# 5.4 Functions: Proteins

Protein is an important aspect of both the function and maintenance of the human body. Without protein, the muscles, bones and even skin would not be able to function correctly. One unique aspect of protein is that the body has no way to store it for future use, as it can store carbohydrates and fats. Many people use this as an excuse to overconsume protein through everything from protein shakes to specialized protein bars. Unfortunately, too much protein can actually do more harm to the body than good. This excess protein can be converted to fat and then stored in the body. Just like any other macronutrient, protein in excess is not good. http://www.livestrong.com/article/32424-excess-protein-diet/.

## 5.4.1 Cell and tissue synthesis

It is understood that proteins are very versatile. They have the ability to grow, repair, and replace tissue.
Proteins are known as the building blocks of the body, and are the main structural component of all the body's cells. For example, in the process of building bone, the protein generates a matrix in collagen.
* Matrix: the basic substance that gives for to a developing structure.
* Collagen: the structural protein that form the foundations of bone and teeth.
Then, the proteins add minerals, such as calcium, phosphorus, magnesium, and fluoride, that give the bone it's strength.
The protein collagen plays a very important role superficially and deep to the skin. When you get a scar after a cut or scratch, that is the college fibers that knit the separate parts of torn tissue together. Also, collagen is vital to the circulatory system. It provides the materials of ligaments and tendons and the strength between artery walls that allows them to be flexible enough while blood pumps through them; this is because of collagen's elasticity.
There is another fibrous protein, called keratin, that is found all throughout the body, but mostly in the epidermis. A specific type of keratin filament is abundant in the skin, in epithelial tissue, which makes the skin tough and creates a natural water barrier. As the epithelial cells in the epidermis die, cells from the next layer (there are 5 layers within the epidermis) take their place. The protein that make up the keratinocytes help replace damaged or dead cells that are found in the skin.
Rolfes, S., & Whitney, E. (2013). Understanding Nutrition (pp. 179). Stamford, CT: Cengage Learning.
Alberts B, Johnson A, Lewis J, et al. (2002). Epidermis and Its Renewal by Stem Cells. Molecular Biology of the Cell. 4th edition. New York: Garland Science. Available from: http://www.ncbi.nlm.nih.gov/books/NBK26865/

