TCA cycle

After glycolysis has occurred  once oxygen is available, Acetyl-CoA is produced and it enters the Krb’s or TCA cycle which takes place in the matrix of the mitochondria. TCA cycle is easily explained in the form of a diagram:

tca themedicalbiochemistrypage.org

 

The following videos are also very useful!

http://www.youtube.com/watch?v=9EFRHRXPDWo

http://www.youtube.com/watch?v=juM2ROSLWfw

http://www.youtube.com/watch?v=WXHpTHb1MQM

Kreb’s/ TCA Cycle Video Review

As i previously mentioned, I usually watch a few youtube channels when studying, as it often makes learning fun and easy. Another one of my favourite channels is ThinkWell, who also has a website with a lot of great information on biology and chemistry topics. I came across one of his videos on TCA and will now do a review on it:

http://www.youtube.com/watch?v=9EFRHRXPDWo

Summary of the video:

The video basically breaks down TCA step by step, showing and explaining the mechanisms of each reaction, and ending with the first reactant being the last product, hence emphasizing the cyclic part of the Kreb’s Cycle.

  • His animated voice as well as excessive hand gestures kept the video interesting as well as full attention throughout the entire video.
  • Every single reaction of TCA is explained individually and in depth with mentions including but not limited to: reactions, reactants,  chemical structure of products and reactants, enzymes and by-products.
  • Cutting of compounds showed the physical breaking and forming of bonds example S-CoA.
  • The type of each reaction occurring is mentioned which included but is not limited to: oxidation, NAD reduction, destabilisation, exothermic reactions and subtrate-level phosphorylation.
  • The way in which each reaction occurs and products formed is demonstrated.
  • A downloadable paper to follow along with the video is available on the channel’s offical website: http://www.thinkwell.com

However, one way in which the video can be improved is if a white board is used instead of so many paper so that paper can be saved.

In conclusion, i believe that the video is amazing, makes learning fun and easy while at the same time covering the necessary information.

goodbye (1) www.tangrammedia.com

 

Enzyme video reveiwed

While cramming for subjects, i usually use a couple youtube channels that has concise information about topics. One of my favourite channel is BrightStorm2 which has a range of topics in biology,chemistry,physics and math. The following is a video from their channel on Enzymes:

http://www.youtube.com/watch?v=870MWm0peRI

Summary of the video:

The lecturer talked about enzymes being a protein catalyst, having a substrate specific active site, induced fit theory, and the effect of pH and temperature.

  • Firstly, i thought that the video was concise, but filled with enough information to give you a general idea of Enzymes.
  • His animated voice kept your attention throughout the entire video.
  • The use of a diagram of an Energy vs Time graph on the white board gave you a visual understanding of how enzymes work as a catalyst and lowers activation energy and speeds up the rate of reaction.
  • The use of main points on the white board also gave a visual of the main characteristic of Enzymes that should be known. these main points were also discussed in the video: Protein catalyst, active site, specific to substrate, induced fit theory, pH and temperature.
  • The use of the scissors gave a real life application and therefore better understanding of enzymes being a catalyst and the active site being substrate specific.
  • The use of assistant Laura also gave the video an added touch of familiarity and proved that enzymes act as catalyst and make reactions easier to occur.
  • Diagram of induced fit theory gave a visual, hence better understanding of how the theory works.

 

However, the video can be improved in multiple ways:

  • The video could have been edited so that Laura ripped the paper correctly the first time, proving that enzymes make reactions occur easier.
  • Other topics such as Inhibition, Nomenclature, Enzyme classes, Inorganic catalyst vs biological catalyst, M-M equation, Line-weaver Burk plot and Allosteric enzymes could have been covered. This could have given the video a sense of depth instead of a general idea. In this way, students at university level would find the video very useful.
  • Other graphs such as pH and temperature graphs could have been used.
  • pH and temperature effect on enzymes could have been explained more, instead of simply mentioned.

