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Biochemistry I Spring/Summer 2023 Lecture 6 April 17, 2023 Textbooks: Mark’s Basic Medical Biochemistry 5th Edition And Harper’s Illustrated Biochemistry 30th Edition 3 tests March/April/May.

[Audio] We have agreed to have tests covering the content of Mark’s Basic Medical Biochemistry 5th Edition and Harper’s Illustrated Biochemistry 30th Edition for Lecture 6. Please read chapters 7,8,9 of Mark’s Basic Medical Biochemistry 5th Edition for Lecture 6. I will send Homework 5,6 shortly. Our tentative list of topics and chapters for the rest of the semester includes: Chapter 7 Structure-functional relationships in proteins Chapter 8 Enzymes as catalysts Chapter 9 Regulation of enzymes Chapter 10 Relationship between cell biology and biochemistry Chapter 11 Cell signaling.

[Audio] Today, we will be discussing the catalytic triad of chymotrypsin, a serine protease involved in protein breakdown. We will also discuss induced fit, activation energy, and the 1st enzyme mechanism. Understanding enzyme kinetics is crucial for understanding enzyme function. We will be discussing the important parameters that help us understand enzyme kinetics such as Vmax, Km, and kcat. This chapter is important for students as it prepares them for the upcoming tests on April 17th. We will be covering the enzyme and enzyme catalysis in Basic Medical Biochemistry 5th Edition and Harper’s Illustrated Biochemistry 30th Edition. We hope this information is helpful and look forward to discussing it further in class..

[Audio] Today, we will discuss the Induced Fit Model for Enzymes. Enzymes are biological catalysts that increase the rate of a reaction by modifying their shape and conformation slightly. The equation E plus S ↔ ES ↔ ES* ↔ EP ↔ E plus P represents the steps involved in the Induced Fit Model. The active site of an enzyme is the region or domain where the substrate binds, and it may contain cofactors. In conclusion, we explain how enzymes are changed transiently during the conversion of substrates into products, and return to their original configuration when the reaction is complete..

[Audio] We will be covering the Basic Medical Biochemistry 5th Edition and Harper’s Illustrated Biochemistry 30th Edition on Lecture 6. Our focus will be on the functional groups of amino acid residues and cofactors in the active site, as well as the formation of the transition-state complex. Through studying ES* and learning about the different functional groups and cofactors involved in the active site, we hope to gain a deeper understanding of the mechanisms of enzyme function and how they catalyze chemical reactions. This knowledge will be invaluable in our future studies and careers in biology and chemistry..

[Audio] We have agreed to have three tests during Lecture 6, covering the content of Harper’s Illustrated Biochemistry 30th Edition, and testing our understanding of the concepts presented in Lecture 6. One of the key principles we will be covering is E plus P D, the idea that the products of a reaction dissociate, causing the enzyme to return to its original conformation. This is important to understand as it helps us grasp how enzymes function and interact with other molecules in the body. To fully grasp E plus P D, we need a strong foundation in both biology and chemistry. We will test our understanding of this concept through three tests, working together as a class to review and understand the material presented in Lecture 6. We are excited to learn more about Basic Medical Biochemistry and Harper’s Illustrated Biochemistry and are confident in our ability to understand and apply the concepts presented in these texts through our collective efforts..

[Audio] We will discuss the chemical reactions that occur in the body. We will focus on the reactions between E and S, which are key components of the body's metabolism. We will discuss the reaction E plus S ↔ ES, which is an important reaction that occurs in the body and is responsible for the formation of new compounds. We will also discuss other reactions, such as ES* ↔ EP, which are also important for the proper functioning of the body. It is important for us to understand these reactions and their significance in the body. By studying these reactions, we can gain a better understanding of the complex processes that take place in the body and how they are affected by various factors, such as diet and exercise. In conclusion, the chemical reactions that occur in the body are crucial for the proper functioning of the body. By studying these reactions, we can gain a better understanding of the complex processes that take place in the body and how they are affected by various factors..

[Audio] ΔG° = ΔH° TΔS° Enzymes use the equation ΔG° = ΔH° TΔS° to increase the velocity of a reaction. By decreasing the ΔG°, Enzymes make it easier for the reactants to proceed to the transition state and convert to the products..

