publish paper reviews

Division of Bioorganic Chemistry and Molecular Pharmacology, Washington University School of Medicine.2011. “Reversible high affinity inhibition of phosphofructokinase-1 by acyl-coA. A mechanism integrating glycolytic flux with lipid metabolism” April 8th 2011. http://www.jbc.org/content/286/14/11937.full

Review of “Reversible high affinity inhibition of phosphofructokinase-1 by acyl-coA. A mechanism integrating glycolytic flux with lipid metabolism”

In this review I learnt that glycolysis and lipid metabolic flux are two processes that are linked or intertwined and must be regulated simultaneously to maintain cellular bioenergetic homeostasis. Fatty acids can surpress the glycolytic flux reaction. Acetyl coA which is generated from fatty acid beta oxidation leads to accumulation of citrate which is a potent inhibitor of PKF-1.The researchers identified a direct mechanism through which the branch point metabolite in fatty acid anabolic and catabolic metabolism, acetyl-coA regulates the phosphorylation of fructose 6-biphosphate to fructose1,6-bisphospate by the PFK-1 enzyme. This is the rate determining step in glycolysis. Different tests were carried out using rabbit muscle and varying reagents. The results of the tests showed that potent and reversible inhibition of PFK-1 by low concentrations of long chain acyl-coA is reversed by APT-1. The acylation of PFK-1 by palmitoyl CoA at four cysteine residues and the covalent acylation of PFK-1 are also reversed by APT-1. Acylation of PFK-1 increases the affinity of the enzyme for the membrane layers. PFK-1 membrane binding was regulated by acyl-coA. In this experiment I learnt that an increase in cytoplasmic citrate levels leads to direct inhibition of PFK-1 activity at the citrate regulatory site and accumulation of glucose 6-phosphate. Increase in glucose 6-phosphate leads to decrease hexokinase activity and thus decrease net glucose uptake. Free fatty acids are inhibitor for both glucose uptake and inhibition. This paper reinforced the enzymes I learnt in glycolysis but the information was a bit confusing because a lot of new terms were introduced to me. However I did grasp the overall concept of the experiment. One of the weaknesses in this experiment were was that the researchers tried to test for too much information and this made the paper very confusing.

US national library of medicine national institutes of health.2011. “Carbohydrate Metabolism is Essential for the Colonization of streptococcus thermophilus in the gastrointestinal tract of Gnotobiotic rats.” December 22nd 2011. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245227/

Review of “Carbohydrate Metabolism is Essential for the Colonization of Streptococcus Thermophilus in the gastrointestinal tract of Gnotobiotic rats.

In this paper I learnt that streptococcus Thermophilus bacteria are a dairy bacterium that is known for its exceptional performance in milk fermentation and resistance to elevated temperature. It is used in probiotics and it promotes a healthy system in the body.
Live yogurt cultures are beneficial because they aid in digestion of the sugar lactose in humans that lack the ability to digest it. Research brought data on the streptococcus Thermophilus bacteria and their metabolic adaptations in the gastrointestinal tract (GIT) of the rats. From the experiment it was found that the streptococcus Thermophilus bacteria were in higher concentration in the GIT of the rats which contained lactose than in the rats that did not contain lactose. The presence of the lactose allowed the bacteria to enhance and diversify the metabolism of diverse carbohydrate sources. The presence of lactose therefore enhanced the fermentation activity of the bacteria leading to higher levels of luminal lactate when compared to another strain of bacteria. Streptococcus Thermophilus bacteria had a high colony formation in the GIT and the addition of lactose boosted the bacteria’s carbohydrate metabolism. Due to a constant supply of lactose the bacteria recruited proteins involved in glycolysis and induced the metabolism of alternative sugars such as sucrose, galactose and glycogen. This paper was related to what I learnt in my carbohydrate lectures. It was very informative and it helped me understand the concept of lactose intolerance. I now understand that the bacteria thrive on the lactose and multiply when lactose is present. I can relate this to my lectures because I now that a by product of bacteria breaking down lactose is gas. Therefore the more bacteria in the stomach the more gas is produced and the only way there can be more bacteria is if there is a greater concentration of lactose. In essence I have learnt that the more lactose a lactose intolerant person consumes, the more gas they produce.

