Glycolysis part 2&3

Glycolysis:

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·       Image 92

The fates of pyruvate

What is the fate of pyruvate in the cell? Well, that depends on whether the conditions are aerobic or anaerobic…

If oxygen is available, then the pyruvate moves to the mitochondria through active transport. In the mitochondria the pyruvate is changed to Acetyl CoA this is known as the link reaction. During this reaction CO2 and H + is removed from the pyruvate which is a 3C compound. NAD which stands for nicotinamide adenine dinucleotide is a coenzyme which is needed for the reaction to follow through, NAD is reduced. . The enzyme responsible for this reaction is pyruvate dehydrogenase, the remaining 2C pyruvate combines with the coenzyme A to produce acetyl CoA. Most of the ATP is made through aerobic conditions. The link reaction produces 5 ATP molecules, this is of course theoretically!

Now, what if there was no oxygen present? Well, under anaerobic conditions the pyruvate is turned into lactate.  This conversion occur in mature red blood cells which depend on glycolysis for its energy. Why convert pyruvate to lactate? Well, there is limited NAD therefore if the NAD is used up then glycolysis stops… Therefore when the pyruvate is converted to lactate in the presence of lactate dehydrogenase the NAD+ is regenerated. Thus no ATP is generated! An example of this occurring in the body… during vigorous exercise the decreasing oxygen allows the lactate or lactic acid to accumulate which then causes muscular cramps.

Also, under anaerobic conditions there is another fate for the pyruvate that is; in yeast fermentation ethanol and carbon dioxide are produced. The enzymes; pyruvate decarboxylase and alcohol dehydrogenase are involved. The pyruvate is first changed to acetaldehyde by the enzyme pyruvate decarboxylase and carbon dioxide is removed or decarboxylation occurs. For this to occur it needs TPP(thiamine pyrophosphate), which is a cofactor for the enzyme. In the second step the acetaldehyde is converted to ethanol. Then H+ is removed by NAD and it is during this step that the NAD+ is regenerated.  

 Image 93

·       FEEDER PATHWAYS FOR GLYCOLYSIS:

 

So far we have spoken extensively about glucose and its metabolism. However, we have failed to recognize that glucose is not the only carbohydrate consumed in the daily human diet. Other carbohydrates such as fructose and galactose also contribute to the energy levels within the human body.

 

·       Metabolism of fructose:

The main source in which fructose is consumed is from sucrose. For fructose to be metabolized by the body it has two steps involved; phosphorylation of fructose and cleavage of fructose-1-phosphate.

In the phosphorylation of fructose, fructokinase is the enzyme that catalyses the reaction. A phosphate group is added to the fructose molecule (i.e.phosphorylation) to produce fructose-1-phospahte. This allows the energy level of the fructose compound to be higher thus allowing it to participated in the second step. The phosphate group is from the ATP molecule.  In the next step, another enzyme aldolase B disintegrate the fructose-1-phosphate to the products; dihydroxyacetone phosphate and glyeraldehyde. Note that aldolase B is found in the liver. The dihydroxyacetone phosphate can then enter glycolysis.

 

·       Image 94

Metabolism of galactose:

Image 95

 

The source of galactose in the diet is from milk products. The metabolism of galactose is similar to that of fructose. For instance the galactose is phosphorylated to galatose-1-phosphate which is catalysed by the enzyme galactokinase. Galactose-1-phosphate is then changed to UDP-galactose. In this reaction the UDP-glucose reacts with the galactose-1-phosphate which produces UDP-galactose and glucose-1-phosphate with the aid of the enzyme galactose-1-phosphate uridyltransferase. Then the UDP-galactose is converted to a C4 epimer which is UDP-glucose by the enzyme UDP-hexose 4-epimerase. The UDP-glucose can then enter the glycolytic pathway.

 Image 96

References:

Google Books. “Biochemistry.” 2014. http://books.google.tt/books?id=-Lhp0ppRYWoC&pg=PA137&dq=metabolism+of+fructose&hl=en&sa=X&ei=IicSU-WBOMafyQGy1YHoCw&ved=0CCUQ6AEwAA#v=onepage&q=metabolism%20of%20fructose&f=false (accessed 1 Mar 2014).

Unknown. Fructose metabolism – Acumen. Fructose metabolism – Acumen. 2014. http://www.breakspearmedical.com/files/documents/fructosemetabolism230910_AM_.pdf. (accessed 1 Mar 2014).

 

Aside

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 3

Image

 IMAGE 79

M-M Equation

Leoner Michaelis and Maude Menten proposed a model that shows that an enzyme can increase the kinetic rate of a reaction and also showed that the rate of a reaction depends on the concentration of the enzyme and the substrate.

