Tca cycle/ krebs cycle/ citric acid cycle……………..

What is it???

Where does is take place???

What is its significance???

 

Image 98

The pyruvate that was formed in glycolysis  goes through oxidation and result in carbon dioxide and water using oxygen. All of this happens in the matrix of the mitochondria and involves the Kreb’s cycle.

First there is a transition stage  . In the matrix each pyruvate molecule enters and there is the conversion into an acetyl group.  These are carried by coenzyme A as acetylcoenzyme A. There are two carbon atoms in the acetyl  groups so when the pyruvate  which contains 3 carbons  is converted to the  acetyl which has two carbons there is the loss of a carbon. This is lost as a result of carbon dioxide in a decarboxylation reaction.  There is also a dehydrogenation  as there is the reduction of NAD.

STEP 1.  There is the combination of   the acetic acid subunit of acetyl CoA which has two carbon  with a 4 carbon oxaloacetate to form  the six carbon  compound citrate. After this step  due to the process of hydrolysis the coenzyme is released  so that it can be able to combine with other acetic acid molecule to start over the Krebs cycle

STEP 2.  Isomerization of the citric acid molecule takes place.  There is the removal of both a hydroxyl group  and a hydrogen molecule and this happen in the form of water. A double bond is formed between the two carbons until there is the replacement of the water molecules. And this result in the formation of isocitrate.

STEP 3.  At this stage an NAD molecule oxidizes  the isocitrate molecule. The hydrogen atom and the hydroxyl group causes the NAD molecule  to become reduced. There is the binding of the NAD  molecule and a hydrogen atom. The NAD also  takes away the other hydrogen atom leaving behind a carbonyl group. The resulting structure is not stable so there is the release of a carbon dioxide molecule and the resulting structure is a 5 carbon compound known as alpha-ketoglutarate.

STEP 4.  Here is where there is the return of the coenzyme A . It comes back to oxidize the alpha-ketoglutarate. There is another reduction of NAD to NADH  leaving with another hydrogen.  There is instability once again and to restore this a carbonyl group is kicked out as carbon dioxide and there is the replacement of a thioester  bond  between the previous alpha-ketoglutarate and the coenzyme A creating succinyl coenzyme A complex.

STEP 5. Being generous the water molecules gives its hydrogen atoms to coenzyme A. A greedy free phosphate floating group then pushes out the coenzyme A and this leads to the formation of a bond with the succinyl complex.

STEP 6. Here a molecule of Flavin adenine dinucleotide  (FAD) oxidizes succinate. This FAD takes away both of the hydrogen from the succinate forcing a double bond to form between two carbon atoms formingggggg……. fumarate.

STEP 7. Hmmmm  To the fumurate an enzyme adds water and this creates malate. This malate is a result of adding to a carbon a hydrogen atom. And then to the carbon that is next to the terminal carbonyl group the addition of a hydroxyl group

STEP 8. Woosh finally the last step…. A NAD molecule oxidizes the malate molecule.  The carbon that was initially carrying the hydroxyl group is now turned into a carbonyl group. The final product is the four carbon compound oxaloacetate. This compound can start over the Krebs cycle by combining with acetyl coenzyme A.

 

https://i0.wp.com/guweb2.gonzaga.edu/faculty/cronk/biochem/images/citric-acid-cycle-summary.gif

 Image 99

THE LINK BETWEEN CHEMIOSMOSIS AND THE GENERATION OF ATP IN THE MITOCHONDRIA!!!!!!!

 

  To understand how ATP is generated in the mitochondria by chemiosmosis, we need to break things down first.   

    Firstly, what is Chemiomosis?????????????????

 

This is when ions move across a selectively permeable membrane, down an electrochemical gradient. It is paired with ATP generation by moving hydrogen ions across a membrane when cellular respiration is taking place.

CELLULAR RESPIRATION

  Cellular respiration involves the breaking down of food (more specifically glucose) to yield energy. This energy is in the form of chemical energy and in the body. The cells of our body recognise this energy in another form known as ATP, so they convert the energy from the food we into ATP which they can use.

Image 100 

 

 There are a few terms that we should be familiar with at this stage, but if you’re not, here’s a quick reminder:

  • Glucose- this is the main energy source of the body and it is a sugar that consists of 6 carbons.
  • ATP- (Adenosine Triphosphate) – This is what we would call the main energy or “money source” of the cell. It has a large amount of energy in storage and it also transports that energy in the cell.
  • NADH An electron carrier with high amounts of energy. It is what transports the electrons made in Glycolysis and Kreb’s cycle to the Electron Transport Chain. In other words, “The Shuttle service.”
  • FADH2 Also an electron carrier with a high amount of energy, this is also a “Shuttle Service.”

Cellular respiration takes place in three main steps:

  1. GLYCOLYSIS

This is when the glucose molecule from food sources is divided into two molecules known as pyruvate. Two ATP molecules are made and also 2 NADH molecules. So for every 1 glucose molecule, we get pyruvate, 2 ATP and 2 NADH.

 

2. KREB’S CYCLE

Here the pyruvate molecule made in glcolysis is use to 2 ATP and some FADH2 and NADH are also made for the 3rd step.

 

3. ELECTRON TRANSPORT CHAIN

The NADH and FADH2 made previously are used to form a proton gradient which eventually forms 32 molecules of ATP.

 

Now that we have recapped what cellular respiration entails, we can now make the link between chemiosmosis and the generation of ATP in the mitochondria.

 

In the mitochondria of cells, there is something we would call a proton gradient, which is the inner membrane of the mitochondria.

  Electrons are journeying through the electron transport chain, hydrogen ions are pushed or pumped out from the mitochondria into a space known as the inter-membrane space.

