PUBLISHED PAPER #2

PUBLISHED PAPER #2

 

Panfoli, Isabella,Daniela Calzia, Silvia Ravera, Alessandro Morelli.2010. “Inhibition of Hemorragic Snake Venom Components: Old and New Approaches”. Accessed April 12, 2013. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3153198/

 

 

Snake venoms are mixtures of biologically active proteins, metal ions, peptides and organic compounds. There are over 600 species of venomous snakes which can be classified into several groups. Most of the world’s envenomation’s are due to crotalidae and viperidae venoms. Venoms which affect the cardio-vascular system are classified hemotoxic whereas those that affect the nervous system are classified as neurotoxic.

Hemotoxic venoms contain various enzymes, isoenzymes and non-enzymatic proteins that either activate or inhibit factors that affect hemostasis. Many of the toxins in the venom affect platelet function by inhibiting or inducing platelet aggregation. Phospholipase A2 (Pla2) isoenzymes are responsible for inflammation and can be found in large numbers in both hemotoxic and neurotoxic venoms. Hemorrhages are caused by enzymes degrading proteins and components of the hemostatic system. This can be lethal as the hemostatic system is responsible for stopping bleeding and wound healing, which is the opposite of hemorrhage.

The extract of protein from horses and sheep are used as antivenins as they neutralize the toxins in humans. The administration of these toxins may be risky. Neutralization of toxins using inhibitors in plant extract may be used. Inhibitors of PLA2’s form soluble complexes with PLA2 enzymes, inhibiting their effects. Electric currents can also be used as a neutralizer at low voltages against metalloproteases and PLA2. There are many approaches to inhibit hemorrhagic venom which present advantages as well as disadvantages.

Most people, if not aware of how, know that some snakes possess poisonous venoms which can be lethal. It is known that poison affects the body in a negative way, but I have never known how or why. From this paper I have learnt that venoms are composed of proteins which are responsible for attacks on specific system which, if not treated, will bring down the body from within. I also learnt that inhibitors play a positive role in preventing these damaging proteins and so are the major components in antivenins. This paper may be difficult for someone without a biochemistry, biology or chemistry background to follow. It is also too wordy.

Essential and Non-Essential Amino Acids

Essential and Non-Essential Amino Acids

There are 20 amino acids required for adequate health. Some of these 20 amino acids are esseital amino acids as well a non-essential amino acids.

Essential Amino Acids – these are amino acids that cannot be synthesized by the body and have to be acquired through the diet.

Non- essential Amino Acids can be synthesized by the body.

Complete Protein

  • contain all 10 amino acids
  • proteins are derived from animal sources
  • Bears contain some complete proteins

Incomplete Protein

  • lack one or more of the essential amino acids 
  • most vegetable proteins are incomplete
  • Beans are an exception to this generalization

FACTORS AFFECTING ENZYME ACTIVITY

Factors affecting enzyme activity

  • Substrate concentration
  • Enzyme concentration
  • Temperature
  • pH

Velocity (V) – the number of substrate molecules converted to product per minute.

Initial Velocity (Vo) – rate of reaction measured as soon as the enzyme and substrate.

Max velocity is also known as Vmax

Km – reflects enzyme-substrate affinity. It is numerically equal to the substrate concentration at which the reaction velocity is equal to ½ Vmax.

  • Small Km , high enzyme-substrate affinity due to a low [S] being needed
  • High Km , low enzyme-substrate affinity due to a high [S] being needed

Substrate Concentration

As substrate concentration[S] increases, so does the rate of enzyme-catalysed reactions until it reaches Vmax. This can be seen by the steady increase of the curve. The plateauing off of the curve at Vmax reflects saturation(X). This is due to all the active sites on the enzyme molecule being occupied with substrate. At this point the reaction cannot occur any faster and does not have any effect on the rate of the reaction, therefore the curve plateaus.

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Enzymes Concentration

The substrate concentration, temperature, and pH are kept constant in order for the enzyme concentration to have full effect. As enzyme concentration increases, so does the rate of the enzyme-catalysed reactions. This is because more enzymes will be colliding with substrate molecules. However this would only be up to a certain concentration where the enzyme concentration would no longer be a limiting factor.

