Lipids so far

Well I can only give the basics of what I learned in class because I have not reached that far in studying Biochemistry as yet.

Fats are generally solids at room temperature while oils are liquids. Oils contain unsaturated hydrocarbon chains meaning they have at least 1 C=C double bond. They can have several.

Short chain fatty acids have 6 carbons in the chain or less. Medium chains have 6-12 and large chain fatty acids have 14+ carbons in the chain.

Fats are very good sources of energy. 1 gram of fat produces more energy than 1 gram of glucose. It can serve as an energy reserve and is stored as TAG in adipose tissue. It also provides insulation and can protect vital organs.

Fats can be burned in oxygen(combustion) to release energy by oxidation just like with glucose but since fats are in a more reduced state they are easier to break down to produce energy.

Fats can be classified by delta designation.

As fatty acid chain length increases their melting point increases.

Lipids classification obtained from http://1.bp.blogspot.com/-hingIz7sYLI/Tq7mRRFHZQI/AAAAAAAAABc/9Q9y8DT4_GQ/s1600/lipids.png

Well that’s all for now. Until next time, Corporal out!

Blair's house full

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Exams and Farewell?

Well Biochemistry was interesting. It seems to be a very complex area for me and even with Mr. Matthew’s help I still did not find it as appealing. It was nice to blog and the layout of the course was different and innovative. Thanks Sir for teaching us so well!!!!

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“I know there isn’t ‘a one size fits all approach to learning. We all learn differently. My intention is to employ a range of teaching strategies to assist with that. Please make every use of all the recourses this course has available.”

“And as usual I am here to assist. Meet me in the digital universe if you have any problems.SincerelyYour Hokage Biochem JM”

Mr. Jason Matthews. 2013.

Final Examinations!!

Gather your knowledge and your courage we shall not bow to Biochemistry!

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Come Demon Do Your Worst!

The Kreb’s Cycle

The components and reactions of the citric acid cycle were established in the 1930s by seminal work from the Nobel laureates Albert Szent-Györgyi (Left) and Hans Adolf Krebs (right).

I remember them as Comrade Szent and Kraut Adolf Krebs. 🙂

The citric acid cycle — also known as the tricarboxylic acid cycle (TCA cycle), the Krebs cycle, or the Szent-Györgyi–Krebs cycle is a series of chemical reactions used by allaerobic organisms to generate energy through the oxidization of acetate derived from carbohydrates,fats and proteins into carbon dioxide. In addition, the cycle provides precursors including certain amino acids as well as the reducing agent NADH that is used in numerous biochemical reactions. Its central importance to many biochemical pathways suggests that it was one of the earliest established components of cellular metabolism and may have originated abiogenically.

The name of this metabolic pathway is derived from citric acid (a type of tricarboxylic acid) that is first consumed and then regenerated by this sequence of reactions to complete the cycle. The NADH generated by the TCA cycle is fed into the oxidative phosphorylation pathway. The net result of these two closely linked pathways is the oxidation of nutrients to produce usable energy in the form of ATP.

In eukaryotic cells, the citric acid cycle occurs in the matrix of the mitochondrion. Bacteria also use the TCA cycle to generate energy, but since they lack mitochondria, the reaction sequence is performed in the cytosol with the proton gradient for ATP production being across the plasma membrane rather than the inner membrane of the mitochondrion.

Cycle obtained from http://upload.wikimedia.org/wikipedia/commons/0/0b/Citric_acid_cycle_with_aconitate_2.svg

Information found on the Wikis.

A simpler illustration of the cycle:

Obtained from http://content.answcdn.com/main/content/img/oxford/Oxford_Chemistry/0192801015.krebs-cycle.1.jpg

My blogs are due for marking very soon so I amgoing with quantity over quality. Afterwards I will explain the Kreb’s cycle in detail.

For a more on each step of the cycle see this site: http://www.incolor.com/mcanaday/Krebs%20Phases.htm

fsn

IT’S TIME TO BLOG!!!!!!!!!

