PART 2
Use the following key to answer the question below
A.1,2 and 3
B.2 and 4
C.3 and 1
D.1,2,3 and 4
What are the enzymes/enzyme that catalyze the reaction/s where substrate-level phosphorylation occurs?
1. Phosphofructokinase-1
2. Pyruvate kinase
3. Glucose 6-phospahte
4. Phosphoglycerate kinase
So this is my second published paper and i choose to do it on the ever interesting and rare Maple Syrup Urine disease. I came across this in one of the videos i was listening to pertaining to the amino acids and proteins topic. So i had to do some research on it since i have never actually heard about this disease.
Reference: D.Y Mackenzie, L.I Wolf. 1959. ‘Maple Syrup Urine Disease, An Inborn error of the metabolism of valine,leucine and isoleucine associated with gross mental deficiency.’ Maple Syrup Urine Disease. 1959 January 10;1(11514): 90-91. Accessed April 4th 2013. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1992202/
What exactly is this disease,first question that came to find and secondly how did was it named?. Maple Syrup Urine Disease is a disorder that as you can guess from the title affects the metabolism (breakdown) of valine, leuicne and isoleucine. As you know these three are amino acids and therefore are used for the production of proteins,when not in used they would therefore be broken down for the production of energy. When the smell of the urine is sweet which resembles the smell of Maple syrup this is a early sign that belongs to infants.
In the article a case study was done where where the patient was at infant stage and did not have any history of mental disorder in the family. She displayed symptoms such as the cease in sucking to get food and had to be fed via tubes,this further escalated at just 4 moths old to jerkiness of body parts and breathlessness. As these symptoms got worse tests were carried out to figure what exactly was wrong. For the option of a disease to be rule out named phenylketonuria a test was done where the results of urine from a fresh specimen was gather,this sample was very similar to maple syrup. Using a test which intertwines two dimensional paper chromatography of the amino acids named above were found in large amounts,these are valine,leucine and isoleucine.
What exactly caused the maple syrup smell? well this is due to the α-hydroxyl-acids which are modified by the ketones. Keto-acids are found to be present in the urine at large amounts. The two dimensional chromatography showed derivatives of large amounts of indoylacetic and indoyllactic acid.
It can be concluded that from the article the patient suffered from inborn error in the break down of the amino acids leucine,valine and isoleucine. In the disease the amino acids are metabolized as seen below at the bottom where the stages B or C are blocked this may be due to a enzyme not being peresent and there is a build up of keto acid,if there is a build up of this there is abuild up of amino aicds . Path D would decreased the amount keto acid and the three amino acids along with there production of keto acids and hydroxy-acids are excreted in large amounts.Keto-acid is said to be the cause of this disease as it is a metabolite and there is a large increase in it due to the failure to metabolize it at the second stage. This build up would cause the brain dysfunctions of the patient and interferes with trypotophan breakdown which if your are confused is the reason for indolylacetic and indolyllacetic excretion. There would be proteins that break down the amino acids and forms complex (BCKD) and it is made up of the branched chained alpha ketoacid dehydrogenase). They would therefore be lacking one of the proteins to break it down the three amino acids. Causing as said above high amounts if amino acids in their bloods and results in degradation of the brain cells and even death. This paper concluded that the keto-acid and blood concentration has to reach a critical level before enough amino acid that is brought about by the transamination if formed to exceed the renal threshold. Diets low in leucine,valine and isoluecine would be aid if a patient has this disease to prevent brain defects and dysfunction.
I have thoroughly enjoy learning about this diseases. I didn’t not know about it before but i must say it has opened my mind,i did not know about a deficiency in proteins to break down amino acids could caused a life threatening disease where brain dysfunction and improper metabolism of amino acids happen, that occur mostly in babies. I do hope you read about it and understand from a article that showed a experiment to a discussion that explained what exactly it the disease is about. I guess the name is really pertaining to the disease. =)
Hello again,this is my published paper 1 and it centers around the Alzheimer’s Disease.
