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Biomolecules

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

 Extracts compounds & subjects extract: separation technique


 Isolates & purify compound
 All carbon compounds from living tissues— biomolecules

 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

 Weighs ↓ living tissue & dry


 All H2O evaporates &remaining material: dry weight

 If tissue— fully burnt, all C compounds oxidize— CO2 & water vapour & removed
 Ash— Inorganic elements (Ca, Mg, Cl)

Inorganic compounds like SO4, PO4— acid-soluble fraction

 Lipids— not strict macromolecule


 Size—< 800 Da
 In cell membrane & other membranes
 Grind tissue— disrupt cell structure
 Cell membrane & other membranes— broken: pieces
 Form vesicles (water insoluble)
 Membrane fragments – form (vesicles) separated: acid ip
 Hence— macromolecular fraction

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

Essential (8) Semi-essential (2) Non-essential (10)


Not synthesized—body synthesized: adults Synthesized by body
Needed: diet not—children not needed: diet

Based—no. amino & carboxyl groups

1. Acidic (glutamic acid)—Basic ph


(-) charge (COOH group donates H+ to basic: OH-)
COO- charge

2. Basic (lysine) — acidic pH


(+) charge (NH2 gains H+ = NH3+)

3. Neutral (valine) — gavil

Zwitterion— at isoelectric pH: (+) & (-) charge: ionizable nature: COOH & NH2— dipolar ion

Aromatic amino acids


1. Tryptophan: precursor of
 Indole aceitic acid
 Melatonin
 Niacin
 Serotonin

2. Tyrosine (OH group)


 Dopamine
 Melanin
 Adrenaline/Nor adrenaline
 Thyroxin

3. Phenylalanine
 Tyrosine precursor

Nucleic acids

5 N bases – adenine, guanine, cytosine, uracil (RNA) & thymine


Purine— 2 heterocylic ring (a, g)
Pyrimidine— 1 heterocylic ring (c, u, t)
 NB + ribose (pentose)/deoxy-ribose = nucleosides
[RNA] [DNA]

 Phosphate group + nucleoside= nucleotides

 NB + ribose= Adenosine, guanosine, thymidine, uridine & cytidine (nucleosides)


 NB + deoxy-ribose (DNA) = de-oxy prefix (not uridine)
 Nucleoside + phosphate= Adenylic acid, thymidylic acid, guanylic acid, uridylic acid & cytidylic acid

DNA & RNA— nucleotides only

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

Only single c bond +nt 1 or< double c bond +nt


Solid (room temp) Liquid
↑ boiling & melting point ↓ boiling/melting point

Palmitic acid—16 C Oleic acid 18 C 1 double bond 9(position of bond)


Arachidic acid—20 C Linoleic acid 18 C 2 9, 12
Stearic acid— 18C Linolenic acid 18C 3 9, 12
Arachidonic acid 20 C 4 5, 8, 11, 14

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

Primary Metabolites Secondary Metabolites


Growth, development & reproduction not: growth, development &reproduction
Formed: all living cell Plant, fungi & microbial cells
Primary metabolism, respiration No primary metabolism
Formed: growth phase: cell Formed: end— growth phase
Nucleic acid, lactic acid, amino acid Cellulose, drugs

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

 Polypeptide/protein: AA linked: peptide bond


Carboxyl group (1AA) reacts— amino group (AA)
Eliminate water

 Collagen— abundant protein (animal world)


 RuBisCO— ↑ abundant protein (biosphere)

 Collagen— Intercellular ground substance & provide strength


 Trypsin— protein— peptides
 Insulin— hormone
 Antibody— fight infectious agents
 Receptor— sensory reception
 GLUT-4— Glucose transport
Structure of Proteins

 A protein imagined— line


 Left end represented— 1st AA (N-terminal AA) & right end— last amino acid(C-terminal AA)

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

 Carbohydrates— optically active compounds having polyhydroxy group— aldehyde/ketone


 Long glucose chains/ glucose polymer
 In polysaccharide chain: right end— reducing end & left end— non-reducing end

1. Monosaachrides— Simple carbohydrates: not hydrolysed further


i. 3-7 C
ii. Ribose, Erythrose
2. Oligosaachrides— Small carbohydrates: condensation— 2-9 Monosaachrides
i. Sucrose, lactose

