Magical, Compelling,Questionable, ….the answers revealed!

  “The farther backward you can look, the farther forward you will see.”Gideon quoting Winston Churchill.

Criminal Minds, Season 1, Episode 1, Extreme Aggressor 

So after we have come to the end ..

.

 

Yes, it’s time for us to bid you good-bye and wish you well on your biochemical adventures. It has been a couple fun-filled weeks …well mostly 😀 So we hope you enjoyed viewing our blog and using the interactive stuff.

 

Answers to the MCQs previously posted for those who attempted them

1) C

Ribosomes have no membranes and are not membrane bound therefore none of the other options were suitable answers.

2) C

Phosphofructokinase is the enzyme which catalyzes the reaction of  Fructose 6- Phosphate to  produce 1,6-biphosphate  according to the glycolysis pathway where we see in the post  glycolysis the process and glycolysis the process continues…

3) C

Acetly CoA, NADH and  ATP can competitvely inhibit pyruvate dehydrogenase.

4) B

The possible fates of pyruvate include; fermentation which leads to the formation of lactate in erythrocytes or muscle tissues; or ethanol in yeast as well as aerobic respiration where the products of the link reaction lead to the citric acid cycle.

But….please don’t forget your biochemistry!!! Especially you who have Finals soon!

 

Blog Views!

This is our blog views thus far! We’re so happy that we were able to reach so many people from all over the world and hoped that we have been helpful at some point. A total of 589 views! *feels accomplished* 🙂

We just wana’ wish everyone good luck in their upcoming exams! All the best ya’ll ! 🙂

*From the Biochemical Minds® Team! Happy studying!

 

Something Phat …

“All truths are easy to understand once they are discovered. The point is to discover them.” Morgan quoting Galileo.

Criminal Minds, Season 6, Episode 12, “Corazón”

Hi guys, this is Shammi and I will be doing a video review on Lipids (Fats). The link for this video is shown below.

http://www.youtube.com/watch?v=CdKbO7qwJvM

The title of the video is “Macromolecules: Lipids (Fats) – Biology at West – Biochemistry”, done by Aaron Williams and edited by Justin Higgins. This video focuses on the structure and functions of Lipids.

Lipids are very diverse and have a variety of bodily functions. There are different types of lipids such as cholesterol, fatty acids, triglycerides and phospholipids.

The types of atoms that make up lipids are similar to carbohydrates, which are carbon, hydrogen and oxygen but carbohydrates and lipids are different because of the structure of the compound and that lipids tend to form long chains with carbon to carbon bonds.

Saturated fats are formed when all carbon atoms are single bonded to each other, they also bond to hydrogen and tend to be solid at room temperature. For example lard and butter are common ones. On the other hand, unsaturated fats are formed when a single carbon is double-bonded to another carbon and these tend to be liquid at room temperature, for example, vegetable oil.

A single lipid molecule constitutes a monomer which can join with other monomers to form a chain or polymers which may be composed of different monomers for example, generally, 3 fatty acids chains and 1 glycerol make up a triglyceride.

Some examples of polymers include:

• Hormones. e.g. testosterone
• Steroids. e.g. messenger molecules
• Cholesterol.

Function of lipids include:

• They store energy.
• They form biological membranes.
• They form chemical messengers.

This video was relatively short and contained most of the basic information about lipids, however it lacked detail necessary concerning the functions and properties of fats which would have been useful as well as the characteristics of lipids. This information would have improved the video. Nevertheless it was a concise but informative video.

 

Have a laugh ^_^

As we are now in the midst of preparing for our finals this semester, we are all under abit of stress. Nonetheless, make studying fun and enjoyable and here are some pictures that might just tickle the funny bone and make you smile! Enjoy 😉 xo

          

        

 

 

 

 

 

 

Magical, Compelling, Questionable?

HEYYY, so here are some questions to test your biochemical knowledge!

We shall post the answers a bit later.

