Paper Review 2

Paper review 2

Glycolysis inhibition for cancer treatment

Hey readers! Nasir here again and for this post I will be giving a review on an interesting excerpt I uncovered while researching glycolysis..so have a read!

This paper consisted facts on the metabolic pathway known as glycolysis and how the knowledge on said metabolic pathway can profit medicine a promising step into battling the deadly disease known as cancer. The paper highlighted that most cancer cells tend to show an increased rate of glycolysis for the generation of ATP and these may be as a result of one of or a combination of 1) mitochondrial defects 2) adaptation to hypoxic environment in cancer tissues and 3) abnormal expression of certain metabolic enzymes. (As seen in previous posts, ATP is one of the main universal energy currencies for the cell.) This increase in the rate of glycolysis (described by Otto Warburg) is known as the Warburg effect. More importantly, this increase in metabolic activity provides a biochemical basis for a design into therpeudic strategies to preferentially kill cancer cells by inhibiting glycolysis. 

Now, many advances into the destruction of cancer cells have been developed; such as target specific agents designed to interact with the key cells that contribute to cancer without damaging normal cells. However this paper illustrates several attempts that can be undergone to kill malignant cells effectively by inhibiting phases in glycolysis. As is known by the scientific community, the process of glycolysis undergoes 10 important reactions, each catalysed by a specific enzyme to generate 2 ATP. The paper decribes that recent studies have provided evidence that inhibition of glycolysis is more prominent on cells with a higher rate of glycolysis because of either genetic defects or a lack of oxygen. For instance if the enzyme hexokinase is inhibited by 3-BrPA, it causes a rapid decrease in the generation of ATP and can lead to massive cell death. The paper goes on to explain that if glycolysis is inhibited, the intact normal mitochondria in normal cells tend to utilise other materials such as fatty acids and amino acids as a means to generate ATP. As such, normal cells are expected to be less sensitive to the agents that will inhibit glycolysis and are relatively unaffected. Another agent mentioned is 3-Bromopyruvate, and inhibits hexokinase to abolish ATP production and cause severe cellular depletion of ATP; it also shows tendencies to target cells exhibiting high glycolytic rate and rapidly dephosphorylate the substrate leading to massive cell death. Furthermore the inhibitor Oxythiamine is also mentioned tasked with the inhibition of pyruvate dehydrogenase leading to a block in aerobic respiration.

The paper was very informative in that it helps highlight the many important pathways in glycolysis and also allows an informative insight into how cells can be influenced on a biochemical basis to achieve a much desired outcome; in this case, battling cancer.

I hope this was an informative read! Please do not forget to comment.

~Nasir

References: Pelicano H, Martin DS, Huang P.(2006) “Glycolysis inhibition for cancer treatment” accessed 12/04/14. Published by University of Texas MD Anderson Cancer Center, Houston,TX,USA.

Toxicity of weight loss agents

In today’s world there is a large amount of the population that obese and desire to become thinner. Some goes on extreme diet plans while the others go on unhealthy weight management strategies such as diet pills and laxatives. However, this summary would only be on diet pills and its content such as 2,4- dinitrophenol (DNP) and guar gum.

        DNP was historically used as a dye, wood preserver, herbicide, and photographic development but then was discovered by Murice Tainter as a weight loss supplement. However, after its discovery, DNP became popular but then it causes a significant amount of death due to its used as a weight loss pill. DNP causes uncoupling of oxidative phosphorylation in which there would be a decrease in ATP production and hence the body would be energy deficient and start breaking down fat to make ATP. Uncoupling of oxidative phosphorylation causes a buildup of pyruvic and lactic acid  and also competitively inhibits ATP formation which causes a rise in body temperature above normal. Therefore DNP can cause hyperthermia, tachycardia (increase heart rate), Diaphoresis ( perspiring abnormally due to increase heat), tachypnea (abnormal breathing rate) and cardiac arrest hence if taken in a large amount can lead to death.

