Review of Biological Principles and Academic Study Guide

Structure and Function of Organic Molecules

Organic Compounds: These are carbon-containing compounds found in all living organisms.
Carbohydrates: * Serve as a major energy source. * Consist of sugars and starches. * Chemical Composition: Made of carbon, hydrogen, and oxygen with a hydrogen-to-oxygen ratio of $2:1$ . * Functions: Utilized by both plants and animals to maintain cellular structure. * Molecular Example: Glucoe ( $C_6H_{12}O_6$ ).
Proteins: * Nitrogen-containing compounds formed from chains of amino acids. * Variety: There are $20$ different amino acids that combine to create a vast variety of protein molecules. * Functions: Essential for composing enzymes, hormo nes, antibodies, and structural components within the body.
Lipids: * Water-insoluble compounds including fats and oils. * Chemical Composition: Composed of carbon, hydrogen, and oxygen. * Structure: Formed from glycerol and fatty acids. * Saturated vs. Unsaturated: Saturated lipids contain single bonds and are saturated with hydrogen, while unsaturated lipids contain double bonds. * Functions: Provide insulation, energy storage, cushioning for internal organs, and are primary components of biological membranes.
Nucleic Acids: * Direct the instructions for protein synthesis. * Contain the genetic information passed from parents to offspring. * Types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). * Building Block: The nucleotide, which consists of a phosphate group, a sugar, and a nitrogenous base. I

Cell Structures and Organelles

Nucleus: Houses DNA; serves as the control center for all cellular activities.
Ribosome: Responsible for protein production.
Mitochondria: Transforms energy through the process of respiration.
Chloroplast: Captures solar energy for photosynthesis; found in plant cells and some algae.
Golgi Body: Functions in packaging and distributing cellular products.
Lysosomes: Responsible for digesting food particles and excess or worn-out products.
Vacuole: Acts as a storage site for various substances.
Cell (Plasma) Membrane: A phospholipid bilayer that encloses and protects the cell; maintains homeostasis and regulates transport.
Cell Wall: A rigid second outer layer providing protection and enclosure; found in plants l and some bacteria.
Cytoplasm: A fluid-like substance containing membrane-bound structures (organelles) that perform specific functions.
Endoplasmic Reticulum (ER): The site of chemical reactions. * Rough ER: Studded with ribosomes. * Smooth ER: Responsible for lipid production.
Cytoskeleton: Provides internal structural support. * Microfilaments: Fibrous structures. * Microtubules: Cylindrical structures.

Cell Types and Theory

Cell Theory: 1. The cell is the basic unit of life. 2. All organisms are composed of cells. 3. All cells originate from pre-existing cells.
Unicellular Organisms: Exist as a single, independent cell.
Multicellular Organisms: Exist as specialized groups of cells organized into tissues. Tissues form organs, and organs form organ systems.
Prokaryotes: Lack a nuclear membrane; nuclear material is located in the center of the cell but not enclosed. They lack membrane-bound organelles. Examples include bacteria and blue-green bacteria.
Eukaryotes: Feature a clearly defined nucleus enclosed by a nuclear membrane and possess membrane-bound organelles. Examples include plants, animals, fungi, and protists.

Cell Specialization and Hierarchy

Organizational Hierarchy: cells $\rightarrow$ tissues $\rightarrow$ organs $\rightarrow$ organ systems $\rightarrow$ organism.
Functional Diversity: Each cell type performs a specific function for a given tissue or organ. Design and shape are dictated by the cell's specific function and working conditions.
Maturation: As cells mature, their shape and internal contents change. Specialized cells may contain unique organelles (e.g., plastids, cell walls, vacuoles, centrioles) not found in all cells.
Multicellular Examples: Red blood cells, nerve cells, and gland cells show high levels of specialization.

Cell Transport Mechanisms

Passive Transport: Movement of substances across the plasma membrane without energy expenditure (moving with the concentration gradient). 1. Diffusion: Movement from high concentration to low concentration. 2. Osmosis: The specific diffusion of water across the membrane from high to low concentration. 3. Facilitated Transport: Use of carrier molecules embedded in the membrane to move substances from high to low concentration.
Active Transport: Movement across the plasma membrane requiring cellular energy and carrier molecules (moving against the concentration gradient from low to high concentration). 1. Endocytosis: Bringing large particles into the cell. 2. Exocytosis: Releasing large particles out of the cell.
Effects of Concentration (Tonicity): * Hypotonic: Water moves into the cell; the cell may burst. * Hypertonic: Water moves out of the cell; the cell shrivels. * Isotonic: No net movement of water; the cell maintains equilibrium.

