Core Concepts in General Biology: Chemistry of Life, Macromolecules, and Biological Molecules

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The concept of pH is fundamental to understanding biological systems, as it measures the hydrogen ion concentration in a solution.

Definition of pH: pH is a logarithmic scale used to specify the acidity or basicity of an aqueous solution. It is calculated as the negative logarithm (base 10) of the hydrogen ion concentration:
pH Scale: Each unit change in pH represents a tenfold change in hydrogen ion concentration. Lower pH values indicate higher hydrogen ion concentrations (more acidic), while higher pH values indicate lower hydrogen ion concentrations (more basic).
Acids, Bases, and Neutral Solutions: Acids have pH values less than 7, bases have pH values greater than 7, and neutral solutions have a pH of 7.
Strength of Acids and Bases: The strength of an acid or base is determined by its ability to donate or accept protons (H+ ions).

Buffers are crucial in maintaining stable pH levels in biological systems.

Definition: A buffer is a solution that resists changes in pH when acids or bases are added.
Biological Importance: Buffers help maintain homeostasis in organisms by stabilizing the internal pH, which is essential for enzyme function and metabolic processes.
Example: The bicarbonate buffer system in blood helps maintain a stable pH.

Ocean acidification refers to the decrease in ocean pH due to increased absorption of atmospheric carbon dioxide (CO2).

Effect: Increased CO2 leads to the formation of carbonic acid, which lowers ocean pH and affects marine life, especially organisms with calcium carbonate shells.
Biological Impact: Acidification can disrupt marine ecosystems and food webs.

Carbon is the backbone of all biological molecules due to its unique chemical properties.

Versatility: Carbon can form four covalent bonds, allowing for a variety of stable and complex molecules.
Importance: Carbon's ability to form chains and rings makes it essential for the structure of carbohydrates, lipids, proteins, and nucleic acids.

Functional groups are specific groups of atoms within molecules that have characteristic properties and chemical reactivity.

Examples: Hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), phosphate (-PO42-).
Biological Role: Functional groups determine the properties and functions of organic molecules.

Isomers are molecules with the same molecular formula but different structures.

Types: Structural isomers (different covalent arrangements), geometric isomers (different spatial arrangements), and enantiomers (mirror images).
Significance: Isomers can have different chemical and biological properties.

Biological macromolecules are often polymers, made up of repeating subunits called monomers.

Monomer: A small molecule that can join with others to form a polymer.
Polymer: A large molecule composed of repeating monomer units.
Examples: Amino acids (monomers) form proteins (polymers); nucleotides form nucleic acids.

These are key chemical reactions in the formation and breakdown of biological macromolecules.

Dehydration Synthesis: A reaction in which two monomers are joined by removing a water molecule, forming a covalent bond.
Hydrolysis: A reaction in which a polymer is broken down into monomers by the addition of water.
Example: Formation and breakdown of polysaccharides, proteins, and nucleic acids.

Carbohydrates are essential macromolecules that serve as energy sources and structural components.

Monosaccharides: Simple sugars (e.g., glucose, fructose) that serve as the building blocks of carbohydrates.
Disaccharides: Formed by joining two monosaccharides (e.g., sucrose, lactose).
Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose) important for energy storage and structural support.

Lipids are a diverse group of hydrophobic molecules, including fats, oils, steroids, and phospholipids.

Hydrophobicity: Lipids are "hydrophobic," meaning they do not mix well with water.
Types: Fats (triglycerides), oils, steroids (e.g., cholesterol), and phospholipids.
Phospholipids: Major component of cell membranes, with hydrophilic (water-attracting) heads and hydrophobic (water-repelling) tails.

Proteins are polymers of amino acids and perform a wide range of functions in cells.

Amino Acids: Building blocks of proteins, each with an amino group, carboxyl group, hydrogen atom, and a variable "R" group.
Peptide Bond: Covalent bond formed between amino acids during protein synthesis.
Levels of Protein Structure:
- Primary: Sequence of amino acids.
- Secondary: Local folding (alpha helices, beta sheets) stabilized by hydrogen bonds.
- Tertiary: Overall 3D shape of a single polypeptide chain.
- Quaternary: Association of multiple polypeptide chains.
Importance of Hydrogen Bonds: Hydrogen bonds stabilize protein structure at various levels.
Protein Folding: Proper folding is essential for function; misfolding can lead to diseases (e.g., sickle-cell disease).

Nucleic acids (DNA and RNA) store and transmit genetic information.

Monomer: Nucleotide, composed of a phosphate group, a five-carbon sugar, and a nitrogenous base.
DNA vs. RNA: DNA contains deoxyribose sugar and is double-stranded; RNA contains ribose sugar and is usually single-stranded.
Structure: Nucleotides are linked by phosphodiester bonds to form long chains.

Macromolecule	Monomer	Function	Example
Carbohydrate	Monosaccharide	Energy storage, structure	Glucose, starch, cellulose
Lipid	Glycerol & fatty acids	Energy storage, membranes, signaling	Triglyceride, phospholipid, steroid
Protein	Amino acid	Catalysis, structure, transport	Enzyme, hemoglobin
Nucleic Acid	Nucleotide	Genetic information storage & transfer	DNA, RNA

"R" group in amino acids determines the chemical nature and function of each amino acid.
There are 20 standard amino acids found in nature.
Sickle-cell disease is caused by a single amino acid substitution in hemoglobin, leading to abnormal protein folding and function.
Be able to label the parts of a nucleotide: phosphate group, sugar, and nitrogenous base.