Proteins are made up of polypeptide chains, which are amino acids joined together with peptide bonds. Amino acids are joined together by the peptide bond which is formed in between the carboxyl group and amino group of successive amino acids. Proteins are formed from 20 different amino acids, depending on the number of amino acids and the sequence of amino acids. Amino acids are molecules containing an amine group (NH2), a carboxylic acid group (R-C=O-OH) and a side-chain (usually denoted as R) that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen.
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Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids.
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There are four levels of protein structure:
1. Primary structure
- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure
1. Primary structure
- The linear sequence of amino acids forming the backbone of protein.
- They are non-functional protein.
2. Secondary structure
- Refers to the coiling or folding of a polypeptide chain that gives the protein its 3-D shape.
- There are two types of secondary structures observed in proteins:
- Refers to the coiling or folding of a polypeptide chain that gives the protein its 3-D shape.
- There are two types of secondary structures observed in proteins:
- Alpha (α) helix
- Resembles a coiled spring and is secured by hydrogen bonding in the polypeptide chain
- Hydrogen bonds form between the oxygen of the C=O of each peptide bond in the strand and the hydrogen of the N-H group of the peptide bond four amino acids below it in the helix
- The hydrogen bonds make this structure especially stable.
- Appears to be folded or pleated and is held together by hydrogen bonding between polypeptide units of the folded chain that lie adjacent to one another.
- The polypeptide N-H and C=O groups form hydrogen bonds to stabilize the structure. These bonds are formed between neighbouring polypeptide beta strands.
- Two or more parallel or antiparallel adjacent polypeptide chains of beta strand stabilised by hydrogen bonds form a beta sheet.
- Side chains project alternately upward and downward from the sheet.
- The bond angles along the peptide backbone produce a regular zigzag pattern within this linear structure.
- The major constituent of silk (silk fibroin) consists mainly of layers of b sheet stacked on top of each another.
3. Tertiary structure
- The spatial arrangement of secondary structure (α helices, β strands, and loops) results in the formation of the tertiary structure or fold of a protein.
- Types of bonds and forces that holds a protein in its tertiary structure:
- The spatial arrangement of secondary structure (α helices, β strands, and loops) results in the formation of the tertiary structure or fold of a protein.
- Types of bonds and forces that holds a protein in its tertiary structure:
- Hydrophobic interactions
- Greatly contribute to the folding and shaping of a protein.
- The "R" group of the amino acid is either hydrophobic or hydrophilic. The amino acids with hydrophilic "R" groups will seek contact with their aqueous environment, while amino acids with hydrophobic "R" groups will seek to avoid water and position themselves towards the center of the protein.
- In the polypeptide chain and between amino acid "R" groups helps to stabilize protein structure by holding the protein in the shape established by the hydrophobic interactions.
- Occur between the positively and negatively charged "R" groups that come in close contact with one another.
- Oxidation of the sulfhydryl groups on cysteine is an important aspect of the stabilization of protein tertiary structure, allowing different parts of the protein chain to be held together covalently.
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4. Quaternary structure
- Two or more polypeptide chains may bind to each other to form a quaternary structure.
- Each polypeptide chain is referred to as a subunit.
- Eg:
- Two or more polypeptide chains may bind to each other to form a quaternary structure.
- Each polypeptide chain is referred to as a subunit.
- Eg:
- Hemoglobin found in the blood, is an iron containing protein that binds oxygen molecules. It contains four subunits: two alpha subunits and two beta subunits. Its function is to carry oxygen around in the blood, and it is facilitated in doing so by the presence of the haem group which contains a Fe2+ ion, onto which the oxygen molecules can bind.
- Collagen is a fibrous protein consisting of three polypeptide chains wound around each other. Each of the three chains is a coil itself. Hydrogen bonds form between these coils, which are around 1000 amino acids in length, which gives the structure strength. This is important given collagen's role, as structural protein.