YOUTUBE VIDEO REVIEW: Krebs/ Citric Acid Cycle.

YouTube. “Khan Academy Krebs/ Citric Acid Cycle.”http://www.youtube.com/watch?v=juM2ROSLWfw

The video being reviewed is produced by the Khan Academy and they introduce the Krebs/Citric Acid/TCA Cycle to those who are unfamiliar with it. The video prior to this one is based on glycolysis which highlights the sequence of events that produces two molecules of pyruvate/pyruvic acid (3-carbon) from one molecule of glucose (6-carbon).

The process of glycolysis was not recapped in this video but the net production of 2ATP molecules, 2NADH+H+ and two molecules of pyruvate was mentioned. Then a diagram of the cell was drawn followed by a diagram of a mitochondrion to show that glycolysis occurs in the cytoplasm of the cell and glycolysis occurs within the matrix of the structure in the mitochondria. The pyruvate oxidation to Acetyl Coenzyme A (CoA) known as the preparatory step for the TCA cycle followed by a summarized look at the entire cycle was given. Individual steps were not looked at into detail. The overview was to illustrate the production of ATP, NADH+H+, CO2 and FADH+H+ in glycolysis and the Krebs cycle. This includes the production of 2ATP molecules and 2NADH+H+ molecules in glycolysis along with 2 molecules of NADH+H+, in the preparatory reaction (oxidation of pyruvate to acetyl CoA) and 6NADH+H+ (3 molecules × 2), 2ATP and 2FADH+H+ (1 molecule × 2) from Krebs Cycle.

The number of molecules for each one produced was multiplied by two, which is from the two pyruvate molecules formed from glycolysis. This was used to show the generation of ATP from NADH+H+ and FADH+H+ in the Electron Transport Chain, where one molecule of NADH+H+ produced 3 molecules of ATP and FADH+, H+ produced three. Therefore in total, theoretically there must be a total net gain of 38ATP molecules for metabolic activities in the cell.

From this information a more complex diagram of the Krebs cycle was shown and the same molecules produced were highlighted. No further detail was given, but, it was still very understandable and thorough. Khan Academy was not addressing an audience of University students in particular, but instead catered to a more basic knowledge of the topic, such as the number of carbons in each step, the purpose of the Krebs Cycle (to generate NADH+H+ and QH2/FADH+H+ for use in the ETC), the linkage reaction from glycolysis to the Krebs Cycle and how the total amount of ATP molecules were calculated etc.

If there was more detail in the video for example if the enzymes for each reaction were mentioned and their catalysis was explained, showing the EC number in relation to the type of reaction (by the major class of the enzyme). It should also be addressed that the 2FADH+H+ produced is now being termed as QH2, since after recent studies which shows that the FAD+ molecule is a prosthetic group (permanently/covalently linked) on the enzyme succinic dehydrogenase. Therefore the QH2 is the final product.

However, the video is concise although more detail is needed, but it is good for a quick review and basic comprehension of the topic.

REFLECTION 10 NUCLEOTIDES AND NUCLEIC ACIDS

Nucleic acids:

Nucleic acids are biopolymers, which contain the genetic material that is responsible for the transmission and the storage of hereditary characteristics in an organism. In nature there are two common nucleic acids: Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA). The basic unit of nucleic acids is a nucleotide. Nucleotides are the ‘building blocks’ upon which the genetic material DNA (deoxyribonucleic acid) and its derivative (transmission of the stored genetic material for the synthesis of functional complex protein molecules within the cell) RNA (ribonucleic acid) are composed from. There is both a structural and functional difference between DNA and RNA.

Nucleosides:

A nucleoside is either sugar (from DNA or RNA) bonded to a base. In other words:

Nucleoside = Sugar + Base

Nucleotide = Sugar + Base + Phosphate group

An Example of a nucleotide is Adenosine Triphosphate (ATP):

 

DNA and RNA sugars:

Nitrogenous Bases:

There are two groups of the Nitrogenous bases:

  • Pyramidines: The three pyramidines that is present in RNA and DNA are cytosine, thymine and uracil. Cytosine and thymine are present in DNA only. Cytosine and uracil are present in RNA only.
  • Purines: The two purines that are present in both DNA and RNA are adenine and guanine.
  • Watson and Crick postulated the bonding between these bases is complementary hydrogen bonding and they are between a pyramidine and a purine. A and T are complementary. C and G are also complementary.
  • The base pairs interact by 2 to 3 hydrogen bonds per base pair. Hydrogen bonds are not strong bonds individually, but collectively they produce a very strong effect.

DNA (Deoxyribonucleic Acid):

  • 5-membered furanose ring (2-Deoxy-α-D-ribfuranose ring) sugar + Inorganic Phosphate group + Base = 1 Nucleotide
  • 5’ End bonded by a phosphodiester bond/bridge to 3’ End containing a hydroxyl group (-OH)
  • Described as having a deoxyribose sugar phosphate backbone with nitrogenous bases attached to both backbones which form hydrogen bonds with each other cross ways to its complement (as a base pair), as proposed by Watson and Crick.
  • Bases present in the DNA molecule are classified into two groups: Pyramidines and Purines. The base pairs are A (Adenine) and T (Thymine), G (Guanine) and C (Cytosine)
  • There are two antiparallel strands of the DNA molecule bonded together to form a double α helix. These strands are referred to as ‘antiparallel’ since they are bonded at opposite ends to each other. Therefore, one strand will start from the 5’ End and the other strand will start from the opposite end which is the 3’ End.
  • The DNA strands coil, and super coil in the nucleus to form chromosomes.

RNA (Ribonucleic Acid):

  • 5-membered furanose ring (α-D-ribofuranose ring) sugar + Inorganic Phosphate group + Base = 1 Nucleotide
  • 5’ End bonded by a phosphodiester bond/bridge to 3’ End containing a hydroxyl group (-OH)
  • Described as having a ribose sugar, which is single stranded (in comparison to DNA which is a double stranded helical structure) and is used for the transcription and translation in the synthesis of functional proteins from the DNA helix found in the nucleus of the cell.
  • There are different forms of RNA. These include mRNA (messenger RNA), tRNA (transfer RNA)
  • The four bases present in RNA strands are Cytosine, Adenine, Uracil, and Guanine.
  • The base pairing is Guanine to Cytosine and Uracil to Adenine.

REFERENCES:

Talaro, Arthur and Kathleen. Foundations in Microbiology. Wm. C. Brown Publishers, 1993.

“Nucleic acids.” https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/nucacids.htm

“DNA Structure.” http://www.ucl.ac.uk/~sjjgsca/DNAstructure1.html

“Nucleoside.” http://web.pdx.edu/~newmanl/nucleoside.GIF

“Structure of DNA.” http://faculty.rhodes.edu/lindquester/molbiol/dnastructure.html

PUBLISHED PAPER REVIEW: British Journal of Anaesthesia, Oxford Journals. “Weight loss and 2,4 dinitrophenol poisoning.”

British Journal of Anaesthesia, Oxford Journals. “Weight loss and 2,4 dinitrophenol poisoning.” http://bja.oxfordjournals.org/content/102/4/566.full 

BY: A. Tewari, A. Ali, A. O’Donnell and M. S. Butt

The paper that will be reviewed is closely related to the severity of the dangers of purchasing unknown drugs via the internet which make ridiculous claims of weight loss, enhancement drugs and supplements etc. This article focuses on the dangers of the internet commercialised weight loss drug that has resurfaced via the internet known as DNP (2, 4-dinitrophenol – C6H4N2O5).  First, the author mentions the rebirth of the drug on the internet and its growing prevalence, and gives a brief history of the drug and the serious health consequences attached with it.

