ∆S
3. Resonance: The average of several Lewis structures describes the
and product formation
bonding 4. An exergonic step can overcome an
3. Each step passes through an energy
Example: The peptide bond has some >C=N< character endergonic step
barrier, the free energy of activation
B. Molecular Structure Example: ATP/ADT/AMP reactions
(Ea), characterized by an unstable
Typical Behavior of C, N & O configuration termed the transition are exothermic and exergonic; these
state (TS); Ea has an enthalpy and provide the energy and driving force
Atom sp3 sp2 sp
entropy component to complete less spontaneous
C4 e– 4 bonds -C-C- >C=C< -C≡C- biochemical reactions; Example:
N 5 e – 3 bonds, 1 lone pair >N- R=N- -C≡N Endothermic Exothermic ATP + H2O => ADP + energy

Potential energy
O6 e– 2 bonds, 2 lone pairs -O- >R=O Transition state E. Equilibrium
P
Ea 1. LeChatlier’s Principle
Ea
∆H R
1. Geometries of valence electron hybrids: a.Equilibrium shifts to relieve the stress
H O ∆H P
R due to changes in reaction conditions
sp2 - planar, sp3 - tetrahedral, sp - linear C
2. Isomers and structure R
Reactants Reaction progress Products
P b.Keq increases: Shift equilibrium to the
a.Isomers: same formula, different bonds H C OH product side
b.Stereoisomers: same formula and bonds, B. Key Thermodynamic Variables c.Keq decreases: Shift equilibrium to the
different spatial arrangement H C OH reactant side
1. Standard conditions: 25ºC, 1 atm,
c.Chiral = optically active: Produces + or – solutions = 1 M 2. Equilibrium and temperature
H
rotation of plane-polarized light
2. Enthalpy (H): ∆H = heat-absorbed or changes
d.D: Denotes dextrorotary based on clockwise D(+) - Glyceraldehyde
produced a.For an exothermic process, heat is a
rotation for glyceraldehyde
e.L: Denotes levorotary based on counter-clockwise H O
∆H < 0 exothermic product; a decrease in temperature
rotation for glyceraldehyde; insert (–) or (+) to ∆H > 0 endothermic increases Keq
C
denote actual polarimeter results C. Standard Enthalpy of Formation, b.For an endothermic process, heat is a
f. D/L denotes structural similarity with D or L HO C H ∆H0f reactant; an increase in
0 0
glyceraldehyde 1. ∆H = Σ prod ∆Hf – Σ react ∆Hf temperature increases Keq
H C OH
g.Chiral: Not identical with mirror image 2. Entropy (S): ∆S = change in disorder 3. Entropy and Enthalpy factors
h.Achiral: Has a plane of symmetry
H 3. Standard Entropy, S0: ∆G = ∆H – T∆S
i. Racemic: 50/50 mixture of stereoisomers is ∆S = Σ prod S0 – Σ react S0 a.∆H < 0 promotes spontaneity
L(–) - Glyceraldehyde
optically inactive; + and – effects cancel 4. Gibbs-Free Energy (G): b.∆S > 0 promotes spontaneity
j. R/S notation: The four groups attached c.If ∆S > 0, increasing T promotes
∆G = ∆H – T∆S; the capacity to
to the chiral atom are ranked a,b,c,d by CH3 CH3
complete a reaction spontaneity
molar mass
Br H Br H ∆G = 0 at equilibrium d.If ∆S < 0, decreasing T lessens
•The lowest (d) is directed away from C
= steady state Keq = 1 spontaneity
the viewer and the sequence of a-b-c
C Br ∆G < 0 exergonic Note: T is always in Kelvin;
produces clockwise (R) or counter- H Br H
spontaneous large Keq K = ºC + 273.15
clockwise (S) configurations CH 3
CH3
•This notation is less ambiguous than
D/L; works for molecules with >1 Three- Fischer
dimensional projection
chiral centers
k.Nomenclature: Use D/L (or R/S) and +/– in the compound name:
KINETICS: RATES OF REACTIONS
