ATP, Energy & Thermodynamics

ATP: Structure, Function, Storage, and Release

• ATP consists of adenine, ribose, and three phosphate groups.
• ATP serves as the primary energy carrier in cells.
• Energy is stored in ATP's high-energy phosphate bonds.
• ATP hydrolysis (ATP → ADP + Pi) releases energy, whereas ATP synthesis occurs through cellular respiration.

Potential vs. Kinetic Energy & Thermodynamics

• Potential energy refers to stored energy, such as that in chemical bonds.
• Kinetic energy is the energy of motion, like molecular movement or muscle contractions.
• The First Law of Thermodynamics states that energy is only converted, not created or destroyed.
• The Second Law of Thermodynamics says that energy transformations increase entropy, or disorder.

Major Types of Chemical Reactions

• Synthesis (anabolic) reactions involve small molecules combining to form larger ones, such as A + B → AB (e.g., protein synthesis).
• Decomposition (catabolic) reactions involve large molecules breaking down into smaller ones, such as AB → A + B (e.g., glycogen breakdown).
• Exchange (oxidation-reduction) reactions happen when molecules exchange atoms or electrons.
• Oxidation is the loss of electrons, while reduction is the gain of electrons.

Classification of Chemical Reactions

• Anabolic reactions build up molecules and are endergonic.
• Catabolic reactions break down molecules and are exergonic.
• Endergonic reactions need energy input (e.g., ATP synthesis).
• Exergonic reactions release energy (e.g., ATP hydrolysis).
• Reversible reactions can proceed in both directions, while irreversible reactions proceed in one direction only.

Reaction Rate, Activation Energy, and Catalysis

• Reaction rate indicates the speed at which a chemical reaction occurs.
• Activation energy is the minimum energy needed to start a reaction.
• Uncatalyzed reactions occur slowly because of high activation energy.
• Catalyzed reactions use an enzyme to lower activation energy, increasing reaction speed.

Enzymes: Structure, Function, and Importance

• Enzymes are protein molecules with a specific 3D shape.
• Enzymes accelerate chemical reactions by lowering activation energy.
• Enzymes are essential for metabolism, digestion, and cellular processes.

Mechanism of Enzyme Action

• The active site is the specific region on an enzyme where the substrate binds.
• An enzyme-substrate complex forms temporarily, facilitating the reaction.
• Cofactors, which are non-protein molecules (e.g., vitamins, metal ions), assist enzymes.

Factors Affecting Enzyme Activity

• More substrate increases reaction rate until saturation is achieved.
• Optimal temperature for enzymes is around 37°C (body temperature); high temperatures cause denaturation, while low temperatures cause slower reactions.
• Optimal pH range varies by enzyme (e.g., pepsin works best at pH ~2, amylase at pH ~7); extreme pH levels denature enzymes.

Enzyme Inhibition

• Competitive inhibition happens when an inhibitor binds to the active site, blocking substrate binding, and can be overcome by increasing substrate concentration.
• Noncompetitive inhibition occurs when an inhibitor binds to an allosteric site, changing the enzyme's shape and function, and cannot be reversed by adding more substrate.

Metabolism & Metabolic Pathways

• Metabolism is the sum of all chemical reactions in the body.
• Metabolic pathways consist of a series of chemical reactions regulated by enzymes (e.g., glycolysis, Krebs cycle, electron transport chain).
• Negative feedback happens when a product of a metabolic pathway inhibits an earlier step, helping maintain homeostasis (e.g., ATP production regulation).

DNA Structure & Bonds

• DNA is a double helix made of nucleotides (sugar, phosphate, nitrogenous base).
• Adenine (A) pairs with Thymine (T), and Cytosine (C) pairs with Guanine (G).
• Hydrogen bonds exist between nitrogenous bases.
• Covalent bonds (phosphodiester bonds) exist between sugar and phosphate.

Levels of DNA Organization

• Nucleotides form strands of DNA, which form chromatin (loosely coiled DNA + histones), which then form chromosomes (tightly packed DNA during cell division).

DNA Processes: Replication, Transcription, and Translation

• DNA replication takes place in the nucleus and produces two identical DNA strands.
• Transcription takes place in the nucleus and produces mRNA (messenger RNA).
• Translation takes place in the ribosome (cytoplasm or rough ER) and produces protein.

mRNA modifications

• A 5' cap protects mRNA and assists ribosome binding.
• A poly-A tail increases mRNA stability.
• Splicing removes introns (non-coding regions) and joins exons (coding regions).