## 5.4.2 Enzymes

Enzym [greek: enzym; en = in; zume = sourdough, yeast; enzym = in sourdough). The old name for enzyme is 'ferment'.
Except for a small group of RNA molecules, enzymes are proteins that operate as a biological catalyst, i.e. an accelerator of (bio)chemical processes that occur in living organisms. ( RNA: ribonucleic acid ) History
About 10000 BC: Fermentation; the proces that resulted in the discovery of enzymes.
2000 BC: Egyptians and Sumarians developed fermentation for the use in brewing, bread baking and the manufacturing of cheese.
800 BC: the stomachs of kalves and the enzyme chymosine were used for the manufacturing of cheese.
Middle ages: alchemists identify alcohol as a product of fermentation.
Alcoholic fermentation is undeniably the oldest known enzyme reaction. These and other phenomena where until 1857 thought to be spontaneous reactions. In 1857 concluded the French chemist Louis Pasteur that alcoholice fermentation is catalysed by 'ferments' and will only take place in the presence of living cells. Subsequently discovered the German chemist Eduard Buchner in 1897 that a cellfree extract of yeast can cause alcoholic fermentation. The old puzzle was solved; the yeast cells produce the enzym that controls the fermentation.
In 1877, German physiologist Wilhelm Kühne (1837–1900) first used the term enzyme.
Enzymes are biological catalysts that speed up chemical reactions and allow them to occur more efficiently than if the reactants, also called substrates, had come together by chance. Though the enzyme participates in the chemical reaction, it always comes away unchanged and does not affect the chemical equilibrium. Most enzymes in biological systems are proteins, though some RNA molecules do also participate in catalysis.
The amino acid side chains are what give each protein enzyme its specific catalytic properties. The different types of amino acid side chains are as follows:
* Hydrophobic amino acids include: Gly, Ala, Val, Met, Leu, Pro, Ile, Phe, Tyr, and Trp.
* Polar, uncharged amino acids include: Ser, Thr, Cys, Asn, and Gln.
* Positively-charged, polar amino acids include: Lys, Arg, and His.
* Negatively-charged, polar amino acids include: Asp and Glu.
The properties of these groups can speed up reactions by positioning the substrate in the optimal conformation for a reaction to occur, such as when a hydrophobic substrate situates itself into a hydrophobic “pocket” of amino acids in the enzyme active site. Some of the side chains of the polar amino acids can also participate in nucleophilic reactions and form hydrogen bonds with the substrates, which aids in catalysis. In addition to the side chains, the amino (NH2) and carboxyl (COOH) termini of the proteins can assist in these reactions. Only globular proteins, which are soluble in water, can act as enzymes in biological systems. In these proteins, the hydrophobic amino acids are clustered on the inside of the folded protein, while the hydrophilic, polar amino acids are on the outside. This property gives them their solubility.
There are six main classes of enzymes. These classes are based on how the enzyme functions in catalysis. The first class, oxidoreductases, catalyzes the movement of hydrogen atoms, oxygen atoms, and electrons between substrates. The second class, transferases, transfers chemical groups, such as a methyl group, between substrates. The third group, hydrolases, catalyzes the splitting of a substrate using water. The fourth type, lyases, catalyzes the removal of groups from substrates without using water. These enzymes often leave behind double bonds. The fifth class, isomerases, catalyzes the rearrangement of atoms within the substrate. For example, a major enzyme in the glycolytic pathway, triose phosphate isomerase, catalyzes the conversion of the intermediate dihydroxyacetone phosphate to glyceraldehyde 3-phosphate. The last class of enzymes, ligases, catalyzes the synthesis of new chemical bonds. These enzymes use the energy of nucleotide triphosphates, such as ATP, to drive the reaction forward.
Enzymes of all types are involved in the metabolism of the major macromolecules during and after digestion. Protein enzymes are involved in the regulation of the major metabolic pathways, as well. These enzymes often act through phosphorylation by protein kinases and dephosphorylation by protein phosphatases. The whole system of activation or deactivation is called an enzyme cascade. An example of an enzyme cascade is the system that activates and deactivates the breakdown of carbohydrates. These cascades are started when a hormonal messenger, such as glucagon or insulin, bind to a receptor protein on the outside of the cell. In the case of glucagon, a chain of reactions is initiated that eventually end in the activation of protein kinase A. Protein kinase A phosphorylates the hydroxyl groups of amino acids in enzymes that will eventually lead to an increase in gluconeogenesis and glycogenolysis and decrease in glycogenesis and glycolysis. The binding of insulin has the opposite effect. It stimulates the autophosphorylation of tyrosine residues on its receptor tyrosine kinase, which activates a protein phosphatase that will dephosphorylate other enzymes. The end result is an increase of glycolysis and glycogen breakdown and decrease in gluconeogenesis and glycogenolysis. The metabolism of other macromolecules is mediated in a similar way. In this way, enzymes are involved in nearly every step of metabolism. In this way, the unique properties of the amino acids in proteins affect how an enzyme functions in catalysis. Without enzymes, chemical reactions in biological systems would occur too slowly for life to exist. Therefore, enzymes have a very important role in life.
References Nelson, D. L., & Cox, M. M. (2013). Lehninger principles of biochemistry (6th ed.). New York, NY: W.H. Freeman and Company. Palmer, T., & Bonner, P. L. (2007). Enzymes: biochemistry, biotechnology, clinical chemistry (2nd ed.). Cambridge, UK: Woodhead Publishing Limited. Whitney, E., & Rolfes, S. R. (2013). Understanding nutrition (14th ed.). Stamford, CT: Cengage Learning.

## 5.4.3 Hormones

Hormone literally means to urge on. Hormones are your body's chemical messengers. They travel in your bloodstream to tissues or organs.
Only a small amount of hormone is required to alter cell metabolism. It is essentially a chemical messenger that transports a signal from one cell to another. The hormone binds to the receptor protein, resulting in the activation of a signal transduction mechanism that ultimately leads to cell type-specific responses.
Hormones can be divided up on the basis of their chemical structure into 5 groups:
* Those derived directly from the amino acid tyrosine, including: thyroxine, triiodothyronine,
adrenaline and noradrenaline
* Those made up of short chains of amino acids, including: adrenocorticotrophic hormone (ACTH), corticotrophin releasing hormone (CRH), thyrotrophin-releasing hormone (TRH), gonadotrophin-releasing hormone (GnRH), growth hormone releasing hormone (GHRH), vasopressin, oxytocin, somatostatin, gastrin, glucagon and calcitonin.
* Those made up of long chains of amino acids, including: insulin, growth hormone (GH), prolactin, parathyroid hormone (PTH), cholecystokinin (CCK)and secretin
* Those made up of proteins linked with glucose molecules forming glycoproteins, including: thyroid stimulating hormone (TSH), follicle stimulating hormone (FSH, luteinising hormone (LH)
* Those derived from cholesterol thus forming lipid soluble steroid hormones, including: oestrogens, progesterones, testosterone, androstenedione, aldosterone and cortisol.
So, the hormones have many function:
* Alter plasma membrane permeability by opening or closing gated ion channels
* Stimulate the synthesis of proteins, more specifically enzymes
* Activate or deactivate enzymes that are already made
* Induce secretory activity
* Stimulate cell division

