Week 13 - Organic Molecules

LECTURE 35

Reactivity and Bond Characteristics of Alcohols

• Electronegativity and Polarity: The chemistry of alcohols ($R-OH$) is primarily dominated by the high electronegativity of oxygen. This oxygen atom makes the attached carbon and hydrogen atoms electron-deficient. The $OH$ group is highly polar, allowing it to engage in hydrogen bonding.

• Physical Properties: Due to hydrogen bonding, alcohols possess high boiling points relative to alkanes and alkenes of similar molecular weight. They also demonstrate increased solubility in water.

• Available Electrons: The oxygen atom in an alcohol has four electrons (two lone pairs) available for chemical reactions.

• Reactions and Catalysis:

  • Loss of both hydrogen atoms (attached to the oxygen and the alpha-carbon) leads to oxidation.

  • Base treatment (e.g., using sodium hydride, $NaH$) can remove the acidic proton from the hydroxyl group, though it requires a very strong base to do so.

  • Alcohols do not readily accept a proton ($H^+$); in the presence of acid, the equilibrium for protonation lies heavily to the left.

  • pKb Values: Methanol has a $pKb$ of $18.9$, while 2-propanol has a $pKb$ of $18.7$.

  • $H^+$ acts as a catalyst in the formation of esters from alcohols and carboxylic acids: $R-COOH + R'-OH \rightleftharpoons R-COOR' + H_2O$.

Acidity of Alkanols versus Phenols

• Classification of Alcohols:

  • Primary ($1^o$) alcohol: $R-CH_2OH$.

  • Secondary ($2^o$) alcohol: $R_1R_2CHOH$.

  • Tertiary ($3^o$) alcohol: $R_1R_2R_3COH$.

• Acidity and pKa Values for Alkanols:

  • Methanol ($CH_3OH$): $pKa = 15.5$.

  • Ethanol ($CH_3CH_2OH$): $pKa = 15.9$.

  • 2-propanol (isopropanol): $pKa = 17$.

  • tert-butanol ($(CH_3)_3COH$): $pKa = 18$.

• Acidity and pKa Values for Phenols (Ar-OH):

  • Phenol: $pKa = 9.2$.

  • Other substituted phenols: $pKa = 10.2$ and $pKa = 10.5$.

• Induction and Solvation:

  • Tertiary alkoxides are the least stable conjugate bases in water. This instability arises because it is harder to solvate them due to steric hindrance, which interferes with ion-dipole and hydrogen-bonding intermolecular forces.

  • The conjugate base of a stronger acid is more stable. Phenols are significantly more acidic than alkanols because their conjugate bases (phenoxides) are stabilized by resonance/polarization.

Bond Conjugation and Molecular Orbitals

• Definition of Conjugation: Conjugated systems occur when two or more p orbitals exist in an uninterrupted sequence, allowing for the formation of delocalized $\pi$ orbitals. In Lewis structures and line notation, these are represented as alternating single and double bonds.

• Bond Properties in Different Environments:

  • Alkanes ($C-C$): Bond length of $154\,pm$, bond strength of $356\,kJ/mol$.

  • Alkenes ($C=C$): Bond length of $133\,pm$, bond strength of $636\,kJ/mol$.

  • Benzene: Bond length of $139\,pm$, bond strength of $518\,kJ/mol$.

• Delocalization Effects: $\pi$ electrons in delocalized orbitals lie above and below the plane of the molecule. Consequently, the single bonds in conjugated systems remain shorter than expected and do not rotate as freely as standard single bonds.

• Conjugated Examples and Bond Lengths:

  • 1,3-butadiene: Features alternating bond lengths such as $134\,pm$, $146\,pm$, and $134\,pm$.

  • 1,3,5-hexatriene: Features lengths of $134\,pm$, $145\,pm$, $134\,pm$, $145\,pm$, and $134\,pm$.

  • 1,3,5,7-octatetraene ($C_8H_{10}$): Demonstrates electrons in highly delocalized orbitals. These $\pi$-type bonding orbitals are low-energy quantum states where electrons are bound by more than two nuclei.

Characteristics and Requirements of Aromaticity

• Benzene vs. Polyenes: Unlike 1,3,5-hexatriene, benzene is not simply three alternating double bonds in a ring. Its bonds are identical in length ($139\,pm$) and the ring is perfectly flat (planar).

• Resonance and Stability: Resonance structures for aromatic molecules are simplified representations of delocalized $\pi$ molecular orbitals. Aromatic molecules exhibit enhanced stability and reduced reactivity.

