Biology Placement Exam Review Flashcards

Scientific Methodology

  • Science as a Process: Science is characterized by systematic inquiry through defined logical steps.

  • Steps of the Scientific Method:

    • Hypothesis: Formulating a testable explanation for a phenomenon.

    • Testing the Hypothesis: Conducting experiments to evaluate the validity of the hypothesis.

    • Variables: Identifying factors that can change within an experiment.

    • Data: Collecting and analyzing the results obtained from testing.

    • Supporting/Falsifying: Assessing whether the gathered data aligns with the original hypothesis or proves it incorrect.

Principles of Chemistry and Matter

  • Matter: Defined as anything that occupies space and has mass.

  • Elements: Pure substances consisting of only one type of atom.

  • Atoms: The fundamental units of matter.

    • Atomic Number: Represents the number of protons in an atom.

    • Atomic Mass: The total mass of an atom, primarily the sum of protons and neutrons.

    • Subatomic Particles: The constituent parts of an atom, including protons, neutrons, and electrons.

  • Chemical Bonds:

    • Ionic Salts: Formed through the transfer of electrons between atoms, resulting in electrostatic attraction between ions.

    • Covalent Molecules: Formed when atoms share pairs of electrons.

    • Hydrogen Bonds: Weak attractions between a hydrogen atom and an electronegative atom in different molecules or parts of a molecule.

Chemical Properties and Biological Roles of Water

  • Polarity of the Molecule: Water (H2OH_2O) is a polar molecule due to the uneven distribution of electrons.

  • Electro-negativity: Oxygen possesses a high electronegativity, pulling electrons towards it and creating partial charges.

  • Hydrogen Bonds (H bonds) Between Molecules: These bonds form between the partial positive charge of one water molecule and the partial negative charge of another.

  • Water as a Good Polar Solvent: Its polarity allows it to dissolve various substances.

    • Ionic Compounds: Easily dissociated and dissolved by water.

    • Electrolytes: Substances that conduct electricity when dissolved in water.

    • Polar Compounds: Most biochemicals are polar and therefore soluble in water.

  • Adhesion and Cohesion:

    • Cohesion refers to water molecules sticking to each other.

    • Adhesion refers to water molecules sticking to other surfaces.

    • Surface Tension: A result of cohesive forces that makes the surface of water resist external force.

  • Thermal Properties:

    • High Heat of Vaporization: Significant energy is required to transform water from liquid to gas.

    • High Heat of Fusion: Significant energy removal is required to turn water into ice.

    • High Specific Heat: Water can absorb or release large amounts of heat with minimal change in its own temperature.

pH, Buffers, and Acid-Base Chemistry

  • pH: A measure of the concentration of hydrogen ions (H+H^+) in a solution.

  • Acids: Substances that increase the H+H^+ concentration of a solution.

  • Bases: Substances that decrease the H+H^+ concentration or increase the concentration of hydroxide ions.

  • Buffers: Substances that minimize changes in the concentrations of H+H^+ and OH−OH^- in a solution, maintaining stable pH levels.

Carbon Foundations and Functional Groups

  • Carbon Compounds: Organic chemistry is the study of carbon-based molecules.

  • Hydrocarbons: Molecules consisting entirely of carbon and hydrogen.

  • Functional Groups: Specific groups of atoms that confer distinct chemical properties to molecules:

    • Hydroxyl: −OH-OH

    • Carboxyl: −COOH-COOH

    • Amino: −NH2-NH_2

    • Sulfhydryl: −SH-SH

    • Phosphate: −PO42−-PO_4^{2-}

    • Carbonyl: −C=O-C=O

Biological Macromolecules: Structure and Synthesis

  • Polymerization: The process of combining small units called monomers to form large chains called polymers.

    • Dehydration Synthesis (Condensation): The removal of a water molecule to join two monomers together.

    • Hydrolysis: The addition of a water molecule to break the bonds within a polymer.

  • Carbohydrates:

    • Functional Groups Involved: Hydroxyl and carboxyl.

    • Structure: Monosaccharides (single sugars) are joined to form polysaccharides (complex carbohydrates).

    • Examples: Glucose (monosaccharide) is used to build starch, glycogen, and cellulose.

    • Functions: Serve as primary energy sources and structural components within the cell.

  • Lipids:

    • Insolubility: Lipids are not water-soluble.

    • Composition: They consist of a high proportion of hydrocarbon chains with very little oxygen, making them largely nonpolar.

    • Fatty Acids: Chains of hydrocarbons; can be saturated (no double bonds) or unsaturated (containing one or more double bonds).

    • Triglycerides: Composed of glycerol and three fatty acids.

    • Phosphoglycerides: Major components of cell membranes.

    • Steroids: Lipids characterized by a carbon skeleton consisting of four fused rings.

Protein Complexity and Enzymatic Function

  • Proteins (Polypeptides):

    • Building Blocks: Amino acids.

    • Bonding: Amino acids are linked by peptide bonds.

    • Levels of Structure:

      • Primary Structure: The unique sequence of amino acids.