## 5.4.4 Fluid balance

Fluid balance is maintaining the correct amount of fluid in the body. It is the continuance of the fluid input and output of the body. Fluid balance can alter with disease and illness.
Body fluids are regulated by fluid intake, hormonal controls, and fluid output.
5 KEY POINTS
* Fluid balance is the balance of the input and output of fluids in the body to allow metabolic processes to function
* To assess fluid balance, nurses need to know about fluid compartments in the body and how fluid moves between these compartments
* Dehydration is defined as a 1% or greater loss of body mass as a result of fluid loss. Symptoms include impaired cognitive function, headaches, fatigue and dry skin. Severe dehydration can lead to hypovolaemic shock, organ failure and death
* The three elements to assessing fluid balance and hydration status are: clinical assessment, body weight and urine output; review of fluid balance charts; and review of blood chemistry
* Fluid balance recording is often inadequate or inaccurate often because of staff shortages, lack of training or lack of time

## 5.4.5 Acid-base regulation

What's normal? Proteins also act as acid-base regulators. Since proteins have negative charges on their surface they attract the positive charge of hydrogen ions. By accepting and releasing hydrogen ions, proteins act as buffers, maintaining the acid-base balance of the blood and body fluids (A.C.).A normal range for arterial pH is 7.35 to 7.45. Acidosis is a pH less than 7.35; alkalosis is a pH greater than 7.45. Because pH is measured in terms of hydrogen (H+) ion concentration, an increase in H+ ion concentration decreases pH and vice versa.
Changes in H+ ion concentration can be stabilized through several buffering systems: bicarbonate-carbonic acid, proteins, hemoglobin, and phosphates.
Acidosis, therefore, can be described as a physiologic condition caused by the body's inability to buffer excess H+ ions. Acid-base equilibrium is closely tied to fluid and electrolyte balance, and disturbances in one of these systems often affect another. Fluid metabolism is discussed in Fluid Metabolism, and electrolytes are discussed in Electrolyte Disorders.
Thus, the body has three compensatory mechanisms to handle changes in serum pH:
Physiologic buffers, consisting of a weak acid (which can easily be broken down) and its base salt or of a weak base and its acid salt.
Pulmonary compensation, in which changes in ventilation work to change the partial pressure of arterial carbon dioxide (PaCO2) and drive the pH toward the normal range.
Renal compensation, which kicks in when the other mechanisms have been ineffective, generally after about 6 hours of sustained acidosis or alkalosis. Alkalosis results from a deficiency in H+ ion concentration. Acidemia and alkalemia refer to the process of acidosis or alkalosis, respectively, occurring in arterial blood.

## 5.4.6 Transporters

Transport proteins arehttp://www.minahealth.com/what_are_transport_proteins.htm:
* proteins within the membranes of cells that transport substances such as molecules and ions across the membrane or within the cell, or can be involved in vesicular transpor
* in blood plasma bind and carry specific molecules or ions from one organ to another.
* Hemoglobin of erythrocytes binds oxygen as the blood passes through the lungs.
* Other kinds of transport proteins are present in the plasma membranes and intracellular membranes of all organisms; these are adapted to bind glucose, amino acids, or other substances and transport them across the membrane.
Here are some functions of transporters: - hemoglobin: carries oxygen from the lungs to the cells - Lipoproteins: transport lipids around the body.
In living beings transport phenomena are essential, either to carry a hydrophobic molecule through an aqueous medium (transport of oxygen or lipid through the blood) or to transport molecules across barriers polar hydrophobic (transport across plasma membrane). Carriers and channels are always biological proteins.
Membrane proteins, such as channels and pumps, are important for the transport of some compounds across the cell membrane. Adsorbed nutrients must cross four barriers to reach the bloodstream:
* The mucus layer, a diffusion barrier which is rather thin in the small intestine.
* The enterocyte apical membrane- a lipid bilayer, which requires transport proteins for water- soluble molecules
* The enterocyte- a metabolic barrier which may metabolise the nutrient.
* The basolateral membrane- a lipid bilayer which again requires transport proteins for water- soluble molecules.
In addition to transport proteins, absorption is enhanced by metabolic compartmentation or zonation within the enterocyte, which prevents excessive metabolism (e.g. only 10% of absorbed glucose).
The classification of transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the Union of Biochemistry and Molecular Biology. This system is hared on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily and (iii) substrate specificity. Almost all of the more than, 250 identified families of transporters include members that function exclusively in transport. Channels (115 families), secondary active transporters (uniporters, symporters and antiporters) (78 families), primary active transporters (23 families), group translocators (6 families), and transport proteins of ill-defined function or of unknown mechanism (51 families) constitute distinct categories. Although different transporters carry very different substrates, they share many common structural features. They have regions of hydrophobic amino acids that can fold into helices which, when grouped together like the staves of a barrel, span the membrane and form a ‘pore’ through which substrates can be transported. Parts of the protein (bearing a sugar polymer) are outside the membrane and can act as a signaling receptor to allow other compounds to control the rate of transport of the main substrate. Transport may be either passive, allowing ten transported nutrient to come to equilibrium across the membrane, or active, permitting a higher concentration to be achieved on one side of the membrane than the other.

