Chemistry of Life: Organic and Biological Chemistry – Study Notes

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Chemistry of Life: Organic and Biological Chemistry

Overview

This section introduces the foundational concepts of organic and biological chemistry, focusing on the structure, nomenclature, and reactivity of organic compounds, as well as the chemistry of amino acids and proteins. These topics are essential for understanding the molecular basis of life and are directly relevant to General Chemistry.

Structure of Organic Compounds

Common Geometries

Organic compounds exhibit distinct molecular geometries based on the hybridization of carbon atoms:

Tetrahedral: Carbon bonded to four atoms; bond angle ≈ 109.5°.
Trigonal planar: Carbon bonded to three atoms; bond angle ≈ 120°.
Linear: Carbon bonded to two atoms; bond angle ≈ 180°.

These geometries arise from the spatial arrangement of electron pairs around the central carbon atom.

Hydrocarbons

Types and Properties

Hydrocarbons are compounds containing only carbon (C) and hydrogen (H) atoms, with stable carbon-carbon bonds. They are classified into four basic types:

Alkanes: Saturated hydrocarbons with only single C–C bonds.
Alkenes: Unsaturated hydrocarbons with at least one C=C double bond.
Alkynes: Unsaturated hydrocarbons with at least one C≡C triple bond.
Aromatic hydrocarbons: Cyclic compounds with delocalized π electrons (e.g., benzene).

Alkanes

Properties and Classification

Alkanes are saturated hydrocarbons containing the highest possible number of hydrogen atoms per carbon atom. Their general formula is:

Only C–C single bonds exist.
Boiling point increases with chain length due to greater van der Waals forces.

Molecular Formula	Condensed Structural Formula	Name	Boiling Point (°C)
CH4	CH4	Methane	-161
C2H6	CH3CH3	Ethane	-89
C3H8	CH3CH2CH3	Propane	-42
C4H10	CH3(CH2)2CH3	Butane	0
C5H12	CH3(CH2)3CH3	Pentane	36
C6H14	CH3(CH2)4CH3	Hexane	69
C7H16	CH3(CH2)5CH3	Heptane	98
C8H18	CH3(CH2)6CH3	Octane	126
C9H20	CH3(CH2)7CH3	Nonane	151
C10H22	CH3(CH2)8CH3	Decane	174

Organic Nomenclature

Systematic Naming of Organic Compounds

Organic compounds are named using three main components:

Base: Indicates the number of carbon atoms in the longest continuous chain.
Suffix: Specifies the type or family of compound (e.g., -ane, -ene, -yne).
Prefix: Describes the nature and position of substituent groups attached to the chain.

For example, in 2-methylpropane:

Base: propane (3 carbons)
Prefix: 2-methyl (methyl group on carbon 2)
Suffix: -ane (alkane family)

Steps to Name a Compound

Find the longest carbon chain and determine the family of molecule.
Number the chain from the end nearest the first substituent encountered.
List substituents as prefixes, along with the number of the carbon(s) to which they are attached.
If two or more types of substituents are present, list them alphabetically. Use prefixes such as di-, tri-, tetra-, etc., for multiple identical groups.

Structural Isomers

Definition and Examples

Structural isomers are compounds with the same molecular formula but different connectivity of atoms. They can be straight-chain or branched hydrocarbons.

Example: C5H12 can be n-pentane (straight chain), isopentane, or neopentane (branched).

Structures of Alkanes

Bonding and Hybridization

Carbon atoms in alkanes are sp3-hybridized, resulting in tetrahedral geometry and 109.5° bond angles.
Alkanes form σ-bonds with hydrogen atoms (using 1s orbitals).
Only C–C single bonds exist, allowing free rotation about the bond axis due to end-to-end orbital overlap.

Hybridization:

Reactions of Alkanes

Chemical Reactivity

Alkanes are generally unreactive at room temperature; they do not react with acids, bases, or strong oxidizing agents.
This low reactivity is due to the lack of polar bonds and the strength of C–C and C–H bonds.
Alkanes are excellent non-polar solvents.