 When this happens, a concentration gradient is formed or a more in depth term would be “proton motive force.”

Proton motive force is simply the energy that causes the movement of protons or the “driving force” of protons. 

This causes the protons to move from an area of high concentration to one of lower concentration by diffusion, which in turn, causes the ion to be diffused back into the cell by a process called ATP synthase.

ATP synthase is a form of enzyme that produces ATP by chemiosmosis and it is what allows the protons to be able to go through the membrane.

So to recap: ATP is made in cells that respire by an electrochemical gradient that is found across the inner membrane of the mitochondria. It uses the NADH and FADH2 as the energy source.

Now that the protons have moved back into the membrane by ATP synthase, this same energy that does this, supplies a sufficient amount of energy for ADP to join together with inorganic phosphate to thus form ATP (oxidative phosphorylation).

 This is what it mainly looks like………………………………………………..

Image 101

References for Images:

 

 

http://blog.cholesterol-and-health.com/2012/01/we-really-can-make-glucose-from-fatty.html

http://guweb2.gonzaga.edu/faculty/cronk/CHEM440pub/L30-index.cfm

http://apps.cmsfq.edu.ec/biologyexploringlife/text/chapter7/concept7.4.html

http://en.wikipedia.org/wiki/Electron_transport_chain

 

 

Nowwwwww here is where it gets trickyyyyyyyy!!!!!!!!!!!

Oh nooooo its MCQss…….

 Image 97

  1. Select the correct multiple answer using one of the following keys A,B, C,D or E

A. Only 1 is correct

B. 1 and 2 are correct

C. All are correct

D. 1,2 and 3 are correct

E. Only 4 is correct

Which of the following describe the lysosome organelle

  1. They exist  in animal cells only
  2. Contain both  proteases that break down protein and lipases that break down lipids
  3. It is the site where  aerobic respiration takes place
  4. It is composed of a network of microtubules

2. Which of the following statements about enzymes is not true?

A. In the lock and key hypothesis  the key is symbolic of the substrate

B. They speed up a chemical reaction

C. Products and substrate have the same shape

D. Enzymes are divided into 6 major categories

E. Some of them are actually RNA molecules

Feel free to place your answers!

References for Image:

http://alifetimeofwisdom.com/category/thoughts/

Enzymes 2

terminator21013

IMAGE 71

Welcome back folks, we did enzymes part 1, now it’s on to part 2.

YAYYYYYYYYYYYYYYYY!!!!!!!!!!!!!!!!!!!!!!!

To start off let’s continue with the features of enzymes. The catalytic power of enzymes was dealt with in part 1, so we will now focus on the specificity of Enzymes.

Try not to bite your tongue saying SPECIFICITY!!!!!

SPECIFICITY OF ENZYMES

A certain enzyme, is one that is very selective, we can also say that they are “picky” or “stush”. They are very selective on what substance they react with and also in the reaction they catalyse.

The substances that the enzymes work on are what we call SUBSTRATES.

IMAGE 72

Also, in a reaction where an enzyme is present, or, an enzyme catalysed reaction, there are NO by products, or waste products and all reactions tend to yield a great percentage of product.

The products that are formed from an enzyme catalysed reaction are also “stush enzymes”.

In the chemical reaction involving enzymes, the substrate, has to stick or bind to the enzyme by a process called MOLECULAR RECOGNITION.

All this is saying is that the substrate compliments or suits the enzyme perfectly, it’s like a match made in heaven. Like peanut butter and jam, like ice-cream and cake, like biology and chemistry. This way, they form a mutual relationship, they both benefit from each other.

IMAGE 73

The substrate binds to a specific area on the enzyme called THE ACTIVE SITE.

So, let’s talk about this active site!!!!!!!!!!!!!!!!!!!!!!

The active site is a pocket or cleft that is made to recognize certain substrates and thus, catalyse chemical transformation.

It is formed in the 3D structure by the group of a variety of Amino Acid residues. These Amino Acid residues are either adjacent or not in the primary formation.

At the ACTIVE SITE, the substrate associates or mingles with the active site via hydrophobic, electrostatic, hydrogen and Vanderwaal’s interactions. These are the same forces that cause the structure of protein to be stable and they are all weak forces of attraction.

The active site of enzymes can also, provide catalytic groups. These groups are the “R” groups of Amino Acids residues and they give certain interactions and allow chemistry which stabilizes the transition state form for the chemical reaction to occur.

When a substrate binds together with an enzyme at the active site by the weak forces we discussed above, a complex is formed. This complex is called THE ENZYME SUBSTRATE COMPLEX.

IMAGE 74

There are different Hypotheses models to explain how enzymes are catalytic and specific.

The two major ones are:

  1. THE FISCHER’S LOCK AND KEY HYPOTHESIS
  2. THE KOSHLAND’S INDUCED FIT HYPOTHESIS.

Let’s talk about Fischer’s hypothesis first; it implies the lock and key method.

Look at the figure below!!!

494a8e8421b688f627e00d62c7fd6522

IMAGE 75

In the diagram, we can clearly see that the key is analogous to the substrate, while the lock is the enzyme. The key fits into the lock perfectly. In the same way, the substrate fits into the enzyme perfectly forming the enzyme substrate complex. There shape coincides so the complex is formed. If however, another substrate was to try to fit into the active site of this enzyme, the complex would not be formed since the substrate doesn’t match the enzyme’s active site.

In the same way, my car keys can only start my car, if I were to try to start someone else’s car with my keys nothing would happen because they DO NOT MATCH.

The product that is formed, is different from that of the substrate in terms of shape, thus, it is unable to fit into the active site and is released for another substrate of the same shape to bind to the active site once again.