(1) Ribosomes have __________ ?

a) Single membranes

b) Double membranes

c) No membranes

d) Triple membranes

e) None of the above

 

2) Fructose 6- Phosphate can be phosphorylated to produce 1,6-biphosphate by ______.

a) aldolase

b) enolase

c) phosphofructokinase

d) phosphoglucose isomerase

e) none of the above

 

3) Pyruvate Dehydrogenase can be inhibited by the following:

(i) Acetly CoA

(ii) NADH

(iii) ATP

(iv) FADH₂

a)      (i),(Iv)

b)      (i),(ii),(iv)

c)       (i),(ii),(iii)

d)      (II),(Iii)

 

4) The possible fates of pyruvate are:

(i) promotion

(ii) fermentation

(iii) aerobic respiration

(iv) reduction

 

a) (i),(ii)

b)(ii),(iii)

c) (ii)

d) (iii),(iv)

Respiration, Breathe the Oxygen !

“What we do for ourselves dies with us.  What we do for others and the world remains and is immortal,” Gideon quoting Albert Pine.

Criminal Minds, Season 1, Episode 15, “Unfinished Business”

Here’s a little video review…more fun!!!

https://www.youtube.com/watch?v=aA8d-tt6dII

This video pretty much sums up Glycolysis, TCA/Kreb’s Cycle and the Electron Transport Chain. Enjoy!

Cellular Respiration

Summary:

This video focuses on the “big picture” starting with the equation for respiration. The analogy of the use of money is made in comparison to the way that energy is used and made in respiration. When using this analogy, the money represents glucose, the item that cells need in order to perform their functions.

Glucose on its own can’t be used to help cells work, as it needs to be converted into a usable form. This usable form is called ATP. Therefore the objective of cellular respiration is to convert glucose to ATP like converting a cheque to cash via a bank in order for it to be used to buy food.

Mitochondria are the main organelle responsible for the conversion of glucose to ATP. The conversion efficiency is about 40% efficient at breaking down the energy from the food that we eat and converting it into ATP. The rest of the energy is lost as heat in the conversion process.This is the method Antoine Lavoisier used to study cellular respiration.  He did so using a calorimeter and guinea pigs. He had an outer chamber which he kept at a constant temperature with ice in the middle chamber and the guinea pig was placed on the inside. Through this experiment, he found out that the guinea pig produced heat.  He collected the water from the melted ice in the middle chamber and found what the guinea pig was doing in respiration.

The process where glucose is converted to ATP begins with glycolysis. Glycolysis is a 9 step process that occurs in the cell cytoplasm where glucose (a six carbon sugar) is converted to two 3 carbon, pyruvate molecules.These molecules of pyruvate will go into the mitochondria. The mitochondrion is a double membrane organelle where there is an outer mitochondrial membrane and an inner mitochondrion membrane (cristae) which is folded in order to increase surface area. The space inside the inner membrane is called the mitochondrial matrix.

This is where the citric acid cycle takes place. Before entering the citric acid cycle, pyruvate is groomed onto Acetyl-CoA. As bonds break, carbons are released which combine with oxygen to form CO_2, hence the CO₂ we exhale. Most of the high energy bonds get oxidized, thus electron carriers are reduced. These electron carriers, when reduced leave the citric acid cycle and interact with proteins on the inner-mitochondrial membrane to generate ATP.

The electrons being carried by the electron carriers go to a series of proteins built into the inner-mitochondrial membrane called the electron transport chain. As the electron carriers give up their electrons, they become oxidized and the proteins in the chain get reduced. As the electrons move through these different proteins, energy is given off each time. This energy is used to pump protons into the inter-membrane space. These proteins have increasing electron affinity. This creates a proton gradient. The final electron acceptor is oxygen.

During aerobic respiration one glucose molecule can generate up to 34 molecules of ATP. However, during anaerobic respiration, without oxygen, only 2 ATP can be produced (from glycolysis).The space between the inner and outer membrane is called the inter-membrane space.

New knowledge obtained:

–          where exactly the energy is used for in the body and that the liver actually requires more energy than the brain.

–          background into the beginning of the study of cellular respiration.

–          It helped to visually enhance the viewer’s understanding of the places where the processes took place as well how the processes work in relation to the functions of the body.

This video could have been improved by giving more details about the enzymes and molecules involved in glycolysis, the TCA Cycle and the Electron Transport Chain.

Great Glycolysis!!!

“Better than a thousand days of diligent study, is one day with a great teacher,” Morgan quoting a
Japanese proverb. 