The drug was first introduced in the 1930s to facilitate weight loss where studies proved that it increases an individual’s basal metabolic rate by 36% to 95% in just a matter of weeks. Due to the health risks that the drug caused users such as cataracts, liver failure, agranulocytosis (lowered white blood cell count), it was removed from the market. The author then used this information to give an example of an actual patient, a 27 year old woman who was admitted to emergency and accident after symptoms of nausea, fatigue and profuse sweating. According to the standard tests done, she was at optimal health and there was no other medical explanation other than the over dosage of the diet supplement that was bought via the internet containing the drug.

After mentioning the dilemma of the patient, the biochemical aspects of why this occurs comes into play. The author explains what happened is that the DNP molecule is acting as an uncoupling agent which reduces the rate of oxidative phosphorylation occurring within the mitochondria. What is occurring is an uncoupling reaction where the DNP molecule is a weak lipophilic anion (containing an overall negative charge) and it is capable of transferring H+ ions (overall positive charge) across the inner membrane of the mitochondria in its unionized form (no charge). This therefore reduces the electrochemical gradient formed between the two membranes. Therefore a rapid increase in respiration occurs to compensate for the disturbed electrochemical gradient. With a rapid increase in respiration (which produces a lot of heat and water), there is an increase in body heat and increase in sweat production which explains what happened to the patient since there was an overdose of the drug, there was an increase in the uncoupling effect that it has on the mitochondria in the cell.   

The author also referred to the uncoupling of oxidative phosphorylation as a trigger for the release of calcium ions which causes increased muscle contractions and hyperthermia in individuals containing a certain dosage of the drug.

This article was a very interesting and informative and precautionary for persons who are considering trying diet pills and other gimmicks on the internet in an ad hoc fashion that can be detrimental to one’s health. You should definitely read this paper if you’re a nutrition fanatic like me.

REFERENCES:

Graham J. M. and Rickwood D. Subcellular Fractionation: A Practical Approach. Oxford University Press, 1997.

LIPIDS

 

WEEK 10: LIPIDS

Hi guys, hope all is well. So Lipids, also know known as fats and oils, also known to get people like this…

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Fats can be either good or bad for you depending on how your body uses it.

Fats and oils go hand in hand. Fats are solid at room temperature and fats can sometimes be in liquid form (oils). Fats contain saturated hydrocarbon chains while oils contain unsaturated hydrocarbon chains.

Here is a pic of some foods that contain fats and oils.

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FACTS ABOUT FATS: 

  • Although fats are mostly said to be bad for you, it is actually needed by the body to survive.
  •  Fats provide insulation for the body when it’s too cold.
  •   It surrounds the organs in the body and cushions it from any damage.
  •   It also provides the body with absorption and transportation of vitamins A, D, E and K (fat soluble vitamins) as they depend on fat for this.
  •   Provides storage for energy.
  •   Fats make foods taste better.
  •   Assists in the process of steroid hormones and in the formation of cell membranes.

 

  • SATURATED FATS AND TRANS-FATS:

Are not healthy because it comes from most animal sources such as butter, dairy products and meat, and this contributes to diseases such as heart disease, diabetes, cancer, low cholesterol and lipoprotein levels. Trans-fat may be even a tad bit worse for you as it is produced as a by-product when hydrogen is added to vegetable oil through a hydrogenation process.  Trans-fat raises LDL and causes heart disease.

 

Chemical structure of a saturated fatty acid

It has a methyl group at one end and a carboxyl group at the other end. All carbons are bonded to hydrogen.

stearic

 

UNSATURATED FATS:

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This type of fat is said to be healthy for you. It comes from soya bean, avocado, nuts, olive oils and fish, seeds and plant oils. This fat is mostly oil, liquid at room temperature. Unsaturated fat can either be polyunsaturated or monounsaturated and they both do not raise the level of LDL. Omega-3 fatty acid is an essential fatty acid that is contained in polyunsaturated fat which is good for the heart, teeth and bones.

 

Chemical structure of an unsaturated fatty acid

This fatty acid has C=C bond and a carboxyl group

stearic

ESSENTIAL FATTY ACIDS:

These fatty acids are required by the body to help with certain illnesses. The body cannot make these fatty acids because our bodies cannot produce the C-C double bonds so we must take this up from our diets. Two of these include:  alpha-linolenic acid and linoleic acid.

 

NON-ESSENTIAL FATTY ACIDS:

These fatty acids are not required by the body as we can produce these acids from carbohydrates and unsaturated fats. Omega-9 is an example of a non-essential fatty acid and this helps to control blood sugar and lower bad cholesterol.

 

Melting points of saturated and unsaturated fats

The melting points of a fatty acid depend on numerous reasons:

  • The number of methylene group
  • Chain length
  • The ionized state of the fatty acid, and last but not least
  • Molecular weight

 

HYDROLYSIS OF FATS:

This is the breakdown of fat to fatty acids and glycerol.

The formation of three fatty acids and a glycerol makes a phospholipid

Phospholipid

 

MEMBRANE LIPIDS

These lipids assist in forming the surface layer of all cells. The three types of membrane lipids are phospholipids, glycolipids and cholesterols. These lipids contribute too many functions in a cell. Phospholipids help carry protein messengers through the cell. Glycolipids help with the cells shape, fuel storage and special functions. While cholesterol serves as the metabolic precursor for steroid hormones. They are also used to build membranes and synthesize hormones.

CellMembraneComplex

 

Check this out!! It demonstrates lipid digestion in the body.

http://www.wiley.com/college/grosvenor/0470197587/animations/Animation_Lipid_Digestion_and_Absorption/Energy/media/content/dig/anima/dig5a/frameset.htm

 

Ok gals and girls, hope you learnt something interesting, and remember which fats you can and can’t eat!

TOODLES!🙂

http://www.livestrong.com/article/546145-advantages-disadvantages-of-fats/

http://livehealthy.chron.com/advantages-disadvantages-eating-fats-1331.html

http://answers.ask.com/Fitness_and_Nutrition/Nutrition/how_are_trans_fats_made

http://www.sciencedaily.com/articles/u/unsaturated_fat.htm

http://fitnessfusion.com/the-difference-between-essential-and-non-essential-fatty-acids/

http://biology.stackexchange.com/questions/7252/melting-point-of-a-fatty-acid

http://en.wikibooks.org/wiki/Structural_Biochemistry/Lipids/Membrane_Lipids

 

Week 9-Overview of Metabolism Part 2

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Hope you all are awesome🙂

I don’t know about you guys but I was never a fan of Electron Transport Chain but after researching and actually taking the time to understand what it is really about I realized it’s not so bad after all.

ImageLet us get straight to it!!

 

 

At this point we all should be familiar with Glycolysis and different pathways of aerobic and anaerobic conditions.

This week we will be focusing on the last stage of aerobic respiration which is the Electron Transport Chain.

What is Electron Transport Chain?

Well, this is a process the cell uses to obtain energy from reducing electron carriers, such as, NADH+H+ and FADH2. The energy is converted into a proton gradient which produces ATP (Adenosine Triphosphate) from ADP (Adenosine Diphosphate) and a phosphate group.

Where all the fun of the synthesizing of ATP occurs?

The formation of ATP occurs in the inner membrane of the mitochondria.

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 http://rosekennedyproject.weebly.com/photosynthesis–respiration-processes.html

 

What happens to the energy from the food that we consume?

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This is what happens:

All the energy that the food contains is stored in chemical bonds.

   

The food is broken down during Glycolysis and the Krebs cycle.

     ↓

 The energy is passed on to the electron carriers, NADH+H+ and FADH2

        ↓

Electrons from NADH+H+ are transferred across the membrane.

       ↓ 

When the electrons move from one location to the next it is a reduction-oxidation reaction, hence the molecules will have a lower energy state.

 
   

 

 

         

Hydrogen ions, which are protons, are able to move across the membrane when energy is released.