3. Derived monosaachride— modified monosaachride (deoxy-ribose)

Monosaccharides— linked: glycosidic bond


Formed— dehydration
2 C atoms (2 adjacent monosaccharides)

Cellulose— polymeric polysaccharide consisting 1type: monosaccharide glucose


 Homopolymer
 6000 β glucose residues
 β-1,4 linkage

Starch— Amylose & Amylopectin


o Amylose— 200-1000: ᾳ-1, 4
o Amylopectin—2000-200,000 & ᾳ-1, 4 linkages
o Branching—ᾳ-1, 6 & after 25 units
 Glycogen— 30000 glucose residues
 ᾳ-1,4 & Branching: ᾳ-1,6 & after 10-14 residues
 Red color: I2

 Starch— helical secondary structures (Branched)


o Hold I2 mol: helical portion (blue)
 Cellulose— no complex helices & not hold I2

 Inulin— fructose polymer


 Plant cell walls— cellulose
 Paper & cotton fibre— cellulosic
 Chitin— Exoskeletons of arthropods (N-acetyl glucosamine)

Nucleic Acids
 Polymers— nucleotide
 Adenine & Guanine— substituted purines
 Rest— substituted pyrimidines
 Nucleic acid: deoxyribose— deoxyribonucleic acid (DNA)
 Ribose— ribonucleic acid (RNA)

 Ester bond: phosphate & hydroxyl group (sugar)


 Phosphate links 3’-C (sugar): 1 nucleotide— 5’-C (sugar): nucleotide
 1 ester bond: either side: phosphodiester bond

Watson - Crick Model

 DNA— exists double helix


 2 strands— polynucleotide: antiparallel (opp dir)
 Backbone formed by— sugar-phosphate- sugar chain
 N bases— projected ↑ or ↓ — backbone: face inside

 A & G: 1 strand— base pairs with T & C, respectively: other strand


 All bp : 1 Purine & 1 Pyrimidine & 2 complementary strands: complementary b pairing

 2 H bonds between A &T


 3H bonds between G & C.

 Each strand appears— helical staircase.


 Each step of ascent represented— base pair

 Each step of ascent, strand turns 36°


 1 full turn: helical strand: 10 steps/base pairs
 Pitch = 34Å
 Rise /base pair = 3.4Å.

A DNA = 11 base pair


C DNA = 9bp
D DNA = 8bp
Z DNA = 12 bp

Dynamic state of body constituents

Living organisms— contain biomolecules (certain conc mol/cell or mol/L)


Turn over no. — no: substrate mol changed/min (enzyme)

Metabolic reactions: Break & make & transform biomol

a. Anabolic: simple → complex (consume J)


Aceitic acid → cholesterol
Amino acid → Protein

b. Catabolic: Degradation complex → simple (release J)


Glucose → Lactic acid (glycolysis)

 Living organism— trap J (degradation)


 Store— as chemical bond
 Bond J— biosynthetic, osmotic & mechanical work
 ATP— Bond J
J currency
Adenosine + 3 phosphates

Metabolic transformations—
 Remove CO2 (amino acids) — amine
 Remove: amino group (nucleotide)
 Hydrolysis: glycosidic bond (disaccharide)— monosaachride

Metabolic reactions— not isolated


Linked— other reactions

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)

 Catalysts— hasten metabolic conversation rate


Proteins

 Metabolic flux— molecule turn over (metabolic pathway)

 Chemical/ physical process— move spontaneous to equilibrium (eb)


Systems (eb) — no work

 Living/ steady state— non-eb state


 Living organisms— work continuously & not afford: reach eb

 To perform work— constant effort (prevent falling: eb)


J input required

 Metabolism—J production

 Living state & metabolism— ≡


 No metabolism— No living state

Enzymes

 Enzymes— proteins (catalytic power)

 Nucleic acids— like enzymes: ribozymes

 Has— primary (AA protein sequence) secondary & tertiary structure

 Active Site
Crevice / pocket: substrate fits
Tertiary— backbone (p chain) folds: itself
 Chain criss-crosses itself & pockets made
 Catalyse reactions— ↑ rate

 Enzymes— isolated (org: ↑ temp)


Stable & retain catalytic power— ↑ temp (80°-90°)

 Thermal stability— imp Isolated (thermophilic)


Inorganic Catalysts Enzyme
↓ & simple inorganic mol (minerals) Proteins & complex mol organization