Example: D (–) lactic acid A.Determination of Rate stabilized complex; the enzyme
l. Fisher-projection: Diagram for chiral compound reaction may be 103-1015 times faster
For a generic reaction, A + B => C:
m.Molecular conformation: All than the uncatalyzed process
Alkene 1. Reaction rate: The rate of producing
molecules exhibit structural variation
H H H Me C (or consuming A or B) 2. Mechanism:
due to free rotation about C-C single
C C C C 2. Rate-law: The mathematical dependence Step 1. E + S = k1 => ES
bond; depict using a Newman-
Me Me Me H of the rate on [A], [B] and [C] Step 2. ES = k2 => E + S
diagram
Cis Trans 3. Multiple-step reaction: Focus on Step 3. ES = k3 => products + E
n.Alkene: cis and trans isomers;
[E] = total enzyme concentration,
>C=C< does not rotate; common in rate-determining step - the slowest
Chain Positions
[S] = total substrate concentration,
fatty acid side chains step in the mechanism controls the
[ES] = enzyme-substrate complex
C. Common Organic Terminology R overall rate
C C C C C C C concentration, k 1 - rate ES
1. Saturated: Maximum # of Hs (all C-C) δ γ ββ αγ δ B. Simple Kinetics formation, k2 - reverse of step 1,
2. Unsaturated: At least one >C=C< 1. First-order: Rate = k1[A] k3 - rate of product formation
3. Nucleophile: Lewis base; attracted to the + charge of a nucleus or cation Examples: SN1, E1, aldose 3. Data analysis:
Michaelis-Menten
4. Electrophile: Lewis acid; attracted to the electrons in a bond or lone pair rearrangements Examine steady Equation:
Vmax [S]
of ES formation v = K + [S]
Carbon-chain Prefixes 2. Second order: Rate = k2[A]2 or state of [ES]; rate
m
1 meth- 7 hept- 13 tridec- 19 nonadec- k2[A][B]
2 eth- 8 oct- 14 tetradec- 20 eicos- Examples: SN2, E2, acid-base, equal rate of
3 prop- 9 non- 15 pentadec- 22 docos- hydrolysis, condensation disappearance
4 but- 10 dec- 16 hexadec- 24 tetracos- C. Enzyme Kinetics Km = (k2 + k3)/k1 (Michaelis constant)
5 pent- 11 undec- 17 heptadec- 26 hexacos- 1. An enzyme catalyzes the reaction of a v – reaction speed = k3[ES]
6 hex- 12 dodec- 18 octadec- 28 octacos- substrate to a product by forming a Vmax = k3 [E]
2
 4. Practical solution: 1

Lineweaver-Burk approach:
v
1
ORGANIC ACIDS & BASES
1/v=Km/Vmax(1/[S])+1/Vmax Vmax
Acid Base 6. Pyrimidine: Nucleic acid H
The plot “1/v vs. 1/[S]” is C
aqueous H3O+ aqueous OH–
component: cytosine (4-amino- N3 4
1 Km Arrhenius 5 CH
linear Km slope = V 2-hydroxypyrimidine), uracil
max
Brønsted-Lowry proton donor proton acceptor 2
Slope = Km /Vmax , 1 (2,4-dihydroxypyrimidine) & HC 1
6
CH
y - intercept = 1/Vmax [s] Lewis electron-pr acceptor electron-pr donor thymine (5-methyluracil) N
x - intercept = –1/Km Lineweaver-Burke electrophile nucleophile D. Buffers Pyrimidine
Calculate Km from the data A.Amphoteric 1. A combination of a weak acid and salt of a weak
D. Changing Rate Constant (k) 1. A substance that can react as an acid or a base acid; equilibrium between an acid and a base that
1. Temperature increases the rate constant: 2. The molecule has acid and base functional can shift to consume excess acid or base
Arrhenius Law: k = Ae–Ea/RT groups; Example: amino acids 2. Buffer can also be made from a weak base and salt
• Determining Ea: Graph “ln(k) vs. 1/T”; calculate 3. This characteristic also allows amphoteric
Ea from the slope of weak base
compounds to function as OH 3. The pH of a buffer is roughly equal to the pKa of