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Temperature

As temperature (heat energy) increases more moles of substrate will have enough activation energy, therefore the number of substrate moles that bind to the active site(s) to form product will increase substantially. This leads to a high rate of reaction as a result of high collision rate between substrate molecules and active sites due to a high kinetic energy. This is seen in the high increase of the curve. The curve then peaks towards optimal temperature(X) and then quickly decreases. At optimal temperature the bonds of the tertiary structured enzyme cannot take it anymore and become denatured. When denaturation occurs the hydrogen bonds, hydrophobic, electrostatic and van der waal interactions begin to break. This breaking is a co-operative process, therefore as one bond breaks, it makes it easier for the others to break. As a result of this the enzyme’s shape changes and can no longer bind to the substrate.

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pH

pH is the measure of hydrogen ions concentration in a solution. The higher the hydrogen ion concentration, the lower the pH, vice versa. Most enzymes function efficiently over a narrow pH range. A change in pH above or below this range reduces the rate of enzyme reaction considerably. Changes in pH lead to the breaking of the ionic bonds that hold the tertiary structure of the enzyme in place. The enzyme begins to lose its functional shape, particularly the shape of the active site, such that the substrate will no longer fit into it, the enzyme is said to be denatured. Also changes in pH affect the charges on the amino acids within the active site such that the enzyme will not be able to form an enzyme-substrate complex.

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Enzyme Specificity!!! Can you be a little more specific?!

Enzymes are specific!

  • Specificity of enzymes

Intermediate interaction between enzymes and its substrates occurs through molecular recognition based on complementary structure. This specific site on enzymes where the substrate and enzyme bond is a cleft called the active site . At this site the complementary substrate bonds using hydrophobic, electrostatic and van der waals interactions as well as hydrogen bonding.

Types of specificity

  • Relative specificity – enzymes to substrates that contain similar structures and the same type of bonds
  • Absolute specificity – enzymes only catalyse one reaction
  • Group specificity – enzymes only bind to n=molecules that have a specific functional group
  • Linkage specificity – enzymes only bind to a particular kind of chemical bond, regardless of structure of molecule
  • Stereochemical specificity – enzymes bind to certain steric or optical isomers

Hypotheses of Enzyme-Substrate Interactions

  • Fischer’s lock and key hypothesis (Emil Fischer 1894)

This theory states that the substrate (key) is perfectly complementary to the active site (lock). Only if the substrate fits perfectly would it be catalysed, showing that enzymes can only catalyse specific substrates.

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  • Kushland’s induced fit hypothesis

Although the both theories are recognized, the induced fit is the more accurate of the two.the induced fit hypotheses explains that the shape of the enzyme molecule changes to fit the shape of the substrate when they encounters , thereby enabling the substrate to bind more effectively.

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http://www.elmhurst.edu/~chm/vchembook/571lockkey.html

http://scienceaid.co.uk/biology/biochemistry/enzymes.html

Enzymes Video Review

Enzymes are biological catalysts that speed up chemical reactions without being changed in the end. This is achieved by the enzymes providing an alternative pathway with a lower activation energy. Activation energy is the minimum amount of energy needed for a reaction to occur. This can be seen using an energy profile diagram. Most enzymes are protein molecules although some are RNA molecules called ribozymes.

Enzymes are important as they allow metabolic reactions necessary for the sustenance life to occur in seconds. Without them, these reactions would occur to slow for life to be sustained. During these reactions the substrate’s bonds are broken to form the product. The highest energy arrangement of atoms that contains a structure intermediate between that of the reactants and products is referred to as the Transition State. The distinctive features of enzymes include their catalytic power, their regulation and their specificity. The number of molecules of substrate converted to product per enzyme molecule per second is called the turnover number or Kcat.

Enzymes are named based on their substrates, based on the action they perform and some just end in ‘ase’. Enzyme names usually end in ‘ase’, however there are a few exceptions. They are given numbers called enzyme commission numbers (EC), based on their class, subclass and sub-subclass. There are six classes of enzymes, oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases, each with categorizing functions. Enzymes need non-protein components to help them work called cofactors. This can be subdivided into inorganic cofactors and organic cofactors. Organic cofactors can be transiently associated in which case they are Cosubstrates or permanently associated in which case they will be Prosthetic groups.

