Biochemistry

6 Pages·2009·5.155 MB·English

by  Inc. BarCharts

BarCharts,Inc.® WORLD’S #1ACADEMIC OUTLINE
BIOCHEMICAL PERIODIC TABLE
11
Key Elements in the Body
H
1. Hydrogen 15. Phosphorus 29. Copper
Hydrogen 3. Lithium 16. Sulphur 30. Zinc
33 6. Carbon 17. Chlorine 32. Germanium 66 77 88 99
7. Nitrogen 19. Potassium 33. Arsenic
Li C N O F
8. Oxygen 20. Calcium 34. Selenium
9. Fluorine 22. Titanium 35. Bromine
Lithium 11. Sodium 25. Manganese 50. Tin Carbon Nitrogen Oxygen Fluorine
1111 1122 12. Magnesium 26. Iron 53. Iodine 1133 1144 1155 1166 1177
Na Mg 13. Aluminum 27. Cobalt Al Si P S Cl
14. Silicon 28. Nickel
Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine
1199 2200 2222 2255 2266 2277 2288 2299 3300 3322 3333 3344 3355
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
5500 5533
Sn I
Tin Iodine
GLUCOSE BROADER CHEMICAL PRINCIPLES
A.Intermolecular Forces Energy = 1 q1.q2 2.Hydrophilic = Lipophobic: Affinity for polar
H 1.iEnlteecratrcotisotna tbiect:ween ioSntsr;o fnogr ε r12 Egrxoaump;p sloelsu:ballec oinh owl,a taemr, irneep, eclalerdb obxyy nliocn apcoidlar
O H charges q and q;separated byr , Polarizability 3.Amphipatic: Polar and nonpolar functionality;
1 2 12
H C and solvent dielectric constant, εε; R common for most biochemical molecules: fatty
water has large εε; stabilizes C Oδ- acids, amino acids and nucleotides
C C.Behavior of Solutions
zwitterion formation R
1.Miscible: 2 or more substances form 1 phase;
2.Polarizability, αα: 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
layers; compounds are partitioned between the
DNA 3.Dipole moment, µµ: Asymmetric Nδ- 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 µµ 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
hypotonic to a hypertonic region; the flow produces
H HC H HHH CCH H H HHCHHCHHCHHC H 6.sHdbteiryptewdonlregeoet hng eibnnoc nreidnabetsdoee rnsHa dwcitaniitonghdn :µµ EnHhayndcreodgen Bleoδs-sn dstianbgle ΠΠ:Osam footricc ep,r tehsesu orOsem s(imont ΠΠoiactt mi==pc r) iiePMMsrsRReuTTsres,u orne the hypertonic side
H C C H H C H the lone-pair of N i:Van’t Hoff factor = # of ions per solute molecule
H neighboring O, Nor S; Hδ+ H H M:Solution molarity (moles/L)
H C H C H H C H gives “structure” to Ammonia R:Gas constant = 0.082 L atm mol–1K–1
HHHCCHCCHH HH CHCCCHH H HHHHCCC HHH laaaimlmqcuoiininhdoeo wsal,sc a,it desrsfu;a gsttaoyrl us,b aicliaizdnesds, HRδ+AOlδc-o.h..olHδ+ Oδ- Hδ+Water T4:.AaS.bolHsilqouelunutiirtdoey in’tsse s pm Lropofaep wrgoaa:rttusiTroeehsn e(ai ln at oKm teohluevn ipnta )rotfia lg parse sdsiusrseo lovfe tdh ei ng aas
H H C H H C H H H C O B.Types of Chemical δN- b.Carbon dioxide dissolves in water to form carbonic acid
H C H H C C O C Groups R R R cd..POoxlylugteann tiss caanrdr iteodx binys h deimssoogllvoeb iinn ibno tdhiely b lfoluoidds; react
H C H H H C O 1.Hydrophobic = Amine with tissue and interfere with reactions
H
HHC CH HCH O C CH H bLyip pooplahri lgicr:ouRpe;p ienlsleodluble in water; affinity for Eacxidasm; polzeosn:eS ouxlfiudriz oexs ilduensg a tnisds uneit;r ohgyednro ogxeind ecsy aynieidlde
H C C C non-polar disables the oxidation of glucose
H H O O H H Examples:alkane, arene, alkene
BONDS & STRUCTURE IN REACTIONS, ENERGY & EQUILIBRIUM
ORGANIC COMPOUNDS
A.Mechanisms ∆G > 0endergonic
A.Bonding Principles Resonance 1.Biochemical reactions involve a not spontaneous small K
eq
1.Most bonds are polar covalent; the more
