Monthly Archives: March 2013

Multiple Choice Questions ^______^

i)   In amino acids , a zwitterion  is formed when;

A)  The carboxylic group donates a proton to the R group.

B)  A hydrogen from the amino group is lost as proton and accepted by the carboxylic group.

C)  The R group donates a proton to the carboxylic group.

D)  The amino group donates a proton to the R group

E)  A hydrogen from the carboxylic group is lost as a proton and accepted by the amino group.

 

ii)  Which of the Following amino acids have aromatic R groups?

1)  Serine

2)  Phenylalanine

3) Lysine

4) Tyrosine

A)   1,2 and 3 only

B)   1 and 3 only

C)   2 and 4 only

D)  Only 4

E) All are correct

 

iii) Which of the following enzymes is responsible for the splitting in glycolysis?

A)  Aldolase

B)  Enolase

C)  Pyruvate Kinase

D) PFK-1

E) Hexokinase

 

iv)   Which of the following enzymes is the most regulated in glycolysis

A)   Hexokinase

B)   Aldolase

C)   Phospho-fructokinase-1

D)  Enolase

E)  Pyruvate kinase

 

v)  Which of the following organelles contain DNA

1)  Mitochondria

2)  Chloroplasts

3)  Vacuole

4)  Nucleus

A) 1,2,3 only

B) 1 and 2 only

C)  1,2 and 4 only

D) 4 only

E)  All are correct

 

vi)  Which of the following are disaccharides?

1)  Lactose

2)  Sucrose

3) Maltose

4) Fructose

A) 1,2 and 3

B) 1 and 2 only

C)  1,2 and 4 only

D) 4 only

E)  All are correct

 

vii) A zwitterions has a net charge of;

A)  1+

B)  2+

C)  0

D)  1-

E)   2-

 

viii)  The biuret test is used to identify;

A)  Proteins

B)  Amino acids

C)  Carbohydrates

D)  Reducing sugars

E)   None of the above

 

ix)   The Ninhydrin test is used to identify;

A)  Proteins

B)  Amino acids

C)  Carbohydrates

D) Reducing sugars

E)  None of the above

 

x)  What is the net gain during  glycolysis?

A)  2 ATP

B)   4 ATP

C)   2 ATP and NADH

D)  4 ATP and 4 NAD+

E)   4 NADH

 

xi)   Which of the following is not found in animal cells?

A)   Nucleus

B)    Mitochondria

C)    Chloroplast

D)   Rough ER

E)    Cell Membrane

 

xii)   How many irreversible reactions are in the energy investment phase of glycolysis?

A)   2

B)    1

C)    3

D)   0

E)   None of the above

 

xiii)   Which enzyme is used in the 1st priming reaction of glycolysis?

A)  PFK-1

B)   Hexokinase

C)   Aldolase

D)   Enolase

E)   Pyruvate kinase

 

xiv)  How many ATP molecules are used in the energy investment phase of glycolysis?

A)   1

B)    2

C)    3

D)   4

E)   None of the above

 

xv)  Sucrose is a non-reducing sugar?

[] True

[] False

 

xvi) The R group in Glycine is H , a single hydrogen atom.

[] True

[] False

 

xvii) Uncompetitive enzymes bind to the substrate active site.

[]True

[] False

 

xviii) The primary structure of a protein refers to the;

A)  Folding of the structure

B)  Type of bonds holding the protein together

C)  The sequence of amino acids making up the protein

D)  Structure being in an alpha helix or beta pleated sheet

E)   None of the above

 

xix) Which of the following is true about Globular proteins?

1)  They are water soluble.

2)  They function in dynamic roles.

3)   They can function as enzymes.

4)   They have one dominating secondary structure.

A) 1,2 and 3 only

B) 1 and 2 only

C)  2 and 4 only

D)  1 and 3 only

E)   All of the above

 

xx)  Which of the following amino acids is not allowed in an alpha helix?

A) Serine

B) Alanine

C)  Glutamine

D) Glycine

E) Valine

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