THE INDUCED FIT HYPOTHESIS!!!!!!!!!!!!!!

This hypothesis is self explanatory. The fit of the substrate to the active site is induced. Initially, it does not have a perfect fit; however, as the substrate is brought towards the active site or is on its way to the active site, it induces its shape into the enzyme. The active site now becomes an exact fit when the substrate is in the active site of the enzyme.

The products formed, also have a different shape so they are set free for more substrates to enter.

The diagram below shows the Induced Fit hypothesis:

https://i2.wp.com/upload.wikimedia.org/wikipedia/commons/thumb/2/24/Induced_fit_diagram.svg/648px-Induced_fit_diagram.svg.png

IMAGE 76

 

THE FACTORS AFFECTING REACTION RATE OR REACTION VELOCITY.

There are a number of factors that can affect the rate of reaction velocity, involving enzymes that is. They include:

  • Ø Substrate concentration
  • Ø Enzyme concentration
  • Ø Temperature
  • Ø pH

SUBSTRATE CONCENTRATION

IMAGE77

In the graph above, the main focus is on the blue line known as Michaelis Menden curve. At first, as substrate concentration increases, reaction rate increases steadily. This is because; there are more collisions between substrates and the active site, more effective collisions. The point at which the line plateau or levels off, is the point where saturation level has been reached.

That is, the amount of substrate level is continuously increasing but there are no more active sites available so they have to wait on the next available active site. The reaction is still in process; however, the rate is not increasing. In this illustration, the only variable is the substrate concentration. Temperature, enzyme concentration and pH are kept constant.

References for Images:

https://biochem1362blog.files.wordpress.com/2014/02/terminator21013.jpg

http://bltshop.deviantart.com/art/Enzyme-Substrate-173836053

http://cheezburger.com/6579483392

http://roadshowhaberleri.com/wp-content/gallery/most-mobile/enzyme-active-site-substrate-and-product

https://biochem1362blog.files.wordpress.com/2014/02/494a8e8421b688f627e00d62c7fd6522.jpg

http://emptyemptyme93.blogspot.com/2010/08/lock-and-key-paradox.html?zx=ae0a35ad410040b5

http://csls-text.c.u-tokyo.ac.jp/active/07_03.html

 

Enzymes 1

ENZYMES PART 1

IMAGE 64        

Enzymes are biological catalysts. In simpler terms, they are very little structures that perform a very important job in the body; they speed up the chemical reactions that take place in different areas of our body by providing a different pathway with lower activation energy. This activation energy is simply the amount of energy needed to start a chemical reaction. They are essential for life since they speed up a number of reactions that we all need to survive. I know what you are thinking………………………………………………………………….

Well take a lot at the diagram below!!!!

IMAGE 65

In this diagram the red curve indicates the activation energy needed to convert reactants to products. If we were to compare the red curve with the green curve, it is clear to see that the activation energy of the green curve is a lot lower than that of the red curve, therefore, less activation energy needed to convert reactants to products.  Note also that the amount of reactants and products remains the same. SO, although the enzyme speeds up how fast reactants are converted to products it does not change the amount of reactants or products and remains itself unchanged.

IMPORTANCE OF ENZYMES!!!!!!!!!!!!!!!!!

In cellular respiration, sucrose (table sugar) and oxygen are converted to carbon dioxide, water and of course energy by the following reaction;

C12H22O11  + 12O2————à 12CO2  +   11H2O + ENERGY

This reaction occurs in seconds in the cells of the body, however, table sugar is able to stay on the shelf or on the table for years and years. The mere fact that in the body, a reaction like this can occur in seconds compared to years outside the body highlights the many talents and importance of enzymes. Some of you may be thinking about stocking up on lots of sugary stuff to get energy from looking at this reaction but it also has a down side to it, so be very careful.

Most enzymes are proteins!!!!!!!!!!!

In this sense, they are called biomolecules.

Some RNA molecules pretend to be enzymes.

Yes it’s true some RNA (Ribo Nucleic Acid) molecules can act as enzymes. We can also call them RNA catalysts, or biologically, RIBOZYMES and although they are not enzymes they are qualified for their acting role in a number of ways:

IMAGE 66

  • They are substrate specific( which we will discuss in more detail later on)
  • They speed up the reaction rate
  • They come out from the reaction just as they went in, they don’t change their structures.

There are also ABZYMES, which are antibodies that have features similar to catalysts. *Antibodies are a special kind of protein that is found in fluids of the body, they are also blood travellers.

IMAGE 67

TRANSITION STATE.

The transition state in a reaction is the point at which the substrate is no longer a substrate, that is, it is on its way to becoming a product but it is still not fully converted to a product. Let’s use an analogy to break things down a little.

The popular TV series TEEN WOLF!!

IMAGE 68

In the show, a teenage boy named Scott discovers that he is half human: half wolf and it certain instances, he undergoes a change from human to wolf. The point at which Scott’s nails get long and sharp, his body becomes covered with hair, his back arches and his teeth become long and sharp and deadly, that extreme point of pain where all these events are occurring is his transition state. He is not yet a full wolf but he is no longer a human teenage boy.

TRANSITION STATE

Let’s apply this to chemical reactions now, the transition state is the point where the reactants or should we say atoms are at its highest level of organization in the middle of the structure of reactants and that of the products. So, as soon as some bonds in a reaction are being broken, some are also being formed.

Enzymes have three features that make them unique:

  1. They have catalytic power
  2. They are specific (Specificity)
  3. They are regulators

For now, we’ll focus on the catalytic power of enzymes.

A lot of enzyme catalyzed reactions are very effective, an enzyme can make a reaction occur over ONE MILLION times faster than if the reaction had no enzymes present.

