Ending enzymes with an INTRO.

Enzymes serve the purpose of being “biological catalysts” in that is “speeds” up the rate of chemical reactions. Enzymes are highly specific (absolute or relative) and selective, meaning that they catalyze only a certain type of substrate to form a product. Absolute specificity, meaning that the enzyme will catalyze one type of substrate alone. On the other hand, in relative specificity, the enzyme would catalyze another substrate type that has the same bond type and structure similar to the complimentary substrate for the particular enzyme.

Enzyme + Substrate                  Product

Figure1 below- the various types of enzymes and their definition

Nearly all enzymes are considered proteins. The design of a particular site on the enzyme, the active site, determines if which substrate would be complimentary. “Amino acid residues” are located on the “cleft” of the active site on the enzyme. Substituent groups are contained within these groups and this is where the catalysis of the substrate takes place. This is so because an enzyme-substrate complex is formed when hydrogen and ionic bonding occurs because of the binding of the active site and the substrate molecule. Enzymes show relative or absolute specificity. Relative, meaning it would bind to another type of substrate if the substrate resembles the complimentary one of the enzyme. However absolute specificity reveals that the enzyme would only bind to one particular type of substrate molecule and no others. Part of the experiment is to show how enzymes reaction rate is affected by substrate type. How specific enzymes are will be revealed by that method. During catalyzing reactions, enzymes may introduce some cofactors such as inorganic and organic molecules to assist. Nearly all living cells need enzymes to sustain life because they maintain the rates of reactions at an appropriate value. Enzymes work on the principle of lowering a reaction’s activation energy without being consumed by the reactions as well as they do not change the reactions’ equilibrium. Various molecules could afflict the activity of enzymes thus changing the speed of the process. If an enzyme is broken down into is subsequent amino acid then its ability to perform catalysis will be destroyed. Primary, secondary, tertiary and quaternary designs of an enzyme –protein are valid information for its catalysis purposes.

Figure 2 shows the designs of protein:Upon disruptions of the enzyme-protein’s active site, these various structures will cooperatively change (eg. Denaturation but does not affect the primary structure) affecting catalysis.

Molecules such as activators which increase activity and inhibitors which slow down the reaction rate attributes to catalytic activity of an enzyme. Temperature, chemical environment such as pH, concentration of substrate and pressure also tampers with the activity of enzymes. The experiment also deals with temperature on enzyme action as well. Boiling an enzyme far surpasses the optimum temperature and so leads to denaturation. Boiling the enzyme affects the, “ hydrogen bonds, Van der waals forces, hydrophobic interactions and electrostatic interactions,” which is responsible for keping thetertiary as well as quaternary design of enzymes. Boiling thus affects “spatial configuration” of revealed residues on the active site of the enzyme. The enzyme needs this in order to bind to the relevant substrate. . In enzyme kinetics, there are four types of  reversable inhibitors. These include competitive, non-competitive, uncompetitve and mixed inhibition.

Figure 3 above shows Lineweaver- Burk plots for the various types of inhibition.

Table 1 below shows the characteristics of the following inhibitors mentioned above.

Type of inhibitor	Does inhibitor resemble substrate	Inhibitor binds where	Effects on           V-max	Effect on Km
Competitive	Yes	Free enzyme alone	No change	Increase
Non-competitive	No	Free enzyme and Enzyme-substrate complex	Decreases	No change
Uncompetitive	No	Enzyme-substrate complex	Decrease	Decrease
Mixed	No	Allosteric site, free enzyme or Enzyme substrate complex	Decrease	Increases or decreases

Figure 4

Figure 4 above: The graph illustrates that when Vmax is reached, the point of saturation where all the active site of the enzyme have been binded to, increasing the concentration of the substrate would have no effect on the rate of the reaction hence the tapering of the curve at the saturation point.The rate will drastically increase as there are more substrates to collidewith the enzyme hence the steep increase of the graph which would remain so until the saturation point is reached.

Figure 5: Graph illustrating the effect of temperature on enzymatic activity. As the optimum temperature is decreased or increased, the slope of the graph is either negatively skewed or positively skewed. Low temperatures will inactivate the enzyme whilst high temperatures would denature it. The highest rate of reaction is where the optimum temperature is reached and where the enzyme could work efficiently.

references:

David Hames, Nigel Hooper. Instant Notes in Biochemistry. New York: Taylor and Francis

Group,2005.

David L. Nelson, Michael M. Cox. Lehninger Principles of Biochemistry. New York: W. H.