2. Catalyst: Lowers the activation energy; reaction single-component buffers for
occurs at a lower temperature biological studies O P OH
the acid, or pKb of the base, for comparable
3. Enzymes B. Acids amounts of acid/salt or base/salt
a. Natural protein catalysts; form substrate-enzyme OH 4. Buffer pH is approximated by the Henderson
complex that creates a lower energy path to the product
1. Ka= [A–][H+]/[HA]
pKa = –log10(Ka) Phosphoric acid Hasselbalch equation
b.In addition, the enzyme decreases the Free Energy of
Activation, allowing the product to more easily form 2. Strong acid: Full dissociation: HCl, H2SO4 Note: This is for an acid/salt buffer
c.Enzyme mechanism is very specific and selective; and HNO3: Phosphoric acid
3. Weak acid: Ka << 1, large pKa Henderson Hasselbalch Equation:
the ES complex is viewed as an “induced fit” pH = pKa + log (salt/acid)
lock-key model since the formation of the 4. Key organic acid: RCOOH
complex modifies each component Examples: Fatty acid: R group is a long
Common Buffers
Enzyme + Substrate Enzyme/Substrate Enzyme + Product hydrocarbon chain; Vitamin C is abscorbic acid;
complex nucleic acids contain acid phosphate groups Buffer composition approx. pH
Active acetic acid + acetate salt 4.8
site
Common Acids & pKa
ammonia + ammonium salt 9.3
Acid pKa Acid pKa
Enzyme Enzyme Enzyme
Acetic 4.75 Formic 3.75 carbonate + bicarbonate 6.3

E+S E/S complex E+P Carbonic 6.35 Bicarbonate 10.33 diacid phosphate + monoacid phosphate 7.2

E. Energetic Features of Cellular Processes H2PO4– 7.21 HPO42– 12.32 E. Amino Acids COOH
1. Metabolism: The cellular processes that use H3PO4 2.16 NH4+ 9.25 1. Amino acids have amine (base)
nutrients to produce energy and chemicals H2N C H
and carboxylic acid functionality;
needed by the organism C. Organic Bases H the varied chemistry arises from R
a. Catabolism: Reactions which break molecules apart; 1. Kb=[OH–][B+]/[BOH] C N
these processes tend to be exergonic and oxidative N1 6 5 C 7 the chemical nature of the R- group L Amino acid
pKb = –log10(Kb)
8 CH • Essential amino acids: Must be
b.Anabolism: Reactions which assemble larger 2. Strong base: Full HC 2 3 4 C 9
molecules; biosynthesis; these processes tend to N provided to mammals in the diet
dissociation: NaOH, KOH N -
be endergonic and reductive 3. Weak base: Kb << 1,
H 2. Polymers of amino acids form COO
2. Anabolism is coupled with catabolism by ATP, Purine proteins and peptides
large pKb +
NADPH and related high-energy chemicals 4. Organic: Amines & derivatives • Natural amino acids adopt the L H3N C H
3. Limitations on biochemical reactions Examples: NH3 (pKb = 4.74), hydroxylamine configuration R
a.All required chemicals must either be in the diet or be 3. Zwitterion; self-ionization; the
(pKb =7.97) and pyridine (pKb = 5.25) Zwitterion
made by the body from chemicals in the diet; harmful
5. Purine: Nucleic acid component: “acid” donates a proton to the “base”
waste products must be detoxified or excreted
b.Cyclic processes are common, since all reagents adenine (6-aminopurine) & • Isoelectric point, pI: pH that produces balanced
must be made from chemicals in the body guanine (2-amino-6-hydroxypurine) charges in the Zwitterion
c.Temperature is fixed; activation energy and
enthalpy changes cannot be too large; enzyme
catalysts play key roles
TYPES OF ORGANIC COMPOUNDS
Type of Compound Examples
MAJOR TYPES OF
Alkane ethane C2H6, methyl (Me) -CH3, ethyl (Et) -C2H5
