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Introduction to Metabolism
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Today, we're going to discuss metabolism, which is essentially the sum of all the chemical reactions that occur within living cells. Can anyone tell me what the two main categories of metabolism are?
Catabolism and anabolism!
Correct! Now, catabolism involves breaking down larger molecules to release energy. Can someone give me an example of a catabolic process?
Glycolysis!
Yes, glycolysis is a perfect example! Now on the flip side, what about anabolism? What does that involve?
It's the synthesis of complex molecules from simpler ones.
Exactly! An example would be protein synthesis. Now, enzymes play a crucial role in metabolism. What does an enzyme do? Can anyone describe its function?
Enzymes are catalysts that speed up reactions by lowering the activation energy.
Very good! Lowers activation energy! Remember the mnemonic 'EASE' for Enzymatic Action Speeds up Efficiency. Itโs important as it means reactions happen quickly enough to support life.
To summarize, metabolism is the sum of all reactions, divided into catabolism and anabolism, and is enabled by enzymes that lower activation energy. Next, we will explore enzyme kinetics!
Enzyme Kinetics and Regulation
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Now that we have set the foundation, let's dive deeper into enzyme kinetics and regulation. Does anyone know what Michaelis-Menten kinetics describe?
It describes the rate of enzymatic reactions.
Exactly right! The Michaelis-Menten equation helps us determine reaction rates based on substrate concentration. Can someone explain what V_max and K_m are?
V_max is the maximum rate of the reaction, and K_m is the substrate concentration at which the reaction rate is half of V_max.
Great explanation! Remember, a low K_m indicates a high affinity between the enzyme and substrateโanother mnemonic is 'Low K's, High E's' for low K_m means high enzyme affinity. Now let's move on to inhibitors. Who can explain the different types of inhibitors?
There are competitive inhibitors that compete with the substrate, non-competitive inhibitors that bind elsewhere, and uncompetitive inhibitors that bind only to the enzyme-substrate complex.
Excellent! Inhibition can alter enzyme activity significantly, and understanding these mechanisms is fundamental for studying metabolic pathways. In summary, we covered how enzymes interact with substrates through kinetics and various types of inhibition. Next, we will dive into metabolic pathways.
Metabolic Pathways Overview
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Now letโs discuss the various metabolic pathways like glycolysis, the citric acid cycle, oxidative phosphorylation, and more! Who can remind us where glycolysis occurs?
In the cytosol!
Correct! And whatโs the main product of glycolysis?
Two molecules of pyruvate and a net gain of two ATP!
Absolutely! What happens to pyruvate next?
It's converted into acetyl-CoA in the link reaction, which occurs in the mitochondrial matrix.
Excellent! Next, during the citric acid cycle, acetyl-CoA is further oxidized. What are the products generated per acetyl-CoA?
Three NADH, one FADHโ, and one GTP or ATP!
Precisely! Now remember these products as they play a crucial role in ATP generation during oxidative phosphorylation. To wrap up, we highlighted glycolysis, the link reaction, and the citric acid cycle. Let's move on to respiration and photosynthesis in our next session!
Cell Respiration and Photosynthesis
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In this session, we will dive into cellular respiration in more detail. How is aerobic respiration different from anaerobic respiration?
Aerobic respiration uses oxygen, while anaerobic respiration does not.
Correct! During aerobic respiration, glycolysis, the link reaction, the citric acid cycle, and oxidative phosphorylation work together to produce around 30 to 32 ATP per glucose. Now, can anyone describe what happens during fermentation?
In fermentation, pyruvate is converted to either lactic acid or ethanol and COโ, and it only yields 2 ATP per glucose.
Exactly right! Now let's move on to photosynthesis. What are the two main stages of photosynthesis?
The light-dependent reactions and the light-independent reactions, or Calvin cycle.