Criminal Minds, Season 8, episode 6, “The Apprenticeship”

Hey guys and gals, we have another fun review to enrich your learning……..ok fine maybe not entirely fun but it will help you someday in your biochemical life 😀

 

Review of “Synthetic non-oxidative glycolysis enables complete carbon conservation”

Igor Bogorad, Tzu-Shyang Lin and James C. Liao. 2013. “Synthetic non-oxidative glycolysis enables complete carbon conservation.” Nature. Pgs 693-698.

Glycolysis is an ancient metabolic pathways that is fundamental to life since it plays a major role in decomposing sugars in almost all organisms. You should be able to recall that it involves the splitting of a six carbon glucose molecule into two three- carbon molecules called pyruvate. Under aerobic conditions, the pyruvate dehydrogenase complex converts the two pyruvate molecules into two acetyl-coA which participates in the TCA cycle (or citric acid cycle) to create NADH and FADH (ATP). This step however, is quite inefficient because the reaction is one of oxidative decarboxylation where carbon sources are lost in the form of carbon dioxide.

As a result, three keen researchers of the University of California developed a cyclic and non-oxidative pathway that essentially conserves all the carbon molecules in sugar catabolism allowing for a greater production of acetyl-coA. Acetyl-coA is a precursor molecule for biofuels such as ethanol and butanol and therefore, this synthetic route will improve yields of these useful chemicals especially in the biorefinery industry. The biorefinery industry are facilities which integrate biomass conversion processes for the production of fuels, power, and chemicals. It is a relatively new industry catering for the creation of a new domestic bio-bases industry (NREL 2009) .

The unique pathway, known as non-oxidative glycolysis (NOG) is comprehensively described in the article. As opposed to the natural glycolysis pathway, three glucose molecules are converted into three fructose 6-phosphate molecules which are then broken down into three molecules each of acetyl phosphates (ACP) and erythorse 4-phosphate (E4P) via the enzyme phosphoketolase. The E4P molecules undergo a process known as carbon rearrangement to form two fructose 6-phosphate and subsequently three ACP molecules. These three ACP molecules are essentially converted to acetyl-coA. Therefore, this route is fitting since it gives a net gain of three acetyl-coA molecules and there are no loss of carbon atoms.

The researchers tested the pathway to ensure its validity by performing an in vitro and in vivo experiment in Escherichia coli. Firstly, in the in vitro experiment a number of enzymes were used namely phosphoketolase, Tkt, Rpi, Rpe, Tpi, Fba, and Fbp. DHAP; Ru5P except Tal which is responsible for the carbon rearrangement step (Igor Bogorad, Tzu-Shyang Lin and James C. Liao. 2013). The concentrations of ACP molecules were measured and it was concluded that there was a higher level of ACP when the enzyme Tal was present than when it was not.

Secondly, the in vivo experiment gave a similar result. Using the enzymes in the same manner and known concentrations of fructo 6-phosphate and glyceraldehydes 3-phosphate, ACP molecules were formed. It was confirmed that the pathway and enzymes were in fact necessary to produces the respective products. Thus the NOG was deemed valid and is widely used to improve efficiency and sustainability of biofuel production.

References

NREL. 2009. What is a Biorefinery? Accessed april 9th, 2014. http://www.nrel.gov/biomass/biorefinery.html.

Igor Bogorad, Tzu-Shyang Lin and James C. Liao. 2013. “Synthetic non-oxidative glycolysis enables complete carbon conservation.” Nature. Pgs 693-698.

 

Something interesting…

“It’s not so important who starts the game, but who finishes it.” JJ quoting the Legendary basketball coach John Wooden.

Criminal Minds, Season 2, Episode 8, “Empty Planet”

Hey Guys and Gals , this is our first review of a journal article. Please read, like, comment!

Journal Article Review :Chromatin Proteins and Modifications as drug targets

Kristian Helin, Dashyant Dhayak. 2013. “Chromatin Proteins and modifications as drug targets.” Nature International Weeky Journal of Science 480-488.

The article “Chromatin Proteins and Modifications as drug targets” by Kristian Helin and Dashyant Dhanak discusses the importance of chromatin associated proteins and post-translational modification (PTM) of histone proteins and DNA for transcriptional control and normal development. The article explains that the generation of new classes of specific inhibitors have been tested and are promising to treat diseases that affect proteins and DNA. This introduction of new technology would allow for epigenetic control over diseases such as Cancer.

