Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function.

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; however, in certain organisms the genetic code can include selenocysteine and—in certain archaea—pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by posttranslational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes.

Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism. Broken down proteins are often used for their amino acids which are collected by certain tRNA and held until needed by a ribosome which has been told by mRNA to synthesize the amino acid into a protein. Protein is a recyclable in that sense.


 * Different Stages of Protein Structure**

__Primary Structure__: Primary structure of proteins involves the order of amino acids in a polypeptide chain. This order is determined during translation, when a codon, transported by an RNA molecule, is deciphered by a ribosome and codes for a specific amino acid sequence.

__Secondary Structure__: Secondary structure is how different amino acids interact with others in close vicinity to them. These interaction happen between amino acids that are 3 or 4 spaces away. This determines whether the amino acid forms an alpha helix structure or a beta pleated sheet structure.

__Tertiary Structure__: Tertiary structure is how different amino acids interact with others much farther away. This determines the folding and overall structure of the protein.

__Quaternary Structure__: Quaternary structure is how proteins interact with other proteins. Examples of proteins that involves quaternary structure include collagen and hemoglobin.

We need protein in our diet to survive (along with carbohydrates, etc.) Here is a list of things that contain protein
 * steak
 * peanut-butter
 * sausage
 * ham
 * turkey
 * bologna
 * fish
 * dog (eaten in north korea)
 * maggots
 * beans
 * protein bars
 * pork
 * brats
 * ribs
 * pastrami
 * salami
 * pepperoni

Synthesis
A ribosome produces a protein using mRNA as template. The [|DNA] sequence of a gene [|encodes] the [|amino acid] sequence of a protein. Proteins are assembled from amino acids using information encoded in [|genes]. Each protein has its own unique amino acid sequence that is specified by the [|nucleotide] sequence of the gene encoding this protein. The [|genetic code] is a set of three-nucleotide sets called [|codons] and each three-nucleotide combination designates an amino acid, for example AUG ( [|adenine] - [|uracil] - [|guanine] ) is the code for [|methionine]. Because [|DNA] contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code, with some amino acids specified by more than one codon. [|[6]] Genes encoded in DNA are first [|transcribed] into pre- [|messenger RNA] (mRNA) by proteins such as [|RNA polymerase]. Most organisms then process the pre-mRNA (also known as a //primary transcript//) using various forms of [|Post-transcriptional modification] to form the mature mRNA, which is then used as a template for protein synthesis by the [|ribosome]. In [|prokaryotes] the mRNA may either be used as soon as it is produced, or be bound by a ribosome after having moved away from the [|nucleoid]. In contrast, [|eukaryotes] make mRNA in the [|cell nucleus] and then [|translocate] it across the [|nuclear membrane] into the [|cytoplasm], where [|protein synthesis] then takes place. The rate of protein synthesis is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second. [|[7]] The process of synthesizing a protein from an mRNA template is known as [|translation]. The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its [|base pairing] [|anticodon] located on a [|transfer RNA] molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme [|aminoacyl tRNA synthetase] "charges" the tRNA molecules with the correct amino acids. The growing polypeptide is often termed the //nascent chain//. Proteins are always biosynthesized from [|N-terminus] to [|C-terminus]. [|[6]] The size of a synthesized protein can be measured by the number of amino acids it contains and by its total [|molecular mass], which is normally reported in units of //daltons// (synonymous with [|atomic mass units] ), or the derivative unit kilodalton (kDa). [|Yeast] proteins are on average 466 amino acids long and 53 kDa in mass. [|[5]] The largest known proteins are the [|titins], a component of the [|muscle] [|sarcomere] , with a molecular mass of almost 3,000 kDa and a total length of almost 27,000 amino acids. [|[8]]

Chemical synthesis
Short proteins can also be synthesized chemically by a family of methods known as [|peptide synthesis], which rely on [|organic synthesis] techniques such as [|chemical ligation] to produce peptides in high yield. [|[9]] Chemical synthesis allows for the introduction of non-natural amino acids into polypeptide chains, such as attachment of [|fluorescent] probes to amino acid side chains. [|[10]] These methods are useful in laboratory [|biochemistry] and [|cell biology], though generally not for commercial applications. Chemical synthesis is inefficient for polypeptides longer than about 300 amino acids, and the synthesized proteins may not readily assume their native [|tertiary structure]. Most chemical synthesis methods proceed from C-terminus to N-terminus, opposite the biological reaction. [|[11]]

Enzymes
The best-known role of proteins in the cell is as [|enzymes], which [|catalyze] chemical reactions. Enzymes are usually highly specific and accelerate only one or a few chemical reactions. Enzymes carry out most of the reactions involved in [|metabolism], as well as manipulating DNA in processes such as [|DNA replication] , [|DNA repair] , and [|transcription]. Some enzymes act on other proteins to add or remove chemical groups in a process known as posttranslational modification. About 4,000 reactions are known to be catalyzed by enzymes. [|[27]] The rate acceleration conferred by enzymatic catalysis is often enormous—as much as 1017-fold increase in rate over the uncatalyzed reaction in the case of [|orotate decarboxylase] (78 million years without the enzyme, 18 milliseconds with the enzyme). [|[28]] The molecules bound and acted upon by enzymes are called [|substrates]. Although enzymes can consist of hundreds of amino acids, it is usually only a small fraction of the residues that come in contact with the substrate, and an even smaller fraction—three to four residues on average—that are directly involved in catalysis. [|[29]] The region of the enzyme that binds the substrate and contains the catalytic residues is known as the [|active site].