The great Glycolysis Metabolic Pathway

Glycolysis is the metabolic pathway that converts glucose , into pyruvate. The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).
Glycolysis is a determined sequence of ten reactions involving ten intermediate compounds (one of the steps involves two intermediates). The intermediates provide entry points to glycolysis. For example, most monosaccharides, such as fructose, glucose, and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful. For example, the intermediate dihydroxyacetone phosphate (DHAP) is a source of the glycerol that combines with fatty acids to form fat.
It occurs, with variations, in nearly all organisms, both aerobic and anaerobic. The wide occurrence of glycolysis indicates that it is one of the most ancient known metabolic pathways. It occurs in the cytosol of the cell.
The entire glycolysis pathway can be separated into two phases:
1. The Preparatory Phase – in which ATP is consumed and is hence also known as the investment phase
2. The Pay Off Phase – in which ATP is produced.

The Pathway is described as the most ancient metabolic pathway and is basically glucose splitting from its name:

GLYCO- glucose, LYSIS- splitting  6 carbon glucose is split into two 3 carbon Pyruvate molecules.

A basic summary of the reactions of glycolysis can be seen below:

glycolysispathway-a

 

This first phase is also called the energy investment phase because 2 ATP is used or invested.

glycolysispathway-b

 

This second part is called the energy generation or payoff phase as 2 ATP is produced for each molecule of pyruvate giving 4 ATP molecules. Overall a net gain of 2ATP is seen.

For greater detail visit http://themedicalbiochemistrypage.org/glycolysis.php or see the video by Mr.Jason Matthews at:http://www.youtube.com/watch?v=33JUjeo6-lE

I also described a practical use of glycolysis inhibition  here: https://biochemnoob.wordpress.com/2013/04/09/glycolysis-inhibition-uses/

Basically glycolysis consists of ten steps using ten enzymes to convert glucose to 2 molecules of pyruvate.

It’s just a basic overview of glycolysis but go into more detail later. We learned about each reaction and the importance of each enzyme. It is a task to memorize all the ten steps but hopefully with some practice I will learn it.

break1-concept

 

Biochem is getting complicated!!!!

Let the enzymes begin!

This will be my second review of a video. This time it is about enzymes and it was made by BiochemJM on Youtube.

Here’s the link http://www.youtube.com/watch?v=qcA57r2gBL8

It is a very good video  for introduction of enzymes at level 1.

The video starts with the introduction of some scientists that contributed greatly to the enzyme theories. One of them was Louis Pasteur (left) who observed that yeast contained ferments that converted sugar to ethanol which gave rise to the vitalism view. The yeast cell has to be intact to convert the sugar to ethanol. However, Edward Buckner obtained yeast extract that converted sugar to ethanol without the entire yeast cell.

James Sumner was able to isolate and crystallize the first set of enzymes. He saw that the enzymes were made up of proteins only.

John Burdon Sanderson Haldane proposed that the enzymes and substrates bind with weak bonds.

Enzymes are biological catalysts. They speed up a chemical reaction by providing an alternative reaction pathway with a lower activation energy.

They are made up of proteins. But some RNA molecules can act as enzymes called Ribozymes which fir the same criteria of a catalyst. This criteria being lowering activation energy and being unchanged by the reaction it catalyzes. Some antibodies also have catalytic properties and are called abzymes.

Enzymes are very important!! For example sucrose produces alot of energy when it is oxidized which can be used by cells but sucrose bonds will not break down easily under normal conditions. This reaction takes place in sceonds in the cells by respiration. This is made possible only by the presence of ENZYMES. Life would not occur if there were no enzymes present.

An example of an enzyme catalyzed reaction is given below. It shows the main difference in activation energy.

Image from: http://upload.wikimedia.org/wikipedia/commons/thumb/f/fe/Carbonic_anhydrase_reaction_in_tissue.svg/504px-Carbonic_anhydrase_reaction_in_tissue.svg.png

The enzyme only lowers the activation energy of the reaction. Therefore the reaction occurs faster.

The video then goes on to describe the transition state which is described as the highest energy arrangement of atoms that is intermediate in structure between the structure of the reactants and the structure of products.

Activation energy is the minimum amount of energy needed for the reaction to occur. The minimum amount of energy is deemed as important.

So more substrate molecules will be converted to product per unit time because they will have the energy required to be converted. The enzyme does not change the free energies of the reactants or products hence it will not change the equilibrium of the reaction.

There are three distinctive features of enzymes: they have tremendous catalytic power, they are specific and are regulated.

Enzymes are highly efficient in being catalysts. They can speed up reactions about one million times faster than if there was no enzyme. The number of molecules converted to product per enzyme molecule per second is the turnover number or kcat.