        Apart from DNP and electron transport chain, Guar Gum which is used in weight loss pills which has a toxic effect. Guar Gum is used in ice cream making and also as a food thickener. It causes weight loss by increasing fecal excretion since it lowers cholesterol from the enhance excretion of bile acid into feces and in turn decrease the absorption of dietary lipids. Moreover, since it delays gastric emptying it gives a sense of fullness which can cause a decrease in consumption of food and hence weight loss. Therefore too much Guar Gum intake can cause abdominal pain, flatulence, diarrhea, and cramps, also to an extent abdominal obstruction which have to be treated by urgent surgical means.

         Since the rise in obesity, there has been an increased in the usage of diet pills, deaths due to these pills and thus the awareness towards its dangerous effects.  

 

Reference:

Yen May, and Michele Burns Ewald. 2012. Toxicity in Weight

        Loss agents. Journal of Medical Toxicology 8(2):

        145-152. Accessed April 10, 2014.

        http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3550246/

Think Lipids !!!

here are some more MCQ’s on lipids…
LIPIDS MCQ’S
1. Which one of these statements is NOT TRUE about FATS:
a. They are usually solids and liquids at room temperature
b. They contain saturated hydrocarbon chains
c. They do not contain a C=C bond.
d. They are made up of carbon, hydrogen and oxygen.

2. Does oils contain unsaturated hydrocarbon chains and are also known as Polyunsaturated.
a. TRUE
b. FALSE

3. van der Waals forces are present in the fatty acids
a. FALSE
b. TRUE

4. As fatty acid chains increases the melting point decreases
a. TRUE
b. FALSE

5. What are the functions of lipids:
1. Natural protective layer in fruits and vegetables
2. Provides insulation to the body from the cold environment
3. Source of energy
4. Protects the vital organs

a. 2,3
b. 1,3,4
c. 2,3,4
d. 1,2,3,4

ANSWERS:
1) a-Fats are solids at room temperature while oils are liquids at room temperature
2) a
3) b
4) b- As fatty acid chains increases the melting point increases
5) d

Mcq’s- Fig 1

MCQ’s for BIOL 1362
1. What events occur in the TCA cycle?
1. Dehydration
2. Hydration
3. Oxidative carboxylation
4. Substrate-level phosphorylation
5. Dehydrogenation

a. 1,2,3,4
b. 2,3,4,5
c. 1,2 and 3
d. 3,4,5
e. 1,2,3,4,5

Using figure 1 below to answer questions 2

2. Which letter (X, Y, and Z) represents the steroid nucleus?
a. X
b. Y
c. Z
d. None of the above
e. All of the above

Answers
1. E
2. c

enzyme word search

THE END IS NEAR!!!!

The End is Near…. and no I am not talking about the world I am talking about exam time and the near of another semester.

We, the bcbionx, had a wonderful experience in doing these blogs and by “We” I mean Nasir, Sabita, Sade, Philip and  I (Dominique).

Where we put all our creativity and humour in these blogs, examples like the “Trinidad as a cell” was does by Nasir ,the ” Classic Cartoons” was done by me, some of the the videos’ reviews were done by Philip and some reflections were done by Sabita and Sade. 

However that is just a summary if I was to go in complete details, this blog will but too long. As the team leader of the bcbionx I just want to say thank you to all that have been viewing our blogs, asking us questions about the topics we researched and just supporting us.

We all in the bcbionx group are grateful.

Thank you.

Hi everyone …….it’s me again, Sade from BC Bionx!!!!!!!! And today I’m discussing RNA structure and synthesis. So I’m going right into it, so what we remember from CAPE level that RNA is made from transcription that is, the copying process during which DNA strand serves as a template for the synthesis for transcription. Transcription produces messenger RNA, ribosomal RNA, transfer RNA and additional small RNA molecules that perform specialized catalytic, structural and regulatory functions that are not translated also known as ncRNA, non coding RNAs so the final product can be an RNA or protein.

