Category Archives: Week in review

lipids

Lipids

These are naturally occurring organic compounds that are insoluble in water.

Lipids functions as:

  • Energy Storage
  • Making Biological Membranes
  • Insulation eg. Animal fat (blubber)
  • Protection – e.g. protecting plant leaves from drying up
  • Acting as hormones

They are made from two molecules: Glycerol and Fatty Acids. They may be saturated or unsaturated.

A fatty acid is saturated if every possible bond is made with a Hydrogen atom, such that there exist no C=C bonds. Saturated fatty acids on the other hand do contain C=C bonds.

If fatty acids are unsaturated, it does contain C=C bonds  and so because of this their shape is altered from a saturated molecule so the molecules in the Lipid push apart, thus making it more fluid and oily.

Types of lipids

Triglycerides

Basically one glycerol molecule bonded with three fatty acid molecules as seen below . Triglycerides are hydrophobic and so insoluble in water.

 

Phospholipids

Phospholipids are similar to triglycerides in they consist of a glycerol ‘back bone’ and fatty acid ‘tails’

This means the phosphate group will orientate itself towards water and away from the rest of the molecule, and also gives rise to the special properties that allow phospholipids to be used to form membranes

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Prostaglandins Thromboxanes & Leukotrienes

Natural hormones have an extraordinary range of biological effects. They can lower gastric secretions, stimulate uterine contractions, lower blood pressure, influence blood clotting and induce asthma-like allergic responses.

Steroids

Steroids may be recognized by their tetracyclic skeleton, consisting of three fused six-membered and one five-membered ring, as shown in the diagram to the right. The four rings are designated A, B, C & D as noted, and the peculiar numbering of the ring carbon atoms (shown in red) is the result of an earlier misassignment of the structure. The substituents designated by R are often alkyl groups, but may also have functionality. The R group at the A:B ring fusion is most commonly methyl or hydrogen, that at the C:D fusion is usually methyl. The substituent at C-17 varies considerably, and is usually larger than methyl if it is not a functional group. The most common locations of functional groups are C-3, C-4, C-7, C-11, C-12 & C-17. Ring A is sometimes aromatic.

steroid

Cholesterol

Cholesterol is a waxy steroid which is produced by the liver. Cholesterol is vital for normal body function. Every cell in our body has cholesterol in its outer layer.

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DNA

DNA is sometimes called “the blueprint of life” because it contains the code, or instructions for building and organism and ensuring that organism functions correctly. It is the chemical component of chromosomes, which are located in the nucleus of every cell. Stretches of DNA (or stretches of chromosomes) code for genes.

The shape of the DNA molecule is a double-helix (like a twisted ladder). The sides of the ladder are composed of alternating sugars (deoxyribose) and phosphates. The rungs of the ladder are composed of nucleotides.

Nucleotides pair in a specific way – called the Base-Pair Rule

Adenine pairs to Thymine

Guanine pairs to Cytosine

How I remember it A,T or  At and gato means cat or G-C

Chargaff’s Rule

In DNA, the amount of A = the amount of T and the amount of C = the amount of G

RNA

RNA is a copy of DNA that goes out into the cytoplasm and basically tells the cell which proteins to make. RNA has the same shape as DNA except that it is a single stranded the R stands or ribonucleic acid and that there are

Uracil (U)

Adenine (A)

Guanine (G)

Cytosine (C)

This animation helps a lot with explaining how DNA works to make protein http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter3/animation__how_translation_works.html

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

Video Review Glycolysis

Video Review on Glycolysis

These are videos on glycolysis and  the author or rather creator happens to be my lecturer for biochemistry at my university and I am not being biased when I say he did a great job. I can certainly attest to the fact that I struggled my royal off trying to understand and cram glycolysis in A-levels or form 6 kind of like pre university if you are not familiar.

It was tough so tough that when I had to do this topic it seemed completely new to me


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However because of my lectures methods I found myself understanding rather than cramming ….And the best advice I can give you if you are having problems is to clear your mind nothing is too difficult and just do it   …. Not for passing the course sake but try to fully understand what you are learning and doing … this method had worked wonders for me I can type this entire blog video review just based on my memory of the video and what I learnt and understood so YaY ME !!!

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Well firstly we have to appreciate that for each step of glycolysis there is an associated enzyme that helps catalyses the steps and since have done enzymes just by looking at the names and the reaction we can get an idea of what the enzymes in glycolysis are doing. Glycolysis can be viewed as well studying you have to give to get , meaning you have to give your time, effort and other things to get a good grade , a good job and well to pass a course. Now the purpose of glycolysis is to gain energy in the form of ATP and NADH and we will see how these are made and I don’t even need to go into detail you can look at this picture and get the jest of the entire pathway.

