So this morning before I could even have my ceylon tea, my-friend-slash-colleague-slash-gym-slash-running-sprinting-buddy No-e, well let's juz say was sulking like there's no 'morrow. Gahh!! She juz kept dumping all her desk stuff on mine like crazy! There goes her fave stuffed bulldog animal. Her NU desk clock...aaand more..'til I was, like whaaaaaaaaaaat the!! No-e!! One of my best bud GB took the friggin' stuff animal and went like ooh can I have this??? (all forgetting to stop the poor girl from her emo trip). So left me no choice but to grab 'em back and told No-e, noooo eeeee!! and again, whaaaaat the.....
Unless she's pretty much sure she's dying, in which who is to tell right? There really is no reason to give her things away like that. Sheesh! No-e! Sometimes I dunno really whether to crack or cry. Told her the usual preppy pep, not to make decision at the peak of her emotion. Especially when she juz got her promotion, hey that rhymed! So can you see why I kept saying whaaaaaaaaat the!!! Why do all sorts of people resign when they're emo?
How 'bout you guys? How do you deal with setbacks? When you pretty much know it's part of life and thus happens to the best of us! Me, I always and forever got my entourage of bashers too, but I keep telling No-e how I always take their perspective at face value. And besides people are balls hard, you just can't change them. Also, we already know how entitled they are with their views and whatnot. Oh well, as Britney Spears put it, it's their prerogative, love that song by the way. In a nutshell vayvee, if ya can't change the people around you, then choose the people you choose to be around. Pretty much how you chose your bridesmaids and maid of honor. Also, remember not to invite on your wedding day those who aren't so thrilled with you for the past days and so.
Btw, today's post seeecret seems to have been written juz for you, gawsh, f*ckyea cuz you're the dashing bride my betch.
So, P. S. Always keep in mind to keep zennnn sistah. oooommmmm. aaand repeat.
So today we had team building. Guess every team needs that every once in a while..and some serious drinkage of course, although booze are so so, kinda bitin actually. Only got roasted juz a teenie bit. Me gots some ball of anger puke in my throat that can only be vanished by some cuervo jose! Meanwhile... wuz able to score some watermelons on our way home! Nommmmmmmmm! Me love watermelon. Sweet or even the not so sweet kind so long as it refreshes me, I'm a happy camper!
Credits to Biochem
students Carlos, Shenelle, Liniker, Latisha, et. al
This video started with a revision session of Glycolysis.
Things that we learnt before:
Glycolysis is the splitting of Glucose (a 6 Carbon Sugar) into 2 Pyruvate molecules (2 3-Carbon molecules).
It occurs in the cytosol of cells, he stated that Glycolysis takes place in the cytoplasm of the cell which is not true.
It produces a net gain of 2 Atp and 2 NADH moleules.
In the video he told us that Glycolysis take place in the presence or absence of Oxygen (Aerobic or Anaerobic conditions).
New Material
The Krebs Cycle is also known as the Citric Acid Cycle (substance found in orange juice).
It takes place in the inner space of Mitochondria (Power House of cells).
Mitochondria has a double membrane outer and inner.
The inner membrane of the mitochondria is called the ‘Crista’ (plural Cristae).
Therefore it has 2 compartments
The outer compartment.
The Matrix.
A combination of Acetyl CoA (2 Carbon molecule) and Oxaloacetic Acid( 4 Carbon molecule) to form Citric Acid (6 Carbon molecule) is what enters the Krebs Cycle.
All reactions are catalyzed by enzymes.
Carbons are lost via Co2 gas.
The Purpose of the Krebs Cycle is to generate ATP, NADH, FADH2 etc.
NADH and FADH2 produced here will go into the ETC (Electron Transport Chain) to generate much more ATP than in the Glycolysis Pathway and the Krebs Cycle.
Enzymes are proteins that are referred to as a biological catalyst that speeds up an chemical reaction. If enzymes did not exist our important life processes will not occur therefore they are VERY important to life.
Enzymes are not changed when they perform there function and can be used over and over. Each enzyme in the body has one particular function. Therefore the enzyme can fit only into a certain substrate.
LOCK AND KEY THEORY AND INDUCED FIT THEORY!!
The lock is the enzyme and the key is the substrate. Only the correctly sized key (substrate) fits into the key hole (active site) of the lock (enzyme).
