Protein

A representation of the three-dimensional structure of myoglobin, the oxygen carrier in muscle. Max Perutz and Sir John Cowdery Kendrew received a Nobel Prize in Chemistry for their eludicidation of myoglobin's structure in 1958; it was the first protein whose structure was solved using X-ray crystallography. The colored alpha helices represent myoglobin's secondary structure (see below).

Alongside polysaccharides, lipids, and nucleic acids, proteins are a major class of the bio-macromolecules that make up the primary constituents of biological organisms. A protein is a complex, high-molecular-mass, organic compound that consists of amino acids joined by peptide bonds. As suggested by the Greek origins of the term protein (from the word protas meaning "of primary importance"), proteins are essential to the structure and function of all living cells and viruses.

Different proteins perform a wide variety of biological functions:

• Some proteins are enzymes, which catalyze chemical reactions.
• Other proteins play structural or mechanical roles, such as those that form the struts and joints of the cytoskeleton, which is like a system of scaffolding within a cell.
• Still more functions filled by proteins include immune response
• the storage and transport of various ligands.

Proteins are essentially polymers made up of a specific sequence of amino acids. The details of this sequence are stored in the code of a gene. Through the processes of transcription and translation, a cell reads the genetic information and uses it to construct the protein. In many cases, the resulting protein is then chemically altered (post-translational modification), before becoming functional. It is very common for proteins to work together to achieve a particular function, and often physically associate with one another to form a complex.

In nutrition, proteins are broken down through digestion back into free amino acids for the organism, including those the organism may not be able to synthesize itself. explain need for dietary protein to get essential amino acids

Proteins are among the most actively-studied molecules in biochemistry, and were discovered by Jöns Jakob Berzelius in 1838. expand to include some reasons for study of proteins and major areas of investigation.

The structure of proteins

Components and synthesis

Proteins are polymers built from 20 different L-alpha-amino acids. Proteins are assembled from amino acids using information present in genes. Genes are transcribed into RNA, RNA is then subject to post-transcriptional modification and control, resulting in a mature mRNA that undergoes translation into a protein. mRNA is translated by ribosomes that match the three-base codons of the mRNA to the three-base anti-codons of the appropriate tRNA. The enzyme aminoacyl tRNA synthetase catalyzes the addition of the correct amino acid to their tRNAs.

The two ends of the amino acid chain are referred to as the carboxy terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the functional group on each extremity.

The four levels of protein structure

The four levels of protein structure.

Proteins fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native state, which is determined by its sequence of amino acids. Thus, proteins are their own polymers, with amino acids being the monomers. Biochemists refer to four distinct aspects of a protein's structure:

• Primary structure: the amino acid sequence
• Secondary structure: highly patterned sub-structures — alpha helix and beta sheet — or segments of chain that assume no stable shape and are formed by hydrogen bonding. Secondary structures are defined, meaning that there can be many different secondary motifs present in one single protein molecule.
• Tertiary structure: the overall shape of a single protein molecule; the spatial relationship of the secondary structural motifs to one another; primarily formed by hydrophobic interactions, but hydrogen bonds, ionic interactions, and disulfide bonds are usually involved too.
• Quaternary structure: the shape or structure that results from the union of more than one protein molecule, usually called protein subunits in this context, which function as part of the larger assembly or protein complex.

File:ProteinStructure.jpg

An example of the three-dimensional structure of protein.

In addition to these levels of structure, proteins may shift between several similar structures in performing their biological function. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as "conformations," and transitions between them are called conformational changes.

The process by which the higher structures are formed is called protein folding and is a consequence of the primary structure. The mechanism of protein folding is not entirely understood. Although any unique polypeptide may have more than one stable folded conformation, each conformation has its own biological activity and only one conformation is considered to be the active one. This assumption has been recently challenged by the discovery of intrinsically unstructured proteins, which can fold in multiple structures with different biological activity.

Major functions of proteins

Proteins are generally large molecules, having molecular masses of up to 3,000,000 (the muscle protein titin has a single amino acid chain 27,000 subunits long) however protein masses are generally measured in kiloDaltons (kDa). Such long chains of amino acids are almost universally referred to as proteins, but shorter strings of amino acids are referred to as "polypeptides," "peptides" or rarely, "oligopeptides". The dividing line is undefined, though "polypeptide" usually refers to an amino acid chain lacking tertiary structure which may be more likely to act as a hormone (like insulin), rather than as an enzyme (which depends on its defined tertiary structure for functionality).

Proteins are generally classified as soluble, filamentous or membrane-associated (see integral membrane protein). Nearly all the biological catalysts known as enzymes are soluble proteins. Antibodies, the basis of the adaptive immune system, are another example of soluble proteins. Membrane-associated proteins include exchangers and ion channels, which move their substrates from place to place but do not change them; receptors, which do not modify their substrates but may simply shift shape upon binding them. Filamentous proteins make up the cytoskeleton of cells and some of the structure of animals: examples include tubulin, actin, collagen and keratin, all of which are important components of skin, hair, and cartilage. Another special class of proteins consists of motor proteins such as myosin, kinesin, and dynein. These proteins are "molecular motors," generating physical force which can move organelles, cells, and entire muscles.