 

In conclusion, i believe the video is best for cramming purposes, because it give a general sense of Enzymes and their characteristics.

goodbye www.maurilioamorim.com

Is Methylene Blue a cure for a disease? [Published paper #2]

Source: http://www.scientificamerican.com/article.cfm?id=common-lab-dye-found-to-i

So there I was browsing through scientific websites looking for a topic to do my assignment on, and I came across a chemical that I’ve used in biology and chemistry labs before, and apparently it has properties that help in Huntington’s Disease.  This is being researched by Leslie Thompson, a neurobiologist at University of California–Irvine and her team. Leslie Thompson is in the picture below:

Imagehttp://faculty.uci.edu/profile.cfm?faculty_id=4708

Huntington’s disease (HD) is a genetic disorder that disturbs muscle coordination and results in mental deterioration and psychiatric issues. It is usually recognizable in adults in their 30s and 40s. HD is the most common genetic cause of abnormal involuntary writhing movements called chorea. Huntington’s disease occurs when the C-A-G sequence of DNA base pairs repeats too often on the HTT gene, creating a long version of the Huntington protein, which therefore folds incorrectly and produces clumps in the brain. HTT is a protein that interacts with many other proteins as well as has many biological functions. HD is not caused by inadequate production of HTT, but by an accumulation of the toxic function mHTT. It is a neurodegenerative disease, which causes a gradual loss of structure or function or death of neurons.

Imagefolding.stanford.edu

Below is a microscope image of a neuron with inclusion (stained orange) caused by HD, image width 250 µm:

Imagehttp://en.wikipedia.org/wiki/Huntington’s_disease

Methylene blue is said to disrupt the formation of mHTT protein clumps in HD. Methylene blue was used to treat ailments from cyanide poisoning to malaria from since 1897. However, Food and Drug administration has never officially acknowledged it as a therapy for any diseases or illness. There is currently no drug produced to stop HD progression. Methylene blue itself is not harmful to humans.

The research team is currently experimenting with flies and mice. Drosophila flies with mHtt gene were given food mixed with methylene blue for seven days. Results of the flies’ brains showed that protein clumps had been reduced by 87 percent compared with a control group. The mice with the mHTT gene were tested for mobility. The 2-month old treated mice demonstrated irregular clasping of their hind claws only 20 percent of the time in a reflex test, while the untreated mice clasped at a 60 percent rate. Less clasping meant healthier mice. However, the amount of mice used was not large enough to give statistically feasible results and the difference in the tests “dropped off” after 9 weeks.

Imagehight3ch.com

The research team says a lot more research on methylene blue is needed but they are hopeful because the early steps of clumping of the mHTT protein is significantly altered in test tubes, the flies and also the mice. They state that methylene blue may prevent mHTT from sticking to itself. Thompson highlights that “Methylene blue would absolutely require further testing in mouse models and would need safety and efficacy trial before it could be used for humans.”

Now think about the difference that a chemical we use as a stain and indicator..has the ability to save the millions of people that suffer from HD worldwide. Furthermore, what other chemicals purposes are being underrated and not utilized? I really hope that the clinical trials go well and methylene blue is approved as a therapy for Huntington’s Disease.

Imageblogs.nature.com

Glycolysis Quiz

Its quiz time once again..so put on your thinking caps and make me proud biochemists!

blog26

1) What is the most regulated enzyme?

a)      Adolase

b)      Phosphofructokinase-1

c)       Phosphohexoseisomerase

d)      Enolase

e)      Pyruvate Kinase

2) What co-factor is needed for the conversion of Pyruvate to Acetyl-CoA?

a)      Mg2+

b)      TPP

c)       Cu2+

d)      Vitamin C

e)      All the above

3) What is the co-factor that all kinase enzyme require?

a)      Fe2+

b)      Cu2+

c)       Vitamin A

d)      TPP

e)      Mg2+

4) Which reaction is the only oxidation phase in glycolysis?

a)      Fructose-6-phosphate to Fructose-1,6-bisphosphate

b)      1,3-BPG to 3-Phosphoglycerate

c)       G3P to 1,3-BPG

d)      Phosphoenolpyruvate to Pyruvate

e)      Glucose to Glucose-6-Phosphate

5) In which reactions are ATP produced?

a)      1st and 10th reactions

b)      All reactions of the Energy Generation phase

c)       7th and 10th reactions

d)      Reactions vary according to cell

e)      ATP is produced in the Citric cycle and consumed in Glycolysis

6) In which reactions are ATP consumed?

