ENZYMES

http://www.youtube.com/watch?v=ok9esggzN18

Enzymes are Biological catalysts (proteins) that speed up a chemical reaction by lowering its activity. Enzymes are not consumed during a reaction. One such example is catalase which is an enzyme that is found in all living cells. This enzyme breaks down hydrogen peroxide (H2O2).

Chemical reaction:

2H₂O₂   à 2H₂O + O_2.

The enzyme catalase breaks down H2O2 into water and oxygen.

Ebzymes contains active site, where substrate fits into. This substrate will be catalysed. The substrate in this example above was H2O2.

Substrates bind to the active site of the enzyme by two theories;

1. Lock and key – this is where the substrate is identically shaped to the active site and fits perfectly into the active site
2. Induced fit – this is where the substrate is not identical to the active site but still binds to the enzyme for a reaction to occur.

Enzymes are turned on (activated) and turned off (deactivated or inhibited)

Enzymes are turned off/ inhibited;

This is done by inhibition. It can either be competitive or non competitive inhibition. Competitive inhibition is when the inhibitor competes with the substrate for the active site of an enzyme and non competitive is where the inhibitor binds to another part (allosteric site)of the enzyme and causes a conformational change of the enzyme.

Enzymes are activated by;

1. They are only produced when needed – this is a regulating method for reactions. These enzymes are activated when needed.
2. Enzymes are activated using either cofactors (inorganic) or coenzymes (organic). These are small that are added to enzymes to activate the enzymes.
3. Example of cofactor – Heme contained in hemoglobin
4. Example of coenzyme – Thiamine (Vitamin B1)

Enzyme reactions are affected by;

1. Substrate concentration
2. Enzyme concentration
3. Temperature
4. pH
5. Competitive inhibitors
6. Non competitive/ allosteric inhibitors

Example of enzyme reaction vs temperature

As temperature increases, enzyme reaction increases until optimum temperature. Optimum temperature is the temperature or range of temperatures that the enzymes functions at its best. After this optimum temperature is passed enzymes becomes denatured and rate of reaction decreases as enzymes cannot bind to substrates due to conformational changes and breaking of chemical bonds within the active site and entire enzyme.

VIDEO REVIEW – GLYCOLYSIS

Glycolysis!

In this video, Khan aims to explain fully the Glycolysis process. He firstly explained that glycolysis is one of the major processes that take place during cellular respiration. He stated that glycolysis is simply the splitting of glucose. Glycolysis can occur either with oxygen or without oxygen. If oxygen is not present, we go to the fermentation process; if oxygen is present, we proceed to the Kreb’s Cycle.
Glycolysis consists of 2 phases: the investment phase and the payoff phase. In the investment phase, 2 ATP molecules are used which produces 2 ADP. At the end of this phase, we end up with 2 phosphoglyceraldehyde molecules. The molecules then lead us into the payoff phase. Unlike the investment phase, the payoff phase uses 4 ADP molecules and 2 NAD+ molecules which produce 4 ATP and 2 NADH molecules respectively.
Khan stated that:
Glucose + 2 NAD+ + 2 ATP + 4 ADP + 4Pi undergoes the process of Glycolysis and produces
2 Pyruvate + 2 NADH + 2 ADP + 4 ATP.

Khan then proceeds to explain each step of the glycolysis process. Firstly, Glucose forms Glucose-6-phosphate with the enzyme HEXOKINASE. In this reaction, ATP is used and produces ADP. Glucose-6-phosphate then reacts with the enzyme PHOSPHOGLUCOSE ISOMERASE to produce Fructose-6-phosphate which then forms Fructose-1,6-bisphosphate when reacted with the enzyme PHOSPHOFRUCTOKINASE-1. In this reaction, another ATP molecule is used which is converted to ADP. This Fructose-1,6-bisphosphate molecule then reacts with the enzyme FRUCTOSE BISPHOSPHATE ALDOSE and forms Glyceraldehyde-3-phosphate and Dihydroacetone phosphate. However, for the reactions in the payoff phase to occur, we need to convert the Dihydroacetone phosphate into Glyceraldehyde-3-phosphate. To do this, we need the help of another enzyme, TRIOSEPHOSPHATE ISOMERASE.

In the payoff phase however, because we begin with 2 molecules of Glyceraldehyde-3-phosphate, for every reaction, product, or reactant used it needs to be timed by 2 as everything is done twice, once per Glyceraldehyde-3-phosphate. The first step of the payoff phase is where the Glyceraldehyde-3-phosphate is converted to 1,3-bisphosphate by the enzyme GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE. In this reaction, NAD+ is used to produce NADH+H+. The 1,3-bisphosphate molecule then reacts with the enzyme PHOSPHOGLYCERATE KINASE which produces 3-phosphoglycerate. In this reaction, not 1 but 2 ADP molecules are used and produce 2 ATP molecules. Then, 2-phosphoglycerate is formed from 3-phosphoglycerate with the enzyme PHOSPHOGLYCERATE MUTASE. No ADP or NADH molecules are used in this reaction. This molecule of 2-phosphoglycerate then converts to Phosphoenol pyruvate. The enzyme ENOLASE is used to catalyse this reaction. This next reaction then produces the 2 final molecules of Pyruvate. These pyruvate molecules are formed from the Phosphoenol pyruvate molecules and this reaction is catalysed by the enzyme PYRUVATE KINASE. Here, 2 ADP molecules are used and produce 2 ATP molecules.
Pyruvate is a 3C structure. This is the end product of glycolysis as the glucose molecule was split. The carbons from the glucose molecule was oxidised hence the number of carbon is reduced, forming pyruvate.
The NADH molecules produced would be used in the ETC to produce ATP molecules per NADH molecule.
NET GAIN IN GLYCOLYSIS: 2ATP, 2NADH, 2PYRUVATE 