##### Osmosis

Proteins are not involved. Osmosis is the diffusion of water across a semi-permeable (or differentially permeable or selectively permeable) membrane. The presence of a solute decreases the water potential of a substance. Thus there is more water per unit of volume in a glass of fresh-water than there is in an equivalent volume of sea-water. In a cell, which has so many organelles and other large molecules, the water flow is generally into the cell. Water, carbon dioxide, and oxygen are among the few simple molecules that can cross the cell membrane by diffusion (or a type of diffusion known as osmosis. The effect of this water movement is to dilute the area of higher concentration. Reverse osmosis is the passage of water from a more concentrated to a less concentrated solution through a semi-permeable membrane by the application of pressure. Hypertonic solutions are those in which more solute (and hence lower water potential) is present. Hypotonic solutions are those with less solute (again read as higher water potential). Isotonic solutions have equal (iso-) concentrations of substances.
One of the major functions of blood in animals is the maintain an isotonic internal environment. This eliminates the problems associated with water loss or excess water gain in or out of cells. Again we return to homeostasis.

##### Passive diffusion

Diffusion is one principle method of movement of substances within cells, as well as the method for essential small molecules to cross the cell membrane. Passive diffusion or transport driven by a difference in concentration of the element between the two sides of the membrane and the mucosa. Passive transport does not require energy and moves with a concentration gradient. Transmembrane movement of ions occurs through pores or channels within the membrane and is an energy-independent process. Proteins are not involved in all types of passive transport of nutrients. A significant amount of passive transport across the intestinal mucosa may occur through a paracellular pathway, or the transport between cells aross intercellular right junctions.
Some examples of how is the movement of nutrients from an area of higher concentration (with the concentration gradient) to an area of lower concentration without the help of a protein (passive transport) are: ethanol absorbtion into the enterocyte; 75% of Vitamin B6 from foods; Thiamin uptake and absorption is believed to be an efficient process that is passive when thiamin intake is high and active when thiamin intakes are low.

