BIO notes

Unit 1: Cell Theory

• Definition of Cell Theory:

  • All living organisms are composed of one or more cells.

  • The cell is the structural and functional unit of life.

  • Cells arise from pre-existing cells.

  • Cells contain DNA, the hereditary material passed onto daughter cells (except for mature red blood cells).

• Living vs. Non-living:

  • Cells are the fundamental units of living things that carry out all life processes, including:

  • Movement

  • Metabolism

  • Respiration

  • Growth

  • Reproduction

  • Responding to stimuli

  • Excretion

  • Viruses are not considered to be cells or alive because they possess some but not all characteristics of life, thus not complying with cell theory.

• Cell Membrane:

  • A thin boundary that separates and controls the movement of materials between the cell’s internal environment and its external environment.

  • Described as a semi-permeable layer allowing some molecules to pass while preventing others (such as large or charged molecules).

Lipids in the Cell Membrane

• Types of Lipids:

  • Phospholipids:

  • Composed of phosphate and glycerol (head) and two fatty acid chains (tails).

  • The hydrophilic head attracts water (water-loving) while the hydrophobic tails repel water (water-fearing).

  • Cholesterol:

  • A lipid that is sandwiched between phospholipids, restricting their movement which prevents the membrane from becoming too solid or too fluid.

  • Glycolipids:

  • Lipids with carbohydrate groups attached, found on the surface of cell membranes, extending into the extracellular environment, maintaining stability and facilitating cellular recognition.

Membrane Proteins

• Composition:

  • A mosaic of nearly 100 different proteins imbedded in the fluid region of the phospholipid bilayer.

• Types of Proteins:

  • Integral (Intrinsic) Proteins: Span the entire membrane.

  • Peripheral (Extrinsic) Proteins: Embedded in but do not span the membrane.

Functions of Membrane Proteins

1. Transport:

   • Channel Proteins (without ATP) and Carrier Proteins (with ATP) transport hydrophilic materials across the membrane.

2. Receptors:

   • Recognize and bond to target molecules (e.g., hormones) causing internal cellular changes.

3. Enzymes:

   • Catalyze substrate-specific reactions at the membrane's boundary or within it.

Cell Recognition

• Glycoproteins:

  • Integral and peripheral proteins with carbohydrate molecules attached that serve as markers recognized by membrane proteins on other cells.

Unit 2: Prokaryotic and Eukaryotic Cells

Prokaryotes

• Features:

  • Cell Wall: Provides rigidity and structural support, maintaining the shape of the cell.

  • Capsule: An external covering offering protection from host cells; sticky for adhesion.

  • Fimbriae (Pili): Thin protein fibers that serve to attach bacteria to surfaces, other bacteria, and target cells.

  • Flagella: Fibrous projections in motile bacteria for movement.

  • DNA: A single, continuous circular molecule located in the nucleoid region.

  • Plasmids: Circular DNA molecules separate from the chromosome, containing a few genes for metabolism, virulence, and antibiotic resistance.

Common Features of Prokaryotes and Eukaryotes

• Common Features:

  • Cell Membrane: Surrounds cytoplasm, controlling substance entry/exit.

  • Ribosome: Site of protein synthesis without an outer membrane.

  • Nucleic Acids: Polymers of nucleotides (DNA and RNA).

  • Proteins: Essential for myriad cell functions, polymers of amino acids.

  • Cytoplasm: Fluid containing enzymes, salts, organelles.

  • ATP: An energy-storage molecule produced during respiration.

Comparison: Eukaryotic and Prokaryotic

Eukaryotes

• Types: Animal, Plant, or Fungal

Key Organelles and Their Functions

• Nucleus:

  • Contains chromosomes; site of DNA replication and transcription.

• Nucleolus:

  • Site of ribosomal RNA synthesis.

• Mitochondrion:

  • Site of later stages of aerobic respiration; contains its DNA and ribosomes.

  • Generates most of the cells supply of ATP

• Chloroplast:

  • Light-absorbing organelles for photosynthesis in plants; contains DNA and ribosomes.

• Vacuole/Vesicle:

  • Vacuoles store water (large in plants); vesicles contain materials for secretion.

