Final reflection..:(

I can honestly say that this semester went by the fastest thus far. Starting the semester was hard, because I knew I had to repeat the dreaded Biochemistry I. But this time I can say I learnt sooo much, that I never learnt the first time around doing the course. The course content was well delivered by Mr.Mattew, via his very interactive lectures and tutorials. Although, I was sacred at the beginning of this course, since I failed already, this vast knowledge I gained, has made me confident for the final exam. I learnt concepts that I had no clue about previously, which helped me put together all the missing pieces from last year and make sense of what was being taught. I  enjoyed doing the course and look forward to having Mr.Matthew and his very effective teaching strategies next semester, for the second Biochemistry course!

Good luck all…:D

Revision time..:)

Found these videos to be quite useful in revision:

Glycolysis:

http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_glycolysis_works.html

Electron Transport Chain:

http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__electron_transport_system_and_formation_of_atp__quiz_1_.html

Nucleic Acids:

http://telstar.ote.cmu.edu/biology/MembranePage/index2.html

Catalytically perfect enzyme

Also, while learning about we came upon the term, “perfect enzyme”.

A catalytically perfect enzyme or kinetically perfect enzyme is an enzyme that catalyzes so efficiently, that almost every time enzyme meets its substrate, the reaction occurs. The specificity constant, kcat/Km, of such enzymes is on the order of 108 to 109 M-1 s-1, indicating high efficiency. Catalytically perfect reactions are only limited by substrate diffusion rate.

Some catalytically perfect enzymes are triose-phosphate isomerase, carbonic anhydrase, acetylcholinesterase, catalase, fumarase, β-lactamase, and superoxide dismutase.

Some enzymes operate with kinetics which are faster than diffusion rates, which would seem to be impossible. Several mechanisms have been invoked to explain this phenomenon. Some proteins are believed to accelerate catalysis by drawing their substrate in and preorienting them by using dipolar electric fields. Some invoke a quantum-mechanical tunneling explanation whereby a proton or an electron can tunnel through activation barriers, although proton tunneling remains a somewhat controversial idea.

Sources:

http://en.wikipedia.org/wiki/Catalytically_perfect_enzyme

 

 

 

Thermophiles-Thermophilic organisms

While learning about enzymes we learnt that different organisms have different optimum temperatures, at which they can function, they can range from 37C, (humans), to 105C.

Microorganisms can be grouped into broad (but not very precise) categories, according to their temperature ranges for growth.

• Psychrophiles (cold-loving) can grow at 0^oC, and some even as low as -10^oC; their upper limit is often about 25^oC.
• Mesophiles grow in the moderate temperature range, from about 20^oC (or lower) to 45^oC.
• Thermophiles are heat-loving, with an optimum growth temperature of 50^o or more, a maximum of up to 70^oC or more, and a minimum of about 20^oC.
• Hyperthermophiles have an optimum above 75^oC and thus can grow at the highest temperatures tolerated by any organism. An extreme example is the genusPyrodictium, found on geothermally heated areas of the seabed. It has a temperature minimum of 82^o, optimum of 105^o and growth maximum of 110^oC.

It must be stressed that the temperature ranges for the groupings above are only approximate. For example, we would use different criteria to classify prokaryotes and eukaryotes. The upper temperature limit for growth of any thermophilic eukaryotic organism is about 62-65oC. And the upper limit for any photosynthetic eukaryote is about 57o – for the red alga Cyanidium caldarium, which grows around hot springs and has a temperature optimum of 45oC. In contrast to this, some unicellular cyanobacteria can grow at up to 75oC, and some non-photosynthetic prokaryotes can grow at 100oC or more.

Below, we consider two major types of thermophile – the microbes that grow in geothermal sites, and those that grow in “self-heating” materials such as composts. However, some very recent reports suggest that these different types of environment can share some common organisms.

