Summary Of Fates of Pyruvate/TCA

• Pyruvate is combined with oxygen to produce Acetyl-CoA which then goes through the citric acid cycle to form CO2 and H2O. Eventually, through oxidative phosphorylation, NAD+ is regenerated from NADH and even more ATPs are made from ADP.

• Production of Lactate.  In Lactic Acid Fermentation NAD+ is regenerated from NADH by an enzyme called Lactate dehydrogenase. Lactate dehydrogenase adds a water molecule across the C=O of pyruvate. This produces the molecule lactate, which builds up in the muscles of aerobes under anaerobic conditions.

• Alcohol Fermentation – Here NAD+ is regenerated by the fermentation of pyruvate to ethanol and carbon dioxide. However, that is not the end story of this pathway. This pathway requires the enzyme pyruvate decarboxylase and alcohol dehydrogenase, both of which we’ll discuss here.

 

Pyruvate —-> Ethanol

Pyruvate —> Lactate.

Glycolysis

The above picture is a summary of steps in glycolysis.

Step 1

The enzyme hexokinase phosphorylates (adds a phosphate group to) glucose in the cell’s cytoplasm. In the process, a phosphate group from ATP is transferred to glucose producing glucose 6-phosphate.

Glucose (C₆H₁₂O₆) + hexokinase + ATP → ADP + Glucose 6-phosphate (C₆H₁₁O₆P₁) 

Step 2

The enzyme phosphoglucoisomerase converts glucose 6-phosphate into its isomer fructose 6-phosphate. Isomers have the same molecular formula, but the atoms of each molecule are arranged differently.

Glucose 6-phosphate (C₆H₁₁O₆P₁) + Phosphoglucoisomerase → Fructose 6-phosphate (C₆H₁₁O₆P₁)

Step 3

The enzyme phosphofructokinase uses another ATP molecule to transfer a phosphate group to fructose 6-phosphate to form fructose 1, 6-bisphosphate.

Fructose 6-phosphate (C₆H₁₁O₆P₁) + phosphofructokinase + ATP → ADP + Fructose 1, 6-bisphosphate (C₆H₁₀O₆P₂) 

Step 4

The enzyme aldolase splits fructose 1, 6-bisphosphate into two sugars that are isomers of each other. These two sugars are dihydroxyacetone phosphate and glyceraldehyde phosphate.

Fructose 1, 6-bisphosphate (C₆H₁₀O₆P₂) + aldolase → Dihydroxyacetone phosphate (C₃H₅O₃P₁) + Glyceraldehyde phosphate (C₃H₅O₃P₁) 

Step 5

The enzyme triose phosphate isomerase rapidly inter-converts the molecules dihydroxyacetone phosphate and glyceraldehyde phosphate. Glyceraldehyde phosphate is removed as soon as it is formed to be used in the next step of glycolysis.

Dihydroxyacetone phosphate (C₃H₅O₃P₁) → Glyceraldehyde phosphate (C₃H₅O₃P₁)

Net result for steps 4 and 5: Fructose 1, 6-bisphosphate (C₆H₁₀O₆P₂) ↔ 2 molecules of Glyceraldehyde phosphate (C₃H₅O₃P₁)

Step 6

The enzyme triose phosphate dehydrogenase serves two functions in this step. First the enzyme transfers a hydrogen (H^–) from glyceraldehyde phosphate to the oxidizing agent nicotinamide adenine dinucleotide (NAD⁺) to form NADH. Next triose phosphate dehydrogenase adds a phosphate (P) from the cytosol to the oxidized glyceraldehyde phosphate to form 1, 3-bisphosphoglycerate. This occurs for both molecules of glyceraldehyde phosphate produced in step 5.

A. Triose phosphate dehydrogenase + 2 H^– + 2 NAD⁺ → 2 NADH + 2 H⁺

B. Triose phosphate dehydrogenase + 2 P + 2 glyceraldehyde phosphate (C₃H₅O₃P₁) → 2 molecules of 1,3-bisphosphoglycerate (C₃H₄O₄P₂) 

Step 7

The enzyme phosphoglycerokinase transfers a P from 1,3-bisphosphoglycerate to a molecule of ADP to form ATP. This happens for each molecule of 1,3-bisphosphoglycerate. The process yields two 3-phosphoglycerate molecules and two ATP molecules.

2 molecules of 1,3-bisphoshoglycerate (C₃H₄O₄P₂) + phosphoglycerokinase + 2 ADP → 2 molecules of 3-phosphoglycerate (C₃H₅O₄P₁) + 2 ATP 

Step 8

The enzyme phosphoglyceromutase relocates the P from 3-phosphoglycerate from the third carbon to the second carbon to form 2-phosphoglycerate.

2 molecules of 3-Phosphoglycerate (C₃H₅O₄P₁) + phosphoglyceromutase → 2 molecules of 2-Phosphoglycerate (C₃H₅O₄P₁)

Step 9

The enzyme enolase removes a molecule of water from 2-phosphoglycerate to form phosphoenolpyruvic acid (PEP). This happens for each molecule of 2-phosphoglycerate.

2 molecules of 2-Phosphoglycerate (C₃H₅O₄P₁) + enolase → 2 molecules of phosphoenolpyruvic acid (PEP) (C₃H₃O₃P₁) 

Step 10

The enzyme pyruvate kinase transfers a P from PEP to ADP to form pyruvic acid and ATP. This happens for each molecule of PEP. This reaction yields 2 molecules of pyruvic acid and 2 ATP molecules.

2 molecules of PEP (C₃H₃O₃P₁) + pyruvate kinase + 2 ADP → 2 molecules of pyruvic acid (C₃H₄O₃) + 2 ATP

My Summary of Enzymes

What are Enzymes?