• Hückel’s Rule and Aromatic Criteria:

  1. The system must be conjugated with all species $sp^2$ hybridized.

  2. The conjugated system must be cyclic.

  3. The system must contain $4n + 2$ $\pi$ electrons, where $n = 0, 1, 2, \dots$ (Hückel’s Rule).

  4. The system must be planar (within reasonable geometric limits).

• Aromatic Heterocycles: Aromatic systems can include non-carbon elements (heteroatoms). Examples include:

  • Pyridine ($N$)

  • Pyrrole ($NH$)

  • Phosphole ($PH$)

  • Furan ($O$)

  • Imidazole ($NH, N$)

• Prevalence of Aromatic Rings: Aromatic rings are essential components in natural and synthetic organic compounds, including:

  • Painkillers: Aspirin, Paracetamol, Ibuprofen.

  • Opioids: Morphine, Heroin, Codeine.

  • Anaesthetics: Propofol, Ketamine.

  • Amino Acids: Phenylalanine, Tryptophan.

  • Hormones: Estradiol, Norepinephrine.

Amines: Structure, Basicity, and Classification

• General Structure: Amines consist of one or more organic groups ($R$) bonded to a nitrogen atom. General formulas include $RNH_2$ (primary), $R_2NH$ (secondary), and $R_3N$ (tertiary).

• Basicity: The nitrogen lone pair is an effective proton acceptor, making amines basic. The conjugate acid of an amine (ammonium ion) is positively charged at low pH. Quaternary ammonium salts possess a permanent positive charge.

• Aliphatic vs. Aromatic Amines (pKb Values):

  • Aliphatic primary amine ($RNH_2$): $pKb ≈ 3.13$.

  • Pyridine: $pKb = 8.75$. The nitrogen is $sp^2$ hybridized, which forms a weaker bond to $H^+$ than the $sp^3$ orbitals on aliphatic amines. The lone pair is not part of the aromatic $\pi$ system.

  • Pyrrole: $pKb = 13.6$. It is a very weak base because its nitrogen lone pair is part of the aromatic $\pi$ system and is unavailable for protonation.

  • Imidazole: $pKb = 6.9$ (alternate value mentioned: $14.4$). It contains two nitrogen sites; one is a basic lone pair (similar to pyridine) not part of the $\pi$ system, and the other is part of the $\pi$ system and non-basic (similar to pyrrole).

Biological and Nitrogen-containing Functional Groups

• Neurotransmitters and Hormones:

  • Adrenaline (secondary amine)

  • Serotonin (primary amine, aromatic amine)

  • Acetylcholine (quaternary ammonium)

  • Dopamine (primary amine)

• Psychoactive Drugs and Stimulants:

  • MDMA ("E"): Contains a secondary amine.

  • Nicotine: Contains a tertiary amine and a tertiary aromatic amine.

  • Cocaine: Contains a tertiary amine.

  • Heroin: Contains a tertiary amine.

• Other Nitrogen Groups:

  • Amide: $NH$ attached directly to a carbonyl group ($C=O$).

  • Urea: $NH_2$ attached to a carbonyl and another nitrogen heteroatom.

  • Urethane (Carbamate): Nitrogen attached to a carbonyl and an oxygen heteroatom.

  • Imine: Nitrogen is $sp^2$ hybridized in a $C=N$ bond.

  • Nitrile: Nitrogen is $sp$ hybridized in a $C\equiv N$ bond.

Questions & Discussion

• Tranexamic Acid Case Study:

  • Tranexamic acid is used to prevent major blood loss by mimicking amino acid receptor sites on plasminogen.

  • Comparison of amino acids for mimicry:

    • Asparagine: $pKa = 2.1$ (carboxyl), $8.80$ (amino).

    • Lysine: $pKa = 2.15$ (carboxyl), $9.16$, $10.67$ (amino).

    • Arginine: $pKa = 2.18$ (carboxyl), $9.09$ (amino), $13.8$ (guanidino).

  • The molecule's existence as a zwitterion in solution depends on the pH range relative to the carboxyl and amino $pKa$ values.

• Aromaticity Example: The cyclopropane cation (cyclopropenium) is aromatic. It follows Hückel's Rule where $n=0$ ($2$ $\pi$ electrons), is cyclic, and planar.

LECTURE 36

Carbonyl Functional Groups and Structural Arrangement

• Orbital hybridization and Valence Shell Electron Pair Repulsion (VSEPR) theory determine the three-dimensional arrangement around reactive heteroatoms in functional groups.

