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

It’s true

Enzyme Wordle

<a href="” title=”Enzyme Wordle”>Enzyme Wordle

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).

GLYCOLYSIS

This week is all about glycolysis…… It is a bit difficult to grasp at first but with a little time and alot of drawing you would get it!!!!!!!

All tissues use the glycolytic pathway for the breakdown of glucose to provide energy. This energy is in the form of ATP.

Glucose to pyruvate takes place in two stages these are:

The first five reactions of glycolysis correspond to an energy investment stage

The other five reactions of glycolysis constituted energy generating stage

Below shows a diagrammatic explanation of the steps in glycolysis it is simple yet effective.

The Fate of Pyruvate

Diagram showing the fate of pyruvate under different conditions:

Aerobic conditions

FATE NUMBER 1:

This is where pyruvate is converted to acetyl CoA. The enzyme pyruvate dehydrogenase (PDH) uses Thiamine prophosphate (TTP) to catalyse the  reaction. It is irrevisible.

NOTE: The most ATP is generated in this fate.

Anaerobic conditions

These two fates can sometimes  be referred to as fermentation.

This process helps regenerate NAD+.

FATE NUMBER 2

Pyruvate is converted to lactate by the enzyme lactate dehydrogenase (LDH).

FATE NUMBER 3

Pyruvate decarboxylase uses TPP to convert pyruvate to acetaldehyde

THEN

Using alcohol dehydrogenase acetaldehyde is convert to ethanol

NADH is converted to NAD+

NOTE: No ATP is generated.

 

 Feeder Pathways for Glycolysis

In glycolysis most carbohydrates except glucose are  transformed into one of the glycolytic intermediates:

1.     The storage polysaccharides glycogen and  starchh

2.   The disaccharides maltose, lactose, trehalose and sucrose

3.    The monosaccharides  fructose, mannose and galactose

Metabolism of Fructose

takes place via two  routes

1. Adipose tissue muscle and kidney

Fructose                    to  (enzyme used is Hexokinase )                                      Fructose 6 phosphate

It can then undergo glycolysis

2.  In the Liver

The enzyme used is glucokinase this does not phoshorylate the frustose. Here fructose is metabolised.

POINTS TO NOTE:

• Glycolysis takes place in the cytosol of  cells.
• There are two phases  in glycolysis  these are: The Energy investment phase & Energy generation phase
• Glycolysis produces 2 pryuvate  molecules.
• ATP is initially  needed.
• ATP is  generated.
• The fate of the pryuvate form differs depending on the conditions.
•  There is a disease called Galactosemia which  is a genetic disease caused by the inability of the body  to convert galactose to glucose.

REFERENCES

https://www.google.tt/search?q=fates+of+pyruvate&espv=210&es_sm=93&tbm=isch&imgil=x7vITESRmLrS3M%253A%253Bhttps%253A%252F%252Fencrypted-tbn0.gstatic.com%252Fimages%253Fq%253Dtbn%253AANd9GcQBnmmjP4QoGkFv9-hWtcF2lSsuSCaPIqiIG8owpGMHuzxDeq582g%253B640%253B372%253Bol0s-ZnMxbjT0

https://www.google.tt/search?q=glycolysis&espv=210&es_sm=93&source=lnms&tbm=isch&sa=X&ei=ybUfU6TFF8udkQe6-4HQAQ&ved=0CAkQ_AUoAQ&biw=1092&bih=507#facrc=_&imgdii=_&imgrc=Ef2-LosnGEc9sM%253A%3BkmJmFJLj3xG4hM%3Bhttp%253A%252F%252Fwww.accessexcellence.org%252FRC%252FVL%252FGG%252Fecb%252Fecb_images%252F13_01Glycolysis-Steps_6-10.jpg%3Bhttp%253A%252F%252Fwww.accessexcellence.org%252FAB%252FGG

Enzymes

From enzymes part 1 we learnt what are enzymes as well as some key facts relating to enzymes such as how they are useful as well as their different classes. In this section we would examine the lock and key hypothesis as well as the induce fit and how the substrate binds to the enzymes.

Substrates are the substances which react with enzymes. Specific enzymes react best at its optimum environment conditions. Certain enzymes react in high ph conditions and other in low ph conditions. Temperature is key as well as a very high temperature denatures enzymes preventing any reactions. Enzymes react with a specific substrate and hence the lock and key hypothesis. This site where they substrate bind to the enzyme is called the active site. Each cleft on the enzymes recognises a specific substrate which it reacts to. After joining together, the enzyme and the substrate is referred to as the enzyme-substrate complex.

There are many different hypotheses that were developed to illustrate the way substrates react with the enzymes. The two main hypotheses are the Fisher’s Lock and Key hypothesis and the Kushland’s induced fit hypothesis.

The Fisher’s Lock and Key Hypothesis.

This as the name implies suggest that a specific substrate acts as a key and the enzymes are various locks. Each lock requires a specific key as to with the substrate and the enzyme. The substrate acts as a key and the enzymes is the lock. When the substrate binds at the active site of the enzyme (lock) and it is complimentary with it will cause a reaction to take place between the substrate and the enzyme. When this occurs the product is form and is now of a different shape from the enzyme’s active site. However the lock and key hypothesis suggested the enzyme was too rigid which isn’t so and this gave way to the kushland’s induced fit hypothesis. Figure one shows the lock and key hypothesis.

The Induced Fit Hypothesis.

Unlike the lock and key hypothesis the induced fit states that the substrate doesn’t completely match with the active site on the enzymes. However as the substrate nears or even touches the enzyme it somewhat conforms to match the shape of the substrate allowing it to react and give a product. Figure 2 shows the induced fit hypothesis.

Rate of Reaction Factors

There are many factors that affect the rate of reaction. Enzyme and substrate concentration as well as temperature and ph level all play a part in rate of reactions. As substrate and enzyme concentration increases so too does the rate of reaction as there are more substrate and active sites to react resulting in a faster reaction rate. Increase in temperature increases the rate of reaction as it speeds up the collision frequency between the substrate and the active site. In humans that max temperature is 37 degrees. However there are other types of enzymes that can withstand even higher temperatures than enzymes in humans. Denaturing is the unfolding or opening of the enzymes as a result of extremely high temperatures. The optimum ph values for enzymes vary depending on the enzymes. Pepsin for example requires a ph value of 2. Trypsin unlike pepsin cannot function at ph value 2 and requires a high ph value to function.

Carbohydrates Crossword

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