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2

ENERGY

energy (rom the sun is stored in "high nergy" bonds when CO2 and H ° ar~ combined by photosynthesis 10 form carbohydrates. Ultimately it IS this energy which drives all the reactions necessary to mainlainlife on this planet.

I\s these processes arc repeated, energy ami matter ar continually C msurncd and recycled throughout llle chain of life. Life produces and reproduces itself by the processes of replication, transcription, and translation, using the instructions of the genetic code stored in DNA.

I. Replication:

DNA --+- DNA

Photons (Irom ~lInlighl)_ excited electrons in chlorophyll O,+H'0--1

phOlosyntJle 'is

. ~

hi.gh energy careen-carbon bonds (carbohydrates)

~ .

catubollc metabolism (enzyme linked oxidarion-rcduction)

~ ·°2

electrons (211 in NADH or FADH:J .,._ in higher 'Organisms

02~

pH20

el tron transport chain

f

high energy phosphate bonds (ATP)

~

anabolic metabolism + enzymes + substrnro» (building blocks)

~

complex biologic 11101 .cules

2. Transcription:

DNA~ RNA

3. Translatlon:

RNA --+ Proteins

ACID-BASE

11+: Hydrogen ion.

[ I : Conccnuauon, i.e .. [H"] = concentration of hydrogen ions.

pH: -log [I-I" J.

Unlie: H' acceptor.

Acid: 1-1+ donor.

Weak Acid: donates few of us W.

Strong Acid: donates almost all of its HI and forms II wcnk conjugate bnse.

K: used 10 symbolize a constant,

K .. : constant which correlates with the extent an acid gives lip its H", (the strong r the acid the higher U1C Kn)

IjK n : -log Kfl

HEN[)ERsoN-H~SSELBACH E~UATION

Complc,.; biologic lIloleade<! catabolic ITIclnbolisrn

anabolic 1mboli'" En."", + metabolic pL~

HI>: hydrogen ion. A-: conjugate base,

HA: An uudissociated acid.

K _ [A-l x [1-1+ 1 _ conjugal!! h:lse concentration x hydrogen ion cone.

a - [HAl - undissociar'd acid cone.

If you solve this cquaticn ~ r IH+I:

I)-I 1= K [HAl u x [A-I

Now if you remember how to lise Logarithms, you con rearrange this equation:

MAJTER

Plants and bacteria also ex IraCI nitrogen and CO:!. from the atmosphere, minerals from the soil. and synthesize molecules whi h become IJP building blocks f biomnttcr. Other organisms consume and in orporatc these building blocks int their substance hy Lit processes of growth, maintenance, all I reproduction.

1

-log [H+] = -log K I'" (-log lHA] I {A-J but remember-log NB = +Iog B/A.

So you get: 1111= pKIl + .Iog ~1

Which is the Hender.fOlI-flas!u!/bach equation!

GfNEf1AL BIOCHEMISTRY

3

~U;:~t.ion that ists changes in its pH when a id or base arc added. Co,'~tains nid nJugale base pairs, b~I'fcrin9 is src:aICSI when pH = pK'l!:nd Wh~' ~shappeus,the conccnuation of acid and J!S ~nJugate base ~ equal ( I~C:, [A. ] - rHA]). The proton release or acceptance IS directly proportional 10 the pH.

META.BOLISM

The process in which mailer from outside an organism is transformed into -'nefgy 01' material for the organism, In bacteria, metabolism talcc~ place inside the cytoplasm and along the cell membrane. In ~ighcr organisms, metabolism occurs in the cytoplasm and in the mitochondria.

C"TABOUSM

Reactions that break lite bonds or complex. molecules. In the body, Ijlc..~e reaclions may be linked 10 enzyme catalysts allowing for storage of the released energy in the form uf ATP (adenosine triphosphate). P lymcrs yield energy when Uu~y arc converted 10 inlcnnedintcs.

ANABOLISM

Reactions which synthesize complex molecules from simpler molecules using AT? IL~ an energy source. Simpl molecules bccom • polymers.

ATP (Adenosine Triphosphate)

lIergy medium for reactions inside rhe cell.

Oxldal.ion Loss of .J sctrons Reduction Gain of electrons

C.ALORIE (C) In nutrition, equals one scientific kilocalorie (Kcal). BOMB CALORIMETER

lnsulatcd chamber in which samples of food nrc oxidized and the amount of heal generated is accurately measured.

MAXIMUM BUFFERING CAPACITY

. Occurs III the pH represented by pK a

2 4

6 8 10 l2

pH

TyPES OF TRANSPORT .

Osmosis is the rnigrution of water Irom the side of it III mbranc thnt IS hypo-

osmotic [0 the side thal is hYJV.,:r,oslTIotic.

Facilitatcd trnnsport uses carriers:

. I rt f '01: eule "ct wn the c ncentration gra-

I'fJ.fS;W: transport IS t ic transpo 0 a m - cc

diem" by" carrier; docs not lise energy.

Active transport is the transport of a molecul (i. e., Na~. Glucose. Amino acid) by u carrier which uSCS energy.

a-transport, n typ of active transport. transport» an ion al.~ng ,:,ith a mole: cule as in the case of the glucose-No"/K" ATPuse pump. 1.lllS :.yslcm~lscs energy from ATPlo o-lrans()Ql1 sodium and rlucosc From lutestinal epithe-

lial cells into the blood.

Carbohydrales Proteins Alcohols

PaIS

4 KcaJIgrom 4· K.cllllgratll.'" 7 KcaJ/gnun 9 Kcallgram

.ProtCi.ll would yield 5 KeaVgrnr!l if iL WIlI'I: completely mewbolized but thili would produce oompoundB too toxic 10 the Pody. InstcJJd urea is the ultimate excretor;y rorm and still has some ClIllfgy len in it which can be ulill~d by baeteri ... Baeteri .. can mCLDbolizc urea to Ilnunooill, E.Lhanul is 111.elllboli7.cd in the liver. Alcohollnhibit., gluoolleogOl1esls.

4

I

'2

META80USM 5

NAD1c NADH NAO" NADH

BUlanol \.4 Acetaldehyde \..4 Acetate

Aim/wi d), lIc~wlrfrl!ydt: M

NAD'" = 111e oxidized form; the electron acceptor

NAOH '" The chemically reduced form; the electron donor,

Each reaction above is a reduction reaction = the gain of an electron (H+).

ENERGY STORAGE

Energy sources arc xidizcd to produ c energy. Excess Calori . ar slor d in the body. In nutrition, the "70 Kg Mall" is the defined stand xl with the following composition:

AmOl.lnt

6 Kg Prot~In

:25 ~g Catbobydrn~C}S

GI,VCOOEN

A starch made in [he liver and muscle. II is the first fuel used LO power activity. Carbohydrates arc NOT (I cause of any diseases-the only problem may be adding dental caries.

FAT

rat (tnacylglycerol) is the IlH\ior energy store ill the body. Adipose tissue is an efficient way to store energy because [HI is twice as energy den e as carbohydrate or protein, und has less WOller as ociuted WiUI it. When ixcess calories arc taken in, only limited amounts of carbohydrates and protein 'an be stored (unlc. s they arc converted to fal which uses energy). Fats need Iiulc processing and Me easily stored; this is (me '11. on 100 much ill in the diet 'an be a prohlcm. The urrent perccntag of fat in the U.S, diet is near 42 percent, and the g01l1 is to reduce the rOl caloric to ~ 30 percent of the total calorler (fill, cerbohydratcs and protein intake). Olive oil and anoia oil [If' mono unsaturated 1~IIS, All plant» have unsalurated fill (contain double bonds and ure more Iluid), except coconut and palm oil. which life saturated filts and increase the risk lor cardiovascular disease,

PflorEIN

Pro lei II is not mctubcllzcd liS an energy source in healthy, well-nourished people, hUI there is sume turnover due 10 repair lind fen swal of tissue, 'Ole biologic value f animal proteins is high 'SI compared 10 plants (which may be missing

6 BIOCHEMISTRY

several essential amino acids), This is why the lowest Iut nnd inexpensiv . form of protein sources would be n combination of animal und plant derived foods.

Tlisue

Energy Sources Utilized

Muscle

at fCSt! fm

w~en active; carbohydrates cQ(bohydratc.'l

Brain

RESPIRATORY QUOTIENT (R.Q.)

O2 mall' and 02 used by atissuc when a given type of energy source is oxidized.

CO2 produced R.Q. = z consumed

Par Pr¢~ejn.1 Carbohydrate

0.7 0.8 1.0

A body at rest will have an overall R,Q. of -0..8 because resting muscl is utillung fnl, brain is using carbohydrates, and there is some turnover or prot sin, As 11 body becomes active the R.Q. approaches 1,0 since muscle begin. [0 usc carbohydrates.

ENERGY REqUIREMENTS

BMR + Physical Activity + SDA = otal Energy Requirement (TEI~) SDA (specific dynamic action): Tho amoum . r energy used secondary to the increase in the metabolic rille lhal occurs during the digestion and absorption

r food. This small number is ten left out of calculations. (Thermic effect. f food is about 10% of the energy ·onsumption.)

Physical Activity: Energy used by physical activity. In a sedentary person accounts for about 15-25% of the "fER, in a very active person can b as mueh as 50%. (Physical ucrivhy is about 30% of the energy consumption.)

BMR (Basal Metabolic Rate) = TER - [SDA + Physical AcLivily]I3MR is the energy required for the maintenance (unctions of the body, i.e., energy needed for the brain. respiration, and 10 rnaintnin homeostasis. (This is about 60% of the energy ell pcndiui rc of a resu rig person.)

BMR Call be estlmared I\S 24 Kelll/kg for adult moles and [8 Kcal/kg for adult females (per 24 hours), or 24 kcal/kg X 70 kg malc e 1,680 kcnVday minimum caloric necessity.

Side Chains: _

Nonpolar SlrudllfC

(EiCClm(IS nrc 8~~1I1'1 distributed)

AMINO ACIDS

There arc 20 amino acids in animal metabolism, bul more occur in nature. Amino !1cids,lhe buildjng blocks ·of proteins. have differenl side chains which arc connected 1.0 a common backbone, AI physiologic pH, all amino acids have both positive and negative charges.

Valine Vill

V

Structure of amino odd:

H I

+H3N -C-COOH

I

Leucine Leu

L

Isoleucine Uc

1

NH] - amino group COOH = carboxyl group

I'

-C- '" alpha carbon (O:'GflIbon)

I

Mclhioninc Mel

M

Phenylaninc Phe

p

When the pK is small, then the proton comes: off easily (readily). When the pK is very large. (hen il is difficult ~Io remove the proton, and you must add u base (Lil:rllle) lind remove the protons,

Tryptophan TI'l'

W

Side Chains': .

Nonpolar Struc(urt

(Ele<;lruns arc <I'wl), ui.Lrlbtllcll)

Glycine -1:1

Gly

G

Simplified Abbrcvilltion

-H

Proline Pro

p

A lnn inc Ala

A.

-c

7

Simplified Abbreviation

-c-c

/ \ c C

-C

I \ c ,

c

-c-c-s-c

-c-v

t.__ aromatic side chain

C

/IMINO ACIDS IWD PROTEINS

9

:1. 0 BIDCHfMfSmr

Proline is an imino acid wilb. a side chain lhnt forms II ring will' me amino group of the buc,kbone.

Valine, Leucine, and Isoleucine arc hydJophobi,c and bond together through hydrophobic interaction. (Imagine oil and water: Val, Leu. lind Ile are the oil and they try 10 avoid water.)

Physiologic pH = 7.4

Side Chains:

Polar Slruclurc

(Elecuons nrc unevenly dislril)I.Ued)

Continued

Polar Bas-Ie (+1 Chlll'ge)

Side Chains:

Lysine Lys

K

Simplified Abb~vllldlln

PoilU' SIru:cture

( lectrons are UrleVeJI'y distributed)

Serine Ser

S

ystcine Cy~

Threonine The

T

1Yros,il1t:

Tyr y

Polllr Amide Asparngino

Asii

N

Glutamine GIn

Q

Polar Acidic Aspartic Acid Asp

I)

Glutamic Acid III

E

-C-OJI

-C-SH

Arginine Arg

R

H- H3

I

on

-CH1~OH

-c

I

ou

-eVOH

Histidine His

H

'H2- -NB2 - -NBl
II II
0 0
-CH1-CH1 -NH2 -C- -NU2
II II
0 0
H2 11 H
II II
0
'112- H2 - H -C-C-OH
II It
0 0 Simpllncd Abbreviation

-CH2-C1-12-CH:z-N H

I

c

/~

H2N NH2+

-C-C-C-NH I

c

/~

H2N NH2+

-CH2-C- NH+ II II HC C

\ I N I H

-CH2-C- NH+

'1'1 II c c

\ I N I H

Note: • Phenylalanine, Tyrosine and Tryptophan have aromatic side chains. .~ Cysteine and Methionine contain sul.rur.

• Proline is an lmioo acid and forms a ring with its own backbone,

• 111e other 19 nrc amino acids.

SIQNIRCANCE OF SIDE CHAIN CHARACTERISTICS

Side chains am what ulLimale)y determine the function o( tile protein that they make up,

Non-Polar Side Chains: AJ"c hydrophobic (fear water). so regions of a prole in with many non-polar amino acids will try 10 Slay away from water, 111is tendency may contribute to the three dimensional shape of a protein.

Ty~osine has, n. polar side chain but il is still somewhat hydrophobic because of I.fS aromaucny.

AMINO Ac;ws .AND P'WTfINS 11

12 BrocllfMISrIlY

Charged side chains: Aspartate (-), Glutamate (-). Lysine (+), Argini.nc (+), HisHdlnc (+) ma.y take part in ionleinteraetions,

Histidine has an imidazole ring; .il. also offers buffering at physiologic pH 10 protein. Histidine is decnrboJt!ylated 10 histamine (3 vasodilator).

Serine and threonine contain bydrollyl groups which. can Conn hydrogen bonds.

ZWITT£RIONS

Dipolar ions. Amino acids have II dipolar (+ and ») cbarge atneunal pH. From Ute protcnated amino group (NHc"), and ionized cafboltylgroup (COO-).

OPTIC~L "cflvm

Polarized IighLpa~sing Ulrough an optically active sample .is rotated. to lheleft or right. The alpha-carbon of all amino acids, ClICCpl glycine, is bound to 4 differ. ent groups so it .is called "chiral" and Litis makes amino acids optically active.

Cysteine:

• The SUlfllydryl grouj' is animportaat purl of Lhe active site of many cnz.ymcs.

• In addition. two side chains may Iorm a covalent disulfide bond which may join two different proteins or two differcn; regions of the same protein.

CONAGURATION

Amino acidsare in 2 configurations: "L" or "D." In mao. they arc usually L· amino a.cids (remember, L-amino acids and D-sugars).

[L = Ic,,"orotalory ; rotation to theleft]

[D = delttrQfOLalory ; rotation 1'0 the right]

(dexter = Latin WOld for rigllt)

A disulfide bond (Cystine)

Higher orgarUsms contain only L-amino acids illlheir proteins, but V-amino adds do occur in the pcptidoglycans of bacterial cell walls,

EssENTIAL AMINO AcIPS

I. .Phenylalanine

2. Valin!!

3. Tryptophan

4. Threonine 5 .. Isoleucine

6. Methionine

7. Leucine

8. Lysine

Cystine is fonned by a disulfide bond joining of two cysteine residues. Keratin eontains alol of cystine ..

Glycine is used in flrst step of heme sYlllhcsi~:

Glycine + succinyl CnA·_" lj·ALA (6·uminoicvu}inic acid).

Lysine has an aliphatic side chain and a highly basic amino group III phys.it)· logic pH. Blood glycoprereins in diabetics contain glucose linked to lysine.

Tryptophan has the larges; side chuin; it is hydrophobic whhan aromatic ring. Tryptophan deficiency cancausc Hartnup disease ami Pellagra. (Trp .... Niacin) Tryptophan is a precursor of Serotonin (S·HT), Tryptophan is hydroxylated (0 5.Hydroxytryptophnn .. (lnd decarboxylated (0 5.Hydrox.ytryplnmine.

RE1A.I1VELY Es!>ENTIAL AMINO ACIDS'"

1. Hisli{Linc

2. Arginine

Alanine curries nitrogen. from peripheral tissues to the liver.

These amino acids are not essential in dIe short term. A small. amount of Arginine is made in the body. but not enough forgrow.ing children.

Hi~ljdinc is not. made atall,

It is recycled. but must eventually be consumed.

essENTIAL AMINO ACIDS (may be easier for you to memorize these only) These are theamino acids whoseintake is essential for proper body funclion-since they cannot be syOlbesized.

Remember "Pri\lme tim Hall" (PVTTIM HALL).:

PhcIJylwlIJlLuC., Valine, Tryptophan, Threonine, Isoleucine. Methionine. Hjstidine·. Arginine·, Leucine. Lysine ..

Proline disrupts an n-helix in II polypeptide, Proline is uSl!ally Ihe residue at the p·tum in a'plealed shee Is (SCI: secondary structure).

Serine is tile phosphorylatlon sile of enzyme modification. Serine may be dehydrated and deaminated directly. In glycoprotein!!. serine is often linked 10 the carbohydrate group.

Glm umirtcis dearninuted hy glutaminase re.'ll.lilillg in the fonllation of ammonia, IL is <I major carrier of ni,rogcn 1.0 the liver (fromperipherallisslIcs).

AMINO ACIDS AND POOrl!lNS 1.3

14 BIOCNliMlSTFlr

NON-€$SENTlAL AMINO ACIDS

Amino, aeidsthnt can be synlbCllizcd in sufficient amounts in humans or lIml may be made from precursors.

i, a., Arginine (in adults). tyrosine (hydroxyl group on Phe), cysteine, proline.

BIOLOGIC VALUE

The relative ability of a protein source 10 provide all the essential amino acids. Animal sources have the highest biclogic value while individual vegetable sources are 'lower (because they lack enough of one or more of the essentia! amino acids). However. combined different vegetable sources can result in meals of higb biologic value !h(it provide enough of all the essential amino acids,

mr Added

NITROGEN BALANCE

Nitrogen balance is a measure of UIC protein status of the body. Most of the nitrogen in the body is [rom consumption of amino acids. Wh n not nough protein is ingested, the body breaks down its own protein and excretes more nitrogen than wbnl is taken in; the body is ill negative nitrog en balance. On the other hand, growing children with adequateprotein intake will sror more nitrogen in their new muscles Ulan they excrete and will be in positive nitrogen balance.

pH

(-COOH)

BUFfER REGION

This is the area where theleast amount of change in the pH occurs with the addition of a bose.

DISEASES OF MALNUTRITION IN CHILI mEN:

1.0

Buffer Region> I.e;"" amount of ,....._""--., change ln pH whh LlII: addltlon of base,

Kwashlorttor

This disease is due 10 lUI inadequate intake of protein, but an adequate irll1lke of calories. Symptoms: Unpigmented hair which appears reddish. fauy liver, edema due 10 low serum albumin producing a protruding abdomen ("pOI belly").

Titration Curve

'Marasmus

Disease due (0 lin inadequare intake of calories and protein. Total caloric dcficicncy and protein deficiency. Symptoms: Retarded growth. emaciation. "cachexia", but no low albumin or edema,

Of

Added 0.5

PROTEINS

THE PEPTlbE BONO

Amino acids arc joined linearly by peptide bonds which are formed by a reaction called dehydration. One molecule of H20 is produced per peptide bond formed, The peptide bond has a partlU] double bond cllllrnctcr and is rigid.

PEPTIDES

2 amino aeids joined by a peptide bond arc called a dipeptide; many amino acids joined by peptide bonds are called polypeptides. By convention polypeptides are written From the N-Icmlinal to U1C C-tcnninrtl. (Amino end 10 carboxyl end-remember A before C)

3 4 4.8

6

7

pH

AMmo ACIDS AND PROT£INS 15

16 B,OCHEMISTRY

H 0 I II

_---+H3N-C-C-O-

I

R2

the same polypeptide chain (actually 3.6 amino acids pc.r lura). Hydrogen bonds are parallel to the axis of U1C helix, lind U,C R-groups come off the sides. The a-hclix is !I rod-like structure and in man is usually a righI-hand d helix. The side chains point away from the center of the rod. An a-helix is disrupted by Proline. Regions with many charged or bulky side chains (l.e., tryptophan) can also disrupt the helix.

jl-Ploatod Sheeta

There arc two types of j}-Plcalcd Shoots, Pilrallel sheets and Allti-paralle' sheets. Hydrogen bonds occur between '2 different polypeptide chains or

2 regions of the same chain. .

Peptide Bond

Parallel sheets run in the same di rection as compared to their terminal ends:

N.TcrlllinaJ

Rigid Unit I

C·Tcrrninal

N -lr----l-----Ii----l-----rr----l-----ii

o H 0 Ii 0 H 0

H 0 H 0 H 0 H

N .J ll J. .ll. L H .l c

Anti-parallel ShCC1.9 run in opposite dirCGlions:

C --------------------------------------- N N --------------------------------------- C

STRUCTURE OF PROTEINS

A protein may consist of a single polypeptide chain Or more than one chain. 111e ultimate shape of a protein is tJ1C result of U1C following:

1. PRIMARY SlRUCTlJRE

equence of amino acids ill polypeptide chain, Le.:

N-Icu·met·-glu-vnl-ala-Icu-gly-gly-phc-C

Theprimary structure is important for deciding the higher structure of proteins. h is simply the amino acid sequence. II also determines the location of dlsu I fide bonds.

3_ TERTIARY STRUCTURE

The overall 3-dimcnsional shape of a protein. Most proteins are globlf/ar. Some proteins arojibrolls, like collagen. The tertiary structure is the result of the combination of the primary structure. secondary structure and the Intcraclions. between the different side chains. l.c.:

a-HoliK

The a-helil!: is stabilized by hydrogen bonds. Hydrogen bonds are between a carboxyl and an amino group, and occur four amino Ii.cids away in

• Covalent disulfide bonds between 2 cystelnes. This anchors two chains and is found in proteins designated for export. Hydrophobic side chains are oriented tothe inside of globular proteins and away from water.

• Hydrogen bonds between the sid' chains of threonine and serin

• Ionic interactions between the charged side chains,

Remember:

Hydrophilic amino acid side chains arc usually located on the outside of proLeins, Hydrophobic amino acid side chains arc usually on the inside, Charged amino acid side chains are usually IOC<lLed on t.he outslde of proteins. ovalent bonds in proteins also include IJII~ peptide bond and the sulfilydril bond.

2. SECOND-'RY STRUCT\lR£

IF present, .it is Ihc.rcsull of hydrogen bonding between thc C= of one peptide bond and the N-H of another P 'ptide bond, This hydrogen bonding produces regularly repealed structures, the most important of which arc the a.·helix and ~-pleated hccis. However, these structures sre not present ill <\11 polypeptides.

AMINO A.CIOS Nit) PRoTEJNS 17

18 B'QCflEMlsmv

Domains: . . . 'th' th

Tertiary structure may result in separate highly organized un~ts WI .m. e

same polypeptide often with distinct functions, i.e., an acnve sue or blDding site of an enzyme.

Bends may fonn from the steric reilltions.ltip of amino acids aWII.y from each other.

4. QuATERNARY STRUCTURE • . • . I

Some proteins arc made up of mUltiple subunits, each of wlUch.conlrun a slIlg c polypeptide chain, Tbese su.bu~L'> joi~ to form a single ~roLell1 held logeth.er by Ute same forces Utat mamUllO ter,tlary structure. The number of .subumls and their spatial arrangement compnse quaternary struc.lUre. 10 general, .fe~eralpolypcptidcs make n protcinftmcilorllli. Examples Include: Hemoglobin and Myoglobin.

Naermin»! oll1illo acid:

1. Sanger'. method

Fluorodinitrobenzcne labels the free amino group 011 the N-lerminnJ of a polypeptide with adinitropheuyI (DNP) group. Then, acid is used. to hydrolyze aWRY Ute remaining amino acids in the chain and the labeled N-terminal amino acid is idenlilietJ using ion exchange chromatography.

2. Edman'. IReagent

Also labels the free amino group OIl the N-tcnnina1, but the labeled amino acid can be removed from the rest of thepolypeptide chain and Lhe process repeated untll the entire amino acid sequence of a small protein can be determined.

DETERMINATION OF AMINO ACID SEQUENCE

Therefore, EdJJlWl degradation removes one amino acid at a lime, sequenlially. Phenyl isolhioeyanaleis used in this process,

HYDROlVSIS

The dehydralion reaction Illat forms the peptide .bond em! be rev~rsed by a reaction called 'Iydrolysj,f. In II strong ~CIC;t sol.ul1o~ lit 43 C (110 F) :~r 24 hours aU thepeptide bonds of II polypeptide cham WIll be broken and the individual amino acids released.

A sample comalning One type of polypcptid~ is ~)'drolyzed _ Llt~n placed in. an amino acid analyzer. which uses 2 steps 1.0 IdentIfy and quantitate the ammo acids in the sample:

1. Ionic Exchange Chromatography

In an acidic solution. amino acids have a posit;vechargc .and become bound to .Q. negatively charged resin in the chromatographic apparal~s. Then, solutions of varying pH and ionic strength cause ~he amino aCIds. to become negatively charged and rcl~ascd frol~l th? resm. Each type ~t amino acid is identified by the specific combinarion of pH and rome strength at which it is released. Then each of the di Ifcrem . types. of amino acids goes onto the !lex.1 step, This tells you which amino acids arc in the original polypeptide,

2. Spectrophotometry

Amino acids arc labeled with f)inhydrill using l~cal. A: spectrophotomcrer measures the absorbance of each labeled ,1I00no ".tld. The amount of light absorbed by each type of amino acid i~ proportional 10 the amount of that amino acid in lhe original polypeptide (i.e., Ih~ most abundant amino acid absorbs the rnOSI light. amino acids present In the same propertlon absorb the same amount of light),

Absorption f lighl III 280 nm: Trp > Tyr > Phe > Leu

It is possible 10 determine the am.in~ acid sequence (primary SLruCIU{C) of a polypeptide by using the followmg methods:

C-lemu'nat amino acid:

1. Hydrazlne

Binds to the -COO-s in the peptide bonds but not to Ihe -cOO- al the end of the C'lenninlll; litis la.Sl amino acid can be released nnd identified.