 
   

        ↓

Potential energy increases in the form of electrochemical gradient due to the movement of the hydrogen ions.

     

       ↓

 

 
   

The formation of ATP occurs when the enzyme ATP synthase use the potential energy.

 

The above is a brief insight on what happens to the energy.

The Electron Transport Chain comprises of four huge proteins referred to as complexes.

So let us go a little bit deeper.

Image

 

http://chemwiki.ucdavis.edu/Biological_Chemistry/Electron_Transport

 

Imagine NADH dancing his way through to get to the inner membrane.He made it happily, so now he enters the electron transport chain at Complex 1. NADH+H+ donate two electrons to Flavin Mononucleotide (FMN). Complex 1 has an Iron-Sulphur (Fe-S) centre which is an electron carrier and the two electrons will be given to Coenzyme Q (ubiquinone).  Coenzyme Q is mobile so it will travel through the membrane and it will reduce cytochrome B.

FADH2 is now jealous so he makes his grand entrance at Complex 2. Succinate dehydrogenase reduces FAD to FADH2 . Coenzyme Q transfers two electrons to cytochrome B in Complex 3.

One thing to always remember is that Complex 2 is the only one that does not pump protons across the membrane.

The two electrons are transferred to the Fe-S centre which is then transferred to cytochrome C1. Cytochrome C1 transfers the two electrons to cytochrome C.

Cytochrome C is mobile so it transfers the electrons to Complex 4. It then transfers the electrons to cytochrome a. This complex is referred to as cytochrome C oxidase. Cytochrome a will transfer the electrons to cytochrome a3, which will reduce oxygen. Water will be produced.

Protons go through the ATP synthase complex. Energy that comes from the moving protons is used to form ATP from ADP and phosphate.

Image

gifsoup.com/view/2568261/atp.html#prettyPhoto

So we have real our goal🙂 ATP is formed!!!

 

References

Mathur, Meenakshi Mehta.2002.Bio-Chemistry 1st Edition.

In-text citation:

(Mathur and Mehta 2002, 126-130)

Nelson, D.L.and Cox, M.M.2008.Lehninger Principles of Biochemistry 5th Edition.

In-text citation:

(Nelson and Cox 2008,529)

http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter7/electron_transport_system_and_atp_synthesis.html

http://www.elmhurst.edu/~chm/vchembook/596electransport.html

http://www.dbriers.com/tutorials/2012/04/the-electron-transport-chain-simplified/

Well I hope I helped you in anyway to understand the Electron Transport Chain

Keep focus & love Biochemistry!

Buh-Byes

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Overview of Metabolism

BIOL 1362: BIOCHEMISTRY I

DATE: Sunday 16th March, 2014

NAME OF BLOG: World of Biochem

BLOG’S WEB ADDRESS: https://worldofbiochem.wordpress.com/

OVERVIEW OF METABOLISM 1

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Metabolism is simply a term used to sum up all the chemical reactions in a cell and therefore the organism. Catabolism and Anabolism are the two groups of metabolism. The process of molecules being broken down to obtain energy is known as catabolism and the process of synthesis of compounds needed by cells is known as anabolism.

Mostly carbohydrates, proteins (amino acids), and lipids are involved in metabolism and all of these macronutrients’ catabolic pathways eventually connect into the Glycolysis and citric acid pathways, which is glucose catabolism, which leads to the formation of Acetyl CoEnzyme A (Acetyl CoA), whose destination is the tricarboxylic acid cycle (TCA) and the electron transport chain.

Glycolysis is the first part of carbohydrate metabolism and it converts glucose to pyruvate in a ten step process as seen in the previous Glycolysis reflection. We know it produces two pyruvate molecules, two hydrogen ions, two water molecules, and two ATP. The pyruvate is converted to Acetyl Coenzyme A which either enters the TCA cycle or can be converted to fat and stored. Now when oxygen is present, both pyruvates lose one of their carbon atoms from their three carbon structure and gain a molecule of coenzyme A which then combines with the two carbons that remained from the pyruvate to form the Acetyl CoA. The Acetyl CoA is a two carbon molecule. Carbon dioxide is the waste product formed when the third carbon combines with oxygen thus forming carbon dioxide which is lost through the lungs.

Fats are broken down to fatty acids which can be converted to acetyl CoA. This can be achieved when the coenzyme A is added to the carboxylic end of the fatty acid chain, therefore forming acyl CoA. This acyl CoA is a long chain which a carrier molecule can simply help to cross the membrane of the mitochondria. Upon entering the mitochondria, the fatty acid is taken apart two carbon fragments at one time via beta oxidation starting at the carboxyl end of the fatty acid. Now another CoA joins the two carbon pairs, therefore converting it to acetyl CoA. This is a continuous process until all the carbons are oxidized and used up in the reaction.

Proteins are made up of amino acids and these amino acids ccan be converted to acetyl CoA just as carbohydrates and lipids. It can also be converted to glucose which can enter glycolysis or other TCA molecules that can enter the cycle directly.

So we see that these three macronutrients-proteins, carbohydrates and lipids come together at a point, meaning whatever their metabolic pathway, they all have a common destination: to become acetyl coenzyme A, which then enters the TCA cycle to provide energy.

Not only is energy produced by the TCA cycle, but reducing power is also generated. For every turn that the TCA cycle makes, one acetyl CoA molecule is converted to two molecules of carbon dioxide, four molecules  are reduced (NAD+, NADP+, or quinine to NADH, NADPH and quinol), and phosphorylation of one GDP to GTP. The reduced molecules act as electron donors for the process of oxidative phosphorylation in which the flow of electrons leads to a terminal acceptor. On their way, they power proton pumps which transport protons across membranes therefore generating a proton motive force (PMF). The protons will eventually return to their original location, but on their way, powers enzymes that catalyze the phosphorylation of ADP to ATP (ATPase).

References:

http://www.news-medical.net/health/What-is-metabolism.aspx

http://www.biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=TCA

http://www.pearsonhighered.com/blake1einfo/assets/pdf/Blake_Chapter08.pdf

WEEK 6 AND 7 REFLECTION – GLYCOLYSIS PART 1 AND 2

 BABY YØU LIGHT UP OUR WORLD WITH YOUR ATP 

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This week we will be focusing on Glycolysis

Let us break it up:

Glyco-meaning sugar (glucose) and lysis-meaning breaking

Tadaaaa: It is the breaking down of glucose

Glycolysis is the first step in cellular respiration. This is where enzyme reactions convert glucose to pyruvate (2) and it is also important for the production of ATP (Adenosine Triphosphate).

Something you should know:

Glucose is one of the most crucial substances that our body require to function properly and it supplies organisms with the correct amount of energy needed.

So, where does all the excitement occurs?

Glycolysis takes place in the cytoplasm, this is where all the enzymes are present to break down glucose.

Who were the scientists involved in discovering Glycolysis???

The scientists who were involved in discovering Glycolysis were:

Gustav Embden                     Otto Meyerhof                      Jakub Karol Parnas

Image                                   Image                                                 Image

What enzymes are involved in the reactions? How many enzymes are used?

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Well, there are ten (10) enzymes involve in Glycolysis, they are as follows:

1)    Hexokinase

2)    Phosphohexose isomerase

3)    Phospho-fructokinase-1

4)    Aldolase

5)    Triose phosphate isomerase

6)    Glyceraldehyde 3-phosphate dehydrogenase

7)    Phospho-glycerate kinase

8)    Phospho-glycerate mutase

9)    Enolase

10)   Pyruvate Kinase

The diagram below outlines each step involve in Glycolysis:

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Okay, so don’t get a huge headache by trying to understand the picture. Below has an outline on what is occurring in each step, hopefully you all should understand.