Induced fit theory is when the substrates change the shape of the active sites in enzymes in order to fit.
DEPENDENT ON ENZYMES: While doing some research on enzymes i found out that without them life processes would take almost 2.3 millions years to occur. Also for creating the building blocks for DNA without enzymes would take 78 million years according to the biologist Richard Wolfenden. Therefore it is a good thing we have enzymes present to help speed up these reactions. Here we have a picture of the six major class of enzymes:
An enzyme is a biological catalyst (protein or RNA molecules) which speeds up a chemical reaction, because it creates an alternative pathway with a lower activation energy.
Now enzymes comprises of 2 important parts.
Substrate- the molecule that binds to the enzyme.
Enzyme itself- this contains the Active site (the binding site) where the substrate binds to the enzyme via Hydrogen bonds.
Now the things that make these molecules sooooo fascinating are:
These molecules are specific, meaning that they have a specific complementary shaped active site to the substrate coming in. Say for instance I tried using my key for my house to open the door for your house it wouldn’t work because the lock on your door is different from that of my door. 2. Enzymes speed up reactions, meaning that the time a reaction will take with an enzyme will be less than the time taken without an enzyme. It is said that without enzymes some biological reactions can take up to 2.5 million years to occur.
Say for instance the reaction without an enzyme is Wile.E Coyote and the reaction with an enzyme is Roadrunner. Now for you would don’t know the cartoon Wile.E Coyote never catches Roadrunner because Roadrunner is so much faster than Coyote. This is the basis in the enzyme world. The reaction with the enzyme is so much faster than the reaction without the enzyme.
For example Maltase is the enzyme used to convert Maltose into 2 Glucose molecules.
Glucose can enter the Glycolysis Pathway via addition of a Phosphate group (Phosphorylation) with the help of the enzyme Hexokinase, which converts it into Glucose-6-Phosphate. This molecule will then undergo various other reactions with the help of different enzymes until the end product of pyruvate.
3. Enzymes have the ability to take part in the reaction but remain unchanged in the end!
The video firstly focused on the enzyme called catalase. Catalase is found in almost all living cells. Catalase breaks down hydrogen peroxide. Hydrogen peroxide is the substrate which feeds into the catalase and break down into H2O +O2.
According to the video an enzyme has an area called the active site. (This is the area where the substrate is going to fit in). As described, the active site is going to be part of the enzyme with a “hole” in it where the substrate fits in. This describes the Lock and key hypothesis. When the substrate fits into the active site there is going to be a “sort of tug” which will result in making it easier for chemicals to break off as describe. The tug is referred to as the lowering of the activation energy. The presenter further states that enzymes can be turn on or turn them off as described in the video.
Credits to Biochem
students Carlos, Shenelle, Liniker, Latisha, et. al
Turning on the enzyme:
There are cofactors according to the video. This is small chemicals which are inorganic because they are not made up of carbon. Heme is an example of a cofactor. Coenzymes were also described. These are enzymes that act as a cofactor and help the enzyme to work. When cofactors and coenzymes are present only then the enzyme actually functions. If they are removed the enzyme stops.
Turning off the enzyme:
In trying to stop the substrate from binding, an inhibitor is used. Competitive inhibition was described as where another chemical/compound is used to bond with into the active site. If the bond occurs then the substrate cannot fit and the reaction will be stopped.
Allosteric inhibition is where it changes shape from the substrate. It is described as an inhibitor that bonds to the allosteric site and covers up the active site so that the substrate cannot bind.
Another method of allosteric inhibition is where the inhibitor bonds to the allosteric site and it changes the shape of the active site. There by the substrate will be unable to fit.