Apoenzyme- inactive protein part

Cofactor- non-protein part

Haloenzyme- active enzyme

The apoenzyme with the cofactor gives the haloenzyme .

Inorganic catalyst can be compared to enzymes by looking at industrial processes such as the haber and contact process .These inorganic catalysts, unlike enzymes which work at normal body temperature, require very high temperatures and pressures in order to work. Enzymes are more efficient and due to their specificity and like inorganic catalysts, they do not have any side reactions occurring, thereby ensuring 100% product manufacture. Inorganic catalyst cannot be regulated are may be poisonous.

This video was very informative and well put together. I appreciated the use of colour to highlight important point and also as a separator, as a person who gets bored quickly it helps. there was one badly coloured part however, the equation with sucrose, where I found it difficult to follow, and had to really focus to read it. I’m not sure if this was the intention of the individual, but if so, mission accomplished. the beginning of the video was also a bit unclear as I could not clarify the names of the scientist being mentioned and therefore went on a google hunt with the bits of name that I could make out. I would have also preferred if the photo of the scientist was a little bigger, although I am aware that they are not apart of the major topic, but I would have still preferred to see their ingenious faces. Generally I enjoyed the video, despite these one or two issues, it did what it was intended to which makes it very successful in my eyes.

Enzyme Classes – Shhhhh!!! Class is in session. . .

Six major classes of enzymes

enzyme classes wordle

Oxidoreductases – catalyses oxidation- reduction reactions

Transferases – catalyses the transfer of C,Nor Pcontaining groups

Hydrolases – catalyses the cleavage of bonds by the addition of water

Lyases – catalyses the cleavage of certain C-C, C-S and certain C-N bonds

Isomerases – catalyses the racemization of optical and geometrical isomers

Ligases – catalyses the formation of bonds between carbon and O, S, N coupled to hydrolysis of high energy phosphate. 

ENZYME INHIBITORS

Enzyme inhibitors are molecules that bind to enzymes and decrease the velocity of enzyme-catalysed reaction. There are irreversible inhibitors that permanently bond to enzymes through covalent bonds, as well as    reversible inhibitors that temporarily bond through non-covalent bonds. Reversible inhibitors comprise of competitive, non-competitive, mixed and uncompetitive inhibitors.

Competitive Inhibitor

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FIGURE  1.

  • Similar shape to substrate
  • Binds to active site
  • Vmax (max velocity) remains the same
  • Km increases

Non-competitive Inhibitor

noncompetitive_inhibition1310425351769

FIGURE 2.

  • Does not resemble substrate
  • Binds either to free enzyme or enzyme substrate complex (ES)
  • Vmax decreases
  • Km remains the same

Mixed Inhibitor

  • Binds the same as a noncompetitive inhibitor, either to the free enzyme or ES cmplex, except the EIS cmplex has residual enzymatic activity.
  • Vmax decreases
  • Km  can either increase or decrease

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FIGURE 3.

Uncompetitive Inhibitor

  • Binds ONLY to the EIS complex
  • Both Vmax and Km are reduced by the same amount

 

 

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                                                                                                                                       FIGURE 4.

ENZYME CROSS WORD PUZZLE- LET’S GET CATALYSED!!!

ENZYMES CROSS WORD PUZZLE

Image

ACROSS

6 – type of enzyme with more than one active site

8 – inhibitor that produces residual enzyme activity

9 – inhibitor that binds to the ESI

11-non-protein components that help enzymes work

12-substances that diminishes velocity of an enzyme-catalysed rxn

13-catalyses chemical reactions

14-molecular recognition based on structural complementarity

DOWN

1 – enzymes are what type of biological molecule

2 – binds with active site to form product

3 – point at which all active sites are occupied with substrate

4 – inhibitors that bind permanently

5 – catalyses cleavage of bonds by addition of water

6 – location where substrate binds

7 – numerically equal to the [s] at which rxn velocity is equal to half vmax

10-number of moles of substrate converted to product per enzyme mol per second