😀

ENZYME WORD CLOUD: The Key!

I used the shape of a key to do my word cloud as it depicts the lock and key hypothesis of enzymes. The lock and key hypothesis is where the substrate has a precise or specific shape to fit the active site of the enzyme. We say that the shape of the substrate is complementary to the shape of the active site on the enzyme molecule. 🙂

Enzyme Activity Factors

WHAT AFFECTS ENZYME ACTIVITY?

Enzyme activity is affected by many factors such as the presence of inhibitors, temperature as well as changes in pH. These factors tend to denature the enzyme by reducing the enzyme activity henceforth altering the enzyme’s its shape and orientation. When it changes shape, a substrate can no longer fit perfectly into the active site. When binding does not occur, the reaction discontinues therefore reducing the amount products being formed. These enzyme molecules can function up till a certain temperature and pH known as optimum temperature and optimum pH. This is because after these rates, enzymes begin to denature.

After experiencing heat above optimum temperature, the enzyme becomes denature therefore it changes shape and orientation where it can no longer bind to the substrate. 

naribiochemwiz007 🙂 ♥

Enzyme Inhibition Made Simple

Inhibitors are known as the molecules that disrupt the functioning of an enzyme. There are two types of enzyme inhibitors; specific and non-specific. There are also reversible and irreversible specific inhibitors. There are four types of reversible inhibitors. These are known as competitive, mixed, uncompetitive and non-competitive inhibition. Competitive inhibition is where both substrate and inhibitor competes to bind with the active site of the enzyme molecule as these competitive inhibitors possess similar shapes to the substrate.

Competitive inhibition can be overcome when there are relatively high concentrations of substrate, resulting in Vmax remaining constant. However, as this happens, Km increases due to the fact that higher concentrations of substrate is needed to reach half Vmax. Mixed inhibition is very similar to competitive inhibition as the inhibitor tends to bind at the same time as the substrate. Not only can these types of inhibitors bind to the active sight of an enzyme, they can also bind to different sites of the enzyme. These types of enzymes are called allosteric enzymes as they possess more than one active site.

 <<<<< showing how competitive inhibitors slow down the rate of reaction of the enzyme as opposed to without inhibitors.

Uncompetitive inhibition is where the inhibitor only binds to the enzyme substrate complex, and causes Vmax to decrease while simultaneously increasing Km.

 

Uncompetitive inhibition should not be confused with non-competitive inhibition as these two possess very different characteristics. As opposed to uncompetitive inhibitors, non-competitive inhibitors are a form of mixed inhibition where upon binding to the enzyme’s active site, enzyme activity is reduced.

Figure: showing how non-competitive inhibitors affect the rate of reaction as compared to without the use of an inhibitor. The rate of reaction is decreased and also Vmax is decreased.

CAPTAIN ENZYME TALKS ABOUT ENZYMES

Enzymes are a set of highly specialized globular protein molecules which act as biological catalysts. This means that they speed up biochemical reactions in the body by lowering the activation energy required for a reaction to commence. Therefore little energy is desired to start a reaction hence little energy needs to be produced which allows the reaction to occur quicker as well as more efficiently. Enzymes are essential in carrying out specific metabolic and biochemical reactions and remain unchanged after each reaction takes place. Enzymes contain active sites which are highly specific to fit the substrates to be catalysed. Enzymes maybe specific for certain types of chemical bonds for the reaction to occur.

Overall, there are four very distinct types of enzyme specificity known to man. There is absolute specificity where the enzyme will catalyse only one reaction. Another is group specificity; this is where the enzyme molecules will perform only with molecules that possess specific functional groups. Examples of such molecules are phosphate, amino and also, methyl groups. There is linkage specificity where the enzyme molecule acts on a certain type of chemical bond no matter its molecular structure. And finally, the last type of enzyme specificity is stereo-chemical specificity. Stereo-chemical specificity means that the enzyme molecule will work on a precise steric/optical isomer.

Consequently, enzymes can catalyse only one type of reaction. The chemical reaction of the substrate and the functional group of the enzyme’s active site can also be responsible for this. In the active site of the enzyme, the substrate binds causing the reaction to occur. Hydrogen bonds and ionic bonds form as the substrate reacts with the functional groups or amino acids from within the active site of the enzyme forming an enzyme-substrate complex.