The video explains each step very closely so I have no idea what to say because the video speaks for itself. It explains each step in detail, it explains why  ATP can be produced at only 2 steps in the pathway and it also explains how much ATP is made how much is the net gain and also how NAD+  is regenerated. So please have a look.

The second video deal with the faith of pyruvate after it’s made it.

Under aerobic the pyruvate is converted to acetyl coA which enters the TCA cycle via the enzyme PDH in the link reaction.

Under anaerobic it is converted to lactate as in fermentation in muscles, in red blood cells and ethanol be produced as in the process with yeast.  And fermentation is a process which gains energy without the use of oxygen. And yes red blood cells do carry oxygen but the thing is they can’t use it since they have no mitochondria which is the site of aerobic oxidative phosphorelation or where ATP is produced (this is  products of TCA are used).It shows how red blood cell regenerates NAD+ via converting pyruvate into lactate.angry cell

The video also explains how lactic acid is formed in muscles after vigorous exercises this reaction is catalysed by LDH.

Finally the video gives an insight into how yeast makes ethanol from pyruvate by the following pathway:

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.

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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.

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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.

Enzymes 3

Enzymes Nomenclature or naming of enzymes:

There are 6 main classes of enzymes and each are assigned a number. From these classes are sub classes and sub sub-classes which are also assigned a number. When we lay out these numbers to which a particular enzyme belongs to we get what is known as the EC. Number or Enzyme Commission number and this was developed by the International Union of Biochemistry and Molecular Biology  to properly classify enzymes in an orderly manner. Without further ado the following is a list of the major classes of enzymes and the number each class was assigned:

EC 1- Oxidoreductases

EC 2- Transferases

EC 3- Hydrolases

EC 4 –Lyases

EC 5 –Isomerases

EC 6 –Ligases

Now you might be thinking OMG this is soo hard to remember (i did to) but let’s just look at it its only 6 categories come on man you can learn that (what i told myself and i did). I am a strong advocate against acronyms because for; 1 they confuse you and you sometime don’t remember the original name of the think you are trying to remember, 2 if you can remember an acronym you can defiantly remember your work so stop that craziness and just learn you work… anyways.

1)     oxidoreductase

Basically enzymes which catalyse oxidation reduction reactions, between substrates.

A + B → A + B

A is the reductant (electron donor) and B is the oxidant (electron acceptor)

Real life example: In  glycolysis

Pi + glyceraldehyde-3-phosphate + NAD+ → NADH + H+ + 1,3-bisphosphoglycerate

NAD+ is the oxidant, and glyceraldehyde-3-phosphate is the reductant. This process is perfomed by the enzyme glyceraldehyde-3-phosphate dehygrogenase .

2)     Transferase

Catalyses the reaction which involve group transfer reactions. They allow the transfer of a  from one molecule to another.

A–z + B → A + B–z

Real life example: In  glycolysis

Glucose + ATPàglucose-6-phosphate + ADP

And this reaction is conducted by the enzyme hexokinase.

http://www.youtube.com/watch?v=Tn7HJphCBgc

3)     Hydrolyses

Brings about hydrolysis reactions with braking of bonds (using H2O)

A–B + H2O → A–OH + B–H

Example : nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids.

4)     Lyases

Enzymes which catalyze the removal of group from substrates not using hydrolysis. Often forming a new double bond

Example: Decarboxylases that cleave carbon-carbon bonds

5)     Isomerase

Enzymes act an inter-conversion of one optical of geometric or positional isomer to other.

Example: In glycolysis

Dihydroxyacetone phosphate àglyceraldehyde-3-phosphate

This reaction is catalysed by triose phosphate isomerise

6)     Lagases

Catalyse the reaction in which two compounds linked with breaking of phosphate bond in ATP of any similar compound providing energy.

Enzymes can also be divided by their specify:

Those that react with molecules with specific function groups example alcohol groups are said to exhibit group specify, some enzymes act on certain bonds/linkages such as amide linkages these are enzymes that are linkage specific while others react on optical and steric isomers which are called sterochemical specific enzymes.

Did you know that some fruits, vegetables and just general foods are great sources of these enzymes and we can observe the activity of these enzymes by simply using the tissue of such foods some common ones found in fruits and did you know that these enzymes can also help with our overall health? The following is a list of fruits and their enzymes put forward by www.everynutrient.com so feel free to have a look.

Pineapple (bromelain) – The bromelain in most digestive enzyme supplements is
extracted from pineapple stems, since they have the highest concentration of the
nutrient.  The core and flesh of pineapple fruit contains good amounts of bromelain
as well.  Bromelain is a group of powerful proteolytic digestive enzymes and provides
several other health benefits, most of which are still under investigation.  Studies
have revealed that bromelain is also effective in fighting cancer growth.  It blocks
growth of a broad range of tumor cells in several types of cancer including breast,
lung, colon, ovarian, and melanoma.  Pineapple is also a great source of several
other nutrients including manganese, vitamin C, and potassium.