Wonderful! The light-dependent reactions occur in the thylakoid membranes, capturing sunlight, while the Calvin cycle takes place in the stroma of chloroplasts. Remember the acronym 'LDP-Low Power' to link light-dependent reactions with their crucial role in energy metabolism. Summarizing, we covered cellular respiration stages and processes of photosynthesis. In the next session, we will discuss interactions between these processes.
Interdependence of Metabolism and Photosynthesis
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Now, letโs consider the ecosystem-wide importance of both cellular respiration and photosynthesis. How do these processes interconnect?
Photosynthesis produces glucose and oxygen, which are utilized in cellular respiration to produce ATP!
Exactly! And what's the overall equation for photosynthesis?
6 COโ + 6 HโO + light energy โ CโHโโOโ + 6 Oโ.
Great memory! And how about the equation for cellular respiration?
CโHโโOโ + 6 Oโ โ 6 COโ + 6 HโO + ATP.
Perfect! This highlights the cyclical relationship between these two essential processes. In summary, cellular respiration and photosynthesis are fundamentally linked for sustaining life on earth, providing energy and matter necessary for the functioning of ecosystems. All right! Let's wrap up with a final review of the whole section.
Introduction & Overview
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Quick Overview
Standard
In this section, we examine metabolism's dual componentsโcatabolism and anabolismโalongside the critical roles of cell respiration and photosynthesis. By dissecting the underlying mechanisms, enzyme functions, and metabolic pathways involved in these processes, we highlight their importance in maintaining life and energy flow in biological systems.
Detailed
Detailed Summary
Metabolism is defined as the sum of all chemical reactions occurring within cells, divided into two categories: catabolism, which breaks down larger molecules to release energy, and anabolism, which synthesizes complex molecules from simpler ones requiring energy input. Enzymes, primarily proteins that catalyze these reactions, reduce the activation energy required for reactions to proceed, thus enabling vital biological processes to happen efficiently.
- Enzyme Structure and Function: Enzymes have specific structural features, including primary, secondary, tertiary, and quaternary structures, crucial for forming active sites that bind specific substrates. The 'lock and key' model and the 'induced fit' model describe how enzymes interact with their substrates.
- Mechanism of Action: Enzymes accelerate reactions by lowering activation energy through various mechanisms like proximity and orientation, altering the microenvironment, covalent catalysis, and acid-base catalysis.
- Enzyme Kinetics: Michaelis-Menten kinetics govern many enzyme-catalyzed reactions, with key parameters such as maximum velocity (V_max) and Michaelis constant (K_m) providing insights into enzyme-substrate interactions.
- Inhibition and Regulation: Enzymes are regulated through mechanisms including reversible and irreversible inhibitors, allosteric regulation, covalent modifications, and feedback inhibition, ensuring metabolic pathways maintain homeostasis.
- Metabolic Pathways: Several metabolic pathways are outlined, such as glycolysis, the citric acid cycle, and oxidative phosphorylation, each contributing to cellular respiration and energy production. Anaerobic respiration and fermentation pathways are discussed as alternatives when oxygen is limited.
- Photosynthesis: The section concludes with an exploration of photosynthesis, detailing the light-dependent and light-independent (Calvin cycle) reactions that convert solar energy into chemical energy, illustrating how these processes complement cellular respiration in the ecosystem.
Overall, understanding the intricacies of metabolic processes, cellular respiration, and photosynthesis reveals not only the energy flows within living organisms but also their interdependence, providing foundational knowledge pertinent to the theme of interaction and interdependence in biology.
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Definitions and Overview of Metabolism
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โ Metabolism refers to the sum of all chemical reactions that occur within living cells. It can be divided into two broad categories:
โ Catabolism: the breakdown of larger molecules into smaller ones, often releasing energy.
โ Anabolism: the synthesis of complex molecules from simpler precursors, typically requiring an input of energy.
โ Enzymes are biological catalystsโalmost always proteins (with an exception of certain catalytic RNAs)โthat accelerate metabolic reactions by lowering the activation energy (ฮGโก) required for the reaction to proceed. Without enzymes, many metabolic reactions would proceed too slowly to sustain life.
