BIOCHEMISTRY MAIN MACROMOLECULES CARBOHYDRATES

THE CELL- basic unit of life General formula: (CnH2nOn)

 Cell membrane 1. CARBOHYDRATES: MONOSACCHARIDE 1 SU
Components: (human) phospholipid, monosaccahrides
glycoprotein, cholesterol, arachidonic acid DISACCHARIDE 2 SU
(Plants) cellulose (Bacteria) peptidogycan glycosidic bonds OLIGOSACCHARIDE 3-10 SU
(Fungi) chitin- N-acetylglucosamine POLYSACCHARIDE >10 SU
 Organelles 2. LIPIDS: **not a biopolymer
 Mitochondria: powerhouse
 Lysosomes: suicide sacs
 MONOSACCHARIDE/ SIMPLE SUGAR
 Ribosomes: protein synthesis 3. PROTEINS:  Glucose/ Physiologic sugar/
 RER: protein synthesis amino acid, dextrose/blood sugar/ grape
 SER: fat/lipid synthesis peptide bond sugar
 Golgi bodies: storage site of CHON  Fructose/ Levulose / fruit sugar
 Microtubule: guide to chromatids
 Cell wall only in plants fungi bacteria 4. NUCLEIC ACID:  Galactose
 Vacuole only in plants nucleotides,  Mannose
 Plastids only in plants  Ribose, deoxyribose (pentose
 Nucleus: control/brain center phosphodiester bond
sugar) *STRUCTURE- pyran
 Chromosomes: 46,23 pairs- DNA code
 Nucleolus: ribosome assembly site 5. VITAMINS AND ENZYMES
 Nuclear membrane, pore: (+) eukaryote
 DISACCHARIDE
 Sucrose / Table sugar SUGAR RELATED CONDITIONS: CARBOHYDRATE METABOLISM
 Matose / malt sugar GLUCOSE Inc: hyperglycemia (DM) CATABOLIC
 Lactose/ milk sugar Type 1 DM: damage pancreas, insufficient  break down, produce energy
insulin (txt: insulin) ANABOLIC
 OLIGOSACCHARIDE Type 2 DM: undamaged pancreas, sufficient
 build up, utilized energy
 Raffinose- Gal Glu Flu (RAGAGUFU) insulin, insulin resistance (txt: OHA)
 Maltotriose- Glu Glu Glu (MAGU) **COMPLICATIONS: retinopathy, AMPHIBOLIC
 Sucralose- Glu Fru Gal (SUGUFUGA) neuropathy, nephropathy  combination eg. KREB CYCLE
 Gentianose- Glu Glu Fru (GEGUGUFU)
GALACTOSE Inc: Galactosemia- causing ADENOSINE TRIPHOSPHATE (ATP)
 POLYSACCHARIDE mental retardation
Basis of Type of deficiency: -energy currency of cell
 Starch- storage form of glu in plants
*amylase alpha 1,4 Gal-1-PO4 uridyl transeferase (classical) -traps energy
*amylopectin alpha 1,4 & alpha 1,6 @ every Galactokinase -adenosine + phosphate
25 glu unit Galactose epimerase ATP 2 HEPB
 Glycogen- storage form of glu in animals; ADP 1 HEPB
alpha 1,4 & alpha 1,6 @ every 8-10 glu units LACTOSE: lactose intolerance- GI distress
AMP NO HEPB
 Cellulose beta 1,4 glycosidic bond
* high energy phosphate bond (HEPB)

COENZYMES: NAD & FAD Fate of Glu in the body:

