Like Pacman, enzymes have specific shapes, act on smaller molecules and can be destroyed by external factors.
Like Pacman, enzymes have specific shapes, act on smaller molecules and can be destroyed by external factors. Enzymes are made of proteins - each having a unique structure for a specific function.(1:10) Melanie explains lactose intolerance (3:30) before straightening her hair for a night out (5:43). There are several environmental factors which influence enzyme functioning (6:41). Disrupt those hydrogen bonds or R group interactions and lose structure as well as function.
The Question of the Day asks (9:38)Which amino acid corresponds to the start codon - AUG?
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Hi and welcome to the APsolute Recap: Biology Edition. Today’s episode will recap Enzymes and their unique structures
Zoom out:
Unit 3 - Cellular Energetics
Topics 3.1-3.3
Big idea - Energetics
Pacman? Did she say Pacman? Yup - For those of you who weren’t gaming in the 80s - Pacman is a classic arcade game where a small pie shaped character (missing a slice) goes through a maze trying to consume dots and not be destroyed by blinking ghosts. What in the WORLD does this have to do with enzymes? Like Pacman, enzymes have specific shapes, act on smaller molecules and can be destroyed by external factors.
Let’s Zoom in:
Enzymes are made of proteins - each having a unique structure for a specific function. Proteins are polymers (or polypeptides) of the monomer amino acids - of which there are 20 different varieties. Their diversity in structure is the greatest of all the biological molecules. An amino acid is made up of one central carbon atom that forms four single covalent bonds – one is to hydrogen, another to a carboxyl, and a third is to an amino group. The fourth covalent bond is to a variable “R” group. This R group is a substitute for different side chains that give each of the 20 different amino acids their unique properties (like size, charge, and pH). Amino acids join together through dehydration synthesis between an amino group of one monomer and the carboxyl group of the other at a ribosome during the process of translation. (Check out episode 20 for a recap of the Central Dogma). The covalent bond formed between adjacent amino acids is referred to as a peptide bond.
Proteins have four levels of structure as it bends and folds in upon itself. Primary structure is a chain of amino acids, the sequence of which is dictated by a particular gene of DNA. Protein chains vary greatly in length from hundreds to tens of thousands of amino acids. Secondary structure forms an alpha helix coil or a beta pleated sheet. The particular folding is due to local hydrogen bonding between the oxygen of a carbonyl and hydrogen of an amino group. Tertiary structure forms when alpha helices and beta sheets fold further inwards as a result of R group interactions. These interactions may involve hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces. Additionally, a special type of covalent bond can also form - a disulfide bridge. This is found between cysteines which contain the element sulfur in their side chain. The final structure is quaternary, which has two separate amino acid chains, bent and folded and interacting together. Due to their unique 3D shapes - proteins are often referred to as “globular.”
Enzymes are biological catalysts, are not used up in a reaction and are substrate and condition specific. For an enzyme catalyzed reaction to occur, the charge and shape of the substrate must be compatible with the enzymes active site. Consider the enzyme lactase. It has a specific active site which fits the substrate lactose, a disaccharide sugar found in milk. Collectively, this is lactose and lactase are called the enzyme substrate complex and has an induced fit. An induced fit brings the reactants and enzyme closer together with a microenvironment chemical interaction at the active site. Lactase facilitates the catabolic reaction of lactose with water into the monomers glucose and galactose. Products are released, and the enzyme can be used again with another molecule of lactose. (as an aside, this is a common pattern for the carbohydrate enzymes to end in -ase and be named after the substrate it acts upon). Individuals who are lactose intolerant often don’t make enough lactase enzymes and experience symptoms such as bloating and an upset stomach when consuming dairy. Want to learn more about catalysis? Check out the APsolute RecAP Chemistry Edition: Episode 25.
Imagine you are getting ready for a night out. You’re showered and dressed, but now it's time to tackle that hair. Heating up a straightening iron, you run it through your locks until they are pin straight and volume free. You run out the door only to realize its raining and your hair begins to curl up to its original shape. Your hair is made of protein, and just like enzymes, is influenced by environmental factors. The addition of heat disrupted hydrogen bonds and R-group interactions - denaturing the protein from its 3D shape. However - you did NOT break the peptide bonds of primary structure. The addition of water from the rain assisted in reforming some bonds and regaining hair shape. Chemical hair straightening is more permanent, as it breaks and reforms disulfide bridges while in a new hair shape.
Enzyme rates are influenced by similar factors. They are influenced by pH, substrate concentration, temperature, and competitive molecules. Generally, increasing the substrate concentration and temperature will increase the rate of reaction. However, there is a ceiling to the reaction rate due to the amount of available enzymes no matter how many substrates there are. Additionally, increasing temperature increases kinetic energy and the likely collisions of active sites with substrates. But be warned - increase too much, and the protein may denture. In some instances, enzyme denaturation is reversible, allowing the enzyme to regain functioning. Enzymes can also be inhibited by the presence of other molecules such as poisons, pesticides, and antibiotics. If these molecules bind to the active site, they are classified as competitive inhibitors while those that bind elsewhere are called noncompetitive.
Enzyme function can be further regulated through cofactors (like magnesium) or coenzymes (like NAD+). These molecules cause conformational changes to the active site. Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another. (Allo meaning other) An example of this is with feedback inhibition - where the end product of a metabolic pathway shuts down the pathway itself. Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed.
Time for unit connections. Enzymes are in nearly every unit - and with some, you are required to know their specific name and role. Know ATP Synthase in Unit 3. Unit 6 has several - DNA polymerase, ligase, RNA polymerase, helicase, and topoisomerase. Don’t forget lysosomes which contain hydrolytic enzymes for intracellular digestion! We learned about this organelle in unit 2. Alright - what about the exam? Enzymes provide a strong opportunity to test Science skill 4 - representing and describing data. You may be asked to analyze a graph of enzyme activity with an increase in temperature until reaching optimum and then denaturing. Don’t freak out - but it is also highly probable that you will read about enzymes and substrates in a question that you’ve never heard of. Trust your gut! Every enzyme has its goldi-locks zone - go beyond that, and you’ll likely see decreased activity and denaturation.
To recap……
Enzymes are like Pacman, substrates like the dots, and environmental factors that cause denaturing? Ghosts. These biological catalysts are substrate and condition specific. Disrupt those hydrogen bonds or R group interactions and lose structure as well as function.
Coming up next on the Apsolute RecAP Biology Edition: Calvin vs. Krebs
Today’s question of the day is about amino acids
Question of the day: Which amino acid corresponds to the start codon - AUG?