Detailed Explanation
Metabolism encompasses all chemical processes that occur within a cell to maintain life. It consists of two main parts: catabolism and anabolism. Catabolism breaks down larger molecules into smaller ones, releasing energy in the process. For example, the digestion of food involves catabolic reactions that convert complex carbohydrates into glucose. On the other hand, anabolism is the process of building complex molecules from simpler ones, requiring energy input, such as synthesizing proteins from amino acids. Enzymes play a crucial role in both processes as they act as catalysts, speeding up reactions by lowering the activation energy, which is the energy needed to start a reaction. Without enzymes, essential reactions would be too slow for life to function effectively.
Examples & Analogies
Think of enzymes like a key in a lock. The lock (a chemical reaction) requires the right key (enzyme) to turn smoothly (occur efficiently). Without the key, even a simple lock might take a long time to open, just like a chemical reaction would take too long without its enzyme.
Enzyme Structure and Active Site
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- Primary Structure (Amino Acid Sequence)
โ The linear sequence of amino acids (often several hundred residues) determines folding patterns via peptide bonds. - Secondary Structure (ฮฑ-Helices and ฮฒ-Sheets)
โ Hydrogen bonding between backbone amide and carbonyl groups leads to local structures: ฮฑ-helices (coiled) and ฮฒ-sheets (folded). - Tertiary Structure
โ Further folding stabilized by interactions (hydrophobic interactions, ionic bonds, hydrogen bonds, disulfide bridges) culminates in a unique three-dimensional conformation.
โ The active site is typically a cleft or pocket formed by this tertiary arrangement. - Quaternary Structure (where applicable)
โ Some enzymes are multisubunit complexes, with each polypeptide chain (subunit) contributing to the overall catalytic function (e.g., hemoglobin-type tetrameric structure, but in the case of enzymes such as aspartate transcarbamoylase, the subunits cooperate allosterically). - Active Site and Specificity
โ The active site is composed of specific amino acid residues (often called catalytic residues) that bind substrate(s) with high specificity via complementary shape, charge, hydrogen bonding, and hydrophobic interactions.
โ The concept of โlock and keyโ has been superseded by the โinduced fitโ model, wherein substrate binding induces a conformational change in the enzyme, optimizing the geometry for catalysis.
Detailed Explanation
Enzymes have specific structures that determine their function. The primary structure consists of the amino acid sequence of the enzyme, which dictates how the enzyme folds into secondary and tertiary structures. In secondary structure, alpha helices and beta sheets form due to hydrogen bonding between the backbone atoms. The tertiary structure is the final 3D shape of a protein, stabilized by different interactions. The active site is where the enzyme interacts with its substrates, and its structure is highly specific to fit certain substrates, much like a key fits into a lock. While the traditional model compared enzyme action to a 'lock and key', the modern understanding, known as the 'induced fit' model, suggests that the enzyme changes shape slightly to better fit the substrate upon binding, enhancing its catalytic efficiency.
Examples & Analogies
Imagine a puzzle piece (enzyme) that only fits perfectly into its corresponding slot (substrate) on a board (the active site). Initially, the shape you see might not appear to fit perfectly, but as you push the piece into place, it wiggles a bit and molds itself to fit snugly (induced fit), ensuring that the whole puzzle (reaction) comes together successfully.
Mechanism of Enzyme Action
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- Lowering Activation Energy (ฮGโก)
โ Enzymes stabilize the transition state of the substrate, thereby reducing the energy barrier.
โ Mechanisms include:
โ Proximity and Orientation: Bringing substrates into close proximity in the correct orientation.
โ Microenvironment Alteration: Creating a local environment (e.g., slight acidity or basicity) that favors the reaction.
โ Covalent Catalysis: Forming transient covalent bonds with the substrate (e.g., serine proteases).
โ Acid-Base Catalysis: Donating or accepting protons during the reaction.
