lecture outline 2

Page 1

• 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 (-).

Page 14

• 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.

Page 28

• 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.

Page 31

• 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.

Page 36

• 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.