Results for "Organic Molecules"

8. Introduction to organic molecules

2. Bonding of carbon and other atoms in organic molecules

Properties of organic molecules

Biology - Ecology, Biogeochemical Cycles, Organic Molecules, and Cell Systems

Organic molecules

endomembrane system Semi-autonomous organelles Protein sorting to organelles Systems biology of cells Cell Biology & Cell Theory Cell biology: The study of individual cells and their interactions. Cell Theory (Schleiden & Schwann, with contributions from Virchow): All living organisms are composed of one or more cells. Cells are the smallest units of life. New cells arise only from pre-existing cells through division (e.g., binary fission). Origins of Life: Four Overlapping Stages Stage 1: Formation of Organic Molecules Primitive Earth conditions favored spontaneous organic molecule formation. Hypotheses on the origin of organic molecules: Reducing Atmosphere Hypothesis: Earth's early atmosphere (rich in water vapor) facilitated molecule formation. Stanley Miller’s experiment simulated early conditions, producing amino acids and sugars. Extraterrestrial Hypothesis: Organic carbon (amino acids, nucleic acid bases) may have come from meteorites. Debate exists over survival after intense heating. Deep-Sea Vent Hypothesis: Molecules formed in the temperature gradient between hot vent water & cold ocean water. Supported by experimental evidence. Alkaline hydrothermal vents may have created pH gradients that allowed organic molecule formation. Stage 2: Formation of Polymers Early belief: Prebiotic synthesis of polymers was unlikely in aqueous solutions (water competes with polymerization). Experimental evidence: Clay surfaces facilitated the formation of nucleic acid polymers and polysaccharides. Stage 3: Formation of Boundaries Protobionts: Aggregates of prebiotically produced molecules enclosed by membranes. Characteristics of a protobiont: Boundary separating the internal & external environments. Polymers with information (e.g., genetic material, metabolic instructions). Catalytic functions (enzymatic activities). Self-replication. Liposomes: Vesicles surrounded by lipid bilayers. Can enclose RNA and divide. Stage 4: RNA World Hypothesis RNA was likely the first macromolecule in protobionts due to its ability to: Store information. Self-replicate. Catalyze reactions (ribozymes). Chemical Selection & Evolution: RNA mutations allowed faster replication & self-sufficient nucleotide synthesis. Eventually, RNA world was replaced by the DNA-RNA-protein world due to: DNA providing more stable information storage. Proteins offering greater catalytic efficiency and specialized functions. Microscopy Microscopy Parameters Resolution: Ability to distinguish two adjacent objects. Contrast: Difference between structures (enhanced by special dyes). Magnification: Ratio of image size to actual size. Types of Microscopes Light Microscope: Uses light; resolution = 0.2 micrometers. Electron Microscope: Uses electron beams; resolution = 2 nanometers (100x better than light microscopes). Light Microscopy Subtypes Bright Field: Standard; light passes directly through. Phase Contrast: Amplifies differences in light phase shifts. Differential Interference Contrast (DIC): Enhances contrast for internal structures. Electron Microscopy Subtypes Transmission Electron Microscopy (TEM): Thin slices stained with heavy metals. Some electrons scatter while others pass through to create an image. Scanning Electron Microscopy (SEM): Heavy metal-coated sample. Electron beam scans the surface, producing 3D images. Cell Structure & Function Determined by matter, energy, organization, and information. Genome: The complete set of genetic material. Prokaryotic vs. Eukaryotic Cells Feature Prokaryotic Cells Eukaryotic Cells Nucleus ❌ Absent ✅ Present Membrane-bound organelles ❌ None ✅ Yes Size Small (1-10 µm) Large (10-100 µm) Examples Bacteria, Archaea Plants, Animals, Fungi, Protists Prokaryotic Cell Structure Plasma Membrane: Lipid bilayer barrier. Cytoplasm: Internal fluid. Nucleoid Region: DNA storage (no nucleus). Ribosomes: Protein synthesis. Cell Wall: (Some) Provides structure & protection. Glycocalyx: Protection & hydration. Flagella: Movement. Pili: Attachment. Eukaryotic Cell Structure Nucleus: Contains DNA & controls cell functions. Organelles: Rough ER: Protein synthesis & sorting. Smooth ER: Lipid synthesis, detoxification. Golgi Apparatus: Protein modification & sorting. Mitochondria: ATP production (Powerhouse of the Cell™). Lysosomes: Digestive enzymes for breakdown & recycling. Peroxisomes: Breakdown of harmful substances. Cytoskeleton: Provides structure (microtubules, actin filaments, intermediate filaments). Plasma Membrane: Regulates transport & signaling. Endomembrane System Includes: Nucleus, ER, Golgi apparatus, lysosomes, vacuoles, and plasma membrane. Nuclear Envelope: Double membrane structure. Nuclear pores allow molecule transport. Golgi Apparatus: Modifies & sorts proteins/lipids. Packages proteins into vesicles for secretion (exocytosis). Lysosomes: Contain acid hydrolases for macromolecule breakdown. Perform autophagy (organelle recycling). Semi-Autonomous Organelles Mitochondria Function: ATP production (cellular respiration). Structure: Outer & inner membrane (inner folds = cristae for increased surface area). Mitochondrial matrix houses metabolic enzymes. Chloroplasts (Plants & Algae) Function: Photosynthesis (light energy → chemical energy). Structure: Outer & inner membrane. Thylakoid membrane (site of photosynthesis). Contains chlorophyll. Endosymbiosis Theory Mitochondria & chloroplasts evolved from free-living bacteria that were engulfed by an ancestral eukaryotic cell. Protein Sorting & Cell Organization Co-translational sorting: Proteins destined for ER, Golgi, lysosomes, vacuoles, or secretion. Post-translational sorting: Proteins sent to nucleus, mitochondria, chloroplasts, peroxisomes. Systems Biology Studies how cellular components interact to form a functional system

