You Tube Video #2

http://www.youtube.com/watch?v=VGHD9e3yRIU

This video is titled “Lipids” and it is done by bozemanbiology.

Published on Nov 12, 2012

In this video Paul Andersen describes the lipids (of the fats). He explains how they are an important source of energy but are also required to cell membranes. He explains how the hydrocarbon tails in triglycerides contain energy available for life. He also explains how phospholipids construct, and cholesterol molecules main the cell membrane.

Intro Music Atribution
Title: I4dsong_loop_main.wav
Artist: CosmicD
Link to sound: http://www.freesound.org/people/Cosmi..

Creative Commons Atribution License

I found this video to be very helpful when studying for lipids. It was concise, short, straight to the point, short, well-explained and did i mention short! LOL However, even thought the vid was only 7mins and 05sec. there were a lot of things that he went through. I especially liked his method of teaching as the video was generally fun to watch as well as listen to.

Some of the Key points discussed in the video are:

• lipids /fats that is found in butter or olive oil is what we call a triglyceride.
• it contains a glyceral head and 3 fatty acid tails
• the tail is where the energy lies
• when we eat fat it is broken down by enzymes called lipases
• this is where we get the energy from
• energy is stored via fats in the body and then we burn these fats when needed.
• fats in addition to providing energy also provides thesurroundings such as cholesterol with a bilayer phospholipid head.
• energy comes from the hydrocarbons.
• saturated fats are solid at room temp, because of the single bonds.
• unstaurated fats because of the double bonds, puts a bend in the tail causing it to be kinky. therefore it cannot be packed together so it is a liquid at room temp.

Reflection on Labs…

For biochem labs i was placed in the evening class because apparently when i had signed up it didn’t go through. 😦 this kind of affected my mood toward enjoying my labs because can you imagine having labs on a FRIDAY evening >.< lol however, all in all my labs were good. Each time i got great demonstrators who always explained the labs and helped us…even though the labs were quite simple enough for one to understand by themselves. 🙂 All in all, i had a great experience in the lab and i have learned my lesson when signing up for labs next semester!!!!! 😀 😀

Reflection on Tutorials…

Biochem is the 1st tutorial out of all my other courses that i actually looked forward to every other week. 🙂 i generally enjoy having tutorials with J.M because he challenges us to study and come well prepared before the tutorial starts. It is fun for me because i was lucky enough to sit on the side of the class that is filled with smart people so i never really got a low mark for any tutorial hehe 😀

TCA cycle and ETC

 

 

 

 

 

 

 

REFERENCES:

http://www.google.tt/search?q=tca+cycle&hl=en&tbm=isch&tbo=u&source=univ&sa=X&ei=oSJqUdf1JYjM0AH9qICYDw&sqi=2&ved=0CD0QsAQ&biw=1241&bih=606#imgrc=8ixrd6eydmJJiM%3A%3B6ekHXuTaZuZtiM%3Bhttp%253A%252F%252Fsustainabilityworkshop.autodesk.com%252Fsites%252Fdefault%252Ffiles%252Fstyles%252Flarge%252Fpublic%252Fcore-page-inserted-images%252Fkrebs_cycle_from_wikimedia-tweaked.jpg%3Bhttp%253A%252F%252Fsustainabilityworkshop.autodesk.com%252Fbuildings-products%252Fdoing-biomimicry-mechanical-principles%3B1000%3B796

 

 

Reflection!

At the beginning of doing the topic i found glycolysis very difficult to grasp as there was simply too many enzymes and reactions to remember. However, being the topic that was stressed the most in the course, and after looking at the video posted up by J.M i actually find glycolysis to be the topic stuck in my head and and also the easiest to remember now! Hopefully i will remember it during the final exam  *hides face*……But seeing as how it is my last exam that gives me enough time to review everyting i would need to! Woohoo 😀

YOUTUBE VIDEO #1

http://www.youtube.com/watch?v=33JUjeo6-lE&feature=youtu.be 

Glycolysis was a difficult topic to remember because of all the different reactions taking place. However, i found the video by J.M video on glycolysis part 1 to be very helpful as it was well explained and concise. i generally enjoyed listening to this video because i understood everything that was thought in the video and the pictures and diagrams of the reactions made it easier to remember.