• Relevant heteroatoms in these groups typically include nitrogen ($N$), oxygen ($O$), sulfur ($S$), and chlorine ($Cl$).

• Key Carbonyl Functional Groups:

  • Aldehyde: $R-CHO$ (where $R' = H$).

  • Ketone: $R-CO-R'$.

  • Acyl Chloride (Acid Chloride): $R-COCl$.

  • Carboxylic Acid: $R-COOH$.

  • Ester: $R-COOR'$.

  • Primary Amide: $R-CONH_2$ (where $R' = R'' = H$).

  • Acid Anhydride: $R-CO-O-CO-R$.

  • Thioester: $R-CO-SR'$.

Activation and Interconversion of Carboxylic Acid Derivatives

• Activating Carboxylic Acids: Carboxylic acids are generally less reactive and can be converted into highly reactive acyl chlorides (acid chlorides) using thionyl chloride ($SOCl_2$).

  • Reaction: $R-COOH + SOCl_2 \rightarrow R-COCl + SO_2 + HCl$.

• Reactivity of Acyl Chlorides: Once formed, acyl chlorides are easily transformed into other functional groups:

  • Amide Formation: $R-COCl + NH_2-R' \rightarrow R-CONHR' + HCl$.

  • Ester Formation: $R-COCl + R'-OH \rightarrow R-COOR' + HCl$.

• Alternative Amide Synthesis: Amides can also be formed by reacting an ester with an amine and applying heat.

Hydrolysis of Carboxylic Acid Derivatives

• Definition: Hydrolysis (from "hydro" for water and "lysis" for breaking apart) involves the reaction of these derivatives with water to break chemical bonds.

• Reaction Pathways:

  • Acyl Chloride: $R-COCl + H_2O \rightarrow R-COOH + HCl$.

  • Acid Anhydride: $R-CO-O-CO-R + H_2O \rightarrow 2 R-COOH$.

  • Ester: $R-COOR' + H_2O \xrightarrow{H^+} R-COOH + R'OH$.

  • Amide: $R-CONHR' + H_2O \xrightarrow{HCl, \text{ heat}} R-COOH + R'NH_3^+Cl^-$.

  • Thioester: $R-COSR' + H_2O \rightarrow R-COOH + R'SH$.

• Catalysts and Conditions:

  • $H^+$ (e.g., $HCl$) acts as an acid catalyst.

  • Under acidic conditions ($HCl$), amine products are protonated (e.g., $R'NH_3^+$).

  • Under basic conditions ($NaOH$ and heat), the carboxylic acid product is deprotonated to form a carboxylate salt ($R-COO^- Na^+$).

Rates of Hydrolysis and Electronic Effects

• Reactivity Hierarchy: The rate of hydrolysis depends on the reactivity of the functional group. The order from most reactive to least reactive is:

  1. Acid Chlorides (most reactive)

  2. Acid Anhydrides

  3. Esters

  4. Amides (least reactive)

• Condition Requirements:

  • Acid chlorides and anhydrides hydrolyze in water at $pH\,7$.

  • Esters require an acid ($H^+$) or base ($OH^-$) catalyst and heat.

  • Amides require concentrated acid ($H^+$) or base ($OH^-$) and prolonged heating.

• Electronic Factors:

  • Induction: $O$, $N$, and $Cl$ are all more electronegative than Carbon, pulling electron density away from the carbonyl carbon.

  • Resonance: $O$ and $N$ form delocalized orbitals. The resonance effect is significantly greater for Nitrogen than Oxygen due to the similarity of p-orbital energies between Carbon and Nitrogen, which stabilizes the amide group and reduces its reactivity.

Biological Applications: Thioesters and Cofactors

• Acetyl Coenzyme A (Acetyl CoA): Thioesters are critical in biological systems, specifically as cofactors.

• Function: Coenzyme A acts as a "molecular crane" for the delivery of acetate ($CH_3CO$) in biosynthetic processes, such as fatty acid biosynthesis.

• Metabolic Oxidation:

  • The metabolism of alcohol involves the conversion of Ethanol to Acetaldehyde (a toxic intermediate) and then to Acetate.

  • The enzyme Aldehyde Dehydrogenase facilitates the conversion of acetaldehyde to acetate using the cofactor $NAD^+/NADH$.