Codons & Their Function

• A codon is a sequence of 3 nucleotides in mRNA that codes for an amino acid.
• Start codon (AUG - methionine) initiates translation.
• Stop codons (UAA, UAG, UGA) signal the end of translation.

How Proteins Leave the Cell

• Proteins travel: Ribosome (Rough ER) → Golgi Apparatus (modifies & packages) → Vesicle → Plasma Membrane (exocytosis).

Mitosis vs. Meiosis

• Mitosis is for growth and repair, whereas meiosis is for gamete (sperm/egg) production.
• Mitosis involves 1 division, while meiosis involves 2.
• Mitosis results in 2 cells produced, while meiosis results in 4.
• Mitosis has no genetic variation, whereas meiosis does (crossing over).
• Mitosis maintains a diploid (2n) chromosome number, whereas meiosis halves it to haploid (n).

Cell Cycle Phases

• Interphase occurs for growth and DNA replication.
• In prophase, chromosomes condense and the spindle forms.
• In metaphase, chromosomes align at the middle of the cell.
• In anaphase, sister chromatids are pulled apart.
• In telophase, the nuclear envelope reforms.
• Cytokinesis is when the cytoplasm divides, creating two daughter cells.

Cell Theory

• All living things are made of cells
• The cell is the basic unit of life
• All cells arise from pre-existing cells

Definitions

• Proliferation is cell division leading to growth.
• Differentiation is the specialization of cells.
• A zygote is a fertilized egg (first cell of a new organism).

Functions of Cellular Organelles

• Nucleus: stores DNA and controls cell activities.
• Nucleolus: produces ribosomes.
• Plasma Membrane: Controls what enters/exits the cell.
• Endoplasmic Reticulum (ER)
• Rough ER handles protein synthesis
• Smooth ER handles lipid synthesis and detoxification.
• Golgi Apparatus: modifies, packages, and ships proteins.
• Lysosomes: digests cellular waste.
• Peroxisomes: breaks down fatty acids and toxins.
• Mitochondria: produces ATP (cellular respiration).
• Ribosomes: handles protein synthesis.
• Centrosome: organizes microtubules (important for cell division).
• Proteasomes: breaks down damaged or unneeded proteins.

Cell Surface Structures

• Cilia: moves substances along the cell surface (e.g., in the respiratory tract).
• Flagella: propels cells (e.g., sperm).
• Microvilli: increases surface area for absorption (e.g., intestines).

Passive vs. Active Transport

• Passive transport does not require energy, while active transport does (ATP).
• Passive transport moves from high to low concentration, while active transport moves from low to high concentration.

Passive Transport Examples

• Simple Diffusion: Small, nonpolar molecules (O₂, CO₂) move without energy from high to low concentration.
• Facilitated Diffusion: Large or charged molecules move via transport proteins without energy from high to low concentration.
• Osmosis: Water moves from high to low concentration.

Effects of Solutions on Cells

• Hypertonic solutions cause water to move out of the cell, causing it to shrink (crenation).
• Isotonic solutions cause no net water movement, so the cell stays the same.
• Hypotonic solutions cause water to move into the cell, causing it to swell (lysis).

Exocytosis vs. Endocytosis

• Exocytosis exports materials when vesicles fuse with the membrane and release contents (e.g., neurotransmitters).
• Endocytosis imports materials when the plasma membrane engulfs substances.

Connective Tissue Functions & Characteristics

• Connective tissue functions include support, protection, binding, insulation, and transportation.
• Connective tissues consist of few cells and abundant extracellular matrix.
• Most connective tissues are vascular, excluding cartilage.
• Connective tissue is diverse in structure and function.

Components of Connective Tissue

• Cells of various types provide structure and function.
• Protein fibers provide support and strength (collagen, elastic, reticular).
• Ground substance is a gel-like material that fills spaces between cells and fibers.

Extracellular Matrix Components

• Ground substance acts as a fluid to solid material that supports cells and fibers.
• Protein Fibers:
• Collagen fibers are strong and resist stretching.
• Elastic fibers are flexible, stretch, and recoil.
• Reticular fibers are thin and form a supportive meshwork.

