bio study guide

Chapter 2: Basic Chemistry

Properties of Atoms

• Atom: The fundamental unit of matter, consisting of protons, neutrons, and electrons.

  • Protons: Positively charged particles located in the nucleus.

  • Neutrons: Neutral particles also found in the nucleus.

  • Electrons: Negatively charged particles that orbit the nucleus in electron shells.

Electron Shells & Bonding

• Electron Shells:

  • First Shell: Max of 2 electrons.

  • Second & Third Shells: Max of 8 electrons each.

• Valence Electrons: Outer shell electrons that determine the atom's bonding capacity.

• Bonding by Atoms:

  • Hydrogen: Forms 1 bond.

  • Oxygen: Forms 2 bonds.

  • Nitrogen: Forms 3 bonds.

  • Carbon: Forms 4 bonds.

Chemical Bonds

1. Covalent Bonds: Sharing of electrons.

   • Example: Water (H₂O).

2. Ionic Bonds: Transfer of electrons resulting in the formation of ions.

   • Example: Table salt (NaCl).

3. Hydrogen Bonds: Weak bonds between polar molecules.

   • Example: Bonds between water molecules.

Electronegativity and Polarity

• Electronegativity: The ability of an atom to attract electrons in a compound.

• Polarity: Occurs due to unequal sharing of electrons in covalent bonds.

  • Example: Water (H₂O) is polar because oxygen has a higher electronegativity.

Unique Features of Carbon

• Capable of forming 4 covalent bonds.

• Forms the basis for organic molecules.

• Can create chains, rings, and complex structural formations.

Solutions, Solvent, and Solute

• Solution: Homogeneous mixture.

• Solvent: The substance that dissolves another (e.g., water).

• Solute: The substance being dissolved (e.g., salt).

Unique Properties of Water

• Cohesion: Water molecules attract each other.

• Adhesion: Water molecules interact with different surfaces.

• High Specific Heat: Water resists changes in temperature.

• Universal Solvent: It can dissolve a variety of substances.

Chapter 3: Organic Molecules

Four Classes of Organic Molecules

1. Carbohydrates: Serve as energy storage (e.g., glucose, starch).

2. Lipids: Energy storage and insulation (e.g., fats, oils).

3. Proteins: Function as enzymes and structural components (e.g., hemoglobin, keratin).

4. Nucleic Acids: Store and transmit genetic information (e.g., DNA, RNA).

Monomers and Polymers

• Monomers: The building blocks (e.g., amino acids).

• Polymers: Large chains made of monomers (e.g., proteins, polysaccharides).

Dehydration Reactions and Hydrolysis

• Dehydration Reaction: Joins monomers by removing water.

• Hydrolysis: Breaks polymers apart by adding water.

Saturated vs. Unsaturated Fats

• Saturated Fats: Do not contain double bonds; solid at room temperature.

• Unsaturated Fats: Contain one or more double bonds; liquid at room temperature.

Hydrophilic vs. Hydrophobic

• Hydrophilic: Substances that dissolve in water.

• Hydrophobic: Substances that do not dissolve in water.

Chapter 4: Cells

Cell Organelles and Categories

1. Genetic Control: Nucleus, ribosomes.

2. Energy Processing: Mitochondria, chloroplasts.

3. Endomembrane System: Endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles.

4. Support/Movement/Communication: Cytoskeleton, plasma membrane.

Prokaryotic vs. Eukaryotic Cells

• Similarities: Both have DNA, cell membrane, cytoplasm, ribosomes.

• Differences:

  • Prokaryotes: Lack a true nucleus, smaller with no membrane-bound organelles.

  • Eukaryotes: Possess a nucleus and membrane-bound organelles.

Animal vs. Plant Cells

• Similarities: Both contain a nucleus, mitochondria, endoplasmic reticulum (ER), Golgi apparatus, cytoplasm.

• Differences:

  • Plant Cells: Have cell walls, chloroplasts, and large vacuoles.

  • Animal Cells: Contain lysosomes and centrioles.

Chapter 5: Energy and Transport

Types of Energy

• Kinetic Energy: Energy of motion.

• Potential Energy: Stored energy.

Exergonic vs. Endergonic Reactions

• Exergonic: Release energy (e.g., cellular respiration).

• Endergonic: Require energy input (e.g., photosynthesis).

ATP (Adenosine Triphosphate)

• Structure: Composed of adenosine bonded to three phosphate groups.

• Function: Serves as the energy currency of cells.

