Řӟƒƪӟςϯїδή 4 ώӟӟʞ 6

Hey peeps it’s Neerie here, thinking about how time is flying sooooo fast and I am already in week 6 of my second semester as a year 1 student…yaayy!!! Well…today we started  ЀлӠұϻӟŞ. As you all should know enzymes are biological catalysts. Why is enzymes called biological catalysts? Well…it’s simply because they are large molecules that speed up the chemical reactions inside cells. Each type of enzyme does on specific job. Enzymes are protein in nature which are made from long chains of different amino acids.

Enzymes are soluble protein molecules that can speed up chemical reactions in cells. These reactions include respiration, photosynthesis and making new proteins. For this reason enzymes are sometimes called biological catalysts. Enzymes speed up (catalyse) chemical reactions occurring inside and outside of living cells including:

  • DNA replication
  • Protein synthesis
  • Digestion

Each enzyme will only speed up one reaction as the shape of the enzyme molecule needs to match the shape of the molecule it reacts with (the substrate molecule). The part of the enzyme molecule that matches the substrate is called the active site.

GRAPH SEEN TODAY IN MY LECTURE: (:

figure06-14

A few points to note about this graph:

  • it is an exothermic reaction
  • the reactants for both the catalyzed and uncatalyzed reactions start at the same point
  • the enzyme only lowers the activation energy from Ea (blue) to Ea (pink)

There are three distinctive features of enzymes:

  • catalytic power
  • specificity
  • regulation

There are 6 major classes of enzymes:

Only Think His Love ILiving each day with you and only you in mind :p lol (an easy way to remember the order of classes in exams)

  • Oxidoreductase
  • Transferase
  • Hydrolase
  • Lyase
  • Isomerase
  • Ligase
Oxidoreductase: Oxidoreductases catalyze oxidation reduction reactions.  At least one substrate becomes oxidized and at least one substrate becomes reduced.
Transferase:  Transferases catalyze group transfer reactions- the transfer of a functional group from one molecule to another.
Hydrolase:  In hydrolysis reactions, C-O, C-N, and C-S bonds are cleaved by addition of H2O in the form of OH and H+ to the atoms forming the bond.
Lyase: Lyases cleave C-C, C-O, C-N, and C-S bonds by means other than hydrolysis or oxidation.
Isomerase: Isomerases just rearrange the existing atoms of a molecule, that is, create isomers of the starting material.
Ligase: Ligases synthesize C-C, C-S, C-O, and C-N bonds in reactions coupled to the cleavage of high energy phosphate bonds in ATP or some other nucleotide.

Enzymes and temperature relationship:

At low temperatures enzymic reactions are slow but increases as the temperature rises until an optimum temperature is reached. After this point the reaction will slow down and eventually stop. This is where protein denaturation has taken place.

20_biology

Enzymes and pH relationship:

Most enzymes work fastest in neutral conditions. By making the solution more acidic or alkaline it will slow the reaction down. At extremes of pH the reaction will stop altogether.

21_biology

Enzymes and substrate concentration:

Enzymes will work best if there is a lot of substrate available. As [S] increases so does the enzyme activity. However, the enzyme activity does not increase without end. This is because the enzyme can’t work any faster even though there is plenty of substrate available.

What is Denaturing of enzymes???

The important part of an enzyme is called the active site. This is where specific molecules bind to the enzyme and the reaction occurs.

Anything that changes the shape of the active site stops the enzyme from working. The shape of the active site is affected by pH and temperature.

REFERENCES:

http://www.bbc.co.uk/schools/gcsebitesize/science/add_edexcel/cells/enzymesrev3.shtml

http://faculty.une.edu/com/courses/bionut/distbio/obj-512/Chap8-enzyme%20classes.html

http://sarahssureshots.wikispaces.com/Focus+on+Proteins

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Lets go back in time…

lThe oldest known enzyme reaction is alcoholic fermentation until Louise Pasteur proved otherwise in 1857. Pasteur found that fermentation was caused by yeast cells digesting sugar for their own nourishment. He said that there was something called fermence that was able to convert the sugar to ethanol.

buchnerIn 1897  Eduard Buchner discovered that fermentation actually does not require the presence of living yeast cells. Buchner made an extract of yeast cells by grinding them and filtering off the remaining cell debris. Then he added a preservative ‘sugar’ to the resulting cell-free solution to preserve it for future study. He observed that fermentation, the formation of alcohol from sugar, occurred. Buchner then realized that living cells were not required for carrying out metabolic processes such as fermentation. Instead, there must be some small entities capable of converting sugar to alcohol. These entities were enzymes. After Buchner’s discovery, most scientists assumed that fermentation and other metabolic reactions were caused by enzymes.

sumnerAll attempts to isolate and determine the chemical nature of enzymes were unsuccessful until 1926. An American biochemist James Sumner isolated the enzyme urease from the jackbean after nine years of research. The enzymes pepsin and trypsin were isolated. It was later shown that enzymes are proteins.