2. Cartloxypeplldase

An enzyme that cleaves the peptide bonds sequentially startlng QI. the Cterminnl, Carboxypeptidase is a zinc protease,

SEQUENCING OF l..oNOER POLYPEPTIDES

Larger polypeptides can be cleaved into smaller fragments, and dIe sequence of these fragments can be determined. By using different agents (to generate Iragmems thnt overlap): the entire sequence or larger proteins can be determined.

Cyanogen Bromide

Cleaves polypeptides at the carboxyl side of methionine.

Trypsin

Digestive enzyme produced by tile pancreas which cleaves polypeptides on the carboxyl side of either (lrgitrine or lysine. (Acts on the basic amino acids wiUI cationic amino side chains.)

Act~ as 1\ scrim: protease.

Chymotrypsin

Unreliably cleave.'! polypeptides at the carboxyl side or tryptoplrall. tyrosine, Or phenylalanine (aromatic amino acids). AclS as a serine protease (most pancreatic enzymes are serine. proteases).

PlromNS COMPOSED OF MULnPlE POLYPEPTioES

The quaternary structure of some proteins arc composed of subunlta madc up of more than one kind ofpoJypcptide chain. Denaturing agents disrupt the

AMINO ACIDS AND PROTEINS 19

20 Biocfl/!.MISTRY

ENZYMES

'Kioase:eatalyzes reactions adding or removing nucleoside triphesphates (usually ATP).

Dehydrogenase: removcsH'

ENZYME-6UBS1'RNTE COMPI£X.

The inlermedi!ll.c product of an enzyme c8taJyz.ed reaction.

kl• "2' k, ::; Rate Censtants

forces that maintain tertiary and quaternary strUClllrc, This separates Ute different polypcpl.ides so they can be sequenced .. The 2 common denaturing agents are: U .. en and GuauJldine hydrocb1oride. Afler the indlviduel polypeptide chains are separated they may undergo amino acid analysis.

ENEROY OF A.cnVATI(lN

The amount of energy which must be added 10 areacdon 10 allow il. to go forward. Enzymes (CIlI.IlIYSl.'i) decrease the enc.rgy of activation,

Energy of Activation

Km=k2+k3 kJ

Free Energy

Fn:IlJi;nergy Un~otutyzcd _01 ACOVlltiOU

. ~':"~}- l

: CIlt:aJy;wd reaction

.. (the: catalyst decreases the Energy of ncuvatlon)

SUBSTRATE

TIJC substance which is recognized by the enzyme and is transformedInto the

product by the reaction. .

Reaction---

PRODUCT

TIle product is. the substance formed by the interaction of the substrate lind enzyme. Removal of the produer helps thereactionto proceed.

ACTIVE Sri!

I. binds the specific substrate

2. thepart of the enzyme which is calaly,tic ..

'REACTION VELOCITY

This Is UIC rate that II. reaction occurs.

AmNITY

Attraction between enzyme and substrate

CATALYSTS

Ca!nIY~lB increase the speed of u reaction by itlwerillg the reaction '8 energy of acuvanon,

SPECIFICITY

'~le binding site of lin enzyme mlly be so "specific" thai it recognlzes and binds 1.0 Oll~y one optical isomer of II given molecule: or may beless specIfic

lind recogm7.c several closely relaled molecules. .

Isomerase: converts one isomer 1.0 another Epimcrilllc: ccnverts one eplmer 10 another Carboxylase: adds carboKyt group '10 a molecule

Lock and Key 1'heory

Substrate andenzyme always fil each other,

/,!duced Fir Theory

Substrate an.dcnzYflle fir mlly at birufing,.

ISOENZVMES

Ellzy.mes which have different amino acid sequences, but catalyze the same reacnons .. (Isoenzymes have different electrophoretic mohiJilies and nre made of ~iff~ronl pn:>l.cins.). For axample, LDH or Lactate dehydrogenase or H4-whichIs found m the heart and Iddncy r: and M.4--which is found in liver and

skeletal Dluscle. . .

E.NZYME

A protein catalyst, which may require II vitamin or mineral cofactor. Buzymes may increase the rate of a reaction between uthousand and a million limes the uncatalyzed rate, Enzy!m:s also lower thetemperature al which reactions take place to 0 temperature compatible witlllife. Bnzymes. catalyze .OO(lctiOl1S by decreasing the free energy of activation (Gibb's free energy of aotivation). The active site is a small crevice whichinitialjy weakly binds substrates, Metal ions may net us cofaetors oy keeping an enzyme in its active conformation.

22 BIOCIIf'M15TRY

AMINO ACIDs 111'10 PROTEINS

21

HOLOENlYME

An enzyme which requires a co-factor 10 be active.

2. TEMPERATURE

increasing the temperature increases the rate because more molecules can achieve the energy of activation, until the increased .Iempera~urc causes t~le protein in the enzyme to either de/om! to a conformation thaL IS not catalytlc, or to denature.

APoENZYME

Protein part of a holoenzyme,

Co-F'.lCTO R

Vitamin or mineral. Apoenzyme + ofactor = Holoenzyme

3. pH.

Different enzymes have different optimal pH values for a maximal reaction

rate.

PROSTHETIC GROUP

A co-factor which is permanently cornplexed with its enzyme.

KINETIC ORDER

Homotropic enzyme substrate molecules: the binding of subs'mle causes enzymes to have a oonfonnational change, which increases the binding of other substrate molecules and the velocity. The homotropic enzyme's mbSlrate is alseits effector.

Zero Order

AuOSTERIC ENZYME

An nllostcric enzyme, contains another site, different from Lhe active site, ~It which MI effector binds. Positive effectors ;11CreOSI! the rate al which Ule nzyrnc wiU c.1Ialyz.e II reaction. "ogotiv effectors slow the rate. These enzymes IIJ'C often Ihe [mlstep or branch peint in fI metabolic pathway, wi!h the product of ihe pathway serving IlS II negative effector and excess substrates as positive effectors.

Zero Order

Reactions where the rate is independent from substrate concentration.

Heterotroplc enzym substrate molecules: different Bgand interactions. A positive heterotropic effector is all activator . .A negative hoterorropic effector i an inhibitor, (This does NOT change the equilibrium of th reaction.) 1110 Heterotroptc enzyme has a different molecule a.~ lin effeclor (i.e., tho end product of the pathway).

V", K{S]U

ALlOSTERIC ENZYME

An allosteric enzyme may increase or inhibit substrate binding. Substrate bhlding (0 one site CRn alter other sites, The plot of substrate concemration VS. velocity is sigmoidal, and does N T follow Michaelis-Menlen kinetics (which is a hyperbolic plot). (See plots)

FIrat Order

Reactions where the rate is dependent 011 the substrate concentration; the rate decreases over the time as Ihe substrate concentration decrease. s, The rate is proportional to Ule substrate concentration.

V", K{S]1

second Order

PHOSPHORYLATION

Activating or inactivating regulatory enzymes. TIle reaction is catalyzed (or activared) by pho.sphorylase kinase. Par example, inactivcpllOsphoryiase bis activated (0 phosphorylase a. II is deactivated by phosphatase,

v = K(S]2

v = velocity Of rate of reaction, [S) '" substrate concentration, K .. rate CORSlnn!.

FACTORS THAT AFFECT THE RATE OF A REACTION:

MICH.t.ws-MENTEN EQUATtON

8Jlzymcs that follow Michl.otis-Menlen kinetics have a hyperbolic curve (unlike allosteric enzyme reactions, which have a sigmoid curve).

Assumes:

I. IS] much greater than [E], so all binding sites are filled

2. [ES) is constant

3. [P) is low

1. Su851R.ATE CONcENTRAnON (5)

Iacrcaslngtbe substrate will increase the reaction rate until all of UIC enzyme bjnding sites are occupied, at the Maximal Velocity (Vm). Remember, the

enzyme is like a door nly so many people can go through at once.

AMINO ACIDS AND PROTEINS 23

24 B,OOIIEMISmy

v = ·Vm[S] Km + [51

INHIBITION

v = veloclty

Vrn = maximal velocity at saturation

Km = Michaells 'onslant; the substrai concentration which gives half the VOl.

k., k2• k) = Rate onstants.

A. R£vERSIBU!

L Competitive

Mechanism: Inhibitor is shaped similar 1.0 the substrate and temporarily competes with it for binding sites.

Reversed: By mcreasing (S) (subslr8te conccnnation)

Km: Higher (II (inhibitor concentration) increases Km-simulating decreasing enzyme-subSlr8lC afflDity.

Vm: Not changed

Kill =.!Q±.!QI kJ

Competitive Jnbibilor of enzyme thai increases K.n' bur has NO effect onV_.

Micltnelis-Menten Plot

Competn .... e Inhibition

+lnhibitor

Vm ----------------------:,:-:.,::-,_,,- _---

(hyperbolic curve)

112 Vmax

Km increases

Knl (5]

Km

[S ')

2. Non-Competltlve

Mechanism: Binds temporarily 10 enzyme somewhere other than active

site but halts catalysis. Has the same effect as reducing [E) (enzyme concentration)

By increasing [E)

Not changed

Lowered

When v = In VOl, then Km::::; (S] Higher enzyme-substrate ojJi,dty ::::; Lower Km

A lower affinity of the enzyme for the substrate means a larger Km,

IJNEWEAVER-BURKE PLOT

TIle Lineweaver-Burke equation rearrange the Michaelis-Menlen equation so Ihul tJ1C line plottedis Slrnight which makes finding VOl easier.

1"" Krn +_1_

v Vm(Sl Vm

Reversed:

Km:

Vrnax:

Non-eompetiuvc inhibition decreases V . and has NO effect on Km. This inhibitor binds 10 both enzyme and't!nzymc.Substrolc complex.

Non-c.ompetltlvG InhlblUGn

Ltaeweaver-Burke Plot for example

lIYmall

,

/ +lnhibllur

, ,

, ,

liS

AMINO AciDS AND PRaWNS 25

B. IRREVERSIBLE

IrroV81"81ble InhlbltOQl (fton.compettthte InhlbH.o ....

Bind covalently to enzymes and penuanenlly inactivate them (i.e., organophosphates, used in nerve gO.5 and insecticides, bind permanently 10 acctylcbollncstcrase) are not plotted on Michnclis-Mcnten graphs,

Free Energy (60)

Allt)sterie Emym_

Usull.lly these arc multimcric (Hb, a2~2).TIlcy catalyze irreversible reactions and are usually the commined step in the pathway-s-and tile slowest step of the reaction (like HMO CoA rcduclal-lc). These enzymes are found at metabolic brach points.

Reactants

Rca.cUQIl -->

Non~Micbaeli5~Menten (Allosteric Enzyme, Sigmoid Curve)

Free Energy ( .... 0)

II2 Vmax

Reaction -_>

BIOENERGETICS

COUPUNO

Coupling r~actions will cause a reaction to occur that would not normally occur. II WIll encourage the other reaction 10 occur by changing the reaction fr?1O a +.60 to II -.60. A large negatlve free energy reaction will "couple" ~IUI ~ smalle~ positive ~rec energy reaetlon 1.0 yield an overall Tlcgorive renelion. Illl:.:iO of~TP IS -7,3?O cal/mo! because of the high energy phosphates. Therefore. In the K+IA rPase pump, the overall sum of th reactions will lead LO a spontaneous reaction because 60 ;; +S .j- (-7) ;:::: -2.

EN"ntMPY ('&H)

dH is the change in heal of reactants and products (i.e .. the heat given off with lighting a match).

ENTROPY (AS)

6S is tile change in randomness or disorder of the reactants and products.

EXAMPLES OF ENZYMES

FREE ENEROY

AG = The chungc in free energy. If 6G is negative, then the reaction occurs spontan 'ously. rf 60 is poslti ve, then the reacticn does NOT occur spontancously. flO" = the: char) c in free energy under standard condition» (standard free energy change).

AO "" AH-TAS

R = 1.987

T "" {> K = °C + 273

I . \ • •. i :..

A6parUltc I:r'tln;\!curban.J

'\

licJCokiiulSfl' ,

(NO~ g]u.oo'ki:na~)

P&O"lpbofrUotokio,AS~

ll.GO::; -RT In Keq

Pyruvate kinase

~TP . I

AMINO Ac/OS lIND PmmilNS 27

28 BIOCHEMISTRY

I "

hi

Avi<Jjn

Decreased (iflinjty of bemoglobin for oxygen results from: Increased levels of CO2, increased levels of 2 .. 3-DPG (diphosphogJycerllte) in RBC's. acidosis or lowered pH (tho Bohr effect), and increased temperature (all sltifllhe oxygendissociation curve to the rig"t).

Decreased partial pressure of 02 will decrease lite percent of oxygen saturation of hemoglobin. Binding of carbon monoxide and cyanide 10 Hb is tighter OllID oxygen. binding to Hb. Carbon mouoxidc ,inhibits cytochrome oxidase and tnerefore cellular rosplration. Carbon monox ide binds to Hb at the same site as oxygen. Deoxyhemoglobln is stabilized by sail bridges that cross-link polypeplJde chains. Deoxyhemoglebin is a wenker acid than oxyhemcglobln.

Methemoglobin cannot carry-cxygen since the iron is in the ferric state (Fe3'·). Small amounts of methemoglobin and carboxyhemoglobin are found in normal people.

Glycosylatcd Hfl: Hb Ale concemratlon may be increased in patients with diaberes mellitus. The amount of glycosylated hemoglobin depends on the glucose level in the blood; a normal value is between 3 [0 9% of the Hb (<<zP::-gJucose). The Hb AI concentration reflects the blood glucose level for 1I1eprevioos few months. ori'd is helpfulln assessing if the patient is compliant with insulia trCDtment and diabetes control.

Siclde cell anemia results from substitution of valine' for glutamate at position' on the p-chnins in hemoglobin (HbS). Valine has 8 neulral charge., and it replaces glutamate (-I). The sickle shape favors the dooxy foun and Lhis leads to a cri is.

HbC is another hemoglobin variant !bat has II modified j3-chain lit position '. but in HbC, lysine (+ I charge)'repJaccs glutamate.

PhO$P~9Q: a,se :ehosph~ Pyroval~ carb ;Il)'l~ Pyruvale de~yd.mQO~Ase I

1s.ociftalO d~ydrogC)1a.SeJ F'rucUtse~l ,6JbiSphQ phulIISe Glycogen synthetase

ICiIrl),I.e O(UC08e-6- PhQ$pbate

PvRUVAT! DEHVOROOErtASE

Involvedin oxidatlve decarboxylation. lt uscs COraClO!':I, like the o-kctogluIn~al(l dehydrogenase reaction, Pyruvate dehydrogenase reaction joins glycolYSIS 10 the T A cycle, Arnulrienzyrne complex: is used in rhis reaction.

PAPAIN

Proteolytjc enzyme with esterase, transamidase, and lhiol protease activity.

PROENZVMES (INACTIVE ZYMOGENS)

Proenzymes arc PI' 'cursors of enzymes like: trypsin, chymotrypsin, pepsin, and carboxypeptidase (N01' ribonuclease).

PEPSIN

Pepsinogen is released into the sternach, and this proenzyme is activated by acid hydrolysis 10 form pepsin. It acts as nn acid protease or carboxyl I)' lease and is activo only ill the ncidily of the stomach, (Hycif IY7.es peptid bonds at low pH.)

OTHER PROTEINS

The majority or proteins ill U1D body ar norenzymes, but the structural pr -

tcins thet make up most of the tissues Of rhe body. .

HEMOGLOBIN (HB)

Hemoglobin is a globular protein made UI' of 4 polypeptide chains; 2 alpha and 2 bela ~hajll!i, Hemoglobin A subunit structure in adults: Clz'h. Each chain contams 0 heme molecule. A heme molecule contains one iron 310m (Pel+ or ferrous stme for normal hemoglobin), Each iron CRn hind I oxygen molecule (02), Therefore. since there nrc four chains in a heme molecule, a lola] of 4 oxygen can be carried by each hcrn globin. Th maj( r rib 01 bjrtJl:

HbF, with subunit structure f1..z'Y ,Hemoglohin . binds oxygen lighter than HbA docs. Hemoglobin an transport Oz.

AMINO ACIDS lIND PRoTEJ/'IS 29

30 BIOCllEMlsrnr

OLYCOSAMINOGLYCANS

GlycosnminogLycaos include: hyaluronic acid, heparin, chondroitin sulfate, hcparnn sulfate, dermatan sulfate. and kcratan sulfate. (NOT collagen). Glycosaminoglycans are in the extracellular matrix of connective tissue,

PROTEOGL YCANS

Proteoglycans == Protein core + Glycosaminoglycans. Protccglycans arc found in &«!u nd substance.

COUAO.EN

Collager; goes through Hydroxylation then giycosyfmion. Three pro-a strands join to Forni II singlclriplo helix preeollagcn strand. (Gly-X- YHO Iy-T -UHOly-. , .) The procollagen strand is transported from the cell, Segments of the N and C terminals of the polypeptides are removed. These procollagcn strands spontaneously form the triple helix collagen molecules kn WI} as troPOCQII(lgCII. Then, crosslinks between the strands form. This occurs between 11 Iysyf 011 om: strand and a Iysyl on another strand (11..'1 well !IS hydroxylysyl),

Unlike elastin, collagen is sriff. Type I collagen is found in bone and skirr. The primary structure of procollagen contains many lysines, hydroxylysines, and glycine .. ely ine allows rotation (0 occur within the procollagen strands, 01- lagen is the major protein of connective tissue, tendons, bone, and cartilage. II contain. increased glycine, proline, alanine, hydroxylcucine, hydroxyproline, and hydroxylysinc residue)'; as H re 'ull of IJOSI-ml/lslatiotl(ll modijicQlioll. Collagen requires ascorbic add in order to hydroxylate. SClln'Y results from a deficiency of Vitamin C, nnd results in increased bleeding, loose teeth in gum and other problems associated with collagen defects,

ELASTIN

Blastin is also found in connective tissue and will stretch (clastic properties) and recoil. Enzymes culled elastoses can brenk the elastin fibers down. A deficiency in a}-anlitrypsin can result in the chronic obstructive pulmonary disease empitysema. Normally o'l-llnlirrypsin inhibits elastase. ]f there is a gene defect, and the liver cannot produce the a,-nntiLrypS~lI, then the individual muy develop thls loss of pulmonary function (Non-smokin ' cause of emphyscma).

K£RAnN

Keratin is II protein or intermediate filament found in eplthellalcells (epidermis). JI is high 10 cystine and sulfur (due to increased disulfide amino acids).

IMMUNOGLOBULINS

Immunoglobulins are structural proteins made of pairs of polypeptide chains (light and heavy chains). Immunoglobulins are also classified according 10 the properties or the H chains. Immunoglobulins form the antibodies. Light chains are the K or }.. chains. Heavy chains determine the Class: IgO = 'Y. IgA = ex, IgM ... 11, (gD '" 0, 19B." E. (For more 011 imfmmog/oblllilIS. refer W Microbiology &: /l1JJmlllolo8Y of this review series,)

MYOSIN

Myosin is found in skeletal muscle, and myosin fib rs are th "lick filaments (15 urn), Myosin is COnsidered an ATI'(lse involved in contraction-it binds LO the thin filaments,

Oxygen Dissociation Curve

p02 In tlssues

20

o

100

% se. 60

(% SUI. = % of binding IImL is lchicvcd)

2,3-DjPHOSPHOOLYCERATt (2,3-0PO) ." ,

Also known as 2.3~blsphosphoglyce(ate. 2,3~I?PO IS an IRlcrmcdia~e Ih~t plays a role inregulntiog the affmily of hemogl.ohm for ox.ygc~. ~t pbysiologic pH. 2.3·DPO has a nct negotlve charge. In ~d blood' cells, It infhiences the oxygen affillhyand. binds to deox.ybemoglobm (T form of Hb)-NO'! 100:<'Yhemoglobin (R form of Hb). This increase in 2,3-DPO causes a sllift 10 tbe right in the exygen-bindlng curve.

PORPHYRINS

porphyrins have side chains attached to ea.ch ~f the 4 pyr;ole rillgs.(\n example is uroporphyrin Ill. Congelli/of erythropoietic {JOrpIIYflO can be diagnosed by the pathognomonic type I porphyrin in .the u~lne. AC~/e intermittem poryphyria is NOT photoscnsaive, and results m anl~crease ~ &-ALA and po~hobilinogen. The urine darkens ill the pre.<;coC4? of bght o.r ru.r. Sbm~ med_lCatlOnS are contraindicated in porphyrias (i.e., barbIturates), smce U1017 IS an tncrease in cytocllfomc p450 and heme 10 produce cytochrome p450; thiS decreases the amounl of heme even more.

AMINO ACIDs IINO POOTEINS 31

32 810CHEJdlsmr

ACTIN

Actin is in skeletal muscle, and il is the thin filaments (7 nm), 111Crc are two forms of actin: the Fibrous (F-actin) ronn and the Globular form (G-nclin).

TROPONIN.c

Troponin-Cinili!ltes skeletal muscle COli traction by binding Cilicium.

HOMoomrlSATE _

Otherwise known as "A lka[Jlon".'This acid is an lntermedlate of tyrosine breakdown Ih(11 accumulates in "black urlne disease." or alkaptonuria (autosomal recessive disease). It is caused by a deficiency of hornogentisaie 1,2-dioxygenasc. It is part'of'the dclrrndntionpnthwuyofPhenylalanjnc ........ Tyrosine ........ fumarate + acetoacetate (Lack ojhomogeTlJisate oxidase).

IONOPMOR£S

lonophorcs form acomplex with u certain ion and can increase membrane permeability La the ion. In some circumstances, antibiotics can act as ionophorcs. They have 11 hydrophilic inside (carboxyl groups).

HEMI! OEQRADA.OON Hemoglobin----+- Heme + Q~bIn

(The conversion of Heme to Bilirubin is the only reaction in the body [hal makes carbon raonoxide.)

Bt.OOD

o, CO, Pe3+. NADP~ HEME\...._4'Biliverdin _. Bilirubin

.In blood) ---------------------.f-------------------------

OUirobin.Albumin

(In liver) ----------·----------l~-liDP-gi~:;~~i~-~~i-d---·

Bmrubin diglucuronlde

(till. b the eonjllg_led f{N'!n "r nlllrubln)

(In InLutlne) -------------------Jr------------------------

BILE

+

BilirubIn

-.

Stercobilin .. . Urobilinogen (no color)

i!locn:!od [n 0],. [".""01",, (kldnoYI "~C!1:!O til urlee)



Urobilin!> (brown &10.0) color)

Tho average life span for a red blood cell is 120 dnYH,

SVNTHESIS OF HEMf;

The Ilynlhesis of heme occurs in all cells except mature red blood cells (beCOllSC they lack mitochondria).

Succinyl eoA + Glycine

Y AlA .• fcylltflll.fe (lsi commuted step)

ill milOdwndria 6·amlnolevul.onll: add (ii-ALA)

iiicYfOSO;--- -------~----.---.- --rAiA'diii;,;/i-;;J7;;-- --. --------------

_________________ . Porphobiltnogcn (linCilr structure: " mclcculcs needed)

Photo~ell~hlvc I .• PorphClbllinogtn deaminnse

2, Uroporphyrloogtll c"~ynlh(lUlse

(~d end) (rillt alrucurrc) (iJcnd end)

Uroporphrrinllgclll Uroporphyrinogcn m-e- Uroporphyrin In

,. t dccnruox.y.IA5C (inhibiled hy iron ~nl15)

Coprophyrinogen I Coproporphyrlnogen III

----------- --------------- ------ -----------. - f'!~~~::e---- --------- - ---- _

1)~r4irl ",lwrllQ/ldr;a Protoporphyrinogcn IX

ProIOPO~I)Yrin IX

Fc" ~ rcmx:lw!'\IJ'sc'

l'fEME

"ALA dehydrase and :Pcrrm:hcla'asc (Ire UlI: IWO enzymes nffccted by lead pflis(miflg. Therefore, ALA andccpropcrphyrinincroasc.

Stercobilin'

n,us is the degraded product of hemoglobin Ilia. creates the brown color of feces.

IypeO Blood Indlvldllall (Unlvsl'l" dono,.)

Type 0 Blood indivlduals have the H speeiflclty on glycoproreins in secr~ lions. They haveihe H geneand produce fuccsyltransferase, TIley have 81111- A and anLl-.B anubodiea in Lhe serum-'Ihey do NOT have A or B antigens.

Type A Blood Individual. . c c

H8.ve anti-B antibodies in lh.c serum. They have the A antigen. They cannot receive a blood transfusion [Tom type B blood. The A antigen specificity may

I

Q

o

1

-

I=Q

~ I

~

'"

~ a

H r

~~ ~-~

,---.-----~----------

34 BlocHEMlsm ...

be determined by !he terminal monosaccharide on the oligosaccharide of glycoproteins and glycoliplds.

TypeB Blood individuals

Have anti·A antibodies in the serum. They have the B antigen.

Ty,pe AB ,Blood Indlvlduala

Have A and B antigens on gJycoprolcins in body nuids, They also synthesize the H antigen.

Bleeding can be caused by:

Decrea.fed tnromboxane A2, Viuunio K, Pactor VITI or antihemophilin A factor, and ~-aotiplasmjn.

Thrombos'- (clottlng) i5 prevemed by:

Prostaeyclin, Heparin, Dicoumarol, Antithrombin III (NOT antiplasrnin).

thrombin

Bnzyme formed from prothrombin that cause s blood clotting. Removes Iibrinopeptides from fibrinogen. COil verts fibrinogen to fibrin (NOT plasminogen to plasmin).

PlasmIn

An enzyme with proteolytic action that dissotv s a clot. Acts as a fibrinase.

33

36 BlocHEMlsmr

PHOSPHATE

o

I O=P-O

I 0-

DNA AND RNA

REPUCAnON

DNA

DNA

RNA (mRNA, tRNA,. rRNA)

NUCLEOSIDE

A nucleoside is a nitrogen base and a penrose su.gar. Most anti-cancer drugs are nucleoside ana Jogs.

TRANSCRIPTtON DNA

TRANSLATION mRNA (codons)

1 tRNA (anti-eodons) + activatcti amino acids rRNA_"'"

Proteins (structural. enzymes, globins, contractife, etc.)

NOCl£OTlDE

A nucleotide is a nucleoside plus pbosphate joined at penrose sugar; nucleotides are tho building blocks of RNA and DNA. Also. nucleetides serve as the medium of energy exchange inside the cell, most commonly in the form of ATP.

Remember, )lQU "translate" nucleic acids 'lifo proteins.

AlP (ADEHoSINE TRIPHOSPHATE)

A ribose nucleoude which stores energy from catabolic metabollsm in its high energy phosphate bonds.

