last blog post

Hey Guys, so this is it the last and final biochem blog post. YAYYY!!!!

As happy as it sound I’m actually sad, I am really going to miss blogging. I never thought I was going to miss blogging since I didn’t really liked the idea of blogging at the beginning. 

WHAT CAN I SAY IT GROW ON ME. LOL

I must admit, blogging about biochem was quite helpful, it allowed me to retain so much more information faster than before because when blogging I use my our own words and involved in me doing additional reading and research whereas before we just learn off stuff.  Also blogging about topic thought in class allowed me to be up to date with what is being thought since we had to make regular blog post.

Blogging is a really good teaching technique.

I would like to thank my lecturer Jason Matthew for making biochem so much easier, interesting and also a challenge sometimes like in those tutorial session.

THANK YOU SIR !!!!!

FAREWELL GUYSSS TILL NEXT TIME 🙂

enzyme puzzle :)

 ENZYME PUZZLE- FEEL FREE TO TAKE A TRY

Y C K Y A L T E R N A T I V E O C X T H G W O Y T T C R C N R V J N B I Y E I X R F Q N Y I K A O M Y O Z B B R M A Q M E Q G O C R C I F E N C T O O P Q C T U N C O M P E T I T I V E H I E N M T P R E R R R Y C N V F S M P G R B B D I R E Z Z T I A M B T C I O U A O U I A V O W R B E R U W D G R R C T B B R X H E T O B B E M I X E D D A U E U U N D V N E L G T G S R V H Y R R T X P A K O Y R I E N Z Y M E S H O E L U I O S A I W H N I F T I Q R Q T V X N E X O R C N U J S G A S V N X F S M O T I F U N C W O N M S E Y E Y D S C I I D C Z H H E V Z A D U H L W V Q U T S O N O I T A L U G E R B X A P I I A C R N T L J B J E I X E E S R T Y D V T E E R F X F Q A R Z X X I T U A N I H D I A D U S Y X Q A N U S L R Q C T Z U U N T P K N W M T T R Z K C A G C R C N S N B E C V D Z P E W P V L T A J T G I U Y A C P Z O Z E S G N B H E G A Y T I C O L E V M P N W X C D Z S B S B I O L O G I C A L O F B W X E D D E B O E Y G B E D O W Y M C R F U P U O Y N X V Y T R Z J X K U G P N Z F N I V ACCELERATES ACTIVATION ACTIVE ALTERNATIVE BIOLOGICAL BOND CATALYST COMPETITIVE CONCENTRATION ENERGY ENZYMES HYDROGEN HYDROPHOBIC INDUCED INHIBITOR INTERACTION LOWER MIXED OXIDOREDUCTASE PROTEINS REGULATION SITE SPECIFICITY SUBSTRATE TEMPERATURE TRANSITION UNCOMPETITIVE VELOCITY

THE PUZZLE WAS MADE USING THE SITE
http://puzzlemaker.discoveryeducation.com/WordSearchWithMessageSetupForm.
asp.

PUBLISHED PAPER 2 – peroxidase

My second published paper review is based on the enzyme peroxidase.

Peroxidases are enzymes that belong to the class oxidoreductase, its EC number is 1.11.1.x. There are 15 different EC number for peroxidase which is grouped into different families and subfamilies.  Peroxidase activity is involved in physiological, biological and developmental processes base on the type of organism they are present in; plants or animal species. For example auxin metabolism, ligin, suberin formation and hormone regulation in plants and animals species respectively. The enzyme peroxidase is also involved in aiding the immune system of human in the defense against pathogenic diseases and other diseases.  Peroxidase is present in almost all living organism, they use hydrogen peroxide as electron acceptor in order to catalyze their oxidative reaction.

