CH2 | Peptide Bonds Flashcards
What are peptides?
Short chains of amino acids linked together.
What type of bond links two amino acids together, and what molecule is created?
A peptide bond (a substituted amide linkage) forms between two amino acids, creating a dipeptide.
How is a peptide bond formed?
Dehydration reaction – the removal of a water molecule from the carboxyl group of one amino acid and the amino group of another.
What is the role of the α-NH2 group in peptide bond formation?
It acts as a nucleophile, displacing the -OH group of another amino acid’s carboxyl group.
What kind of reaction is involved in forming a peptide bond?
It’s called a dehydration (or condensation) reaction.
What is a dipeptide?
A peptide composed of two amino acids.
What is a tripeptide?
A peptide composed of three amino acids.
What is a tetrapeptide?
A peptide composed of four amino acids.
What is an oligopeptide?
A peptide composed of a few amino acids.
What is a polypeptide?
A peptide composed of many amino acids.
Can peptides have a biological function? Name two examples.
Yes. Angiotensin and oxytocin are examples of peptide hormones.
How many amino acids can a peptide have?
It is composed of two or more amino acids covalently linked by peptide bonds.
What is a “residue” in the context of peptides?
An amino acid unit within a peptide.
What are the N-terminal and C-terminal residues?
N-terminal: residue with a free α-amino group. C-terminal: residue with a free carboxyl group.
How is a peptide chain’s sequence written by convention?
N-terminal (free amino end) on the left, C-terminal (free carboxyl end) on the right.
In which direction are amino acid sequences within peptides read?
From the N-terminus to the C-terminus (N→C).
How are amino acid residues named within a polypeptide, what are the common suffixes?
Suffixes (-ine, -an, -ic, or -ate) changed to -yl, except for the C-terminal amino acid.
Name a tripeptide with N-terminal valine, glycine in the middle, and C-terminal leucine.
Valylglycylleucine.
List the seven amino acids that have ionizable R groups.
Asp, Glu, Arg, Lys, His, Cys, Tyr
How many free α-amino and α-carboxyl groups does a tetrapeptide have?
One free α-amino group and one free α-carboxyl group.
How do you calculate the number of peptide bonds in a peptide?
Number of amino acids in the peptide minus 1.
Which groups in a peptide can ionize, contributing to their overall acid-base properties?
The free α-amino group (N-terminus), the free α-carboxyl group (C-terminus), and any ionizable R groups.
Why do the α-amino and α-carboxyl groups of non-terminal amino acids in a peptide not contribute to its acid-base behavior?
They are involved in peptide bonds (covalently joined), so they cannot ionize.
What factors determine the overall acid-base behavior of a peptide?
The nature and number of its free α-amino group, free α-carboxyl group, and ionizable R groups.
Do peptides have a characteristic isoelectric point (pI)? If so, what does it mean?
Yes, peptides have a characteristic pI where they do not move in an electric field (they have a net charge of zero).
What kind of curves are characteristic of peptides, as they are of amino acids?
Peptides, just like amino acids, show characteristic titration curves.
What are the five main characteristics of a peptide bond?
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.
How stable are peptide bonds in proteins?
Quite stable.
Why does peptide bond hydrolysis occur slowly?
Because it has a high activation energy.
Can heating or high salt concentration break peptide bonds?
No.
What can break peptide bonds?
1) Strong acids or bases (at elevated temperatures for a long time). 2) Specific enzymes (like digestive enzymes).
What kind of linkage is a peptide bond?
Amide covalent linkage.
Why is a peptide bond shorter than a typical single bond?
Due to resonance, there’s a partial sharing of electron pairs between the carbonyl oxygen and the amide nitrogen.
What is “resonance” in the context of peptide bonds?
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.
In a peptide bond, which atom carries a partial negative charge, and which carries a partial positive charge?
Oxygen: partial negative. Hydrogen (bonded to nitrogen): partial positive. This creates a small electric dipole.
Where are the electrons delocalized over in a peptide bond?
Over the carbonyl oxygen.
Are the -C=O and -NH groups in a peptide bond polar or nonpolar?
Polar.
What type of bonding are the polar groups in a peptide bond involved in?
Hydrogen bonding (e.g., in α-helices and β-sheets).
Can the -C=O and -NH groups in a peptide bond ionize within the pH range of 2-12?
No, they are uncharged (not ionized) in that pH range.
What are the only charged groups typically present in a polypeptide?
1) N-terminal (α-amino) group, 2) C-terminal (α-carboxyl) group, and 3) Any ionized R groups in the side chains.
Can peptide C-N bonds rotate freely? Why or why not?
No, because the partial double bond character makes them rigid.
Which bonds in a polypeptide chain have limited rotation?
The N-Cα and Cα-C bonds.
What limits the rotation of N-Cα and Cα-C bonds?
The size and character of the R groups.
What are the three torsion (dihedral) angles that define peptide conformation? What do they represent?
φ (phi), ψ (psi), and ω (omega). They represent the three repeating bonds in the peptide backbone.
Which two torsion angles describe the rotation around the bonds on either side of the Cα atom? What are their possible values?
φ (phi) and ψ (psi). Any value between –180° and +180°.
In a polypeptide chain, which bond is described by the ω (omega) angle? Can it rotate?
The C-N peptide bond. No, it is not free to rotate.
Which bonds in a polypeptide chain are described by the φ (phi) and ψ (psi) angles? Can they rotate?
N-Cα (phi) and Cα-C (psi). Yes, but their rotation is limited.
What prevents φ and ψ from both being 0°?
Steric interference between atoms in the polypeptide backbone.
What is the value of predicting torsion angles for a protein?
It would allow us to predict its fold (conformation).
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.
Torsion, also known as twisting or dihedral angles.
What is a Ramachandran plot?
A plot of ψ (psi) versus φ (phi) torsion angles of the protein backbone.
What is the purpose of a Ramachandran plot?
To test the quality of three-dimensional protein structures.
What do the different colors in a Ramachandran plot represent, and what information is displayed in them?
Different shades represent favored, allowed, and disallowed torsion angle combinations. They display information about potential steric clashes and energetically favorable conformations.
Are peptide bonds generally in the cis or trans configuration? Why?
Trans, because it avoids steric interference of R-groups.
What does “steric interference” mean in the context of peptide bond configuration?
The R-groups clash (occupy the same space) when they are in the cis configuration.
Which amino acid is more likely to adopt the cis configuration in a peptide bond? Why?
Proline, because its cyclic structure reduces the energy difference between cis and trans forms.
Which configuration is characterized by proximity of R-groups, trans or cis?
Cis.