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Glycolysis consists of ten steps which are divided into two sections which includes the preparatory phase and payoff phase where pyruvate, ATP and NADH are formed.

 Preparatory Phase 

Step1: This is where phosphorylation occurs and the reaction is irreversible. The enzyme Hexokinase is responsible for glucose to react with ATP to produce glucose-6-phosphate, where the adding of the phosphate group to the glucose molecule makes it unstable, hence promoting the reaction.

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Step 2: glucose-6-phosphate is converted to fructose-6-phosphate with the help of the enzyme Phosphohexose isomerase.

Step 3: Another enzyme, phospho-fructokinase-1 removes the phosphate group from ATP giving it to fructose-6-phosphate to form fructose 1, 6-bisphosphate. Phospho-fructokinase-1 is the most important regulating enzyme and this reaction is also irreversible.

 

Step4: An Aldolase enzyme reaction split the fructose 1, 6-bisphosphate into Glyceraldehyde 3-phosphate and Dihydroxyacetone phosphate.

Step5: This is where the enzyme Triose phosphate isomerase makes its presence and rearranges the Dihydroxyacetone phosphate to form a second Glyceraldehyde 3-phosphate. At this stage in Glycolysis glucose has been metabolised to Glyceraldehyde 3-phosphate (2) and two ATPs have been consumed.

We have completed the Preparatory Phase

Image Let us see what happens in the Payoff Phase

PAYOFF PHASE

Step6: The two Glyceraldehyde 3-phosphates are oxidised to 1, 3-Bisphosphoglycerate (2) by the enzyme Glyceraldehyde 3-phosphate dehydrogenase. This step produces one NADH (Nicotinamide adenine dinucleotide) for each oxidise 1, 3-Bisphosphate, giving a total of two NADH. These NADHS are used later on to produce more ATP for the cell.

Step7: A Phospho-glycerate kinase transfers a phosphate group from the 1, 3-Bisphosphoglycerate to ADP to for ATP and 3-Phosphoglycerate (2). This step results in two ATPS and two 3-Phosphoglycerate molecules.

Step8: This involves a Phospho-glycerate mutase reaction which moves the phosphate group in the third carbon of 3-phosphoglycerate to the second carbon to form 2-phosphoglycerate.

Step9: An Enolase enzyme reaction removes the water from the 2-phosphoglycerate to form two Phosphoenolpyruvate. This step occurs for the two molecules of 2-phosphoglycerate

Step10: Pyruvate kinase enzyme reaction removes a phosphate group from Phosphoenolpyruvate and donates it to ADP to produce ATP and Pyruvate. This step is similar to reactions 1and 3 where it is irreversible. At this stage two pyruvate molecules, four ATPs and Two NADH are formed for each glucose that was broken down for Glycolysis.

ATP IS AN IMPORTANT ENERGY MOLECULE REQUIRED FOR MANY BIOCHEMICAL PATHWAYS, ESPECIALLY FOR LIFE!

While I was researching I came across some harmful effects of Glycolysis which alarmed me. I never knew Glycolysis could be a bad thing but I guess in life there will always be good and bad characteristics in everything that exist, hence proving the point that no person or thing is perfect.

This is just a brief insight on two of the effects caused by Glycolysis.

It is known that malignant tumour cells can be caused when Glycolysis levels are way higher than those of normal tissues. Otto Warburg was the scientist who discovered this in the 1930s and it is referred to as the Warburg effect.

The second disease caused by an imbalance in Glycolysis is Alzheimer. This is a very unsafe disease which affects the nervous tissues of our brain and also it interferes with its functions.

So next time you think of sitting down with a bag of chocolates or candies Glycolysis will punish you!!! 

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REFERENCES:

Harvey, Denise R. Ferrier.2011.Lippincott’s Illustrated Reviews Biochemistry 5th Edition.

In-text citation:

(Harvey and Ferrier 2011, 90-92)

Nelson, D.L.and Cox, M.M.2008.Lehninger Principles of Biochemistry 5th Edition.

In-text citation:

(Nelson and Cox 2008,529)

Mathur, Meenakshi Mehta.2002.Bio-Chemistry 1st Edition.

In-text citation:

(Mathur and Mehta 2002, 126-130)

“10 Steps of Glycolysis.” About.com Biology. (accessed March 2, 2014). http://biology.about.com/od/cellularprocesses/a/aa082704a.htm

In-text citation:

(Biology 2014)

“Things to Know About Glycolysis | Glycolysis.” Things to Know About Glycolysis | Glycolysis. (accessed March 2, 2014) http://www.glycolysis.org/things-to-know-about-glycolysis.html.

In-text citation:

(Glycolysis 2014)

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http://i5.glitter-graphics.org/pub/1728/1728675fik7v1bctx.gif

http://cdn1.sbnation.com/imported_assets/382485/sm-face.jpg

http://gifsoup.com/view/4970989/hexokinase.html

PART 2 OF GLYCOLYSIS

In case you missed some information on EACH STEP OF THE GLYCOLYTIC PATHWAY HERE IS A LITTLE MORE INFORMATION FOR YOU GUYS:

Steps in the Metabolic Pathway of Glycolysis which are Enzyme-Controlled Reactions:

The glucose is formed from the hydrolysis of glycogen and starch. The glucose formed is kept in low concentrations to favor the conditions of Le Chatelier’s Principle (Equilibrium Principle), which states that,

If there is a change in the equilibrium of a chemical system, may it be in concentration, temperature, pressure or volume, the position of equilibrium will ‘shift’ or will be changed to accommodate a new established equilibrium.

There are ten steps in glycolysis. The first five reactions are the first phase which consumes energy. In the other five reactions, there is a net production of ATP and hence, energy. The reactions are outlined as follows:

Step 1: The first step in the glycolytic pathway is the phosphorylation (addition of a phosphate group) of glucose to glucose-6-phosphate (charged to avoid diffusion through the cellular membrane) by an ATP molecule. The enzyme that catalyses this reaction is from a family of enzymes known as hexokinases with the cofactor* being Mg2+. The concentrations of glucose are kept low to allow the shift of the reaction to the right (formation of glucose-6-phosphate).

Step 2: The second step involves the reaction involving the conversion of glucose-6-phosphate (pyranose ring) to its isomer fructose-6-phosphate (furanose ring). The enzyme which catalyses this reaction is phosphoglucoisomerase which is an isomerase. This reaction is reversible, but due to the low concentrations of fructose-6-phosphate, the position of equilibrium shifts to the right allowing more production of fructose-6-phosphate.

Step 3: The third step involves the phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate. This consumes one molecule of ATP which is used for two purposes: to add a phosphate group to the fructose-6-phosphate molecule and to provide energy for this reaction. This reaction is catalysed by the enzyme phosphofructokinase-1 which is a kinase with the coenzyme being Mg2+ and this reaction is irreversible. This step is necessary since the fructose-1,6-bisphosphate is a very unstable, charged molecule that will form two charged molecules which cannot diffuse across the non-polar cellular membrane.

Step4: The fourth step is where the destabilization of the fructose-6-phosphate to fructose-1,6-bisphosphate causes the molecule to split roughly down the middle into two triose sugars. The enzyme catalysing this reaction is aldolase which is a lyase and is a reversible reaction. The two products or triose sugars formed are: D-glyceraldehyde-3-phosphate (GADP/GAP) and Dihydroxyacetone phosphate (DHAP), which are both carboanions.

Step 5: In the fifth step, dihydroxyacetone phosphate (DHAP) is immediately interconverted to D-glyceraldehyde-3-phosphate (GADP/GAP). The enzyme that catalyses this reversible reaction is triose phosphate isomerase which is an isomerase. This gives simplicity to the reactions that follow since one specific triose sugar is used (D-glyceraldehyde-3-phosphate/GADP/GAP). Therefore the net gain of steps 4 and 5 are two molecules of D-glyceraldehyde-3-phosphate (GADP/GAP).