  • The ultimate oxidation of acetate to $CO_2$ and $H_2O$ releases significant energy: $\Delta_{rxn}G^{\circ} = -1325\,kJ\,mol^{-1}$ (for full combustion) or $\Delta_{rxn}G^{\circ} = -215\,kJ\,mol^{-1}$ for specific intermediate steps.

Oxidation States (O.N.) in Organic Chemistry

• Definition: Oxidation state represents the hypothetical charge on an atom if all bonds were treated as ionic. It measures the number of electrons associated with an atom.

• Core Rules for O.N.:

  1. Pure elements (e.g., $Na$, $O_2$, $Cl_2$) = $0$.

  2. Monatomic ions = the charge on the ion (e.g., $Fe^{3+} = +3$).

  3. Sum of O.N. in a neutral compound = $0$.

  4. Sum of O.N. in a polyatomic ion = the charge of the ion.

  5. Fluorine ($F$) = $-1$.

  6. Group 1 elements = $+1$; Group 2 elements = $+2$.

  7. Oxygen ($O$) = $-2$ (except in peroxides where it is $-1$, in $O_2/O_3$ where it is $0$, and in $OF_2$ where it is $+2$).

  8. Halogens = $-1$ (unless bonded to Oxygen or a smaller halogen).

  9. Hydrogen ($H$) = $+1$ when bonded to non-metals; $-1$ when bonded to metals.

• Organic Specific Rule: $C-C$ bonds do not contribute to the oxidation number of carbon.

Oxidation and Reduction Reactions

• Oxidation: Involves increasing Oxygen content and/or decreasing Hydrogen content, which increases the O.N. of Carbon atoms in or near functional groups.

  • Primary ($1^{\circ}$) Alcohol: $R-CH_2OH$ ($O.N. = -1$) oxidizes to Aldehyde ($O.N. = +1$) and then to Carboxylic Acid ($O.N. = +3$).

  • Secondary ($2^{\circ}$) Alcohol: $R_2CHOH$ ($O.N. = 0$) oxidizes to Ketone ($O.N. = +2$).

  • Tertiary ($3^{\circ}$) Alcohol: $R_3COH$ ($O.N. = +1$) cannot be oxidized further because there is no $C-H$ bond to break.

  • Common Oxidants: Potassium permanganate ($KMnO_4$) and Sodium dichromate ($Na_2Cr_2O_7$). These are reduced to $MnO_2(s)$ or $Cr^{3+}$.

• Reduction: The reverse of oxidation.

  • Strong Reducing Agent: Lithium aluminium hydride ($LiAlH_4$) supplies the hydride anion ($H^-$) and can reduce carboxylic acids to primary alcohols.

  • Mild Reducing Agent: Sodium borohydride ($NaBH_4$) can reduce ketones and aldehydes but lacks the reactivity to reduce carboxylic acids due to Boron's higher electronegativity compared to Aluminum.

Practice Problems

• Problem 1: Predict the product of oxidation with a strong oxidizing agent like permanganate ($MnO_4^-$) for:

  • a) 1-methylbutan-1-ol (Secondary alcohol): Produces a Ketone (2-pentanone).

  • b) 2-methylbutan-1-ol (Primary alcohol): Produces a Carboxylic acid (2-methylbutanoic acid).

  • c) 1,1-dimethylbutan-1-ol (Tertiary alcohol): No reaction.

  • d) 1,2-dimethylbutan-1-ol (Secondary alcohol): Produces a Ketone (3-methyl-2-pentanone).

• Problem 2: Determine the Oxidation Number (O.N.) of the carbonyl carbon in various functional groups (e.g., in a carboxylic acid, the carbonyl carbon typically has an O.N. of $+3$).

LECTURE 37

Cultural Acknowledgement and Copyright Information

• The School of Chemistry stands on lands that always was and always will belong to the Gadigal people of the Eora Nation.

• Respect is paid to Elders past, present, and emerging, as well as all Aboriginal and Torres Strait Islander people.

• Knowledge shared in teaching and research is contextualized within the Aboriginal Custodianship of Country.

• Material from the University of Sydney is protected under the Copyright Act 1968 (the Act) and Copyright Regulations 1969.

• Images provided are reproduced from Blackman, Bottle, Schmid, Mocerino, and Wille, Chemistry, 2012 (John Wiley & Sons), ISBN: 9 78047081 0866.

Carbonyl Compounds and Their Derivatives

• Carbonyl compounds are classified into diverse categories based on their functional groups:

  • Primary carbonyls: Aldehydes ($R-CHO$), ketones ($R-CO-R$), and carboxylic acids ($R-COOH$).

