metabolism

Metabolism: An Overview

• Metabolism encompasses all life-sustaining chemical reactions in organisms
• Its main purposes are converting food to energy, converting food to building blocks for molecules like proteins, lipids, and nucleic acids, and eliminating metabolic wastes
• It involves hundreds of enzymatic reactions organized into discrete pathways
• These pathways involve many specific chemical intermediates transforming substrates to end products
• Catabolism is oxidative and exergonic, breaking down complex molecules to release energy
• Anabolism is reductive and endergonic, building complex molecules requiring energy

Structure of BS2003 - Biochemistry II

• Students are provided with a booklet, "Essentials and Beauty of Biochemistry," as foundational material
• Pre-recorded lectures are made available electronically, allowing for flexible learning
• Weekly tutorial sessions and online coffee sessions are provided for clarification
• The first online coffee session, on August 13th at 8:30 AM, is scheduled to address questions and reinforce learning outcomes
• Practical course content related to carbohydrate catabolism, and lipids and fatty acids is covered in weeks 8 and 9, respectively

BS2003 - Biochemistry II - Learning Outcomes

• Identifying classes of organic molecules in food
• Describing metabolic processes of proteins, carbohydrates, and nucleic acids, and fatty acids,
• Classifying key catalysts involved in metabolic processes
• Determining relationships between pathways related to the digestion and synthesis of amino acids, fatty acids, and nucleic acids, as well as carbohydrates

Recommended Textbooks

• Voet & Voet: Biochemistry, 3rd edition, John Wiley & Sons
• Mathews, van Holde, Ahern: Biochemistry, 4th edition
• Berg, Tymoczko & Stryer: Biochemistry, 5th edition, Spectrum
• Horton, Moran, Scrimgeour, Perry & Rawn: Principles of Biochemistry, 4th edition
• Essentials and Beauty of Biochemistry

Metabolic Fuels and Dietary Components

• The body requires synthesizing the components it cannot acquire from the diet and protecting itself from toxins from the environment
• It metabolizes dietary components through pathways such as fuel oxidation, fuel storage and mobilization, biosynthesis, and detoxification.
• Our diet provides energy in the form of calories from elements like carbohydrate, fatty acids, and proteins.

Carbohydrates: Monosaccharides

• Monosaccharides typically exist in ring structures, with a carbonyl group reacting with a hydroxyl group within the same molecule
• Rings formed are five or six-membered
• The anomeric carbon is a result of intramolecular bonding from the carbonyl group and the hydroxyl group
• These molecules also undergo mutarotation, a process where the a and ß positions spontaneously interconvert when the ring opens and closes

Carbohydrates

• A disaccharide contains two monosaccharides linked by an O-glycosidic bond
• Oligosaccharides contain 3 to roughly 12 monosaccharides
• Polysaccharides have tens or thousands of monosaccharides
• Starch and glycogen are examples of branched polymers of glucosyl residues
• Polysaccharides can be found as components in the cell walls, and in animals, as energy storage molecules.

The Three Key Polysaccharides Made From Glucose Monosaccharides

• Cellulose, starch, and glycogen differing in linkage and branching
• Cellulose — used for structural support
• Starch — energy storage in plants
• Glycogen — energy storage in animals

Energy Content of Food Constituents

• Energy content of fat, glycogen, protein, glucose is discussed in kJ/g and total amounts in a human
• Important advantages of storing energy in fatty acids compared to sugars or amino acids relate to fatty acid structure and their suitability form storage tissue

Saturated and Unsaturated Fatty Acids

• Fatty acids can be saturated or unsaturated, based on the presence or absence of double bonds in the carbon backbone
• Melting point varies based on the degree of saturation—saturated are typically solid at room temperature, while unsaturated are typically liquid
• Trans fats differ from naturally occurring fatty acids, and are often used in food substitutes

Amino Acids and Peptide Formation

• Twenty amino acids are building blocks of proteins
• Amino acids differ in their side chains, which contain various atoms, and groups
• Amino acids are categorized based on their properties

The Acidic and Basic Amino Acids

• The pKa values differentiate acidic and basic amino acids
• It correlates with their ability to gain or lose a proton
• The isoelectric point (pI) identifies the pH at which the net charge of an amino acid is zero

Dissociation of Side Chains of Amino Acids

• Describes how the amino acid side chains can gain or lose protons depending on the pH of the environment
• pKa values indicate at what pH half the molecules in the solute will become ionized

Enzymes as Catalysts

• Enzymes are proteins that catalyze chemical processes including creating more products
• Enzymes speed up reaction rates by lowering the activation energy needed to initiate a reaction
• Enzymes are not consumed, meaning they are not consumed during the transformation of substrates to products

Antibiotic Penicillin as a Transition-State Analog

• Penicillin is a transition analog, tightly binding to an enzyme creating a specific enzyme-substrate complex
• This binding site is irreversible, inhibiting the normal function of the enzyme involved in bacterial cell wall synthesis