Diffusion and Osmosis

• Diffusion: Movement of molecules from high to low concentration.

• Osmosis: Specific diffusion of water across a semipermeable membrane.

Transport Mechanisms

• Passive Transport: Does not require energy, moves down the concentration gradient.

  • Example: Diffusion.

• Active Transport: Requires energy to move substances against the concentration gradient.

• Facilitated Diffusion: Passive transport through protein channels.

Membrane Structure

• Semipermeable: Membranes selectively allow substances to pass through.

• Fluid Mosaic Model: Describes the structure as a phospholipid bilayer with embedded proteins.

Chapter 6: Cellular Respiration

Basic Equation

Glucose + O₂ → CO₂ + H₂O + Energy (ATP)

Stages of Cellular Respiration

1. Glycolysis: Breakdown of glucose into pyruvate (occurs in the cytoplasm).

   • Reactants: Glucose.

   • Products: 2 pyruvate, 2 ATP, 2 NADH.

2. Citric Acid Cycle: Completes glucose breakdown (occurs in mitochondria).

   • Reactants: Acetyl-CoA.

   • Products: CO₂, NADH, FADH₂, ATP.

3. Electron Transport Chain: Generates the majority of ATP (occurs in mitochondria).

   • Reactants: NADH, FADH₂, O₂.

   • Products: H₂O, ATP.

Fermentation

• An anaerobic process that produces lactic acid or alcohol.

Chapter 7: Photosynthesis

Basic Equation

CO₂ + H₂O + Light → Glucose + O₂

Stages of Photosynthesis

1. Light Reactions: Convert solar energy to chemical energy (ATP, NADPH).

   • Reactants: Light, H₂O.

   • Products: O₂, ATP, NADPH.

2. Calvin Cycle: Utilizes ATP and NADPH to produce glucose.

   • Reactants: CO₂, ATP, NADPH.

   • Products: Glucose.

Chloroplast Structures

• Thylakoids: Site of chlorophyll and light reactions.

• Grana: Stacks of thylakoids.

• Stroma: Fluid-filled area where the Calvin Cycle occurs.

Chapter 8: Reproduction

Asexual vs. Sexual Reproduction

• Asexual Reproduction:

  • Involves one parent.

  • Offspring are genetically identical (clones).

  • Example: Binary fission, budding.

• Sexual Reproduction:

  • Involves two parents.

  • Offspring exhibit genetic diversity.

Binary Fission

• A type of asexual reproduction occurring in prokaryotes involving:

  1. DNA replication.

  2. Cell elongation and separation of DNA.

  3. Cell division into two identical cells.

Genes

• Sequences of DNA that code for proteins, located on chromosomes.

Haploid vs. Diploid

• Haploid (n): One set of chromosomes (e.g., gametes).

• Diploid (2n): Two sets of chromosomes (e.g., somatic cells).

Body Cells vs. Gametes

• Somatic Cells:

  • Diploid (2n).

  • Comprise body tissues.

  • Divide via mitosis.

• Gametes:

  • Haploid (n).

  • Participate in sexual reproduction.

  • Produced by meiosis.

Chromosomes and Cell Division

Relationship Between Chromosomes, DNA, Genes, and Chromatin

• DNA: Carries genetic information.

• Gene: Segment of DNA encoding specific traits.

• Chromatin: Uncoiled form of DNA in the nucleus.

• Chromosome: Condensed chromatin visible during cell division.

Sex Chromosomes

• Determine an organism's sex (e.g., X and Y in humans).

• Females: XX, Males: XY.

Homologous Chromosomes

• Pairs of chromosomes, one from each parent with the same genes at corresponding loci but potentially different alleles.

Mitosis

• Somatic cell division for growth, producing two identical diploid daughter cells.

Phases of Mitosis

1. Prophase: Chromatin condenses; spindle apparatus forms.

2. Metaphase: Chromosomes align at cell's equatorial plane.

3. Anaphase: Sister chromatids are pulled apart.

4. Telophase: Chromosomes decondense; nuclei reform.

Homologous Chromosomes vs. Sister Chromatids

• Homologous Chromosomes: One from each parent.

• Sister Chromatids: Identical copies from DNA replication, joined at a centromere.

Chapter 9: Mendelian Genetics

Genotypes vs. Phenotypes

• Genotype: Genetic makeup (e.g., BB, Bb, bb).

• Phenotype: Observable traits (e.g., color of eyes).

Mendel and His Experiments

• Conducted research on pea plants to study inheritance of traits with clear forms (tall vs. short).

