Multiple choice questions

Questions:

  1. Which combination of the following organelles is specific to animal cells?

I ribosomes

II golgi apparatus

III lysosomes

IV centrioles

V Plasmodesma

VI smooth ER

(A)I, IV, II

(B)  V, III, VI

(C)  III and IV only

(D)I, III,V

(E)  all of the above

 

2. Which of the following statements are true about Glycolysis:

I    The entire reaction contains 10 enzymes in which all are reversible

II    At the end of glycolysis the net formation of ATP is 2

III   Glycolysis is the only means by which ATP is produced

IV   PFK-1 is the most regulated enzyme

V    Only one Pyruvate molecule is formed at the end of glycolysis

(A)II, IV and V

(B)  II

(C)  I, III and IV

(D)II and IV

(E)  I and IV

(F)   All of the above

“Obesity and Cancer: A Gut Microbial Connection”

Ohtani, Naoko, Shin Yoshimoto and Eiji Hara. 2014. “Obesity and Cancer: A Gut Microbial Connection”. The Journal of Cancer Research (7): 1883-1884. Accessed April 8, 2014. http://cancerres.aacrjournals.org/content/74/7/1885.full

 

According to the Oxford dictionary, cancer being one of the top five leading causes of death globally is described as “a disease caused by an uncontrolled division of abnormal cells in a part of the body”. Not only does genetics have a role in cancer, but one’s lifestyle choices such as smoking, diet and physical activity are major contributions towards the development of cancer. Hence obese persons certainly pose a high risk of developing cancer. In the Journal of Cancer Research article, through experimentation and analysis of mice, the authors present and explain the direct relationship between attributes of obesity, particularly in the gut and cancer.

The researchers proved through the comparison of mice fed a high-fat diet and a normal diet that various changes occur which in turn contribute to cancer development. At first no changes were detected between the mice, but this was altered upon changing the sterile surrounding environment of the mice. By treating both types of mice with a chemical carcinogen 7, 12-dimethylbenzanthracene (DMBA) and altering their genes to cause bioluminescence to occur this lead to some conclusions being made. Over a period of 30 weeks it was found that only the obese mice developed tumors within the liver portraying that obesity is in fact related to cancer development.

As this was established it was further inferred that not only does being obese cause cancer, but alterations that occur in the gut due to obesity contributes to cancer as well. It was seen that obesity caused the bacteria of the gut to undergo activation upon which promotes cancer growth. Therefore not only was obesity enough on the system to induce cancer, but obesity coupled with changes incurred to intestinal bacteria are highly linked to cancer growth. Fortunately by further experimentation researchers found a way to counteract the bacteria of the gut through antibiotic treatment.

Overall, it was amazing to see how important something such as diet – which can be taken for granted – is a major factor that can put anyone at risk to cancer. Additionally, another astonishing revelation concerning the intestinal bacteria and its relation to cancer was an mysterious interesting piece of information to be obtained from this article. This therefore should be of great warning to all persons that unhealthy eating, lack of exercise and obesity poses double the risk of developing cancer. It definitely instills such a sense of fear concerning one’s health, but at the same time it is also intriguing to understand the complexity and diversity of the body. Ohtani, Yoshimoto and Hara, the authors of this journal, have definitely done a great job in educating and promoting the need for healthier living. Persons should heed to the information given and truly take control of one’s life by making adjustments to poor lifestyle habits. If this is done it is quite possible that a healthy future can be attained globally.

“Application and Functions of Stabilizers in Ice Cream”

Bahramparvar and Mostafa M. Tehrani. 2011. “Application and Functions of Stabilizers in Ice Cream”. Food Reviews International, 27:4, 389-407, DOI. Accessed March 4, 2014. http://dx.doi.org/10.1080/87559129.2011.563399.

 

Now, I know everyone has either eaten, seen or heard of ice cream. If not, I will be more than happy to personally direct you to the nearest ice cream shop. However, have we ever realized that aspects of Biochemistry are involved in the ice cream making process?

Although we love ice cream, there are tons of ingredients, additives and technical attributes that go into its creation. I certainly did not know that until I met this article by Maryam Bahramparvar and Mostafa Mazaheri Tehrani of Ferdowsi University of Mashhad in Iran. The article “Application and Functions of Stabilizers in Ice Cream” is found in the journal Food Reviews International published by Taylor and Francis. The authors’ review extensively educates the reader on the types of stabilizers used in ice cream, their functions and limitations. Stabilizers refer to a specific group of substances that are added to enhance the overall quality of ice cream for consumption. According to Bahramparvar and Tehrani, the main uses of stabilizers are:

  • To produce smoothness in body and texture
  • Retard or reduce ice and lactose crystal growth during storage
  • Provide uniformity to the product
  • Provide some degree of shape retention during melting
  • Contribute to mix viscosity
  • Stabilize the protein in the mix to avoid wheying off
  • Help in suspension of flavoring particles
  • Create a stable foam with easy cut off and stiffness at the barrel freezer for packaging
  • Slow down moisture migration from the product to the package or the air
  • Assist in preventing shrinkage of the volume during storage.

