Lecture 2: Chemical Organization Level

Properties of Water

• Exhibits cohesion by allowing molecules to stick together.
• Moderates temperature by absorbing significant energy before temperature changes; plays a crucial role in climate regulation.
• Expands upon freezing, causing ice to float due to the lattice structure formed by hydrogen bonds.
• Functions as a solvent, effectively dissolving polar and charged substances (hydrophilic) while not dissolving nonpolar substances (hydrophobic).
• Buffers help maintain a stable pH, essential for biological functions; blood pH is maintained between 7.35-7.45.

Organic Molecules

• Composed of matter, which is governed by chemical and physical laws.
• Saturated fats contain saturated fatty acids; unsaturated fats can be monounsaturated or polyunsaturated.
• Phospholipids have a glycerol backbone linked to two fatty acids and a phosphate group, featuring hydrophilic heads and hydrophobic tails, making them amphipathic.
• Steroids consist of four fused carbon rings; cholesterol serves as the precursor for other steroids and maintains membrane fluidity.

Proteins

• Composed of carbon, hydrogen, oxygen, and nitrogen; account for 12-18% of body mass.
• Made up of amino acids, which are the building blocks linked by peptide bonds through dehydration synthesis.
• Protein structure is organized into primary (amino acid sequence), secondary (α-helices and β-sheets stabilized by hydrogen bonds), tertiary (3D shape driven by various interactions), and quaternary (arrangement of multiple polypeptides) levels.
• Fibrous proteins are water-insoluble and form structures like hair and muscle filaments; globular proteins are water-soluble and include enzymes and antibodies.
• Denaturation results in the loss of protein structure and function, rendering proteins inactive.

Nucleic Acids

• Comprise DNA and RNA, containing carbon, hydrogen, oxygen, nitrogen, and phosphorus.
• DNA is transcribed to RNA, which is subsequently translated to proteins; genes are sections of DNA that code for proteins.
• Nucleotides are the monomers, consisting of a nitrogenous base, pentose sugar, and phosphate group.
• DNA features a double helix structure with base pairing between purines (A, G) and pyrimidines (C, T), while RNA contains uracil (U) instead of thymine (T).
• DNA replication involves creating a new double helix using one original strand as a template; mutations can occur from changes in the nucleotide sequence.

Energy Currency: ATP

• Adenosine triphosphate (ATP) is a crucial nucleotide that serves as the energy currency for cells.
• Comprises three phosphate groups bound to adenosine; energy is released upon hydrolysis of the terminal phosphate.
• ATP is generated by exergonic cellular reactions and consumed in endergonic reactions to perform work.
• ATP synthesis is catalyzed by ATP synthase during aerobic respiration.

Summary of Biological Molecules

• Four classes of biological molecules: carbohydrates, lipids, proteins, and nucleic acids.
• All classes are polymers of monomers except for lipids, which do not have a common monomer.
• The structure of biological molecules is intrinsically linked to their specific functions.

Organic Molecules

• Organic molecules primarily consist of carbon atoms.
• Carbon skeletons form the backbone, held together by covalent bonds.
• Hydrocarbons are organic molecules composed solely of carbon and hydrogen.
• Functional groups are additional atoms or molecules attached to carbon skeletons, influencing chemical properties and functions.

Biological Molecules

• Composed of complex organic compounds.
• Cells contain trillions of organic molecules organized into a limited number of structural subunits.
• Most biological molecules are polymers made from monomers.

Classes of Biological Monomers

• Four main classes include carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates

• Formed of carbon, hydrogen, and oxygen; make up 2-3% of total body mass.
• Monosaccharides (simple sugars) serve as the monomers for carbohydrates.
• Monosaccharides can link through dehydration synthesis to form more complex carbohydrates.

Lipids

• Saturated fats consist mainly of saturated fatty acids, while unsaturated fats contain mono- or polyunsaturated fatty acids.
• Monounsaturated fats include oils from olive, canola, and avocado; polyunsaturated fats include corn and fish oils.

Phospholipids

• Composed of glycerol, two fatty acids, and a phosphate group.
• Amphipathic properties stem from polar (hydrophilic) phosphate heads and nonpolar (hydrophobic) fatty acid tails.

Steroids

• Comprised of four fused carbon rings; cholesterol is a precursor for steroid synthesis.
• Cholesterol contributes to membrane fluidity and is categorized as a sterol if it has a hydroxyl group, making it slightly amphipathic.

Other Lipids

• Eicosanoids are 20-carbon compounds that include immune signaling molecules like prostaglandins.
• Fat-soluble vitamins (D, E, K) are essential in the diet.

Proteins

• Comprised of carbon, hydrogen, oxygen, and nitrogen; account for 12-18% of body mass.
• The building blocks are amino acids (20 natural types), each with a central carbon connected to an amino group, carboxyl group, and an R group that defines its properties.
• Amino acids are linked via dehydration synthesis to form peptide bonds, creating polypeptides from individual amino acids.
• Proteins can be simple (single polypeptide) or complex (multiple polypeptides).
• Protein structure levels:
  • Primary: sequence of amino acids
  • Secondary: α-helices and β-sheets stabilized by hydrogen bonds
  • Tertiary: 3D shape influenced by various bonds and interactions
  • Quaternary: arrangement of multiple polypeptide chains.

Types of Proteins

• Fibrous proteins (e.g., keratin) are insoluble and form structures like hair.
• Globular proteins (e.g., antibodies) are water-soluble and involved in metabolic functions.
• Denatured proteins lose their structure and biological activity.

Nucleic Acids

• Include DNA and RNA, made of carbon, hydrogen, oxygen, nitrogen, and phosphorus.
• DNA contains genes, sequences essential for coding specific proteins.
• DNA transcription converts its information into RNA, which is then translated into proteins by ribosomes.

Nucleotide Structure

• Monomers are nucleotides composed of a nitrogenous base, pentose sugar, and phosphate group.
• DNA and RNA base pairing:
  • DNA: adenine (A), guanine (G), cytosine (C), thymine (T)
  • RNA: adenine (A), guanine (G), cytosine (C), uracil (U)
• The DNA structure is a double helix, while RNA is single-stranded.

ATP (Adenosine Triphosphate)

• ATP serves as the energy currency of cells, composed of adenine, ribose, and three phosphate groups.
• Energy is released during hydrolysis of ATP, particularly when the terminal phosphate group is removed.
• ATP is regenerated via ATP synthase during aerobic respiration.

Summary

• Biological molecules, including carbohydrates, lipids, proteins, and nucleic acids, possess diverse structures linked directly to their functions, with lipids being the exception as they are not formed from polymerized monomers.

This quiz covers Lecture 2, focusing on the chemical level of organization. It requires understanding of atomic and molecular structure, properties of water, acid-base chemistry, and chemical reactions. Be sure to review the relevant textbook pages for a comprehensive understanding.