Detailed Explanation
Enzymes work by lowering the activation energy (the energy required to start a reaction) for chemical reactions, which speeds up the process. They achieve this through several mechanisms. By positioning substrate molecules closely and correctly, they increase the likelihood of interactions (proximity and orientation). They can also alter the local environment of the substrate to favor the reaction, such as creating acidity or basicity that may help break or form chemical bonds. In some cases, enzymes can form temporary chemical bonds with substrates, stabilizing the transition state, making it easier for the reaction to proceed. They may also facilitate proton transfer (acid-base catalysis), enhancing the breakdown or formation of substrates.
Examples & Analogies
Picture trying to build a sandcastle (a chemical reaction). If you just throw wet sand together, you might struggle to create a stable structure (high energy barrier). However, if you put the sand in a mold (enzyme), it holds the sand in the right shape, ensuring each grain fits together perfectly (lowering activation energy) so your castle comes together smoothly and quickly.
Enzyme Kinetics
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โ Michaelis-Menten kinetics describe many enzyme-catalyzed reactions (single-substrate, non-cooperative). Two key parameters:
โ Vmax: the maximum rate achieved when the enzyme is saturated with substrate.
โ KM: the substrate concentration at which the reaction rate is half of Vmax.
โ The Michaelis-Menten equation: v=Vmax[S]KM+[S] where v = initial reaction velocity and [S] = substrate concentration.
โ Interpretation:
โ A low KM indicates high affinity between enzyme and substrate (i.e., half-maximal velocity achieved at low [S]).
โ Vmax depends on the concentration of active enzyme ([E]total) and kcat (turnover number, the number of substrate molecules converted to product per enzyme per second under saturation conditions).
Detailed Explanation
Enzyme kinetics studies the rates of enzymatic reactions and how they change in response to changes in various factors, including substrate concentration. Michaelis-Menten kinetics is a model that describes the rate of enzymatic reactions for single-substrate systems. It introduces two important parameters: Vmax, which is the maximum speed of the reaction when all enzyme active sites are filled, and Km, which indicates how much substrate is needed to reach half the maximum velocity. A low Km means that the enzyme has a high affinity for the substrate, allowing the reaction to occur quickly at lower substrate concentrations. The Michaelis-Menten equation allows us to graph this relationship and understand how enzymes behave under different conditions.
Examples & Analogies
Think of a well-trafficked restaurant (enzyme) that can seat a limited number of customers (substrate). Vmax is like the maximum number of guests that can be served at peak times. If you have a table for everyone, you serve quickly (high rate). However, if too many diners arrive (high substrate concentration) and people can't get seated (active sites filled), not everyone can be served at full speed, and the rate of service slows until relaxation (low Km) allows more diners in comfortably.
Inhibition and Regulation of Enzymes
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โ Reversible Inhibitors:
โ Competitive Inhibition: Inhibitor competes with substrate for binding at the active site. Effect: increase apparent KM (i.e., more [S] required to reach ยฝ Vmax), Vmax unchanged.
โ Noncompetitive Inhibition: Inhibitor binds to the enzyme at a site other than the active site (allosteric site), equally affecting enzyme-substrate complex and free enzyme. Effect: Vmax decreases, KM unchanged.
โ Uncompetitive Inhibition: Inhibitor binds only to the enzyme-substrate complex. Effect: both Vmax and KM decrease.
Detailed Explanation
Enzymes can be regulated by various inhibitors that affect their activity, often through reversible means. In competitive inhibition, an inhibitor mimics the substrate, competing for the active site, which raises the Km (more substrate needed to achieve half-maximal velocity) but does not affect Vmax. Noncompetitive inhibitors bind to a different part of the enzyme and reduce enzyme activity regardless of substrate concentration, lowering Vmax without affecting Km. Lastly, uncompetitive inhibitors bind only to the enzyme-substrate complex, decreasing both Km and Vmax, suggesting that the complex is less likely to produce the product.
