Biochemistry Deep Dive

Cheatsheet Content

### Biomolecules: Structure and Function #### Carbohydrates - **Monosaccharides:** Simple sugars (glucose, fructose, galactose). - **Structure:** $(CH_2O)_n$, typically 3-7 carbons. Exist in linear and cyclic forms (hemiacetal/hemiketal). - **Function:** Primary energy source (e.g., glucose in cellular respiration), structural components (e.g., ribose in RNA). - **Disaccharides:** Two monosaccharides linked by a glycosidic bond (e.g., sucrose = glucose + fructose, lactose = glucose + galactose). - **Polysaccharides:** Long chains of monosaccharides. - **Storage:** Starch (plants), Glycogen (animals) - branched polymers of glucose. - **Structural:** Cellulose (plants) - linear polymer of glucose with $\beta$-1,4 linkages, Chitin (fungi, arthropods) - polymer of N-acetylglucosamine. #### Lipids - **Structure:** Diverse group, characterized by hydrophobicity. Primarily composed of C, H, O. - **Fatty Acids:** Long hydrocarbon chains with a carboxyl group. - **Saturated:** No C=C double bonds, straight chain, solid at room temp (e.g., palmitic acid). - **Unsaturated:** One or more C=C double bonds (mono- or polyunsaturated), kinked chain, liquid at room temp (e.g., oleic acid). - **Triglycerides:** Glycerol backbone esterified to three fatty acids. - **Function:** Major energy storage, insulation. - **Phospholipids:** Glycerol backbone, two fatty acids, and a phosphate group (often with an additional head group). - **Structure:** Amphipathic - hydrophilic head, hydrophobic tails. - **Function:** Major component of cell membranes (lipid bilayer). - **Steroids:** Four fused hydrocarbon rings (e.g., cholesterol, steroid hormones). - **Function:** Membrane fluidity (cholesterol), signaling molecules. #### Proteins - **Monomer:** Amino acids (20 common types). - **Structure:** Central alpha carbon, amino group ($NH_2$), carboxyl group ($COOH$), hydrogen atom, and a variable R-group (side chain). - **Classification:** Based on R-group (nonpolar, polar uncharged, acidic, basic). - **Peptide Bond:** Amide linkage between carboxyl of one amino acid and amino of another. - **Levels of Structure:** - **Primary:** Linear sequence of amino acids. - **Secondary:** Local folding ( $\alpha$-helices, $\beta$-sheets) stabilized by H-bonds in backbone. - **Tertiary:** 3D folding of a single polypeptide chain, stabilized by various interactions (hydrophobic, ionic, H-bonds, disulfide bridges). - **Quaternary:** Arrangement of multiple polypeptide subunits (e.g., hemoglobin). - **Function:** Enzymes, structural support, transport, signaling, immunity. #### Nucleic Acids - **Monomer:** Nucleotides. - **Structure:** Pentose sugar (ribose in RNA, deoxyribose in DNA), nitrogenous base (A, G, C, T/U), and 1-3 phosphate groups. - **Bases:** Purines (Adenine, Guanine - double ring), Pyrimidines (Cytosine, Thymine, Uracil - single ring). - **Phosphodiester Bond:** Linkage between 3'-hydroxyl of one sugar and 5'-phosphate of another. - **DNA (Deoxyribonucleic Acid):** - **Structure:** Double helix, antiparallel strands, sugar-phosphate backbone, bases paired (A-T, G-C) via H-bonds. - **Function:** Genetic information storage. - **RNA (Ribonucleic Acid):** - **Structure:** Typically single-stranded, contains Uracil instead of Thymine, ribose sugar. - **Types:** mRNA (messenger), tRNA (transfer), rRNA (ribosomal) - each with distinct functions in gene expression. ### Biological Membranes: Structure, Action Potential, and Transport #### Membrane Structure - **Fluid Mosaic Model:** Describes the cell membrane as a dynamic, fluid structure. - **Lipid Bilayer:** Primary component, formed by phospholipids (hydrophilic heads face aqueous environment, hydrophobic tails face inward). - **Fluidity:** Influenced by temperature, cholesterol (buffers fluidity), and degree of fatty acid saturation. - **Membrane Proteins:** - **Integral (Transmembrane):** Span the entire bilayer, often with hydrophobic regions interacting with lipid tails. - **Peripheral:** Loosely associated with the surface, often via non-covalent bonds with integral proteins or lipid heads. - **Functions:** Transport, enzymatic activity, signal transduction, cell-cell recognition, intercellular joining, attachment to cytoskeleton/ECM. - **Glycocalyx:** Carbohydrate chains covalently linked to lipids (glycolipids) or proteins (glycoproteins) on the outer surface, involved in cell recognition and