BIOCHEMICAL REACTIONS C C

Addition Add to a >C=C< Hydrogenate Alkene >C=C< ethene C2H4, unsaturated fatty acids
Nucleophilic: Nucleophile attacks Hydrate
Electrophilic: >C=O Hydroxylate Aromatic ring -C6H5 benzene - C6H6, phenylalanine

Substitution Replace a group Amination Alcohol R-OH methanol Me-OH, diol = glycol (2 -OH), glycerol ( 3 -OH)
Nucleophilic: on alkane (OH, NH2) of R-OH Ether R”-O-R’ ethoxyethane Et-O-Et, or diethyl ether
SN1 or SN2 deamination
Aldehyde O methanal H2CO or formaldehyde, aldose sugars
Elimination: Reverse of addition, Dehydrogenate
R-C-H
E1 and E2 produce >C=C< Dehydrate
Ketone O Me-CO-Me 2-propanone or acetone ketose sugars
Isomerization Change in bond aldose =>
R-C-R’
connectivity pyranose
Carboxylic acid O Me-COOH ethanoic acid or acetic acid
Oxidation- Biochemical: Oxidize: ROH to >C=O
RC-OH Me-COO- Acetate ion
loss of e- Add O or remove H
Reduction- Reduce: Reverse of Hydrogenate Ester O Me-CO-OEth, ethyl acetate, Lactone: cyclic ester, Triglycerides
gain of e- oxidize fatty acid RC-OR’
Coupled Metals: Change Amine N-RR’R” H3C-NH2, methyl amine, R-NH2 (1º) - primary, RR'NH (2º) - secondary,
Processes valence
RR'R"N (3º) - tertiary
Water breaks a bond, Hydrolyze
Amide O H3C-CO-NH2, acetamide Peptide bonds
Hydrolysis add -H and -OH to peptide, sucrose
form new molecules triglyceride R-C-NRR'

Condensation R-NH or R-OH Form peptide Cyclic Ethers:

combine via bridging or amylose O O
O or N Pyran Furan
3
BIOCHEMICAL COMPOUNDS
A.Carbohydrates: Polymers of Monosaccharides e.Disaccharides Disaccharide Common Fatty Acids
1. Carbohydrates have the general formula • 2 units M-OH + M-OH → M-O-M Common
(CH2O)n • Lactose (β-galactose + β-glucose) β (1,4) link Name Systematic Formula
2. Monosaccharides: Simple sugars; building •Sucrose (α-glucose + β-fructose) α, β (1,2) link Acetic acid ethanoic CH3COOH
• Maltose (α-glucose + α-glucose) α (1,4) link
blocks for polysaccharides Butyric butanoic C3H7COOH
Common Sugars CH2OH CH2OH Valeric pentanoic C4H9COOH
Triose 3 carbon glyceraldehyde O O Myristic tetradecanoic C13H27COOH
H H H H H H
Pentose 5 carbon ribose, deoxyribose
Palmitic hexadecanoic C15H31COOH
Hexose 6 carbon glucose, galactose, fructose
OH H O OH H Stearic octadecanoic C17H35COOH
HO OH
a.Aldose: Aldehyde CHO CH2OH Oleic cis-9-octadecenoic C17H33COOH
type structure: H OH H OH
H C OH C O Linoleic cis, cis-9, 12 C17H31COOH
H-CO-R Maltose - Linked α D Glucopyronose
HO C H HO C H octadecadienoic
b.Ketose: Ketone type
structure: H C OH H C OH f. Oligosaccharides Linolenic 9, 12, 15- C17H29COOH
R-CO-R • 2-10 units octadecatrienoic (all cis)
H C OH H C OH
c.Ribose and • May be linked to proteins (glycoproteins) or
CH2OH CH2OH Arachidonic 5, 8, 11, 14- C19H31COOH
deoxyribose: fats (glycolipids)
eicosatetranoic (all trans)
Aldose Ketose •Examples of functions: cellular structure,
Key component in
D Glucose D Fructose enzymes, hormones
nucleic acids and O OH O OH
ATP g.Polysaccharides
• >10 units C C
CH2OH CH2OH Examples:
O O
- Starch: Produced by plans for storage
H H
- Amylose: Unbranched polymer of α (1,4)
linked glucose; forms compact helices
H H H H H
H OH OH - Amylpectin: Branched amylose using
α (1,6) linkage
OH OH OH H
- Glycogen: Used by animals for storage;
Ribose Deoxyribose
highly branched polymer of α (1,4) linked
d.Monosaccharides cyclize to ring structures in water Saturated Unsaturated
glucose; branches use α (1,6) linkage Stearic Acid Oleic Acid