NITROQEJt BASES Pyrimidines: ("CUT')

Cytosine (C), Uracil (U), Thymine (T) Purines:

Adenine (A). Guanine (0)

fo-r-o-r-Q-H~do BASE (adenine)

000 Phosphate

OH OH SlIsar

Note that the basic structure of the purines is an imidazole ring joined at carbons 5 and 6 of the pyrimidine ring. The sum of purines is equal to the pyrimidines.

PENrOSE (5 CARBON) SUIlARS

H--C=O

I

H-C-OH....:-

I II-C-Oll

I

H-C-OH

I H-C-Oa

I

H

Ribose

H-C=O I

H-C-B1-

I H-C-OH

I H-C-OH

I

H-C-OH

I

H

DNA (D£OxmIBONUCL!lC ACID)

Polynucleotide chain formed by joining together deoxyribose nucleotides with phospbodiester bonds between the 5'-hydroxyl and the 3'·hydroxyl groups on adjacent deoxyriboses. By convention, the sequence of DNA is written (rom the free 5' end of the molecule to the free 3'·hydroxyl end. DNA encodes instructions which comprise the genetic code. Ribose is converted to deoxyribose by the enzyme ribonucleotide reductase. This enzyrnc insures that Lbe amount of Adenine will be equivaJenl to Thymine, and Guaruno equivalent to Cytosine.

RNA (RI80NUCtnc ~CID)

Contains ribose nueleotidcs and the nitrogon base Uracil instead of Thymine (see below). [I is involved with carrying out the instructions encoded for by DNA. The penrose phospbate pathway makes ribose. The 2' Hydroxyl group con be ionlzcd; therefore, RNA is less stahle than the DNA.

Deoxyribose

35

DNA, RNA. lIND PRoI IN SYNTHESIS 37

38 B,OCHE.MISTRY

DNA AND RNA PURINES = Adenine, Guanine

DNA P'l'RIMIDINe; ::::l Cytoslne, Thymine

P"LlNI)ROME . .

A short series of nuclcotides whieh has (he same sequence ~~ 1':1 cOIll~lem~n.

lary strand and is read from 5' to 3' ... 11 can be read I~e same ~n ellher (hrccILO~ (i.e., S'-GAATTC-J' .......... 3'-CTrAAG-S'). Notice lhol III the e~~~lple,. J[ reads th same in the 5' 10 3' dtrection, GAATI'C. An BeoR 1 restriction Sl~C can allow eleavc3ge and fC-lIliglll11elll with other genes 10 clone and express

genes.

RNA PYRIMIDINES "" Cytosine, Uracil IluE PAIRS

Nitrogen bases form complementary base pair8 by hydrogen bonding between 0))0 purine and 01\0 pyrimidine. The sum of the purines is equal 10 the pyrimidine . Charkors Rule is A=T and G=C, so as long as you know one of ihe values, you can calculate the other three, In humans, 30% is A (30% is therefore 1) and 20% is 0 (20% is therefore ). for II total of 100% of bases.

• Guanine only base pairs with cytosine (3 H-bonds; O=C)

• Adenine base pairs with a thymine from DNA, or an uracil from RNA (2 H-bonds; A=1", A=U)

• Base pairing can hold 2 di.H:"c.rcnt poJynucleotidcs logethet

read
S' 3'
G A A T T C
T T A A G
3' 5'
read EcoR I restriction site

MELlING nMPERATURE

The more O-C bonds between I.ho two strands of dsDNA. the more they arc stablllzed. This willincrease I}IC Tm (melting temperature) 1.1.1 wttich tbe two strands will separate.

DNA STRUtmJltE •

• Double Helix, xcept in some viruses (ParvovlflJs s. hav~ ss,DNA),

2 IlnlipandleJ polynucleotide chains aile strand runmng ~ -;-3 and the other 3'-5', held together by complementary base painng. Contained in C)llOplm'f1I ofprokaryctes (before the nucleus). Conlained in the nucleus of eukaryotes (true nucleus).

TIle middle of the helix. is held together by IlydroCt!TI bonds.

• Is Lliildly acidic.

Milochondria nave their own DNA. .

.J' 10 5' plwsplwdie.\'ler OQ1I(1.1' hook the nucl.oolJdes ~ogelher.

MOSl proteins bind in uic major grQ{)ve.~ (not the mmor grooves).

NOOI.£ASES

NucJea es are enzymes which hydrolyze ph sphodlester bonds

Endonucl8M8

Break polynucleotide by cleaving at nucleotides inside of III chain.

3 TYPES OF DOUBLE HEUX .

B form: rlghr-handed helix with 10.5 base ~alrs per turn. '. •

A fonn:right.bandcd helix will, 11 base prurs per tum and IS formed by

dehydrating B foml.. '. . ' .

Z form: fe/t-ha.nded helix with 12 base pairs per turn occu~ I~l small

sections or DNA. It has an alternating anI i- and syn-glycoSldlc bond

conformation.

Exonuclease

Cleaves auclcotides (rom the end of a polynucleotide chain

RestrictIon Endonuclea&es

I3I1,,-ymes, produced by bacteria and viruses, which recognize and cleave nl short specific sequences of a polynucleotide called palindromes. The e enzymes are used in genetic engineering. 'They arc bacterial detense mechanisms used 1.0 fend off an invading DNA. They protect by mcthylaticn,

~~o:"~:~eRLlS "before the nucleus;" it. includes bacterin and blue-green algae.

PROKARV011O DNA

One large circular DNA chromosome located in the cytoplasm

no nuclear membrane to hold on 10.

. ince there is

DNA. RNA. AND PROrE:IN SYN1HI£SlS 39

40 8IoeHEMISTflY

PLA6MIDS

Small cir ular DNA molecules also found Jn 1JI0 ylop/aslII of some bacteria code Ior extrachromosomal genes. Replication and inheritance of these gen cs is independent from lhltl of l11e chromosome. M re limn one ly.~ of plasmid Illay be present in a bacteria and a single bacteria can have hundreds of plasm ids. Pia mid genes have often boon found 10 carry genes encoding for anubiouc rcsistcece. Under certain circumstances plasmid DNA is lncorporsted into the large circular chromosome and irs DNA is lhen replicated and inherited with it.

MITOCHONDRIAL DNA

Circular DNA chromosome similar to lJ1C large bacterial chromosome.

EliKARYOTIiS

Eukaryote means "true nucleus." ukaryotes arc highly organized organisms; plants. animal s and single-celled organisms, except baeicria nnd blue-green algae. Their genetic material is contained within an intracellular nuclear membrane.

ElIl(ARYOTtC DNA

DNA organized into chromosomes andloceted inside of the nucleus.

CHROMOSOME

Prokary tes have 1 bug> chromosome which replicates and divides at the lime of cell division. Eukaryotes have much more DNA, which is divided into 11 number of chromosomes. Every organism has a specific number of chromosomes (46 in humans). 'ach chromosome is replicated and Ihen evenly divided during cell division assuring thai each cell gel' ~he righl number of chromosomes. HUmans arc dtplotd meaning III t therc arc 2 of each of the 23 types of chromosomes (one inherited from the father and J from the mother).

Heterochromatin

This is very denseJy packed and inactive chromatin.

euchromatin

111is is active chromatin;

REPUCATION OF DNA

DNA __,.. DNA

Replication is by semieonservative replication:

PACKING OF DNA

After replication each of the flew double helixesis made of one original strand

and one newly synthesized strand. .

I. Double stranded DNA unwinds and 2 single strands are exposed fonning a "replication fork" which move. s along the cham as DNA is repheated, This OCcurs in b011l directions WitJl 2 replication forks in an anti-parallel. 5' to 3' direction. These processes arc facilitated by the following enzymes:

DNA HelIcaM

Binds 10 single stranded' DNA at the replication fork. and opens the double stranded DNA similar to pu hing a zipper apart, This unwinds the DNA, and it requires ATP to open the DNA.

Helix-de.tablllzlnc protei ..

Bind' to and stabilizes single strands of DNA. Th belix-destabiJi7jng proteins arc also called ssONA.bindil1g proteins. As 1110 replication fork proceeds it causes twisting which is relieved by topoisemerases.

NUClEOSOMES

DNAisorgani1.cd into clumps called nucieosames by complcxing wid) histones. giving it the appearance of "threaded bends." DNA WI<lpS around IJ10 histone 2 limes. A nuclcosorne is a DNA-wrnpped histone corel ~!!:'!~

