Biology Study Guide: Foundations of Life, Chemistry, and the Cell

Properties and Organization of Life

Eight Properties of Life

Living organisms share a set of fundamental characteristics that distinguish them from nonliving matter.

• Order: Highly ordered structure, such as cells and tissues.

• Evolutionary Adaptation: Populations evolve over generations through adaptations that enhance survival and reproduction.

• Response to Environment: Ability to sense and respond to environmental stimuli.

• Regulation: Maintenance of internal balance (homeostasis).

• Energy Processing: Use of energy to power activities and chemical reactions.

• Growth and Development: Consistent growth and development controlled by inherited information.

• Reproduction: Ability to produce new organisms.

• Cellular Organization: Composed of one or more cells, the basic units of life.

Evolutionary Adaptation vs. Response to Environment: Adaptation refers to inherited traits that enhance survival over generations, while response is an immediate reaction to stimuli.

Emergent Properties

New properties arise at each level of biological organization that are not present at the preceding level. For example, a functioning organ system exhibits properties not found in individual cells.

Reductionism vs. Systems Biology

• Reductionism: Breaking down complex systems into simpler components for study.

• Systems Biology: Study of interactions among parts of a system to understand the whole.

Levels of Biological Organization

• Biosphere: All life on Earth and all places where life exists.

• Ecosystems: All living organisms in a particular area plus nonliving components.

• Communities: Different populations inhabiting a particular ecosystem.

• Populations: Individuals of the same species in a given area.

• Organisms → Organs → Tissues → Cells → Organelles → Molecules

Cells and Genetic Information

Prokaryotic vs. Eukaryotic Cells

• Prokaryotic Cells: Lack a nucleus and membrane-bound organelles; DNA in nucleoid region; domains Bacteria and Archaea.

• Eukaryotic Cells: Have a nucleus and membrane-bound organelles; domain Eukarya.

DNA, Genes, and Genome

• DNA (Deoxyribonucleic Acid): Hereditary material; double helix structure.

• Genes: Segments of DNA coding for proteins or RNA.

• Genome: Entire set of genetic instructions in an organism.

Gene Expression

Process by which information from a gene is used to synthesize a functional product (protein or RNA).

• DNA → (transcription) → mRNA → (translation) → Protein

Genomics, Proteomics, and Bioinformatics

• Genomics: Study of whole sets of genes and their interactions.

• Proteomics: Study of sets of proteins and their properties.

• Bioinformatics: Use of computational tools to analyze biological data.

Feedback Mechanisms

• Negative Feedback: End product slows or stops the process (e.g., insulin regulation of blood glucose).

• Positive Feedback: End product speeds up its own production (e.g., blood clotting).

Evolution and Classification

Evolution, Adaptation, and Natural Selection

• Evolution: Change in genetic composition of a population over generations.

• Adaptation: Inherited traits that enhance survival and reproduction.

• Natural Selection: Process by which individuals with advantageous traits survive and reproduce more successfully.

Darwin’s Observations and Inferences

• Observations:

  1. Individuals in a population vary in traits.

  2. Traits are inherited from parents to offspring.

  3. Species produce more offspring than the environment can support.

• Inferences:

  1. Individuals with advantageous traits are more likely to survive and reproduce.

  2. Favorable traits accumulate in the population over generations.

Taxonomy and Classification

• Taxonomy: Science of naming and classifying organisms.

• Hierarchical Groups (from broadest to most specific):

  1. Domain

  2. Kingdom

  3. Phylum

  4. Class

  5. Order

  6. Family

  7. Genus

  8. Species

• Three Domains: Bacteria, Archaea, Eukarya

• Four Eukaryotic Kingdoms: Plantae, Fungi, Animalia, Protista (sometimes split further)

Scientific Method and Experimental Design

Scientific Method

• Observation: Gathering information about phenomena.

• Hypothesis: Testable explanation for observations.

• Experiment: Controlled test of hypothesis.

• Data: Qualitative (descriptive) or quantitative (numerical).