 Peroxidase can be haem or non haem proteins. Based on the peroxidase having haem or non haem proteins they are found in different families. Haem peroxide are found only in fungi, plants, bacteria and animals whereas non haem peroxidase is found in five (5) independent families;  thiol peroxidase, alkylhydroperoxidase, non-haem haloperoxidase, manganese catalase and NADH peroxidase

Mammals contains haem peroxidase which is involved in disease prevention and human pathologies, this occurs when the haem peroxidase uses hydrogen peroxide (H2O2) to develop more aggressive oxidants to fight off intruding bacteria.

PeroxiBase is an database system that stores data on peroxidase superfamilies which is used to follow the evolution of peroxidase in living organism. It is also involved in compiling information regarding the transcriptional regulation and function of peroxidase for medical uses and research.

The database currently has over 6000 peroxidase encoding sequences from 94 organisms. A new has been developed to classify new peroxidase number based on PROSITE profile methodology. The main purpose of this database is to make information with grading peroxidase readily easy to attain.

In our last biochemistry lab we dealt with different enzyme, one of which was peroxidase, hence the reason for selecting this paper to review. After reading this paper I have learned so much more about peroxidase whereas before I knew so little. I was so shock to see how peroxidase activity in our body is of major importance. For example, I did not know peroxidase enzyme in our body is involved in fighting diseases among their other functions. Another interesting fact I came across while reading is the amount of sub classes and sub- sub classes there are for peroxidase and each class plays an important functional role in living organism (plants or animals).

I must admit this article was really interesting as I learned so much interesting facts about peroxidase, mostly how they work to fight bacteria and diseases in human.

 

REFERENCE:

Koua Dominique, Lorenzo Cerutti, Laurent Falquet, Christian J. A. Sigrist, Grégory Theiler, Nicolas Hulo and Christophe Dunand.2008. “PeroxiBase: a database with new tools for peroxidase family classification.” Accessed April 3rd 2013. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686439/

 

Reflection***

Hey Guys,,,

Today was our last teaching day in class since we have reached the end of the syllabus.

YOU KNOW WHAT THAT MEANS TEACHING IS OVER!!!! yayyy

😦 NOOO dat means study time begins :/

In class today Sir thought us the last topic left in the syllabus- ATP. 

  ATP is often called a high-energy phosphate compound, and its phosphoanhydride bonds are referred to as high-energy bonds. ATP is an energy-rich molecule because of its triphosphate unit contains two phosphoanhydride bonds and when hydrolyzed releases large amount of free energy.(Berg, Tymoczko, and Stryer, 2002)

However in class today we learned that ATP has an high phosphoryl transfer potential.

Three factor responsible for the high phosphoryl transfer potential of ATP:

1. electrostatic replusion

2. resonance stabilization

3. stabilization due to hydration

After doing some reading I came across that not only ATP has an high phosphoryl transfer potential but also phosphoenolpyruvate (PEP) and 1,3-bisphosphoglycerate (1,3-BPG), in fact they have an higher phosphoryl transfer potential.

The term PEP and 1,3-BPG is not something new to me, I came across these terms when studying glycolysis.It actually makes sense these two molecules having high phosphoryl transfer potential since their role in glycolysis is to make ATP from ADP so the high phosphoryl transfer potential of these molecules are used to phosphorylate ADP to form ATP.

NOTE TO REMEMBER: ATP IS A NUCLEOTIDE SINCE IT COMPRISES OF A RIBOSE SUGER, A PHOSPHATE GROUP (triphosphate unit) AND A BASE (adenine).

Continue reading

FACTORS AFFECTING ENZYME ACTIVITY

Here is just a quick recap about factors affecting enzymes activity.

WHAT ARE FACTORS THAT AFFECT ENZYMES ACTIVITY?

– Substrate concentration

– pH

– Enzyme concentration

-Temperature

– Inhibitor

HOW DOES SUBSTRATE CONCENTRATION AFFECTS ENZYMES ACTIVITY?

