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 SUGAR RELATED CONDITIONS: CARBOHYDRATE METABOLISM

 Sucrose / Table sugar GLUCOSE Inc: hyperglycemia (DM) CATABOLIC
 Matose / malt sugar Type 1 DM: damage pancreas, insufficient  break down, produce energy
 Lactose/ milk sugar insulin (txt: insulin) ANABOLIC
Type 2 DM: undamaged pancreas, sufficient
 build up, utilized energy
 OLIGOSACCHARIDE insulin, insulin resistance (txt: OHA)
 Raffinose- Gal Glu Flu (RAGAGUFU) **COMPLICATIONS: retinopathy, AMPHIBOLIC
 Maltotriose- Glu Glu Glu (MAGU) neuropathy, nephropathy  combination eg. KREB CYCLE
 Sucralose- Glu Fru Gal (SUGUFUGA)
 Gentianose- Glu Glu Fru (GEGUGUFU) GALACTOSE Inc: Galactosemia- causing ADENOSINE TRIPHOSPHATE (ATP)
mental retardation
Basis of Type of deficiency: -energy currency of cell
 POLYSACCHARIDE
 Starch- storage form of glu in plants Gal-1-PO4 uridyl transeferase (classical) -traps energy
*amylase alpha 1,4 Galactokinase -adenosine + phosphate
*amylopectin alpha 1,4 & alpha 1,6 @ every Galactose epimerase ATP 2 HEPB
25 glu unit ADP 1 HEPB
 Glycogen- storage form of glu in animals; LACTOSE: lactose intolerance- GI distress
alpha 1,4 & alpha 1,6 @ every 8-10 glu units
AMP NO HEPB
 Cellulose beta 1,4 glycosidic bond * high energy phosphate bond (HEPB)

OXIDATION VS REDUCTION COENZYMES: NAD & FAD Fate of Glu in the body:
1. ATP
Oxidation/ Dehydrogenation 2. GLYCOGEN
Nicotinamide Adenosine Dinucleotide
 +O2 3. FATS
(NAD) 4. PROTEINS
 -H
 Vitamin component: Niacin Glu convertion to ATP processes
 LEORA 1. Glycolysis/ embden meyer hof
(Vit. B3)
 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 tricarboxylic acid cycle
Riboflavin (Vit. B2)
 +H 4. Electron transport chain
 GEROA Glu convertion to Glycogen process
***
 ANABOLIC REACTIONS 1. Glycogenesis
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) TYPES OF PHOSPHORYLATION: Intermediate reaction
 Rate Limiting Enzyme:  SUBSTRATE LEVEL 2 pathway of 2 pyruvic acid from
Phosphofructokinase (PFK) PHOSPHORYLATION glycolysis
 Production Of 2 Pyruvic Acid/ Pyruvate 4 ATP – 2 ATP= 2 ATP (left) 1. Anaerobic pathway (cytosol):
From 1 Glucose  OXIDATIVE PHOSPHORYLATION produces lactic acid via lactate
 Utilize 2 ATP (Hexokinase 1. Glycerol phosphate pathway dehydrogenase
&Phosphofructokinase) @brain and skeletal muscle 2. Aerobic pathway (intermediate
 Produces 2 NADH (Glyceraldehyde 3 1 NADH= 2 ATP space) : produces2 acetyl coA
PO4 Dehydrogenase) and 2 NADH via pyruvate
 Produces 4 ATP 2. Malate aspartate pathway dehydrogenase
(Phosphoglyceratekinase, Pyruvate
@heart, liver and kidneys
kinase) 2 Acetyl coA proceed to Kreb cycle
1 NADH= 3 ATP
 Happens In The Cytosol, Must Undergo
SUMMARY 2 NADH proceed to Electron transport
Translocation
4 ATP PRODUCED – 2 ATP UTILIZED = chain (ETC)
 Glyceraldehyde 3 PO4 –
2 ATP (LEFT)
Dihydroxyacetone phosphate (triose Accumulation leads to muscle fatigue
PO4 isomerase) : reversible step 2 NADH=4 ATP (GPP) OR
2 NADH=6 ATP (MAP)
 2 pyruvic acid produced proceed to SUMMARY
TOTAL: 6-8 ATP produced
intermediate reaction 2 NADH *3= 6 ATPS

