# 5.3 Synthesis

The process of protein synthesis can be broken up into two main steps: transcription and translation. Transcription is the process of creating mRNA from DNA, and translation is the process of creating a protein from the mRNA.
The DNA in our cells holds all the necessary information for protein synthesis. In the nucleus of a cell, RNA polymerase unzips the DNA to begin the formation of the RNA. C and G nucleotides match up and A and T nucleotides match up. However, whenever an A is found on the DNA, the RNA polymerase places a U on the RNA. For example, if the sequence of amino acids on the DNA were ATCG, the sequence on the mRNA would be UAGC. This is the process of transcription to messenger RNA, or mRNA. The mRNA is carried outside the nucleus into the cytoplasm (Dobson, 2000).
It is important to note that the mRNA will not code for the entire DNA, it will code for a portion of the DNA strand that is necessary to create the protein needed at that time. (Teacher’s Pet, 2014) Once the new mRNA is formed, transcription will occur. Transcription can be broken down into three main steps: initiation, elongation, and termination.
Once the mRNA is outside of the nucleus and inside the cytoplasm of the cell, two ribosomal subunits attach to the mRNA. Ribosomes can be found on the rough endoplasmic reticulum (Farabee, 2007). They can be thought of as protein making machines; they themselves are made up of protein and RNA. This linking step between the mRNA and ribosomes is called initiation.
The ribosome reads the nucleotides from the mRNA in groups of threes, known as a codon. It begins at a start codon, which is usually AUG. Transfer RNA, or tRNA, delivers the necessary amino acids in order to add the amino acids to the chain and create a protein. The codon of the mRNA is matched to three nucleotides on the tRNA, known as an anticodon. The anticodon is on one side of the tRNA while the amino acid that will be added to the chain is on the other. In elongation, the ribosome has three tRNA binding sites, known as the acceptor (A) site, the peptidyl (P) site, and the exit (E) site. The tRNA that has the chain of amino acids attached to it binds to the P site, and the new tRNA with an anticodon binds to the A site to be read and checked that it has the correct next anticodon. When the two tRNAs are next to each other, a bond forms between the amino group of one amino acid, and the acid group of the other. One of the tRNAs continues to the E site where it exits the ribosome and then goes back to the cytoplasm to find new amino acids. The protein grows until a stop codon is reached (Farabee, 2007).
The bonds between amino acids are called peptide bonds, and a strand of 10 or more amino acids is known as a polypeptide. Once the chain of amino acids is complete, termination takes place and the new protein is released from the ribosome (Teacher’s Pet, 2014), ready to perform one of the many functions of proteins which will be described in the next section.

## Works Cited

Dobson CM (2000). "The nature and significance of protein folding". In Pain RH (ed.). Mechanisms of Protein Folding. Oxford, Oxfordshire: Oxford University Press. pp. 1–28. ISBN 0-19-963789-X. Retrieved November 10, 2015.
Farabee, M.J. (2007). Protein Synthesis. Retrieved November 9, 2015.
[Teacher’s Pet]. (2014, December 7). Protein Synthesis. [Video File]. Retrieved November 9, 2015 from https://www.youtube.com/watch?v=2zAGAmTkZNY.

