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The ETC Rollercoaster

It seems like a fun ride if your and electron you see NADH and FADH act as electron stores or transporters and when they get to complex I of the electron transport chain the electrons are passed from the molecules to complex and then from that complex to the other complexes. NADH is oxidized to NAD in this process and at Complex II FADH is oxidised adding more electrons for the chain.

So basically the electrons are fully of energy like “YEAHH this is fun” as they move from complex to complex


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However as the electrons move through the chain from complex to complex they lose their energy thus at complex III, no additional electrons enter the chain, but electrons from complexes I and II flow through it.

When electrons arrive at complex IV, they are transferred to a molecule of oxygen. When the oxygen, get the electrons water is produced and so the electrons are like “aww i just so tired i had enough i think ill just turn into water and chill.”

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But its not just a free fun ride it serious business because while these electron ride from complex to complex, H+ move through complexes I-IV from the matix to the outside the membrane or in the intermembrane space where it accumulates. As a result, a net negative charge builds up in the matrix space while a net positive charge builds up in the intermembrane space this is where the last complex comes into play this complex is called ATP synthase.

In an attempt to meet and equilibrium between the charges the H+ in the intermembrane space tries to find a way back into the matrix however the only way back is through the ATP synthase molecule that harnesses the energy of the H+ flowing back into the matrix and thus in the process uses the energy to make ATP by combing ADP +Pi. This process is also called oxidative .phosphorelation and this process takes place within the intermembrane of the  mitochondria.

here is another really cool way of looking at it

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Well i am almost at the end of this blog but i did promise you one last video and that video would be on protein denaturing and then we end with a bang 😀 i hope you had fun with me on my biochem journey ….

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check this out http://www.science.smith.edu/departments/Biology/Bio231/etc.html

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TAC my second video review

Second video review

This person has helped my through Alevels and even though his videos aren’t in such detail as need for university it is pretty good to get the general idea of the topic before actually doing it for your course which would obviously be in greater detail.

This video review is on the TCA cycle or citric acid cycle and it’s pretty much very good it starts of with the products of glycolysis which is pyruvates and 2 ATP and 2 NADH.

Mistakes he made were that he said that glycolysis took place in the cytoplasm but we know that it’s not so much the cytoplasm but rather the cytosol, he also fails to mention the enzyme responsible for the link reaction in which pyruvate is converted to acetyl coA that enzyme is pyruvate dehydrogenase.

However he is very clear about the actual cycle where acetyl-coA enters the critic acid cycle.

Firstly the acetyl coA combines with oxaloacetate to form citric acid. We should note that it is this cycle and process in respiration that produces the CO2 for every carbon that is cleaved off. One pyruvate molecule produces 3 CO2 thus for a molecule of glucose 6 CO2 is produced. At the end of the cycle we should also note that oxaloacetate is reformed thus making this a cycle. And the steps are quite simple and given below in the diagram.

http://en.wikipedia.org/wiki/File:Citric_acid_cycle_with_aconitate_2.svg

We should note however the amount of products we produce per turn of the cycle which is:

3 NADH

1ATP

1 FADH

We should also note that for each glucose molecule 2 pyruvate is produces and so per glucose molecule the TCA occurs twice thus 2 times the number of products are actually produced. One last thing remember that respiration is a 3 part process we are done with 2 which means that all of this preparation is done to facilitate the third step and here we will see how we utilize the FADH and NADH produced thus far.   My next post is about the electron transport chain which is the last step for respiration. I still have one more experiment to upload and hopefully i will get that done but i am coming to the end of this blog as i am almost done with teh topics covered in my course.

TCA has always been a tough topic and i know i said that about glycolysis but it’s true for the entire topic of cellular respiration i was basically lost in secondary school even at A levels which made me mess up my CAPE biology exams (equivalent to A levels) and i always put a block against this topic but though this biochemistry course i am actually understanding the topic and i think the mind block has been removed 🙂 So study up i know finals a in a few weeks and i think Alevels and CAPE are close also so just keep studying and just because something looks daunting or intimidating and you think you don’t have the ability to do it (which is what i always though) trust me when you truly take the time understand a topic or a process and not just learn it for passing an exam you will definitively never forget it . Happy Dance for me because i understand finally 😀

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Enzymes 2

sgBanner471_88544Stained Cancer Cells

NOTE:

Km  – the rate constant or it can be explained as how much substrate concentrationis required by an enzyme to reach to the half of maximum rate or velocity of enzyme.