Homeostasis and Feedback Mechanisms

Definition: A self-regulating mechanism maintaining internal equilibrium within cells, organs, and systems (e.g., body temperature, respiration, nutritional balance).
Regulatory Process: Cells communicate needs via messengers released through membranes. These chemical signals reach the hypothalamus in the brain.
The Hypothalamus: Acts as the ruler of homeostasis, adjusting the internal environment (interstitial fluid) via neural and chemical signals to glands and organs.
Negative Feedback: Systems like glucose and insulin levels where the response reduces the initial stimulus.
Positive Feedback: Systems like blood platelets and clotting where the response enhances the initial stimulus.

Biochemical Reactions and Bioenergetics

Cellular Respiration: Converts food molecules into energy. * Stage 1: Glycolysis (anaerobic, occurs without oxygen). * Stages 2 & 3: Citric Acid Cycle and Electron Transport Chain (aerobic, require oxygen). * Chemical Equation: $C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{ENERGY (36 ATP)}$ .
Photosynthesis: Conversion of solar energy into chemical energy (carbohydrates) by plants. * Chemical Equation: $6CO_2 + 6H_2O + \text{ENERGY (Sunlight)} \rightarrow C_6H_{12}O_6 + 6O_2$ . * Note: In Chemosynthesis, organisms use sulfur or nitrogen as an energy source instead of sunlight.
ATP (Adenosine Triphosphate): Stores and releases energy. * Energy Release: Removing a phosphate group turns ATP into ADP, releasing energy: $\text{ATP} \rightleftharpoons \text{ADP} + \text{P} + \text{ENERGY}$ .
Fermentation: Occurs when oxygen is unavailable to continue ATP production. * Lactic Acid Fermentation (Muscle cells): $\text{Glucose} \rightarrow \text{Lactic Acid} + 2\text{ATP}$ . * Alcoholic Fermentation (Plant cells): $\text{Glucose} \rightarrow CO_2 + \text{Alcohol} + 2\text{ATP}$ .

Enzymes

Enzymes are specialized proteins that regulate biochemical reactions. They act as catalysts, speeding up reactions without being consumed.
Functions: Provide energy, build new cells, aid digestion, and break down substrates (reactants).
Factors Affecting Enzymes: pH, temperature, and quantity.

Comparison of DNA and RNA

DNA (Deoxyribonucleic acid): * Structure: Double-stranded, twisted helix. * Sugar: Deoxyribose. * Bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T). * Pairing: $G-C, A-T$ (Purines opposite Pyrimidines), held by weak hydrogen bonds. * Location: Never leaves the nucleus. * Function: Controls protein production; coiled into chromosomes; small sections are genes. * Replication: DNA unravels and each strand makes an exact copy for mitosis.
RNA (Ribonucleic acid): * Structure: Single-stranded. * Sugar: Ribose. * Bases: Adenine (A), Guanine (G), Cytosine (C), Uracil (U). * Pairing: $G-C, A-U$ . * Location: Leaves the nucleus to work in the cytoplasm. * Types: Ribosomal (rRNA), Messenger (mRNA), Transfer (tRNA). * Transcription: mRNA is made from a DNA strand to carry messages to ribosomes. * Translation: mRNA is translated into protein at ribosomes; tRNA transfers amino acids.

Cellular Reproduction: Mitosis and Meiosis

Mitosis: * Purpose: Growth, repair, and replacement in multicellular organisms; reproduction in unicellular organisms. * Cycle: Interphase (longest part; DNA replication), Mitosis (Prophase, Metaphase, Anaphase, Telophase), and Cytokinesis. * Result: Two identical diploid daughter cells. Human diploid number is $46$ ( $23$ homologous pairs).
Meiosis: * Purpose: Production of gametes (sex cells). * Process: Two cell divisions, one chromosome replication (reduction division). Phases repeat (I and II). * Result: Four haploid daughter cells ( $n = 23$ ) with genetic variation. * Sperm Production: One primary cell results in four haploid sperm cells of equal size with whip-like tails. * Egg Production: One primary cell results in one large haploid egg cell and three smaller polar bodies (which disintegrate).

Genetics and Heredity

Gregor Mendel: Conducted sweet pea experiments in the $1800$ s, leading to the laws of heredity.
Terminology: * Gene: Instructions for traits (alleles). * Homozygous: Two identical alleles ( $BB$ or $bb$ ). * Heterozygous: Two different alleles ( $Bb$ ; "hybrid"). * Genotype: Genetic makeup (letters). * Phenotype: Physical appearance (description).
Mendel's Laws: 1. Law of Dominance: Dominant alleles mask recessive ones. 2. Law of Segregation: Gene pairs separate during gamete formation. 3. Law of Independent Assortment: Gene pairs separate independently of each other.
Inheritance Patterns: * Sex-Linked Traits: Traits on the X chromosome (e.g., colorblindness, hemophilia). * Polygenic Inheritance: One trait controlled by many genes (e.g., skin color). * Codominance: Both alleles expressed (e.g., checkered chickens, sickle cell anemia). * Incomplete Dominance: Intermediate phenotype (e.g., red + white = pink flowers).
Probabilities: * Heterozygous Monohybrid Cross: $1:2:1$ genotype ratio; $3:1$ phenotype ratio ( $75\%$ dominant phenotype probability). * Heterozygous Dihybrid Cross: $9:3:3:1$ phenotype ratio.