Coenzymes in Catalysis

• Coenzymes, non-protein organic molecules, function similarly to amino acid side chains
• Two general types are oxidation-reduction coenzymes and activation-transfer coenzymes
• Thiamine pyrophosphate (TPP), coenzyme A (CoA), biotin, or pyridoxal phosphate are examples of activation-transfer coenzymes derived from vitamins

Regulation of Enzyme Activity

• Enzyme activity, crucial for maintaining equilibrium in biological systems
• Methods like allosteric regulation, covalent modification, proteolytic cleavage by isoenzymes, enzyme availability, and compartmentalization, are explained
• Hormonal regulation as a final mechanism modifying enzyme activation and activity

Allosteric Interaction

• Allosteric interaction describes a sigmoid plot between the reaction rate and substrate concentration
• Example of homotropic interaction includes hemoglobin, where binding of one oxygen molecule changes the subsequent binding affinity for oxygen molecules within the same enzyme
• The altered affinity of different oxygen-binding sites for oxygen is crucial for the function of hemoglobin, to increase binding in regions with high oxygen demands within the body

Regulation by Covalent Modification

• Reversible, covalent changes in enzymes altering their activities
• Phosphorylation of specific amino acid side chains within the enzyme (Ser, Thr, Tyr) is common regulation method
• The change in side chain chemistry directly affects the overall function of the enzyme

Regulation By Compartmentation

• Compartmentalization within compartments limits diffusion of substances.
• Selective permeability of compartmental membranes control the rate of movement of metabolites
• This compartmentalization creates distinct areas within cells where specific metabolic reactions are regulated, ensuring appropriate metabolic function.

Energy-Related Organelles

• Mitochondria and chloroplasts are crucial for energy generation
• Photosynthesis in chloroplasts and cellular respiration in mitochondria convert energy from one form to the other
• Cellular respiration is also related to ATP production within the mitochondria and the usage of energy within the cell

Metabolism Overview

• Catabolism is the breakdown of complex molecules, releasing energy.
• Anabolism is the synthesis of complex molecules, requiring energy
• These processes are interconnected and regulated to maintain homeostasis

Transport and Fate of Major Carbohydrates and Amino Acids

• Glucose, proteins, amino acids, and other metabolites are transported throughout the body
• Organs such as the liver and kidneys, are central in transporting and converting metabolites
• Metabolism within the different parts of the body are coordinated, ensuring regulated transportation and utilization of metabolites

Energy Relationship Between Pathways

• The process of catabolism and anabolism are simultaneous
• Catabolism is oxidative and releases chemical energy in the form of ATP and NADPH
• Anabolism is reductive, using the energy from catabolism to synthesize complex molecules such as proteins, nucleic acids, and carbohydrates

NADH and NADPH as Sources of Free Energy

• Coenzymes NADH and NADPH are crucial in transferring electrons and hydrogen during biochemical reactions. The oxidation of NADH and NADPH are associated with energy release
• NADH and NADPH are involved in driving important cellular processes like biosynthesis, synthesis, and energy transfer

ATP Serves in a Cellular Energy Cycle

• ATP serves as the primary energy currency in the cell
• Hydrolysis of ATP releases energy, which powers many cellular processes like biosynthesis, muscle contraction, active transport, and osmotic work

Corresponding Pathways of Cata- and Anabolism

• Pathways are regulated to ensure they proceed efficiently and independently
• Reactions are localized or separated within compartments to prevent conflicting processes and maintain appropriate metabolic function

Multienzyme Systems Carrying out Metabolic Pathway

• Multienzyme systems facilitate and organize sequential reactions
• The organization can take several forms: physically separate soluble entities, multienzyme complexes, or membrane-bound structures
• Multienzyme systems increase efficiency of metabolism by concentrating enzymes and controlling processes

Metabolic Pathways Are Compartmentalized Within Cells

• Compartmentalization of metabolic pathways in cells isolates enzymes and other components involved in metabolic reactions
• Different compartments within cells house different metabolic reactions, e.g., glycolysis in the cytosol, citric acid cycle and oxidative phosphorylation in mitochondria

State of Reduction of Carbon Atoms in Biomolecules

• The level of reduction of carbon atoms in molecules determines their potential to release energy when oxidized

Biochemical Reaction Types

• Nucleophilic substitutions, nucleophilic additions, carbonyl condensations, eliminations, oxidation and reductions are the common types of transformations within biochemistry

Nucleophilic Substitution

• Carbonyl carbons, protonated imines, and phosphates are common examples of electrophiles, commonly interacting with nucleophiles to form covalent bonds

Quiz Regarding Biochemistry

• Several multiple-choice questions and explanations were not included regarding this topic

Explore the fundamentals of metabolism, including the critical processes of catabolism and anabolism. This quiz covers the essential pathways and reactions involved in converting food into energy and building blocks for cellular function. Ideal for students studying Biochemistry II.