Allyson Martinez Period 3 Benchmark SC.912.L.18.1 Allyson Martinez Period 3

Molecular structures Carbohydrate Lipids Proteins Nucleic acid

Carbohydrates A carbohydrate is a compound that is composed of atoms of hydrogen, carbon, and oxygen in a ratio of 1 carbon atom, 2 hydrogen atoms, and 1 oxygen atom. Some carbohydrates are small molecules, the most important to us is glucose which has 6 carbon atoms. These simple sugars are called monosaccharide, which is any class of sugars that cannot be hydrolyzed to give a simpler sugar.

Lipids Lipids may be divided into eight categories: fatty acids, glycerol lipids, glycerophospho lipids, sphingo lipids, saccharolipids, and polyketides sterol lipids, and phenol lipids. Although the term lipid is sometimes used as a synonym for fats, fats are a subgroup of lipids called trilycerides. Lipids also encompass molecules such as fatty acids and their derivatives, as well as other sterol-containing metabolites such as cholesterol . Although humans and other mammals use various biosynthetic pathways to both break down and synthesize lipids, some essential lipids cannot be made this way and must be obtained from the diet. There are 2 classes of lipids Simple containing C, H and O and compound contains C, H, O, fatty acids and glycerol. It is a macromolecule, which is a molecule containing a very large number of atoms.

Proteins Each protein is a polymer; specifically a polypeptide, that is a sequence formed from various amino acids. By convention, a chain under 40 residues is often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations, driven by a number of non-covalent interactions such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. Protein structures range in size from tens to several thousand residues. Proteins are classified by their physical size as nano-particles. Very large aggregates can be formed from protein subunits: for example, thousands of actin molecules assemble into a microfilament. A protein may undergo reversible structural changes in performing its biological function. The alternative structures of the same protein are referred to as different conformations, and transitions between them are called conformational changes.

Nucleic acids The base components of nucleic acids are heterocyclic compounds with the rings containing nitrogen and carbon. Adenine and guanine are purines, which contain a pair of fused rings; cytosine, thymine, and uracil are pyrimidines, which contain a single ring. The acidic character of nucleotides is due to the presence of phosphate, which dissociates at the ph found inside cells, freeing hydrogen ions and leaving the phosphate negatively charged. Because these charges attract proteins, most nucleic acids in cells are associated with proteins. In nucleotides, the carbon atom of the sugar (ribose or deoxyribose) is attached to the nitrogen at position 9 of a purine (N9) or at position 1 of a pyrimidine (N1).

Primary functions Carbohydrates: The primary function of carbohydrates is for short-term energy storage. A secondary function is intermediate-term energy storage, as in starch for plants and glycogen for animals. Other carbohydrates are involved as structural components in cells, such as cellulose which is found in the cell walls of plants. Lipids: One function for Lipids is that of Energy storage. Lipids contain a lot of calories in a small space. Since Lipids are generally insoluble in polar substances such as water, they are stored in special ways in your body's cells. Lipids can also function as structural components in the cell. Phospholipids are the major building blocks of cell membranes. Lipids are also used as hormones that play roles in regulating our Physiology (metabolism). Most lipids are composed of some sort of fatty acid arrangement. The fatty acids are composed of methylene (or Methyl) groups, and are not water soluble. Proteins: Proteins are very important molecules in our cells. They are involved in 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 twenty amino acids and have distinct three-dimensional shapes. Nucleic acids: Nucleic acids allow organisms to transfer genetic information from one generation to the next. There are two types of nucleic acids: deoxyribonucleic acid, better known as DNA and ribonucleic acid, better known as RNA.

How do enzymes speed up the rate of a biogeochemical reaction by lowering the reaction’s activation? Enzymes work by lowering the activation energy of a biochemical reaction thus enabling the reaction to occur at a greater rate than it could under the temperature, pressure and environment of a biological environment. This extra energy for the reaction to occur is called the activation energy. It has nothing to do with the initial and final energy states. Activation energies can be extremely high and is why many ordinary chemical reactions need a source of heat.  You can't heat a biochemical reaction of course so enzymes lower this activation energy. The way they do this is complex and there are different types of mechanisms. In many case the substrate and enzymes for enzyme - substrate complexes through binding at the active site of the enzyme. Then enzyme - product complexes are formed before the product is released. The enzyme is not consumed during these reactions and that is one of the properties of a catalyst. These complexes bring substrates into very close proximity

How concentration affects enzyme activity? As the enzyme concentration increases the rate of enzyme activity increases up to a level where it becomes constant.  This happens because the more the enzymes are available, the more substrates are broken in less time.  It then becomes constant as the substrate acts as a limiting factor, which means that there aren’t enough substrates to be broken down compared to the number of enzymes.

How does PH affect enzyme activity? Changes in ph may not only affect the shape of an enzyme but it may also change the charge properties of the substrate so that either the substrate can’t bind to the active site or it cannot undergo catalysis. Extremes in pH can denature enzymes. In general an enzyme has a ph optimum. However the optimum is not the same for each enzyme. A change in ph disrupts an enzyme's shape and structure. Ph measure acidity, water is neutral and has a ph of 7. When the ph changes an enzyme's structure, the enzyme can't do its job. Changes in ph break the delicate bonds that maintain an enzyme's shape. An enzyme will unravel, or denature, and become useless in a different ph.

How does temperature affect enzyme activity? Drastic changes from optimal temperature agitate the bonds that create an enzyme and that bind it to the substrate. It denatures the secondary and tertiary structure of enzymes However, increasing temperature also increases the vibration energy that molecules have, specifically in this case enzyme molecules, which puts strain on the bonds that hold them together. As temperature increases, more bonds, especially the weaker hydrogen and Ionic bonds, will break as a result of this strain. Breaking bonds within the enzyme will cause the Active Site to change shape. This change in shape means that the Active Site is less Complementary to the shape of the Substrate, so that it is less likely to catalyze the reaction. Eventually, the enzyme will become Denatured and will no longer function. As temperature increases, more enzymes molecules' Active Sites' shapes will be less Complementary to the shape of their Substrate, and more enzymes will be Denatured. This will decrease the rate of reaction. In summary, as temperature increases, initially the rate of reaction will increase, because of increased Kinetic Energy. However, the effect of bond breaking will become greater and greater, and the rate of reaction will begin to decrease. The temperature at which the maximum rate of reaction occurs is called the enzyme's Optimum Temperature. This is different for different enzymes. Most enzymes in the human body have an Optimum Temperature of around 37.0 °C.