Not— living cells Living cells +nt

Not specific Specific


Catalyse ↑ reactions Catalyse ↓ reactions

Efficient— ↑ temp & Pa Damaged— ↑ temp (> 40)

↓ efficient ↑ efficient

Chemical reactions

 Physical change— change: shape & state (no breaking of bond)


 Old bonds: broken & new bonds formed (transformation) — chemical reaction

 Rate (physical/ chemical) — amount: product formed / unit time


 Velocity if dir specified
 Influenced— temp
 Rate— 2X / ↓ (1/2): every 10°C change (either dir)

 Catalysed reactions proceed ↑ rates > uncatalysed


 Enzyme catalysed reactions ↑ rate > same uncatalysed reaction

 Enzyme –nt— slow reaction


 200 H2CO3 mol— 1 hour

 Carbonic anhydrase +nt— reaction ↑


 600,000 molecules— 1s
 Reaction: a (10 million times)

 Glucose— pyruvic acid (10 diff enzyme catalysed metabolic reaction)


 Skeletal muscle— lactic acid
 Yeast (fermentation) — ≡ pathway: ethanol production
 Chemical converted to product— substrate
 Enzymes: substrate— product

 S— bind enzyme: active site (as)


 Diffuse: as
 Obligatory form— ES complex (transient phenomenon)

 State— S bound: enzyme as


New structure (S) — transition state (TS) structure

 Bond breaking/making— completed


Product— released (as)

 S structure — transformed: P structure


 Transformation pathways— go through TS structure
 ↑ unstable intermediate altered structural states— bw stable S & P

 Stability— J status of mol

 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

 P— ↓ level < S— exothermic


 P—↑ level > S— endothermic

Nature of enzyme action

1. S binds to enzyme AS (fitting AS): E-S complex


i. Short-lived
ii. Dissociates: P & unchanged enzyme (as EP complex)

2. Substrate binding— induce enzyme: alter shape: fit tightly around S

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

 Enzymes function— narrow range: temp & pH change

 ↑ Activity: particular temp & pH— optimum temp & pH

 Activity declines— ↑ & ↓ optimum value

 Low temp— preserve enzyme (inactive state)

 ↑ Temp— destroy enzymatic activity & denature proteins

Substrate Conc

 ↑ S conc = ↑ velocity: enzyme reaction

 Reaction reaches— max velocity not exceeded: further ↑ S conc

 Enzyme mol: < S molecules


 After saturation (mol) — No free enzyme molecules: bind S mol

 Km value— S conc: 1/2 Vmax (enzyme catalysed chemical reaction)

Inhibition

Enzyme activity— sensitive: specific chemicals (bind)


When binding— shuts off enzyme activity (inhibition & chemical: inhibitor)

Competitive Inhibition

Inhibitor resembles— S (mol structure) & inhibits enzyme activity


Close structural ≡: S inhibitor compete substrate binding site

S— not bind & enzyme action ↓

Inhibition: succinic dehydrogenase: malonate (resembles S succinate structure)


Control— bacterial pathogens

Vmax remains ≡
Km value ↑ (↑ substrate: ½ Vmax: inhibitor +nt)
Nomenclature & classification of enzymes

6 classes each: 4-13 subclasses & named: 4-digit number

1. Oxidoreductases/dehydrogenases— catalyse oxidoreduction bw 2 S— S & S’


S reduced + S’ oxidised → S oxidised + S’ reduced

2. Transferase— catalyse transfer: 1 group (not H) bw : 2 S— S & S’


S - G + S → S + S’ – G

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

5. Isomerases— catalyse inter-conversion: optical, geometric / positional isomers


6. Ligases: link 2 compounds (C-O, C-S, C-N, P-O bonds)

Co-factors

 Non-protein constituents bound: enzyme & make catalytically active


 Protein portion— apoenzyme
 Catalytic activity lost: co-factor remove

1. Prosthetic groups (PG) — organic compounds


Tightly bound— apoenzyme

In peroxidase & catalase— break hydrogen peroxide: water & O2


Haem (PG)

2. Co-enzymes— organic compounds


Transient association: apoenzyme (during catalysis)
Co-factors— ↑ diff catalyzed reactions
Vitamins

Nicotinamide adenine dinucleotide (NAD) & NADP—niacin

3. Metal ions— form coordination bonds (side chains at AS)


 Form 1 < cordination bonds (with S)
 Zn— carboxypeptidase (proteolytic)

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