a)      1st and 3rd reactions

b)      All reactions of the Energy Investment Phase

c)       2nd and 5th reactions

d)      ATP is only produced not consumed

e)      Glucose to Glucose-6-phosphate ONLY

7) Where does glycolysis occur in the cell?

a)      Cytosol

b)      Cytoplasm

c)       Mitochondria

d)      Nucleus

e)      Directly outside the cell

8) Multiple Answer MCQ:

Select the correct multiple choice answer using ONE of the keys A,B,C,D or E below:

a)      1 and 4 are correct

b)      2 and 3 are correct

c)       Only 4 is correct

d)      1 and 3 and 4 are correct

e)      2 and 4 are correct

8) Which reactions are irreversible?

1)      Glucose-6-Phosphate to Fructose-6-Phosphate

2)      Glucose to Glucose-6-phosphate

3)      DHAP to G3P

4)      Phosphoenolpyruvate to Pyruvate

9) Why is/are this/these reaction(s) irreversible?

a)      Backward reaction is not energetically feasible

b)      Not enough product is made for a reverse reaction

c)       Backward reaction produces too much heat

d)      Change in structure of product prevents reactants from being made.

e)      All of the above

10) What enzyme is used to convert Glucose-6-Phosphate to Fructose-6-Phosphate?

a)      Aldolase

b)      Enolase

c)       Phosphohexose isomerase

d)      Phosphofructokinase-1

e)      Glucose-6-Phosphase

11) What is the by-product when Enolase converts Phosphoglycerate to Phosphoenolpyruvate?

a)      NADH

b)      H2O

c)       ATP

d)      DHAP

e)      TPP

12) What happens to pyruvate when oxygen is unavailable?

a)      It is converted to L-Lactate

b)      It is converted to Ethanol and enters Citric cycle

c)       It is converted to Acetaldehyde and enters Citric cycle

d)      It is converted to Acetyl-CoA and enters Citric cycle

e)      All the reactions of Glycolysis are reversed

Glycolysis…this is friggen awesomeeeeee

gly5

Stop whatever you are doing and watch this AMAZING video!!!

Now tell me that song isnt stuck in your head and you’ve already learnt and memorized BOTH glycolysis and TCA!!!

Regardless of that vid, in case you’re not a huge rap fan..allow me to break it down for you!

Glycolysis is the process that breaks down Glucose into Pyruvate and produces ATP along the way. ATP is used for energy. ATP is like money to cells, if you aint got no ATP, you aint got no game. And guess what? Glycolysis is going on in your body RIGHT NOW! As you read this, 10 different enzymes are working hard to convert that sandwich you ate into pyruvate. How you ask? This picture should give you a good explanation:

gly2

In the first reaction, glucose is converted to glucos-6-phosphate because the phosphate group makes it more reactive as well as prevents it from passing through the glucose transporter.

All kinases enzyme require Mg2+ as a cofactor. All these enzymes are induced-fit.

Also, wherever a Kinase is involved, ATP is either being broken or formed.

The enzyme in the third reaction; Phosphofructokinase-1 is the most regulated enzyme, and the this reaction is also the second priming reaction.

The sixth reaction is the only oxidation reaction in glycolysis by the enzyme Glyceraldehyde-3-phosphate dehydrogenase, and hence forth, 2molecules of everything is produced in each reaction.

There are 3 irreversible reactions in glycolysis and this is because the forward reaction has a high negative deltaG value and hence a high positive deltaG value will be needed to overcome for a backward reaction to occur.

The 3 irreversible reactions are:

1st reaction: Glucose –> Glucose-6-phosphate

3rd reaction: Fructose-6-phosphate –> Fructose-1,6-bisphosphate

10th reaction: Phosphoenolpyruvate (2) –> Pyruvate (2)

The 2 enzymes involved in sub-level-phosphorylation are;  Phosphoglycerate kinase and Pyruvate kinase.

Fate Of Pyruvate:

After pyruvate has been made, 3 things can happen depending on if oxygen is available or not.

If oxygen is available:  Pyruvate is converted to Acetyl-CoA by enzyme Pyruvate dehydrogenase complex and NADH is produced as a by-product. Acetyl-CoA then enters the TCA cycle.

If oxygen is unavailable:

Pyruvate is converted to L-Lactate by the enzyme Lactate dehydrogenase and NAD+ is produced as a byproduct.