The video proceeds to how enzymes are named. They are based on substrates used eg. sucrose enzyme is sucrase. Some enzymes get their names from the actions they do. eg. pyruvate carboxylase. But some enzyme names are like Trypsin and Pepsin. It gets confusing as some enzymes have different names for the same enzyme. However the IUBMB( International Union of Biochemistry and Molecular Biology) divided them into classes and given numbers. Each enzyme can have 4 numbers. These numbers are called EC numbers.

Enzymes were classified as:

Oxidoreductases

Transferases

Lyases

Isomerases

Ligases

Each of these classes were described in the video

Table from: http://images.tutorvista.com/content/cellular-macromolecules/enzymes-classification.jpeg

From this system the names of enzymes became less ambiguous and more specific.

An example was  also given in the video to explain the significance of each EC number. This showed how the naming system became specific. eg. Glucose 6 phosphotransferase has an EC of 2.7.1.2

The first number shows that it falls into the second class of enzymes which are transferases. However the common names are used because the systematic names can be cumbersome.

Most enzymes are proteins but sometimes a non protein component is needed to help the enzyme to work more effectively. These are called co factors which can be inorganic or organic.

Apoenzyme+ Cofactor = Holoenzyme

The apoenzyme is the inactive protein part

The cofactor is the non protein part

the Holoenzyme is the active enzyme.

These were the general ideas given in the video and they were a good start to the enzyme part of the course. It was nice and short and to the point. The other two enzyme videos by Mr. BiochemJM seem to be much longer but they go in depth into the specifics of enzymes and their characteristics. The video should have introduced the different hypotheses on how enzymes turn substrate into products.

 

2nd Proteins reflection and youtube video review.

This is my second reflection on proteins which I will also be using as a video review of a video by BiochemJM on Youtube.

Here’s the link: http://www.youtube.com/watch?v=ZWLNkEJloJA

His videos are a good source of Biochemistry related material.

This review will focus on proteins. Basically there are four main structures associated with proteins being Primary structures, secondary structures, Quaternary structures and Tertiary structures.

Image obtained from: http://4.bp.blogspot.com/_ee2yOd0wTkk/TLfmPbTNEXI/AAAAAAAAAAs/eyaXy8fKMwg/s1600/0048.gif

In the primary, secondary and tertiary structures the main structures are the single polypeptide chains. There is increased folding no folding  in the chain from primary to some folding in the secondary to more folding in the tertiary.

All proteins will have a primary and secondary structure but only some will develop tertiary structures and fewer will form quaternary structures. The folding relies on the protein and its function.

The primary level of structure is a linear sequence of amino acids joined together by peptide bonds. This sequence is determined by the nucleotide sequences and the encoding of the protein by the gene.

The secondary structure is the regular folding in regions of the polypeptide chain and the most common are the alpha helix and beta pleated sheets.

In the video the alpha helices are then described as being an arrangement of the amino acids in the regular helical formation. There is hydrogen bonding between the oxygen in the peptide bonds and the hydrogen of every 4th amino acid where the hydrogen bonds running nearly parallel to the axis of the helix (C=O —-NH2). There are 3.6 amino acid residues for every turn in the helix and their R groups face the outside and perpendicular of the cylindrical helix axis.

Images from:


In the video Mr. BiochemJM describes the Alpha helix in considerable depth. He describes it as wrapping around an imaginary central rod in a coiling configuration.

The alpha helix is the most common form of coiling and forms more readily because of the optimal use of internal hydrogen bonding. All the peptide bonds in the helix are involved in hydrogen bonding except the ones at the ends. Each successive turn in the helix is held together by 3 or 4 hydrogen bonds which gives the helix collective stability.

In the helix some amino acids are considered undesirable because they can weaken the structure. One of these is proline which has that ring structure that has bonding with the alpha amine group (NH3) so there is one less hydrogen available for bonding. It produces a destabilizing ‘kink’ in the helix. Thus it is usually found at the ends of the alpha helix and it can sometimes terminate the helix by causing alterations in the direction of the polypeptide chain.

According to Mr. JM, “We can lebel proline as a bad boy.”

Glycine can also compromise the structure of the alpha helix. Its R group is the smallest atom being hydrogen so it has high conformational flexibility.

