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Chemical analysis
Living tissue & grind: trichloroacetic acid (Cl3CCOOH) (mortar & pestle)
Thick slurry
Strain through cheesecloth/ cotton
2 fractions—filtrate/acid-soluble pool
Retentate / acid-insoluble pool
Acid soluble pool—mol weights: 18-800 Da ( glucose, amino acids & nucleotides)
Cytoplasmic composition
Acid insoluble—mol weights > 10000 Da (lipids, carbs, proteins, nucleic acids)
Cytoplasmic macromolecules & organelles
If tissue— fully burnt, all C compounds oxidize— CO2 & water vapour & removed
Ash— Inorganic elements (Ca, Mg, Cl)
Amino Acids
Organic compounds— amino group & acidic carboxyl group: substituents – same ᾳ-carbon
Substituted methanes
Optical isomerisation
4 groups occupy: 4 valency position
H, carboxyl group, amino group & variable group designated: R group
Only 20 occur (proteins)
R group— hydrogen— glycine
Methyl— alanine
Hydroxy methyl— serine
Zwitterion— at isoelectric pH: (+) & (-) charge: ionizable nature: COOH & NH2— dipolar ion
3. Phenylalanine
Tyrosine precursor
Nucleic acids
Lipids
Glycerol/ Trihydroxy propane + fatty acids
Fatty acids (FA) — long chain of alkyl group containing –COOH group
Water insoluble
A carboxyl group attached: R group
Methyl /ethyl/ ↑ no –CH2 groups
Saturated FA Unsaturated FA
1. Simple Lipids
Neutral fat, wax, suberin/cutin
a. Neutral fat— monoglycerides (1 glycerol)
Diglycerides (2 glycerol)
Triglycerides (3 glycerol)
Phospholipid—
Glycerol + phosphate + 2 FA + Choline
Lecithin— cell membrane & alveoli
Neural tissues (cephaline)
Primary & Secondary Metabolites
Proteins
Proteins – polypeptides
Linear chains: amino acids linked – peptide bonds
Polymer: amino acids
Heteropolymer & not homopolymer (1 type— monomer repeating n times)
Transport nutrients, fight infectious organisms, hormones, enzymes
1. Primary Structure
The sequence— amino acids: arranged—polypeptide chain
Positional information (AA)
2. Secondary structure
Protein thread— not exist: extended rod
Chain folded: helix form (only ↓ portions)
Only right handed helices observed
ᾳ helix: interaction 4th AA by intramol. H bond (Keratin)
β pleated: 2 or< polypeptide chains: intermolecular H bond (Fibroin)
3. Tertiary Structure
Long protein chain— folded upon itself (hollow woolen ball)
tertiary structure
Imp— ↑ biological activities (proteins)
Form active site (enzyme)
4. Quaternary Structure
Some proteins— assembly: > 1 polypeptide subunits
Manner— Individual folded polypeptides/subunits arranged: — quaternary structure
Hb— 4 subunits
2 ᾳ subunits & 2 β subunits
Polysaccharides
Nucleic Acids
Polymers— nucleotide
Adenine & Guanine— substituted purines
Rest— substituted pyrimidines
Nucleic acid: deoxyribose— deoxyribonucleic acid (DNA)
Ribose— ribonucleic acid (RNA)
Metabolic transformations—
Remove CO2 (amino acids) — amine
Remove: amino group (nucleotide)
Hydrolysis: glycosidic bond (disaccharide)— monosaachride
Metabolic Pathways— multistep chemical reaction: 1 step: catalysed (≡ / diff enzyme complex)
Convert metabolites: other
Linear/ circular
Crisscross— each other (junctions)
All chemical reaction— catalysed
No uncatalysed meta conversion (living systems)
Metabolites— specific conc
Blood conc (glucose) — 4.2— 6.1 mmol/L
Hormones— ng/mL
Living organisms— steady-state characterized: conc
Dynamic state: definite rate & dir of metabolite flow (metabolic pathway)
Metabolism—J production
Enzymes
Active Site
Crevice / pocket: substrate fits
Tertiary— backbone (p chain) folds: itself
Chain criss-crosses itself & pockets made
Catalyse reactions— ↑ rate
↓ efficient ↑ efficient
Chemical reactions
Y-axis— PE content
X-axis— progression: structural transform through TS
S— go through ↑ J state / TS
Diff. — average J content (S) from that of TS— activation J
Enzymes— bring down activation J: easy S→P
3. Enzyme AS— close S proximity: breaks its chemical bonds & form EP complex
4. Enzyme release— reaction products & free enzyme: bind another S mol
Factors affecting enzyme activity
1. Temperature & pH
Substrate Conc
Inhibition
Competitive Inhibition
Vmax remains ≡
Km value ↑ (↑ substrate: ½ Vmax: inhibitor +nt)
Nomenclature & classification of enzymes
3. Hydrolases— catalyse hydrolysis (ester, ether, peptide, glycosidic, C-C, C-halide / P-N bonds)
4. Lyases— catalyse removal: groups from S (other than hydrolysis) leave double bonds
Co-factors