Fermentation can also occur: Pyruvate is converted to Acetaldehyde which is then converted to Ethanol by enzyme Pyruvate decarboxylase and alcohol dehydrogenase respectively. For the enzyme Pyruvate decarboxylase; co-factors include Mg2+ and TPP (thiamine pyrophosphate) and CO2 is produced as a by product. Conversion of Acetaldehyde to ethanol produces NAD+ as a by-product.

 

And that folks, is Glycolysis! Hope you learnt a thing or two! catch ya next time.

 

 

 

 

Enzymes Quiz (:

Its quiz time again! and i KNOW you are all excited! So lets go!

1. Antibodies with catalytic properties are called?

a) Izoenzymes

b) Holozymes

c) Abzymes

d) Co-factors

e)None of the above

2. Which is an example of inorganic co-factor?

a) Vitamin C

b) Au+

c) Ag+

d) Mg2+

e) Urea

3. The active enzyme is called?

a) Holoenzyme

b) Abzyme

c) Co-factor

d) Actenzyme

e) None of the above

4. What is the catalyst used in the Contact Process?

a) LDH

b) Vanadium (V) oxide

c) Fe

d) SDH

e) Silicon

5. Allosteric enzymes show what type of curve?

a) Sigmoid

b) Symmetrical Curve

c) Hyperbolic Curve

d) It produces a line, not curve

e) None of the above

6. When [S] is much less than km and velocity is proportional to [S], what is the rate of reaction?

a) Zero order

b) First order

c) Second order

d) Third order

e) None of the above

7. What is the competitive inhibitor of Malonate?

a) LDH

b) Succinate Dehydrogenase

c) HCl

d) Urea

e) Malonase

Multiple answer MCQ:

Select one of the correct multiple answer using ONE of the keys A,B,C,D or E as follows:

a)      ONLY 1 is correct

b)      2 and 3 ONLY are correct

c)       All options are correct

d)      1 and 4 ONLY are correct

e)      All except 1 are correct

8. Inhibitor that binds to the enzyme at a site besides active site is called?

1) Competitive

2) Uncompetitive

3) Non Competitive

4) Mixed Competitive

9. Why does allosteric enzymes have more than one active site?

a)  Multiple folding

b) Presence of hydrophobic interactions

c) New active sites form when inhibition occurs

d) Multiple polypeptide chains

e) Gene that produces active sites is mutated

10. What takes part in negative feedback mechanism?

a) Homotrophic effectors

b) Heterotrophic effectors

c) Both Homo trophic and heterotrophic effectors

d) Apoenzymes and Co-factors

e) Only inorganic catalyst

 

Release your inhibitions!

So its 1:45am and here i was thinking that “The Perfect Fit” would be my last enzyme blog entry. Then i turned the page in my notebook and BAM, a whole other section about inhibition of enzymes. Weh. This is pretty simple to understand though, it just needs to be remembered. So without further discussion of non-bio things, Let’s begin:

  1. Competitive inhibition
  2. Non-Competitive inhibition
  3. Uncompetitive inhibition
  4. Mixed inhibition

Four easy yet useful stuff!

All inhibitors change the shape of the active site of the enzyme, thereby preventing a reaction from occurring since the specific shape of the substrate cannot bind to this new shape. Its like cock-blocking at a molecular level.

Reversible inhibition: inhibitors can bind to enzymes through weak non-covalent interactions ( ionic bonds, hydrophobic interactions, and hydrogen bonds) but because reversible inhibitors do not form any chemical bonds or reactions with the enzyme, they are formed rapidly and can be easily removed. Thus the enzyme and inhibitor complex is rapidly dissociated in contrast to irreversible inhibition.