Vmax- that point is the saturation point or maximum substrate concentration to have maximum rate of the reaction.

So what are the effects of changing variables on enzymic reactions?

What if we increased the substrate concentration

As the concentration of substrate increases, the rate of reaction also increases until the point saturation occurs. It means as you increase the concentration, rate keeps increasing and then one point comes when all the enzymes are occupied and there is excess substrate. Thus after this point, increasing the concentration will result in the graph tapering off.

substrateconc

Effect of temperature on enzyme activity

If the temperature is too high, there is enough energy to break down the tertiary structure of the enzyme this alters the shape of the active site so that the substrate no longer fits; the enzyme is said to be denatured. However if the temperature is to low the substrate molecules simple do not have enough energy and so the reaction cannot take place.

add_ocr_bi02005a

Effect of pH on enzyme activity:

The optimum pH for each enzyme is different based on the job of the enzyme and where they work. Some enzymes work in acidic conditions such as those in our stomach like pepsin while others work under basic or normal conditions. This is because of the proteins that might be present at the active site and just like the effect of temperature deviation for the optimum pH can cause a conformational change in the shape of the active site.

ie22

OH INHIBITORS  !!!!! : (

inhibitor

Inhibitors are molecules that combine to enzymes and prevent the substrate from attaching to the active site by changing the shape of the active site or the affinity of the enzyme these result in decreses in the rate of reactions which can be plotted on a graph called the Linweaver – Burk plot or even the Michealist- menten curve.

There are many types of inhibitors some are reversible while others are irreversible:

Some reversible inhibitors are:

enzyme-inhibition

Competitive inhibition (Slide B)

Substrate and inhibitor cannot bind to the enzyme at the same time, the inhibitor having an affinity for the active site of an enzyme and the inhibitor having a complementary shape that resembles the substrate. Thus inhibitor compete for access to the enzyme’s active site. This type of inhibition can be reversed by increasing the concentrations of substrate thus the vmax is left unchanged however since there is more substrate the Km or 1/2Vmax point will be increased.

Non-competitive inhibition(Slide C)

Bind at different sites than the active site. When both the substrate and the inhibitor are bound, the enzyme-substrate-inhibitor complex cannot form product and can only be converted back to the enzyme-substrate complex or the enzyme-inhibitor complex. The Vmax is decrease since the enzyme substrate complex or the active state is disrupted, however the Km remains the same since binding of the enzyme to the substrate is not affected.

Uncompetitive inhibitor (Slide D)

Enzyme inhibitor binds only to the complex formed between the enzyme and the substrate the Vmax decreases as well as the Km at equal proportions since formation of the enzymes substrate complex is affected or however the enzyme affinity is increased.

Mix inhibitor

The inhibitor may bind to the enzyme whether or not the enzyme has already bound the substrate but has a greater affinity for one state or the other. The binding of the inhibitor to the enzyme reduces its activity but does not affect the binding of substrate. Vmax will decrease due to the inability for the reaction to proceed as efficiently, but Km will remain the same as the actual binding of the substrate, by definition, will still function properly.

Learning about the different types of inhibitors was new to me and was sort of challenging but once you understand the basics of   the Lineweaver- burk plot and how each inhibitor works you can easily figure out how the graph would change and look. Have a look at this page it’s an interactive that explains enzymes quite well. http://www.wiley.com/college/boyer/0470003790/animations/enzyme_inhibition/enzyme_inhibition.htm

Refferences:

http://medicine.yale.edu/cancer/research/excellence/index.aspx

Disclaimer: The pictures and some text used are not of my own.