##### Facilited diffusion

Facilitated diffusion is the transfer of an element across the membrane by carrier proteins embedded in the membrane. Facilitated transport resembles simple diffusion because it is not energy dependent and is driven by a difference in the ion concentration between two sides of a membrane. Facilitated transport occurs much more rapidly than simple diffusion and is saturable because of a finite number of carrier proteins.
These comprise facilitated transporters and ion channels, which permit the transfers of a solute across the membrane in either direction. Transport therefore takes place down a concentration gradient (so-called ‘downhill transport’). Net accumulation of the transported material in the cell can occur as a result of either onward metabolism to a compound that does not cross the membrane (e.g. vitamin B6 is accumulated intracellulary by phosphorylation to pyridoxal phosphate) or by binding to cytosolic proteins (e.g. ferritin, which binds iron).
The definition of a ’’’channel’’’ (or a pore) is that of a protein structure that facilitates the translocation of molecules or ions across the membrane through the creation of a central aqueous channel in the protein. This central channel facilitates diffusion in both directions dependent upon the direction of the concentration gradient. Channel proteins do not bind or sequester the molecule or ion that is moving through the channel. Specificity of channels for ions or molecules is a function of the size and charge of the substance. The flow of molecules through a channel can be regulated by various mechanisms that result in opening or closing of the passageway. So, a transport protein may be linked to another regulatory protein that can chaperone the transporter into the membrane and thus modulate transport capacity.
Membrane channels are of three distinct types'. The α-type channels are homo- or hetero-oligomeric structures that in the latter case consist of several dissimilar proteins. This class of channel protein has between 2 and 22 transmembrane α-helical domains which explain the derivation of their class. Molecules move through α-type channels down their concentration gradients and thus require no input of metabolic energy. Some channels of this class are highly specific with respect to the molecule translocated across the membrane while others are not. In addition, there may be differences from tissue to tissue in the channel used to transport the same molecule. As an example, there are over 15 different K+-specific voltage-regulated channels in humans.
The transport of molecules through α-type channels occurs by several different mechanisms. These mechanisms include changes in membrane potential (termed voltage-regulated or voltage-gated), phosphorylation of the channel protein, intracellular Ca2+, G-proteins, and organic modulators.
* Aquaporins
Aquaporins(AQP) are a family of α-type channels responsible for the transport of water across membranes. At least 11 aquaporin proteins have been identified in mammals with 10 known in humans (termed AQP0 through AQP9). A related family of proteins is called the aquaglyceroporins which are involved in water transport as well as the transport of other small molecules. AQP9 is the human aquaglyceroporin. The aquaporins assemble in the membrane as homotetramers with each monomer consisting of six transmembrane α-helical domains forming the distinct water pore. Probably the most significant location of aquaporin expression is in the kidney. The proximal tubule expresses AQP1, AQP7, and AQP8, while the collecting ducts express AQP2, AQP3, AQP4, AQP6, and AQP8. Loss of function of the renal aquaporins is associated with several disease states. Reduced expression of AQP2 is associated with nephrogenic diabetes insipidus (NDI), acquired hypokalemia, and hypercalcemia.
The β-barrel channels (also called porins) are so named because they have a transmembrane domain that consists of β-strands forming a β-barrel structure. Porins are found in the outer membranes of mitochondria. The mitochondrial porins are voltage-gated anion channels that are involved in mitochondrial homeostasis and apoptosis. The pore-forming toxins represent the third class of membrane channels. Although this is a large class of proteins first identified in bacteria, there are a few proteins of this class expressed in mammalian cells. The defensins are a family of small cysteine-rich antibiotic proteins that are pore-forming channels found in epithelial and hematopoietic cells. The defensins are involved in host defense against microbes (hence the derivation of their name) and may be involved in endocrine regulation during infection.

##### Examples of Passive Transport in Human Nutrition

* Carbohydrates
Fructose and sugar alcohols are carried by passive transporters, while glucose and galactose are taken up by the same active (sodium-linked) transporter. This means that only a proportion of fructose and sugar alcohols can be absorbed, and after a large dose much may remain in the lumen, leading to osmotic diarrhea.
* Water and electrolytes
It is not known how water is transported, several hypotheses have been proposed. Water absorption is a passive process by which water passes across paracellular and transcellular pathways in response to osmotic gradients created by transcellular absorption of sodium and other solutes. Simple osmosis may account for some water uptake, but the osmolality difference is only 3-30 mosmol/kg, and this would mean that enterocytes replaced their entire fluid volume evety few seconds. While some water is co-transporter itself, enterocytes do not have enough transporters to account for all the water absorbed. Specific water transporters (aquaporins) occur in the cells of secretoty epithelia, and studies in gene knockout nice suggest they may be quantitatively the most important factor in water absorption. The colon acts as an organ of water and electrolyte salvage, but its capacity is limited. Rapid infusion of 500 ml or more of water into the colon will provoke diarrhea through reflex defecation and this is the basis of rectally administered enemas. Sugar alcohols, used as sweeteners, such as xylitol, lactitol and sorbitol, are poorly absorbed and will enter the colon with sufficient water to maintain luminal isotonicity before fermentation and the absorption of SCFAs (short-chain fatty acids), water and Na+. If the colonic fermentation capacity is exceeded then osmotic diarrhea ensues because the excess water cannot be absorbed. Most minerals are absorbed by carrier-mediated diffusion (not passive).
* Vitamins
The water-soluble vitamins are absorbed by specific transport proteins. An example of passive transport of water-soluble vitamins are the phosphorylated derivatives of vitamins B1,B2, and B6 are dephosphorylated in the intestinal lumen, which are absorbed by facilitated transporters, then trapped inside the cells by rephosphorylation. Vitamin B12 is absorbed bound to intrinsic factor, a glycoprotein that is secreted by the parietal cells of the gastric mucosa.