adhesion. #### Transport Processes Across Membranes - **Passive Transport:** Movement down a concentration gradient, no energy required. - **Simple Diffusion:** Small, nonpolar molecules (O2, CO2, benzene) pass directly through the lipid bilayer. - **Facilitated Diffusion:** Requires membrane proteins (channels or carriers) for polar molecules or ions. - **Channels:** Form hydrophilic pores (e.g., ion channels, aquaporins). - **Carriers:** Bind specific molecules, undergo conformational change to move them across (e.g., glucose transporters). - **Osmosis:** Diffusion of water across a selectively permeable membrane. - **Active Transport:** Movement against a concentration gradient, requires energy (ATP hydrolysis). - **Primary Active Transport:** Uses ATP directly (e.g., Na+/K+ ATPase pump, creating electrochemical gradients). - **Secondary Active Transport (Co-transport):** Uses energy stored in an electrochemical gradient created by primary active transport. - **Symport:** Two substances move in the same direction (e.g., Na+-glucose cotransporter). - **Antiport:** Two substances move in opposite directions (e.g., Na+-Ca2+ exchanger). - **Bulk Transport:** For larger molecules or particles. - **Endocytosis:** Cell takes in substances. - **Phagocytosis:** "Cell eating" (large particles). - **Pinocytosis:** "Cell drinking" (fluids and solutes). - **Receptor-mediated Endocytosis:** Specific uptake via receptors. - **Exocytosis:** Cell expels substances. #### Action Potential - **Resting Membrane Potential:** - Neurons maintain a negative charge inside relative to outside (typically -70 mV). - Established by Na+/K+ ATPase (pumps 3 Na+ out, 2 K+ in) and differential permeability of the membrane to ions (more K+ leak channels than Na+). - **Depolarization:** Stimulus causes Na+ channels to open, Na+ rushes into the cell, making the inside less negative (more positive). - **Threshold Potential:** If depolarization reaches a critical level (e.g., -55 mV), voltage-gated Na+ channels rapidly open, leading to a rapid influx of Na+. - **Rising Phase:** Rapid and massive influx of Na+ ions, causing the membrane potential to become positive (up to +30 mV). - **Repolarization:** Voltage-gated Na+ channels inactivate, and voltage-gated K+ channels open, allowing K+ to flow out of the cell, making the inside negative again. - **Hyperpolarization (Undershoot):** K+ channels close slowly, leading to a brief period where the membrane potential is more negative than resting. - **Refractory Period:** Period during which a new action potential cannot be generated or is harder to generate (due to inactivated Na+ channels and open K+ channels). - **Propagation:** Action potentials are propagated unidirectionally along the axon due to the refractory period and myelin sheath (saltatory conduction). ### Enzymes: Classification, Kinetics, and Mechanism of Action #### Enzyme Classification - **Definition:** Biological catalysts, primarily proteins (some RNA - ribozymes), that speed up biochemical reactions without being consumed. - **Specificity:** Highly specific for their substrates and reactions. - **Nomenclature:** Often end in "-ase" (e.g., lactase, dehydrogenase). - **Six Major Classes (IUBMB System):** 1. **Oxidoreductases:** Catalyze redox reactions (transfer of electrons/H atoms). 2. **Transferases:** Catalyze transfer of functional groups (e.g., methyl, phosphate). 3. **Hydrolases:** Catalyze cleavage of bonds by addition of water. 4. **Lyases:** Catalyze cleavage of bonds without water or oxidation, often forming double bonds. 5. **Isomerases:** Catalyze intramolecular rearrangements (isomerization). 6. **Ligases:** Catalyze formation of bonds coupled with ATP hydrolysis. #### Enzyme Kinetics - **Activation Energy ($E_a$):** Enzymes lower $E_a$ by stabilizing the transition state, thus increasing reaction rate. They do not change $\Delta G$ (overall free energy change) or equilibrium. - **Active Site:** Specific region on the enzyme that binds the substrate. - **Induced Fit Model:** Substrate binding induces a conformational change in the enzyme, resulting in a tighter fit and optimal catalysis. - **Michaelis-Menten Kinetics:** Describes the rate of enzyme-catalyzed reactions. - **Assumptions:** Single substrate, irreversible reaction, steady-state (ES complex concentration is constant). - **Equation:** $V_0 = \frac{V_{max}[S]}{K_m + [S]}$ - **$V_{max}$ (Maximum Velocity):** Maximum rate when