The video had information which I find very useful but some descriptions were very confusing. Firstly, there are more than 2 types of inhibition. The process of mixed inhibition and Un-competitive and Non-competitive inhibition was not mentioned. Furthermore, Allosteric enzymes change its conformation to fit the substrate and have more than one site to bind. The inhibition was confusing slightly in the video. This was not described accurately. For enzymes Video, I found it odd that the direct link to the Induce Fit Hypothesis and Lock and Key Hypothesis was not made. There could have been more examples when it came to the cofactors and coenzymes. A proper definition and processes should have been used. The presenter also spoke very fast. This made it hard to truly understand what he was saying. Overall the video was slightly okay in terms of content but lacked information crucial to the topic. References http://waynesword.palomar.edu/images/enzyme5.gif
Primarily, Carbohydrates are called such because it contains essential hydrates of carbon and are composed of water and carbon. Carbohydrates can be given by the equation (CH2O) n.
naming the biomolecule
Carbohydrates have four distinct functions. These are,
1. Used as a storage medium (starch in plants and glycogen in animals)
2. Used as an energy source since it can be broken down easily
3. Used as a Precursor Molecule in the synthesis of certain bio molecules
4. Has a structural function (Cellulose in plants and Chitin in exoskeletons or insects)
These biomolecules are classed as Monosaccharide, Disaccharide, Oligosaccharides and Polysaccharides. Each is structurally different in terms of the amount of simple sugars it contains.
Monosaccharide simple sugars with multiple –OH groups bonded on a number of carbons.
Disaccharide -2 monosaccharide covalently linked.
Oligosaccharides- few monosaccharides linked covalently together.
Polysaccharides – polymers consisting of chains of monosaccharide units.
The bond which is formed between Carbohydrates is called a Glycosidic bond . These biomolecules can be classed into Reducing and Non-reducing sugars. A Reducing sugar is a carbohydrate that serves as a reducing agent due to its free aldehyde or ketone functional groups in its molecular structure. Glucose, fructose, lactose, and maltose are examples of reducing sugars since these have free aldehyde or ketone functional groups in its molecular structure. A Non-reducing sugar is a carbohydrate that is not easily oxidized by a weak oxidizing agents in basic aqueous solution. In basic aqueous solution, non-reducing sugars do not generate compounds containing an aldehyde group. One such example is sucrose, which contains neither a hemiacetal group nor a hemiketal group.
In terms of the video, “TheNewBoston” introduces the topic as carbohydrates and makes an important note that we have learnt before- Carbohydrates are biomolecules. He also states that the Human Body “loves” Carbon, which makes up the back bone of a carbohydrate. He implies that the body actively uses molecules made of carbon. Describing carbohydrate structure, he illustrates using a drawing the ratio to which carbohydrates is made up, which is a 1:2:1 ratio, in terms of Carbon, Hydrogen and Oxygen respectively. In the video, “TheNewBoston” only makes a slight suggestion to where we, humans, obtain carbohydrates. He also describes that we use carbohydrates as a source of energy, also giving the example Glucose and how it used in a brief description.
How are carbohydrates classified?
These biomolecules are classed as Monosaccharide, Disaccharide, Oligosaccharides and Polysaccharides. Each is structurally different in terms of the amount of simple sugars it contains.
Monosaccharide -simple sugars with multiple –OH groups bonded on a number of carbons.
Disaccharide -2 monosaccharide covalently linked.
Oligosaccharide- few monosaccharides linked covalently together.
Polysaccharides – polymers consisting of chains of monosaccharide units.
Carbohydrate Class
Credits to Biochem
students Carlos, Shenelle, Liniker, Latisha, et. al
The bond which is formed between Carbohydrates is called a Glycosidic bond . Note its position on the diagram. In Carbohydrates part 1 we mentioned the importance of Carbohydrates and structure. When carbohydrates bond, its functions change.
Diagram with Glycosidic Bond
References: “Nonreducing Sugar.” OChemPal. science.uvu.edu/ochem/index.php/alphabetical/m-n/nonreducing-sugar/. “Tollen’s Test.” OChemPal. science.uvu.edu/ochem/index.php/alphabetical/s-t/tollens-test/. “What is the principle of the Fehling’s test.” The Q&A wiki. http://wiki.answers.com/Q/What_is_the_principle_of_the_Fehling’s_test. http://images.tutorvista.com/cms/images/38/structure-of-carbohydrates.png http://12angrymen.files.wordpress.com/2008/06/sucrose.jpg?w=510
What are tests for Reducing sugar and Non-reducing sugars?
A Reducing sugar is a carbohydrate that serves as a reducing agent due to its free aldehyde or ketone functional groups in its molecular structure. Glucose, fructose, lactose, and maltose are examples of reducing sugars since these have free aldehyde or ketone functional groups in its molecular structure.