Amino acid residues with charges can also stabilize or destabilize the helix. Like charges repel each other which may cause ‘kinks’ in the helical structure. Large R groups can cause steric interference which will stop the formation of the helix. The amino acids with the large R groups cannot bond closely to give proper turns in the structure. The turn in the helix can facilitate the critical interactions of the amino acid side chains. The positive and negative side chains are usually located 3 – 4 residues away so an ion pair can form when there is the twist. Two aromatic amino acid residues similarly spaced from each other can lead to hydrophobic interactions which will in turn stabilize the helix.

Electric dipoles are also formed at the ends of the helix. This is due to hydrogen bonding. The negatively charged end is on the amino terminal as not the amino acid residues do not bond fully by hydrogen bonding. The positively charged end is the carboxyl end where the negative end of the helix is stabilized.

Image from http://ars.els-cdn.com/content/image/1-s2.0-S0005273612003860-gr1.jpg

The video then goes on to describe the second structure of beta pleated sheets.

In the beta pleated sheets the hydrogen bonds from between the peptide bonds on the same or different polypeptide chains. The planarity of the peptide bonds forces the polypeptide to be pleated with side chains of the amino acids protruding from above and below the sheet. The sheets can be parallel or anti parallel which depends on the C and N terminal end orientation. It is parallel when the terminals are the same on one end and in anti parallel sheets the Terminal ends alternate.

The tertiary structure refers to the spatial arrangement of amino acids that are far apart in the linear sequence as well as those residues that are adjacent. The main driving force for the tertiary structure in a globular protein is the hydrophobic effect where the hydrophobic groups and hydrophilic groups react differently and fold according to the medium to which they are exposed. eg, when exposed to water the hydrophobic groups will fold towards the interior of the structure while the hydrophilic groups are on the surface. This is the hydrophobic effect. Once folded the 3D structure is also maintained by electrostatic forces, hydrogen bonding and if present the covalent disulphide bonds.

The strengths of these bonds are also described. The disulphide bonds are the least frequent and don’t really contribute to the maintenance of the structure. The hydrophobic interactions are weak but collectively they are really strong.

Image obtained from :http://www.dynamicscience.com.au/tester/solutions/chemistry/foodchemistry/proteinstrct.gif

The ionic bond is also called the salt bridge. The tertiary structure is based on interactions of the R groups of the amino acid residues.

Mr. JM then moves on to describe in detail the main details of each type of bond which was in depth and properly explained. This explanation was useful because it linked the bonds to the turns in the secondary structure which gave the importance of the turns in the alpha Helix.

The hydrophobic forces are important in determining protein structure, folding and stability. They try to minimize contact with water. It increases entropy which makes it energetically favored. All the other bonds are also important.

The video then goes on to describe the effects of changes in the sequence of the chain as in sickle cell anemia where glutamate is replaced by valine in the structure of hemoglobin.

Image obtained from :http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/Gifs/HBBmutseq_2.gif

A question was asked on the importance of this substitution with respect to the amino acids themselves. It provided crucial information into why the substitution can be problematic.

Finally the video deals with the Quaternary structures which deals with at least 2 polypeptide chains. These structures provide more stability. They also participate in substrate channeling. This occurs in Oligomers because they are basically structures with more than one polypeptide chain.

Proteins can become denatured. Their natural or native structures may be altered and their biological activity changed or destroyed but the primary structure is not affected. Denaturing refers to the loss of folding dealing with the primary or secondary structure. Based on the conditions some proteins can return to their native form but under extreme conditions like excessive heating the process is irreversible.

Several factors can denature proteins like:

denature

This information was obtained directly from the video.

In heat denaturation the main bonds being broken are the hydrogen bonds. It is a cooperative process because the destabilizing of some parts will reduce the stability of other parts. This is shown by the abrupt change in enzyme activity over a slow increase in temperature .The structure can change for example in frying eggs the albumins unfold and coagulate which drastically reduces the solubility of the proteins.

Enzymes lose all catalytic activity when denatured. The video then goes on to describe the different types of denaturation and their applications in a lab setting like chemical denaturation.

The Anfinsen Experiment is also described.

From the size of this blog post alone there was only one problem with the video and it was its sheer length and volume of information provided. It cannot be watched in one straight sitting. It could be divided where basics and alpha helix are 1 video and the remainder in the other Otherwise the video was very informative from a level 1 perspective and it it covers all the bases. Thanks for another wonderful video Mr. BiochemJM!

Next I will briefly cover Enzymes! As always thanks for reading! 🙂

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So many Topics so little time!!!!!!