##### Active Transport

Active transport
* Synopsis:
The difference between passive and active transport whether energy is required and whether they move with or against a concentration gradient. Passive transport does not require energy and moves with a concentration gradient. Active transport requires energy to move against the concentration gradient. The energy for active uptake/transport is provided by adenosine triphosphate (ATP), which is the energy currency in the body. ATP stores energy in its high-energy phosphate bonds.
Active transport and the role of carrier proteins is a lot like an enzyme substrate reaction. Each type of carrier protein has at least one binding site for its specific substrate or solute. The carrier protein brings the solute across the lipid bilayer of a membrane expose the solute-binding site first on one side of the membrane and then on the other. Competitive inhibitors or non competitive inhibitors can both interrupt and block the binding of a solute, just like what happens with enzymes. Competitive inhibitors compete for the same binding site while noncompetitive inhibitors bind elsewhere indirectly alter the shape of the carrier protein, hindering its ability to have it's specific substrate bind to it. The process of active transport is done in three ways:
1. Coupled carriers couple the uphill transport of one solute across the membrane to the downhill transport of another. Energy is provided by ATP hydrolysis
2.ATP-driven pumps couple uphill transport to the hydrolysis of ATP. By a downhill flow of another solute (such as Na+ or H+) that has released energy
3. Light-driven pumps, which are found mainly in bacterial cells, couple uphill transport to an input of energy from light.
Alberts B, Johnson A, Lewis J, et al. (2002). Carrier Proteins and Active Membrane Transport. Molecular Biology of the Cell. 4th edition. New York: Garland Science. Available from: http://www.ncbi.nlm.nih.gov/books/NBK26896/
* REFERENCES
* ↑ Rolfes, S., & Whitney, E. (2013). Understanding Nutrition (pp. 179). Stamford, CT: Cengage Learning.
* ↑ http://www.ncbi.nlm.nih.gov/books/NBK26865/
* ↑ http://www.nlm.nih.gov/medlineplus/hormones.html
* ↑ http://www.news-medical.net/health/What-are-Hormones.aspx
* ↑ http://www.endocrinesurgeon.co.uk/index.php/what-types-of-hormones-are-there
* ↑ http://www.nursingtimes.net/nursing-practice/clinical-zones/nutrition/measuring-and-managing-fluid-balance/5032614.article
* 1 2 http://journals.lww.com/nursing/fulltext/2008/09002/understanding_acid_base_balance.3.aspx
* 1 2 Pacha 2000/[2]
* 1 2 3 4 5 6 7 8 9 Geissler and Powers 2005/[3]
* ↑ Saier, MH. 2000/ [4]
* ↑ Purves 1992/[5]
* 1 2 Lindsay and Prentice 2012/[6]
* ↑ Gropper et al., 2008/[7]
* 1 2 3 4 5 Michael, W King 2013/[1]
* ↑ http://www.ncbi.nlm.nih.gov/books/NBK26896/
* 'Full References:
[1] Pacha, J. 2000. Development of intestinal transport function in mammals. Physiological Review. 80(4) 1633-1677.
[2] Saier, MH. 2000. A functional-phylogenetic classification system for transmembrane solute transporters. Microbiology and Molecular Biology Reviews. 64(2):354-411. DOI:10.1128/MMBR.64.2.354-411.2000.
[3] Geissler, C. and Powers, H. 2005. Human Nutrition. 9th Ediotion, Elsevier Limited.
[4] Purves et al., 1992. Life: The Science of Biology, 4th Edition by Sinauer Associates and WH Freeman.
[5] Lindsay H. Allen and Andrew Prentice. 2012. Encyclopedia of Human Nutrition, 3th Edition.
[6] Gropper SS, Smith JL, Groff JL. (2008). Advanced nutrition and human metabolism. Belmont, CA: Wadsworth Publishing.
[7] Michael, W King. 2013. http://themedicalbiochemistrypage.org/membranes.php info@themedicalbiochemistrypage.org
[8] Alberts B, Johnson A, Lewis J, et al. (2002). Epidermis and Its Renewal by Stem Cells. Molecular Biology of the Cell. 4th edition. New York: Garland Science. Available from: http://www.ncbi.nlm.nih.gov/books/NBK26865/
[9] Rolfes, S., & Whitney, E. (2013). Understanding Nutrition (pp. 179). Stamford, CT: Cengage Learning.
[10] Alberts B, Johnson A, Lewis J, et al. (2002). Carrier Proteins and Active Membrane Transport. Molecular Biology of the Cell. 4th edition. New York: Garland Science. Available from: http://www.ncbi.nlm.nih.gov/books/NBK26896/
* Websites
- International Union of Biochemistry and Molecular Biology
- Michael W King, PhD© 1996–2013 [themedicalbiochemistrypage.org],info@themedicalbiochemistrypage.org - Sinauer Associates [www.sinauer.com]
- WH Freeman [www.whfreeman.com]