Paul L Wood. 2012. ‘Lipodomics of Alzheimer’s Disease:current status’. Alzheimer’s Research and Therapy 4-5. doi:10.1186/alzrt103.
Firstly i needed to get acquainted with this disease,what exactly is Alzheimer’s Disease? Well in simple terms this is a form of dementia where the person whom had no issues before progressively loses brain functions. This gets worse over time and there is no cure for this particular disease which would eventually result in death. It is therefore a cognitive disorder that result in a various neuropathologies. Whilst describing this disease some of the symptoms are relayed across which are neurofirillary.neuronal shrinage,neuroflammation just to name a few. They say that only older people are susceptible to this disease which is not entirely true, Various hypothesis have been carried out to prove what exactly is happening to a person when they are a patient of Alzheimer’s. Sporadic AD which as you can tell is a form of Alzheimers,it is actually the dominant form of dementia where research have came to show that (genomics) the ε4 allele of a apolipoprotein E which is a lipid transport or a chaperone is a susceptible factor in the cause of AD. Going more indepth the paper reveals that lipids play a very important role in the case of AD where when there is a deficiency in lipids glycerophospholipids and sphingolipids in the brain and changes/modifications of these very complex structural lipids which play the role of signaling molecules that is a contributing factor to AD. Therefore in this the changes/modifications and therefore with regards to the AD,there lipids roles in the pathphysiology are observed. I found this to be interesting and mind opening as many people you know suffer with AD and not have the slightest clue as to what exactly contributes to this horrid disease.
The brain comprises of tons of lipids and is literally enriched with lipids,from this i started to think if the brain is enriched with lipids and AD is the loss of brain function and the paper is says that i may be linked to the alterations made to the certain lipids that play a important contributing role to AD then if all comes together doesnt it?. Late onset AD is can be caused by the ε4 allele of apolipoprotein E (ApoE), this is a lipid transport/chaperone protein and also that when there is intense cases of cerebral macrostrucutral atrophy which also cause AD is due to the loss of the strucutural lipids….. The lipids that were observed were glycerophospholipids and sphingolipids.
The paper shows that glycerophospholipids are separated into different groups firstly,Ethanolamine glycerophospholipids. In the cases of AD there were decreased number of phopholipids found and also later on following this the ethanolamine was also in decreased amounts,this is a phospholipid precursor. In AD there showed levels of increased glycerophosphoethanolamine which degrades the brain. Ethanolamine plasmalogens are subclasses to phosphatidylethanolamine and the plasmalogens belong to the group of glycerophospholipids,peroxisomes (remember these-proteins that degrade fatty acids and amino acids) are responsible for the ether linkage of the plasmalogens. These decrements of phosphatidylethanolamine are very specific,which means that if you did research on other diseases such as Huntington’s you would not find this. The experiments carried out showed that whit matter phosphatidylethanolamine was decreased and gray matter phosphatidylethanolamines was also decreased,but there were no changes observed in the gray matter phosphatidylethanolamine in the late stage.Only phosphatidylethanolamines were very specific and the other lipids remained unchanged/unaltered (glycerophospholipids and inositol glycerophospholipids). So even though we said that changes in these lipids contribute to AD it shows that these lipids remained unaltered??????
The body gets Docosahexaenoic (DHA) from diet,this is the grey matter spoken about above. DHA is also derived form peroixisome dependent synthesis and gastrointestinal. For phosphatidylethanolamines to be formed peroxisomes are needed,this is where the researchers came up the idea that there was deficiency in peroisomes that caused AD. It shows that the DHA numbers were also decreased in patients that have AD,this is metabolized only by peroxisomes and can be seen to have higher/increased levels in the liver. The decreases of phosphatidylethanolamines are caused by a a peroxisomal deficiency,the research showed that decrements that are located in the brain liver and plasma all are connected to the deficiency of brain function in AD patients.In AD decrements of the lipids in the brain (polyunsaturated fatty acids and also phosphatidylethanolamines) which results in the loss of white matter in the brain and also gray matter phosphatidylethanolamines. This can only be due to a deficiency of peroxisomal located in the brain and liver. Another type of glycerophospholipids are Choline glycerophospholipids which as well Ethanolamine glycerophospholipids plays a role in AD due to the deficiency of peroxisomes which causes a decrease in the number of choline plasmalogens and therefore changes the Choline glycerophospholipids. Glycerophospholipids are constantly remodeling themselves as they release arachidonic acid(also eicosanoids mediators of neuroinflammation) which is a indicator of AD patient brain.
