BIOCHEMISTRY

PREPARED BY:

EDWIN S. TATAD JR., RPh

MODULE 2 – PHARMACOGNOSY (15%)

1. BIOCHEMISTRY
2. PLANT CHEMISTRY
BIOCHEMISTRY – is the study of chemical and physicochemical
processes that occur in plants, animals and microorganisms.
4 BIOMOLECULES:

1. PROTEINS
2. CARBOHYDRATES
3. LIPIDS
4. NUCLEIC ACIDS
1. PROTEINS

-constitute to 70% of the organic matter of a cell. The simplest

unit of proteins is called AMINO ACIDS, and proteins are
polymers of these repeating units linked together by a
PEPTIDE BOND.
1A. AMINO ACIDS

-are building blocks/ monomers of proteins

-are organic molecule containing both CARBOXYL and AMINO
FUNCTIONAL GROUPS.
-there are about 300 amino acids occurring in nature BUT only
20 are commonly occurring and are constituents of proteins
(PROTEINOGENIC AMINO ACIDS).
-Amphoteric
ALL THE 20 PROTEINOGENIC AMINO ACIDS CONTAIN:

1) Alpha Carbon - holds the functional groups. The alpha

carbon is a CHIRAL CENTER.

2) NH2/Amino Group – basic; the focus of D and L isomers of

amino acids.

3) COOH/Carboxylic Acid – acidic

4) R Group/Alkyl Group
THEORY ACID BASE

ARRHENIUS Yields H+ Yields OH-

BRONSTED-LOWRY Proton donor Proton acceptor

LEWIS Electron acceptor Electron donor

(metals) (EDTA, Ligands)
BRONSTED-LOWRY THEORY
*Acid – proton donor
*Base – proton acceptor

COOH IONIZATION COOH- (when acids ionize they bear

negative charge)

NH2 IONIZATION NH3+ (when bases ionize the bear

positive charge)
CLASSIFICATIONS OF AMINO ACIDS:

1) BY R GROUP
a. Nonpolar – C-H or C-C
b. Polar – OH, SH, NH
c. Acidic – has 2nd COOH
d. Basic – has 2nd NH2

2) BY METABOLIC FATE
a. Ketogenic
b. Glucogenic
c. Both Ketogenic and Glucogenic

3) BY IMPORTANCE IN DIET
a. Essential
I. BY R GROUP

IA. NONPOLAR AMINO ACIDS

1. Glycine (Gly, G)
-smallest
-the only ACHIRAL amino acid (chiral: has 4 different substituents/functional groups)

2. Alanine (Ala, A)
-the frequently transaminated Amino Acid (ALT)

3. Phenylalanine (Phe, F)
-aromatic amino acid (tyrosine, tryptophan)
*XANTHOPROTEIC TEST:
-Rgt: Conc. HNO3
-(+): yellow ppt

4. Valine (Val, V)
5. Leucine (Leu, L)
6. Isoleucine (Ile, I)
-Valine, Leucine and Isoleucine are BRANCHED AMINO ACID
-Increased levels: MAPPLE SYRUP URINE DISEASE
7. Methionine (Met, M)
-Sulfur-containing Amino Acid
-test for the presence of Sulfur: LEAD ACETATE TEST
*Rgt: Pb Acetate
*(+): Black ppt
-”thioether” R-S-R

8. Tryptophan (Trp, W)
-aromatic
-Indole-containing
-test for the presence of Indole: HOPKINS-COLE TEST
*Rgt: Glyoxylic acid
*(+): violet ring
-precursor of serotonin (5-HT)

9. Proline (Pro, P)
-an imino acid
-NINHYDRIN TEST: general test for Amino Acids
*(+): violet
*(-): yellow (proline)
IB. POLAR AMINO ACIDS

10. Serine (Ser, S)

11. Threonine (Thr, T)

12. Cysteine (Cys, C)

-Sulfur-containing (LEAD ACETATE TEST: black ppt)
-thiol-containing
-test for the presence of thiol: NITROPRUSSIDE TEST
*(+): Red
-component of Glutathione (together with glycine and glutamic acid)

13. Tyrosine (Tyr, Y)

-aromatic
-the only phenolic amino acid
-test for the presence of Phenol: MILLON’S TEST
*Rgt: Hg2+/Mercuric Ion
*(+): pink/rose
-precursor of catecholamines (Epi, NE, Dopamine)

14. Asparagine (Asn, N)

15. Glutamine (Gln, Q)
-Asparagine and Glutamine are AMIDE AMINO ACIDS
IC. ACIDIC AMINO ACIDS

16. Aspartic acid (Asp, D)

17. Glumatic acid (Glu, E)

ID. BASIC AMINO ACIDS

18. Lysine (Lys, K)

19. Histidine (His, H)

-imidazole-containing
-test for the presence of imidazole: PAULY’S TEST
*rgt: diazotized sulfanilic acid
*(+): red
-precursor of Histamine

20. Arginine (Arg, R)

-guanido-containing
-test for the presence of guanido: SAKAGUCHI TEST
*rgt: alpha-naphthol
*(+): red
II. BY METABOLIC FATE

1. Ketogenic (LL)
-Lysine
-Leucine

2. Glucogenic
-the REST

3. Both Ketogenic and Glucogenic (FITTT)

-Phenylalanine
-Isoleucine
-Tyrosine
-Threonine
-Tryptophan
III. BY IMPORTANCE IN DIET

1. Essential/Indispensable Amino Acids

“PVT TIM HALL”

* P – Phenylalanine
* V – Valine
* T – Threonine

* T – Tryptophan
* I – Isoleucine
* M – Methionine

* H – Histidine
* A – Arginine
* L – Lysine
* L - Leucine
IONIZATION OF AMINO ACIDS

*NH2: pka value = 8

*COOH: pka value =2

decrease pka value = increase ka (acid dissociation constant) = increase acidity

If PH < PKA = protonated (with H or with more H)

if PH > PKA = deprotonated (without H or with less H)

ex.

1. COOH >>>>>>>> COO-

(p) (d)

2. NH2 >>>>>>>> NH3+

(d) (p)
IONIZATION OF AMINO ACIDS

*NH2: pka value = 8

*COOH: pka value = 2

1. Determine the charge of Amino Acid X at pH=1

*NH2: pH < pka (protonated)

*COOH: pH < pka (protonated)
*charge: +1

2. Determine the charge of Amino Acid X at pH=4

*NH2: pH < pka (protonated)

*COOH: pH > pka (deprotonated)
*charge: 0 (zwitterion)

3. Determine the charge of Amino Acid X at pH=12

*NH2: pH > pka (deprotonated)

*COOH: pH > pka (deprotonated)
ISOELECTRIC PH CALCULATION

*Isoelectric pH – the average of 2 pka values flanking zero

*if the Amino Acid is ACIDIC, get the average of 2 SMALLER pka values.

*if the Amino Acid is BASIC, get the average of 2 HIGHER pka values.
1B. PEPTIDE STRUCTURES

-Peptides are small proteins, containing two or more amino acids connecting to each other through amide formation involving the
carboxyl group of each amino acid and the amino group of the next amino acid held together by a PEPTIDE BOND.
PEPTIDE BOND

-A chemical bond that formed when carboxyl group of one molecule reacts with the amino group of
another molecule, releasing a molecule of water.

-A bond that holds 2 amino acids together

-An amide type of covalent chemical bond

-has a partial double characteristic

-Rigid, strong; proteins are not easily moveable

LEVELS OF ORGANIZATION

1. PRIMARY LEVEL
- sequence from N-terminus to C-terminus.
- involves formation of peptide bonds
- refers to the linear number and order of the amino acids present.

