Chapter 1-5 General Biology Review Flashcards
The Process and Method of Science
Definition of Science and Scientific Method:
The scientific method is a systematic method of research characterized by defined steps including experiments and careful observation.
A fundamental aspect of the scientific method is the testing of hypotheses through repeatable experiments.
A hypothesis is a suggested explanation for an event, which can be tested.
A theory is a tested and confirmed explanation for observations or natural phenomena.
Scientific endeavors represent a serious, ongoing, and organized effort to explore, measure, and understand the natural world using the scientific method.
Forms of Scientific Reasoning:
Inductive Reasoning: A form of logical thinking that uses related observations to arrive at a general conclusion. It involves analyzing large amounts of data to formulate inferred generalizations. Data collected can be qualitative or quantitative and may be supplemented with drawings, pictures, photos, or videos.
Deductive Reasoning: A form of logical thinking that begins with a general principle or specific question/problem and works outward to predict specific results or solutions.
Descriptive (or Discovery) Science: Usually inductive; aims to observe, explore, and discover biological phenomena.
Hypothesis-Based Science: Usually deductive; begins with a specific question or problem and a potential testable answer or solution.
Steps of the Scientific Method:
The scientific process typically begins with an observation (often identifying a problem to solve) that leads to a question.
Proposing a Hypothesis: Researchers propose one or several hypotheses to answer the question. A prediction is derived from a hypothesis and typically follows the format: "If… then…."
Testing a Hypothesis:
A valid hypothesis must be testable and falsifiable (meaning experimental results can disprove it).
Experiments are conducted to eliminate disproven hypotheses.
Variable: Any part of the experiment that can vary or change during the experiment.
Independent Variable (the cause): The specific factor that the researcher purposely changes or manipulates.
Dependent Variable (the effect): The outcome observed and measured in response to changes in the independent variable.
Controlled Variables (experimental conditions): All external conditions that could potentially affect the outcome and must remain constant across all experimental setups.
Control Group: The untreated comparison group that contains every feature of the experimental group except it does not receive the specific experimental manipulation.
Replication: Repeating the experiment using multiple subjects in each group rather than testing a single subject.
Sample Size: The total number of subjects included in an experiment. A larger sample size reduces the likelihood that an unusual individual outlier will skew the overall results.
Plant Growth Experiment Example:
Question: Does fertilizer make a plant grow taller?
Hypothesis: If a plant receives fertilizer, then it will grow taller than a plant that does not receive fertilizer.
Independent Variable: The fertilizer applied (one group receives fertilizer, the other does not).
Dependent Variable: Plant growth, measured precisely in centimeters.
Controlled Variables: Amount of water, sunlight exposure, soil composition, plant species, pot size, and ambient temperature.
Control Group: The plant or group of plants receiving no fertilizer.
Replication & Sample Size Example: Using fertilized plants and unfertilized plants yields a total sample size of plants.
Data Research (In Silico Research):
An emerging approach to testing hypotheses resulting from the exponential growth of biological databases.
Uses computer algorithms and statistical analysis of database data to provide computational data analysis and interpretation.
Creates significant career opportunities for specialists trained in both biology and computer science.
Basic Science vs. Applied Science:
Basic Science ("Pure" Science): Seeks to expand knowledge regardless of short-term application. Its primary goal is knowledge for knowledge's sake, though it often forms the groundwork for future practical applications.
Applied Science ("Technology"): Aims to use scientific knowledge to solve real-world problems (e.g., improving crop yields, curing diseases, or mitigating natural disasters).
Applied science cannot exist without the baseline foundation provided by basic science.
Human Genome Project Example: A fundamental bridge between basic and applied science. Researchers mapped and analyzed each human chromosome to determine the precise sequence of DNA subunits and exact gene locations. An individual's complete collection of genes is defined as their genome. Basic research on simple model organisms laid the groundwork for mapping the human genome, which is now utilized in applied research for early diagnoses and treatments of genetic diseases.
Reporting Scientific Work:
Scientists present findings in peer-reviewed manuscripts published in scientific journals.