!JII'iIiU'_' ....... _

~~~~~~~~~~-u~~~~~~-9~.~~~

TOPOtaomerasn

Type I (swivelase) binds 10 IlIId cleaves orr of the single strand, .. of ON A (nuclease activity), allows the .DNA to untwist around the axis of the pbosphodiester bond of l11e inhlcl DNA strand and then reconnects the siQgle strand (li8a~o activity).

Type D (gyra.se) binds 10 and cleaves botli single sLnnds at the same time and results in negative t.wlsling which relaxes both strand., und then reseals the strands. Quinolones inhibit DNA gyrase.

HISTONI!S Small arginine nnd lysine rich basicprotelns:

-0- .1-1 I I molecule c mplexed with thread portion of DNA.

-0- Histone core is formed from 8 histone molecules around

which -140 base pairs, rc wound comprised of:

H2A 2 molecules H20 2 molecules H3 2 molecules H4 2 molecules

uc-

Connect two strands of DNA end to end, This enzyme seals the DNA strands. The process requires ATP or NAD+.

2. Primasc (1lII RNA polymerase) uses triphosphate riboauclcotides to form II short strand of RNA complementary 10 DNA near the replication fork which serves as th.e double stmndedprlmer necessary for DNA polymerase

CHROM~Tf"

Further packing of DNA due to hydrophobic interactions and in association with other non-histone proteins compacts it into chromatin.

DNA, RNA. AND PRoTEIN SYI'fTH£SIS 41

m. Later, DNA polymerase I (exouuclease) removes the RNA primer and replaces it with DNA.

3. DNA polymerase m reads each of the old strands in the 3' to 5' direction and uses the appropriate triphosphate deoxyribonucleotides 10 synthesize new complementary strands in the S' to 3' direction. The energy to drive these reactions is provided by the high energy triphosphate groups; these are cleaved QJ1d Iorm the monopbosphatee thai are incorporated inlo. the DNA chain. DNA polymerase JlI also proofreads !he newly syolhe~uzed strands removing any incorrect nucleotide and inserting the correct OnC. This enzyme IS supposed 10 correct the 1110,000 mutations occurring during DNA replication. The 3'-5' exonuclease aClivity (proofreading) allows Cor checking the new cbain as it grows in the 5'-3' direction.

4. The new strand being synthesized complementary 10 the old 3' 1:0 5' strand is called the leading strand and can be synthesized without interruption (it is copied continuously),

5. The new strand complcmcutary to the old 5' to 3' strand is caned the lagglogstraod and is synthesized as [r~gmonlscallcd ,?kazaki rr~gmc~ts, which arc later joined together by ligases. The laggmg strand IS copied "discontinuously" .

42 BIOCHfMISTRY

Types of polymerase DNA Polymerase (l DNA Polymerase j3 DNA Polymerase Y

Funcllon

DNA replication DNA repair

(replication in mitochondria)

Template sequence 5'-ApCpTpGpGp-3' would make the complementary structure: S'-CpCpApGpTp-3', This is determined by forming C for G, and A for T; then, always write 5' ~ 3' (using 3' ...... 5' originaJ sequence). If this

is RNA replication, 'lien place a "0" for any :'A'." .

DNA syntheSis aJway.r occurs in the unidirectional. 5' to 3' direction. DNA synt.hesis alwllls fCQu.i[cs a p"!mer-RNApolymcrase or primase is required (RNA syntheSIS doe not reqUIre a primer).

DNA REPAIR

1. RADI.lTlON

u.v. endonucleaae

Removes pyrir.nidipc-pyrimidine dlrners that occur, usually between l~O thymines (T-T), in the same strand due to exposure to ultraviolet hgbL Then polymerase 1 or 11 fills hi the gap with the appropriate nucltolidCII •. Dimers can lead tb mutations. There,fol'e, fipdinglhc mis-

take and repairing it is lmportant, .

PROKMVOT£5

Have I site of initiation of replication celled the "origin of replication," or replicon. In DNA repair or excision, DNA polymerase f recognizes the .gap (nick), removes the RNA primer, and flUs the gap. DNA polymerase IU IS responsible for synthesizing tho new DNA.

Xerodenna Plamentosum·

I?isease oocurriog in people who cannot repair. dllmage caused by U.V. Iight, oft~n due 10 a defect or deficiency in V.V. endonuclease. This leads [0 skin cancer-malignant melanoma.

2. DEAMINI.TlON

Loss of an amino group.

Types of polymerase DNA Polymerase I DNA Polym 'rase JI DNA Polymerase 1lI

Function

DNA repair Chain elongation DNA repllcatlon

Alkylatlng Agents

Remove -NA3 groups ~rom A, G, or C, Ioruilng mutant bases,

Nitrous A.cld

Alkyla[ing agcm produced in cells by metabolism of nitrites and nitrates which arc often used as foOd preservatives.

EUKAAYOTES

Have many sites al which replication of DNA may be initialed.

Cytosine

Can spontaneously lose its -NH) group forming uracil.

Mutant Baae Endonuclease.

A group or enzymes each of which recognize and remove a specific mutant base containing nucleotides,

DNA,. RNA, ANfJ PtroTElN $VNT"IIfSIS 43

44 BIOCHEMISTRY

Mutent BaH QlytO,yl .. .,.

Enzymes which rccogllil.e ano remove specific mutant nitrogen bases frernthelr deoxyribose.

L TATAAT known as Pribnow box, -10 bases before lhermlt transenpted DNA sequences.

2, TOTTG -35 bases before the [mi. IrnnSCriPled DNA sequences,

Promoter

DNA TR.ANscRIPnON TO RNA (RNA SYNTHESIS) DNA ---:-+- RNA

RNA

Here are some generalizations for RNA: RNA is single-strandedexcept In some viruses (i.e., Rotavlrus or Reovirus). Il contains ribose instead of deoJlyribose. and uracil instead of thymine. Base pairing may occur within the single strand, Base pairing can occur. between RNA IIDd DNA. There are 3 types of RNA involved in protein syntht:sis:mRNA, tRNA. and rRNA.

5'-//-- TGTIO -------TATAAT------Transcriploo DNA--11-3' 1..-- - 35 bases----+ol

:++1

-10 bases

CONSENSUS SEQUENCE

A DNA sequence which is representative of many 'promolers from different 'bacteria.

PROKARYOTIC RNA POLYMERASE

There is only ene RNA polymerase inprekaryctes, Thisis a DNA·directed RNA polymerase. A holoenzyme iscomposed of 5 subunits: ao;.~~'O' [twoof the ()'. unit, oneeaea of the ~and p' units (~~' = care enzyme), plus II cofactor called <Y (lligma), which js .required for the recognition of the promoter during initiation). Sigma/actor (8 subunit of RNA pelymnrasc) glvesthc specificity of illiliating transcripuon of RNA. In bacteria, both the sigma foclOr and the core enzyme of RNA polymerase are required for RNA synthesis ..

PROI(AJlYOTlC DNA TRANSCRIPTION .INTO .RNA Takes place in Ill\} cYloplasm.

I. INrrI~.'ION

A. short area. of single stranded DNA is exposed by the binding of RNA polymerase lit II site known as the promoter region. A holoc.Jlzy.I:ne (e-factor complex) recognizes !.his specific DNA hinding site, The promoter is the region of DNA LhQ[ binds the RNA polymeraseto initiate transcripl!On. Usually the first base is a purine (Adenine).

II. ELONGA.TION

As RNA polymerase moves along, it maintains an area of single stranded DNA on either side of it. RNA rolynHm~sc. reads the DNA strand in the 3' In S direction and uses triphosphate rtbonuclcorides to symlreslze an RNA strand In the S' 1.03' direction at> ill DNArc:plicalion (aJways grows in the S'Lo 3' direction). There is NO proofreading in RNA polymerase since there is NO RNA ]' 1.0 5' exonuclease Ilclivi!y-lhis results fn more errors whcnlranscrihlng DNA 1.0 RNA (compared 10 the rclatlvelycrror-Irec DNA 10 DNA replication).

III. TERMINATION

1. Rho-independenttermination, In prokaryotes, termination of RNAsynlhc:if:) is coded for by palindrome DNA sequences. RNA transceibed from these sequences ClUJ base pair within the sequence fonnlngs hairpin loop causing termination.

2. p (Rho) facter destabilizes RNA and DNA, and may help in the tcrminalion of transcription.

NOLe: trail scribed is synonymous with lrnnNcriplcd.

PROKARyotES

Promoter allows RNA polymerase to transcribe DNA, and it contains 2. sped fie cousens us sequences:

TyPES OF PROMffYOnC RNA

I. mRNA

Containslhc cedens (Ule 3 nucleotide sequences) which specify each of the amino acids in n polypeptidechain .. m_RNA may be translated into II protein without frnthc.f processing. Translation can begin at the free 5'cud before Ule mRNA is completely transcribed. Prokaryotic mRNA does not cordalll 0 "cap" on ilS 5' cnd--cukaxyoHcrnRNA docs. mRNA contains many "ciarons" (polyclstronic) one after the other, each cistron cooing for one protein. Many proteins may be translated from Ihe some mRNA at the same lime, one after the other, It has a ~l1ort hl.llf·lifc ..

II,. tRNA

Contains theantl-codons which are complementary to the cedens of the mRNA. Cedoas and anti-codons base pair during translation (protein synthesis). Transports activated amino acids; is cleaved from a larger precursor. Dloop and T",C loop are areas lhal do 1)01 base pair. The cloverleaf structure of lRNA is short, has 701090 bases, and n'lI:my unusua! bases.

III. rRNA

A 30S precursor rRNA molecule is cleaved 1.0 form one or each: II 5S rRNA, a 16S .rRNA, and II 238 rRNA Ribosomal RNA.

S (Svodbergunlt)

A measure of the sedimentation role of a. molecule.

DNA, RNA, AND PRoTEIN SrN111ESlS

45

46 BIOCHEMJSTRY

PRoKARV:onc RIBOSOMES

I. The small 30S ribosomal subunit is made [rom two 16S rRNAs

2. The lar~c 50S subunit is made from 5S and 23S rRNAs. .

3. The entire 70S ribosome contains one 30S subunit and one 50s subunit,

chain. Approximately 80% of RNA in cells is rRNA. 11 i' found in ribosomes and the nucleolus.

II. mRNA

• Contains codons (the 3 nucleotide sequences which specify Ute

individual amino acids),

• Tho RNA chai" syn~hesizcd by RNA p<>lymcrasc n is called

heterogenous RNA (hnRNA). .

Some ImRNAs contain intervening RNA sequences called "tntrons" which do not code for amino acids and which mUSI be removed from the chain before translation can occur, and before mRNA is iransporred Qui or the nucleus (post-trtmscripriolla/

ll1odificntiOll).

• "ExQfls" which conlain Lhe codons that ar Irnnslalcd into proteins

are spliced together in II IlTOCCSS which uses small nuclear RNA (snRNA) .. !lnRNA I1r~ small nuclear RNAs, and fU"C found itl Apiiceosomcs. snRN'P, "snurp," is snRNAond Protet« (ribonucleo-

protein complex .. RNP).

• Poly (A) polymc;rase synthesizes a tail connected to UIC 3' end made up of many adcnoNine nucleotidcs of some mRNi\s ill the nucleus; after transpcrt into the cytoplasm the toil i removed.

• Guanosine lriphosphlllC Is attached 10 the 5' end and 11\ '11 gets a melhyl -CH\ group on cnrbon number 7, forming a "Cap" on thot

end. '

• POSI_II,(III.\'criPliollo/lllOoiliClIlion occurs only with I!.ukhryolic

mRNA:

l , Addition of 5'-7-met.Out1nosinc cap helps in tmnsbltion-lhis is

a rare 5' 10 5' linkage.

2. Addition of 3' Poly-A tail for stabilizatlon,

3. Rcmovnl of introns or illl""'61!;IIg S(;(/Ill/liCes.

EUKARYOTIC DNA mANSCRIPTION INTO RNA

• Takes place in the nucleus and then the finished RNAs (except for small. nuclear ~NAs) am transported into lite cytoplasm, where p~t?1Il synlhcsis IIlkes place on Ihe ribosomes.

Slm,l!l!' to transcriptiou in. prokaryotes with the following· exceptions:

EUKARYOTIC PRoMOTERS

1. TATA!AA-known as Hogness box or TATA box -25 bases prior to transcripted DNA.

2. GO~AATcr-knowJ) as CAA"! box -70bas.cs before transcnptcd DNA.

3. GC rich 'lr~as (GC boxes) occumng approximately 40 to 11.0 bases before the transcripted DNA.

5'-II--(GCOC--.1--0GTCAAT r----·TATATAA---- trnnscriptcd DNA--II - 3'

I - 40·11 0 bases I

I....,_ - 70 bases _...

1 ..... 1

- 25 bases TRANSCRIPTION FACTOR (TF)

TF is .sin1i1ar I~ the prokaryotic sigma factor. Transcription factor binds to DNA 111 the major groove.

EUKARYOT1C RNA POLYMERASE

T1_rcre are 3 types of RNA polymerase

RNA polymerase I: synthesizes a 45 precursor rRNA wtucn .i. cleaved to form: a 5.8S, a 18S. and a 28S rRNA.

RNA polymerase II: synthesizes mRNA.

RNA pclymerasc III: synthesizes tRNA and UIC SS rRNA.

EuKARYOTlC RNA

ukaryotic .mRNA is always monocistronic. RNA is single stranded (ss), it has a lIe8t1II~e. charge at ~clltral pH, and it has Ribose. usar (not deoxyribose D~A~. Modlly cukaryotic IllRNA aner transcription with ]'-polyadcnylalc

rails. Ihc 5'- aps only occur in eukaryotic mRNA. .

TyPES OF EUKARYOTIC RNA

III. tRNA

Contains IInti-codons complemenlary to mRNA codons. A CCA sequence Is

added to the 3' ond. Contains unusua! nitrogen bases-nol analogs (N-acctylcylosinc, pseucouracll, and dimclhyladenioc). Made trom larger precursor.

EUItARVOllC RIBOSOMES

• The small 40S ribosomal subunit is Formed from two 18S RNAs.

• 111C large 60S ribosomal subunit is formed from proteins and the

5S. 5.8S, and 288 rRNAs.

• The entire 80S ribosome is ('onnc,d from one 40S and one 60S

ribosomltl.snbuniL

I. rRNA

45S precursor synthesised by RNA polymerase I is cleaved 10 form th 58S ISS, and 2BS rRNA chains, RNA polymerase III synthesizes the 5S crRNA

RevERSE TR~NSCAIP110N

SYI\lhcsis of DNA from RNA using viral "RNA directed DNA polymerase."

POST-TRANSCRIP'TIONAL MODIFICATION

Again, uris is modifiClltion of RNA. It com occur by rne addition of terminal

sequences; for example: althc3'cnd, addition of 5··CCA-3' 10 the (RNA. Also,

DNA, RNA, AND PnOTEJN SYN'I11ESl9 47

methylation of bases (mer-Guanine) and methylation of sugars (2'·OH gTOUp can be methylated), Furthermore, cleaving a ribonucleotide or removing introns.

IF·2 binds to the i-IRNA-fon7l,Y1 methionine and they bind to the 30S subunit.

TRANSlATION Polypeptide (protein) SynlhesiR

As the large 50S ribosomal subunit re-assoclates with the small 30S subunit fonning It complete.ribosome and the initiation factors are released.

Release of the i.nhiation factors uses energy from GTP (guanosine lriphosphal~) being cleaved to GOP + Pi.

The Initiation complex has now been assembled.It includes:

TIle complete ribosome (30S and 50S ribosomal subunits) bound 10 mRNA at the Shinc-Dalgerne sequence.

RNA _.. PROTEIN

Polypeptides arc syl1thesiY.c<i from thc.ir amino 10 their carboxyl end. PROMARYOTtC PROTEIN SYNTHESIS

I ... Aatlvatlon

Each type of amino acid is activated by joining [0 AT? using Ii specific aminoacyl-tRNA synthetase (Activation with ATP).

TIle speeifip aminoncyl-LRNA synthetase iA also responsible for binding each typo of amino acid 1.0 its correct tRNA.

TIle amin acid~monophosphate-LRNA is called II charged IRNA.

The energy to drive these reactions comes from ATP btillg Cleaved to AMP and 2 inorganic phosphates (Pi + Pi).

II. Initiation

An 70S ribosome complex. is made of 308 and 50S ribo:,-ollwi SIIIJllTlil s ; the ribosome contains amino (A) and peptide (P) binding sites, (Note:

Streptomycin inhibits initiatioll.)

IF-3 binds ICJ the 30S rlbnsomal subunit and causes Ir to dissociate from the 50S subuelt, <IF", initiationJactor)

Then, mRNA and IF-I bind to IlIC small 30S ribosomal subunit.

The iniliator-tRNA-formyIOlethionine. with ils anticodon (CAU) base paired to the mRNA's codon (AUG), held in U1C ribosome's pep tid (P) site with the ribosome's Amino (A) site is vacant.

• Eukaryotes have several eukaryouc initiation factors (eIFs).

• Thc initial fonnylmethionine amino acid COIl later be removed from dlCpolypeptidc.

III. Elongation

The mRNA al the A site contains the next codon.

When another charged LRNA-phospho amino acid moves into the vacant A site, its anticodon base pairs with the mRNA codon and it also binds 10 the ribosome's A site, 111is process consumes GTP and requires the elongation factor, EF-l'lI ..

The 5' end of each J\1RNA has 1\ Shine-Dalgamo sequence (5'-AOCAGGA-3'), about 7 bases before the first codon, (Not a 5'-Guanosine cap like cukaryotcs.)

Peptidy! transferase, an enzyme thaI is pari of the 50S subunit, catalyzes a reaction that forms a peptide bond between the carboxyl group on the amino acid at the P siteand the amino group or the amino acid at the A sne. (Puromycin and Chloramphenicol. inhibit elongation at this srcp.)

The J 65 rRNA of the small ribosomal subunit has II sequence complementary to the Sbinc-Dnlgnrno sequence which binds 10 it.

The polypeptide grows from the amino side (N-tcrminal) to the carboxyl side

(C-IenninuL). .

M 'Iilionine binds to a specific inililllor IRNA (i-IRNA). Arter binding 10 ;-IRNA methionine receives a formyl group.

N lO·formyltctrnhydroJ''ohllt! is the formyl group donor in II reaction catalp_.cu by methionine transformylasc.

Formation of the peptide bond is driven by Ole hydrolysis of the pnospharc bond from the P site amino acid. This results in an uncharged P site I.RNA no longer bound to all amino add, and the A sire tRNA being bound to 2 amino acids (0 dipeptide).

111C ribosome looks For the first AUO mRNA codon that it comes to. TIllS fk'lt mRNA codon (AUG) always codes for the amino acid methionine,

And the whole process above may be repeated.

Bukaryotes also have termination factors (eTF} that will end synthesls.

DNA, RNA, liND PRoTEIN SYmHEsIs 49

50 BIOCHEM/STRY

(Telracyclines preventeloagation.) IV. Tramlocatlon

(lransJocate tRNA-peptide complex from the A site to the P site)

The ribosome moves 3 nucleotides down toward the mRNA's 3' end.

Polysorne

The uncharged tRNA is released.

The dipeptide tRNA moves to the P site,

N~\" P,'prill".

-'I c.--- .... r>" ,-------- .... ----------

J ") ".,)

5'--- -- ndlNA- g-- --- ---a--- --- --~ --- -- -- ---J'

A new lRN A pbospho amino acid binds to the A silo consuming another mO.Iecule of GTP and requiring EF-Tu, and elongation is repealed. (use 20TP'sJ peptide bond)

GENmCS

OP£RON

DNA of the regulator. promoter. operator. and structural genes,

Diphtheria toxill alters BF-2 and SlOpS elongation-CWl'1 translocate, (ClIndamycin and Brythromycla inhibit transtocauon.)

V. rennlnatlon

When ODe of the mRN A Slop CodODS reaches the A site, releasi 118 factors (RF) cause U1C mRNA and the new polypeptide to be released. (Stop codons or non-sense codons ;:: UAA. UAG, and UGA.)

RF-lrccogni .. .es UAA or UAG.

RF-2 recOgnizes UAA or UOA.

Regulator

Genes for repressor protein synthesis. Repressor protein will bind In the opera lor, preventing RNA polymerase from binding to the promoter region; inhibits synthesis. (Prevents transcription of structural genes.) A positive regulator enhances production ofproducts (CAP = Catabolite gene IIcti~alor. located upstream from Ihe promoter).

Inducer

Binds 1.0 the repressor; tnduces or allows synthesis of RNA.

GENEJl'AJ. CONCEPTS IN PROTEIN SYNTHESIS: (nlRNA -+ Proteins)

Lact~e

Lactose activates the lac operon 10 allow formation of: (3..SlllaclosicJase (z gene), galactoslde permease (y gene), and thiogalaclosidc transaectylase (8 gene). (Glucose decreases cAMP and inhibits the lac operon. Lactose increases cAMP which activates the lac operon),

The enzymes produced will break down lactose.

General Sequence:

L Activate amino acids,

2. mRNA. initiati.on factors, join with ribosomal subunits, 3, GTP" elongation factors. join with aminoacyl-tRNA,

4. Peptide bond forms,

S. Peptidyl-tRNA is translocated,

,---------opemrl -------~

Use /riCh energy phosphate bonds when:

I. Activate Lbe amino acid.

2. Bind N-formylmcthionyl.tRNA to the initiation codon of mRNA (joining of ribosomal subunits).

3. Bind amiooacyl-tRN A to active site of ribosome,

4. Translocation occurs.

p

b:::1 y I~

structural genes ~

P()lYSONIE

Many ribo.~ol~lCS n~ay be a~ll1ched 10 a ~inglc mRNA, all of them synthesizing new polypcpudcs. nit entire complex IS called a polysome.

WOBllLE

The nucleotide in the 3rd position Iui.s less influence on which amino acid a codon specifies. For example, the codons CUU, cue, CUA, and eua all 'code for the amino acid leucine; this is called wobble.

Notice that while each 3 nucleotide sequence codes for only one kind of amino acid, i.e., eUA always codes forleucine, other CodOIlS can still code for Lhat amino acid.

The genetic code is called degenerate, since more than one codon can specify II given amino acid. It usually does not matter what base is in !he third position.

DNA. RNA. !WD PROUi.IN SYNmESlS 5.1

RE'STRIOTION ENDOHUCl.EA5ES

This allows the mopping of Ihe genotype used in cloning.

u

R€STRlCnOH FRAGMENT LENDTH POLYMORPHISM ~RFlP)

This hews the genetic diffeten c between offspring. I[ is used Cor many Icgal custody battles. Pb'nolypically we mny appear identical, but 8 nClically there i a difference.

MUTATIONS

Are the result of changes In Ihe mRNA odon nucleotide sequence.

,c

FRAME SHin MUTATIONS

Shirt the reading frame Oflhe entire DNA hain after the mutation. include the following:

Deletion mutation

The loss of a single base either epontaneously or duc 1.0 damage,

Insertion mutation

Acridine lntercalates between adjacenl DNA nitrogen bases and gelS read by RNA polymerase causing the addition of extra bases into the newmRNA ..

, Qly

C .A (;

POI," MUTATIONS

Includ the following mutations where only I Ilucleotid is changed:

G

AI

,PI

Ala

Alii

Gill

TranaltJon mutation

When n purine is substituted by apurine.

When II pyrimidine is sub tituted by a pyrimidine.

The genetic code is represented by a 3 nucleotide base sequence in ,mRNA molecules. The mRNA molecules read from the 5' to the 3' end; thiS short sequence is called a codon.

The genetic code is universal, il is the same in all orgunlsms=execpt in ciliated protozoa and in mitochondria.

CONsmUTlvE GENE

This is a gene Ihal continI/lilly forms a product.

REOUlATED GENE

This is a gene expression based on environmental or developmental facIo':!. For example, golaclO:iid(ue increases when there is no glucose, but [here IS galacl.ose to break down.

TranlVeralOn mutation

Sub. titution of a purine for a pyrlmidin«. Subsutution of a pyrimidine for a purine.

Silent mutation, i. ,UUU (Phe) --+ UUC (Phe)

hange codon 10 another codon for {he same amino ,tcid, 50 hIlS no effcel.

Nonae.nae mutatton, i.e., UGG (Try) ----+ UGA (stop)

Chllnge codon 10 top codo« (UGA, VAG, IIJld UAA) and terminal s symhests,

Mlnen .. mutation, i.e., UU (Phe) --+ UUA (Leu)

Changes codon 10 anethor codon for a ciijferellJ amino acid. If the new amino acid is similar 10 (he old One th synthesized protein might function.

DNA. RNA, ANO PIlOUIIN SYNTlIF.SIS 53

ANTIBIOTICS BY· SrrE OF ACTION

Many antibiotics arc selectively IO~C to C!t.~lcr eukaryouc or prokaryotic organisms because Ihoy interfere with specific enzymes of DNA, RNA, or protein synthesis.

54 BIOCHEMISTRY

C. DNA SY/IlTHESIS INHI8f1'ORS

DNA IYrase Inhibitors (DNA synlllc.~.is lnhibiton;)

QllinOWllfJS hind 10 and inhibit DNA gymsc preventing DNA synthesis.

A. PROTEIN SrNTlfESIS INHIBITORS

DNA topolsomorose Inhibitors Nalidixic acid and Novobiocin:

Both inhibit DNA ropoiscrncrasc, stopping NA synthesis,

305 ribosomal subunit

I\minoslyc(}sides (Le .. streptomycin) bind to prokaryotic 30S ribosomal S~bunit and causes misreading (prevents the initiation of pro~ein SYlltllcS1S~. Tetracycline binds to the acceptor site on the prokaryotic :30S subunit proveutieg it from binding the activated amino acid.IRNA complex.

50S ribosomal subunit

Chloramphenicol binds 1.0 prokaryotic 50S subunit and inhibits pep-

I idyl-transferase.

Erythromycin and Clinl/Cllllycin:

SOUl bind to the 235 rRNA within the prokaryotic 50S subunit and pre-

vent translocation.

60S ribosomal subunit

ycfohcximid/! binds 10 the cukaryotic 60S subunit nod inhibits pep-

tidyltransferasc.

A Dnd P sites

Puromycin is an amino acid analog, Ulllt binds to tile A site and. has an amino group which eMI form a peptide bond. No fUI111e£ eiongalJol1 c~n take place, and protein synUlcsis oC both prokaryotes and eukaryotcs IS inhibited,

eEF-2

Diphtheria toxin inhibits cukaryotic elongation factor 2; interrupting

cukaryotic protein synthesis,

B. RNA SYNTHESIS INHIBITORS

PrOkaryotic DNA..dlrected RNA polymem It

Actinomycin; binds 10 double stranded DNA so that RNA polymerase

cannot read it.

Rifompi«: binds to the ~.subunil or RNA polymerase. and inhibits the

start of I ranscrlptlen.

Eukaryotlc RNA polymerase II. ,

Amllll;ta phylloides-thll "Angel of ca~l" mushroom prod~ces a IOXIIl which inhibits RNA polymerase II stopping mRNA production.

Drug·

Erythromycin . ClipdlJD'lycip

. CYOlohexlmlde

.P~fQmyojn

" I

blpbthctia lolf;in

A~linoll\ycirl D RU~ycin :B (Rifampin) I

A~ta phyUpi(les ,

t' I

InhibitS protein ynthellis (Iran,slatiOlj) by binding to Ule

lOS ribosomal s~bunit. '

JnhlbilS 1l'a1l.ll\tjol by bi.l:ldiu the 30S rlb9S0:tnlll sub~l'lit.

, (qhibiff> 1r#I1SlatioQ by \liJ:!ding to tb 50s llubuqJl luld lJllti~irs pe'plidyI~trtUlIIrcraSo. 1

Bind 10 th 23S rRNA ill 50S ubuni{ (inh~bit '1J'1lOS1 ation it!

pmk!l(yOI6S), .

, Il

fJ.inds ·to tbe 60S sllbul~jl, illhib,ts peptidy1trans(crus , prt?veots ~lation '1\ ~1~otCll, , Binds [Q tI;le A site inld~lt8 pt'l)teiQ.syotJ ~is jrrovc::rs)bly'.

lnh.ibjl1l protein elQ~ls:ation by inllctiva~Jlg 'Bfi2.

Inhjbit~ P£I!f'\-d£p-RNA,sYllU tnh\bjlS D~A-d¢p.RN~ synlh ([qbibit$ ltans~riptlOl'\)'

Acts on ~- U~lJpj~ of ~A poiymerils •

; ,Inhibits RNA synlJ.lcsi b~' blocldns I~NA produ ((OJ), ' (fllll'blts RNA poJYJll.~$e m.

Methotrexate

Analog of folic acid that is a competitive inhibitor of DHfiR (dihydr folate reductase), Therefore, il inhibits deoxythyrnldylatc synthesis,

OTHER MED/CAnONS:

.Amlnopterln

Analog of folic acid, and competitive inhibitor of DHFR (dihydrofolaic reducrase) .. Therefore, it inJlibilS deoxYl.hymidylate synthesis.

CARBOHYDRATE STRUCTURE

5-Fluorouracll

11115 drug inhibits ,hymidy/ate synthas« (enzyme for dUMP _,.. dTMP). It inhibits deo}(ylllymidylate synthesis ..

MONOSACCHARIDES

General structure: (CH_zD)1l where Il= 3, 4,. 5, 6,. etc ....

Fo,rm~la

Ohcero]de,byde 'l"Juoosc, ErytltrO~O Ribose. Xylose, Xylulose

Glucose. GalllctoSO. Fhlctose, M"l1nIlOSO

C)H(\03 C4"110~

C5l-IH;P!l

Aldoses (Glucose, Galactose, and Mannose) are monosaccharides which contain an £lfdellYile.

General strucrure: H

I

(CH20)n-C""O

Glucose is an Aldohexose (the aldehyde group is needed for reduction 1.0 occur):

o CBrboll It 0

II II

Aldehyde -.. C-Ii I. C-H

------------1.----------------9--1 -----

H-C-Oll 2 H-C-Oll

I I

I-IO-C-H 3 HO--C-H

I I

H-C--Oll 4 H-e-OH

I I

I-I--C-OH +-5....... HO-C-li .

I I

H-C-OH 6 I·I-C-OH

I I

H H

I)·Glucose

L-GJucose

56

CARBOHYDRATES 57

58 BICXIIEMlsmr

Ketoses (like Fructose) ar moncsaccharidcs which contain ketones,

General structure:

HO I.

OH

H 0 I II

HO-C-C-( H20)"

I H

JiO

-,--_,1-1

~ ..... --vH

-ructosc is a ketonexosc:

Carbon #

H I

H I

H-C-OH J 1.-1 H

--------------1·------------------------1-----

Ketone -'" C=O 2 C=O

===-------1, ·-------------------------1-----

HQ- -H 3 HO-H

I I

IJ-C H 4 H.-.. 'VH

I -OH

1

-01-1

1

II

D-G1UCQSC

HO I HO-C

I 1-I0-C-

I

H

I -01-1

I

H It

D-Mllnnos'

The above example or epirncrs (Mannosc and Glutose) differ 111 -2. Another CX811111lc would be Gala aose und Glucosc-s-whlch differ [It C-4. '11m enzyme, eplmerase, allows UIC conversion between the two sugars,

Stereol80mere or Enantlomof8:

Isomers that differ aL mor than one position. -nnntiomcl'S II mirror images of each other. Monosaccharides can have up [0 2N stercoisomcrs (N '" lhe number of chiral p sitions), unless Uley have a plane of symmetry.

H

I

-1-1

I -OH

I

H

H

II

6

1-1

Ring Forms (Anomers):

H20H

I CH-O

lis \1

4COH

1\ I 2 1/1

HO OH~

J I I

OH

D-Fructos!.!

LsFructcsc

L or D Configuration

'11C position of 111I~ hydroxyl 011 the second to last carbon of II rnonosaccharide (carbon tl5 in hexoscs) iridicat s whether thai monosaccharide is in the Lor D conf 1I r:1U on. Til' last hydroxyl is on the Jeft in L-Cflrbohydrnl.cs and on the righ: in Dscarbuhydratcs. Enantlomers nrc mirror image: of each other.

arl10hydratcs ( ugars) are usually ill the D form. Amino acids arc usually in the L form.

OPTICAL ACTIVITY

arbohydrares can have nllmy asymmetric chiral po itiona (i.c .• arbons 2. 3, 4, and 5 ill glucose; therefor I 4 chiral posiuons) so they arc optically active. Compounds Lhlll rotate ligfJlto the left arc designated "1" and to the right "d" (dexter is Ihe Latin word for riglu), This should not be confused with L + D con figural ions.

a-D-(+)-Glucosc tdownward H)

(i

CI-I20H I

CH-O OH"'_

1/5 \1

~ COH C I

1\1 2 1/1 I-IOC-C

3! I

OH

B·D-( + )·Glucose (upward OH)

(So,oll numbers lndicnre number ~!IS!lcd 10 ell h carbon)

Hydroltyls on the rigid In the linear structure arc down on Lhe rings. Hydroxyls on thcleft in the llnenr structure {Ire Ill) on the rings,

IsomeT'S and EplmolS

Isomers: Have same chemical or molecular formula, i. '., 6H,'20(\. J~ph)ll.'rs: Arc isomers Lhat differ only at lie posili n:

The ring form is the predominaut form thal carbohydrates luke in the real w rid. If you put a sample of a-glucose molecules into solution some or the molecules would spontaneously mutJirotale and equilibrate with the I~-fonn.

and LO a v ry small extent a non-ring linear Form. .

CARUOHYDRllIES 59

60 BIOCHEMlsmy

Anomai1a

When sugars form a ring., the aldehyde or ketone carbon becomes asymmetric and is called "anomeric." TIle Co: and fl (orms or a monosuccharido nrccalled anemers, If a sugar's anomerlc site can be oxidized to a carboxyl, il [Day reduce another molecule so .il is called [I reducing sligar.

POLYSACCHARIDES (POLYMERS)

Disaccharides :

Are 2 monosaccharides joined by 11 glycosldlc bond.

Carbohydrarcs have "0"- glycosidic bonds since J oxygen atom is. joining the different monosaccharides (p·lA~bond).

Sturchcs are made up of glucose Illollosncchnridcs:

Glycoge1l is the starch round in animnls,il has many short branches: . 0.-\ ,6 bonds occur at [he beginning of each branch and ct-I ,4 bonds along the brunches, Glycogen. contains only o-anomers and Ct~bond5.

Sucrose == fwclose + glucose LuciuS!: == galactose + glucose MIl'lto.se == glllcctse + glucose

(sucrose is in I able sugar) (lactose is in milk) (maltose is in beer)

CellulQse, the structural component. of plants, is unbranched, linear, and has only 1)-1,4 bends which CI)nnOI be broken by human enzymes (p.glucose polymer). Some animals have the special bacterla that have ~"antylasc.

Oligosllccharidcs;

Arc several monosaccharides joined by glycosidic bonds.

Polysaccharides arc many monosaccharidesjoined by glycosidic bonds.

Othe» Plnnt Stareue« are mixtures of unbranched, linear, a-I,4 bond starchesand starches similar 10 glycogen hut with longer branches,

2 types of G.lycosidic bonds:

Dietary starch is digested by salivary amylase. pancreatic amylase, maltase. lind (:(·dcxlrinase (NOT by HCI, nor by lactase),

1. o:~bond:

CLINICAL CORRELATIONS

H:;!9H CH20l-1

I I

II CH H H CH-Q H

1/ \1 II ,\1

C 01-1 Ii C1 ole OH H C

1\1 I/\.oy \1 1/1

HO -C C-- -C OH

I I I 1

H 01-1 H OB

SORBITOL

Sorbitol is NOT broken down in palierlt,,> Willl diabetes (it 'is found in the lens, kidneys, and nerves), In diabetes, there is an increase in the glucose level, 1111S increased Glucose is converted into anIncreased amount of Sorbitol by aldose reductase .

ex-Bond

Sorbitolis converted by sorbitol dehydrogenase into (7ruC\ose.

When there is a defect in the enzymes (usually aldose recJllcum:), this may cause ",aWl)' because fructose is needed for the sperm in sernlnalvesicles,

Glucose - aldose reductase -+- Sorbitol - sorbitol ddlydrogl!ntl.fr! -+- Fructose

2··I1·bond:

CH20H 1'1201-1

I 1

H CH-O H CII-O H

1/ \n II \1 oa Ii C\ 04C ON 1·1 1\11/1 U\I 1/1

HO C-' H C-C OH

I I I I

H OH H OH

(Therefore, if glucose increases, thls increases sorbitol.)

In diabetes, check for reducing .mgar.f (like glucosejinthe urine. ThL~ is "spill over" from \11e blood and is filtered through thckidneys=-ovcrproductlcn and underutilization. Gelnctosemia find Pructosemia nlso cause urine reducing .fllgar.~,

The major dietary source of Fructose is through I.WflQY. Fructose is mainly used by the .Ii ver, II docs NOT require insulin to be taken up mro the cells (Glucose does require insulin). Aldolase B cleficiNlcy patients require fructose restriction from their diel-sucr,,!:c will not help the patient.

I3-Bond

62 BIOCHEMIS1Rr

Glucose amounl cOlltributed by organs:

LIVER> Kidney> skeletal muscle

CARBOHYDRATE DIGESTION

Carbohydrate digestion begins with salivary a.·amylase in the mouth, and !he enzyme can break a-I ,4 bonds (fou"d in starch), In the intestine, pancreatic a-amylase breaks Ct.-1.4 bonds. Enzymes thlll are on the intestinal epithelial brush border include:

• a.-g/ucosirillse breaks a.-1A bonds and also removes glucoses from

the non-reducing ends,

• a-Dextrinas« breaks a.~ 1,6 bonds.

Remember: Cellulose cannot be digested because of its P-I,4 bond.

• Specific dtsaccharidases; i.e., maltase, sucrase, lactase etc., release the: monosaccharides from disaccharide. .. (Lactose _.,. Galactose + Glucose).

• Converts glucose into J carbon compounds which enter the Kreh's

cycle. .

• Oluco~inns: is specific for glucose and is II liver enzyme. While hexokinase IS found in every cell.

TIler' are three in-eversible reactions in Glycolysis:

I. GlucQsa - JIt:xokinQJ"C Gluco.~c-6.Ph()splltltc

2. F,rLJctosc-6-.Phosphatc - fJ!lOspllOjrw:lokina:.-e ---.. Fructose-I 6. bl~phosr~hatc, (l'hi5 is the regillaling step or rare limiting reaction'of glycotysls)

3, PEP - pymvate kinase -. PyrUYIlI

.Iyc:olytl Pllthwoys

CUzO-1'

I

-C=O

PII(}$p'tQl",rl().'1Ias~ I

HO-C-

I -C--OH I -C-OH

I

CHzO-/'

"'",moo; I.(i.dir,ho r,hole

4 Aid(IIIIt<'

+---l ~

CHO

1)"/11"" iSOlllcm,ft I

~ ~ ~OH

I

CH20-{' Glyccrnl()chyd ·1'h!)~ph"IC

fUO

-C-OH I HO-C-

I

- :......oH

I -C-OH

I

CH:_OH

1),CUltO!;.

1

JI~J;Qkl,j(uc 01" (illleoJ<inaSII

Clln'lcal conelatlon: Deficiencies of disaccharidase, such as lactase, produce intolerances that cause diarrhea because Lhey draw water Into the colon by osmosis. Furthcnnore, they produce gas (flatulence) when (hey are metabolized by bncteriu in the coJon to CO2, Lactose intolerance is more common in Asians and Africans, and least common in northern Europeans. If you damage theintestine, you will have problems digesting disaceharides into nlOIiOSIlCcharides. But, you will be able to degrade Slorch bcCIIUSC of the salivary and pancreatic amylase, Lactose maldigcstion may result from tissue destruction of 1110 brush border, and can OCcur in children.

