Lec 3 & 4: Comprehensive Notes on Peptide Bonds and Protein Structure
Peptide Bond Learning Goals
Convention for Naming and Writing Sequences: Understand the standard ways to denote sequences of amino acids in proteins.
Diversity of Proteins: Grasp the different sizes, compositions, and structures proteins can exhibit.
Prosthetic Groups and Processing: Learn about non-polypeptide units bound to proteins and how proteins undergo modifications after synthesis.
Terminology: Familiarize with key terms related to proteins and peptides:
Residue: A single subunit of a peptide or protein, typically an amino acid.
Side Chain: The variable part of an amino acid that defines its characteristics.
Backbone: The main chain of a polypeptide that includes the peptide bonds connecting the residues.
Termini: Refers to the ends of the peptide or protein chain (N-terminus and C-terminus).
Subunits: Individual polypeptide chains that can combine to form a larger protein structure.
Chain: A sequence of amino acids linked via peptide bonds.
Peptides: Short chains of amino acids (oligopeptides vs. polypeptides).
Monomer: A single, simple molecule that can join together to form a polymer.
Polymer: A large molecule composed of many repeated subunits (monomers).
Sequence Determines Structure: Recognize that the specific order of amino acids in a protein dictates its three-dimensional structure, which is crucial for its function.
Partial Covalent Character of Peptide Bond: Understand how the nature of peptide bonds introduces limitations on the flexibility and conformations of polypeptides.
Reading Assignments:
Chapter 3, sections 3.2 (pp. 81-83) and 3.4 (90-92)
Chapter 4.1 (pp. 109-110)
Textbook Problems: Complete problems 8, 9, and 10.
Levels of Structure of Proteins
Primary Structure: Refers to the linear sequence of amino acids in a polypeptide chain.
Secondary Structure: Localized folding patterns such as alpha helices and beta sheets formed by hydrogen bonding.
Tertiary Structure: The overall three-dimensional structure formed by interactions between the side chains of the amino acids.
Quaternary Structure: The assembly of multiple polypeptide chains into a functional protein complex.
Example of Amino Acids in Sequence:
Proline (Pro)
Alanine (Ala)
Aspartic Acid (Asp)
Lysine (Lys)
Threonine (Thr)
Valine (Val)
Tryptophan (Trp)
Glycine (Gly)
Peptide Bonds
Proteins are linear chains of amino acids linked by amide bonds known as peptide bonds.
The formation of a peptide bond involves a reaction between the carboxyl group () of one amino acid and the amino group () of the next, resulting in the loss of water (dehydration).
For example:
If R1 = H (for Glycine) and R2 = CH3 (for Alanine), then the peptide is called glycylalanine (Gly-Ala or GA).
This exemplifies how specific combinations of amino acids can create distinct peptides
Combinatorial Diversity of Peptides:
With 2 amino acids: combinations
With 3 amino acids: combinations
With 20 amino acids: combinations exist, leading to a vast diversity of proteins.
Number of Amino Acids in Polypeptides
Protein Comparison Table: Here are examples of several proteins and their corresponding molecular weights, number of residues, and chain numbers:
Protein
Molecular Weight (Da)
# of Residues
# of Polypeptide Chains
Cytochrome c (human)
12,400
104
1
Ribonuclease A (bovine pancreas)
13,700
124
1
Lysozyme (chicken egg white)
14,300
129
1
Myoglobin (equine heart)
16,700
153
1
Chymotrypsin (bovine pancreas)
25,700
245
1
Hemoglobin (human)
64,500
574
4
Serum Albumin (human)
66,000
609
1
Hexokinase (yeast)
107,900
972
2
RNA polymerase (E. coli)
450,000
4,158
5
Apolipoprotein B (human)
513,000
4,536
1
Titin (human)
2,993,000
26,926
1
Peptides and Peptide Structure
In terms of peptides:
Peptides can be defined as oligopeptides or polypeptides, based on their length.
