What are the Differences?
Peptides and proteins, while similar in many respects, are different in ways that are important to understand. Oftentimes, the terms “peptide” and “protein” are used interchangeably, but certain characteristics and biological activities are unique to one or other class of compound. To fully appreciate the differences between proteins and peptides, it is important to understand the structure and biochemistry of their building blocks, the amino acids; and how amino acids, peptides, and proteins are inter-related.
Following the Big Bang, and some nine billion years before the most primitive life forms emerged, amino acids were among the first organic molecules to come into existence in the universe. This event occurred in atmospheric conditions of high pressure, electrical instability, and high levels of CO2, NH3 and SO2 .
Amino acids are small, but biologically vital, compounds containing an amino (NH2) group and a carboxylic acid (COOH) group, as well as a side-chain structure whose composition can vary, depending on the amino acid of interest .
Of the hundreds of amino acids that are known to exist in nature, only twenty are encoded in plant and animal DNA, and all of these are alpha-amino acids. Fig.1 illustrates the structure of the alpha-amino acid, Lysine. According to convention, the alpha-carbon is always carbon-2 of the amino acid, while the alpha-carboxyl group is always carbon-1 .
Fig. 1 – Numbering of carbon atoms in amino acids
In the appropriate conditions, both genetically-encoded and artificially-synthesized alpha-amino acids have the potential to be incorporated into peptides.
The shortest peptide, containing two amino acids, is known as a “dipeptide.” A peptide three amino acids in length is a “tripeptide,” and so on.
Peptides are short chains of amino acids that have been linked by amide (or peptide), bonds. While the term “peptide” generally refers to a compound made up of two or more amino acids, peptides can be further classified as either oligopeptides or polypeptides. Oligo-, meaning “few”, describes peptides that contain generally fewer than 20 amino acids. Poly- , meaning “many” peptides, on the other hand, are composed of between 20 and 50 amino acids. Peptides are defined by their amino acid sequence, which is simply the order in which the different building blocks occur in the peptide, starting from the first (N-terminal) amino acid, to the last (C-terminal) amino acid.
Determination of the peptide/protein sequence can achieved, using a range of different analytical techniques. At Genaxxon bioscience, we offer two broad types of sequence analysis, namely:
- de novo sequencing: for applications in which DNA sequence data are unavailable. This step is preceded by proteolytic digestion of the peptide/protein, followed by high-resolution mass spectrometry of the digested peptides, and finally bioinformatic analysis of the peptide/protein, to elucidate its structure and function. Depending on the aim of the project, further analyses are possible, including: micropreparative HPLC of the peptide fragments, sequencing of the internal fragments, and experimental validation of data, using synthetic peptide analogs.
- N-terminal sequencing (Edman degradation): to elucidate the N-terminal amino acids of a peptide/protein. Identification of the entire protein can be achieved by mass spectrometry, which is more sensitive, and can be applied to a broad range of samples .
Polypeptides and Proteins
Proteins are commonly distinguished from polypeptides according to their size and structure.
In terms of size, a polypeptide composed of 50 or more amino acids, is generally classified as a protein, although the size of an average protein can range between 40-100 amino acids, but this is a general guideline only.
Secondly, proteins and polypeptides differ with respect to their structure. Polypeptides containing fewer than 40-50 amino acids, generally lack the ability to form a stable, tertiary structure. Proteins, however, can fold into a stable, three-dimensional (3-D) conformation.
The structure-function relationship of a protein is also dependent upon its primary sequence and tertiary structure. In the case of haemoglobin, which comprises four polypeptide subunits, genetic mutation, or other perturbations in either or both its primary sequence and/or its 3-D conformation, can negatively impact its stability, oxygen-carrying or oxygen-releasing abilities, leading to one or more clinical disorders, including neonatal jaundice, haemolytic anemia, cyanosis, splenomegaly and polycythemia .
1. KAUFFMAN, SA, JELENFI, DP, VATTAY, G. “The clock of chemical evolution”.
2. LEHNINGER, AL, Nelson, DL, COX, MM (2000). Lehninger principles of biochemistry, 6th ed. New York: Worth Publishers. Chapter 3: “Amino acids, peptides and proteins”.
3. TRÖNDLE, N, “Different methods of protein analysis – characterisation of proteins and peptides” [Genaxxon bioscience]
4. MARENGO-ROWE, AJ. “Structure-function relations of human hemoglobins” Baylor University Medical Center Proceedings 2006; 19: 239-245.