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Questions and Answers
What is the definition of an amino acid?
An organic compound that contains both an amino group and a carboxyl group.
How many naturally occurring amino acids are there, and how many of them are typically present in proteins?
What is the term used to denote the loss of a H+ ion?
deprotonated
The side chains of the amino acids vary in ____, _____, charge, and chemical reactivity.
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Nonpolar amino acids are attracted to water molecules.
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Match the amino acid with its isoelectric point:
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What is the pH at which amino acid solutions have no net charge?
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All acid groups are deprotonated at neutral pH.
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What are the 9 amino acids that the human body cannot produce in sufficient quantities and must be obtained from food?
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Which of the following is an example of a nonpolar neutral amino acid?
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All essential amino acids can be synthesized by the human body in sufficient quantities.
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The structure of ___ of the 20 standard amino acids possess a chiral center.
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How many stereoisomers are possible for the amino acids isoleucine and threonine, which possess two chiral centers?
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Why are most amino acids not very soluble in water?
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What is a zwitterion?
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In acidic solution, the zwitterion ___ a proton to form a positively charged ion.
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Match the following amino acid forms with the given pH values:
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What is the direction of migration for Lysine at pH 12.0?
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What is the direction of migration for Glutamic acid at pH 2.0?
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What is the direction of migration for Serine at pH 5.68?
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Which standard amino acid contains a sulfhydryl group?
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Peptides are unbranched chains of amino acids.
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Peptide chains have _________ because their two ends are different.
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What is the primary protein structure?
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Which biochemist determined the primary structure of the protein hormone insulin in 1953?
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Animal insulin is structurally very different from human insulin.
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What is the function of insulin in the human body?
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What is the abbreviated formula for the tripeptide containing the amino acids glycine, alanine, and serine?
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What are the IUPAC rules for naming small peptides?
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What distinguishes one peptide from another structurally?
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How many constitutional isomers are possible for a peptide containing one of each of four different kinds of amino acids?
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What are the two most common types of secondary protein structure?
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What type of interaction is responsible for both alpha helix and beta pleated sheet secondary structures?
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What atoms lie in the same plane for two amino acids linked through a peptide linkage?
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How many isomers are possible for a pentapeptide containing 5 different amino acids?
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Which of the following are biochemically important small peptides?
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Oxytocin and vasopressin are both nonapeptides.
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Match the small peptide with its function:
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What is the defining line for a protein in terms of amino acid residues?
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Study Notes
Proteins: Characteristics and Structure
- Proteins are the most abundant substances in nearly all cells, accounting for about 15% of a cell's overall mass and almost half of a cell's dry mass.
- They contain the elements carbon, hydrogen, oxygen, and nitrogen, and sometimes sulfur, phosphorus, and iron.
- The average nitrogen content of proteins is 15.4% by mass.
Amino Acids: The Building Blocks of Proteins
- An amino acid is an organic compound that contains both an amino (!NH2) group and a carboxyl (!COOH) group.
- The 20 standard amino acids found in proteins are always a-amino acids.
- The general structural formula for an a-amino acid is:
a-Carbon atom
R Side chain
A Carboxyl group
H2N Amino group
H
Classification of Amino Acids
- Amino acids are classified into four categories based on their side-chain polarity:
- Nonpolar amino acids (9)
- Polar neutral amino acids (6)
- Polar acidic amino acids (2)
- Polar basic amino acids (3)
Nonpolar Amino Acids
- Nonpolar amino acids are hydrophobic ("water-fearing") and are generally found in the interior of proteins.
- Examples: glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan.
Polar Neutral Amino Acids
- Polar neutral amino acids are more soluble in water than nonpolar amino acids and can hydrogen bond to water.
- Examples: serine, cysteine, threonine, asparagine, glutamine, tyrosine.
Polar Acidic Amino Acids
- Polar acidic amino acids have a negative charge at physiological pH.
- Examples: aspartic acid, glutamic acid.
Polar Basic Amino Acids
- Polar basic amino acids have a positive charge at physiological pH.
- Examples: lysine, arginine, histidine.
Essential Amino Acids
- Essential amino acids are amino acids that cannot be synthesized by the human body in adequate amounts and must be obtained from dietary sources.
- The 9 essential amino acids are: arginine*, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, and tryptophan.
- *Arginine is required for growth in children but not by adults.
Protein Classification
- Proteins can be classified based on their shape (fibrous, globular, or membrane) or function (enzymes, hormones, etc.).
- Protein classification is important for understanding their roles in the body and their functions in different biological processes.### Chirality and Amino Acids
- In the standard amino acids, except glycine, four different groups are attached to the alpha-carbon atom.