## 5.4.7 Antibodies

Proteins are involved in defense, specifically against foreign invaders. Antibodies are the specialized proteins that do this job, they defend the body against antigens and are used by the immune system to protect the body against bacteria, viruses, and other foreign substances (A.C.). Antibodies are large Y-shaped proteins. They are recruited by the immune system to identify and neutralize foreign objects like bacteria and viruses.
How do Antibodies Work? Antibodies circulate in the blood stream and can appear anywhere throughout the body. If circulating antibodies come in contact with the target or antigen they were generated to fight, then the antibodies bind to the target. Depending on the antigen, the binding may impede the biological process causing the disease or may recruit macrophages to destroy the foreign substance.
As functions:
Types of Antibody: Type: 1. IGG: two identical heavy chainsand two identical light chains arranged in a Y-shape typical of antibody monomers. (also called "gamma globulin") is the most abundant antibody in the human immune system. It is found in blood and tissue liquids. IgG is the only antibody capable of crossing the placenta to provide immune protection to a developing fetus. IgG antibodies appear about one month after an infection, so their presence indicates a mature antibody response to a foreign pathogen.
2. IGM: hich is found mainly in the blood and lymph fluid, is the first to be made by the body to fight a new infection.
3. IGA: Immunoglobulin A (IgA), as the major class of antibody present in the mucosal secretions of most mammals, represents a key first line of defence against invasion by inhaled and ingested pathogens at the vulnerable mucosal surfaces. Exist 2 specie IgA1 and IgA2:
* IgA1 is the predominant IgA subclass found in serum. Most lymphoid tissues have a predominance of IgA-producing cells.
* In IgA2, the heavy and light chains are not linked with disulfide, but with noncovalent bonds. In secretory lymphoid tissues (e.g., gut-associated lymphoid tissue, or GALT), the share of IgA2 production is larger than in the non-secretory lymphoid organs (e.g. spleen, peripheral lymph nodes).
4.IGE: IgE primes the IgE-mediated allergic response by binding to Fc receptors found on the surface of mast cells and basophils. Fc receptors are also found on eosinophils, monocytes, macrophages and platelets in humans.
5.IGD: one of the five classes of antibodies produced by the body. It is found in small amounts in serum tissue. Although its precise function is not known, IgD increases in quantity during allergic reactions to milk, insulin, penicillin, and various toxins. The normal concentration of IgD in serum is 0.5 to 3 mg/dL

## 5.4.8 Energy and Glucose

The energy in glucose is stored in the covalent bonds between the molecules, and most importantly, in the hydrogen electrons. The hydrogen electrons were boosted to a "higher energy level" in the process of photosynthesis (which is transfered by plants from sunlight) during the photosystem I in plants. These hydrogen electrons will than pass through the electron transport chain during aerobic cellular respiration, and the hydrogen ions become stable.]
1.8 5.4.8 Protein Function- Energy and Glucose
In the instance of severe carbohydrate insufficiency, protein can be diverted from its usual function to provide the brain and nervous system with energy in the form of glucose. (Berg, Tymoczko, & Stryer, 2002). However, protein yields significantly less energy than carbohydrates and lipids (4 kcal/gram to 9 kcal/gram), and using protein as fuel sacrifices its other unique functions. Restricting carbohydrates and therefore relying on protein as a primary energy source can be a risky dietary choice if not regulated by a physician. Proteins are incorporated into energy pathways as their building block molecules- amino acids. Prior to metabolism, the amino group (NH2) must be removed from the backbone carbon skeleton of the amino acid through a process called deamination. The nitrogen containing amino group is synthesized with carbon dioxide in the liver to form urea, which is sent to the kidneys before excretion through the liver (Schutz, 2011). The carbon skeleton is retained for entry into the energy pathways. Glucogenic amino acids are converted to pyruvate, which can either form Acetyl CoA and enter the TCA cycle, or form glucose. Ketogenic amino acids are converted directly to Acetyl CoA and therefore cannot form glucose. Both glucogenic and ketogenic amino acids can provide the body with energy or form body fat through the TCA cycle, but only glucogenic amino acids can provide the body with additional glucose.
Figure: Gluconeogenesis from a glucogenic amino acid
References Benson, D. (n.d.). Gluconeogenesis. Retrieved November 29, 2015, from UC Davis Chemistry: http://chemwiki.ucdavis.edu/Biological_Chemistry/Metabolism/Gluconeogenisis Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Section 16.3: Glucose can be Synthesized From Non Carbohydrate Precursors. In J. M. Berg, J. L. Tymoczko, & L. Stryer, Biochemistry (5 ed.). New York: W H Freeman. Retrieved November 28, 2015, from http://www.ncbi.nlm.nih.gov/books/NBK22591/ Schutz, Y. (2011, March). Protein turnover, unreagenesis, and gluconeogenesis. International Journal for Vitamin and Nutrition Research, 81(23), 101-107. doi:10.1024/0300-9831/a000064

