lecture outline 2

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  • Title: Cell Chemistry 1

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  • Cells are Made of Molecules

    • A molecule consists of one or more atoms bonded together.

    • Atom: Comprised of an equal number of protons and neutrons in the nucleus.

    • Electrons:

      • Negatively charged (-) and orbit the nucleus.

      • Same number of electrons and protons: neutral.

      • More electrons than protons: anion (-).

      • Fewer electrons than protons: cation (+).

    • Hydrogen (H): Unique as it has no neutrons.

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  • Electron Shells

    • Electrons occupy discrete areas around the nucleus known as shells.

    • Each shell has a maximum capacity for electrons.

    • The closest shells to the nucleus must be filled first.

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  • Unfilled Electron Shells

    • Atoms with partially filled outer shells are less stable than those with filled outer shells.

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  • Stability and Interaction

    • Atoms attempt to fill their outer shells for increased stability.

    • Methods to achieve this:

      • Covalent Bonds: Share electrons.

      • Ionic Bonds: Transfer electrons.

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  • Covalent Bonds

    • Atoms with nearly filled outer shells share electrons to form a covalent bond, resulting in a molecule.

    • Covalent bonds are relatively strong and stable.

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  • Types of Covalent Bonds

    • Single Bonds: Flexible and allow rotation.

    • Double Bonds: Shorter, stronger, less flexible.

    • Triple Bonds: Less common (e.g., nitrogen gas N2, acetylene C2H2).

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  • Strength of Covalent Bonds

    • Bond strength is the energy difference between free atoms and the molecule formed.

    • Stronger bonds (e.g., CO2, H2O) are more stable with less energy.

    • Weaker covalent bonds can store energy (e.g., CH2O).

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  • Electron Sharing

    • Electronegativity: Different atoms attract electrons to varying degrees.

    • Atoms with different electronegativities can create polar molecules.

    • Polar molecules are crucial in biology.

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  • Polar Covalent Bonds

    • Small differences in polarity can lead to attractions between polar molecules.

    • Hydrogen Bond: A vital electrostatic attraction between hydrogen and electronegative atoms.

    • Although individually weak, many hydrogen bonds can collectively form strong interactions.

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  • Acids and Bases

    • When polar differences are large, molecules act as acids or bases.

    • Acids can donate protons (H+) in polar bonds, often interacting with water, forming hydronium ions (H3O+).

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  • Water as an Acid

    • Water can act as an acid, donating H+ to bases, maintaining a dynamic equilibrium of H+ in cells, essential for cellular chemistry.

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  • Electron Transfer to Fill Outer Shells

    • Atoms can transfer electrons to fill outer shells, resulting in cations (+) and anions (-).

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  • Ionic Bonds

    • Ionic compounds, or salts, are formed from the electrostatic attraction between oppositely charged ions.

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  • Nature of Ionic Bonds

    • Ionic bonds exhibit strong electrostatic attraction, similar to hydrogen bonds but much stronger due to full charges.

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  • Dissolution of Ionic Bonds

    • Ionic bonds are strong but can dissolve in polar solvents like water.

    • Approximately 70% of a cell is water, keeping most salts in ionic form.

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  • Other Interactions

    • Hydrophobic Interactions: Nonpolar molecules tend to associate and avoid water.

    • Van der Waals Attractions: Weak attractions between the fluctuating electron clouds of polar molecules.

    • Van der Waals Radii: Defines the minimum distance between two atoms based on electron cloud dimensions.

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  • Summary of Interactions

    • Interactions defined:

      • Covalent Bonds: Strong and stable.

      • Ionic Bonds: Strong in nonpolar environments.

      • Hydrogen Bonds: Common interaction in polar molecules.

      • Van der Waals Attractions: Weak but significant in number.

      • Hydrophobic Interactions: Weak interactions.

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  • Complementary Molecules

    • Characteristics:

      1. High degree of fit between three-dimensional shapes.

      2. Multiple weak non-covalent interactions allow alignment and stability.

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  • Biological Molecules

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  • The Most Important Biological Molecule

    • Water: Essential for life; makes up approximately 70% of cell weight.

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  • Biological Molecules

    • Biological molecules possess special properties; main atoms involved include:

      • Hydrogen (H), Carbon (C), Nitrogen (N), Oxygen (O).

      • Less common but essential: Sodium (Na), Magnesium (Mg), Phosphorus (P), Sulfur (S), Chlorine (Cl), Potassium (K), Calcium (Ca).