As substrate concentration increases the rate at which enzyme substrate complex formed increases because there are more substrate available for free enzymes active site to bind with. Also with an increase in substrate concentration the greater the collision frequency of substrate to enzyme active site. However at Vmax all the enzyme active site is occupied by substrate therefore the rate of reaction is constant so increasing [S] doesn’t affect the rate of reaction. When observing the effects of substrate concentration on enzyme activity the following variables must be kept constant pH, temperature and enzyme concentration. The effect of substrate concentration can be illustrated by using either line weaver Burk plot (equation) or Michaelis–Menten graph (equation).

FIGURE 1: ILLUSTRATES THE EFFECT OF SUBSTRATE CONCENTRATION ON ENZYME ACTIVITY.

 

HOW DOES pH AFFECT ENZYME ACTIVITY?

When the pH is too acidic or too basic for an enzyme, its hydrogen bonds begin to break resulting in the enzyme active site losing its shape. Each enzyme operates within an pH range (optimal pH). For example: lipase in the stomach operates within the optimum pH 4-5.

FIGURE 2: ILLUSTRATES THE EFFECT OF pH ON ENZYME ACTIVITY.

HOW DOES TEMPERATURE AFFECT ENZYME ACTIVITY?

As temperature increase the rate of reaction increases however beyond the point of optimum temperature the rate of enzyme catalyzed reaction decreases because the hydrogen bond and the hydrophobic interaction in the enzyme structure is being broken. When this occur enzyme losses it shape and the substrate is unable to bind properly to the active site thus reducing enzyme activity. Furthermore, as temperature increases the amount of kinetic energy increases in the system thus increasing the rate of reaction since the collision frequency between the substrate and the enzyme active site increases. Also as temperature increases the substrate molecules gain more energy to overcome the activation barrier hence forming more ES complex which alternately increases rate of enzyme reaction.

FIGURE 2: ILLUSTRATES THE EFFECT OF TEMPERATURE ON ENZYME ACTIVITY.

HOW DOES INHIBITORS AFFECT ENZYME ACTIVITY?

There are irreversible inhibitors and reversible inhibitors which affect rate of enzyme reaction. Reversible inhibitors binds to the enzyme by non- covalent bond therefore dilution of the enzyme-inhibitor complex releases the inhibitor and the enzyme can carry on its activity. There are four types of reversible inhibitors are competitive, uncompetitive, mixed and non-competitive.

1. Competitive inhibitors compete with the substrate for the active site, therefore the shape of the inhibitor resemble the shape of the substrate. When the inhibitor binds to the active site it reduces the rate of enzyme reaction since the substrates unable to bind to the active site because the inhibitor is currently occupying the active site .  Competitive inhibitor increases Km therefore more substrate is needed to achieve ½ Vmax. Vmax however is unaffected by competitive inhibitor.

FIGURE 3: ILLUSTRATES THE EFFECT OF COMPETITIVE INHIBITOR ON Vmax AND Km IN LINEWEAVER- BURK PLOT.

2. Non-competitive inhibitor binds to free enzyme or ES complex; it doesn’t bind to the active site. Therefore the shape of the inhibitor is different from the substrate. This type of inhibitor reduces the ability of the enzyme to convert substrate into product. Vmax is reduced and Km remains the same since the substrate can still bind to the active site as well as before the inhibitor is present.

FIGURE 4: ILLUSTRATES THE EFFECT OF NON-COMPETITIVE INHIBITOR ON Vmax AND Km IN MICHAELLIS MENTEN CURVE AND LINEWEAVER- BURK PLOT RESPECTIVELY.

3. Uncompetitive inhibitor occurs when the inhibitor binds only to the ES complex. They do not bind to free enzymes. It reduces both Vmax and Km in the same amount. The slope of the graph will remain constant because both the Km and Vmax will be changing proportionally to each other and so the line will simply be observed to shift up and to the left.

