Chemistry of Life!

300px-CHONPS.svg.png - Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur

Oxygen.jpg

There are FOUR chemical elements in living things that show up over and over. THEY ARE AS FOLLOWING:

  1. Carbon
  2. Hydrogen
  3. Oxygen
  4. Nitrogen

Carbon, Hydrogen, Oxyen, and Nitrogen are reoccuring chemical elements. However, there are other elements that are also needed by living organisms. THEY ARE AS FOLLOWING:
  1. sulfur
  2. calcium
  3. phosphorus
  4. iron
  5. sodium


Sulfur- It is an essential element for life. It is also found in two amino acids, cysteine and methinoine.sulfur1.jpg



Calcium- The purpose or function for calcium is to produce strong bones, muscle tissue, nerve function, and teeth. It regulates heart beats, and blood clotting
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Phosphorus- It is needed for healthy bones, and teeth. It is also needed in energy metabolism. *You can find phosphorus in milk, grains, lean meats, and food additives.*
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Iron- It's needed by the body in order to make hemoglobin rich blood, which then transports oxygen to the cells. During pregnancy, Iron is also essential for proper placental growth.
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Sodium- It helps to regulate the amount of water in your body's cells. Too much or too little of it can cause health problems. Sodium also regulates blood pressure.

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http://www.youtube.com/watch?v=7CQcRa1HiKI&feature=related


3.1.4 -- Draw and label a diagram showing the structure of water molecules to show their polarity and hydrogen bond formation.
external image water_molecule_full_size_landscape.jpghttp://www.sciencelearn.org
This is a water molecule. The "H" represents a hydrogen atom and the "O" represents an oxygen atom. As shown in the diagram, water molecules are polar molecules because of their positive and negative charges at opposite ends. The hydrogen atoms are positively charged and the oxygen atom has a slight negative charge. Because of the polarity of water and its ability to form hydrogen bonds, it has many unique properties. Hydrogen bonds are formed when a charged end of the water molecule attaches to another atom with the opposite charge. An example of this is many water molecules attaching to each other. The positively charged hydrogen end of one molecule will form a weak bond with the negatively charged oxygen end of another water molecule.

3.1.5 -- Outline the thermal, cohesive and solvent properties of water.

Thermal Properties:
a) High Specific Heat- The amount of heat or the number of calories required to raise the temperature of one gram of that substance by one degree Celsius. This means that it can absorb or lose a large amount of heat without having a drastic change in temperature. Waters high heat capacity allows it to stabilize the inner temperature of organisms.
b) Heat of Vaporivation- The heat of vaporization is the amount of heat necessary to vaporize or evaporate one gram of liquid water. Water evaporates at a decent rate to assist in the cooling of organisms. Waters heat of vaporization property allows it to transfer heat well.

Cohesive Properties:
a) Cohesion- The property that allows water to attract to other water molecules.
b) Adhesion- Adhesion is waters ability to attract to other molecules other than water. Waters polarity allows it to be both cohesive and adhesive because the charged poles will attract to oppositely charged atoms.
c) Surface Tension- Surface tension is another cohesive propery of water. It is the cohesion of water molecules near the surface of a body of water. This property allows things to rest on top of the water without breaking through the surface.
d) Capillary Action- Capillary action uses waters property of adhesion to cling to the sides of thin tubes and therefore, climb them. The molecules adhere to the oppositely charged di-poles of the substance that it is climbing. This property makes water accesible to the top of plants.

Solvent Properties:
a) Good Solvent- This property is due to waters polarity. Water molecules are relatively small so they can easily surround other molecules. The positive di-poles attract to the negative end of the solute and vice versa.

3.1.6 -- Explain the relationship between the properties of water and its uses in living organisms as a coolant, medium for metabolic reactions, and transport medium.

Waters heat of vaporization allows it to act as a coolant for living organisms. Its ability to carry heat and evaporate help to cool organisms. The organisms excrets sweat that is holding heat, and that sweat evaporates taking the heat energy away with it. Waters ability to readily dissolve other substances makes it a good medium for metabolic reactions. Water can easily break down other molecules. Water is also very stable and non-reactive. Water is an excellent transport medium because it has a strong ability to adhere to other substances. Also, waters cohesion trait allows it to bond to itself in order to carry substances with its flow. An example is blood, which is mainly water based, and easily transports necessary nutrients around the body.

3.2.1 - Organic compounds generally contain Carbon and are found in living things. An inorganic compound is a compound of non-biological origins; this doesn't neccersarily mean that they were made in a lab; inorganic compounds such as minerals can be found in nature. Some generalizations about inorganic and organic compounds are: inorganic compounds can form salts and organic compounds can't, organic compounds have Carbon-Hydrogen bonds and inorganic compounds don't, and inorganic compounds contain metals when organic compounds don't. These, however, are just generalizations and are not always true.

3.2.2 -

Solvent Properties:
a) Good Solvent- This property is due to waters polarity. Water molecules are relatively small so they can easily surround other molecules. The positive di-poles attract to the negative end of the solute and vice versa.