Many of the prokaryotes that grow in the most extreme environments are archaea – a group that is clearly distinguishable from both the present-day bacteria and the eukaryotes. There is little doubt that many of them still remain to be discovered and described, but this is a difficult field of research because of the problem of reproducing their natural growth conditions in a laboratory environment. Members of the genus Sulfolobus (archaea) are among the best-studied hyperthermophiles. They are commonly found in geothermal environments, with a maximum growth temperature of about 85-90o, optimum of about 80o and minimum of about 60oC. They also have a low pH optimum (pH 2-3) so they are termed thermoacidophiles. Sulfolobus species gain their energy by oxidising the sulphur granules around hot springs, generating sulphuric acid and thereby lowering the pH.

The study of extreme environments has considerable biotechnological potential. For example, the two thermophilic species Thermus aquaticus and Thermococcus litoralis are used as sources of the enzyme DNA polymerase, for the polymerase chain reaction (PCR) in DNA fingerprinting, etc. The enzymes from these organisms are stable at relatively high temperatures, which is necessary for the PCR process which involves cycles of heating to break the hydrogen bonds in DNA and leave single strands that can be copied repeatedly. Another thermophile, Bacillus stearothermophilus (temperature maximum 75oC) has been grown commercially to obtain the enzymes used in ‘biological’ washing powders.

Sources:

http://archive.bio.ed.ac.uk/jdeacon/microbes/thermo.htm

Snake Skin-Made up by the same material as our hair and nails?

Did you know that snake skin/scales are made up of keratin, the same material of our hair and nails?

Epidermis: characterized by complete covering of keratin (the same stuff that makes up mammalian hair and mammalian, avian, and reptilian nails/claws also makes up the plates we call “scales”). The keratin may be thick, as on the belly and tail, or thin, as on the dewlap. The hard spikes on such lizards as bearded dragons and horned lizards are just harder bits of integument, as are the keeled ridges on many snakes’ scales and some lizards, such as some iguanas. The keratin is composed of many layers of very thin, flat cells. The closer they get to the surface of the reptile, the more highly compacted they are as they are pressed against by new keratin cells being formed lower down in the epidermal layer, the stratum germinativum. Three such layers of increasingly compacted keratin cells are formed called, from the surface inward toward the stratum germinativum, the Oberhautchen layer, the beta-keratin layer, and the alpha-keratin. Some reference the epidermis as being three layers:

Stratum corneum: heavily keratinized outer layer.

Intermediate zone: composed of stratum germinativum cells in various stages of development.

Stratum germinativum: the deepest layer, consisting of cuboidal cells. Undergoes mitosis to form the intermediate zone.

During shedding (ecdysis), the mitosis in the stratum germinativum forms the new cells moved up to the intermediate zone and those cells up to the stratum corneum. It is during this time that the skin is metabolically active and it in this period of activity that healing will occur. Otherwise, skin is essentially inert.

Exception to the norm… The exception to the above is the chelonians. Their shell, which many people think is just bone, is actually covered with living tissue composed of keratinized epidermis covering the underlying dermal plate which is itself the chelonians vertebrae and rib cage. (Thus, the practice of piercing a chelonians’s shell to put a ring in with which to tether chelonian (which is in itself inhumane), or to decorate it with stud earrings, is akin to our puncturing our skulls.)

Dermis: consists of connective tissue. In some reptiles, there may be small bones called osteoderms. These are what form the distinctive specialized scales on savannah monitors and crocodilians, for example.

Reptile skin heals much more slowly than mammalian skin, often taking about 6 weeks for the defect to be fully restored.

 Sources:

http://www.anapsid.org/basicdermatology.html

 

 

Published paper #2-The Potential Toxicity of Artificial Sweeteners

Whitehouse CR, Boullata J, McCauley LA. 23 JUN 2008. ‘The potential toxicity of artificial sweeteners.’Accessed 12^th April 2013  http://www.ncbi.nlm.nih.gov/pubmed/18604921

There has been a lot of talk about artificial sweeteners, in the past and even today. Some people swear by it and others don’t. This article goes into a lot of details about the different type of sweeteners, its uses and chemistry and its potential effects on health.

The main idea about artificial sweeteners is that they provide the sweetness of natural sugars without the calories. Since everyone nowadays is limiting their daily calorie intake, they often turn to these artificial sweeteners to avoid the extra calories. But is this really the way to go?

