Unit 1: Introduction and Biological Molecules – Study Notes

Unit 1: Introduction and Biological Molecules

Overview

This unit introduces foundational concepts in biology, focusing on the characteristics of life and the major classes of biological molecules. Understanding these topics is essential for further study in general biology.

Chapter 1: Introduction

The Three Domains of Life

• Domains: Life is classified into three domains: Bacteria, Archaea, and Eukarya.

• Distinguishing Features:

  • Bacteria and Archaea are prokaryotic (lack a nucleus), while Eukarya are eukaryotic (have a nucleus and membrane-bound organelles).

  • Eukarya includes plants, animals, fungi, and protists.

• Phylogenetic Tree: Shows evolutionary relationships among organisms based on genetic data.

Defining Features of Living Organisms

• Cellular Organization: All living things are composed of cells.

• Metabolism: Ability to acquire and use energy.

• Homeostasis: Regulation of internal environment.

• Growth and Development: Organisms grow and develop over time.

• Reproduction: Ability to produce new organisms.

• Response to Stimuli: React to environmental changes.

• Evolution: Populations change over generations.

Laws, Theories, and Hypotheses

• Hypothesis: A testable, falsifiable statement explaining an observation.

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

• Law: A statement describing consistent, universal relationships in nature (often mathematical).

• Comparison Table:

Term	Description	Testability
Hypothesis	Proposed explanation	Testable, falsifiable
Theory	Comprehensive explanation	Supported by evidence
Law	Describes phenomena	Often mathematical, universal

Elements of a Scientific Experiment

• Variables: Independent (manipulated), dependent (measured), and controlled (kept constant).

• Control Group: Used for comparison to the experimental group.

• Replication: Repeating experiments to ensure reliability.

• Data Collection: Systematic recording of observations.

Chapter 2: Water and Carbon Chemistry

Atomic Number and Mass Number

• Atomic Number (Z): Number of protons in an atom's nucleus.

• Mass Number (A): Total number of protons and neutrons.

• Average Mass Number: Weighted average of all isotopes of an element.

• Equation: $A = Z + N$ (where N = number of neutrons)

Covalent vs. Ionic Bonds

• Covalent Bonds: Atoms share electron pairs (e.g., H2O).

• Ionic Bonds: Atoms transfer electrons, forming charged ions (e.g., NaCl).

• Comparison: Covalent bonds are generally stronger and found in organic molecules; ionic bonds are common in salts.

Polar vs. Nonpolar Bonds

• Polar Covalent Bonds: Unequal sharing of electrons, resulting in partial charges (e.g., H–O in water).

• Nonpolar Covalent Bonds: Equal sharing of electrons (e.g., O2).

Interactions Between Molecules

• Hydrogen Bonds: Attraction between a hydrogen atom and an electronegative atom (e.g., water molecules).

• Van der Waals Forces: Weak attractions due to transient charge differences.

• Hydrophobic Interactions: Nonpolar molecules aggregate to avoid water.

• Ionic Interactions: Attraction between oppositely charged ions.

Chapter 3: Proteins

Amino Acids: Protein Monomers

• Monomer: Amino acid

• Functional Groups: Amino group (–NH2), carboxyl group (–COOH), hydrogen atom, and R group (side chain).

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

Determining Amino Acid Chemistry

• Four steps to identify amino acid chemistry:

  1. Examine the R group.

  2. Determine if it is polar, nonpolar, acidic, or basic.

  3. Assess its ability to form hydrogen bonds or ionic bonds.

  4. Classify based on side chain properties.

Peptide Bonds

• Peptide Bond: Covalent bond formed between the carboxyl group of one amino acid and the amino group of another via a condensation reaction.

• Equation: $\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

Condensation vs. Hydrolysis Reactions

• Condensation Reaction: Joins two molecules, releasing water.

• Hydrolysis Reaction: Breaks a bond by adding water.

Protein Structure Hierarchies

• Primary Structure: Sequence of amino acids.

• Secondary Structure: Local folding (α-helix, β-sheet) via hydrogen bonds.

• Tertiary Structure: Overall 3D shape due to interactions among R groups.

• Quaternary Structure: Association of multiple polypeptide chains.

• Forces: Hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bridges.

Chapter 4: Nucleic Acids

Types and Monomers

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

• Monomer: Nucleotide

• Functional Groups: Phosphate group, pentose sugar (deoxyribose or ribose), nitrogenous base.

Phosphodiester Bonds

• Bond: Phosphodiester linkage connects nucleotides between the 3' hydroxyl and 5' phosphate groups.

• Equation: $\text{Nucleotide}_1 + \text{Nucleotide}_2 \rightarrow \text{Dinucleotide} + H_2O$

Watson and Crick: DNA Structure

• Critical Information:

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

  • X-ray diffraction data (Rosalind Franklin)

  • Double helix model and antiparallel strands

RNA vs. DNA

• Differences:

  • RNA contains ribose; DNA contains deoxyribose.

  • RNA uses uracil; DNA uses thymine.

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

• First "Living" Molecule: RNA is considered the first genetic material due to its ability to store information and catalyze reactions (ribozymes).

Chapter 5: Carbohydrates

Naming Strategies

• Hexose: Six-carbon sugar (e.g., glucose).

• Aldose: Sugar with an aldehyde group.

• Ketose: Sugar with a ketone group.

• Naming: Based on number of carbons and type of carbonyl group.

Types of Carbohydrates

• Monosaccharide: Single sugar unit (e.g., glucose).

• Disaccharide: Two monosaccharides joined (e.g., sucrose).

• Polysaccharide: Many monosaccharides linked (e.g., starch, cellulose).

Carbohydrates as Energy Molecules

• Energy Storage: Carbohydrates are easily metabolized to release energy.

• Glucose: Central to cellular respiration.

• Equation: $C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{energy}$

Common Polysaccharides and Functions

Polysaccharide	Function	Example
Starch	Energy storage in plants	Potatoes, grains
Glycogen	Energy storage in animals	Liver, muscle
Cellulose	Structural support in plants	Plant cell walls
Chitin	Structural support in fungi and arthropods	Fungal cell walls, exoskeletons

Additional info: These notes expand on the brief points in the slides, providing definitions, examples, and context for each major concept. This structure is designed to help students prepare for exams and understand foundational biology topics.