Publised paper review 3

Wilson, Lawrence. 2014. ‘How Nutrition Affects Emotions And Behavior’. Drlwilson.Com. http://www.drlwilson.com/articles/emotions_and_behavior.htm.

 

Something occurred to me recently and it was that we’ve studied the chemical composition of foods and basically the body’s reaction to them; by creating pathways and systems to support and perform a healthy function; with the use of these chemicals/ the nutrition given to the body. This article actually reads on the psychological and therefore behavioural reactions that the body undergoes due to the consumption of particular chemicals. Many mental diseases with physical manifestations and social implementations are touched on, ranging from Autism to biochemical depression, even to disorders such as Obsessive Compulsive Disorder [OCD] and Schizophrenia.
Learning disabilities are also linked to a poor nutrition, intestinal dysbiosis, food allergies and an imbalance of the chemicals Mercury, Calcium, Magnesium, Zinc (found in vaccinations or pharmaceutical drugs). The previously mentioned chemicals function as sedatives to the nervous system and so can assist in the calming of a hyperactive mind and/or body. However, extremely high levels of these chemicals in the system can result in biochemical depression – causing a suppression of the nervous activity, immense fatigue, impaired thyroid gland and adrenal glandular function.
There are a few concise case studies in the article explaining the possible defects and how they may have developed due to an unbalanced nutrition, as well as the human behavioural aspects due to nutritional deficiencies.
It is important to have a balanced diet and gain full nutrition from your foods as it not only affects the physical health but the mental, emotional and by extension social health as well. So maybe you can check it out, you may learn something new.

A decade of molecular cell biology: achievements and challenges

PUBLISHED PAPER REVIEW 2

 

Asifa Akhtar, Asifa. 2014. ‘A Decade Of Molecular Cell Biology: Achievements And Challenges’. Nature Reviews. Molecular Cell Biology 12 (10): 669. doi:10.1038/nrm3187. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282063/.
A 10 year anniversary was celebrated by Nature Reviews Molecular Cell Biology so in honour of this, different researchers where asked to comment on the evolution of molecular cell biology over the past decade including the achievements and challenges. The researchers’ names are as follows: Asifa Akhtar, Elaine Fuchs, Tim Mitchison, Reuben J. Shaw, Daniel St Johnston, Andreas Strasser, Susan Taylor, Claire E. Walczak and Marino Zerial.
A question was raised as to what they thought was the most significant new concepts in the field of molecular cell biology and whether the progress was aided by a specific technical advance. (The researchers’ initials are used)
A.A. spoke about epigenetics, the discovery that a combination of four transcription factors can induce a pluripotent state which would help in stem cell research (E.F. also mentioned this point but in greater detail) and also, the involvement of non-coding RNAs in some cellular and nuclear processes. T.M. mentioned Reaction – diffusion gradients specifying positional information inside cells. Gradients inside cells can now be used as a spatial organising concept. R.J.S mentioned that he was amazed by the amount of information we still lacked on the cell due to their advances in autophagy. D.St J. said that the most important technical advance is the use of RNA interference to knock down gene function. A.S. talked about the ability to reprogram differentiated cells to take on a pluripotent stem cell fate. S.T. mentioned Genomic science and sequencing technology and how the play a great role in the advancing or evolutionary biology. C.E.W and M.Z. spoke about RNA Interference and genome organisation.
A lot of amazing information can be learned and was learned from this article. It’s extraordinary to see how far Science can take us as a species. I do hope that in the years to come, more advances can be made in the field of Molecular Cell Biology.

 

 

 

MULTIPLE CHOICE QUESTIONS

Eukaryotic cells possess 80s ribosomes. What does the “s” unit of measurement stand for?

A. Schwann
B. Szilard
C. Schrödinger
D. Svedberg
E. Sarutobi
 

 

Select the correct multiple answer using ONE of the keys A, B, C, D or E as follows:
A. 1, 2 and 3 are correct
B. 1 and 3 are correct
C. 2 and 4 are correct
D. only 4 is correct
E. all are correct

What is/are the function(s) of carbohydrates?
1. Energy production
2. Energy storage
3. Precursor molecules
4. Basic genetic material

Publish Paper 1 Review – Regional Aerobic Glycolysis.

