The four levels of protein structure are primary, secondary,tertiary and quaternary structure. Each of these levels is basically a different stage in the formation of a complete protein. The primary structure is the unique sequence of amino acids that make up the protein itself. This is the basis for the protein, and the first stage in its development. The secondary structure is the folding of the polypeptide chains as a result of the hydrogen bonds forming between the nucleotides. This folding either occurs as a pleated sheet, or beta structure, or a helix, alpha structure. The tertiary structure is the point when the overall shape of the protein begins to emerge. The side chains interact with each other, and they begin to fold into shapes. This is a result of hydrophobic interaction, which causes the hydrophobic sides of the polypeptide chain to fold towards the middle. This helps them to avoid contact with water, and results in a specific type of folding. This folding eventually shapes the chains into the shape of a protein. The final structure, the quaternary structure, is the overall protein structure that is a result of the combining of the polypeptide subunits that are the tertiary structure. This combination make the structure into its final stage and its final structure.

Fibrous and globular proteins are the two structures and forms that you will find in the world. Fibrous proteins are more for structural function, whereas the globular structure is more for metabolic reactions and things that take place inside the body. A prime example of the fibrous proteins would be skin, as it is a completely structural function. It protects the body from contaminants and serves as a protective barrier. Globular proteins, such as hemoglobin are usually not seen and function inside the body. An example of this would be hemoglobin, which brings oxygen through the blood to the cells of the body.

Proteins have many functions in the body, one of which is hemoglobin. Hemoglobin is a globular transport protein that transports oxygen through the body to the cells. This is essential to life, because the body would not function without oxygen in the cells. Another important structural protein is the fibrous protein keratin, which is skin. This is of major structural importance as it serves as a protective barrier, keeping contaminants out of the body. Keratin is also in hair, which keeps many organisms warm in the natural world. Proteins also are used in defense of the body, as antibodies are proteins. Antibodies attack germs and keep the body safe from diseases. Proteins also are used for cell signaling, as specific proteins on the brain cells of humans bind to endorphins which produces euphoria and relieves pain. This is how opiate drugs work, as they mimic endorphins, mimicking their effects.



Metabolic Pathways consist of chains and cycles of enzyme catalyzed reactions. The map below shows the products of Metabolic pathways. The "Pathways" themselves are actually series of reactions that take place to fulfill a metabolic function of the body, for example Glycolysis, the map under the larger one shows the metabolic pathway of Glycolysis.
external image Metabolism_790px_partly_labeled.png

external image glycolysis.gif
The Induced Fit model: this is a model of how an enzyme breaks apart or puts together substrates. The Induced-Fit model is more modern, realistic, and accurate way of showing enzyme reactions. This is because the model shows the enzymes active site( the area in which the substrate is acted upon) slightly conforming to the shape of the substrate so that it can fit.

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

Enzymes speed up reactions. They do this by finding a "short cut", which is decreasing the activation energy. Enzymes lower activation energy by temporarily fusing with the substrate and reacting with its chemicals to produ​ce the products. The majority of enzymes are specified to only one unique substrate, therefore releasing the same products over and over. The activation energy is the amount of energy needed for a reaction to occur.
Ea - Activation Energy, G - Energy
Ea - Activation Energy, G - Energy
Competitive and non-Competitive Inhibition are ways in which a substance, other than the specified substrate, attach to the enzyme. Competitive Inhibition is when a substance masks or replicates the original substrate to bind to the enzyme. Competitive Inhibition is based also based on concentration. If the concentration of the inhibitor is higher than the concentration of the substrate then the inhibitor will hold more enzymes and less substrates will be catalyzed, and vice versa.

