Published Paper 2 – The Biochemistry Of Cancer

Cancer, scientifically known as malignant neoplasm,  is the condition whereby the unregulated growth of cells occurs , which often leads to the formation of tumours , this papers goes in depth  focusing on the biochemistry behind cancer , and its effects at the cellular level.

Cancer in cells causes changes firstly in the cell membrane , in malignant cells the plasma membrane is altered , leading to loss of density , decrease in anchorage potential and the loss of tissue barriers. All of the above changes in the cell membrane , lead mainly to one thing , that is the extreme increase in cell growth and reproduction which is characteristic of tumours. Malignant cells also experience agglutination  , that is the clumping together of particles and cells , this is why cancer is usually centralised into a single place (the exception being cancers of the blood as they are transferred throughout the body) , this agglutination is caused by the increased production of lectins such as concavalin (Con A) an phytohemagglutinin (PHA) , lectins are glycopoteins which bind to certain sites on cell membranes , however in malignant cells , they are more sites on the cell membrane due to alterations in the plasma , so the lectins bind fully onto the cells , and clumping occurs.

Malignant cells also produce altered glycoproteins  and antigens , this can be attributed to the presence of glycopeptides  with a high molecular weight as well as altered glycosylation patterns in malignant cells. The biochemical changes in said antigens can be attributed to incomplete synthesis of carbohydrate chains , rearrangement of glycolipids and over production of the enzymes known as glycotranferases .  The fact that tumours contain their own antigens leads to them being  difficult for the body’s own immune system to destroy them.

Malignant cells have other ways to increase the rate of growth , they do this by modifying the ECM (Extracellular Matrix Components) , the ECM is used in the moderating of cell differentiation  , however when it comes to tumours , the ECM is modified to aid in the development of a blood supply by altering the mesenchymal stroma which is where the tumour cells grow , hence the stromal structure is constantly altered changing in vasculature , rerouting blood into the tumour , increasing the rate at which it grows , it is this characteristic of malignant tumours that leads to the death of the patient that is suffering from the cancer.

Overall this paper was well written , the point flow well , and the writer goes in depth into the biochemistry associated with cancer, it is extremely informative and  I would recommend this paper to anyone studying biochemistry or anyone researching cancer at the cellular level.

References:

National Institutes Of Health

http://www.ncbi.nlm.nih.gov/books/NBK20906/

Published paper 1 -The Biochemistry Of Diabetes

Diabetes as we all know is the bodies inability to produce insulin , weather due to organ failure or genetic predisposition , diabetics in some way or the other ,lack the ability to convert glucose in the blood, this paper goes into the biochemistry of what happens as a result of this. In diabetic patients it is found that the fasting blood glucose level  is raised , directly proportional to the hepatic glucose output , that is the amount of glucose produced by the liver.

A surprising consequence of the hyperglycaemia sometimes seen in diabetes mellitus patients , is an increase in the glucose metabolism in the sorbitol pathway, a pathway which helps in the breakdown of glucose to produce energy.  This pathway is catalysed by aldose reductase , an enzyme used in the reduction of glucose to sorbitol , and by sorbitol dehydrogenase which catalyses the oxidation of sorbitol to glucose. In diabetic patients , the enzymes have a low affinity to glucose and hence do not bind to it , this leads to chain reaction where firstly the conversion of NADPH to NADP+ does not occur , this then leads to decreased concentrations of cofactors  which ultimately causes decreased synthesis of reduced glutathione,nitric  oxide and myo-inositol . Myo inositol is used primarily in the proper functioning of nerves and hence a decrease in this leads to the loss of feeling some diabetics experience in their lower extremities.

Diabetics are also susceptible to liver disease and detoxification problems within the body , this is due to excessive lipolysis during insulin deficiency , the consequence of this is he excessive mobilization of fatty acids in the liver , the fatty acids are converted by the liver to Co enzyme A esters , the majority of this is converted to acetonate  and 3-ydroxybutyrate. In normal patients this process happens at a relatively moderated rate , however in diabetic patients because of the large amounts of fatty acids the rate becomes very high and hence can lead to liver damage and therefore detoxification problems within the body.

It can be seen therefore that the problems associated with the lack of insulin in diabetic patients go further than simply and inability to convert glucose to fat , it leads to problems regarding nerves , various biochemical pathways , it can inhibit glucagon production and even disrupt HGH , human growth hormone production in men.
Overall it must be said that this paper is well written , it is highly informative , it not only list the symptoms of diabetes but goes into detail about the biochemistry behind the disease , the points are well laid out and they flow one into the other , therefore I would fully recommend this paper to be read by anyone interested in biochemistry or anyone wanting to learn about diabetes.

References:
National Institutes of Health
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1148905/

Amino Acids :D

Amino acids are the subunits of proteins , they have general formula in which a Carbon atom is bonded to four groups , a carboxylic group , an amino group , a hydrogen and an R group , this R group is what makes an amino acid different from another .