Glucose Structure
external image glucose.gif
Ribose Structure
external image Ribose_structure_2.png
Fatty Acid Structure


3.2.3 - Examples of Monosaccharides - Glucose, Galactose, Fructose
- Examples of Disaccharides - Maltose, Lactose, Sucrose
h- Examples of Polysaccharides - Cellulose, Glycogen, Starch

3.2.4 - Glucose - Provides energy for animals.
Lactose - Also an energy provider for aninmals.
Glycogen - Short term energy storage in animals

Fructose - Quick energy source in plants.
Sucrose - Is used for energy storage in plants.
Cellulose - Used to make cell walls in plants.



The
Chemistry of Life: Focus on Protein


7.5.1 -- Explain the four levels of protein structure, indicating the significance of each level.

Primary Structure: The primary structure of a protein is its unique amino acid sequence. In other words, the primary structure is the pattern that the amino acids create when bonding together to form a protein. The primary structure is very important because there are thousands of different ways to arrange amino acids in a polypeptide chains. This arrangment designates the specific function and use of the protein. Lastly, the precise primary structure is determined by inhereted genetic information.

Secondary Structure: This structure refers to the coils and folds that contribute to the proteins overall conformation. These coils and folds are the result of hydrogen bonds between the polypeptide backbone. The positively charged hydrogen atom attached to the nitrogen atom has a weak attraction towards the oxygen atom of a nearby peptide bond. One type of secondary structure is the alpha helix. The alpha helix is a coil held together by hydrogen bonds between every fourth amino acid. The other type is the beta pleated sheet. This type of secondary structure includes two polypeptide chains that lay parallel to one another in terms of their backbones. Hydrogen bonding connects parts of these two parallel backbones.

Tertiary Structure: In the third structure of proteins, the secondary structures are manipulated to get the overall shape of the polypeptide chains. This occurs because of interactions between the "R" groups of the various amino acids. For example, one of these interactions is called a hydrophobic interaction where the hydrophobic side chains cluster in the center of the protein. Another one of these interactions are called disulphide bridges. Disulphide bridges are covalent bonds between the sulpher atoms of two cysteine monomers. All of these interactions when completed fold and bend the protein to form its tertiary structure.

Quaternary Structure: The overall protein structure resulting from the aggregation of many polypeptide subunits. This is the final shape of the protein macromolecule. The two main types of quaternary structure are globular and fibrous.

7.5.2 -- Outline the difference between fibrous and globular proteins, with reference to two examples of each type of protein.

Fibrous Proteins: Polypeptide chains that run parallel to each other in the quaternary structure. These weaving chains are linked by disulphide chains and cross bridges which give the protein its strength. Fibrous proteins usually have structural functions. Two examples are collagen which is a type of connective tissue and keratin which is the protein in hair.

external image CE256000FG0010.gif

Globular Proteins: Become globular in the tertiary or quaternary structure. They are usually soluble because the hydrophobic side chains usually reside in the center of the sphereical shape. Their solubility means that they have a large role in metabolic reactions. An example is hemoglobin which has four polypeptide chain subunits would together in a globular shape. Another example is the transthyretin protein which also folds in a globular manner.

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7.5.4 – State four functions of proteins, giving a named example of each.
1) Framework for connective tissue- Collagen.
2) Transport of other substance- Hemoglobin.
3) Support- Silk and Keratin.
4) Storage of amino acids- Ovalbumin and Casein.

7.6.1- metabolic pathways consist of chains and cycles of enzyme catalyst reactions. Enzymes are catalysts that speed up biological reactions, which means less energy is being used, without being consumed in the process. The reactions are connected by their reactants/substrates the enzyme attaches itself to the substrate and speeds up the process by either binding or breaking apart bonds.

Example
:

external image Metabolism_790px_partly_labeled.png

7.6.2 - The induced fit model is when the enzyme changes its shape to bind to the substrate. This is good because it allows reactions to occur with limited specificity. The bad side is that a virus or bacteria may disguise itself as a substrate and bind to the enzyme(s) and eventually attack the immune system.

Example:


File:Induced fit diagram.svg
File:Induced fit diagram.svg




Click on the following link to see how enzymes work:


http://www.youtube.com/watch?v=VXNsr6Rc6ok


7.6.3 - Enzymes lower the activation energy of the chemical reactions the catalyse. The activation energy is the amount of energy a reaction must overome in order to work. Enzymes are catalyst, which means that they speed up a procees which means less energy is needed( they assist/ help out the reactors). So on regular reaction with no enzyme the activation energy is higher but reactions that use enzymes require less energy so the activation energy is lower but the outcome is still the same.


Example:



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7.6.4 - Enzyme inhibitors, selectively ihnibits activity of certain enzymes. It can have a permanent effect on the enzyme and the way they work. The inhibition may be reversed. There are two types inhibitors; competitive and non- competitive.
Competitive Inhibitors:
They take the place of a substrate at the active site of enzymes and substrates. Hence they block the actual substrate from binding with the enzyme. This form of inhibition is able to be reversed by taking an enzyme supplement/ increasing the concentration of substrates.

Example:


external image Competitive_inhibition.png
Non-competitive Inhibitors:
Impete enzymatic reactions by binding on a part of the enzyme. This causes the enzyme to change its shape. It is also like a leech which allows the reaction to go on bt in a much slower pace that is if the enzyme was not dentatured in the process. This process is irreversible.

Example:


external image 400px-Comp_inhib3.png