Attracting Abundance

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The Law

Belief - X

Our Cellular Biology - IX

Recall that proteins are end products of the decoding process that starts with the information in cellular DNA. Each gene in the DNA contains the code for a unique protein structure. Not only are thee proteins assembled with different amino acid sequences, but they also are held together by different bonds and folded into variety of three dimensional structures. The folded shape, or conformation, depend on the sequence of amino acid of the protein.

Note: The building blocks of proteins are amino acids which are small organic molecules that consists of a central carbon atom linked to an amino group, a carboxyl group, a hydrogen atom and a side chain. While the rest of the structure of amino acid molecules remains same for all amino acids, their uniqueness is derived for the side chain composition which is variable.(See the diagram on the right). Proteins are built from a chain of 20 amino acids each of which has a unique side chain. The side chains of amino acids have different chemistries.  the largest group of amino acids have non-polar side chains. Several other amino acids have side chains with positive or negative charges, while others have polar but uncharged side chains.  Based on the propensity of the side chain to be in contact with polar solvent like water, it may be classified as hydrophobic (low propensity to be in contact with water), or hydrophillic or polar or charged (energetically favorable contact with water). 

Within a protein, multiple amino acids are linked together by peptide bonds, thereby forming a long chain. The linear sequence of amino acids within a protein is considered as the primary structure of the protein.

Note: A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). This is also known as a condensation reaction, and usually occurs between amino acids. (See the diagram on the left)






The chemistry of amino acid side chain 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. Because of side chain interactions, the sequence and location of amino acids in a particular protein guides where the bonds and folds occur in that protein.

When connected together by a series of peptide bonds, amino acids form a polypeptide, another word for protein. The polypeptide will then fold into a specific conformation depending on the interaction (dashed lined) between the amino acid side chains

The final shape adopted by a newly synthesized protein is typically the most energetically favorable one. As proteins fold, they test a variety of conformations before reaching their final form, which is unique and compact. Folded proteins are stabilized by thousands of noncovalent bonds between amino acids. In addition, chemical forces between a protein and its immediate environment contribute to protein shape and stability. For example, the proteins that are dissolved in the cell cytoplasm have hydrophilic (water-loving) chemical groups on their surfaces, whereas their hydrophobic (water-averse) elements tend to be tucked inside. In contrast, the proteins that are inserted into the cell membranes display some hydrophobic chemical groups on their surface, specifically in those regions where the protein surface is exposed to membrane lipids. It is important to note, however, that fully folded proteins are not frozen into shape. Rather, the atoms within these proteins remain capable of making small movements.

Note: A covalent bond, also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms. A noncovalent bond is a type of chemical bond that typically bond between macromolecules. They do not involve sharing a pair of electrons. Noncovalent bonds are used to bond large molecules such as proteins and nucleic acids.

In theory, once their constituent amino acids are strung together, proteins attain their final shapes without any energy input. In reality, however, the cytoplasm is a crowded place, filled with many other macromolecules capable of interacting with a partially folded protein. Inappropriate associations with nearby proteins can interfere with proper folding and cause large aggregates of proteins to form in cells. Cells therefore rely on so-called chaperone proteins to prevent these inappropriate associations with unintended folding partners. Chaperone proteins surround a protein during the folding process, sequestering the protein until folding is complete.

Note: A protein family is a group of proteins that share a common evolutionary origin, reflected by their related functions and similarities in sequence or structure.Protein families are often arranged into hierarchies, with proteins that share a common ancestor subdivided into smaller, more closely related groups.

Chaperone proteins are abundant in cells. These chaperones use energy from ATP to bind. Chaperones also assist in the refolding of proteins in cells. Folded proteins are actually fragile structures, which can easily unfold. Although many thousands of bonds hold proteins together, most of the bonds are non-covalent and fairly weak. Even under normal circumstances, a portion of all cellular proteins are unfolded. Increasing body temperature by only a few degrees can significantly increase the rate of unfolding. When this happens, repairing existing proteins using chaperones is much more efficient than synthesizing new ones. Interestingly, cells synthesize additional chaperone proteins in response to "heat shock."

All proteins bind to other molecules in order to complete their tasks, and the precise function of a protein depends on the way its exposed surfaces interact with those molecules. Proteins with related shapes tend to interact with certain molecules in similar ways, and these proteins are therefore considered a protein family. The proteins within a particular family tend to perform similar functions within the cell.

Proteins from the same family also often have long stretches of similar amino acid sequences within their primary structure. These stretches have been conserved through evolution and are vital to the catalytic function of the protein. For example, cell receptor proteins contain different amino acid sequences at their binding sites, which receive chemical signals from outside the cell, but they are more similar in amino acid sequences that interact with common intracellular signaling proteins. Protein families may have many members, and they likely evolved from ancient gene duplications. These duplications led to modifications of protein functions and expanded the functional repertoire of organisms over time.

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Prabir

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