Biochemistry: Molecular Genetics and Macromolecules
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Questions and Answers

What is the primary reason why water serves as the universal intracellular and extracellular medium?

  • Its ability to dissolve ionic compounds
  • Its high dielectric constant
  • Its ability to form hydrogen bonds and its polar character (correct)
  • Its ability to hydrate ions

    • What is the term used to describe substances that can readily dissolve in water?

  • Polar
  • Hydrophobic
  • Ionic
  • Hydrophilic (correct)

    • What is the main reason why ionic compounds like NaCl can dissolve in water?

  • The polar character of water
  • The formation of hydration shells and the high dielectric constant of water (correct)
  • The high dielectric constant of water
  • The formation of hydrogen bonds between NaCl and water

    • What is the term used to describe the shells of water molecules that surround ions in solution?

    <p>Hydration shells</p> Signup and view all the answers

    What is the result of the interaction between the negative ends of the water dipoles and cations, and the positive ends and anions?

    <p>The hydration of ions</p> Signup and view all the answers

    Why do nonpolar substances like hydrocarbons show only limited solubility in water?

    <p>Because they cannot form hydrogen bonds</p> Signup and view all the answers

    What is the outcome of the energy released in the interaction between ions and dipolar water molecules?

    <p>The overcoming of charge-charge interactions stabilizing the crystal</p> Signup and view all the answers

    What is the timeframe represented by successive frames in the schematic 'motion picture'?

    <p>Picoseconds</p> Signup and view all the answers

    Which of the following macromolecules is responsible for storing and transcribing genetic information?

    <p>Nucleic acids</p> Signup and view all the answers

    What is the main function of lipids in biological systems?

    <p>Energy storage and membranes</p> Signup and view all the answers

    Which of the following is NOT a characteristic of prokaryotic cells?

    <p>They have a true nucleus</p> Signup and view all the answers

    What is the role of pili in prokaryotic cells?

    <p>They aid in attaching the organism to other cells or surfaces</p> Signup and view all the answers

    What is the location of the DNA in prokaryotic cells?

    <p>In the form of one or more molecules that exist free in the cytosol</p> Signup and view all the answers

    Which of the following is an example of a biological function of proteins?

    <p>All of the above</p> Signup and view all the answers

    What is the term for the process of forming macromolecules through condensation reactions of monomers?

    <p>Polymerization</p> Signup and view all the answers

    What is the field of study that seeks to understand heredity and the expression of genetic information in molecular terms?

    <p>Molecular genetics</p> Signup and view all the answers

    What is the primary function of the dihydrogen phosphate–hydrogen phosphate system in cells?

    <p>To control intracellular pH</p> Signup and view all the answers

    Which system provides significant buffering capacity in blood?

    <p>The carbonic acid–bicarbonate system</p> Signup and view all the answers

    What is the definition of a system in bioenergetics?

    <p>Any part of the universe that we choose for study</p> Signup and view all the answers

    Which of the following is an example of a closed system?

    <p>A sealed bottle of soda</p> Signup and view all the answers

    What is the primary difference between an open system and a closed system?

    <p>The ability to exchange matter</p> Signup and view all the answers

    Should a human be considered an open, closed, or isolated system?

    <p>An open system</p> Signup and view all the answers

    What is the definition of internal energy (U) in a system?

    <p>The total energy of a system that can be exchanged through simple physical processes or chemical reactions</p> Signup and view all the answers

    What is the characteristic of an isolated system?

    <p>It can exchange neither energy nor matter</p> Signup and view all the answers

    What is the direction of a thermodynamically favored process?

    <p>In the direction that minimizes free energy</p> Signup and view all the answers

    Which of the following is a characteristic of exergonic processes?

    <p>Negative free energy change</p> Signup and view all the answers

    What is the role of a catalyst in a thermodynamically favored process?

    <p>It increases the rate of the reaction</p> Signup and view all the answers

    What is the significance of the entropy of an open system?

    <p>It can decrease in certain cases</p> Signup and view all the answers

    What is the equation that describes the folding of proteins?

    <p>ΔG = ΔH - TΔS</p> Signup and view all the answers

    What is the significance of the free energy change, ΔG?

    <p>It is a measure of the maximum useful work obtainable from a reaction</p> Signup and view all the answers

    What is the consequence of life involving a temporary decrease in entropy?