Peer Review: A process where qualified expert colleagues judge whether research is original, significant, logical, and thorough prior to publication or grant funding.
Publishing allows external researchers to reproduce experiments under similar or different conditions to expand knowledge.
Scientific Writing Style: Must be succinct (brief, clear, and expressed in very few words without losing meaning) and accurate, avoiding being verbose (using or containing more words than necessary).
IMRaD Structure of Scientific Papers:
Abstract: Concise summary at the beginning of the paper.
Introduction: Broad background information, current knowledge, research rationale, and stated hypothesis/question.
Materials and Methods: Complete, thorough description of substances, tools, and protocols used to enable exact replication without unnecessary verbosity.
Results: Narrative description of findings formatted with tables and graphs, presenting raw findings without duplicate data representation or deeper interpretation.
Discussion: Interpretation of results, explanation of variable relationships, and contextualization within the broader scientific landscape.
Conclusion: Summary of experimental findings and their scientific significance, leading to new research questions.
Additional sections include Acknowledgments and References.
Scientific Ethics and Bioethics:
Scientists must prevent undue harm to humans, animals, and ecosystems.
Research and communication must remain free of bias while balancing financial, legal, safety, and replicability considerations.
Bioethics: Evaluates the ethical implications of emerging technologies, such as gene editing (e.g., creating organisms that might displace natural species, or creating "designer" humans). Ethicists weigh potential positive outcomes (disease prevention, enhanced therapies) against negative risks.
The field of bioethics arose historically following unethical research practices where biological subjects were harmed or denied basic human dignity.
Characteristics and Organization of Life
Eight Key Properties of Life:
Order: High structural organization consisting of one or more cells.
Sensitivity or Response to Stimuli: Movement or reaction to environmental factors (e.g., plants bending toward light [phototropism], climbing walls, or responding to touch).
Reproduction: Single-celled organisms duplicate their DNA and split equally during cell division. Multicellular organisms produce specialized reproductive cells (gametes: oocytes and sperm). Fertilization (fusion of oocyte and sperm) produces a new organism. Genes in DNA ensure offspring resemble their parents in species traits, size, and shape.
Adaptation: Evolutionary "fit" to an environment resulting from natural selection across lineages. Examples include heat-resistant Archaea surviving in boiling hot springs, and nectar-feeding moths whose tongue lengths match deep flower corollas.
Growth and Development: Cellular growth directed by specific genetic instruction sets.
Regulation / Homeostasis: Maintenance of a stable internal environment ("steady state") necessary for life functions. Examples include nutrient transport and blood flow. Body temperature regulation in hot environments occurs via perspiration in humans or panting in dogs.
Energy Processing: Utilization of energy sources for metabolic activities. Autotrophs capture solar energy and convert it to chemical energy; heterotrophs ingest chemical energy via food.
Evolution: Changes in hereditary material (mutations) over time, allowing populations to adapt to dynamic environments through natural selection.
Levels of Biological Organization:
Atom: Smallest and most fundamental unit of matter that retains elemental properties. Consists of a central nucleus surrounded by electrons.
Molecule: Chemical structure consisting of at least two atoms held together by chemical bonds.
Macromolecule: Large complex molecule formed by polymerization (combining smaller units called monomers). Example: Deoxyribonucleic acid (DNA).
Cell: Smallest fundamental unit of structure and function in living organisms. Viruses are non-living (acellular) because they are not composed of cells and must hijack a host cell's machinery to replicate.
Tissue: Group of similar cells working together to perform a specific function.
Organ: Collection of tissues performing a common physiological function (found in both animals and plants).
Organ System: Higher-level organization of functionally related organs working in tandem.
Organism: Individual living entity. Single-celled prokaryotes and single-celled eukaryotes are unicellular organisms (microorganisms).
Domain Classification & Phylogenetic Tree:
Life is categorized into three distinct domains introduced by Carl Woese:
Bacteria: Prokaryotic microbes lacking membrane-bound nuclei and organelles.
Archaea: Prokaryotic microbes lacking membrane-bound nuclei, distinct from bacteria, often inhabiting extreme environments.
Eukarya: Organisms possessing eukaryotic cells with membrane-bound nuclei and organelles; includes unicellular/multicellular protists, fungi, plants, and animals.