There are a variety of stabilizers available in the ice cream industry, but this article highlights the main stabilizers used:

  • Gelatin
  • Guar Gum – obtained from the seeds of a tropical legume Cyamoposis tetragonolba grown in India and Pakistan.
  • Sodium Carboxymethyl Cellulose
  • Locust Bean Gum (Carob Bean Gum) – obtained from the beans of the Ceratonia siliqua tree mostly grown in the Mediterranean.
  • Carrageenan (Irish Moss) – majorly sourced from tropical red sea weeds which are commercially farmed in the Phillipines, Indonesia and Tanzania.
  • Xanthan
  • Alginates
  •  Microcrystalline Cellulose

Although all of the stabilizers mentioned above are used minimally in ice cream, they function in the following ways according to the results of the research by Bahramparvar and Tehrani:

 

  •     Prevent phase separation which occurs when the polysaccharides in the ice cream mix are unable to completely blend        with milk proteins present and “a visual separation of clear serum is seen”.
  •     Increase the volume/viscosity of ice cream mix as stabilizers reduce the air size present to improve the ice cream quality.
  •     Improve aeration and body of ice cream.
  •     Control the melting rate by increasing “the melting resistance”.
  •     Restrict growth of crystals of ice through storage which is related to ice cream viscosity.
  •     Improve sensory characteristics of ice cream by retarding iciness, enhancing creaminess and decreasing wateriness.

Even though ice cream is an internationally recognized and widely consumed product, Bahramparvar and Tehrani educate readers of the unknown ingredient of stabilizers in ice cream and their effects.

Nucleotides and Nucleic acids

The central dogma of biology as we know it is built around the little molecule that we know as DNA. For this is transcribed into RNA which is then translated to protein molecules (inclusive of enzymes). When DNA molecules are broken down into their simplest constituents, they come down to many nitrogenous bases, pentose sugars and phosphate structures. When one of each is put together it is known as a nucleotide. Then many of these nucleotides sequentially joined together forms polynucleotides aka nucleic acids.

 

 

Nitrogenous Bases can be classified as either purines or pyrimidines. They can be found in both DNA and RNA molecules. Purines present in both molecules are Adenine (A) and Guanine (G). On the other hand, Cytosine(C), Thymine (T) and Uracil (U) are pyrimidines but note that Uracil is not present in DNA. In RNA, Uracil is present instead of Thymine. These nitrogenous bases are distributed along the length of the DNA double helix molecule. Their alignment allows for Adenine (A) and Thymine (T) to be bonded to each other via two hydrogen bonds and Cytosine (C) and Guanine (G) to be bonded to each other via three hydrogen bonds. This is the only arrangement of these base pairs. This shows that the purines binds to its complementary pyrimidine to hold the anti-parallel DNA strands in a double helical structure.

In addition, Erwin Chargaff studied the ratios of the bases in the DNA molecules of different organisms. From this he realized that the ratio of Purines to Pyrimidine is approximately 1:1 which suggests that they occur in almost the same frequencies.

structure of DNA

NB:  Thymine only binds to Adenine and Guanine only binds to Cytosine.

DNA strands

These DNA strands are considered as anti-parallel because they both possess a (3)three prime end and a (5) five prime end.  The 3 end of one strand aligns with the 5 end of the other while the strands remains parallel to each other. another DNA strand

NUCLEOTIDES

Nucleotides are comprised of Nucleosides and a Phosphate group. As far as naming them, from the table below one can see that names of nucleosides ends with “sine” or “dine” and nucleotides end with “ate” from phosphate.

table

One thing to note is that by convention, the naming of a nucleotide = name of nucleoside + prefix indicating no. of attached phosphate molecules + Phosphate at the end. An example:

  • Adenosine Triphosphate (ATP), which is an energy carrier within cells.

(By hydrolysis of its bonds with phosphate, energy is released).

  • Nicotinamide Adenine Dinucleotide (NAD+) contributes to cofactors of enzymes. They remove hydrogen from molecules (dehydrogenation reactions).

 NUCLEIC ACIDS

These molecules are made in the nucleus of the cells and are of two types: DNA and RNA.

                       TYPES FUNCTIONS
 

DNA

Houses genetic material in its structure that codes for the production of functional proteins and RNA molecules via transcription.
Ribosomal RNA (rRNA) Single strand bearing a specific base sequence that codes for the production of specific functional proteins. For e.g. Enzymes.

It works hand in hand with the ribosome.

Messenger RNA (mRNA) Transfers genetic codes to the ribosomes in the cytosol from genes on DNA molecules.
Transfer RNA (tRNA) It helps to decode/translate the genetic codes presented to the ribosomes via mRNA. By this translation, proteins are synthesized.
RNA Some of these molecules possess catalytic abilities.

As mentioned earlier the nucleotides joined together forms nucleic acids. The bonds formed between the neighbouring nucleotides are known as phosphodiester linkages. They are formed between the phosphate group of one and the -OH group of the 3 carbon of another nucleotide.

Phosphodiester linkage

STABILITY OF NUCLEIC ACIDS

The stability of nucleic acids is highly dependent on the hydrophobic interactions within them. On the other hand, the stability of the DNA double helix and the secondary structure of RNA are dependent on hydrogen bonding. Such stabilities can be disrupted by strongly acidic and high temperature conditions that causes hydrolysis of core bonds and denaturation. Strongly alkaline solutions tautomerize the nucleic acid thus disrupting its stable configuration. This results in the denaturation (unwinding) of the helical structure. However, when these molecules are denatured, renaturation can achieved by both rapid and slow cooling.

