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The subcomponents of biological molecules & their sequence determine the properties of that molecule: The structure of macromolecules determine their function; as such, differently shaped proteins or lipids etc have different functions in the body. If a macromolecule changes its structure, its function may also be altered. CARBOHYDRATES: The subcomponents of starch and cellulose are both glucose. Yet their sequence, or the way they’re linked, makes them very different. In starch, the glucose monomers all have the same orientation; the glucose is alpha-linked. In cellulose, the glucose is beta-linked, meaning that each glucose molecule is “upside down” from its neighbors (with beta-ringed structures, the hydroxyl group is reversed with the hydrogen). This difference makes starch molecules helical, and cellulose straight. Plants use starch as their food storage, and cellulose as the tough cells that enclose their cells. Their different structures allow for different functions. LIPIDS: A saturated fatty acid is different from an unsaturated fatty acid in both their structure and their properties. A saturated fatty acid is ‘saturated’ with hydrogens; are there are no double bonds in the fatty acids. Their tails don’t have kinks and are straight. An unsaturated fatty acid has one+ double bonds, with one less hydrogen molecule for each double bond occurring. Each double bond creates a kink in the hydrocarbon chain tail. Saturated fatty acids saturated fat = animal fats (ex: lard/butter) and are solid at room temperature. Unsaturated fatty acids unsaturated fat = fats from plants or fish, and usually liquid at room temperature (ex: vegetable oil/cod liver oil). This is because the kinks in the hydrocarbon tails prevent the molecules from packing tightly together and solidifying at room temperature. On the other hand, a phospholipid has two fatty acids and a phosphate group joined to the glycerol head. The phosphate group is electronegative, and small polar molecules can link to the phosphate group to create a variety of phospholipids. PROTEINS: Proteins are composed of a string of amino acids (20 possible amino acids). During primary structure, the amino acids are bonded covalently. If one amino acid is substituted for another, the molecule could be different and may fold differently. In secondary structure, the carboxyls and amines bind and form a backbone through hydrogen bonds between oxygen and hydrogen molecules. Secondary protein structure can take the form of either an alpha-helix or beta-pleated sheet. Primary structure can impact the form proteins take in secondary structure. Hydrogen bonds between polar side chains (from secondary structure) affect tertiary structure. In tertiary structure and ionic bonds form between positively & negatively charged side chains and disulfide bridges form between cysteine groups. Additionally hydrophobic interactions form between hydrophobic molecules, held together by van der Walls interactions. o IF the primary structure is different, the amino acids that are hydrophobic might turn out hydrophilic, or there might be another hydrophobic amino acid somewhere else on the polypeptide chain. It would cause the protein to fold differently. o IF in secondary structure, the hydrogen bonds form differently o THIS ALSO AFFECTS quaternary structure. An incorrectly/differently folded protein in tertiary cannot fold with other proteins the same way in quaternary structure. For sickle cell disease, a glutamine is substituted with a valine. This causes the protein to fold incorrectly, and it’s function is therefore affected. NUCLEIC ACIDS: Replacing one nitrogenous base with another means replacing its complementary base too because A always bonds with T/U and C with G. Since DNA codes for proteins through mRNA, changing a base will result in a change in the proteins structure and/or function. EXAMPLE: Hemophilia, where a mutation on the Xchromosome causes the lack of a coagulation factor in the person’s blood. Interactions between molecules affect their structure and function Different molecules have separate properties, so it makes sense that interactions between molecules affect each molecule’s structure and function. Interactions between reactive molecules affect their structure as they bond, and their function as they become a compound. Interactions between molecules in our body fuel metabolism through the processes of releasing and/or utilizing energy. A great example to demonstrate and thoroughly explain how interactions between molecules affect their structure and function is the activity of enzymes and their substrates. An enzyme’s purpose is to catalyze chemical reactions in an organism so they can perform all their necessary processes quickly enough to survive. Below (right) is a picture from the textbook explaining the interaction between enzymes and substrates – the enzyme turns the substrates into different products with different functions. If there is no enzyme to interact with the substrate and catalyze reactions, the rate of the reaction would be much slower (below left: textbook picture displaying a graph of enzyme versus no enzyme in reaction). There are multiple factors that affect the interaction between enzymes & substrates, each affecting the structure & function of both; under different conditions the interactions between the two occur differently. There are seven scenarios that will be discussed in this blog post; the first two address interactions but not structure and function as much (they’re more of a background to explain the process of enzyme-substrate