Branches of Biological Study:
Molecular Biology & Biochemistry: Investigation of biological processes at molecular and chemical levels, including DNA, RNA, protein interactions, and metabolic pathways.
Microbiology: Study of the structure and function of microscopic, single-celled organisms. Sub-disciplines include microbial physiology, microbial ecology, and microbial genetics.
Chemical Foundations of Life
Matter and Chemical Elements:
Body structure and cellular activities are chemical in nature.
Matter is composed of chemical elements—substances that cannot be broken down into simpler substances by ordinary chemical processes.
Chemical symbols use abbreviated letters (e.g., Calcium = \t\text{Ca} , Phosphorus = \t\text{P}).
Four primary elements make up of total human body weight: Oxygen (\t\text{O}), Carbon (\t\text{C}), Hydrogen (\t\text{H}), and Nitrogen (\t\text{N}).
Structure of Atoms:
Atom: The smallest unit of matter that retains the chemical properties of an element.
Subatomic Particles:
Protons (\t\text{p}^+): Positively charged particles located in the central nucleus.
Neutrons (\t\text{n}^0): Uncharged (neutral) particles located in the central nucleus.
Electrons (\t\text{e}^-): Negatively charged particles orbiting the nucleus in an electron cloud.
Chemical Bonds and Molecules:
Molecules: Formed when two or more atoms share or transfer electrons, defined by molecular formulas (e.g., Water = \t\text{H}_2\text{O}).
Ionic Bonds:
Formed between ions with opposite electrical charges.
Cation: A positively charged ion formed when an atom donates/loses electrons (e.g., \t\text{H}^+, \t\text{Na}^+).
Anion: A negatively charged ion formed when an atom accepts/gains electrons (e.g., \t\text{OH}^-, \t\text{Cl}^-).
Ionic compounds generally exist as solids but dissociate into free ions in aqueous solutions. These dissolved ions are called electrolytes (e.g., \t\text{Na}^+, \t\text{K}^+, \t\text{Ca}^{2+}), which are essential for nerve impulse conduction, muscle contractions, and fluid balance.
Example: Sodium Chloride (\t\text{NaCl}) formed by ionic attraction between \t\text{Na}^+ and \t\text{Cl}^-.
Covalent Bonds:
Strongest chemical bonds in biological systems.
Formed when atoms share one, two, or three pairs of valence electrons.
Intramolecular bonds (occur within a single molecule, such as the covalent bonds between hydrogen and oxygen atoms in a water molecule).
Hydrogen Bonds:
Weak intermolecular bonds formed between polar molecules or between different regions of large three-dimensional macromolecules.
Maintain 3D configurations of DNA strands and protein structures.
Responsible for water cohesion and high surface tension.
Physical and Chemical Properties of Water:
Polarity: Hydrogen and oxygen atoms form polar covalent bonds. Oxygen holds a slight negative charge and hydrogen holds a slight positive charge, creating polar water molecules that attract each other.
Three Physical States of Water:
Liquid: Hydrogen bonds continuously form, break, and reform.
Gas: Increased kinetic energy from heat breaks hydrogen bonds, allowing water molecules to escape into the atmosphere.
Solid: Reduced thermal energy allows a rigid crystalline lattice to form. Water molecules are spaced farther apart in ice than in liquid water, making ice less dense than liquid water.
High Specific Heat Capacity: Water absorbs or loses large quantities of heat energy before changing temperature, regulating thermal fluctuations.
High Heat of Vaporization: Water boils at (). Considerable energy is required to break hydrogen bonds to transition water from liquid to gas.
Solvent Properties: Water dissolves polar and ionic compounds.
Solutes: Substances dissolved in water.
Hydrophilic ("water-loving"): Polar or charged substances that readily dissolve in water.
Hydrophobic ("water-fearing"): Nonpolar substances (e.g., oils, fats) that do not interact with or dissolve in water.
Cohesion and Adhesion:
Cohesion: Water molecules sticking to each other at the liquid-gas interface, creating high surface tension.
Adhesion: Water molecules adhering to non-water surface charges inside narrow tubes, driving capillary action required for water transport from plant roots to leaves.
pH, Acids, Bases, and Buffers:
In aqueous solutions, inorganic substances dissociate into constituent ions:
Acids: Dissociate into \t\text{H}^+ ions and one or more anions.
Bases: Dissociate into \t\text{OH}^- ions and one or more cations.
Salts: Dissociate into cations and anions, neither of which is \t\text{H}^+ or \t\text{OH}^-.
The pH Scale: Measures hydrogen ion concentration ([\t\text{H}^+]) on a scale from to ().
Pure water undergoes slight auto-ionization: [\t\text{H}^+] = 1 \times 10^{-7}\,mol\,dm^{-3} and [\t\text{OH}^-] = 1 \times 10^{-7}\,mol\,dm^{-3}, defining a neutral \t\text{pH} = 7.
Acidic Solutions: [\t\text{H}^+] > [\t\text{OH}^-], corresponding to a \t\text{pH} < 7
Alkaline (Basic) Solutions: [\t\text{H}^+] < [\t\text{OH}^-], corresponding to a \t\text{pH} > 7
Buffers: Solutions that absorb excess \t\text{H}^+ or \t\text{OH}^- ions to maintain physiological pH within narrow life-sustaining ranges.
Biological Macromolecules
Organic vs. Inorganic Molecules:
Inorganic Molecules: Usually lack carbon and possess simple chemical structures (e.g., \t\text{H}_2\text{O}, \t\text{O}_2, \t\text{N}_2).
Organic Molecules: Always contain carbon (\t\text{C}) and hydrogen (\t\text{H}), and frequently oxygen (\t\text{O}) and nitrogen (\t\text{N}).
Biological Macromolecules: Large organic polymers constructed from monomer subunits linked by covalent bonds. Make up the bulk of cellular dry weight.
Class 1: Nucleic Acids (DNA and RNA):
Carry the genetic code of living organisms. Located in eukaryotic nuclei, mitochondria, chloroplasts, and prokaryotic cytoplasm.
Double-helix structure discovered in 1953.
Deoxyribonucleic Acid (DNA):
Double-stranded polymer containing a deoxyribose sugar backbone.
Formed from nucleotide monomers. Each nucleotide contains three components: a five-carbon sugar (deoxyribose), a nitrogenous base (Adenine [ ext{A}], Thymine [ ext{T}], Cytosine [ ext{C}], or Guanine [ ext{G}]), and a phosphate group.
Chargaff's Rules: Amounts of Adenine equal Thymine ([\t\text{A}] = [\t\text{T}]) and Cytosine equals Guanine ([\t\text{C}] = [\t\text{G}]).
Strands held together by hydrogen bonds between complementary nitrogenous base pairs.
Directionality & Antiparallel Structure: Carbon atoms in the sugar ring are numbered . One end has a free phosphate, and the opposite end has a free hydroxyl (\t\text{OH}) group. DNA strands run antiparallel ( opposite ).
Genes: Specific sequence of DNA nucleotides containing coding instructions for synthesizing proteins. Human DNA carries approximately genes.
Self-replicating molecule prior to cell division.