 

another DNA strand

Due to nucleic acids capability to absorb UV light via their nitrogenous base, a method for their detection, assessment of their purity, quantitation and other properties and features is established.

Circular DNA molecules are more resistant to the unwinding of the helical structure than the relaxed DNA molecules. This is due to their super coiling. These two configuration of DNA molecules are known as topo-isomers of each other. The only difference between them is their degree of coiling which is regulated by the enzyme topoisomerase.

REFERNCES

  • Nelson, David L. and Michael M. Cox. Lehninger Principles of Biochemistry Fourth Edition
  • Matthew, Jason. Nucleotides and nucleic acids  pptx-Powerpoint

Lipids

Lipids or commonly called fats are organic molecules mostly composed of a carboxyl end and a long hydrocarbon tail. The names and structures of these Lipids are:

name of lipids

Short chain fatty acids are made of less than six carbon (C) atoms, medium chain fatty acids are about six to twelve C atoms long, whilst fatty acids more than 14 C atoms long are referred to as long chain fatty acids.

When fatty acids combine with a long chain alcohol, waxes are formed. These waxes can be found in fruits where they act as a natural protective layer. They can also be used in the pharmaceutical industry as a base, an example of which is the wool wax Lanolin, a main ingredient used in Olay due to its easy absorption into the skin

Functions and Properties of Lipids

Lipids have many functions and uses in the body which can be seen in the following points

  • Provides energy as per gram of fat, 9kcal is produced.
  • Acts as an energy reserve as excess/ unused energy from carbohydrates, proteins and lipids will be stored in adipose tissues in the form of Triacylglycerol.
  • Acts as an insulator to keep the body warm protecting it from very cold temperatures.
  • Provides mechanical insulation acting as a cushion around vital organs protecting it from any mechanical shock.
  • Supplies the body with essential fatty acids called Linolenic Acid and Linoleic Acid.
  • Aids in the formation of cell membranes in which phospholipids are responsible i.e. the phospholipid bilayer.
  • Steroids are a class of lipids, from which cholesterol can be derived. Cholesterol can be found within cell membranes and is used to make steroid hormones.
  • Through the presence of fat, vitamins A, D, E and K can be retained in the body hence why they are called fat soluble vitamins.
  • Increases the palatability of foods
  • When digestion of fats takes place in the body this gives longer feeling of fullness known as satiety as fats digest longer within the body.

In the second point made about the storage of excess energy in adipose tissue in the form of Triacylglycerol (TAG), this molecule plays an important role in animals and energy production. In the case of Polar bears that undergo long periods of hibernation, under the skin of these bears a lot of TAG will be created as it provides a great deal of insulation and energy to maintain survival during hibernation period. As Triacylglycerol is a more reduced form carbon, more energy is produced per gram compared to the carbohydrates glycogen and starch.

 

Saturated Fats vs. Unsaturated Fats

Lipids can be found in two physical states, solid and liquid. The reasoning behind these two different states is due to the bonding that occurs within the molecule. As fats such as margarine and butter remain solid at room temperature this is because within their structure they are made up of straight chain hydrocarbon chains that have a single bond between the C atoms. Therefore they are saturated and can be referred to as saturated fats. However, fats such as oils remain liquid at room temperature as double bonds are present in the bonding taking place between the C atoms that make up the hydrocarbon chain. As such, they are unsaturated and are therefore called unsaturated fats.

SATURATED FATS UNSTAURATED FATS
No double bonds present

C-C-C-C

Double bonds present

C-C=C-C

At room temperature: solid At room temperature: liquid
Found in most animal fats Found in plant and fish fats
Does not form kinks, so molecules are packed closely together Forms kinks within structure, so molecules are not packed closely together

 

butter

oil

 

 

 

 

Nomenclature of Fatty Acids

In the naming of Fatty Acids:

  1. Fatty Acids have both an ethyl end and a carboxyl end

CH3(CH2)7CH=CH(CH2)7COOH

                                                                                             Methyl end                                          Carboxyl end

  1. To count the number of carbons present in the fatty acid, one must start counting from the carboxyl end.
  2. The number of double bonds if present should also be counted where the first carbon atom that is encountered when counting from the carboxyl end is the one which will be present in its naming.
  3. When naming the fatty acid it should be written in the following form. As this structure is Oleic acid it would be written as:

18:1 (∆9)

                                                                                             no. of C                   no. of double      the no C atom at which

                                                                                     atoms present            bonds present        the double bond is present

 

Trends in the Physical properties of Lipids

The two properties that can be examined in fatty acids are the melting point (oC) and solubility (mg/100 mL in H2O).

Melting point (oC)

–         Melting point increases as the number of C atoms present in saturated fatty acids increases.

–         Melting point is lower in unsaturated fatty acids as compared to saturated fatty acids which have a higher melting point. Hence when more double bonds are present, the melting point decreases.

Solubility (mg/100 mL in H2O)

– As the number of C atoms present in fatty acids increases, solubility decreases.