*Changing the sequence, changes the function of amino acids

-ex:

*Regular Insulin: short-acting

*Insulin Lispro: rapid-acting
*Insulin Detemir: long-acting
2. SECONDARY LEVEL
-addition of Hydrogen bonds.
-repeating patterns

-ex.

*Alpha Helix
*Beta Pleated sheets
*Collagen Helix
*Beta turn
*Random coil
3. TERTIARY LEVEL
-refers to the complete 3D arrangement of single peptide chain.
-involves residue interactions.

-ex:

*Hydrogen bonding
*Hydrophobic interactions
*Electrostatic Interactions – are Ionic interactions
*Disulfide Bonds – bond between 2 sulfurs
*Van der Waals forces

”Native” Conformation
-default/normal conformation of proteins
-Folded proteins – functional proteins

Denaturation
-deviation from native state
-example of denaturing agents:
*heat
*extremes of pH
*Chemicals (urea, guanidine, mercaptoethanol)
 -if proteins are denatured, it lose its function

Renaturation
-return form denatured form to its native state

PROTEIN MISFOLDING DISEASES

-Functional proteins: folded
-misfolding of proteins causes diseases

a. Alzheimer’s Disease

Amyloid Precursor
Proteins (APP) secretase AB40 + AB42 misfolding aggregates/fibrils (brain)
(triggered by Aluminum)

b. Bovine Spongiform Encephalopathy (BSE)

-aka “Mad Cow Disease”
-caused by Abnormal/Misfolded proteins
-was first thought as viral disease
-Manifestations in cows/cattles: restlessness, paralysis
c. Creutzfeldt-Jakob Disease
-caused by prions
-rare, kuru-like infections causing dementia

d. Variant Creutzfeldt-Jakob Disease

-transmission of BSE from cows/cattles to humans
-abnormal prions are heat and protease resistant and can make a normal prion misfold

e. Kuru Disease
-aka “laughing death”
-cannibalism
-it started from a tribe
4. QUATERNARY LEVEL
-associate with 2 or more peptide chains/subunits.

-ex:

*Myoglobin : single unit (Tertiary level)

*Hemoglobin : tetramer (Quaternary level)
-contain 2 Alpha globins and 2 Beta globins
CLASSIFICATIONS OF PEPTIDE

1. BY SHAPE

a. Globular Proteins
-water-soluble
-compactly folded and coiled

-ex:

*Plasma Proteins
Albumin- binds acidic drugs
Alpha-acid glycoproteins- bind basic drugs

b. Fibrous proteins
-water-insoluble
-filamentous or elongated

-ex:

*Structural Proteins
2. BY COMPOSITION

a. Simple Proteins
-are composed of amino acids only
-ex:
*globulins
*albumins
*glutelins
*prolamines
*histons
-glutelin and prolamines are collectively called GLUTENS
-inability to digest glutens can lead to CELIAC DISEASE

b. Conjugated Proteins
-have additional components
-ex:
*chromoprotein (Hgb)
*lipoproteins (LDL, HDL)
*Glycoproteins (mucus)
*nucleoproteins
3. BY FUNCTION

a. Structural Proteins
-ex:
*collagen
*keratin
*elastin

Collagen
-most abundant protein the body
-triple helix; rich in lysine and proline

proline hydroxyproline
lysine hydroxylysine
-they need cofactor: Vit C/Ascorbic Acid/Cevitamic Acid (old name: Antiscorbutic acid)
-Scurvy: defiency of Vit. C, bleeding gums
b. Transport Protein
-ex: Hemoglobin (Chromoprotein)

c. Storage Protein
-ex: Myoglobin

d. Regulatory Proteins
-peptide hormones
-ex:
*Insulin (decreases blood sugar level)
*Glucagon (increases blood sugar level)

e. Defense proteins
-ex:
*antibodies
*immunoglobulins (G, A, M, E, D)

f. Catalytic Proteins
-enzymes
1C. ENZYMES

-catalytic proteins/biological catalyst that significantly speed up the rate of all of the chemical reactions
that take place within the cell. They are vital for life and serve a wide range of important functions in the
body, such as aiding in digestion and metabolism.
-the molecule to which enzymes may act are called substrates, and the enzyme converts the
substrates into different molecules known as products.

-most enzymes are proteins (some are ribozymes)

-binding is necessary
-ALL enzymes are specific. ALL enzymes are saturable (they have limitations)
THEORIES OF BINDING

a. Lock-and-Key
-rigid
-requires on 1 subtrate

b. Induced Fit
-involves conformational adjustment in the active site of the enzyme to make the
substrate fit.
COMPONENTS OF ENZYME

*Apoenzyme: protein portion, inactive

*Cofactor: nonprotein portion, activator
*Holoenzyme: apoenzyme + cofactor, active form of enzyme.

COFACTOR- may be organic or inorganic

a. Inorganic- obtained from metal ions/trace minerals (Fe2+/Fe3+, Co, Cu, Zn, etc)
b. Organic- aka “coenzyme”, derived mainly for B Vitamins.
-ex:
*B1 (Thiamine) – TPP (Thiamine Pyrophosphate)
*B2 (Riboflavin) – FAD (Flavin Adenine Dinucleotide)
*B3 (Niacin) – NAD (Nicotinamide Adenine Dinucleotide)
*B5 (Pantothenic acid) – CoA
*B6 (Pyridoxine) – PLP (Pyridoxal Phosphate)
*B9 (Folic acid) – THF (Tetrahydrofolate)
CLASSIFICATION OF ENZYMES
-based on Enzyme Commission (EC)
-based on the chemical reactions they perform
- “O T H L I L”

EC #1: OXIDOREDUCTASES – catalyze redox reactions and have NAD+/NADH/FAD+/FADH cofactor

Oxidation Reduction
-addition of O -removal of O
-removal of H -addition of H
-increases number -decrease number
of bonds of bonds

ex:

a. Oxidase/Dehydrogenase
b. Reductase/Hydrogenase
EC #2: TRANSFERASES – catalyze the transport of 1 functional group from one molecule to another.

ex:

a. Hexokinase f. Aminotranferase
b. Pyruvate kinase g. Transcarboxylase
c. Phosphofructokinase
d. Glucose-6-phosphatase
e. all enzymes in PHASE 2 METABOLISM

EC #3: HYDROLASES
-perform hydrolysis/breakdown by addition of water
ex: NEPULAM

a. Nuclease f. Pepsin, Trypsin and Chemotrypsin (for Hydrolysis of CHON)

b. Esterase
c. Protease, Phosphatase, Peptidase
d. Urease
e. Lipase, Lactase
f. Amylase
g. Maltase
EC #4: LYASES
-catalyze nonhydrolytic cleavage
-removal of a functional group to form double bond or breaking of a double bond by an interaction of a
functional group.

ex:

a. Deaminase (remove NH2)

b. Decarboxylase (remove COOH)
c. Dehydratase/anhydrase (remove H2O)

Carbonic Acid Carbonic anhydrase CO2 + H2O

(H2CO3)

EC #5: ISOMERASES
-interconvert isomer and catalyze intramolecular rearrangement of atoms

ex: RIME

a. Racemase
b. Isomerase
c. Mutase
d. Epimerase
EC #6: LIGASES/SYNTHETASES
-perform condensation reactions
-catalyze reactions that join 2 molecules forming a covalent linkage using an energy released
from hydrolyzing a pyrophosphate bond.

ex:

a. Synthase
b. Synthetase
c. Carboxylase (add COOH)
ENZYME KINETICS

-is the study of the rates of enzyme-catalyzed chemical reactions.

