ATP synthesis and the Mitochondria

Hey guys!

so we just had a little entertaining, CREATIVE, comic about cyanide. A few of you are probably wondering, how is atp made anyways? Yes there were a couple diagrams in the previously ingeniously creative comic strip, however I thought i’d go through a little more in depth with you just about just what REALLY goes on inside our little powerhouses (mitochondria) in our cells.

 

The chemiosmotic hypothesis explains how ATP is generated in the mitochondria :

Within the mitochondria, an ETC, or electron transport chain is found, where NADH and FADH containing electrons, have a high energy potential. This is located within the inner membrane of the mitochondria.

For simplification purposes, one can say that the ETC consists of four complexes which, within the ETC looses an electron, an oxidative process, giving off energy. Complexes 1, 3 and 4 uses this energy to pump protons into the membrane. Complex 2 does not use energy to pump protons even though energy is given off. It instead has succinate dehydrogenase from the TCA cycle, where FADH reacts

The high electrochemical gradient generated by these oxidative processes generates a high proton motive force.

How does it generate this force?

Well, protons cannot cross the inner membrane of the mitochondria matrix. It must therefore pass through an ATP synthase protein molecule, which must undergo a conformational change in order to produce ATP.

ADP + Pi —> ATP

This is generated from the electron motive force.

Cyanide, as seen in the previous comic, bind to comples 4, inhibiting the ETC from functioning.

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Enzymes

Hey guys ! It’s me again ūüôā giving yet another posts on enzymes. Whooo hooo!!

Okay so before we get started I thought i’d make reference to the very informative videos that I have obtained all my information which I am about to summarize for you ūüôā

Video Link : 

So let’s start shall we!

Summarizing, as we’ve learnt before, enzymes are biological catalyst which can speed up the rate of a chemical reaction by providing an alternative pathway for the reaction to occur at a lower activation energy.

Let’s pause for a cause here :

What do we mean by activation energy?

Well activation energy refers to the minimum amount of energy for a reaction to occur.

Okay. We can continue ūüôā

As seen in the video, some RNA molecules or ribozymes can act as enzymes since they are substrate specific, enhance reaction rates, and emerge from the reaction unchanged.

Again. Let’s pause.

What are some features of these biological catalysts? ( ….. you might ask.)

  1. They have catalytic power, meaning the ability to speed up a reaction while the molecule itself remains unchanged.
  2. They can be regulated or controlled in some way

Also something fascinating noted in the video was that some antibodies, which prior to this I thought dealt strictly with the body’s immune system, have catalytic properties. These special antibodies are referred to as abzymes. This got me thinking about how so many different small little things work together to make our magnificent bodies function properly, as these factors work together. Truly remarkable if you ask me!

Next, in the lecture, a Transition State was mentioned. This referred to the highest energy arrangement of atoms that is intermediate in structure between the structure of the reactant and the structure of products.

Noting that :

Changes

structure of substrate ————–> structure of product

 

So now we ask, how do we name these enzymes?

  • based on their substrate : like lipase and sucrose
  • based on a description of the action/reaction performed : Example pyruvate carboxlase
  • And sometimes, well sometimes we just find outta timin’ enzymes, like trypsin pepsin and catalase

Another way to classify enzymes is by the EC number, where there are six main categories that we should know:

  1. Oxidoreductoses —> Catalyzes oxidation reduction reactions
  2. Transferases —> Catalyzes transfer of C, N, or P containing groups
  3. Hydroloses —> Catalyzes cleavage of bonds by addition of water
  4. Lyases —> Catalyze cleavage of C-C, C-S and certain C-N bonds.
  5. Isomerases —> Catalyzes racemization of optical or geometrical isomers
  6. Ligases —> Catalyzes formation of bonds between carbon and O, S, N coupled to hydrolysis of high energy phosphates.

SO. To be honest. memorizing these categories are gonna be quite a challenge for me. But through¬†practice¬†I think, like everything else we should be able to get the hang of it !:) now that we’ve gotten that FUN part ( extreme sarcasm here) out of the way, we can finally move on to Cofactors!

