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    1 IntroThermo

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    Saghar Asi Awan
    The document summarizes key points from a biochemistry lecture, including: 1) It discusses the central themes of biochemistry that will be covered - the chemical basis of life, complementarity of form and function, and the four S's (size, shape, solubility, stability). 2) It outlines the molecular components that make up living cells, such as water, proteins, nucleic acids, carbohydrates and lipids. 3) It explains how living organisms are able to work against the second law of thermodynamics by coupling exergonic and endergonic reactions through mechanisms like ATP hydrolysis.

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    1 IntroThermo

    Uploaded by

    Saghar Asi Awan
    19 views9 pages
    The document summarizes key points from a biochemistry lecture, including: 1) It discusses the central themes of biochemistry that will be covered - the chemical basis of life, complementarity of form and function, and the four S's (size, shape, solubility, stability). 2) It outlines the molecular components that make up living cells, such as water, proteins, nucleic acids, carbohydrates and lipids. 3) It explains how living organisms are able to work against the second law of thermodynamics by coupling exergonic and endergonic reactions through mechanisms like ATP hydrolysis.

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    Is is I is a little more than

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    1_IntroThermo

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    The document summarizes key points from a biochemistry lecture, including: 1) It discusses the central themes of biochemistry that will be covered - the chemical basis of life, complementarity of form and function, and the four S's (size, shape, solubility, stability). 2) It outlines the molecular components that make up living cells, such as water, proteins, nucleic acids, carbohydrates and lipids. 3) It explains how living organisms are able to work against the second law of thermodynamics by coupling exergonic and endergonic reactions through mechanisms like ATP hydrolysis.

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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
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    19 views9 pages

    1 IntroThermo

    Uploaded by

    Saghar Asi Awan
    The document summarizes key points from a biochemistry lecture, including: 1) It discusses the central themes of biochemistry that will be covered - the chemical basis of life, complementarity of form and function, and the four S's (size, shape, solubility, stability). 2) It outlines the molecular components that make up living cells, such as water, proteins, nucleic acids, carbohydrates and lipids. 3) It explains how living organisms are able to work against the second law of thermodynamics by coupling exergonic and endergonic reactions through mechanisms like ATP hydrolysis.

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    You are on page 1of 9

    9/6/20

    Lecture 1 (9/4/20)
    • Reading from Wed: Ch1, 1-5, 12-14 Sfwjfx!
    • Reading for today: Ch1, 8-11, 15-16, 21-27 pg!PSHP
    Sfwjfx!pg!IT! Ch13, 496-497 Sfwjfx!pg!
    DFMM!CJPMPHZ UIFSNP
    Ch2, 47
    • Problems for today: Ch1 (text) 1,2,3,4,7
    Ch13 (text) 1,2,3,4
    Ch2 (text) 3 (study guide) 1,2
    NEXT
    • Reading: Ch2, 47-58

    • Problems: Ch2 (text) 1,2


    Ch2 (study guide) 3,4,5,6,7

    Lecture 1 (9/4/20)
    OUTLINE
    What is Biochemistry?

    Themes throughout the Course

    Molecular Components of Life

    Thermodynamics

    WATER

    1
    9/6/20

    Biochemistry Definition

    A living cell is a self-assembling, self-adjusting,


    self-perpetuating isothermal open system. This
    system consists of many consecutive, linked
    organic reactions that are promoted by organic
    catalysts produced by the cell; it operates on the
    principle of maximum economy of parts and
    processes.

    Biochemistry Is
    the Chemistry of Living Matter
    Living matter is characterized by:
    • a high degree of complexity and organization
    • the extraction, transformation, and systematic use of
    energy to create and maintain structures and to do
    work
    • the interactions of individual components being
    dynamic and coordinated
    • the ability to sense and respond to changes in
    surroundings
    • a capacity for fairly precise self-replication while
    allowing enough change for evolution
    In order to understand these processes, biochemists have tended
    to isolate individual components and study them: reductionists

    2
    9/6/20

    Central Themes of Biochemistry I


    There are THREE repetitive themes:
    1. Chemical Basis: try to explain life in terms of
    equilibria, kinetics, reactivity, and thermodynamic
    quantities
    2. Complementarity: Form & Function.
    3.
    3. The
    Do 4they
    S’s:still teach the 3 R’s?
    Size
    (Reading, ‘Riting, ‘Rithmatic)
    Shape
    Solubility
    Stability
    For each of the biological components of life, we will
    describe them in these terms.