electronegative atom is the “–” end of the bond C O C O- nfourmmb ae rm oefc shiamnpislem steps that together e∆qGu il=ib r–iuRmT ln(Keq) – connection with
Example:For >C=O, Ois negative, Cis positive <=>
N N+ 2.Some steps may establish equilibria, D.Standard-Free Energy of
2.Simplest Model: Lewis Structure: Assign
since reactions can go forward, as well Formation,∆∆G0:
valence electrons as bonding electrons and non- f
bonding lone-pairs; more accurate bonding models include valence- amse bchacaknwisamrd, ; tthhee srlaowtee-sdt estteerpm iinn itnhge 1.∆∆G= Σprod ∆G0f – Σreact ∆G0f
bonds, molecular orbitalsand molecular modeling 2.For coupled reactions:Hess’s Law:
step, limits the overall reaction rate
3.Resonance: The average of several Lewis structures describes the 3.Combine reactions, add ∆G, ∆H, ∆S
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
(E ), characterized by an unstable
Typical Behavior of C, N & O a are exothermic and exergonic; these
configuration termed the transition
Atom sp3 sp2 sp state (TS); Ea has an enthalpy and provide the energy and driving force
entropycomponent to complete less spontaneous
C 4 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 + HO => ADP + energy
2
y
O1 .6Gs pee2–o2-m pbeolatnrndiase,r s, 2so plfo3 vn-ae tlpeeatnrircaseh eedleraclt,r sopn-O -h -lyinberaidrs: >R=O H O REa ∆PH otential energ RTransitio∆EnHa stateP E.1E.qaL.uEdeiuCqleiuhb italoritb ilcurihiemuarmn’sg sePhsr iifintns c rteiopa clreteiloinev ceo tnhdei tsiotrnesss
C P
2.Isomers and structure R Reactants Reaction progress Products P b.Keq increases: Shift equilibrium to the
a.Isomers:sameformula, differentbonds H C OH product side
b.Stereoisomers: same formula and bonds, B.Key Thermodynamic Variables c.Keqdecreases: Shift equilibrium to the
different spatialarrangement H C OH 1.Standard conditions: 25ºC, 1 atm, reactant side
c.Chiral = optically active: Produces + or – H solutions = 1 M 2.Equilibrium and temperature
d.Dro:tatDioenn oofte psl adneex-ptroolaroritzaerdy libgahsted on clockwise D(+) - Glyceraldehyde 2.Enthalpy (H):∆H = heat-absorbed or changes
produced a.For an exothermic process, heat is a
rotation for glyceraldehyde
∆H < 0 exothermic product; a decrease in temperature
e.L:Denotes levorotary based on counter-clockwise H O
∆H > 0 endothermic increases K
rotation for glyceraldehyde; insert (–) or (+) to C eq
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 ∆∆H0 reactant; an increase in
f
g.gClhycirearal:ldNeohty dideentical with mirror image H C OH 12..E∆∆Hntr=o pΣy p (rSo)d: ∆∆HS 0f=– c hΣarnegaec ti n∆ dHis0forder 3.Entetmroppeyra taunred inEcrnetahsaelsp Ky eqfactors
h.Achiral:Has a plane of symmetry 3.Standard Entropy,S0: ∆G = ∆H – T∆S
H
i.Ropatciceamllyic i:na5c0ti/v5e0; +mainxdtu –ree ffoefc tss tcearneoceislomers is L(–) - Glyceraldehyde 4.∆GSib =b sΣ-Fprroede SE0n–e rΣgyre (aGct) S:0 ba..∆∆HS >< 00 pprroommootteess ssppoonnttaanneeiittyy
j.R/S notation:The four groups attached
∆G = ∆H – T∆S; the capacity to c.If ∆S > 0, increasing T promotes
to the chiral atom are ranked a,b,c,d by CH3 CH3 complete a reaction spontaneity
molar mass
Br H Br H ∆G = 0at equilibrium d.If ∆S < 0, decreasing T lessens
•The lowest (d) is directed away from C
the viewer and the sequence of a-b-c = steady state Keq= 1 spontaneity
cplroocdkuwceisse c(Slo)c ckownifsieg u(rRat)i oonrs counter- H C Br H Br ∆G < 0espxoerngtaonneiocus large Keq NKo =te º:C T +is 2 a7l3w.a1y5s in Kelvin;