Cofactors refer to a non protein component which allows an enzyme to function properly.

Cofactors can either be inorganic or organic.

Inorganic cofactors can usually refer to metal ions, examples being Zinc 2+, or Mg 2+

Organic factors however, can lead to something known as “co enzymes” which are frequently derived from vitamins where¬†transparent¬†association can lead to “co substrates” where as permanently associated vitamins can lead to what we know as a “prosthetic group.”

Which leaves me to conclude about inorganic catalyst.

These kids never get 100% of the product and cannot be regulated. Examples where inorganic catalysts are used include the haber process, and the contact processes within the industry .

Alright folks! That’s it for this post! I know there’s plenty more to write about here. Hopefully by the next two days i’ll be able to catch up. Also a new quiz will be coming up soon! so make sure you’re on top of your game! ūüôā

Enzymes! :)

References:

See J. E. and E. T. Bell, Proteins and Enzymes (1988).

The Columbia Encyclopedia, s.v. “enzyme,” accessed March 16, 2013, http://www.credoreference.com/entry/columency/enzyme

Hey guys!

So previously we had covered amino acids and their linkages, that is polypeptides bonds and the structures that are formed along with them. This Week we’ve moved on to a somewhat more exciting topic. ENZYMES!

Now this is a HUGE topic, but to help us along i came across a little article that could help us.

According to “Credo Reference” an enzyme, also known as a biological catalyst,¬†accelerates¬†the rate of a reaction without being permanently chemically changed. Enzymes achieve this phenomenon by providing a different reaction pathway for the reaction to occur, thus lowering the activation energy required for the reaction to take place.

Factors which affect the rate at which the enzyme work include specific temperature ranges, pH ranges. The efficiency of a particular enzyme can also be measured usually by a turnover rate, measuring the number of molecules of compound opon which the enzyme works per molecule of enzyme per second. A useful example given in the article was of Carbonic anhydrase which has a turnover rate of 106  for removal of carbon dioxide from the blood binding it to water. Thus this rate means that one molecule of the enzyme can cause a million molecules of carbon dioxide to react in one second.

Also briefly mentioned in the helpful post, is the occurence of denaturation, where a denatured enzyme refers to an enzyme which has been altered in its chemcial and physical structure, so much so that it can no longer serve its purpose. Once an enzyme loses its shape, it can no longer catalyze its reactions since enzymes are selective for the molecules upon which they act, known as substrate molecules. Most enzymes will react with a small group consisting of closely related chemical compounds, demonstrating absolute specificity, thus having one substrate molecule, appropriate for the reaction.

An interesting fact, about enzymes is that some require non protein molecules, not excluding coenzyme molecules. These nonprotein components which are tightly bound to the protein are also referred to as prosthetic groups.

The active site is known as the region on the enzyme where the catalytic event takes place. Prosthetic groups, as mentioned above are usually located there. The side-chain groups of amino acid residues make up the enzyme molecule also participating in the catalytic event.

Another example given is in the enzyme trysin which brings together a histidine residue from one section of the mlecule with glycine and serine residues from another. Conclusively the side chains of these residues in this particular geometric arrangement produce the active site which accounts for the enzyme’s reactivity.

One may ask the question: How can these enzymes be identified and classified? Well, through crystalization of the amino acid sequence, and X-ray crystallography.

The informative post also mentions enzyme deficiency, where a number of metabolic diseases are known to be caused by deficiencies or malfunctions of the enzyme. An example of this is in albinism, caused by the enzyme responsible for the production of cellular pigments.

 

Tertiary Structure

Hello again!!

This is just a short closing post on tertiary and Quaternary structured proteins, just some general notes to fill in any blank spaces we might have been missing out.

In case we forgot, a tertiary structure of a protein basically refers to amino acids that are far apart in the linear sequence, as well as residues that are adjacent to each other.