S. Neil Vaishnavi, M. E. R. 2010. Regional aerobic glycolysis in the human brain. Accessed 8th April 2014. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955101/

In this paper an experiment using 33 right-handed neurologically normal young adults at rest was used to calculate the regional distribution of aerobic glycolysis using positron emission tomography. Aerobic glycolysis can be defined as the state where glucose metabolism exceeds that used for oxidative phosphorylation despite sufficient oxygen to metabolize glucose to carbon dioxide and water. It was stated that aerobic glycolysis normally increases with increase cellular activity. This experiment was used to further help understand the role of glycolysis in the human brain at rest. Also to determine whether there is variations in glycolysis in the brain and how this in turns affect overall brain energy utilization.
Aerobic glycolysis is traditionally assessed in terms of the molar ratio of oxygen consumption to glucose utilization and a number less than 6 is indicative anerobic glycolysis is present. From the results gathered it was seen that the regions of the brain with high aerobic glycolysis included prefrontal cortex, lateral parietal cortex, posterior cingulate/precuneus, lateral temporal gyrus, gyrus rectus, and caudate nuclei. Whereas low aerobic glycolysis was found in the inferior temporal gyrus and throughout the cerebellum. Thus from the results it can be seen that the levels of aerobic glycolysis are not strictly related to the levels of brain energy metabolism but factors for ongoing aerobic glycolysis in the brain may be: 1) Energy – because the brain needs to suport membrane bound processes which needs ATP it would need to perform aerobic glycolysis to get the required energy. 2) Biosynthesis and 3) redox states.
Therefore from this research it can be seen that not only brain activity affects the level of aerobic glycolysis but there may be many other contributing factors. Thus research in this area should continue as it may help in the prevention/ curing of brain functioning related diseases.

This article is very appealing and everyone interested in biochemistry should take a look at it!!!! 🙂

LIPIDS ARE PHAT YO!

What rhymes with lipid? Well, that doesn’t matter right now, the better question is, what is a lipid? Anyone? OKAY OKAY, I’ll tell you. Basically it’s a group of organic compounds comprising waxes, oils or fats. Useful fact about oils is that they contain unsaturated hydrocarbon chains c=c bonds however, fats contain the opposite which are saturated hydrocarbon chains… and because of this, fats are solids and oils are liquids at room temperature. Waxes are just waxes (fatty acid = long chain alcohol) .

 

Wait, what’s that? Fatty Acids?

A fatty acid is not what’s behind Beyonce, but it is really a carboxylic acid consisting of a hydrocarbon chain and a terminal carboxyl group usually found as esters in fats and oils. They are used by the body as a source of energy, provide insulation from the cold and protects vital organs.

Why fat?

Well; it helps in the formation of cell membranes, provides the steroid nucleus with hormones, carries fat soluble vitamins, adds flavour to foods.

 

Straight Talk.

* Saturated fats have no double bonds, they are long straight chains. They contribute however to cardiovascular disease, the build-up of plaque in the arteries and even arteriosclerosis.

* Unsaturated fats have double bonds present. (‘cis’ form double bond, forming a kink) This prevents the fat molecules from packing tightly (healthier fat)

* The double bonds in monosaturated fatty acids occur between C9 and C10 and in polysaturated fatty acids more double bonds are found at C12 and C15.

* As the number of carbon atoms increase in a fatty acid, the melting point also increases… however the solubility in water decreases.

* Most fats are comprised of a mixture of saturated, monounsaturated and polyunsaturated fatty acids.

* There are both essential and non-essential fatty acids.

* Trans Fats and saturated fats both put your hearts health at risk!

 

* Essential fatty acids! OMEGA – 6 – LINOLEIC acid and OMEGA-3 ALPHA- LINOLENIC acid.

