Proteins are assembled from a set of only twenty amino acids, each with a unique side chain. The sequence of these amino acids is known as the primary structure of the protein. The side chains of amino acids have different chemistries, with the largest group having nonpolar, hydrophobic side chains, while others have polar, charged side chains. The chemistry of these side chains is critical to protein structure, as they can bond with one another to hold a length of protein in a certain shape or conformation. This conformation is determined solely by its amino acid sequence.
| Characteristics | Values |
|---|---|
| What are proteins built from | A set of 20 amino acids |
| Amino acid structure | An alpha (central) carbon atom linked to an amino group, a carboxyl group, a hydrogen atom, and a variable component called a side chain |
| Amino acid sequence | Known as the primary structure of the protein |
| Amino acid sequence variability | Amino acids can have nonpolar, positively charged, negatively charged, or polar but uncharged side chains |
| Importance of side chains | The chemistry of amino acid side chains is critical to protein structure as they can bond with one another to hold a length of protein in a certain shape or conformation |
| Types of bonds formed by side chains | Ionic bonds, hydrogen bonds, and hydrophobic bonds via weak van der Waals interactions |
| Secondary structure | Stretches of polypeptide chain that form α helices and β sheets |
| Tertiary structure | The full three-dimensional organization of a polypeptide chain |
| Quaternary structure | The complete structure of a particular protein molecule formed as a complex of more than one polypeptide chain |
| Protein folding | Proteins fold into unique three-dimensional shapes, and this folding is often assisted by special proteins called molecular chaperones |
What You'll Learn
- The primary structure of a protein
- The secondary structure of a protein
- The tertiary structure of a protein
- The quaternary structure of a protein
- The importance of amino acid side chains
The primary structure of a protein
Proteins are composed of multiple amino acids linked together by peptide bonds, forming a long chain known as a polypeptide chain. Each amino acid consists of an alpha (central) carbon atom bonded to a hydrogen atom, an amino group, a carboxyl group, and a variable side chain. The side chains can be nonpolar and hydrophobic, negatively or positively charged, or reactive, giving each amino acid its unique properties. The sequence and number of these amino acids vary in different types of proteins, and this sequence is what defines the primary structure.
The primary structure is essential to the overall conformation of the protein. The amino acid sequence determines how the protein will fold and interact with other molecules in the cell. This folding process is often assisted by molecular chaperones, especially in the crowded environment of the cytoplasm, ensuring the protein folds along the most energetically favourable pathway.
Additionally, proteins from the same family often share similar stretches of amino acid sequences within their primary structure. These conserved sequences are vital to the catalytic function of the protein and have been passed down through evolution.
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The secondary structure of a protein
The α-helix is a right-handed helix with amino acid residues spaced at 3.6 residues per turn and a rise of 0.54nm per turn. This structure is formed when two or three α-helices wrap around each other, with their nonpolar (hydrophobic) side chains facing inward. This creates a particularly stable structure known as a coiled-coil, which provides the structural framework for many elongated proteins such as α-keratin in the skin and myosin molecules responsible for muscle contraction.
The β-pleated sheets and β-turns are other common secondary structures. The specific amino acids that prefer to adopt helical conformations in proteins include methionine, alanine, leucine, glutamate, and lysine ("MALEK" in amino-acid 1-letter codes). In contrast, large aromatic residues (tryptophan, tyrosine, and phenylalanine) and Cβ-branched amino acids (isoleucine, valine, and threonine) tend to favour β-strand conformations.
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The tertiary structure of a protein
The amino acid sequence of a protein is known as its primary structure. This primary structure determines whether a segment forms an alpha helix or a beta-pleated sheet structure. The full three-dimensional organisation of a polypeptide chain is referred to as the tertiary structure.
As a polypeptide folds into its correct shape, amino acids with nonpolar side chains typically cluster at the core of the protein, avoiding contact with water. Weak van der Waals forces then stabilise the protein. Hydrogen bonds and ionic interactions between polar, charged amino acids also contribute to the tertiary structure. Although individually weak in a cellular environment, their cumulative effect is crucial in determining the distinctive shape of the protein.
The folding of a polypeptide chain into its correct three-dimensional shape is often assisted by special proteins called molecular chaperones. These chaperones are vital in the crowded conditions of the cytoplasm, as they prevent the exposure of hydrophobic regions in newly synthesised polypeptides. Prediction of the tertiary structure of a protein relies on knowing its primary structure and comparing the possible predicted tertiary structure with known tertiary structures in protein data banks.
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The quaternary structure of a protein
Quaternary structures can be homomeric or heteromeric. When two identical protein monomers come together, they form a homomeric structure, or a homo-dimer. On the other hand, two different protein monomers create a heteromeric structure, or a hetero-dimer. Examples of proteins with quaternary structures include haemoglobin, DNA polymerase, ribosomes, antibodies, and ion channels.
It is not always possible to obtain a precise determination of the subunit composition. However, bioinformatics methods have been developed to predict the quaternary structural attributes of proteins based on their sequence information by using various modes of pseudo amino acid composition.
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The importance of amino acid side chains
Amino acids are the building blocks of proteins. They are linked together in long chains called polypeptides. The amino acid sequence is known as the primary structure of a protein.
Amino acid side chains can be classified into four groups based on the polarity of their R groups (side chains). Group I amino acids, including glycine, alanine, and valine, have hydrophobic R groups, which cause globular proteins to fold into three-dimensional shapes, burying these hydrophobic side chains within the protein's interior. This is essential for the stability of the protein.
Group II amino acids, such as serine and threonine, have R groups with functional groups that can form hydrogen bonds with water and other molecules. These hydroxyl groups are subject to phosphorylation, a crucial post-translational modification. Group II also includes cysteine, which contains a highly chemically reactive sulfur atom.
The imidazole side chain of histidine, a Group II amino acid, is unique among standard amino acids. It allows histidine to function in both acid and base catalysis near physiological pH values, making it a key component of active sites in protein enzymes.
Additionally, amino acid side chains within proteins can undergo chemical modifications, increasing the diversity of their structures and functions. For example, lysine, an essential amino acid, can be modified to form acetyllysine, hydroxylysine, and methyllysine. These modifications can affect ionization, deionization, or have no impact on the charge.
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Frequently asked questions
The primary structure of a protein is the linear sequence of amino acids within it.
Amino acids are molecules that contain an amine group, a carboxylic acid group, and a side chain. When amino acids are linked together by a series of peptide bonds, they form a polypeptide, another word for protein.
The sequence of amino acids in a protein can be determined by forming an immune complex of MAb H6-3C4 with its antigenic molecule, which is then fractionated by SDS-PAGE.
The sequence of amino acids in a protein guides where the bends and folds occur in that protein. The conformation of a protein is determined by its amino acid sequence. The chemistry of amino acid side chains is critical to protein structure because these side chains can bond with one another to hold a length of protein in a certain shape or conformation.