Molecular surface of several proteins showing their comparative sizes. From left to right are: Antibody (IgG), Hemoglobin, Insulin (a hormone), Adenylate kinase (an enzyme), and Glutamine synthetase (an enzyme).

Proteins are involved in practically every function performed by a cell, including regulation of cellular functions such as signal transduction and metabolism. Several particularly important functional classes may be recognized:

1. enzymes, which catalyze all of the reactions of metabolism;
2. structural proteins, such as tubulin, or collagen;
3. regulatory proteins, such as transcription factors or cyclins that regulate the cell cycle;
4. signalling molecules or their receptors such as some hormones and their receptors;
5. defensive proteins, which can include everything from antibodies of the immune system, to toxins (e.g., dendrotoxins of snakes), to proteins that include unusual amino acids like canavanine.

Proteins in the human diet

Sources and absorption

In nutrition, proteins are broken down through digestion, which begins in the stomach. Proteins are broken down by proteases into smaller polypeptides to provide amino acids for the organism, including those the organism may not be able to synthesize itself. Pepsinogen is converted into the enzyme pepsin when it comes into contact with hydrochloric acid. Pepsin is the only proteolytic enzyme in the human digestive system that digests collagen, the major protein of connective tissue ^{[citation needed]}. Most protein digestion takes place in the duodenum with the overall contribution from the stomach being small. Almost all protein is absorbed when it reaches the jejunum with only 1% of ingested protein left in the feces. Some amino acids remain in the epithelial cells and are used for synthesis of new proteins, including some intestinal proteins, constantly being digested, recycled and absorbed from the small intestine.

Proteins, like carbohydrates, contain 4 kilocalories per gram as opposed to lipids which contain 9 kilocalories and alcohols which contain 7 kilocalories. Proteins can be converted into carbohydrates through a process called gluconeogenesis.

Dietary requirements

Toasted soybeans

When we think of dietary protein, we tend to think of animal meats. While these are rich sources of this vital dietary element, protein is also found in plant foods, such as grains and legumes, and in eggs and dairy products, such as milk and yogurt. In order to obtain the full range of essential amino acids, you should eat a variety of protein foods. Many people choose red meat (beef, pork, lamb and veal) as their main source of protein, and eat it regularly through the week. Animal meats commonly contain excess fat and lack other important vitamins and minerals, such as complex carbohydrates and dietary fiber. Plant foods, such as legumes, nuts, seeds, and grains, also provide protein. Soy products are particularly popular (e.g. tofu) but contain phytoestrogens, which can be harmful in excessive quantities.

Protein is an important macronutrient to the human diet, supplying the body's needs for amino acids, the building blocks of proteins. Mammals cannot synthesize all 20 amino acids, so protein from the diet is necessary to acquire those that cannot be synthesized, known as essential amino acids (9 in human). The exact amount of dietary protein needed to satisfy these requirements for humans, known as an RDA may vary widely depending on age, sex, level of physical activity, and medical condition.

Soybeans are a source of complete protein. A complete protein is one that contains significant amounts of all the essential amino acids that must be provided to the human body because of the body's inability to synthesize them. For this reason, soy is important to many vegetarians and vegans. Soy protein is similar to that of other legume seeds, but has the highest yield per square meter of growing area, and is the least expensive source of dietary protein. The only non-legume to have an almost identical protein profile to soy is the cereal oat (Avena sativa), and perhaps quinoa. However, rapeseed/Canola may actually even have a better amino acid profile than soy protein.

According to the recently updated Dietary Reference Intake guidelines, the recommended daily consumption of protein for adult men and women is the following: Women aged 19-70 need to consume 46g of protein per day. Men aged 19-70 need to consume 56g of protein per day. The difference is due to the fact that, in general, men's bodies have more muscle mass than those of women.

Other recommendations suggest 1g of protein per kilogram of bodyweight while some extreme sources suggest that higher intakes of 1-2 grams of protein per pound of bodyweight are desirable. Higher levels of protein intake have not been proven to be necessary and may be harmful due to increased stress on the kidneys and liver.

How much protein you need in your daily diet is determined, in large part, by your overall energy intake, as well as by your body's need for nitrogen and essential amino acids. Physical activity and exertion as well as enhanced muscular mass increase your need for protein. Requirements are also greater during childhood for growth and development, during pregnancy or when breast-feeding in order to nourish your baby, or when your body needs to recover from malnutrition or trauma or after an operation.

Because the body is continually breaking down protein from tissues, even adults who do not fall into the above categories need to include adequate protein in their diet every day. If you do not take in enough energy from your diet, your body will use protein from the muscle mass to meet its energy needs, and this can lead to muscle wasting over time.

Protein deficiency and other dietary imbalances

Protein deficiency can lead to symptoms such as fatigue, insulin resistance, hair loss, loss of hair pigment, loss of muscle mass, low body temperature, hormonal irregularities, as well as loss of skin elasticity. Severe protein deficiency, encountered only in times of famine, is fatal, due to the lack of material for the body to construct its own proteins (see kwashiorkor).

