Another enzyme worlde (:

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FML ))):

So last week..i had a chem exam that i knew nothing for..and i came up with what i thought was a genius idea! I decided to all-night monday into tuesday, and tuesday into wednesday to study chemistry. Monday’s all-nighter went great but i began to feel sick in the morning because caffeine makes me feel sick, and i missed the biochem lecture.

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So..i was like no scene..i’ll just all-night in school tuesday and go straight into biochem lecture wednesday morning. But OFC 6am i’m running 48hrs withour sleep…dying..thinking 3 more hours to biochem lecture is more than infinity hours and i leave school at 7am. Then to find out we had two exams each day! And also TCA which was taught in class is the only topic with NO podcasts!

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Great. FML. I’ll have to do my own research to be able to blog this week. WEHH Happy easter to me ūüė¶

Glycolysis…this is friggen awesomeeeeee

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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:

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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.

 

 

 

 

How unicorns are made (:

Unicornase is an enzyme found in horses. Inside of a horse’s brain cells, unicornase attaches to the substrate HORn. The enzyme catalyzes the reaction by lowering the activation energy needed to start the horn making process. With each attachment of unicornase to HORn, one unit of HORn is made as well as a molecule of sparkles. The HORn travels to the top of the frontal lobe. And the sparkles go to the heart. Over time,the amount of HORn will pile up creating a horn on the top of the horse’s head.

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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

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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

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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

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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!

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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.

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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:

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academic.pgcc.edu

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

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en.wikibooks.org

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