• Golgi Body:

  • Modifies proteins and lipids, packaging them into vesicles for transport.

• Endoplasmic Reticulum (ER):

  • Interconnected membrane system; Rough ER has ribosomes and synthesizes proteins; Smooth ER is for lipid synthesis.

• Lysosome:

  • Contains digestive enzymes for digestion of old organelles and cells.

• Cytoskeleton:

  • Supports the cell structure, shapes, and enables movement of organelles; involved in transport and cell division.

• Cell Wall:

  • Provides structure, support, and protection; composed mainly of cellulose in plants, chitin in fungi.

• Internally Folded Membranes:

  • Increase surface area for metabolic processes; significant in mitochondria, chloroplasts, Golgi body, and ER.

Unit 3: Energy Transformations

Autotrophs and Heterotrophs

• Autotrophs:

  • Primary producers synthesizing their own food from inorganic substances via energy conversion.

  • Photoautotrophs: Use light for glucose production (e.g., plants).

  • Chemo-autotrophs: Use inorganic molecules for generating organic food (e.g., certain bacteria).

• Heterotrophs:

  • Obtain food from consuming autotrophs or other heterotrophs.

Photosynthesis

• Process:

  • The sun transfers energy via electromagnetic radiation.

  • Chlorophyll: Light-absorbing pigments in plants, stored in chloroplasts, used for photosynthesis.

  • Occurs in thylakoids which are membrane structures increasing the reaction surface area.

Aerobic Respiration

• Definition:

  • The breakdown of glucose in the presence of oxygen to release energy.

• Process:

  • In prokaryotes occurs in the cytoplasm and cell membrane.

  • In eukaryotes, consists of three stages:

  1. Glycolysis: Non-aerobic steps in the cytoplasm, yielding 2 ATP and pyruvate.

  2. Kreb’s Cycle: Occurs in mitochondria.

  3. Oxidative Phosphorylation: Also in mitochondria.

• Total ATP Yield: 36-38 ATP molecules.

Anaerobic Respiration

• Definition:

  • Involves the incomplete breakdown of glucose without oxygen.

• Process:

  • Begins with glycolysis; pyruvate is converted to lactic acid (in animals) or alcohol (in plants/yeast).

• Energy Yield: 2 ATP molecules.

• Lactic Acid Fermentation: In animals and anaerobic bacteria.

Metabolism

• Definition:

  • Refers to chemical reactions maintaining life processes in cells, involving energy changes.

Anabolic Reactions

• Definition:

  • Synthesis of larger molecules from smaller ones, absorbing energy.

• Examples:

  • DNA replication: from nucleotides to DNA.

  • Transcription: from RNA nucleotides to mRNA.

  • Translation: from amino acids to polypeptides.

  • Photosynthesis: from carbon dioxide and water to glucose or starch.

Catabolic Reactions

• Definition:

  • Breakdown of larger molecules into smaller molecules, releasing energy.

• Examples:

  • Oxidation of hydrogen peroxide to water and oxygen.

  • Aerobic respiration: from glucose to carbon dioxide and water.

  • Anaerobic respiration: from glucose to lactate or ethanol and carbon dioxide.

  • Hydrolysis: of proteins, polysaccharides, and lipids.

ATP

• Definition:

  • Adenosine triphosphate, a molecule used to store and release energy in living organisms.

• Composition:

  • Made of adenine (base), ribose (sugar), and three phosphate groups.

• Properties:

  • Small and water-soluble, facilitating transport within cells (which are 80% water).

ATP Cycle

• Synthesis:

  • ATP is synthesized from adenosine diphosphate (ADP) and inorganic phosphate (Pi).

  • Reaction:

  • $ext{ADP} + ext{Pi} <br>ightarrow ext{ATP}$

• Energy Release:

  • Upon removal of a phosphate group, energy is released, and ADP is formed.

Unit 4: Movement of Substances into and out of Cells

Inputs and Outputs

• All cell types require a constant input of energy and raw materials, alongside waste removal to maintain life processes.

• Inputs and outputs differ between autotrophs (e.g., plants) and heterotrophs (e.g., animals) due to their metabolic processes.

Plant Inputs

• Metabolic processes:

  • Each process requires specific raw materials.

