Biochem 2.1 Amino Acids and Peptides
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Questions and Answers

What is the pKa of the amino group at the N-terminus of a peptide?

  • 2.2
  • 6.0
  • 8.3 (correct)
  • 3.5

At physiological pH, which side chains predominantly contribute a positive charge to a peptide?

  • Arginine and lysine (correct)
  • Tyrosine and histidine
  • Aspartate and glutamate
  • Cysteine and aspartate

At what pH does histidine predominantly exist in a positively charged form?

  • 8.0
  • 7.4
  • 6.0 (correct)
  • 5.0

Which functional group has a pKa near 3.5 in the C-terminus of a peptide?

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

What does the net charge of a peptide at physiological pH assume regarding side chain pKa values?

<p>They remain constant regardless of proximity to other groups (C)</p> Signup and view all the answers

What type of reaction occurs during peptide bond formation?

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

What happens to the amino acids during the formation of a peptide bond?

<p>They lose one oxygen atom and two hydrogen atoms. (D)</p> Signup and view all the answers

What term is used to describe the individual units in a polypeptide after peptide bond formation?

<p>Residuals of amino acids (D)</p> Signup and view all the answers

Which process is thermodynamically favorable under physiological conditions?

<p>Peptide bond hydrolysis (A)</p> Signup and view all the answers

What must occur for peptide bond formation to take place in living cells?

<p>Energy input is required. (B)</p> Signup and view all the answers

Why do peptide bonds remain intact for a long time despite thermodynamic favorability towards hydrolysis?

<p>Hydrolysis has a high activation energy barrier. (A)</p> Signup and view all the answers

What is the result of adding a water molecule across a peptide bond?

<p>Peptide bond hydrolysis (A)</p> Signup and view all the answers

What is essential for peptide bonds to hydrolyze at a significant rate?

<p>Enzymes such as proteases (C)</p> Signup and view all the answers

Why is the process of peptide bond formation considered endothermic overall?

<p>Energy input is required to form peptide bonds (D)</p> Signup and view all the answers

What characterizes the bonding in a peptide bond?

<p>It has partial double bond character (B)</p> Signup and view all the answers

What geometric configuration do atoms involved in a double bond exhibit?

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

What effect does the partial double bond character have on peptide bond rotation?

<p>Limits rotation unless the pi bond is broken (C)</p> Signup and view all the answers

Which configuration do most peptide bonds adopt to minimize steric overlap?

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

Which residue commonly causes peptide bonds to be found in either cis or trans configurations?

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

What primarily causes the restriction of conformations in peptides and proteins?

<p>Partial double bond character of peptide bonds (B)</p> Signup and view all the answers

What is the effect of resonance in the amide group of a peptide bond?

<p>It stabilizes the peptide bond (D)</p> Signup and view all the answers

Which configuration do most peptide bonds adopt?

<p>Z (B), Trans (D)</p> Signup and view all the answers

What are the ends of a dipeptide referred to as?

<p>N-terminus and C-terminus (C)</p> Signup and view all the answers

What happens to the amino and carboxyl groups during the formation of a peptide bond?

<p>They are consumed and converted into a single bond (B)</p> Signup and view all the answers

In which direction are amino acid sequences conventionally written?

<p>N-terminus to C-terminus (B)</p> Signup and view all the answers

Which of the following peptides have distinct biological properties despite containing the same amino acids?

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

How do biological systems synthesize peptides?

<p>Starting from N-terminus and growing toward C-terminus (A)</p> Signup and view all the answers

What is the configuration of peptide bonds preceding proline?

<p>Can be either cis or trans (C)</p> Signup and view all the answers

What does the term 'polarity' refer to in the context of peptides?

<p>The distinct ends of a peptide having different groups (A)</p> Signup and view all the answers

What effect can the arrangement of amino acid residues in a peptide have?

<p>It can result in diverse chemical and biological properties (B)</p> Signup and view all the answers

What is the consequence of forming a tripeptide from three amino acids?

<p>It retains one N-terminus and one C-terminus (C)</p> Signup and view all the answers

How many different ways can a tripeptide composed of one alanine (A), one arginine (R), and one glutamic acid (E) be arranged?

<p>6 (B)</p> Signup and view all the answers

If all 20 proteinogenic amino acids can be used in a tripeptide of four residues, how many different arrangements are possible?