GAlACTOSEMI.

Infant is unable to efficiently catabclisc galactose (because of defective galactokinase), but can synthesize galactose from glucose. A~ a result, there is an increased galactcse-l-phosphatc, II is diagnosed by cord blood assay.

3

ADSORPTION

Monosaccharides are absorbed into imestinal epithehal cells by passive transport and then from the epithelial cells into the blood stream by Ntr'lK· cotransport,

F-6·P

GLYCOLYSIS

Blood carries glucose \0 the cells of the body, where it is transported across

(he cell membrane by carrier molecules. .

• This process is fnciliulled by insulin mainly in adipose and muscle tissues.

• Transport of glucose is 'lot faciliuned by insulin in red blood cells, imeslinal mucosa, brain, and liver.

• Takes place in the cytopl asm ,

• Produces some energy.

CHO I

-C-OI-I

I HO-C-

I

-C-OII

I -C-OH

I

CllzO-P

Glllcosc-6 .. PhosphfiIC

2

CH20

I

1'liosplto/l/llco_rt C = 0

ISOtl/1WI$, I

..... I---.~ HO-C- -+

I

-"-OU

I ~C-OH

I

CHzO-P

I 'ruClllS"'('.I>III)~[1Io"IC

5

CAfiBOHYOflA7 s 63

64 B/()Cf1EIIIISTIlY

o

6 II

C-o-P

()I"....,.f4t.~/, H'bo,pM" IkA1"'""'ff'" I

I H-C-OU

NAO" + PI-~ NADH +11' I

CH'l0-P 1.3·Dlnh 5phoglycCltllIO

°

7 II

1'1i""IWtl)'c_,.16 C--Q-

KlJwe I

H-C---Olf ..._..

ADf- ... ATP I

CH20-P

3.Pho,phoglyc:emle

o

II C-O-

I 1--- __ ... H-C-O-P

I

eH20H

9

o

II ,.,,.,,~c

e-o- k:lnl!ll

I

c-O-P ADI' ..... ATI'

II

CH2 Phosphocllol ">' IIJVI\l.

10

°

II

e-o-

I

c=o

I

til Pyruvale

Step 1#2. Phosphofructoklnaso

Is lh rate limiting reaction.

Acucns are facilitated by high concentrations of AMP, and by fruc-

tos 2,6-bisphosphntc, ,

AHostcric inhibition by cilralo, high concentrations of ATP,. and by

Cataly,,;ed reaction is irrevcrslble. .

linlcal correlation: You may misdiagnose a/rucwkiM.\'.e ~lefl I'lley fructosuria) whlch is a "benign dtseasc," for diabetes. This 15 because the reducing sugars will appear in the urine.

What. you need to know about. the otner glycolylic enzymes nOI specifically dlscusscdis that U1CY arc reversible, do not use or nut~e energy. and are nol regulatory, Just know the functions from the pathway diagram.

Epinephrine activates glycolysis lind glycogenolysis ill muscle. Epinephrine inhibits glycogen synthesis.

8

mUIlUC

b'101we ..__._..

\.._H10

• Hexokinase

In every cell of the body,

Less specific can phosphorylate different hexoscs, •. e., man nose, fructose, glucose.

Inhlbtted by glucosc-6-phosphale.

Has low K . -high affinity 80 can continuo phosphoryllzation even when low gl'lIcose levels are low.

Catalyzes glucose phosphcrylarlou, ill first step of glycolysis. Catalyzed reaction is irreversible.

Hexokinase is able 10 phosphorylate all: D~glucose, Donannese, lind D·fructosc.

The above Is aerobic glycolysis. [0 SOfOC' cells with no mltochondria, red blood cells, and anoxic muscle tissue, anaerobic glyeolysis may also occur. ln aaaerobic glycolysis, Pyruvate is then reduced to L etate,

IMPORTANT STEPS IN GLYCOLYSIS

Rellliatol)l E~mes

These enzymes occur in in:eversibJe reactions. They include; Hexoklnase, Phosphofructokinase, and Pyruvate kinase, and regulate glycolysis.

Step' 1. Glucokinase and Hex.oIdnaIe

• Glucokinase Pound in the liver,

Catalyzes gillcose phospborylaLion in Ihe first step of glycolysis in the liver.

Insulin Jacnitates its actions. High K and high V .

PrimruY~esp<lnsibilitY is to handle increased post-mea.1 glucose surge, CatalYl,cd reaction is irreversible.

GLUCONEOGENESIS

The production of glucose from orgunic precursors pl'oduc~d by glycolysis, ?r the degradation of amino acids, or glY~I'~I. rfon~ tngl~ccrldes. ~~ny .s~cps In gluconeogenesis mak usc 01' the reversibiluy of c()rlllJl~ enzyme SICP~ UI glycolys is. This process occurs ill the Iiv r (90%) and the kidney (I~%). Ihc best way 1.0 learn glu 'on 'ogcllcsi!; is 10 memorize the steps that differ from U1C reverse glycolysis:

CARBOHYfJfI/I rES 65

66 grOCHfMISTRY

Gl.UCON EOGEN ESIS:

PEP (phcsphoenolpyruvate)

[Oxaloacctau; is oxidized to malate and shuulcd across U1C mitochondrial membrane into the cytoplasm where it is changed back to cxalaacetate.]

2. Oxaloacetate is converted 10 phcspbocnclpyruvatc (P "P) by"hospho-

enolpyruvate carbaxykinase.

From 'Iris point glyco'y.~is is reversed until fru itose- ',6-bi,\·pho.l'plwte is formed.

3. Fructose-Lo-bisphosphatc is converted 10 frucrosc-ti-pltospbetc by fmcIO.fe-J,6-bfspho.fphatase.

4. Fructoso-o-pbosphate (using rhe reversible gJyco.lytic enzyme, phosphoglucoisomerase) is convert 'r! 10 gluccse-ti-phosphate. Then. gJIiI·;,ls(!-6-pJIO.l'phatase cleaves the phosphate group. and produces glucose. Glucose- 6-phosplwtose is found in liver (not in skcleta! muscle),

The synthesis of each molecule of glucose COIlJ'!llIles: 4 ATP. 2 GTP, and 2 NADl-I.

OM (oxlllollcetarc)

1 o'n>

2. N,'P carlliM)'kinlLtC r \...ODP+t>

2-.PO (2-phosJ'boglyccmtc)

G-3-P (glyccrnltl.cbyde-3-phosphalC)

( NADH

\.. NAO" + II;'

GLVCOGEN

Contains branched chains of IX-lA-glycosidic links and cx-I.6-glyc()sidic links. Mndc of D-gItJCOSC residues. Glycogen supplies most of Ule glucose released by the liver in the post-absorptive state. 0;-1 ,4-links produce the linear portion of glycogen. and the U-I.6-liuks produce the branched portion. Clinical correlation: normally. the ratio of a-1.4 100.-).6 is 8: I: In a patient. with a glycogen storage disease the rarlo will increase 10 1.000: I (majority comprised of linear chain. rather than the branched chains),

3-PG (3-phosphoglyeeratc)

t

1.3 ·DPG (1.3-dipilosplloglycerale)

DHAP

(dihydroxyacetone phosphate)

GLYCOGENESIS The initial step in giyco;?€n synthesis is:

Glucose-6-phosphfJlc-pIIOspllOglm;0I11I"U'\'e~ Glueosc-f-phosphatc

P-6·P (fruct.ose-6-phosph.31.C)

Then,

GlllCOse-l-phosphatc-UDP-j/iucosc pyropllOsphOlylase ~ HDP·Glueose

("UCliV3tcd glucose")

UDP-Olucos 'lycogeFl syntllilse-(Ihis enzyme adds glucose onto (X-I ,4 bonds, non-reducing cnds)-Gluco,~yl.(4:6)-.translerase lhis enzyme breaks U1C a-I.4 bond. nod creates branches by making a-1,6 bond) ..... GLYCOGEN.

F-I.6-DP (fruclosc-I.,6·diphosphate) 3.!mClos.·J.6.dlpllD"phnliIJr t

0-6·P (glucosc-6-phospluue) 5. glu,·osl:.(j·pllolfll"'ltIs~ ..

GL YCOi1ENOL YSIS

The degradation of glycogen occurs in the cytosol by adding enzymes and water \0 remove the phosphates and glucose. The enzymes arc considered "acid hydrolases' since Lhey work in low pH.

The sequence of events is as follows:

Glycogen-glycogen pllospIJorylase (l-(thjs enzyme adds phosphate and breaks off a glucose from the glycogen chain, leaving 8 minimum of four gfuCOSc.5()n the glycogen chnin) ~ Glucosc-l-phosphate + Glycogen

I. JII the mitochondria. pyruvate is converted to oxaloacctare by pyruvate carboxylase (acetyl CoA increases the activity of litis enzyme).

CllfllJOHYDRATES 67

BI()CllriMISTRY

This glycogca is considered a "limit dextran." As a clinical correlation, MeAnlle'.I· disease is II deficiency hi muscle glycogen phosphorylase; there-

fore, there will be an accumulatlou of glycogen. -

Glycogen then goes l.h.mugh a'Icw more steps: the main enzymes include:

l. Glacosy! (4:4) lrans!emse-(Ibis debranching enzyme cuts all the glucoses off, but leaves I glucose 10 remain on the glycogen branch.)

2. Amylo (.1 :6) e/ucosidase-(this debranchlng enzyme adds water and the

sequence conti niles to remove Glucose.)

Glycogen -+ -+ Glucosc.].phosphab.l-hexokiluMIi -+ Glueosc·6-phosphlllC. Note: Glycogenolysis (glycogen breakdown) will occur if thl!tc is an .increased cAMP, Bplnephrine, Ca2+, fictive protein kinase, nctive phosphorylase kinase. active phosphorylase a, or a DeCTaQ,f(Jd glucose level. The first product of glycogenolysis is GIu.cosc:·I-pbosphate.

CYrOCtlROME

Hemoprotein that transports electrons or bydrogen, Four types: cytochrcrne a, b, c, and d. Cytochrome a has n large standard reduction potential. The brm'n 11M Ilte highest lise ofeytochromclllld therefore. cynnldeClll1 IdlJ. (See table bei()tv for othe;' inMbitors of the cy.tachrome oxidase chni,l.)

KETOSIS

Increased levels of ketones, Ketoacidosis can occur in starvation Wid uncontrolled diabetes mellitus (which mimics starvation because insulin deficiency does not allow glucose to enter many cells). These disease stales result in deflciency of Kreb's Cyc.lc mtcrmedlates and lower the blood pH. If unrrceicd, ketoacidosis may result in deaUl. Examples ofkclone bodies include: Acetone, acetoacetate, ami ~-hydroxybulyf[llC. Ketone bodies arc used as fuel by the heart (Ketone bodies arc NOT used as fuel by the liver).

Ketones arefi)rmed ln the liver:

2 Acetyl CoA _.. Acetoacetyl CoA ~ 3-Hydroxy-3-rnclhylgJutaryl CoA ._. Acetoacetate ~ ~-hydroll.ybulyratc.

O:ddation is the loss of electrons (H") nne! Reduction is the gain or electrons.

III

IV

ACTIVE TAAttsPORT orGL.IJ(:o$E 111'1'0 CEU.S

Requires Nn1'1K+ ATPase active transport of Na+.ll1c m.clhodof transport ig

rhrougbsodium. sndglucose symport. .

MATU.RE. REO BLOOD CElJ.

Mature ROC's do not synthe.sizc nucleic acidsand proteins. They use reduced glutathione and glutathione peroxidase (0 mClabolizeH.:p2' Glucose is metaboliwd by lheglycolylic pathway (anaerobic glycolysis) and the pentose phosphale pathway (pPP).. (Th.e rbc docs NOT fcm1'l ATP by the electron Il"allsport system.) Toe PPP gencrates NADPH. and NAOPH is used to maintain reduced gluwlliioll 06PD is ne.c~ary.PPP metabolizes only llboullO% of the g,lucosc .. Lactate is anend-product of glucose melaoolism.

QUITATHIOHE

Glutathione is a tripeptide. eoruainsa sulfhydl:)'l.group (from Cysteine). Gloullhionc-SH is oxicUied 10 G-S·.s~G. NADPH.depcndcnt glu(alhjonc roductasekeeps il in II reduced 81a1.c. In 1111;1 .rbc,gIUlaihione (when inthe reduced stale) p.fotects other su.lfhydIyl groups from oxidation. G6PD deficient patients may be affected by oxidizing agents like antimalarial drugs, aspirin, irJ/eclioll, lind/alia beans that wiU Jead to hemolysis of rod blood celli and eventually 'Ie,noly.ric anemia. Old rbc'sare vc.ry vulnerable, and yO!lng cells .a:(iC left, Therefore. on the second exposure, there is tess of ani effect. Dielary nnti·oxidon!s include Vhamin. C, Vitamin E, llnd~-cnrotene (Vilamin. A); Hydrogen peroxide is detoxified bythe fol:lowjng enz.ymes: 1. Catalase, 2. Superoxide dismutase, Dud 3. Glutathione pe.rox.id:iRe.

ELECTRON TRANSPORT CHAIN (RESPIRATORY CHAIN} Protons arc transferred across lile irmar mitochondrial membrane. electrons flow through the chitin starting with NADH.llnd end with the final electron carrier, oxygen. In mitochondria, the sites where ATP il:lproduccd arc between:

t. NADH and tlavoptolcin,

2. Cytochrome b and cytochrome c,

3. Cytochrome c lind cytochrornes a, 113.

1 II

NAOH ........ FMN -+ CoQ _.,.. Cytochrome c.hain

Electrons pass thrQugh rhc cyrochrome oxidase chain:

(cytochrome) b -+ C 1-+ C -+ II -+ n3 -+ Oxygen

CAR80nrORATI!S 69

70 BIOClll;MISmy

PENrOSE PHOSPHATE PATHWAY

(PPP or Hexose monopll05phale shunt)

The penrose phosphate pathway acts 1.0 supply NADPH and penteses (S-car. boo slIgon) for nucleic acid synthesis. It also converts pentoses to hexoses and trioscs, NADPH is the reducing equivalent for biosyntheticreactions. 111(~ PPJ> is the only producer of NADPH in red blood cells.

It also forms most reduciog equivalents (NADPH) used in Falty Acid synthesis. In the irreversible first 81.01', G·6-PDH (Olucosc-6-phospblile dehydrogenase) is the regulatory enzyme thai is positively regulated by NADP~. The enzymes of the PPP arc in the cytosol, in the PPP schematic helow, we begin with II 6·carboll glucose, and lose UU} carbon #1 (lIS CO2) to eventually create ribcse-Ssphosphate.

PEl'ffOSE PHOSPHATE PATHWAY:

CITRIC ACID CYCLE (TCA, KRES'S CYCLE)

~Ol1!: Memorize ellery/hill I in thill section. This is a short section and it will likely be cov red on your exam.

CUrie Acid Cycle (TCAt Kreb's Cycle)

NAor' NADPII + H+

Glucose-e-Phcsphete \ ..(';,-PhOSPhOgIUCOnO-a-laclonc

" +

6-Phosphogluconatc

NADP ~

NADPH + Hi" ~~ CO2

Ribulose-5-Phosphate

&I~yoj~ C:MSII~C02

Pyrl'YOIC ?""I:I: 'III~IW

[ NIIIJII ~11t

f£~:'I'" ),yr9l'l1()'pi,.,. O;ll:IlI()JI(;ellilt~>-'""'C:O~A"'~1I Cit r,\l"Itc

.11",1< Id

6rfti')'/~( 1\

(sod.rDlf

_..__----- Ribose-5·P

r

Rioose-S-f>'" XyluI0S(:·5·P ....... Olyecrnldchyde-3-P + Se()ohepwIQsc·7.P

NI:.'T;

The ~ilri.C ~eid Cycle is inhibited by an anaerobic environment. arsenite. (or other inhibitors), mnlonare, and fluoroacetutc (NOT Iluorouraeu).

F.AD aCI~ O.S ~ cofactor for the cxidaticn of succinate, FAD fJ/(ivill adenine dinucleotide) IS the prosthetic group of succi note dehydrogenase.

COfl~CrliJ1g Su~cin8le directly 10 oxaloacetare produces a maximum of 5 ~ TP s. (NOI goms through cilrale-2 ATP's come from PADHz' and ATP's come from NADH.) The t.o18.1 number of ATP produced comes from:

3 NADH x 3_:; 9 A ~P--(Malale-Aspal1alc Shuttle)

+ 1 PADHl X 2 = 4 A fP-{Olycero.I-3-phosplwleIDHAP Shuttle) ± J CITP .. l ATP

S..,d(>l~pluI0$<:·7·P ... ClyccrnJdenytlll·3·.P .... UryUlrosc-4·p + FruCIO e-6-P

Z X)'IIIIQ«C.S-P + Rlbose-S·P .. _' (]lyccroldchydo·3.P·~ 21':1')(1<=-6.1' Enzymes include;

Isomerase, transketclase (requires thiamine pyrophosphate), transaldolase, cpimerase.

PPP is ,I very active pathway in tissues that synthesize lipids or steroids (adipocytcs, adrenal cortex, lactating mammary glands, and the Ilver), Percentage or metabolized glucose by this pathway varies for different tissues of lit· body. Reactions OCCur in the cytoplasm of the cell. CO2 ill generated from glucose in the red blood cell from this pathway. PPP activity is very low in skeletal muscle,

This is 12 ATP equiValents per Acetyl CoA

x 2 .Acelyl CoAlgIucose = 2410ltJl ATP.

There are 1111'00 NA[)!'-dependcnl dehydrogcnascs: IS0ci I rate. t1ehydrogcmlse. a-Ketoglutarate dchydrogenase, Malate dehydrogenase.

CAllllOllYOllArfS 71

Pyruvate dehydrogenase lind a-Ketoglu/tlrate deirydro8ent1,l'e require the following cofactors in the mitochondrial complex: oA (Coenzyme A), NAD+, FAD, Lipoic acid, and thiamine py,rophospllllIC.

Thc vitamin B complex is imporrant in the oxr'dal!Q~r ~J ilia/me, '~Jld fa:: !h: decaroxylalion of I)-keTOglutarate. flurthcrmorc, 1I IS unportant III creatmg Acyl-GoA intermediates.

Remember, the Malare-Aspanale Sf"dlle occurs in the liver. kldney, and heart (0 generate 3 ATPINADH. T!lC Glycerol- -p"~splJaleiDNAP Shllll/e occurs in skeletal muscle and the brain to generate 2 A fPIFADH2·

GENERAL STRUCnJRE OF UPIDS

THE CORI CrCLE

Exercising muscles converts glucose from the blood into Iactntc, This Inctatc then enters the blood, and is changed by the liver back to glucose (and the

cycle repeats itself).

H I

II--C--OH

I H-C-OH

I H-C-..()I:I

I

H

o II

-O-C-R

o II

~CHz)Il-CH3

.~atty Acid (FA)

Saturated Fatty Acid

Glycerol

The Cori Cycle

o II

-O-C-[(CHZ}rl-CH=CH-(CH2)n]n-CHJ

Unsaturated Fotty Add

Liver

Triaeylglycerol (TO) CI" VEftS08 TRANH=ATTY ACIDS

The more trans-falty acids, then the worse off you are for health (thick, hard fat)1 Remember, the "softer' the buuer=-the better the flu. This is why olive oil is 0 "good" oil, sincelt has the least amount of ',Oris-fatty acids.

5ATURATl!PFATTY ACIDS

Saturated fatty acids occur Ilaturally as cis-rauy acids. They have no double bonds and almost all the carbons have 2 hydrogens auached to them, so they arc "saiurared with hydrogens". Saturated falty acids include: ~t.earic acid, and

72

LIPIDS 73

74 B,OC,H1MISffir

Lauric acid. Furthermore, Pahnltle acid (16 carbons) find stearic acid (18 carbans or 18:0) are the major human saturated fally acids. (When we write 18:0 Ll'IiS means 18 = 11 of arbons, and 0 = lilt: number of double bonds.)

MONo-tINSATlJR_ATEO' FATTY ACIDS

These fully acids have I carbon-carbon double bond (-"CH=CB-). Palmitoleic acid (16:1, with the dcublc b nd at carbon #9), and Oleic acid (18:.]) ar the major human mono-unsaturated FA 's. Many plants lind vegetable OIls BIC muno-unsaturated fauy acids, and therefore nrc good for you.

POLY-UNSATURATED FATTY ACIDS

These Iauy acids have marc than one carbon-carbon double bond. Examples include: UrlOleic acid (18:2). Linolenic acid (18:3). and arachidonic acid (20:4). Linoleic acid and Linolenic acid are considered essl'lItfol/aIlY acids, and must be taken in. tromtlie diet. Arachidonic acid is II 1J!'!C'.!fSOf for Dro~!.!1~!?::~;;;; uno teukctricnes. Arachidonic !!.l:id may be essential ir there is lillliied dietary linoleic acid=since linoleic acid forms arachidonic acid,

.ARACHIDONIC ACID'

Arachidonic acid is sy ruhesized from essential fatty acids. It forms cicosanoids (20 carbons) like: Prostaglandins. Icuk trienes, lind thrcrnboxancs. Essential folly acids (like linoleic acid Irorn thc diet) (onns linolenic acid which forms Arnchidonic acid. Arachidonic acid is released from the membrane: by phospholipase A2. (See diagram below)

DIGESTION

Dietary triglycerides enter the small intestine where bile salts-produced by the liver and stored in tile llallbladder-are secreted and emulsify the triglycerides, Then, pancreatic liposes cleave the triglyceridcs into free folly acids and 2-monoglycerld s. These hydrophobic compounds aggregate into small droplets called "micelles" which are absorbed at the intestinal microvilli. Bile 5[l1tS are then reabsorbed in the ileum and then reprocessed in. the liver.

2· MonQglyceride

Prostaglandin & Leukotriene Synthesis

LIPIDS

In fat tissue, lriucyfglycsrol (TG) is synthesized ill/VI cells front precursors. lt is a fOlly acid ester of glycerol TGin the ehylomicron is degraded by lipoprotein lipase (from adipose tissue) into fmc fUlly acids (FFA's) and glycerol. The PFA ofTG is the major energy store of the body. Glycerol is used by the liver and forms glyceroJ·3-phosphiltC.

OICI~'1' Linoleic Id

I

PhoSDhoUpid , ... , .... y..u"i. Arachidonic Add

{htlllrl !-tIIIM:I'nl!ilWII} WI'>I!! 1.:1' "lid 1'0 ~yntl,oll. i. ,,,hil,lled by Co}l,lcOJI.oroIJo)

11\11 NSAlOI (lI.pin". ImlomcIJl3CI". phonylbUluono) l"hlbi!I>(l.Ylllhui.]

,

The bulk of dietary lipids arc triacylglycerol, Lipids are part of the membrane structure, and are in oluble in water or hydrophobic. They are transported with protein in rh body as "lipoproteln panicles" (l.c., cbylcrnicrons, VLDL. LDL, and HDL). In lipid digestion, liplds in the duodenum are emulsified by "detergents" or bile salts. The main function of bile acids is lh formation of micelles. Bile salts holp ill the absorption of cholesterol. Fatty acids with a chain length less than 12 carbons will pass lhrough the mucosal cell directly into the blood stream. The primary she tor lipid absorption is at the mucosal cells of the intestine.

1

Lcukotriene 1\,.

/"-..

L:fBd LT II LTD4 LTE4

Pro lagl ndln (I'GG1)

1 ... ",-,_

Aspirin inhibils the. cn7..ymc Cycl(loxygell(Js . II therefore inhibits the aynthesis or prosluglulldillS nnd Lhrolllbo~anos. I\s yO\1 can sec from Ihe diagrum, h. docs NOT inhibilliplJ"ygf!fIlJSe nor the synthesis of lcuk.oiricnc.",

Lipases break down lipids (TG'~) (0 micas Ole fatty acids. Lingua! lipase degrades TO's in the mouth, Gastric lipase degrades short 10 rncdium-chuin llpids, and works III a pH of 4 10 5-wltich is the pH Or a hal}), 's stomach, but not very useful in adults. When a food bolus reaches the small intestine, pancreatlc lipase acts as all esterase and removes fatlY acids (from It I and 413) or the triacylglycerol. Furthermore, phospholipase A2 removes a flllly acid off em, and cholestero! esterase brcaka fallY acids off of cholesterol. CQII,m1w.is secretedin the pancreatic juice. Colipase is a small protein that stabilizes pancreatic lipase.

An increase in cAMP activarcs triglyceride lipase and regulates lipolysis. Hormone sensitive lipase is lin enzyme that mobilizes triacylglycerols from adipose rlssue.

LIPIDS 75

76 B,OCuEMIsTI1r

MiXl,?lJ micelles contain bile salts, 2-lllonoacylglyccrol, and FF.A's.

Clinical correlation: Malabsorption f lipids results in steatorrhea, because tho excess lipids remain in the feces. This gives the stool II greasy appearnnce and the stool will float, The cause ofthls caninclude liver disease (not enough bile is being produced), gall stones (the bile is occluded), pancreatic disc .. se (enzyme disorder, 01' intestinal mucosal cell defect.

HDL

HDL is importanlin removing cholesterol from peripheraltissues. HDL is made in the liver. HDL contains an apolipoprotejn that activates lecithin choIesterol acyl transferase (HDL is associated with LCAT). Tangier's disease has a deficiency of this lipoprotein.

leCITHIN CHOI.ESTERO,L ACYL TRANSFEflASE (LCAT)

LCAl' converts cholesterol to 1\ cholesterol ester .. LCAT is activated by apoprotein-A T, an important part of HDL (not VLDU LDL).

APOPROTEINB 48

This is needed to package the TO for forming chylomlcrona In the small intestine.

Chylomicr ns arc much larger than mixed micelles and arc made of approxirnntely 90% TO, Vitamins A, D, E, and K, phospholipids, cholesterol esters, Wid apoprotein B-48. Chylcmicrons have a hydrophilic charged surface and are released by exocytosis into the lymphatics (chylomicrons lhat arc formed in the rntcstinal mucosa). Chylomicrons are made in the Intestinal epithelial cells when IUl individunl eats a meal. They have tho hig/resr trincylglyccrol content (>80%TG)-lhey transport dietary tnglyccrtdes, 'Ihey are II substrate for lipoprotein lipase, (See illustration lie/OW for schematic chylomicron [ormation.]

APOLJPOPROTEIN 8-1.00

Thls is made in the liver, and is a portion of VLDL, B-1 00 receptor deficiency would increase blood cholesterol.

Also, not all "fat" is bad. Notice: "fat" is needed for proper absorption of lipid-soluble vitamins as well [ other fuuctions.

Chylomicron Formation

APOPROTEIN C II

This activates extracellular lipoprotein lipase. and degrades TO's into PFA's

and Glycerol. .

Apoprorcln B-48

LIPOPROTEIN UP""

Lipoprotein lipase acts on chylomicrons.lt requires (andis activated by) apolipoprotein C, The enzyme is found attached to capillaries. Exogenous hypertriglyceridemla is caused by lock of lipoprotein lipase; causing a severe chylernlcrcnemia. Familial dysbctaflpoproteinemia (hypertriglycer:idemin) is due to deficient apoprotein E; causing increased ehylomicrcn remnants.

Choli'stcroJ + .?IIJ1IlP)'l CoA FoHY.~o,I.~

FAMIUAL HYPERC'HOLESTEROLEMIA

This is an autosomal dominant disorder (deficient LOL receptors). The decreased LOL plasma membrane receptors results in increased LDL anti c1lOlesterollevels; therefore, these patients have an increased risk of coronary artery diseuse.

Cholesterol -- (tksmolostl) -. pregnenolone ~ I~gesterone-' fQrmIng aldosterone, cortisol, and Nell hormones.

GREATEST TO loWEST DENSITY

LOL - lOL - VLDL (TO)-+ Chylomicron

The lowest density means the hlghest arnouru or Iriglyccridcs and the largest size (increased far, d 'creased protein).

CHOLESTEROL SYNTHESIS

The rale-centrolling step (rAte-limiting step) is: 3-Hydroxy-3-melhylglumryl CoA ~ Mevalonic Acid HMO-CoA reductase

LDt

Lipoprotein lipase actiun on VLDL or IDL will form LDL. LDL transport cholesterol to pcriphera! tissues . .A cause of hypercholesterolemia is all LDL receptor defleioney. LDL is symheslzed in the serum and plasma, NOT the liver. LDL contains mainly cholestero! and holesierol esters.

Cholesterol synthesis requires molecular oxygen,

HMG-CoA REDtJCTASE

This enzyme is involved in the rate-limiting step of cholesterol synlhesis. Ills i(lllibiled by eholesterol or Lovastatin, and activated by insulin.

UPIOS 77

78

a,OCHfM'STilY

SQUALENE .

Mevalonic acid is phosphorylated into Squalene. whit ,h foro"; Lanosterol and finally, Cholesterol.

malonyl CoA, and the flll.ly acid chain grows O .. e .. 16 carbon chain = palmitate; saturated FA),

Citrate is the carrier of acetyl groups ow of Ute mltochondria and allows the continuation of lipogenesis.

Fatly qcid syntheSis uses reduced NADPI·l in fnu)' acid synthesis derived from the malate-citrate, shuttle (malate 10 pyruvate), and rrom the penrose phosphate pathway. NADPH is also required for steroid biosynthesis in U1C adrenal gland. [t acts as a cofactor of fatty acid synlhesis.

Coenzyme A (CoA) links to lnterrncdlercs in f!llly acid oxidation. Remember, the inner mltochondrial membrane is impermeable 10 CoA.

FA's arc transported bound to serum albumin. They arc transported from adipose lis ue 10: the muscle, liver and kidney.

PA's are stored us rnono-, di-, and Iri-ncylglyccrols (Iriglycerides); which arc FA molecules esterified with glycerol.

Mq{ollyl-ncyl carrier protein is the precursor form used in the elongation reaction producing palm.ltate.

OvernIl FA Synthesis:

Condensation ... Reduct!" -+ Dehydration __.. Reduction.

FATTY ACID SyNTHESIS

Short-term control i.s by acetyl CoA carboxylase and futty acid synthase. Long-term regulation is by diet and induction of enz .ymcs. Fauy acid synthesis occurs in the cytosol, and oxidizes fatly acids In lfu .t mitochondria for energy. Citrate "carries" the fally acid oul of (he nutochon {lrill. (See diDgram blJlow.)

Fatty A:cid Syntbe sis (milking Palmilute C 16)

/\rnlno Acids

\

p.J[""~' Glut~ ----1.,J'ynmue

T

Mlllmc Mato"yl CoA

t 11""-"_r:T'CM C'woo,.,.t...JIIi'

OAA X Acelyl QlA CifrullfljJu"

CoASH ,.1(1"1:' Citrate -.

DE NOIo/O: FA.TTY ACID SYNTHESIS

Acetyl-CoA carboxylase is the rate-limhing step. Synthesis occurs in the cytoplasm, Acyl-carder protein and N ADPH are required,

J. Synthesis of cytoplesmle acelyl eoA. Transfer of acetate from acetyl CoAfrom rile mitocIlOl1d"/1l 10 rlre cytoplasm. ( oA cannot cross Lhe luitocbondrial membrane). This is called lrmrsiocatiofl of citrate. It occurs if laocitratc dehydrogenase is inhibited (by an increase in ATP tUl.d citrate).

2. Acetyl CoA carboxylated to malonyl eoA. Acetyl CoA carboxylase (with bioiltl all a cofactor); this is Ute rate limiting slep und Is &l.imulnted by citrate. MalonyloA or the end product palmiloyl CoA willldecrease the activity of acetyl oA carboxylase,

. FaUy acid syntJuase acts as a complex. Acetyl CoA-ACP uansacy- 1.1I8e transfers acetate off the acetyl eoA 10 the acyl carrier protein (AC1». Joins cysteine, then malonate from mnlonyl CoA binds to the ACP. goes through reductase, dejlydral!lllC, and anotherreductnse reaction and forms a 4·carbon chain. The repetition adds 2-cadJOlls from the

FATTY AqlD DEGRADATION

I

OxidaLion is the flrst reaction. Overall FA Degradation:

o.~idtl(;OII ...... Hydration ... Oxidation -+ Thiolysis.

The major fuel storage = FA's in fat tissue. Acetyl CoA is the final product of the path.

Hormone.sensitive lipase (h.s.l.) is activated by cAMP·dep protei» kinase, and removes FA from Cltl or C#3 of tbe TO:

Ailellylale cyclase is activated by glucagon and epinephrine. Adenylate cyclase is inbibited by insulin and glucose. Activation Causes an increase in cAMP which acuvarcs pretcin kinase. Prote» .iuse activates h.s.I, in the presence of A1'P; (phosphatase inactivates h.s.,

H.s.'!. can then form fally acid and diaeylglycerol (from a triacylglyccrol).

P-OXIDATJON

This is FA degradation or Ule catabolic pothwuy of FA's which removes 2 C fragmcrus from the carboxyl cnd and forms acetyl CoA (by oxidizing tile p. carbon). Each cycle of fally acid oxidation yields: Acetyl CoA. Fauy acylCoA. FADHz' and NADH.

!l-Oxjda~ioD or fauy acids requires these substrate» (cofactors): FAD, NAD, and CoA.

LIPIDS 79

80 BlOClJI1MISTnv

jl-Ox.idation occursinthe mitochondrla, and the FA needs to be transported across the inner mjlochondrial membrane, but the bulky CoA cannot !let across and must be "carried" across bycarnltine,

Camltln"ac:yl tranlJ.terat8 I (CAT)

This is 1110 rate-lirnitlng step in fatty acid ox.idatiol1.

Candtlne is tile carrier tblllirnnsporls acyl groups in the "carnitine slunUc". It isinv.olved in trrui.sacylation. II is on amineacid involved in lipid merabolism,. _wd requlre.d for (he transport of long chain fOlly acidsfrom the cytosol mto the mitochondria. Carnitine deficiency resuUs in decreased falty acid oxidation.

i.e .• an 11 Carbon FA will yield: lIil)(12=60

(5 -1) x 5"" 20 -7

-2

71 total ATP yield from 1Il1 1'1 carbon £lA.

«.o.I('IDATlON'

Would build.up phytQflic tU:id if lacking. a.-Oxidation of fall.y acids occurs at lhe slIIoOlh endoplasmic .retiCfllum.

Mal .. n,' Co.A

Inhibits camittne acyltrallsfflra.~e I. (Thus, it cannot transfer new FA into the mitochondria.) II is formed inthe cytoplasm by a.cetyl CoA carboxylase, When malonyl CoA is increased, it causes a decrease in ~oxidation of tong chain fally acids (greater than 12 carbons),

OTHER LIPID TOPICS

OXIDATION OF FA's OF EVF.N"NUM8ER OF C.RBON8 "'I):

(n/2) - 1

Calculate the ATP yield ItSillS ,/lis sharI-cut;

1. from FA-CoA to Acetyl CoA (3 ATPINADH)

2. from FA-eoA 10 Metyl CoA (2 ATPIFADlt,)

3. from Acetyl CoA [0 CO2 andH-z0 (TeA .cyde)

4. loss from brooking energy bonds (thiokinnse reaction)

[(nJ2) - I)x 3 [(nl2) - 1] x 2 (nJ2)X 12 -z

BILE ACIDS

Cholic andchenedeoxychofie acids are p,.,I'maty bile ucids.Dc()xychoJi.c and liUlOChoHc acids are :recoll~/~.ry bile acids. Bile acids are lmportanr in dlgestion.They arc synthesized in (he liver rrom. choleSlerol. Bile acids + Glycine or Taurine fonns BHe Salts. Bile salts nrc secretedIn bile 10 tile duodenum and go back '(0 the Hver. [)jile contains bUe SlIhs and bile cmu'lsilies lipids. Bile i~ the number olle way (0 remove cholesterol from UU~ body. Lung surCaculUl.is dlpal,lIiloyl pnospfiotidyl choline. which dccrcR.~es the surface tension in the lungs. In premature infants. this is nOI formed and the infant has diJlicuhy brcolhjng because offhelack of type II pneumocyte production.

Total ATP yield

i.e., paJmJtoy.I-CoA (whJch is a .16 Carbon PAl would yield:

I. (16/2-1) x 3 :;;;21 '"

2. (7) x 2 = 14

3. ('8) x 12 = 96

4. -2

TAUROCHOLATE

Taurocholate is involved in ihe digcst.ion of dietary fal in the small intestine. In 'the liver, cholesterol forms Ihe prilll.(lr}, bile acids: cholk lind chcnodco.xychelle acids, In the ;1!lcMim'"liUfocholh; and deoxycholic acids (secondary bile adds) are fOIDlI:d. from the primary ac.ids. Then •. in dH: liver the bile acids are conjugaled with glycine (10 form glyooch[)!'luc-Il bile saHli andtaurine Uo fonn taurocholate-a bile selt).

total== 129 ATP yield

CEREBROSLDE

11)is is a .simp.le glycolipid (single sugar bound to Bpid). 11 is madeof a. sphingosine and an JfA chain •. plus one gluen.!;c or one galactose,

OXIDATION OF FA's OF ODD-NUMIIER OF CARDON CHAINS:

Same, but tile las! step forms Ii 3-C compound, prOpiOll)l{ GoA. Calculate this wily:

I. Through the ETC (2 from FADH2, 3 from NADH) [(n; J) -I] x S

n-l

2-)(12

SPHINGOSINE

This Isthc backbone of gang.liosidc.ceri!brosidc. ce.rnmide and sphingomyelin.

SPHINGOMYELIN

A sphingolipid. sJ1hjn~oni.yelin comes from .rp1,i"8o;rine + FA + ceramide.

2_ Goillg througb the TCA cycle

3. musrscbtrscr 7 since coming into TeA cycle late (only make S instead of 12 ATP's)

4. loss from origination (lhioldnase)

-7

SPHINClOUP,IDSYNTHES'tS

Pyri!ioltlli phosphate and NADPH arc required co·fal:tors. Palll1iloyl·CoA and Serine are precursors. Inomlaiion ofcemplex sphingolip.ids, ccramide i.s a major intermediato. SphingoHpids are main!.y found inthe brain andjn nerve

-2 .

Tottll ATI') yield

LJPIDS 81

CERAMIDE

A eeramide is a sphingosine plus all FA (i.e .• an 18 carbon sphingosine attached to a flltly acid by an amide bond). Ceramide is lUI integral part In lhc. ro~nalion of sphingolipids. It i.s an intermediate in the formation of gangbosldclt. sulfaiides, and sphingomyelin (NOT with Diacylglycerol).

7

tissue, Tay-Sach's Disease, a hpid-slorage disease, is a defect in the lysosomal enzyme hexosamlnidase A.

VITAMINS

Viremins am received from the e1i'l and are needed or growth,

PH05PHOUPIDS

Phospholipids ate amphlpatbic, and aU have phosphate. TIley serve an.importanr membrane function and in bile and surfactant. May be synthesIzed de nOVO from CDP-djacylglycerol and a polar alcohol. Have a polar head made of an amino alcohol or II sugar alcohol. (It is NOT an important storage form of lipid.) Phospholipase Al degrades phospholipids and is inhibited by gtucocorticolds, Ph.ospholipase C ill an enzyme that degrades the membrane and relc.a.'ics the second messenger, and il aUacks the phosphatidyl inositol.

BROWN FAT

Brown fat.may produce heat. The excess celeries of the diet may induce beat production.

FAT-SOLUBLE VITAMINS

Vitamins A, D, E. and K. Pat-soluble vitamins are SL f d and th ref re, diffi- 011 t meta lize,

VITAMIN A

'Three [arms:

Retinol (vitamin A alcohol and the trunsport form), Retinol' (vitarnjll A IIId.ehydc),

Retinoic acid (vIl!lmlo A acid; excites "rowtllllnd cpith Iinl cells),

In vision, retinal combines with opsin and forms the pigment. rhod psin. is-retinal chang s 10 trans-r ninal on exposure to light, wilh release f pain.

In the retina, trans-retinal is reduc 'd 10 trans- tinel. Then, in the liver il chang' 10 cis- tin I.

Cis-retinol goo. ba k to rh r tina and becomes is-retinal again, which then binds with opsin and forms rhodopsin again, Vitamin A is stored in the liver,

Vitamin A plays important roles in reproduction, growth, And cpitlPlillJ tissue upkeep. e leiellcy resulls in impaired night. vision, "nigh I. blindIICSS," as well IIR xcropl1lhnJm.in. Deficiency mil)' cause til' male to be unable 10 form sperm cell», and may retard growth. Vitamin A maintains epiUleljaj ussu s aml nvolds cornea! atrophy.

l3-carolcllc can form 2 r "tillill molecules, it may also deer lise th risk for lung cancer and other nrcincmas.

VITAMIN D

PHOSPHOlIPID EXCHANGE PROTEINS

Move phospholipids between the tntracetlular membranes.