There are different types of amino acids , for example , there are the non-polar , aliphatic amino acids such as Proline , polar uncharged amino acids such as Cysteine , aromatic amino acids such as tyrosine  , negatively charged amino acids such as glutamate and positively charged amino acids such as lysine.

An amino acid can be in two forms , a non-ionic form and a zwitterionic form , a zwitterionic form is where the amino acid has a net charge of zero. To form the zwitterion , a hydrogen from the carboxylic group is lost as a proton and accepted by the amino group. Amino acids can be bonded  together by peptide bonds to form long peptide chains , which are covalent bonds formed from a condensation reaction between the alpha amino group of one amino acid to the alpha carboxylic group of another. When writing peptide chains it is important to remember that you start by writing the free alpha amino group on the left and the free carboxylic group on the write, putting a hyphen between each amino acid residue. The free alpha amino end is known as the N terminal end and the free carboxylic end is known as the C terminal end. Amino acids can be conformed into an alpha helix , in which the amino acid residues are arranged in a helical  conformation . The amino acids can also be conformed into a beta pleated sheet where the residues are arranged in a pleated conformation due to the planarity of the peptide bonds.

It must be said however that although both conformations can be formed the alpha helix is more prevalent because it is more stable due to internal hydrogen bonding. Some amino acids however , are not allowed in the helix , bulky amino acids such are tryptophan , due to steric interference may cause to helix to not turn properly , proline isn’t allowed either because of its cyclic nature it cause a kink in the helix . Glysine Is another amino acid that isn’t allowed in the helix , this is because the glysine  has a very small R group , just an Hydrogen atom , this leads to conformational flexibility and because of this it is not allowed .

To test for amino acids in a lab , Ninhydrin can be added , it gives a purple colour in the presence of amino acids.

Proteins (^_______^)

Proteins, the first thing that comes to mind when  we hear the word protein is usually some type of meat. Mmmmmmm  meat (Homer Simpson voice).

Proteins have a wide range of uses in the body, perhaps the most apparent to a biochemistry student would be enzymes , enzymes are biological catalysts and are globular proteins , they increase the rates of chemical reactions in the body and without them life on a complex level such as humans would  not be possible. However proteins have other important uses  such as being structural like collagen in skin , acting as a transport molecule eg. Haemoglobin which transports oxygen in the blood , for storage eg. ferritin in the in the liver and as immune response in the form of antibodies responsible for attacking infections and foreign material in the body.

Proteins can be broken down into three  broad groups , globular proteins , fibrous proteins and membrane proteins. Globular proteins have a variety of secondary structures , they are spherical in shape ,water soluble and function in dynamic roles such as catalysis , regulation transport etc. Fibrous proteins are mainly used in structural role , therefore they are water insoluble as well as possess one dominating secondary structure. Membrane proteins are inserted through membranes and can span over several membranes into cytoplasmic and extra-cellular domains , they function mostly in cell signalling and transport.

Proteins have four main structures , primary , secondary , tertiary , and quaternary. The primary structure of a a protein is the sequence of amino acid residues  in the polypeptide chain. The secondary structure of a protein refers to the conformation of the polypeptide chain , there are two conformations here , the alpha helix conformation and the beta pleated sheet conformation , both of which will be looked at in more detail further down in this post. The tertiary structure refers to the three dimensional layout of the protein as it begins to coil and the quaternary structures refers to the assembly of subunits into one globular three dimensional form.

Proteins can be denatured , that  is have their three dimensional structure unravelled. Heat and ultraviolet radiation denature proteins in relatively the same way , in that they break the hydrogen bonds in the structure through vibration energy , it must also be said therefore that heat denaturation of a protein is a co-operative process meaning that when the proteins starts losing hydrogen bonds , there is a chain effect where the subsequent hydrogen bonds in the structure also break . Organic solvents such as ethanol and acetone can also denature proteins , they accomplish this by changing dielectric constant hence causing the hydration of ionic groups . Proteins can also be denatured by chaotropes and detergents which cause the protein structure to unravel .

One important experiment that is worth looking at is the Afinson experiment , through this experiment , the properties of proteins were more clearly understood. In the experiment he denatures a protein using GnHCl and mercaptoethanol , hence arriving at an unfolded , the next step of his experiment he uses dialysis to separate the protein from the chaotrope , he found that the unfolded protein will re-fold into its original structure , he therefore concluded that the information that codes for the three dimensional protein structure is contained within the primary structure , that is the sequence of amino acid residues.

Protein can be detected in a lab by using the Biuret test , it involves adding Biuret’s reagent to the unknown solution , if there is protein present the solution will change from light blue to purple .

