Unit 1: Introduction and Biological Molecules – General Biology Study Notes

Unit 1: Introduction and Biological Molecules

This unit provides an overview of foundational concepts in biology, focusing on the characteristics of life, the scientific method, and the major classes of biological molecules: proteins, nucleic acids, and carbohydrates. Understanding these topics is essential for further study in biology.

Chapter 1 – Introduction

This chapter introduces the organization of life, the scientific process, and the criteria that define living organisms.

• The Three Domains of Life: Life is classified into three domains: Bacteria, Archaea, and Eukarya. These domains are depicted on a phylogenetic tree, which shows evolutionary relationships.

• Distinguishing Features: Eukarya (the domain humans belong to) are characterized by membrane-bound organelles and a nucleus, unlike Bacteria and Archaea.

• Defining Features of Living Organisms: Living things exhibit organization, metabolism, homeostasis, growth, reproduction, response to stimuli, and evolutionary adaptation.

• Laws, Theories, and Hypotheses:

  • Hypothesis: A testable, falsifiable statement or prediction.

  • Theory: A well-substantiated explanation of some aspect of the natural world, based on a body of evidence.

  • Law: A statement describing consistent natural phenomena, often expressed mathematically.

• Elements of a Scientific Experiment: Key elements include a testable hypothesis, controlled variables, independent and dependent variables, and reproducibility.

Example: The classic experiment by Pasteur disproved spontaneous generation by using swan-neck flasks to show that microorganisms come from other microorganisms.

Chapter 2 – Water and Carbon Chemistry

This chapter explores the chemical basis of life, focusing on atomic structure, chemical bonds, and the unique properties of water and carbon.

• Atomic Number and Mass Number: The atomic number is the number of protons in an atom. The mass number is the sum of protons and neutrons. The average mass number (atomic mass) accounts for isotopes.

• Covalent vs. Ionic Bonds:

  • Covalent bonds involve the sharing of electron pairs between atoms.

  • Ionic bonds involve the transfer of electrons from one atom to another, resulting in oppositely charged ions.

• Polar vs. Nonpolar:

  • Polar molecules have unequal sharing of electrons, leading to partial charges (e.g., water).

  • Nonpolar molecules have equal sharing of electrons and no partial charges (e.g., O2).

• Types of Interactions Between Molecules: Hydrogen bonds, van der Waals interactions, ionic interactions, and hydrophobic interactions.

Example: Water's polarity allows it to form hydrogen bonds, giving it a high specific heat and making it an excellent solvent.

Chapter 3 – Proteins

This chapter covers the structure, function, and synthesis of proteins, which are essential macromolecules in all living organisms.

• Monomer of Proteins: Amino acids are the building blocks of proteins.

• Functional Groups in Amino Acids: Each amino acid contains an amino group (–NH2), a carboxyl group (–COOH), a hydrogen atom, and a variable R group (side chain).

• Individuality of Amino Acids: The R group determines the chemical properties and identity of each amino acid.

• Determining Amino Acid Chemistry (4 Steps):

  1. Identify the R group.

  2. Determine if the R group is polar, nonpolar, acidic, or basic.

  3. Assess the potential for hydrogen bonding or ionic interactions.

  4. Predict the behavior in aqueous environments.

• Bonds Between Amino Acids: Peptide bonds form between the carboxyl group of one amino acid and the amino group of another via a condensation reaction.

• Condensation vs. Hydrolysis:

  • Condensation reaction: Joins two molecules with the loss of water.

  • Hydrolysis reaction: Breaks a bond by adding water.

• Protein Structure: Proteins have four levels of structure:

  1. Primary: Sequence of amino acids.

  2. Secondary: Local folding (α-helix, β-sheet) stabilized by hydrogen bonds.

  3. Tertiary: Overall 3D shape due to side chain interactions.

  4. Quaternary: Association of multiple polypeptide chains.

• Forces Stabilizing Structure: Hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions, and van der Waals forces.

Example: Hemoglobin is a quaternary protein composed of four polypeptide subunits.

Chapter 4 – Nucleic Acids

This chapter discusses the structure and function of nucleic acids, the molecules responsible for storing and transmitting genetic information.

• Types of Nucleic Acids: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

• Monomer of Nucleic Acids: Nucleotides, each consisting of a phosphate group, a five-carbon sugar (deoxyribose or ribose), and a nitrogenous base.

• Functional Groups in Nucleotides: Phosphate group, hydroxyl group (on sugar), and amine groups (on bases).

• Bonds Between Nucleotides: Phosphodiester bonds link the 3' carbon of one sugar to the 5' phosphate of the next.

• Key Information for DNA Structure (Watson and Crick):

  • Chargaff's rules (A=T, G=C base pairing)

  • X-ray diffraction data (Rosalind Franklin)

  • Antiparallel strand orientation

• Differences Between DNA and RNA:

  • DNA contains deoxyribose; RNA contains ribose.

  • DNA uses thymine; RNA uses uracil.

  • DNA is double-stranded; RNA is usually single-stranded.

• First "Living" Molecule: RNA is hypothesized to be the first self-replicating molecule due to its ability to store information and catalyze reactions (the "RNA world" hypothesis).

Example: mRNA carries genetic information from DNA to ribosomes for protein synthesis.

Chapter 5 – Carbohydrates

This chapter examines the structure, classification, and function of carbohydrates, which are vital for energy storage and structural support in living organisms.

• Naming Strategy for Carbohydrates: Carbohydrates are named based on the number of carbon atoms and the presence of aldehyde or ketone groups (e.g., glucose, fructose, ribose).

• Classification:

  • Monosaccharides: Single sugar units (e.g., glucose).

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

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

• Energy Storage: Carbohydrates are efficient energy sources due to their high proportion of C–H bonds, which release energy when oxidized.

• Common Polysaccharides and Their Functions:

  • Starch: Energy storage in plants.

  • Glycogen: Energy storage in animals.

  • Cellulose: Structural component in plant cell walls.

Example: Humans digest starch but not cellulose due to differences in glycosidic bond orientation.

Table: Comparison of Major Biological Molecules

Class	Monomer	Bond Type	Main Functions
Proteins	Amino acids	Peptide bond	Enzymes, structure, transport, signaling
Nucleic Acids	Nucleotides	Phosphodiester bond	Genetic information storage and transfer
Carbohydrates	Monosaccharides	Glycosidic bond	Energy storage, structure

Additional info: Lipids are another major class of biological molecules, but they are not covered in this unit.