FIGURE 5: ILLUSTRATES THE EFFECT OF UNCOMPETITIVE INHIBITOR ON Km AND Vmax IN A LINEWEAVER BURK PLOT.

4. Mixed inhibitor binds to free enzyme or enzyme substrate complex. They do not bind to the active site. When the inhibitor binds to the enzymes it changes the shape of the enzyme thereby reducing the affinity of the substrate to the enzyme active site. Vmax is always reduced whereas Km is either increase or decrease.

Mixed inhibitor may seem similar to non- competitive inhibitor however they are different. When non-competitive inhibitors binds to the enzymes it form the EIS complex that caused the product not to be formed whereas in mixed inhibitor when the inbitor bind to the enzyme forming the EIS complex some product are still formed although the inhibitor is present.

FIGURE 6: ILLUSTRATES THE EFFECT OF MIXED INHIBITOR ON Km AND Vmax USING A LINEWEAVER BURK PLOT.

REFERENCE:

Cox. M.M. and David L. Nelson 1984. Lehninger; Principles of Biochemistry. Fourth Edition.

Worthington Biochemical Corporation.2013. “Introduction to enzymes.” http://www.worthington-biochem.com/introBiochem/substrateConc.html

mymcat.com.2010. “Enzyme Inhibitor.” Accessed March 7th 2013. http://www.mymcat.com/wiki/Enzyme_Inhibition#Noncompetitive

Reflection- week 11 – INCOURSE EXAM

Hey Guys,

So, what you’ll think about that incourse exam??????????

GOOOOD!!!!! rite 🙂

I was so afraid to write the exam but it turned out pretty OK.The only question that I struggled with was the pka question but I have enough time to master that before finals.

Also another factor I have to work on is time management, unfortunately I didn’t complete my paper I was on my last question when the time was up :/

But hopefully before finals all those minor set back will be clarified.

I have Sir to thank for making biochem so much easier for us, all those tutorial session, weekly quiz in class, you tube lectures and blogging about the topic thought in class is finally paying off. While studying for the in course I realize studying for end of term wouldn’t be so hard and would not involve plenty charming because during the semester Sir had us busy, “on our toes” in other words.

The most shocking thing to know that those questions were actually past paper questions :O

I am feeling so confident for finals.

THANK YOU SIR!!!!

PUBLISHED PAPER 1 – Artificial enzymes

Enzyme are biological molecules responsible for the breakdown of substrate into smaller products so that they can we digested in cases of digestion of food or which can produce chemical products necessary for metabolite reaction. Enzymes are essentially important for sustaining life, so important that a lot of research and effort have been put into enzymes. Dr. Jeannette Bjerre while studying for her PhD in chemistry at University of Copenhagen illustrated how a chemzymes was capable of decomposing natural toxin waste.  Chemzymes are artificial enzymes which follows the targeting and efficiency of naturally occurring enzymes i.e they function similar to natural enzyme. Enzymes are present in our body which is responsible for breaking down food, toxin, waste etc. They are also present in our detergents we use every day.

One of the major differences between naturally occurring enzymes and ariticifcal enzymes are that natural enzyme are more complex whereas artificial enzymes are not. This difference however makes chemzymes tasks easier since with fewer parts, there is fewer risk of something going wrong when chemzymes changes structure.

A major factor which affects enzymes whether they occur naturally or are manmade is that change in their structure will affect their reactivity, meaning these enzymes are unable to function properly. Another factor known to affect enzymes are temperature, high temperature denatures the enzymes structure. However artificial enzymes are not affected by heat and solvents, this serves as a major advantages in that chemzymes can be produced using industrial chemical processes. Therefore, these enzymes are being produced readily and quickly under industrial conditions whereas natural enzymes would be more time consuming to produce.

After reading this article I knew this was the one I wanted to do a review on. In class we learn that enzymes are essential to sustain life on earth and they are present in all living organisms. These enzyme present in living organism were responsible for breaking down waste, organic substance, digested food etc to carryout metabolite reaction in the body.

