the biochemGazettE: Sayanora…..\(^o^)/

Well, we have reached the end of the road time to say good bye~

This course had it’s ups and downs for was never smooth sailing but after things got better, and I would like to thank Hokage for his patience and major efforts that may at times seem like he is giving us hell and making our lives miserable, it is a good technique to make us learn and apply what we learn, not just read and regurgitate for exam and have it all forgotten when we’re done. So どうもありがとうございました (Dōmo arigatōgozaimashita) Kyōshi.

One of my all time fav

582826-1366x768-kenshin_swirls

My song of Inspiration T.M Revolution- Heart of the Sword

http://www.youtube.com/watch?v=0LdXiXpS-4w

the biochemGazettE: Electron Transport Chain (ETC)

Mr. Khan he is a life saver, helped me sooo much in understanding this topic!

etf

Reflection: ETC, this one one of the hardest parts of cellular respiration reactions for me to grasp, because of all the hydrogen gradients and moving from outer to inner membrane was so confusing. But I can say now I have thoroughly defeated the enemy Gundam style! \m/

Gundam-WIng2 (1)

So the ETC is where we get all our bulk ATP, so lets do a quick count up

from Glycolysis= 2ATP

from Krebs=2ATP

Other molecules so far

Glycolysis=2 NADH

Krebs= 6 NADH  + 4 CO2

Prepatory stage of pyruvate= 2 NADH + 2CO2

Taotal=10 NADH

Krebs= 2 FADH2

The total according to respiration we are supposed to get is 38 ATP. So far we have 4 ATP

C6H12O6 + 6 O2  6 CO2 + 6 H2O + Energy (38ATP + heat)

The remaining ATP is generated from oxidation of NADH and FADH2, which yield 10 ATP and 4 ATP respectively, giving us the total 38 ATP  . How does it do this?

Well the electrons released from NADH go from a higher energy state to a lower one releasing energy going through the NADH dehydrogenase, Succinate Dehydrogenase, Cytochrome bc1 complex and Cytochrome c oxidase. This energy is then used to pump H+ ions into the outer membrane  by these complexes listed and due to accumulation of H+ in the outer membrane try to get back into the inner membrane to reduce the saturation of H+ in the outer membrane. The H+ goes through the giant protein ATP Synthase which uses the energy from the proton gradient to combine the ADP and inorganic phosphate to combine to form ATP, and from as seen from 1 NADH= 3 ATP and FADH2= 2 ATP. The electrons final acceptor is oxygen which is reduced to water and from the 10 NADH and FADH2 we get 6 H2O.

So, there have it ETC and the compeltion of cellular respiration in a nutshell!

the biochemGazettE: Nucleic Acids.

So what are Nucleic Acids and what do they have to do with use…..well nucleic acids are OUR LIVES! Basically, they are what makes us, you us….DNA and RNA, they are the one of the most important macro molecules.

So DNA( deoxyribonucleic acid, meaning it lacks a oxygen) vs RNA(ribonucleic acid)….

dna vs rna

nucleotides-DNA-RNA

So what are the differences in function and composition between these two

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Structure DNA has a helical structure, this is due to hydrogen bonding between the base pairs in DNA these are:

1. Thymine to Adenine

2. Cytosine to Guanine

Thymine and Cytosine are pyrimidines, while Guanine and Adenine are purines.

References:

Wikipedia.org. “Nucleic Acid” http://en.wikipedia.org/wiki/Nucleic_acid#Nucleic_acid_sequences

diffen. ” DNA vs RNA” http://www.diffen.com/difference/DNA_vs_RNA

the biochemGazettE: Lipids vid Review

This Vid is hella Kawaii!!! Alright enough of that so what did I learn is that Lipids, physical sate is determined by its composition, therefore saturated fatty acids are solid at room temp, because they posses no C=C and are called oils. While unsaturated fatty acids has one or more C=C bonds which forms a kink thus making them unlinear and not able to be compact as saturated fatty acids, therefore they are liquids at room temperature and are called oils.

So, this vid was good for the basic of lipids but it lacked major information as in

1. that all lipids are water hating ie hydrophobic.

2. they are stored as fat in us for energy use.

3. also how they are use in our bodies, in our cell membranes as phospholipids, steriods  and hormones.

4. no mention of different types of lipids, phospholipids, triglycerides, glycerolipids etc.

5. also no mention how we get the bad trans fat, they are cis-trans fats. They arise from Hydrogenation that is the addition of hydrogen  While unsaturated is cis, same side.

transfat1

So what was new I learned from Mr. Hokage is Delta designation…

CH3-CH2-CH2-CH2-CH=CH-CH2-CH2-CH2-CH2-CH2-CH2-CH2-COOH         

We always start from the carboyxlic acid end and count the no. of carbon atoms from there, so in this molecule it is =14

Then we see how much C=C there are in this fatty acid there is only 1

Finally we find the position of that said C=C, which is carbon 9.

thus Delta Designation of this fatty acid is 14: 1(Δ 9).

So jus my tibits on Lipids, fatty acids and all the food we UWI students consume…lol

References:

chemistry.msu. “Lipids” http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/lipids.htm

Wikipedia.org. “Lipid” http://en.wikipedia.org/wiki/Lipid

the biochemGazettE: Real uses

So just wanted to show how we use enzymes in our everyday lives besides in us….there everywhere especially in production of the foods we eat. Today we’re gonna look at how it is used in in Cheese production.