Step 6: The sixth step involves the dehydrogenation of the D-glyceraldehyde-3-phosphate (GADP/GAP) and the addition of a phosphate group from the cytosol in the form of H3PO4 (aq.). Both of these reactions are catalysed by glyceraldehyde phosphate dehydrogenase, an oxidoreductase, which is reversible. First, the glyceraldehyde phosphate dehydrogenase is used to reduce 2NAD+ molecules (a hydrogen carrier) to NADH+H+ (reduced NAD+), then the inorganic phosphate group is added (phosphorylation). The product formed is D-1,3-Bisphosphoglycerate which is a stable molecule.

Step 7: The seventh step involves the conversion of D-1,3-Bisphosphoglycerate to 3-phosphoglycerate by the removal of an inorganic phosphate group and the generation of two ATP molecules (from the two D-glyceraldehyde-3-phosphate/GADP/GAP molecules formed in Step 5). The enzyme involved in this reversible reaction is phosphoglycerate kinase which is a kinase with the cofactor being Mg2+.

Step 8: The eighth step involves the conversion of 3-phosphoglycerate to 2-phosphoglycerate. The enzyme catalysing this reversible reaction is phosphoglycerate mutase.

Step 9: In the ninth step there is a conversion of the two molecules of 2-phosphoglycerate to two molecules of phosphoenolpyruvate by the removal of water. The enzyme catalysing this reaction is enolase which is a lyase with the cofactor being 2Mg2+.

Step 10: This step is the tenth and final step where the two molecules of phosphoenolpyruvate are converted to two molecules of pyruvate by removal of two inorganic phosphate groups and generation of two ATP molecules. This irreversible reaction is catalysed by pyruvate kinase with the cofactor being Mg2+.

Recall:

  • *Cofactor: a chemical compound which is non-protein that is necessary for the proper functioning of (in most cases) proteins which are enzymes. Cofactors also balance the charges in a molecule (for example ATP) and they assist conformational proteins.
  • From Steps 1-5 there is the consumption of two ATP molecules for phosphate groups and for energy.
  • From Steps 6-10 there is the production of four ATP molecules and two NADH+H+ (reduced NAD+) molecules.
  • Therefore there is a net gain of two ATP molecules and two NADH+H+ (reduced NAD+) molecules
  • All products from Steps 6-10 are multiplied by two since two D-glyceraldehyde-3-phosphate/GADP/GAP molecules are produced in Step 5.
  • From the two pyruvate molecules formed, their fate may be either the TCA cycle in the presence of oxygen or formation of lactate or alcoholic fermentation (formation of ethanol).

E.C. NUMBER OF EACH ENZYME:

  1. Hexokinase: 2.7.1.1. (Transferase)
  2. Phosphoglucoisomerase: 5.3.1.9. (Isomerase)
  3. Phosphofructokinase-1: 2.7.1.11. (Transferase)
  4. Aldolase: 4.1.2.13. (Lyase)
  5. Triose Phosphate Isomerase: 5.3.1.1. (Isomerase)
  6. Glyceraldehyde phosphate dehydrogenase: 1.2.1.12. (Oxidoreductase)
  7. Phosphoglycerate Kinase: 2.7.2.3. (Transferase)
  8. Phosphoglycerate Mutase: 5.4.2.1. (Isomerase)
  9. Enolase: 4.2.1.11. (Lyase)
  10. Pyruvate Kinase: 2.7.1.40. (Transferase)

 Fates of the pyruvate (5 different possibilities):

Anaerobic Conditions:

In the absence of oxygen, two main forward reactions can occur in the presence of certain enzymes. The reactions are separately classified due to the difference in the metabolism of the pyruvate (pyruvic acid). Both processes are known as Fermentation Reactions. These are processes which produce ATP under anaerobic conditions (the absence of oxygen). But, more importantly, fermentation reactions are those that regenerate NAD+ from NADH+H+. Fermentation was first discovered by Louis Pasteur who referred to it as “a life without air”.

  1. The first possibility is the conversion of  pyruvate to L-lactate by reduction of the pyruvate molecule by NADH+H+ in the presence of the enzyme lactate dehydrogenase (EC: 1.1.1.27.) in a reversible reaction.

Note:

  • This is an important reaction in Erythrocytes which are mature red blood cells. They depend only on glycolysis as their main source of energy.
  • The purpose of production of lactate on the erythrocytes? Firstly, they are red blood cells which do not contain organelles within their structure, which includes mitochondria. Therefore the only means of production of ATP is through glycolysis.

If we look back at the sixth reaction of glycolysis, there is the conversion of two molecules of glyceraldehyde-3-phosphate to two molecules of 1,3-bisphosphate. The enzyme catalyzing this reaction is glyceraldehyde-3-phosphate dehydrogenase. In this reaction an inorganic phosphate will bond to the glyceraldehyde-3-phosphate molecule, with the phosphate group being removed from the cytosol in the form of H3PO4 (aq.). This reaction alone is not energetically feasible. This explains the coupled oxidation reaction occurring with the phosphorylation, in which NAD+ is converted to NADH+H+ (reduced NAD+). NAD+ is a hydrogen carrier, which is present in low concentrations in the cell and once it is reduced, it cannot revert back to its oxidized state. This is where the conversion of pyruvate to lactate comes into play. The reaction regenerates NAD+ for use in glycolysis. If this is the only source of energy, if all NAD+ is used up, the glycolytic pathway stops. Again, erythrocytes do not contain mitochondria and therefore, there is no use of the TCA cycle or ETC for synthesis of ATP.

  • Lactate is produced under specific conditions in the body. Mostly during vigorous exercise where the muscle tissue is deficient of a steady supply of oxygen to it, there is a rampant increase in the lactate production. Lactate in its ionized form is acidic and it is toxic in large quantities to the body, which causes muscle cramps signaling the body to stop vigorous activity.
  1. The second possibility, under anaerobic conditions, is the conversion of pyruvate to ethanol through two metabolic reactions. The first reaction involves the removal of carbon in the form of carbon dioxide from the pyruvate molecule. It is converted to acetaldehyde/ethanal + CO2 by the enzyme pyruvate decarboxylase with the cofactors being TPP (Thiamine Pyrophosohate) and Mg2+. This reaction is irreversible.

The second reaction involves the conversion of the acetaldehyde/ethanal to ethanol in a reversible reaction. This reaction is where the NAD+ is regenerated from the NADH+H+ (reduced NAD+) in a reduction reaction. The enzyme catalyzing the reaction is alcohol dehydrogenase.

Aerobic conditions:

  1. The third possibility is under aerobic conditions, where pyruvate is converted into Acetyl Coenzyme A (CoA) in an irreversible reaction. The enzyme and cofactors are pyruvate dehydrogenase complex (E1 + E2 + E3) and TPP (thiamine pyrophosphate), Coenzyme A (CoA with a sulphide linkage -SH), lipoate and FAD respectively. NAD+ is also converted to NADH+H+ (reduced NAD+), in an oxidation reaction. This is a high energy reaction which produces a ΔG˚= -33.4 KJmol-1 (very negative) and therefore is not energetically feasible to be a reversible reaction.
  2. The fourth possibility is the conversion of pyruvate back to glucose in a process known as gluconeogenesis/glucogenesis.
  3. The fifth possibility is the transamination of the pyruvate to the amino acid alanine. Transamination is the process whereby an amine group is transferred from one molecule (usually glutamate) to α-keto acid in an enzyme catalyzed reaction by enzymes known as aminotransferases. This is where glutamate transfers an amine group to pyruvate in a reversible reaction to form alanine and α-ketoglutarate. The enzyme catalysing this reaction is alanine transaminase.