-in Enzyme Kinetics, the reaction rate is measured and the effects of varying conditions of the reaction are investigated.
-is illustrated by Michaelis-Menten Plot and Lineweaver-Burk Plot/Double Reciprocal Plot
*Assumption: Increase # of Substrates (S) = Increase Enzyme Activity (V)
Km (Michaelis Constant)
-amount of substrate required to reach ½ of Vmax
-reflects a substrates’ affinity for an enzyme
-”how well the binding is”

*Increase Km = Decrease affinity

*Decrease Km = Increase Affinity

-Km is INVERSELY PROPORTIONAL with affinity

EXTERNAL FACTORS AFFECTING KINETICS

a. Temperature
-each enzyme has a temperature range in which the maximal rate of reaction is achieved. This
maximum temperature is known as Optimum Temperature. The optimum temperature for most enzyme
is 98.6 F/37 C
-beyond optimum temperature: enzyme is denatured

b. pH
-the pH in which the enzymes are most active is knowns as Optimum pH.
-the Optimum pH of an enzyme depends on which it normally works. For example, enzymes in
small intestines have an optimum pH of 7.5, but stomach enzymes have an optimum pH of 2.
ENZYME INHIBITION

-interference with normal enzyme activity

-an enzyme inhibitor is a molecule that binds to an enzyme and decreases the enzyme’s activity.
-when an inhibitor binds to the enzyme’s active site, the inhibitor reduces the compatibility of the substrate and enzyme which
leads to the inhibition of ES complex, preventing the catalysis of the reaction and decreasing the amount of product produced by
the reaction.
-Basis of many drugs
-Types:

a. Competitive Inhibition – inhibitor targets the active site

b. Noncompetitive Inhibition – the inhibitor, instead of binding to active site, targets different site known as the “allosteric site”
c. Uncompetitive Inhibition – the inhibitor binds to the ES Complex
- still an allosteric site
*Competitive Inhibition
-Vm: Same
-Km: Increase
*Noncompetitive Inhibition
-Vm: Decrease
-Km: Same
*Uncompetitive Inhibition
-Vm: Same
-Km: Increase
2. CARBOHYDRATES
2A. INTRODUCTION

-Hydrates of Carbon, Carbon with H2O

-contain Carbon, Hydrogen and Oxygen
-polyhydroxyaldehydes or polyhydroxyketones
-classified by the number of units
-can be polymeric
-General formula: CnH2nOn or (CH2O)n
CLASSIFICATION OF CARBOHYDRATES

1. Monosaccharides – also called “simple sugars”, are the simplest form of sugar and the most basic
form of carbohydrates.
- cannot be hydrolyzed because they have no glycosidic bonds yet.
- further classified by:

a. Functional group
*Aldose: glucose, galactose, xylose, ribose
*Ketose: fructose, mannose, xylulose, ribulose

b. # of Carbons No. of Carbons Category Name Example

3 Triose Glyceraldehyde and Dihydroxyacetone

4 Tetrose Erythrose and Threose

5 Pentose Arabinose, Ribose, Ribulose, Xylose,
Xylulose

6 Hexose Glucose, Galactose, Fructose, Mannose

7 Heptose Sedoheptulose
9 Nonose Neuraminic acid/Sialic acid
2. Oligosaccharides- 2-10 units
Disaccharides- 2 units

ex:
*Sucrose: glu + fru
*Maltose: glu + glu
*Lactose: glu + gal

Sugars- are either mono or disaccharides that taste sweet.

3. Polysaccharides – many units

-further classified into:

a. Homoglycan – same repeating units

*Starch – glucosan, storage polysaccharides in plants
*Glycogen – glucosan, storage polysaccharides in humans and animals
*Inulin- fructosan
*Dextran – glucosan, from Leuconostoc mesenteroides, plasma explander (A/E: Anaphylaxis)
*Cellulose - glucosan, structural polysaccharides in plants
*Chitin – homoglycan of NAG (N-acetylglucosamine)

b. Heteroglycans – different repeating units

*Gums and Mucilages
USES OF CARBOHYDRATES

a. Energy
*Immediate: glucose (mono)
*Stored: glycogen (poly)

b. Structural – cell walls

*Cellulose: plants
*Chitin: fungi, exoskeleton of crustaceans

c. Signalling
*ABO Blood types

d. Pharmaceutic
*Lactose: diluent in tablets
*Sorbitol and sucrose: sweetener

e. Pharmacologic
*Lactulose: stimulant/irritant laxative
*Sucralfate: anti-ulcer
*Mannitol: osmotic diuretic (parenteral); osmotic/saline laxative (PO)
*Heparin: anticoagulatant
2B. LINEAR STRUCTURE
-illustrated by Fischer Projection and Ball-and-stick Model

PENULTIMATE OH- OH of the 2nd to the last carbon

*Right: D
*Left : L
2C. CYCLIC STRUCTURE
-sugars cyclize in aqueous solution
-cyclization: Penultimate O attaches to the Carbonyl (C=O)
-illustrated by Haworth Projection
Anomer – only applicable for cyclic structure
* OH up: Beta
* OH down: Alpha

D-glucose cyclize D-glucopyranose (Racemic)

D-fructose e cyclize a-D-fructofuranose

2D. ISOMERISM

1. Anomers – for cyclic

2. Epimers – only 1 chiral carbon difference
3. Enantiomers – ALL chiral carbon difference
4. diastereomer – neither #2 nor #3

ex:

* D-glucose and D-mannose: 2-epimer

* D-glucose and D-galactose: 4-epimer
* D-glucose and L-glucose: enantiomers
* D-mannose and D-galactose: diastereomer
 MIRROR IMAGE SUPERIMPOSABLE/
SYMMETRICAL

MESO COMPOUNDS YES YES

-same compounds

DIASTEREOMER NO NO

ENANTIOMER YES NO
-same physical properties
-only differ in the rotation of plane
polarized light
2E. REACTIONS

Review:

Primary Alcohol oxidation Aldehyde Acid

oxidation
reduction

Secondary Alcohol oxidation Ketone

oxidation
X
reduction

Tertiary Alcohol oxidation X

Carbohydrates:

Sugar Alcohol reduction Sugars oxidation Sugar Acid

1. REDUCTION

a. D-mannose reduction Mannitol

(sugar) (sugar alcohol)
reduction
b. Ribose Deoxyribose

2. OXIDATION

a. Galactose weak OA (Cu2+) Galactonic

(Aldose) (Aldonic)

b. Galactose strong OA (HNO3) Galactaric

(Aldose) (Aldaric)

c. Galactose strong OA + protecting group Galacturonic

(Aldose) @ CHO (Alduronic)

3. CONDENSATION – 2 or more sugar units are joined together by a glycosidic bond to form a more complex and larger molecule accompanied by
loss of water.

a. Sucrose: glu + fru (Alpha-1,2)

b. Maltose: glu + glu (Alpha-1,4)
c. Lactose: glu + gal (Beta-1,4)
d. Lactulose: fru + gal (Beta-1,4)
e. Cellobiose: Beta-glucose + Beta-glucose (Beta-1,4)

NOTE: Humans don’t have enzymes to break glycosidic bonds

2F. QUALITATIVE TESTS

1. Molisch Test – general test

-rgt: alpha-naphthol
-(+): violet

2. Iodine Test – for starch

-(+): blue/violet (1st: orange)

3. Bials Test – for pentoses (ARRXX)

-rgt: orcinol
-(+): green

4. Seliwanoff’s Test – for ketoses (fructose, mannose,

ribulose, xylulose)
-rgt: resorcinol
-(+): cherry-red

5. Osazone/Kowarsky Test – specific for mannose

-rgt: phenylhydrazine
-(+): yellow crystals
6. Mucic Acid Test – specific for galactose
-rgt: HNO3
-(+): crystals

7. Fehling’s Test – for reducing sugars; unstable

-rgt: *Fehling’s A (Cupric Sulfate)
*Fehling’s B (Sodium Potassium Tartrate/Rochelle’s Salt)
-(+): brick red/red ppt

8. Benedict’s and Barfoed’s Test – for reducing sugars; more stable

-rgt: Modified Fehling’s A (Cupric Sulfate)

9. Tollen’s Test – for reducing sugars

-rgt: Ammoniacal/Ammoniated Silver Nitrate
-(+): silver mirror

NOTE: *Monosaccharides & Disaccharides are reducing (except sucrose & trehalose)
*Polysaccharides are nonreducing
3. LIPIDS
3A. INTRODUCTION
-Organic compounds with variable structure that are insoluble in water but soluble in nonpolar solvents.
They include fats, waxes, oils, hormones that function as stored energy and chemical messengers.