Unsaturated Hydrocarbons

Alkenes and Alkynes

Unsaturated organic compounds have fewer than the maximum number of hydrogen atoms per carbon.
They contain one or more multiple bonds, which significantly affect their structure and reactivity.
Alkenes (olefins) contain at least one carbon–carbon double bond.
General formula for alkenes:

Multiple Bonding: Nature of π Bonds

Bonding Characteristics

Two p orbitals overlap side-by-side to form a π bond.
π bonds are generally weaker than σ bonds due to less orbital overlap.
Alkenes cannot rotate freely about the double bond; rotation requires breaking the π bond.

Hybridization:

Nomenclature of Alkenes

Geometric Isomers

Geometric isomers differ in the spatial arrangement of groups about the double bond.
Chain is numbered so the double bond gets the smallest possible number.
cis-Alkenes: Substituents on the same side of the double bond.
trans-Alkenes: Substituents on opposite sides.

Structures and Properties of Alkenes

Physical Properties

cis- and trans-isomers have different physical properties, such as boiling points.
Example: C4H8 structural isomers show varying boiling points due to differences in structure.

Reactions of Alkenes

Addition Reactions

Addition reactions are characteristic of alkenes; two atoms (e.g., bromine) add across the double bond.
One π bond and one σ bond are replaced by two σ bonds, typically releasing energy (ΔH is negative).

Example reaction:

Mechanism of Addition Reactions

Two-step mechanism:
1. First step is slow (rate-determining); π bond is broken and a cationic intermediate is formed.
2. Second step is fast; bromide anion donates electrons to the cation, forming a new σ bond.
Arrows in mechanisms show electron flow from electron-rich to electron-poor atoms.

Aromatic Hydrocarbons

Structure and Stability

Aromatic hydrocarbons (e.g., benzene) are cyclic, planar, and highly symmetric.
Each carbon has a p orbital; π electrons are delocalized over the ring, resulting in unusual stability.
Resonance structures represent the delocalization of electrons.

Reactions of Aromatic Compounds

Electrophilic Aromatic Substitution

Unlike alkenes, aromatic compounds do not undergo addition reactions due to electron delocalization.
Instead, they undergo substitution reactions, where a hydrogen atom is replaced by another substituent (e.g., nitration).
Example: Nitration of benzene

Chirality

Optical Isomerism

Compounds with a carbon atom bonded to four different groups are chiral (non-superimposable mirror images).
Mirror images are called enantiomers (R and S forms).
Enantiomers have identical melting and boiling points but behave differently in chiral environments and reactions.

Example: 2-bromopentane

Thalidomide Case Study

Thalidomide drug contained both enantiomers:
(R)-enantiomer: Effective against morning sickness.
(S)-enantiomer: Teratogenic, causes birth defects.

Amino Acids and Proteins

Structure and Function

Proteins are polymers of α-amino acids, which exist as zwitterions at neutral pH.
Alanine (R = CH3) is chiral; only the left-handed (L) form is found in nature.
A condensation reaction between the amine end of one amino acid and the acid end of another produces a peptide bond.

Amino Acid	Structure
Alanine (Ala)	CH3CH(NH2)COOH
Glycine (Gly)	H2NCH2COOH
Serine (Ser)	HOCH2CH(NH2)COOH

Protein Structure

Primary structure: Sequence of amino acids.
Secondary structure: Coils and helices formed by intermolecular forces (e.g., hydrogen bonding).
Tertiary structure: Overall 3D shape determined by folding and kinking of the chain.
Most enzymes are proteins; their active site shape fits the substrate (lock-and-key model).

Additional info: These notes cover the essential aspects of organic and biological chemistry relevant to a General Chemistry course, including molecular structure, nomenclature, isomerism, reactivity, and biomolecules.