IMAGE 80

The M-M equation demonstrates how the velocity of a reaction varies with the concentration of the substrate.

IMAGE 81

 

Assumption in Deriving the M-M Equation.

Steady State assumption- the enzyme- substrate concentration is constant since the rate of its formation is equal to its rate of degradation.

Relative Concentration of Enzyme and Substrate- the concentration of the substrate is larger than the concentration of the enzyme.

Initial Velocity- measures the rate of the reaction as soon as the enzyme and substrate are mixed. At that point the concentration of the product is very small so the back reaction is neglected.

Conclusions of M-M Equation

1)      Characteristic of Km

Km is a feature of an enzyme and its substrate. Km numerically is equivalent to the concentration of the substrate at which the velocity of the reaction is equivalent to 1/2Vmax. Km does not change with the concentration of the enzyme.

Small Km – Gives a high affinity of the enzyme for substrate.

Large Km – Gives a low affinity of the enzyme for the substrate.

2)      Order of the Reaction

The velocity of the reaction is proportional to the concentration of the substrate when the concentration of the substrate is less than the Km. the reaction is 1st order with respect to the concentration of the substrate.

The velocity of the reaction is constant and equal to the Vmax when the concentration of the substrate is greater than the Km. The reaction is independent of the substrate concentration and therefore a zero order reaction with respect to the substrate concentration.

Lineweaver – Burk Plot

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The hyperbola curve of the M-M equation is transformed into a straight line. The straight line is obtained by taking the reciprocal of each term in the M-M equation. The Lineweaver –Burke Plot can be used to obtain Km , Vmax  and the mechanism of the enzyme inhibitors.

Inhibitors

Any substance that stops an enzyme catalysed reaction. There are irreversible inhibitors and reversible inhibitors.

Irreversible Inhibitors forms covalent bonds with enzymes. Once the enzyme is inhibited it cannot be reversed.

Reversible Inhibitors forms non-covalent bonds with enzymes. When the enzyme is inhibited the process can be reversed.

Types of Reversible Inhibitors

Competitive

Non- competitive

Uncompetitive

Mixed inhibition

Competitive Inhibitors

IIMAGE 83

 

Bind to the same site as the substrate. The inhibitor has a similar shape as the substrate.

Non- competitive Inhibitors

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Binds to a different site on the enzyme. This can bind to the enzyme or the enzyme substrate.

 

Uncompetitive Inhibitors

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Binds at a different site only on the enzyme substrate.

Mixed inhibition

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Binds on separate sites of either the enzyme or enzyme substrate while decreasing the affinity of the enzyme for substrate.

IMAGE 87

 

Table Showing how the different Inhibitors Affect Km and Vmax

Reversible Inhibitor Km Vmax
Competitive Increases Constant
Non-competitive Constant Decreases
Uncompetitive Decreases Decreases
Mixed Can increase or decrease Decreases

 

Allosteric Enzymes

Allosteric enzymes have more than one binding site. Effectors which are modifiers regulate these enzymes. Effectors bind non-covalently to another binding site of the allosteric enzyme. Effectors can change the affinity of the enzyme for substrate or can change the enzyme’s maximal catalytic activity. Effectors that inhibit the enzyme are negative effectors while effectors that increases the affinity of the enzyme are positive effectors.

Homotrophic and Heterotrophic Effectors

Homotrophic effectors are substrates that act as an effector while a heterotrophic effector is an effector other than a substrate

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References for Images:

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

http://biochemistry.wur.nl/CellCycle/CCMMKinetics.html

http://www.namrata.co/category/semester-paper/

http://course1.winona.edu/sberg/308s09/Lec-note/EnzymesB.htm

http://www.elmhurst.edu/~chm/vchembook/573inhibit.html

http://click4biology.info/c4b/7/pro7.6.htm

http://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Uncompetitive_Inhibitor

http://csrri.iit.edu/~howard/biochem/lectures/enzymeinhibition.html

http://forum1.aimoo.com/chemistrycorner/General-Discussion/Michaelis-inhibition-question-1-1524444.html

http://www.biology.arizona.edu/biochemistry/problem_sets/energy_enzymes_catalysis/03t.html

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Published Paper Review 2 on Pancreatitis (Enzymes)

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What is Pancreatitis????