• 5-member ring: Furanose (ala furan) - Cellulose: Structural role in plant cell wall;
•6-member ring: Pyranose (ala pyran) 4. Common fatty acid compounds
polymer of β (1,4) linked glucose
a.Triglyceride or
• The ring closing creates two possible - Chitin: Structural role in animals; polymer of R1 CO O CH2
triacylglycerol: Three
structures: α and β forms β (1,4) linked N-acetylglucoamine R2 CO O CH
fatty acids bond via
•The carbonyl carbon becomes another chiral 3. Carbohydrate Reactions ester linkage to glycerol R3 CO O CH2
center (termed anomeric) a.Form polysaccharide via condensation b.Phospholipids: A Triglyceride
•α: -OH on #1 below the ring; β: OH on #1 b.Form glycoside: Pyranose or furanose + alcohol phosphate group bonds
above the ring c.Hydrolysis of polysaccharide to one of three positions of fatty acid/glycerol;
d.Linear forms are reducing agents; the aldehyde - -
•Haworth figures and Fischer projections are R-PO4 or HPO4 group
used to depict these structures (see figure for can be oxidized 5. Examples of other lipids
glucose below) e.Terminal -CH2-OH can be oxidized to a.Steroids: Cholesterol and hormones
carboxylic acid (uronic acid) Examples: testosterone, estrogen
Fischer Projection Haworth Figure f. Cyclize acidic sugar to a lactone (cyclic ester)
R = Nearly always methyl R''
g.Phosphorylation: Phosphate ester of ribose in R' = Usually methyl R
12 17
nucleotides R'' = Various groups 11 13 16
H C OH 6 CH OH
2 h.Amination: Amino replaces hydroxyl to form
R H
14 15
5
O amino sugars 1 9
H C OH H
H H H 2 10 8 H
i. Replace hydroxyl with hydrogen to form deoxy
4 1
HO C H O sugars (deoxyribose) 3 5 7
Fatty Acid 4 6
HO OH H OH B. Fats and Lipids H
H C OH Generic Steroid
3 2 1. Lipid: Non-polar compound, R
H C H OH insoluble in water b.Fat-soluble vitamins:
C O
Examples: steroids, fatty acids, • Vitamin A: polyunsaturated hydrocarbon, all trans
CH2OH triglycerides HO
• Vitamins D, E, K
α-D-Glucopyronose 2. Fatty acid: R-COOH 6. Lipid reactions 3 Fatty Acids + Glycerol
2.Polysaccharides Essential fatty acids cannot be synthesized by a.Tr i g ly c e r i d e : R1 CO OH HO CH2
the body: linoleic, linolenic and arachidonic T h r e e - s t e p R2 CO OH
a.Glucose and fructose form polysaccharides HO CH
3. Properties and structure of fatty acids: p r o c e s s :
b.Monosaccharides in the pyranose and furanose R3 CO OH HO CH2
a.Saturated: Side chain is an alkane dehydration
forms are linked to from polysaccharides; b.Unsaturated: Side chain has at least one reaction of fatty acid and glycerol
dehydration reaction creates a bridging oxygen >C=C<; the name must include the position # b.The reverse of this reaction is hydrolysis of the
c.Free anomeric carbon reacts with -OH on and denote cis or trans isomer triglyceride
opposite side of the ring c.Solubility in water: <6 C soluble, >7 insoluble; c.Phosphorylation: Fatty acid + acid phosphate
d.Notation specifies form of monosaccharide form micelles produces phospholipid
and the location of the linkage; termed a d.Melting points: Saturated fats have higher melting d.Lipase (enzyme) breaks the ester linkage of
glycosidic bond points; cis- unsaturated have lower melting points triglyceride
4
BIOCHEMICAL COMPOUNDS continued
C. Proteins and Peptides - Amino Acid d.Quaternary structure: The conformation of 3. Cyclic nucleotides: The
Phosphate
Polymers R2 protein subunits in an oligomer phosphate group attached to
