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 chemical and molecular basis of life. Topics include the domains of life, characteristics of living organisms, scientific methodology, and the structure and function of biological macromolecules.

Chapter 1 – Biology: The Study of Life

The Three Domains of Life

• Bacteria, Archaea, and Eukarya are the three domains represented on a phylogenetic tree.

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

• Distinguishing features: Eukarya have complex cellular organization, including organelles such as mitochondria and, in plants, chloroplasts.

Defining Features of Living Organisms

• Cellular organization: All living things are composed of one or more cells.

• Metabolism: Living organisms carry out chemical reactions to obtain and use energy.

• Homeostasis: Regulation of internal environment to maintain stable conditions.

• Growth and development: Organisms grow and develop according to genetic instructions.

• Reproduction: Ability to produce new organisms.

• Response to stimuli: React to environmental changes.

• Evolution: Populations change over time through genetic variation and natural selection.

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 under specific conditions (e.g., Mendel's Laws).

• Comparison: Hypotheses are tentative; theories are broader and supported by evidence; laws describe patterns but do not explain mechanisms.

Elements of a Scientific Experiment

• Independent variable: The factor manipulated by the researcher.

• Dependent variable: The factor measured in response.

• Control group: Baseline group for comparison.

• Replication: Repeating experiments to ensure reliability.

• Standardization: Keeping conditions consistent except for the independent variable.

Chapter 2 – Water and Carbon: The Chemical Basis of Life

Atomic Number and Mass Number

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

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

• Average mass number: Weighted average of all isotopes of an element.

• Example: Carbon has atomic number 6; common isotopes are $^{12}C$ and $^{13}C$.

Covalent vs. Ionic Bonds

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

• Ionic bonds: Electrons are transferred, creating 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: Electrons are shared unequally, creating partial charges (e.g., O-H in water).

• Nonpolar covalent bonds: Electrons are shared equally (e.g., C-H, O2).

Interactions Between Molecules

• Hydrogen bonds: Attraction between partial charges in polar molecules (e.g., between water molecules).

• Van der Waals interactions: Weak attractions due to transient charge fluctuations.

• Ionic interactions: Attraction between oppositely charged ions.

• Hydrophobic interactions: Nonpolar molecules aggregate to avoid water.

Chapter 3 – Protein Structure and Function

Amino Acids: Monomers of Proteins

• Amino acid: The monomer unit of proteins.

• Functional groups: Each amino acid has an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a unique R group (side chain).

Individuality of Amino Acids

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

• Classification: Amino acids can be nonpolar, polar, acidic, or basic based on their R group.

• Four steps to determine chemistry: Examine charge, polarity, size, and functional groups of the R group.

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: Two molecules join, releasing water.

• Hydrolysis reaction: A molecule is split by adding water.

Protein Structure Hierarchies

• Primary structure: Sequence of amino acids.

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

• Tertiary structure: Overall 3D shape, stabilized by interactions among R groups.

• Quaternary structure: Association of multiple polypeptide chains.

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

Chapter 4 – Nucleic Acids and the RNA World

Types and Structure of Nucleic Acids

• DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are the two types found in cells.

• Nucleotide: Monomer of nucleic acids, composed of a phosphate group, a five-carbon sugar (deoxyribose or ribose), and a nitrogenous base.

Bonds in Nucleic Acids

• Phosphodiester bond: Covalent bond linking the phosphate group of one nucleotide to the sugar of another.

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

Watson and Crick's DNA Structure Discovery

• Key information:

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

  • X-ray diffraction data (Rosalind Franklin's images)

  • Helical structure and antiparallel strands

RNA vs. DNA

• RNA: Contains ribose sugar, uracil base, usually single-stranded.

• DNA: Contains deoxyribose sugar, thymine base, double-stranded helix.

• First "living" molecule: RNA is considered more likely due to its ability to store information and catalyze reactions (ribozymes).

Chapter 5 – An Introduction to Carbohydrates

Naming Carbohydrates

• Monosaccharides: Named based on number of carbons (triose, pentose, hexose) and functional group (aldose, ketose).

• Example: Glucose is a hexose aldose.

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

• High energy bonds: Carbohydrates store energy in C-H and C-C bonds.

• Rapid metabolism: Easily broken down to release energy for cellular processes.

Common Polysaccharides and Their Functions

Polysaccharide	Function	Organism
Starch	Energy storage	Plants
Glycogen	Energy storage	Animals
Cellulose	Structural support	Plants
Chitin	Structural support	Fungi, arthropods

Additional info: These notes expand on the brief points in the slides, providing definitions, examples, and context for each concept. Equations are included for relevant chemical reactions. The table summarizes major polysaccharides and their biological roles.