 

 

 

 

 

Figure 1 showing the transcription of DNA into RNA molecules

Now there three types of RNA molecules needed for the synthesis of protein: ribosomal and transfer and messenger RNA. But like the DNA molecule, these three RNA molecules have polymeric, unbranched molecules composed of nucleoside monophosphates joined by phosphodiester bonds. Sooo yea, interesting stuff …….RNA structure and synthesis always seemed simple at A’level but now….not so much lol. But they be similar in structure but differ in terms of size with RNA being smaller than DNA, contains ribose instead of deoxyribose, uracil rather than thymine and can exist as single strands that are capable of folding into  complex  structures. There is also differentiation between the three types of RNA terms of size, function and structure.rRNA as we all know exist as ribosomes in the cell and is the site of protein synthesis and together makes up for 80% of total RNA .tRNA is the smallest of all RNA

molecules and together 15% of the total RNA in the cell. For every 20 amino acids commonly found in proteins, there at least one specific type of tRNA mole

 

Figure 2 showing the Characteristic structure of tRNA molecule

 

      From the diagram above, you can see that tRNA contain unusual bases e.g. dihydro uracil and have an extensive intrachain base-pairing that leads to its secondary and tertiary structure. Each tRNA functions as an adaptor molecule that carries its specific amino acid covalently bonded to its 3’ end to the site of protein synthesis. Now we come to the mRNA which carries the genetic information from the nuclear DNA to the cysotol, where it’s used as a template for protein synthesis and only makes 5% of the total RNA in the cell. Now we’re almost finish so just bear with me.

 

We finally come to RNA synthesis which can be divided into three stages….initiation, elongation and termination. Initiation involves the binding of RNA polymerase holoenzyme (the holoenzyme allows the RNA polymerase to recognize the promoter regions in the DNA and the RNA polymerase are the signals that control transcription) to the promoter region on  the DNA, which  is not transcribed. Then elongation: once the promoter  region  has been recognized  and bound to the holoenzyme , the DNA helix begins to unwind and the RNA polymerase  begins to synthesize a transcript of the DNA sequence.The elongation phase is said to begin with purine and exceeds ten nucleotides in length. Sigma subunit is then released and the core enzyme  leaves the promoter region and moves along the template strand continuing the process of transcription and a short DNA-RNA helix is formed. Now in termination, the elongation of single stranded RNA chain continues until the termination signal on reached. Termination can be spontaneous or dependent on a protein known as the rho factor. And now my blog entry is finished….TADAAAA!!!!!!!!!

 

 

 

THE END IS NEAR!!!

The end is near…..and I don’t mean the world ending. It simply means exams are approaching and its time to recall what we should know for this Biochemistry course. However, before I start listing out the topics we should study, I will like to introduce myself and thank the members in the bcbionx group.
I am Dominique who is the leader of the bcbionx and the members of this group were Nasir, Sabita,Sade and Phillip. I will like to greatly thank them for all that they have done with this blog.
Nasir for being creative in creating the ‘Trinidad as a cell’
Sabita for always assisting me especially in the topic on Honey
Sade for doing the TCA and ETC which is informative
and Phillip for always presenting humour in the group reflections.

These are the people who make up the bcbionx.
So placing the gratitude aside, bcbionx will be posting up MCQ’s and two publish papers very soon

Review on lipid video

Hey readers, Nasir here, and for this post I decided to do a little insight into that all important bio molecule our world is becoming filled with…yes lipids!!

In my search for interesting facts on lipids, I came across a video that was so informative I thought I should do a little review on it…so have a read!

The video highlighted the important reasons as to why lipids are so needed in the diet. It clearly explains the types needed such as phospholipids, steroids, tri glycerides and even discusses the age old thoughts on the benefits or harm when consuming saturated fats versus unsaturated fats. The purposes these groups serve in making biological systems more efficient are also examined. The various forms of useful and harmful lipid molecules are also highlighted, and for the harmful forms, which are usually man made; the process of their manufacture as well as an insight into why the over consumption of them is harmful, is discussed. Among these are the heart stopping trans fats that we all love but need to stay away from. The reason these are so dangerous as well as the daily recommended amounts based on statistics and nutritional facts are also worked out by the maker of the video so no math here!
It was very useful in that it used various pictures and colours to illustrate the main points on the topic allowing its viewers to clearly grasp the simple concepts lipids have to offer. Apart from the fact that slight humour and facts also help to create a more comfortable learning experience while viewing the video, the most interesting part of the video for me was the fact that the numbers for quantity placed in the nutritional facts for snacks were based on a ‘per serving’ intake; which is interesting because snacks nowadays are packaged so sparsely that most consumers buy more than the usual amount to be satisfied. This means the serving intake is increased and therefore intake of the undesired ingredient, but because the quantity number says zero, most people would over look this little detail.
The video was composed so well that it leaves little room for error, but I would say a little elaboration on why Omega 3 and Omega 6 polyunsaturated fats promote a healthy heart would be interesting to know, but I guess not all answers are a giveaway.