References:

http://www.discoveriesinmedicine.com/Enz-Ho/Enzyme.html

ȨƞƉ ŏƒ Ąϻȋñö Ąċȉďs & Ƥřȯƫȇȉñs…

Amino Acids-

Proteins are polymers of amino acids joined by peptide bonds. There are 20 different amino acids that make up all proteins on earth. Each of these amino acids has a fundamental design composed of a central carbon (also called the alpha carbon) bonded to:

  • a hydrogen

  • a carboxyl group

  • an amino group

  • a unique side chain or R-group

The characteristic that distinguishes one amino acid from another is its unique side chain and it is the side chain that dictates an amino acids chemical properties. Examples of three amino acids are shown below: 

amino

Glycine is the smallest amino acid. Except for glycine which has a hydrogen as its R-group there is asymmetry about the alpha carbon in all amino acids. All amino acids except glycine can exist in either of two mirror-image forms called stereoisomers which refer to D and L configurations of amino acids. D is more common than the L configuration.

d-lysine

The unique side chains confer unique chemical properties on amino acids, and dictate how each amino acid interacts with the others in a protein. Amino acids can thus be classified as being hydrophobic versus hydrophilic, and uncharged versus positively-charged versus negatively-charged.

 AminoAcids1

Proteins-

Amino acids are covalently bonded together in chains by peptide bonds. If the chain length is short <20 it is called a peptide. Longer chains are called polypeptides or proteins. Peptide bonds are formed between the carboxyl group of one amino acid and the amino group of the next amino acid. Peptide bond formation occurs in a condensation reaction involving loss of a molecule of water. 

l

 

 

 

Levels of Protein Structure:

Structural features of proteins are usually described at four levels of complexity:

  • Primary structure: the linear arrangment of amino acids in a protein and the location of covalent linkages such as disulfide bonds between amino acids.
  • Secondary structure: areas of folding or coiling within a protein; examples include alpha helices and 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. 

a

 

 The different bonds in a protein structure: 

bonds

Proteins are very important molecules in our cells. They are involved in virtually all cell functions. Each protein within the body has a specific function. Some proteins are involved in structural support, while others are involved in bodily movement, or in defense against germs. Proteins vary in structure as well as function. They are constructed from a set of 20 amino acids and have distinct three-dimensional shapes. Below is a tab;e of several types of proteins and their functions.

The table below are some examples of protein functions:

functions

Why You Need Amino Acids Daily?

Foods with amino acids are the building blocks of protein. That means they are responsible for strength, repair and rebuilding inside your body. Your tissues, your cells, your enzymes and your brain all get their nourishment and protection from amino acids. Amino acids make up 75% of the human body and are vital to every part of human function.

You Can’t Store Amino Acids…The problem with amino acids is that they deteriorate. The body will store extra starch and protein as fat, to use later. Amino acids are not stored, but they can be replaced. There are upwards of twenty different kinds of amino acids that form proteins. Some of these the body makes. The ones it cannot make, called the essential amino acids, it must get from constant consumption of food.

The Best Foods: Meat, eggs, and dairy are sources but it is difficult for strict vegetarians and vegans to get all their essential amino acids. Most vegetarian protein foods, such as beans and seeds, contain only portions of the essentials. An exception to this is soy which contains complete proteins.

 

REFERENCES:

http://ghr.nlm.nih.gov/handbook/howgeneswork/protein

http://alevelnotes.com/Protein-Structure/61

http://www.muscleandstrength.com/articles/the-importance-of-amino-acids.html

http://www.fitday.com/fitness-articles/nutrition/vitamins-minerals/foods-rich-in-amino-acids-for-every-meal.html#b

http://www.vivo.colostate.edu/hbooks/genetics/biotech/basics/prostruct.html

http://biology.about.com/od/molecularbiology/a/aa101904a.htm

garden_vegetables_wit_a_ha      Vegetarians have a difficult time:

This post is based on the topic of amino acids and proteins. I can surely tell you from experience it is difficult for a vegetarian to obtain all their essential amino acids by not supplying meat to their daily diet. As a result there must be a presence of a lot of beans to supply the needed nutrients into the body.

What is an essential amino acid?

An essential amino acid is a building block of protein molecules that our bodies cannot produce and need to get from a food source. They are essential because we can not synthesize them from other amino acids or smaller building blocks. Ultimately they are needed to make proteins which build tissues in our bodies.  They are to be obtained from our daily diet.

