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

Anfinsen Experiment

Anfinsen used the protein RNase A (has a single polypeptide chain with 8 cysteines). Anfinsen wanted to know if there are substances within cells (enzymes?) that cause other proteins to fold properly into their appropriate 3D shapes.

His first step was to apply mercaptoethanol alone to the RNase and that caused the S-S bonds between the cysteins to break, but no unfolding. Then he applied urea alone and that caused unfolding but didn’t change the sequence of the amino acids. Both mercaptoethanol and urea caused the RNase to lose it’s enzymatic function.

he decided to remove these reagents (urea and mercaptoethanol) in 2 ways:
Method 1: remove mercaptoethanol first and then remove urea
Method 2: remove urea first and then remove mercaptoethanol

Method 1 resulted with very little activity in the RNase.

Method 2 resulted with the RNase regaining almost all of it’s enzymatic function.

Review of Amino Acid + Protein Lecture 2

Protein

Proteins are polymers of amino acids joined together by peptide bonds.

Each of these amino acids has a fundamental design composed of a central carbon (also called the alpha/chiral carbon) bonded to:

• a hydrogen
• a carboxyl group
• an amino group
• a unique side chain or R-group

Peptide bonds are formed between the carboxyl group of one amino acid and the amino group of the next amino acid. Peptide bond formation occurs in a condensation reaction involving loss of a molecule of water. The head-to-tail arrangment of amino acids in a protein means that there is a amino group on one end and a carboxyl group on the other end.

Levels of Protein Structure

Structural features of proteins are usually described at four levels of complexity:

• Primary structure: the linear arrangement of amino acids in a protein and the location of covalent linkages such as disulfide bonds between amino acids. In the primary structure, it tells you what amino acid is present and the sequence of that amino acid.
• Secondary structure: areas of folding or coiling within a protein; examples include alpha helices and pleated sheets, which are stabilized by hydrogen bonding.
• Tertiary structure: the final three-dimensional structure of a protein, which results from a large number of non-covalent interactions between amino acids.
• Quaternary structure: non-covalent interactions that bind multiple polypeptides into a single, larger protein. Hemoglobin has quaternary structure due to association of two alpha globin and two beta globin polyproteins.

Summary 🙂

1. Primary
Animo acid sequence

2. Secondary
Alfa helix
Beta plates
Hydrogen bonds with the polypeptide backbone

3. Tertiary 
Basic structure of the protein; alpha helixes and beta plates arranged in the protein
Hydrogen bonds, Ionic bonds, Covalent bonds, Sulfide bonds
They are important interacting with the side chains

4. Quaternary
Interactions between tertiary structures/polypeptide chain
Hydrogen bonds, Ionic bonds, Van der Waals interactions, Disulfide bridges
They are important interacting with the side chains

Denaturing Proteins

Denaturation of proteins involves the disruption and possible destruction of both the secondary and tertiary structures. Since denaturation reactions are not strong enough to break the peptide bonds, the primary structure (sequence of amino acids) remains the same after a denaturation process. Denaturation disrupts the normal alpha-helix and beta sheets in a protein and uncoils it into a random shape.

Denaturation occurs because the bonding interactions responsible for the secondary structure (hydrogen bonds to amides) and tertiary structure are disrupted. In tertiary structure there are four types of bonding interactions between “side chains” including: hydrogen bonding, salt bridges, disulfide bonds, and non-polar hydrophobic interactions. which may be disrupted. Therefore, a variety of reagents and conditions can cause denaturation. The most common observation in the denaturation process is the precipitation or coagulation of the protein.

Heat, Ultraviolet radiation, Strong Acid/bases, Urea, Some organic solvents, agitation are all conditions that can lead to denaturing a protein. 

Review Of Amino Acid + Protein Lecture 1

Important things to remember about amino acids

Amino acids differ because they have different ‘R’ groups attached to the molecule. The 20 amino acids are subdivided into different categories based on the ‘R’ groups:

• Nonpolar, aliphatic R groups

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine. Glycine = Smallest Amino Acid – the ‘R’ group is hydrogen. Proline = Special because the ‘R’ group is attached to the amino group and forms a ring structure.

• Polar, uncharged R groups.

Serine, Threonine, Cysteine, Asparagine, Glutamine. These are polar because there are atom’s present which differ in electronegative thus giving a polar bond being formed. Eg Oxygen in serine, Sulphur in Cysteine.

• Aromatic R groups.

Phenylalanine, tyrosine and tryptophan. Aromatic ring has double bonds in conjugated form.

• Positively charged R groups.

Lysine, Arginine, Histidine.