Examples & Analogies
Imagine a traffic jam (competitive inhibitor) where a single lane is blocked (active site) by an obstacle. Cars (substrates) can still move, but it becomes harder (higher Km) for them to get through. In contrast, a toll booth (noncompetitive inhibitor) affects all cars regardless if they're eager to go through or not (Vmax decreases). An additional layer is a toll that can only be paid after parking (uncompetitive inhibitor), slowing down the entire process as it adds steps (both Km and Vmax decrease).
Metabolic Pathways and Compartmentalization
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- Glycolysis (occurs in cytosol)
โ A series of ten enzymeโcatalyzed reactions converting glucose (CโHโโOโ) to two molecules of pyruvate (CโHโOโ), with a net production of two ATP (via substrateโlevel phosphorylation) and two NADH.
โ Key regulatory enzymes: hexokinase/glucokinase, phosphofructokinaseโ1, pyruvate kinase.
Detailed Explanation
Glycolysis is the initial metabolic pathway for glucose breakdown. It takes place in the cytosol and consists of ten enzyme-catalyzed reactions, converting one glucose molecule into two pyruvate molecules. This process also produces two molecules of ATP and two NADH, which can be used in further processes. The main regulatory enzymes, such as hexokinase, phosphofructokinase-1, and pyruvate kinase, control the speed and efficiency of glycolysis based on the cell's energy needs. These regulatory mechanisms ensure that glucose is processed effectively in response to the cell's demands.
Examples & Analogies
Think of glycolysis as a quick assembly line in a factory where raw materials (glucose) are quickly converted into parts (pyruvate) that are ready for further processing. Just like how some workers (regulatory enzymes) manage the flow of materials based on demand, these enzymes ensure that only the right amount of parts is produced at any time, preventing unnecessary waste.
Cellular Respiration Overview
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Cellular respiration is the process by which cells extract chemical energy (from organic molecules like glucose) and convert it into adenosine triphosphate (ATP), the cellโs energy currency. This process can be aerobic (using oxygen as the terminal electron acceptor) or anaerobic (using alternative electron acceptors or substrateโlevel phosphorylation).
Detailed Explanation
Cellular respiration is essential for generating ATP, which provides energy for all cellular processes. In aerobic respiration, oxygen is used as the final acceptor to produce ATP, while in anaerobic respiration, different methods are employed to generate ATP in the absence of oxygen. This is crucial for organisms that operate under low oxygen conditions or in environments devoid of it. Both pathways begin with glycolysis, which breaks down glucose to extract energy, leading to further reactions either in the presence or absence of oxygen.
Examples & Analogies
Imagine cellular respiration as a process of charging your phone (a cell). When you plug it into a wall outlet (aerobic respiration), it charges quickly because of the steady flow of electricity (oxygen). However, if you're using a portable power bank (anaerobic respiration), it can still work, but the charging speed is slower and not as efficient as using a direct outlet. Each method allows the phone (cell) to stay powered and functional, just as ATP powers the cell's activities.
Aerobic Respiration Pathway
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- Glycolysis (Cytosol)
โ Glucose Uptake and Activation: - Hexokinase/Glucokinase (muscle/liver): Phosphorylates glucose โ glucose-6-phosphate (G6P), trapping it inside the cell. Consumes 1 ATP.
- Phosphoglucose Isomerase: Converts G6P โ fructose-6-phosphate (F6P).
- Phosphofructokinase-1 (PFK-1): Phosphorylates F6P โ fructose-1,6-bisphosphate (FBP). Major regulatory step (activated by AMP, ADP, fructose-2,6-bisphosphate; inhibited by ATP, citrate). Consumes 1 ATP.
โ Cleavage and Oxidation: - Aldolase: Splits FBP into glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP).
- Triose Phosphate Isomerase: Reversibly converts DHAP โ G3P. Only G3P continues.
- Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH): Oxidizes G3P โ 1,3-bisphosphoglycerate; reduces NADโบ โ NADH + Hโบ.
