Biology Study Guide BIO.1A - BIO.5.7

Characteristics of Life and Biological Organization

To differentiate between living and non-living things, biologists examine eight primary criteria: - Cellular Basis and Genetic Material: All living entities are composed of one or more cells. These cells contain genetic material in the form of DNA (deoxyribonucleic acid). - Reproduction: All living things have the capacity to reproduce, either through sexual reproduction (requiring two parents) or asexual reproduction (requiring only one parent). - Growth and Development: All living organisms undergo a process of growing and developing throughout their lifespan. - Responsiveness to Stimuli: Living things exhibit the ability to detect and respond to various internal and external stimuli. - Metabolism and Energy Acquisition: All living things must obtain and utilize energy. Metabolism consists of the chemical processes used to maintain life. - Homeostasis: Living organisms maintain a fairly stable and balanced internal environment despite external changes. - Adaptation: Individual organisms respond to changes in their specific environment. - Evolution: As a collective group, living species change over time through the process of evolution.

The Principles and Development of Cell Theory

The Cell Theory is defined by three fundamental principles: - The cell constitutes the basic unit of life. - All existing cells originate from pre-existing cells via processes such as mitosis, meiosis, or fertilization. - Every living organism is composed of at least one or more cells.
Key historical contributions to the development of the cell theory include: - Hook: Recognized as the first individual to name and observe living cells using a microscope. - Schleiden and Schwann: Identified that all organisms are composed of cells; specifically, Schleiden focused on plants while Schwann focused on animals. - Virchow: Formulated the tenet that all cells must come from pre-existing cells.

Biological Classification of Viruses

Biologists classify viruses as non-living entities based on several specific criteria: - Viruses are not composed of cells. - They lack the ability to produce their own food, ingest food, or produce metabolic waste products. - Viruses do not react to environmental stimuli.
Functional characteristics of viruses: - They can only replicate or multiply when they inhabit a host cell. - Their structure consists of genetic material, which can be either DNA or mRNA, encased within a protective protein coat (capsid). - Bacteriophage: A specific type of virus that attaches to a bacterium, eventually destroying or lysing the cell to release additional phage particles.

Structure and Function of Organic Macromolecules

All organic compounds contain carbon and are essential to living things. There are four primary classes:
Carbohydrates (CHO): - Elementary Units: The monomer is a monosaccharide, and the polymer is a polysaccharide. - Function: They serve as a major source of energy and include sugars and starches. They often have names ending in the suffix "-ose." - Composition: Composed of carbon, hydrogen, and oxygen with a ratio of $1:2:1$ . - Structural Role: Utilized by both plants and animals to maintain cellular structure.
Nucleic Acids (CHONP): - Elementary Unit: The monomer is the nucleotide. - Function: They direct protein synthesis instructions and store genetic information inherited from parents. - Types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
Proteins (CHON): - Elementary Units: The monomer is an amino acid, and the polymer is a polypeptide. - Structure: Compounds containing nitrogen made of linked chains of amino acids. There are $20$ different amino acids that can combine to create a vast variety of proteins. - Examples: They make up enzymes, hormones, antibodies, and structural components.
Lipids (CHO): - Elementary Unit: Fatty acids. - Properties: Water-insoluble substances including fats and oils. They are composed of glycerol and fatty acids (containing carbon, hydrogen, and oxygen). - Function: Provide insulation, store energy, and are key components of cell membranes. - Types: Saturated lipids (linked by single bonds and saturated with hydrogen) and unsaturated lipids (containing double bonds).

Enzymes and Biochemical Reactions

Enzymes are specialized proteins that regulate nearly every biochemical reaction within a cell.
Mechanism: Described as a "lock and key" mechanism. This means each enzyme is specific to a particular substrate.
Active Site: The location on the enzyme where the substrate binds to trigger the reaction.

Cellular Organelles and Specialized Functions

Nucleus: Holds the genetic information within DNA.
Nucleolus: Located inside the nucleus; its primary function is the creation of ribosomes.
Ribosomes: Responsible for protein synthesis. They are found either attached to the rough endoplasmic reticulum or floating freely in the cytoplasm.
Smooth Endoplasmic Reticulum (SER): Facilitates the production of lipids (fats) and the transport of nutrients inside the cell.
Golgi Apparatus (Golgi bodies): Prepares and packages proteins for import into or export out of the cell.
Mitochondria: Known as the "powerhouse" of the cell, it generates energy in the form of ATP (adenosine triphosphate).
Chloroplast: Exclusive to plant cells; it captures solar energy to create glucose/food.
Cytoskeleton: A network of protein fibers that provides structural shape, comparable to human bones.
Vacuoles: Act as storage units for water and essential nutrients.
Cell (Plasma) Membrane: A phospholipid bilayer that encloses and protects the cell, regulating entry and exit.
Cell Wall: A rigid outer layer for protection found in plant cells, fungus cells, and some bacteria.