activity), while three through seven address the main question (both). ONE In conditions where enzyme concentration is greater, the rate of substrates being catalyzed increases, because there are more enzymes for substrates to interact with. Products Produces vs Time (One Enzyme) 24 21 18 15 12 9 6 3 0 0 10 20 30 40 Total # of Products Made Total # of Products Made Products Produced vs Time (Two Enzymes) 24 19 14 9 4 -1 Time (sec) 0 10 20 30 40 Time (sec) Likewise, if there are fewer enzymes present, less substrates will get converted into products. Even in the amount of substrates present is at the maximum level, an enzyme can only work so fast. Differences in reaction rate can be observed below: TWO If there are more substrates, more of them will interact with the enzyme, resulting in a faster rate of reaction, up to a point where the amount of substrates are at the maximum level and an enzyme cannot work faster. Reaction Rate (products/s) Reaction Rate vs Time as Substrate Concentration Increases 1000 900 800 700 600 500 400 300 200 100 0 0 1 2 3 4 5 6 7 8 Time (sec) THREE Increasing the temperature of a solution/within an environment where enzymes and substrates react affect both their interaction and the structure and function of the enzyme. Increased temperature facilitates greater kinetic energy, which makes collisions of enzymes and substrates more likely. As such, the rate of reaction will increase. Enzymes have optimal temperatures that they work best in. However, an enzyme will denature if the temperature is too high; their structure will change and make their active sites unsuitable to binding enzymes. Their ability to turn reactants into products will decrease. As seen in the graph below, higher temperatures are favorable until the point of denaturation, when the temperature is high enough to alter the shape of the enzyme. Reaction Rate (products/sec) Reaction Rate vs Temperature 600 500 400 300 200 100 0 23 28 Temperature (˚C) 33 FOUR Increasing the pH of the environment also changes the way enzymes interact, and their structure and function. Similarly to temperature, different types of enzymes have different optimal pH levels. Usually, if a solution/the environment is too acidic or basic, the enzyme’s structure will change (denaturation), resulting in a worse ability to catalyze reactions. A neutral pH (pH 7) is usually suitable; however, as the earth’s ancient oceans are speculated to be slightly acidic, a pH level between 5-7 can be optimal too. The more acidic pH could alter the active sites to bind better to substrates (an example would be the peroxidase enzyme, which seems to work best at a slightly acidic pH). In the graph below, the enzyme works best at pH7, and is denatured to a point where they are less effective when out of the range of pH 5-8. FIVE Competitive inhibitors do not change the structure of the enzymes themselves, but are imitate the structure of the substrate. Its function is to inhibit the substrates from attaching to the active site. Examples are toxins/poisons such as sarin. The Rate of Reaction vs Time with Inhibitors 30 25 20 15 10 5 0 0 2 4 6 8 Total # Products Made Total # of Product Made Rate of Reaction vs Time Without Inhibitors Time (sec) interaction between competitive inhibitors affect the structure of an enzyme; now, substrates can no longer bind because there is only one active site, now taken up by the inhibitor. It also affects the function; the enzyme is no longer able to act as a catalyst for reactants for the while the inhibitor is stuck on the active site. Increasing the number of substrates can help increase the reaction rate, as there are more substrates to compete with the competitive inhibitors for an active site. Competitive inhibitors slow the rate of reaction. SIX: Allosteric inhibitors regulate the amount of products enzymes catalyze from reactants. They are especially useful for metabolic pathways that 30 25 20 15 10 5 0 0 5 Time (sec) 10 involve multiple products being generated, which are used for reactants in the next step of the pathway. Allosteric inhibitors ensure that there is the right amount of reactants and products to ensure maximum pathway efficiency. A picture from the textbook on the right shows how they work. Interactions of enzymes with allosteric inhibitors affect their structure; they change their shape so they are stabilized and don’t need a substrate in their active site for that purpose. Their function alters too; they can no longer catalyze substrates due to their stable form and shape. Their active sites are occupied. They can only take up substrates when inhibitors dissociate from the enzyme. This slows the rate of reaction. Refer to the graphs above to compare reaction rate; the rate for competitive and allosteric regulators compare approximately equally to the rate of reaction without inhibitors. SEVEN Cofactors are nonproteins assisting the process of catalytic activity. They can be inorganic or organic; examples are vitamins. They can either bind tightly and permanently (covalently) to enzymes or loosely and reversibly to substrates with weaker bonds; either way of interacting with these two will have the same results. They serve to increase the rate of reaction; for example, their interaction with substrates may involve shifting the substrates to be in cloze proximity to enzymes, and their interaction with enzymes helps the enzyme better recognize and attract/repulse a substrate. Rate of Reaction With Cofactors 50 40 30 20 10 0 0 2 4 Time (sec) 6 8 Total # of Products Made Total # of Product Made Rate of Reaction Without Cofactors 50 40 30 20 10 0 0 2 4 Time (sec) 6 8