# 5.1 Defining Proteins

All living cells are made up of proteins (n.d.) including substances such as hormones, enzymes and antibodies that are necessary for that organism to function correctly. Proteins are essential for life. They are a group of complex organic chemical compounds that are made up of carbon, hydrogen, oxygen and sometimes sulfur that is composed of one or more chains of amino acids. They are the true workhorses of the body. Proteins perform a vast array of functions within living organisms, including replicating DNA, catalyzing metabolic reaction and responding to different stimuli. They are an essential part of an organism and take part in nearly all processes that go on within the cells. They are extremely essential in animal diets as some amino acids cannot be synthesized and must be obtained from our food. Amino acids are used in metabolism after they are broken down through digestion.
Some foods that are rich in proteins include eggs, milk, meat, fish, tofu and legumes.
There are three different types of proteins based of their composition.
* Simple proteins
* Conjugated proteins
* Derived proteins
Simple proteins are proteins that are made up of amino acids joined by peptides bonds. Some examples are globulin, albumins, histones, albuminoids, protamines, and glutelins.
Conjugated proteins are simple proteins joined with a prosthetic group or cofactor. Some examples are phospho- proteins, chromo proteins, nucleoproteins and glycoproteins.
Derived proteins are obtained from simple proteins using the actions of chemical agents and enzymes and they are not naturally occurring proteins. Some examples include peptides, peptones and metaproteins.
Simple proteins are proteins that are made up of amino acids joined by peptides bonds. Some examples are globulin, albumins and gliadins.
Conjugated proteins are simple proteins joined with a prosthetic group or cofactor. Some examples are phospho- proteins and chromo proteins.
Derived proteins are obtained from simple proteins using the actions of chemical agents and enzymes and they are not naturally occurring proteins. Some examples include peptides and peptones.
Amino acids and proteins are the building blocks of life. When proteins are digested or broken down, amino acids are left. The human body needs a number of amino acids to:
* Break down food
* Grow
* Repair body tissue
* Other body functions
Amino acids are classified into three groups:
There are three types of amino acids: essential amino acids, nonessential amino acids and conditional amino acids.
* The essential amino acids, we don't produce this, so we have to eat the food for obtain. The amino acids isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine can not be synthesised by the body and therefore must be essential components of the diet.
* Nonessential amino acids the body produce, so people don't need to eat for obtain this amino acids. They are: alanine, asparagine, aspartic acid, and glutamic acid.
* Conditional amino acids: If your system is stressed, out of balance, or diseased, these amino acids become essential and you must get them from food or supplements. They are: arginine, glycine, cystine, tyrosine, proline, glutamine and taurine.

