Chapter 3: Carbon and the Molecular Diversity of Life – Study Notes

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Carbon and the Molecular Diversity of Life

Overview of Biomolecules

Biomolecules are the fundamental molecules that make up living organisms. They include carbohydrates, lipids, proteins, and nucleic acids. Each class of biomolecule has unique structures and functions essential for life.

Biomolecules: lipids, nucleic acids, carbohydrates, proteins

3.1 Carbon Atoms Can Form Diverse Molecules by Bonding to Four Other Atoms

Properties of Carbon

Carbon is the backbone of organic molecules due to its ability to form four covalent bonds, allowing for a wide variety of molecular shapes and sizes. This versatility is key to the diversity of life.

Organic compounds contain carbon and are large, complex, and varied.
Carbon's four valence electrons enable it to bond with many elements, including hydrogen, oxygen, nitrogen, and other carbons.
Macromolecules are large molecules composed of smaller subunits.

Carbon as the structural basis for four classes of biological molecules

Formation of Bonds with Carbon

The number of covalent bonds an atom can form is determined by its valence, which is the number of unpaired electrons in its outer shell. Carbon can form single, double, or triple bonds, affecting the shape and flexibility of molecules.

Single bonds allow rotation, while double bonds restrict movement and create flat regions in molecules.
Carbon can bond with other carbons to form chains, rings, and branched structures.

Molecular shapes: tetrahedral and flat

Carbon Chain Skeletons

Carbon chains form the skeletons of most organic molecules. These chains can vary in length, branching, double bond position, and ring formation, contributing to molecular diversity.

Length: Number of carbons in the chain.
Branching: Chains may be straight or branched.
Double bonds: Presence and location of double bonds.
Rings: Some carbon skeletons form rings.

Branching in carbon skeletons Length variation in carbon skeletons Double bond position in carbon skeletons Presence of rings in carbon skeletons

Isomers

Isomers are compounds with the same molecular formula but different structures, resulting in different properties. There are three main types:

Structural isomers: Differ in covalent arrangement of atoms.
Cis-trans isomers: Differ in arrangement around double bonds.
Enantiomers: Mirror images of each other, often only one is biologically active.

Types of isomers: structural, cis-trans, enantiomers

Functional Groups

Functional groups are chemical groups attached to carbon skeletons that affect molecular function and participate in chemical reactions. Seven functional groups are most important in biological chemistry: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl.

Functional groups are not unique to one biomolecule and are found in many different molecules.

ATP: Important Energy Source for Cellular Processes

Adenosine triphosphate (ATP) is an organic molecule consisting of adenosine attached to three phosphate groups. ATP stores potential energy and releases it upon reaction with water, fueling cellular processes.

ATP hydrolysis releases energy used by cells.

ATP structure ATP hydrolysis reaction

3.2 Macromolecules Are Polymers, Built from Monomers

Polymers and Monomers

Macromolecules are polymers, long molecules made of repeating units called monomers. The synthesis and breakdown of polymers involve dehydration and hydrolysis reactions, facilitated by enzymes.

Dehydration reaction: Joins two monomers by removing a water molecule.
Hydrolysis reaction: Breaks a polymer by adding water.

Dehydration and hydrolysis reactions

Carbohydrates

Structure and Function

Carbohydrates are sugars and polymers of sugars. The simplest carbohydrates are monosaccharides, which serve as fuel and building material for cells. Glucose is the most common monosaccharide.

Monosaccharides: Simple sugars, classified by carbon number and carbonyl group placement.
Disaccharides: Formed by joining two monosaccharides via a glycosidic linkage.
Polysaccharides: Carbohydrate polymers with storage (starch, glycogen) and structural (cellulose, chitin) roles.

Monosaccharide structure Glycogen and starch structure Cellulose vs. chitin structure

Lipids

Structure and Function

Lipids are hydrophobic molecules that do not form true polymers. They include fats, phospholipids, and steroids. Lipids are important for energy storage, membrane structure, and signaling.

Fats: Constructed from glycerol and three fatty acids, forming triacylglycerol.
Saturated fats: No double bonds, solid at room temperature.
Unsaturated fats: One or more double bonds, liquid at room temperature.
Phospholipids: Two fatty acids, one phosphate group, and glycerol; form cell membranes.
Steroids: Four fused rings; cholesterol is a key steroid in membranes.

Synthesis and structure of a fat Saturated, trans, and cis fatty acids Phospholipid structure and bilayer Steroid structure

Proteins

Structure and Function

Proteins are polymers of amino acids and account for more than 50% of the dry mass of most cells. They perform diverse functions, including defense, storage, transport, communication, movement, and structural support.

Constructed from 20 amino acids.
Amino acids differ by their side chains (R groups), which determine protein structure and function.
Polypeptides are formed by peptide bonds between amino acids.

Protein structure: primary, secondary, tertiary, quaternary Protein secondary structure: alpha helix and beta sheet Protein tertiary and quaternary structure

Protein Structure Determines Function

The function of a protein is determined by its three-dimensional structure, which is organized into four levels:

Primary structure: Sequence of amino acids.
Secondary structure: Coils and folds (alpha helix, beta sheet) due to hydrogen bonding.
Tertiary structure: Overall shape from interactions among R groups.
Quaternary structure: Association of two or more polypeptides.

Quaternary protein structure

Sickle-Cell Disease

A single amino acid substitution in hemoglobin causes sickle-cell disease, demonstrating how primary structure affects protein function and health.

Protein Denaturation

Physical and chemical conditions such as temperature, pH, and salt concentration can disrupt protein structure, leading to denaturation and loss of function. Denaturation is sometimes reversible.

Protein denaturation and renaturation

Nucleic Acids

Structure and Function

Nucleic acids store, transmit, and help express hereditary information. DNA and RNA are polymers of nucleotides, each consisting of a nitrogenous base, a pentose sugar, and one or more phosphate groups.

DNA: Double-stranded, uses deoxyribose, bases A, T, G, C.
RNA: Single-stranded, uses ribose, bases A, U, G, C.
Genes are segments of DNA that encode proteins via mRNA.

Nucleotide structure Nucleoside and nucleotide components Phosphodiester linkage in nucleic acids

DNA and RNA Structure

DNA consists of two antiparallel polynucleotide strands forming a double helix. Nitrogenous bases pair via hydrogen bonds (A-T, G-C). RNA is usually single-stranded, with A-U pairing.

Genomics and Proteomics

Modern Molecular Biology

Genomics and proteomics are fields that analyze large sets of genes and proteins, respectively. Bioinformatics uses computational tools to interpret genome and proteome data, advancing our understanding of evolution and biological function.

DNA and protein sequences are used to assess evolutionary relationships.