Chromatin is a complex or mass of DNA and proteins which condense to form chromosomes in a cell’s nucleus. The basis of epigenetics is denoted by the inheritance of chromatin in either the euchromatic (active) state or the heterochromatic (inactive) state (Bernstein 2005). Epigenetics is important for the correct transcriptional processes to occur for each cell.

The main cause of diseases such as cancer is the deregulation of epigenetic control. Epigenic systems are heritable and reversible. Abnormal epigenic patterns are found in tumours therefore, epigenic markers can be used to predict if patients respond to anti-cancer drugs which blocks DNA Methylation. Consequently, the function of the genes are affected so effector proteins can remove histone markers or recognize them.

The correct transcription of DNA is therefore necessary in maintaining the identity of a cell through the processes of epigenetic regulation which are proliferation, development, differentiation, and genome integrity.  Proliferation is the process of growing or multiplying by the rapid production of new tissue. These tissues can develop and undergo differentiation depending on the proteins being coded for, which in turn is dependent upon the histones responsible for DNA packaging. Histones are affected by PTMs such as methylation, phosphorylation and acetylation which cause steric changes in the structure of the chromatin.

DNA Methylation has an important role in causing cancer. A methyl group is added to adenine or cytosine DNA nucleotides in the biochemical process of DNA methylation. DNA methylation has a complex relationship with gene expression but when methylation occurs less, there is a higher level of gene expression. The discovery by scientists is that, treatment  in the form of irreversible inhibitors known as azacitidine (5-azacytidine) and decitabine (5-aza-2ʹ-deoxycytidine) bind to DNA methyl- transferase enzymes DNMT1 and DNMT3 (Kristian Helin 2013). The PTMs are removed and the histones undergo modifications after being sufficiently prepared.

Therefore, with this next generation technology, correct gene coding for DNA sequencing of proteins can be obtained.

The unfolding of the genome sequence is initiated by the transcription of DNA and RNA sequences. De-lineation of the protein coding genes is the initial step after completing the genome sequence. The new classes of specific inhibitors will regulate DNA methylation patterns.

The discovery of chromatin associated proteins are an important part of cancer mechanisms and factors involved in chromatin facilitated events, including transcription. Studying the post- translational modifications of the N terminal tails of histone proteins can allow the modification of histones at specific genome regions. Continuous research, development and use of this new advancement in chromatin proteins and modifications will follow in the future as indicated in the article.

 

 

 

References

Bernstein, Emily and C.David Allis. 2005. “RNA meets chromatin.” Genes and Development. Accessed 04 07, 2014. http://genesdev.cshlp.org/content/19/14/1635.long.

Kristian Helin, Dashyant Dhayak. 2013. “Chromatin Proteins and modifications as drug targets.” Nature International Weeky Journal of Science 480-488.

Jennifer Harrow, Alinda Nagy, Roderic Guigó.2009.” Identifying protein-coding genes in genomic sequences.”Genome Biology.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687780/

Guy Riddihough, Laura M. Zahn.2010. “What Is Epigenetics?” .Science. Accessed 04 07, 2014.https://www.sciencemag.org/content/330/6004/611

 

Finding Neverland: Nucleotides, Nucleosides and Nucleic Acids

“There is no formula for success, except perhaps an unconditional acceptance of life and what it brings,” Hotchner quoting Arthur Rubinstein.

Criminal Minds, Season 3, Episode 15, “A Higher Power”

This is Sara here and this week we’ll discuss the topic of Nucleic acids and nucleotides. So what are nucleotides and why do we care? Well, we cannot exist without nucleotides!They are the elementary structures used to make nucleic acids, such as DNA and RNA.

A nucleotide is an organic compound made up of a phosphate group, nitrogenous base and a sugar, and it contains the following elements of carbon, nitrogen, oxygen and phosphorous. 

 

Now in order to understand nucleic acids and nucleotides, we need to familiarize ourselves with some new terms or may be not so new. The first is Pyrimidines, which are aromatic heterocyclic organic compounds similar to pyridine, (a simple heterocyclic organic compound (C₅H₅N). They occur in DNA as cytosine and thymine, which are the pyrimidines in RNA.