•This notation is less ambiguous than CH3 CH3
D/L; works for molecules with >1 Three- Fischer
dimensional projection
chiral centers KINETICS: RATES OF REACTIONS
k.Nomenclature: Use D/L (or R/S) and +/– in the compound name:
Example:D(–) lactic acid A.Determination of Rate stabilized complex; the enzyme
l.Fisher-projection:Diagram for chiral compound For a generic reaction, A + B => C: reaction may be 103-1015 times faster
m.Molecular conformation: All
Alkene 1.Reaction rate:The rate of producing than the uncatalyzed process
molecules exhibit structural variation
H H H Me C (or consuming A or B) 2.Mechanism:
due to free rotation about C-Csingle
bond; depict using a Newman- C C C C 2.Rate-law:The mathematical dependence Step 1.E + S = k1 => ES
diagram Me Me Me H of the rate on [A], [B] and [C] Step 2.ES = k2 => E + S
n.Alkene: cis and trans isomers; Cis Trans 3.Multiple-step reaction: Focus on Step 3.ES = k3 => products + E
[E] = total enzyme concentration,
>C=C< does not rotate; common in rate-determining step - the slowest
fatty acid side chains Chain Positions step in the mechanism controls the [S] = total substrate concentration,
[ES] = enzyme-substrate complex
C.Common Organic Terminology R overall rate
1.Saturated:Maximum # of Hs(all C-C) Cδ Cγ Cβ Cα Cβ Cγ Cδ B.Simple Kinetics cfoornmcaetnitorna,t iokn, - rke1vers-e orfa tset ep E1S,
2
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:
1 meth- 7 hepCt-arbon-chai1n3 Ptrreidfiexce-s 19 nonadec- 2.Sk2e[cAo]n[dB ]order: Rate = k2[A]2 or sotfa tEe So f f[oErSm]a; triaotne v = Vmax [S]
2 eth- 8 oct- 14 tetradec- 20 eicos- Examples: SN2, E2, acid-base, equal rate of Km + [S]
3 prop- 9 non- 15 pentadec- 22 docos- hydrolysis, condensation disappearance
4 but- 10 dec- 16 hexadec- 24 tetracos- C.Enzyme Kinetics K = (k + k)/k (Michaelis constant)
m 2 3 1
5 pent- 11 undec- 17 heptadec- 26 hexacos- 1.An enzyme catalyzes the reaction of a v – reaction speed = k[ES]
3
6 hex- 12 dodec- 18 octadec- 28 octacos- substrate to a product by forming a Vmax = k3[E]
2
4.Practical solution: 1
v ORGANIC ACIDS & BASES
Lineweaver-Burk approach: 1
1/v=Km/Vmax(1/[S])+1/Vmax Vmax Acid Base 6.Pyrimidine: Nucleic acid H
STlhloienp eepa l=or tK “m1//vV mvasx. ,1/[S]” is K1m slope = VKmmax1 ABrrørhnestneidu-sLowry apqrouteoonu ds oHn3oOr+ apqrouteoonu as cOceHp–tor c2(2o-h,m4y-pddorinohexynydtpr:o yxcriyymtpoyisdriiinnmee i)d(, 4in-aemu) rianco&i-l HCN32 C14 56CCHH
y - intercept = 1/Vmax [s] Lewis electron-pr acceptor electron-pr donor thymine (5-methyluracil) N
x - intercept = –1/K Lineweaver-Burke electrophile nucleophile D.Buffers Pyrimidine
m
Calculate Kmfrom 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 acidor 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 of weak base
E from the slope
2.Caatalyst:Lowers the activation energy; reaction csionmglpeo-cuonmdsp ontoe nt fubnucftfieorns faosr OH 3.The pH of a bufferis roughly equal to the pKaof
occurs at a lower temperature the acid, or pK of the base, for comparable
biological studies O P OH b
3.Enzymes B.Acids amounts of acid/salt or base/salt
a.Natural protein catalysts; form substrate-enzyme 1.K= [A–][H+]/[HA] OH 4.Buffer pH is approximated by the Henderson
complex that creates a lower energy path to the product a Phosphoric acid
pK = –log (K) Hasselbalchequation
b.In addition, the enzyme decreases the Free Energy of a 10 a
