General Biology: Biomolecules, Functional Groups, and Macromolecular Structure

Organic Chemistry and Biomolecules

Introduction to Organic Chemistry

Organic chemistry is the study of carbon-containing compounds and their properties. Carbon is unique due to its ability to form four covalent bonds, allowing for a diversity of stable molecules essential for life.

• Importance of Carbon: Carbon can form single, double, or triple bonds, and can bond with many elements, including hydrogen, oxygen, nitrogen, and other carbons.

• Organic Molecules: Molecules containing carbon, often with hydrogen, oxygen, and nitrogen.

• Hydrocarbons: Compounds composed only of carbon and hydrogen; nonpolar and hydrophobic.

Functional Groups

Definition and Properties

Functional groups are specific groups of atoms within molecules that have characteristic properties and chemical reactivity. They determine the behavior of organic molecules in biological systems.

• Structure: Each functional group has a specific arrangement of atoms.

• Properties: Functional groups confer polarity, acidity/basicity, and reactivity to molecules.

Group	Structure	Properties	Found in
Carbonyl	>C=O	Adds polarity, makes molecules more hydrophilic	Sugars
Hydroxyl	-OH	Adds polarity, makes molecules more hydrophilic	Sugars & Alcohols
Carboxyl	-COOH	Acidic	Proteins (amino acids), Fatty acids
Sulfhydryl	-SH	Allows for covalent bonds (disulfide bridges)	Proteins
Phosphate	PO4	Negative charge, strongly hydrophilic	ATP, Proteins, Phospholipids, Nucleotides
Amino	-NH2	Basic	Proteins (amino acids)
Methyl	-CH3	Hydrophobic	DNA (ubiquitous)

Polymers and Monomers

Dehydration and Hydrolysis Reactions

Biological macromolecules are polymers made from monomer subunits. The formation and breakdown of these polymers involve dehydration and hydrolysis reactions.

• Dehydration Reaction: Joins monomers by removing a water molecule, forming a covalent bond.

• Hydrolysis Reaction: Breaks covalent bonds by adding water, splitting polymers into monomers.

Carbohydrates

Structure and Types

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen. They serve as energy sources and structural components.

• Monosaccharides: Simple sugars (e.g., glucose, fructose).

• Disaccharides: Two monosaccharides joined by a glycosidic bond (e.g., sucrose).

• Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose).

• Structural vs. Energy Storage: Cellulose (structure in plants), starch and glycogen (energy storage).

Macromolecule	Bonds	Monomers
Carbohydrates	Glycosidic	Monosaccharides
Proteins	Peptide	Amino acids
Triglycerides & Phospholipids	Ester	Glycerol (backbone) & 3 Fatty acids; Glycerol, 2 Fatty acids, phosphate, positively charged group
Nucleic Acids	Phosphodiester	Nucleotides

Lipids

Types and Functions

Lipids are hydrophobic molecules, including fats, phospholipids, and steroids. They function in energy storage, membrane structure, and signaling.

• Triglycerides: Composed of glycerol and three fatty acids; used for energy storage.

• Phospholipids: Glycerol, two fatty acids, and a phosphate group; major component of cell membranes.

• Steroids: Four fused carbon rings; function as hormones (e.g., cholesterol).

Proteins

Structure and Levels of Organization

Proteins are polymers of amino acids with diverse functions, including catalysis, structure, and transport. Their function depends on their structure, which is organized into four levels.

• Amino Acids: Building blocks of proteins, each with a central carbon, amino group, carboxyl group, hydrogen, and R group (side chain).

• Peptide Bonds: Covalent bonds linking amino acids.

Protein Structure	What is it?	What bond(s) stabilizes it?
Primary	Sequence of amino acids	Covalent (peptide)
Secondary	α Helix, β pleated sheet	Hydrogen
Tertiary	3D structure of a fully folded polypeptide	Covalent, Ionic, Hydrogen, Van der Waals
Quaternary	More than one polypeptide required for function	Covalent, Ionic, Hydrogen, Van der Waals

Nucleic Acids

Structure and Function

Nucleic acids (DNA and RNA) store and transmit genetic information. They are polymers of nucleotides, each consisting of a sugar, phosphate group, and nitrogenous base.

• DNA: Double-stranded, contains deoxyribose sugar, bases A, T, C, G.

• RNA: Single-stranded, contains ribose sugar, bases A, U, C, G.

• Purines: Adenine (A), Guanine (G).

• Pyrimidines: Cytosine (C), Thymine (T, in DNA), Uracil (U, in RNA).

• Directionality: Nucleic acids have 5' to 3' directionality.

• Complementary Base Pairing: A pairs with T (or U in RNA), C pairs with G.

General Structure of a Nucleotide

• Phosphate group attached to 5' carbon of sugar

• Pentose sugar (deoxyribose in DNA, ribose in RNA)

• Nitrogenous base attached to 1' carbon of sugar

Key Concepts and Examples

• Hydrolysis Example: Breaking a disaccharide into two monosaccharides by adding water.

• Dehydration Example: Forming a peptide bond between two amino acids with the release of water.

• Enzyme Specificity: Amylase breaks glycosidic linkages in starch but not cellulose due to the specific form of glucose monomers.

• Protein Folding: Hydrophobic amino acids are typically found in the interior of globular proteins.

• DNA Replication: Complementary base pairing allows DNA to replicate accurately.

Sample Questions and Applications

• Which bond is a peptide bond? The bond between the carboxyl group of one amino acid and the amino group of another.

• Which group is a carbonyl functional group? >C=O

• Which group is basic and can accept H+? Amino group (-NH2).

• Which macromolecule is not formed by dehydration reactions? Fatty acids.

• What stabilizes secondary protein structure? Hydrogen bonds.

• What is the structural feature that allows DNA to replicate? Complementary pairing of the nitrogenous bases.

• What type of bond holds the two DNA strands together? Hydrogen bonds.

Additional info: The above notes synthesize and expand upon the provided study guide, tables, and practice questions, offering definitions, examples, and context for each major topic relevant to a General Biology course.