 

Essential Fatty Acids

When a substance is considered essential, this means that the body can synthesize it and subsequently only through the diet can this substance be obtained. This is exactly what is meant by an essential fatty acid. As our bodies cannot synthesize fatty acids composed of double bonds located before the ninth carbon from the methyl end, they have to be obtained through the dies. These fatty acids are Omega-3 and Omega-6 also called Alpha-Linolenic Acid and Linoleic Acid respectively.

Omega infers the position of the first double bond in relation to the methyl end.

CH3(CH2)7CH=CH(CH2)7COOH

                                                                                         Methyl end

Therefore in Omega-3 and Omega-6, the first double bonds are found at C atom 3 and at C atom 6 respectively, both of which are found when counting from the methyl end.

CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH

Alpha-Linolenic Acid, Omega-3

Sources: flaxseed, soybean oil, dark green leafy vegetables, salmon, tuna

CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH

Linoleic Acid, Omega-6

Sources: seeds, nuts, sunflower oil, cottonseed oil

 

Trans Fatty Acids

 When unsaturated fatty acids are hydrogenated, hydrogen is applied converting the double bonds present to single bonds where the new bonds formed have added hydrogen bonds to them. The process of hydrogenation also creates Trans fatty acids which can be found in fried foods. These Trans fats are very unhealthy as they increase the formation of LDL cholesterol which leads to a high risk of heart disease. However fatty acids are naturally found in abundance in the cis configuration, therefore mostly cis fatty acids are found in the diet except for in fried foods as stated before.

 

Formation of Triacylglycerol (TAG)

Triacylglycerol also commonly known as triglycerides are formed when the three hydroxyl groups on glycerol and the carboxyl group of three fatty acids (the fatty acids could be the same or different) undergo a condensation reaction. In a condensation reaction water is removed from between the molecules as the OH group from the fatty acids and the hydrogen from the glycerol are removed forming water. As these groups have been removed and are no longer present, the glycerol and fatty acids form ester bonds thereby creating a Triacylglycerol or a Triglyceride.

triglyceride

 

When fats are hydrolysed, the opposite occurs where water is added to the Triglyceride/Triacylglycerol, splitting into glycerol and three fatty acids. This reaction is catalyzed in the body by the enzyme lipase. Strong bases can be used in the hydrolysis of fats such as sodium hydroxide NaOH or potassium hydroxide KOH. However instead of fatty acids being produced, instead the sodium or potassium salt of a fatty acid is produced with glycerol.

glycerol

Membrane Lipids – Formation of Phosphotidate

In the formation of Phosphotidate, this incorporates the combination of glycerol-3-phosphate with two fatty acids. In glycerol-3-phosphate, the third carbon atom is bonded to a phosphate group. On C atoms 1 and 2 an ester linkage is formed between two fatty acids where one fatty acid is saturated and the other unsaturated. The third C atom contains the phosphate group at which X in the diagram denotes the bonding of a group. When hydrogen is present in the position that X is located the structure is therefore a Phosphotidate. Therefore it can be stated that in the general structure of Phosphotidate, it entails a glycerol backbone bonded to a phosphate group at the third carbon and a saturated and unsaturated fatty acid bonded to carbon atoms one and two. As the second carbon atom is unsaturated, this causes the fatty acid to have a kink within its structure which is beneficial to the membrane making it less compact and more fluid. All naturally occurring fatty acids would have the cis configuration meaning that the hydrogen atoms bonded remain on one side of the double bond. However, the hydrogen atoms in the trans configuration are located on the opposite sides of the double bond. As stated before the trans configuration / trans fats are unhealthy.

 

Non polar tail, hydrophobic end

structure Polar head, hydrophilic end

Due to the structure of Phosphotidate it can be stated that it is amphipathic. There are two parts to the molecule, the hydrophilic (water loving) and the hydrophobic (water hating) parts which are the phosphate and fatty acid groups respectively. The hydrophilic part is referred to as the polar head and the hydrophobic part the nonpolar tail.

Membrane Lipids – Formation of Sphingosine

Sphingosine comprises of an unbranched 18 carbon alcohol. It has a trans configuration between C-4 and C-5, with hydroxyl groups at C-1and C-3 and at C-2 an amino group.

sphingosine

With sphingosine, the lipid that can be formed is ceramide where sphingosine is the backbone and at the amino group on C-2, a fatty acid forms and amide bond.

amide bond

Membrane Lipids – Formation of Cholesterol

In cholesterol, there is a sterol nucleus at which there are four fused rings, three rings have six carbons and one has five carbons. An alkyl side chain at carbon 17 is present along with a double bond between C-5 and C-6 and a hydroxyl group at C-3 and. In all cholesterol comprises of a total of 27 carbon atoms.
cholesterol structure

 

 

 

Sterol Nucleus

 

 

Polar head

Hydrophilic end

 

Cholesterol is predominantly present in cell membranes of animals through orientation in the phospholipid membrane. How this occurs is that hydroxyl group of the cholesterol molecule aligns itself with the polar head of phospholipid molecule and a hydrogen bond is formed between the oxygen (O) of the ester linkage that is formed within the phospholipid molecule, i.e. the glycerol and fatty acids. The cholesterol’s sterol nucleus and alkyl side chain also act together with the fatty acid hydrocarbon chains of the phospholipids.