Generations in Mendelian Genetics

• P Generation: Parent plants.

• F1 Generation: Offspring from the P generation (mostly heterozygous).

• F2 Generation: Offspring from F1 (3:1 phenotypic ratio).

Alleles and Chromosomes

• Alleles: Different forms of a gene located at the same locus on homologous chromosomes.

• Homozygous: Two identical alleles (AA or aa).

• Heterozygous: Two different alleles (Aa).

• Dominant vs. Recessive:

  • Dominant: Masks the effect of a recessive allele.

  • Recessive: Only expressed in homozygous condition.

Mendel’s Four Hypotheses

1. Genes exist in different forms (alleles).

2. Organisms inherit two alleles per gene, one from each parent.

3. Dominant alleles mask recessive alleles.

4. Alleles segregate during gamete formation (Law of Segregation).

Punnett Square

• A predictive tool for determining the genotype and phenotype ratios of offspring.

Laws of Inheritance

• Law of Segregation: Aleles separate during meiosis, leading to gametes that carry one allele per gene.

• Law of Independent Assortment: Non-linked genes assort independently during meiosis.

Chapter 10: DNA and RNA

Nucleic Acids, Nucleotides, and Structure

• Nucleotides: Monomers of nucleic acids, composed of a sugar, phosphate group, and nitrogenous base.

• Polymers: DNA and RNA made up of chains of nucleotides.

• Key Differences:

  • DNA: Double-stranded, deoxyribose, bases A, T, C, G.

  • RNA: Single-stranded, ribose, bases A, U, C, G.

DNA Structure

• Double Helix with a sugar-phosphate backbone and paired bases (A-T, C-G) through hydrogen bonds.

Base Pairing Rules

• A with T and C with G in DNA.

• A with U in RNA.

Semiconservative DNA Replication

• DNA strands separate and serve as templates for new strands.

Transcription and Translation

• Transcription: Process of converting DNA to RNA in the nucleus.

• Translation: Process of translating RNA into proteins at ribosomes.

Relationship Between DNA, RNA, and Proteins

• Sequence: DNA → mRNA → Amino Acids → Polypeptide Chains → Proteins.

Replication Direction

• DNA replication occurs in the 5’ to 3’ direction.

Chapter 12: Cancer and Gene Expression

Normal vs. Cancer Cell Cycles

• Normal Cell Cycle: Controlled division.

• Cancer Cell Cycle: Uncontrolled growth and division.

Growth Factors

• Proteins that regulate the cell division cycle.

Tumors

• Benign Tumors: Non-invasive and localized.

• Malignant Tumors: Invasive and capable of metastasis.

Oncogenes and Proto-Oncogenes

• Proto-Oncogenes: Normal genes that regulate cell growth.

• Oncogenes: Mutated genes leading to uncontrolled cell growth associated with cancer.

Gene Expression Control

• Gene expression is regulated by the action of transcription factors and modifications to histones.

Eukaryotic Differentiation

• Specialization based on gene expression depending on cell types.

Chapter 13: Evolution by Natural Selection

Definition of Evolution by Natural Selection

• Evolution: Refers to the change in allele frequencies in populations over time.

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

Adaptations

• Features that enhance survival and reproduction in a specific environment.

Homologous Structures

• Similar anatomical features arising from a common ancestor (e.g., vertebrate limb structure).

Key Points on Evolution by Natural Selection

1. Populations evolve, not individual organisms.

2. Natural selection acts on existing variation.

3. Traits influencing evolution must be heritable.

Significance of Allele Frequency Changes

• A population is considered evolving when there are observable changes in allele frequencies over generations.

Hardy-Weinberg and Population Genetics

• Hardy-Weinberg Equation: p² + 2pq + q² = 1

  • p: Frequency of dominant alleles.

  • q: Frequency of recessive alleles.

  • Conditions for equilibrium: no mutations, migration, selection, genetic drift, or mate preferences.

Microevolution

• Refers to minor evolutionary changes within a population.

Gene Pool

• Total collection of alleles within a population.

Chapter 14: Genetic Drift and Gene Flow

Genetic Drift

• Random changes in allele frequencies, more pronounced in small populations.

  • Examples: Bottleneck effect, founder effect.

Gene Flow

• Movement of alleles between populations (e.g., via migration).

Comparison of Genetic Processes

• Genetic Drift: Random alterations, reduces variation.

• Gene Flow: Introduces new alleles and increases diversity.

