MBoC Chapter 2: Weak Forces, Building Blocks, and pH
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Questions and Answers

In the amino acid cysteine, what is the name of the oxidized, cross-bridging form of the sulfhydryl group?

disulfide

What is the stable ion formed from phosphoric acid in the context of phosphate?

  • Phosphate ion (correct)
  • Hydroxyl ion
  • Hydronium ion
  • Hydrogen ion

    • The dissolved substance in a liquid is termed a _______.

    solute

    Compounds with a high-energy bond are easily broken down in cells.

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

    Biological macromolecules are mostly polymers of small organic molecules composed of which of the following atoms?

    <p>Carbon, Nitrogen, Hydrogen, Oxygen</p> Signup and view all the answers

    Hydrogen bonds in water are long-lived and not easily broken by thermal motions of molecules.

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

    What role do hydrophobic molecules play in aqueous solutions?

    <p>Hydrophobic molecules interact with each other in aqueous solutions to minimize disruption of water structure.</p> Signup and view all the answers

    Weak, non-covalent attractive forces drive most important biochemical ________.

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

    Match the following chemical groups commonly encountered in biological molecules with their descriptions:

    <p>Amines and amides = Compounds containing a carbon linked to a nitrogen Hydroxyl group = Contains an -OH group and is positively charged Alcohol = Compounds containing a carbon bonded to an oxygen</p> Signup and view all the answers

    What are substances that release hydrogen ions into a solution called?

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

    What are substances that reduce the number of hydrogen ions in a solution called?

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

    What is the term for a high-energy bond found in molecules such as ATP?

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

    Weak acids only partially dissociate in water.

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

    _______ ions can move from one water molecule to another and create two ionic species in solution.

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

    What is the functional group called that consists of a carbon atom double-bonded to an oxygen atom?

    <p>carbonyl group</p> Signup and view all the answers

    Which functional group is called as 'carboxylic acid'?

    <p>−COOH group</p> Signup and view all the answers

    Amides are charged in water.

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

    An example of a condensation reaction is the formation of esters by combining an acid and an ______.

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

    What is the common name for a compound formed from a phosphate and a free hydroxyl group?

    <p>phosphate ester</p> Signup and view all the answers

    What do buffers resist?

    <p>changes in pH</p> Signup and view all the answers

    Buffers maintain a solution within a wide pH range.

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

    Blood is buffered by _________ acid.

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

    What is the primary role of bicarbonate in buffering blood?

    <p>Absorbing H+ ions</p> Signup and view all the answers

    What is the purpose of using a logarithmic scale for pH?

    <p>Provide a more simplified notation for the concentration of H+ ions.</p> Signup and view all the answers

    PH is defined as pH = _log10[H+].

    <p>pH = -log10[H+]</p> Signup and view all the answers

    What is a weak base?

    <p>Compounds that partially reduce the number of hydrogen ions in a solution.</p> Signup and view all the answers

    What is the pH value at which an acid is half dissociated?

    <p>pH = pKa</p> Signup and view all the answers

    Study Notes

    Biological Macromolecules and Weak Forces

    • Biological macromolecules are mostly polymers of small organic molecules, including sugars, fatty acids, nucleotides, and amino acids.
    • These molecules are composed of a handful of atoms, including carbon, nitrogen, hydrogen, and oxygen.

    Properties of Water

    • Water molecules are polar, with oxygen attracting electrons more strongly than hydrogen, resulting in a weak negative charge on oxygen and weak positive charges on hydrogen.
    • This polarity enables water molecules to form weak non-covalent bonds, known as hydrogen bonds, which are responsible for many of water's unique properties.
    • Hydrogen bonds in water are short-lived and rapidly broken by thermal motions of molecules.

    Cohesive and Hydrophobic Properties

    • Hydrogen bonding in water makes it cohesive, with high surface tension, and requires relatively high temperatures to be converted to a gas.
    • Polar molecules that can form hydrogen bonds dissolve readily in water, while ions that can interact with water also dissolve readily.
    • Non-polar or hydrophobic molecules cannot dissolve in water and are forced to interact with each other in aqueous solutions.

    Carbon-Containing Molecules

    • Nearly all molecules in cells are based on carbon, which can form large molecules because it can form four covalent bonds.
    • The C-C bond is highly stable and is used to form diverse molecules.