enzyme is saturated with substrate. Proportional to enzyme concentration. - **$K_m$ (Michaelis Constant):** Substrate concentration at $1/2 V_{max}$. Reflects affinity of enzyme for substrate (lower $K_m$ = higher affinity). - **Lineweaver-Burk Plot:** Linearizes Michaelis-Menten equation ($1/V_0$ vs $1/[S]$) for easier determination of $V_{max}$ and $K_m$. - **Enzyme Inhibition:** - **Reversible:** - **Competitive:** Inhibitor resembles substrate, binds to active site. Increases apparent $K_m$, $V_{max}$ unchanged. Can be overcome by increasing [S]. - **Non-competitive:** Inhibitor binds to allosteric site (not active site), changes enzyme conformation, reducing catalytic efficiency. Decreases $V_{max}$, $K_m$ unchanged. - **Uncompetitive:** Inhibitor binds only to ES complex, preventing product formation. Decreases both $V_{max}$ and apparent $K_m$. - **Irreversible:** Inhibitor forms a permanent covalent bond with enzyme, inactivating it (e.g., penicillin, nerve agents). #### Mechanism of Action - **Transition State Stabilization:** Enzymes bind the transition state more tightly than the substrate or product, lowering its energy. - **Proximity and Orientation:** Bring substrates together in optimal orientation for reaction. - **Acid-Base Catalysis:** Donate or accept protons to facilitate reaction. - **Covalent Catalysis:** Form transient covalent bonds with substrate. - **Metal Ion Catalysis:** Metal ions act as electrophiles, stabilize charges, or participate in redox. - **Cofactors/Coenzymes:** Non-protein molecules required for enzyme activity. - **Cofactors:** Inorganic ions (e.g., $Mg^{2+}$, $Zn^{2+}$). - **Coenzymes:** Organic molecules, often derived from vitamins (e.g., NAD+, FAD, CoQ). - **Regulation:** - **Allosteric Regulation:** Binding of a molecule at a site other than the active site (allosteric site) affects enzyme activity (activators or inhibitors). - **Covalent Modification:** Reversible addition/removal of groups (e.g., phosphorylation by kinases, dephosphorylation by phosphatases). - **Zymogen Activation:** Inactive precursor (zymogen) activated by proteolytic cleavage. - **Transcriptional/Translational Control:** Regulating enzyme synthesis. ### Basic Concepts and Designs of Metabolism #### General Principles - **Metabolism:** Sum of all chemical reactions in a living organism. - **Catabolism:** Breakdown of complex molecules into simpler ones, releasing energy (exergonic). (e.g., cellular respiration). - **Anabolism:** Synthesis of complex molecules from simpler ones, requiring energy (endergonic). (e.g., photosynthesis, protein synthesis). - **ATP (Adenosine Triphosphate):** Universal energy currency. Hydrolysis of high-energy phosphate bonds releases energy. - **NAD+/NADH, FAD/FADH2:** Electron carriers, crucial in redox reactions. #### Carbohydrate Metabolism - **Glycolysis:** Breakdown of glucose (6C) into two pyruvates (3C). - **Location:** Cytosol. - **Phases:** Energy investment (consumes 2 ATP), Energy payoff (produces 4 ATP, 2 NADH). - **Net Yield:** 2 ATP, 2 NADH, 2 Pyruvate. - **Anaerobic Fate of Pyruvate:** Lactic acid fermentation (animals), alcoholic fermentation (yeast). - **Pyruvate Oxidation:** Pyruvate converted to Acetyl-CoA ($CH_3COSCoA$). - **Location:** Mitochondrial matrix. - **Yield:** 1 NADH, 1 CO2 per pyruvate (2 NADH, 2 CO2 per glucose). - **Citric Acid Cycle (Krebs Cycle):** Acetyl-CoA combines with oxaloacetate to form citrate. - **Location:** Mitochondrial matrix. - **Yield per Acetyl-CoA:** 3 NADH, 1 FADH2, 1 ATP (or GTP), 2 CO2. - **Net Yield per Glucose:** 6 NADH, 2 FADH2, 2 ATP (or GTP), 4 CO2. - **Gluconeogenesis:** Synthesis of glucose from non-carbohydrate precursors (lactate, amino acids, glycerol). - **Location:** Liver (primarily). - **Importance:** Maintain blood glucose levels during fasting. - **Glycogenesis:** Synthesis of glycogen from glucose (storage). - **Glycogenolysis:** Breakdown of glycogen to glucose. - **Pentose Phosphate Pathway:** Produces NADPH (for reductive biosynthesis) and ribose-5-phosphate (for nucleotide synthesis). #### Lipid Metabolism - **$\beta$-Oxidation of Fatty Acids:** Breakdown of fatty acids into Acetyl-CoA. - **Location:** Mitochondrial matrix. - **Process:** Fatty acid chain shortened by 2 carbons in each cycle, producing 1 FADH2 and 1 NADH per cycle. - **Acetyl-CoA:** Enters citric acid cycle. - **Fatty Acid Synthesis:** Synthesis of fatty acids from