                                                                                                      Figure 1 showing structure of cytosine                                                                        Figure 2 showing the structure of thymine

Next, are Purines which are heterocyclic aromatic organic compounds which occur as adenine and guanine in DNA and RNA.

                                                              

Figure 3 showing structure of adenine                                                               Figure 4 showing structure of guanine

So, Nucleotides are necessary to us as most importantly, they are used as an energy currency in cellular respiration, in the form of ATP, as allosteric effectors (see enzymes) as well as the structural components of enzyme co-factors. Nucleotides are the phosphoric esters of nucleosides.

 Then we also have Nucleosides which are pyrimidine or purine N-glycosides of D-ribofuranose. The purine or pyrimidine part of a nucleoside is referred to as a purine or pyrimidine base. The main component of a nucleoside is the phosphate group as it is necessary for nucleotide polymerization.

Pyrimidine and purine nucleosides of D-ribofuranose include Uridine and Adenosine. Uridine contains a uracil group linked to a ribose ring by a Beta-N₁ glycosidic bond while Adenosine has a molecule of adenine bonded to a ribose ring by a beta-N₉ glycosidic linkage.

Figure 6 showing Uridine and Adenosine structures

Nucleotides form Nucleic acids which include DNA and RNA.DNA has two strands, is a deoxyribose sugar and is characterized by 4 bases; Guanine (G), Cytosine (C), Adenine (A) and Thymine (T).

RNA also has four bases, G, A, C and instead of T, there is Uracil (U). It possesses a single strand and can have the form of rRNA (RNA + Protein), mRNA, and tRNA.

 

OK, well, rRNA are ribosomal RNAs which function in protein synthesis, mRNA are messenger RNAs which transport genetic information from genes to ribosomes. tRNA are transfer RNAs which translate information from mRNA to amino acid sequences.

Nucleic acids are formed by nucleotide monomers forming phosphodiester linkages between the 3’-OH of one nucleotide and the phosphate of another nucleotide.They can have 3 different forms: A, B and Z. A is common for RNA and DNA, B is favoured by RNA and Z does not occur generally but can form for some DNA sequences.

Figure 7 showing A, B and Z forms of DNA and RNA

The major molecule which encodes genes containing information for the formation and function of most if not all living organisms is…yes you know it, DNA! The ‘backbone’ of DNA (deoxyribose sugar) comprises of five carbons which are numbered as 1¹, 2¹, 3 ¹, 4 ¹and 5 ¹ and three oxygen. Phosphate groups are linked by the hydroxyl groups present at carbons 3¹and 5 ¹. The A, G, C and T bases can extend from the chain in order to stack on top each other which contributes to the stability of the nuclei acid as this is more energetically favourable.

Figure 8 showing the structure of DNA

Base pairs are similar in size and shape which allows for more efficient packing into the double helix. Bases are linked by hydrogen bonding and are hydrophobic and therefore located to the inside of the helix, perpendicularly stacked and the phosphate groups are polar so they are located to the outside. This is described as being hypochromic which also makes bases less susceptible to UV absorption.

DNA molecules are generally circular in shape in eukaryotes and are usually negatively coiled as this form has a higher torsional energy allowing for unwinding of the helix during transcription or replication. Having supercoiling in the DNA tertiary structure reduced the problem of the lack of space, as the number of base pairs and length per 360 degree turn was equivalent to one meter!

Things seem to be going well for DNA and RNA but acids, alkalis and other chemicals can have negative effects on the structure of DNA and RNA. Denaturation can also occur due to chemicals such as urea and formamide which disrupt H bonding and hydrophobic effects and thermally by high temperatures which destroy double stranded H bonded regions. However renaturation can occur by rapid cooling, annealing (base pairing of short regions complementarily) and hybridization.

Well, that’s all for now!

 

Loving Lipids ?

So continuing on the topic of Lipids…

Essential FAs (fatty acids) are those that cannot be synthesised by the body and must be obtained from our diet. This comprises of two important polyunsaturated FAs – Omega – 3 (ω-3) and Omega – 6 (ω-6) FAs. Referring to Fig.2 in the last post, the carbon of the methyl group most distant from the carboxyl group is called the ω (omega) carbon and designated as number 1.The polyunsaturated FAs with a double bond between carbon 3 – 4 are called Omega – 3 (ω-3) FAs while those with a double bond between carbon 6 – 7 are known  as Omega – 6 (ω-6) FAs.