A Non-reducing sugar is a carbohydrate that is not easily oxidized by a weak oxidizing agents in basic aqueous solution. In basic aqueous solution, non-reducing sugars do not generate compounds containing an aldehyde group. One such example is sucrose, which contains neither a hemiacetal group nor a hemiketal group.
Primarily, one can use a series of tests to differentiate carbohydrates. Benedict’s reagent is used to determine the presence of a reducing sugar, i.e. when a mixture contains sugar it will turn from blue to green to orange to red after this test – an indication that the reducing sugar is present. Fehling’s reagent also has the same result. If the mixture stays blue, it is a Disaccharide. One can further perform the Modified Barfoed’s test to indicate if the reducing sugar from the Benedict’s test is either Disaccharide or a Monosaccharide. This can be followed by the Seliwanoff’s test to determine if the sugar is a ketose or an aldose sugar. If the sugar is a ketose sugar, the mixture will turn pink while if the sugar is an aldose sugar, the mixture is colourless. In addition one can determine if the sugar is pentose or not by performing the Bail’s test. A positive test results in the mixture turning green while a negative result results in the mixture remaining yellow.
MORE ON PROTEINS AND AMINO ACIDS!
Amino Acids and Proteins were one of the 3 bio-molecules we studied in class. Amino acids are defined as a simple organic compound containing both a carboxyl (COOH) and an amino (NH2) group. Proteins are defined as any of a class of nitrogenous organic compounds that consist of large molecules composed of one or more long chains of amino acids and are an essential part of all living organisms. Amino acids have the basic structure seen in the diagram where R can be given by different groups (highlighted in red). The central carbon is referred to as the Alpha carbon.
There are 20 essential Amino acids for survival which can be classed as either Essential or Non-Essential Amino Acids.
An Essential amino acid is one that is required by animals that cannot be synthesize by them and must be supplied in the diet. (marked)
Non essential amino acids are those that are synthesized by the body. (unmarked)
Furthermore Essential Amino Acids can be described as either Complete Proteins or Incomplete Proteins. Complete proteins contain all 10 essential amino acids and are derived from animal sources while Incomplete proteins lack one or more of the essential amino acids and most a vegetable based.
How are Amino acids and Proteins classed by structure?
Amino acids bond together to from Proteins. These bonds are called peptide bonds. As a result of bonding Amino acids can be arranged into the following long chain structures;
Peptide- short polymer of amino acids
Di-peptide- contains 2 amino acids joined by a peptide bond.
Tri-peptide- a molecule with 3 amino acids joined by peptide bonds.
Polypeptide- a macro-molecule containing many amino acids.
Protein- a biological molecule of molecular weight 5000g/mol that is made up of polypeptide chains.
How can we identify Amino Acids from Proteins?
We can use to chemical tests to determine which compounds are amino acids or proteins. These are the Ninhydrin Reaction and the Biuret Test.
Ninhydrin reacts with amino acids to from a Purple colour imino derivative. This derivative is a positive test for amino acids which are commonly colourless.
The Biuret test involves using biuret reagent which is light blue in colour. It contain Copper(II) ion in an alkaline solution. Biuret turns purple when mixed with a solution contain proteins. Biuret reagent interacts with peptide bonds of proteins. The purple colour formed is a positive test for proteins.
Credits to Biochem
students Carlos, Shenelle, Liniker, Latisha, et. al
How are Proteins classed in terms of structure?
Proteins are classed by the arrangement and the number of polypeptide chains it contains and the level of folding that occur. Protein folding occurs due to Hydrophobic Interactions, Ionic Bonding, Hydrogen bonding and Disulphide bonding. Protein structure can be either Primary, Secondary, Tertiary or Quaternary.
Primary structure: the linear arrangment of amino acids in a protein and the location of covalent linkages such as disulfide bonds between amino acids. These Disulphide bonds are not denatured.
Secondary structure: areas of folding or coiling within a protein; examples include alpha helices and Beta pleated sheets, which are stabilized by hydrogen bonding.
Tertiary structure: the final three-dimensional structure of a protein, which results from a large number of non-covalent interactions between amino acids.
Quaternary structure: non-covalent interactions that bind multiple polypeptides into a single, larger protein. Hemoglobin has quaternary structure due to association of two alpha globin and two beta globin polyproteins.
Protein Structure
Folding can be denatured in several ways.