Freeman and Company, 2008.

“Specificity of Enzymes,” Worthington Biochemical Cooperation, accessed April 07, 2013,

http://www.worthington-biochem.com/introbiochem/specificity.html

“ Six Types of Enzyme Catalysts,” Cliff Notes, accessed April 02, 2013,

http://www.cliffsnotes.com/study_guide/Six-Types-of-Enzyme-Catalysts.topicArticleId-   

 24998,articleId-24970.html

T. W. Graham Solomons, Craig B. Fryhle. Organic Chemistry. New Jersey: John Wiley & Sons,

2006.

“ Types of Inhibition,” NIH Chemical Genomics Center, accessed April 03, 2013,

http://assay.nih.gov/assay/index.php/Types_of_Inhibition

Mayo Clinic Researchers Identify New Enzyme To Fight Alzheimer’s Disease

An enzyme that could represent a powerful new tool for combating Alzheimer’s disease has been discovered by researchers at Mayo Clinic in Florida. The enzyme — known as Beta-secretase 2( BACE2 )— destroys beta-amyloid, a toxic protein fragment that litters the brains of patients who have the disease.

Alzheimer’s disease is the most common memory disorder. It affects more that 5.5 million people in the United States. Despite the disorder’s enormous financial and personal toll, effective treatments have not yet been found.

The Mayo research team, led by Malcolm A. Leissring, Ph.D., aneuroscientist at Mayo Clinic in Florida, made the discovery by testing hundreds of enzymes for the ability to lower beta-amyloid levels. BACE2 was found to lower beta-amyloid more effectively than all other enzymes tested. The discovery is interesting because BACE2 is closely related to another enzyme, known as BACE1, involved in producing beta-amyloid.

“Despite their close similarity, the two enzymes have completely opposite effects on beta-amyloid — BACE1 giveth, while BACE2 taketh away,” Dr. Leissring says.

Beta-amyloid is a fragment of a larger protein, known as APP, and is produced by enzymes that cut APP at two places. BACE1 is the enzyme responsible for making the first cut that generates beta-amyloid. The research showed that BACE2 cuts beta-amyloid into smaller pieces, thereby destroying it, instead. Although other enzymes are known to break down beta-amyloid, BACE2 is particularly efficient at this function, the study found.

Previous work had shown that BACE2 can also lower beta-amyloid levels by a second mechanism: by cutting APP at a different spot from BACE1. BACE2 cuts in the middle of the beta-amyloid portion, which prevents beta-amyloid production.

“The fact that BACE2 can lower beta-amyloid by two distinct mechanisms makes this enzyme an especially attractive candidate for gene therapy to treat Alzheimer’s disease,” says first author Samer Abdul-Hay, Ph.D., a neuroscientist at Mayo Clinic in Florida.

The discovery suggests that impairments in BACE2 might increase the risk of Alzheimer’s disease. This is important because certain drugs in clinical use — for example, antiviral drugs used to treat human immunodeficiency virus (HIV) — work by inhibiting enzymes similar to BACE2.

Although BACE2 can lower beta-amyloid by two distinct mechanisms, only the newly discovered mechanism — beta-amyloid destruction — is likely relevant to the disease, the researchers note. This is because the second mechanism, which involves BACE2 cutting APP, does not occur in the brain. The researchers have obtained a grant from the National Institutes of Health to study whether blocking beta-amyloid destruction by BACE2 can increase the risk for Alzheimer’s disease in a mouse model of the disease.

Reference: Mayo clinic.2012.Mayo Clinic Researchers Identify New Enzyme To Fight Alzheimer’s Disease.http://www.mayoclinic.org/news2012-jax/7087.html

Here’s your lucky day to find out how Jell-O is formed

What is Jell-O? How does it turn from a liquid to a solid when it cools?

 

David J. McClements, an assistant professor in the Biopolymers and Colloids Research Laboratory at the University of Massachusetts at Amherst, provides this more extensive overview of dessert science:

“The principal component responsible for the transition from a liquid to a semisolid gel on cooling is gelatin. Gelatin is a protein derived from collagen, the major component of the connective tissue of animals. Jell-O and other, similar products consist of powdered gelatin mixed with sweeteners, flavorings and coloring agents.

“In its natural state, collagen exists as fibers that contain three polypeptide chains entwined into a helical structure. Collagen is converted to gelatin by heating it in the presence of water. This procedure breaks down the relatively weak (noncovalent) bonds holding the three polypeptides together, as well as some of the stronger, covalent bonds, and produces a solution in which the polypeptides are arranged into a predominantly amorphous structure.

