Cell Structure and Function

Cell Structure and Function

• Cells are the fundamental units of life.
• Cell theory states that all living organisms are composed of cells, the cell is the basic structural and functional unit of life, and all cells arise from pre-existing cells.
• Prokaryotic cells (bacteria and archaea) lack a nucleus and other membrane-bound organelles.
• Eukaryotic cells (protists, fungi, plants, and animals) have a nucleus and other membrane-bound organelles.
• Major organelles in eukaryotic cells include the nucleus (contains DNA), endoplasmic reticulum (protein and lipid synthesis), Golgi apparatus (modifies and packages proteins), mitochondria (cellular respiration), lysosomes (digestion and waste removal), and chloroplasts (photosynthesis, in plant cells).
• The plasma membrane is a selective barrier that regulates the passage of substances into and out of the cell, composed of a phospholipid bilayer with embedded proteins.
• Membrane proteins can function as transport channels, enzymes, receptors, or for cell recognition.
• Cell size is limited by surface area-to-volume ratio. As a cell grows, its volume increases faster than its surface area, affecting the efficiency of transport of materials in and out of the cell.
• Plant cells have a cell wall made of cellulose, providing support and structure.
• Animal cells lack a cell wall but have an extracellular matrix for support and cell communication.
• Cell junctions (tight junctions, desmosomes, gap junctions) allow cells to interact with each other, facilitating communication and organization in tissues.

Heredity and Evolution

• Heredity is the transmission of traits from parents to offspring.
• Genes are the units of heredity, composed of DNA, and are organized into chromosomes.
• Sexual reproduction involves the fusion of gametes (sperm and egg), resulting in offspring with a combination of traits from both parents.
• Asexual reproduction involves a single parent and produces offspring that are genetically identical to the parent.
• Gregor Mendel's laws of inheritance include the law of segregation (each individual has two alleles for each trait, and these alleles segregate during gamete formation) and the law of independent assortment (genes for different traits assort independently during gamete formation).
• Genetic variation is generated through mutation, sexual reproduction (crossing over, independent assortment, random fertilization).
• Evolution is the change in the genetic makeup of a population over time.
• Natural selection is the process by which individuals with traits that are better suited to their environment are more likely to survive and reproduce, leading to the adaptation of populations to their environment.
• Evidence for evolution includes the fossil record, comparative anatomy, comparative embryology, biogeography, and molecular biology.
• Mechanisms of evolution include natural selection, genetic drift (random changes in allele frequencies), gene flow (migration), and mutation.
• Speciation is the process by which new species arise, which can occur through reproductive isolation (prezygotic and postzygotic barriers).
• Phylogeny is the evolutionary history of a species or group of species, often represented as a phylogenetic tree.

Molecular Genetics

• DNA (deoxyribonucleic acid) is the molecule that carries genetic information.
• DNA structure: double helix made of nucleotides, each nucleotide containing a deoxyribose sugar, a phosphate group, and a nitrogenous base (adenine, guanine, cytosine, or thymine).
• DNA replication is the process by which DNA is copied. It is semi-conservative, meaning each new DNA molecule contains one original strand and one newly synthesized strand.
• RNA (ribonucleic acid) is involved in protein synthesis and gene regulation.
• RNA structure: single-stranded molecule made of nucleotides containing a ribose sugar, a phosphate group, and a nitrogenous base (adenine, guanine, cytosine, or uracil).
• Transcription is the process by which RNA is synthesized from a DNA template.
• Translation is the process by which proteins are synthesized from RNA (mRNA) using ribosomes and tRNA.
• The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA) is translated into proteins.
• Mutations are changes in the DNA sequence. They can be spontaneous or induced by mutagens and can have varying effects on the organism.
• Gene regulation controls the expression of genes. Mechanisms include transcriptional control, post-transcriptional control, translational control, and post-translational control.
• Biotechnology involves the use of biological systems to develop technologies and products, including genetic engineering, gene cloning, and DNA sequencing.
• Polymerase chain reaction (PCR) is a technique used to amplify specific DNA sequences.
• Gel electrophoresis is a technique used to separate DNA fragments based on size.

Organismal Biology

• Organ systems: groups of organs that work together to perform specific functions. Examples include the digestive system, respiratory system, circulatory system, nervous system, and endocrine system.
• Homeostasis: the maintenance of a stable internal environment.
• Feedback mechanisms (positive and negative) regulate physiological processes.
• Plant structure: roots, stems, leaves, vascular tissue (xylem and phloem).
• Plant reproduction: sexual (involving pollination and fertilization) and asexual (vegetative propagation).
• Animal behavior: innate behavior (instinct) and learned behavior (modified by experience).
• Animal communication: visual, auditory, chemical, and tactile signals.