Enzymes are globular proteins which speeds up the rate of a reaction. They are biological catalyst. Enzymes, lowers the activation energy of a reaction. Enzymes contain an active site which the substrate binds to by weak interactions

and form an enzyme-substrate complex.They are highly specific, they bind to complementary substrates to be converted to products. Some enzymes require a cofactor. 

What is a cofactor?

A cofactor can be described as compounds to ensure their catalytic activity. The presence of a cofactor and enzyme binded together is called a haloenzyme.

Apoenzyme + Cofactor = Holoenzyme

According to Holum, the cofactor may be:

1. A coenzyme – a non-protein organic substance which is dialyzable, thermostable and loosely attached to the protein part.

2. A prosthetic group – an organic substance which is dialyzable and thermostable which is firmly attached to the protein or apoenzyme portion.

Types of specificity of Enzymes.

Although enzymes exhibit great degrees of specificity, some are more specific than others. 

• Absolute specificity – the enzyme will catalyze only one reaction.
• Group specificity – the enzyme will act only on molecules that have specific functional groups, such as amino, phosphate and methyl groups.
• Linkage specificity – the enzyme will act on a particular type of chemical bond regardless of the rest of the molecular structure.
• Stereochemical specificity – the enzyme will act on a particular steric or optical isomer.

Classification of Enzymes

Enzymes can be classified by the kind of chemical reaction catalyzed.

What are the Factors that affect Enzymes?

Several factors affect the rate at which enzymatic reactions proceed – temperature, pH, enzyme concentration, substrate concentration, and the presence of any inhibitors or activators.

Temperature:-

As graph shows, the rate of an enzyme-catalyzed reaction increases as the temperature is raised, the reaction rate increases with temperature to a maximum level, then abruptly declines with further increase of temperature. Because most animal enzymes rapidly become denatured at temperatures above 40°C, most enzyme determinations are carried out somewhat below that temperature.

Substrate Concentration:

When all factors are kept constant and substrate concentration is increasin, the reaction  velocity increases, this occurs until it reaches it’s maximum, at that point, increasing substrate concentration will no longer increase the velocity. At that point, all enzymes are in the process of releasing a product hence substrates not binded to enzymes have to wait until an enzyme’s active site is free. We say that the reaction has reached Vmax.

Important to note from graph:- The Michaelis constant Km is defined as the substrate concentration at 1/2 the maximum velocity.

• A small Km indicates that the enzyme requires only a small amount of substrate to become saturated. Hence, the maximum velocity is reached at relatively low substrate concentrations.
• A large Km indicates the need for high substrate concentrations to achieve maximum reaction velocity.
• The substrate with the lowest Km upon which the enzyme acts as a catalyst is frequently assumed to be enzyme’s natural substrate, though this is not true for all enzymes.

pH:

Enzymes are affected by changes in pH. The most favorable pH value – the point where the enzyme is most active – is known as the optimum pH.

Extremely high or low pH values generally result in complete loss of activity for most enzymes. pH is also a factor in the stability of enzymes. As with activity, for each enzyme there is also a region of pH optimal stability.

The optimum pH value will vary greatly from one enzyme to another.

Inhibitors:

Enzyme inhibitors are substances which alter the catalytic action of the enzyme and consequently slow down, or in some cases, stop catalysis. Inhibition can be reversible and irreversible. For course we focused on reversible inhibition.

Reversible inhibition is divided into competitive, non competitive, uncompetitive and mixed.

Summary of inhibition:

 

References:-

http://www.worthington-biochem.com/introbiochem/inhibitors.html

BiochemJm channel – Youtube videos

 

 

Published Paper – Is a Calorie a Calorie?

Researchers tested free living adults for obtaining results based on a study to investigate whether a high protein/low carbohydrate diet yields greater weight loss that a high carbohydrate/ low fat diet. Study showed that, the high protein/low carbohydrate diet had greater weight loss than that of the high carbohydrate/ low fat diet. Results also introduced new questions as to whether a calorie is indeed a calorie. Different aspects of energy were investigated to reassure result findings.

By definition, a calorie is known a unit of energy which is equated to 4.184 Joules. The first law of thermodynamics states that energy cannot be created nor destroyed, but it is converted from one form to the other. The consumption of food the human body constantly transforms energy by combusting food ingested to produce heat. Scientist Lavoisier and Crawford both conducted experiments to conclude that respiratory exchange is combustion and thus from a purely thermodynamic point of view, a calorie is indeed a calorie.

Another concept which was used to determine whether a calorie is actually a calorie was to measure the energy expenditure of the various macronutrients. The gross energy of the faces and urea was examined for this experiment. Although an individual consuming high protein/low carbohydrates energy composition was less than an individual consuming high carbohydrate/low fat. This concluded that the high protein/low carbohydrate diet yield less energy for body and hence greater weight loss also the gross energy did however show that a calorie is a calorie.

It was indicated that; the human body is not a perfect engine and thus the thermodynamic concept was re-examined. The concept of “metabolizable energy” was introduced; it was now known that energy liberated from food combustion isn’t identical to energy available to the body from consumption of that food. Many experiments were conducted but could not prove that the thermodynamic concept was inaccurate.

In conclusion, greater weight loss is indeed prominent with the high protein/low carbohydrate diet than the low fat/high carbohydrate diet based on short experiment conducted. Protein is not stored in the body long term. Protein is stored as muscle and briefly as free amino acids in the blood stream; whereas carbohydrates are stored in the body glycogen which is converted to fats. Based on research of whether a calorie is actually a calorie, from purely a thermodynamic point, it is clear because living organism does not have the ability to create or destroy energy but we convert energy from one form to another.

Reference:

http://ajcn.nutrition.org/content/79/5/899S.long#ref-19