REFERENCES

 

http://telstar.ote.cmu.edu/biology/MembranePage/images/representation.jpg http://myhealthyfriends.blogspot.com/2013/08/packaged-foods-have-much-more-trans-fat.html http://courses.washington.edu/conj/membrane/fattyacids.htm

KREB and DUMPLIN

TCA CYCLE

Today, we learn about the TCA cycle as known as the famous Krebs cycle for all our scientist out there and is sometimes called the Citric Acid cycle. TCA stands for tricarboxylic acid. So what is the purpose or the end product of the TCA cycle? Well the easy answer would be energy but as a tertiary level student, more information would be needed to express the level of knowledge and understanding that I should be at. The TCA cycle can be defined as a continuation of different chemical reactions to produce energy in the form of ATP (Adenosine Triphosphate) via the oxidation of acetate. The TCA cycle can be considered as the step following glycolysis in the breakdown of sugar towards producing energy. Be sure to remember that the cycle takes place in ALL aerobic organisms and must take place under aerobic condition to generate ATP via oxidative phosphorylation.

So if glycolysis takes place in the cytosol, where does the TCA cycle take place? The answer to that would be in the mitochondria. Remember those little things? In eukaryotic cells? I’m sure you do. Yes, so the cycle takes place on the inner cristae within the mitochondria.

We need to link glycolysis to the TCA cycle via a reaction. This reaction will be:

Pyruvate + CoA+ NAD⁺      →     acetylCoA + CO2 + NADH

The primary substrate in the TCA cycle is Pyruvate(3C) but it is immediately turned into acetylCoA(2C) which is the main product of the reaction above. The above reaction is catalysed by three enzymes and collectively, they are called the pyruvate dehydrogenase complex. Once this is produced, our eight chemical reactions can begin. For our level, we must know these 8 enzymes used in the reactions. So let’s list them.

ü  Citric synthase- Synthesises Citrate(6C) from Oxaloacetate(4C) + acetyl CoA(2C)

ü  Aconitase- produces cis-aconitate(6C) and isocitrate(6C)

ü  Iso-citrate dehydrogenase- produces α-ketoglutarate (5C)

ü  α ketoglutarate dehydrogenase- produces succinyl CoA(4C)

ü  Succinyl-Coenzyme A synthetase- produces succinate(4C)

ü  Succinate dehydrogenase- produces fumerate(4C)

ü  Fumerase- produces malate(4C)

ü  Malate dehydrogenase- produces olaloacetate(4C)

 

TIPS

• An easy way to remember these reactions is by abbreviating but I’m sure everyone will have their own special way to remember.
• Always pay close attention to the carbon balance when learning and doing the Krebs cycle
• The TCA cycle is not an easy topic so be sure to go it over in much more detail.

 REFERENCES

Wikipedia. “Citric acid cycle with aconitate 2.svg.” 2014. http://en.wikipedia.org/wiki/File:Citric_acid_cycle_with_aconitate_2.svg (accessed 23 Mar 2014).

N-Zymez homie!

What the heck are enzymes?

You don’t know what enzymes are? Really?! Ok that’s fine. An enzyme is simply a biological catalyst. It speeds up a biological reaction with out being used or changed and it is specific, meaning each enzyme only works on a specific substrate. For example lipase hydrolyses lipids and only lipids. (How do enzymes speed up reactions though? ) OMG glad you asked! They just create a different pathway that has lower activation energy than the original pathway.

Most enzymes are proteins, some are RNA molecules known as ribozymes (they satisfy mostly all of the enzymatic criteria eg. they are substrate specific, they speed up the reaction rate, and they remain unchanged after the reaction. Some antibodies have catalytic properties and these are called abzymes.

What’s the big deal about enzymes?

Without enzymes life is literally impossible! Enzymes allow for respiration to occur. Which means, no enzymes à no energy à no life. Thank goodness for enzymes right? Yeah… trust me I know.