The fluidity of the cell membrane is regulated by cholesterol. As cholesterol is situated between the phospholipids it helps to maintain membrane fluidity through the various temperature changes that occur within the body and in turn affect the membrane. When there is an increase in temperature, cholesterol decreases the fluidity of the membrane by limiting the movement of phospholipids, while at lower temperatures, cholesterol inhibits the membrane from becoming more compact by maintaining fluidity.

 

References

  • Garrett, Reginald H. and Charles M. Grisham. 2010. Biochemistry. Fourth edition. Boston: Brooks/Cole, Cengage Learning.
  • Whitney, Ellie and Sharon R. Rolfes. 2012. Understanding Nutrition. California: Wadsworth
  •        Cengage Learning

TCA and ETC cycle

The tricarboxylic acid (TCA) cycle and the electron transport chain (ETC) are both very important to the metabolic pathways within the mitochondria of the eukaryotic cell. In essence the products of glycolysis (pyruvate molecules) acts as the substrates for the TCA cycle and the electron transport chain. When the pyruvate molecules are produced they are oxidised by the various reaction of the TCA cycle in which they give off electrons. These free electrons then flows through the electron transport chain. In doing so it powers the process of oxidative phosphorylation which generates most of the cell’s ATP. Hence, due to oxidative phosphorylation, the mitochondria is viewed as the cells energy chamber.

Here we’ll take a closer look at the TCA cycle which takes place in the matrix of the mitochondria. The TCA cycle starts with the oxidised pyruvate molecules known as Acetyl-CoA. These molecules undergoes a series of enzyme catalysed reactions which include condensation reactions, dehydrogenation, decarboxylation, phosphorylation, hydration and dehydration. With these reactions, these molecules takes several physical forms that possesses varying properties. In chronological order these forms are known as Citrate, Isocitrate, α-Ketoglutarate, Succinyl-CoA, Succinate, Fumarate, Malate and lastly Oxaloacetate. Furthermore, below is an outline of the TCA cycle.

TCA cycle

For clarity

  • IDH- Isocitrate Dehydrogenase enzyme  (remove hydrogen from isocitrate)
  • α-KGDH- α-Ketoglutarate Dehydrogenase enzyme (remove hydrogen from α-Ketoglutarate)
  • CoA or CoASH- Co enzyme A (carrier of acetyl groups)
  • MDH- Malate Dehydrogenase (remove hydrogen from malate)
  • OAA- Oxaloacetate

 

>> A much simpler outline of the TCA cycle……

Acetyl coA

Another important thing to note is that Succinyl-CoA undergoes substrate level phosphorylation which results in the generation of ATP and Succinate. At different stages within the cycle electrons are released and this provides feed for the electron transport chain (ETC). The electron transport chain is where greater ATP synthesis is powered.

ETC Cycle

In the inner membranes of the mitochondrion there are complex molecules (electron carrier molecules) including proteins and cytochromes which makes up the electron transport chain. When the NAD molecule is produced in the matrix of the Krebs cycle, the hydrogen atom released splits into a hydrogen ion (H+) and an electron.

                               H –> H+ + é

The electrons from NADH + H+ are transferred to the electron carrier protein (NADH dehydrogenase) which is reduced as it gained an electron and the reduced NAD is oxidised since it lost hydrogen. The electrons are carried along the ETC, the protons are transferred to the outside of the membrane and NAD returns to the Krebs cycle to be reused as the coenzyme to pick up hydrogen. Coenzyme Q accepts protons from inside the cell membrane and transports it along the ETC increasing the proton gradient.

As the first electron carrier transfers the electron to the second, it is oxidised and the second electron carrier is reduced. Energy is released throughout the chain forming ATP. At the end of the ETC and during aerobic respiration cytochrome C allows the electron to combine with an electron acceptor oxygen and hydrogen to form water. The hydrogen ions diffuse down the electrochemical gradient and ATP synthase is an enzyme which uses the proton force produced to synthesize ATP from ADP and Pi. This is chemiosmosis.

ETC

 

Glycolysis part 2

Fates of pyruvate

Aerobic conditions

1)     Entry into the TCA cycle

The two pyruvates formed from glucose is converted to acetyl-CoA under aerobic conditions and with the use of an enzyme pyruvate dehydrogenase. The CoA is further broken down into carbon dioxide and water which enters the TCA cycle. Most ATP is produced with this reaction. Activation energy sums up to -33.4KJmol-1.

16979-004-83CCEC5C

Anaerobic conditions

2)     Conversion to lactate

Pyruvate converts to lactate with an enzyme lactate dehydrogenase (LDH) and NADH is regenerated to NAD+. No ATP is regenerated and this reaction can only occur with mitochondria. This type of fate occur in erythrocytes (red blood cells). Even though red blood cells carry oxygen they do not contain mitochondria hence the conversion to lactate can occur under anaerobic conditions.

lactate dehydrogenase

3)     Ethanol fermentation

Ethanol fermentation occurs in two steps each containing a different enzyme. Firstly the pyruvate is converted to acetaldehyde with a thiamine pyrophosphate (TPP) cofactor and pyruvate decarboxylase enzyme where carbon dioxide is lost. Secondly the acetaldehyde is converted to ethanol with an alcohol dehydrogenase enzyme. NADH is converted into NAD+ which allows glycolysis to continue a cycle.

cycle

Fermentation is the removal of ATP where oxygen is not used up and the NAD+ or NADH concentration is not changed.