[Audio] In this slide, we will discuss the concept of catalysis in biochemistry and the three ways in which catalysts facilitate chemical reactions: 1) by preferentially binding to the transition state through complementary noncovalent bonding interactions, 2) by distorting the substrate and/or active site, which promotes reduction of the activation energy, and 3) by altering the reaction pathway to include intermediate states. Understanding these mechanisms of catalysis allows us to appreciate the role of catalysts in biochemical processes, such as metabolism and protein folding. We can also design new catalysts for a wide range of applications, such as drug discovery, biofuels production, and environmental remediation. The study of catalysis in biochemistry is a crucial area of research that has the potential to greatly impact our understanding of the natural world and the development of new technologies for a more sustainable future..

[Audio] We will discuss the glucokinase enzyme. Glucokinase enzyme is a crucial regulator of glucose metabolism in the body. Its function is to convert glucose into A-T-P--, which is the primary energy of our cells. The enzyme has two parts: the N-terminal and C-terminal domains. The N-terminal domain binds glucose, while the C-terminal domain transfers the phosphate group from glucose to A-T-P--. Glucokinase enzyme is important for maintaining proper glucose metabolism and preventing diseases such as diabetes. Understanding its function is crucial..

[Audio] Boa tarde a todos, bem-vindos à aula de hoje. No slide número 11, iremos abordar um tema bastante importante para os alunos de Biologia e Química: as três provas que serão realizadas no dia 17 de abril, abordando o conteúdo das edições básicas da Bioquímica Médica de Mark e da Bioquímica Ilustrada de Harper. Este slide mostra a importância do sítio de ligação à glicose na enzima glicocinase. Podemos ver que a glicose, em vermelho, é mantida em seu sítio de ligação por múltiplas ligações de hidrogênio entre cada grupo hidroxila e aminoácidos polares de diferentes regiões da sequência aminoacídica da enzima. A posição do resíduo de aminoácido na sequência linear é indicada pelo seu número. Essas múltiplas interações permitem que a glicose induza grandes mudanças conformacionais na enzima, conhecido como "ajuste induzido". No entanto, essa especificidade enzimática é ilustrada pela comparação da galactose e da glicose. A galactose, mesmo sendo muito similar à glicose, apresenta uma diferença crucial no grupo hidroxila em vermelho. E é por causa dessa diferença que a galactose não é fosforilada em uma taxa significativa pela enzima, tornando-se necessário o uso de uma galactocinase separada para o metabolismo dessa substância pelas células. É importante entender esses conceitos para compreendermos melhor a atuação e a especificidade das enzimas em nosso organismo. Na próxima aula, iremos abordar outros aspectos importantes desse tema..

[Audio] Three tests covering the content of Mark’s Basic Medical Biochemistry 5th Edition and Harper’s Illustrated Biochemistry 30th Edition for Lecture 6 have been agreed upon. Our first test will focus on enzyme function and activity. Please review the relevant sections of the textbooks and prepare thoroughly for this test..

[Audio] 1. Substrate specificity and pocket 2. Oxyanion hole 3. Enzyme-substrate complex formation 4. Tetrahedral intermediate formation 5. Cleavage and acyl-enzyme intermediate formation 6. Hydrolysis of the peptide bond Study the following sections from the textbook for this topic: * Section 2: Substrate Specificity and Pocket * Section 4: Oxyanion Hole * Section 5: Enzyme-Substrate Complex Formation * Section 6: Tetrahedral Intermediate Formation * Section 7: Cleavage and Acyl-Enzyme Intermediate Formation..

[Audio] Enzyme kinetics is the study of enzyme-catalyzed reactions and how to optimize these reactions for maximum efficiency. We will discuss the equation for enzyme kinetics, which shows that the rate of enzyme-catalyzed reactions is dependent on the substrate concentration. We will also explore the optimization techniques that can be used to increase the rate of enzyme-catalyzed reactions. It's important to note that this equation is used to simplify the complex process of enzyme kinetics, and in reality, there are many factors that can affect the rate of these reactions..

