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Proteins
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Proteins - 02-15-2013, 10:02 AM

posted by: andrew.peplin

Basic Overview:

Just about every function of living depends on the function and use of proteins. The word "protein" is derived from the ancient Greek word proteios, meaning the "first" or "primary". Proteins are essential to everyday life and are used in a spew of different chemical reactions, one of the most important proteins is the enzyme, enzymes act as a catalyst and speed up chemical reactions. Although enzymes are important the human has tens of thousands of proteins each with a specific structure and function.

Polypeptides:

Though there are tons of diversified proteins, they are all unbranched polymers constructed from the same 20 amino acids and each protein is folded and coiled into a specific three dimensional structure. This structure is vital and with one simple flaw can cause a spew of problems.
Now I would like to take a detour to talk about amino acids. All amino acids share a common structure and at the center of an amino acid is a asymmetric carbon atom referred to as the alpha carbon. This alpha carbon partners with a carboxyl group and a variable group symbolized by R (Google an amino acid side chain), the R group is also called the side chain. This side chain differs with each amino acid. There are three primary groups of amino acids according to their properties non polar hydrophobic, polar hydrophilic, and electrically charged hydrophilic (positive or negatively charged side chains).
Now that we have taken a look at amino acid we can talk about how they are linked to form polymers. When two amino acids become positioned, so that the carboxyl group of one is adjacent to the amino group, they become joined through a dehydration reaction, this results in a peptide bond. If this occurs over and over again we have a polypeptide bond, polypeptides range in length from a few amino acids to thousands. Although its important to take in to account that one end of the polypeptide has a free amino group (N-terminus) while the other end has a free carboxyl group (C-terminus) and that the side chains far outnumber their terminal groups (this makes the chemical nature of the molecule dependent on side chains).

protein structure and Function:

Now we can get to the fun stuff! The function and specific activities of the protein depend upon their three dimensional architecture and at the simplest level their amino acid sequencing. One of the most inspirational men of his time who was determined to find the amino acid sequencing of proteins was Frederick Sanger who with his colleges worked on the hormone Insulin. By using specific chemical methods and agents to break polypeptides, they eventually succeeded in doing so. Although just a side note, though a protein consists of polypeptides the relationship is somewhat analogous to that of a long strand of yarn and a sweater. As it comes down to the shape and structure of the protein. Most proteins are roughly spherical ( globular proteins) while others are long like fibers (fibrous proteins), hmm I wonder what long fibrous proteins could do?

Definition:

Catalyst: chemical agents that speed up a reaction without being consumed during the reaction.

Polypeptides: polymer of amino acid

protein: a biologically functional molecule that consists of one or more polypeptides.

amino acid: is an organic molecule possessing both an amino group and carboxyl group.

dehydration reaction: a reaction by which a water molecule is lost.

Alright so this is all the time I have to type for today but I will probably continue in this thread tomorrow, hope you guys like it!





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Part 2
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Part 2 - 02-15-2013, 10:03 AM

protein structure and Function (continued):

A proteins function depends on its ability to recognize and bind to some other molecule. For a great example look up the common flu virus and its anti virus.

Subcategory: Four levels of protein Structure

With the goal of understanding the function of a protein, its important to learn about its structure. Although proteins have a great diversity all proteins share three superimposed levels of structure. These are known as primary,secondary, and tertiary structure although a fourth, Quaternary structure, arises when a protein consists of two or more polypeptide chains.

Primary Structure: is an organized series of linked amino acids with a unique sequence. for the sake of an example lets consider Transthyretin a globular blood protein that transports vitamin A and one of the thyroid hormones throughout the body. Transthyretin is made up of four identical polypeptide chains, each of these chains are composed off 127 amino acids . This would be a primary structure because this protein is determined not by ran*** linking of amino acids buts by the precise chain. The primary structure in turn dictates the secondary and tertiary structure due to the chemical nature of the backbone and side chain groups (R) positioned along the side of the chain.

Secondary structure: Secondary structure is the result of hydrogen bonds forming between repeating constituents of the polypeptide backbone. The oxygen atoms have a partially negative charge while the hydrogen atoms connected to the nitrogen have a partially positive charge. This results in the a helix or b pleated sheet, and these hydrogen bonds are weak. The bonds actually break down and get all tangled when cooked, this breakdown is called denaturation and your body will perform renaturation to return the protein to its original form.

Tertiary Structure: is the overall shape of polypeptide resulting from interactions between the side chain groups (R) of various amino acids. One type of interaction that contributes to this is called a hydrophobic interaction. As the peptide folds into shape the amino acids with hydrophobic (non polar) side chains will end up in clusters. Covalent bonds called disulfide bridges may further reinforce the shape of the protein.

Quaternary structure: is the overall protein that results from the aggregation of the polypeptide sub units. These proteins consist of one or more polypeptide chains. A great example of this is collagen or even red blood cells.

protein Folding in the Cell:

Biochemists now know the amino acid sequences for more than 10 million proteins and the three dimensional shape for more than 20,000 and researchers have put a lot of time into correlating the three dimensional shape with the primary structure of many proteins to discover the rules of protein folding. Although its not to simple as most proteins go through a series of different shape before becoming stable. One of the most important to the folding process's are chaperonins, which are protein molecules that will assist other proteins in proper folding. They act like a shield keeping the polypeptide from any bad influences, as it creates a hydrophilic environment for the folding of the polypeptide. Misfolding of polypeptides is a serious problems and many diseases are a result of misfolding, so this process is crucial.

Alright, those are the basics from proteins. I am thinking of doing carbohydrates next, so stay tuned for more!





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02-15-2013, 12:24 PM

Dam I learn something new everyday..wish I was in college cause I'd put more effort into chemistry and not beer 101.
   
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