Ribonucleic Acid (RNA):
Single-stranded nucleic acid containing ribose sugar (possessing one additional oxygen atom compared to deoxyribose).
Bases: Adenine ( ext{A}), Uracil ( ext{U}) (replacing Thymine), Cytosine ( ext{C}), Guanine ( ext{G}).
Example DNA strand:
T G C A T C A G AComplementary mRNA transcribed strand:
A C G U A G U C UFunctional RNA categories:
Messenger RNA (mRNA): Intermediary transcript carrying genetic information out of the nucleus for protein synthesis (transcription).
Transfer RNA (tRNA): Adaptor molecule matching nucleic acid codons to specific amino acids during translation.
Ribosomal RNA (rRNA): Structural and catalytic component of ribosomes.
Class 2: Proteins:
Most abundant organic molecules in living systems ("prota" = of primary importance).
Constructed from standard amino acid monomers linked linearly by peptide bonds (covalent bonds).
Amino acid representations: Valine = V / Val, Aspartic Acid = D / Asp.
A chain of amino acids is called a polypeptide, synthesized on ribosomes.
Protein Functions:
Regulatory: Peptide hormones regulate physiological cellular processes.
Structural: Form cellular cytoskeleton, maintaining structural integrity.
Protective: Form antibodies that neutralize infectious pathogens.
Transport: Hemoglobin transports oxygen (\t\text{O}_2) throughout systemic circulation.
Contractile: Actin and myosin drive muscular contraction and cell shape changes.
Enzymatic: Catalyze bio-chemical metabolic reactions.
Four Levels of Protein Hierarchy:
Primary Structure: Unique linear sequence of amino acids in a polypeptide chain encoded by the gene (e.g., lysozyme contains amino acids; insulin consists of an A chain and a B chain joined by disulfide bonds).