2.Strong acid: Full dissociation: HCl, HSO Note: This is for an acid/salt buffer
Activation, allowing the product to more easily form 2 4
and HNO: Phosphoric acid
c.Etlhonecz kyE-mkSee y cm oemmcpohldaenexli s miss i invsci veewe retyhd se p aesfc oiarfnmic a“atininoddn us ecleoedfc tiftvihte”e; 43..KWeeya ko ragcain3dic: Kacaid<:< R 1C, lOarOgeH pKa HendeprHs o=n p HKaas+s leolgb a(slcahlt/ aEcqidu)ation:
complex modifies each component Examples: Fatty acid: R group is a long
Common Buffers
hydrocarbon chain; Vitamin C is abscorbic acid;
Enzyme + Substrate Enzyme/Substrate Enzyme + Product
complex nucleic acids contain acid phosphate groups Buffer composition approx.pH
Active Common Acids & pK acetic acid + acetate salt 4.8
site a
ammonia + ammonium salt 9.3
Acid pK Acid pK
Enzyme Enzyme Enzyme a a
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 HPO 2.16 NH+ 9.25 1.Amino acids have amine (base)
nutrients to produce energy and chemicals 3 4 4 and carboxylic acid functionality; H2N C H
needed by the organism C.Organic Bases H the varied chemistry arises from R
ab..CtAmbheaneo tsealaeenbb cpdoourellloiiresscgsmme;os ::bnsReiioRcse sateayecanntnciddotth n irtoesoesn wdbissueh ; icwecttxhhhieev ibrsecrgeheo a pnkar iosmcscaeoenmlsedscbe uolslex e tisedl anaaprdtgai vrettoer; 312...KpSWdKitbser=sbaoo[k=nOc gib–Ha lta–ois]og[enB1::0b +(KNaK]/sa[beBO<):<OH H1, ,K]FOuHll HCN12 CN36 54CC 7NNH98CH 2.•tPhopEelr sycosmhveiendemteridasic lta oola fnmm aaaitnmumormei n aaooclfs i d taihsnce: i tRdhMes- ugdsfiroteo rtubmpe LAminoC OacOi-d
2.Anabolism is coupled with catabolism by ATP, large pK b Purine proteins and peptides +
NADPH and related high-energy chemicals 4.Organic:bAmines & derivatives • Natural amino acids adopt the L H3N C H
3.aL.Aimll irteaqtuioirneds cohne mbiicoaclsh memusitc eailth reer abcet iino nthse diet or be E(pxKam=p7l.e9s7:) NanHd3 py(priKdibne= ( p4K.74=), 5.h2y5d)roxylamine 3.Zcwointfteigruiorant;io nself-ionization; the ZwitteRrion
made by the body from chemicals in the diet; harmful b b
5.Purine:Nucleic acid component: “acid” donates a proton to the “base”
waste products must be detoxified or excreted
adenine (6-aminopurine) & • Isoelectric point, pI: pH that produces balanced
b.Cyclicprocesses are common, since all reagents
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
BIOCHEMICAL REACTIONS Alkane C C ethane C2H6, methyl (Me) -CH3, ethyl (Et) -C2H5
Addition Add to a >C=C< Hydrogenate Alkene >C=C< ethene CH unsaturated fatty acids
2 4,
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 HCO or formaldehyde, aldose sugars
Elimination: Reverse of addition, Dehydrogenate 2
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: ROHto >C=O
RC-OH Me-COO-Acetate ion
loss of e- Add Oor 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” HC-NH, methyl amine, R-NH (1º) - primary, RR'NH (2º) - secondary,
Processes valence 3 2 2
RR'R"N (3º) - tertiary
Water breaks a bond, Hydrolyze
Amide O HC-CO-NH, acetamide Peptide bonds
Hydrolysis add -Hand -OHto peptide, sucrose 3 2
form new molecules triglyceride R-C-NRR'
Condensation R-NHor R-OH Form peptide Cyclic Ethers:
combine via bridging or amylose O O
Oor 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
(CH O) •Lactose (β-galactose + β-glucose) β(1,4) link Name Systematic Formula
2 n
•Sucrose (α-glucose + β-fructose) α,β(1,2) link
2.Monosaccharides: Simple sugars; building Acetic acid ethanoic CHCOOH