Some of the key points in the video are:

• Glycolysis is the splitting of glucose.
• there are two phases: energy investment phase and the energy generation phase.
• In both phases, it requires 5 enzymes to break down each glycolytic reaction.
• The 1st phase contains 2 irreversible (goes in one direction) enzymes and 3 reversible (goes in both direction) enzymes.
• The 2nd phase phase contains 1 irreversible enzyme reaction and 4 reversible enzyme reactions.
• One molecule  of glucose is needed to convert into two molecules of pyruvate.
• for every glucose molecule entering glycolysis, 2 ATP and 2 NAD+ are used, and 4 ATP and 2NADH are generated.
• Therefore there is a net gain of 2ATP and 2NADH.
• The 1st 5 enzymes in the investments phase are: Hexokinase, which requires Mg2+ in order to stabalize some of the negative charge on the ATP molecule and prevents water from entering, Phosphohexose isomerase which converts an aldose sugar to a ketose sugar. Phospho-fructkinase-1 which is catalysed by the reaction PFK-1. This is an important enzyme in terms of regulation. Aldolase which splits the fructose 1,6-bisphosphate into 2 glyceraldehyde 3-phosphate and dihydroxyactone. Triose phosphate isomerase which converts the DHAP to G3P.
• At the end of the 1st phase there will be 2 molecules of G3P.
• The 2nd 5 enzymes in the pay-off phase are: Glyceraldehyde 3-phosphate dehydrogenase, Phosphoglycerate kinase, Phosphoglycerate mutase, Enolase and Pyruvate Kinase.
• For glycolysis to continue 2NAD+ needs to be converted 2NADH + H+
• If there is no more NAD in the cell then glycolysis cannot occur.
• NAD conc. is low in the cell then they need to regenerate NADH back into NAD

 

Glycolysisssss…..

Glycolysis is the metabolic pathway that converts glucose C₆H₁₂O₆, into pyruvate, CH3COCOO⁻ + H⁺. The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).

Glycolysis is a determined sequence of ten reactions involving ten intermediate compounds (one of the steps involves two intermediates). The intermediates provide entry points to glycolysis.

It occurs, with variations, in nearly all organisms, both aerobic and anaerobic. The wide occurrence of glycolysis indicates that it is one of the most ancient known metabolic pathways. It occurs in the cytosol of the cell.

The entire glycolysis pathway can be separated into two phases:

• The Preparatory Phase – in which ATP is consumed and is hence also known as the investment phase
• The Pay Off Phase – in which ATP is produced.

The overall reaction of glycolysis is:

 

Preparatory phase

The first five steps are regarded as the preparatory (or investment) phase, since they consume energy to convert the glucose into two three-carbon sugar phosphates (G3P):

•  The first step in glycolysis is phosphorylation of glucose by a family of enzymes called hexokinases to form glucose 6-phosphate (G6P). This reaction consumes ATP, but it acts to keep the glucose concentration low, promoting continuous transport of glucose into the cell through the plasma membrane transporters. In addition, it blocks the glucose from leaking out – the cell lacks transporters for G6P, and free diffusion out of the cell is prevented due to the charged nature of G6P. Glucose may alternatively be formed from the phosphorolysis or hydrolysis of intracellular starch or glycogen.

 

• G6P is then rearranged into fructose-6-phosphate (F6P) by glucose phosphate isomerase. Fructose can also enter the glycolytic pathway by phosphorylation at this point.The change in structure is an isomerization, in which the G6P has been converted to F6P. The reaction requires an enzyme, phosphohexose isomerase, to proceed. This reaction is freely reversible under normal cell conditions. However, it is often driven forward because of a low concentration of F6P, which is constantly consumed during the next step of glycolysis.