Amino-acids and Protein Wordle

Amino-acids and Protein Wordle

Carbohydrates (SUGARS FTW)

Carbohydrates, countless diets have given this macronutrient a bad rap , but they are immensely importantly for the proper functioning of our bodies. Unlike most nutrients, carbohydrates  give our bodies immediate energy . I like to think sometimes , if there is a GOD , then maybe his favourite molecule is a carbohydrate , glucose , I mean think about it , all life comes from the sun , primary producers(plants) trap sunlight and use it to synthesize glucose , animals eat plants , and the cycle of life goes on. This means that glucose is the first dietary molecule formed in the entire food chain.

Ok enough of my random ramblings , I’ve compiled a list of  what I think are the main points  covered during the carbohydrates lectures.

Carbohydrates are used for energy , storage , structure and as precursor molecules. Plants store carbohydrates as starch while animals store carbohydrates in the form of glycogen. An example of a  structural carbohydrates are cellulose ,as seen in plants , is a beta-D-glucose polymer .Dietary fibres are found in complex carbs but not simple sugars.

D or L configurations of a carbohydrate refers to the position of the OH(hydroxyl) group on the asymmetric carbon farthest from the aldehyde or keto group, if the OH group is on the right its refered to as D-conformation , if it’s on the left , its referred to as a L-conformation ( the most naturally occurring sugar is the D isomer) . An epimer is where you have two sugars which differ only in the configuration around one carbon atom. It is also very important to note what are dissacharides  , such as maltose , sucrose and lactose. When two monosaccharides  form a glycosidic bond by condensation , a disaccharide is formed.

Polysaccharides are chains of monosaccharides , starch , glycogen and cellulose are all examples of polysaccharides , being polymers of glucose. Starch is made by storing glucose as amylase or amylopectin, Amylose is a glucose polymer with an alpha 1 to 4 linkage. There are two types of sugars , reducing and non-reducing sugars , a reducing sugar can reduce compounds , being itself oxidised . Sucrose is an example of a non-reducing sugar , because it has no free anomeric carbon .

Test for reducing sugars are;

1)      Tollen’s test (silver mirror test) : Ag+ ————> Ag.  (silver ppt)

2)      Fehling’s test or  Benedict’s test : Cu2+ (blue ———>Cu+ (red ppt)

Reference : Biochem JM

Science Fact Of The Day :D

The first synthetic human chromosome was constructed by US scientists in 1997.

The Biochemistry behind Valentines day <3 _ <3

This particular post isn’t directly related to the course specifically but it contains a lot of biochemistry and seeing that valentines day  is just around the corner I thought I might talk about something that we’ve all felt or experienced in one way or the other. LOVE ❤ , that attraction to people that we really can’t describe , but I’m not talking about brotherly or friendly love , no , I’m talking about the kind of love that bands like The Goo Goo Dolls (Iris) , Lifehouse(You and me , hanging by a moment ) ,The Fray ( How To Save A Life) and Hinder (lips of an Angel) sing about , yup , that’s right , I’m talking about boyfriend girlfriend kind of love. Truth is , just like most emotions and reactions in the body , love is controlled by chemicals that affect how we feel and act towards certain people , these chemicals or hormones control if we like someone , if we think someone is cute or handsome etc. There are several hormones that have a say in who we like or are attracted to and how we react when we see or come into contact with , them, I’ll try to break down and analyse the 3 main stages of love , the first encounter , Falling in love and getting attached from a biochemistry point of view.

1)     The first encounter , Adrenaline – this chemical is usually produced during flight or fight responses for example when we are in trouble or danger , however this chemical is secreted by the body when induced by hormones such as testosterone. Lets say for example you see a really hot girl,long legs , bright smile , pretty eyes , your body produces adrenaline , it immediately increases your heart rate , your core body temperature goes up , the blood vessels in your eyes dilate causing them to spasm leading to eye twitches , pupils dilate, the blood supply is rerouted to major muscles in the body , hands and legs , taking blood away from parts of your body like the stomach causing those butterflies you feel in your stomach ,and making your palms sweaty.

2)     Falling in love, Phenylethylamine or PEA – This is an amine that naturally occurs in the brain ,It is a stimulant, much like an amphetamine, that causes the release of dopamine. This chemical is found when you are falling in love. It’s responsible for the head-over-heels, elated part of love. So the next time you find yourself not being able to stop thinking about that one particular person , blame the PEA 😀 .

3)     Getting attached, Oxytocin – Also known as the cuddle hormone it is released by touch and sex and deals with forming life long bonds , this hormone peaks immediately after sex and is extremely powerful casing feelings of  attachment and deep connection  to the other person .

LOVE will continue to be something of a mystery to people but it is a very important emotion, aiding in reproduction and hence directly attributing to the continuation of the human species.

Science fact of the day :D

Polar Bears are nearly undetectable by infrared cameras, due to their transparent fur.

The first photo of the DNA Helix taken by Enzo di Fabrizio from the University of Genoa, Italy, using an electron microscope.

The first photo of the DNA Helix taken by Enzo di Fabrizio from the University of Genoa, Italy, using an electron microscope.