•Maltose (α-glucose + α-glucose) α(1,4) link 3
blocks for polysaccharides
Butyric butanoic CHCOOH
3 7
Common Sugars CH2OH CH2OH Valeric pentanoic C4H9COOH
Triose 3 carbon glyceraldehyde O O Myristic tetradecanoic C H COOH
H H H H H H 13 27
Pentose 5 carbon ribose, deoxyribose
Palmitic hexadecanoic C H COOH
15 31
Hexose 6 carbon glucose, galactose, fructose
HO OH H O OH H OH Stearic octadecanoic C17H35COOH
a.tAylpdeo sster:uctAurlde:ehyde CHO CH2OH H OH H OH Oleic cis-9-octadecenoic C17H33COOH
H-CO-R H C OH C O Maltose - Linked ααD Glucopyronose Linoleic cis, cis-9, 12 C17H31COOH
b.Ketose:Ketone type HO C H HO C H octadecadienoic
structure: H C OH H C OH f.Oligosaccharides Linolenic 9, 12, 15- C17H29COOH
R-CO-R H C OH H C OH •2-10 units octadecatrienoic (all cis)
•May be linked to proteins (glycoproteins) or
c.Rdeiboxoyser iabnodse: CH2OH CH2OH fats (glycolipids) Arachidonic e5i,c 8o,s 1at1e,t r1a4n-oic (all trans) C19H31COOH
Aldose Ketose •Examples of functions: cellular structure,
Key component in
D Glucose D Fructose enzymes, hormones
nucleic acids and
g.Polysaccharides O OH O OH
ATP
•>10 units C C
CHOH CHOH Examples:
2 O 2 O -Starch:Produced by plans for storage
H H
-Amylose: Unbranched polymer of α (1,4)
linked glucose; forms compact helices
H H H OH H H H 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 glucose; branches use α(1,6) linkage Saturated Unsaturated
Stearic Acid Oleic Acid
•5-member ring: Furanose(ala furan)
-Cellulose: Structural role in plant cell wall;
4.Common fatty acid compounds
•6-member ring: Pyranose(ala pyran) 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: αand βforms β(1,4) linked N-acetylglucoamine fatty acids bond via R2 CO O CH
•The carbonyl carbon becomes another chiral 3.Carbohydrate Reactions ester linkage to glycerol R3 CO O CH2
center (termed anomeric) a.Formpolysaccharide 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;
- -
•Haworth figures and Fischer projections are d.Linear forms are reducing agents; the aldehyde R-PO or HPO group
4 4
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
f.Cyclize acidic sugar to a lactone (cyclic ester)
Fischer Projection Haworth Figure R = Nearly always methyl R''
g.Phosphorylation: Phosphate ester of ribose in R' = Usually methyl 12 R 17
nucleotides R'' = Various groups 11 13 16
H C OH 6CH2OH h.Amination: Amino replaces hydroxyl to form
H C OH H 5H O H i.aRmepinlaoc seu hgyadrsroxyl with hydrogen to form deoxy 2 1 R10H9 8 H14H 15
HO C H O 4 1 sugars (deoxyribose) 3 5 7
HO OH H OH B.Fats and Lipids Fatty Acid 4 H 6
H C OH 3 2 1.Lipid: Non-polar compound, R Generic Steroid
H C H OH insoluble in water C O b.Fat-soluble vitamins:
Examples: steroids, fatty acids, •Vitamin A: polyunsaturated hydrocarbon, all trans
CH2OH triglycerides HO •Vitamins D, E, K
αα-D-Glucopyronose 2.Fatty acid:R-COOH 6.Lipid reactions 3 Fatty Acids + Glycerol
Essential fatty acidscannot be synthesized by
2.Polysaccharides a.Triglyceride: R1 CO OH HO CH2
the body: linoleic, linolenic and arachidonic
a.Glucose and fructose form polysaccharides Three - step R2 CO OH HO CH
3.Properties and structure of fatty acids:
p r o c e s s :
b.Monosaccharides in the pyranose and furanose
a.Saturated:Side chain is an alkane dehydration R3 CO OH HO CH2
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 formmicelles produces phospholipid