WOWWWWWWWWWWWWWWWWWWWW!!!!!!!!!!

SO HOW THEN DO WE NAME ENZYMES???????????????

 

Image 69

 

The nomenclature for enzymes can sometimes be easy. Some enzymes are named based on the substrate they work on.

For example: Lipase is the enzyme that hydrolyses lipids and sucrose is the enzyme that hydrolyses sucrose.

Simple enough right??????

It can get even simpler, anything ending with the suffix “ase” are most likely enzymes in biochemistry.

What about trypsin and pepsin??  They are also enzymes but their name doesn’t provide us with any clues that they are enzymes.

To make things more complicated, some enzymes have more than one name, for example: Glyceraldehyde-3- phosphate, Triose phosphate and 3-phosphoglyceraldehyde refers to the same enzyme.

So how are we supposed to deal with a situation like that?????????

Thankfully, a brilliant group of people from the International Union of Biochemistry and Molecular Biology, or IUBMB, came up with a system of naming. In this system the enzymes are put into 6 main classes.

Each class has subclasses and each subclass has sub-subclasses.

The classes, subclasses and sub- subclasses, as well as single participants are given a specific number, in this way, a chain of up to 4 numbers relate to a certain enzyme or the Enzyme Commission number (EC).

The six main classes are illustrated below:

Class What it catalyses
1. Oxidoreductases
  • redox reactions
2. Transferases
  • transfer of molecules
3. Hydrolases
  • cleaving of bonds by adding water
4. Lysases
  • reactions where a double bond is formed by removing a group or adding a group a double bond
5. Isomerases
  • reactions where intramolecular arrangements are present
6. Ligases/Synthesases
  • reactions that join 2 molecules to each other

THAT IS THE END OF ENZYMES PART 1 FOLKS!!!!!!!!!!!!!!!!!!

STAY TUNED FOR PART 2………………………..

IMAGE 70

References for pictures:

 

http://www.quickmeme.com/meme/36fg4g/

http://www.biologyreference.com/Dn-Ep/Enzymes.html

http://www-ssrl.slac.stanford.edu/research/highlights_archive/ribozyme.html

http://www.wiley.com/college/boyer/0470003790/cutting_edge/catalytic_ab/tumor_drug.gif

http://blog.zap2it.com/frominsidethebox/2012/08/teen-wolf-finale-recap-death-and-fate-in-beacon-hills.html

http://funnyanimalz-90.blogspot.com/2011/06/funny-chimp-photos.html

http://www.keepcalm-o-matic.co.uk/p/keep-calm-and-we-ll-be-right-back-3/

protein funny

IMAGE 47

AMINO ACIDS AND PROTEINS 1

 

What are Proteins?

Proteins are macromolecules or large biological molecules that are made up of a single or a number of chains of amino acids.

 It’s has a number of important functions in living organisms:

 . As Receptors, receptor proteins are basically used for the intercommunication between cells carrying messages to cells around the entire body, some examples are cytokine receptors and guanine nucleotide binding protein receptors.

 . Channels – channel proteins or ion channels forms pores that help in establishing and controlling a small voltage gradient across the plasma membrane of cells .These pores allows ions and small molecules to pass though via the process of diffusion.

 . Storage – an example of this is ferritin which is a protein that stores iron in the liver as well as release it in a controlled fashion..

.Enzymes – there are many different enzymes which are responsible for catalyzing many major biological reactions.

. Structural Function – these are fibrous and provide support, examples are collagen and elastin in skin and provide support in connective tissue and keratin in hair.

. Immune Response – there are specalised proteins which are called antibodies and help the body defend against antigens.

. For Transport – a well known organic molecule called hemoglobin which is the taxi or transport vessel for oxygen as well as carbon dioxide around the body.

  Image

 IMAGE 48

  Now let’s talk about the stuff that make up the proteins.

 

 What are amino acids?

 Image

IMAGE 49 

Amino acids are very important organic compounds which are made up of an amine (-NH2) and carboxylic acid (-COOH) functional groups, a hydrogen H and an R group which is specific to each amino acid.

Image

example of an amino acid basic structure

 IMAGE 50

  

Ok now these R groups which make each different type of protein different from each other.

  

The R Groups

 Image

 IMAGE 51

 NON POLAR ALIPHATIC R GROUPS

 

This group is also hydrophobic and that increases as the number of C in the hydrocarbon chain increases. The name of the amino acids in the groups are glycine, alanine, proline, valine, leucin, methionine and isoleucine, amino acids prefer to remain inside the protein molecule but glycine and and alanine are like rebels and are ambivalent which means they can be inside and outside.

 

 POLAR, UNCHARGED R GROUPS

This group consists of five amino acids serine, threonine, cysteine, asparagine and glutamine. These are polar because of the oxygen O which is much more electronegative than the carbon C and hydrogen H thus polar bonds form.

 

 AROMATIC R GROUPS

 This group of amino acids are relatively non polar to a degree and all absorbs ultraviolet light. The amino acids in this group are tyrosine, tryptophan, phenylalanine.

 

  POSITIVELY CHARGED R GROUPS

  This group includes lysine, arginine and histidine. They have pH values pKa‘s and are very hydrophilic. They are positively charged because of the  positive charge from the group ammonia. 

 

 NEGATIVELY CHARGED R GROUPS

 This groups consists of aspartate and glutamate and there is an acidic group.

 Image

IMAGE 52

ZWITTERION

 Amino acids have nonionic form and a zwitterionic form. This happen when the proton which is the hydrogen H on the carboxylic group is lost and the amino group NH2 will accept it.

   https://i2.wp.com/images.tutorvista.com/cms/images/44/internal-salt.png

IMAGE 53

 Essential Amino Acids

 There are 20 amino acids essential for the human body and 10 of the 20 the human body cannot produce and must rely on a proper diet to obtain them.