Ecology

• Ecology is the study of the interactions between organisms and their environment.
• Population ecology: focuses on factors that affect population size, density, distribution, and demographics.
• Community ecology: focuses on interactions between different species in a community, such as competition, predation, mutualism, and commensalism.
• Ecosystem ecology: focuses on the flow of energy and nutrients through ecosystems.
• Biomes: major types of ecological communities characterized by distinctive climate conditions and plant/animal communities (e.g., forests, grasslands, deserts, aquatic biomes).
• Food chains and food webs: describe the transfer of energy and nutrients from one organism to another in an ecosystem.
• Trophic levels: the position an organism occupies in a food chain (e.g., producers, primary consumers, secondary consumers, decomposers).
• Nutrient cycles: the movement of essential elements (e.g., carbon, nitrogen, phosphorus) through ecosystems.
• Biodiversity: the variety of life in the world or in a particular habitat or ecosystem.
• Conservation biology: the study of the conservation of nature and of Earth's biodiversity.
• Human impacts on the environment: pollution, deforestation, climate change, habitat destruction, and overexploitation of resources.

Cell Communication

• Cell signaling is the process by which cells communicate with each other.
• Types of signaling: direct contact, paracrine signaling, endocrine signaling, synaptic signaling.
• Signal transduction pathways convert signals on a cell's surface into cellular responses.
• Components of signal transduction pathways: receptors, relay proteins, second messengers, transcription factors.
• G protein-coupled receptors (GPCRs): cell-surface receptors that work with the help of a G protein.
• Receptor tyrosine kinases (RTKs): cell-surface receptors that can trigger multiple signal transduction pathways at once.
• Ion channel receptors: ligand-gated ion channels that open or close in response to a specific signal molecule.
• Second messengers: small, nonprotein, water-soluble molecules or ions that relay signals to intracellular proteins (e.g., cAMP, Ca2+).
• Cellular responses to cell signaling: changes in gene expression, enzyme activity, or cell shape.

Cellular Energetics

• Energy is the capacity to do work.
• Thermodynamics: the study of energy transformations
• Laws of thermodynamics: energy cannot be created or destroyed (1st law), and every energy transfer increases the entropy (disorder) of the universe (2nd law).
• Metabolism: the totality of an organism's chemical reactions
• Catabolic pathways: break down complex molecules into simpler ones, releasing energy.
• Anabolic pathways: build complex molecules from simpler ones, consuming energy.
• ATP (adenosine triphosphate): the primary energy currency of cells.
• Enzymes: biological catalysts that speed up chemical reactions by lowering activation energy.
• Factors affecting enzyme activity: temperature, pH, substrate concentration, inhibitors.
• Cellular respiration: the process by which cells break down glucose to generate ATP.
• Stages of cellular respiration: glycolysis, pyruvate oxidation, citric acid cycle (Krebs cycle), electron transport chain and oxidative phosphorylation.
• Glycolysis: occurs in the cytoplasm and breaks down glucose into pyruvate.
• Citric acid cycle: occurs in the mitochondrial matrix and completes the breakdown of glucose.
• Electron transport chain: located in the inner mitochondrial membrane and generates a proton gradient that drives ATP synthesis.
• Oxidative phosphorylation: ATP synthesis powered by the flow of H+ ions across the inner mitochondrial membrane through ATP synthase.
• Photosynthesis: the process by which plants and other organisms convert light energy into chemical energy.
• Stages of photosynthesis: light-dependent reactions and the Calvin cycle.
• Light-dependent reactions: occur in the thylakoid membranes and convert light energy into chemical energy (ATP and NADPH).
• Calvin cycle: occurs in the stroma and uses ATP and NADPH to convert CO2 into glucose.

Chemistry of Life

• Matter: anything that takes up space and has mass.
• Elements: substances that cannot be broken down into other substances by chemical reactions (e.g., carbon, hydrogen, oxygen, nitrogen).
• Compounds: substances consisting of two or more different elements combined in a fixed ratio (e.g., water, glucose).
• Atoms: the smallest unit of matter that retains the chemical properties of an element.
• Structure of an atom: protons (positive charge), neutrons (no charge), electrons (negative charge).
• Chemical bonds: forces that hold atoms together.
• Types of chemical bonds: covalent bonds (sharing of electrons), ionic bonds (transfer of electrons), hydrogen bonds (attraction between a hydrogen atom and an electronegative atom).
• Water is essential for life due to its unique properties: cohesion, adhesion, high specific heat, evaporative cooling, and solvent properties.
• pH: measure of the acidity or alkalinity of a solution.
• Organic chemistry: the study of carbon compounds.
• Carbon can form diverse and complex molecules due to its ability to form four covalent bonds.
• Functional groups: specific groups of atoms attached to carbon skeletons that give organic molecules their unique properties (e.g., hydroxyl, carbonyl, carboxyl, amino, phosphate).
• Macromolecules: large polymers composed of smaller repeating monomers.
• Four major classes of organic macromolecules: carbohydrates, lipids, proteins, and nucleic acids.
• Carbohydrates: composed of sugars (monosaccharides, disaccharides, polysaccharides) and provide energy and structural support.
• Lipids: hydrophobic molecules including fats, phospholipids, and steroids, and provide energy storage, insulation, and structural components of cell membranes.
• Proteins: composed of amino acids and have diverse functions: enzymes, structural proteins, transport proteins, hormones, antibodies.
• Protein structure: primary (amino acid sequence), secondary (alpha helices and beta sheets), tertiary (3D shape), quaternary (arrangement of multiple polypeptide chains).
• Nucleic acids: DNA and RNA, composed of nucleotides, and store and transmit genetic information.