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Review of the Anfinsen Experiment

This video was very informative whilst being short and precise. It helped me understand the Anfinsen experiment with the use of the colorful diagrams and cleared up every bit of confusion that I had. The video consisted of two parts. The first part of the video talked about the addition of the urea and beta mercaptoethanol to a folded protein known as the native ribonuclease. Urea disrupts the hydrogen bonds of the protein while beta mercaptoethanol disrupts the disulphide linkages. These disruptions caused the protein to unfold. To refold the protein, urea and beta mercaptoethanol were removed using dialysis. This showed that all the information needed for the folding of the peptide chain back into its native form was contained in the primary amino acid sequence of the peptide.
In the second part of the experiment only beta mercaptoethanol was removed from the unfolded protein via dialysis. When this was done the protein refolded, however it was a scrambled form of ribonuclease and it was inactive because specific bonds were not formed. Following this, traces of beta mercaptoethanol were added and the active, native form of the protein was reformed. An interesting fact that I learnt was that there 105 ways to renature the protein. However, the native form of the protein has the thermodynamically most stable structure because this is the only form that has the correct interactions and bonds made.
The weakness of the video was that the speaker was talking a bit to fast and it was difficult to understand him at times because he was mumbling and stuttering in some sentences. Two things he could have mentioned that I learnt from my lecturer was the fact that the dialysis tubing had small pores in it to allow the urea and beta mercaptoethanol to escape but not the protein itself and that the urea was a chaotrope and it also disrupted hydrophobic interactions.

video review on enzymes

The main things discussed in this enzyme video were enzyme specificity, the lock and key hypothesis, the induced fit hypothesis and the factors affecting reaction velocity. The video was very informative and it helped me understand this aspect of enzymes even better. The main strengths of this video were the picture diagrams, the graphs and the fill in the blank questions. My favorite part of the video was answering the fill in the blank questions. This kept me interested in the video and boosted my confidence when I got the questions correct. The only weakness I found in this video was that some of the slides were packed with information and that was a bit overwhelming. Some of the main points in this video are that in the lock and key hypothesis the substrate and the active site on the enzyme have a complimentary fit and the product has a different shape to the substrate. In the induced fit hypothesis the substrate and active site on enzyme do not have an exact fit but as the substrate gets closer to the active site and one part binds to it, the active site conforms to fit the shape of the substrate. I also learnt that [S],[E],temperature and pH affect the reaction velocity. as the [S] increases the active sites become saturated and the rate of the reaction increases, however when all the active sites are saturated the rate of the reaction does not continue to increase and velocity remains the same as substrates have to wait for the next free active site. Increased [E] will cause the rate to also increase, however when all the substrates are bound to the enzyme then the rate remains constant. If temperature is increased then reaction rate increases as molecules have more kinetic energy and thus more frequent collisions. However when temperature gets too high, hydrophobic bonds and hydrogen bonds are broken and the enzyme becomes denatured. This causes the rate of the reaction to decrease very quickly. Changes in pH affect the rate of the reaction because the enzymes can be denatured and the ionization the active site can be affected. The catalytic activity depends on ionization or unionization of the chemical groups of the active site and substrates. Also the structure of the catalytically active protein molecule depends on the ionic character of the amino acid side chains, therefore if an alkaline pH is needed for the reaction to occur then a decrease in Ph will denature the substrate and enzyme and the rate of the reaction will decrease gradually as the solution becomes more acidic.
To improve this video animation could have been shown, to make it more appealing and slides could have been less packed.

Multiple choice questions

  1. Which enzymes use TPP as a cofactor?

A. 1, 2 and 3 correct

B. 1 and 3 correct

C. 2 and 4 correct

D. All are correct

1. phosphofructokinase-1

2. Pyruvate dehydrogenase

3. Trios phosphate isomerase

4. Pyruvate decarboxylase

2. What type of reaction is involved when ATP is made from mitochondria?

A. reduction

B. oxidation

C. condensation

D. hydrogenation

3. Which of the following organelles break down lipids?

A. 1, 2 and 3 correct

B. 1 and 3 correct

C. 2 and 4 correct

D. All are correct

1. Lysosomes

2. Smooth ER

3. Peroxisomes

4. Ribosomes

Amino acids and proteins word search puzzle

D I H T N W G M O G Y E I R P U S E N E 
I H M Y P Q B T N X H D Q E X Y D I C N 
S N I E T O R P S U O R B I F G N B D I 
U D T H R E O N I N E H L P L H O R D C 
L S N L Q U J U W R E E F O Y H B U Y Y 
P A T O Y Z B P B A H E B D C R N K O L 
H Z S I B W B E T A C U R H D D E K Y G 
I E T P U T N H H A L I I P F K G F K D 
D D N Y A I N P T A N O T G Q B O P A B 
E S K I D R L E R N A O T L X L R O B F 
B D V A E A T P L I J E T U S Z D J M B 
R O L Z R T R A V A U W G T G C Y S Z R 
I A J L M O S C T H V F B A I X H F S S 
D E M V T T Z Y Y E N O U M A Z F O D R 
G J T E T B Z U C S P N C A D V Y H N S 
E W I P R O L I N E T S O T L H D O V E 
S N Z T R N W F H F P I W E D I K E B R 
S I N Y Q E K B I H O G N X J N L U R I 
W W E P Y A W N K F T Q E E A H H Q N N 
K O E W N Z W I X N D E R U T A N E D E 

ALADINE
ALPHAHELIX
ASPARTATE
COVALENTBONDS
CYSTEINE
CYSTINE
DENATURED
DISULPHIDEBRIDGES
FIBROUSPROTEINS
GLOBULARPROTEINS
GLUTAMATE
GLYCINE
HEAT
HYDROGENBONDS
NINHYDRIN
PROLINE
SERINE
THREONINE

PROTEINS AND HAIR.