• Controlled Experiment: Only one variable is changed at a time.

• Independent Variable: Factor manipulated by the experimenter.

• Dependent Variable: Factor measured in the experiment.

• Theory: Broad explanation supported by evidence.

• Scientific Law: Statement describing consistent natural phenomena.

Chemical Context of Life

Elements and Compounds

• Element: Substance that cannot be broken down by chemical means.

• Compound: Substance consisting of two or more elements in a fixed ratio.

• Elements making up 96% of living matter: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N)

Atomic Structure

• Proton: Positively charged particle in nucleus.

• Neutron: Neutral particle in nucleus.

• Electron: Negatively charged particle orbiting nucleus.

• Atomic Number: Number of protons.

• Atomic Mass: Number of protons plus neutrons.

Isotopes and Radioactivity

• Isotope: Atoms of the same element with different numbers of neutrons.

• Radioactive Isotope: Unstable isotope that decays, emitting radiation.

• Half-life: Time for half the atoms in a sample to decay.

Chemical Bonds

• Octet Rule: Atoms tend to have eight electrons in their valence shell.

• Valence Electrons: Electrons in the outermost shell.

• Ionic Bond: Transfer of electrons between atoms.

• Covalent Bond: Sharing of electrons between atoms.

• Polar Covalent Bond: Unequal sharing of electrons.

• Nonpolar Covalent Bond: Equal sharing of electrons.

• Hydrogen Bond: Weak attraction between a hydrogen atom and an electronegative atom.

• Electronegativity: Atom's ability to attract electrons.

• Chemical Equilibrium: Forward and reverse reactions occur at the same rate.

Water and Life

Properties of Water

• Cohesion: Water molecules stick together via hydrogen bonds.

• Adhesion: Water molecules stick to other substances.

• High Specific Heat: Water resists temperature change.

• High Heat of Vaporization: Large amount of energy needed to vaporize water.

• Ice Floats: Solid water is less dense than liquid water.

• Solvent of Life: Many substances dissolve in water.

Kinetic and Thermal Energy

• Kinetic Energy: Energy of motion.

• Thermal Energy: Total kinetic energy of molecules.

• Temperature: Average kinetic energy of molecules.

Hydrophilic vs. Hydrophobic Substances

• Hydrophilic: Substances that dissolve in water (e.g., salts, sugars).

• Hydrophobic: Substances that do not dissolve in water (e.g., oils).

Acids, Bases, and pH

• Acid: Substance that increases H+ concentration.

• Base: Substance that decreases H+ concentration.

• pH Scale: Measures H+ concentration; ranges from 0 (acidic) to 14 (basic).

• Buffer: Substance that minimizes changes in pH.

Key Equation:

$\mathrm{CO_2 + H_2O \leftrightarrow H_2CO_3 \leftrightarrow H^+ + HCO_3^-}$

Mole and Molarity: A mole is 6.022 x 1023 molecules; molarity is moles per liter.

Calculating [H+] and [OH-]: At 25°C, $[H^+][OH^-] = 1 \times 10^{-14}$

Carbon and Molecular Diversity

Carbon Bonding and Isomers

• Carbon: Forms four covalent bonds, allowing for diverse molecules.

• Isomers: Compounds with same formula but different structures.

• Structural Isomers: Differ in covalent arrangement.

• Cis-trans Isomers: Differ in spatial arrangement around double bonds.

• Enantiomers: Mirror images of each other.

• Racemic Mixture: Contains equal amounts of enantiomers.

Functional Groups

Seven key functional groups in biological molecules (see slides 13 & 14):

• Hydroxyl (-OH)

• Carbonyl (C=O)

• Carboxyl (-COOH)

• Amino (-NH2)

• Sulfhydryl (-SH)

• Phosphate (-OPO32-)

• Methyl (-CH3)

Large Biological Molecules

Monomers, Polymers, and Reactions

• Monomer: Small building block molecule.

• Polymer: Long molecule made of monomers.