GLYCOUPIDS

These are membrane components like II ganglioside. It is made from an FA + sphingosine to yicld a cernmide. The ceramide joins willi 8 sugar 10 form ~broside, The cerebroside jolns with glucose to become II "glucose cerebroside."

VII.miD D Syntilesill

?dehydrocholesterol

1 is d~{H't'(1 tJ)' "Rill (in Skin)

holcc.'llciferol (also n:oci.ved from diet)

1 U}'drv).yllll~ (in Llv,e.r)

lS-lIydroxy holecaleifbrol (the major storage fonn)

j 25-lIydrQ. 'l'IIvleco[r./f"",'I.hydm<ylflu (ill the KIdney)

l.lS-Dihydrolly hoi CCII lei rero I

(the flllol. active und mOSllm/~'" form of Villlmill I ,

82

V,TAM,NS AND NORMO(,!ES 83

84 BIOCHCMISTRY

Yilamin 0 maintains calcium levels by:

Increasing resorption of calcium Irom bone, Decreasing kidney excretion of calcium,

Increasing the calcium-binding proteins and absorption of calcium (increase calcium uptake) in theIntesrlne.

Il increar s es serum calcium and phosphate levels by bone resorption (in the presence of required parathyroid hormone).

Vitamin 0 is the most toxic vitamln, A de.ficiellcy of Vitamin D in children is called Rick u's, A deficiency ill adults is called OSlcOlllulacill.,

VITAMIN E

ACIS as an antioxidant. His fonned of tocopherols and is relatively nontoxic. (Least toxic fat-soluble vitamin.) High doses of Vitamin e may decrease the risk for coronary artery disease,

VITAMIN K

Vitamin K is a required vitamin (it acts as u cofactor) for prothrombin (clotling factor 2) and clolling factors 7.9, and 10 in blood coagulatiou Toxicity may cause. hemolytic uncmin nnd jaundice, A dcfici ncy may cause A decreased carboxylation of the glutamic acid residues of prothrombin, and a decreased formaticn of fibrin monomers (from flbrinogcn). Also. a deficiency may cause a decrease ill (he bil~ding of en'" to prothrombin (factor Il), Bacteria in the intestine make Vitamin K except in newborns or antirnicroblal therapy, tilis is a reason newborns 1'CCClve a shot of Vitamin K.

cllzyme if! either me rC(lCU1I11S or rlr produ Is W" "YOII see "mimI acid rearttons=you carl fed comfortable to guess" Vitamin 86" 0" your c;tnm. Otherwise, memnrize III [otlowing reactions, Vitamin Bf> is iJlvalved in:

I. TrunSl,mhwtion 2, DC<'arboxylation Deaminntion

4. Condensation

(OAA Glu ++ Asp + IX-.kg) (Histidine_'" CO. + Hi, tamlne) (Sorlnc _..,., NH.,'; Pyruvate)

Glydn + Suceinyl oA _,.. a·ALA)

eficicncy is assooiat d with Isoniazid anti-tuber ulosis lr almont (therefore, pyrid x.inc is given. In g meral. Ivaler-solubie vitamins arc 11 I usually t xi , but vitamin B(j is aclUaUy a 10 ic vitamin thaI c n result in gail problen rom NS toxlcity.

VITAMIN B~ (COBAlAMIN)

Contains cobal! ill the center err a corrin dug.

Meillylcobalamin contains a methyl group, and cYl1llOcobalamin COn-

tains N on a coordinate area. -

Involved in th followin reactions:

I. Homocysteine - ~fl/.e'''ylcobalaJ11in) ----IJ. M thionirt

2. Mclhylmalonyl oA - (deo.l)'aderro.l'ylcobalrunin) _.. SuccinyJ oA

INATER..sOLUB.L.E VITAMINS

Vitamin B'2 binds t jilt/in i faci for absorption. Deli iency results from d creased parictal c'U secretion of intrinsle fa I J' (IF) in the stomach, causing pernicious megaloblastic anemia. This is due 10 decreased [P, ami therefore decreased absorption ofvitaminBl2• Vilamin B'l deficiency will. abo CIlUSC neurologic problems (folale deficiency only I'C uJIs in mogaloblllstiellflcmia).

The remalning 9 vitamins, Those vitamins are not considered toxic since the stored levels are low, and aI hi.gh levels nre then excreted in the urine. They include the B vitamins, biotin, pantothenic acid, folic acid. and ascorbic acid,

VITAMIN B~ (THIAMINE)

Acuvc fonn: Tluamine pyrophosphate (fPP). acts as a cofactor in oxidative decarboxylation of (X-keto acids and by transketolase reactions.

Deficiency can result in Beri-beri and Wcmickc-Korsakoff syndrome.

VITAMIN B:it (RIBOFlAVIN)

Active cofactor forms: Flavin mononucleotide (PMN) and Plavin adcnine dinucleotide (FAD).

FAD and FMN bind with hydrogen 10 form FADH lind FMNH~. Deficiency results in dcrmeutis, glossitis, and cheilosis ~cJ·!lck.ing 01 the comer of the mouth),

VITAMIN Be (PYRIDO)UNE)

Pyridoxine. pyridoxamine, and pyridoxal arc precursor of active pyridoxal phosphate (a coenzyme). As a general rule, this vitamin is a co-

NIACIN (NlconNIC ACID)

Active eofsct r Coons: NAD+ and NADP->.

They are coenzyme in oxidatlon-redueucn reaeuons. nd ar reduced to NADH and NADPII. 'Tryptophan is able 10 fonn niacin. A d riei ency results in Pel/agro: d'rmalitis, diarrhea, and dementia (the" -D's"),

BIOTIN

Au imidazole derivative. Acts as a carrier of carbon dioxide ill carboxylatlon reactions, It is found in II arly all food. The nly dcfi.cien y may appear w.ilh eating a di 'I of raw egg whites (tbal have avidin). Avidin [lrevenlsab~orpli()n by binding 10 biotin.

Til biotin .requiring reactinns that are important to know:

Acetyl CoA-- Bio(;n _. Malonyl eoA

Pyruvale Heo - + 1\ TP-8ioli/l + A.cely/ QA _.. AA + ADP + Pi

86 BIOCIli!MISTRY

PAN11lDlENIC A.elD

Part of Coenzyme A,. thai participates in the transfer of acyl g,rolipS. Pantothenic acid is II groWt11 factor that is a part of acyl carrier protein,

Fouc ACID .

Mude of p-aminobenzoic acid (pABA) bound lOA pterin riog and glutamic acids, The active form .is Tetrahydrofolate (THF), which :is formed by reducing felate witb theeazyme, dihydrofolarc reductase (OKF - dihydr%/aJe reductase -+ 1HF). PABA aotdogs (su]fruulamide) will inhibit synthesis of folate. THE" transfers carbon Cor 1110 synthesis of purines, lhymidylic acid (a pyrimidine) lind amino acids. Deficiency results in megaloblastic anemia (frequently seen in alcoholics and pregnant wormen; very common). Prognll_ot women must receive folic ncid early in fetal developmentto ovoid neural tllbe defects (i.e .• spina blfida) and growth failute .. II Is recommended to begin vitamin snpplmncnts be/ore copceptioe.

AsCORBIC AC'ID (VITAMIN C)

V:ilamin C is a reducing agent oxidized by oxygen. It nels lIB a cofactor in fOfming hydroxyl.ysylresidues. and is required in the hydroxylation of collagen. It helfs ill the a.bsorption of iron by reducing Ferric (PcJ+) to tho Ferrous (Pc +) form inthe stomach. Excretion of increased levels of vitamin C may result in kidney stones by calcium SIIIt deposits Qf oxalate (a. breakdown producL). Deficiency results in SCII"'Y: deficient hydroxylation of collagen and tllcrcfore, connective tissue problems which include sore gums and loose teeth, as well 115 anemia.

HORMONES

Hormones may be either p()lypep.tide hOlluone.s or steroitlhormones. They act as chemical messengers and cause a responsein a target tissue or tissues. Hormones have different slgnaling methods: I. Hormone will enter the cell and redircct: !tow the gene aCIS, These are the steroid hormones, Vitamins 0 and A, and thyroxine. 2. Rcceptor-medlated will change the shape and signal !.he iaterior of the cell. This occurs in the cell membrane, NOT insidelhe cell. II causes a cascade effect Ion-channels may open up next to. tile receptor. which allows ions In flow in or out of the cell.

lnsulin. rut anabolic hormone, acts by signaling the membrane receptor and activating tyrosine kinase. Oiucagon nets by chaagmg UH~ shape of the G-proleins and acting Oil adetlylate cyclase to convert ATP to cAMP. This excites protein kinase which phosphorylates proteins.

INSUUN

Insulin is a peptide hormone made by pancreatic islet P.·cells. wilh anabolic effects, It binds 10 speciflcreceptorsin lhe cell membrane of tissues like liver, muscle. andadipose tissue, and. increases the transport of glucose and amino acids acr-osslfle plasma membrane, Insulin .ill creases protein, triglyceride, and

VitAMINS AND HORMONES 87

88 BlocN£MISml'

glycogen synthesis in the liver and muscle. By acting Oil the receptor, il activates or inhibits nzymcs in the c II, Per example, when insulin si nals the [t~ 'lTIbran~ recept r, it activates (causes the phosphorylation of) tyrosine kinase which then places phosphates au Tyrosine residues of target proteins. Another action of insulin is Its ability to decrease UIC blood conccnuation of glucose. Furthermore, it deer ascs UIC fatty acid level by inhibiting hormonesensitive lipase in fn!. As II response to stress, epinephrine wilJ decrease the ill~ulJn release. ~nsulil1 secretion is increased by increased glucose. amino acids, and secretin.

CHOLECY&TOKII'tIN (CCK)

CK is (I hormone made by the Intestinal endocrine cells or the jejunum and the last part of the duodenum. and is increased in the presence of fm. . K causes the gallbladder to release bile und the pancreas 1.0 releaseenzymes.

K decreases motiliry (less movement of gastric matorial LO rhc small intcsline). This peptide hormone stimulates III' coniracuon of the gallbladder.

S£C~ETIN

Secretin is released when there is an increase in fata, II low pH (increased gastric hydrochloric acid), and chyme. Secretin causes the pancr as to release bicarbonate (pancreatic juice secretion) into the duodenum.

Overall, insulin acts to illC:f'C1ISC 1Jm synthesis of glycog '11, protein, and trlacylglycerol-it. is considered an anabolic hormone.

G-.sTRIN

This hormone is secreted in the pylorlc-antral area or tJ1C stomach. 11 increases the H 1 secretion of parietal cells. A gustrinoma is a gastrin-secreting tumor thnt is associated Wi1JI Zolling r-Ellison syndrome.

Preprolnsulln _,. Proinsu1in ---+- Insulin (active form).

GLUCAGON

Glucagon is II peptide hormone 1.I1:lt .iN secret d by pan 'realic islet c-ccus. Il malntains ~Iood glucose by Increasing liver glycogenolysis and gllLcollcogcnesis. Glucagon increases blood sugar, breaks down liver glycogen. Ilnd increases gluconeogenesis (docs NOT break down muscle glycogen). II is increased in ;esponse to hypoglycemia, 10 increase tIle glucose level. Remember. glucagon IS mcreasoll by: II decreased blood glucose level, an increased epinephrine (stress), and a. high amino acid diet (I} high protein meal needs to counter the hypoglyccnuc~fccl1J1lIIjnsulin WOUld. creal ), A sudd JI increase of glu ngon wouJd mcreasc!lVI.~r cAMP levels and liver glycogenolysis. Glucagon increases the l:rilnsfofmfllJon of pyruvate LO phosphoenolpyruvate. It also increases fructose-I ,G-diphospbme conversion to fructo8e~6-phosphIlIC.

CALCITONIN

alcitonin decreases blood calc! urn levels. (Think of "calcium toning" 10 decrease the calcium level.)

TRIIOOOTHYRONINE (Ta) AND THVROKINE (T4)

These Ihyroid hormones increase hem production and xygen consumption. Cretinism is 1\ prenatal thyroid deficiency that causes defective physlcal and mental growth.

OXYTOCIN

Oxytocin causes uterine contraction, and U1C release of milk during breast feeding ("mjlk let down"). '1lis hormone is released by the posterior pituitary,

THVROID STIMULATING HORMONE (TSH)

Actlvatcs tJ1C secretion of thyroid hormone, Thyroid stimulating hormone causes the synthesls and secretion of T and T.1•

S~OID HORMONES

Steroid hormones arc lipid soluble hormones thot cause effect' at a slower rare. Thisis why you need 10 give corticosteroids for several days before you see an effect. They decrease the protei n synthesis. They activate nuclear receptors of the target ussue and cause an increase in mRNA and protein synthesis to occur.

VASOPRESSIN

Antidiuretic hormone (AOH) or vasopressin increases sodium and water reabsorption in the kidney. This bormonc .is released by the posterior pituitary,

GROWTH HORMONE

Growth hormone increases amino acid uptake nnd growth. Somatotropin is c?n~idered a growth hormone. Growth hormone is rcloased by tile anterior prnutary,

CALMO.DULIN

alrnodulin acts as an intracellular receptor for Cal •. It activates myosin light chain kinase and binds reversibly 10 C:l2 ... (in muscle comraction).

ADDITIONAL REVfEW

ACTH (AoRENOCtiRTICOTROPIN HORMONE)

ACTH stimulates growlh of the adrenal cortex, This hormone ,is released by Ute anterior lobe of the piluitary (hypophysis),

CATECHOLAMrN£5

Catecholamincs include: Dopamine. Norepinephrine, and pinephrin. A and NE arc ncurotransmiuers or the brain. NE and Epinephrine are released from the adrenal medulla. atecholarnines are synthesized from Tyrosine (which is from Phenylalanine):

PARATHYROID HORMONI;

~rH in.crta.,'es· blood calcium levels. 11 decreases plasma phosphate levc.1 by increasing the excretion of phosphatc.

VlTAMIIIIS AIIIO HORMONES 89

Tyrosine - I ... Dopa - 2 -+ Dopamine - 3 -+ NE - 4 _.. Epincpluin()

L Hydroxylase (ratc-limhing step; uses tctrahydrobiopterln) 2. ecarboxylasc

3. r3.Hydroxylllse

4. N-MclhyHransfcrasc (uses SAM)

TETR.AHYDROBIOPTERIN (BH4) ..,

BH is needed in tyrosine. catecholamine, and serororun synthesis, The 101- low1ng schematic should be memorized:

Phenylalanine - BH.I .... Tyrosine -- IlH4 -+- 0 I'll Tryptophan - BH ...... 5-Hydrox.y tryptamine -to- 5-HT (Serotonin)

CHRONIC GRANULOMATOUS DISEASE

!:?cficicncy .of NADPH oxidase. This results in chronic pyogenic infections since there IS n respiratory burst,

DfABETES MELLITUS

Insulin dcficieney that results iJI increased glucose level. glucosuria. and Con Increase ketogenesis. (See /101'. 7)

TYPE I DIABETES MEWT\JS (INSUUN-DEPENDENT DM, JUVENILE DM)

ln type I :OM, Il-cells arc destroyed and there is no insulin production. This occurs as II child and can result in ketoacidosis. 'TIle treatment is insulin to suslfl.in lire. Insulin deficiency results in increased glucose level, glucosuria, and kerogen sis.

GALACTOKINASE DEFICIENCY

Deficient ~alactolci~\usc, nn autosornn] recessive disease, resulting in increased galactose III 0e unnc. Remember tlwt most mzymc deficiencies arc autosomal recesstve.

TYPE II DIABeTES MELUTUS (ADULT-<lNSET DM)

This occurs as ;J rcsuh Or "lazy" ~.cc.lIs and peripheral rcslstanecof insulin. II occurs in individuals over 35 years old, and is [ISS ciarcd with obesity. II includes about 90% of all dlaberics. The treatment is dieting' and then oral hypoglycemics if there is poor compliance or dif lculty in controlling the blood sugllr levels.

AMINO ACID DISORDERS

HOMOCYSrlNURIA

Jncreas~ uri.ne levels of h~mocystlne. May tn~al with dietary Vitamin Be. (~y~doxme) and cysteine. Cannot methylate homo ystcincirno mcthlonm,c. (Homocysteine is oxidized into homocystine.) Deficiency of cystatluomnc synthetase.

MINERALS

PHENYUUiTONURIA (PKU)

PK.U results f~on.l (I deficiency of phenylalanine hydroxy lase , The p!llle~1 I~USl Ch!nlll~le p.henylallmin' from Ute diet. Tyrosine must be SUppll<:<! ID the dlCI sl~ce II cannot be made from phenylalanine. Neonatal screemng test: Guthrie Test may show false negative il' done ar birth,

ALKAPTONURIA

Dcflcicncy of homogentisare oxidase. auses darkened urine when standing.

IRON

Iron is trunsported in (he blood by transferrin. (OrGIlC of extra iron is by ferrltln and 1"III()si(/erin. Heme iron is nbsorbcd by mucosal cells of intestine more than non-heme ir n, Primary hemochromatosis ntily accumulate iron by lncreuscd absorptlon frum the die!. Dietary aseorblc acid increases iron absorplinn. Phospharcs bind with iron and decrease absorption. Iron is absorbed mainly in the duodenum and the proximal jejunum.

CALCIUM

The nutritionnl source for calcium is milk, Bones arc II reservoir or calcium lind they "fill up will! calcium' until about 21 years of age, After that lime. hones an: III (I continuous drainage of calcium. Menopausal women 'Ire of tell placed on ("tlrog!'11 replacement to decrease the amount of calcium loss and Ihe number of bone fractures, This ill why meuopausnl women have II sleep decrease ill the cal 'ium IIlId their 1)I)III!s become more Irngile, Weight-bearing ixcrclscs and <lClivily can help maintain hom: calcinru,

UREA CYCLE DISORDERS

Carbamoyl pbosphate synthat09.& denclency auses hyperaO'llllollemia,

Omlthlne trM.c:arbamoylu8 deflclency

Causes hyperan)nlonelllia. as welt ns orotic aciduria,

90

BIOCHEMICAL DISORDERS 91

92 SlfJCNEMlsrt/r

Citrulllnemia

Deficiency of argininosucclnate synthetase. auses increased citrullin level.

FAMILIALIPOPROTEIN UPAS DEFICIENCY D Iieiency of lipoproreln lipuse

In 'llSe4 Iev 'Is of 'hylomicr n triglyecrid .

FAMILIAL lCAT DEFICIENCY

'Ii ieney r lecithin: ch Icsterol acyltransferase.

TANaLER'S OIIJEASE

Defeerlv HDL synthesis,

Elevated ch lestero] in Ii. su and I decreased plasma HDL level.

FAMILIAL OY6BETALlPDPROTli.INEMIA D lid 'ncy f Apo , 3.

ABETAUPOPROTEINEMIA

fecuve synthesis of AI)O B-lipid • mplcx.

ArgJnlnornla

D 'fioieney of argminosuccinasc.

auscs ar ininosuccinatc excretion in (he urine,

MAPLE SYRUP tJRINE DISEASE

This disease was named because of UI.O "sw 'l urin " Deficiency of keto-acid (branched-chain) dchydrogcnas . Therefore. branched-chain keto acids ill urine.

(branched-chain amino acids fire isoleucine, leu in • and valine) To treat, Ute dlci must be low in branched-chain amino acids.

GLYCOGEN STORAGE DISORDERS (12 TYPES OF GSD)

(Most arc autosomal recessive, with the exception of phosphorylase h kinase deficiency)

VON GIERKE'S (TYPE I GSD)

Deficien ''I of glucesc-e-pheaphatasc. Hcpntornegnty is seen.

POMPE'S (TYPE II GSO)

Deficiency of Ct.I.4-gluco.~itlnse and Iysosomal acid maltase (0 dcbranching enzyme).

Cardiomegaly, restrictiv cardiomyopathy, occurs !IS the heart stores glycogen.

CORl'S

Deficiency of the dcbranching enzyme, arnylo-I.6-glucClsidasc. Errccis limit dextrin conversion 10 glucose.

McARDLE'S (TYPE V GSO)

Deficiency of musele phosphorylase,

Increased glycogel1 sine CIIIl'I break down glycogen 10 glucose. There is weakness and cramps in the II1l1seJ '.

LYSOSOMAL STORAGE DISEASES

Lysosome have hydrol~tic enzymes, When these enzyrncs decrease. thcr if> OIl nc .urnulauon of sphin olipids and sulfates. et .

MUCOPOlYSACCHAR100SES

Hunt "8

X-linkcd r csslvc de I • ency f ldur nosulfate sulralas . 111lS causes un lncreas . in dermutan and hcpamn sulfate.

auscs menIal an ! physical retardatlun .. (N corn' I cI uding)

5thelols

Autosomal recessive deficiency of a-L-iduronidltsc.

Causes '1 tiding of th com '3. joint d 'generation, and heart d;, • casco These individuals hove II /lumia/life expectancy,

Docs NOT cause retardation,

HERS

Defici 'ney of liver ph sphorylase. lncrcnscd glycogen.

PHOSPHORYLASE 8 HINASE DEACIENCY

Defici 'ncy of liver ph sphorylase b kinase.

Increased glycogen due to inability to activate 10 the phosphorylase a,

Hurlor's

LIPID DfSORDERS

fi i 'ney or (X-L-iduron.idll

Increased dcrmnran and hcparan sulfate,

nuscs loudlng of th 'urne;], m '11101 and physical rcrnrdntl n, and ca Iy doth.

Snnnllppo's

J)e/iciem:y b Type; A: N- ulrala, •

B: N-Il·tylglucosominjdasl!,

; N-accLyl 01\; C1~gl'ucosnminc-acctyhJ'ansfcr a se, : N-n 'lyl·Ct- -gill 'osamin'- -sul ntase.

This in rcascs hepnran SUirlll Causes severe mental rctardmlon, Type IJJ muccpolysnc haridos] ..

FAMILIAL HYPERCHOLESTEROLEMIA

Mutated LDL receptors thai reduce binding of LDL. Increased level of cholesterol.

94 BJOCllt;MJSmr

SPHINGOLIP1OOSES

aMi,gangllosldosls

Defective iJ.-gangliollidase A.

Remember, Adenosine dcaminnse was the fir.~t gene unnsplanted lnto human cell DNA 10 develop theirnrnune system. Adenosine is convertcdinto Inosine (Set! purine nucleotide dl'graflmioll) .. An adenosine deficiency will shut off dcexyrlbose production, and t.hi~ dCCfCIISCS the immune system. Think of the "Bubble baby"

Tay.Sa<:haDlsease

Deficiency of hexosaminldase A. Increased OM2-gtmghol>idcs.

This disease is associated with Ashkenu2i(EMlern European) Jews, and a macular ch« rry-red spot.

Causes rcmrdutien and early death.

ORonCACIDURIA

Deficiency oI orotate pho.sphoribosyhransferase.

Causes megaloblastic anemia andjncreascd oroiate excretion in the urine,

Niomann-Plck'il

Deficiency of sphingcmyclinase, Increased ~phingomyclin.

This is associated with severe mental retardation and cady death.

XEROl)EAMl PtQMENTOSUM

DefIciency of U. V. endonuclease,

Result of the loss of exclsion-repalr LO remove thymine dimers (created by UV radiation formiug dimersin DNA).

Repair dimers by 3 enzymes:

1. Speciflc exonuclease-protein complex

2. DNApolymcf:lsc J

3. DNA ligase

Gauc:her"e

Deficiency of glucocerebrosidase, Increased glueocerebresides.

Fabry's

Deficiency of a-galactocerebrosidasc A. Increased ceramide uihexcsidcs.

This is LIm only sex-linked recessive .YIIljalic/osis.

Ligase is a repair enzyme oflhyrninc dimers [rom excessive sun expo" sure, It is involved in DNA repair ami synthesis, and in the formation of phosphodiester bonds between dsDNA molecules. (Sl:'e Chap. 4)

OTHER DISORDERS

PURINE AND PYRIMIDINE D.ISORDERS

W,LSON'S DISEASE

Increased serum copper due 10 deflcicncy of ceruloplasmin, Causes hcpatolenticular degeneration as wen as dermatitis.

LEsCH-NYI1I\N

Deficiency of HGPRT (bUI, has xanthine oxidase), Self-mutilating diseuse thai occurs only in IHIlIe.':. Lesch-Nyhan Syndrome isassocialed with:

Gout, increased serum urare,

increased phosphoribosylpyrophosphulC (f>RPP). increased hypoxunthine (due lO HGPln deficiency), sell-dcstrucuon, and menial retardation.

Allopurinol (thetreatment for Rout) is an analogue of xanthine and is used 10 inhibit xanthine oxldas«, this decreases hypoxanthine conversion [0 urate, (BUI. still have neure prohlerns.) Allopurinol inhibits urie acid production and urate crystal fommtlon.

Xanthine oxidase is involved in the degradation of purines: two oxidation react iuns:

Hypoxanthine -----+- Xanthine ~ Uric acid. (Xunrhine is ulso :1 pl'CClirsor 01" guanine)

ACUTE INTERMlnENT PORPIfVRIA

Deficient porphobilinogen deaminase.

lncrcased levels or o.aminolevulonic acid (I)-ALA)

CRIGLER-iNAJJAR SYNDROME

Defective formation of bilirubin glucuronide.

Deficiency of hepatic bilil'Ubin-UDP·glucuwnyltransferasc. Nonhcmolytic jau ndice, hypcrhi I irubinemin,

May cause irreversible brain damage.

HEMOSIDEROSIS

Excessive iron storage, (Hemochromatosis),

Can occur if receive many blood transfusions,

HEMOQI.ODINOPAntlES

AOENOSINE OEAMINASE(ADA) DEFICIENCY

Defectin gene for mll'lIu!'iinu deaminase, leads 10 severe combined immunodeflcicncy dis~a~(' (SClD).

Sickle cell' anemia

Substitution of valiNc for glutamate til posit jon 6 on fj·chuins in hemoelobin.

Abnormal Hemoglobin S.

TIle deoxygclIIolcd hemogJobin ill les» soluble than UII.} oxygenated h moglobin.

lcctrcpborcsis dern nstrates Hemoglobin band.

(Sickle ceil/rail demonstrates both hemoglobins S and A)

96 8/0CHCM/STRY

TholasaAmlas

ause defective synlh is (abnormal quantity r ex- and ~-h rnoglobin chains,

Normal function of thechains.

(l-Ihalassemiu patient may produe hcmogtobin H; decreased 0:-

hain synthesis.

il-Ula1asscmill has decreased ~-chflin synthesis.

p-lIl11lasscmia may be caused by a gene deletion or II mutation lhut may affect the processing of mRNA O( premature chain tcrminauon.

CONNECTIVE Tissue DISORDERS

Ehlers-Oanlos Syndrome 'oJ lagen defc IS.

Can occur with decreased Jysyl oxidase or Iy:;yl hydroxylase. Elastic skin and loose joints. These individuals nrc "bondable."

Disorder'

Deficiency

Clinical Presentation

Mart'an'g Syndromo

Deficiency of type J collagen formation. Elastin defect. TaJl stature, arachnodactyly (long spider ringers). Weak arteries can lead 10 a disscctmg aortic aneurysm.

Ostoogene&ls Imperf eta

ecreascd collagen synthesis.

"Brittle bone syndrome," bones bend and break.

HARTNUP DISEAS£

Trarrsport defect of tryptophun ill intesunal and renal systems.

CYSTINURIA

DC[!·CI·ivc cystine, lysine, arginine, and ornithine transport, Cystine crystals and stone fonnatlon.

BLOOD COAGULATION OEFlCIE)llCIES

Classic homophllla

Factor 8 deficiency or Hemophi lia A. X-li_nkctl recessive.

Th sse individuals have probl ms with blood coagulation and will have massive hemorrhage iller trauma or an opcrati n, They I ave normal bleeding time, but a prolonged coagulation lime. Treatment: FIIClor Yin concentrate,

Chrlatma: dlaea e

Factor 9 deficiency or Hemophilin B. X-linked recessive.

hronic granulornutous dis.

Diabetes Mellitos

Ga lactoklnase deficiency

Homocystinuria

Phenylketonuria

Alknptonuria

Carbamoyl phosphate synthetase d 'udeney

Ornithine trnnscarbameylase d 'ficicncy

Arginincmia

NADPH oxidase

Insulin

Galacrokluase

ysrathionine synthetase

Phenylalanine hydroxylase

Hornogcntlsatc oxidase

arbarnoyl phosphate synthcras

Ornithine trmrscarbamoylase

Arglninosuccinase

Increased: Glucose level, glucosuria. and possible ketogencsis

Increased galactose in will

Increased homocytine ill urine

Must be given tyrosine in diet, Musl eliminate phenylalani no from diet.

Darkened urine when staud

Hyperamrnoncrnia

Hypetammoncm la, orotlc aciduria

Increase urine excretion of'

A rgini nosucci nate

Disorder

Def1clenc),

BIOCHEM/CIIL DISOIIDERS 97

Clinical Presentatlon

Maple syrup urine disease

Von Gierke's Cod's

McArdle's Hers

Phosphorylase b kinase de fie,

Keto add dehydrogenase

Ghicose-fi-phospharase D 'branching enzyme,

runylo-I.6-glucosidas

MllscI ph sphorylasc Liver phosphorylase Liver pbosphorylasc

b kinase

Familial LDL receptors mulaled

hypercholesterolemia

I1am i rial tipoprotcin Lipoprotein lipase

lipase deficiency

Familial AT

defici ncy

Tangier's disease

Familial dysbetatlpoprotei ncrnia

Abctalipoprotci ncmia

Hunter's

Schcic's

Hurler's

Lecithin: cholesterol acyltransfcrasc

Defective HDL syruhesis

ApoB

Defective synUI 'sis of Apo-B lipid complex

Iduronare Rulflilase

a-L-iduronidase

n-L i tJ uronidasc

Increased urine ketoacids. (branched chain A.A.'s) Sweet smell of Linne.

Hepatic glycogenosie.

Increased glyc gen

i!

In rcascd hole ter I

Increased chylomicron TO

Increased holcstcrol, Decreased HDL level

Mental lind physical retardation.

N com-a! clouding

Joint degeacration, corneal clouding, NO retardation

Mental and physical retardation, corneal clouding, Early death.

98 BIQCH£MISrl/V

Disorder

Def1clency

Clinical Presentation

Sanfllippo's

OM l-gangl iosidosis 'Fay-Sachs discs e

Gaucher'S Nicmann-Plck's

Pabry's

Lesch-Nyhan Syndrome

Goul

ADA deficiency Orotic aciduria

Type A: N-sulfnlasc Type B:

N-3ectylgluco· snml n idase

Severe mental retardation

'1'ypc 111 mucopolysaccharidosis •

Type C: N-o.cclyl CoA: Hepatomegaly

. o:-gluC()saminc-

acctyltrnnsfcrase

Type D: N-acctylct-D-glueosamine- 6·sulfalnse

fi-gangliosidase A

Hexosaminldase A Retardation, early

death. Cherry-red spots from deposits of N-acetylgalactosamine in tJ1C retina and brain. OM2 gangliosides,

Glucocei ebrosidase Sphingomyellnase

n-gaJac[osidnse A

HGPRT (totallyabsenl)

HGPRT Is decreased Adenosine deaminase Ororate phospho-

ribosyltransferase

Also, Cherry-r d SpOI.S_

Skill lind kidney accumulation of cerami de trisacchari des.

Gout, MenIal retardation, self-destruction. Increased: serum urate, phosphoribosylpyrophosphate (PRPP). hypoxanthine.

Urate crystals, SCID

MegalobJaslic anemia Increased urine excretion or oroiatc

Disordor

Deficiency

Cllnlca' SUMMARY OF ENERGY PRODUCTION AND CONSUMPTION

Prosontatlon

Skin d:U!UlS ' from sun CAp sur'

Jncrca~l:d serum pper, Hcpo.l.olenLicu I· r d'S ne li n, rmatltls.

tnerc cd &'A A

Juundi e, Hypc.rbiJirubin mia, (Uflconjtrgalcd bilirubin) Irreversible brain damage may occu .

• xc zssivc ron storu se

Hemolysi , Ulcers, lufarcts oC

bon 111ld splceu. Autosplcncctomy.

Hcmoglobinopathy

Collagen defects

Blood cuagulatlon pr blcm • Bleeding,

Blood e agulali n problems ..

Blc din.

Sk o[ etnl abnormulity, hildhr d d nih.

Xerod rma

Pi mentes urn

Wilson'. iseuse

Acute Intermittent Porphyria

rigfer-Najjnr Syndrnm ,

Homo ldero: is

Sickle cell anemia

1l1l1i1nlscm.in

l3h1crs-Dwtlos Syndrom'

las le Hemophilia

hrislmos Diseas

1- ell Disease

uv endonuclease

Porph bilinogcn dcnminOJl

Hepatic bilirubiu-UDPglucoronyl uansfemsc

uuscd by 0 puint mutauon thnt

sub, tillllCS valin« ~ r glutamate at position 6 n ~-chains in Hb

0;. nnd ~.hClnoglobjll

halns

LYliylllltidru;c, Lysyl hydroxyl.

Factor 8

-acior 9

Mannose phosphorylation is decreased

:LOa

MISCEllANEOUS 101

102 BIOCIiEMISTnV

PH ENVLA.1.AN1NE,

w"enY/O/fIIl$" hydroxylase wlth COfnCiQT. Tl:1I"i'lhyd.robiol'leril1 (TIIB)1

Tyrosine . Melanill

H ~"-d

omogenusie aCI

Fumaric aeikCClOaCetiC acid ~ Acetyl eoA

FIJMI\RATE AHD AsPARTATE

Conncct th citric acid cycle with the urea cycle

UREA CYCLE

Nitrogenous waste products are removed through (he urea cycle. Urea is formed ill UIC liver. enters the blood and is excreted in the urine. One nitrogen is from ammonium (NH4" via carbamoyl phosphate). the other is from aspartate. Reactions occur in the cytosol and mitochondrial matrix.

5-ADENOSVLMETHIONINI: (SAM,

onates methyl group.

SAM of .. S-lldcnosyUiomocystei",

S·lIdenosyllto/rlocysre;'re of .. Homocysteine + Adenosine.

R{!(lc!;o,,~ involving SAM: (Donates methyl group) Pho.'!~h?lIdyle{!,afl~/o/1lilll! __.. Ph sphatidy.lcholine. Guanidinoacetic acid __.. rca Line.

Gualli~c --.. Terminal Z-methylguanylerc ap (5'-(;<11'). Norepinephrine ----+ Epinephrine.

Posl.-lrallscript.ioll!ll modificalion re .. ictions

(i.e .• J ·II/elily/adcnine in tRNA)

Firs! two reactions occur in. (fie mifocilOmJria:

I. arbnmoyl phosphate synthetase reaction

2ATP+CO +NH/+ Hp __.. arbamoy] phosphnlc+2 A.DP+ PI

2. Ornithine carbamoyl transfernscreactlon

Ornithine + nmamoyl phosphate _. Citrulline + PI

Tire remaining reactions occur in til cytosol:

3. Argininosuccinate synthetase reaction

Citrulline + Aspnrtale + ATP ----+- Arginino8uccinalc + AMP + PPI

4. Argininosuccinate lyase rcaction

Arglnlncsucclnntc _. Pumarate + Arginine

5. ArgiJlase reaction

Arginine ----+- Ornithine + UREA

(Ornithine retUffill into the mitochondria. While, the (oxic Nli:, is released

$U~J -

S·A.denollyl.melliioluDIl

Urea:

NH2-C-NH2

. II

o

MISCELlANEOUS 103

j04 BIOCN[MISI~'(

4 moles of high energy phosphate bonds arc released in the synthesis of I mole or urea,

Urea Cycle

Uv()r C'ylo.101

Arginine

Pum~t

v

Ttueonine -+- Glycine -+- S nne _. Pyruvate

Throollin' _., Propionyl oA -+- MeUlylmaJollyl CoA ___.. Suecinyl oA rtomocys(cinc - (meilly/cobillamin) -+ M'lhioninc

ospartau: amlnotran rfi rase

Aspartate -I- o:-kclogl.ularal'.. ~ xalonc Ulle +- GIUlonlot •

Amino Acids lIlId Kreb's Cycle

• • rnlc-li mill ns enzyme

- I

p- o-p-

I 0-

AMINO ACID CATABOUSM

(The use of amaas in m tabolic pathways):

Glw;l)genic

Alln - Asr. - Oxnloaeerme

!

Mnlnlc

t

[Pile, l'yr] - PurnarlllC

Succinate

Till·

/

NUCLEOTIDE METABOUSM

Nuel ofides are important for the synthesis of lipids, cllrbohydralcs,llI1d prot ins. '01 y S tv in the formatlen of cofact and ar ere i J for III tabolic pathway:;. '01 two types f bas s: purin (A. ) and pyrimidine ( • U, n. are syntbesizcd de '10\10 or by alvage prllhwaY:l.

PlJRINE NUCL£OTlDE SYNTHESIS

ISOCiJmto Gin -i Ills

a-ltctog]UlBfllIC - Glu I'm

I II.rg

uccinyl oA

t

MclhylmoJony'· oA

t

ProPiOC',COA

II .. M .. ,_ Thr_ Val

DE. Novo SYNTHEsas

Ac:lenin and Guanine)

Purine r 08 structure has several sources for ils atoms:

Purine Structure (AIJimilu! Imd uanlne)

Iy jilt!

I

Mel/llmylfr'fralrytiro/(}lic (I II' (TIfF)

MrSCfLt.ANEOUS 105

106 BIOCHfMISTRI'

PURINE NUCLEOTIDE SYNTHESIS (colllimwd) 5.pho.~phoribosyl- J .. pyrophosphate (I'RPJ»

Riboso--S-phosphate + ATP --------- .. PRPP rlbosephosphnte pYlVpllOsrhokill!.l~~

Au.OPURINOL

This drug inhibits xanthine oxidase, and is useful ill th trcatm nt of LeschNyhaa gOU1.

Then, the committed step:

CI"lll.mi" ph<)sph riMyl pymphosrhlll.Cl tlffiinOlrnn~fQm.!c

PRPP -I- ;Iulnmlrw ~ 5-.phospho.~.D·ribosyJarninc + OIUlIlfIUlle

Silvernl steps proceed 10 Corm Inosine mono phosphate (IMP)

IMP is an unusual base found in LRNA. Glycine. Mcthcnyl-THF. Glutamine, ATP, 02, Aspartate. and Formyl-t trahydrofolate enter thepath to form IMP.

FinliUy, IMP is converted to AMP and GMI) (I(/Ctlylo.fllf:dllfJ/c :;,111/1(1.'1<:

IMP + Aspartic acid ... GTP _., Adcnylosuccinate + DP + PI

Adenylosuccinatc AMP + Fumarate

THE SALVAGE PATHWAY OF PURINES

This path allows undcgrsded purines from the cellular turnover or diet 10 be reuse? by tho bod~. Unlike de novo, thiH path occurs in e.drahcpatic tissues, Adenine phcsphcribosyhransferasc and hypoxanthine-guanine phosphoribosyltranllfcrll8c (l-lt?PRT) nIC the two enzyme." involved. PRPP is used by these enzymes f~r the nbose-5-phosphalc group. linical correlarion: Lesch-Nyhan Syndromeis the result of HOPRT deficiency, is X-linked recessive. and leads 10 increased uric acid and sclt-mutilauon,

PYRIMIDINE SYNTHESIS

SYlllh~is of the llyn midjn~ ring occurs before a ttachrnent to ribose 5-phosphate. PRPP IS the donor for the nbose-5-phosphntc. Aspartate tr'dIlscarbru:noylas . is the

enzyme for the committed step. .

Pyrimidine ring source s :

~orm~lioll of the pyrimidine ring from carbamoyl phosphate and asparIIC acid.

IMP t/qh.wimgl!lwsC

[Mp + NAD' Xanthosine monophosphate + NADIi + Ii'

Xanmosine monophosphate + Glutarnin + ATP -----

GMP -I- Glummme + AMP + 1'[>1

(As AMP increases il will inhibit adenylosuccinate synthase and as GMP increases il will inhibit IMP dehydrogenase; resulting in decreased conversion of IMP to AMP and OMP)

Pyrimidine Synthesis

(

PURINE NUCLEOTIDE DEGRADATION

111C linal degradation product of the purine nucleetrdcs is uri acid. which is excreted in the urine.

Ad<nolinc Adtl~ln.~IO I,. (n.''''loOlld ... )

dearnlnas

Inosine

I (pliO'pl'OI)'I ... j Hypoxanthine

I (xanthine oxidase) Xanthine

! (.anlhl". ()~ld05e)

URI' ACID

Pyrimidines (" . U.To") '::::r yrosinc U=Umcil T=TI1)lmille

I (rn'l;lc~i(b._..c:)

Guanosine (nLl~I.~oMe r",,,,)

I

Guanine

108 BIOCIIEMIS1IIY

M'SCI£UAN ·()US 107

PYRIMIDINE NUCLEOnOE DEGRADATION

The oonlmitted step: AsportfJ/ trans arbamoylas«

arbnmoyl phosphale + Asp arbamoylaspartat

H20 1

DihydroorOliite

N. AD' ~ .f)1h)l/","'''WI' tklo "<1101/""1-"

NADII +11' ,

rotate

