Peptide sequence
A peptide sequence, also referred to as an amino acid sequence, denotes the specific order in which amino acids are linked together by peptide bonds. These bonds form short chains known as peptides, or longer chains called polypeptides, which can constitute proteins. There are twenty naturally occurring amino acids, each characterized by a unique side chain (R group) alongside a carboxyl and an amino group. The sequence in which these amino acids are arranged is critical because even slight variations can lead to different structures and functions of proteins.
The primary structure of a protein is dictated by the linear arrangement of amino acids, which is encoded by corresponding DNA sequences. Proteins may also exhibit secondary structures, such as alpha helices and pleated sheets, as well as tertiary and quaternary structures that determine their overall shape and function. These structures play a vital role in biological processes, including enzyme activity and hormone signaling, where proper alignment and organization are essential for interaction and functionality. Ultimately, peptide sequences are fundamental to the creation of proteins, which are indispensable for life, forming the building blocks of muscles, organs, enzymes, and hormones.
Peptide sequence
Peptide sequence, also known as amino acid sequence, describes the order in which amino acids (organic molecules) are linked together through peptide bonds. These peptide bonds can form short chains, commonly called peptides, or longer chains of polypeptides, which include proteins.
What Is an Amino Acid?
Amino acid molecules are essential to the creation of peptides and proteins, which are important building blocks for life. There are twenty naturally occurring amino acids, all of which have a similar structure. All amino acids have a carboxyl group (–COOH) and an amino group (–NH2). The carboxyl group contains a carbon atom that is double bonded with an oxygen atom and joined to an alcohol group. The amino group is made up of one nitrogen atom bonded to two hydrogen atoms. Each amino acid also has an R group, which is a side chain that determines the unique characteristics of that particular amino acid.
Two amino acids join when the carboxyl group of one amino acid reacts with the amino group of another amino acid. This process releases one molecule of water and forms a peptide bond.
What Is a Peptide?
Peptides are simply two or more amino acids joined together by a peptide bond. A compound of two amino acids joined in this way is called a dipeptide, and a compound of three amino acids joined by a peptide bond is called a tripeptide. Longer chains of amino acids are called polypeptides, which make up proteins.
Peptide Sequence
Peptide sequence, also known as amino acid sequence, begins when two amino acids form a peptide bond. A sequence of amino acids in a peptide or polypeptide is often described from left to right. The free amino group, or N-terminus, of one amino acid will be on the left, while the free carboxyl group, or C-terminus, of another amino acid will be on the right. The combination of amino acids in this sequence is important. For example, an amino acid sequence of X-Y-Z would be different from an amino acid sequence of Z-Y-X because the free amino and carboxyl groups would come from different molecules.
Sequence and the Structure of Proteins
The sequence of amino acids is particularly important in the formation of proteins, which have one or more polypeptide chains. The deoxyribonucleic acid (DNA) sequence of a particular protein gene controls the sequence of the amino acids in these chains and creates the primary structure of the protein.
The primary structure is simply the linear arrangement of amino acids that form the polypeptide chain. However, three other types of structures can be used to describe a protein. The interactions of the various R groups of the amino acids with one another and with a solvent (which is usually water) often help determine the protein's function and its shape.
It is common for polypeptide chains to develop a secondary structure. This occurs when hydrogen bonding between amino acids creates either a pleated sheet or an alpha helix structure. A pleated sheet, which has peaks and valleys, looks like a fan made from a piece of paper. An alpha helix structure resembles a spiral. This structure is found in some of the proteins that make up nails, hair, wool, and skin.
The side chains, or R groups, which may attract or repel each other depending on their charges, determine the tertiary structure of a protein. The interactions of these side chains may result in folds, bends, or loops in the protein chain. The tertiary structure determines the protein's overall shape, which is usually globular (spherical) or fibrous (stringy).
Quaternary structures occur in complex proteins that have two or more polypeptide chains. Hydrogen bonding between polypeptide chains is usually responsible for the quaternary structure. Hemoglobin, a structure in the blood that carries oxygen to different parts of the body, is an example of a protein with a quaternary structure.
The Importance of Peptide Sequence
In general, peptide sequence is important because it leads to the formation of proteins, which are necessary components of life. Blood, muscle, and various organs and tissues all contain proteins. Proteins also make up enzymes, which are catalysts that aid in certain biological reactions. Protein structure plays an important role in enzyme reactions because an enzyme must bond with a substrate (reactant) to create the desired reaction. The enzyme and substrate work much like a lock and key. Therefore, if the structural alignment of the enzyme is not correct, the reaction will not occur.
Some hormones, or chemical messengers, also are made from proteins and amino acids. Like enzymes, hormones function using the lock-and-key method. To deliver its chemical message, the hormone must bind to a target cell. Once again, structural alignment is crucial to this process. The hormone will not be able to deliver its chemical message if it cannot bind with the target cell.
Bibliography
"Amino Acid." Biology. Ed. Richard Robinson. New York: Macmillan Reference USA, 2009, n.p.
"Amino Acids and Protein." CK-12. CK-12 Foundation. 2014. Web. 22 Dec. 2014. http://www.ck12.org/book/CK-12-Chemistry-Intermediate/section/26.2/
"The Chemistry of Biology." Fact Monster. Pearson Education. 2014. Web. 22 Dec. 2014. http://www.factmonster.com/cig/biology/proteins.html
Ophardt, Charles E. "Tertiary Protein—Structure" Virtual Chembook. Elmhurst College. 2003. Web. 22 Dec. 2014. http://www.elmhurst.edu/~chm/vchembook/567tertprotein.html
"Peptide." World of Biology. Gale, Science in Context. 2006. Web. 22 Dec. 2014.
"Protein." World of Biology. Gale, Science in Context. 2006. Web. 22 Dec. 2014.
Solomon, Eldra P., Charles E. Martin, Diana W. Martin, and Linda R. Berg. "Polarity of Molecules." Biology. 10th ed. Boston: Cengage Learning, 2018, 59–62. Print.
"What Is a Peptide Sequence?" WiseGeek. Conjecture Corporation. 2014. Web. 22 Dec. 2014. http://www.wisegeek.com/what-is-a-peptide-sequence.htm
"What Is an Amino Acid Sequence?" WiseGeek. Conjecture Corporation. 2014. Web. 22 Dec. 2014. http://www.wisegeek.org/what-is-an-amino-acid-sequence.htm