Detailed Explanation
The aerobic respiration pathway starts with glycolysis, where glucose is broken down into two molecules of pyruvate. Initially, glucose is phosphorylated by hexokinase, using one ATP to form glucose-6-phosphate, preventing it from leaving the cell. Several enzymes further transform glucose through various steps, including isomerization and phosphorylation, leading to the production of glyceraldehyde-3-phosphate, which undergoes oxidation to produce NADH, a carrier of electrons. NADH plays a vital role in the next stages of cellular respiration, which will occur in the mitochondria.
Examples & Analogies
Consider glycolysis as the initial steps of baking cookies โ you start by measuring and mixing ingredients (glucose phosphorylation), then you modify the mixture to ensure clumps of dough (pyruvate) are formed, which are critical for baking (energy production) later. By preparing the ingredients correctly early on, you set yourself up for a successful batch of cookies (ATP).
Definitions & Key Concepts
Learn essential terms and foundational ideas that form the basis of the topic.
Key Concepts
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Enzymes: Biocatalysts that lower activation energy to facilitate biochemical reactions.
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Metabolic Pathways: Sequential series of reactions in metabolism, including glycolysis, Krebs cycle, and oxidative phosphorylation.
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Cellular Respiration: Process of converting biochemical energy from nutrients into ATP, which is used as energy.
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Photosynthesis: Conversion of light energy into chemical energy stored in glucose.
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Regulation of Metabolism: Mechanisms like enzyme inhibition, allosteric regulation, and feedback inhibition maintain metabolic homeostasis.
Examples & Real-Life Applications
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Examples
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The process of glycolysis transforms glucose into pyruvate with the net production of 2 ATP and 2 NADH.
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Photosynthesis is outlined by the reaction 6 COโ + 6 HโO + light energy โ CโHโโOโ + 6 Oโ, showing the conversion of carbon dioxide and water into glucose and oxygen.
Memory Aids
Use mnemonics, acronyms, or visual cues to help remember key information more easily.
๐ต Rhymes Time
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To gain some power, glucose we should devour, metabolism's the key, for energy!
๐ Fascinating Stories
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Imagine a factory with enzymes as workers. Theyโre quick and efficient, making sure every molecule is transformed into energy or useable parts. The flow of materials represents catabolism breaking down to produce energy while assembly lines symbolize anabolism putting together the building blocks of life.
๐ง Other Memory Gems
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For glycolysis, remember 'GLYCO - DROP' which stands for Glucose, Lyse to Pyruvate, OH, ATP! Using GLUCOSE to make energy!
๐ฏ Super Acronyms
Remember 'CAP' for the phases of metabolism
- Catabolism
- Anabolism
- and Photosynthesis.
Flash Cards
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Glossary of Terms
Review the Definitions for terms.
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Term: Metabolism
Definition:
The sum of all chemical reactions occurring within living cells, including catabolic and anabolic processes.
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Term: Catabolism
Definition:
The breakdown of larger molecules into smaller ones, often releasing energy.
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Term: Anabolism
Definition:
The synthesis of complex molecules from simpler precursors, typically requiring an input of energy.
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Term: Enzyme
Definition:
A biological catalyst that accelerates metabolic reactions by lowering the activation energy.
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Term: Enzyme Kinetics
Definition:
The study of the rates of enzyme-catalyzed reactions and how they are affected by various factors.
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Term: V_max
Definition:
The maximum rate achieved by an enzyme-catalyzed reaction when the enzyme is saturated with substrate.
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Term: K_m
Definition:
The substrate concentration at which the reaction rate is half of V_max.
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Term: Oxidative Phosphorylation
Definition:
The final stage of cellular respiration, where ATP is produced using energy from electrons transferred through the electron transport chain.
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Term: Photosynthesis
Definition:
The process in which light energy is converted into chemical energy in the form of carbohydrates.
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Term: Calvin Cycle
Definition:
The light-independent reactions of photosynthesis that fix carbon dioxide into glucose.