Example of Competitive Inhibition: The picture below shows two substances, Sulfanilamide and para-aminobenzoic acid (PABA). PABA is the normal substrate and Sulfanilamide, an antibiotic, can competitively inhibit the enzymeImage15.gif
non-Competitive Inhibiton is when a substance other than the enzymes specified substrate, obstructs the enzymatic reaction by binding onto a part of the enzyme. This causes the enzyme to change its shape. This can slow down reactions and/or denature the enzyme. Example: Sarin nerve gas is a non-Competitive Inhibitor which paralyzes the enzyme Acetylcholinesterase. This enzyme controls basically the whole nervous system, and being paralyzed means the body is paralyzed

3.2.5 Outline the role of condensation and hydrolysis in the relationships between monosaccharides, disaccharides and polysaccharides; between fatty acids, glycerol and triglycerides; and between amino acids and polypeptides

condensation reaction- the loss of a water molecule causes a covalent bond between 2 molecules. Another name for this is a dehydration reaction, and the opposite is called hydrolysis.

Monosaccharides can bond together through a condensation reaction to form disaccharides, the bond being called a glychosidic linkage. Hydrolysis can also occur between monosaccharides; when a water molecule is added to a disaccharide, the glychosidic linkage breaks and the disaccharide breaks apart into the original monosaccharides. An example, of fructose and glucose binding through a condensation reaction to form sucrose, is shown below.
external image tmp.bmp
This can also happen with polysaccharides. When a polysaccharide is hydrolyzed, it is often for the purpose of providing sugar for the cells.

A fat molecule, aka triacylglycerol or triglyceride, is made up of a glycerol and 3 fatty acids. The fatty acids and the glycerol are bonded through a condensation reaction. This is shown below.
external image glycerol,%20fatty%20acids,%20triglyceride.gif
The circled atoms form H2O and are removed, bonding the glycerol and fatty acids.

Amino acids also bond together through a condensation reaction. The reaction occurs between the carboxyl group of one amino acid and the amino group of another, and only happens when these groups are adjacent to each other. The bond is called a peptide bond when it is between 2 amino acids, and when it is repeated many times it forms a polypeptide with a free carboxyl group at 1 end and a free amino group at the other. A protein is made up of a folded polypeptide.

c 3.3.1 -- Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate.
DNA is made up of nucleic acids (aka polynucleotides), which are made up of mucleotides. Nucleotides are made up of a phosphate group, covalently bonded to a sugar, covalently bonded to a nitrogenous base.

The base is alwways either a pyrimidine or a purine. Pyrimidines have a hexagon shape and are made up of nitrogen and carbon atoms. Mambers of the pyrimidine family are ​cytosine, thymine (found only in DNA), and uracil (found only in RNA). The larger purine family have a hexagon shaped ring attached to a pentagon shaped ring. The members of the purine family are adenine and guanine.

The sugar is deoxyribose in DNa and ribose in RNA. Deoxyribose does not have an oxygen on the second carbon in the sugar ring, while ribose does. This is the only difference. The atoms on the sugar ring are numbered with a (# ') format. 5' is the carbon that sticks up from the ring, in the molecule that is bonded to the phosphate group. In the diagram below, it is the carbon in the CH2 molecule and the 1' carbon is the one furthest to the right.

A nucleotide looks like this:
external image nucleotide.jpg

c 3.3.2 -- State the names of the four bases in DNA.
Thymine, adenine, guanine, and cytosine are the 4 bases in DNA. Thymine bonds with adenine through hydrogen bonding, and guanine bonds with cytosine through hydrogen bonding.

DNA nucleotides are linked together by covalent bonds into a single strand because the phosphate group of one nucleotide links to the sugar of another nucleotide by covalent bonds.

A DNA double helix is formed between the bases of two strands of DNA. Its formed by using complementary base pairing and hydrogen bonding because there are four bases in DNA, thymine, adenine, guanine, and cytosine. Those four bases only pair off and form hydrogens bonds with one other specific base. Thymine and adenine form a hydrogen bond when they pair off together and cytosine and guanine also form a hydrogen bond when the pair off together.

external image DNA.jpg