PROTEINS!!

So everyone knows what proteins are and how they have different functions! Of all the proteins I LIKE HAIR THE MOST!!

LETS TALK HAIR!!

Do you REALLY know what is hair ? “funny rite… but!”

“Live hair cells are generated inside the follicle by the papilla. As the new cells grow, the older cells die and are forced along the follicle towards the scalp. The dead cells are compressed to form a protein called keratin. The hair shaft that we see is the keratin emerging from the scalp. 

The cuticle – “the outer most part that we can see, a protective coating of the hair is formed from overlapping scales and can be several layers thick” this is the part of the hair that gives the hair its flexibility. It is translucent so that you can see the color of the hair (from the cortex).

This is definitely the most popular part of the hair as we can see it. The popularity of hair is all based on the texture of the hair or the texture determined to be achieved.This hair blog focuses on how this protein is affected by heat and chemicals.

Since we all have hair made of keratin then WHY IS EVERYONE’S HAIR TEXTURE DIFFERENT?

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At the molecular level, hair is composed mostly of chains of keratin molecules. These chains are cross-linked by chemical bonds in much the same way that the sides of a ladder are held together by rungs. The bonds include very strong links between sulfur atoms found in cysteine and much weaker electrical attractions between hydrogen atoms in other parts of the keratin molecules.

In straight hair, bonds form between atoms located at approximately the same sites on neighboring keratin chains. This creates relatively level “rungs” that allow the sides of the “ladder” to remain straight. In wavy or curly hair, molecules from different sites along adjacent keratin chains are attracted to each other, forming arching bonds that cause the sides of the keratin ladder to bend or loop around.”

HEAT PRESSED HAIR VS CHEMICALLY RELAXED HAIR

so we know that when we press or flatiron our hair it becomes straight and when we chemically relax our hair it is also straight. But the difference is that one process is reversible and the other isn’t!!! WHY IS THAT?!!!

So how does heat actually straighten hair?? “Heat straightens hair by breaking up the bonds that make hair wavy or curly. These curling bonds are hydrogen bond, and they are responsible for producing a wave or curl. Heat has the unique capability of modifying and relaxing the hair. When using a straightening iron, the heat gives the power needed to shape the hair while the flat shape of the iron molds each strand into a flat shape, removing the curl temporarily.The effect of heat, however, is temporary, over time the hydrogen bonds eventually return to their original form and the hairs goes back to the way they were. This rearrangement happens because moisture in the air hydrates the proteins. Hydrating the proteins in hair causes your hair to swell and allows the proteins (which like to exist in water) to become more “at home,” and your hair will take its original form again.   Therefore when the hair becomes wet it reverts to its original curl pattern.

RELAXER

The main reason hair is curly is because the keratin proteins contain amino acids called cysteines. These cysteines link to each other by disulphide bonds (two sulfur atoms connected to each other). The more disulphide bonds, the curlier the hair.Relaxers simply break these disulphide bonds and cap them so that they cannot chemically reform.The bonds between the keratin chains are rearranged in such a way that the hair becomes straight. Disulphide bonds however, are not affected by water so, when you break the bonds and cap them (in the case of relaxers) they will not go back to their original state and thus the hair cannot revert to its original curl pattern.

 

carbohydrates

I have noticed that since I have entered UWI I have gained weight. I wondered why and then I realised that my carbohydrate intake had increased significantly. I started eating more fast food and sweets for quicker bursts of energy.

    ARE CARBS MAKING ME FATTER?

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The answer is yes!!!  There are 2 groups of carbs known as simple and complex carbs. simple carbs are known as sugars and complex carbs are known as starches. I was eating more  unrefined simple carbs which released glucose into my blood stream much faster thancomplex carbs would. This spiked  my blood glucose levels and released energy fast. However, the energy did not last and I soon became tired again. To get more energy I consumed more food which had high calorie content and I did not burn them off, so the excess glucose was converted to glycogen and stored as fat in my body and in my liver. Now I know why I was gaining  weight and I plan to eat less unrefined carbs and eat more natural complex and simple carbs which are converted and released more steadily into my blood stream.

reflection of my introduction to biochem

my name is khadija nurse and i attend the university of the west indies. I am currently doing a degree in biology and environmental and natural resource managment. I love the environment and I am a member of the EMA youth ambassadors.I like participating in events that uplift our environment, so i am also a member of 2 environmental clubs.
I would like to be an environmentalist in the future.my first biochemistry class and tutorial was very exciting it was exactly what i hoped it would be.The cell was a good introduction to the biol 1362 course, it was very simple to understand. I used a very catchy,fun cell song that I found on youtube to help me remember the parts of the cell and its functions.This is the link to the video http://www.youtube.com/watch?v=KzMviiBoRtA. I hope it is very useful to all.