USES:

a. Stored energy: TAGs (Triacylglycerol/triglycerides/fats)

b. Structural: Phospholipids
c. Pharmaceutic: waxes, volatile oils, and stearic acid
d. Regulatory: hormones, steroids and eicosanoids

Lipids can be:

a. Saponifiable – lipids that contain Fatty acids
b. Nonsaponifiable – do not contain Fatty acids

SAPONIFICATION – is the alkaline hydrolysis of fatty acids

fatty acid + NaOH soap + H20

3B. FATTY ACIDS
-are long chain carboxylic acids (with at least 6C)
-could it either be Saturated or Unsaturated Fatty Acids

1. Saturated Fatty Acids

-obtained from animals, unhealthy, no double bonds, compact.
-solid at room temperature

# of Carbons Trivial Names # of Carbons Trivial Names

6 Caproic 18 Stearic
8 Caprylic
20 Arachidic
10 Capric
12 Lauric 22 Behenic
-major component of coconut
oil
24 Lignoceric

14 Myristic 26
-insulin detemir Cerotic

16 Palmitic
2. Unsaturated Fatty Acids
-obtained from plants, healthier, have double bonds, not as compact.
-liquid at room temperature
-can be:

a. Monounsaturated FA (MUFA) – 1 double bond

-ex:
*Palmitoleic acid
*Oleic acid
*Nervonic acid

b. Polyunsaturated FA (PUFA) – more than 1 double bond

-ex:
*Linoleic acid – precursor of arachidonic acid
*Arachidonic acid – precursor of eicosanoids (PG, TX, LT: short-term response to stress
producing inflammation)
*Alpha-linolenic – precursor of EPA & DHA (omega-3; important in brain development)
*EPA (Eicosapentaenoic acid)
*DHA (Docosahexaenoic acid)
3. REACTIONS OF FA

a. Auto-oxidation/Rancidification
oxidation
Unsaturated FA broken down into short chain aldehydes

b. Reduction/Hydrogenation – conversion of liquid oil to semi-solid fat

-catalyst: Pd/Ni
-pass H2 gas
reduction
Unsaturated FA Saturated FA
Side re -break down the double bonds to increase the t90
a ction

*still has double bond, changed isomer

*TRANSFAT: increases the risk of CAD

c. Sulfation – reaction of double bonds with H2SO4

- the sulfates you get can now be used as surfactants (surface active agents ; emulsifier)
3C. SAPONIFIABLE LIPIDS

1. Triacylglycerol/Triglycerides (TAGS)
- major form of fat in human diet
- component: glycerol triester with 3 fatty acids
-neutral lipids (no charge)
-may be:
a. Simple TAGS – same fatty acids
b. Mixed TAGS – different fatty acids
-stored in fat tissues
-used for energy
2. Glycerophospholipids
-similar to TAGS, except that 1 fatty acid is replaced with phosphate
-component: 1 glycerol, 2 FA, Phosphate (where the “x”/head group attaches)
-acidic lipids
-used as structural lipids (phospholipid bilayer of the cell membrane)
-ex:

a. Phosphatidic acid – simplest glycerophospholipid, parent compound

b. Phosphatidylcholine – aka “lecithin”
c. Phosphatidylethanolamine – aka “cephalin”
d. Phosphatidylinositol – related to secondary messengers (IP, DAG)
3. Sphingolipids
-contain the sphingosine backbone instead of glycerol
-still has “x”/head group
-ex:

a. Ceramide – simplest sphingolipid, parent compound

b. Cerebroside – glu/gal
c. Globoside – neutral oligosaccharide
d. Ganglioside – acidic oligosaccharide/polysaccharide (acidic due to Sialic/Neuraminic acid)
e. Sphingomyelin – phosphate + choline

-Sphingolipids are the primary structural lipid of nerve tissue in the brain.
4. Waxes
-esters of fatty acids with long chain monohydric alcohol
-has a very long hydrocarbon chain
-water-repelling and extremely nonpolar
3D. NONSAPONIFIABLE LIPIDS

1. Fat-Soluble Vitamins – “ADEK”

a. Vit. A – aka “retinoic acid” (most toxic vitamin)

b. Vit. D – sunshine vitamin
*D2 – ergocalciferol
*D3 – cholecalciferol
c. Vit. E – D-a-tocopherol
d. Vit. K
*K1 – phytomenadione
*K2 – menaquinone
*K3 – menadione
2. Terpenes – wide class of natural products based on Isoprene (5C) backbone.

1 terpene = 2 isoprene unit

-ex:

a. Monoterpene – 2 isoprene (10 C)

*volatile oils
b. Sesquiterpene – 3 isoprene (15 C)
*Artemisinin & Chamazulene
c. Diterpene – 4 isoprene (20 C)
*taxanes
d. Sesterpene – 5 isoprene (25 C)
e. Triterpene – 6 isoprene (30 C)
*steroids
f. Tetraterpene – 8 isoprene (40 C)
*B-carotene
*Lycopene
3. Sterols – contain CPPP (cyclopentanoperhydrophenanthrene) backbone
-ex:
a. Cholesterol – humans & animals, mostly stored in liver
b. Ergosterol – fungi
c. Phytosterol – plants

USES OF CHOLESTEROL

a. regulates the fluidity of cell membrane

b. precursor of Vit. D
c. precursor of Bile acids (used to break down food)
i. Primary Bile acids – directly synthesized in the liver
-ex:
* Cholic acid
* Chenodeoxy Cholic acid – conjugated with glycine and taurine
ii. Secondary Bile acids – fermented by the gut flora ; removal of OH
-ex:
* Deoxycholic acid
* Lithocholic acid
d. precursor of steroid hormones
i. Mineralocorticosteriod – aldosterone
ii. Glucocorticosteroid – cortisol
iii. Sex hormones – estrogen, testosterone
3E. TEST FOR LIPIDS

1. Liebermann-Burchard Test
-most sensitive test for sterol
-rgt: H2SO4 + Acetic anhydride
-(+): green

2. Salkowski Test
-also a test for steroid
-rgt: conc. H2SO4 (the cholesterol is dissolved first in chloroform)
-(+): red or violet

3. Acrolein Test
-for glycerol
-rgt: KHSO3 (potassium bisulfite) + heat
-(+): burn fat odor/acrid odor

4. Test for Phosphates (Phospholipids)

-rgt: ammonium molybdate
-(+): yellow ppt

5. QC Tests
4. NUCLEIC ACIDS

4A. INTRODUCTION
-2 Types: *DNA
*RNA
-responsible for storage and expression of genetic
information including all inborn information
-polymers of nucleotides

4B. NUCLEOTIDES
-monomers/building blocks of nucleic acids
-composed of 3 parts:
i. Phosphate
ii. Sugar
iii. Base (nitrogenous)
-sugar & base are collectively called Nucleoside
-Nitrogenous base could either be Purine or Pyrimidine
PURINE: “purGA” PYRIMIDINE: “pyrCUT”
*Guanine *Cytosine
*Adenine *Uracil
*Thymine
 BASE NUCLEOSIDE NUCLEOTIDE
-base + sugar -phosphate + base +
sugar
Adenine Adenosine Adenosine Phosphate