 

Complete Proteins

 

Complete proteins are protein food source that contain all the essential amino acids that we can’t produce on our own. Proteins from animals alone with the exception of beans have all the essential proteins.

 Image

IMAGE 54 

Incomplete Proteins

 These are proteins that do not contain all the essential amino acids and are found in vegetables with the exception of beans.

Ninhydrin Reaction

This is a reaction that tests for amino acids. Amino acids are mostly colourless but if you conduct the ninhydrin test and it is positive it give a purple colour which says that amino acids are present.  is a white or yellow toxic, crystalline or powdery compound that reddens when heated above 100°C and is soluble in water and alcohol.

 Image

 IMAGE 55

 

Amino Acids and Proteins 2

 

Proteins can have four levels of structure.

Primary

Secondary

Tertiary

Quaternary

quaternary-structure-of-protein

IMAGE 56

The level of the structure is based on the level of folding due to;

Hydrogen Bonding

Electrostatic Forces

Disulphide bonds

Hydrophobic forces

Hydrogen Bonding

Bonding between hydrogen and an electronegative atom like nitrogen or oxygen in protein folding. Bonds range from .27 to .31 nm. Hydrogen bonding is stronger than van der Waal forces but weaker than covalent bonds.

Electrostatic forces

Interactions between groups of opposite charge. The bond is referred to as a salt bridge.

 Disulphide Bonding

Formed by the oxidation of two cysteine residues to form a cystine residue. Also called a disulphide bridge

Hydrophobic Forces

Interactions between non-polar molecules in order to avoid contact with water.

tertiary_structure

IMAGE 57

Primary Structure

This level of structure has no folding. It is a linear sequence of amino acids joined by peptide bonds. The primary structure tells you what amino acids are present and what sequence they are in.

primary-structure-of-a-protein

IMAGE 58

Secondary Structure

This level of structure has regular folding of the polypeptide chain. This folding can either be  helices and beta pleated sheets. Both are held together by hydrogen bonding.  Alpha helix is a conformation where the amino acids are arranged helical. Hydrogen bonding occurs between the carbonyl oxygen in each peptide bond to the hydrogen on the amino group. In the alpha helix there are 3.6 amino acids per turn. This conformation is more common because there is optimal use of internal hydrogen bonding which gives the helix stability. Beta pleated sheeting is formed by hydrogen bonding between peptide bonds of the polypeptide chain or between different polypeptide chains. The polypeptide is pleated with the amino acids above and below the sheet. Beta pleated sheets can be parallel or anti-parallel. The parallel beta pleated sheet has both C-terminal ends running along the same side while the anti-parallel beta pleated sheet has the C-terminals alternating.

IMAGE 59

Tertiary Structure

This level of structure has irregular folding of the polypeptide chain. Hydrophobic forces are the main cause for such folding. The chain folds itself in way that the hydrophobic side chains are in the interior with the polar molecules on the outside. Besides hydrophobic forces there are electrostatic forces, hydrogen bonding and covalent disulphide bonds.

interactions involved in tertiary strucutre

IMAGE 60

Quaternary Structure

Quaternary_Protein_Structures

IMAGE 61

This is a level of structure containing more than one polypeptide chain eg. Haemoglobin. Theses chains are held together by hydrogen bonding, electrostatic forces, hydrophobic forces and disulphide bonds.

Denaturation of Proteins

2f6a9abcf84141bf47246a4549726a867de7a73023f3f61c2b72c43d84a50271

IMAGE 62

The disruption and or destruction of the quaternary, tertiary and secondary structures of proteins. The primary structure is not changed. When a protein is denatured the bonds are broken and can return natural structures under good conditions. Under extreme conditions, however, the protein cannot return to its natural state. Proteins can be denatured by heat, UV radiation, some organic solvents (ethanol and acetone), strong acids or bases, urea and agitation.

Now that you know about proteins, go forth into the world and share the good news about proteins!!!

prot

IMAGE 63

References for pictures

https://trainelite.com/10-hilarious-supplement-memes/

http://www.kulfoto.com/funny-pictures/34960/transport-proteins-and-a-cell-wall

https://biochem1362blog.files.wordpress.com/2014/02/20590244.jpg

https://biochem1362blog.files.wordpress.com/2014/02/image4.gif

https://biochem1362blog.files.wordpress.com/2014/02/f_a5ab36acd90fe560059f9d8a2c730175r18-logo.jpg

https://biochem1362blog.files.wordpress.com/2014/02/negativelychargedrgroup.jpg

http://images.tutorvista.com/cms/images/44/internal-salt.png

https://biochem1362blog.files.wordpress.com/2014/02/funny-bear-grylls-lion-king.jpg

https://biochem1362blog.files.wordpress.com/2014/02/biuret2.jpg

https://biochem1362blog.files.wordpress.com/2014/02/primary-structure-of-a-protein.png

https://biochem1362blog.files.wordpress.com/2014/02/quaternary-structure-of-a-protein.png

https://biochem1362blog.files.wordpress.com/2014/02/tertiary_structure.jpg

https://biochem1362blog.files.wordpress.com/2014/02/importance_f3.gif

https://biochem1362blog.files.wordpress.com/2014/02/interactions-involved-in-tertiary-strucutre.jpg

https://biochem1362blog.files.wordpress.com/2014/02/quaternary_protein_structures.jpg

https://biochem1362blog.files.wordpress.com/2014/02/2f6a9abcf84141bf47246a4549726a867de7a73023f3f61c2b72c43d84a50271.jpg

https://biochem1362blog.files.wordpress.com/2014/02/prot.jpg

What are Carbohydrates????