O H Sugar Base
1. Pe p t i d e s a r e 6. Chemical reactions of proteins: the 3’ position bonds to the
C OH N C H Nucleotide
formed by H a.Synthesis of proteins by DNA and RNA 5’ carbon 3’, 5’ cyclic AMP =
COOH
linking amino H2N C H + b.Peptides are dismantled by a hydrolysis reaction cAMP and cGMP
acids; all R1 breaking the peptide bond 4. Additional Phosphates
natural peptides 2 Amino acids c.Denaturation: The protein structure is a.A nucleotide can bond to 1 or 2 additional
contain L-amino acids disrupted, destroying the unique chemical phosphate groups
a.Dipeptide: Two linked amino acids features of the material b.AMP + P => ADP - Adenosine diphosphate
b.Polypeptide: Numerous linked amino acids d.Agents of denaturation: Temperature, acid, ADP + P => ATP - Adenosine triphosphate
c.The peptide bond is R2 base, chemical reaction, physical disturbance
H c.ADP and ATP function as key biochemical
the linkage that 7. Enzymes
O N C H energy-storage compounds
connects a pair of a.Enzymes are proteins that function as
C 5. Glycosidic bond: Linkage between the sugar and
amino acids using a COOH
biological catalysts
dehydration reaction; H2N C H base involve the anomeric carbon (carbon #1)
b.Nomenclature: Substrate + - ase
the N-H of one amino R1 >C-OH (sugar) + >NH (base) => linked sugar
Example: The enzyme that acts on phosphoryl
acid reacting with the - Dipeptide - base
OH of another => -N- bridge groups (R-PO4) is called phosphatase
6. Linking Nucleotides: The
d.The dehydration reaction links the two units; 8. Enzymes are highly selective for specific B
polymer forms as each S
each amino acid retains a reactive site reactions and substrates
phosphate links two sugars; #5 P
2. The nature of the peptide varies with amino Six Classes of Enzymes
acids since each R- group has a distinct (Enzyme Commission) position of first sugar and #3
S B
chemical character Type Reaction position of neighboring sugar
1. Oxidoreductase Oxidation-reduction 7. Types of nucleic acids: P
a.R- groups end up on alternating sides of the
polymer chain Examples: oxidize CH-OH, >C=O or CH-CH; Double - stranded D NA S
Oxygen acceptors: NAD, NADP B
b.Of the 20 common amino acids: 15 have neutral (deoxyribonucleic acid) and
2. Tranferase Functional group transfer Linking
side chains (7 polar, 8 hydrophobic), 2 acidic and single - stranded R NA Nucleotides
Examples: transfer methyl, acyl- or amine group
3 basic; the variation in R- explains the diversity (ribonucleic acid)
3. Hydrolase Hydrolysis reaction
of peptide chemistry (see table, pg. 6)
Examples: cleave carboxylic or phosphoric ester 8. Components of a nucleotide: sugar, base and
3. Proteins are polypeptides made up of
4. Lysase Addition reaction phosphate
hundreds of amino acids
Examples: add to >C=C<, >C=O, aldehyde a.Sugar: ribose (RNA) or deoxyribose (DNA)
a.Each serves a specific function in the organism
5. Isomerase Isomerization b.Bases: purine (adenine and guanine) and
b.The structure is determined by the interactions
Example: modify carbohydrate, cis-trans fat
of various amino acids with water, other pyrimidine (cytosine, uracil (RNA) and
6. Ligase Bond formation, via ATP
molecules in the cell and other amino acids in thymine (DNA))
Examples: form C-O, C-S or C-C
the protein 9. In DNA, the polymer strands pair to form a
4. Types of proteins: 9. An enzyme may require a cofactor double helix; this process is tied to base