Guanine Guanosine Guanosine Phosphate

Cytosine Cytidine Cytidine Phosphate

Uracil Uridine Uridine Phosphate

Thymine Thymidine Thymidine Phosphate

*Phosphoester Bond – bond between a Phosphate and a sugar

*Phosphoanhydride Bond – bond between Phosphate (PO4-PO4)
*Phosphodiester Bond – linkage between the 3’ C atom of one sugar molecule to the 5’ C atom of
another
*Hydrogen Bond – bond between base pair (Base-Base)
4C. POLYNUCLEOTIDE STRUCTURE
 RNA DNA

Sugar Ribose Deoxyribose

Bases AGCU AGCT

# of strands 1 2

Variation *mRNA – messenger *B-DNA

*rRNA – ribosomal *A-DNA
*tRNA - transfer *Z-DNA
B (most common)
A & Z (made in the lab)
LEVELS OF ORGANIZATION

1. Primary Level – sequence of nucleic acids

-ex:
5’-CGA AGT CGA TCA-3’

2. Secondary Level – formation of base pairs due to H-bonds

-includes double helix

3. Tertiary Level – further organizations; coiling beyond normal

-ex:
*supercoiling, plasmids

4. Quaternary Level – involves complexation with proteins

-ex:
*histones
PROPERTIES OF DOUBLE HELIX
-isolated by Rosalind Franklin
-elucidated by Watson & Crick
-double helix is a double strand

1. Both strands have the same exact sequence

2. Complementary Base pairing : “Watson-Crick Base Pairs” : AT and CG
*Chargaff’s Rule:
%A=%T
%C=%G
% (A + G) = % (C + T)
3. Handedness (spin CW or CCW)
-CW: right-handed (ex: B-DNA, A-DNA)
-CCW: left-handed (ex: Z-DNA)
4. Antiparallel
-ex:
5’-------------------------3’
3’-------------------------5’
PRACTICE PROBLEM:

If a DNA sample contains 21% A, what is the percentage of others?

CENTRAL DOGMA
4D. REPLICATION (Initiation, Elongation, Termination)
-DNA synthesis
-occurs in the nucleus
-promoted during a cell’s S-Phase

1. DNA Replication is SEMI-CONSERVATIVE 4. DNA Replication is BIDIRECTIONAL

2. The two DNA strands are ANTI-PARALLEL 5. INITIATION

5’-----------------------3’ -Helicase: has to recognize first the origin
3’-----------------------5’ of replication.
3. DNA strands have complementary base pairing -separate the 2 strands together by breaking
5’-ATTGATCGTCCGTAAGTC-3’ the H-bonds that hold the nucleotides
3’-TAACTAGCAGGCATTCAG-5’ together (unwinding)
*AT – 2 H-bonds
*GC – 3 H-bonds
 *Tension/Torsional strains – is relieved by DNA Gyrase,
a type of Topoisomerase II.
-DNA Gyrase relieve positive coiling ahead of the

Replication/Bubble Fork
*SSB (Single Strand Binding) Proteins – stabilize the
two strands to prevent them from cleavage or from
cleavage or from snapping back together.
-it makes the parent strands remain unwinded.

6. DNA Replication requires RNA PRIMER to begin

*RNA Primer: is a sequence of RNA Nucleotides ; added by Primase

7. ELONGATION
-DNA Polymerase III adds nucleotides in 5’ to 3’ direction
8. DNA Replication is SEMI-DISCONTINUOUS
*Leading Strand – moves in the same direction as the replication fork
-only needs 1 RNA primer and DNA Replication goes continuously
*Lagging Strand – needs more than 1 primer and DNA Replication goes discontinuously.

9. DNA Polymerase I on a 5’-3’ exonuclease activity removes RNA primer and replace it with a DNA
material.

10. TERMINATION
-DNA ligase seals the gap/spaces between Okazaki fragments
*Okazaki Fragments – are short sequences of nucleotides on the lagging strand.

11. PROOFREADING – when DNA Polymerase III adds a wrong nucleotide, it will stop, remove the
wrong nucleotide and replace it with the right one.
-DNA Polymerase I & DNA Polymerase III on a 3’-5’ exonuclease activity

12. DNA REPAIR – by DNA Polymerase I on a 5’-3’ exonuclease activity

4E. TRANSCRIPTION (Initiation, Elongation, Termination)
-RNA synthesis
-conversion of DNA to RNA
-occurs in the nucleus
-produces a premature mRNA strand
-UNIDIRECTIONAL: uses only 1 strand
-RNA Polymerase – big enzyme; does not need a primer
*sigma subunit
*rho subunit
*core subunit

1. INITIATION
-RNA polymerase binds to the promoter region of DNA
-the promoters direct the RNA polymerase upstream (unwinding)
*Promoter Region – short DNA sequence
a. TATA box/Hogness box – short sequence of TATAA

2. ELONGATION
-sigma subunit is ejected
-core subunit performs elongation
*RNA Polymerase reads the DNA strand in 3’-5’ (Template strand)
*RNA synthesizes mRNA from 5’-3’
*Template/Antisense strand (3’-5’)
-one being used in mRNA synthesis
-one with RNA polymerase is active upon

*Nontemplate/Sense strand/Coding strand (5’-3’)

-it is called coding strand because it’s nucleotide is the same with mRNA except that Thymine is
found in DNA and Uracil is found in mRNA.

5’-G C G G A C A A T G C T-3’ (Nontemplate/sense/coding)

5’-G C G G A C A A U G C U-3’ (mRNA)
3’-C G C C T G T T A C G A-5’ (Template/antisense)
3. TERMINATION
-2 mechanisms:
i. Rho-dependent – Rho subunit will signal dissociation
ii.Rho-independent – produces premature mRNA

4. POST-TRANSCRIPTIONAL MODIFICATION
*EXONS – short sequence of nucleotide
- coding; one being used to synthesize proteins
-remain

*INTRONS – long sequence of nucleotides

- uncoding
-removed

*RNA SPLICING – removal of introns

*Capping at 5’ – addition of 7-MG (7-methylguanosine)
*Polyadenylation at 3’ – addition of approximately 100-200 Adenosine

mature mrNA : 7-MG-5’-EXONS-EXONS-EXONS-EXONSE-3’-AAAAAAAAA

4F. TRANSLATION (Initiation, Elongation, Termination)
-protein synthesis
-conversion of mRNA to proteins
-occurs in the ribosomes
*64 codons
*61 – coding
*3 – noncoding
-Stop codons/Nonsense (UAA, UAG, UGA) – terminate translation
-ex:
*UUU – Phe
*UUC – Phe
*AUG – Met ; the only start codon

-Ribosomal subunit:
*Prokaryotes (70s) : 30s ; 50s
*Eukaryotes (80s) : 40s ; 60s

-facilitated by tRNA
*each codon codes for a specific anti-codon
*each codon codes for a specific amino acid
*tRNA carries the anti-codon and it is covalently linked to a specific amino acid

A site – aminoacyl
P site – peptidyl
E site - exit
RULES OF GENETIC CODE

1. Almost universal
2. Degenerate/Redundant (1 Amino acid = many codons)
3. Nonambiguous (1 codon = 1 amino acid)
4. Commaless – no skipping
5. Nonoverlapping – no repeat

1. INITIATION – validated by Chain Initiating sequence/mRNA Binding Site

*Chain Initiating Sequence:
a. Eukaryotes – kozak
b. Prokaryotes - Shine Dalgarno

2. ELONGATION

3.TRANSPEPTIDATION

4. TRANSLOCATION

5. TERMINATION
-if the next codon is still coding then repeat the process
-if stop codon, elongation terminates

product: PROTEIN (not native)

6. POST-TRANSLATIONAL MODIFICATION
-occurs in the Golgi Apparatus

1. FOLDING – formation of residue interactions needed to become native

-sometimes assisted by chaperone proteins (ex: HSP – Heat Shock Protein)