Water soluble globular proteins.

In proteins such as myoglobin,while folding of chains occur spontaneously, the energy required to bury the non polar amino acids in the hydrophobic interior away from the surrounding hydrophilic aqueous medium is the driving force behind the folding of the polypeptide chain.

One may ask, How is this folding maintained, i.e. the confrontational 3D biologically active (native) conformation.

  • Hydrophobic interactions
  • electrostatic forces
  • hydrogen bonding
  • covalent disulphide bonds (if present)

Amphipathic

  • An amphiphathic molecule is one with two different affinities. i.e: Hydrophobic and hydrophilic. ( where hydrophobic is not water loving, and hydrophilic is water loving.)

A final note on Electrostatic Forces:

Electrostatic Forces refers to ionic groups of opposite charges which are attracted to each other. Like ammonium groups of Lys for example. They can also be referred to as an ion pair or a salt bridge.

 

 

Finally My last note is on Denaturation:

There are several ways in which a protein can be denatured.

  • Heat : An abrupt change, which occurs over a narrow temperature range. It is referred to as a co-ooperative process as Hydrogen bonds are continuously quickly broken.
  • UV : Causes Hydrogen bonds to once again be disrupted
  • Organic Solvents : Causes a change in hydration of ionic groups resulting in a change in the di elective constant.
  • Strong Acids/Bases through salt formation causing disruption of Hydrogen bonds
  • Chemicals : Such as Chaotrops which disrupts hydrophobic interactions. Detergents is another example of chemicals which can cause denaturation of proteins.

Amino Acids Part 2

So I promised that this time we’d take a closer look at secondary structures, that is alpha helices and beta pleated sheets.

The Alpha Helix

Image

Here are some basic pointers about this secondary protein structure:

  1. The o from the CO bond is hydrogen bonded to the H on the NH2 group of the 4th amino acid.
  2. Hydrogen bonds run parallel to the axis of the helix.
  3. There are 3.6 amino acids per turn of the helix, which are 0.54nm long
  4. Each aa residue is 0.15nm of the axis of the helix.
  5. Any side chains, are found on the outside of the helix.
  6. The abundance of hydrogen bonding gives the structure of the helix its stability.

If we take a closer look at this marvelous naturally occurring structure, we will see that certain amino acids are less often found in alpha helices than in others.

For examples:

Proline:

      The N atom in proline is a part of a rigid ring within the amino acid itself.This causes a destabilizing kink in the helix since rotation about the N-C bond is not possible.

Having trouble imagining what I’m referring to? Here’s a diagram to remind you about the structure of proline.

Image

 

 

 

The type of bonding exhibited in proline also prevents it from forming the correct pattern of H bonds due to the lack of H on the NH2 group. Because of these bonding factors, Proline is more suitable for, and mostly found at the end of an alpha helix where it alters the direction of the polypeptide chain, terminating the helix.

Another example of an amino acid which can destabilize an alpha helix is Glyceine since the R group, is the small, that is H, which allows high conformational flexibility.

 

Structure of Glyceine

 Image

 

 

Beta Pleated Sheet

Image

 

 

REFERENCES:

“Chubblyemonscience.” Last modified 2012. Accessed March 9, 2013. http://chubbylemonscience.blogspot.com/2012/11/secondary-structure-of-proteins-alpha.html.

Accessed March 9, 2013. http://commons.wikimedia.org/wiki/File:L-proline-2D-skeletal.png.

Accessed March 9, 2013. http://commons.wikimedia.org/wiki/File:Glycine-2D-flat.png.

Kaiser, Gary,Dr. “Doctor Kaiser Microbology.” Last modified 2005. Accessed March 9, 2013. http://webcache.googleusercontent.com/search?q=cache:http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit3/viruses/beta.html.

 

 

Amino Acids

Hey guys ūüôā

I know its been a while since I’ve posted anything ( a week to be exact ) but ive been quite the busy bee! So that being said I decided to give a major post on the basics for amino acids ūüôā

So let’s start off with the basic stuff.

question

and Last but NOT least:

question

What are amino acids?