Competitive inhibition: inhibitors bind reversibly to the same site (active site) that the substrate would occupy. By increasing substrate concentration, effect of inhibitor is reduced.

academic.pgcc.edu

enz7

Non-Competitive inhibition: inhibitors and substrate binds on different sites of the enzyme. The inhibitor can either bind with free enzymes, or the enzyme-substrate complex. Concentration of substrate would therefore not affect inhibitors since it can bind elsewhere.

http://www.tutorvista.com

enz8

Uncompetitive inhibition: inhibitor binds only to the enzyme-substrate complex, at a separate site from the substrate binds, and not with free enzymes.

en.wikibooks.org

enz9

Mixed inhibition: inhibitor binds at a separate site from the substrate’s active site, to either free enzymes or enzyme-substrate complex. It sounds similar to non-competitive inhibition doesn’t it? However the difference is that the enzyme-substrate complex has residual enzymatic activity.

en.wikipedia.org

Now you guys know how much i love my youtube videos! its a little longer than usual, but its worth it!

The Perfect Fit!

Enzymes are SO picky when it comes to substrates! they would never react with any old substrate, and due to this specificity, two hypothesis were created;

  1. Fisher’s Lock and Key hypothesis
  2. Koshland’s Induced Fit hypothesis

The lock and key hypothesis states that the enzyme’s active site shape is very rigid and therefore the substrate must have this exact shape in order for a reaction to occur.

The induced fit hypothesis however, indicates that the active site is flexible and only assumes its catalytic conformation after the substrate binds to it. Crystallography shows that proteins are flexible. Lock and key hypothesis is as if you are a strong independent woman with high standards and accept nothing less of a man! While induced fit hypothesis is like when you change some of your personal traits to better suit your mates’ own, to make the love work. Ah, i bet you get it now, don’t you?

In the video, Milo is an catabolic reaction enzyme which active site affects the bonds in the substrate so that they are easier to break. Barry however is an anabolic reaction enzyme and brings substrate molecules together.

The following video shows how enzymes work in the body, and although this is not on the syllabus, you should still view it for general knowledge and pleasure (:

Allosteric enzymes have a quaternary structure and hence has more than one active site present. why do you think this is? Its because allosteric enzymes are composed of more than one polypeptide chain, since each chain has a least one active site, allosteric enzymes has multiple active sites. They therefore show sigmoid curve when plotted. i know what you’re thinking, allosteric enzymes are like the Channing Tatum of enzymes!

Image

If you’ve watched no podcasts so far from this blog entry, i recommend you watch this one. Its a fun summary of everything enzymes!

Enzymes!

Enzymes are biological catalysts that speeds up chemical reactions by providing an alternative pathway with a lower activation energy. Allow me to break down that definition by explaining key words. Catalysts are substances that increases the rate of a reaction without itself being changed in the process. Activation energy is the least amount of energy required for a reaction to occur. Now re-read the first sentence…got it now? great!

 

Enzymes are mostly proteins though some are RNA molecules.

ENZYMES ARE HIGHLY SPECIFIC! ..and yes, i had to use shouty-caps, cause that characteristic is very important to know. The relationship between enzymes and substrates is like a love story:

Just as a girl heart is specific for that one guy..”the one”..an enzyme’s active site is also highly specific.

When that girl meets that perfect guy..they have a relationship..just as the enzyme and substrate forms an enzyme-substrate complex.

Eventually,the guy changes,and turns out to be the person you thought he was, and yall break up…just as the substrate shape changes to form products and the complex is broken.

The enzyme remains unchanged,free to bind with more subtrate while the girl may however be changed.

enz5

http://theewanderingkind.tumblr.com/

LOL slight toat, but anyways, you get the point!

Catalytic Power: the number of molecules of substrate converted to product per enzyme molecule per second is called “turnover number”  or “kcat”

Co-Factors: essential for proper functioning of enzymes.

Non-protein component: can be organic (derived from vitamins) or inorganic (metal ions)

‘Cosubstrates’ are not bound, while ‘Prosthetic groups’ are bound.

Apoenzyme + Cofactor –> Holoenzyme

Active site is formed when proteins undergo complex folding of the amino acid chain,pockets formed by such structures containing a functional group responsible for the reaction forms an active site.

Weak forces of attraction exists between the active site and the substrate.

Biological catalyst are more efficient than Inorganic enzymes which include Fe catalyst for Haber Process and Vanadium (V) Oxide catalyst for contact process.

Graph showing reaction with and without  enzyme present:

enz4

academic.pgcc.edu

Graph showing effect of Temperature, pH and substrate concentration on velocity of enzyme catalyzed reactions:

Image

en.wikibooks.org

Please read Part two of this Enzyme Blog…toodles for now.