Acetyl-CoA. - **Location:** Cytosol. - **Requires:** NADPH (from pentose phosphate pathway). - **Lipogenesis:** Synthesis of triglycerides for storage. - **Lipolysis:** Breakdown of triglycerides into fatty acids and glycerol. #### Amino Acid Metabolism - **Protein Turnover:** Continuous synthesis and degradation of proteins. - **Amino Acid Degradation:** - **Transamination:** Transfer of amino group to $\alpha$-ketoglutarate to form glutamate. - **Deamination:** Removal of amino group, often as ammonia ($NH_3$). - **Urea Cycle:** Converts toxic ammonia to urea for excretion (mammals). - **Carbon Skeletons:** Remaining $\alpha$-keto acids can be converted to intermediates of glycolysis or citric acid cycle (glucogenic or ketogenic amino acids). - **Amino Acid Synthesis:** Cells can synthesize non-essential amino acids. #### Nucleic Acid Metabolism - **De Novo Synthesis:** Synthesis of nucleotides from simpler precursors. - **Salvage Pathway:** Recycling of pre-existing bases and nucleosides. - **Degradation:** Nucleotides are broken down to nucleosides and then bases, which are further catabolized (e.g., purines to uric acid). #### Photosynthesis - **Overview:** Conversion of light energy into chemical energy (glucose) by plants, algae, and cyanobacteria. - **Location:** Chloroplasts (thylakoid membranes and stroma). - **Equation:** $6CO_2 + 6H_2O + \text{light energy} \rightarrow C_6H_{12}O_6 + 6O_2$ - **Light-Dependent Reactions:** - **Location:** Thylakoid membranes. - **Process:** Light energy excites electrons in chlorophyll (Photosystems II & I). Water is split (photolysis), releasing O2, electrons, and protons. Electrons move through electron transport chain. - **Products:** ATP (via chemiosmosis/photophosphorylation) and NADPH. - **Light-Independent Reactions (Calvin Cycle):** - **Location:** Stroma. - **Process:** Uses ATP and NADPH from light reactions to fix CO2 into glucose. - **Phases:** Carbon fixation (RuBisCO enzyme), Reduction, Regeneration of RuBP. #### Respiration and Electron Transport Chain #### Cellular Respiration (Aerobic) - **Overview:** Breakdown of glucose (or other organic molecules) to generate ATP. - **Equation:** $C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{Energy (ATP + heat)}$ - **Stages:** Glycolysis, Pyruvate Oxidation, Citric Acid Cycle (covered above), Oxidative Phosphorylation. #### Oxidative Phosphorylation - **Location:** Inner mitochondrial membrane. - **Components:** Electron Transport Chain (ETC) and Chemiosmosis. - **Electron Transport Chain (ETC):** - **Process:** NADH and FADH2 (from glycolysis, pyruvate oxidation, Krebs cycle) donate electrons to a series of protein complexes (Complex I-IV). - **Electron Flow:** Electrons move from higher to lower energy levels, releasing energy. - **Proton Pumping:** Energy released is used to pump protons ($H^+$) from the mitochondrial matrix into the intermembrane space, creating a proton gradient. - **Final Electron Acceptor:** Oxygen ($O_2$) accepts electrons and protons to form water ($H_2O$). - **Chemiosmosis:** - **Process:** Protons flow back into the mitochondrial matrix down their electrochemical gradient through ATP Synthase (Complex V). - **ATP Synthesis:** The flow of protons drives the rotation of ATP synthase, catalyzing the phosphorylation of ADP to ATP. - **Yield:** Most of the ATP (approx. 26-28 ATP) is generated here. #### Bioenergetics - **Thermodynamics in Biology:** - **First Law:** Energy cannot be created or destroyed, only transferred or transformed. - **Second Law:** Every energy transfer or transformation increases the entropy (disorder) of the universe. - **Gibbs Free Energy ($\Delta G$):** - **$\Delta G = \Delta H - T\Delta S$** - **Exergonic Reactions:** $\Delta G < 0$, spontaneous, release energy. - **Endergonic Reactions:** $\Delta G > 0$, non-spontaneous, require energy input. - **Equilibrium:** $\Delta G = 0$. Cells are rarely at equilibrium. - **Coupling Reactions:** Cells couple exergonic reactions (e.g., ATP hydrolysis) with endergonic reactions to drive unfavorable processes. - **Redox Reactions:** Transfer of electrons. - **Oxidation:** Loss of electrons. - **Reduction:** Gain of electrons. - **Reducing Agent:** Electron donor. - **Oxidizing Agent:** Electron acceptor. - **Standard Reduction Potential ($E_0'$):** Measure of a molecule's tendency to gain electrons. Higher $E_0'$ means stronger oxidizing agent. Electron flow occurs from lower to higher $E_0'$.