Glutamate + Pyruvate ↔ Alanine + α-Ketoglutarate (catalyzed by alanine transaminase)

REFERENCES:

Campbell, Mary, Farrell, Shawn. Biochemistry 7th edition. Cengage Learning, 2011.

Conn, Eric E. Outlines of Biochemistry. John Wiley and Sons, Inc., 1976.

Fruton, Joseph S., Simmonds Sophia. General Biochemistry. John Wiley and Sons, Inc., 1953.

Gonzaga.edu. “Biochemistry Dictionary” http://guweb2.gonzaga.edu/faculty/cronk/biochem/P-index.cfm?definition=pyruvate

MCQ FOR YOU TO TRY:

What is the importance of fermentation?

  1. To break down pyruvate due to its toxicity.
  2. Since there is a negative value of ΔG˚ the energy is lost as heat which is needed by the organism.
  3. To regenerate the NAD+, since is not present in high concentrations in the cell and is needed for the catalysis of the sixth reaction in the glycolytic pathway.
  4. To produce alcohol, needed by yeast cells.
  5. The provision of ATP for use of metabolic reactions in the cell.

Hope you all enjoyed

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 For now

ENZYMES!

ENZYMES!!

Ok guys, let’s learn about Enzymes!

 

ImageEnzymes are a group of proteins also known as a biological catalyst that’s speeds up chemical reactions.

 

 

 

 

 

DID YOU KNOW?

  • There are many different enzymes in a person’s mouth, stomach, pancreas and intestine? They all serve a different purpose.

This table shows some important enzymes and their function in the body:

                                         ENZYMES

FUNCTIONS

Amylase

Converts starch to simple sugars

 

Pepsin

Converts proteins in small peptides

 

Lipase

Converts triglycerides into fatty acids and glycerol

 

Trypsin

Converts proteins to amino acids

 

Sucrase

Converts sucrose to disaccharides and monosaccharides

 

Maltase

Converts maltose to glucose

 

Lactase

Converts lactose to glucose and galactose

 

ENERGY PROFILE DIAGRAM!

Enzymes also make an alternative pathway for the reaction and lower the activation energy which is required. The enzyme does not alter the reactants or products.

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ACTIVE SITE!

An active site is probably the most important part in learning about how enzymes work.

ImageThe active site is used to recognize specific substrates that will bind together with the enzyme producing a chemical reaction.

This is called the lock and key hypothesis. It shows that a specific substrate will preferably bind to a specific enzyme.

Joke: Can I be your enzyme? Because my active site is dying for a chemical reaction😉

INDUCED FIT HYPOTHESIS!

This method is where the active site of an enzyme continues to change itself until a substrate is able to fit into it to perform its catalytic function.

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DENATURING OF ENZYMES!

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Enzymes are denatured when the pH are too high or unfavourable. This means that the enzyme will not be able to carry out its specific task. The enzyme loses its shape due the breaking of ionic and hydrogen bonds. So guys be careful, once these enzymes are denatured they won’t be able to reform their original shape K The optimum temperature for most human enzymes are between 35 to 40 degree Celsius.

SOME USES OF ENZYMES!

  • Foods and Beverages
  • Textiles
  • Detergents
  • Stickies Removal
  • Leather
  • Biodegradable Plastic

HERE IS A REACTION THAT IS CATALYZED BY AN ENZYME!

Glucose + ATP ——-> Glucose-6-phosphate + ADP

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So guys based on this awesome information that you just read, can you answer these true (T) or false (F) questions?

  1. Enzymes are proteins that lower the rate of a chemical reaction. T/F
  2. The enzyme amylase converts starch to proteins? T/F
  3. The activity of an enzyme can be altered by a high pH? T/F
  4. The active site is where the substrate binds? T/F
  5. If an enzyme loses its shape, it can always reform to its original shape. T/F

HERE ARE THE ANSWERS

1. F   2.T   3.T   4.T   5.F

COFACTORS AND COENZYMES!

Cofactors are a non-protein chemical compound (helper molecules) that attaches to an enzyme and is used to catalyse biochemical reactions.

Coenzymes are organic molecules and are required by enzymes to carry out catalysis. Some coenzymes are nicotine adenine dinucleotide and coenzyme A.

SOME DISEASES CAUSED BY ENZYME DEFICIENCY!

  • G6PD Deficiency- caused by lack of
  • Congenital Adrenal Hyperplasia
  • Gaucher’s Disease
  • Pyruvate Kinase Deficiency

 

http://pickuplinesgalore.com/biochem.html

http://www.agscientific.com/molecular-biology/molecular-biology.html

https://www.google.tt/search?q=pictures+of+enzymes&tbm=isch&tbo=u&source=univ&sa=X&ei=oDoJU_uwLaWMyQHX7ICIBg&sqi=2&ved=0CCQQsAQ&biw=1242&bih=607#q=imags+of+an+enzyme&tbm=isch&imgdii=

_http://www.buzzle.com/articles/list-of-digestive-enzymes.html

http://www.youtube.com/watch?v=FPKAJlgMCbE&feature=youtu.be

http://www.biology-online.org/biology-forum/about472.html?hilit=Disulphide

http://www.austincc.edu/emeyerth/quizenz.htm

http://www.biology-online.org/dictionary/Induced_fit_model

http://answers.yahoo.com/question/index?qid=20080227223133AA5PvN7

http://academic.brooklyn.cuny.edu/biology/bio4fv/page/coenzy_.htm

http://www.livestrong.com/article/325010-list-of-diseases-caused-by-lack-of-enzymes/

 

Carbohydrates

Carbohydrates are an essential food group to us humans as well as other living organisms as it provides energy, bearing in mind that the sun is our indirect energy provider. This is so as the sun provides energy to plants directly as they can use it to make carbohydrates because they are the only organisms which can accomplish this task by photosynthesis.

As we understand, carbohydrates are so called as they are the hydrates of carbon, comprising hydrogen, oxygen and water. They function as an energy source, storage molecules, for structure and as precursor molecules.

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Carbohydrates provide energy by metabolism of glucose when it is broken down into carbon dioxide and water. This releases a lot of energy allowing us to fulfill our daily needs and activities. They are stored in the form of starch in plants and glycogen in animals.  Cellulose and chitin are the major carbohydrates used for structural purposes. Cellulose is composed of polymers of the β-D-glucose molecule and makes up most of plants cell walls as it is a strong fibre material. Chitin is used to build the structure of exoskeletons in insects. It is a strong and flexible material. Carbohydrates are also used in the synthesis of other molecules such as DNA and RNA.

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Monosaccharides, disaccharides, oligosaccharides and polysaccharides are all categories that belong to the carbohydrates. Monosaccharides are the simple sugars and can be aldoses or ketoses. Aldoses have an aldehyde group at one end and ketoses normally have a keto group at carbon 2. An example of an aldose is D-glucose and a ketose is D-fructose.

There can be different forms of molecules like the D and L isomers. An isomer is another form of a molecule with the same molecular formula but different structural formula. D and L isomers are determined  by the configuration about a single asymmetric carbon in glyceraldehydes, but for sugars with more than one chiral centre, it is based on the asymmetric carbon furthest away from the aldehyde or keto group. A chiral carbon atom or centre is one in which all the groups attached to it are different from each other. If the hydroxyl group on this carbon is on the right, then it is the D form, and if it is on the left of this carbon then it is the L form, and indeed D and L forms are mirror images of each other. Epimers are two sugars that are different only in the configuration around one carbon atom. For sugars/carbohydrates the most common form of the isomer is the D form.

Carbohydrates such as hexoses and pentoses can be cyclic as a result of the aldehyde or ketone reacting with a distal hydroxyl group. Glucose forms two cyclic  structures which are the alpha (α) and beta (β), where the hydroxyl group is below the plane of the ring on the first carbon in the alpha structure and the hydroxyl group is above the plane of the ring in the beta structure. These cyclic structures are representations of the Haworth projection.

