CH2 | Peptide Bonds

Question 1

What are peptides?

Answer 1

Short chains of amino acids linked together.

Question 2

What type of bond links two amino acids together, and what molecule is created?

Answer 2

A peptide bond (a substituted amide linkage) forms between two amino acids, creating a dipeptide.

Question 3

How is a peptide bond formed?

Answer 3

Dehydration reaction – the removal of a water molecule from the carboxyl group of one amino acid and the amino group of another.

Question 4

What is the role of the α-NH2 group in peptide bond formation?

Answer 4

It acts as a nucleophile, displacing the -OH group of another amino acid’s carboxyl group.

Question 5

What kind of reaction is involved in forming a peptide bond?

Answer 5

It’s called a dehydration (or condensation) reaction.

Question 6

What is a dipeptide?

Answer 6

A peptide composed of two amino acids.

Question 7

What is a tripeptide?

Answer 7

A peptide composed of three amino acids.

Question 8

What is a tetrapeptide?

Answer 8

A peptide composed of four amino acids.

Question 9

What is an oligopeptide?

Answer 9

A peptide composed of a few amino acids.

Question 10

What is a polypeptide?

Answer 10

A peptide composed of many amino acids.

Question 11

Can peptides have a biological function? Name two examples.

Answer 11

Yes. Angiotensin and oxytocin are examples of peptide hormones.

Question 12

How many amino acids can a peptide have?

Answer 12

It is composed of two or more amino acids covalently linked by peptide bonds.

Question 13

What is a “residue” in the context of peptides?

Answer 13

An amino acid unit within a peptide.

Question 14

What are the N-terminal and C-terminal residues?

Answer 14

N-terminal: residue with a free α-amino group. C-terminal: residue with a free carboxyl group.

Question 15

How is a peptide chain’s sequence written by convention?

Answer 15

N-terminal (free amino end) on the left, C-terminal (free carboxyl end) on the right.

Question 16

In which direction are amino acid sequences within peptides read?

Answer 16

From the N-terminus to the C-terminus (N→C).

Question 17

How are amino acid residues named within a polypeptide, what are the common suffixes?

Answer 17

Suffixes (-ine, -an, -ic, or -ate) changed to -yl, except for the C-terminal amino acid.

Question 18

Name a tripeptide with N-terminal valine, glycine in the middle, and C-terminal leucine.

Answer 18

Valylglycylleucine.

Question 19

List the seven amino acids that have ionizable R groups.

Answer 19

Asp, Glu, Arg, Lys, His, Cys, Tyr

Question 20

How many free α-amino and α-carboxyl groups does a tetrapeptide have?

Answer 20

One free α-amino group and one free α-carboxyl group.

Question 21

How do you calculate the number of peptide bonds in a peptide?

Answer 21

Number of amino acids in the peptide minus 1.

Question 22

Which groups in a peptide can ionize, contributing to their overall acid-base properties?

Answer 22

The free α-amino group (N-terminus), the free α-carboxyl group (C-terminus), and any ionizable R groups.

Question 23

Why do the α-amino and α-carboxyl groups of non-terminal amino acids in a peptide not contribute to its acid-base behavior?

Answer 23

They are involved in peptide bonds (covalently joined), so they cannot ionize.

Question 24

What factors determine the overall acid-base behavior of a peptide?

Answer 24

The nature and number of its free α-amino group, free α-carboxyl group, and ionizable R groups.

Question 25

Do peptides have a characteristic isoelectric point (pI)? If so, what does it mean?

Answer 25

Yes, peptides have a characteristic pI where they do not move in an electric field (they have a net charge of zero).

Question 26

What kind of curves are characteristic of peptides, as they are of amino acids?

Answer 26

Peptides, just like amino acids, show characteristic titration curves.

Question 27

What are the five main characteristics of a peptide bond?

Answer 27

Amide Covalent Stable Linkage: Forms a strong, stable connection between amino acids. Polar but Uncharged: The -C=O and -NH groups are polar, contributing to hydrogen bonding, but the bond itself doesn't carry a charge. Partial Double Bond Character: Due to resonance, the bond is shorter and stronger than a typical single bond. Rigid and Planar: The partial double bond character prevents free rotation around the peptide bond, making it rigid and planar. Trans-configuration: The α-carbons of adjacent amino acids are typically positioned on opposite sides of the peptide bond (trans configuration), which is energetically more favorable because it reduces steric hindrance.

Question 28

How stable are peptide bonds in proteins?

Answer 28

Quite stable.