So in the cheese production the enzyme Lipase is used to give a creamy-texture and rich flavour to either hard or soft cheese, whithout losing that dairy taste. So what is lipase and how does it do this?

” Lipase is an enzyme that catalyzes the formation or cleavage (hydrolysis) of fats (lipids)”. What Lipase does it attach to the fat globes of the raw milk and break them down, which then causes the fatty acids to be released. The  fatty acids then in turn creates the aroma, texture and sharp taste common (and desired) in most Italian cheeses, as well as some Feta and Blue Cheeses. Lipases are present in the milk itself. But, most of it is lost in the process so additional lipase is needed they come from kids, lambs or calves.

So fun fact about how we get the good tasting cheese…

 

References:

Curd-Nerd. ” Lipase- A helpful busy little enzyme” http://curd-nerd.com/lipase-what-is/

the biochemGazettE: TCA Vid Review….

krebs_cycle-46b152fcf30abdad1e42cce4ded6e2d99d00f458-s6-c10

Well back again, this time am gonna review the TCA/ Krebs/ Citric Acid Cycle it gonna be a vid review  part reflection

Reflection: TCA that’s another old foe. He was scary but he ain’t, so this cycle unlike glycolysis needs oxygen and it occurs in two cycles for every 1 glucose molecule and where it actually occurs is in the matrix of the mitochondria. Also something new i learn’t maybe due to my ignorance is that one of the enzyme Succinate Dehydrogenase is found in the inner membrane of the mitchondria unlike the rest of the enzymes which are in the matrix.

This vid came from the same ppl who I reviewed on the Glycolysis, can’t help it love the voice and the clear drawings. So, Krebs cycle is the 3 step in glycolysis if we’re gonna count the preparatory step as one in this cycle we’re oxidizing 2 Acetyl-CoA to form:

4 oxygen+ 2ATP + 6 NADH+ 2FADH2

So , he started of with identifying that pyruvate is the krebs cycle primary substrate although their are other substrate than can be used eg. fatty acids. He also looked at the preparatory stage where the pyruvate from glycolysis is converted to Acetyl-CoA by pyruvate dehydrogenase complex and that it had other substance assisting it in the conversion ie. cofactors.  He cleary went through all the steps, but also he identified the enzymes involved in each intermediate conversion which was a bonus

Enzymes:

1. Citrate Synthase- forms citrate from acetyl-CoA and oxaloacetate

2. Aconitase- converts citrate to cis-aconitate

3. Aconitase again converts cis-aconitate back to isocitrate (a isomer of citrate)

4. Isocitrate Dehydrogenas- converts isocitrate to alpha-ketogluterate and gives off the first NADH and first CO2

5. Alpha-Ketogluterate Dehydrogenase Complex- converts alpha-ketogluterate to succinyl-CoA and gives off the second CO2 and NADH.

6. Succinyl-CoA Synthetase- converts succinyl-CoA to Succinate and gives off GTP which is a form of ATP.

7. Succinate Dehydrogenase- converts Succinate to Fumarate and givess of the ony FADH2.

8. Fumarase- converts fumarate to Malate.

9. Malate Dehydrogenase- converts malate back to oxaloacetate and the final NADH of this cycle.

So all in all a good and concise overview of the Krebs Cycle.

the biochemGazettE: Fate of Pyruvate!!!!!

ballgob-fig20_017

Well it should be more the Fates of Pyruvate, but whatever. So as we can see from the lovely little pic above there three ways pyruvate can go…

1. Converted into Acteyl-CoA and enter Krebs Cycle, a AEROBIC process.

2. Converted into Lactate which happens in organisms ie. us, a ANAEROBIC process.

3. Converted into Ethanol the good stuff…NEVER! It’s bad for you! A ANAEROBIC process in microorganisms.

1. Acetyl-CoA path, here 3c pyruvate is converted to 2C Acetyly-CoA which is the molecule used in the krebs cycle. The enzyme that does this is Pyruvate dehydrogenase complex and remembering that anything with dehydrogenase in the name NADH is formed and yes it is along with one CO2. Pyruvate Dehydrogenase is a complex thus it has buddies helping him, well cofactors which are

a. TTP (thiamine pyrophosphate)

b. NAD+

c. FAD

d. Lipoate

e. Coenzyme A

Pyruvate oxidation

2. Pyruvate to Lactate, this happens to all of us when we do strenuous activities were you get cramps in your muscles and soreness. This reaction is important because it gives back NAD+ which is vital for Glycolysis to proceed, as it is used in step 6. The enzyme at work here is Lactate dehydrogenase, it adds a water molecule across the C=O in the pyruvate to give the lactate/ lactic acid. These reactions are also seen in Erythrocytes our red blood cells and jus a lil reminder it is a anaerobic process. ie. no oxygen is present.

Pyruvate_to_lactate 3. Finally the last path pyruvate can go is to Ethanol by fermentation, another anaerobic process but occurs in microorganisms. There are two enzymes at work here:

a. Pyruvate decarboxylase- this enzyme requires TTP  coenzyme and Mg2+ cofactor to work it removes a carbon atom

(decarboxylates) from the pyruvate and forms Acetaldehyde.

b. Alcohol Dehydrogenase- another dehydrogenase, but we get NAD+ instead of NADH, thus why this reaction is another form of

gaining back NAD+ and finally Ethanol is formed.

Pyruvate_decarb_1So there it is folks Fate of Pyruvate, hope it was as helpful!:D

References:

afoggyone.tripod. “Fates of Pyruvate”.http://afoggyone.tripod.com/pyruvate1.html