      • Secondary Structure: Coils and folds (alpha helices and beta-pleated sheets).

      • Tertiary Structure: The overall three-dimensional shape of a polypeptide.

      • Quaternary Structure: The structure resulting from the aggregation of two or more polypeptide subunits.

    • Functions: Serve as enzymes (biocatalysts), structural supports, and agents of motility.

  • Enzymes:

    • Function: Proteins that act as catalysts to lower the activation energy of chemical reactions.

    • Active Site: The specific region where the substrate binds.

    • Allosteric Site: A site on an enzyme other than the active site where a molecule can bind and regulate activity.

    • Inhibition:

      • Competitive Inhibitor: Competes with substrate for the active site.

      • Noncompetitive Inhibitor: Binds to another part of the enzyme, changing its shape.

      • Feedback Inhibition: The end product of a metabolic pathway shuts down the pathway.

Nucleic Acids and Bioenergetics

  • Nucleic Acids:

    • Nucleotide Structure: Composed of a pentose sugar (ribose or deoxyribose), a phosphate group, and a nitrogenous base.

    • Polymers: Nucleotides link to form nucleic acids.

    • Types: DNA (deoxyribonucleic acid), RNA (ribonucleic acid), ATP (adenosine triphosphate), $NAD^+$, and $FAD$.

  • Metabolic Reactions:

    • Activation Energy: The initial energy needed to start a chemical reaction.

    • Endergonic Reactions: Reactions that absorb free energy from the surroundings.

    • Exergonic Reactions: Reactions that proceed with a net release of free energy.

Cellular Structure and Organelle Function

  • Cell Classification:

    • Prokaryotic Cells: Lack a membrane-bound nucleus and organelles.

    • Eukaryotic Cells: Contain membrane-bound organelles and a nucleus.

  • Nucleus: The control center of the cell.

    • Nuclear Envelope: Double membrane surrounding the nucleus.

    • Nucleolus: Site of ribosome synthesis.

    • Genetic Material: Organized as chromosomes, chromatin, and DNA.

  • Ribosomes: Sites of protein synthesis; can be free (floating in cytoplasm) or bound (attached to the Endoplasmic Reticulum).

  • Endoplasmic Reticulum (ER):

    • Rough ER: Studded with ribosomes; involved in protein synthesis and membrane production.

    • Smooth ER: Lacks ribosomes; involved in lipid synthesis and detoxification.

  • Golgi Apparatus: Functions in modification, sorting, and packaging of proteins and lipids for secretion or delivery to other organelles.

  • Lysosomes: Contain digestive enzymes for breaking down waste and macromolecules.

  • Vacuoles: Membrane-bound sacs used for storage.

  • Mitochondria: The site of cellular respiration.

    • Cristae: Folds of the inner membrane.

    • Matrix: The innermost compartment of the mitochondrion.

The Cytoskeleton and Cellular Motility

  • Microtubules: Thick hollow tubes.

    • Centrioles / Basal Bodies: Involved in organizing microtubule assembly.

    • Flagella / Cilia: Microtubule-based projections for cell movement.

    • Mitotic Spindle: Distributes chromosomes during cell division.

  • Microfilaments: Composed of actin.

    • Function: Involved in cell shape and movement; forms the cleavage furrow in animal cells during division.

  • Intermediate Filaments: Provide mechanical strength and structural support to cells.

Membrane Dynamics and Cellular Transport

  • Membrane Structure: Described as a phospholipid bilayer with embedded proteins.

    • Phospholipids: Feature nonpolar (hydrophobic) tails and polar (hydrophilic) heads.

    • Proteins: Can be integral (spanning the membrane) or peripheral (attached to the surface).

  • Cell Communications: Involves transmembrane channels and signaling.

  • Mechanisms of Transport:

    • Diffusion: Movement of molecules from high concentration to low concentration (down a gradient).

      • Rate Increase: Higher temperature, smaller molecule size, or higher concentration gradient increases the rate.

    • Osmosis: The diffusion of water across a selectively permeable membrane.

      • Hypertonic: Higher solute concentration outside; water leaves the cell.

      • Hypotonic: Lower solute concentration outside; water enters the cell.

      • Isotonic: Equal solute concentration; no net water movement.

    • Facilitated Diffusion: Uses membrane channel or carrier proteins to move polar or charged molecules down their gradient without energy.

    • Active Transport: Moves polar or charged molecules against their concentration gradient; requires energy (ATP) and membrane channels/carrier proteins.

    • Exocytosis: Transport of materials out of the cell via vesicles.

    • Endocytosis: Transport of materials into the cell via vesicles.

Cellular Bioenergetics and Respiration

  • Metabolism Phases:

    • Anabolism: Building complex molecules from simpler ones (requires energy).

    • Catabolism: Breaking down complex molecules to release energy.

  • Energy Currency: ATP (Adenosine Triphosphate).

  • Redox Reactions: Involves oxidation (loss of electrons) and reduction (gain of electrons).