Kreb’s cycle (aerobic) Electron transport chain Pentose Phosphate Pathway

 Amphibolic reaction  Electron transporter transport  Production of:
 2 GTP were produced from succinyl coA electron to O2 to produce water
 Final electron acceptor: O2
Ribose 5 po4(rna)
via succinyl coa synthase NADPH (reduced form of NAD)
 Final products: ATP &H2O
 2 FADH2 were produced from succinate  Complex I- NADH-Coenzyme Q reductase
 Glutathione + H= reduced
via succinate dehydrogenase NADH dehydrogenase, release of H, NADH = Glutathione--- cells protected
 6 NADH were produced from NAD
isocitrate(isocitrate dehydrogenase), from free radicals
 Complex II- Succinate Coenzyme Q reductase
alpha ketoglutarate (alpha FADH dehydrogenase FADH = FAD
ketoglutarate dehydrogenase+ vit b5 +  Complex III- Cytochrome c reductase **G6PD deficiency premature
coA), malate coversion (fumarase) release of H; inhibited by CO death of RBC = HEMOLYTIC
 Complex IV- Cytochrome C Oxidase ANEMIA
O2+2H = H2O, H release; Inhibited by
SUMMARY ** CI: Sulfonamide, methyldopa,
cyanide
2 GTP= 2 ATP *ADP + PO4 VIA H & ATP synthase become ATP NSAID, anti malarials, fava beans
6 NADH= 18 ATP **coenzyme Q10/ UBIQUINONE
2 FADH2= 4 ATP **OXYGEN FREE RADICALS DEACTIVATED BY
TOTAL= 24 ATP CATALASE, PEROXIDASE, SUPEROXIDE
DISMUTASE

PROCESSES AND THEIR LOCATION

LIPIDS
CYTOSOL: CATABOLISM OF FATS
Soluble in hexane benzene ether etc.
 Glycolysis  VIA LIPASE AND H2O to yield
1. FATS/ LIPIDS
 Glycogenolysis glycerol and fatty acid
2. LIPOPROTEINS
 HMP Shunt/ Pentose PO4  Glycerol converted to
3. STEROIDS
Pathway glyceraldehyde 3 PO4 to
4. PHOSPHOLIPIDS
 Fatty Acid Synthesis 5. EICOSANOIDS produce ATP
 Lactate Dehydrogenase
 Fatty acids undergo beta
Pathway FATS: oxidation converted to acetyl
 ester of 1 glycerol and 3 fatty acids coA to become ATP
MITOCHONDRIA:
 for protection, heat insulator,  Lipase id inhibited by ORLISTAT
 Kreb’s Cycle (Matrix) energy
 Electron Transport Chain AE: steatorrhea, Vit ADEK
 saturated FA: no double bonds
(Cristae) deficiency
 unsaturated FA: with double bond
 Fatty Acid Oxidation  essential FA: Vit. F Linoleic acid
 Intermediate Reaction (omega 6, 18:2) and Linolenic acid
(INTERMEMBRANE SPACE) (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 +

