Protein Structure and Amino Acids
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Questions and Answers

What is the primary function of enzymes in relation to proteins?

  • They act as antibodies against infections.
  • They transport oxygen in the bloodstream.
  • They provide structural support in cells.
  • They facilitate metabolic processes. (correct)

How many amino acids are commonly found in mammalian proteins?

  • 100
  • 20 (correct)
  • 300
  • 50

What characterizes the carboxyl group of amino acids at physiological pH?

  • It is protonated and positively charged.
  • It forms a peptide bond.
  • It is dissociated and negatively charged. (correct)
  • It remains uncharged.

Which statement about amino acid side chains is true?

<p>They determine whether the amino acid is polar or nonpolar. (B)</p> Signup and view all the answers

What type of amino group does proline have?

<p>Secondary amino group (C)</p> Signup and view all the answers

What role do immunoglobulins play in the body?

<p>They fight infectious bacteria and viruses. (C)</p> Signup and view all the answers

Which type of bond typically stabilizes protein structures through amino acid interactions?

<p>Hydrogen bonds (D)</p> Signup and view all the answers

What occurs to carboxyl and amino groups during peptide formation?

<p>They combine through peptide linkage. (C)</p> Signup and view all the answers

What is the isoelectric point (pI) of alanine?

<p>5.7 (D)</p> Signup and view all the answers

At pH above the isoelectric point of plasma proteins, what is the charge on the proteins?

<p>Negative (C)</p> Signup and view all the answers

Which statement accurately describes the function of the Henderson-Hasselbalch equation?

<p>Predicts how pH responds to weak acid and salt concentrations. (C)</p> Signup and view all the answers

What defines an amino acid as being amphoteric?

<p>It has both acidic and basic functional groups. (B)</p> Signup and view all the answers

Which amino acid has an additional potentially charged group in its side chain?

<p>Lys (A)</p> Signup and view all the answers

For a weak acid like aspirin, which form is more likely to permeate cell membranes?

<p>The uncharged form (HA) (D)</p> Signup and view all the answers

Which of the following describes the primary amino group in amino acids at physiologic pH?

<p>It is protonated and positively charged. (C)</p> Signup and view all the answers

Which term describes substances such as amino acids that can act as both acids and bases?

<p>Ampholytes (B)</p> Signup and view all the answers

What is the impact of pH on the mobility of proteins in an electric field?

<p>Proteins may move towards the positive or negative electrodes based on their net charge. (D)</p> Signup and view all the answers

Which form of a weak base is typically charged?

<p>Protonated form (BH+) (B)</p> Signup and view all the answers

What is the result of the hydrophobic effect in proteins located in aqueous environments?

<p>Nonpolar side chains fill the interior of folded proteins. (B)</p> Signup and view all the answers

How does proline differ from other amino acids?

<p>It has a rigid, five-membered ring structure. (D)</p> Signup and view all the answers

Which amino acids have side chains that can lose a proton at alkaline pH?

<p>Cysteine and tyrosine. (A)</p> Signup and view all the answers

What type of bond forms between the –SH groups of two cysteines in proteins?

<p>Disulfide bond. (C)</p> Signup and view all the answers

Which amino acid is known to play a buffering role in proteins like hemoglobin?

<p>Histidine. (C)</p> Signup and view all the answers

At physiologic pH, which of the following amino acids carries a negative charge?

<p>Glutamic acid. (A)</p> Signup and view all the answers

What site can the hydroxyl group of serine serve as in glycoproteins?

<p>Oligosaccharide chain attachment site. (D)</p> Signup and view all the answers

Why is glycine unique among amino acids?

<p>It has no side chain. (B)</p> Signup and view all the answers

In proteins found in a hydrophobic environment, where are nonpolar R groups typically located?

<p>Outside surface of the protein. (A)</p> Signup and view all the answers

What is the charge on lysine's side chain at physiologic pH?

<p>Positive. (A)</p> Signup and view all the answers

Which amino acids can participate in hydrogen bond formation due to their polar hydroxyl groups?