Green Papaya (papain) – Like the bromelain in pineapple, papain is a group of
proteolytic digestive enzymes.  Papain, often extracted from papaya, is another
major ingredient in digestive enzyme supplements.  Papain is also added to most
enzyme supplements that are formulated specifically for pain relief (arthritis, sports
injuries, etc.).  Papain may also have anti-inflammatory properties.  Papaya is an
excellent source of several other nutrients including potassium, calcium, vitamin C,
vitamin A, folate, beta-carotene, lutein, and zeaxanthin.

Mangoes (magneferin, katechol oxidase, and lactase) – In India, green mango
powder (amchur) is often used as a tenderizing agent for meats.  Mango lassi is a
common drink in Indian restaurants and it’s made from a combination of mangoes,
yogurt, and spices.  Not only are mangoes a rich source of digestive enzymes,
they’re also an excellent source of potassium, vitamin A, and beta-carotene.
Mangoes are also a good source of vitamin C, vitamin D, calcium, phosphorus,
magnesium, and fiber.

Kiwifruit (actinidin) – The actinidin enzyme in kiwifruit eases digestion due to it’s
proteolytic enzyme qualities.  Actinidin is also found in pineapples, papayas, and
mangoes.  Aside from kiwi being a great source of digestive enzymes, it’s also a
great source of several other nutrients including vitamin C (almost twice the amount
in an orange), magnesium, and potassium.  Kiwi also acts as a blood thinner without
the adverse side effects of asprin.

Figs (ficin) – Used as a meat tenderizing agent, ficin is another protease (proteolytic)
enzyme that eases digestion.  Ficin is found primarily in figs.  Figs provide several
other health benefits as well.  They’re an excellent source of fiber and a good source
of calcium, magnesium, and potassium.

Experiments and published papers coming soon along with structured multiple choice questions.

Enzymes

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“So enzymes are biological catalysis that speeds up chemical reaction via providing an alternate pathway with lower activation energy.”JM

Remember from my protein post we can see that enzymes are proteins but are all enzymes proteins?

Nope…. some are RNA molecules called ribozymes and then we can also use some antibodies called abzymes (but also proteins).

Do we need a faster reaction why not just wait for it to happen naturally?

Well the answer to that is because you will die  :/ see some reaction within our bodies may take up to a trillion years if enzymes were not involved , according to Dr. Richard Wolfenden a distinguished professor of biochemistry, biophysics and chemistry at the University of North Carolina without a particular enzyme, a biological transformation he deemed “absolutely essential” in creating the building blocks of DNA and RNA would take 78 million years.

Can you believe that? Obviously we would be a cluster of carbon in the ground by that time however because of enzymes this reaction and many more can take place in a matter of milliseconds. Wolfenden also said “Without catalysts, there would be no life at all, from microbes to humans,” and this is certainly true.

We can show how enzymes work on a simple graph like the one below where we see how enzymes physically lowers the activation energy and as you should know the activation energy is the energy need to start the chemical reaction and a lower activation energy allows the reaction to take place faster.

energy-level-diagram-activation-energy

So how exactly do enzymes work??

Enzymes attach to substrate via there active site and a molecule called an enzyme substrate complex is formed, this complex then quickly breaks down to form the product as well as the original enzyme. During this reaction bond or formed and broken and it is important to note that the enzyme substrate complex or intermediate has the highest energy since this is where the chemical reactions take place. We should also appreciate that there is no change to the enzyme, the enzyme remains the same after the reaction as it was before and when the product releases the enzyme moves on to another substrate molecule.

NOTE:

The active site is a cleft in the enzyme’s protein structure formed by the folding of amino acid residues, each active site is different this is because each enzyme contains a different protein structure and the properties of the active site that facilitate the combination of the substrate is due to the R groups of the proteins within the active site cleft, creating a complementary shape to the substrate that they bind to. Enzymes DO NOT make permanent bonds to substrate instead they bond via weak temporary bonds.

 

There are main theories about how enzymes and substrates react and bond:

1) Fischer’s lock and key hypothesis

This was developed by a scientist named Hermann Emil Fischer and he basically said that each enzyme it’s substrate fits perfectly together and complement each other forming the enzyme substrate complex and then the products which is a different shape from the substrate. The enzyme therefore acts as a lock and the substrate the key and only the key (substrate) for that lock (enzyme) would work or react to form a product. Once the products are formed they are released from the active site.


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Although from this theory we can see that enzymes are highly specific and can only react with a certain substrate which must be perfectly complementary it is too strict as we know that this may not be the case in nature as most molecules are not perfect copies of each other thus another theory explains how enzymes react in this situation.