  • Derivatives of carboxylic acids: Acid chlorides ($R-COCl$), esters ($R-COOR$), thioesters ($R-COSR$), and amides ($R-CONH_2$).

• These derivatives form the building blocks for various macromolecules:

  • Polyamides: Chains containing repeated amide links.

  • Polyesters: Chains containing repeated ester links.

  • Peptides and proteins: Natural biopolymers formed by amino acid linkages.

• Polymer structures can be categorized as:

  • Homopolymer: Consists of a single type of monomer unit.

  • Copolymer: Consists of multiple types of monomer units (e.g., $R_1, R_2, R_3$).

Principles of Condensation Polymerisation

• Condensation polymerisation (step-growth polymerisation) occurs when compounds with multiple, complementary functional groups join at their ends to form a chain.

• There are two primary methods for forming a condensation polymer:

  1. Two monomers, each possessing two identical functional groups ($X-R-X + Y-R'-Y$), react together. The resulting repeat unit consists of both monomers. Examples include Poly(ethylene terephthalate) (PET) and Nylon 66.

  2. One monomer possessing two different functional groups ($X-R-Y$) reacts in a "head to tail" fashion. The repeat unit consists of just one monomer. An example is poly(lactic acid).

• In condensation polymerisation, chains can grow in large steps by joining functional groups at the ends of already long chains.

• The backbone of condensation polymers contains functional groups (such as esters or amides) interspersed with carbon chains.

Principles of Addition Polymerisation

• Addition polymerisation (chain-growth) involves adding alkene (vinyl) monomers one at a time to a growing chain.

• Most addition polymers contain only $C-C$ single bonds along their backbone. An exception is Poly(ethylene glycol), which contains an ether linkage along the backbone.

• Common addition polymers based on the substituent $R$ on the monomer ($CH_2=CHR$):

  • $R = H$: Polyethylene

  • $R = CH_3$: Polypropylene

  • $R = Cl$: Polyvinylchloride (PVC)

  • $R = Ph$ (Phenyl): Polystyrene

  • $R = COOH$: Poly(acrylic acid)

  • $R = OOCCH_3$: Poly(vinyl acetate)

• Polymer chains are inherently flexible due to $C-C$ single bond rotation, which allows for various chain conformations.

Degree of Polymerisation and Molecular Weight

• The degree of polymerisation ($n$) represents the number of repeat units along a polymer chain.

• The molecular weight of a polymer is calculated as: $\text{Molecular Weight} = n \times \text{Molecular weight of the repeat unit}$.

• Polymers can range in size from 100 or fewer repeat units to molecular weights in the millions.

• Chain flexibility and conformations:

  • If each bond in a chain can adopt three possible conformations (anti, gauche+, or gauche-), a polymer with $n$ monomers can adopt $3^{2n}$ different conformations.

Functionalised Polymers and Chemical Reactions

• Functional groups on polymer chains undergo the same chemical reactions as small organic molecules.

• Acid/Base Chemistry:

  • Treatment of certain polymers with $NaOH$ creates ionised groups, which increases the polymer's solubility in water. In these cases, solubility is pH-dependent.

• Ester Hydrolysis:

  • Poly(vinyl alcohol) (PVA) cannot be prepared directly from a monomer. It is produced through the hydrolysis of poly(vinyl acetate) using $CH_3OH$.

  • Partial hydrolysis can lead to a copolymer featuring different functional groups distributed along the chain.

• Alcohol Oxidation:

  • Secondary (2^) alcohol groups on a polymer can be oxidized. While hydrolysis increases water solubility, oxidation generally decreases it.

Physical Properties: Solubility, Crystallinity, and Fibres

• Solubility and physical properties are determined by functional groups and chain architecture.

• Crystallinity:

  • Areas of high order (crystallinity) along a thread improve tensile strength.

  • Bulky side groups on the polymer chain can disrupt this ordering, affecting the material's properties.

• Fibre Production:

  • Fibres are thin threads produced by extruding thermoplastic polymers.

  • Drawing and stretching these polymers while cooling aligns the areas of crystallinity.

• Intermolecular Strengthening:

  • Hydrogen bonding ($NH ∙∙∙ O=C$) between amide groups on adjacent chains significantly strengthens materials.

  • Examples of high-strength polymers utilizing these interactions include Nylon and Kevlar.

Cross-linking and Three-Dimensional Polymers

• Cross-linking moves beyond linear chains to create network structures.

• Bakelite (phenol-formaldehyde resin) was the first synthetic polymer discovered and is a non-linear resin.