“When the solution of gelatin cools below a certain temperature, the molecules tend to associate with one another in order to regain some of their original helical structure. In this way, junction zones are formed. The junction zones mark a local return of the original form: three polypeptide chains in a helical formation. If there is enough gelatin present, a gel will form. The gel consists of a three-dimensional network of gelatin molecules linked by these junction zones, which is capable of en-training large amounts of water through capillary forces. This gel has solid-like characteristics, although it is really a viscoelastic material.

“Gelatin is a thermoreversible, cold-setting polymer: if the gel is reheated, it will convert back to a liquid because the forces favoring the amorphous state (mainly configurational entropy) outweigh those favoring the aggregated state (mainly hydrogen bonds). For this reason, gelatin cannot be used in ‘cook and serve’ products such as puddings that are supposed to form gels when heated. These products must incorporate a heat-setting polymer, such as starch.”

Reference: Scientific American.2000.What is Jell-O?How does it turn from a liqiud to a solid  when it cools?http://www.scientificamerican.com/article.cfm?id=what-is-jell-o-how-does-i

 

Image kidnapped from; http://1.bp.blogspot.com/-_5polj3VbC4/TXVnnNwdNfI/AAAAAAAACfE/yxGbOzjoRE0/s1600/mallow-jello.jpg

Die protein…….Die…….

So i have been learning about protein and amino acids and i came across this interesting topic:

Cooked Protein Vs. Raw Protein

Do you think that cooking food has any effect on its protein content in terms of its quality and availability to the cells of our body? For some, this question may have never crossed your mind, especially if you’re new to the idea of a raw foods diet.

How Does Heat Effect Protein?

Most people are unaware that cooking food drastically changes the chemical composition of those foods, including the extreme molecular change to protein. The fact that cooking food destroys protein is not news.“Essentials to Human Anatomy & Physiology”, Elaine N. Marieb writes:

“The fibrous structural proteins are exceptionally stable; the globular functional proteins are quite the opposite. Hydrogen bonds are critically important in maintaining their structure, but hydrogen bonds are fragile and are easily broken by heat and excesses of pH. When their three-dimensional structure are destroyed, the proteins are said to be denatured and can no longer perform their physiological roles.”

Cooked Proteins Become Substantially Useless to Our Bodies

When we apply high heat to food, over 115 degrees Fahrenheit,the hydrogen bonds are destroyed and the amino acids fuse together with enzyme-resistant bonds that preclude them from being fully broken down by the body, creating coagulated proteins. This changes the particular structure of proteins, which are three-dimensional. Their particular functions depend on their specific structure, rendering them unable to ‘fit’ and interact with other molecules of complementary shape, ultimately becoming useless to the body. For example, the protein molecule hemoglobin can then no longer fit with and transport oxygen and is useless to perform its specific function.According to the Max Planck Institute, cooking foods coagulates at least 50% of the protein, making them less bio-available to the body.

Cooked Proteins & Toxicity

Now we have these newly created molecules – from cooked proteins, which the body absolutely can’t recognize as ‘food’. Now these partially broken down proteins, called polypeptides, are targeted as ‘foreign invaders’ and it becomes a toxic substance that the body needs to work extremely hard to remove. This causes the immune system has to focus energy on protecting the body from something that was eaten, instead of focusing on other areas of the body that may need immune support, causing the entire system to work and perform extremely inefficiently. This is one of the reasons why there is such a dramatic increase in white blood cell count (the immune system’s army) after cooked food is eaten.

Proteins, in order to be usable by the body need to be broken down into amino acids. Digestive enzymes can’t easily break down these ‘fused’ together proteins into simple amino acids because they’ve coagulated, putting extra strain on the digestive system and the pancreas.

To top it all off, undigested proteins are one of the main culprits for allergies, arthritis, leaky gut and auto immune diseases. Eating proteins in their raw state does not have this same effect at all, and are actually more bio-available (usable) by our bodies.

It seems quite obvious, once explained, that the body would recognize these mutant protein molecules as ‘foreign’ and not as food as this is not what’s found in nature – one of the most intuitive explanations supporting the consumption of a primarily raw foods diet.

This information was obtained from:

Sacred Source Nutrition.2013. Cooked Protein vs Raw Protein.http://sacredsourcenutrition.com/cooked-protein-vs-raw-protein/

Image obtained from: https://spie.org/Images/Graphics/Newsroom/Imported-2012/004149/004149_10_fig1.jpg