According to Ask.com, in the human body approximately 2700 enzymes can be found. These enzymes are separated into three major groups, which are: metabolic enzymes, food enzymes and digestive enzymes. Their location in the body depends on their function. Enzymes can be found in the mouth in saliva, in the stomach and everywhere else in the body. Without enzymes we are nothing!

This is an energy profile diagram.

This diagram shows exactly how enzymes speed up the reaction to produce product.

But what is activation energy? Activation energy is the minimum energy needed for a reactant to react.

How do enzymes get their name?

Um… their parents obviously name them at birth just like everyone else! No, just kidding. Enzymes are either named based on the substrate they react on, the action they perform, they end in ‘ase’ or they just have some random name that has nothing to do with them. Because names were getting out of hand, our homies at The International Union of Biochemistry and Molecular Biology, IUBMB for short, decided to come up with a naming system. They divided the enzymes into 6 classes. In each class is a sub class and in each subclass there is a sub-subclass. Each is numbered and therefore a series of 4 numbers specifies a specific enzyme (this is called the Enzyme Commission [E.C.] number.

The 6 major classes are: 

1. Oxidoreductases – Catalyze oxidation-reduction reactions
2. Transferases – Catalyze the transfer of C,N or P containing groups
3. Hydrolases – Catalyze cleavage of onds by adding water.
4. Lyases – Catalyze clevage of C-C, C-S an some C-N bonds
5. Isomerases – Catalyze isomerizaton of optical or geometric bonds
6. Ligases – Catalyze the formation of bonds between C and O, S, and N couples to hydrolysis of high energy phosphates.

Holoenzyme?? Hol up.. holo what??

Omg chillllll! Its simple! A holoenzyme is just a biochemical compound that is a combination of an enzyme and a coenzyme. And before you go a-wall!  A coenzyme is just a substance that is necessary for an enzyme to function.

Inorganic Catalyst v.s Biological Catalyst

Well incase you didn’t know, biological catalyst are THEE (emphasis on thee) fastest by far when compared to inorganic ones. Biological catalysts are also the most efficient. For example: during the Haber process, which makes ammonia, the temperature needed is 450 degree Celsius, at 1000 atm! What? Amylase breaks down starch to maltose in my mouth and at less than 100 degrees Celsius! And unless you’re a fire-breathing dragon it does the same for you!

So whenever you’re feeling on top of the world, and feel that you can take on a lion, tiger or bear… give enzymes a quick shout out, because with them my good friend… you are without life.

Here’s some pickup lines! Use them wisely.

In that order!

Chao for now!

“Title about Protein”

 

So, last week we discussed Amino Acids… now, let’s be blunt, let’s be quick, let’s talk PROTEINS.

Protein Structure: There are four levels of protein structures and those are as follows
v  Primary

v  Secondary

v  Tertiary

v  Quaternary

But, what determines these levels of protein structure?
Who says polypeptide chains? Who says the linear sequence of amino acids? Who says both? Well I obviously don’t know who said what, but if you said both, you’re right!

Now let’s talk about how the levels are determined…

 

 

 

 

RECAP!!

As blogged before, the bond between two amino acids is called a peptide bond.

Peptide bonds are formed removing a water molecule from two different amino acids. The sequence of amino acids determines the positioning of the different R groups and this positioning determines the order in which the proteins fold and essentially the structure of the molecule.

PRIMARY STRUCTURE:

The linear sequence of amino acids that make up the polypeptide chain is determined by the genetic encoding of the sequence of nucleotide bases in the DNA.

 

SECONDARY STRUCTURE:

 

This is the regular folding of regions of the polypeptide chain. Two of the most common types of ‘protein folds’ are called the α – helix (coiled) and the β pleated sheet;  which is folded.

Compared to other conformations, the α-helix if formed more readily due to its optimal use of internal hydrogen bonding.