<p>160,000 (C)</p> Signup and view all the answers

What is the term for the side of an amino acid residue closer to the N-terminus?

<p>N-terminal side (C)</p> Signup and view all the answers

What distinguishes protease enzymes that cleave on the C-terminal side from those that cleave on the N-terminal side?

<p>They target different amino acids. (B)</p> Signup and view all the answers

Which group in amino acids contributes to the ionizable properties of peptides?

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

What is the pKa value of amino groups in free amino acid backbones typically near?

<p>9.6 (D)</p> Signup and view all the answers

Which enzyme cleaves peptide bonds on the N-terminal side of aspartate?

<p>Asp-N endopeptidase (B)</p> Signup and view all the answers

What primarily contributes to the diverse functions of peptides and proteins in living cells?

<p>Exponential increase in arrangements (D)</p> Signup and view all the answers

Which term describes the amino acid residues that do not have backbone amino or carboxyl groups?

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

In order to carry out biochemical functions, what aspect of amino acids is crucial?

<p>Their ability to be ionized (C)</p> Signup and view all the answers

Flashcards

Peptide Bond

A chemical bond formed between the carboxyl group of one amino acid and the amino group of another amino acid, releasing a molecule of water.

Proteases

Enzymes that break down proteins by hydrolyzing peptide bonds.

Hydrolysis

The process of breaking a chemical bond by adding water.

Exothermic vs. Endothermic

The formation of a new chemical bond results in the release of energy, while breaking a bond requires energy.

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Partial Double Bond Character of Peptide Bonds

The double bond character comes from electron delocalization, where electrons are shared across multiple atoms, giving the bond partial double-bond characteristics.

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Planarity of Peptide Bonds

The planar geometry of the peptide bond forces all atoms linked to the carbon and nitrogen into the same plane.

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Restricted Rotation of Peptide Bonds

The partial double bond character restricts rotation around the peptide bond, limiting the possible conformations of a protein.

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Trans Configuration of Peptide Bonds

The most common conformation of a peptide bond, where the groups on either side of the partial double bond are on opposite sides.

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Cis Configuration of Peptide Bonds

The amino acid proline can adopt either a trans or cis conformation due to the cyclic structure of its side chain.

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Peptide

The joining of two or more amino acids through peptide bonds. The length can range from two amino acids (dipeptide) to thousands (polypeptide).

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Hydrolysis of Peptide Bonds

The process of adding a water molecule to break a peptide bond. This separates the amino acids.

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Condensation Reaction

The formation of a peptide bond from two amino acids, accompanied by the release of a water molecule.

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Amino Acid Residue

The remaining unit of an amino acid after forming a peptide bond. It lacks the carboxyl group or the amino group that participated in the bond.

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Thermodynamically favorable

The tendency of a system toward a lower energy state. For peptide bonds, hydrolysis is favored under physiological conditions.

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Kinetically stable

The rate at which a reaction occurs, regardless of energy favorability. While peptide bond hydrolysis is thermodynamically favorable, it has a high activation energy.

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Amino Acid Sequence

The arrangement of amino acids in a polypeptide chain, starting from the amino terminus (N-terminus) to the carboxy terminus (C-terminus).

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Amino Terminus (N-terminus)

The end of a peptide chain that has a free amino group. It is the starting point of the amino acid sequence.

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Carboxy Terminus (C-terminus)

The end of a peptide chain that has a free carboxyl group. It is the ending point of the amino acid sequence.

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Trans Configuration (Z)

A type of isomerism that describes the spatial arrangement of substituents around a peptide bond. Most peptide bonds are in this configuration, where the groups attached to the α-carbon are on opposite sides of the peptide bond.

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Cis Configuration (E)

A type of isomerism that describes the spatial arrangement of substituents around a peptide bond. It is less common than the trans configuration, and is often found in peptides involving the amino acid proline.

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Peptide Backbone Flexibility

The flexibility of the peptide backbone, determined by the rotation around certain bonds. The bond between the nitrogen and α-carbon and the bond between the α-carbon and the carbonyl group can rotate. This allows for different conformations of the protein chain.

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Cis-trans Isomerization

A peptide bond, particularly the one preceding a proline residue, that can exist in either cis or trans configuration. Proline's unique structure influences the flexibility of the backbone.