- Glycine is achiral, while the other 19 standard amino acids are chiral, meaning they have a chiral center and can exist in two non-superimposable mirror-image forms (enantiomers).
- In nature, only L-amino acids are found, and they are the preferred form.
Drawing Fischer Projection Formulas
- Rules for drawing Fischer projection formulas for amino acid structures:
- The —COOH group is at the top, the R group is at the bottom, positioning the carbon chain vertically.
- The —NH2 group is in a horizontal position, with positioning on the left denoting the L isomer and on the right denoting the D isomer.
Chiral Centers
- Two standard amino acids, isoleucine and threonine, possess two chiral centers, resulting in four stereoisomers.
- Only one of the L isomers is found in proteins.
Acid-Base Properties of Amino Acids
- Amino acids are white crystalline solids with high decomposition points and low solubility in water due to strong intermolecular forces.
- Both acidic (—COOH) and basic (—NH2) groups are present on the same carbon in an alpha-amino acid, making them charged species.
- In neutral solution, an amino acid molecule reacts with itself, resulting in a zwitterion, a molecule with both positive and negative charges but no net charge.
- Zwitterions can exist in equilibrium with positively and negatively charged ions, depending on pH.
pH-Dependent Forms of Amino Acids
- At low pH, the zwitterion accepts a proton to form a positively charged ion.
- At high pH, the zwitterion loses a proton to form a negatively charged ion.
- The structure of an amino acid changes with pH, resulting in three different forms: zwitterion, negative ion, and positive ion.
Isoelectric Points
- The pH at which an amino acid solution has no net charge is called its isoelectric point.
- At the isoelectric point, almost all amino acid molecules (>99%) are present in their zwitterion form.
- Every amino acid has a different isoelectric point, with 15 of the 20 amino acids having isoelectric points in the range of 4.8-6.3.### Amino Acids and Electrophoresis
- The three basic amino acids have higher isoelectric points, while the two acidic amino acids have lower isoelectric points.
- The isoelectric point of an amino acid is measured by observing its behavior in an electric field.
- In an electric field, a charged molecule is attracted to the electrode of opposite charge.
- At a high pH, an amino acid has a net negative charge and migrates toward the positive electrode.
- At a low pH, the opposite is true; with a net positive charge, the amino acid migrates toward the negative electrode.
- At the isoelectric point, migration does not occur because the zwitterions present have no net charge.
Separation of Amino Acids using Electrophoresis
- Mixtures of amino acids in solution can be separated by using their different migration patterns at various pH values.
- Electrophoresis is the process of separating charged molecules on the basis of their migration toward charged electrodes associated with an electric field.
- Amino acids can be separated via electrophoresis techniques, which involves applying a current to the solution and observing the migration patterns.
Cysteine: A Chemically Unique Amino Acid
- Cysteine is the only standard amino acid that has a side chain that contains a sulfhydryl group (SH group).
- The presence of this sulfhydryl group imparts to cysteine a chemical property that is unique among the standard amino acids.
- Cysteine readily dimerizes, that is, reacts with another cysteine molecule to form a cystine molecule, in the presence of mild oxidizing agents.
- The covalent disulfide bond of cystine is readily broken, using reducing agents, to regenerate two cysteine molecules.
Peptides
- A peptide is an unbranched chain of amino acids, each joined to the next by a peptide bond.
- Peptides are classified by the number of amino acids present in the chain, such as dipeptide (2 amino acids), tripeptide (3 amino acids), and so on.
- The name oligopeptide is loosely used to refer to peptides with 10 to 20 amino acid residues, and the name polypeptide is used to refer to longer peptides.
- A polypeptide is a long unbranched chain of amino acids, each joined to the next by a peptide bond.
Nature of the Peptide Bond
- The bonds that link amino acids together in a peptide chain are called peptide bonds.
- Peptide bonds are formed through a condensation reaction, where the carboxyl group of one amino acid interacts with the amino group of another amino acid.
- The products of this reaction are a molecule of water and a molecule containing the two amino acids linked by an amide bond.
- The peptide bond is a covalent bond between the carboxyl group of one amino acid and the amino group of another amino acid.
Directionality of Peptide Chains
- A peptide chain has directionality because its two ends are different.
- There is an N-terminal end and a C-terminal end.
- By convention, the sequence of amino acids in a peptide is written with the N-terminal end amino acid on the left.
- The end with the free H3N group is called the N-terminal end, and the end with the free COO group is called the C-terminal end.
- The individual amino acids within a peptide chain are called amino acid residues.
- An amino acid residue is the portion of an amino acid structure that remains, after the release of H2O, when an amino acid participates in peptide bond formation as it becomes part of a peptide chain.
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Description
This quiz covers the characteristics, building blocks, and structural characteristics of proteins, including amino acids, peptides, and more.