• Negatively charged R groups

Aspartate, Glytamate which is both acidic.

How Cystine is formed.

Two cysteine undergoes a a oxidation reaction where the sulphur hydroxyl reacts and loses the Hydrogen and forms disulphide linkage to form one cystine molecule. This process can be reversed where you reduce the disulphide linkage and form the two cysteine molecules. See Image below.

Nonionic forms  Zwitterion

To form a zwitterion, the hydrogen (proton) from the carboxylic group is lost as a proton and the amino acid group accepts the proton. Having two charges on a molecule forms a zwitterions (ie – a positive and negative group).

• Test to distinguish Amino acids – Ninhydrin – turns purple = positive conformation of presence of amino acid.

• Test to distinguish Protein – Biuret

Every amino acid has an amino and carboxyl group.  When a bond is formed between an  amino group and a carboxylic group; a peptide bond is formed. This peptide bond is covalent in nature. The reaction is a condensation reaction. 

Reference

Lecture 1 – Amino Acid + Protein

Multiple choice!!!!

1.Glycine and proline are the most abundant amino acids in this structure:

(a)  Insulin

(b) Myoglobin

(c)  Haemoglobin

(d) Collagen

 2. Which of the amino acid cannot participate in hydrogen bonding.

(a)  Valine

(b) Theronine

(c)  Cysteine

(d) Serine

3.Which of the following amino acids can form hydrogen bonds with their side (R) groups?

A)  Asparagine

B)   Aspartic acid

C)   Glutamine

D)  All of the above

 4. The isoelectric point of an amino acid is defined as the pH

A)  Where the molecule carries no electric charge

B)   Where the carboxyl group is uncharged

C)   Where the amino group is uncharged

D)  The maximum electrolytic mobility

 5. All of the following are considered “weak” interactions in proteins, except:

A)hydrogen bonds.

B)hydrophobic interactions.

C)ionic bonds.

D)peptide bonds.

E) van der Waals forces.

 6. In the αhelix the hydrogen bonds:

A) are roughly parallel to the axis of the helix.

B) are roughly perpendicular to the axis of the helix.

C) occur mainly between electronegative atoms of the R groups.

D) occur only between some of the amino acids of the helix.

E) occur only near the amino and carboxyl termini of the helix

7. Which of the following statements is false?

A) Collagen is a protein in which the polypeptides are mainly in the α-helix conformation.

B) Disulfide linkages are important for keratin structure.

C) Gly residues are particularly abundant in collagen.

D) Silk fibroin is a protein in which the polypeptide is almost entirely in the β conformation.

E) α-keratin is a protein in which the polypeptides are mainly in the α-helix conformation.

 8. In an α helix, the R groups on the amino acid residues:

A) alternate between the outside and the inside of the helix.

B) are found on the outside of the helix spiral.

C) cause only right-handed helices to form.

D) generate the hydrogen bonds that form the helix.

E) stack within the interior of the helix.

9.Which statement about the zwitteronic form of an amino acid is trueA)    The zwitterions acts only as an acid B)    The zwitterions ion is neutral overall C)    The zwitterions acts only as a base. D)   T he zwitterions ion carries an overall charge which can be positive or negative. What are proteins composed? A)    Enzymes B)    Peptides C)    Precursors D)    Pepsin E)     Amino Acids

http://wordsearchaday.com/amino-acids-the-essence-of-life/2008/05/31/

 

Facts Corner!!!

1. There ESSENTIAL and NON ESSENTIAL amino acids!!!

2. ESSENTIAL MEANS YOU HAVE TO EAT THEM!! :- Our bodies can’t produce essential amino acids, so we have to get them from the foods we eat. There are 10 essential amino acids… 1. Arginine. 2. Histidine. 3. Isoleucine. 4. Leucine. 5. Lysine. 6. Methionine. 7. Phenylalanine. 8. Threonine. 9. Tryptophan. 10. Valine!!!

3. If you are not able to obtain enough of even ONE of the TEN most essential amino acids, then there is certain degradation in your body’s proteins. IT IS VERY IMPORTANT TO GET THE RIGHT AMOUNT OF PROTEIN IN YOUR DIET!!!

4. On average, we need 40 to 60 gm of protein per day. This is necessary in one’s diet to be healthy. The exact amount of protein needed everyday can be calculated, the RDA is 0.8 grams per kilogram of lean bodyweight!

5. Most amino acid supplements sold over the counter have no side effects if they are taken properly and accordance with their daily-recommended allowance!! Its generally safe!!! 🙂

6.There are arguements that excessive protein consumption can cause a variety of body ailments–such as kidney and heart disease, constipation, and osteoporosis. :O :O :O