• The energy expenditure of another ATP in this step is justified in 2 ways: The glycolytic process (up to this step) is now irreversible, and the energy supplied destabilizes the molecule. Because the reaction catalyzed by Phosphofructokinase 1 (PFK-1) is coupled to the hydrolysis of ATP, an energetically favorable step, it is, in essence, irreversible, and a different pathway must be used to do the reverse conversion during gluconeogenesis. This makes the reaction a key regulatory point. This is also the rate-limiting step. Furthermore, the second phosphorylation event is necessary to allow the formation of two charged groups (rather than only one) in the subsequent step of glycolysis, ensuring the prevention of free diffusion of substrates out of the cell.

• Destabilizing the molecule in the previous reaction allows the hexose ring to be split by aldolase into two triose sugars, dihydroxyacetone phosphate, a ketone, and glyceraldehyde 3-phosphate, an aldehyde. There are two classes of aldolases: class I aldolases, present in animals and plants, and class II aldolases, present in fungi and bacteria; the two classes use different mechanisms in cleaving the ketose ring. Electrons delocalized in the carbon-carbon bond cleavage associate with the alcohol group. The resulting carbanion is stabilized by the structure of the carbanion itself via resonance charge distribution and by the presence of a charged ion prosthetic group.

• Triosephosphate isomerase rapidly interconverts dihydroxyacetone phosphate with glyceraldehyde 3-phosphate (GADP) that proceeds further into glycolysis. This is advantageous, as it directs dihydroxyacetone phosphate down the same pathway as glyceraldehyde 3-phosphate, simplifying regulation. 

 

Pay-off phase

The second half of glycolysis is known as the pay-off phase, characterised by a net gain of the energy-rich molecules ATP and NADH. Since glucose leads to two triose sugars in the preparatory phase, each reaction in the pay-off phase occurs twice per glucose molecule. This yields 2 NADH molecules and 4 ATP molecules, leading to a net gain of 2 NADH molecules and 2 ATP molecules from the glycolytic pathway per glucose.

• The triose sugars are dehydrogenated and inorganic phosphate is added to them, forming 1,3-bisphosphoglycerate. The hydrogen is used to reduce two molecules of NAD⁺, a hydrogen carrier, to give NADH + H⁺ for each triose. Hydrogen atom balance and charge balance are both maintained because the phosphate (Pi) group actually exists in the form of a hydrogen phosphate anion (HPO₄^2-), which dissociates to contribute the extra H⁺ ion and gives a net charge of -3 on both sides.

• This step is the enzymatic transfer of a phosphate group from 1,3-bisphosphoglycerate to ADP by phosphoglycerate kinase, forming ATP and 3-phosphoglycerate. At this step, glycolysis has reached the break-even point: 2 molecules of ATP were consumed, and 2 new molecules have now been synthesized. This step, one of the two substrate-level phosphorylation steps, requires ADP; thus, when the cell has plenty of ATP (and little ADP), this reaction does not occur. Because ATP decays relatively quickly when it is not metabolized, this is an important regulatory point in the glycolytic pathway.

 

• Phosphoglycerate mutase now forms 2-phosphoglycerate.

• Enolase next forms phosphoenolpyruvate from 2-phosphoglycerate. Cofactors: 2 Mg2+: one “conformational” ion to coordinate with the carboxylate group of the substrate, and one “catalytic” ion that participates in the dehydration.

• A final substrate-level phosphorylation now forms a molecule of pyruvate and a molecule of ATP by means of the enzyme pyruvate kinase. This serves as an additional regulatory step, similar to the phosphoglycerate kinase step. Cofactors: Mg2+

 

REFERENCES:

http://www.google.tt/search?q=glycolysis&hl=en&tbm=isch&tbo=u&source=univ&sa=X&ei=P_hpUbyoCZSm8ASv94D4Cg&sqi=2&ved=0CDIQsAQ&biw=1241&bih=567

http://biology.about.com/od/cellularprocesses/a/aa082704a.htm

Published Paper #2…..