OXIDATION VS REDUCTION 1. ATP
2. GLYCOGEN
Oxidation/ Dehydrogenation Nicotinamide Adenosine Dinucleotide 3. FATS
 +O2 (NAD) 4. PROTEINS
 -H  Vitamin component: Niacin Glu convertion to ATP processes
 LEORA (Vit. B3) 1. Glycolysis/ embden meyer hof
 CATABOLIC REACTIONS 2. Intermediate reaction/ formation of
acetyl coA/ lactate dehydrogenase
Flavin Adenosine Dinucleotide (FAD) pathway
Reduction/ Hydrogenation  Vitamin component: 3. Kreb cycle/ citric acid cycle/
 -O2 Riboflavin (Vit. B2) tricarboxylic acid cycle
 +H 4. Electron transport chain
Glu convertion to Glycogen process
 GEROA *** 1. Glycogenesis
 ANABOLIC REACTIONS B1: TPP Glycogen convertion to ATP
B2: FMN, FAD 1. Glycogenolysis
B3: NAD Glu formation from fats and proteins
1. Gluconeogenesis
B5: CoA Other Glu utilization in the body
B7: Carboxylase reactions 1. Pentose phosphate pathway /
hexose monophosphate shunt
GLYCOLYSIS (anaerobic)
 Rate Limiting Enzyme:
Phosphofructokinase (PFK)
 Production Of 2 Pyruvic Acid/ Pyruvate
From 1 Glucose
 Utilize 2 ATP (Hexokinase
&Phosphofructokinase)
 Produces 2 NADH (Glyceraldehyde 3
PO4 Dehydrogenase)
 Produces 4 ATP
(Phosphoglyceratekinase, Pyruvate
kinase)
 Happens In The Cytosol, Must Undergo
Translocation
 Glyceraldehyde 3 PO4 –
Dihydroxyacetone phosphate (triose
PO4 isomerase) : reversible step
 2 pyruvic acid produced proceed to
intermediate reaction
Kreb’s cycle (aerobic)
 Amphibolic reaction
 2 GTP were produced from succinyl coA
via succinyl coa synthase
 2 FADH2 were produced from succinate  Complex I- NADH-Coenzyme Q reductase
via succinate dehydrogenase
 6 NADH were produced from
isocitrate(isocitrate dehydrogenase),
alpha ketoglutarate (alpha
ketoglutarate dehydrogenase+ vit b5 +  Complex III- Cytochrome c reductase
coA), malate coversion (fumarase)
SUMMARY
2 GTP= 2 ATP
6 NADH= 18 ATP
2 FADH2= 4 ATP
TOTAL= 24 ATP
PROCESSES AND THEIR LOCATION
CYTOSOL:
 Glycolysis
 Glycogenolysis
 HMP Shunt/ Pentose PO4
Pathway
 Fatty Acid Synthesis
 Lactate Dehydrogenase
Pathway
MITOCHONDRIA:
 Kreb’s Cycle (Matrix)
 Electron Transport Chain
(Cristae)
 Fatty Acid Oxidation
 Intermediate Reaction
(INTERMEMBRANE SPACE)
TYPES OF PHOSPHORYLATION: Intermediate reaction
 SUBSTRATE LEVEL 2 pathway of 2 pyruvic acid from
PHOSPHORYLATION glycolysis
4 ATP – 2 ATP= 2 ATP (left) 1. Anaerobic pathway (cytosol):
 OXIDATIVE PHOSPHORYLATION produces lactic acid via lactate
1. Glycerol phosphate pathway dehydrogenase
@brain and skeletal muscle 2. Aerobic pathway (intermediate
1 NADH= 2 ATP space) : produces2 acetyl coA
and 2 NADH via pyruvate
2. Malate aspartate pathway dehydrogenase
@heart, liver and kidneys
2 Acetyl coA proceed to Kreb cycle
1 NADH= 3 ATP
SUMMARY 2 NADH proceed to Electron transport
4 ATP PRODUCED – 2 ATP UTILIZED = chain (ETC)
2 ATP (LEFT)
Accumulation leads to muscle fatigue
2 NADH=4 ATP (GPP) OR
2 NADH=6 ATP (MAP)
SUMMARY
TOTAL: 6-8 ATP produced
2 NADH *3= 6 ATPS
Electron transport chain Pentose Phosphate Pathway
 Electron transporter transport  Production of:
electron to O2 to produce water
 Final electron acceptor: O2
Ribose 5 po4(rna)
NADPH (reduced form of NAD)
 Final products: ATP &H2O
 Glutathione + H= reduced
NADH dehydrogenase, release of H, NADH = Glutathione--- cells protected
NAD
from free radicals
 Complex II- Succinate Coenzyme Q reductase
FADH dehydrogenase FADH = FAD
**G6PD deficiency premature
release of H; inhibited by CO death of RBC = HEMOLYTIC
 Complex IV- Cytochrome C Oxidase ANEMIA
O2+2H = H2O, H release; Inhibited by
** CI: Sulfonamide, methyldopa,
cyanide
*ADP + PO4 VIA H & ATP synthase become ATP NSAID, anti malarials, fava beans
**coenzyme Q10/ UBIQUINONE
**OXYGEN FREE RADICALS DEACTIVATED BY
CATALASE, PEROXIDASE, SUPEROXIDE
DISMUTASE
LIPIDS
CATABOLISM OF FATS
Soluble in hexane benzene ether etc.
 VIA LIPASE AND H2O to yield
1. FATS/ LIPIDS
glycerol and fatty acid
2. LIPOPROTEINS
 Glycerol converted to
3. STEROIDS
glyceraldehyde 3 PO4 to
4. PHOSPHOLIPIDS
5. EICOSANOIDS produce ATP
 Fatty acids undergo beta
FATS: oxidation converted to acetyl
 ester of 1 glycerol and 3 fatty acids coA to become ATP
 for protection, heat insulator,  Lipase id inhibited by ORLISTAT
energy
AE: steatorrhea, Vit ADEK
 saturated FA: no double bonds
deficiency
 unsaturated FA: with double bond
 essential FA: Vit. F Linoleic acid
(omega 6, 18:2) and Linolenic acid
(omega 3, 18:3)
LIPOPROTEIN STEROIDS: 3. Bile acids
(LIPID + PROTEIN) Cyclopentanoperhydropenantherene a) Primary (cholic acid, chenodeoxycholic
Snthesis rate limiting enzyme: HMG-COA 1. Sterols acid)
REDUCTASE a) Cholesterol, in animals or fluidity b) Secondary (lithocholic acid, deoxycholic
1. Chylomicrons : acid)
b) Phytosterol in plants (beta
Carry dietary lipids **emulsify fats
2. VLDL:
sitosterol) 4. **cholesystokinin- contract gall bladder
Endogenous lipids c) Ergosterol, fungi cell membrane VIT. D/ SUNSHINE VITAMIN
3. LDL: d) Stigmasterol, soy bean & calabar PRECURSOR:
Bad cholesterol, deposit bean a) 7 DEHYDROCHOLESTEROL + UV
cholesterol for repair, if inc 2. Sex hormones becomes cholecalciferol (D3) further
result to atherosclerosis a) Estrogen, 2’ female char. at liver and kidney to become calcitriol
4. HDL: b) Progestin, pregnancy hormone, (most active form)
Good cholesterol, remove excess implantation b) Ergosterol become D2 -ergocalciferol
cholesterol in the blood c) Androgen, 2’male char 5. CORTISONE (glucocorticoid)
Use: natural ant-inflammatory agent
d) Testosterone, most impt sh
6. ALDOSTERONE (mineralocorticoid)
Use: sodium and water retention

