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.

 

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!

 

Powerful Proteins !

“He who controls others may be powerful but he who has mastered himself is mightier still,” Hotch, quoting Philosopher Lao Tzu. 

Criminal Minds, Season 3, Episode 3 , “Scared to death”

Continuing on the topic of amino acids and proteins, it occurred to me that many people also relate to bodybuilding so I decided to do a little digging and write about the relation, since many people are unaware of how amino acids and proteins work to help build muscles and promote strength and fitness.

In terms of bodybuilding, amino acids facilitate growth and repair of muscle tissues. Different amino acids are necessary to perform different functions in the body therefore people need to be aware of what supplements are required. So we know that there are 10 essential amino acids and 10 non-essential ones.  But, before we talk about some of the amino acids necessary for bodybuilding we will discuss proteins and their role in the diet of a bodybuilder.

Picture 1: A popular brand of supplements among the bodybuilding community.

As we already know protein is one of the major food groups necessary for a balanced diet and more importantly, the diet of a bodybuilder. But, how many know of how they really work? Proteins exist in four types of structures: Primary, Secondary, Tertiary and Quaternary structures. Characterizing proteins are based on the level of folding there is in the polypeptide chain.

For the primary structure there is no folding, in fact it’s just a linear chain of amino acid residues joined by peptide bonds. The secondary structure has regular folding, described as being helical in nature (referred to as the α-helix) which is a spiral conformation or beta pleated sheets. The alpha helix is formed easily due to the optimal energy usage of hydrogen bonding providing stability occurring with peptide bonds. The twisting of the structure ensures critical interactions occur between an amino acid side chain and the side chain 3 or 4 residues away.

The beta pleated sheets (β-pleated sheet) contain hydrogen bonds which form between  peptide bonds in different sections of a polypeptide chain or different polypeptide chains either top or bottom of amino acids so the C terminal end (carbonyl group) and N terminal end (amino group) line up (parallel) or alternating of C and N terminal ends resulting in being anti-parallel.

In tertiary structures, the polypeptide chain is folded into a 3-Dimensional structure which is kept stable by hydrogen bonds but important hydrophobic interactions are necessary. There are also electrostatic forces of attraction and if present, covalent disulfide bonds. Quaternary structures consist of many polypeptide chains in a multiple sub-unit compound. They can be either fibrous or globular.

Diagram 1: Structures of Proteins.

When the proteins have been broken down to their constituent amino acids, these amino acids are then selectively grouped to form new proteins which will be used for different functions in the body. E.g. for aiding in muscle building. So certain proteins will have to be specifically made for that purpose. Many of the protein supplements today are from both animal sources such as milk, meat, egg or plants sources like soy. Whey protein is a milk derivative and an example of a protein powder commonly used by professional athletes and bodybuilders. It is considered to be a complete protein as it contains 9 essential amino acids. It is absorbed quickly in the body and provides an immediate supply of amino acids.

Picture 2: A commonly used protein powder (whey protein).

What amino acids are helpful in building muscle? Well there are those such as histidine, phenylalanine, lysine, leosine, threonine, cysteine, glutamine, arginine and valine to name a few.  They are involved in the manufacture of certain proteins that have roles in tissue repair and muscle building. Carnithine for example has a specific role in fat metabolism. Arginine becomes nitric oxide in the body and is known as a vasodilator. It dilates or widens blood vessels so more blood can reach the heart and muscles faster therefore making them work harder and grow in size and strength.

Professional athletes and bodybuilders often eat high protein diets or take supplements that contain high amounts of proteins.  During weight training, muscles are forced into breaking down proteins, amino acids are split to be oxidized into energy or to be synthesized into new proteins. To promote muscle growth, exercise induced breakdown of proteins requires the ingestion of adequate protein. The proteins which are ingested into the digestive system and then it is broken down into specific amino acids by enzymes know proteases for example pepsin in the stomach and trypsin in the small intestine. Now, a protease is an enzyme and enzymes are proteins as well. Well look at that! A protein structure functioning to break down another protein.

So in essence, amino acids are very important in bodybuilding because after the proteins have been digested in the body, there are specific amino acids responsible for making the different proteins that are necessary for the goal of muscle building. Protein supplements however should not be consumed if a person is getting enough protein from their diet as too much protein can cause dehydration and more severely, an increase in the risk of gout and kidney stones.

What we haven’t considered so far is that proteins are affected by biological activity and can be denatured by extreme conditions. Some conditions are high heat which causes breakage of hydrogen bonds and therefore loss of structure and strong acidity or alkalinity which cause the disruption of hydrogen bonds as well as salt formation and precipitation of the protein. Organic solvents cause changes in the dielectric constant, hydration of ionic groups and consequently the precipitation of proteins. Chaotropic agents such as perchlorate cause an enhanced solubility of non-polar compounds by disordering water molecules which solvate groups on the interior of the proteins

So I hope you enjoyed the topic of proteins and learned at least one interesting thing about proteins.