COMPOSITION:
EICOSANOIDS
PHOSPHOCHOLINE /
 GLYCEROL  PROSTAGLANDIN
PHOSPHOETHANOLAMINE
 2 FATTY ACID  SMOOTH MUSCLE
**AMINO ALCOHOL: SPHINGOSINE
 PHOSPHATE CONTRACTION AND
**CERAMIDE
 ORGANIC MOLECULE RELAXATION
: AMIDE OF SPHINGOSINE +FATTY ACID
FUNCTION: Component of cell membrane :CORE STRUCTURE OF  GASTRIC SECRETION
 Lecithin/ phosphatidylcholine GLYCOSPHINGOLIPIDS  PLATEKET AGGREGATION
 Cephalin/ phosphatidylethanolamine  INLAMMATORY RESPONSE
GLYCOSPHINGOLIPIDS (W/  THROMBOXANE
CARBOHYDRATE)  PLATELET AGGREGATION
SPHINGOLIPID
COMPOSITION: a) CEREBROSIDES= CERAMIDE+  LEUKOTRIENES
 SPHINGOSINE MONOSACC  CHEMOTAXIS
 FATTY ACID b) GLOBOSIDES= CERAMIDE +  ALLERGIC REACTIONS
 POLAR HEAD GROUP DISACC / NEUTRAL OLIGOSACC  INFLAMMATION
FUNCTION: COMPOSITION OF NEURAL
TISSUES
c) GANGLIOSIDES= CERAMIDE +
CHARGED OLIGOSACC
PROTEINS Characteristics: CLASSIFICATION OF AMINO ACIDS
COMPOSED OF AMINO ACIDS Amphoteric Aromatic: Phe Tyr Typ
 Glycine: smallest, simplest, only aa not Optically active Basic: His Arg Lys
optically active, inhibitory NT, used in @low ph positively charged Acidic: Asp A Glu A
heme syn @high ph negatively charged Amidic: Asp Glu
 Phenylalanine: converted to tyrosine via AA conversions:
Phe hydrolase, associated with
Branched chain: Leu Iso Val
Histidine- histamine S containing: Cys Met
phenylketonuria Tyrosine- melatonin, catecholamines,
 Tyrosine: only aa with phenol grp, used in Alcohol cont: Ser Thr
thyroid
cathecholamine and melanin syn
Tryptophan- serotonin
(tyrosinase) Polar: CT TAGS
Glutamate- GABA
 Tryptophan: only aa with indole grp, used
Arginine- Nitric oxide  Cysteine
in the syn of 5HT/ serotonin/ happy
KETOGENIC (LEUCINE, LYSINE)  Tyrosine
hormone and melatonin  Threonine
GLUCOGENIC (13)
 Histidine: histamine syn
BOTH  Asparagine
 Arginine: converted to NO (vasodilation)
 Cysteine: aa in gluta **cystine(dimer)  PHENYLALANINE  Glutamate
 Proline: no amino, has imino grp,  ISOLEUCINE  Serine
hydroxyproline (derivative)  TYROSINE
 THREONINE
 TRYPTOPHAN
 Essential: PVT TIM HALL POLYPEPTIDE PRODUCTION: Fibrous:
 Phenylalanine AMINO ACIDS LINKED BY PEPTIDE BOND  Collagen
 Valine  Keratin
 Threonine DEHYDRATION PROCESS: FORMED BET  Elastin
 Tryptophan THE CARBOXYL AND AMINO GRP
 Isoleucine Globular:
 Methionine LEVELS OF STRUCTURE
 Primary: specific amino acid  Albumin
 Histidine
sequence (left to right)  Immunoglobulin
 Arginine
 Secondary: spatial relation of  Antibody
 Leucine
neighboring aa, hydrogen bond
 Lysine
forms helices and pleated sheets Tertiary Structure Stabilized By:
 Tertiary: spatial relation of more  H-Bonds
Aliphatic:
distant residues, determine shape  Non-Covalent Bond
 Alanine
Quaternary: spatial relation between  Disulfide Bond
Glycine
individual polypeptide chains in a
multichain protein

Classification of proteins Enzymes

Contractile
Structural protein Catalyze chemical reactions
 Actin, myosin (muscle)
 Collagen Governed by michaelis- menten equation
 Troponin C, I, T (heart)
 Keratin
Part:
 Elastin Chromoproteins
 Apoenzyme: protein portion
 Glycoproteins (mucin)  Melanin (dark)  Co-factor: nonprotein portion
 Hemoglobin (heme-red)  Proenzymes/ zymogens: inactive
Transport proteins: enzyme
Protective
 Hemoglobin, Myoglobin (O2)  Plasminogen- plasmin
 Immunoglobuins  Trypsinogen- trypsin
 LDL, HDL
 Albumin  Pepsinogen- pepsin
Hormones
 Alpha acid glycoprotein  Fibrinogen- fibrin
 Growth hormone
 Holoenzyme: apoenzyme + co-
 Insulin, Glucagon factor: active enzyme
Nutrient
 Casein Catalyst
 ovalbumin  enzymes

Properties of enzymes: Nucleic acids

Enzymes Functions DNA RNA
1. Temperature dependent 35-40 SUGAR DEOXYRIBOSE RIBOSE
Oxidoreductases REDOX
d. optimal 37 d. Transferases Transfer of PURINE ADENINE, ADENINE,
2. Ph dependent, pepsinogen functional group
GUANINE GUANINE
PYRIMIDINE THYMINE, URACIL,
(HCl)- pepsin Hydrolases Hydrolytic CYTOSINE CYTOSINE
3. Very specific to target Isomerases Isomerization STRAND DOUBLE SINGLE
*lock and key theory: Ligases Join functional
groups NUCLEOSIDE: BASE + SUGAR
complementary to substrate
Lyases Removal of  GUANINE +R - GUANOSINE
*induced fit theory: change functional groups  ADENINE + R - ADENOSINE
structure to fit  CYTOSINE + R - CYTIDINE
4. Naming: prefix- substrate; **ribozyme: RNA molecule that act  URACIL + R - URIDINE
suffix- ase asenzyme  THYMINE + D – DEOXYTHYMIDINE