## 5.4.9 Protein Regulation

Proteins are responsible for an astounding number of functions in the cell from DNA replication to helping produce proteins themselves. Without proteins, we would be unable to survive. With proteins being such an important aspect of our biology, nature is sure to have made several checks and balances so that they are able to function correctly and prevent them from damaging our cells. This section will provide a basic overview one of the protein regulation mechanisms; protein inhibition.
Many of the pharmaceutical medications that we use to treat various illnesses or symptoms involve using protein inhibition. Inhibition works to slow down, stop, or speed up the activity of a certain enzyme and thus the desired effect can be made. For example, Penicillin acts by inhibiting and blocking the enzyme some bacteria use to make their cell walls and without a cell wall the bacteria cannot survive (Berg et. al, 2002). There are a few different types of inhibition including competitive, noncompetitive/allosteric, and feedback inhibition.
Competitive Inhibition: Each enzyme has its own active site where it binds to a given reactant, or substrate. These substrates can vary from other proteins to water molecules and much more depending on what the enzyme’s specific role in the cell is. An active site will only bind substrates that perfectly fit into its shape. Competitive inhibition surrounds the binding of the active site of a given enzyme. A competitive inhibitor will compete with a given reactant for the chance to bind to an enzyme’s active site. Think of an enzyme with a circular shaped active site, which binds to its given circular shaped reactant normally in a given cell. If a competitive inhibitor is added to this cell that is also circular shaped, the reactant and the inhibitor will fight their spot in the enzyme’s active site and thus decrease the rate of the reaction of a given enzyme. How well a competitive inhibitor works is dependent on its binding affinity (Stretlow et. al, 2012), a concept that will not be explored in this section.
Several enzymes have an alternate site other than their active site, called an allosteric site. Some small molecules act as inhibitors by being able to bind to these allosteric sites which can therefore change the active site of the enzyme. Through this mechanism, allosteric inhibitors do not directly compete with the active site and can change the shape of active site, preventing the normal substrate from binding to the active side.
Feedback Inhibition: Feedback inhibition is a specific type of allosteric inhibition where the product of a series of enzymatic reactions allosterically inhibits the first enzyme in the series to effect the sequence of reactions. This type of inhibition can be divided into positive or negative feedback, where the reaction product will either increase or decrease the amount of product produced. An example of this is the feedback inhibition of Angiotensin on Renin (Antonipillai et. al, 1998) which is a topic we covered in class and involves positive feedback.
1. Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002. Section 8.5, Enzymes Can Be Inhibited by Specific Molecules. Available from: http://www.ncbi.nlm.nih.gov/books/NBK22530/
2. Strelow J, Dewe W, Iversen PW, et al. Mechanism of Action Assays for Enzymes. 2012 May 1 [Updated 2012 Oct 1]. In: Sittampalam GS, Coussens NP, Nelson H, et al., editors. Assay Guidance Manual [Internet]. Bethesda (MD): Eli Lilly & Company and the National Center for Advancing Translational Sciences; 2004-. Available from: http://www.ncbi.nlm.nih.gov/books/NBK92001/
3. Antonipillai, I., Nadler, J., & Horton, R. (n.d.). Angiotensin Feedback Inhibition on Renin Is Expressed Via the Lipoxygenase Pathway*. Endocrinology, 1277-1281.

## 5.4.10 Other Functions

Proteins also take part in some background roles like blood clotting and vision. When injured a sequence of events occurs that leads to the production of fibrin, a stringy, insoluble mass of protein fibers that forms a solid clot from liquid blood. After clotting occurs, protein collagen forms to create a scar that replaces the clot and heals the wound.
Source: Protein Function. (2015). Retrieved October 20, 2015, from http://biology.about.com/od/molecularbiology/a/aa101904a.htm Updated by A.C.
* ↑ http://www.news-medical.net/health/Antibody-What-is-an-Antibody.aspx
* ↑ http://pdl.com/technology-products/how-do-antibodies-work/
* ↑ http://dermatology.about.com/od/glossaryi/g/igg.htm
* ↑ http://kidshealth.org/parent/system/medical/test_immunoglobulins.html
* ↑ http://medical-dictionary.thefreedictionary.com/immunoglobulin+D