There are 10 essential amino acids:

  1. arginine
  2. histidine
  3. isoleucine
  4. leucine
  5. lysine
  6. methionine
  7. phenylalanine
  8. threonine
  9. tryptophan
  10. valine

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The failure to obtain enough of even 1 of the 10 essential amino acids has serious health implications and can result in degradation of the body’s proteins. Muscle and other protein structures may be dismantled to obtain the one amino acid that is needed. Unlike lipid and starch the human body does not store excess amino acids for later use.

References:

http://hyperphysics.phy-astr.gsu.edu/hbase/organic/essam.html

http://www.biology.arizona.edu/biochemistry/problem_sets/aa/aa.html

Video

Bial’s Testing in Carbohydrates:

This is a short video showing the simple test for carbohydrates to determine which sugar is a pentose or hexose.

A pentose reacts with acid and is converted to furfural which condenses with orcinol in the presence of ferric ions to yield a bluish green colour.
A hexose reacts with orcinol to produce a 5-hydroxymethyl furfural which firms a yellow brown colur.
Bial’s test is a qualitative test.

P_sickle_cell1

                                         One of the most important aspects of a protein is its shape. The shape of a protein is critical to its function, and this holds true for hemoglobin. The shape of a protein is largely based on the amino acids it contains and whether or not they are charged, attracted to water or repelled by water. According to the sickle cell center at Harvard University, the amino acid substitution that causes sickle cell disease is a mutation of the sixth amino acid from glutamic acid to valine. This is relevant because glutamic acid is a charged amino acid and, as a result, is very attracted to water, whereas valine is repelled by water. This simple substitution occurs at a spot that is critical for the hemoglobin protein’s shape, causing it to have an unusual structure and to be poor at binding to oxygen. Sickle cell anemia is a disease passed down through families in which red blood cells form an abnormal sickle or crescent shape.

images (2)                          sickle-cell-anemia                  images (1)

Picture sowing the various areas                                                                                                                                 affected by sickle cell anemia

The effects of sickle cell anemia cause pain and damage to the organs. Irregularly shaped red blood cells become sluggish, and move more slowly, causing clumping. Red blood cells are normally round, and carry oxygen rich blood. Oxygen is carried by hemoglobin in red blood cells, but in individuals with sickle cell anemia, abnormal hemoglobin levels cause red blood cells to take on a C shape. Red blood cells that are abnormally shaped, as in sickle cell anemia, die before new ones can be produced.

Sickle cell anemia can destroy the organs of the body. Pain and swelling in the toes, feet and ankles might be one of the first signs of sickle cell anemia. Blocked blood vessels can also cause pain in the hands. Sickle cells can block blood flow to other organs, including the spleen, lungs, brain, eyes and the blood vessels that supply the heart and lungs. Infection and pneumonia are possible.
Eye damage, disability from hemorrhagic or ischemic stroke (from lack of oxygen to the brain), enlargement of the spleen, and pulmonary artery hypertension (increased pressure in the lungs) are possible effects of sickle cell anemia. Leg ulcers can occur from poor blood flow to the skin. Kidney failure can occur. Red blood cell destruction that releases too much bilirubin into the bloodstream can lead to gallstones and gallbladder attacks that cause nausea and abdominal pain.

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A child suffering from sickle cell anemia

               lcdmf

            As the daughter of a victim of sickle cell anemia from Madagascar, I spent my whole childhood with sickle cell disease without knowing its name, but aware of the suffering and the pain it causes. After the disease was diagnosed in my daughter a few years ago when she was two, I decided to dedicate myself to ensuring that families, mothers and patients no longer had to live through the hell of ignorance. So in 2008, we set up the first association to fight against sickle cell disease in Madagascar.

sicklecell-anemia-symptom                                                                                                   shortened finger

Treatment: There isn’t a cure for sickle cell anemia, but symptoms can be well-handled with treatment. Antibiotics are used by infections patients and  Hydroxyurea are used to manage pain and reduce simple crises. In severe cases, blood transfusions or bone marrow transplants may be performed.

References:

http://www.ehow.com/how-does_5185869_amino-cause-sickle-cell-anemia_.html

http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001554/

http://www.leffortcamerounais.com/2011/08/catuc-hosts-first-international-sickle-cell-conference.html

http://www.fondation-sanofi-espoir.com/en/ngo_lcdmf.php

http://www.youtube.com/watch?feature=player_embedded&v=iKQmQHh4E2w

http://www.youtube.com/watch?v=qe59ar-GZmg

http://www.youtube.com/watch?v=skWYKOcptLQ

There are three videos about patients coping with this disease which are informational.

Amino acids & Proteins Quiz

You have 15 minutes to complete 20 questions:

Image

TRUE / FALSE

  1. All proteins have both a primary and secondary structure.
  2. Denaturing proteins disrupts their primary structures only.
  3. Urea is a chaotrope which disrupts the hydrophobic interactions causing the protein to loose its tertiary structure.
  4. A typical amino acid has an amino group, a hydrogen atom and a carbonyl group bonded to a central carbon.
  5. The biuret test is only done to determine the presence of proteins not amino acids in a solution.

