Focus on Proteins

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3.2.5-- Outline the role of condensation and hydrolysis in the relationships between monosaccharides, disaccharides, and polysaccarides ; between fatty acids, glycerol, and triglycerides; and between amino acids and poly peptides.

Condensation- Is the chemical process in which two molecules join to form an even larger and more complex molecule, that also results in the loss of water.
Carbohydrates- A monosaccharide is a member of the -OH group which will result in a disaccharide when it combines with another -OH group and when water is removed. The dissaccaride will have an oxygen bridge between the two monosaccarides. On one monosaccaride the bond will be on carbon1 while the other monosaccaride the bond would be on carbon 4 or carbon 6. These bonds are glysidic bonds which can be extended many times resulting in a polysaccaride.
Proteins- The sub units are amino acids. The -H comes from the amino group while the -Oh comes from the carboxyl acid group. When two amino acids join a peptide bond is formed which results in a dipeptide. This can also be extended several times which will then result in a polypeptide.
Lipids- Glycerol has up to 3 fatty acid chains which can react to fatty acids which will result in an ester bond.When glycerol binds with a fatty acid chain it is called a monoglyceride. When glycerol binds with three fatty acid chains it will result in a triglyceride.

Hydrolysis- Is pretty much the opposite of condensation. A large molecule will result in smaller molecules by breaking a bond adding -H to one part and -OH to the other, this results in simple molecules. What hydrolysis pretty much is, is the addition of water to a molecule. Hydrolysis is like condensation but in reverse.

3.3 DNA Structure

3.3.1 Nucleic acids are macromolecules that exist as polymers called polynucleotides. As indicated by the name, each polynucleotide consists of monomers called nucleotides. A nucleotide itself is composed of three parts: a nitrogenous base, a pentose (a five-carbon sugar), and a phosphate group. The portion of this unit without the phosphate group is called a nucleoside.

3.3.2 There are two families of nitrogenous bases: pyrimidines and purines. A pyrimidine has a six-membered ring of carbon and nitrogen atoms. The members of the pyrimidine family are cytosine, thymine, and uracil. Purines are larger, with a six-membered ring fused to a five-membered ring. The purines are adenine and guanine. Thymine is found in only DNA and uracil only in RNA.

3.3.3 Adjacent nucleotides are joined together by covalent bonds called phosphodiester linkages between the –OH group on the ‘3 carbon of one nucleotide and the phosphate on the ‘5 carbon of the next. This bonding results in a backbone with a repeating pattern of sugar-phosphate units.
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3.3.4 Cellular DNA have two polynucleotides that spiral around an imaginary axis, forming a double helix. The sugar-phosphate backbones are on the outside of the helix, and the nitrogenous bases are paired on the interior of the helix. The two polynucleotides, or strands, as they are called are held together by hydrogen bonds between the paired bases and by van der Waals interactions between the stacked bases. Most DNS molecules are very long, with thousands or even millions of base pairs connecting the two chains.

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7.5 Proteins

Primary Structure- Refers to the amino acid sequence of the peptide chain coding the function and use of the protein.
Secondary Structure- Is the overall shape of the protein. examples of this would be an alpha-helix coil, or a beta pleated sheet.
Tertiary Structure- Is the 3D physical structure of any single polypeptide chain, so it indicates the physical formation of the secondary structure. The two kinds of tertiary structures are globular and fibrous.

Quaternary structure- Describes when several proteins are bonded together to form are large molecule like Hemoglobin which supplies oxygen in the bloodstream.

The two kinds of tertiary structures globular and fibrous and different in nature. globular proteins are usually enzymes of other similar proteins involved in either the condensation or hydrolysis of substrates. The are circular and with a hydrophobic center which is commonly known as the active site. Two examples of globular proteins are hemoglobin (or red blood cells) which as a transport medium to distribute oxygen throughout the body, and lactase the enzyme needed to break down the sugar lactose into galactose and glucose which is found in dairy products. Fibrous proteins on the other hand are long groups of parallel polypeptide chains commonly held together by disulfide bonds. Fibrous proteins are strong and make up most visible tissues in the body such as bones, skin, and keratin found in hair and nails.

Transport medium- Hemoglobin or red blood cells act as a transport medium to distribute oxygen throughout the body.
Breakdown of Polymers- Cellulase and enzyme which breaks down the sugar cellulose providing energy for the body and aiding in digestion.
Provides Structure- Collagen is a protein that makes up the framework of most connective tissues throughout the body such as ligaments and tendons.
Provide Shelter- Silk a protein found mostly in insects and arachnids is used to build cocoons and webs in which the organism can live.
7.6 Enzymes

7.6.1-- State that metabolic pathways consist of chains and cycles of enzyme catalysed reactions.

Metabolic pathways are a series of chemical reactions occuring within a cell to fufill a metabolic function of the body, these pathways consist of chains and cycles of enzyme catalyzed reactions. In a metabolic pathway, one enzyme takes the product of another enzyme as a substrate. After the catalytic reaction, the product is then passed on to another enzyme and the cycle continues on. One example of such a pathway wuld be glycolysis.

7.6.2-- Describe the induced-fit model.

The induced-fit model is a modification on the lock and key model. The induced-fit model states that the active site of an enzyme does not fit perfectly to the substrate, as a lock and key would, but instead isn't the most precise so when the substrate binds with the enzyme, the enzyme will change it's shape to fit the substrate. An example of this is the way a glove changes it's shape slightly to fit a hand, at first the glove (the enzyme) is roughly the right shape of the hand (the substrate) that combines with it, but when the hand is put into the glove, the glove will change slightly to fit the hand perfectly. Also the binding of the substrate to the enzyme's active site can weaken the bonds within the substrate and cause the reaction to happen more readily.


7.6.3-- Explain that enzymes lower the activation energy of the chemical reactions they catalyze.

Every chemical reaction involves both bond breaking and bond forming. The bonds of the reactants of a reaction only break when they have absorbed enough energy, usually measured in heat, to be activated enough to become more reactive and get to the transition state. This activation energy provides a barrier that determines the rate of the reaction, the reactant must absorb enough energy so that the reaction can occur, if the activation energy is high then it will take longer for the reactants to have the energy that they need for the reactions to occur. What an enzyme does is find an alternative pathway for the reaction to occur, this alternative path way will have a lower activation energy than the original reaction would, resulting in a faster rate of reaction.

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7.6.4-- Explain the difference between competitive and non-competitive inhibition, with reference to one example of each.
The difference between the two is that competitive inhibition is when the inhibitor is structurally similiar to the substrate and binds to the active site of the enzyme thus preventing catalytic activity from occurring.

While in non-competitive inhibition the inhibitor interacts in some other site other than the active site which can contort the active sites shape so the substrate is not allowed to bind properly if at all. This can result in lower catalytic activity or none at all while competitive inhibition results in no activity at all.