Comparative Cell Biology

Prokaryotes: Simple structural organisms that lack a membrane-bound nucleus and membrane-bound organelles. Examples include bacteria and blue-green algae.
Eukaryotes: Complex cells containing a clearly defined nucleus (enclosed by a nuclear membrane) and membrane-bound organelles. Examples include plants, animals, fungi, and protists.
Virus vs. Cell Comparison: - Similarities: Both contain genetic material at their core and possess a protective outer layer (lipid membrane for cells, capsid for viruses). - Differences: Viruses lack organelles and cannot undergo protein synthesis independently. Therefore, they must utilize a living host cell for reproduction.

Cell Transport Mechanisms and Homeostasis

Passive Transport: Movement across the plasma membrane without energy expenditure, following the concentration gradient (high to low). - Diffusion: Movement of substances from high to low concentration. - Osmosis: The diffusion of water across the membrane from high to low concentration. - Facilitated Transport: Use of carrier molecules to move substances down the gradient.
Active Transport: Movement requiring cellular energy (ATP) and carrier molecules to move substances against the concentration gradient (low to high). - Endocytosis: Process of bringing large particles into the cell. - Exocytosis: Process of large particles leaving the cell.
Sodium-Potassium Pump: Uses ATP to move two potassium ( $K^+$ ) ions into the cell and three sodium ( $Na^+$ ) ions out into the extracellular fluid. This is crucial for transmitting nerve impulses.
Tonicity and Concentration Effects: - Hypotonic: Water moves into the cell, causing it to swell and potentially burst or "pop." - Hypertonic: Water moves out of the cell, causing it to shrivel. - Isotonic: There is no net movement of water; the cell maintains equilibrium.

The Cell Cycle and Cellular Reproduction

The Cell Cycle: The longest phase is Interphase ( $G_1, S, G_2$ ).
Mitosis Phases: - Prophase: Chromosomes shorten and thicken. - Metaphase: Chromosomes "Meet in the Middle." - Anaphase: Chromosomes pull "Away" from each other. - Telophase: The nucleus splits into "Two" and moves to opposite ends.
Cytokinesis: The actual division of the cytoplasm.
Cancer and Abnormalities: - Cancer: A disease resulting from an unregulated cell cycle at genetic checkpoints, leading to uncontrollable growth and tumors. - Tumor Types: Benign tumors are referred to as cysts; malignant tumors are cancerous and can destroy healthy tissue. - Metastasis: The aggressive spread of cancer cells to other body parts. - Apoptosis: Regulated cell death consisting of a series of molecular steps. This can be blocked in cancer cells.

Modes of Reproduction

Asexual Reproduction: Offspring are produced by one parent and are genetically identical clones. This allows for rapid reproduction and ensures favorable traits are preserved without needing a partner. - Budding: Offspring grow out of the parent body (e.g., corals, sponges, yeast). - Fragmentation (Regeneration): The parent body breaks into pieces that each become offspring (e.g., worms, starfish). - Binary Fission: Prokaryotes split into two (e.g., bacteria, Amoeba). - Vegetative Propagation: Taking a plant cutting to produce a clone.
Sexual Reproduction: Two individuals produce offspring with combined genetic traits, increasing variation and survival odds in changing environments. - External Fertilization: Eggs are laid in wet environments and fertilized outside the female body (e.g., frogs, fish). Many offspring often perish before adulthood. - Internal Fertilization: Fertilization occurs within the female tract (e.g., mammals, birds, reptiles). This typically results in fewer offspring with higher levels of parental care.
Mixed Reproduction: Some organisms like plants, fungi, jellyfish, and aphids can utilize both types. Plants may use asexual reproduction to quickly cover land in favorable conditions and switch to sexual reproduction when environments change.

Bioenergetics: Photosynthesis and Respiration

Photosynthesis: - Definition: Autotrophs (plants) convert radiant electromagnetic energy from sunlight into chemical energy contained in glucose ( $C_6H_{12}O_6$ ). - Location: Occurs in chloroplasts, specifically in stacked membranes called thylakoids. - Pigments: Chlorophyll (green) absorbs red and blue wavelengths and reflects green. It converts light into chemical energy. - Steps: 1. Light-Dependent Reactions: Occur in thylakoid membranes. Electrons in pigments absorb light, converting ADP into ATP and $NADP^+$ into NADPH using the enzyme ATP synthase. 2. Light-Independent Reactions (Calvin Cycle): Occur in the stroma. Six molecules of $CO_2$ are combined using ATP and NADPH to build a stable 6-carbon sugar (glucose). - Factors: Affected by temperature, light intensity, and water availability.
Energy Comparison: A glucose molecule is more stable and contains over $90$ times the energy of an ATP molecule. ATP is used for immediate energy transfer, while glucose is used for long-term storage.
Cellular Respiration: - Definition: The process of releasing energy from food in the presence of oxygen (aerobic). - Location: Occurs in the cytoplasm and the mitochondria. - Energy Yield: Glycolysis, the Krebs cycle, and the electron transport chain produce approximately $36-38$ ATP molecules from one glucose molecule. Energy is released by breaking bonds between phosphate groups to reduce ATP to ADP.
Anaerobic Respiration (Fermentation): - Occurs only in the cytoplasm in the absence of oxygen. It is inefficient, producing only $2$ ATP per glucose molecule. - Alcoholic Fermentation: Used by yeast and some bacteria. Produces ethyl alcohol and $CO_2$ (used in baking and beverages). - Formula: $\text{Pyruvic Acid} + ext{NADH} \rightarrow ext{Alcohol} + CO_2 + NAD^+$ - Lactic Acid Fermentation: Occurs in the food industry (yogurt, cheese, sauerkraut). In humans, it occurs during high-intensity activity without enough oxygen, causing lactic acid buildup cleared by heavy breathing (oxygen debt). - Formula: $\text{Pyruvic Acid} + ext{NADH} \rightarrow ext{Lactic Acid} + NAD^+$