<p>Serine, threonine, and tyrosine. (A)</p> Signup and view all the answers

Which of the following refers to the fully ionized forms of aspartic acid and glutamic acid?

<p>Aspartate and glutamate. (D)</p> Signup and view all the answers

What is the three-letter abbreviation for valine?

<p>VAL. (A)</p> Signup and view all the answers

Which configuration of amino acids is predominant in mammalian proteins?

<p>L configuration (C)</p> Signup and view all the answers

What causes an amino acid to act as a buffer in a solution?

<p>The dissociation of its α-carboxyl and α-amino groups (B)</p> Signup and view all the answers

How does the pH of a solution relate to the concentration of a weak acid and its conjugate base?

<p>It is defined by the Henderson-Hasselbalch equation (D)</p> Signup and view all the answers

What is the primary role of a buffer solution?

<p>To resist changes in pH upon addition of acids or bases (D)</p> Signup and view all the answers

At what pH level does maximum buffering capacity occur?

<p>At a pH equal to the pKa of the buffer system (B)</p> Signup and view all the answers

What is a zwitterion?

<p>A molecule with both positive and negative charges but an overall neutral charge (A)</p> Signup and view all the answers

Which property describes the second titratable group of alanine?

<p>It is a weaker acid than the carboxyl group (D)</p> Signup and view all the answers

Which statement about the dissociation constants of amino acids is true?

<p>K1 is always larger than K2 for amino acids (B)</p> Signup and view all the answers

When both the α-carboxyl and α-amino groups of alanine are fully protonated, what is the overall charge?

<p>Positive (B)</p> Signup and view all the answers

What happens to the carboxyl group of alanine when the pH is increased?

<p>It donates a proton to the solution (A)</p> Signup and view all the answers

Which amino group form is predominant above its pKa value?

<p>Deprotonated form (A)</p> Signup and view all the answers

In the titration curve of alanine, what indicates equal amounts of two forms in solution?

<p>The point where pH equals pK1 or pK2 (D)</p> Signup and view all the answers

What characterizes the behavior of a weak acid in relation to its dissociation constant?

<p>Acids with larger Ka almost completely dissociate in solution (C)</p> Signup and view all the answers

Flashcards

What are proteins?

Proteins are the most abundant and versatile molecules in living organisms, essential for countless life processes.

What are some examples of protein functions in the body?

Enzymes and polypeptide hormones are examples of proteins that control and direct metabolism in the body.

How does protein contribute to bone structure?

Collagen, a protein found in bone, provides a framework for calcium phosphate crystals, similar to the steel reinforcement in concrete.

How do proteins facilitate transport in the body?

Hemoglobin carries oxygen in the blood, while albumin transports other essential molecules, demonstrating protein's role in transport.

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How do proteins contribute to immune defense?

Immunoglobulins, a type of protein, protect the body against harmful bacteria and viruses.

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What is the basic structure of a protein?

Proteins are linear polymers, meaning they are made of chains of smaller units, in this case, amino acids.

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How many types of amino acids are typically found in mammalian proteins?

While there are many different amino acids, only 20 are commonly found in mammalian proteins.

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Describe the basic structure of an amino acid.

Each amino acid has a carboxyl group, an amino group, and a unique side chain (R group) attached to a central carbon atom.

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Isoelectric point (pI)

The pH at which an amino acid exists in its electrically neutral form, with an equal balance of positive and negative charges.

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Amphoteric

A substance that can act as both an acid and a base, like amino acids which have both carboxyl and amino groups.

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Henderson-Hasselbalch equation

The equation used to calculate the pH of a solution containing a weak acid and its conjugate base, helping to understand how changes in concentrations affect pH.

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pKa

The relative strength of an acid or base, measured as the negative logarithm of the acid dissociation constant (Ka).

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Permeant form of a drug

The form of a drug that can pass through cell membranes more easily, usually the uncharged form.

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Impermeant form of a drug

The form of a drug that cannot pass through cell membranes easily, usually the charged form.

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Side chain (R group) of an amino acid

The chemical group that distinguishes one amino acid from another, giving it its unique properties.