Let’s start with a basic structure :

Reference: http://www.ucl.ac.uk/~sjjgsca/ProteinStructure.html

So there we have it folks! the basic structure of an amino acid, containing an amino group, a carboxyl group, and a variable R group also known as the “side chain.” Later on we will see that the interactions between the varying side chains, as well as the amino group play an important role in forming different types of bonds for various structures.

Two amino acids, come together, through condensation, to form a peptide bond.

Peptide bond

Reference: https://courses.worldcampus.psu.edu/welcome/biol011/lesson02_09.html

Later on in this blog, we will refer back to peptide linkages, and polypeptide chains, so make sure you understand the basics!!

Moving on we ask;What are amino acids used for?

Well to begin with, there are two different types of amino acids, Essential, and non essential amino acids. Naturally I am sure you will be able to guess the difference between two.

Essential amino acids :

These amino acids ust be obtained from the diet, since they cannot be synthesised on their own. There are roughly ten essential amino acids.

Non-Essential amino acids:

The body is able to synthesize these amino acids. Usually the body uses already exsisting carbon skeletons, and convert them to the respective amino acids. One example of this is the conversion of alanine to pyruvic acid.

Here’s a general picture of whats happening for the curious ones:

c01f010

Reference: https://kubon-sagner.e-bookshelf.de/products/reading-epub/product-id/595941/title/Essential%2BBiochemistry%2Bfor%2BMedicine.html?autr=%22Mitchell+Fry%22

Finally we move on to some chemical reactions involved with amino acids! ūüėÄ

Here’s a look at general peptide chain:

peptide1

Reference:http://www.ucl.ac.uk/~sjjgsca/ProteinStructure.html

From these peptide bonds, polypeptide chains can be formed,which can cause further structures to be created, as the polypeptide chain begins to fold. The polypeptide chain folds as a  result of different interactions between the different amino acids and the formation of hydrogen bonds, sometimes various sulphide bonds The different degrees of folding in the structure, classifies it as either primary,secondary or tertiary.

Primary and Secondary structures.

Reference: http://www.mhhe.com/biosci/ap/ap_prep/chemH5.html

Let’s Pause for a cause here and get some definitions under our belt.

Here’s a useful website I found describing everything in a pretty concise understandable manner.

http://www.mhhe.com/biosci/ap/ap_prep/chemH5.html

They give a concise definition of amino acids stating that they are a ¬†“Class of organic acids that comprise the building blocks for proteins.”

They also explain hydrogen bonding in an easy, understandable way stating that hydrogen bonds are, ”¬†¬†A weak attraction between a slightly positive hydrogen atom on one molecule and a slightly negative oxygen or nitrogen atom on another molecule, or between such atoms on different parts of the same molecule; responsible for the cohesion of water and the coiling of protein and DNA molecules, for example.”

Understanding hydrogen bonds is important seeing as they form the basis for primary, and therefore secondary and tertiary structures.

So now that we’ve taken a moment to understand, let’s dive straight into these amazing structures ūüėÄ

Primary structures:

  • ¬†These are a linear sequence of amino acids joined by peptide bonds
  • The nucleotide bases in the gene encoding the protein determines this sequence.

Secondary structures:

  • Regular folding of regions in polypeptide chains are observed.
  • Two examples of secondary protein structures can be seen in the alpha helix and beta pleated sheet.

Tertiary Structures:

  • These are usually globular
  • For soluble globular proteins, they are usually folded in away that the hydrophobic links are buried within the structure, while the hydrophilic chains are on the outside.

protein-structure

Reference : http://www.umass.edu/molvis/workshop/prot1234.htm

So there you have it folks! ūüôā the basics of amino acids.

Hope you had a fun time learning ūüėÄ

Next time we’ll go into detail about the secondary structures of proteins, that is, alpha¬†helices¬†and beta pleated sheets.

Until next time

Au Revoir