Meiosis and Chromosomal Abnormalities

Meiosis: The production of haploid gametes ( $n=23$ ). - Sperm Formation: One primary cell develops into four equal-sized haploid cells with tails for movement. - Egg Formation: One primary cell develops into one large nutrient-rich haploid cell and three small polar bodies that disintegrate. - Crossing Over: Genes are exchanged between chromosomes during meiosis to increase genetic variation.
Chromosomal Errors: - Nondisjunction: Failure of homologous pairs to separate during meiosis, leading to extra chromosomes (trisomy) or missing chromosomes (monosomy). - Trisomy 21 (Down Syndrome): Caused by a third copy of the $21^{st}$ chromosome. - Klinefelter Syndrome (XXY): Male genitals with female secondary characteristics (e.g., enlarged breasts). - Turner Syndrome (XO): Female external genitals, stunted growth, and lack of menstruation.
Karyotypes: Charts used to study chromosome pairs. Females are $XX$ and males are $XY$ .

Genetics and Patterns of Inheritance

Key Terms: - Gene: Inherited instructions; alleles are different versions of a gene. - Homozygous: Identical alleles ( $BB$ or $bb$ ). - Heterozygous: Different alleles ( $Bb$ ; also called hybrid). - Genotype: Genetic makeup (the letters). - Phenotype: Physical appearance (what is seen).
Mendel’s Laws: - Law of Dominance: The dominant allele prevents the expression of a recessive allele. - Law of Segregation: Gene pairs separate during gamete formation so each gamete has only one allele. - Law of Independent Assortment: Different gene pairs separate independently (Anaphase II of Meiosis).
Probabilities: - Heterozygous monohybrid cross ratio: $1:2:1$ . - Heterozygous dihybrid cross ratio: $9:3:3:1$ .
Complex Inheritance: - Incomplete Dominance: Alleles blend (e.g., Red + White = Pink carnations). - Codominance: Both alleles are expressed (e.g., Black + White speckled chickens). - Sex-Linkage: Traits carried on the $X$ chromosome (e.g., Hemophilia, Color blindness).

DNA Technology and Evolution

DNA Bases: Adenine pairs with Thymine, Cytosine pairs with Guanine. In RNA, Adenine pairs with Uracil.
Protein Synthesis: - Transcription: Information from DNA is copied to mRNA. - Translation: mRNA is decoded to build proteins. - Codon: Three bases on mRNA representing one amino acid. - Anticodon: Three bases on tRNA that pair with mRNA codons.
Evolutionary Evidence: Comparative anatomy (homologous structures), fossils, and biochemical similarities serve as evidence of common ancestry.
Cladograms: Diagrams showing evolutionary relationships; organisms sharing more characteristics are assumed to have diverged more recently.
Natural Selection: Darwin's theory where environments favor organisms best adapted to them. Drivers include competition (resource limitation), overproduction (too many offspring), and reproductive success.
Isolation Mechanisms: - Geographic: Physical barriers (volcanoes). - Temporal: Different reproductive cycles. - Behavioral: Different courtship rituals/songs.

Ecology and Environment

Ecological Hierarchy: Organism → Population → Community → Ecosystem → Biome → Biosphere.
Habitat vs. Niche: Habitat is where an organism lives; a niche is the organism's specific role in the ecosystem.
Nutrient Cycles: - Nitrogen Fixation: Converting $N_2$ gas into $NH_4^+$ for organic compounds. - Phosphorus: Found in cell membranes; moves between rocks, soil, and water without entering the atmosphere.
Symbiosis: - Mutualism: Both benefit. - Parasitism: One benefits, one is harmed. - Commensalism: One benefits, one is unaffected.
Population Growth: Limited by density-dependent factors (food, water) and density-independent factors (disasters).
Succession: - Primary: Starts with no soil (glaciers/volcanoes); starts with pioneer species like lichen. - Secondary: Occurs after a disturbance that leaves soil intact (forest fire/plowing).
Global Issues: Acid rain (caused by burning fossil fuels releasing sulfur/nitrogen oxides into the air) and Global Warming (increase in greenhouse gases).