    Four Major Families of Small Organic Molecules

    • Sugars
    • Fatty acids
    • Nucleotides
    • Amino acids

    Polymers and Macromolecules

    • Sugars, nucleotides, and amino acids can be covalently linked together to form polymers.
    • These long-chain macromolecules are largely responsible for the extraordinary properties of living organisms and constitute a large fraction of cellular mass.

    Weak Non-Covalent Interactions

    • Three kinds of weak non-covalent interactions play important roles in cells:
      • Electrostatic interactions (ionic bonds or salt bridges) between oppositely charged molecules.
      • Hydrogen bonds between molecules, which are stronger when all three atoms in the bond form a straight line.
      • Van der Waals interactions between electrons in neighboring atoms, which are highly distance-dependent.

    Hydrophobic Effects

    • Hydrophobic molecules are non-polar and cannot interact with water.
    • Hydrophobic molecules displace water molecules and disrupt the hydrogen bonding network of water.
    • Hydrophobic effects drive many important molecular interactions in cells, including formation of lipid bilayers, protein folding, and interactions between proteins.

    Functional Groups

    • Biological molecules have a number of functional groups that are used again and again in biochemical events.
    • Common functional groups include:
      • Amines and amides
      • Carbonyl groups
      • Hydroxyl groups
      • Carboxyl groups
      • Esters
      • Phosphates
      • Sulfhydryl groups### Phosphate Groups and Acid Anhydrides
    • Phosphate groups are often attached to proteins and can form a very stable structure with a carboxyl group or two or more phosphate groups, giving an acid anhydride.
    • These compounds are easily hydrolyzed in the cell and are sometimes said to contain a "high-energy" bond.

    Sulfhydryl Group

    • The sulfhydryl group is a functional group found in the amino acid cysteine.
    • It can exist in a reduced form or more rarely in an oxidized, cross-bridging form.

    Phosphates and Water

    • Inorganic phosphate is a stable ion formed from water and can dissolve in water.
    • Phosphate groups can be attached to proteins and are often written as Pi.
    • Water is an excellent solvent for many substances due to its polar bonds.

    Hydrogen Ion Exchange

    • Positively charged hydrogen ions (H+) can spontaneously move from one water molecule to another, creating two ionic species.
    • pH is a measure of the concentration of hydrogen ions in a solution.

    Acids and Bases

    • Substances that release hydrogen ions into solution are called acids.
    • Substances that reduce the number of hydrogen ions in a solution are called bases.
    • pH is a measure of the acidity or basicity of a solution.
    • Strong acids readily release a proton in water, whereas weak acids only partially dissociate their proton.

    Example of Weak Acid

    • The carboxyl group is an example of a weak acid, which dissociates to give a hydronium ion and a hydroxyl ion.### Acids and Bases

    • A weak base reduces the number of H+ ions, making OH- ions that combine with H+ ions to form water.

    • A strong base, like sodium hydroxide, directly removes H+ ions from water.

    pH Scale

    • pH is defined as the concentration of H+ ions.
    • pH = -log10[H+] is used to provide a simple notation for the concentration of H+ ions.
    • pH scale is a logarithmic scale used to measure the acidity of a solution.

    Bases

    • Bases are substances that reduce the number of H+ ions in a solution.
    • Weak bases, like ammonia, contain an amino group (-NH2) and have a weak tendency to accept an H+ ion from water.
    • Strong bases, like sodium hydroxide, directly combine with H+ ions.

    Buffers

    • Buffers resist changes in pH and maintain a solution within a tight pH range.
    • Buffers are weak acids or bases that can bind or release H+ ions within a specific range.
    • Buffers work best to maintain pH around their pKa.

    Biological Importance

    • The interior of the cell is kept close to pH 7 by the presence of buffers.
    • Blood is buffered by carbonic acid, which releases a proton to form bicarbonate and H+ ions.
    • Bicarbonate acts as a buffer by absorbing H+ ions released into the blood.

    Laboratory Applications

    • Numerous buffers are used in the laboratory to maintain the pH of solutions near physiological levels.
    • Buffers are essential to maintain the pH of solutions in biological experiments.

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    Description

    This lecture covers the basic structure of biological macromolecules, including their composition and functional groups. It also introduces weak forces and pH in the context of biochemistry.

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