2. Trimming of N- or C- Terminal portions

3. Residue Modifications – addition of functional groups to proteins

4. Degradation
-ex: Ubiquitination
4G. MUTATION c. Nonsense Mutation – production of Stop Codon
-alteration in the normal DNA sequence -ex: UGG  UAG
-caused by mutagens (Trp) (stop codon)
-leads to disease
-some mutations are inborn (ex: Sickle cell anemia) COMMON MUTATIONS
-types:
1. Pyrimidine Dimers

1. Point Mutation – substitution of a single base -caused by UV from sunlight

a. Transition: pur  pur or pyr  pyr -when pyrimidine becomes dimers it will no
b. Transversion: pur  pyr or pyr  pur longer be readable  blisters/lesions
-ex: -repair: DNA Photolyase
CAC  UAC -decrease photolyase: Xeroderma pigmentosum
AAG  AAA
UAA  UAU 2. Depurination/Depyrimidination
-done by most mutagens
2. Frameshift Mutation – addition or deletion of base -repair: Excision repair
-result:
a. Silent Mutation – nothing changes 3. Oxidative Stress
-ex: UUU  UUC -due to ROS
(Phe) (Phe) -can cause cell death : IRREVERSIBLE
b. Missence Mutation – changed amino acid -repair: Antioxidant
-ex: AUG  AUA
(Met) (Ile)
 METABOLISM

I. CELL RESPIRATION II. LIPID METABOLISM

a. Glycolysis a. Fatty Acid Synthesis
b. Fates of Pyruvate b. Lipolysis
c. Gluconeogenesis (GNG) c. Fates of HMG-CoA
d. Fates of Glucose-6-Phosphate (G6P) i. Mevalonate Pathway
i. Pentose Phosphate Pathway (PPP) ii. Ketogenesis
*Oxidative Phase
*Non-oxidative Phase III. NUCLEOTIDE & AMINO ACID
ii. Glycogen Metabolism METABOLISM
*Glycogenesis a. Nucleotide Metabolism
*Glycogenolysis b. Shikimic Acid Pathway
e. Kreb’s Cycle c. Amino Acid Derivative
f. Electron Transport Chain (ETC) d. Inborn Errors of Amino acid
Metabolism
e. Nitrogen Disposal
METABOLISM
-Sum total of all the chemical reactions in the body
-broken down in pathways
-a pathway must have:
i. a direction
ii. a goal

*Anabolism – conversion of small to big molecule

- production of big molecule from small molecule
- requires energy
*Catabolism – breakdown of big molecule into small molecule
- generates/produces energy

“Energy” – ATP or NADH (2.5 ATP)

FADH2 (1.5 ATP)
I. CELL RESPIRATION
-The opposite of photosynthesis

C6H12O6 + O2  CO2 + H2O

(glucose)
A. GLYCOLYSIS

-breakdown of glucose into 2 molecules of pyruvate

-catabolism
-occurs in the cytosol
-reduces blood sugar level
-during fed state : (+) Insulin (a hormone that tells your body to reduce blood sugar)
-consists of 10 steps
-has 2 phases:
a. Energy investment (1-5)
b. Energy payoff (6-10)
TYPE OF REACTION:

1. Phosphorylation (Irreversible)
2. Isomerization
3. Phosphorylation (Irreversible)
4. Reversible Aldol Condensation and
Isomerization
5. Isomerization
6. Oxidation/Dehydrogenation
7. Phosphoryl Group Transfer
8. Isomerization
9. Dehydration
10. Phosphoryl Group Transfer
*Energy Yield: 2 ATP
2 NADH
2 PYRUVATE

*Universal: both aerobic and anaerobic

*Irreversible Step:
i. 1 – Hexokinase/Glucokinase
ii. 3 – Phosphofructokinase (PFK)
iii. 10 – Pyruvate Kinase

*Steps 1 & 3: are the ‘energy-spending’ steps

*Steps 7 & 10: are the substrate level phosphorylation which produce ATP

*”Rate Limiting Step” or “Committed Step”

-finalizes the direction of a substrate
-STEP 3 (PFK – rate limiting step)
B. FATES OF PYRUVATE

Glucose

glycolysis gluconeogenesis
(fed) (fasted)

PYRUVATE
Aerobic Respiration Anaerobic in Yeast
pyruvate kinase pyruvate decarboxylase

Anaerobic Respiration

ACETYL COA lactate dehydrogenase ACETALDEHYDE

Alcohol dehydrogenase

LACTATE
Kreb’s Cycle “fermentation” Ethanol
“fermentation”

FERMENTATION – is a process occurring in an Anaerobic condition

C. GLUCONEOGENESIS (GNG)

-conversion of a noncarbohydrate substrate (pyruvate, amino acid, glycerol, lactate) into glucose
-Anabolism
-exclusive in the Liver
-direction is the reverse of glycolysis

*Reversible steps use same enzymes

*Irreversible steps use different enzymes:

i. 1 – Hexokinase (glucose  glucose-6-phosphatase

glucose-6-phosphate)
*glucose-6-phosphate GLUCOSE

ii. 3 – Phosphofructokinase (fructose-6-phosphate  fructose-1,6-bisphosphate)

*fructose-1,6-bisphosphate Fructose-1-6-bisphosphatase fructose-6-phosphate

iii. 10 – Pyruvate kinase (phosphoenolpyruvate  pyruvate)

*pyruvate pyruvate carboxylase oxaloacetate carboxylase phosphoenolpyruvate

*
D. FATES OF GLUCOSE-6-PHOSPHATE (G6P)

Glucose

Ribose-5-phosphate PPP G6P Glycogen metabolism Glycogen

pyruvate

1. PENTOSE PHOSPHATE PATHWAY

-not part of Respiration
-aka “Hexose Monophosphate Shunt”
-overall reaction:

Glucose-6-Phosphate  Ribose-5-Phosphate

-occurs in cytosol
-2 phases:
i. Oxidative Phase
ii. Non-oxidative Phase
a. OXIDATIVE PHASE

Glucose-6-Phosphate Ribulose-5-phosphate (Ru5P)

Glu
co se-6 NADPNADPH
-ph
osp
hate
deh
ydr
o gen
ase

Phosphogluconolactone

*NADPH – antioxidant; not used in making ATP

*G6PD DEFICIENCY: Decrease NADPH  decrease reduced GSH

 increase H2O2  increase oxidative stress  increase CELL DEATH (ex: Hemolysis)
-advantage: Immunity to malaria
b. NON-OXIDATIVE PHASE
Ribulose-5-Phosphate

Xylulose-5-Phosphate RIBOSE-5-PHOSPHATE
(Xu5P) (R5P)

Glyceraldehye-3-Phosphate Sedoheptulose-7-Phosphate
(G3P) (S7P)

Fructose-6-Phosphate Erythrose-4-Phosphate
(F6P) (E4P)
2. GLYCOGEN METABOLISM
-occurs in the cytosol
*Glycogen: a polysaccharide, stored in the liver and muscle for energy
-is made up many glucose units, highly-branched

*Alpha-1,4 Glycosidic bond – linearity (broken by Glycogen phosphorylase)

*Alpha-1,6 Glycosidic bond – branching (broken by Debranching enzyme)
 GLYCOGENESIS VS. GLYCOGENOLYSIS

-Glycogen synthesis -Glycogen breakdown

-direction of glucose: -direction of glucose:
*blood  liver *liver  blood
-increase durinfed state -increase during fasted state
*(+): insulin *(+): glucagon