~~~~l~l!l~

1'1';1

OMP t/.j·tlrl"""fa,tc OMP

Pyrimidine rings are able to open and can be further used by me body.

Thymine Dihydrothyminc _.,. Ureldeisobutyratc

U 'I' P , ~b

mCI ·ammoso utyrau:

FORMING RIBONUCLEOTIDES FROM DEOXYRIBONUCLEOTIDES

RlbOtlllcieos;de ruiucltJ.l'eis specific for the diphosphares:

ADP. P, GOP, UDP.

Tliloredoxin donates III hydrogen atoms I reductas enzym lind reduces the. ribonucleotide to cleo ribonoclectide, Later, NADPH + Ii'· and lhiorcd xin rcdu Ilise can convert the thioredoxin back 10 it.'! reduced form and repent its function.

UMP

1

ongratulatlon • YOIl have reviewed all of (II important topics in Rioc/wm;SII)'!

UTP IUlllmine t liTP

C7~' sY" thnse

(JIularrnllc 1\1 P 1 1'1

CfP

dUMP+ HE'

1 f/.ymidyilJlo S ,"h~II'U

dTMP+ DH'

TAP gives up a iarbon unit and a hydrogen nl~'~, .r· ultlng in. ~H : ~I-l(l is reduced 10 TH wilh dibydfOfohllC redut lase. I Ills cnzyrnu IS ,mlllbltc~ by amin ptcrin and m lh trcxatc an~ theref r~.dccr>ru;c th~ amount firTH.F. 111C reduced TIIF causes a decrees In the punne synthesIs lind the mability to methylat dUMP to dTMP. TIle result: Inhibited DNA symhesls.

'OlC cull product-e-l.lMl', (us well as AMP) inhibit pyrimidin . synthe is. ATP .. and I'npp activate synthesis, Kinase: form diph phates from monophosphates.