and the location of the linkage; termed a d.Melting points:Saturated fats havehigher melting d.Lipase (enzyme) breaks the ester linkage of
glycosidicbond points; cis- unsaturated have lower melting points triglyceride
4
BIOCHEMICAL COMPOUNDScontinued
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
1.Peptides are O H 6.Chemical reactions of proteins: the 3’position bonds to the Sugar Base
C OH N C H Nucleotide
formed by H a.Synthesis of proteins by DNA and RNA 5’carbon 3’, 5’cyclic AMP =
linking amino H2N C H + COOH 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 base, chemical reaction, physical disturbance
R2 c.ADP and ATP function as key biochemical
the linkage that H 7.Enzymes
connects a pair of O N C H energy-storage compounds
amino acids using a C COOH a.Enzymes are proteins that function as 5.Glycosidic bond: Linkage between the sugar and
biological catalysts
dehydration reaction; H2N C H b.Nomenclature:Substrate + - ase base involve the anomeric carbon (carbon #1)
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
groups (R-PO) is called phosphatase
OH of another => -N- bridge 4
6.Linking Nucleotides: The
d.The dehydration reaction links the two units; 8.Enzymes are highly selective for specific B
polymer forms as each
each amino acid retains a reactive site reactions and substrates S
phosphate links two sugars; #5
2.The nature of the peptide varies with amino Six Classes of Enzymes P
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
a.R- groups end up on alternating sides of the 1.Oxidoreductase Oxidation-reduction 7.Types of nucleic acids: P
polymer chain Examples: oxidize CH-OH, >C=O or CH-CH; Double-stranded DNA 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 RNA 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
b.The structure is determined by the interactions 5.Isomerase Isomerization b.Bases: purine (adenine and guanine) and
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 (Mg2+, Zn2+ or pairing
helices or sheets; typically serve a structural Cu2+); vitamins (called coenzymes) 10.Chargaff’s Rule for DNA:
function
10.Inhibition:An interference with the enzyme a.Adenine pairs with thymine P P
Examples:keratin, collagen, silk
structure or ES formation will inhibitor block (A:T) and guanine pairs with S-T...A-S
b.Globular: Tend to be compact, roughly
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 1.Nucleotide: A phosphate group and organic genetic information for Rule
fibrinogen 450,000 Physical structures
base (pyrimidine or purine) attached to a sugar reproduction and cellular control
hemoglobin 68,000 Binds O
2 (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-RNAthen passes from the
•Ala-Ala-Cys-Leu or A-A-C-L denotes a
adenine deoxyriboside = deoxyadenosine
peptide formed from 2 alanines, a cysteine and nucleus into the cell and directs the synthesis of
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
START; a protein is synthesized as different
•Factors:H-bonding, hydrophobic interactions, cytosine Cytidine Cytidylic acid, CMP
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
5
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 pK pI
a UUU UUC
MW pK R-pK -R A aa alanine M aa methionine
b a
essential - e • Thr adenine - purine base Molar (moles/L)
ACU ACC
Alanine Ala A 2.33 6.00 hydrophobic
HC- ACA ACG Ala aa alanine m milli (10-3)
89.09 9.71 3
Arginine Arg R 2.03 10.76 basic • Lys ADP adenosine diphosphate Man mannose sugar