Glucose

glucose-6 phosphatase

Glucose-6-phosphate
phosphoglucomutase

Glucose-1-Phosphate

glycogen pyrophosphorylase

Glycogen
E. KREB’S CYCLE
-aka “Citric acid cycle” or “Tricarboxylic acid cycle”
-converts 1 Acetyl-CoA to 2 molecules of CO2
-occurs in:
*Mitochondrial matrix – eukaryotes
*Cytosol – prokaryotes
-energy synthesis through oxidation of Acetyl-CoA
1. Oxaloacetate + Acetyl-CoA

citrate synthase

2. Citrate (6C)

acotinase (isomerization)

3. Isocitrate (6C)

NADNADH isocitrate dehydrogenase (oxidation) ; CO2

4. a-ketoglutarate (5C)

NADNADH a-ketoglutarate dehydrogenase (oxidation) ; CO2

5. Succinyl-CoA (4C)

GTP succinyl CoA synthase/succinate thiokinase

6. succinate

FADFADH2 succinate dehydrogenase (oxidation)

7. fumarate

fumarase

8. malate

NADNADH malate dehydrogenase (oxidation)

9. oxaloacetate

GTP (Guanosine Triphosphate) – is an energy rich nucleotide analogous to ATP

- Guanine, Ribose and 3 Phosphate groups
ENERGY YIELD:

NADH : 3 x 2.5 = 7 ATP

FADH2: 1 x 1.5 = 1.5 ATP
GTP = 1 ATP
10 ATP/Acetyl Coa ; 2 molecules of CO2

1 glucose = 2 pyruvate = 2 acetyl-CoA

NADH : 6 x 2.5 = 15 ATP

FADH2: 2 x 1.5 = 3 ATP
GTP : 2 = 2 ATP
20ATP/glucose ; 4 molecules of CO2
KREB’S CYCLE
-Amphibolic ( both anabolism and catabolism)
*oxaloacetate : part of gng
*citrate : fat/lipid synthesis
*a-ketoglutarate : amino acid catabolism
*succinyl-CoA : heme synthesis

-NADH & FADH2 will proceed to ETC

F. ELECTRON TRANSPORT CHAIN (ETC)

-series of e- transfer that produces an H+ gradient that leads to ATP synthesis

-aka “oxidative phosphorylation”
-occurs in the inner mitochondrial membrane
-uses 4 e- carrying complexes/enzyme complexes/protein complexes:

complex 1 : NADH dehydrogenase/NADH oxidoreductase

complex 2 : Succinate dehydrogenase/succinate CoQ dehydrogenase
complex 3 : Cytochrome C reductase
complex 4 : Cytochrome C oxidase (inh. by: cyanide)
complex 5 : ATP synthase
4 H+ = 1 ATP

Complex 1 – 4 : ETC
Complex 5 : Chemiosmosis

ETC + Chemiosmosis = Oxidative Phosphorylation

SUMMARY: CELL RESPIRATION

Glucose

7 ATP

2 Pyruvate

5 ATP

2 Acetyl-CoA

20 ATP

CO2

Total : 32 ATP/glu
II. LIPID METABOLISM
A. FATTY ACID SYNTHESIS (Anabolism)
-occurs in the cytosol
-increase during fed state
-(+) : insulin
-RLS:

Acetyl-CoA carboxylase Malonyl-CoA (Building block of FAS)

(2C) (3C)

CO2
B. LIPOLYSIS (Catabolism)
-breakdown of TAGs
-occurs in fasted or carb-deficient states
-(+): glucagon

Triacylglycerides

Glycerol Fatty acid

Glycerol Phosphate “B-oxidation”

DHAP

“Gluconeogenesis”
B-OXIDATION
-’’Fatty Acid Oxidation”
-occurs in Mitochondrial matrix
-involves continuous removal of 2 C from a fatty acid, which will become Acetyl-CoA molecules
-every step has 4 cycles;

Acyl-CoA
dehydrogenation (1 FADH = 1ATP)
Cleavage Acyl-CoA
ketoacyl-CoA enoyl-Coa

dehydrogenation hydration
(1 FADH2 = 1.5 ATP)
Hydroxyacyl-CoA

Product: 4 ATP/Cycle
C. FATES OF HMG-COA

2 excess Acetyl-CoA

Thiolase

Acetoacetyl-CoA

HMG-CoA Synthase

HMG-CoA (B-hydroxy-B-methylglutaryl-CoA)

Mevalonate Pathway Ketogenesis

(fed) (fasted)

Sterol Ketone bodies

(cytosol) (mitochondria)
MEVALONATE PATHWAY
KETOGENESIS

HMG-CoA

HMG-CoA Lyase

Acetoacetate/Acetoacetic acid

Non-enzymatic degradation D-B-Hydroxybutyrate dehydrogenase

Acetone D-B-Hydroxybutyrate/
-the only true ketone D-BHydroxybutyric acid
KETOGENESIS
-production of ketone bodies
-Ketone bodies are emergency sources of energy (esp. brain)
-increase during fasted state (+) glucagon

KETOSIS – state of high ketone production

KETOMENIA – ketone bodies in blood
KETONURIA – ketone bodies in urine
KETOACIDOSIS – lowered pH due to increase levels of ketones
- hyperventilation
- acetone brain
*DKA (Diabetic Ketoacidosis) – complication of DM 1
- decreased insulin ; increased ketone bodies
KETOGENIC DIET
-weight loss?
-Decrease carbs ; increase fats
-it works
-originally for children with frequent seizures

*risk:
-Lethargy
-Heart disease
-Ketoacidosis
III. NUCLEOTIDE AND AMINO
ACID METABOLISM
A. NUCLEOTIDE METABOLISM
-separate for purine and pyrimidine metabolism

a. De Novo Metabolism – from scratch

b. Salvage Metabolism – from wastes materials

PYRIMIDINE METABOLISM (DE NOVO)

5 STEPS

Orotidine Monophosphate (OMP)

UMP (Uracil)

dUMP UTP

dTMP (Thymine) CTP (Cytosine)

Orotidine Monophosphate (OMP) – parent pyrimidine; 1st pyrimidine that our body synthesizes

Methylation Reaction
dUMP (uracil) dTMP (thymine)
Thymidylate Synthase
-Inh. by: 5-fluorouracil (Competitive Inhibition)

FOLATE METABOLISM

Pteridine + PABA

DHP synthetase (inh. by: Sulfonamides)

Dihydropteroic Acid

glutamate DHF synthetase

Dihydrofolate (DHF)

DHF reductase (inh. by: Trimethoprim/TMZ)

Tetrahydrofolate (THF)
* Cotrimoxazole = TMZ (Trimethoprim) + SMX (Sulfamethoxazole)
Trade Names: Bactrim and Septrim

* Drugs are similar to substrates that should fit in the active site of enzymes

* x folic acid = x thymine = x DNA  Bacterial Cell Death

PURINE METABOLISM

a. De Novo

11 steps

Inosine Monophosphate (IMP)

Adenylosuccinate Xanthosine Monophosphate (XMP)

Adenosine Monophosphate (AMP) Guanosine Monophosphate (GMP)

* Inosine Monophosphate – parent purine (aka “Inosate”)

- base: Hypoxanthine
* Xanthosine Monophosphate
- base: Xanthine
b. Salvage Metabolism

AMP GMP

Adenine Guanine

Hypoxanthine

Xanthine

Xanthine Oxidase - inh. by: Allopurinol & Febuxostat (Competitive Inhibition)

URIC ACID – final product in purine metabolism; excreted in urine

B. SHIKIMIC ACID PATHWAY – important in plant chemistry

* Phe (F) & Tyr (Y) – precursors of phenylpropanoids

-ex: volatile oils
flavonoids
tannins

*Humans cannot undergo Shikimic Acid Pathway

C. AMINO ACID DERIVATIVES

1. Tyrosine (Tyr, Y) Tyr  DOPA  Dopamine  NE  Epi

a. Catecholamines
-ex: Dopamine, NE, Epi
b. Thyroid Hormones Tyr  Thyroxine
-ex: T3 – Triidothyronine
T4 – Thyroxine
c. Melanin – pigment of skin and eyes