  • Cellular Respiration Pathways:

    • Complete Oxidation of Glucose: The full extraction of energy from glucose molecules.

    • Coenzymes: $NAD^+$, $FAD$, and Coenzyme A act as electron carriers.

    • Glycolysis: Occurs in the cytoplasm; the initial breakdown of glucose.

    • Intermediate Step: Transition between glycolysis and the Krebs cycle.

    • Krebs Cycle: Occurs in the mitochondrion; metabolic cycle that completes the breakdown of glucose.

    • Electron Transport System (ETS): Occurs in the mitochondrion; generates the majority of ATP.

  • Respiration Types:

    • Aerobic Respiration: Oxygen serves as the final electron acceptor.

    • Anaerobic Respiration: Occurs in bacteria; utilizes incomplete oxidation of glucose.

    • Fermentation: An organic molecule serves as the final electron acceptor.

The Cell Cycle and Mitosis

  • The Cell Cycle: Consists of Interphase and M-phase.

    • Interphase: $G_1 ightarrow S ightarrow G_2$. In the $S$ phase, DNA is replicated.

    • Mitotic Phases: Prophase $ ightarrow$ Metaphase $ ightarrow$ Anaphase $ ightarrow$ Telophase.

    • Cytokinesis: The division of the cytoplasm.

  • Outcome: One diploid cell divides to produce two identical diploid cells.

  • Key Terms: Chromosome, chromatid, centromere, centriole, kinetochore, spindle.

Meiosis and Sexual Reproduction

  • Objective: Reduction of chromosome number from diploid ($2n$) to four haploid ($n$) nuclei.

  • Zygote: Formed when a haploid sperm and haploid egg fuse during fertilization.

  • Cycle: $G_1 ightarrow S ightarrow G_2$, followed by two rounds of division.

  • Meiosis I:

    • Prophase I: Includes synapsis (pairing of homologous chromosomes), tetrad formation, and crossing over (exchange of genetic material).

    • Metaphase I: Homologous pairs align at the equator.

    • Anaphase I: Homologous chromosomes separate.

    • Telophase I: Nuclear membranes may reform.

  • Interkinesis: A resting period between Meiosis I and Meiosis II; no DNA replication occurs.

  • Meiosis II: Phases include Prophase II, Metaphase II, Anaphase II, and Telophase II (followed by Cytokinesis), where sister chromatids finally separate.

  • Nondisjunction: The failure of chromosomes to separate properly during meiosis.

Principles of Genetics and Inheritance

  • Basic Terminology:

    • Dominant vs. Recessive: Patterns of trait expression.

    • Genotype: The genetic makeup (alleles).

    • Phenotype: The physical appearance or observable traits.

    • Gene: The unit of heredity.

    • Allele: Alternative versions of a gene.

    • Homozygous: Having two identical alleles ($AA$ or $aa$).

    • Heterozygous: Having two different alleles ($Aa$).

  • Genetic Crosses:

    • Monohybrid Cross: A cross focusing on a single trait.

    • Dihybrid Cross: A cross focusing on two different traits.

  • Gene Interactions:

    • Pleiotropy: A single gene affects multiple phenotypic traits.

    • Polyallelic: Genes that have more than two possible alleles (e.g., blood types).

    • Polygenic: Traits controlled by the additive effect of two or more genes.

    • Incomplete Dominance: The phenotype is an intermediate mix of the parents.

    • Codominance: Both alleles are expressed equally in the phenotype.

  • Chromosomal Inheritance:

    • Linked Genes: Genes located close together on the same chromosome that tend to be inherited together.

    • Sex Linked: Genes located on sex chromosomes.

    • Crossing Over: Occurs between linked genes, providing genetic variation.

    • Gene Mapping: Determining the relative positions of genes on a chromosome.

Molecular Genetics and Gene Expression

  • DNA Structure and Function:

    • Function: DNA is defined as the genetic material where genes are stored.

    • Replication Process: Semi-conservative copying of DNA.

    • Enzymes of Replication:

      • Helicase: Unwinds the DNA double helix.

      • Primase: Lays down an RNA primer to begin replication.

      • DNA Polymerase: Synthesizes new DNA strands by adding nucleotides.

      • Ligase: Joins DNA fragments (Okazaki fragments) together.

    • Strand Synthesis: Leading strand (continuous) and lagging strand (discontinuous).

  • Gene to Protein (The Central Dogma):

    • Transcription: RNA polymerase synthesizes mRNA from a DNA template.

    • RNA Processing (Eukaryotes):

      • Addition of a $5'$ cap and a poly-A tail.

      • Spliceosomes (snRNPs) perform the excision of introns (non-coding regions) and splicing of exons (coding regions).

    • Translation: The process where ribosomes read mRNA and use tRNA to assemble amino acids into a polypeptide chain.

  • Mutation: Changes in the DNA sequence.

  • Regulation of Transcription in Prokaryotes:

    • Operons: Functional units of genomic DNA containing a cluster of genes under the control of a single promoter.

    • Components: Operator (the switch), promoter (binding site for RNA polymerase), and the structural genes.