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?

Carboxyl group Signup and view all the answers

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

They remain constant regardless of proximity to other groups Signup and view all the answers

What type of reaction occurs during peptide bond formation?

Condensation reaction Signup and view all the answers

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

They lose one oxygen atom and two hydrogen atoms. Signup and view all the answers

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

Residuals of amino acids Signup and view all the answers

Which process is thermodynamically favorable under physiological conditions?

Peptide bond hydrolysis Signup and view all the answers

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

Energy input is required. Signup and view all the answers

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

Hydrolysis has a high activation energy barrier. Signup and view all the answers

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

Peptide bond hydrolysis Signup and view all the answers

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

Enzymes such as proteases Signup and view all the answers

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

Energy input is required to form peptide bonds Signup and view all the answers

What characterizes the bonding in a peptide bond?

It has partial double bond character Signup and view all the answers

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

Planar Signup and view all the answers

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

Limits rotation unless the pi bond is broken Signup and view all the answers

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

trans (Z) Signup and view all the answers

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

Proline Signup and view all the answers

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

Partial double bond character of peptide bonds Signup and view all the answers

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

It stabilizes the peptide bond Signup and view all the answers

Which configuration do most peptide bonds adopt?

Z Signup and view all the answers

What are the ends of a dipeptide referred to as?

N-terminus and C-terminus Signup and view all the answers

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

They are consumed and converted into a single bond Signup and view all the answers

In which direction are amino acid sequences conventionally written?

N-terminus to C-terminus Signup and view all the answers

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

ERA and ARE Signup and view all the answers

How do biological systems synthesize peptides?

Starting from N-terminus and growing toward C-terminus Signup and view all the answers

What is the configuration of peptide bonds preceding proline?

Can be either cis or trans Signup and view all the answers

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

The distinct ends of a peptide having different groups Signup and view all the answers

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

It can result in diverse chemical and biological properties Signup and view all the answers

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

It retains one N-terminus and one C-terminus 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?

6 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?

160,000 Signup and view all the answers

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

N-terminal side 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?

They target different amino acids. Signup and view all the answers

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

Carboxyl group Signup and view all the answers

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

9.6 Signup and view all the answers

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

Asp-N endopeptidase Signup and view all the answers

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

Exponential increase in arrangements Signup and view all the answers

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

Interior residues Signup and view all the answers

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

Their ability to be ionized Signup and view all the answers

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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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.