IMAGE 26

They are made up of carbon and water and have the formula (CH2O)n

The functions  of carbohydrates are

Energy source–  Monosaccharides and disaccharides are broken down to form glucose and sucrose

Storage–  Starch and glycogen are the main storage polysaccharide

Remember — Starch is used by plants while Glygogen is used by animals.

When glucose concentration in the body is high the pancreas produces insulin. This converts the glucose into glycogen and it is then stored in the liver and muscle. The secretion of insulin is VERY IMPORTANT  as it is the only hormone that lowers the blood glucose level. When insulin production is low  this result in diabetes mellitus .

When the glucose concentration is low  the hormone glucogon is produced. This converts the glycogen into glucose.

Structure-  The most significant component of the cell wall in plants is cellulose.  It is a polymer of β-D- glucose. Approximately 50% of  the carbon found in plants is in cellulose.  It has tremendous tensile  strength.  This protects the cell and prevents it from bursting when osmosis occur and water enters.

Chitin  -This is found is some fungi  and animals , the arthropods. It is made up of bundles of long parallel chains similar to cellulose.

Precursor molecule–  It is involved in the making of other biomolecules.

Carbohydrate metabolism:  Glycolysis

IMAGE 27

Monosaccharide these are simple sugars that contain  many OH groups.  Monosaccharide with three carbons are called triose, with four tetrose , with five pentose, with six hexose.

 

                                                       IMAGE 28

Disaccharides is formed when two monosaccharide  combine through condensation.

Oligosaccharide contains a few monosaccharide that are linked covalently 

Polysaccharide – This is polymers made up of chains of monosaccharide units.

 

                                               IMAGE 29

There are two types of monosaccharide

Aldose and Ketose…

Aldose  contains an aldhyde group at one end CHO

Ketose contains a keto group C=O

IMAGE 30

Chiral compound- is where there are  four different groups attached to a carbon. There are mirror images of each other.

 

IMAGE 31

D AND L designations???

This  refers to the arrangement about the single asymmetric carbon in glyceraldehyde, where the asymmetric carbon had four different group attached to it. The OH group can be present on two different sides of the asymmetric carbon. If on the right hand side , it is called a D isomer , if it is on the Left hand side it is called a L isomer.

 

IMAGE 32

Whenever you have sugars that contain more than one chiral carbon the D or L configuration is usually the chiral carbon, that is the furthest from the aldehyde or ketone group.

D and L are mirror images of each other

Points to note: When aldehyde reatcs with alcohol it forms hemiacetal

                         When a ketone reacts with an alcohol is forms hemiketal

 

IMAGE 33

Diabetes????

 

IMAGE 34

What is it?  It is a disease where person has high blood glucose due to low insulin production or as a result of the body cells not responding to insulin.

There are three types

  1. Type 1  – There is no production of insulin in the body.
  2. Type 2- Insufficient amounts of insulin is being produced in the body for normal functioning.
  3. Gestational Diabetes- This occurs during pregnancy.  In some women glucose levels are very high and adequate amounts of insulin is not produced to carry all the glucose into their cells, this leads to high glucose levels.

Do you have it?

 Frequently urinating?

Always thirsty?

Always hungry?

Feeling tired?

Seeing blurry?

Long healing cuts or bruises?

Are you losing weight even though you are consuming more food?

 Is there a tingling, a pain or are you getting a numbness in your hand or feet?

 

CARBOHYDRATES PART 2

 

IMAGE 35

When you hear the word carbs, what comes to mind????????

Looks good doesn’t it, but looks can be very deceiving sometimes. Because too much of this and no exercise can lead to…………………….

 

IMAGE 36

They are good for you to a certain extent, that is in the right amounts at the right times but i like to call them “THE DELICIOUS DEVILS”.

  Let’s dig deeper to find out more about carbohydrates……….   

GLYCOSIDIC BONDS!!!

  A glycosidic bond is formed when two monosaccharides join together using condensation. The two OH or hydroxyl groups line up side by side, where one combines with a hydrogen atom from the other and form a water molecule. An “oxygen bridge” is formed joining the two molecules together forming a disaccharide.  In alpha glucose the OH group is always below.

DISACCHARIDES

  “Di” here, meaning two, so a disaccharide is two monosaccharides joined together by a glycosidic bond. The three main dissaccharides that we should know are: maltose, lactose and sucrose.

MALTOSE

 Maltose is formed by the joining of two glucose molecules. (Maltose = glucose + glucose). It is a disaccharide with 1-4 glycosidic bonds. That is the glycosidic bond is formed between the 1st carbon on one glucose molecule and the 2nd carbon on the other.

 

IMAGE 37

Here, you can see that the oxygen bridge forms perfectly between the two glucose molecules, since their OH group is at the bottom.

SUCROSE

Or what we know as “table sugar”

IMAGE 38

Sucrose is a combination of glucose and fructose. Glucose which is an example of an aldose, that is it has an aldehyde group has an anomeric, carbon 1, while fructose, which is a ketose, meaning it contains a ketone group, has an anomeric carbon 2. So the glcosidic bond is formed on carbon 1on glucose and carbon 2 on fructose.

  This causes sucrose, to be a non- reducing sugar, since both anomeric carbons are involved in the glycosidic bond, or in other words, there are no free anomeric carbons. It looks like this………………

IMAGE 39

LACTOSE

Lactose is what we call “milk sugar”

                                                                           IMAGE 40  

Lactose is a combination of glucose and galactose, it is formed by a beta 1-4 linkage. Glucose has its OH group below while galactose has its OH group above, so for them to come together, the galactose has to be flipped upside down.