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Buffer

A molecule that resists changes in pH, helping to maintain a stable pH in a solution.

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Enantiomers (D- and L-isomers)

Mirror-image forms of a molecule that are non-superimposable, like left and right hands.

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L-isomer of amino acids

The form of amino acids found in proteins synthesized by the human body.

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Nonpolar Amino Acids

Nonpolar amino acids have side chains that do not participate in hydrogen or ionic bonds. They tend to cluster together in the interior of proteins in aqueous solutions, promoting hydrophobic interactions.

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Hydrophobic Effect

The tendency of nonpolar amino acid side chains to cluster together in the interior of proteins to avoid contact with water.

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Proline

Proline's side chain and α-amino nitrogen form a rigid ring structure, making it unusual. This creates a kink and disrupts α-helices, but contributes to collagen's fibrous structure.

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Disulfide Bond

The formation of a covalent bond between the sulfhydryl groups of two cysteine residues, creating a strong linkage. This stabilizes many extracellular proteins.

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Side Chain Attachment Sites

The polar hydroxyl groups of serine, threonine, and tyrosine can attach to phosphate groups, while the amide group of asparagine and the hydroxyl group of serine/threonine can attach to oligosaccharide chains.

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Acidic Amino Acids

Aspartic acid and glutamic acid are acidic amino acids. At physiological pH, their side chains are negatively charged (carboxylate groups).

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Basic Amino Acids

Lysine and arginine are basic amino acids. At physiological pH, their side chains are positively charged. Histidine can be either positively or neutral depending on the environment.

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Amino Acid Abbreviations

The standard three-letter and one-letter codes used to represent each amino acid in protein sequences.

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Chirality of Amino Acids

The α-carbon of amino acids (except glycine) is asymmetric, meaning it has four different groups attached. This allows for two mirror-image forms, D and L.

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Amino Acid Sequencing

The process of arranging amino acids in a specific sequence to form a polypeptide chain.

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Primary Structure

The structure of a protein that is determined by the linear sequence of amino acids.

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Secondary Structure

The local folding patterns of a protein, including α-helices and β-sheets.

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Tertiary Structure

The overall three-dimensional shape of a protein, determined by the interactions between amino acid side chains.

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Quaternary Structure

The arrangement of multiple polypeptide chains (subunits) in a protein.

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Protein Denaturation

The process of changing a protein's shape or conformation, often due to changes in temperature, pH, or the presence of other molecules.

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Acid Dissociation

The process of an acid releasing a proton (H+).

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Conjugate Base

The ionized form of a weak acid. It is the result of the acid donating a proton.

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Dissociation Constant (Ka)

A constant that describes the extent to which a weak acid dissociates in solution. It is the equilibrium constant for the dissociation reaction.

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Titration

The process of determining the concentration of an unknown solution by reacting it with a solution of known concentration.

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Zwitterion

A molecule with both a positive and a negative charge, but an overall neutral charge.

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Isoelectric Point

The point at which a molecule has a net charge of zero.

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Titration Curve

The curve that shows the change in pH of a solution as a base is added to a weak acid. It is used to determine the pKa values of the acid.

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Buffer Pair

A pair of molecules that can work together to maintain a stable pH. Often consists of a weak acid and its conjugate base.

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Study Notes

Protein Structure and Properties

  • Proteins are the most abundant and diverse molecules in living systems, pivotal to all life processes.
  • Proteins have diverse roles: enzymes/hormones regulate metabolism, contractile proteins facilitate movement, collagen in bone provides structure, hemoglobin/albumin transport molecules, and immunoglobulins combat infections.
  • Structurally, proteins are linear polymers of amino acids.

Amino Acid Classification

  • Only 20 standard amino acids are common in mammalian proteins. These are encoded by DNA.
  • Each amino acid contains a carboxyl group, an amino group (except proline), and a unique side chain (R group) attached to the α-carbon.
  • At physiological pH (~7.4), the carboxyl group is negatively charged (-COO⁻) and the amino group is positively charged (-NH₃⁺).
  • The R group dictates an amino acid's function within a protein, categorizing them as nonpolar or polar (acidic/basic).