Thanks for reading! Have a look at the video, and don’t forget to leave your comments!
~ Nasir

Getting Down and Funky with DNA!!!

Hey all, Phillip hear again and this week it’s my pleasure to share a little on Deoxyribonucleic acid or DNA as most people call it.

So what is DNA?

Well DNA is a molecule that contains all the genetic  codes need to create  living organism.

Here are some interesting facts about DNA:

1)      DNA is known to have codes for all he information needed to make an organism but the actual DNA molecule is made up of four basic nucleotides: adenine, guanine, thymine and cytosine.

2)      Every human being shares 99% of his DNA with every other human. I mean how awesome that is!

3)      There are so many DNA strands of DNA in your body that if you were to line them up end to end the DNA would reach from earth to the sun over 600 times!!!

4)      Between you and your parent there is a 99.5% similarity in DNA

5)      Get this. You can actually call a chimpanzee your family because there is a 98% similarity. Awesome your family with a chimp 😛

6)      Did you know that if you typed 60 words per minute for eight hour a day it would take almost  50 years to type out the human genome

7)      DNA is so fragile that about a thousand times a day errors occur. These errors lead to mutations that can be repaired or non-repairable. Some mutations are good; others don’t do anything whilst others are helpful.

8)      Wow take this in….you have common DNA to a mud worm. So if anyone calls you a worm in the future you can tell them thank you.

9)      Well ok it seems that we have common DNA with everything….first was a chimp then was a mud worm now you also have common DNA with a cabbage, 40-50% common DNA actually.

So now that you know what DNA is we can go a little more into it. DNA is a double stranded anti parallel structure. It is a double stranded helix structure. As stated in the interesting facts there are four nucleotides that make up DNA. These are then split into Pyrimidines and Purines. In DNA the Pyrimidines are cytosine (C) and thymine (T). In Purines DNA has adenine (A) and guanine (G). The back-bone of the DNA molecule is what we call a sugar phosphate because nucleotides are products of sugars, bases and phosphate. So pyrimidines always bonds with a purine via hydrogen bonging, there are no purine to purine bonds, same goes for pyrimidines. Cytosine always bonds to guanine and thymine always bonds to adenine. The reason for this bonding is because A and T both had two complementary hydrogen bonding pairs while C and G had three hydrogen bonding pairs. The bonds were covalent bonds.

As noted, DNA is made up of anti-parallel strands. One strand runs from five prime (5’) to three prime (3’); the other strand runs in the opposite direction 3’ to 5’. For the DNA molecule to form the purines and pyrimidines have to be on the inside to join, the outside has phosphate and sugars.

DNA is a tertiary structure that has a spring like look. It is described as being super coiled. Within the structure there is a minor grove and a major grove. The minor groove occurs when the back bones are close together. The major groove occurs when they are far apart.

DNA is a nucleic acid. In DNA there are genes to synthesize functional proteins and RNAs. It also contains segments that take part in regulation of gene expression.

High pH changes the tautomeric state of bases. This causes the DNA to become denatured.

To actually get DNA of a person from a blood sample it must go through a centrifugation process. After this process is complete the blood is split up into different layers, each one for every constituent of blood.

For DNA to be replicated it goes through a series of processes. There are three processes: transcription, translation and initiation or replication.
In transcription the double helix structure splits into two strands.
In translation nucleotides join on to the single strands.
in replication the new DNA strand is formed.

 

This concludes my little something I have to offer on my knowledge of DNA.

Thank you for reading, please leave comments.

References:

http://chemistry.about.com/od/lecturenoteslab1/a/10-Interesting-Dna-Facts.htm

https://tandem.bu.edu/knex/grooves.knex.html

http://en.wikipedia.org/wiki/DNA#Base_pairing