Reference: National Institues Of Health (NIH).2012.‘‘Pancreatitis” Accessed February 22, 2014. http://www.digestive.niddk.nih.gov/ddiseases/pubs/pancreatitis/

This is caused as a result of inflammation in the pancreas. As we should know the function of the pancreas is to secrete enzymes through the pancreatic duct to the duodenum. These enzymes then combine with bile to digest food. Another function of the pancreas as mentioned in an earlier reflection is to produce insulin and glucagon into the bloodstream. These enzymes are not active till they arrive at the small intestine. However when the pancreas is inflamed, the enzymes inside it attack and damage the tissue that produce them. This leads to infection, bleeding and there may be permanent damage to the tissue.
There are two types chronic and acute
Chronic. This is where there is no healing of the pancreas and this can be permanent. Here the enzymes attack the pancreas and causes a lot of pain.
Causes???—If you have high calcium levels in the body
If you consume large amounts of alcohol
If you have high levels of fat in the body
Certain medicines
If you have hereditary disorders of the pancreas
Cystic fibrosis can also lead to it
How do you know if you have it???
A pain in the upper abdominal region.
Have you been vomiting?
Losing weight?
Having diarrhoea or oily stools?

Diagnosis-Many times acute is mixed up with chronic.
-A medical history can be conducted
-The doctor can carry out a physical examination.
-Blood tests – to find out if the pancreas is producing sufficient digestive enzymes.
-Blood urine and stool test
-X-rays of the abdomen CT scan EUS and MRCP

Cure– Patient may need treatment for managing the pain and IV hydration. If weight loss is continuous patient may require nasogastric feeding.
When the pancreas returns to a normal diet they may use synthetic pancreatic enzymes if the pancreas does not produce sufficient amounts.
Then a dietician is recommended to a plan a small but frequent low fat diet.
Patients must consume a lot of fluids and must stay of caffeinated and alcoholic drinks as well as cigarettes.

Acute -Sudden inflammation in the pancreas that goes away with a few days treatment.
Causes??? When persons have gallstones- When these are passing through the common bile duct they cause inflammation in the pancreas
Can occur within two days of drinking alcohol.
Other causes
Having trauma in the abdominal region
Having infections, tumours or genetic abnormalities in the pancreas.
How do you know you have it????
-Do you experience pain sudden or gradual in the upper region of your abdomen?
-Do you suffer from swollen and tender abdomen?
-Experiencing nausea and vomiting?
-Have a fever?
-Having fast pulse?

Diagnosis-Due to the location of the acute pancreatitis it is difficult for diagnosis.
So……… an abdominal ultrasound, Computerized tomography CT scan, endoscopic ultrasound and Magnetic resonance cholangiopancreatography must be performed.
Cure Similar to that of chronic
Hope this was an informative piece about pancreatitis as I, myself have learnt a lot !!
See you next time… 🙂

Reference for Image:

http://static.someecards.com/someecards/usercards/9474665a2298a28741ec882d8eae2762.png

 

Aside

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

 

Aside

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!!

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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………………………..

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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/

Aside

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

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 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

Aside

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

Discovery of the cell

The Cell

How was the cell discovered?  The discovery of the cell was credited to a microscopist, Robert Hooke. He attempted to ask a simple question as to why cork stopper ( which were made from the wood of a tree)  that were used to bottle toppers was suitable to maintain air in the bottle. He took a sample of the cork and examined it under a microscope which revealed that it contained pores. In his assessment he compared the porous material to that of the structure of a honeycomb and thus named the pores “cells” due to their memory of the cells that monks lived in the monastery.  Hooke was also able to further his findings when he noted that the cork cells which as we know it today are plant cell, they had cell walls. This revelation about cells led to the further discovery of microscopic organisms such as bacteria by Leeuwenhoek. His findings were confirmed by Robert Hooke in 1678.

Image 25  of Robert Hook and the discovery of cells from a cork stopper.

Cell Theory?

Following the discovery of the cell that is the basic unit that is characteristic of  all life.  A botanist by the name Robert Brown observed the plant cell and noted the presence of the nucleus. Following the publication of Brown’s findings another botanists, Matthias Schleiden proposed the ideas that cells made the basis of plants and that the nucleus was an important part of the functionality of the cell.  Then later on Theoder Schwann a biologist related the ideas of Schleiden to animals. In that both plants and animals were made of cells and they both had the nucleus present.

References of picture

http://www.bing.com/images/search?q=robert+hooke+and+his+discovery+cork+cell&qs=n&form=QBIR&pq=robert+hooke+and+his+discovery+cork+cell&sc=1-31&sp=-1&sk=#view=detail&id=0025CCF122BF46C3EB6088FB788D99CDAF80BC41&selectedIndex=2