 

 

 

The Hydrogen bonding in the secondary structure occurs between atoms in the peptide bond

TERTIARY STRUCTURE:

Tertiary… this is a three dimensional structure and is formed by the twisting of the polypeptide chain. The linear sequence of amino acids is usually folded into a compact structure and becomes stable by many non-covalent interactions between the side groups of the amino acids.

 

QUARTERNARY STRUCTURE:

Not many proteins reach to this stage of folding (protein structure) but one example of a protein that has the structure is Haemoglobin. This structure is formed by the combination of more than one polypeptide chain. Interactions between them are; ionic, disulphide, hydrogen bonds and hydrophobic (not afraid of water, but rather ‘water hating’) interactions.

 

 

 

RANDOM FACTS ABOUT PROTEINS.

• About 18-20% of the body’s weight is protein.

 

• Hair is made up of a protein called keratin, which forms a helical shape. It contains sulphur bonds and so the more sulphur links present, the curlier a person’s hair can be. (I LOVE CURLS)

 

• Protein is a macronutrient; these provide calories/energy and are essential for survival.

 

• The lifespan of most proteins lasts two days or less.

 

• Without Albumin, the human body would begin to swell. (When I think of Albumin, I think of eggs.. when I think of eggs, I think of PROTEIN)

 

• Protein in semen acts on the female brain to prompt the ovulation process. #fertilize #dontgetideas #okaygetideas

 

• Errors in protein function can cause diseases such as Alzheimer’s and cancer.

 

•  The body needs protein to grow, heal, and carry about nearly every chemical reaction in the body.

 

• Complete or Whole Proteins contain all nine of the essential amino acids.

 

• Insufficient protein in diets can prohibit weight loss.

 

 

References:

Pictures

http://www.vitalityfitnesscalgary.com/protein-4-reasons/

http://www.slapcaption.com/josh-nichols-weight-loss-success/

http://hanguyenbiologyhlblog.blogspot.com/2013/01/proteins-homework.html

 

Information

http://www.bodybuildingpro.com/proteinrating.html

http://www.nature.com/horizon/proteinfolding/background/disease.html

http://www.youtube.com/watch?v=ZWLNkEJloJA&feature=youtu.be

 

 

 

AMINO ACIDS AND PROTEINS!

CALL ME ACID…… AMINO ACID *brings in intro music*

Amino!!!!!!! I think I’ll name my daughter that. Anyways, onto the topic of amino acids and proteins. Amino acids are the initial structures for one of the most important biological compounds out there i.e. PROTEINS. Proteins have many functions in the world we live in today that we know of and don’t know of. To generalise, some of these functions include receptors, channels, transport, enzymes, storage, structural and immune response. Let go a bit deeper into the biochemistry of the building blocks which make up proteins, i.e. amino acids.

 

ALL THAT R GIRL!!!!!!!!!!

Soooooooooo….. If I show you a Fischer diagram of a molecule, how would you know if it’s an amino acid or not. What’s that? You don’t know? Well I’m not shockedJ.  In my own words, an amino acid can be described as an α carbon bonded to four different groups. But not just any four groups. The four groups must be a hydrogen atom, a carboxylic group, an amino group and a R group.

 

 

Another question: So how can we distinguish between the different amino acids?

Answer: Via the R groups of course.

What makes each amino acid different is the R group. The R group can range from very small for example Glycine (smallest amino acid) to very large e.g.  Tryptophan (largest standard amino acid). The R groups can be split up into different categories.

1. Non polar, aliphatic R groups e.g. Glycine.
2. Polar, uncharged R groups e.g. Serine.
3. Aromatic R groups e.g. Tyrosine
4. Positively charged R groups e.g. Lysine
5. Negatively charged R groups e.g. Glutmate.

 

 

AMINO ACID ABBREVIATIONS

The names of some amino acids can be abbreviated for the purpose of ease. Here is a chart showing some names and abbreviations which can be a three letter code or a one letter code.

 

 

MARRIAGE OF CYSTEINE 

When two cysteine molecules react with each other, they go through an oxidation reaction where they lose hydrogen. A bond between the sulphurs in the molecules form. This bond is called a disulphide linkage and the new molecule is called cystine. A reduction reaction can take place in cystine where hydrogen is gained and the two cysteine molecules are reformed.