The second lipid mentioned were Sphingolipids,this lipid unlike the other was no new to me. They are structural lipids in the central nervous system. So what is the connection to AD? Well remember when earlier i spoke about AD whit and grey matter> well the metabolism of shingolipids will be affect by this. These causes changes and alterations that can be seen in pathology the AD.
So lets tie everything together to how exactly these lipids work to contribute to AD. Myelin has to be rich in plasmalogen and sulfatides to be able to be a structural lipid. Along with this is also phosphatidylethanolamine which is a structural lipid. When there is loss of these two together it shows the signs of a process that occurs in AD which is named hypoyelination. Studies that have been conducted have shown that AD patients would have showed signs of changes in myelin. Due to the process of hypoyelination and the the loss of plasmologen this can account for the dysfunction of AS cortical neurons and nucleus projections which results in the dysfunction of the cognitive brain function. In the end it concludes that a deficiency in perosisome in AD also leads to ethanolamine and choline plasmalogens which causes the neuronal negative affects that is a major symptom in AD. The lipid sphinolipids would be due to the myeline changes which also occur in AD. The two named lipids glycerophospholipids and sphingolipids change/alterations very early on in the AD which causes the symptoms in AD.
Looking at this paper,i thought it is very interesting but also confusing. This disease is well known and i wanted to know what its association with lipids as the last topic that we covered was lipids in BioChem class. It enlighten me to the fact that it was not only the lipids but more the deficiency in perosisome that cause the alterations and changes that enable the symptoms of AD to occur with respect to the brain and in some cases the liver. I must say that it enlighten me and opened my mind,i did enjoy doing this paper.
Was just strolling through some videos and came across this,its very cute and helps you remember,its just a by the way thing.:)
THIS WORDLE IS MADE IN THE SHAPE FOLLOWING FISCHER’S LOCK AND KEY HYPOTHESIS,WHERE THE SUBSTRATE AND THE ENZYME ACTIVE SITE HAVE COMPLEMENTARY SHAPES 🙂
E N O I T I S N A R T E X E N S V R O T C A F O C L S N N O H C I E V I T C A B E Z O T I Y N O T V H U J I S Y N I E T D O E M I E H S A M C H T M A R I T Z P T R R E O A Y A P Z O T A C E E E S M K Q D V E I P C T X V M T P I D N R I R L H A S E O K E I M B M O T A I O E R S C T R Y T O L G C T B B R I O I S I T E I C E A U A I A L T Y G R E N E V N K R T C L I N E W E A V E R E U E S P V S P E C I F I C I T Y D Y E S A T X U D E R O D I X O R ACTIVATION ACTIVE COFACTOR COMPETITIVE ENERGY ENZYME HYDROGEN HYDROPHOBIC IRREVERSIBLE ISOMERASES KEY LINEWEAVER LOCK NONCOMPETITIVE OXIDOREDUXTASE REACTION REVERSIBLE SITE SPECIFICITY STABILIZATION STATE TEMPERATURE TRANSITION UNCOMPETITIVE USE THIS LINK TO MAKE ONE ALSO:http://puzzlemaker.discoveryeducation.com/code/BuildWordSearch.asp
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So for my second youtube video i choose,i choose to pick the topic cells. The name of the video is A Tour of the Cell from the youtube channel bozemanbiology. The person carrying out the podcast was a teacher named Paul Anderson. I do hope you enjoy this summary and learn something valid 😀
As we know cells are small by the question is why? In the video it explains stating that cells are small for material to move in and out of the cell by diffusion,also for oxygen to go in and carbon dioxide to move out. When the surface’s area is increased and the volume is the same the distance for the materials and the gases to travel would be small. Cells are made up of different macromolecules and they are complex contrary to what you would think when you were younger. Until microscopes were invented we did’nt know the depth of the cells and the structures that lie within them. There are two types of microscopes which are the optical that uses light and electron which uses a number of magnets->scanning electron microscope and transmission electron microscope. In the electron microscope the specimens are dead. To help better understand he gived a example where the way a electron microscope operates is similar to that of putting a magnet close to a computer screen what happens is that the part of the electrons are changed increasing the magnification of the specimen.