## 5.1.1 Structure

There are four levels of organization for proteins to take on. Each level lends a new layer of physical intricacy, and in turn, more diverse functionalities. The phrase “form fits function” is an appropriate mantra for proteins. The four levels are as follows:
Primary Structure
Proteins at their most basic level are patterned strings of individual amino acids linked together by peptide bonds. Think of a single protein as a beaded necklace, strung with different beads that all have unique properties (Whitney, E., & Rolfes, S., 2013). Each protein has its own pattern of amino acids that makes its form different, and thus its function different. The different effects the arrangement of amino acids has comes into play in the next level of organization.
Secondary Structure
Now is when the string of proteins starts to take a distinct shape. The forming is driven by the weak electrical attractions the individual amino acids have to other amino acids (Whitney, E., & Rolfes, S., 2013). According to Geoffrey Cooper, This is the major form of guidance for the protein, and why the sequence of amino acids in the primary structure determines the functionality of the future protein. Also, molecular chaperones aid in protein folding, and their sole purpose is to help the protein fold in ways it already is predisposed to fold (Cooper, G., 2000).
Some forms that protein strings can take are pleated sheets and helixes (Whitney, E., & Rolfes, S., 2013). Elmhurst University describes the helix shape as spring-like, with the form stabilized by the hydrogen bonding between the nitrogen and hydrogen of an individual amino acid with that of the carbon and oxygen on the amino acids that is 4 amino acids down the string from it. Elmhurst University also states that beta pleated sheets are sheets of protein strings that are bonded side to side by hydrogen bonds, and is planar in contrast to helixes.
Tertiary Structure
The tertiary structure of proteins is when form really starts to represent function. The alpha and beta riddled strings of amino acids begin to fold in on themselves, with the hydrophilic amino side groups facing outward in an aqueous environment, and the hydrophobic side groups facing inwards (Whitney, E., & Rolfes, S., 2013). It is now easy to see how the order of amino acids in the primary structure is vital to the correct form and function of a protein.
Quaternary Structure
In some cases, proteins need to be organized beyond tertiary structure. Multiple proteins that have attained tertiary structure, otherwise known as polypeptides, can group together to create a larger form (Whitney, E., & Rolfes, S., 2013).
Misfolding
Protein folding is a complex process and directly influences the function of the protein. Proteins will only properly work in the body if the 3D structure is correct. While most proteins are correctly folded, some can be misfolded or become unfolded during the process. This leads to inactive proteins that cannot be used by the body. Misfolded proteins are a result of proteins not having enough energy to fold to their correct state and can be influenced by temperature or a limited amount of space in the cell (Gregersen, 2006). This is a common occurrence in the cell and is generally corrected by mechanisms in the body. Misfolded proteins can be refolded through chaperone systems, which refold the protein, or destroyed through denaturing (Gregersen, 2006). However, some proteins that are not folded properly may become detrimental to one’s health. Misfolded proteins that accumulate in the body can replicate and cause degenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s (Reynaud, 2010). The risk of getting degenerative diseases increase with age because the body is not as efficient in protein refolding processes (Reynaud, 2010).
Denaturing
Denaturation is the process by which proteins are broken down (Ophardt, 2003). During this process, the 3D tertiary structure becomes uncoiled. Because the tertiary structure is unraveled, proteins can no longer function properly. Denaturation can be induced through a strong acid or base, salt, detergent, heat, or mechanical force (Ophardt, 2003). Protein folding is caused by hydrogen bonding, which is a weak interaction; thus, it does not take much effort to denature proteins. After denaturation, the protein is in a “random coil” structure (Ophardt, 2003). This random coil structure is not related to the primary, secondary, tertiary, or quaternary structures. After a protein has been denatured, it cannot fold back into its secondary and tertiary structures (Ophardt, 2003). Since it cannot reform its tertiary structure, it no longer can function as it originally did, if it can function at all. Denaturation is almost entirely an irreversible process. Denaturation causes changes in cell activity and even potentially cause cell death (Ophardt, 2003). However, denaturation can also just cause minor changes in color, texture, and physical form. Denaturation is a common occurrence; it is needed in the body to digest food. An example of denaturation that happens in every day life is the hardening of egg whites and yolks when cooked (Ophardt, 2003). In order for the egg to be edible, it must be denatured through heat. Denaturation is also why meat turns firm when cooked. Proteins derived from food are denatured when they come in contact with stomach acid (Ophardt, 2003).
Complete and Incomplete Proteins
Complete proteins contain all nine essential amino acids in quantities that meet the body’s needs. These are found mostly in animal-based proteins such as meat, fish, dairy products, and eggs. These proteins typically have better absorption and availability to the body. Incomplete proteins do not contain all essential amino acids, or not in sufficient quantities. Incomplete proteins come from plant foods such as grains, vegetables, nuts, seeds, and legumes. They can be combined to form complete proteins (Morrow, 2012).
Protein Breakdown
Proteins are broken down into amino acids in a catabolic process. Once these amino acids are broken down, they are reassembled into thousands of different forms the body can use for hormones, enzymes, and neurotransmitters. In order for proteins to break down, the stomach secretes a hormone called gastrin which causes the stomach to secrete gastric juices. The stomach also produces pepsinogen which is converted to pepsin by the hydrochloric acid found in gastric juices. Pepsin is the enzyme that breaks down proteins to peptides. Another digestive enzyme that is secreted by the stomach is protease. Once these peptides move to the duodenum and the pancreas they are broken down further by the enzyme trypsin. In the intestines, digestion of peptides into amino acids is completed with help from peptidase, and these amino acids are absorbed into the bloodstream by the small intestine (Gromisch, 2014).
Transamination and Deamination
When too much protein is consumed, amino acids must be broken down and excreted as urea. In order to begin the catabolism of an amino acid, its amine group, NH3, must be removed. An amine group can be removed by transamination or deamination. Transamination is the transfer of an amine group from an amino acid to a keto acid. This is a reversible reaction, as the reverse is used to synthesize nonessential amino acids. Deamination occurs mostly in the liver with the help of catalysts called deaminases. In this process, ammonia is removed and converted into urea, which is less toxic to the body. The urea is then excreted from the body after passing through the kidneys. Transdeamination is a combination of these two types of reactions, otherwise known as coupled reactions. It occurs when transamination is directly followed by oxidative deamination. These processes are both part of the urea cycle. In the urea cycle, the free ammonium ions released from deamination reactions are condensed with bicarbonate ions to form urea. With each cycle, a molecule of ornithine is produced which keeps the cycle in motion. Some genetic mutations can prevent production of ornithine and, therefore, cause malfunction in the urea cycle. This can be life-threatening, as excess ammonia in the body is toxic (Yudkoff, 1999).