PHOSPHOLIPID **SPHINGOMYELIN: CERAMIDE + EICOSANOIDS

COMPOSITION: PHOSPHOCHOLINE /  PROSTAGLANDIN
 GLYCEROL PHOSPHOETHANOLAMINE  SMOOTH MUSCLE
 2 FATTY ACID **AMINO ALCOHOL: SPHINGOSINE CONTRACTION AND
 PHOSPHATE **CERAMIDE RELAXATION
 ORGANIC MOLECULE : AMIDE OF SPHINGOSINE +FATTY ACID  GASTRIC SECRETION
FUNCTION: Component of cell membrane :CORE STRUCTURE OF
 Lecithin/ phosphatidylcholine
 PLATEKET AGGREGATION
GLYCOSPHINGOLIPIDS
 Cephalin/ phosphatidylethanolamine  INLAMMATORY RESPONSE
 THROMBOXANE
GLYCOSPHINGOLIPIDS (W/
 PLATELET AGGREGATION
CARBOHYDRATE)
SPHINGOLIPID  LEUKOTRIENES
COMPOSITION: a) CEREBROSIDES= CERAMIDE+
 CHEMOTAXIS
 SPHINGOSINE MONOSACC
  ALLERGIC REACTIONS
FATTY ACID b) GLOBOSIDES= CERAMIDE +
 POLAR HEAD GROUP DISACC / NEUTRAL OLIGOSACC  INFLAMMATION
FUNCTION: COMPOSITION OF NEURAL
TISSUES
c) GANGLIOSIDES= CERAMIDE +
CHARGED OLIGOSACC

PROTEINS Catabolism of AA
COMPOSED OF AMINO ACIDS Characteristics:
 Glycine: smallest, simplest, only aa not Amphoteric KETOGENIC
optically active, inhibitory NT, used in Optically active  LEUCINE
heme syn
@low ph positively charged  LYSINE
 Phenylalanine: converted to tyrosine via
Phe hydrolase, associated with @high ph negatively charged
phenylketonuria GLUCOGENIC
 Tyrosine: only aa with phenol grp, used in AA conversions: (13)
cathecholamine and melanin syn Histidine- histamine
(tyrosinase)
Tyrosine- melatonin, catecholamines, BOTH
 Tryptophan: only aa with indole grp, used  PHENYLALANINE
in the syn of 5HT/ serotonin/ happy thyroid hormone
 ISOLEUCINE
hormone and melatonin Tryptophan- serotonin
 TYROSINE
 Histidine: histamine syn Glutamate- GABA
 Arginine: converted to NO (vasodilation)
 THREONINE
Arginine- Nitric oxide  TRYPTOPHAN
 Cysteine: aa in gluta **cystine(dimer)
 Proline: no amino, has imino grp,
hydroxyproline (derivative)
CLASSIFICATION OF AMINO ACIDS Essential: PVT TIM HALL POLYPEPTIDE PRODUCTION:
Aromatic: Phe Tyr Typ  Phenylalanine AMINO ACIDS LINKED BY PEPTIDE BOND
Basic: His Arg Lys  Valine
Acidic: Asp A Glu A  Threonine DEHYDRATION PROCESS: FORMED BET
Amidic: Asp Glu  Tryptophan THE CARBOXYL AND AMINO GRP
Branched chain: Leu Iso Val  Isoleucine
S containing: Cys Met  Methionine LEVELS OF STRUCTURE
Alcohol cont: Ser Thr  Histidine  Primary: specific amino acid
 Arginine sequence (left to right)
Polar: CT TAGS  Leucine  Secondary: spatial relation of
 Cysteine  Lysine
neighboring aa, hydrogen bond
 Tyrosine forms helices and pleated sheets
 Threonine  Tertiary: spatial relation of more
Aliphatic:
 Asparagine  Alanine
distant residues, determine shape
 Glutamate  Quaternary: spatial relation
 Glycine between individual polypeptide
 Serine
chains in a multichain protein