[Audio] We are here to discuss the upcoming test for Basic Medical Biochemistry. Our agreement states that we will have three tests covering the content of Mark’s Basic Medical Biochemistry 5th Edition and Harper’s Illustrated Biochemistry 30th Edition for Lecture 6 on April 17th. The first test will be on k1, which is the first topic we covered in the previous lecture. The second test will be on kE, which includes the topics we covered in the second part of the previous lecture. The third test will be on ES, which contains the topics we covered in the third part of the previous lecture. It is important to note that the tests will be cumulative, meaning that the marks from the previous tests will be added to your final grade. Therefore, it is essential to understand the content and prepare accordingly..

[Audio] Michaelis-Menten equation is a fundamental concept in biochemistry. It describes the relationship between the concentration of substrate, the concentration of product, the rate of reaction, and the constants Km, Kcat, and Vmax. Understanding this equation is essential for understanding the kinetics of enzyme-catalyzed reactions and for predicting the rate of reaction under different conditions..

[Audio] The concept of Kinetic Michaelis Constant, which measures an enzyme's binding affinity for its substrate. It is the concentration of substrate at which the enzyme's rate of catalysis is half of its maximum rate. However, it is important to note that Km is not equal to the maximum rate of catalysis. A low Km value indicates greater affinity, while a high Km value indicates lower affinity. Understanding the concept of Km is crucial for understanding the kinetics of enzyme-substrate interactions..

[Audio] We will discuss the concept of enzyme activity. Vmax is the velocity at which an enzyme is operating at maximum efficiency when it is fully saturated with substrate. It is proportional to the concentration of enzyme used in the experiment and is not useful for comparing enzymes. Instead, we use the concept of kcat, which is the turnover number. This is a numer that represents the rate at which an enzyme converts substrate to product, taking into account the enzyme's efficiency and the concentration of substrate. By dividing both sides of the equation by the concentration of enzyme, we can obtain the turnover number. Expressed in units of time, this number is called kcat. This number is a useful measure of enzyme activity and can be used to compare enzymes. It is important to note that the equation Vmax/ = /( time) is not a valid equation. This equation does not take into account the efficiency of the enzyme and the concentration of substrate, which are important factors in determining enzyme activity..

[Audio] We will continue with our lecture on Basic Medical Biochemistry. We have three tests scheduled to cover the material from Mark’s Basic Medical Biochemistry 5th Edition and Harper’s Illustrated Biochemistry 30th Edition. We will calculate kcat using the formula: kcat = Vmax / Km. We have been given the value of Vmax, which is 75.5 μM/min. We will calculate kcat by dividing Vmax by Km. We will ensure that we are using the correct units for both Vmax and Km. We will convert Km to units of μM/min. Once we have calculated kcat, we can convert it from units of 1/min to units of 1/s by recalling that 60 minutes is equal to 1 hour. We will make sure that we are using the correct information and formula to calculate kcat. We will make sure that we are using the correct units and that we are recalling the time units correctly. Let’s move on to the next slide..

[Audio] Enzyme kinetics and the principles discussed in the slide will be applied in the tests. Enzyme kinetics is the study of enzyme reaction rates and their dependence on substrate concentration, and how these factors affect enzyme function. Enzymes that fall below the diffusion limit may have slower reaction rates, which can affect their overall efficiency and impact the effectiveness of the enzyme in its intended function. By studying enzyme kinetics, we can gain a better understanding of the factors that affect enzyme function and how these can be optimized for maximum efficiency. We can apply this knowledge to improve medical treatments and therapies. Enzymes are important in the medical field..

[Audio] We will discuss the importance of enzyme efficiency and substrate specificity in today's lecture. Enzyme efficiency is calculated by dividing the Michaelis constant by the rate constant. Substrate specificity refers to an enzyme's ability to distinguish between different substrates. For instance, an enzyme that catalyzes the hydrolysis of a peptide bond in proteins has specific binding sites that fit perfectly with its substrate. The ratio between the Michaelis constant and the rate constant is a convenient measure of enzyme efficiency and substrate specificity. This is important for understanding how enzymes function and how they are regulated in the body..

[Audio] Agreed to three tests covering Mark’s Basic Medical Biochemistry 5th Edition and Harper’s Illustrated Biochemistry 30th Edition for Lecture 6. Presentation should include copyright information © 2019, 2016, 2013 Pearson Education Ltd. All Rights Reserved..