Boncompagni, Tatiana.2012.”Enzymes Try to Grab the Spotlight,” Published: February 22, 2012.          http://www.nytimes.com/2012/02/23/fashion/enzymes-once-sidelined-try-to-grab-the-spotlight.html?_r=0

 

This article is for the ladiesss and also for the guys who cares about their appearance… 😀

 

As we all know we are approaching finals soon and that just causes us to be stressed by simply thinking about the fact that its only two weeks away!! :O One of the main problems caused by stress is known as BREAKOUTS (pimples)!!!! >.< hopefully this solution works lol 😀

Found this article to have helpful tips on how to manage your sensitive skin and the solution is ENZYMES!  :O Bet there are many of us (like myself) who did not know this. This article is simply based on the fact that enzymes are also used to treat persons with cases of: irritable bowel syndrome, leg cramps, insomnia, acid re flux, acne, wrinkles and many more. This is a very interesting article for me as I didn’t know they used enzymes clinically to treat these problems that almost everyone face each day.

 

The article states that there are two kinds of enzymes, one being metabolic and the other being digestive enzymes. Metabolic enzymes are found in every living cell of the body which is responsible for various chemical reactions, whilst digestive enzymes are released in the stomach and the intestines to help break down the food into soluble nutrients that the body can use. However, there is a third kind of enzyme known as food enzymes. These are found in uncooked nuts, vegetables and fruits.

When these food enzymes are eaten it is argued that they predigest the nutrients and so the body will use less of its own digestive enzymes and direct more of the energy to other functions such as, organ repair or detoxification.

The enzyme responsible for making the spotlight or in other words the “star ingredient” is Bromelain. This is an enzyme found in pineapple and papain which comes from papaya. This enzyme is the main ingredient in facial masks and the night cream from Rx Skin Therapy.

However, there is a less expensive treatment that you could use and that would be to try this at home by using the peelings from the pineapple and papaya. This is used for sensitive skin and skin prone to acne.

 

This is said to work so good that plastic surgeon Dr. Adam R. Kolker sells a line of products that also includes a papaya face polish.

The article states that enzymes affect the peptide bonds and the protein based adhesion between cells on the dead outer layer of skin cells. This causes the bonds to break and the enzymes speeds up this reaction. Therefore adding this to the skin as you age slows down this process thus, making the skin appear to be dull and flat.

If you are one to believe that beauty comes from within then you might want to consider the Beauty Detox Solution. This is a dietary enzyme supplement that is advised to be taken every day even before eating cooked foods. It is said to be the secret to long life.

However, it is advised by Janine Whiteson, a Manhattan nutritionist to eat pineapple and papaya and drink a lot of herbal tea when experiencing bloating.

 

References for photo:

http://www.google.tt/imgres?imgurl=http://3.bp.blogspot.com/-7dCza1JUvVc/TVO_Fia7JlI/AAAAAAAAADg/N_10FfcD4ic/s1600/papaya-lg.jpg&imgrefurl=http://naturalmedicineworld.blogspot.com/2011/02/papaya.html&h=427&w=640&sz=49&tbnid=jbhlY9KhPqsF0M:&tbnh=89&tbnw=133&prev=/search%3Fq%3Dpictures%2Bof%2Bpapaya%26tbm%3Disch%26tbo%3Du&zoom=1&q=pictures+of+papaya&usg=___1eXWdY75m20wjT9pQX09b16Cnk=&docid=GBDNrhUgV02W0M&hl=en&sa=X&ei=U_ZpUZOsIMHl4AONuoHgDw&sqi=2&ved=0CDIQ9QEwAw&dur=1413

 

Reflection!

For myself i find enzymes to generally be an easy topic to grasp seeing as how it’s the reason why i am alive! However, i find the different graphs to be confusing as there are soo many for each type of reaction taking place with enzymes. If you have the same problem as myself then you will find this very helpful as i am going to post up the graphs for each type of inhibition as well as for each factor that affects enzymatic activity! Hope this helps and do hope you enjoy! ^_^

 

Figure 1: Lineweaver-Burk plot graph showing competitive inhibition.

 

 

Figure 2: Lineweaver-Burk plot graph showing Uncompetitive inhibition.

 

 

 

Figure 3: Lineweaver-Burk plot graph showing Non-competitive inhibition

 

 

 

Figure 4: showing the effect of temperature on enzyme activity.