• Natural Selection: Adaptive, non-random process.

Types of Selection

• Stabilizing Selection: Favors average or intermediate phenotypes.

• Directional Selection: Favors one extreme phenotype.

• Disruptive Selection: Favors extreme phenotypes at both ends.

Pesticide Resistance

• Evolves through natural selection when resistant individuals survive and reproduce after pesticide application.

Bottleneck and Founder Effects

• Bottleneck Effect: Large decrease in population size leads to reduced genetic diversity.

• Founder Effect: New population established by a small number of individuals leads to a different gene pool.

Chapter 15: Speciation and Reproductive Isolation

Species Definitions

• Biological Species Concept: Defined by ability to interbreed and produce fertile offspring.

• Ecological, Morphological, Phylogenetic Definitions: Based on roles in ecosystems, physical traits, and shared genetic characteristics.

Reproductive Isolation Mechanisms

• Prezygotic Barriers: Prevent fertilization (e.g., temporal, behavioral, mechanical).

• Postzygotic Barriers: Prevent viable or fertile offspring (e.g., hybrid sterility).

Mechanisms of Speciation

• Allopatric Speciation: Driven by geographical barriers.

• Sympatric Speciation: Occurs without geographic isolation (e.g., due to changes in chromosome number).

Sexual Selection Explained

• Sexual Selection: Variations in mating success based on traits that improve mating opportunities.

• Differences: Focuses on reproductive success rather than survival.

• Types:

  • Intersexual Selection: Mate choice (e.g., peacock tail).

  • Intrasexual Selection: Competition among same-sex individuals.

Effects of Resource Distribution on Sexual Selection

• Clumped resources reinforce sexual selection while dispersed resources weaken it.

Sexual Dimorphism

• Distinction in appearance between genders within a species.

Chapter 16: Phylogeny

What is a Phylogeny?

• Represents the evolutionary history and interrelations among species.

Key Terms in Phylogeny

• Clade: Group of organisms sharing a common ancestor.

• Monophyletic Group: Contains all descendants of a common ancestor.

• Shared Derived/Ancestral Characters: Unique traits to a clade vs. traits common to more than one group.

• Ingroup vs. Outgroup: Ingroup is the main focus; outgroup provides comparative context.

Building Phylogenetic Trees

• Identify shared traits to construct relationships, showing lineages and evolutionary paths.

Interpreting Phylogenetic Trees

• Note that tree orientations can vary, but relationships should reflect branching patterns.

Chapter 17: Ecology

Levels of Ecological Organization

1. Organism: Individual species member.

2. Population: Members of the same species inhabiting an area.

3. Community: Integrations of different populations.

4. Ecosystem: Community interactions with physical environments.

5. Biome: Clusters of similar ecosystems.

6. Biosphere: Aggregate of all ecosystems.

Species Interactions

• Competition: Resources are contested by different species.

• Mutualism: Both species benefit.

• Predation: One species consumes another.

• Parasitism: One benefits at the other's expense.

• Commensalism: One benefits, other is neither helped nor harmed.

Ecological Niche Definitions

• Fundamental Niche: The full spectrum of potential resources.

• Realized Niche: Actual resources exploited due to competition.

Adaptations of Predators and Prey

• Predatory Adaptations: Camouflage, speed, sharp features.

• Prey Defenses: Mimicry, warning coloration, escape behaviors.

Trophic Structure

1. Producers: Autotrophs such as plants.

2. Primary Consumers: Herbivores.

3. Secondary Consumers: Carnivores eating herbivores.

4. Tertiary Consumers: Top-level predators.

5. Decomposers: Organisms that recycle nutrients (e.g., fungi).

Food Chains and Food Webs

• Food Chain: Direct energy flow.

• Food Web: Interconnected energy dynamics.

• Changes in one species may impact the overall ecosystem.

Chapter 18: Prokaryotes and Protists

Prokaryote Structure and Function

• Cell Wall: Maintains cell shape and provides protection (peptidoglycan in bacteria).

• Flagella: Facilitate movement.

• Pili: Aid in attachment and genetic exchange.

Differences: Gram-Negative vs. Gram-Positive Bacteria

• Gram-Positive: Thick peptidoglycan layer.

• Gram-Negative: Thin peptidoglycan and an outer membrane, often more antibiotic-resistant.