AsPAJ1TATE TRIlNSCARBAMOVlASE

ant rols rate of Pyrimidine synthesis ( • U. T).

Rcgullllcll by allosteric imcracnon.

Inhibited by TP. (End product of pyrimidine syruhesis.)

110 INDEX

Cnlcilonin. (,l! nlmoduliu, 8R nlorin,4

nr'hnmoyillho photo SYlIlhcIIISC, H12 nrbamoyl phosphutc symllCWSQ de.liciel\cy. 90

,Ilrb(}11 rnonoxld«, 26. 68 IrlIQxyl protease, 27 nrbollylnsc, 19

arboxypcplid • 18

CnmiLine,79

IImhlnc, yhnmsr·1'aS<l 1.79 COi.abollsm, 4

Cnlnly$ls. I'

Cntecholnmincs. B8-89 Cellulose. 60

CemmJda.81

Cemlcplnsrnin, 94

ChlrAI. 12

hlorarnphenlccl, 53. 54 holcculciferol, 82

holecysmklnln ( K),88

hotcsterol. 76

brisunas disease, CJS, 99 hromcsome, 39

Chronic llrnnulornu!UlJs Ui~C4ISt, 90 hylernl ron • 75

hyrnorrypsln, IS

itrlllc.70

Cline: neid yde. 10 Chndll nco I 03 luultlnemia, 91

Classic hcmephilin, 95. ')I)

IIndulII)' ill. 53, 54 Cobnllllllln, ij4, 86 Cofn,aQr.2' Colipuse, 74

011 gCII.30 Corupctltivo I nlnbitor, 211 cnfl II r!1I ion , ~7

onneetlve ll ~YC dl ordcrn.95 on~ellsu~ sequence. 43 cpreporphyrlnogen Ill. 3 I

ori cy Ie, 'II

Cori's, 91.97

"ijlcr-NnfCnr 9yndrome. 94, 91'1 ),uoldc.68

C)'OIl1lgcn hrurni,lc. III ycl h¢dmidc, 5 ,54 CycJt)l;)XYIlCIlw.c. R I ),510;110,9, II

rt·ftmnnilin,55 a.-hUlld.59 a.l.le~lfln<l5c, 61

a.golnel n:hronsldDSc /1..93

a.glucmida:le, 61

(t-helix. I -I I tH(elogl~lllrr'IC, 70

a-kologluu.rHt dl:hydrogcno'l:. 70 a-L-i(lllr<,nillaw. <)2 Abetnllpoprolc:incmin, 92. 97 Ah,oqllion, e,l

A 'Iyl oA. 65, fI',. 71l, 77-7'(" 102 AC1l1ytchonnc~,,~rnsc. 25

Acid,2

AClirl,31

Actinomycm, 53

ACiinomY8in O. 54

Active site, 20

Aculc lutermluent IlOrl'hyrill. 94. ')<) Adenille, 35, 37

1111allo~inc II _rnlrcl. e (AOAl deficiency. 93-94 Adcnosmc lfipho~phm", 'I, 6 .s-Otlcilosylrnclhilllrillc (SAM), 10 I ALl.rc"ocofllcOlropjn hcnnone. 87

Amnlly.20

Mfinily Chl'l)1l1I)t(lJ,;fUI1hy. 34 ALA uchydr,ll;C, :11

A lenine, K, 14

Albumlo. 2

Ald<JIII'u,~c. 56

Aldolies. S6

1\1","1110 n, J I

AlkDI'toliuritl, 31. 90. 96. 97 Alkyhllillj; nltcfllli, 42 Allopurinol,9

I\llo.!lcric CIII;yillC. '21. 22 "!]Inniln pltyLloides. 54 Arnlno nci~1 c"Ulboli.~II1, 104 Amirw addll. 7 l\!lIim".cyHRNA,49 Arnill"!l:lyc()~idcs. 53. S4 AlIlimJl1lcrill,55

Amytal. 68

An b()liilll,4

Anomcrs, 59 Anllbiolics.53

A n I it! iu rctic hormone (A DJ I), 87 Autimycin A. 68

Anlilhrombln HI, 34 ApOIlll1.YlIlC. 21

Apolilxll'rulcin B·' 00, 76 AJlOprOlcill-Al,7(\

AI'OrJflllCill'C II. 76

A.nu:hitlolli neid. 7.

Attiilino. 10, 18

Ar&inillollli .. ,91

Ascorbic field, 85, 8(,

I\spl1.mlliil . 10

ASJl~rwle IrQI'~CJlrt"'m')yIM~. 26. 107 A JlAlli~ 114;ld. 10

Aspirin, '/

ATI'. <1

A~idin. !l6

B vunmtn complex, 71

lJ,-100 receptor deficiency, 76 f~bonu. S9

jl-llnngllosldlWl A, 93 !l-hydroJlybulyr::olC.67 l).uxhlmioll.711-'19

p-plcmcd she ts, 16

Ih.qQ,2

Beri-beri, 83. KS

Dlle,32

Bi Ie ncids. so Bilirubin. J2 lIIlivvroli". 32 lIiQIQgk \1111"". \:1 l'liOlin, M. R6

OIl1ck urine ul~cllse. J I Ulceding. 29

mood clllllinlt, 3:1

Blooo CO"t"llllion dcficien<:ic5. 95 BMll,6

Bomb ClIl0rtlllclcr. '" Ilrilile bone syndmmc, 95 nrvwn f~l. 81

!lurrer. 2

109

ySI inc, 12, 30 'YMinurill, 9Ii

yrochrome b- -I reductase, fl8 ylochrornc ehnin, 67

ytochr me ()xidnsc. 27. 6S )'lo;:hrOI1le.~. 67

yhuillc, S. 36.42

O-"l1li"olevulllll;C a 'Id (d-A ). 1.94

,l)cnnlilmrion,42

·/.(lchydJ'ocholcslcml, 8 Dehydrogenase. 2()

Deletion ullltillicm, 52

DCl1lllurlng ngent~, 19 Deoxyhemcglobin. 27

Deoxyribonn lcosldcs, II1K

Dcox y ri bose, )5

DcoxYlhYlnidylntc. S5

Dcxrrorntarory. 12

Di llCl~ I1lcllilus, 27, III .90. c 6 Dinly~is, 34

01 OUIlIllrOI. 29

Dlgc.'lioll.7)

Dihytlro(olfllCYIiCI se. 55 1.2S·dih)'t1ruxycholccnlcifcrol.1I.3

J inhrophcnyl (I NP). 19 DiphoSflll('J,;lyccHilc (2.3·DPG). 29 Diptherln toxin, 53. 54

Disulfide bonds. 17

DNII, 3S, :lB. 53

DNA polymerase I, ·11 DNA polymerase 11.41 DNA f1(Ilyrn 'msc III. til DNA hel lcusc, 40 1}('l'nrn\n·. 88

Double IIdi., :lK

mmIUl'~ rcngcm. 19 em'·:!.,52

EliIcr~ nunlns syndrome, 95, 99 mCCH<I.tllrnnSporl chmn, 67 P.I«lloph()rc~is. 3'1

RlulIgJl ion. 43

r:ndooll .lense, 37

EniJlllluckn ... ll>, ,12

Energy. I. 2.

Ene:fSY oe fJCLiv l,iOll, 20 En7.yrnc, 19.20. 'M En7.ymc-~ubmn(1: complex, 20 Epitncr. 5R

Epimerns ,20 Epinephrine, 88 Erylhromycin, 53. 54

I:!: seRlinl amine ncids, 12 Elho.uol,01

EukJll')'OICS, 38, 4l

xnuuclense, 37 EXlrin~ic plnh, 3

I ubry's. 93, \111

Fnctor 8 delld sncy, 95

nelor 9 dcJi i ney, 9 Factor VLU, 4

r.mili~1 t1ysb<;.lol ipoprotcinemla, 7S,on Famililtl hY))lll1.lhOlcslcrQh;mir., 76, III PamiliAI L AT deficiency, 92

Pnrnilinl lipoprotein lipase d ,n"lency. 92 Fnl.!I

Fnt-soluhle vlunnins, 82

ftlly aeid llcgrodnlion. 78 F' Lly meld synlh,lSC, 77

FUlly ncld ~Ylllh,csi~, 76, 71. 78 !'ibnn.33

l'ibrinog n, 2~, 33

Pi rst order, 23

FlIJVOproIC.irl,67

Pluorodl nhrobenzene, 18 S·PluorOllrn il.;S

FolI.tc.1I6

Polic ncld, 85 Formyllllcthion,,>o, 'l7, 118 Pom\ylmclhjOIl)'I-II~NA. 49 I·omlyhetn,hydrv(olnlc. 47 I~nllnc alMI mutations, 52 Pruclose 1,6 bill'llosph,(tMc, 65 Fumnrnlc. I, 70

o loolokinasc <Iorioienc),. 90. 96 OOluClOsumlt,. 611

Gaucher's, 93, 98

Gel-filtrutlon dll()fl1f1I(1srnphy, 34 Ghu:nt;(III, 86. 101 GlucocerobrosidllSe.93 Glucogonic, 1('111

,llIcokinll.~C, 63, 64

Gluconeogenesis. M, 100

Glucose, 64, 67, 71. 116 GluCQ:lC·Ii-pho~pIJlllC dehydrogenase, 69 Glucosc-e-phosphmnsc, 65

Glu iuronie It 'id, 2

Olllt81llUle. 27 Glutamic acid. 10 Glllilillii" ,10,12 GIIJIniJ1iol1 " 68 Glyt'Crol, 72 Glycine, 8. 12, 31

tycogen, 5. 60. 66

lycogcn slomgc disonlcts. 91 Glyoogenolysis, 66 Glycolysis. 61, 62. 63. 100 Glycolytic palhways. 62

lycoSllJl1inogly lit. 29 Glycosidic bonds, 59 GJyc,osyloscs. 42 GMI'g(lflllliosido~i8, 93. 98 GrOWlh hormone, 87

unn dluo hydrochloride, 19 GII~ni nco 3.5, 3(j

GUlllric test, 90

Gyrnso, 40. 5

rl~i(pill loop. 43 Hartnup diseuse, 12, 95 Bb Ate, 211

tn 1-,79

Helix, JB

Hcl iJ!·dcStnbdi1.1 ng prtncins, 40 ImME. I

Hemoglobin. 28. 9S Herncglobln (Hb). 27 IicmOllti)b\nopothies .. 95 Hernnslderosl . 95. 9!1 Jlcnders_n-lIl1$SClbach.2 I-Ieparin, 29

Hers, 91.97

Hercrouoplc t;117,Y"'c, 21 Hexokinase, 26. 63. (>4

H sxosnmine, 3() Hexcsnminldase A. 93

Hexose. S6

Hexose monophosphme hUIII. ()9 I·IOPItl'.93

II i&Lidinc, 10, II Hisrkllnernln, 96 IIiHI()"C~, 39

HM • "'01\ redIJCII~C. 1 1101 enzyme, 21 Ilolllocy~t<llnc. 103

l lumocystlnurin, 9{), 96 l lomogentisme, I

INOEX 111

H2 IN

110m It nl 'al'- cJ>.ith.'IC, 31 lIomog<ltl tc:-1,2-dil1xygcnll.'C,31 Ilomol'"p'c cnt)llnt, 21

11'~n"o'~ .... n~hiv~ lipase, '1'1.77

H noone •. B6

Hunl'r'$, '} _ 97

Hurler'j, 92, 98

Uyd"'1m~, I B

Hydrol)'si ,17

2~·hyd""X)'ch"l· ,1c]f.:roI,1.I lIydro )'1)'&yl, 29

J-lIyJrm.y- ."'rlh)'lgluIMyl CoA. 7~ IIypcrglycc,n, c e !flXl. 66

Idurn" 1(' sui raIn,' ',9'2.97 Im;no" 111.11 Imll""'Ol\IQb"',,,~. III Induced Illlhcory. 21

Indll r, 'II)

r nhibitOl. • 25 lnirlntlon. .1). 'IH Iniliatlon cUl11pl~~. 'IS 111,1,"111111 lnctor •• I~ tnse II idc.', 2!1 Inseniou nmnniuu, 10""'". Hb, 101 lntnn\,c r~clOr,1! Inlrin,j( 1I",h, 3.1 h"lId ,8S

Inn e h""ge l-nrumllh'£, phy, J.I I"";,, cx,",m'-'I,Ie chrumBIl1I'mphy. 1'/ h""-'I'horc.~, J I

Iml1.119

Incyc,.lhk i.-.hib,lllflo. l'ocilrlHC, 7(1

I.. ;IMle t1t::hydmgcllo5C. 70 1~"/ymc~. 21

tseleu inc, II

r"'''H:I1I>c. II

t.tltl! OCl"O, 58

bun r" kl, t\il

Kn, Kernln.230

K ·to: cid",h. M KCI 'genic, I n~ KClI(,,,,,,,.57 Keto,i •. (,7

Km.",.20

Kin lie order, 2

K~ h'~ cycle, ?(), ICIO Kw.sh,o".lIf, 14

1..11 mse deli icney. 8 I eLlie, 71

>ctole J<lh.ydlo1_;cll t.e.21 lo,~', SO, ~9

lose mnlt_liJie:~1 on, ,R gll;n!! .. ,n.l. 41 Lnuric .CIII. 71

1.1)1.. "19

I, .. mdint: -'I •• nd, 41

I..«itlrln 011111 '1<1(11 ""yl 1r.U\_<re • ..., r A'I. -/1) I ·.,;h·Nyh,,",9 ,!1M

Leuc;ne, M

l.<!ukotricI"" II I

r -"YOl'Olm,)1 Y. 12 I.'e""", .1'1, MI

1IIIc'~;tYcr lJurke plOI, 2·, Liflulerc &1:111, I

Llpid dlsor,1 IS, <) 1 ')2 Lipi.h. 1 , 7,1 L'J>Oprol"rn Iop.cw. 7(, 1.ir'''''Y~.fI nse , K I

Liver py,\JYt>1C k 1""' e, ~~

I ~ ,,,,ol key IJlem}" 20 Lysine, 10,12. lit Lyso,,,mul dj~II'oC~. 1)2- 93 I.y'yl.· Q

M"",,c, /11

Mal. ie dchyd"'Hc"a~c. 70 Molllnlllc, (,7

Mol" u yl C'oA, 77. '/9 Mrolu,," •• ,

Mapl- 'yru" """' ,Ii...::a!.<;, I) I. ')7 M"m,onll~, IS

Mlllfm,'. syr"'n'm~,I)S

Milner. I

I\IlcA"lIc',. 'II. 'n

!\II 'Ilnlohla5li n nna, H·I. M MeI"nin. 102

Melling !llll'IX'lal!lrC, 51 M'crul'Ktllllln. ·1 MClhclIIOglull1l1, 27 MClhioniuc. ~ .. 1-' Me'h[llre~"IC, 4 Mclh~ln'"lol1yl (' .. A,M. !OJ

Mcvaioni !\Cill. 77 Mcvimllin. 110

Mi haells-Mentcn l'.<lIJaliufI. 23 Mi5scn~c lIlulMion, 51 MOI1(lCisIIVnic. S Mono~!)c(hnrides. 56

Mil ·ol'oly sn cdmritill ,,91. Myoglobin. 28

Myosin. :'IU

NAD+ dCl>cndcnl d~h)'urt)gCI1a&Cs. 70 NAI)II.6'l

NADII dehyurogenusc, 68 NAI)I'I'I.dclI"'ld"nl gluunhione, (,R N"II<1ixic !lcill. 53

Ne rve 8:1$. 25

Nmcin, 84. HC,

Nlcolinic acid. 1:14. S6 NiQllmnn-Plck.·s. 93. 9& Ninhydrin. 17

N i1rosen b,,!uncc. 13

Nitrous ecld, tl2 NOfl.compelilivc inhilJition. 25 Nonsense rnulmion. 51 Norcpincphrin·. 88 Novobiocill. 53

N"d,,,, .. ses, 7

(II "cleo, de. 3(i

NuclcOSOnlCS. 39

Nucleotide. _ 6

Nucleotide rnerebolism, 104

Okll:lAki (rnSl1lcnls, ,,! Oleic, 7

Old ociol,73 Oligo$llcchnridcs, 9 Oller n.49

Oro1icill .clivil),. 12. 5g Orll~l1o-phosphnlCS. 2S Ornilhine, Ill)

Ornlthluu cnrhaliloyltrnnsrCtllte. 102 Or"ilhin~ ImnSCnrbl)lIIllylssc deficiency. 90 Olon,le, IQ(,. 107

OrOlic aciduria, 94. 98

O,.m(l,i~. 1

l)81o:"r,~III:~i~ irnllerfccm, 95 O~ICl)III. ineill. 8 . 85 (hl,lollc':llIle, 70

)~ill"Ii'lI1, II. n. 79

ChyS"" diSSOI:ialioil curve, 28

INOex 113

:1.14 INOEX

Proline, 9. 12 l'I'OI11Q(cfS. 45 Prostllc),clin.29 l'roSloglondin, 7' , 8.1 PrO$IIIr;lic gltlllp. 21 Proleln. :I. 49

Protein syntlH:lii. inhibitors. 53 ProlcoglYClIJls. 30 ProlJlrombin, 29. 33 Proloporphyrin.IX, I ProtOllOrphyrinogcn IX, 31 Purine. S.52

PlIrif!Q nu IWLioo dcgm\lnliOIl. IDS Purine nuctceilde ~yntllcsis. 104-105 Purioe ring S1ruChJfC: I Q.I Puromycin, 53, 54

I'yridoxinc, 83. 86

l'yrilllidillC. 35, 52

I yrilllidtnc nucltolicJt d"grtldaliol1. I OS Pyrimidillc ring, 106

11yrirnilHnc ,synlho::sis. J 06

PynlVol c, rho,),1 se, 65

PYnlvOlc dchydrogcnn~c. 26

Pyruvnte kimt~e. 211. 62, 63. 64

1'50. 28

PnlimlrOfllcS, 3'1

J'nlmili . ne,". 73 I'ohuilnleic acid, 73 1'lInnc,"li' lipase, 14 I'nllcn:Mlc lipMCS.1 l'oHtolhcni' Deill, 8'1, 115 Pnpnin.26

l'~mlhyfIJitl harmon e. 87 ('"nng.'''' n, II . M l'enlOsc. 35. 56

l'cntosc phosplUlIC Il~Ulwuy, 69

"ellSin.26 '

('cps i uogen, 2()

l'Cl'li"" bond. l:i

PClnld ·S. 15

Pcplitlyl ImrlSfcl'll.SG. I'cplillyl-IRNA. I "cplidyltrnn5rCm~". S

I'crni ious lIncll\m. 114.116 1)11,22 Phill1yll80tlliocyg!l~IC, III Phenylolnn!n ,8, I. 102 1)1","ylkcwu,,,jn, 90,96 f'hosphoglycemlc kimlsc. M PhoSf,I1~le. J(i Pll()Sphnlldmc. 74

l'hOSI)hOCllolpyrw,nlc c",bo~ykllltlSC, (,6 Pho~phornlclukil1"sc, 26. M Pho~Jlholipids. 81

l'hrn>phoryll1'><l II kinll."C deficiency, 91 Pho,phoryluliull.22

Photons, I

I,K~. '2

Pla~lIIid '. II

l'lMrnill,29

Poi II I mutntiens, 52 I'OlYIJej!li<les. 18 l)ol),sll<:dHlridlls. 59 polysome, 0 Porl,hQbiUnogcII. J I

Il'ri 111ar), uucture, IS l'rimf1se.40 Pm,;ollr'Il¢". 29

I'mdu I. 20 r'rocIl1.yrncs. 26 I'l'uknf)'otes. JS. "II, 43 I'n,k"tyoll' DNA. 38

Qunlcmnry structure, 17 Quinolon<,S. 5

Rnle COl1SLDJlt. 20

Reu blood cell, 68

Reduction. "

Rcgul lor, 50

RC,lliclIlion. 35

RCllres,sOT,50

Respimlury chain, 67 Rc,~pjrtllory quouem, ~ Restrictlon cndonll leftS • 37 RCIlnol,82

Ribonllvin. 113, 86 Rlbcnucleotldes, lOS

Ribose, 35

Ribosomal subunit. 46, 47 RibosomC5,45

Rlckel.s, 83, 8S

Rlrllll1pin, 53

Rjfll.m),oin 1.1, 54

Ring (om18. 58

RNA, 35, 43. M. 45

RNA pelymerase, 43 RNAI.lOlymel'!lSC fT. S3

ROiCIflol1c.67

S-ntlcnos~hnelhionlne (SAM). 101 Snliv:Ir), n-(lIlI.ylnSI), 61

Snl".gc p,lhw3)' of purines, 106 Sonnlillpo·S. 92. 9t\

Sn,"gCJ" n"'lho<l, 18

SIII.ur:Ued rlllty acid, 72. 73 Schcle's, 92, 97

Scurvy. 85. 86

Second onlur. 23

S~ondn.ry structure, 15

Secrelin. 88

Sernlconservndve repllcarlon, 40 S rlne. 9. II, 12

Shlnc·DlIlgDJ1lo sequence, <17.48

i klc-cctl nnernln, 27, !.M. 99 Side chmns. 8

Si81U~. rn~lot. 44

5ilcIII II1Ul. Ii n, 51

Sodium n7jd~, 68

Speciflc dynnnlic nction, 6 Spcc.ifi ily. 20 SpeCt:n'lpIIOl0mclry. 17 SpllingQ1il.ldose. s, 80. 93 s p II ingol i pids, 80 Sphingomyelin, 80 SphlngQIl1)'clloIL1C,93 Sphingosine. ~O

Squnlcne, 77

Sinrehes, 60

SICllric acid, 7

SI rcobllifl, 32

Sum:oi ol11Qf1I.58

Sicroid hormones. 88 SlfCl'tom),cill.53 Subssrnte, 20. 22 SUCC;''''IIl. 70

SUCCiMlc dch.l'dros""n.sc. 67 SIiC inyl oA,31

Sucrose, 59

Sv~Jberg unit, 4S

Swiycln: .. 40

T"ngier's dise se, 92, 97 Tnnrocbelate, 80

'I'ay.Snch·s (Ii case. 81, 9 • 91\ Tcmpernlure. 22

Termlnntion, 43. 49

Tertiary suucturc, l6

Tel.rncycllnc, 53, 54 Tell1\hytlrQbi· pterin, 102 TCLrnliydr"Orolohl. 85

Te trose , 56

111011Jll~cmiu. 95, 99 'Theophylline, 89 111illOlin • 83, 85 l1lI'Cohinc, 9, II, 104 11lrOllIbin. 29. 3 111romoosis, 29 Thromoox.nnc A2. 21) 111)' m I nco 35, 36, 53. 108

Thyroid ~li11lul(ltjng hormone rrsu). 88 Thyroxin (,f4). 88

Topol omerase, '10. "

Talnl energy I'e<lulremc.nl. () Tmnscription, 2. 35. 43.45

Trnnsltlnn muuaion. 52

Trnnslntlon, 2. 35

Tmnsloeauou, 49

1'r.l.I1spon. 3

Transversion mutation, 52 Trlacylglycerol, 75 Triglyceride, 12 Trilcdothyrouluc (n). 88 Triesc, 56

Triplcll code, 5 1

Troponlu- • 30

Trypsin. 28

Tryptophan. 9. 12

1'ypo A blood. 32

Typo AD blOOlJ, 33

Type B blood. 3

Typo 0 btood, '2 Tyro$ino,9, 11,31, 102

iNIJf.)C .U5

U.V. ndomlcJ':t.~I), 42 UI\$lIlumled (ally IIdd. 72 Umcil. 35. J7

Urcll. 19. 103

U['Cj'j cycle, 102-103

Ure" cycle dlsonlcrs, 90-91 Uric acid, lOS Urobilinogen. 2

U roporph yo nogcn Ill, 1

MEDICAL REVIEW SERIES

~

VolillC, 8. 21 V"~OI)rcs..in. 117 Vilamin A. 82. 115 Vitamin Ill, 83. 85 Vitnmln n12. 84. 86 Vitamin 92, 83. 86 Villll)1lfl 86. 83, Sf! Vitamin C. 85 VirllJ11in D. 82. 85 Vilnmin E, 83. 85. 8() Villlm;1l K. 29. 8J, 85 Vitamins. 82-86

Von Gierke'», 91, 97

Biochemistry

Second Edition

Compiled and Wrmen by Nlkos M. Linardakls, M.D. and

Christopher R. Wilson, M.D.

Willer-sol uble vii 1111;11 • 83-85 W-n1id Korsllkorr ~)'ndronle. S3 WiJ.s n's diwa.s', 94,99

Wobble. SO

Xeroderma pigmcfllosul'fI. 42, !).,I, 99

Zero order. '23 Zwhlcrlmu, 12 Zymogen, 27. 3.1

McGRAw-HIll

Health Protesstons Division

New YOlk St. LOllis Sun Francisco I\IJC/(llJnd BogoltJ CtlrlJClIS usoo« t.onnon Madrid MOJ</co City Milan Montreal Now De/Ill San Jue« Singopore Sydney Tollyn Toronto

~ ~

MEDICAL REVIEW SERIES

(;:::::::;=9

Prepare to Iearn r 'nle DigClnB Up the BOlles Medical Review Series is a COITIpilation of concepts fn:qllcnlly seen in course exams and on USMLE Slep I. This volume offers a clear, concise, and to-the-point presentation or the facts you need 10 succeed in Biochemistry. 'Ole Digging Up tire BOlles review series is designed 10 complement your curse work. providing in a brief format items you need to review in a subject. Pay particular attention 10 bold or itolicited words. We recommend placing notes in tl, margins and reviewing the material at least two times. Try 10 make usc of any old exams tha; arc available 10 you, these ar sometimes cam d in your library, by other stud snts in the year ahead of you, or Lhrough the professors who leach the course. A final lip: Usc this book 10 preview material thar will be cover d on the next day of ChillS and you wiJJ be surprised with how much more you gel 01.11 of lectures.

Biochemistry

Best of luck.

Ix

viII

CQl'lrr;NI5

ChapterS

Biochemical Disorders

90

ChI3pter 9 Miscellaneous

100

Index 109

Preface tx

Cf)spier 1

General Biochemistry

1

Chapter 2 Metabolism

4

Chapter 3

Amino Acids and Proteins

7

Chapter 4

DNA, RNA, and Protein Synthesis

35

C/Japter 5 Carbohydrates

56

C/lapter 6 Uplds

7.2

Chapter 7

Vitamins and Hormones

82

vii