    • Carbon is notably important despite not being the most abundant.

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  • Cells are Made From Carbon

    • All non-water molecules in cells contain carbon.

    • Carbon can form covalent bonds with 2, 3, or 4 other atoms due to having 4 missing electrons.

    • Carbon molecules can be small or form large polymers (organic molecules).

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  • Cells as Chemical Factories

    • Reactions within cells predominantly involve four types of organic molecules:

      • Amino acids, Sugars, Nucleotides, Lipids.

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  • Primary Reactions in Cells

    1. Catabolic Reactions: Breakdown of large organic molecules, releasing energy and producing smaller molecules.

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  • Details on Catabolic Reactions

    • Significant energy release during the breakdown of high-energy organic molecules.

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  • Anabolic Reactions

    1. Anabolic Reactions: The small molecules produced during catabolism are built into larger molecules, utilizing some released energy.

    • Metabolism: The sum of catabolic and anabolic reactions occurs at millions per second.

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  • Biochemical Reactions

    • Basic principles, yielding products from reactants:

      • Energetically Favorable: Products have less energy than reactants (exothermic).

      • Energetically Unfavorable: Products have higher energy than reactants (endothermic).

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  • Energy Dynamics in Reactions

    • Energy difference signifies the stability of electrons and molecules.

    • Ionic bonds and other weaker interactions do not store energy.

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  • Energetically Stable States

    • In the presence of O2, carbon's stable state is CO2, and the stable state of hydrogen is water (H2O).

    • Organisms utilize energy to break down CO2 and H2O into free, unstable atoms, later stabilizing them at CH2O.

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  • Photosynthesis Overview

    • Reaction process involves sunlight energy, CO2, and H2O conversion into CH2O and O2 while releasing heat energy.

    • CH2O holds chemical energy between its states.

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  • Importance of CH2O

    • Key points:

      1. Carries chemical energy.

      2. Provides usable carbon source for processes.

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  • Gibbs Free Energy

    • ΔG: Represents the change in free energy between reactants and products.

    • Negative ΔG: Favorable, energy lost in reactions (catabolism).

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  • Positive ΔG

    • Positive ΔG: Unfavorable, requires energy input (anabolism).

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  • Reduction and Oxidation

    • Energy transfer correlated with electron gain/loss:

      • Reduction: Gain of electrons, more negative charge.

      • Oxidation: Loss of electrons, more positive charge.

    • Occurs in complementary redox reactions.

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  • Understanding Electrons

    • Electrons are units of energy and charge; not all have the same energy, influencing processes accordingly.

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  • Second Law of Thermodynamics

    • States that disorder in an isolated system is always increasing.

    • Entropy: Measure of disorder, with elements striving for high entropy (low energy state).

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  • Reaction Rates

    • Favorable reactions result in products with lower energy states, increasing disorder and releasing heat.

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  • Assessment of Reaction Dynamics

    • Rate of reactions can be favorable or unfavorable, independent of product energy assessment.

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  • Reaction Speed example

    • Example of wood decay: a favorable reaction taking time due to necessary molecular contact for bond breaking.

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  • Activation Energy

    • Energy needed to produce sufficient thermal motion for reactions to occur and pass through unstable intermediates.

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  • Influencing Reaction Rate

    • The rate of reactions can be increased (e.g., through heat) while maintaining thermodynamic properties.

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  • Control through Cells

    • Oxidation in cells occurs gradually to allow energy harvesting efficiently through enzymes.

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  • Enzyme Function

    • Enzymes lower activation energy by stabilizing reactants and intermediates, conducting reactions on demand.

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  • Energy Recovery through Enzymes

    • Reaction energy is captured for future use while maintaining ΔG and Δentropy consistency.

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  • Unfavorable Reactions

    • Reactions with positive ΔG require energy input and yield higher energy products that are more organized.

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  • Enzyme Role in Coupling Reactions

    • Enzymes couple unfavorable reactions with favorable ones to drive processes efficiently.

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  • Metabolism Flow

    • Encompasses both catabolism and anabolism, indicating energy transition within biological systems.

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  • Activated Carriers

    • Molecules like ATP serve as activated carriers for energy and biosynthetic pathways, crucial for metabolic processes.

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  • Integrated Control of Biosynthesis

    • Both anabolism and catabolism are coordinated and managed by proteins, ensuring efficiency and stability in cellular chemistry.

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