This play a significant part in human nutrition as Omega-3 FAs are found to help regulate the body’s blood sugar levels and regular intake can reduce the risk of diabetes and obesity. I am sure that you at least know of or take Omega -3 fish oil supplements because of its immense health benefits to the body.

Image taken from: http://www.fatsoflife.com/fats-and-health/omega-3s/omega-3s-in-fish/

An example of an essential FA is Omega-6 Linoleic acid which also works wonders as it has the potential of disease prevention of cancers, cystic fibrosis and dermatitis. You can learn more about Linoleic acid here: http://www.news-medical.net/health/Linoleic-Acid-What-is-Linoleic-Acid.aspx

Amphipathic Lipids

These are lipids that hydrophobic (water-hating) at one end and hydrophilic (water-loving) at the other. They usually contain one or more polar groups making them suitable as constituents of membranes where there are water/lipid interactions like phospholipids for instance. Glycolipids are found in almost every tissue of the body particularly in the brain and nerve tissues (Nelson, David L., Albert L. Lehninger and Michael M. Cox. 2008).

Also included are cholesterols, which are usually wedged between phospholipid molecules in the plasma membranes in which they maintain its fluidity. At warm temperatures, cholesterol molecules prevent the movement of phospholipids thus reducing the fluidity while at low temperatures it maintains the fluidity by preventing tight packing. They synthesise steroid products such as useful hormones, Vitamin D and bile acids. Cholesterols are transported via lipoprotein molecules that can be known as LDL (low density lipoprotein) or HDL (high density lipoprotein). LDLs are proclaimed to be “bad” cholesterol because of its association with the condition atherosclerosis while HDL is the “good” cholesterol which does the good job of course (Good vs. Bad Cholesterol.” American Heart Association).

Image taken from: http://imgfave.com/view/1485033

Fast foods! Those lipid-rich foods that are deep-fried in partially hydrogenated vegetable oils…doesn’t sound too appetizing now does it? Hydrogenation is a commercial process done to increase the shelf life and flavour stability of products. It essentially converts the cis double bonds to trans double bonds in the FAs which raises the melting point of the oil so that it is solid at room temperature.  As a result, most of these fast foods contain a high level of trans FAs or trans fats. Trans fats negatively affects the body in that they increases the blood levels of LDL (“bad” cholesterols) and reduces the levels of HDL (“good” cholesterols). Trans fats are sited in many foods such as margarine, cereals, candies, cookies salad dressings and snack foods (“Lipids (Fats)”, Lipids fats). The Fig. 3 Below shows the trans fat content of some typical fast foods and snacks.

Fig.3 Trans fat content in some typical fast foods and snacks  (Nelson et al. 2008).

Fact: Butter is a main ingredient of many foods and it is essentially milk fat.

Butter is a mixture of triglycerides of many different fatty acids such as oleic, myristic, malmitic, stearic, lauric, butyric, caproric and linoleic acids. Anti oxidants such as butylated hydroxyanisole (BHA),butylated hydroxytoluene (BHT), propyl gallate and mono-terbutylhydroquinone (TBHQ) flavouring (3-hydroxy-2-butanone and diacetyl) and vegetable colours (usually carotene from carrot, a source of Vitamin A) are added. (Singh, Kirpal 2012)

Image taken from: http://www.nickomargolies.com/big/2012/02/butter-melting-in-the-pan/

References:

“Good vs. Bad Cholesterol.” American Heart Association. http://www.heart.org/HEARTORG/Conditions/Cholesterol/AboutCholesterol/Good-vs-Bad-Cholesterol_UCM_305561_Article.jsp

“Lipids (Fats).” Lipids, fats. http://www.healthynutritionguide.info/lipids.htm#wstep

Murray, Robert K..2000. Harper’s biochemistry. 25^th ed. Stamford, Ct.: Appleton & Lange, pgs 111-121.

Nelson, David L., Albert L. Lehninger and Michael M. Cox. 2008. Lehninger principles of biochemistry. 5^th ed. New York: W.H. Freeman, pgs 343-413.

Singh, Kirpal. 2012. Chemistry in daily life. 3rd ed. New Delhi: PHI Learning, pg 30.