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There can be sugar derivatives like sugar alcohol which lacks an aldehyde or ketone; sugar acids where the aldehyde at carbon one or the hydroxyl at carbon six is oxidized to a carboxylic acid; and amino sugars where a hydroxyl group is substituted by an amino group.

Glycosidic bonds are formed when monosaccharides are joined together by a condensation reaction in which water is lost.

Disaccharides are two sugar molecules joined together forming one molecule. For example, two glucose molecules form a maltose molecule when joined, glucose and galactose forms a lactose molecule and glucose and fructose forms a sucrose molecule. Lactose is the sugar found in milk, sucrose is our normal table sugar and maltose is found in germinating seeds.

Carbohydrate malabsorption like lactose intolerance is where the body cannot digest the amount of lactose consumed, sometimes due to the fact that synthesis of the enzyme lactase which breaks down lactose decreases in the body as we get older. This causes discomfort-bloating, abdominal discomfort and diarrhea as the bacteria in our intestines feed on the undigested lactose and produce acid and gas.

Polysaccharides are made up of repeating monomer units joined by the process of condensation forming bonds. As we know, starch, glycogen and cellulose are important polysaccharides, all of them being polymers of glucose.

Carbohydrates as we can see are very important and essential in our lives…therefore it is needed in our diets.

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THE CELL

What is a cell? The cell is the term, which was coined by English Scientist, Robert Hooke in 1665 and it was defined simply as the basic, functional unit of living organisms that is the ‘building block’, and it is capable of performing metabolism or metabolic activities (which are the sum of chemical reactions in the cell, including processes of anabolism –synthesis and catabolism – breakdown), growth and reproduction. In other words, the cell is a self-sustaining unit.

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Sir Robert Hooke

Other significant scientists responsible for further research and development with regards to the Cell Theory are: Matthias Schleiden (German Botanist), Theodor Shwann (German Physiologist) and Rudolph Virchow (German Pathologist, Anthropologist, Prehistorian biologist).

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From the left: Theodor Shwann, Matthias Schleiden and Rudolph Virchow.

With the invention of the microscope: the Compound microscope, Light microscope and the Electron microscope, this has opened a new window of exploration into the microscopic cellular world and has led to fascinating discoveries and conclusions made by these prominent scientists.

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From left: Compound Microscope, Electron Microscope 

To be a self-sustaining unit, there must be components within this unit that perform specific tasks to allow metabolism. The basic cell structure contains the following organelles that are located inside the limits of the cell membrane:

  1. Cell Membrane
  2. Cell Wall (Present in Plant cells and Bacterial Cells, Absent in Animal Cells)
  3. Cytoskeleton
  4. Cytoplasm
  5. Nucleus
  6. Chloroplast
  7. Mitochondria
  8. Endoplasmic Reticulum (Smooth and rough ER)
  9. Golgi Complex (Golgi Apparatus)
  10. Lysosomes
  11. Proteasomes
  12. Ribosomes

The Cell Membrane:

The Plasma phospholipid bilayer otherwise known as the plasmalemma (refers to the cell membrane only and not cell organelles) is the semi-permeable membrane surrounding the cell and enveloping its contents. There is an upper and a lower layer and they both comprise of a phosphate head (hydrophilic) and a two carbon chains (or fatty acid chains which is hydrophobic and non-polar), making them amphipathic in nature and are about 7 nm thick. This membrane forms what is termed ‘the fluid mosaic model’, which represents the various proteins and receptors embedded in the layers of the membrane, which gives it the appearance that it is ‘floating’ on the membrane and hence the term fluid is given. Chemically, the composition of the contents of the membrane is: 50-70% lipids, 20-50% proteins and 1-5% carbohydrates.

The membrane is important for regulation of the substances, which move in and out of the cell such as the raw materials for metabolism, waste products, water etc. and it is also significant for cell-to-cell recognition and interaction (for example, the formation of tissues), receptors for hormones and harmful external bodies such as phagocytes and pathogens. There are thousands of different proteins present and they can be embedded within the membrane (transmembrane or integral membrane proteins) or on the surface of it. These proteins function to maintain fluidity (such as cholesterol), active transport and passive transport (diffusion, osmosis and facilitated diffusion). The carbohydrate portion, which are glycoproteins and glycolipids, have the appearance of ‘antennae’ on the surface of the lipids and proteins. These function as receptors for external stimuli to the cell.

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Cell Wall:

The cell wall is an important feature in plant cells and bacterial cells and is present on the outer surface of the cell, not the cell membrane. Its functions include maintaining turgidity and hence, the shape of the cell and protects against lysis (osmotic pressure which builds up causing bursting). In plant cells, the cell wall is comprised of cellulose fibrils, which is a polymer of beta-glucose that is water permeable and has high tensile strength. In bacterial cells the cell wall is comprised of murein or peptidoglycan layer. This layer contains repeated units N-acetyl glucosamine and N-acetyl muramic acid and has peptide chains from these units, which aid in structural support.

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Structure of a typical Plant Cell

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Structure of a typical Bacterial Cell

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Structure of a typical animal cell 

Cytoskeleton:

The cytoskeleton is the structural frame of the eukaryotic cell and also plays an important role in maintaining the cell’s shape. The cytoskeleton is comprised of microfilaments (5 nm thick), microtubules (25 nm thick) and intermediate filaments that form a network within the cytoplasm of the cell. The microfilaments contain protein and allow movement of cell organelles within the cell such as mitochondria (are moved where there is a high demand for ATP) and microtubules allow cellular movement, which includes vesicular movement during endocytosis and exocytosis.

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Structure of the Cytoskeleton or the ‘framework’ of the cell

Cytoplasm:

The cytoplasm includes all the contents (fluid – soluble, non-soluble and organelles) that span the entire cell excluding the nucleus (surrounded by a nuclear membrane). The cytosol is the soluble, fluid component of the cytoplasm and contains the gel-like, homogenous matrix and salts such as Na+ and other soluble salts.

Nucleus:

The nucleus of eukaryotic cells (contain a true nucleus) is the organelle, which controls all metabolic activities in the cell and is also known as the ‘agent’ of heredity. The nucleus contains all the genetic material otherwise known as DNA (deoxyribonucleic acid that is double stranded), which form chromatin threads (DNA wrapped around proteins known as histones). There can be tightly wound chromatin (heterochromatin visible in interphase of the dividing cell) and euchromatin (less coiled). This DNA contained within the nucleoplasm is linear and contain all the ‘codes’ in base sequences that allow the synthesis of proteins. The nucleoplasm is surrounded by the nuclear envelope, which contain nuclear pores that function in the transport of materials (such as mRNA) from the nucleoplasm to the cytoplasm and vice versa. The nucleolus is located within the nucleoplasm but is separated from the chromatin and stains dark. This is the region of the synthesis of ribosomal subunits (ribosomes).

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Structure of the Nucleus which controls all activities taking place in the cell

Chloroplast:

This double-membraned organelle is present in plant cells only. It functions as the ‘agent’, which performs photosynthesis that converts light energy from the sun into chemical energy in the form of carbon. The chloroplast consists of sac-like membrane bound vesicles that contain pigments attached to its surface (such as primary pigments or chlorophylls). These vesicles are known as thylakoids that are stacked together (in vertical piles) to form grana. The matrix or fluid-like substance that the grana are surrounded by is known as the stroma. This is the region of carbon fixation. Chloroplasts also contain 70 S ribosomes and circular DNA, which is not a true nucleus, but instead is called the nuclear region. This is one of the various factors, which explain the Endosymbiont Theory, which states that chloroplasts and mitochondria have been referred to earlier as free-living prokaryotic organisms that have been engulfed by eukaryotes and they both live in mutualistic relationship.