• Chemical Slime:

  • Made using hydrogen-bonded cross-links between the $-OH$ groups on poly(vinyl alcohol) (PVA) chains and the borate anion derived from boric acid ($B(OH)_3$).

Environmental Impact and Sustainability

• Recyclable plastics (primarily addition polymers) include:

  • High density polyethylene (HDPE)

  • Low density polyethylene (LDPE)

  • Polypropylene (PP)

  • Polystyrene (PS)

  • Polyvinylchloride (PVC)

  • Polyethylene terephthalate (PET) — a condensation polymer known as Dacron, Mylar, or Terylene.

• Biodegradable Biopolymers:

  • Plastics are being redesigned to mimic natural biopolymers for better biodegradability.

  • These are synthesized from microbial or plant feedstocks rather than petrochemicals.

  • Examples include poly-($R$)-3-hydroxybutyrate (PHB) and polylactide (poly(lactic acid) or PLA).

Biopolymers: Carbohydrates, Nucleotides, and Proteins

• Cellulose: A polysaccharide carbohydrate.

• Polynucleotides (DNA & RNA):

  • These are polyphosphate esters and copolymers of nucleotides.

  • A nucleotide consists of a nucleobase and a phosphate ester.

  • DNA adopts a double helix structure supported by hydrogen bonding between complementary base pairs.

  • Geometry: The double helix has a width of approximately 2nm and a distance of 0.34nm between bases along the phosphodiester backbone.

• Proteins:

  • Proteins are polyamides and copolymers of amino acids connected in a specific sequence known as the primary structure.

  • They consist of chains ranging from 50 to over 1000 amino acids.

DNA Structure and Coding

• Complementary Base Pairing via Hydrogen Bonds:

  • Guanine pairs with Cytosine (forming three hydrogen bonds).

  • Adenine pairs with Thymine (forming two hydrogen bonds).

• Genetic Coding:

  • There are 64 possible triplets of bases (codons).

  • These triplets code for the 20 amino acids used to assemble proteins.

Protein Chemistry and Structure

• Synthesis:

  • Amino acids condense to form a peptide (amide) link. Two amino acids form a di-peptide; three form a tri-peptide.

  • The Ribosome serves as the catalyst for this process in biological systems.

  • Polypeptide chains have an N-terminus and a C-terminus.

• Molecular Geometry:

  • Resonance (electron delocalisation) of the $C-N$ amide bond restricts rotation.

  • This creates a rigid backbone where both cis and trans ($E$ and $Z$) peptide isomers can exist.

• Levels of Structure:

  • Primary (1^) structure: The specific order of amino acids.

  • Secondary (2^) structure: Local 3-dimensional structures like $\alpha$-helices and $\beta$-sheets formed by hydrogen bonding and intermolecular forces.

  • Long-range folding: Driven by backbone rigidity and interactions between side-chain groups.

• Denaturation:

  • Intermolecular forces maintaining secondary structure are relatively weak.

  • Denaturing can be caused by heat, pH changes, or chemical reactions.

  • The process is usually irreversible and alters biological and physical properties.

Biological Functions and Pathologies of Proteins

• Proteins comprise 50% of the body's dry mass and are present in all cells.

• Key Functions:

  • Structural support: Collagen.

  • Mechanical work: Actin and Myosin.

  • Catalysis: HIV protease (enzymes).

  • Regulation: Insulin (hormones).

  • Protection: Immunoglobins (disease defense).

  • Storage and Transport: Haemoglobin.

• Protein Misfolding:

  • Linked to diseases such as Alzheimer's, Parkinson's, Mad Cow Disease (BSE), and Creutzfeldt-Jakob Disease (CJD).

Practice Problems & Quantitative Analysis

• Problem 1: Polyethylene, $H-(CH_2-CH_2)_n-H$

  • For a molecular weight of 28,000g/mol: Calculate the number of ethylene monomer units ($n$).

  • Determine the number of $C-C$ bonds along the backbone.

  • Calculate potential conformations if each bond adopts anti, gauche+, or gauche- positions.

  • Repeat the calculation for a molecular weight of 2,800g/mol.

• Problem 2: Combinatorial Possibilities

  • Given 20 naturally occurring amino acids, calculate the number of different possible protein sequences for chain lengths of $n = 50$, $100$, and $1000$.

  • Compare this to a simple copolymer of just two different monomers ($n = 50$, $100$, or $1000$) to determine the specific arrangements along the chain.