a.Fibrous: Composed of regular, repeating Examples: Metal cations (Mg 2+, Zn 2+ or pairing
helices or sheets; typically serve a structural Cu 2+); vitamins (called coenzymes) 10. Chargaff’s Rule for DNA:
function
Examples: keratin, collagen, silk
10. Inhibition: An interference with the enzyme a.Adenine pairs with thymine P P
structure or ES formation will inhibit or block S-T...A-S
b.Globular: Tend to be compact, roughly (A: T) and guanine pairs with
P P
spherical; participates in a specific process: the reaction cytosine (C: G)
S-C...G-S
Examples: enzyme, globin 11. Holoenzyme: Fully functional enzyme plus b.Hydrogen bonds connect the base P P
c.Oligomer: Protein containing several subunit the cofactors pairs and supports the helix S-G...C-S
proteins 12. Apoenzyme: The polypeptide component c.The sequence of base pairs along P P
Common Protein D. Nucleic Acids: Polymers of Nucleotides the DNA strands serves as Chargaff’s
Examples Mol Wt Function genetic information for Rule
1. Nucleotide: A phosphate group and organic
fibrinogen 450,000 Physical structures
base (pyrimidine or purine) attached to a sugar reproduction and cellular control
hemoglobin 68,000 Binds O2
(ribose or deoxyribose) 11. DNA vs RNA: DNA uses deoxyribose, RNA
insulin 5,500 Glucose metabolism
• Name derived from the base name uses ribose; DNA uses the pyrimidine thymine,
ribonuclease 13,700 Hydrolysis of RNA
•Example: Adenylic acid = adenosine-5’- RNA uses uracil
trypsin 23,800 Protein digestion
monophosphate = 5’ AMP or AMP 12. Role of DNA & RNA in protein synthesis
5. Peptide Structure: 2. Nucleoside: The base attached to the sugar a.DNA remains in the nucleus
a.Primary structure: Primary Structure •Nomenclature: Base name + idine (pyrimidine) b.Messenger-RNA (m-RNA): Enters the nucleus
The linear sequence of Ala-Ala-Cys-Leu
or + osine (purine) and copies a three-base sequence from DNA,
amino acids connected by peptide bonds
•Example: adenine riboside = adenosine; termed a codon. m-RNA then passes from the
• Ala-Ala-Cys-Leu or A-A-C-L denotes a
adenine deoxyriboside = deoxyadenosine nucleus into the cell and directs the synthesis of
peptide formed from 2 alanines, a cysteine and
1 leucine Nucleic Acid Components a required protein on a ribosome
•The order is important since this denotes the Base Nucleoside Nucleotide c.Transfer-RNA (t-RNA): Carries a specific
connectivity of the amino acids in the protein adenine Adenosine Adenylic acid, AMP amino acid to the ribosomal-RNA (r-RNA) and
b.Secondary structure: Describes how the Deoxyadenosine dAMP aligns with the m-RNA codon
polymer takes shape guanine Guanasine Guanylic acid, GMP
d.Each codon specifies an amino acid, STOP or
Example: Helix or pleated sheet Deoxyguanisine dGMP
cytosine Cytidine Cytidylic acid, CMP
START; a protein is synthesized as different
•Factors: H-bonding, hydrophobic interactions,
disulfide bridges (cysteine), ionic interactions Deoxycytidine dCMP amino-acids are delivered to the ribosome by t-
c.Tertiary structure: The overall 3-dimensional uracil Uridine Uridylic acid, UMP RNA, oriented by m-RNA and r-RNA, then
conformation thymine Thymidine Thymidylic acid, dTMP chemically connected by enzymes
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COMMON AMINO ACIDS AMINO ACID ABBREVIATIONS USED IN
RNA CODONS BIOLOGY & BIOCHEMISTRY
hydrophobic = yellow, basic = blue, acidic = red, polar = green
• Phe aa amino acid Lys aa lysine
Amino acid pKa pI