Something Crunchy!

“The healthy man does not torture others. Generally it is the tortured who turn into torturers.” Carl Jung quoted by Gideon.

Criminal Minds, Season 1, Episode 8, “Natural Born Killer”

Hi ya’ll, this is Shammi and I am going to be dealing with Proteins and Amino acids. I will be discussing the importance of proteins as well as the common misconception that a vegetarian diet doesn’t provide enough protein. So just to recap of some basic knowledge about proteins and amino acids.

What are amino acids? Well, they are structural components that make up proteins.

Diagram 1 showing structure of an amino acid

The general structure of an amino acid consists of an amino group and a carboxyl group. The R-groups differ and make the specific amino acid unique. The Nitrogen atom is present in proteins unlike carbohydrates. Proteins can be classified based on their polarity and the presence of functional groups. Now, amino acids can link together to form polymers or polypeptide chains. A peptide bond is formed when the amino group of one amino acid reacts with the carboxyl group of another amino acid by a condensation reaction where water is lost.

Diagram 2 showing the condensation process

Amino acids can be named by using the full name, for example alanine, can be identified as Ala or A. Proteins consist of one or more polypeptide chains. They are very diverse and have many important functions throughout the human body including: storage, structural, transport, enzymes, immune response. They exist as primary, secondary, tertiary and quaternary.  Proteins are necessary from the molecular level to the macromolecular level. They are required in the cell as enzymes which allow for biochemical reactions to occur in a timely manner necessary to sustain life, and as polypeptides forming muscle tissue for movement in animals and growth in plants. Proteins can have strange names such as the protein pikachurin, a retinal protein named after…yes you guessed it! Pikachu!

Proteins generally ‘live’ for less than a week but a new discovery by scientists is showing that longer living proteins can lead to a decrease in cell aging. Salk Institute for biological studies discovered a type of protein, referred to as ELLP which are not replaced when damaged in the cell causing aging of the cell. Aging is characterized by a decline in the proper functioning of the body’s organs caused by damage of the internal constituents of the cells in the respective organs. The majority of cells repair their proteins by a process of protein turnover which replaces the damaged proteins with new ones, duplicates of the previous. Transport channels on the nucleus surface are composed of ELLPs which control the entrance and exit of substances. When these are damaged, the transport channels are affected therefore affecting to some extent how much deterioration occurs as toxins may enter the cell’s nucleus. This can cause alteration of DNA and therefore gene activity and enzyme expression causing cellular ageing as there can be the loss of youthful gene expression.

Picture showing microscope image of ELLP proteins on the outside of the nucleus of a rat brain cell.

What interested me in this topic of proteins and amino acids was, the general idea that vegetarian or vegan diets lack proteins. Normally when we think about protein we mainly associate it with animal protein right? Well the majority of people generally think about meat being the only source of proteins. However, there are many proteins in vegetables such as cauliflower and legumes such as beans. There are 20 necessary amino acids required by the body for proper functioning. Complete proteins are proteins which contain all 10 essential amino acids and are generally acquired from animal sources and incomplete proteins are short of one or more of the essential amino acids. Beans are the exception as they are complete proteins.

What is a vegetarian? Well they are people who avoid meat and meat based products, and eat mainly a plant-based diet. There are many types of vegetarians; some that only consume meat from fish, called pescatarians, vegans who stay away from meat, eggs and dairy products.

Now, people normally think of salads and vegetables when they hear about vegetarians. But this is a fallacy! Even vegans can get enough protein if they eat balanced diets. People consuming meat products are known to get certain health diseases such as cardiovascular disease quicker since meat such as pork and beef contain a high amount of saturated fats and cholesterol as opposed to vegetarian sources such as soy which has a much lower amount. This therefore promotes a healthier life.

There are many champion body-builders and athletes that survive on vegetarian or vegan diets and get more than enough protein. There is Dave Scott (6-time ironman triathlon world champion), Mike Mahler (a professional strength trainer) among others.

The proteins in plant-based diets are not as incomplete as thought of, vegetables like broccoli and spinach contain high amounts of protein. Soy products, nuts, dairy, peas and beans contain various essential muscle-building amino acids and proteins.

Wouldn’t it be great to be of an ideal body mass index on a vegetarian diet or to build muscle on a meat-less diet? Well, there are those who love their meat despite the health disadvantages but research proves vegetarianism is a healthier way of life and should be promoted. Supplementation can be taken for any lack in nutrition one may have if necessary with a meat less diet.

I myself am a strict vegetarian who avoids all meat products and my balanced diet to follow .Diet plays an important role to ensure that vegetarians are getting a variety of amino acids necessary for the body.

Bottom line? The idea that vegetarians are lacking protein and not getting enough protein and amino acids is misleading because they can get enough from a smart healthy plant based balanced diet.