2. Tryptophan (Trp, W)
a. Serotonin (5-HT)
Trp 5-Hydroxytryptophan 5-HT
b. Melatonin –Hydroxylation
associated with sleep/wake cycle Decarboxylation

3. Histidine (His, H)
a. Histamine – via Histidine decarboxylase

4. Serine (Ser, S) – choline 7. Arginine (Arg, R) – NO/Nitric Oxide

5. Glutamate (Glu, E) – GABA 8. Glycine (Gly, G) – heme synthesis (w/ succinyl-coA)
6. Lysine (Lys, K) – L-carnitine
HEME
- a porphyrin
- gives red color to RBC
- contains Fe2+ as a cofactor
- metabolized in the liver to bilirubin

BILIRUBIN
- degradation product of Hemoglobin
- protein bound

Heme

Biliverdin (Green)

Bilirubin (Yellow)
-unconjugated
-nonpolar, unionized, water-insoluble
 NOT EXCRETABLE
-causes liver disease (liver cell necrosis) and
Hemolytic Anemia
 Conjugated Bilirubin
- polar, ionized, water-soluble  EXCRETABLE
- can contribute to Gallstones (Biliary obstruction)

STERCOBILIN – feces (brown)

UROBILIN – urine (yellow)
ICTERUS/JAUNDICE – increase serum bilirubin; yellow skin
- tx if chronic: PHOTOTHERAPY
KERNICTERUS – bilirubin in the brain
- neurological damage (permanent brain damage)
- caused by sulfa drugs

VAN DER VERGH TEST

- identification test for increased serum bilirubin
- measures conjugated bilirubin
- produces azobilirubin
- negative : normal level
- Rgt: Equal volume of Sulfanilic acid (diluted with HCl) and Sodium nitrite.
D. INBORN ERRORS OF AMINO ACID METABOLISM

1. ALKAPTONURIA (Tyr) – 1st discovered error in history

- decreased levels of Homogentisate oxidase
- aka “Black Urine Disease”

2. ALBINISM
- decreased tyrosinase
- has no melanin
- poor eyesight

3. PHENYLKETONURIA/PKU (Phe)
- decreased Phenylalanine hydroxylase
- tested during newborn screening (GUTHRIES’ TEST)
- mentally retarded

4. MAPLE SYRUP URINE DISEASE/MSUD (Val, Leu, Ile)

- decreased branched-chain amino acids
- mental retardation
E. NITROGEN DISPOSAL
- Nitrogen refers to proteins (CHON)
- Amino acids in excess are not stored in the body
- Proteins  Amino acids  free ammonia (NH3)  UREA
-toxic in the body -nontoxic; easily excreted in urine
-cannot be excreted
properly
UREA – dissolved in the blood  kidney  excreted in urine
 SPHINGOLIPIDOSIS
DISEASE ENZYME-DEFICIENCY LIPID ACCUMULATING

1. SANDOFF Beta-Hexosaminidase A & B 2-Globoside

2. TAY-SACHS Beta-Hexosaminidase A Ganglioside

3. FABRY Alpha-galactosidase Globotriaosylceramide

4. KRABBE Beta-galactosidase Galactosylceramide

5. GAUCHER Beta-glucosidase/Glucocerebrosidase Glucosylceramide

6. METACHROMATIC Arylsulfatase A 3-Sulfogalactosylceramide

LEUKODYSTROPHY
7. NIEMANN-PICK Sphingomyelinase Sphingomyelin

8. FARBER Ceraminidase Ceramide

TYPE GLYCOGEN
NAME STORAGE DISEASEENZYME DIFICIENCY

GSD 0 Glycogen Synthase

GSD Ia Von Gierke Glucose-6-phosphatase

GSD Ib Glucose-6-phosphate Translocase

GSD II Pompe Lysosomal alpha-glucosidase

GSD III Cori Debranching enzyme

GSD IV Andersen Branching enzyme

GSD V McArdle Muscle Glycogen Phosphorylase

GSD VI Hers Liver Glycogen Phosphorylase

GSD VII Tarui Phosphofructokinase (PFK)

 RATE LIMITING ENZYMES
REACTION RLE
1. Glycolysis Phosphofructokinase (PFK)
2. Gluconeogenesis Fructose-1,6-Bisphosphatase
3. Kreb’s Cycle Isocitrate dehydrogenase
4. Glycogenesis Glycogen synthase
5. Glycogenolysis Glycogen phosphorylase
6. PPP Glucose-6-phosphate Dehydrogenase
7. Fatty acid synthesis Acetyl-CoA Carboxylase
8. Beta-oxidation Carnitine Acyl Transferase
9. Ketogenesis HMG-CoA Lyase/synthase
10. Urea/Kreb’s Henseleit Cycle Carbamoyl PO4 Synthetase I
11. Mevalonate Pathway HMG-CoA reductase
CARBOHYDRATE DIGESTION

1. Mouth : Salivary Amylase/Ptyalin

2. Stomach : Acid Hydrolysis

*Proteins : Enzymatic metabolism (alpha-amylases)

3. Small Intestine : Pancreatic amylases

sucrose  glu + fru

maltose  glu + glu
dextrin  glu units
lactose  glu + gal

LACTOSE INTOLERANCE – unable to fully digest lactose  Increased lactose in large intestine

Lactose  lactate + CH4 + H2

Lactate – produces osmotic effect = DIARRHEA

CH4 & H2 - flatulence
PRIMARY LEVEL OF ORGANIZATION (PROTEINS)

1. SANGER METHOD
- Rgt: 2,4-Dinitrofluorobenzene (DNFB) reacts with N-terminal amino acid residue
- Disadvantage: N-terminal only, the rest are hydrolyzed.

2. EDMAN DEGRADATION
- Rgt: Phenylisothiocyanate reacts with N-terminal Amino acid structure
- Advantage: N  C terminal

3. BIURET TEST
- complexation
- Rgt: CuSO4 complexes with peptide bonds  (+): Violet complex
GLYCEROPHOSPHOLIPIDS/PHOSPHOGLYCERIDES

1. Phosphatidic Acid
2. Phosphatidylcholine (Lecithin) – major phospholipid in the ER and cell membrane
3. Phosphatidylethanolamine (Cephalin)
4. Phosphatidylserine
5. Phosphatidylinositol – precursor of Secondary messengers (IP, DAG)
6. Phosphatidylglycerol (Cardiolipin) – found only in mitochondrial membrane
PERCOLATION

FATS/LIPIDS : HEXANE
RESINS : ALCOHOL
CHLOROPHYL : ACETONE
SOLANINE : ACETIC ACID
CHRYSAROBIN : HOT BENZENE

AMINO ACIDS
- Amphoteric
- All are optically active except GLYCINE
- Exist as Zwitterions/Dipolar ions at physiologic pH
LIPIDS
- TPN : 9 kcal/g
- Chemical messengers (ex: PG)

B-AMYLOID
- a prominent feature of Alzheimer’s disease found in old age

SMOOTH ER – lipid synthesis

ROUGH ER – protein synthesis

HEXOSES – most important monosaccharides

OLIGOSACCHARIDES – contain less than 12 monosaccharides
PENICILLIN : Val & Cys

Gly & Cys : Bile salts synthesis

Gly, Cys & Glu : Glutathione synthesis
Gly, Arg & Met : Creatinine synthesis
Asp & Gln : Pyrimidine synthesis
Asp, Gln, Gly, Ser : Purine synthesis

HAWORTH PROJECTION – closed chain structure

PROTEINS
*Myosin & Actin : for muscular contraction
*Ferritin : storage