2. **Secondary Structure:** Local folding patterns formed by hydrogen bonding along the polypeptide backbone, generating \t\text{\alpha}-helices and \t\text{\beta}-pleated sheets.

3. **Tertiary Structure:** Overall 3D spatial conformation of a single polypeptide chain caused by side-chain interactions (hydrogen bonds, ionic bonds, hydrophobic interactions, and covalent disulfide linkages).

4. **Quaternary Structure:** Association of multiple separate polypeptide subunits functioning as a single protein complex (e.g., Collagen composed of supercoiled helical chains; Hemoglobin composed of globular subunits).

Denaturation: Unfolding of native protein 3D conformation caused by extreme shifts in temperature or pH, leading to total loss of biological activity.
Class 3: Carbohydrates:
Composed of Carbon, Hydrogen, and Oxygen in an approximate ratio of ([\t\text{CH}_2\text{O}]).
Serve as short-term energy sources and structural components.
Categories:
Monosaccharides: Simple single-sugar units (e.g., Glucose used in cellular respiration to produce ATP; Ribose and Deoxyribose in nucleic acids).
Disaccharides: Two monosaccharides joined by a covalent glycosidic linkage formed via condensation.
Maltose = Glucose + Glucose.
Sucrose = Glucose + Fructose.
Lactose = Glucose + Galactose.

- **Polysaccharides:** Long branched or unbranched chains of hundreds to thousands of monosaccharides joined by glycosidic bonds.
- *Glycogen:* Extensively branched glucose storage polymer in animal liver and muscle cells.
- *Starch:* Energy storage polysaccharide in plants.
- *Cellulose:* Structural polysaccharide in plant cell walls.
- *Chitin:* Structural polysaccharide in arthropod exoskeletons and fungal cell walls.
- *Peptidoglycan:* Structural material of bacterial cell walls.
- *Glycoproteins & Glycolipids:* Carbohydrates bound to membrane proteins or lipids, driving cell recognition and adhesion.
Class 4: Lipids:
Non-polar, hydrophobic biological macromolecules composed primarily of hydrocarbons.
Non-polymeric (not built from repeating monomer subunits).
Functions: Long-term energy storage, thermal insulation, hormone precursors, and cellular membrane structure.
Four main types:
Phospholipids: Major constituent of biological membranes. Composed of a glycerol backbone linked to two fatty acid tails (hydrophobic) and a modified phosphate head group (hydrophilic).

2. **Fats and Oils**
3. **Waxes**
4. **Steroids**
Cell Structure, Function, and Transport
Cell Discovery and Cell Theory:
Robert Hooke (1665): Used a compound microscope to examine cork slices, coining the term "cells" (cellulae).
Anton van Leeuwenhoek: Observed living motile microscopic organisms ("animalcules").
Rudolf Virchow (19th century): Postulated "All cells come from cells."
Three Core Principles of Cell Theory:
All living organisms are composed of one or more cells.
Cells are the basic structural and functional units of life.
All cells arise exclusively from pre-existing cells.
Four Common Features of All Cells:
Plasma Membrane: Outer semi-permeable lipid barrier.
Cytoplasm: Internal fluid medium (cytosol) containing cellular components.
DNA: InherITED genetic material.
Ribosomes: Protein synthesis machinery.
Prokaryotic Cell Structure:
Lack membrane-bound nuclei or internal organelle compartments.
Chromosomal DNA is located in an un-enclosed cytoplasmic region called the nucleoid.
Possess cytoplasmic ribosomes, a plasma membrane, and usually a peptidoglycan cell wall.
May possess external capsules, flagella (for movement), or pili (for attachment/conjugation).
Include domains Bacteria and Archaea.