2) Koshland’s Induced fit hypothesis

 This theory states that contrary to fischer’s theory all the enzyme’s active site and substrate are not perfectly complementary, they vary slightly however as the substrate approaches the enzyme changes the shape of its active site to fit the substrate and so the enzyme substrate complex is formed and the products are formed and released. This theory shows that enzymes are flexible and conformationaly dynamic molecules.


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Michealis –Menten Curve

 

The reaction between enzymes and substrates can be expressed on a curve call a michealis –menten curve and this curve plots the velocity of the reaction against the substrate concentration (velocity is the amount of product formed per unit time or the amount of substrate being consumed).  As the enzymes start to bind to the active sites the velocity increases and when all the active sites are occupied the graph remains constant, this point is called vmax and the enzymes are said to be saturated. This graph keeps all variables constant except the concentration of substrate. This graph forms a hyperbolic shape.

NOTE: This graph only shows the reaction for michealis menten enzymes of enzymes with one actives site present.

If an Allosteric enzyme were to be observed and plotted on the graph it would give a sigmoidal shape. Allosteric enzymes are those with more than one active site.

asset4

The black line shows the curve for an enzyme with one active site or a michealis –menten enzyme while the red show the curve for an allosteric enzyme.

This was the end of part one and honestly I never knew this much about enzymes who knew right… during cape (Alevels) we didn’t do much on enzymes unlike that of previous topics so this was all new to me but I coped well and I hope these notes help you . My next post will be a direct continuation from this and after that I will post 2 experiments I conducted recently …. Stay tuned hope you like 🙂

http://learning.covcollege.ac.uk/content/Jorum/MET_Enzyme-control_LM-1.2-05FEB08/page25.htm

http://www.med.unc.edu/biochem/news/without-enzyme-biological-reaction-essential-to-life-takes-2-3-billion-years-unc-study

http://www.activemotif.com/

Proteins

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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

Amino acids

AMINO ACIDS

Amino Acids as its name suggests as always these are molecules made up of an amino group, a carboxylic acid group and well and R group which varies to make each amino acid different. There are 20 different amino acids which can then be further divided based on their properties. These amino acids also carry standard 3 letter abbreviations as well and 1 letter abbreviations along with their names as seen in the table below:

Amino Acid        3 letter     1 letter
alanine                         ala       A
arginine                      arg        R
asparagine                asn        N
aspartic acid            asp        D
cysteine                     cys        C
glutamine                  gln        Q
glutamic acid           glu        E
glycine                        gly        G
histidine                     his        H
isoleucine                   ile        I
leucine                        leu        L
lysine                           lys        K
methionine               met       M
phenylalanine         phe       F
proline                       pro       P
serine                         ser        S
threonine                  thr        T
tryptophan               trp       W
tyrosine                     tyr        Y
valine                          val        V

From a chemical perspective each amino acid can be grouped together as follows and the group names are sort of self explanatory as to their speciality.
20-amino-acids1

When we come to biology they can be grouped into 2 main categories: essential and non essential. Essential amino acids are those which our bodies are not able to synthesis and so we need to get them from our diet and non essential amino acids are those which our body synthesis.

Essential Amino Acids    Non-essential Amino Acids
• Isoleucine                           • Alanine
• Leucine                                • Arginine
• Lysine                                   • Asparagine
• Methionine                         • Aspartic Acid
• Phenylalanine                   • Cysteine
• Threonine                           • Glutamic Acid
• Tryptophan                        • Glutamine
• Valine                                    • Glycine
• Histidine
• Proline
• Serine
• Taurine
• Tyrosine

Right about now you might be asking well why I am talking about amino acids and what are they really. Well amino acids are the building blocks for all proteins in our bodies. Meaning every cell, all enzymes and just about anything made of proteins are made of amino acids!!

Amino acids bond with other amino acids to form peptide bonds or a (-CONH-) bond during this reaction is a condensation reaction and a water molecule is lost and the 2 linked amino acids are called a dipeptide.

dipeptide-bond-formation

Bonding between amino acids can create long chains which are called polypeptides. Proteins are formed from a polypeptide or many polypeptide chains. However what makes each protein different is the sequencing of the amino acids in the chains.

Things to note
• Alanine is THE SMALLEST amino acid with its R group being hydrogen.
• Proline is the only cyclic amino acid besides the aromatic compounds.
• In order for polypeptides to be called a protein they must have a molecular weight of over 5000g/mols.
• Amino acids can form a zwitter ion form where the H from the carboxyl (COOH) group is lost to the amino group (NH2) forming a COO- group and a NH3+ group.
nz_vs_zw

And just so you easily remember the 20 amino acids here is a fun cool picture.

Capture

(This is just the beginning stay tuned for some interesting activities as well as proteins. )