                                 IMAGE 41

The “z” formation shows that the galactose is being flipped. Lactose is the main energy source that is found in nearly all mammalian milk, so it is the also the major food and energy source for growing and developing babies.

 Staying on the topic of lactose. Let’s talk about Lactose intolerance.

LACTOSE INTOLERANCE

 

                                         IMAGE 42

Lactose intolerance is “serious business”, might be a bit nasty but it’s serious.

 We all vary in the amount of enzymes we have in our stomach that digests dairy products. This enzyme, known as lactase, lessens as we age, however one out of two things causes lactose intolerance:

  • The body is producing less lactase enzymes
  • The enzymes, lactase, are not working properly

If this is happening in your stomach, then the lactose in the dairy you consume, is not being broken down. When this happens, the lactose stores water causing bloating, then all this water wants to come out immediately so you get diarrhoea. In addition to that, bacteria love to respire on lactose so the result of that is gas. Not the useful ones, the ones to make you feel to………………………….

 

                                              funny people running

                                                                                     IMAGE 43

So what to do if you know that you cannot consume dairy, the safest thing to do is to stay away from it although it might be very difficult since not everything you eat will say whether or not it is lactose free.

  When that happens walk with your resources…………………………………………

 

                                                                     IMAGE 44

POLYSACCHARIDES

These are polymers (a larger molecule composed of smaller ones, that are chemically bonded together), made up of many monosaccharides formed by condensation reactions and glycosidic bond formation. The three main polysaccharides are:

  • Starch
  • Glycogen
  • Cellulose

STARCH

This is the glucose storage unit specific to plants only. It is made up of amylose (a spiral shaped polysaccharide made up of D glucose with no branches and a 1-4 alpha linkage) and amylopectin ( a polymer  of glucose with a lot of 1-6  branching).

   The types of starches vary according to the proportion of amylose and amylopectin that it contains.

GLYCOGEN

This is the where glucose is stored in animals only and is relatively similar to amylopectin, however, glycogen has more alpha 1-6 branches, that is , every 10 glycosyl residue (every 10 units). This allows the quick release of glucose from glycogen stores in times of need. Animals, require much more energy output than plants, thus, the ability to move glucose to the areas of need from the glycogen stores is of major importance.

 https://i0.wp.com/ppcdn.500px.org/741583/3f46e813281ff81849783df1d9e88db8c21fea41/5.jpg

                                                                                              IMAGE 45

This requires a lot of energy, so bring on the glucose.

CELLULOSE

This is what makes up the cell walls of plants. It is made up of long, linear chains of glucose that has beta 1-4 linkages. As compared to starch and glycogen, it plays a structural role and not a storage role. In cellulose, every other glucose is flipped, this is because of the beta linkage (the OH group being above).

   There are a lot of hydrogen bonds within cellulose which helps it to be straight and rigid and filled with crystalline structures in thick bundles, which we call micro fibrils. This provides it with high tensile strength, meaning, they can stretch without tearing or bursting. Perfect for plant cell wall which has to undergo hydrostatic conditions (water coming into the cell).

                          IMAGE 46

THAT’S ALL FOR NOW FOLKS. HOPE YOU HAD FUN LEARNING ABOUT CARBOHYDRATES!!!!!

References for pictures

http://www.bing.com/images/search?q=funny+carbohydrates+picture&FORM=HDRSC2#view=detail&id=5CFB6ADDE34AABD5F0D8DFCABE820C928A0B4E0E&selectedIndex=6

http://www.bing.com/images/search?q=glycolysis+picture&qs=n&form=QBIR&pq=glycolysispicture&sc=0-0&sp=-1&sk=#view=detail&id=BC6A847C7B66D1DF1EB5B642D6E15B6312E425C1&selectedIndex=51

http://www.bing.com/images/search?q=glucose+fructose+and+galactose++picture&qs=n&form=QBIR&pq=glucose+fructose+and+galactose+picture&sc=0-15&sp=-1&sk=#view=detail&id=F8A5A54D3B96792743C22BB2DE17252B42B6B80B&selectedIndex=2

http://nychieee.blogspot.com/2008/08/summary-of-chapter-52.html

http://www.mikeblaber.org/oldwine/BCH4053/Lecture12/Lecture12.htm

http://lawrencekok.blogspot.com/2011/06/ib-chemistry-stereoisomerism-optical.html

http://www.ncl.ac.uk/dental/oralbiol/oralenv/tutorials/polysaccharides/basics.htm

http://eduframe.net/andc/biology/Sunita-Bio/carbohydrate%20ODL.htm

http://www.dumpaday.com/random-pictures/funny-pictures/funny-pictures-34-pics/

http://paulsjourneytolife.blogspot.com/2012/06/day-74-carbohydrates.html

http://www.chrismadden.co.uk/food/fat-man-food.html

http://www.pearsonhighered.com/mathews/ch09/maltose.htm

http://www.starch.dk/isi/starch/sugar.asp

http://cnx.org/content/m44400/latest/?collection=col11448/latest

http://www.healthguru.sg/general/nutrition-information-milk-condensed-evaporated-coconut-soy-whole/

http://www.scienceofcooking.com/lactose_intolerance.htm

http://funlexia.com/2012/07/12/am-i-lactose-intolerant/

http://thenutsnet.com/funny-people-running.html

http://www.funtroll.com/in-case-of-diarrhea-apocalypse/

http://www.bing.com/images/search?q=cheetah+chasing+animal&qs=n&form=QBIR&pq=cheetah+chasing+animal&sc=0-0&sp=-1&sk=#view=detail&id=4A78075795AA77127558DAE880F1AF96B3CCC096&selectedIndex=14

http://www.bing.com/images/search?q=starch+cellulose+and+glycogen&qs=n&form=QBIR&pq=starch+cellulose+and+glycogen&sc=3-29&sp=-1&sk=#view=detail&id=8A92487918915EBD64E90C186B6F19B89CD3E9F7&selectedIndex=10

 Neurodegenerative diseases a growing concern…

 

Reference:

“Protein aggregation and degradation mechanisms in neurodegenerative diseases”

Accessed January 27, 2014. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601466/

 

                 IMAGE 23                                        

Have you or a member of your family been forgetting important events lately?