Proteins

vs_viral_protein_banner

 

Proteins
In the last post we established that proteins are made of a polypeptide chain/s and each protein is different due to the sequencing of the amino acids within the polypeptide chain. We also learned that in order to be called a protein the chain/s must have a molecular weight of over 5000g/mol. So let’s just get to it 😀
Importance of protein
Proteins are VERY important we are primarily made of proteins and they can be found in every aspect of our body, they can be used for :
Defence:

Antibodies are made of proteins and are used to protect our bodies from antigens by immobilizing them so they can be dealt with bywhite blood cells.Antibody

Movement:
Our muscles are made of proteins which can be easily contracted and relaxed which allows us to move.

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Enzymes:
Very importantly enzymes are proteins that regulate and catalyse chemical reactions within our bodies and are very specific and efficient some speed up reactions by almost 100% .

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Hormones:
Most hormones are made of proteins and act as messengers to help induce bodily activity example insulin for blood glucose concentration maintenance.


Structural support:
Fibrous proteins such as keratin and collagen act as support for connective tissues in ligaments as well as in structure such as hairs, feathers, quills etc.
The hard exoskeleton of insects is made of a glycoprotein called chitin.

americanCockroachAdult


Storage:
Such as the “yolk” of eggs which is made of the protein Ovalbumin which acts as a food store for that developing foetus.

fried-egg


Transport Proteins:
That help transport molecules around the body the most famous being haemoglobin and mayoglobin. As well as Cytochromes that act as a carrier protein in the electron transport chain.


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In other words Proteins are very important and can be found everywhere!!


Levels of Protein Structure:
Proteins can generally have 4 structures:
1) Primary structure:
The actual sequence of the proteins along the chain eg.
[-Serine-Alanine- Leucine-Leucine-Tryrocine-]
Or [-S-A-L-L-Y-]

(see what I did there )

2) Secondary Structure:
This is where the interesting stuff happens; here folding starts to take place and the alpha helix or beta sheet are formed.

Alpha helix – a rod like shape, the primary structure coils and this folding occurs due to hydrogen bonds being formed between the carbonyl oxygen on the pepide bond and the Hydrogen on the amino group. Hydrogen bonds are formed nearly parallel and the side chains or R groups of each amino acid are on the outside of the spiral.
0192801015.alpha-helix.1
NOTE: the alpha helix is mostly dominant due to the maximum use of hydrogen bonding since every peptide linkage (except those on the ends) takes place in H bonding. This enormous amount of bonding gives the helix structure stability.
Proline is not welcomed because it is cyclic and so one of its hydrogen is not available for bonding thus it forms and uneven number of bonds and the structure bends or leans in that direction.
Glycine is also not welcomed because it has a high “conformational flexibility” simply meaning it destabilizes the alpha helix and this is due to the fact that glycine’s R group is H.
Bulky or large R groups destabilise the alpha helix.

Beta pleated sheet- hydrogen bonds form between peptide bond on the same chain or different chain on a horizontal plane. There are parallel and anti parallel sheets.
0192801015.beta-sheet.1

3)Tertiary Structure
Here it gets more interesting as all the different types of bonding start to take place as side chains interact. The protein folds in on its self and forms: hydrogen bonding, salt bridges, disulfide bonds, and non-polar hydrophobic interactions.

Just so you understand how the bonding works:

Disulfide bonds

Oxidation of the sulfhydryl groups on cysteine. Different protein chains or are held together by the strong covalent disulfide bonds.

Hydrogen Bonding:

Where bonding occurs between two alcohols, an alcohol and an acid, two acids, or an alcohol and an amine or amide side groups.

Salt Bridges:
Salt bridges result from the neutralization o

f an acid and amine on side chains. Interaction is ionic between the positive ammonium group and the negative acid group. Any combination of the various acidic or amine amino acid side chains will have this effect.

Non-Polar Hydrophobic Interactions:
The hydrophobic interactions of non-polar side chains are believed to contribute significantly to the stabilizing of the tertiary structures in proteins. The non-polar groups mutually repel water and other polar groups and results in a net attraction of the non-polar groups for each other. This results in the non-polar side chains of amino acids being on the inside of a globular protein, while the outside of the proteins contains mainly polar groups.
(http://www.elmhurst.edu/~chm/vchembook/567tertprotein.html)

proteinstrct

4)Quaternary Structures

Here 2 or more polypeptide chains interact to form large structures one such is haemoglobin. However not all proteins consist of a quaternary structure.

quaternary_structure