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!!!! 🙂

Nucleotides and Nucleic Acids

Holla hommes! Welcome back! On this post we’re talking about Nucleotides and Nucleic Acids…which should be hella obvious from the title, or not, but what-evz! Now you know. So what is a nucleotide? Well that’s pretty simple. A nucleotide is an organic molecule that is a subunit of the nucleic acids DNA and RNA. What are they made up of you may ask? And to this question I shall answer that it is a nucleoside + a phosphate. And now you want to know what a nucleoside is made up of right? Of course you do. A nucleoside made up of a nitrogenous base + five-carbon sugar therefore a nucleotide is a nitrogenous base + five-carbon sugar + phosphate.

 

Okay, so how about we get all up in this nucleotide and see what’s going on with the sugar! By the way, the sugar is the main characteristic of the DNA and RNA. Deoxyribonucleic acid who goes by the street name DNA is made up of deoxyribose and Ribonucleic acid whose street name is RNA (as you may have guessed) is made up of ribose sugar. (The ‘de’ in deoxyribose indicates the lack of oxygen on the second carbon in the ribose sugar.)

 

Our homme DNA

DNA – The mysterious double helix, self-replicating material that makes up our chromosomes and is the carrier for our genetic information. As mentioned before DNA is made up of a five-carbon sugar, a nitrogenous base, and a phosphate. Lets talk about the nitrogenous bases in DNA. There are two categories of nitrogenous bases, single ring and double ring. The single ring bases are known as pyrimidines, which consist of Cytosine (C), Thymine (T) and Uracil (in RNA) and double ring bases are purine, which consist of Adenine (A) and Guanine (G). In DNA a purine always pairs with a pyrimidine by means of a hydrogen bond, which is strong enough to hold them together, but also allows them to be separated when necessary. This bonding creates the ladder seen in the double helix formation. Adenine is paired with Thymine and Cytosine is paired with Guanine. The backbone, which is seen on the outskirts of the double helix, is made of sugar-phosphate pairs. The backbones run from 3’ (3 prime) – the sugar end to 5’ (5 prime) – the phosphate end and are anti-parallel to each other. Therefore one side is 3’ – 5’ and the other side is 5’ to 3’.

 

 

Namingggg! (The simplest part)

For Nucleosides:

–      For purine nucleosides would simply change the ending to “-sine”: Guanosine & Adenosine

–      For pyrimidine nucleosides you would change the ending to “-dine”: Thymidine, Uridine, Cytidine,

For Nucleotides:

–      You would begin with the nucleoside name above and then add “mono-”, “di-”, or “triphosphate” according to the number of phosphates present (Mono=1, Di=2, Tri=3): Adenosine Monophosphate, Cytidine Triphosphate, Deoxythymidine Diphosphate.

 

I know you’re like, seriously though, like what’s the big deal with nucleotides?

Welllllll I’ll tell you what the big deal is! First of all, nucleotides are the building blocks of DNA and RNA. Meaning with out them we’d be nothing, zip, zilch, zero, and nada homie! They can be compared to amino acids in their role in proteins. They are responsible for selectively binding to a protein and regulating its activities. In other words they are allosteric effectors. They serve as an energy currency in cellular metabolism and they make up the structures of many enzyme cofactors?

And now you’re all like, what about nucleic acids!!?

Gosh chill, I was getting there. Well most importantly, DNA has the information needed to create fuctional proteins and RNAs. They also have promoters that assist in the regulation of gene expression. rRNAs or Ribosomal RNAs help to make up ribosomes and they help with the creation of proteins. mRNAs (Messenger RNAs) are like FedEx for genetic information. They transport genetic information from the gene to the ribosome. tRNAs decode information in mRNAs into an amino acid sequence and some RNAs can increase the rate of biochemical reactions

 

Most Famous Nucleotide!! – ATP!!!

Real name, Adenosine Triphosphate isanucleotide containing adenine, ribose, and a triphosphate group.ATP is often wrongly referred to as an energy-storage molecule, however a more accurate term would be an energy carrier or energy transfer agent. ATP diffuses though the cell to make energy so that the cell can perform other work such as ion transport, cell movement and biosynthetic reaction. ATP’s chemical potential energy is made available when one or two of its phosphate groups are relocated to another molecule. This course of action can be denoted by the hydrolysis of ATP to ADP.

 

Forms of Nucleic Acids

B form – This is the most common conformation for DNA.

A form – This is common for RNA and is favored in conditions of low water. Contains deeper minor groove and shallow major groove.

Z form – Contains narrow, deep minor groove and the major groove is hardly existent. This can form for some DNA sequences and requires alternating syn and anti base configurations. It is known as being left handed, meaning that is coil in the left direction. Z form also contains high salt/charge neutralization.

 

And finally: Stability of Nucleic Acids

Nucleic acids contain hydrogen bonding but it is not usually a factor the stability of nucleic acids however it contributes to the double helix in DNA and RNA secondary structure. What does contribute to the nucleic acid stability is the hydrophobic interaction between base pairs. It is favorable for the hydrophobic bases to exclude waters and stack on top of each and this stacking is expand in double-stranded DNA.

 

Thanks so much for reading and I hope you found it informative and helpful.

Chao for now!

 

 

 

 

 

 

 

 

 

Amino Acid Video Review

 

This is a video review on Amino Acid Structure By Tracy Kovach from YouTube. I personally like this video because it is short and gets right to the point and pretty much covers all the necessary information.

In this video Tracy talks about what amino acids do and how they can be illustrated. She starts off by talking about the hemoglobin protein and explains how its job it to pretty much taxi around oxygen by picking it up from the lungs and dropping it off to the tissues where it is needed in the human body. The cells in the tissues then use the oxygen to create ATP, which is needed for all the metabolic processes for life. She then explains how amino acids are the building blocks of the protein hemoglobin and how without them this process would not be able to occur and we would therefore not be able to live.

She goes on to explain the structure of an amino acid. In an amino acid there is and amino group, the carboxylic group and the alpha carbon atom/chiral carbon that links the amino and carboxylic group. A hydrogen atom is connected to the alpha carbon as well as a side chain/R-group. A chiral carbon is a carbon that has four different groups attached to it. The only amino acid that does not possess a chiral carbon is Glycine. Glycine is the simplest amino acid with a R-group of only Hydrogen. Tracy then draws the Fischer projection – an illustration of an amino acid that highlight the four groups surrounding the chiral carbon – of two amino acids. There are two different types of Fischer projection configurations L-Amino Acids and D-Amino Acids. Whether the projection is L or D depends on where the amino group is. If the amino group is on the left it is L and if it is on the right it is D. L and D amino acids are enantiomers, meaning they are mirror images of each other however they can not be superimposed on one another. They are pretty much like your hands. Your hands are mirror images but if you place one on top of the other they would lay differently.

*Fact: L-amino acids are the only configuration found in the human body.

Well that is all for this video review I hope you enjoyed! Remember to subscribe to Tracy Kovach on YouTube!

Chao for now!

 

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