    Central Themes of Biochemistry I


    There are THREE repetitive themes:
    1. Chemical Basis: try to explain life in terms of
    equilibria, kinetics, reactivity, and thermodynamic
    quantities
    2. Complementarity: Form & Function.
    3. The 4 S’s:
    Size
    Shape
    Solubility
    Stability
    For each of the biological components of life, we will
    describe them in these terms.

    3
    9/6/20

    History of Biochemistry

    Regardless of the
    enormity of the field
    of biochemistry, it is
    the study of SMALL
    things.

    Sizes of Things

    Scaler
    http://www.htwins.net/scale2/

    4
    9/6/20

    Cells are complex ORGANIZED units of life

    The Molecular Hierarchy of Structure

    Nucleic Acids

    Proteins

    Lipids

    Carbohydrates

    Nucleic Acids: covalent polymer of nucleotides

    Proteins: covalent polymer of amino acids

    Carbohydrates: covalent polymer of monosaccharides

    Lipids/membranes: non-covalent supramolecular complex of phospholipids

    5
    9/6/20

    Components of Life
    Data from E. coli:
    Component % by weight Complexity*
    Water 70 1
    Protein 15 3000
    Nucleic Acids 7 1001
    Carbohydrate 3 50
    Lipids 2 40
    Small organics 2 500
    Inorganics 1 12
    *number of types
    Before we discuss each component,
    lets review thermodynamics that makes
    these possible

    Energetics of Life
    The laws of thermodynamics (thermo, “energy”;
    dynamics, “change”) apply to all matter and all
    energy transformations in the universe.
    1st & 2nd Laws of Thermodynamics:
    1) Energy can never be created or destroyed,
    but can be interconverted.
    2) The universe tends toward more
    disorder (randomness) [When energy is
    converted from one form to another, some of that energy
    becomes unavailable to do work.]

    6
    9/6/20

    Energetics of Life
    Chemistry of Life: Biochemistry

    Organisms Work Against the Second Law Big-


    Time to Build the Cell

    Complexity and Organization

    Take as the system, the reactions


    creating the cell:

    Chaos ⇌ Cell
    DSsystem = Scell – Schaos
    (small) (large)
    DSsystem = ⊝
    DSuniverse > 0 (⊕) (2nd Law)
    DSuniverse = DSsystem + DSsurroundings Entropy of surroundings can increase by

    ⊕ release of heat by the system: First Law


    to the rescue!!!

    7
    9/6/20

    Organisms Use the First Law Big-Time


    (perform energy transformations) to Stay Alive

    • Living organisms exist in a dynamic steady


    state and are never at equilibrium with their
    surroundings.
    • As the entropy* of the universe increases,
    creating and maintaining order requires work
    and energy.
    • Energy coupling allows living organisms to
    transform matter into energy.
    *Entropy is a measure of the disorder in a system.
    It takes energy to impose order on a system. Unless energy is applied to a
    system, it will be arranged randomly or “disordered.”
    A little more about “coupling”….....

    Equilibrium and ΔG° Measure


    Favorability of a Reaction
    Spontaneity
    Equilibrium and ΔG° Measure
    Not all biochemical reactions are favorable in the
    Favorability
    Spontaneity
    direction that the cell needs.of a Reaction
    Not all biochemical
    Recall reactions are for
    from gen-chem, favorable in the
    a given direction that the cell needs.
    reaction:
    Recall from gen-chem:

    8
    9/6/20

    Organisms Use the First Law Big-Time


    (perform energy transformations) to Stay Alive

    Favorable and Unfavorable Reactions


    • The breakdown of some metabolites
    releases a significant amount of energy
    (exergonic).
    – Their cellular concentration is far higher
    than their equilibrium concentration.
    DS > 0 – Metabolites, such as ATP, NADH, NADPH,
    can be synthesized using the energy from
    sunlight and fuels…..
    • Synthesis of complex molecules and many
    DG°< 0 other metabolic reactions requires energy
    catabolism
    (endergonic).
    – A reaction might be thermodynamically
    unfavorable (DG°> 0).
    DG°> 0 • Creating order requires work and energy.
    anabolism

    Energy Coupling
    • Chemical coupling of exergonic and endergonic
    reactions allows otherwise unfavorable reactions.
    • TWO basic mechanisms:
    – e.g., The hydrolysis of the “high-energy” molecule (ATP),
    which is exergonic, is coupled with an otherwise endergonic
    reaction during an enzyme mechanism.
    – e.g., a series of otherwise endergonic reactions during a
    metabolic pathway are linked in the reaction series to an
    overwhelming exergonic reaction (all catalyzed by enzymes).

    Inorganic phosphate = Pi
    Pyrophosphate = PPi

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