UUU UUC A aa alanine M aa methionine
MW pKb R-pKa -R
essential - e • Thr adenine - purine base Molar (moles/L)
Alanine Ala A 2.33 6.00 hydrophobic ACU ACC
H3C- ACA ACG Ala aa alanine m milli (10-3)
89.09 9.71
Arginine Arg R 2.03 10.76 basic • Lys ADP adenosine diphosphate Man mannose sugar
NH AAA AAG
e 174.20 9.00 12.10 AMP adenosine monophosphate Met
H2N C NH CH2 CH2 CH2 aa methionine
• Leu
UUA UUG Arg aa arginine mL milliliter
Asparagine Asn N 2.16 5.41 polar
O CUU CUC Asn aa asparagine
132.12 8.73 mm millimeter
H2N C CH2 CUA CUG
Asp aa aspartate N aa asparagine
• Ala
Aspartate Asp D 1.95 2.77 acidic GCU GCC atm atmosphere
HOOC CH2 Avogadro’s number
133.10 9.66 3.71
GCA GCG (pressure unit)
Cysteine Cys C 1.91 5.07 polar elemental nitrogen
HS CH2 • Asp
121.16 10.28 8.14 ATP adenosine triphosphate n nano (10-9)
GAU GAC
Glutamate Glu E 2.16 3.22 acidic C aa cysteine
147.13 9.58 4.15
HOOC CH2 CH2 • Glu O orotidine
GAA GAG cytosine - pyrimidine elemental oxygen
Glutamine Gln Q 2.18 5.65 polar
O • Ile elemental carbon
146.15 9.00 P aa proline
H2N C CH2 CH2 AUU AUC
cal calorie phosphate group
AUA
Glycine Gly G 2.34 5.97 polar Cys aa cysteine
-H • Tyr elemental phosphorous
75.07 9.58
UAU D aa aspartate
Histidine His H 1.70 7.59 basic p pico (10-12)
CH2 UAC
e 155.16 9.09 6.04 Dalton
N NH • Cys Phe aa phenylalanine
UGU UGC DNA deoxyribonucleic acid
Pro aa proline
Isoleucine Ile I 2.26 6.02 hydrophobic CH3 CH2 dRib 2-deoxyribose sugar
• Met
e 131.18 9.60 Q aa glutamine
HC START E aa glutamate
CH3 AUG coenzyme Q, ubiquinone
F aa phenylalanine
Leucine Leu L 2.32 5.98 hydrophobic CH3 CH2 • STOP R aa arginine
e 131.18 9.58 UAA UAG Fru fructose sugar
HC CH2 gas constant
UGA
CH3 G aa glycine Rib ribose sugar
• Trp
Lysine Lys K 2.15 9.74 basic UGG guanine - purine base
RNA ribonucleic acid
e 146.19 9.16 10.67 H2N CH2 CH2 CH2 CH2 Gal galactose sugar
• Val
S aa serine
GUU Glc glucose sugar
Methionine Met M 2.16 5.74 hydrophobic GUC Svedberg unit
e 149.21 9.08 CH3 S CH2 CH2 GUA GUG Glu aa glutamate
s second (unit)
• His H aa histidine
Phenylalanine Phe F 2.18 5.48 hydrophobic CAU Ser aa serine
e 165.19 9.09 CH2 h hour
CAC T aa threonine
Proline Pro P 1.95 6.30 hydrophobic Planck’s constant
CH2 CH2 H • Arg thymine - pyrimidine
115.13 10.47
CGU CGC His aa histidine
C absolute temperature
CGA CGG
CH2 N COOH AGA AGG I aa isoleucine
H Thr aa threonine
• Ser inosine
Trp aa tryptophan
Serine Ser S 2.13 5.68 polar UCU UCC elemental iodine
HO CH2
105.09 9.05 UCA UCG Tyr aa tyrosine
Ile aa isoleucine
Threonine Thr T 2.20 5.60 polar CH3 CH • Gln U uracil - pyrimidine
e 119.12 8.96 CAA CAG J Joule (energy unit)
OH V aa valine
• Ser K aa lysine
Tryptophan Trp W 2.38 5.89 hydrophobic CH2 AGU AGC volt (electrical potential)
Kelvin - absolute T
e 204.23 9.34
N • Pro Val aa valine
H elemental potassium
CCU CCC
Tyrosine Tyr Y 2.24 5.66 polar k kilo (103) W aa tryptophan
HO C6H6 CH2 CCA CCG
181.19 9.04 10.10 elemental tungsten
• Asn L aa leucine
Valine - e Val V 2.27 5.96 hydrophobic AAU AAC
CH3 liter (volume) X xanthine
117.15 9.52
HC • Gly Lac lactose sugar Y aa tyrosine
CH3 GGU GGC
GGA GGG Leu aa leucine yr year
Note: Source - CRC Handbook of Chemistry & Physics
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Note: Due to the condensed nature of this chart, use as a quick reference guide, not as a replacement for assigned course work.
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