 

 

 

Figure 5: graph showing the effect of substrate concentration on enzyme activity.

 

REFERENCE:

http://en.wikipedia.org/wiki/Enzyme

 

Enzymessssssss!!!

Enzymes are biological catalyst that speeds up the rate of a reaction. A catalyst is a substance which increases the rate of a chemical reaction without itself being used up in the process. Industrial process use catalysts to speed up the production of important chemicals, reducing the need for high temperatures and pressures. An organism’s metabolism consists of thousands of different reactions. Each of these needs different catalysts to enable the reaction to take place. These catalysts called enzymes; hence an enzyme is also an organic catalyst which speeds up the rate of a reaction.

The substance upon which the enzyme acts is called its substrate. Metabolism consists of hundreds of reactions linked together, where the product of one reaction is the substrate for the next. This is known as a metabolic pathway and each step is catalyzed by a different enzyme.

There are thousands of different reactions taking place in living cells; therefore each reaction needs to have a specific enzyme in order to catalyze the reaction. Enzymes are proteins which are composed of sub-units called amino acids that can be linked to each other in an infinite number of different ways. This therefore means that the primary structure of an enzyme shows the unpredictability needed to achieve specificity.

However, this specificity depends on the shape of a small part of the enzyme called the active site, which is the place where the enzyme actually comes into contact with the substrate.

A property of enzyme that makes them important as analytical and research tools is the specificity that they display relative to the reactions that they catalyze. Some enzymes display absolute specificity. This is where the enzyme catalyse only one particular reaction while other enzymes shows relative specificity which is where the enzyme binds to some structurally related substrates. There are 4 types of specificity and they are; absolute specificity, group specificity, stereochemical specificity and last but not least linkage specificity. Absolute specificity is when the enzyme itself will catalyze only one reaction. Group specificity is where the enzyme itself will act on molecules that have detailed functional group for example, amino, phosphate and methyl groups. Linkage specificity, this is where the enzyme acts on a particular type of chemical bond, no matter of what the rest of the molecule structure appears to be. And sterochemical specificity is where the enzyme itself will act on a particular steric or optical isomer.

Non- covalent bonds is responsible for the binding of reversible inhibitors to enzymes. This non-covalent interaction depends upon what the inhibitors bind to, such as, the hydrogen bonds, the hydrophobic interactions or the ionic bonds.

These are referred to as weak bonds and combines to produce strong and specific bonding. There are 3 kinds of reversible inhibitors and they are competitive, non-competitive and uncompetitive inhibitors.

Competitive inhibitor is where the inhibitor and substrate are in a competitive with each other in order to bind to the enzyme at the same time. This can be overcome by simply increasing the substrate concentration level or in other words out-compete the inhibitor. The second type of inhibition is uncompetitive inhibition. These along with the enzyme’s substrate bind to the enzyme at the very same time. However, this binding of the inhibitor affects the binding of the substrate and vice-versa. This type of inhibition is reduced by simply increasing the substrate concentration. The third type of inhibition is non-competitive inhibition. This type of inhibitor reduces the activity by binding to the active site; however, it does not affect the binding of the substrate.

Temperature, substrate concentration as well as pH are all factors that affect enzyme activity. However, in this lab we focused mainly on temperature and substrate concentration. As you increase the temperature it causes the molecules to move faster and this in turn increases the enzyme activity. This means that there will be collision between the molecules and the enzyme. This therefore affects the rate, meaning that the higher collision rate allows an increase in the reaction rate, but, only up to a certain point. If there is still an increase in the temperature, it will cause the enzyme’s protein to start to denature which is a potentially permanent process. The optical temperature ranges of about 25-40 degrees Celsius.

An increase in substrate concentration will also cause the enzyme activity to increase. This is also due to the increase in collisions between the substrate and the active site. However, at some point, if the substrate concentration still increases, there will have no effect on the enzyme activity because all the active sites will be taken up.

 

REFERENCES:

http://en.wikipedia.org/wiki/Enzyme

http://www.chem4kids.com/files/bio_enzymes.html