Classification of proteins Contractile

Fibrous: Structural protein  Actin, myosin (muscle)
 Collagen  Collagen  Troponin C, I, T (heart)
 Keratin  Keratin
 Elastin Chromoproteins
 Elastin
 Melanin (dark)
 Glycoproteins (mucin)  Hemoglobin (heme-red)
Globular:
 Albumin Transport proteins: Protective
 Immunoglobulin  Hemoglobin, Myoglobin (O2)  Immunoglobuins
 Antibody  LDL, HDL
 Albumin Hormones
Tertiary Structure Stabilized By:  Alpha acid glycoprotein  Growth hormone
 H-Bonds  Insulin, Glucagon
 Non-Covalent Bond Nutrient
 Disulfide Bond Catalyst
 Casein
 enzymes
 ovalbumin

Enzymes
Properties of enzymes: Enzymes Functions
Catalyze chemical reactions
1. Temperature dependent 35-40 Oxidoreductases REDOX
Governed by michaelis- menten equation
Transferases Transfer of
d. optimal 37 d. functional group
Part: 2. Ph dependent, pepsinogen
 Apoenzyme: protein portion Hydrolases Hydrolytic
 Co-factor: nonprotein portion
(HCl)- pepsin Isomerases Isomerization
 Proenzymes/ zymogens: inactive 3. Very specific to target Ligases Join functional
enzyme *lock and key theory: groups
 Plasminogen- plasmin complementary to substrate Lyases Removal of
 Trypsinogen- trypsin functional groups
*induced fit theory: change
 Pepsinogen- pepsin
structure to fit **ribozyme: RNA molecule that act
 Fibrinogen- fibrin
 Holoenzyme: apoenzyme + co-
4. Naming: prefix- substrate; asenzyme
factor: active enzyme suffix- ase
Nucleic acids DNA
DNA RNA PURINE (GuAPu) STORES GENETIC CODE
SUGAR DEOXYRIBOSE RIBOSE  ADENINE STRANDS COILED AROUND HISTONE
PURINE ADENINE, ADENINE,  GUANINE PROTEINS TO FORM CHROMOSOMES
GUANINE GUANINE
PYRIMIDINE THYMINE, URACIL,
PYRIMIDINE (CuTPy) B DNA-
CYTOSINE CYTOSINE
STRAND DOUBLE SINGLE  CYTOSINE  most common form,
 THYMINE  hydrated,
NUCLEOSIDE: BASE + SUGAR  URACIL  right handed
 GUANINE +R - GUANOSINE A DNA-
 ADENINE + R - ADENOSINE  dehydrated,
Base pairing: connects double strand
 CYTOSINE + R - CYTIDINE  right handed
A-T/U: 2 H BONDS
 URACIL + R - URIDINE Z DNA-
G-C : 3 H BONDS
 THYMINE + D – DEOXYTHYMIDINE  rare type,
 left handed,
NUCLEOTIDE  double stranded
B + S + PO4 (BUILDING BLOCKS OF
NUCLEIC ACIS
LEVELS OF STRUCTURAL ORGANIZATION
1. PRIMARY: UNIQUE SEQUENCE
LINKED BY PHOSPHODIESTER
BOND
2. SECONDARY: DNA DOUBLE HELIX
PROPERTIES:
COMPLEMENTARITY: (A-T/U: 2 H
BONDS
G-C : 3 H BONDS)
ANTIPARRALLELISM: STRANDS
ARRANGED IN 5’-3’
DENATURATION:H BOND CAN BE
BROKEN BY INC TEMP OR ALKALI
RENATURATIONL/ ANNEALING:
REFORM
3. TERTIARY: SUPERCOILING
(1.74 M DNA STRAND)