Organic Molecules Quiz

Lecture 3: Organic Molecules

Naming Organic Molecules

Small Organic Molecules

Chapter 5: Organic Molecules

HOMEOSTASIS Maintaining a stable internal environment respond to stimuli Reacting to changes in the environment reproduce and develop Creating new organisms and growing adapt and evolve Changing over time to better suit the environment INDUCTIVE REASONING Making generalizations based on specific observations DEDUCTIVE REASONING Making specific predictions based on general principles Matter Anything that has mass and takes up space elements Substances that cannot be broken down into simpler substances protons Positively charged particles in the nucleus neutrons Neutral particles in the nucleus electrons Negatively charged particles orbiting the nucleus Atomic Number Number of protons in an atom Isotopes Atoms of the same element with different numbers of neutrons Octet Rule Atoms tend to gain, lose, or share electrons to achieve a full outer shell of 8 electrons molecule Two or more atoms held together by chemical bonds compound A substance consisting of two or more different elements IONIC BONDS Bonds formed by the transfer of electrons COVALENT BONDS Bonds formed by the sharing of electrons reactants Starting materials in a chemical reaction products Ending materials in a chemical reaction WATER solvent Dissolves many substances WATER cohesion & adhesion Water molecules stick to each other and other surfaces WATER high surface tension Water's surface resists being broken WATER high heat capacity Water can absorb a lot of heat without changing temperature WATER heat of vaporization Water requires a lot of energy to evaporate WATER varying density Ice is less dense than liquid water acidic solutions Solutions with a pH below 7 basic solutions Solutions with a pH above 7 pH scale Measures the acidity or basicity of a solution buffers Substances that resist changes in pH Organic Molecules Molecules containing carbon carbon The backbone of organic molecules functional groups Chemical groups attached to carbon that give molecules specific properties Macromolecules Large molecules made up of smaller subunits monomers The individual subunits of a polymer polymers Long chains of monomers Dehydration Synthesis Reaction Joins monomers by removing water Hydrolysis Reaction Breaks polymers by adding water Role of Enzymes Speed up chemical reactions Carbohydrates monosaccharides glucose Simple sugars Carbohydrates disaccharides glycosidic bonds Two monosaccharides joined together Carbohydrates polysaccharides starch glycogen cellulose Many monosaccharides joined together LIPIDS Glycerol & Fatty Acids saturated Fatty acids with no double bonds LIPIDS Glycerol & Fatty Acids unsaturated Fatty acids with double bonds PROTEINS Enzymes Proteins that catalyze chemical reactions PROTEINS amino acids peptide bonds The monomers of proteins, joined together PROTEINS protein structure primary The sequence of amino acids PROTEINS protein structure secondary Local folding patterns (e.g., alpha-helices and beta-sheets) PROTEINS protein structure tertiary The overall 3D shape of a single polypeptide PROTEINS protein structure quaternary The arrangement of multiple polypeptides in a protein conformation The 3D shape of a protein denaturation The unfolding of a protein DNA Deoxyribonucleic acid, the genetic material RNA Ribonucleic acid, involved in protein synthesis ATP Adenosine triphosphate, the energy currency of the cell

introduction to organic molecules

Organic Molecules Prefixes

Organic Molecules

Study Guide for Organic Molecules

functional groups, naming and drawing organic molecules

Unit 9 honors organic molecules and biochemistry

Common IR bands for organic molecules

Organic Molecules Functional Groups: Nucleic Acids DNA RNA