 

 

ZWIT ZWIT

Amino acids can exist in the non-ionic form and also the zwitterionic form. It is quite easy to explain how one changes to the other. A proton/hydrogen from the carboxylic group adds itself to the amino group to form the zwitterion. The carboxylic group will now have a negative charge and the amino group will take a positive charge.

 

 

DON’T GET IT TWISTED (Ninhydrin reaction vs Biuret’s test)

Did you know that amino acids are colourless? So how do we know they a part of a substance? We test for them….DUH!!!!!!!! But which test do we use? Ninhydrin or biuret? C’mon, are you for real bro? We use Ninhydrin which ONLY test for amino acids and not proteins. Biuret’s test works on proteins ONLY!!!!! In the ninhydrin test, if a purple colour is observed, then the test is positive for AMINO ACIDS. In the biuret’s test the same purple colour means that the test is positive for PROTEINS.

 

 

PEPTIDE BONDS!!!!!!!!!!

These are the bonds created between amino acids. When two amino acids react, the carboxylic group of one amino acid reacts with the amino group the other amino acid to form a covalent bond called a peptide bond. The two amino acids joined together are now called a dipeptide. The reaction is a condensation reaction meaning that water is given off.

A sick lil cell…

Multiple Nuclei

Multiple nuclei are eukaryotic cells with more than one nuclei present within it. They generally share one cytoplasm within that cell. Multiple nuclei cells are commonly found within cancer cells. The formation or causes can be brought about through many means such as failed cytokinesis as well as multipolar spindles. Failed cytokinesis refers to the cell not being able to fully split during mitosis and therefore isn’t fully separated creating a cell with two nuclei. Mutipolar spindles refer to cells which contain more than three pairs of chromosomes which when splitting, splits in various directions resulting in an abnormal splitting due to chromosomes pulling throughout the various parts of the cells forming various nuclei. An example would be that of Syncytia. This is a natural occurrence caused due to fission of the plasma membrane.

Cytoplasmic Streaming

Commonly called protoplasmic streaming is the movement of a liquid substance within a cell. It transports valuable nutrients, proteins and organelles throughout. Mediated by motor proteins which is a molecule consisting of two protein molecules that use ATP, one protein remains fixed while the other can move organelles through the cytoplasm. It is important as it is difficult for large plant cells to transport nutrients throughout the cell by simple diffusion so this aids in this process. It consist of an outer filament which are long fibrous proteins positioned in rows along with myosin molecules which “tow” the organelles by moving along the filaments and by doing this it also sweeps and gathers other cytoplasmic organelles as well.

Organelles and Disease

Dysfunctional Organelle – This refers to an organelle which is impaired and doesn’t carry out its specific function as it normally suppose to. This is as a result of a disease or a harmful substance which damages the organelle and preventing it from performing its role. An example of this would be mitochondrial disease. This causes death to majority of the cells in the body (all except red blood cells) as it deplete cell energy resulting in eventual cell death.

Pathophysoilogy – the biological and physical disciplines of and within an organism. This can be as a result of an injury causing a functional change within the organism. It doesn’t directly deal with the treatment of a disease but it comes about as a result of one.

Pompe Disease – this is a genetic condition where too much glycogen is present within the body. This can cause cells within the muscles to fail resulting in a lack of many functions being carried out. This can cause even the heart to cease from performing properly which can prove fatal. This disease can make even simple activities such as walking a challenge and is most commonly found in children. The younger an infant is when this disease is found, the more severe the implications.

Tay-Sachs Disease – an inherited disease which can cause damage to nerve and brain cells within the body. More common in Europe it is caused by inheritance in an autosomal recessive pattern. This indicates that both copy of the genes are mutated causing this disease. One indicator of this disease is ‘cherry red spot’ which is a distinct abnormality in the eye of the infant infected.