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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?
The dissolved substance in a liquid is termed a _______.
solute
Compounds with a high-energy bond are easily broken down in cells.
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Biological macromolecules are mostly polymers of small organic molecules composed of which of the following atoms?
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Hydrogen bonds in water are long-lived and not easily broken by thermal motions of molecules.
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What role do hydrophobic molecules play in aqueous solutions?
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Weak, non-covalent attractive forces drive most important biochemical ________.
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Match the following chemical groups commonly encountered in biological molecules with their descriptions:
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What are substances that release hydrogen ions into a solution called?
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What are substances that reduce the number of hydrogen ions in a solution called?
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What is the term for a high-energy bond found in molecules such as ATP?
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Weak acids only partially dissociate in water.
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_______ ions can move from one water molecule to another and create two ionic species in solution.
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What is the functional group called that consists of a carbon atom double-bonded to an oxygen atom?
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Which functional group is called as 'carboxylic acid'?
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Amides are charged in water.
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An example of a condensation reaction is the formation of esters by combining an acid and an ______.
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What is the common name for a compound formed from a phosphate and a free hydroxyl group?
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What do buffers resist?
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Buffers maintain a solution within a wide pH range.
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Blood is buffered by _________ acid.
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What is the primary role of bicarbonate in buffering blood?
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What is the purpose of using a logarithmic scale for pH?
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PH is defined as pH = _log10[H+].
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What is a weak base?
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What is the pH value at which an acid is half dissociated?
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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
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The carboxyl group is an example of a weak acid, which dissociates to give a hydronium ion and a hydroxyl ion.### Acids and Bases
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A weak base reduces the number of H+ ions, making OH- ions that combine with H+ ions to form water.
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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.