Sources of Variation and Mutations

Crossing Over: Exchange of genes between chromosomes during meiosis.
Nondisjunction: Failure of homologous pairs to separate during meiosis, resulting in trisomy (one extra) or monosomy (one less), such as Down's Syndrome (extra $21^{st}$ chromosome).
Mutations: Changes in genetic code. Gene mutations affect single genes; chromosome mutations affect many.

Evidence and Theory of Evolution

Natural Selection: Proposed by Charles Darwin; organisms best suited to the environment survive and pass on traits.
Microevolution: Change within a species (e.g., antibiotic or pesticide resistance).
Macroevolution: Evolution between different species (e.g., speciation).
Geographic Isolation: Physical barriers dividing a population, leading to new species.
Evidence: * Fossils: Records of changes over time found in rock, ice, or amber. * DNA: Genetic similarity indicates close relationships. * Embryology: Similarities in early vertebrate stages.

Taxonomy and Classification

Taxonomy: The grouping and naming of organisms.
History: * Aristotle ( $4^{th}$ Century B.C.): Divided life into "blood" and "bloodless" groups (plants and animals). * Linnaeus ( $1700$ s): Developed binomial nomenclature (Genus and species).
Classification Levels: Kingdom, Phylum, Class, Order, Family, Genus, Species.
Six Kingdoms: 1. Archaebacteria: Ancient, anaerobic bacteria. 2. Eubacteria: True, aerobic bacteria. 3. Protista: Eukaryotic, unicellular or multicellular, mobile (e.g., amoeba). 4. Fungi: Eukaryotic, decomposers, lack chlorophyll (e.g., mushrooms). 5. Plantae: Eukaryotic, multicellular, photosynthetic autotrophs with cellulose cell walls. 6. Animalia: Eukaryotic, multicellular consumers.
Human Classification: Kingdom Animalia, Phylum Chordata, Class Mammalia, Order Primates, Family Homidae, Genus Homo, Species Homo sapiens.

Viruses and Infectious Organisms

Viruses: Considered non-living; composed of nucleic acid with a protein coat. Require a host cell for replication. * Lytic Cycle: Virus injects DNA, replicates immediately, host cell bursts. * Lysogenic Cycle: Viral DNA integrates and remains dormant before entering the lytic cycle.
Pathogens: * Bacteria: Streptococcus pyogenes (strep throat), Escherichia coli (UTIs). * Viruses: Varicella zoster (chicken pox), Rhinovirus (cold). * Fungi: Candida albicans (yeast infection), Tinea pedis (athlete's foot). * Parasites: Enterobius vermicularis (pinworm), Plasmodium falciparum (malaria).

Immune Defense and Health

First Line: Physical barriers like skin, mucous membranes, stomach acid.
Second Line: Inflammation, fever (controlled by hypothalamus; temp > 100^{\circ}F), and white blood cell increase.
Third Line: Immune response producing antibodies (Killer T cells, phagocytes).
Antibiotic Resistance: Caused by overusing antibiotics or not finishing prescriptions, leading to "superbugs."

Plant Biology

Nonvascular Plants: Small, rely on osmosis; require moist environments (e.g., mosses).
Vascular Plants: Possess Xylem (transport water/minerals up) and Phloem (transport sugars down). * Gymnosperms: Cone-bearing plants. * Angiosperms: Flowering plants.
Tropisms: Growth responses to stimuli. * Geotropism (gravity), Phototropism (light), Hydrotropism (water), Thigmotropism (touch), Chemotropism (chemicals).

Ecology and Ecosystems

Energy Flow: Sun $\rightarrow$ Producers (Autotrophs) $\rightarrow$ Consumers (Heterotrophs).
Energy Transfer: Only about $10\%$ of energy is transferred to the next trophic level; $90\%$ is lost to metabolism/heat.
Symbiosis: * Mutualism: Both benefit. * Commensalism: One benefits, other unaffected. * Parasitism: One benefits at the expense of another.
Cycles of Matter: * Water Cycle: Involves evaporation, condensation, and precipitation. * Carbon Cycle: Recycled through respiration, photosynthesis, and combustion. * Nitrogen Cycle: Bacteria break down nitrogen compounds for soil and air.
Succession: * Primary: Colonization of barren land (no soil initially). * Secondary: Changes after disruption to an existing community (soil present).
Human Impact: Extinction, pollution (smog, acid rain, landfills), and global warming. Conservation efforts include the $3$ Rs (Reduce, Reuse, Recycle) and wildlife protection.