ILLUSTRATIONS contrast the structure of an intestinal cell as known from light vs electron microscopy (left and right)
They are two types of cells……Prokaryotic cells and Eukaryotic cells. Prokaryotic cells have no nucleus and are very small whilst eukaryotic cells do have a nucleus. Bacteria and Arachaea belong to prokaryotic cells and plants animals and fungus among others belong to the eukaryotic cells. There are similarities between that all cells have whether prokaryotic or eukaryotic such as nucleic material,cell membranes,cytosol and ribosomes. The difference is that eukaryotic cells have organelles for example mitochondria.
Eukaryotes- animal cells. The video further went on to define and state the function of each organelle that can be found in the animal cell.
Illustration of the animal cell and its organelles.
Nucleolus are found in the nucleus. Here all the chromosomes put all of their genes to make ribosomes,therefore there is alot of proteins so it would stain darker. The nucleolus is the area where ribosomes are assemble in the nucleus. The genetic DNA also reside in the nucleus. There are also pores called nuclear pores in the nucleus that is used for translation where the material can move in and out.
Ribosomes have a small subunit on the bottom and a large subunit on the top. The function of ribosomes are to build proteins. Eukaryotic and Prokaryotic have different ribosomes.
Vesicle- This is a vacuum that moves material around.
Rough ER- ER stands for endoplasmic reticulum. This is a folded membrane that is located coming out from the nucleus,it has ribosomes that are on the outside of the membrane. “Factory behind a cell”,what is this? well as the messenger RNA comes through the rough ER it creates proteins and also produces proteins that are used in the cell.
Illustration of the Rough ER
Golgi Body- Proteins are created in the endoplasmic reticulum and then moved to the Golgi Apparatus,here the proteins are modified by adding for example a carbohydrate and transported off. This is called the shipping part of the cell.
Illustration of the Golgi body
Cytoskeleton- The function of the cytoskeleton is to give the cell physical structure. A analogy was used here where a bridge is described example golden bridge,
where the two thick beams that are supporting it are the microtubules which give compressional support and the thin beams at the top on the left and right side going across are the microfilaments which give tensional support.
Smooth ER-From the name it can be told that there is no ribosomes instead the smooth ER produces lipids and cholesterol. They function in detoxification so the more you drink the greater amount of ER would build up in your body.
Mitochondria-This generates ATP (energy).It looks like a bacteria because it is believed that is becomes part of our cells through the endoplasmic theory where they become parts of the cell,produce ATP for the cell and dwells there. The evidence for this that they have there own DNA and reproduce through binary fission.
Illustration of the Mitochondria
Vacuole: This is found in plants and not exactly necessarily found in animals. It functions where it stored water for turgid pressure. Some protists have contractile vacuole. Animals used there vacuoles for endocytosis and exocytosis.
Illustration of the Vacoule
Cytosol: This can be described as the dissolved material in the cell which contains solutes.
Lyosome: Aka Suicide Sack. Digestive enzymes inside it which are contained by a membrane are able to go next to another vesicle that have material to breakdown and it would then go into the vesicle and break down the materials. Or when the vesicle is popped the digestive enzymes would kill the cells,this is called apoptosis.
Illustration of the lysosome
Lastly Centriole- Where ever this is sets up the location of the other organelles. When the cell divides the centriole would from the spindle pulling the chromosome aside.