NUCLEOTIDE
B + S + PO4 (BUILDING BLOCKS OF
NUCLEIC ACIS
PURINE (GuAPu) LEVELS OF STRUCTURAL ORGANIZATION RNA
PYRIMIDINE (CuTPy) 1. Primary: unique sequence linked TYPES:
by phosphodiester bond mRNA : template for transcription
DNA 2. Secondary: dna double helix tRNA : carries aa to site of
STORES GENETIC CODE Properties:
translation
STRANDS COILED AROUND HISTONE Complementarity: Base pairing:
PROTEINS TO FORM CHROMOSOMES
rRNA: structural component of
connects double strand A-T/U: 2 H
B DNA- ribosomes
BONDS ; G-C : 3 H BONDS
 most common form, SnRNA : removes introns / okazaki
Antiparrallelism: strands arranged in
 hydrated, fragments
5’-3’
 right handed
Denaturation:h bond can be broken
A DNA- CENTRAL DOGMA
by inc temp or alkali
 dehydrated, 1. REPLICATION: DNA- RNA
 right handed
Renaturationl/ annealing: reform
2. TRANSCRIPTION: RNA – mRNA
Z DNA- 3. Tertiary: supercoiling (1.74 m
3. TRANSLATION: mRNA – aa-
 rare type, dna strand)
protein
 left handed, double stranded
**TOPOISOMERASE:PREVENT UNDER
AND OVER WINDING

TRANSCRIPTION: VITAMINS
HELICASE open DNA helix FAT SOLUBLE VITAMINS
MUTATION
PRIMASE creates mRNA primer Vit A / Retinol/ Retinal/ Retinoic Acid
POINT MUTATION  Precursor: Beta Carotene
DNA polymerase start transcription TRANSITIONAL same class  Deficiency: Nyctalopia
(DNA- mRNA) TRANSVERSIONAL interchange from  Most Toxic, Stable, Teratogenic
SnRNA removes introns (non coding) purine to pyrimidine Vit D/ Sunshinevitamin
DNA ligase: joins discontinuous  Precursor: ergosterol- ergocalciferol
strands RESULT OF POINT MUTATION: (D2) &
SILENT- codes to same aa  7 dehydrocholesterol-
RNA polymerase: transcribe info from cholecalciferol (D3) – calcitriol
MISSENSE - codes to diff aa.
DNA- Mrna  Deficiency: rickets, osteomalacia
NON SENSE- codes to stop codon
Vit E/ Alpha tocopheol – anti oxidant
TRANSLATION: FRAMESHIFT MUTATION Vit K –CLOTTING FACTOR (10,9,7,2)
Activation a. INSERTION MUTATION 1. PHYTOMENADIONE /
Initiation start codon AUG methionine b. DELETION MUTATION PHYLLOMENAQUINE
Elongation conversion of codon to aa 2. PRENYLMENAQUINONE
1. Termination: stop codon- 3. MENADIONE
UGA UAA UAG 4. MENADIOL

WATER SOLUBLE VITAMINS  Niemann-Pick disease-  Biuret test- protein peptide bonds
Cevitamic acid / Ascorbic acid/ Vit C sphingomyelinase  Xanthoproteic test- aromatic aa (PTT)
 Deficiency: scurvy  Farber disease- ceramidase  Hopkin’s cole test- indole aa (trp)
 Least stable/ reducing agent  Fabry disease-  Millon’s test/ millo-nase test – phenol
 Impt in syn of collagen alpha galactosidase aa (tyr)
B1: beriberi, wernicke-korsakof syndr  Krabbe disease-  Sakaguchi test- arginine
B2: cheilosis, glossitis, stomatitis, FAD beta galactosidase  Pauly-diazo test- tyrosine, histidine
B3: pellagra, dementia,  Gaucher’s disease –  Ninhydrin test – alpha amino group
diarrhea,dermatitis, dec LDL NAD cerebrosidase (except proline, hydrocyproline)
B5: Chic antidermatitis factor, burning  Tay-sach’s diseases-  Molisch test/ purple ring test-
foot syndrome beta hexoaminidase glycoprotein
B6: peripheral neuritis  Albinism- tyrosinase  Fehling’s, benedict’s, tollen’s,
B7: alopecia  Phenylketonuria- Phe hydroxylase barfoed’s – reducing sugars
B9: megaloblastic anemia, prev spina  Maple syrup urine dse-  Seliwanoff’s test- fructose
bifida, impt in fetal brain development alpha keto acid dehydrogenase (ketohexose)
B12: pernicious anemia, abs through  Hartnup’s dse- tryptophan  Bial’s test, tauber’s test- pentoses
intrinsic factor  Alkaptonuria-  Ozasone test- mannose
homogentisate oxidase  Mucic acid test- galactose