USES OF FERMENTATION

  • Wine making
  • Baking
  • Taste in sour milk
  • Beer brewing
  • Taste and fragrance of sauerkraut
  • Producing biofuels

glucose to lactate

NAD+ must be regenerated in order for glycolysis to be continuous in the fates of pyruvate.

Enzymes that use Thiamine Pyrophosphate (TPP)

Enzyme Pathway
Pyruvate dehydrogenase

α-ketoglutarate dehydrogenase

Synthesis of acetyl CoA, citric acid cycle
Pyruvate carboxylase Ethanol fermentation
Transketolase -Carbon assimilation reactions

-Pentose phosphate pathway

 

Glycolysis feeders pathway

In glycolysis many different carbohydrate molecules are broken down and energy is released. Glucose-6-phosphate is the most common of these molecules. Fructose is another molecule that undergoes glycolysis. It accomplishes this via either the Fructose 1-Phosphate pathway or the Fructose 6- Phosphate pathway. Galactose also undergoes glycolysis but this uses a four step process that reduces it. It is converted to Glucose 1-phosphate by an incoming UDP glucose molecule. This molecule is then converted to glucose 6-phosphate via the enzyme phosphoglucomutase which changes the location of the phosphate group from the 1` carbon to the 6` carbon. This structure is then converted to fructose 6-phosphate which then forms fructose 1,6-biphosphate by the enzyme, phosphofructokinase-1. From these fructose 1,6-biphosphate molecules two simple 3 carbon structures are formed. Glyceraldehyde 3-phosphate and Dihydroxyacetone phosphate are the molecules formed.  Below is an outline of this entire feeders pathway.

galactose metabolism

In Glycolysis it is important for us, not only to learn the various steps in this process, but also to know the enzymes which catalyze each of these reactions.

The multi-step pathway has reaction types including phosphorylation reactions, dehydration reactions, isomeration reactions, lysis etc.

A simple way for us to remember enzymes used in these reactions are to associate the type of reaction to a corresponding enzyme.

For example, we know isomerases catalyze the racemization of optical isomers from previous study of enzymes. So in the glycolysis reactions converting Glucose 6-phosphate to Fructose 6-phosphate, we can deduce in this isomeration reaction, an isomerase is used.

PI

Another isomerase enzyme used in glycolysis is used in the reaction involving Dihydroxyacetone

Phosphate and Glyceraldehyde 3-phosphate

TPI

When we think of phosphorylation reactions in glycolysis we associate them with kinases enzymes as in the following reactions;

Hexokinase

1. The reaction of glucose into glucose 6-phosphate

pyr kinase

2. The reaction of 3-phosphoglycerate to 2-phosphoglycerate

PFK1

3. Fructose 6-phosphate to fructose 1,6 bisphosphate

pyr kinase

4. 1,3-bisphosphoglycerate to 3-phosphoglycerate

The enzyme Enolase is used in the dehydration reaction;

pyr kinase

 

Phosphor glycerate mutase is used to catalyze the reaction;

PM

 

The enzyme Aldolase is used to catalyze the lysis of a 6 carbon sugar into two 3 carbon sugars in the following reaction;

Aldolase

 

The following oxidation reaction is catalyzed by glyceraldehyde 3-phosphate dehydrogenase;

GAP

Glycolysis part one

Glycolysis takes place in every living cell of life. Glycolysis simply means the splitting of glucose. In glycolysis the starting product is glucose but at the end two pyruvate molecules is produced, and this is vital in glycolysis.

Glycolysis can be broken down into two phases;

  1. Preparalary phase – this phase is responsible for the first five enzyme reaction.
  2. The Pay of phase – this is where the last five enzyme reaction take place.

In all there are ten enzyme reactions.

In the first two ATP is used to give two ADP. And in the second phase four ADP is used to get four ATP and two NAD+ is used to get two NADH.

This is an image of what the partway looks like from steps one to ten.

glucose

In the first reaction (1), glucose is converted to glucose 6 phosphate, this is catalysed by the enzyme hexokinase. Hexokinase transfers the terminal phosphate group from ATP and adds it onto an accepter substrate molecule in this case is glucose. This reaction is irreversible.

This reaction is known as the first priming reaction.

The second reaction (2), glucose 6 phosphate is converted to Fructose 6 phosphate, this reaction is catalysed by the enzyme Phosphohexose isomerise.

In reaction three (3), this is where fructose 6 phosphate is converted to fructose 1, 6- bisphosphate. This is catalysed by the enzymes Phosphor Fructoskinase -1. This enzyme is the most regulated enzyme in glycolysis. At this stage it is known as the second priming reaction and is also an irreversible reaction.

The fourth reaction (4), fructose 1, 6- bisphosphate is catalysed by Aldolase to give Glyceraldehyde- 3- phosphate and Dihydrogacetone phosphate but this not go through to the next reaction but is converted to another Glyceralderehyde 3- phosphatein this is done by the last enzyme reaction which is enzyme five (5).The name of this enzyme is Triose phosphate isomerise. At the end of this phase a six carbon molecule is split into two 3 carbon molecules.