Protein deficiency is rare in developed countries, but it can occur in people who are dieting to lose weight, or in older adults, who may have a poor diet. Convalescent people recovering from surgery, trauma, or illness may become protein deficient if they do not increase their intake to support their increased needs. A deficiency can also occur if the protein you eat is incomplete and fails to supply all the essential amino acids.

Because the body is unable to store excess protein, it is broken down and converted into sugars or fatty acids. The liver removes nitrogen from the amino acids, so that they can be burned as fuel, and the nitrogen is incorporated into urea, the substance that is excreted by the kidneys. These organs can normally cope with any extra workload but if kidney disease occurs, a decrease in protein will often be prescribed.

Excessive protein intake may also cause the body to lose calcium, which could lead to bone loss in the long-term. Foods that are high in protein (such as red meat) are often high in saturated fat, so excessive protein intake may also contribute to increased saturated fat.

Some suspect excessive protein intake is linked to several problems:

• Overreaction within the immune system
• Liver dysfunction due to increased toxic residues
• Loss of bone density, frailty of bones is due to calcium and glutamine being leached from bone and muscle tissue to balance increased acid intake from diet (blood pH is maintained at around 7.4). This effect is not present if intake of alkaline minerals (from fruits and vegetables, cereals are acidic as are proteins, fats are neutral) is high. In such cases, protein intake is anabolic to bone. [1]

It is assumed by researchers in the field, that excessive intake of protein forces increased calcium excretion. If there is to be excessive intake of protein, it is thought that a regular intake of calcium would be able to stablilise, or even increase the uptake of calcium by the small intestine, which would be more beneficial in older women .

Proteins are often progenitors in allergies and allergic reactions to certain foods. This is because the structure of each form of protein is slightly different; some may trigger a response from the immune system while others remain perfectly safe. Many people are allergic to casein, the protein in milk; gluten, the protein in wheat and other grains; the particular proteins found in peanuts; or those in shellfish or other seafoods. It is extremely unusual for the same person to adversely react to more than two different types of proteins, due to the diversity between protein or amino acid types.Template:Cite needed

Studying proteins

The first mention of the word protein was from a letter sent by Jöns Jakob Berzelius to Gerhardus Johannes Mulder on 10. July 1838, where he wrote:

«Le nom protéine que je vous propose pour l’oxyde organique de la fibrine et de l’albumine, je voulais le dériver de πρωτειος, parce qu’il paraît être la substance primitive ou principale de la nutrition animale.»

Translated as:

"The name protein that I propose for the organic oxide of fibrin and albumin, I wanted to derive from [the Greek word] πρωτειος, because it appears to be the primitive or principal substance of animal nutrition."

Investigation of proteins and their properties had been going on since about 1800 when scientists were finding the first signs of this, at the time, unknown class of organic compounds.

Proteins are sensitive to their environment. They may only be active in their native state, over a small pH range, and under solution conditions with a minimum quantity of electrolytes. A protein in its native state is often described as folded. A protein that is not in its native state is said to be denatured. Denatured proteins generally have no well-defined secondary structure. Many proteins denature and will not remain in solution in distilled water.

One of the more striking discoveries of the 20th century was that the native and denatured states in many proteins were interconvertible, that by careful control of solution conditions (by for example, dialyzing away a denaturing chemical), a denatured protein could be converted to native form. The issue of how proteins arrive at their native state is an important area of biochemical study, called the study of protein folding.

Through genetic engineering, researchers can alter the sequence and hence the structure, "targeting", susceptibility to regulation and other properties of a protein. The genetic sequences of different proteins may be spliced together to create "chimeric" proteins that possess properties of both. This form of tinkering represents one of the chief tools of cell and molecular biologists to change and to probe the workings of cells. Another area of protein research attempts to engineer proteins with entirely new properties or functions, a field known as protein engineering.

The most commonly used test for the amount of proteins in foods is called the Kjeldah test. This test determines the total nitrogen in a sample. The only major component of most food which contains nitrogen is protein (fat, carbohydrate and dietary fibre do not contain nitrogen). If the amount of nitrogen is multiplied by a factor depending on the kinds of protein expected in the food the total protein can be determined. On food labels the protein is given by the nitrogen muliplied by 6.25, because the average nitrogen content of proteins is about 16%. The reason the Kjeldah test is used is because it is the method the AOAC International has adopted and which is therefore used by many food standards agencies around the world.

External links

• The Protein Databank
• UniProt the Universal Protein Resource
• Human Protein Atlas
• iHOP - Information Hyperlinked over Proteins
• Proteins: Biogenesis to Degradation - The Virtual Library of Biochemistry and Cell Biology
• MIT's Laboratory for Protein Molecular Self-Assembly
• Numerous publications on synthetic biomimetic protein-based biomaterials
• Amino acid metabolism
• Protein Images
• Online Protein viewer with a local PDB database
• NCBI Entrez Protein database
• NCBI Protein Structure database
• TheDailyPlate.com - Protein content details for over 100,000 foods.
• AOAC International

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