## 5.3.1 Protein turnover

Protein turnover is defined as the continuous degradation and synthesis of proteins in our body. This process is important in human and animal cells because it allows them to grow and build the protein we need to survive. The organs in our body make use of this process to repair and build tissues and regulate metabolic pathways. When we obtain proteins from the food we eat, our body digests that food in our small intestines and breaks down the nutrient into smaller parts known as amino acids, which are essentially the building blocks of proteins (W H Freeman, 2002). When proteins are broken down into nitrogen containing amino acids, they are added into the amino acid pool, which is an accumulation of amino acids that are stored in the body for the future. The amount of protein we need in our body from our diet depends on nitrogen balance, which is the balance between the amounts of nitrogen digested versus the amount of nitrogen excreted. In normal cases, the rate of protein degradation equals the rate of protein synthesis. During an anabolic state, organisms or cells are growing therefore the rate of protein synthesis is higher than the rate of degradation. During a catabolic state, the rate of degradation is higher than that of protein synthesis (Doherty & Whitfield, 2011). This constant balancing of metabolic pathways allows our bodies to react to different cellular situations and stay in homeostasis.
There are a lot of factors that influence the rate of protein synthesis and degradation. In protein synthesis, the initiation of transcription as well as the activity of ribosomes has an effect. In protein degradation, the half-lives of proteins in a cell are not always constant and may vary (Cooper, 2000). In some cases degraded proteins are used as regulatory molecules, like in transcription, therefore they must be broken down rapidly. In other cases, proteins are degraded in response to certain signals so they can act as a mechanism in regulation depending on the intracellular environment (Cooper, 2000). In any case protein turnover must be swift in order to change their levels and react to external stimuli.
Protein turnover is a dynamic process that requires certain techniques in order for it to be measured. Some ways protein turnover can be measured include measuring the amount of RNA per DNA or protein, the state of aggregation of ribosomes (i.e. the polyribosome index), the abundance of mRNA for particular proteins, and the enzymatic activity of proteins such as proteases, ribonuclease, etc. (Smith & Rennie, 1996). However, the more common and efficient method of measuring protein turnover involves using a proteomic machine to set a precursor into a protein or amino acid so that quantifiable data can be obtain throughout the process (Doherty & Whitfield, 2011).
In the processes of protein synthesis and metabolism, amino acids can be used to form compounds other than protein in the body, such as neurotransmitters, glucose and adipose cells. But the most important and most common mechanisms of protein synthesis and metabolism occur when amino acids are broken down through deamination and then reconstructed to make nonessential amino acids and other types of proteins through transamination.
The process of deamination can be executed under aerobic or anaerobic conditions as it can be either oxidative or non-oxidative. Deamination occurs in all body tissues, but most notably is found in the liver. During this mechanism, an amine functional group is removed, forming an ammonia molecule that travels into the urea cycle (Ophardt, 2003). This functional group is replaced by a ketone group, thereby converting the amino acid into a keto acid, where the carbon skeleton can then be further broken down for energy, used to form fatty acids or glucose for energy storage, or can continue on to be synthesized into a nonessential amino acid (Diwan, 2008).
Transamination, the process of transferring an amino group to an alpha-keto acid from an amino acid, is essential for anabolic functions in humans, most importantly the synthesis of non-essential amino acids like aspartate and glutamate. There are 12 amino acids that are known as non-essential because they are synthesized in the body from other substances and don’t need to be supplied through the diet (“What is Transamination?”, 2015). The mechanism of this process begins when transaminase, the enzyme used to catalyze this reaction, binds the cofactor pyridoxal phosphate to a lysine residue of enzyme, forming an “aldimine”. Next, the amino group of a new substrate entering the active site displaces the amino group of lysine’s active site. A new bond is created with the alpha-amino group of the substrate, as the active site of lysine moves away. Rearrangement of electrons shifts the double bond to make a “ketamine”, then hydrolysis acts to release PMP, or pyridoxamine-5’-phosphate, as well as an alpha-keto acid. Finally, the PMP molecule combines with alpha-ketoglutarate in reverse of prior steps, and results in the transfer of an amino group to alpha-ketoglutarate, as well as glutamate release (Meister, 2006).
In looking closer at the interaction of amino acids, researchers have found that while most amino acids can undergo deamination, the process occurs primarily with glutamic acid due to the fact that this molecule serves as the end product of a plethora of transamination reactions (Ophardt, 2003). Commonly, the alpha-amino group of amino acids is transferred to alpha-ketoglutarate to make glutamate, which then undergoes oxidative deamination to yield the ammonium ion. Transaminases catalyze this process, and generally guide alpha-amino groups from many different types of amino acids to alpha-ketoglutarate for the creation of a glutamate (Berg, 2002). Through this combination of the deamination and transamination of glutamic acid, which serves in recycling glutamic acid, other amino acids can be deaminated (Ophardt, 2003).

## Works Cited

Berg JM, Tymoczko JL, Stryer L, W. H. Freeman and Company. (2002). “Chapter 23: Protein Turnover and Amino Acid Catabolism.” Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK21182/
Mary K Doherty; Phillip D Whitfield. (2011). “Proteomics Moves From Expression to Turnover.” Retrieved from http://www.medscape.com/viewarticle/745130_2
Geoffrey M Cooper. (2000). “Protein Degradation.” Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK9957/
Smith K, Rennie MJ. (1996). “The measurement of tissue protein turnover.” Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/9022947
Berg, J. (2002). The First Step in Amino Acid Degradation is the Removal of Nitrogen. Retrieved December 3, 2015, from http://www.ncbi.nlm.nih.gov/books/NBK22475/
Diwan, J. (Ed.). (2008). Amino Acid Catabolism - N. Retrieved December 3, 2015, from https://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/amino.htm#glutdeam
Oxidative Deamination. (2003). Retrieved December 3, 2015, from http://chemistry.elmhurst.edu/vchembook/632oxdeam.html
Transamination of Amino Acids. (2006). Retrieved December 3, 2015, from https://www.uic.edu/classes/phar/phar332/Clinical_Cases/aa metab cases/PKU Cases/transaminationofaminoacid.htm
What is Transamination? (2015). Retrieved December 3, 2015, from http://www.wisegeek.org/what-is-transamination.htm