We are now in the next phase of glycolysis called the Pay of Phase

In stage six (6), two molecule of Glyceraldehyde 3 phosphate to give two molecules of 1, 3- Bisphosphateglycerate. The enzyme that catalysed this reaction is Glyceraldehyde 3- phosphate dehydrogenase. This is the reaction that oxidation occurs.

Reaction seven (7) is where 1, 3 – Bisphosphateglyorate is converted to two molecules of 3 phosphoglycerate, this reaction is catalysed by the enzyme phosphor-glycerate kinase.

At this stage is where the first ATP is formed. So the two ATP molecules which were used in the prearalary phase has been generated back.

In reaction eight (8), 3-phosphcycerate is converted to two molecules phosphoglycerate, it is catalysed by the enzyme phosphor-glycerats mulase. The 3 phosphoglcycerate is first converted into an intermediate 2,3-bisphosphoglyarate. Then the phosphor-glycerats mulaseis going to remove the phosphate group to give two molecules of phosphoglyarate.

In reaction nine (9) the two phosphoglycorate is converted to phosphoenalpyruvate due to a dehydration reaction. It is catalysed by the enzyme Enolase.

In the last reaction which is ten (10), the two molecules of phosphoenalpyruvate are converted to two molecules of pyruvate. For every one molecule of phosphoenolpyruvate, one ATP is formed so it adds up to two (2).

This is where the second ATP is formed by substrate-level-phosphorylation. At this stage this is where you make your net gain of ATP. This reaction is catalysed by the enzyme Pyruvate Kinase. In this second phase from reaction six (6) to nine (9) are all revisable except reaction ten (10).

Enzymes

When we think about the metabolic reactions which occur in our bodies, we know that most of these reactions would not take place at such and effective rate without the special help of ENZYMES.

Enzyme

Enzymes provide another pathway containing a lower activation energy in order to accelerate a chemical reaction, therefore acting as a biological catalyst. Majority of enzymes can be made of proteins, and some can be RNA molecules. They are crucial to living organism as enzymes catalyze metabolic reactions in the cell necessary for life. This can by represented graphically in an Energy Profile Diagram

energy profile diagram

In this energy profile diagram the x-axis shows progress of the reaction and the y-axis shows free energy. The blue curve shows the chemical reaction without the presence of a catalyst. Here we can see the activation energy is relatively higher than the reaction with a catalyst present; the red curve. Both reactions start off with the same substrates and give the same products. The difference is the activation energy required for the reaction to occur. With activation energy, the lowest energy needed for a reaction to occur is used.

without and with enzyme

When the activation energy of a reaction is high it requires a lot of energy to convert substrate into products in the reaction. Hence only a few molecules of substrate are converted to product when the activation energy is lowered by the presence of enzymes the conversion of substrate to product is easier and can happen at a faster rate. Although the enzyme lowers the activation energy of the reaction, the enzyme takes no part in the reaction and does not change the equilibrium of the reaction.

Nomenclature

Nomenclature simply describes the naming of enzymes. Enzymes were named based on the substrate, for example: the enzyme Lipase hydrolyses Lipids.

Also some enzymes adapt their name from the function they perform, for example: the enzyme Pyruvate carboxylase catalyses the carboxylation of a carboxyl group to pyruvate.

Other enzymes which aren’t based on substrate or function end in –ASE. For example; catalase

Or  -IN. For example; Trypsin and Pepsin.

nomenclature

These were confusing as the name of some enzyme would not give any indication of its substrate or function. Further, things were more confusing when names such as Glyceraldehyde 3 phosphate/ triose phosphate/ 3-phophoglycetaldehyde are for the same enzyme.

confused face

Enzyme Classes

This confusion led to the systematic naming of enzymes by the International Union of Biochemistry and Molecular Biology (IUBMB). In this system of nomenclature enzymes are divided into six classes. These classes further divide into sub-classes and sub-sub-classes. These groups were all assigned a number; hence every enzyme will have a designated number called the Enzyme Commission (EC) number.

The six enzyme classes are;

1.      Oxidoreductases

2.      Transferases

3.      Hydrolases

4.      Lyases

5.      Isomerases

6.      Ligases

6 features

HOLOENZYMES

Enzymes are proteinaceous molecules but in order for some of these enzymes to work they require assistance from cofactors. Cofactors are non proteinaceous molecules that can be categorized into two groups, Organic and Inorganic. Inorganic cofactors as the name suggests are derived from inorganic molecules, while Organic cofactors are derived from organic molecules/substances such as coenzymes which are mostly obtained from vitamins. These organic cofactors are further divided into two groups, Cosubstrates – referring to coenzymes that bind to enzymes only when they are undergoing a reaction- and Prosthetic Group – referring to coenzymes that permanently bind to an enzyme.

So what is a Holoenzyme?