    <p>Energy is expended</p> Signup and view all the answers

    What is the role of enzymes in biological systems?

    <p>They selectively increase the rate of specific thermodynamically favorable reactions</p> Signup and view all the answers

    What is the characteristic of 'high-energy' phosphate compounds?

    <p>They have very large negative free energies of hydrolysis</p> Signup and view all the answers

    What is the result of the release of the orthophosphate ion in a hydrolysis reaction?

    <p>An entropy increase in the system</p> Signup and view all the answers

    What is the abbreviation for inorganic phosphate?

    <p>Pi</p> Signup and view all the answers

    Why is resonance stabilization important in phosphate hydrolysis reactions?

    <p>It applies to all phosphate hydrolysis reactions</p> Signup and view all the answers

    What is the characteristic of the hydrolysis reactions of biochemically important phosphate compounds?

    <p>They have very large negative free energies of hydrolysis</p> Signup and view all the answers

    What is the role of orthophosphate ion in biological systems?

    <p>It is a byproduct of hydrolysis reactions</p> Signup and view all the answers

    Why are phosphate hydrolysis reactions favored in biological systems?

    <p>They lead to an increase in entropy</p> Signup and view all the answers

    What is the significance of ATP molecule in biological systems?

    <p>It is a source of energy</p> Signup and view all the answers

    What is the branch of science that seeks to describe the structure, organization, and functions of living matter in molecular terms?

    <p>Biochemistry</p> Signup and view all the answers

    Biochemistry can be divided into how many principal areas?

    <p>Three</p> Signup and view all the answers

    Proteins, polysaccharides, nucleic acids, and lipids are examples of macromolecules.

    <p>True</p> Signup and view all the answers

    ___________ are formed by condensation reactions of the monomers.

    <p>Polymers</p> Signup and view all the answers

    What is the basic unit of biological organization?

    <p>The cell</p> Signup and view all the answers

    Match the following macromolecules with their biological functions:

    <p>Polysaccharides = Structure, energy storage Nucleic acids = Storage and transcription of genetic information Proteins = Structure, enzymes, hormones, receptors Lipids = Energy storage, membranes</p> Signup and view all the answers

    What is the equation that expresses the first law of thermodynamics?

    <p>ΔU = q - w</p> Signup and view all the answers

    What is enthalpy defined as?

    <p>H = U + PV</p> Signup and view all the answers

    What does the Gibbs free energy include?

    <p>Both energy and entropy</p> Signup and view all the answers

    Processes with a negative free energy change are endergonic.

    <p>False</p> Signup and view all the answers

    In biological systems, what type of reactions drive countless reactions by coupling with them?

    <p>Exergonic reactions</p> Signup and view all the answers

    Study Notes

    Genetic Biochemistry

    • Genetic biochemistry is the chemistry of processes and substances that store and transmit biological information
    • It's also the province of molecular genetics, which seeks to understand heredity and the expression of genetic information in molecular terms

    Macromolecules

    • Many macromolecules are polymers, formed by condensation reactions of monomers
    • Examples of macromolecules:
      • Proteins
      • Polysaccharides
      • Nucleic acids
      • Lipids

    Biological Functions of Macromolecules

    • Polysaccharides: structure, energy storage
    • Nucleic acids: storage and transcription of genetic information
    • Proteins: structure, enzymes, hormones, receptors
    • Lipids: energy storage, membranes

    Biochemistry as a Biological Science

    • The cell is the basic unit of biological organization
    • Cell types:
      • Prokaryotes (always unicellular, including true bacteria and archaea)
      • Eukaryotes (may be unicellular or multicellular)

    Cell Structure

    • Prokaryotic cell structure:
      • Plasma membrane and cell wall
      • Cytoplasm with cytosol, DNA, and ribosomes
      • Cell surface may have pili and flagellae

    The Role of Water in Biological Processes

    • Water serves as the universal intracellular and extracellular medium due to its:
      • Ability to form hydrogen bonds
      • Polar character
    • Hydrophilic substances can readily dissolve in water
    • Water is an excellent solvent for ionic compounds due to:
      • Hydration shells
      • High dielectric constant

    Energy, Heat, and Work

    • Bioenergetics: the study of how organisms capture, transform, store, and utilize energy
    • Systems:
      • Isolated: exchanges neither energy nor matter
      • Closed: exchanges energy but not matter
      • Open: exchanges both energy and matter
    • Human and organisms are considered open systems
    • Internal energy (U) includes all forms of energy that can be exchanged via physical or chemical processes