Reading this article display an all new view of enzymes to me. Enzymes can also be used to get rid of natural toxin waste. This is so cool, if enzyme can decompose natural toxin waste, they can probably decompose toxic man made waste. I’m also doing a major in Environmental studies so this particular topic was really interesting and informative to me.

So think about it, if scientist developed enzymes to breakdown toxic waste, this will truly be an beneficial research in that it will aid in cleaning up the environment and reducing pollution thus reducing ozone layer depletion etc.

Who knows, probably scientist have already developed such enzymes or are currently doing so…. O.o

depositphotos_2847550-Toxic-waste

REFERENCE:

University of Copenhagen.2010. “Artificial Enzyme Removes Natural Poison.” ScienceDaily. Accessed March 16, 2013. http://www.sciencedaily.com/releases/2010/08/100826122624.htm

THE IMAGE USED ABOVE WAS TAKEN FROM THE SITE:

FATE OF PYRUVATE MADE FROM GLYCOLYSIS

Hiiii Guys,

Today I am just briefly going to discuss the fate of pyruvate.

SO, THE BIG QUESTION IS WHAT HAPPENS TO PYRUVATE AFTER IT IS MADE FROM GLYCOLYSIS.

Well, the fate of pyruvate depend on two factor whether oxygen is present or not.

In the presence of oxygen (aerobic condition) pyruvate is converted to acetyl-CoA by the enzyme pyruvate dehydrogenase which enters the TCA or Kerb cycle where large (most) of ATP molecules is generated.

Image

The diagram above illustrates the conversion of pyruvate to Acetyl CoA

In the absence of oxygen (anaerobic conditions) pyruvate undergoes fermentation either lactic acid fermentation or alcohol fermentation. In this fermentation reaction NO ATP molecules is generated, however reduced NAD+ is generated from fermentation. The NAD+ regenerated is used in the glycolysis process to make ATP. Therefore these cells only get energy (2 ATP) from glycolysis and not from the TCA cycle. Example of such cell are red blood cells.

LACTATE FERMENTATION: occurs in muscle, erythrocytes, and some other cells. The pyruvate made in red blood cells is converted to lactate by the enzyme lactate dehydrogenase. This mite be confusing since there are a lot of oxygen in red blood so why pyruvate isn’t converted to acetyl CoA and enter the TCA cycle. Pyruvate made from glycolysis does not enter the TCA cycle because the red blood cells do not have mitochondria which is the site for the TCA cycle (the TCA cycle occurs in the matrix of the mitochondria). Since NAD+ concentration is low the main purpose of fermentation in red blood cell is to regenerate NAD+ to enter the glycolysis pathway to yield ATP, since glycolysis the main manufacture of energy (ATP) for red blood cells.

Moreover lactate is made in muscles. This occurs when the muscles are under vigorous muscle contraction due to exercise activities, when this occurs lactic acid builds up in the muscles causing cramps and pain. This is one way the brain is telling the body to STOP!!! When oxygen become present in the muscle the pyruvate is convert to acetyl CoA which may enter the TCA cycle to generate ATP.

ETHANOL FERMENTATION: is a two step reaction which uses 2 enzymes; pyruvate decarboxylase and alcohol dehydrogenase. TPP is an co-factor for both of these enzymes.

REMINDER:  2 molecules of pyruvate made from one molecules of glucose therefore two molecules of NAD+ is regenerated.

NOTE: The net gain of ATP molecules made from one glucose molecule which enters the glycolysis pathway is two (2).

Image

The diagram above illustrates the fate of pyruvate in aerobic and anaerobic conditions.

Reference:

THE IMAGES USED ABOVE WAS TAKEN FROM THE SITES:

WEEK 9 reflection; GLYCOLYSIS

HEY GUYS,

This week in class we did the topic glycolysis.