There are classes of artificial sweeteners, nutritive and non-nutritive. The nutritive sweeteners include the monosaccharide polyols (e.g., sorbitol, mannitol, and xylitol) and the disaccharide polyols (e.g., maltitol and lactitol). The non-nutritive sweeteners, better known as artificial sweeteners, include substances from several different chemical classes that interact with taste receptors and typically exceed the sweetness of sucrose by a factor of 30 to 13,000 times . Artificial sweeteners are found in a wide range of products such as soft drinks, juices, jams, jellies and desserts.

The history, chemistry and metabolism, and toxicology, of saccharin, aspartame, acesulfame-K, sucralose and neotame, all common substances that make up artificial sweeteners, were provided in a detailed account throughout the article. The main idea from all this being, that there has been extensive research about the effects of these substances on human health and evidence that suggest that they are associated with health conditions such as cancers, migraines and low birth weights.

There are a lot of controversy surrounding artificial sweeteners since some research scientists  believe that since the compound found in artificial sweeteners are not metabolized by the body they possess no health risks since they are simply excreted as wastes products.

The average daily intake, ADI is defined as an intake that “individuals in a (sub) population may be exposed to daily over their lifetimes without appreciable health risk”, (WHO. 2004). In the USA, aspartame has the highest ADI of 50mg/kg/d, but this value may be subjected to change based on new research discoveries about its health implications.

Diabetics, children, pregnant women, women of childbearing age, breastfeeding mothers, are all populations susceptible to the negative effects of these artificial sweeteners.

Controversy also arises among individuals who are on low calorie diets, who tend to use these sweeteners in their diets. These individual should be warned about the risks and benefits of these substances, and also should be educated about healthy eating habits and exercise to burn off the extra calories they would be consuming if they choose to go the natural sugar way.

All in all, this article provided a very god insight, into artificial sweeteners, without being bias. It gave a wide explanation about the dangers of artificial sweeteners, and the risks they pose to human health. Which one are you? Natural or Artificial?

Published paper #1-Brown Adipose Tissue as a Regulator of Energy Expenditure and Body Fat in Humans

Saito M. 23 FEB 2013, ‘Brown Adipose Tissue as a Regulator of Energy Expenditure and Body Fat in Humans’ Accessed 12^th April 2013  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3579148/

Brown Adipose Tissue, (BAT), was one of the topics suggested to us my Mr Matthew, for our published paper review, but I chose this particular topic because during the semester I learnt a lot BAT. In my second year course Animal Physiology we learnt how animals such as mice use BAT to maintain their body temperature, when placed in cold environments; we also did a lab using a real live mouse to demonstrate how they react to varying temperatures. Quite interesting I must say! Anyways, onto this paper.

Brown Adipose tissue is known as a major site in the body where non shivering thermogenesis occurs during cold exposure, hence controlling energy use and body fat. The study states that BAT had been recently discovered in humans, and has a potential to be used for decreasing body fat in humans. There are two main types of adipose tissue, white adipose tissue (WAT) and brown adipose tissue (BAT).  WAT is used mainly for energy storage and BAT for energy use.  BAT was discovered in human using fluorodeoxyglucose (FDG)-positron emission tomography (PET), together with computed tomography (CT).

The inner membrane of the mitochondria of BAT contains a protein known as unique uncoupling protein 1 (UCP1), which acts to uncouple oxidative phosphorylation from ATP synthesis, releasing heat energy, thereby ensuring thermogenesis. The primary substrates for this process are fatty acids from triglycerides and circulating free fatty acids and lipoproteins.

The existence of metabolically active BAT in adult humans was confirmed by using FDG-PET/CT studies.

In humans, the fact that the metabolic activity of BAT is increased after cold exposure suggests a contribution of BAT to cold-induced thermogenesis, thereby regulating whole body energy expenditure. In humans studies have shown an inverse relationship between the presence of BAT and indices of measuring obesity such as body mass index (BMI). It was observed in past studies that BAT prevalence is lower in patients with a higher BMI. Age also influences adiposity, since cold activated BAT is more than 50% in younger subjects and decreases with age.