Connective Tissue Classification

• Connective Tissue Proper includes loose & dense tissues, such as adipose (fat), tendons, and the dermis.
• Supporting CT provides structural support, such as cartilage and bone.
• Fluid CT transports substances, such as blood and lymph.

Resident vs. Wandering Connective Tissue Cells

• Resident Cells reside in the tissue to maintain structure: --Fibroblasts produce fibers & ground substance. --Adipocytes store fat. --Mesenchymal cells are stem cells for repair. --Fixed macrophages perform immune defense by engulfing pathogens.
• Wandering Cells move as part of the immune response: --Mast cells mediate inflammation. --Plasma cells produce antibodies.

Protein Fibers in Connective Tissue

• Collagen fibers are thick and unbranched to provide strong resistance to stretching as found in tendons and ligaments.
• Elastic fibers are thin and branched to stretch and recoil as found in arteries and lungs.
• Reticular fibers are thin and mesh-like to provide structural frameworks such as in the spleen and lymph nodes.

Epithelial Tissue Functions & Characteristics

• Epithelial tissue functions to provide protection, secretion, absorption, and sensation.
• It is composed of tightly packed cells with little extracellular material.
• Epithelial tissue is avascular (relies on diffusion).
• Epithelial tissue has a high regeneration capacity.

Epithelial Tissue Types & Locations

• Simple Squamous: For diffusion and filtration as found in the lungs and blood vessels.
• Simple Cuboidal: For secretion and absorption as found in kidney tubules and glands.
• Simple Columnar: For absorption and secretion as found in the digestive tract.
• Stratified Squamous: For protection as found in the skin, mouth, and esophagus.
• Stratified Cuboidal: For protection and secretion as found in sweat and salivary glands.
• Stratified Columnar: For protection as found in the male urethra.
• Pseudostratified Columnar: For secretion and movement as found in the trachea and respiratory tract.
• Transitional: For stretching as found in the bladder and ureters.

Classification of Epithelial Tissue

• By Cell Layers: --Simple: One layer. --Stratified: Multiple layers. --Pseudostratified: Appears multilayered but isn’t.
• By Cell Shape: --Squamous: Flat. --Cuboidal: Cube-shaped. --Columnar: Tall, rectangular.

Endocrine vs. Exocrine Glands

• Endocrine Glands secrete hormones without ducts.
• Exocrine Glands secrete enzymes, sweat, and saliva through ducts.
• Examples of Endocrine Glands are the thyroid and adrenal glands.
• Examples of Exocrine Glands are sweat glands and salivary glands.

Muscle Tissue Types & Characteristics

• Skeletal: striated, multinucleated, voluntary; for movement and attached to bones.
• Cardiac: striated, single nucleus, involuntary; pumps blood in the heart.
• Smooth: non-striated, single nucleus, involuntary; moves substances in the walls of organs, such as intestines and blood vessels.

Neurons & Glial Cells

• Neurons transmit electrical signals. --Consist of a cell body, dendrites (receive signals), and an axon (sends signals).
• Glial Cells support and protect neurons.

Four Types of Membranes

• Mucous: epithelial & CT; lines cavities open to the exterior, such as the digestive and respiratory tracts.
• Serous: simple squamous & CT; reduces friction as found in the pleura (lungs) and pericardium (heart).
• Cutaneous: stratified squamous & CT; provides protection as the skin.
• Synovial: CT only; lubricates joints, such as knees and elbows.

Key Terms in Tissue Changes

• Hypertrophy: Increase in cell size.
• Atrophy: Decrease in cell size.
• Hyperplasia: Increase in cell number.
• Metaplasia: Change in cell type (e.g., smoking damages respiratory epithelium).
• Dysplasia: Abnormal cell growth.
• Neoplasia: Uncontrolled cell growth (tumor formation).
• Necrosis: Premature cell death due to injury.

Methods of Tissue Repair

• Regeneration involves damaged tissue being fully replaced by the same type of tissue.
• Fibrosis involves damaged tissue being replaced by scar tissue (collagen), resulting in a loss of function.

Overview of ATP (structure, function), potential vs kinetic energy and the Laws of thermodynamics. ATP is the primary energy carrier in cells, storing energy in its phosphate bonds. Thermodynamics studies energy transformation and entropy.