    Free Energy: The Second Law in Open Systems

    • Free energy (ΔG) determines the favorability of a process
    • ΔG = ΔH - TΔS
    • Processes with -ΔG are exergonic (favorable), while those with +ΔG are endergonic (unfavorable)
    • Enzymes increase reaction rates but do not change the favored direction
    • The entropy of an open system can decrease

    High Energy Phosphate Compounds

    • These compounds have very large negative free energies of hydrolysis
    • Examples:
      • ATP
      • Phosphocreatine
      • Phosphoenolpyruvate
    • Hydrolysis reactions release orthophosphate (Pi), which increases entropy and is therefore favored
    • Resonance stabilization applies to all phosphate hydrolysis reactions

    Biochemistry: Course Overview

    • Attendance in laboratories and seminars is mandatory, with only one allowed absence without excuse and one allowed lateness per semester
    • Late arrivals are considered absences, with a 5-point deduction for every subsequent lateness
    • Students must submit a doctor's excuse for absences within 7 days to the course coordinator

    Assessment Structure

    • Total of 200 points
    • Exam (final): 100 points
    • Midterms (winter and summer): 25 points each
    • Seminars and labs: 10 points each (winter and summer)
    • Lectures: 5 points each (winter and summer)

    Literature

    • Required textbooks: Harpers Illustrated Biochemistry (at least 29th Edition), Lubert Stryer's Biochemistry (at least 4th Edition), and Biochemistry: Concepts and Connections
    • Recommended texts: None listed

    What is Biochemistry?

    • Biochemistry is the study of the structure, organization, and functions of living matter in molecular terms
    • Three principal areas of biochemistry:
      • Structural chemistry of living matter's components and their relationships to biological function
      • Metabolism: the totality of chemical reactions that occur in living matter
      • Genetic biochemistry: the chemistry of biological information storage and transmission

    Biochemistry as a Chemical Science

    • Macromolecules: proteins, polysaccharides, nucleic acids, and lipids
    • Many macromolecules are polymers formed by condensation reactions of monomers
    • Biological functions of macromolecules:
      • Polysaccharides: structure, energy storage
      • Nucleic acids: storage and transcription of genetic information
      • Proteins: structure, enzymes, hormones, receptors
      • Lipids: energy storage, membranes

    Biochemistry as a Biological Science

    • The cell is the basic unit of biological organization
    • Prokaryotes (e.g. bacteria, archaea) are unicellular, with a plasma membrane, cell wall, cytoplasm, and freely floating DNA and ribosomes
    • The cell surface may have pili, flagellae, and other features

    The Matrix of Life: Weak Interactions in an Aqueous Environment

    • Noncovalent interactions:
      • Hydrogen bonds
      • Dipole-dipole interactions
      • Van der Waals forces
    • Importance of weak interactions in biomolecular structures

    The Role of Water in Biological Processes

    • Hydrogen bonding in biological structures
    • Water serves as a universal intracellular and extracellular medium due to its ability to form hydrogen bonds and its polar character
    • Water is an excellent solvent for ionic compounds
    • Hydration of ions in solution
    • Nonpolar substances (hydrophobic, lipophilic) have limited solubility in water

    Ionic Equilibria

    • Brønsted-Lowry definition of acids and bases
    • Strong acids and bases, and their conjugate forms
    • Buffered solutions:
      • Minimize pH changes upon addition of acid or base
      • Functioning near the pKa, where the conjugate acid and base are present in nearly equimolar concentrations

    Energetics of Life

    • Bioenergetics: the study of energy capture, transformation, storage, and utilization in living organisms
    • Energy, heat, and work
    • Internal energy (U): the total energy of a system
    • Thermodynamic systems:
      • Isolated: no exchange of energy or matter
      • Closed: exchange of energy, but not matter
      • Open: exchange of both energy and matter

    Free Energy and Chemical Reactions

    • Gibbs free energy (G): a function of state that includes both energy and entropy
    • Free energy change (ΔG) = ΔH - TΔS
    • Favorable processes: negative ΔG
    • Unfavorable processes: positive ΔG
    • High-energy phosphate compounds:
      • ATP and its hydrolysis reactions
      • Free energy sources in biological systems

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