Illustration of the Centriole
Comments
My comments: I enjoy the way the person carrying out the video communicated with his audience it was free and a very easy mood. What aided in comprehending about cells was the analogies that was made and the easier names to remember the organelles and their functions for example lysosome aka suicide pack. In the end of the video a recap was done where questions were asked at the end,this is always a good way to know if you understand or took away anything from the topic. Furthermore though there were benefits i must say that there were some downfalls,the information given on each organelle was not done indepth,even the information given was somewhat lacking,for example the differences between the two type of cells prokaryotic and eukaryotic cells he just stated the organelles that both have and both,what about there size? the shape of the DNA?…prokaryotic has circular DNA whilst Eukaryote has linear DNA. What are the cells walls made up from? prokaryotic is made up of murein and eukaryotic cells are made up from plants-cellulose. Ribosomes number differ where prokaryotes are 70s and eukaryotes are 80s. Another downfall would be the lack of information given,for the role of the golgi body the cist phase and the transe phase was not mentioned,this occurs before the vesicles are shipped out. Only lysosomes were mentioned and not proteasome or peroxisomes. What i think need to be explained the most was in the area of the lysosome which initially gives me troubled,the lysosome are single celled organelles that contains the digestive enzymes protease etc They were initially formed by the Rough ER. Ribosomes would have synthesize the enzymes ,the rough ER would have carried out the modification(post translational modification) and send it off to the cyst phase this is where it would bind with the Golgi apparatus and they would be modified to go to their destination,the vesicles are accepted from the rough ER sorted and packed to be sent out. On the transe side their would be lysosomes budding off. The lysosme would fuse with a vesicle forming a secondary vesicle during phagocytosis. The cell engulfs some material from the outside forming a food vesicle and this would bind with the primary lysosome forming a secondary lysosome. The contents of the primary lysosome are released into the vesicle and digested ,phagocytosis takes place. I think they should of been explained more indepth like i just explained,due to the fact if a student whom knows nothing about cells watches this podcast they would not entirely know everything about cells. I would also like to add Apoptosis i did not know about this was interesting to learn about. Improvements such as being more indepth with the information and more questions could be done :).
I hope you enjoy and took what i said into account.
http://www.youtube.com/watch?v=1Z9pqST72is -link for the video used.
Websites for the pictures used:
http://www.animalport.com/animal-cells.html
http://micro.magnet.fsu.edu/cells/plants/vacuole.html
http://www.howardmodels.com/fun-stuff/golden-gate-bridge/Golden-Gate-Bridge2.html
http://hyperphysics.phy-astr.gsu.edu/hbase/biology/cell.html
FACTORS AFFECTING ENZYME REACTION:
There are factors affecting this rate of reaction such as temperature, enzyme concentration ,substrate concentration and pH. In temperature the heat increases the molecular motion and increases the molecules of both the enzyme and substrate to move faster and more colliding would occur. The rate of reaction here would therefore increase. When there is maximum activity there it is referred to as optimum temperature. When the temperature goes beyond this point the rate in reaction would decrease because the secondary and tertiary structures would be denature and therefore cannot function.
Image showing the effect temperature has on a enzyme catalysed reaction
In terms of the enzyme concentration when the substrate is also high and the other factors mentioned are constant such as the pH and also the factor of temperature, the rate of reaction would be proportional to the enzyme concentration. Therefore, as the enzyme concentration is increased so will the rate of the enzyme reaction.
Image showing that as the enzyme concentration increases the rate of reaction increases
For the substrate concentration the rate of an enzyme reaction increases with increasing substrate concentration but at a certain point any more added substrate would produce no change as the active sites are already saturated and cannot take any more. They would be high amount of substrate in the active sites of the molecules of the enzymes, this high amount makes the enzymes molecules highly saturated with substrate concentration so for more substrate to go into the active site it would have to wait until the enzyme/complex has free its products that it has produced and then the substrate that was waiting could gain entry to the enzyme active site to go through the same process as the last to produce the products.