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Structure of a chloroplast (present in plant cells only)

Mitochondria:

Mitochondria (chondriosomes) are known as the ‘power-houses’ of the cell. Due to their generation of energy in the form of ATP (Adenosine triphosphate) through the process of aerobic respiration, energy in this form is transported to regions of heavy cellular metabolism or energy-required reactions. The mitochondria have a double membrane consisting of the outer membrane and the inner membrane, which is folded to form cristae (increases surface area). Each of the cristae contain ATPase, the enzyme that catalyses the formation of ATP. Surrounding the cristae in the inner membrane is a fluid known as the matrix. The matrix contains 70 S ribosomes and circular DNA in a nuclear region of the organelle, which is similar to chloroplasts and it, is also associated with evidence of the Endosymbiont Theory.

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Structure of a  Mitochondrion, the ‘power houses’  of the cell

Endoplasmic Reticulum (Smooth and Rough ER):

Endoplasmic Reticulum (ER) is membrane bound sac-like structures that form an intricate interconnected ‘network’ in the cytoplasm. The Rough ER originates and encircles the nuclear envelope and is known as rough ER for its appearance but has ribosomes on the surface of it, which gives it this characteristic. This endoplasmic reticulum functions in protein synthesis and takes part in post translational protein synthesis which means that after the peptide chains are made in the free ribosomes within the cytoplasm, the rough ER modifies the protein by removing or adding substances or adding carbohydrate chains etc. and transporting these proteins out of the cell via the Golgi Complex/Apparatus. The rough ER is functional only for proteins that are to be secreted and are very abundant in secretory cells. They also function in the reorganisation of the nuclear envelope since they originate from the nuclear envelope. The Smooth ER is also membrane bound sac-like structures except do not contain ribosomes and has its origins from the Golgi Complex/Apparatus. It has a wide range of functions such as carbohydrate, sterols, vitamins and lipid synthesis and is also used in the liver for detoxification by having digestive enzymes, which break down toxins.

Golgi Complex/Apparatus:

These are also membrane bound sac-like structures known as cisternae that form a concave system in the cytoplasm (but are not branched and interconnected as in ER) and it functions in packaging and exporting substances from the cell. The Golgi complex forms a network with the ER and the ER transports substances to the Golgi complex and in this complex, protein may be further modified and are then secreted from the cell via vesicles that bind with the cell membrane and allow the substances out of the cell. The Golgi complex also functions in the formation of glycolipids and glycoproteins.

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Structural features including Endoplasmic Reticulum and the Golgi Complex

Lysosomes:

These are membrane bound vesicles, which has its origins from the Golgi complex/apparatus and functions in digestion of waste products of metabolism. It contains hydrolysing enzymes, which can digest almost all organic matter with the exception of cellulose (digested by cellulase). Lysosomes range from 0.2 to 2 micrometres in diameter. Performs phagocytosis of the food external to the cell (food vesicle) and binds with another vesicle from the Golgi apparatus to form a secondary lysosome. This is where digestion of the food takes place.

Proteasomes:

These are enzymes responsible for the degradation or break down of excessive proteins and abnormal proteins. They specify mostly with endogenous proteins. That is, proteins that are synthesised for cell function only. These individual amino acids are reused in further protein synthesis in the cell.

Ribosomes:

These are the sites of protein synthesis. They form the ‘assembly line’ for all the amino acids from the mRNA and place these amino acids in the right conformation to form the primary polypeptide chain that is later modified into a secondary or tertiary protein (translation). Ribosomes are made of a smaller and larger subunit that is synthesised in the nucleolus. In eukaryotic cells, there are 80 S ribosomes and in prokaryotes there are 70 S ribosomes. The S is a Svedberg unit of sedimentation from an ultracentrifuge.

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Structure of a Ribosome, some are more complex and have more structural features

Factors Affecting Cell Size

  • Cell volume increases at a faster rate in comparison to cell surface area. In fact, as cell size increases the ratio of volume to surface area decreases. This can decrease the diffusion rate in a cell and therefore the cell cannot remove wastes or obtain nutrients from outside efficiently which may cause death of the cell either by being poisoned or by starvation.
  • The nucleus contains DNA can affect cell size since it controls all functions of the cell, especially the genetic and hereditary traits and it must control a limited number of organelles for the normal functioning of the cell.
  • Depending on the function of the cell, this can affect the cell size. For example, red blood cells lose their nucleus and form a biconcave shape to fit into vessels of the circulatory system.
  • The cell wall can affect the size of the cell since its tensile strength functions in the maintenance of cell turgidity and the osmotic pressure within the cell can either cause shrinkage or bulging.
  • The cytoskeleton affects the size of the cell since it is the framework that ‘holds’ the cell together.

Differences between Prokaryotic cells and Eukaryotic cells

Characteristic/feature

Prokaryotic cells

Eukaryotic cells

Cell size

      Usually around 0.5 micrometres          Up to 40 micrometres

Type of DNA (Genetic Material)

      Circular DNA          Linear DNA

Nucleus

  • No true nucleus
  • Nucleus is located in a region known as the nuclear area
  • Not surrounded by a nuclear envelope
  • ‘Pro’ meaning before and ‘karyote’ meaning nucleus
  • Has a true nucleus
  • Nucleus is bound by a nuclear envelope
  • Nuclear envelope contains nuclear pores
  • ‘Eu’ meaning after and ‘karyote’ meaning nucleus

Cell wall

  • Contains a cell wall made of peptidoglycan layer (murein)
  • Cell wall only present in plant cells made of cellulose, which is a polymer of beta glucose
  • No cell wall present in animal cells
  • Fungi cell wall made of chitin

Ribosomes

  • 70 S ribosomes which are smaller
  • 80 S ribosomes which are larger

Unicellular or Multicellular?

  • All prokaryotes are unicellular and belong to the kingdom Monera
  • Most Eukaryotes are multicellular
  • The unicellular prokaryotes are termed collectively Protista or protozoans

Characteristics of the organelles present

  • Few organelles present
  • None membrane bound
  • Contain various organelles performing specific tasks
  • Organelles are double and single membrane bound

Applications of Cell Theory: The Discovery of ROS in Mitochondria in Relation to Ageing

ROS is known, as Reactive Oxidative Species are highly reactive molecules that are waste products of the mitochondria after aerobic respiration that cause oxidation of vital materials needed by the body such as DNA, proteins and lipids. Degradation of such materials can greatly affect aging and the decrease of mitochondria was linked to several degenerative diseases that occurs with age such as Alzheimer’s (form of dementia). Although, it has been proven that substances such as antioxidants can decrease the levels of ROS being produced that inhibit cell deterioration from these highly oxidative chemicals and cellular death.

Therefore, mitochondria under oxidative stress can lead to neurological conditions and has a role to play in the many processes which one undergoes when ageing.

References:

  1. Atlas, Ronald M., Microorganisms in our World, 1995, Mosby-Year Book, Inc.
  2. Claus, Harald, Prokaryotic Cell Wall Compound – Structure and Biochemistry, 2010, Springer
  3. Jaypee Brothers, Medical Publishers, Chittiprol, Biochemistry: Instant Notes for a Medical Student, 2006, Jaypee Publishers
  4. Mirsky, Alfred E., The Cell – Biochemistry, Physiology, Morphology, Vol. II, 1961, Academic Press
  5. Staff, E., Human Anatomy and Physiology Review for Premed Students, Examville Study Guides
  6. Talaro, Kathleen and Arthur, Foundations in Microbiology, 1993, Wm. C. Brown Publishers
  7. http://www.hindawi.com/journals/jst/2012/646354/

INTRODUCTION

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