e174.20 9.00 12.10 NH AAA AAG AMP adenosine monophosphate Met aa methionine
H2N C NH CH2 CH2 CH2 • Leu
UUA UUG Arg aa arginine mL milliliter
Asparagine Asn N 2.16 5.41 polar
132.12 8.73 O CUU CUC Asn aa asparagine mm millimeter
HN C CH CUA CUG
2 2 • Ala Asp aa aspartate N aa asparagine
Aspartate Asp D 1.95 2.77 acidic HOOC CH GCU GCC atm atmosphere Avogadro’s number
133.10 9.66 3.71 2
GCA GCG (pressure unit) elemental nitrogen
Cysteine Cys C 1.91 5.07 polar
HS CH • Asp
121.16 10.28 8.14 2 GAU GAC ATP adenosine triphosphate n nano (10-9)
Glutamate Glu E 2.16 3.22 acidic HOOC CH CH • Glu C aa cysteine O orotidine
147.13 9.58 4.15 2 2
GAA GAG cytosine - pyrimidine elemental oxygen
Glutamine Gln Q 2.18 5.65 polar
146.15 9.00 O • Ile elemental carbon P aa proline
HN C CH CH AUU AUC
2 2 2 cal calorie
AUA phosphate group
Glycine Gly G 2.34 5.97 polar -H • Tyr Cys aa cysteine elemental phosphorous
75.07 9.58
Histidine His H 1.70 7.59 basic CH UUAAUC D aa aspartate p pico (10-12)
e155.16 9.09 6.04 2 Dalton
N NH • Cys Phe aa phenylalanine
UGU UGC DNA deoxyribonucleic acid Pro aa proline
eIs1o3le1u.c1i8ne Ile I 92..6206 6.02 hydrophobic CH3 CH2 • Met dRib 2-deoxyribose sugar Q aa glutamine
HC START E aa glutamate
CH AUG coenzyme Q, ubiquinone
3
F aa phenylalanine
Leucine Leu L 2.32 5.98 hydrophobic CH CH • STOP R aa arginine
e131.18 9.58 3 2 UAA UAG Fru fructose sugar gas constant
HC CH2 UGA
CH3 • Trp G aa glycine Rib ribose sugar
guanine - purine base
Lysine Lys K 2.15 9.74 basic UGG RNA ribonucleic acid
e146.19 9.16 10.67 H2N CH2 CH2 CH2 CH2 • Val Gal galactose sugar
S aa serine
GUU
Glc glucose sugar
Methionine Met M 2.16 5.74 hydrophobic GUC Svedbergunit
e149.21 9.08 CH S CH CH GUAGUG Glu aa glutamate
3 2 2 s second (unit)
• His H aa histidine
Phenylalanine Phe F 2.18 5.48 hydrophobic Ser aa serine
e165.19 9.09 CH2 CAU h hour
CAC T aa threonine
Proline Pro P 1.95 6.30 hydrophobic Planck’s constant
115.13 10.47 CH2 CH2 H • CAGrgU CGC His aa histidine thymine - pyrimidine
C absolute temperature
CGA CGG
CH2 N COOH AGA AGG I aa isoleucine Thr aa threonine
H
inosine
• Ser
Trp aa tryptophan
Serine Ser S 2.13 5.68 polar UCU UCC elemental iodine
HO CH
105.09 9.05 2 UCA UCG Tyr aa tyrosine
Ile aa isoleucine
Threonine Thr T 2.20 5.60 polar CH CH • Gln U uracil - pyrimidine
e119.12 8.96 3 CAA CAG J Joule (energy unit)
OH V aa valine
• Ser K aa lysine
Ter2y0p4to.2p3han Trp W 92..3348 5.89 hydrophobic CH2 AGU AGC Kelvin - absolute T volt (electrical potential)
N • Pro elemental potassium Val aa valine
H
CCU CCC
Tyrosine Tyr Y 2.24 5.66 polar CCA CCG k kilo (103) W aa tryptophan
HO CH CH
181.19 9.04 10.10 6 6 2 • Asn L aa leucine elemental tungsten
Valine - e Val V 2.27 5.96 hydrophobic CH AAU AAC liter (volume) X xanthine
117.15 9.52 3
• Gly
HC Lac lactose sugar Y aa tyrosine
GGU GGC
CH
3 GGA GGG Leu aa leucine yr year
Note:Source - CRC Handbook of Chemistry & Physics
U.S. $5.95 CAN. $8.95 free downloads & Customer Hotline # [phone]
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Author:Mark Jackson, PhD. quickstudy.com ISBN-13: 978-142320390-2
ISBN-10: 142320390-9
Note:Due to the condensed nature of this chart, use as a quick reference guide, not as a replacement for assigned course work.
All rights reserved. No partof this publication maybe reproduced or transmitted in anyform, or by any means, electronic or
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