Holoenzymes are the product of the combination of apoenzymes with cofactors, where an apoenzyme is the inactive protein part of the enzyme and the cofactor as described before is the non-protein part of the enzyme.

produces

Apoenzyme + Cofactor      —————>      Holoenzyme

INORGANIC CATALYSTS VS ORGANIC CATALYSTS

Inorganic catalyst Organic catalyst
Is not made up of C, H and O Substance made of C, H and O
Depend on high temperatures such as 450oC ( Haber and Contact process) and high pressures such as 1000 atm Do not depend on high pressure and work at an optimum temperature of around 37 oC. This definitely shows how unique and efficient our bodies are
Side reactions are formed Specific enzyme, no side reactions
Poisonous to the body Not poisonous
Cannot be regulated Can be regulated

ENZYME SPECIFICITY

Enzymes completely react with and catalyse specific substrates, therefore due to this one product is constantly formed with this enzyme meaning that the product is also specific as well. For an enzyme to be able to react with a substrate this depends on the active site which has to complement the substrate. The active site is the particular part of an enzyme where the substrate binds to and is broken down into its products. As enzymes are made of proteins this means that the same characteristics that act in the stability of proteins also act in the structure of the active site. These characteristics are:

  • Hydrophobic Interactions
  • Electrostatic Interactions
  • Hydrogen Bonding
  • Van der Waals Interactions

The R groups of the proteins that make up the active site are referred to as catalytic groups. They are involved on the specificity of an enzyme allowing it to act upon the substrate.

LOCK AND KEY HYPOTHESIS FOR ENZYME SPECIFICITY AND CATALYSES.

lock and key hypothesis

In this hypothesis when the substrates(key) combines with the enzyme(lock) the product has a new shape and therefore cannot fit anymore and is let go. This explains the denaturation of enzymes and the activity loss they undergo.

Tertiary structure of enzyme —->  unfolding —-> 3D shapeless

INDUCED FIT HYPOTHESIS

induced fit hypothesis

FACTORS THAT AFFECT REACTION VELOCITY OF CATALYST

1)      Enzyme concentration

The rate of reaction increases as enzyme concentration increases. However when the active site out numbers the substrate molecule the velocity of the reaction stays the same and gives a plateau on the graph.

enzyme conc graph

2)      Temperature

Increasing temperature also increases the rate of reaction because the substrate and molecules react giving a frequency collision which overpowers the activation energy barrier, until an optimum temperature arises and then rate of reaction decreases. Basically the kinetic energy that was formed vibrates the enzyme tertiary bonds until it begins to unfold (cooperative process).

temp graph

3)      pH

In order for pH to work the substrate and enzyme must possess a chemical group either ionized or unionized. The rate of reaction increases as pH increases until the enzyme is denatured and the reaction decreases. The maximal pH varies for different enzymes because each has a different hydrogen concentration that makes it work. Some enzymes work in acidic, neutral or basic conditions.

pH graph

4)      Substrate concentration

Enzymes can be generally referred to as either Michaelis – Menten enzymes or Allosteric enzymes. These associations are made based on the fact that some enzymes possess only one active site while others possess multiple. Those having only one active site follows the Michaelis – Menten principles, while those bearing several active site follow the Allosteric principles.

Michaelis – Menten Enzymes

These enzymes all possess one reaction style/pattern. When this reaction pattern is represented graphically it takes the form of a hyperbolic curve as illustrated below. We came to the understanding that as the substrate concentration increases, the rate of the reaction also increases then slows down as when maximum possible speed (vmax) is met by the enzymes.

m-m graph

Another graphical representation of these enzymes reaction style using a double reciprocal plot is known as the Lineweaver-Burk plot. It implements straight diagonal lines with both x and y intercepts values. Here the x intercept value is (-1/km) where km refers to the enzymes’ greed for the substrate and the (y) intercept value is (1/vmax), where vmax isthe top velocity that the enzyme activity can reach.

lineweaver graph

These plots are ideal but are subject to change when inhibitors are introduced to the reaction medium. These changes occurs when inhibitors blocks enzyme activities by binding to them both permanently (irreversibly) and temporarily (reversibly). When inhibiting reversibly, it can be done in various ways such as:

  • Competitively- it is like a rush between these inhibitors and substrates to see who can bind first to the enzyme active site which is complementary to them both. This shows that substrate and the inhibitor are similar in shape to each other.

competitive enzyme

  • Non-competitively- here the inhibitor don’t rush for an active site, it just binds elsewhere on the enzyme and changes the enzyme’s shape. This changes the active sites’ shape and the substrate cannot bind they no longer complement each other.
  • Uncompetitive- here the inhibitors binds only to the enzyme-substrate complex and prevents the formation of products

uncomp enzyme

uncompetitive enzyme

where E-enzyme, P-product, I-inhibitor, S-substrate, ES-enzyme substrate complex, ESI or EIS- enzyme inhibitor substrate complex.

  • Mixed inhibitors avoid the enzymes active site but attaches to another site on the enzyme body or they attach to the enzyme-substrate complex. Even though these attachments are formed the enzyme still maintains some of its functional abilities. This separates mixed inhibitors from non-inhibitors.

mixed inhibitor

Allosteric Enzymes

The multiple active sites facilitate cooperative binding to substrates, meaning that one substrate binding to the enzyme alters the tendency of others doing the same. When the attached substrate increases these tendencies it is called a positive effector and vice versa it is called a negative effector. From this we can deduce that an effector is a modifier molecule that attaches to and regulates the enzyme. When these enzymes reaction pattern is represented graphically it takes the form of a sigmoidal or (s) curve as illustrated below.

allosteric    allo