## 5.3.2 Amino acid pool

Definition: The amino acid pool consists of all the amino acids available in the body for protein synthesis at a given time. All these amino acids come from all different sources, and they get mixed up to form a general amino acid pool (Amino acid Pool). Liver is the main organ acting during this process, in which its main function is to regulate blood levels amino acids based on tissue needs. It also plays a role in converting excess of amino acids into carbohydrates when the body is lacking energy to sustain its metabolism. An adult body contains about a hundred grams of free amino acids, in which constitute the amino acid pool (Chaudhary, 2014).
During the process of protein turnover, cells are breaking down proteins and releasing amino acids. These released amino acids, as well as those supplied from our diet, make up the amino acid pool in our blood. Of the 20 common amino acids, nine are essential: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine (Whitney & Rolfes, 2015). Essential amino acids must be consumed in the diet because the body lacks the ability to generate these amino acids (Escott-Stump, 2008). There is a continuous demand for amino acids in the body so that protein homeostasis can be maintained. The amino acid pool is highly regulated, and must be supplied by 3 ways: exogenous proteins from the diet, the breakdown of tissue protein during the process of protein turnover, and de novo synthesis (Schultz, 2011). It's very important to have a varied diet in order to get all of these essential amino acids. Some foods contain a large amount of the essential amino acids, and some contain virtually none. The Protein Digestibility-Corrected Amino Acid Score (PDCAS) reflects the composition of amino acids found in food and the digestibility of these amino acids (Schaafsma, 2000). This score is important because it takes into account not only the composition of amino acids, but also how much of those amino acids the body actually digests and absorbs. Some food sources provide more essential amino acids than others, and the best way to get all the amino acids needed is to consume them naturally form food. Protein powders and amino acid supplements are often unnecessary in today's modern society because most people obtain proper protein and amino acid intake from their diet (Whitney & Rolfes, 2015). Additionally, it is better for the body to breakdown these amino acids from food through the body's natural processes of protein metabolism. Excess amino acids in the body are converted to urea to be excreted.
Contribution of Amino acid Pool: These mixtures of amino acids that are available at one time to the cell contribute to the amino acid pool, and it is produced from our dietary intake, turnover of proteins, synthesis of nonessential amino acids, and breakdown of tissues themselves. Proteins and amino acids are not stored inside our bodies, and that is why there is always a constant turnover of proteins (Protein Metabolism). During the turnover, some proteins are being synthesized while others are being degraded. The cell reaches a state of equilibrium when it takes as much amino acids as it loses. If the cell amino acid loss is greater, the cell wastes. If the cell amino acids gain is greater, the cell grows. This is why a balance of excretion and intake is of crucial importance in our bodies. Negative balance will produce tissue and protein destruction, but a positive balance will promote tissue and protein formation (Chaudhary, 2014). Their presence and availability also varies in the blood for certain proteins, for instance, plasma and liver protein’s duration in the blood is about 180 days while hormones and enzymes contain a half-life from minutes to hours in the blood. Hormones and enzymes are constantly recycled depending of the body needs and metabolism (Protein Metabolism). Amino acids catabolism produces great amounts of energy and ammonia, in which the latter compound is a highly toxic product for the body. In order to maintain low levels of toxicity inside body, ammonia is converted into urea in which is excreted in the urine by the kidneys. Urea can be observed as a “drain” in the amino acid pool because it is the compound that takes the excess of nitrogen, which is found and needed in amino acids synthesis (Protein Metabolism).
Deficiency: It is difficult to understand the necessary amount of each amino acid in the amino acid pool because of the lack of valid indicators of adequacy (Institute of Medicine Committee on Military Nutrition Research, 1999). Deficiencies in certain amino acids or protein in general can cause diseases. To prevent disease it’s important to eat a well-balanced diet that supplies the essential amino acids and other sources of nitrogen to generate amino acids. When a person does not meet adequate protein and caloric intake, the body must degrade proteins to release amino acids to keep metabolic systems functioning properly (Cooper, 2000). It is extremely important to consume enough protein to generate all of the amino acids the body needs to function properly and maintain the balance of amino acids in the amino acid pool.