Since it has been observed that BAT can be used to prevent body fat accumulation, attempts has been made to activate this process. The most effective stimulus discovered in both mice experimental studies and humans for activating BAT was exposure to colder temperatures. In humans a cold stimulus is received by transient receptor potential channels (TRP).  Chemical activation of these receptors (TRPM8 and TRPA1), would mimic the effects of cold exposure. These receptors may be activated by common food ingredients such as menthol, found in mint, mustard and Wasabi. Also mentioned is capsaicin, found in chilli pepper, which can act as a agonists for TRPV1. All these substances can act to mimic the effect of thermogenesis without having to decrease the external environmental temperature.

Also BAT may be relevant in improving insulin sensitivity and enhanced glucose utilization in cold acclimated animals, hence BAT maybe useful for not only treating obesity but also other obesity related diseases.

This concept of using BAT as an energy and body fat regulator in humans is an interesting concept that can be further enhanced by more research into how it can be used to increase metabolism and aid in preventing obesity.

YouTube Video Review #2-Protein Structure

Review of a video that explains protein structure; on all four levels.

The first protein structure discussed in the video was the primary structure. The primary structure consists of the aminoacid sequence that are joined by peptide bonds. The secondary structure; consists of a alpha helix, which is spiral shaped and held together by hydrogen bonds, between the NH–OC. In the video it was said that there are 3.5aa per turn, however, we learnt that there are 3.6aa amino acids per turn of the helix.  Also, the Beta pleated sheets are linear parallel primary structure, that are hydrogen bonded together, that stabilizes the structure. The tertiary structure was then discussed. It was said that the tertiary structure, consists of interactions between R groups. Interactions found in the tertiary structure; covalent disulphide bridges, hydrophobic side chains, Van Der Waals forces and ionic interactions or the salt bridge. In the video the concepts of domains, which are the basic units of the tertiary structure, that are functioning parts. Also the concept of a chaperon was mentioned, which as simply proteins that facilitate the correct folding of other proteins. These concepts, are not required for us to learn at this level. Finally the Quaternary structure was discussed, which are different poly peptide chains that interact to form the entire protein, e.g. hemoglobin. The Quaternary structure are composed of the same interactions as the tertiary structures.

In summary the video was well laid out and straight to the point. It was explained in a manner that was easy to follow and understand. The video also provided a short review about the structure of proteins.

Exam paper MCQ :)

Single answer MCQ

1. Where are the enzymes needed for glycolysis located in eukaryotic cells?

 

A.            intermembrane space

B.            plasma membrane

C.            cytosol

D.            mitochondrial matrix

E.            cytoplasm

 

Multiple answers MCQ

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 3 is correct

E. all are correct

 

Which of the following is/are non-essential amino acids?

1. Lysine

2. Proline

3. Valine

4. Glycine

 

C’mon don’t be shy; give it a try!

YouTube Video Review #1-Enzyme Inhibtion

While doing enzymes the first time around, everything about enzyme inhibition was quite strange to me, especially those graphs. The second time around Mr.Matthews video made it easy to understand what was going on in each type of inhibition, and I learnt a great amount. I found this video on YouTube that summarizes nicely everything we need to know about enzyme inhibition.

• The definition of enzyme inhibition was given as; agents that bind covalently to enzymes and disrupt their functions are irreversible inhibitors.
• There are three main types of inhibitors: Competitive, Non-competitive inhibition and Uncompetitive Inhibition.
• Competitive inhibitors compete with the substrate for the active site by binding irreversibly with non-covalent bonds at the active site. The substrate is blocked from binding to the active site, forming an enzyme substrate complex. Km increases and V max remains the same. Inhibition is overcome by adding more substrate .
• Non-competitive inhibition-states that inhibitors bond non covalently to a site other than the active site and changes the conformation of the enzyme. The substrate is not prevented  from binding to the enzyme. In this case the Vmax is lowered and Km remains the same.
• Uncompetitive inhibition-The inhibitor  binds only to the enzyme substrate complex. Both Vmax and Km decreases.

Each type of inhibition was accompanied by the guy drawing, Line-weaver Burk plots, which he used to explain each type of inhibition and their effects of Vmax and Km. The video was quite good and straight to the point.  The guy had a good explanation that was easy to understand. Though, i felt his illustrations should have been a little bigger, it was still good overall.

The video helped me to reinforce what I learnt about enzyme inhibition and was a good review tool.