## 5.1.2 Classification of Amino Acids

Amino acids are known for their role as building blocks of proteins as well as intermediates in metabolism. Their arrangement within a protein in determined by the sequence of bases within a gene that goes on to encode a protein. The chemical properties of these building block then dictates the function of the protein. (Dayhoff, 2003)
There are 20 different amino acids required the make the variety of proteins needed by the human body. These amino acids can be classified either by their nutritional aspects or by their chemical composition, specifically their variable side chain. (Fantar, 2009)
Essential, Nonessential, and Conditional Amino Acids
The human body can only make some of the amino acids on its own, while others must be consumed in the diet.
Essential amino acids, also known as indispensable amino acids, are ones that are not manufactured in the body, therefore they must be obtained through ones diet. The 9 essential amino acids are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. (Gersten, 2012)
Nonessential amino acids are those that the body produces naturally. They are either created from the breakdown of protein products or from other essential amino acids. These acids include: alanine, asparagine, aspartic acid, glutamic acid, arginine, cysteine, glutamine, glycine, ornithine, proline, serine and tyrosine. (Creative Commons, 2012)
Conditionally essential amino acids are not usually required in the diet; however for some they are required at certain stages of growth or are needed by certain people whose body cannot synthesize them (McAuley, 2015). Often a nonessential amino acid becomes conditionally essential when there is a deficiency of a needed precursor for that amino acid. Other instances amino acids become conditional are during periods of stress, aging, or illness (Helmenstine, 2011). For proper development, children should consume arginine, cysteine and tyrosine in addition to the essential amino acids. Another example is patients with phenylketonuria who must reduce their phenylalanine intake due to their condition, which causes tyrosine to become an essential amino acid to the diet, as its production is reduced by the phenylalanine reduction. The conditional amino acids include: arginine, cysteine, glutamine, tyrosine, glycine, ornithine, proline, and serine. (McAuley, 2015)
Nonpolar, Polar, Basic, and Acidic Amino Acids
Another form of amino acid classification is based on the charged and polarity of side chains known as the R groups. A single amino acid structure consists of a central carbon atom, an amino group, a carboxylic acid group, and the variable side chain that can lead the amino acid to be nonpolar, polar, basic or acidic. (TutorVista, 2013)
Nonpolar amino acids have no charge on their R group and are hydrophobic. These side chains have pure hydrocarbon alkyl groups. The amino acids in this group are alanine, valine, leucine, isoleucine, phenylalanine, glycine, tryptophan, methionine and proline. (TutorVista, 2013)
Polar amino acids will have functional groups such as alcohols, amides, acids, and amines, and they yield a hydrophilic compound. The amino acids in this group include: Asparagine, Glutamine, Cysteine, Serine, Threonine, and Tyrosine. (TutorVista, 2013)
Acidic amino acids have an acid functional group as well as the carboxylic acid, yielding two acidic components. Aspartic and glutamic acids are the two acidic amino acids. (Ophardt, 2003)
Basic amino acids have another amine functional group as their R group, yielding a basic solution because this extra amine group isn’t neutralized by the carboxylic acid. Basic amino acids include: Arginine, Histidine, and Lysine.

## References

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