Image showing the effect of substrate concentration on enzyme catalysed reaction
Various pH have a certain effect on the reactions. Enzymes would function to its best ability when there is a standard temperature and a exact pH range. When there is said to be a optimum pH then here at this pH value the maximum rate of reactions can occur. Therefore when the pH would change to be higher or lesser than this optimum value the rate of activity of this enzyme would reduce. What happens when the pH is changed is that acidic ionic charge and basic groups would be altered, this would lead to the ionic bonds being broken. These ionic bonds aid in keeping the specific shape of the enzyme. The result in this alteration would lead to a change in the enzyme shape and therefore by extension its active site. When the pH values are very extreme and the enzyme crosses path with it the result will be in denaturing of this enzyme.
Image showing the effect on pH on enzyme rate of reaction
Various molecules exists which can reduce the rate of an enzyme controlled reaction. They are called inhibitors. There are competitive inhibitors and uncompetitive inhibition. With competitive inhibitors they prevent the substrate from binding to the active site. The inhibitor therefore plays the role where it competes with the substrate for the active site. Competitive inhibitors occupies the space that is there for the active substrate this mostly due to the fact that the inhibitor resembles and has the same shape as the substrate enabling it to bind with the enzyme at the active site. Secondly the other type of inhibitors are uncompetitive inhibitors, uncompetitive inhibition the inhibitor would not exactly bind to the active site ,it binds to a different site from where the substrate active site. Uncompetitive inhibitors would only bind to the enzyme substrate complex. Found in the group of inhibitors are also mixed inhibitors, this does not bind to both the enzyme and the complex but it binds either one the enzyme or enzyme substrate complex, where like uncompetitive inhibitors it binds at a different site not the substrate active site. Lastly an irreversible inhibitors unlike the rest mention before where there is a functional group it would demolish it or other way it carries out its role is by binding by covalent bonds to the enzyme. These two ways causes a drastic change in the enzyme and therefore it would not be able to carry out its role as a catalyst.
We came across in the lectures Michealis-Menten Curve and Lineweaver Burk Plot.
Fear no more: Michealis-Menten Equation and Curve. Firstly the Michealis-Menten equation describes how the reaction velocity varies with the substrate concentration. The equation is as follows…….(Image below)The equation was based on the fact that at the time it was thought that the enzyme only had one active site…therefore one substrate and one enzyme molecule.
Image showing the Michealis-Menten equation.
Image of Michaelis-Menton Plot
In the terms of the Michaelis-Menten equation, inhibitors can raise Km, lower Vmax, or both.
The type of inhibition, where Km increases but Vmax is unchanged, is called competitive because the inhibitor and substrate compete for the same site on the enzyme (the active site).
Inhibitors that alter both Vmax and Km are called noncompetitive; the inhibitors that alter Vmax only are uncompetitive.
Lineweaver-Burk Plot is when you inverted the Michaelis-Menten equation
and there you can see the effects of the inhibitors using reciprocol plots called the Lineweaver-Burk plot. This equation is linear so that a plot of 1/ v versus 1/[S] and has a slope equal to Km/Vmax and a y-intercept equal to 1/Vmax. The x-intercept of a Lineweaver-Burk plot is equal to–1/Km.
Image showing Lineweaver-Burk Plots for inhibiton
Things to remember:
Apoenzyme————>inactive protein part
Apoenzyme + Cofactor————>Holoenzyme
Cofactor———–> non protein part
Holoenzyme——-> active enzyme
-Allosteric Enzymes are enzymes involved in the regulation of cell processes. These enzymes play a role in cell metabolism by catalyzing various events, like other enzymes, and they can also be used to control the rate of metabolism.