Heat and Ultra Violet Radiation-Hydrogen bonds are broken by increased translational and vibration energy
Strong Acids/Bases- salt formation, disruption of hydrogen bonds
Urea- competion for hydrogen bonds
Agitation-shared hydrogen bonds
Some Organic Solvents- change in dielectric constant and hydration of ionic groups.
Proteins are essential to body function and are useful in life processes. An example of an important protein structure is an Enzyme.
“Definition of terms .” USA rice. http://www.usarice.com/index.php?option=com_content&view=article&id=629&Itemid=258. “Essential Amino acid.” wordnet web. wordnetweb.princeton.edu/perl/webwn?s=essential%20amino%20acid. “The Structure of Proteins.” arbl.cvmbs.colostate.edu. http://www.vivo.colostate.edu/hbooks/genetics/biotech/basics/prostruct.html.
Hey guys now i was watching this video on amino acids and proteins and the first thing that i remembered was that amino acids are the subunits of proteins. Remember when we did glucose and we talked about Monosaccharides and stuff well yea its similar to that. Now the professor said that a protein looks like a slinky.
Which i thought was funny but then i remembered the toy and was like “O yea it really does look like that!!!!!!”.
The structure of an Amino Acid
The Amino Acid contains 4 groupings of elements attached to its central carbon atom or alpha carbon (Ca) which can form 4 covalent bonds to itself, they are:
An Amino group- (NH3+)
A Carboxylic acid group- (COO-)
A Hydrogen atom- H
A alkyl or aryl group (R) which can be as simple as just an H atom or something as complex as (CH2CH(CH3)2.
There are 20 different types of Amino Acids based on what is the (R) group so here you can see how many different combinations of amino acid there are to synthesize different proteins.
When these amino acids bond via peptide bonds or otherwise they can form either; Primary Structures, Secondary Structures, Tertiary Structures or Quaternary Structures.
Based on the diagram you can see that a water molecule is removed. In the video the professor called that Dehydration Synthesis which he said enables the two amino acids to snap together. Now i think this term sounds more complex than the term I’m accustom to which is Condensation. When i hear dehydration i think of drying out or the lost of water and the synthesis part which means coming together for me. So in a nut shell Dehydration Synthesis means the coming together of 2 amino acids by the removal of a water molecule. So for the reverse, to break up the polypeptide chain into amino acid units you add water via Hydrolysis.
NB: ALL PROTEINS CONTAIN PEPTIDE BONDS.
These other structures contain different types of bonds and only when they contain these specific bonds that they go to the next level of structure.
Primary Structures: they will have peptide bonds.
Secondary structures: contains peptide bonds,hydrogen bonds, which occurs between the R groups of the amino acids as a result the structure folds.
Tertiary Structures: peptide bonds, hydrogen bonds, the main bondage Hydrophobic interactions which is responsible for the structures 3-D shape, electrostatic forces and sometimes covalent disulphide bonds.
Quaternary Structures: peptide bonds, hydrogen bonds, Hydrophobic Interactions, electrostatic forces and sometimes covalent disulphide bonds. Now the Quaternary Structure is made up of more than one polypeptide chain where it is referred to as a spatial arrangement.
PROTEINS
DIFFERENCE BETWEEN FIBROUS AND GLOBULAR PROTEINS
AMINO ACIDS Amino acids are an organic group consisting of an amine group and a carboxylic group. Amino acids are subunits of protein. Only 20 amino acids are used to make proteins in the body. They are classed as being essential and non-essential amino acids. Essential amino acids cannot be synthesized by the body therefore it must be supplied in the diet. Examples of some essential amino acids are histidine, leucine, lysine, and methionine. Non-essential amino acids are those that can be synthesized by the body and are produced in the body in certain functions. Example of some non-essential amino acids are alanine, asparagine, aspartic acid, glycine, serine and cysteine.
Lysine is an essential amino acid in humans. Lysine is a nutritional requirement in our bodies. Some good sources we can get Lysine from are meat, egg, soy ,cheese and certain fish like sardines.
Also, L-Lysine is a building block for all the proteins in the body. It plays a major role in calcium absorption, building muscle protein and the body’s production of enzymes, hormones and antibodies.
Credits to Biochem
students Carlos, Shenelle, Liniker, Latisha, et. al