Prokaryotic Energy/Carbon Acquisition Processes

1. Photoautotrophs: Use light and CO₂.

2. Chemoautotrophs: Use inorganic compounds and CO₂.

3. Heterotrophs: Utilize organic molecules for energy.

Archaeal Adaptations to Extreme Environments

• Halophiles: Thrive in high salt environments.

• Thermophiles: Function in high-temperature conditions.

• Methanogens: Produce methane in anaerobic settings.

Toxins in Bacteria

• Exotoxins: Secreted proteins responsible for specific diseases.

• Endotoxins: Released when bacteria die, can trigger immune responses.

Chapter 19: Plants and Fungi

Plant Evolutionary History

• Land plants evolved from green algae roughly 500 million years ago.

Key Adaptations for Terrestrial Life

1. Presence of a waxy cuticle to reduce water loss.

2. Stomata for efficient gas exchange.

3. Development of vascular tissue (xylem and phloem) for resource transport.

4. Seeds allowing reproduction without dependence on water.

Four Key Adaptations

1. Alternation of Generations: Life cycle includes both multicellular diploid and haploid stages.

2. Walled Spores in sporangia for protection.

3. Multicellular Gametangia for reproductive structure.

4. Apical Meristems: Growth regions in plants.

Function of Vascular Tissue

• Xylem: Transports water.

• Phloem: Distributes sugars.

Fungi Nutrition and Structure

• Absorption through Hyphae: Fungi take in nutrients through specialized structures.

• Hyphae: Filamentous structures of fungi.

• Mycelium: Network of hyphae, constitutes the main body.

Ecological Roles of Fungi

• Act as decomposers, mutualistic partners (mycorrhizae), and can be pathogenic.

Chapter 20: Invertebrates

Definition of Animal Characteristics

• Animals are multicellular, heterotrophic, and generally motile during their lifecycle without rigid cell walls.

Developmental Stages in Animals

• Blastula: Initial hollow spherical stage.

• Gastrula: Formation of cell layers that lead to tissue differentiation.

Types of Symmetry

• Radial Symmetry: Symmetry around a central axis (e.g., jellyfish).

• Bilateral Symmetry: Symmetry along a single plane (e.g., humans).

Types of Animal Development

• Protostomes: Mouth forms from the blastopore first.

• Deuterostomes: Anus forms first from the blastopore.

Metamorphosis in Animals

• Transition from larval stage to adult.

Chapter 21: Vertebrates

Derived Features of Chordates

1. Notochord: Flexible rod providing support.

2. Dorsal Hollow Nerve Cord: Forms the central nervous system.

3. Pharyngeal Slits: Openings in pharyngeal area, important for respiration and feeding.

4. Post-Anal Tail: Extends beyond the anus, varies in function.

Evolution of Jaws

• Evolved from modifications of the gill arches in early fishes.

Definition of Tetrapods

• Four-limbed vertebrates (e.g., amphibians, reptiles, mammals).

Endothermy vs. Exothermy in Vertebrates

• Endothermy: Internal regulation of temperature.

• Exothermy: Body temperature regulated by the external environment.

Mammalian Evolution

• Monotremes: Egg-laying mammals (e.g., platypus).

• Marsupials: Carry young in pouches (e.g., kangaroo).

• Placental Mammals: Young develop fully within the uterus.

Hominins

• Group including modern humans and direct ancestors, including interbreeding between Neanderthals and ancestors of modern humans.

Key Prokaryotic and Protist Species

• Rhizobium: Nitrogen-fixing bacteria aiding legumes.

• Cyanobacteria: Essential for oxygen production.

• Diatoms: Important primary producers in aquatic systems.

• Brown Algae: Major habitat-forming multicellular protists.

• Red Algae: Marine algae capable of photosynthesis at varying depths.

• Green Algae: Close relatives of land plants, such as Chlamydomonas and Spirogyra.

Plant and Fungi Relationships

• Mycorrhizae: Mutualistic associations aiding nutrient absorption.

• Bryophytes: Non-vascular plants reliant on water for reproduction.

• Seedless Vascular Plants: Include ferns, reproducing via spores.

• Gymnosperms: Non-flowering seed plants (e.g., pine trees).

• Angiosperms: Flowering plants with enclosed seeds (most diverse).

Animals and Transitional Fossils

• Birds: Descendants of theropod dinosaurs, exhibiting characteristics for flight.

• Tiktaalik: Transitional fossil bridging fish and tetrapods.

• Archaeopteryx: An early feathered dinosaur displaying features of both birds and reptiles.

• Hadrocodium: An early mammalian ancestor with advanced hearing and jaw adaptations.