Question 29

Why does peptide bond hydrolysis occur slowly?

Answer 29

Because it has a high activation energy.

Question 30

Can heating or high salt concentration break peptide bonds?

Answer 30

No.

Question 31

What can break peptide bonds?

Answer 31

1) Strong acids or bases (at elevated temperatures for a long time). 2) Specific enzymes (like digestive enzymes).

Question 32

What kind of linkage is a peptide bond?

Answer 32

Amide covalent linkage.

Question 33

Why is a peptide bond shorter than a typical single bond?

Answer 33

Due to resonance, there's a partial sharing of electron pairs between the carbonyl oxygen and the amide nitrogen.

Question 34

What is "resonance" in the context of peptide bonds?

Answer 34

The delocalization of electrons (partial sharing of two pairs of electrons) between the carbonyl oxygen and the amide nitrogen, resulting in a partial double bond character.

Question 35

In a peptide bond, which atom carries a partial negative charge, and which carries a partial positive charge?

Answer 35

Oxygen: partial negative. Hydrogen (bonded to nitrogen): partial positive. This creates a small electric dipole.

Question 36

Where are the electrons delocalized over in a peptide bond?

Answer 36

Over the carbonyl oxygen.

Question 37

Are the -C=O and -NH groups in a peptide bond polar or nonpolar?

Answer 37

Polar.

Question 38

What type of bonding are the polar groups in a peptide bond involved in?

Answer 38

Hydrogen bonding (e.g., in α-helices and β-sheets).

Question 39

Can the -C=O and -NH groups in a peptide bond ionize within the pH range of 2-12?

Answer 39

No, they are uncharged (not ionized) in that pH range.

Question 40

What are the only charged groups typically present in a polypeptide?

Answer 40

1) N-terminal (α-amino) group, 2) C-terminal (α-carboxyl) group, and 3) Any ionized R groups in the side chains.

Question 41

Can peptide C-N bonds rotate freely? Why or why not?

Answer 41

No, because the partial double bond character makes them rigid.

Question 42

Which bonds in a polypeptide chain have limited rotation?

Answer 42

The N-Cα and Cα-C bonds.

Question 43

What limits the rotation of N-Cα and Cα-C bonds?

Answer 43

The size and character of the R groups.

Question 44

What are the three torsion (dihedral) angles that define peptide conformation? What do they represent?

Answer 44

φ (phi), ψ (psi), and ω (omega). They represent the three repeating bonds in the peptide backbone.

Question 45

Which two torsion angles describe the rotation around the bonds on either side of the Cα atom? What are their possible values?

Answer 45

φ (phi) and ψ (psi). Any value between –180° and +180°.

Question 46

In a polypeptide chain, which bond is described by the ω (omega) angle? Can it rotate?

Answer 46

The C-N peptide bond. No, it is not free to rotate.

Question 47

Which bonds in a polypeptide chain are described by the φ (phi) and ψ (psi) angles? Can they rotate?

Answer 47

N-Cα (phi) and Cα-C (psi). Yes, but their rotation is limited.

Question 48

What prevents φ and ψ from both being 0°?

Answer 48

Steric interference between atoms in the polypeptide backbone.

Question 49

What is the value of predicting torsion angles for a protein?

Answer 49

It would allow us to predict its fold (conformation).

Question 50

Name the type of angle which defines peptide conformation and have values which, if known for a certain protein, can allow us to predict its fold.

Answer 50

Torsion, also known as twisting or dihedral angles.

Question 51

What is a Ramachandran plot?

Answer 51

A plot of ψ (psi) versus φ (phi) torsion angles of the protein backbone.

Question 52

What is the purpose of a Ramachandran plot?

Answer 52

To test the quality of three-dimensional protein structures.

Question 53

What do the different colors in a Ramachandran plot represent, and what information is displayed in them?

Answer 53

Different shades represent favored, allowed, and disallowed torsion angle combinations. They display information about potential steric clashes and energetically favorable conformations.

Question 54

Are peptide bonds generally in the cis or trans configuration? Why?

Answer 54

Trans, because it avoids steric interference of R-groups.

Question 55

What does "steric interference" mean in the context of peptide bond configuration?

Answer 55

The R-groups clash (occupy the same space) when they are in the cis configuration.

Question 56

Which amino acid is more likely to adopt the cis configuration in a peptide bond? Why?

Answer 56

Proline, because its cyclic structure reduces the energy difference between cis and trans forms.

Question 57

Which configuration is characterized by proximity of R-groups, trans or cis?

Answer 57

Cis.