It is understood that when a substrate binds with an enzyme, it is held in precise orientation for the reaction to take place resulting in less energy being wasted since the substrate molecules tend to give off a lot of energy in random motion to achieve this. There are two hypotheses which suggest how enzymes bond to as substrate. There is the ‘lock and key’ hypothesis and the Induced Fit hypothesis.

The ‘lock and key’ hypothesis suggests that each enzyme has a precise place on its surface to which the substrate molecule binds. The enzyme is understood to be exactly complimentary to the substrate molecule.

The other hypothesis is known as the Induced Fit hypothesis where the substrate and the enzyme’s active site are very similar but not the same. In other words, they are not complimentary to each other. When the substrate binds to the enzyme, it experiences small changes which enable the substrate to have a more exact fit into the active site.

PROTEIN WORD CLOUD: Before and After

This is my very own self-created peptide chain. It does not contain any words, etc as it was made specifically to be used for the protein word cloud. This peptide chain is known as the first or primary structure of a protein ans is basically a chain of protein molecules attached via peptide bonds. I chose this to depict my word cloud as this structure of protein is very important. If this does not occur then secondary, tertiary or quaternary structures of proteins cannot be formed. This is my word cloud. 😀

Protein Humor

TWO WORDS:

SASHA. GREY.

You know you laughed!

I am going to hell -_-

Proteins – Important terms to note

TERMS

Amino Acid  –  A class of 20 organic compounds that combine to form proteins.

Deoxyribonucleic acid (DNA)  –  A long polymer of nucleotides joined by phosphate groups, DNA provides the ‘blueprint’ for the proteins that each different cell will produce in its lifetime. It consists of a double stranded helix consisting of a five-sided sugar (deoxyribose) without a free hydroxyl group, a phosphate group linking the two nucleotides, and a nitrogenous base.

Ribonucleic acid (RNA)  –  RNA is a long polymer of ribose (ribose is a five-sided sugar with a free hydroxyl group) and nitrogenous bases linked via phosphate groups. It is complementary to one of the DNA strands and forms the proteins that are specified by the cell.

Primary Structure  –  The first level of protein structure that is simply the linear sequence of its constituent amino acids.

Secondary Structure  –  The second level of protein structure where the linear sequence of proteins begins to fold into regular repeating patterns.

Tertiary Structure  –  The third level of protein structure where side chain interactions dictate the direction of the folding.

Quaternary Structure  –  The fourth level of protein structure that refers to the spatial arrangement of the subunits within the protein.

Zwitterions  –  Amino acids in a form of neutrality where the carboxyl group and amino group are ready to donate and accept protons, respectively.

Polar  – Hhydrophilic or “water loving” qualities of amino acids.

Non-polar  –  Hydrophobic or “water fearing” qualities of amino acids.

Polypeptides  –  Multiple amino acids joined by peptide bonds.

Alpha Helix  –  The secondary structure of proteins that is a tightly coiled polypeptide chain wound in a clockwise or counterclockwise direction.

Beta Sheet  –  The secondary structure of proteins where the polypeptide chains are almost completely extended during the process of folding.

Transamination  –  The synthesis of amino acids in the liver.

Alpha keto acid  –  A precursor molecule for amino acid synthesis.

Aminotransferases  –  Enzymes, derived from vitamin B6, that are important in amino acid synthesis.

Ketogenic  –  The process whereby fatty acids are broken down to produce ketones.

Gluconeogenesis  –  The process of synthesizing glucose from non- glucose precursors such as amino acids.

Pyruvate  –  Pyruvate is a three-carbon compound formed through the degradation of glucose via glycolysis. Two pyruvate molecules are formed per molecule of glucose that enters glycolysis.

PROTEINS PROTEINS PROTEINS!

Proteins are composed of long chains of amino acids joined together by peptide bonds. They are produced through a two step process involving the transcription of deoxyribonucleic acids (DNA) and the subsequent translation of messenger ribonucleic acid (RNA). Even though the same DNA blueprint that contains instructions for all the body’s tissue and organs is found in every cell, only certain proteins are expressed by specific cell types.

Each amino acid is composed of an amino group (NH2), a carboxylic acid group (COOH), Hydrogen (H) and a functional group (R) as seen in the photo above. There are twenty kinds of R groups that distinguish each different amino acid. All twenty amino acids are found in proteins, each contributing to the protein’s overall structure or function. Some of these R groups form covalent bonds within the protein. The following photo shows the 20 amino acids as they are classified into their respective R-group Type.

Due to the diversity of their structures, proteins have many important functions in the body. Enzymes are a special class of proteins that catalyze biological reactions in plants and animals. Other classes of proteins include membrane channels and pumps, functioning within the membranes of cells to regulate the flux of ions and small molecules. It is known that some proteins are also found in the immune system as antibodies that function in the recognition and destruction of foreign particles and antigens.

It is also very important to consider proteins in dietary terms. Non-essential amino acids can be synthesized by the liver through a process known as transanimation while essential amino acids must be obtained through the diet. Both non-essential and essential amino acids are used by the body for the production of proteins that make up and are stored in tissues like the skeletal muscles and even the heart and by extension, the gastrointestinal tract.