## References

Amino acid pool. (n.d.) Medical Dictionary. (2009). Retrieved December 3, 2015 from http://medical-dictionary.thefreedictionary.com/amino+acid+pool
Chaudhary, R. (2014, December 26). Amino acid pool. Retrieved December 3, 2015, from http://www.slideshare.net/RajeshChaudhary10/amino-acid-pool
Cooper, G. (2000). The Cell: A Molecular Approach. Sunderland, MA: Sinauer Associates. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK9957/ (Links to an external site.)
Escott-Stump, S. (2008). Nutrition and Diagnosis-Related Care. Philadelphia, PA: Lippincott Williams & Wilkins.
Institute of Medicine Committee on Military Nutrition Research. (1999). The Role of Protein and Amino Acids in Sustaining and Enhancing Performance. Washington, DC: National Academies Press (US) http://www.ncbi.nlm.nih.gov/books/NBK224623/ (Links to an external site.)
Noss Whitney, E. & Rady Rolfes, S. (2015). Understanding Nutrition. Belmont, CA: Wadsworth Publishing.
Protein Metabolism. (n.d.). Retrieved December 3, 2015, from http://chemistry.elmhurst.edu/vchembook/630proteinmet.html
Schaafsma, G. (2000). The protein digestibility-corrected amino acid score. The Journal of Nutrition, 130(7), 1865-1867. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/10867064 (Links to an external site.)
Schultz, Y. (2011). Protein Turnover, Ureagenesis and Gluconeogenesis. The International Journal for Vitamin and Nutrition Research, 81(23), 101-107. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/22139560 (Links to an external site.)

## 5.3.3 Nitrogen balance

Definition
Nitrogen balance is the relationship between the intake of nitrogen into the body (through protein rich foods) and the output of nitrogen excreted from the body (through urine and feces). The majority of the nitrogen in our bodies comes from protein. (Segen's Medical Dictionary, 2011).
Achieving nitrogen balance
In order to measure nitrogen balance and to determine nutritional competence, track the amount of protein that the body loses in the urine within twenty-four hours. To calculate this protein lost, measure the nitrogen products which are excreted through urine. On average, 0.5g/kg of protein from the diet is enough to ensure a zero nitrogen balance (Segen's Medical Dictionary, 2011). Our bodies require nitrogen in order to complete tissue protein synthesis and to produce nitrogen-containing compounds which are key in several vital functions; some of these important functions include hormones, immune competence, peroxidative defenses, and neurotransmitters (Tomé & Bos, 2000). Our bodies lose nitrogen in several ways, also. Mainly, nitrogen is lost by means of urea, creatinine, and ammonia in the urine; in addition, nitrogen is lost in fecal matter and other miscellaneous losses (Tomé & Bos, 2000).
Nitrogen balance
When the intake of nitrogen through the diet is the same as the output of nitrogen through urine and feces, total body protein does not change; the body is at nitrogen equilibrium/balance which is the normal state in a healthy adult. When intake in nitrogen is greater than the output of nitrogen, total body protein increases; people who experience a positive nitrogen balance are those who are pregnant, growing, or recovering from the body’s protein loss from undernutrition or trauma. When intake of nitrogen is less than the output of nitrogen, total body protein endures a net loss; the body is at a negative nitrogen balance which is abnormal and unhealthy. A negative nitrogen balance is the body’s response to infection, trauma, or the inadequate intake of nutrients to aid in replacing tissue proteins which are turning over (Bender, 2006).
On average, healthy adults consume 80 grams of protein in one day, and the body intakes 70 more grams of protein through digestive enzymes in the gut, intestinal enzymes, and shed intestinal cells. Our bodies hydrolyze the majority of this protein to dipeptides and amino acids, and the dipeptides are then hydrolyzed. The body loses on average ten grams of protein each day through fecal matter; protein that is lost through feces is often indigestible protein from the diet, bacterial protein, or mucin (mucus’s main protein which resists hydrolysis from enzymes). Proteins that are absorbed are utilized for protein synthesis which occurs in recovering adults and growing children. Their bodies must synthesize proteins in order to replace the proteins that are turning over. From the amino acid pool, some of the amino acids are reused, but most are deaminated; amino acids that are newly absorbed in excess for protein synthesis use are also deaminated. The carbon skeletons that remain are utilized for gluconeogenesis, metabolic fuels, or fatty acid synthesis. The amino groups from the amino acids form urea which is the primary nitrogen-containing compound which we excrete through urine (Bender, 2006).

## References

Bender, D. (2006). Nitrogen balance and protein requirements. Retrieved from http://www.ucl.ac.uk/~ucbcdab/simulations.htm
Nitrogen balance. (n.d.). Segen's Medical Dictionary. (2011). Retrieved from http://medical-dictionary.thefreedictionary.com/nitrogen+balance
Tomé, D., & Bos, C. (2000). Dietary Protein and Nitrogen Utilization. Journal of Nutrition, 130, 1868S-73S. Retrieved from http://jn.nutrition.org/content/130/7/1868S.long