The Scientific Method and Biology Overview

The Scientific Method

• Investigative approach to acquiring knowledge through observation, explanation, and testing.
• Hypotheses are testable, falsifiable, tentative explanations.
• Controlled experiments compare experimental and control groups, identifying independent, dependent, and controlled variables.
• Statistical analysis of large sample sizes is crucial for interpreting results.
• Failure to falsify a hypothesis doesn't prove it true; further research is needed.
• Peer-reviewed scientific papers are integral to disseminating findings.
• Scientific theories are well-substantiated explanations supported by extensive experimentation. They are unlikely to be contradicted by future research.
• Observational science uses statistical techniques to infer patterns and causes in situations where controlled experiments are difficult (e.g., astronomy, ecology).

Biology and the Scale of Life

• Biology is the study of living things.
• The cell is the basic unit of life.
• Microscopy (light and electron) allows visualization at various scales.

Matter, Elements, and Compounds

• Matter occupies space and has mass; it consists of pure elements.
• Elements cannot be broken down chemically into other substances.
• Compounds are substances with two or more elements in a fixed ratio.
• 96% of living matter comprises carbon, hydrogen, oxygen, and nitrogen.

Atomic Structure and Isotopes

• Atomic number equals the number of protons.
• Atomic mass equals the sum of protons and neutrons.
• Isotopes are atoms with the same number of protons but different numbers of neutrons (same atomic number, different atomic mass).
• Radioisotopes are unstable isotopes that decay, releasing energy; their decay rate defines their half-life.
• Radioisotopes are used as radioactive tracers to measure chemical processes and substance movement.

Electrons and Chemical Bonds

• The number of electrons usually equals the number of protons in a neutral atom.
• Electrons occupy orbitals within shells. Stable orbitals have paired electrons.
• Valence electrons (outermost shell) determine an atom's reactivity; full valence shells generally indicate inertness.
• Reactive elements form molecules through chemical bonds.

Types of Chemical Bonds

• Ionic bonds: Electron transfer creates ions (cations and anions) with opposite charges.
• Covalent bonds: Atoms share valence electrons, resulting in distinct 3D molecular shapes; the structure relates to function.
• Electronegativity: Measures an atom's electron attraction in a covalent bond; unequal sharing creates polar covalent bonds.
• Polar molecules: Possess partial positive and negative charges due to unequal electron sharing.
• Hydrogen bonds: Occur between a partially positive hydrogen atom and a partially negative atom (e.g., in water). Weaker than covalent and ionic bonds.
• van der Waals forces: Weak attractions between nonpolar molecules due to temporary electron distribution imbalances.

Water and Hydrogen Bonds

• Water's unique properties (high specific heat, density changes with temperature) arise from hydrogen bonding.
• Water is an excellent solvent, dissolving polar molecules and ions through hydration shells.
• Water ionization produces H+ and OH- ions.

pH and Buffers

• pH measures the concentration of H+ ions; acids donate H+, bases accept H+.
• Buffers resist pH changes by absorbing or releasing H+, typically weak acids or bases. The carbonic acid–bicarbonate system buffers blood pH.

Carbon Compounds

• Carbon's tetravalence (four bonds) allows diverse and large molecule formation.
• Hydrocarbon chains vary in length and shape; those with carbon atoms bonded only to hydrogen atoms are called hydrocarbons.
• Functional groups (hydroxyl, carbonyl, carboxyl, amino, phosphate, sulfhydryl) affect molecule reactivity and properties. Structure is related to function.

Dehydration and Hydrolysis Reactions

• Dehydration reactions synthesize polymers by removing water and forming bonds.
• Hydrolysis reactions break down polymers by adding water and breaking bonds.

Carbohydrates

• Sugars and their polymers; function as fuel and building materials.
• Monosaccharides are multiples of CH2O (e.g., glucose, fructose, galactose); isomers have the same formula but different structures and functions (structural isomers, enantiomers).
• Disaccharides are two monosaccharides linked by a glycosidic bond (e.g., sucrose, lactose, maltose).
• Polysaccharides are polymers of monosaccharides; they may be branched or unbranched, and their linkage type influences their properties.

Proteins

• Proteins have diverse structures and functions (structural support, storage, transport, catalysis, communication, movement).
• Proteins are composed of one or more polypeptide chains.
• Polypeptides are polymers of amino acids. There are 20 different amino acids, categorized by their side chains (nonpolar, uncharged polar, charged).
• Peptide bonds (covalent) link amino acids; they are formed via dehydration reactions. Amino acids are added only to the carboxyl end.

Protein Structure

• Primary structure: The linear sequence of amino acids.
• Secondary structure: H-bonds between backbone atoms create α-helices or β-pleated sheets.
• Tertiary structure: All types of bonds between R groups determine the 3D shape and function.
• Quaternary structure: Two or more polypeptides assemble.
• Prosthetic groups are non-protein components necessary for protein function.

Nucleic Acids

• Nucleic acids (DNA and RNA) are polymers of nucleotides. They store and transmit genetic information. RNA also has functional roles (mRNA, tRNA, rRNA).
• Nucleotides consist of a nitrogenous base, a pentose sugar, and one to three phosphate groups.
• DNA uses deoxyribose; RNA uses ribose. Uracil is only in RNA; thymine is only in DNA. ATP and GTP store energy.
• DNA is a double helix; two polynucleotide chains are antiparallel, connected by hydrogen bonds between bases adenine (A), guanine (G), cytosine (C), and thymine (T) or uracil (U).

Lipids

• Nonpolar; not true macromolecules because they lack a defined monomer subunit.
• Have a hydrocarbon backbone. Biological examples include fats, phospholipids, and steroids.
• Fatty acids: Saturated fats have maximal hydrogen atoms and no double bonds. Unsaturated fats have at least one double bond causing bending in the molecule.
• Fats: Formed via dehydration reactions between glycerol and fatty acids. 1g of fat has more energy than 1g of starch.
• Phospholipids: Amphipathic (both hydrophilic and hydrophobic regions) found in cell membranes.
• Steroids: Have four carbon rings; many have dual solubility (polar and nonpolar regions).

Putting it Together

• Living things are made of carbon compounds – carbohydrates, proteins, lipids, and nucleic acids.
• Water is essential due to its solvent properties and hydrogen bonds.
• Interactions between molecules govern cell structure and function.