The peptide backbone consists of a repeating sequence of peptide bonds along with associated side chains (R groups).
The primary sequence is the specific order of residues in the peptide chain, e.g. serylglycyltyrosylalanylleucine (SGYAL).
Peptides exhibit two main terminuses: N-terminal and C-terminal.
Peptide Binds: Only the -carboxyl and -amino groups of the amino acids are typically linked by peptide bonds, with noted exceptions such as glutathione (g-Glu-Cys-Gly), which plays a role in detoxification and reduction of protein disulfides.
Protein Diversity
Each protein has a unique amino acid sequence that is genetically determined.
The sequence of amino acids determines the protein's specific structure, which in turn is essential for its function.
A single substitution of an amino acid can lead to diseases, exemplified by the substitution of Glutamic Acid (Glu) to Valine (Val) at position 6 of the β-chain in Hemoglobin S (HbS), leading to sickle cell disease.
Modifications of Proteins
Various chemical groups can be associated with proteins, including prosthetic groups or cofactors:
Lipoproteins: Lipids bound to proteins.
Glycoproteins: Carbohydrates attached to proteins.
Metalloproteins: Contain metal cofactors (e.g., Iron, Zinc).
Table of Conjugated Proteins
Class
Prosthetic Group
Example
Lipoproteins
Lipids
β1-Lipoprotein of blood
Glycoproteins
Carbohydrates
Immunoglobulin G
Phosphoproteins
Phosphate groups
Casein of milk
Hemoproteins
Heme (iron porphyrin)
Hemoglobin
Flavoproteins
Flavin nucleotides
Succinate dehydrogenase
Metalloproteins
Iron, Zinc, etc.
Ferritin, Alcohol dehydrogenase
Protein Processing
Synthesis of Insulin:
Insulin is synthesized in the pancreas as preproinsulin on ribosomes. A signal sequence targets it to secretory vesicles.
The signal sequence is cleaved during processing, and the remaining proinsulin folds into its stable conformation with disulfide bonds formed.
Insulin is stored in secretory granules in pancreatic B cells and is secreted into the bloodstream through exocytosis.
Modifications of N and C Terminini
Modifications can be made to the N-terminal and C-terminal ends of proteins, such as:
N-formyl
N-acetyl
C-terminal amide
C-terminal methyl ester
Conformation and Structure of the Peptide Bond
The peptide bond exhibits unique electron characteristics leading to a resonance hybrid structure, which gives the C-N bond a partial double bond character. This restricts rotational freedom around the bond.
The length of the C-N bond is approximately between single bond (1.49Å) and double bond (1.27Å).
Configurations: The peptide bond can exist in two configurations:
Trans configuration: More stable and common due to reduced steric hindrance.
Cis configuration: Less common as it can lead to steric interference, particularly in proline residues.
Phi (φ) and Psi (ψ) Rotation Angles
The rotation angles around the alpha carbon (Cα) and the peptide bonds influence the conformation of the protein.
Phi (φ): N-Cα rotation angle.
Psi (ψ): Cα-C' rotation angle.
A Ramachandran plot can illustrate favorable dihedral angles that proteins usually adopt due to steric hindrance.
Not all φ and ψ angles are allowed as they can lead to unfavorable steric interactions, leading to the necessity to examine the specific conformation space available for a protein's structure at a molecular level.
Recap of Learning Goals
Naming and Writing Sequences: Importance of proper nomenclature in peptide/protein sequences.
Protein Diversity: Understanding variety in protein forms.
Prosthetic Groups and Processing: Importance of these features for protein function.
Terminology: Knowing key definitions pertinent to biochemistry.
Sequence Determines Structure: Critical link between sequence and functional conformation.
Peptide Bond Character: Implications of the covalent character of the peptide bond on protein structure and folding.
Follow-up readings suggested from textbook sections mentioned earlier to reinforce learning and understanding.