  • Photosynthesis: Inputs include carbon dioxide and water.

  • Aerobic Respiration: Requires glucose and oxygen.

  • Other processes like nucleotide/phospholipid synthesis, protein synthesis, chlorophyll synthesis, and cell wall synthesis have various nutrient requirements.

Plant Outputs

• Waste products can become toxic at high concentrations.

• Photosynthesis: Produces excess oxygen.

• Aerobic Respiration: Outputs carbon dioxide and water.

• Removal mechanisms include stomata (in leaves), lenticels (in stems), root hairs, and storage of wastes in vacuoles.

Heterotrophs’ Inputs

• Heterotrophs, like humans, acquire glucose and essential organic compounds from other living organisms.

• Metabolic processes in human cells include aerobic respiration (requires glucose and oxygen) and protein synthesis (requires amino acids).

Human Outputs

• Metabolic waste can be toxic.

• Carbon dioxide is removed via gas exchanges, sweat (as bicarbonate ions), and urea in urine.

• Outputs include carbon dioxide and water from aerobic respiration and lactic acid from anaerobic respiration.

Mechanisms of Transport

Diffusion

• Definition:

  • Net movement of small, uncharged molecules across membranes following a concentration gradient without transport proteins.

  • Movement occurs from higher to lower concentration until equilibrium is reached.

  • Examples: O2, CO2, ethanol can pass via simple diffusion due to being nonpolar/hydrophobic.

Facilitated Diffusion

• Definition:

  • Passive process facilitated by transport proteins that assist selected materials moving down concentration gradients between the cell and environment.

• Types of Transport Proteins:

  • Channel Proteins: Facilitate diffusion of ions and hydrophilic materials.

  • Carrier Proteins: Bind selectively to specific materials, changing shape and releasing substrate to the opposite side of the membrane.

Osmosis

• Definition:

  • Diffusion of water from a lower solute concentration (higher water concentration) to higher solute concentration until equilibrium is attained.

• Types of Solutions:

  • Hypotonic: Lower solute concentration outside; water influx causes swelling.

  • Hypertonic: Higher solute outside; water efflux leads to cell shrinkage.

  • Isotonic: Equal solute concentrations; no net movement of water.

Aquaporins

• Specialized protein channels that allow efficient water transport across membranes despite being small and hydrophilic, making diffusion slow.

Active Transport

• Definition:

  • Use of carrier proteins to move materials against concentration gradients (like glucose, ions, amino acids) requiring ATP input.

• Example: Sodium-Potassium Pump, crucial in nerve cells for impulse transmission.

Co-Transport

• Movement of two substances across the membrane simultaneously in the same direction utilizing the gradient generated by the first substance to move the second against its gradient (indirect active transport).

Bulk Transport

• Definition:

  • Transport mechanism for larger molecules that cannot utilize standard transport methods.

• Endocytosis: Vesicle-mediated transport into cells, with specific receptor-mediated entry.

  • Types:

  • Phagocytosis: For solid substances.

  • Pinocytosis: For liquid substances.

• Exocytosis: Vesicle-mediated transport out of the cell, with Golgi body packaging materials into vesicles for transport.

Properties Affecting Transport

• Transport methods depend on physical properties (size/charge) and chemical properties (hydrophobic/hydrophilic).

• Hydrophobic materials diffuse better than hydrophilic; transport proteins assist in hydrophilic material movement.

Unit 5: Cell Metabolism

Features of Mitochondria

• Outer Membrane:

  • Lipid bilayer with embedded proteins and enzymes for cytoplasmic reactions.

• Inner Membrane:

  • Lipid bilayer with channel proteins linked to ATP synthase.

• Cristae:

  • Extensions boosting surface area for ATP synthesis.

• Matrix:

  • Contains mitochondrial DNA, ribosomes, and enzymes for biochemical reactions.

• Intermembrane Space:

  • Area creating proton concentration gradients vital for energy production.

Features of Chloroplasts

• Inner and Outer Membrane:

  • Regulate material transport between stroma and cytoplasm, containing enzymes for some pigments/lipid synthesis.

• Thylakoid:

  • Membrane sacs holding light-absorbing pigments and ATP synthase complexes aiding photosynthesis.