Eukaryotic Cell Structure:
Possess a membrane-bound nucleus and specialized sub-cellular organelles.
Found in animals, plants, fungi, and protists.



Comparative Organelle Summary Table:
Nucleus: Enclosed by double-membrane nuclear envelope; stores chromatin/chromosomes.
Nucleolus: Non-membrane-bound sub-region of nucleus synthesizing rRNA and assembling ribosome precursors.
Ribosomes: Non-membrane-bound complexes translating mRNA into proteins.
Rough Endoplasmic Reticulum (RER): Studded with bound ribosomes; processes and folds proteins.
Smooth Endoplasmic Reticulum (SER): Lacks ribosomes; synthesizes lipids, phospholipids, and steroid hormones.
Golgi Apparatus: Modifies, sorts, and packages macromolecules into secretory vesicles for transport.
Mitochondria: Powerhouse of the cell; produces cellular ATP via oxidative respiration. Contains independent circular DNA and ribosomes.
Lysosomes: Membrane-bound sacs containing digestive enzymes to hydrolyze macromolecules (present in animal cells).
Peroxisomes: Sites of metabolic oxidation-reduction reactions.
Cytoskeleton: Network of microfilaments, intermediate filaments, and microtubules maintaining cell shape and driving transport.
Centrioles / Centrosomes: Microtubule-organizing structures guiding chromosome segregation during cell division (animal cells).
Chloroplasts: Double-membrane photosynthetic organelles containing chlorophyll, independent DNA, and ribosomes (plant cells).
Central Vacuole: Large membrane-bound organelle storing water, regulating turgor pressure, and driving plant cell expansion.
Cell Wall: Rigid external protective layer composed of cellulose (plants) or peptidoglycan (bacteria).
Plasmodesmata: Channels through plant cell walls enabling cytoplasmic movement between neighboring cells.
Plasma Membrane and Transport Mechanisms:
Fluid Mosaic Model: Double phospholipid bilayer containing floating integral membrane proteins, peripheral proteins, cholesterol molecules (maintaining membrane fluidity), glycoproteins, and glycolipids.

Passive Transport: Movement of molecules without cellular energy consumption (ATP).
Simple Diffusion: Unassisted net movement of small, nonpolar, or lipid-soluble molecules down a concentration gradient (from high to low concentration) until dynamic equilibrium is established.
Facilitated Diffusion: Transmembrane transport of larger or charged molecules down their concentration gradient using carrier or channel proteins.
Factors Increasing Diffusion Rate: Higher temperature, steeper concentration gradient, larger surface area, and smaller particle mass.
Active Transport: Energy-dependent movement (requiring ATP) of solute molecules against their concentration gradient.
Osmosis in Plant and Animal Cells:
Osmosis: Net diffusion of free water molecules across a semi-permeable membrane from a region of lower solute concentration (higher free water) to higher solute concentration (lower free water).
Impact on Plant Cells:
Hypertonic Solution: Extracellular solute concentration is higher than cytosol. Water exits the cell, causing loss of turgor pressure and plasmolysis (detachment of the plasma membrane from the rigid cell wall).
Isotonic Solution: Extracellular solute concentration matches cytosol. No net water movement occurs; cell becomes flaccid.
Hypotonic Solution: Extracellular solute concentration is lower than cytosol. Water enters the cell until counterbalanced by mechanical cell wall resistance, creating high turgor pressure (turgid state). Preferred optimal condition for plants.

Impact on Animal Cells:
Hypertonic Solution: Water leaves the cell, causing cell shrinkage (crenation).
Isotonic Solution: No net water flow. Cells maintain optimal normal volume and dynamic shape (e.g., standard red blood cells). Optimal condition for animal cells.
Hypotonic Solution: Water floods into the cell, causing cellular swelling and membrane rupture (lysis).