Nonpolar Amino Acids

  • Nonpolar amino acids lack charged side chains, do not participate in hydrogen or ionic bonds.
  • Their side chains are hydrophobic (lipid-like).
  • In aqueous environments, nonpolar amino acid side chains cluster within the protein interior (hydrophobic effect). This is crucial for protein 3D shape.
  • In hydrophobic environments (e.g., membranes), nonpolar amino acid side chains are exposed on the exterior of the protein.
  • A prominent example of how amino acid structure impacts protein function is sickle cell anemia due to a valine replacing a glutamate in hemoglobin's β-subunit.

Proline

  • Proline's structure differs with a five-membered ring and a secondary amino group, often called an "imino acid."
  • Proline's unique shape influences collagen's (fibrous) structure but disrupts α-helix formation (globular proteins).

Polar Amino Acids

  • Polar uncharged amino acids have side chains that can form hydrogen bonds. These include serine, threonine, tyrosine, asparagine, and glutamine.
  • Cysteine side chains contain a sulfhydryl (-SH) group forming disulfide bonds (-S-S-) that connect cysteine pairs (cystine). These bonds are important for stabilizing protein structures (e.g., albumin).
  • Polar side chains (serine, threonine, tyrosine) can be modified by phosphate groups, and (serine, threonine, asparagine) can be sites for oligosaccharides in glycoproteins.

Acidic Amino Acids

  • Aspartic acid and glutamic acid donate protons.
  • At physiological pH, these amino acids are negatively charged (-COO⁻) side chains as aspartate and glutamate.

Basic Amino Acids

  • Lysine and arginine accept protons.
  • Their side chains have positive charges (+).
  • Histidine is unique. It's side chain's charge can be positive or neutral depending on the protein's environment. Its varying charge is important for buffering by proteins like hemoglobin.

Amino Acid Abbreviations

  • Each amino acid has a 3-letter and 1-letter code, based on rules that involve letter priority, frequency, and phonetic similarity.

Isomers of Amino Acids

  • Amino acids (except glycine) have a chiral α-carbon.
  • They exist as D and L isomers.
  • Proteins in humans use the L-form.

Acid-Base Properties of Amino Acids

  • Amino acids have both acidic (α-carboxyl) and basic (α-amino) groups.
  • They are amphoteric (ampholytes) that can act as buffers (acids donate, bases accept protons).
  • The Henderson-Hasselbalch equation quantitatively describes the relationship between pH and acid/base concentrations in solution. This is important for understanding how these properties influence buffer capacity,
  • Buffers resist pH changes. These involve a weak acid and its conjugate base; buffering is strongest when the pH = pKa.

Titration Curves of Amino Acids

  • Alanine's titration curve demonstrates the stepwise dissociation of protons from the α-carboxyl and α-amino groups. The pKa values characterize the dissociation tendencies of each group.
  • It explains how the pH of a solution affects the ionization state and charge of an amino acid.

Isoelectric Point (pI)

  • The isoelectric point is the pH at which an amino acid has a net zero charge. It's calculated by averaging the pKa values of the titratable groups involved.
  • pI correlates with the predominant dipolar form of an amino acid in a solution.

Protein Separation

  • Plasma proteins are separated by charge, frequently at pHs above their pI. This is how proteins are separated in an electrical field.
  • Differences in protein migration can indicate disease states.

Buffering Systems & Drug Absorption

  • Buffers resist changes in pH, essential for maintaining stable physiological conditions.
  • The Henderson-Hasselbalch equation predicts how pH changes due to concentrations of acid/base components in the buffer.
  • It is also applicable to drug absorption, as the membrane permeability of drug molecules depends on their ionization state (charged vs. uncharged forms) influenced by the pH, and thus the pKa.

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Description

This quiz covers essential concepts of protein structure and amino acid classification. Learn about the roles of proteins in biological systems, the standard amino acids found in mammals, and their unique properties. Test your knowledge on how amino acids contribute to the functions of proteins and the significance of their side chains.

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