Has it been a dilemma in their life?

                                      It is possible that it is due to a neurodegenerative disease such as Parkinson’s or Alzheimer’s which are increasingly becoming

common in society ?

 

Neurodegenerative diseases are the gradual failure of the normal function of areas of the brain. As the name suggests, “neuro” means nerve cell or neuron and the meaning of “degenerative”  is the overtime loss of brain function.  How is the loss of function in the brain caused?  Within regions of the brain extracellular or intracellular components are formed from the collection of disease- specific proteins.  That is the deposition of abnormal protein.

What are the contributing factors?  Well, neurodegenerative disease is either brought about by genetic mutations or environmental stresses.

How does the human body deal with such diseases? The normal functioning of the human body allows mechanisms in which it is able to effectively resolve misfolded proteins by the protein quality control system or PQC. This system detects the misfolded proteins and takes action by either unfolding or degrading it, in which the peptides and amino acids are regenerated. However in the case of neurodegenerative diseases the PQC system is overwhelmed and thus more proteins are accumulated that unfolded.

       IMAGE 24

Is there such a thing as a cure?  There is still no definite cure for such diseases or disorders, scientists have been able to develop treatments, however these only gradually reduce the progression of the diseases.

 References for pictures

http://www.bing.com/images/search?q=Alzheimers+is+no+joke+I+forgot+what+i+was+going+to+type+funny+image&qs=ds&form=QBIR#view=detail&id=D4A57EEDEDD726DE80945A52041D980C2B47C779&selectedIndex=0

http://ehp.niehs.nih.gov/120-a110/

 

Cytoplasmic Streaming

 

IMAGE 18

Do you know what is Cytoplasmic Streaming??????????????     

  Also known as Protoplasmic streaming, involves the movement of cytoplasm throughout the cell facilitating diffusion at a quick rate. This allows the cell to grow larger than the expected surface area to volume ratio without being harmed. Recall that as the surface area increases the volume increases thus restricting the size of a cell. Cytoplasmic streaming allows cells to jump this hurdle. The movement of the cytoplasm causes the movement of materials and organelle around the cell therefore allowing for diffusion to occur at a fast rate even with a large surface area to volume ratio. This is done by motor proteins which are responsible for the movement of proteins and vesicles. Myosin motors, a family of motor proteins acts on actin filaments to generate contractions in the cell. Other motor proteins like kinesin allow movement of organelles and vesicles around the cell.

IMAGE 19

 

References for pictures

http://www.bing.com/images/search?q=funny+picture+thinking&FORM=HDRSC2#view=detail&id=55C84A124B78D3B36E52C441C43E3E8F0C2FCC93&selectedIndex=0

http://www.bing.com/images/search?q=picture+of+cytoplasmic+streaming&qs=bs&form=QBIR#view=detail&id=2BA38C3DF40D6448B1A043699677805CC8DB98CC&selectedIndex=0

 

 

About Us

IMAGE 1.

 

BIOCHEMASTERZ- Our group is a lot of fun as each member is unique and has many diverse ideas. There are four girls and one lucky boy in our blog. Coming from different respective homes and having different cultural background we all share one thing in common a great passion for the biochemistry course.

Ar  –I am 21 years old and is pursuing a degree in biology at the University of The West Indies. I’m from Princes Town and attended Presentation College San Fernando. I never give up on something that I really want but I always try not to bite more than I can chew. I’ve always had an interest in biology, I also love music which is why I play and write music/songs. Additionally I’m the treasurer of a charity organization called Sunnyside Foundation. I’m not the simplest of persons but I’m easy to get along with. I am enjoying the Biochemistry class thus far, as of now I can’t say much about the class but it does hold my attention which is a good thing.

 ReI became intrigued with the science behind common everyday things and since then followed through by studying science at a tertiary level. Biochemistry is extremely interesting and the combination of two fields of science to explain the human anatomy as well as other concepts is quite evolutionary.

HaI am a very outgoing person that likes to engage in outdoor activities, learning new things and doing experiments. I am very passionate about life and its many wonders. As a result this course captivates my attention. I am looking forward to getting more in dept in biochemistry and am aware that it requires hard work and persistence and is willing and open to gain as much knowledge there is to offer.

PriHi , I am currently pursuing a bachelor of science in chemistry and biology. I really like biochemistry and was very happy when I heard we had to do a blog. I thought of it as an exciting and colorful way for us to get a better understanding of this course.

Ay– I am from one of the best places in Trinidad, the humble borough of Point Fortin. Currently  twenty years of age, my dream is to become a pediatrician. At first, when I heard the word biochemistry, I thought to myself , why do they need to add chemistry to spoil it. This may be a tough one or it might be the opposite . Who knows? But after my first lecture of Biochemistry , it turned out to be a lot simpler  and enjoyable than expected and our lecturer is really cool and fun.

IMAGE 1

http://www.bing.com/images/search?q=funny+scientist+picture&FORM=HDRSC2#view=detail&id=2B6F94A230555DB59A5A95C21D6FF0B339CE47E2&selectedIndex=8