WHAT IS THE FIRST THING THAT COMES TO MIND WHEN YOU HEAR THE WORD GLYCOLYSIS?

WELL YOU SHOULD BE THINKING ABOUT: The process which converts glucose molecules into pyruvate molecules.

REMINDER: Glycolysis takes place in the cytosol of the mitochondria and not in the cytoplasm

Glycolysis isn’t something new to me however some of the stuff thought in class regarding the topic glycolysis was a bit new. For example: There are 10 enzymes involved in the metabolic pathway of glycolysis. These ten (10) enzymes are responsible for converting one glucose molecule into 2 pyruvate molecule, also 4 ATP molecules and 2 NADH is generated in this process.

IMPORTANCE OF GLYCOLYSIS:

The main reason for glycolysis is to make pyruvate molecules which may enter the TCA cycle under aerobic conditions to yield ATP molecules. These ATP molecules are used as energy compound which supply cells with energy required for them to carry out their metabolite reaction. Therefore, glycolysis is an very important process without it cells wouldn’t get the energy it needs to carry out it reaction and hence will deteriorate or die causing the organism to become weak and sick. This may even results in death of the organism.

THE DIAGRAM BELOW SHOWS THE PROCESS OF GLYCOLYSIS AND THE 10 ENZYMES THAT ARE INVOLVED IN GLYCOLYSIS.

Image

DISEASE ASSOCIATED WITH GLYCOLYSIS IS: Pyruvate Kinase deficiency.

Pyruvate kinase deficiency is an genetic disease which is inherited from parent to offspring. Pyruvate kinase is the enzyme which is responsible for converting phosphoenolpyruvate into a pyruvate molecule. Deficiency in this enzyme will reduce the rate of the glycolysis process, therefore it would take longer to produce pyruvate, ATP and NADH molecules.

Furthermore, pyruvate kinase deficiency can cause hemolytic anemia which is a form of anemia, that is due to the abnormal break down of erythrocytes. Hemolytic anemia can be inherited or acquired. The average life span of red blood cells in our body is 120 days however in  hemolytic anemia conditions the body immune system destroys our red blood before its expect life span because the immune system does not recognize the red blood cells and consider them to be foreign substance hence they destroy them. Therefore our blood cells are breaken down early than normal, this results in our body not having sufficient amount of red blood cells to transport oxygen since the function of red blood cell is to transport oxygen to the body. Moreover, the cells in the body would become oxygen deprived. Some of the symptoms of hemolytic anemia are shortness of breath, headaches, fatigue, jaundices etc.

Moreover, some cells that lack mitochondria solely relies on glycolysis for energy(ATP)  because mitochondria is require for the TCA cycle to occur. Example of such cell is red blood cells. With deficiency in pyruvate kinase, red blood cell would not acquire sufficient energy since it would take long for pyruvate and ATP molecules to be produce, this therefore results in the membrane of red blood cells becoming weak since the sodium potassium pumps would not work efficiently because it is not acquiring the sufficient amount of ATP molecules.

REFERENCE:

THE IMAGE USED ABOVE WAS TAKEN FROM THE SITE:

PubMed Health. 2012. ‘Hemolytic anemia”. Accessed March 22,2013.http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001597/

COMING UP NEXT IS FATE OF PYRUVATE

SO STAY TUNE 🙂

LAST LAB yayyy!!!! :)

Image

Today was my last biochem lab, couldn’t be more happy. 🙂

However I must admit today lab was pretty OK! We tested factors that may affect enzymatic activity such as heat, concentration and inhibitors. From the lab experiment carried out it can be concluded that enzyme activity is affected by these factors. This conclusion was made by the relevant color change observed. In addition, test tubes that didn’t have enzymes showed no visible color change, therefore it can be concluded that in the absence of enzyme no reaction will occur.

Some of the color change observed were pretty cool, different ranges of colors were observed.

That was pretty much what the lab was based on.

Anyways, GOOD BYE LABS!!!!!!