• Granum: A stack of thylakoids to enhance light absorption and ATP synthesis efficiency.

• Stroma:

  • Gel-like fluid with enzymes to facilitate photosynthesis.

• Stromal Lamellae:

  • Extensions enhancing surface area for pigments and increasing rate of photosynthesis.

Metabolic Pathways

• Metabolic pathways consist of regulated steps requiring specific enzymes.

Reasons for Multiple Steps:

1. Reduce Activation Energy:

   • Enzymes decrease activation energy for each step.

2. Variable Reaction Rates:

   • Reactions adjust according to substrate, product, enzyme concentrations, or inhibitors.

3. Heat Management:

   • Progressive heat release avoids significant enzyme deactivation.

4. Pathway Interconnectivity:

   • Intermediates may participate in alternate metabolic processes.

Environmental Factors Affecting Metabolism

• Temperature:

  • Reaction rates increase to optimum, then decline beyond due to enzyme denaturation.

• Light Intensity:

  • Affects the rate of light-dependent reactions in photosynthesis.

• pH:

  • Alters enzyme structure affecting substrate binding and reaction rates.

• Water Availability:

  • Affects reaction conditions within cells.

• Substrate and Enzyme Availability:

  • Reaction rates depend on concentrations of substrates and enzymes.

Chemical Interference and Metabolism

• Chemicals Affecting Pathways:

  • Antibiotics, chemotherapy drugs, and herbicides affect metabolic pathways in target cells.

• Cofactors and Coenzymes:

  • Assist enzymes by shaping active sites.

Comparison of Chemicals

Unit 6: Cell Division

DNA Replication and Cell Division

• DNA Replication:

  • Produces two identical copies of each DNA molecule.

• Cell Division:

  • Essential for growth, reproduction, and cell replacement.

  • In multicellular organisms, increases cell number; unicellular organisms form new individuals.

  • Eukaryotic Mitosis: Followed by cytokinesis produces two new identical cells; Prokaryotic Binary Fission: Direct duplicated and divides.

Eukaryotic Chromosomes

• Structure:

  • DNA wrapped around histone proteins to form chromatin.

  • Chromosomes condense during division into homologous pairs, one from each parent, carrying the same gene traits.

Mitosis Phases

1. Interphase: Preceding mitosis; replication occurs without visible chromosomes.

2. Prophase: Chromosomes condense, and spindle fibers form, centrioles move to poles.

3. Metaphase: Alignment of chromosomes along the metaphase plate.

4. Anaphase: Spindle fibers pull sister chromatids apart to opposite poles.

5. Telophase: Formation of nuclear membranes around separated chromatids; chromosomes decondense.

6. Cytokinesis: Final division of cytoplasm, forming two daughter cells.

Binary Fission

• Definition:

  • Prokaryotic cell division resulting from the size trigger; takes about 20 minutes for a doubling population.

• Mechanism: Both daughter cells identical to the original; single circular DNA moved to oppose sides before division.

Energy Requirement in Cell Division

• Processes that require energy include DNA replication, membrane pinching during fission/mitosis, forming cell walls, spindle fiber formation, chromosome orientation, and nuclear membrane assembly.

Unit 7: Control of Cell Cycle

Interphase Staging

Checkpoints in the Cell Cycle

• G1 Checkpoint:

  • Checks chromosome integrity, nutrient availability for transition to S (initiation of replication).

• G2 Checkpoint:

  • Ensures all chromosomes replicated and free from damage before mitosis.

• M Checkpoint:

  • Ensures sister chromatids are attached to spindle fibers before anaphase.

Growth Factors and Internal Factors

• Growth Factors:

  • Bind to cell receptors to trigger cell cycle progression.

• Cyclin:

  • Protein synthesized throughout the cycle, binding to or activating Cdk (cyclin-dependent kinase) forming MPF (Mitosis Promoting Factor) for mitosis initiation.

• Low SA:V Ratio:

  • Encourages division to generate smaller cells with higher surface-area-to-volume ratios.

External Factors Influencing Cell Cycle

1. Nutrient Dependence: Cells need nutrients in extracellular fluid for division.

2. Anchorage Dependence: Cells need substrate attachment for division.

3. Density Dependence: Cells require space to split; lack of space inhibits division (notably, cancer cells deviate from this).