MULTIPLE CHOICE QUESTIONS

1. How many different types of amino acids are present?

a. 3

b. 20

c. 100

d. 120

e. none of the above

2. Which of the following forces is the most unfavorable for protein folding?

a. Covalent bonding

b. Vander Waals interactions

c. Conformational entropy

d. Hydrophobic interactions

e. Electrostatic interactions

3. An essential amino acid is one that:

a. readily available in the body

b. the body can synthesize

c. is essentially easy to synthesize

d. the body cannot synthesize

e. none of the above

4. The sequence of letters ‘KNQG’ will represent:

a. alanine, cysteine, proline, glycine

b. lysine, asparagine, glutamine, glycine

c. asparagine, lysine, glycine, glutamine

d. histidine, glycine, asparagine, valine

e. asparagine, glutamine, histidine, glycine,

5. The sulphur containing chain of cysteine is:

a. hydrophobic, highly reactive and capable of reacting with another cysteine

b. hydrophillc, highly reactive and capable of reacting with another cysteine

c. amphiphilic, not reactive with another cysteine

d. amphiphilic, highly reactive and capable of reacting with another cysteine

e. none of the above

6. Which amino acid when exposed to Ninhydrin produces a brown colour?

a.  alanine

b. valine

c. asparagine

d. proline

e. glycine

7. Beta pleated sheets are examples of protein’s:

a. primary structure

b. secondary structure

c. tertiary structure

d. quaternary structure

e. α – helix configuration

8. Sickle cell disease is due to:

a. a mutation in the beta chain of hemoglobin

b. mutation in the secondary structure between Glu and Val residues

c. a mutation in the alpha chain of hemoglobin

d. infection with a parasite

e. none of the above

9. Which one of the following is an essential amino acid?

a. alanine

b. cysteine

c. asparagine

d. glycine

e. valine

10. If an egg white protein of albumin is denatured into a hard boiled egg then which of the following is least affected?

a. the primary structure of ovalbumin

b. the secondary structure of ovalbumin

c. the tertiary structure of ovalbumin

d. the quaternary structure of ovalbumin

e. none of the above

11. Disulphide bonds are formed between:

a. between two cysteine residues

b. between two cystine residues

c. between a alanine and asparagine residue

d. between two glycine residues

e. none of the above

12. Alpha helicies in the secondary structure of proteins are affected by:

a. the interactions between R groups spaced 3 or 4 residues apart

b. the electrostatic repulsion or attraction between successive amino acid residues with charged R groups

c. the bulkiness of adjacent R groups

d. the occurrence of Pro and Gly

e. all of the above

13. The four subunits of hemoglobin represents:

a. primary structure

b. secondary structure

c. tertiary structure

d. quaternary structure

e. none of the above

14. The α-amino acids have a carboxyl group with a pK around __________ , and an amino group with a pK near __________ .

a. 7.0 and 9.0

b. 5.5 and 12.1

c. 2.2 and 9.4

d. 1.0 and 6.3

e. 0.5 and 11.0

15. Refer to the diagram below. Choose the correct answer:Image

a. parallel beta pleated sheet & anti parallel alpha pleated sheet

b. parallel beta pleated sheet & anti parallel beta pleated sheet

c. anti parallel beta pleated sheet & parallel alpha pleated sheet

d. anti parallel beta pleated sheet & parallel beta pleated sheet

e. none of the above

Image

A point to note:

In amylopectin there is glycosidic linkages between the straight chain members at C1 & C4 and on the branched chains at C1 & C5 NOT C1 & C6 although it is said that it has alpha (1-6) linkages.

amylopectin_2

Biochem Lab #1: Carbohydrates, Lipids, Amino acids and Proteins

Today’s lab was FUN! It was really interesting since it involved a variety of tests:

  • Mollisch’s Test- neg test shows the absent of carbohydrates
  • Benedict’s Test – a change from the blue colour  of the benedict’s solution to other colours such as orange, red and brown after heating indicated the concentration of glucose present in the test tube
  • Seliwanoff’s Test – is specific to the presence of ketose sugars
  • Modified Barfoed’s Test – distinguished between monosaccharides and disaccharides
  • Bial’s Test – is a colour reaction specific to pentose sugars
  • Iodine Test – indicates the presence of starch
  • Acid Hydrolysis of Sucrose
  • Sudan lll Test – used for the testing of lipids
  • Emulsion Test – this is also used for testing lipids
  • Biuret Reaction – this is specific  to compounds containing peptide bonds
  • Protein Precipitation
  • Ninhydrin Test

See ‘All about Biochemistry’ to look at some pics 🙂