What exactly are enzymes? Well enzymes are biological catalyst that speeds up chemical reactions by providing an alternative pathway in which has a lower activation energy,the enzyme remains unchanged from the reaction. Most enzymes are globular proteins. These proteins are associated with the increased in rate of a chemical reaction. The chemical in this chemical reaction which the enzyme works on is referred to as the substrates. An enzyme would combine with its substrate to form a enzyme/substrate complex that is very short lived. The specific site on the enzyme where the substrate binds and catalysis occurs is called the active site. Enzyme active sites provide catalytic groups to facilitate and stabilize the formation of the transition state for the chemical reaction.Once the chemical reaction has been carried out the complex would be broken up into product and enzyme. The enzyme would not change at the end of the reaction, it would remain the same as it was when the reaction had begun and it is left free of interact with other substrates. Without enzymes the cell cannot survive, most biological cells need enzymes so that their processes can occur at a faster rate that is needed to fulfill the necessary amount of products so that the cell would not die.
Substrate + enzyme ↔ enzyme/substrate complex ↔ enzyme/product complex ↔enzyme + product(s)
Enzymes are very specific and would only catalyse one reaction. This specificity is based upon the shape of the part of the enzyme molecule where the enzyme would come into contact with the substrate molecule that is the active site. This specificity can be explained more indepth by the “Lock and Key” Hypothesis proposed by Fischer in 1980 and the “Induced Fit” Hypothesis proposed by Koshland. In “Lock and Key hypothesis” the substrate is considered to be the key and its shape is complementary to that of the enzyme, then enzyme is considered to be the key.
Image showing Lock and key hypothesis where the substrate and the enzyme active site have complementary shapes.
The second hypothesis ‘Induced Fit’ was the ‘lock and key’ hypothesis with a few modifications and proposed the ‘Induced Fit’. He stated that there was more flexibility to the enzymes along with their active sites therefore the active sites could be changed or modified when the substrate comes into contact with the enzyme.
Image showing Koshland Induced Fit Hypothesis
The energy that is needed to make the substances react at all is reduced by the presence of enzymes in a chemical reaction is called activation energy.
You may have come across the word Transition state: During a chemical reaction the structure of the substrate would change into the structure of the product. Bonds are broken and formed. The transition state is the highest energy arrangement of atoms that is intermediate in structure between the structure of the reactants and the structure of products.
The enzyme does not change the free energies of the reactants or products. The position of the equilibrium is not changed.
The forces that keep the tertiary structure therefore the active site and substrates are hydrophobic interactions,electrostatic interaction,hydrogen bonding and Van Der Waals interaction.
There are 6 major classes of enzymes:
Oxidoreductases: which catalyse oxidation reduction reactions lactate—->Pyruvate OR Alcohol dehydrogenase converts primary alcohols to aldehydes.
In this reaction, ethanol is converted to acetaldehyde, and the cofactor, NAD, is converted to NADH. In other words, ethanol is oxidized, and NAD is reduced. (The charges don’t balance, because NAD has some other charged groups.) Remember that in redox reactions, one substrate is oxidized and one is reduced.
Transferase: These enzymes, called transferases, move functional groups from one molecule to another. For example, alanine aminotransferase shuffles the alpha-amino group between alanine and aspartate:
Hydrolase:Catalyse cleavage of bonds by addition of water For example, phosphatases break the oxygen-phosphorus bond of phosphate esters:
Lyases: The functional groups transferred by these lyase enzymes include amino groups, water, and ammonia. For example, decarboxylases remove CO2 from alpha- or beta-keto acids:
Dehydratases remove water, as in fumarase (fumarate hydratase):
Deaminases remove ammonia, for example, in the removal of amino groups from amino acids:
Isomerase: Isomerization of functional groups. In many biochemical reactions, the position of a functional group is changed within a molecule, but the molecule itself contains the same number and kind of atoms that it did in the beginning. In other words, the substrate and product of the reaction are isomers. The isomerases (for example, triose phosphate isomerase, shown following), carry out these rearrangements.
Ligases: Catalyse formation of bonds between Carbon and O,S,N coupled to hydrolysis of high energy phosphate such
For example, aminoacyl-transfer RNA amino acids to their respective transfer RNAs in preparation for protein synthesis; the action of glycyl-tRNA synthetase is illustrated in this figure:
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