4. Growth Factors/Hormones: Act as signals to stimulate division.

Cancer

• Mechanism: Genetic mutations in proto-oncogenes and tumor suppressor genes trigger unregulated division.

• Tumor Types:

  • Benign: Non-spreading, non-harmful.

  • Malignant: Spread, harmful to host.

• Metastasis: Tumor cells spread and form secondary tumors elsewhere in the body.

Carcinogens

• Definition: Agents causing mutations leading to cancer; includes ionizing radiation, mutagens, and some viruses.

• Gene Functions:

  • Proto-Oncogene: Promotes normal growth/division.

  • Tumor Suppressor Gene: Inhibits growth/division.

  • Oncogene: Mutated proto-oncogene causing tumors.

Unit 8: Meiosis

Somatic and Gamete Cells

• Somatic Cells:

  • Diploid with complete chromosome sets, formed by mitosis; identical offspring.

• Gametes:

  • Haploid, half the chromosome count, formed from diploid germ cells via meiosis.

Stages of Meiosis

Meiosis 1

• Process:

  • Homologous pairs separate producing haploid cells; preceded by DNA replication.

• Phases:

  • Prophase 1: Homologous chromosomes pair, crossing over occurs; results in genetic variation.

  • Metaphase 1: Pairs align on metaphase plate; independent assortment happens.

  • Anaphase 1: Chromosomes pulled to opposite poles.

  • Telophase 1: Nuclear membranes form; cytokinesis results in two haploid cells.

Meiosis 2

• Process:

  • Separates sister chromatids to yield four unique haploid gametes.

• Phases:

  • Prophase 2: Chromosomes condense; new spindle forms.

  • Metaphase 2: Chromosomes align randomly; leading to additional variation.

  • Anaphase 2: Sister chromatids separate.

  • Telophase 2: Nuclear membranes form; cytokinesis results in four new gametes.

Genetic Variation in Sexual Reproduction

• Sources of variation include:

  1. Mutations

  2. Crossing Over during Meiosis 1

  3. Independent Assortment during Meiosis 1

  4. Fertilization: Joining of gametes increasing genetic diversity.

Asexual Reproduction

• Single-parent division gives identical offspring; mutation is the sole source of genetic diversity.

Comparing Mitosis and Meiosis

Unit 9: Culturing Cells

Definition of Cell Culture

• The growth of cells under controlled conditions used for:

  • Microorganisms

  • Animal cells

  • Plant cells

  • Genetically modified cells

  • Stem cells

  • Fungi

Techniques for Cell Culture

• Tissue removal must use sterilized equipment to prevent contamination.

  • Physical Dissection: Using sharp instruments to isolate cells.

  • Chemical Dissection: Enzymatic digestion of the extracellular matrix for cell separation.

  • Separated cells are incubated in media; purification achieved through selective media and methods.

Conditions For Optimal Cell Growth

• Require appropriate Nutrients for metabolic activity.

• Oxygen: For aerobic cells during culture.

• Growth Factors: To stimulate cell proliferation.

• Osmotic Balance: Controlled water and solute levels to maintain homeostasis.

• Optimal pH: Maintained through buffering agents for enzyme activity.

• Optimal Temperatures: To ensure enzymatic efficiency.

• Antibiotics: To eliminate potential bacterial contaminants, ensuring culture purity.

• Sterile Environment: Essential to prevent contamination; achieved using UV light and sterilizing substances.

Considerations in Cell Culture

• Anchorage-dependent cell-types (e.g., human skin cells) need surface attachment for growth.

• Cancer cells can pile up and do not observe anchorage requirements.

• Anchorage-independent cells (like blood cells) grow freely.

Applications of Cell Culture

• Research: Investigate differing cell types and functions.

• Toxicology: Examine drug effects on cellular structure/function.

• Cancer Research: Study properties of tumors and the responses to treatments.

• Virology Research: Interactions between viruses and cells to develop medications/vaccines.

• Genetic Engineering: Modify and produce transgenic organisms for commercial biotechnology, including GMO plants.

• Food Production: Development of cultured meat technologies.