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Factorial

The number of ways to arrange a set of items, calculated by multiplying the numbers from the set's size down to 1 (e.g., 3! = 3 × 2 × 1 = 6).

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Protein Folding

The ability of a polypeptide to fold into a specific three-dimensional structure, determined by its primary amino acid sequence.

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N-terminus and C-terminus

The ends of a polypeptide chain. The N-terminus has a free amino group, while the C-terminus has a free carboxyl group.

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Peptide Bond Hydrolysis

The process of breaking peptide bonds in a polypeptide chain, often catalyzed by enzymes called proteases.

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pKa of N-terminus

The pKa value for the amino group of a free amino acid backbone (typically around 9.6).

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pKa of C-terminus

The pKa value for the carboxyl group of a free amino acid backbone (typically around 2.3).

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Acid-Base Properties of Peptides

The ability of a molecule to donate (acidic) or accept (basic) protons, influenced by the presence of ionizable groups.

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Isoelectric point of a peptide

The pH at which the net charge of a peptide is zero. This occurs when the positive charges from the protonated amino groups balance the negative charges from the deprotonated carboxyl groups.

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Zwitterionic Peptide Backbone

The predominantly charged ends of a peptide are zwitterionic at physiological pH, meaning the positive charge of the N-terminus cancels the negative charge of the C-terminus.

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pKa Changes in Peptides

The pKa of the amino group at the N-terminus of a peptide is approximately 8.3, while the pKa of the carboxyl group at the C-terminus is around 3.5.

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Predominant Net Charge of a Peptide

The net charge of a peptide can be estimated by considering the charges of its backbone and side chains. The backbone is typically zwitterionic, and only a few side chains significantly contribute to the net charge at physiological pH.

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Net Charge Calculation

The net charge of a peptide can be determined by evaluating the charges of its backbone and side chains. At physiological pH, the backbone is zwitterionic, so the net charge primarily depends on the side chain charges.

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Study Notes

Amino Acids and Peptides

  • Amino acids are the building blocks of polypeptides
  • Polypeptides form when the amino group of one amino acid bonds with the carboxyl group of another, forming a peptide bond.
  • A dipeptide is formed when two amino acids link together. A tripeptide results from three amino acids, and so on.
  • Peptide bonds form through a condensation reaction, releasing a water molecule.
  • Peptide bond formation is thermodynamically unfavorable under normal conditions, requiring energy input.
  • Peptide bonds are kinetically stable, remaining intact for long periods, allowing them to perform their biological functions.
  • Peptide bond hydrolysis is thermodynamically favorable, but slow due to a high activation energy. Enzymes like proteases are required for faster hydrolysis.

Peptide Bond Characteristics

  • Peptide bonds exhibit partial double bond character, restricting rotation around the bond.
  • The atoms involved in the peptide bond (C and N atoms) and adjacent atoms are coplanar.
  • This planarity affects protein folding.
  • The peptide bond typically exists in the trans configuration, minimizing steric clashes.
  • Proline residues can adopt both cis and trans configurations.

Peptide Organization

  • Peptides have an amino-terminus (N-terminus) and a carboxyl-terminus (C-terminus).
  • Amino acid sequences are written from the N-terminus to the C-terminus.
  • Peptides with different sequences, even using the same amino acids, have distinct properties.
  • The sequence of amino acids in a peptide directly influences its structure and consequently, its function.

Peptide Properties

  • The arrangement of amino acids can significantly affect the properties of a peptide.
  • Different arrangements of the same amino acids lead to a substantial diversity in peptide properties.
  • The number of possible arrangements from different amino acid combinations is extensive, increasing exponentially with the size of the peptide.

Peptide and Protein Properties

  • Peptide properties depend on the arrangement of amino acid residues.
  • Even small peptides can exhibit substantial diversity.
  • The arrangement affects how peptides/proteins function.
  • Specific arrangements determine the ability to participate in specific reactions or interactions.

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Peptides Introduction - Biochemistry PDF

Description

Test your knowledge on amino acids and peptide bonds. This quiz covers the formation of polypeptides, the characteristics of peptide bonds, and their role in biological functions. Explore concepts such as dipeptides, tripeptides, and the energy dynamics involved in peptide bond formation and hydrolysis.

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