• Dehydration Synthesis: Joins monomers by removing water.

• Hydrolysis: Breaks polymers by adding water.

Carbohydrates

• Monosaccharides: Simple sugars (e.g., glucose).

• Aldoses vs. Ketoses: Aldoses have an aldehyde group; ketoses have a ketone group.

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

• Polysaccharides: Many monosaccharides (e.g., starch, glycogen).

• Glycogen: Storage polysaccharide in animals.

• Starch: Storage polysaccharide in plants.

Lipids

• Lipids: Hydrophobic molecules (fats, phospholipids, steroids).

• Saturated Fats: No double bonds; solid at room temperature; usually from animals.

• Unsaturated Fats: One or more double bonds; liquid at room temperature; usually from plants.

• Phospholipids: Amphipathic molecules forming bilayers in membranes.

• Steroids: Lipids with four fused rings (e.g., cholesterol, hormones).

Table: Saturated vs. Unsaturated Fats

Property	Saturated Fat	Unsaturated Fat
Double Bonds	None	One or more
State at Room Temp	Solid	Liquid (oil)
Source	Animals	Plants

Proteins

• Monomer: Amino acid (20 types).

• Peptide Bond: Covalent bond between amino acids.

• Levels of Structure:

  1. Primary: Sequence of amino acids.

  2. Secondary: Alpha helix or beta sheet (hydrogen bonds).

  3. Tertiary: 3D folding (R group interactions).

  4. Quaternary: Multiple polypeptides.

• Denaturation: Loss of protein structure and function.

• R Group: Side chain that determines properties of amino acid (polar, nonpolar, charged).

Cell Structure and Function

Plasma Membrane

• Phospholipid Bilayer: Hydrophilic heads face outward; hydrophobic tails face inward.

• Embedded Proteins: Serve as channels, transporters, receptors.

• Semipermeable: Selectively allows passage of substances.

Cell Types and Structures

• All Cells Have: Plasma membrane, cytosol, DNA, ribosomes.

• Animal Cells: No cell wall.

• Plant, Fungi, Bacteria: Have cell walls.

• Bacterial Structure: Single circular chromosome in nucleoid, ribosomes, flagella for movement.

Eukaryotic Organelles

• Nucleus: Contains DNA, nucleolus (ribosome synthesis).

• Ribosomes: Site of protein synthesis.

• Endomembrane System: Includes nuclear envelope, endoplasmic reticulum (ER), Golgi apparatus, vesicles.

• Rough ER: Studded with ribosomes; modifies proteins.

• Smooth ER: Synthesizes lipids, detoxifies drugs.

• Golgi Apparatus: Modifies, sorts, and ships proteins and lipids.

• Lysosomes: Digestive organelles; phagocytosis.

• Chloroplasts: Site of photosynthesis (plants).

• Mitochondria: Site of cellular respiration (ATP production).

• Peroxisomes: Break down fatty acids, detoxify.

• Cytoskeleton: Network of fibers for support and movement; motor proteins move organelles.

Energy Transformations

• Photosynthesis: $\mathrm{Energy\ (sun) + H_2O + CO_2 \rightarrow C_6H_{12}O_6 + O_2}$ (in chloroplasts)

• Cellular Respiration: $\mathrm{C_6H_{12}O_6 + O_2 \rightarrow Energy\ (ATP) + H_2O + CO_2}$ (in mitochondria)

• These processes are reciprocal; products of one are reactants of the other.

• ATP is the main energy currency of the cell.

Summary Table: Prokaryotic vs. Eukaryotic Cells

Feature	Prokaryotic	Eukaryotic
Nucleus	No	Yes
Membrane-bound Organelles	No	Yes
DNA Location	Nucleoid	Nucleus
Examples	Bacteria, Archaea	Plants, Animals, Fungi, Protists

Additional info:

• For diagrams and drawing practice, refer to textbook figures for dehydration synthesis, hydrolysis, and amino acid structure.

• For functional group recognition, practice identifying groups in molecular structures.