Biochemistry Exam 3: Chapter 11, 12, 13, 15 Review Guide

Advantages of Enzyme Complexes in Metabolic Pathways

• Enzymes organized in complexes enhance efficiency by:

  • Proximity: Substrates are close together, reducing diffusion time.

  • Coordination: Enables sequential reactions to occur without releasing substrates into the solution, minimizing side reactions.

  • Regulation: Allows coordinated regulation of multiple enzymes involved in a pathway.

Comparison of Catabolism and Anabolism

• Catabolism (exergonic): Breakdown of complex molecules to release energy. Examples include glycolysis and the citric acid cycle.

• Anabolism (endergonic): Building of complex molecules from simpler ones, requiring energy input. Examples include protein synthesis and gluconeogenesis.

Coupling of Reactions

• Coupling unfavorable reactions with favorable ones allows biochemical processes that would otherwise be thermodynamically not possible to occur. This occurs through the use of shared intermediates and free energy changes being additive.

Structure and Energetics of ATP

• Structure: ATP (Adenosine Triphosphate) consists of adenine, ribose, and three phosphate groups.

• Energetically Favorable Phosphoryl Transfer: The transfer of a phosphoryl group is energetically favorable due to:

  • Resonance stabilization of orthophosphate compared to ATP's phosphoryl groups.

  • Electrostatic repulsion among the negatively charged phosphate groups in ATP.

  • Increased entropy of the hydrolysis products compared to the reactants.

ATP Hydrolysis Power

• ATP hydrolysis powers many biological reactions, enabling processes such as muscle contraction, active transport, and biosynthesis, essentially fueling cellular work.

Energy Sources in Exercising Muscle

• Initially, muscles rely on stored ATP and creatine phosphate.

• As exercise continues, the reliance shifts to glycolysis and anaerobic metabolism, followed by aerobic respiration utilizing carbohydrates and fats for sustained energy production.

Proton Gradients and ATP Synthesis

• ATP synthesis is powered by proton gradients generated during electron transport in oxidative phosphorylation. This chemiosmotic gradient drives ATP synthase, coupling the flow of protons back into the mitochondrial matrix with ATP synthesis.

Stages of Energy Extraction from Food

• Stage 1: Digestion: Breakdown of food into simple building blocks (e.g., amino acids, fatty acids, glucose).

• Stage 2: Activation and Breakdown: Conversion into acetyl CoA and carbon skeletons during glycolysis and citric acid cycle.

• Stage 3: Oxidative Phosphorylation: Electrons from NADH and FADH₂ are transferred via the electron transport chain to produce ATP.

NAD+ and FAD as Electron Carriers

• NAD+ and FAD function as essential electron carriers in various metabolic reactions, particularly in oxidation of fuels, shuttling electrons to the electron transport chain for oxidative phosphorylation.

Coenzyme A and Acetyl CoA

• Structure of Coenzyme A: Contains a pantothenic acid component, with a reactive thiol group (–SH) which forms thioester bonds with acyl groups, facilitating the transfer of acyl groups in metabolic pathways.

• Acetyl CoA is a key substrate that contributes to both central metabolic pathways (Krebs cycle) and fatty acid synthesis.

Key Reactions in Metabolism

• Key metabolic reactions that are repeatedly used include:

  • Glycolysis (oxidation of glucose)

  • Citric acid cycle (Krebs cycle)

  • Oxidative phosphorylation.

Regulation of Metabolic Processes

• Three primary means of regulating metabolic processes:

  1. Enzyme amount control: Regulates synthesis and degradation rates of enzymes.

  2. Substrate accessibility control: Utilizes compartmentalization to separate divergent pathways.

  3. Catalytic activity control: Allosteric regulation or covalent modifications adjust enzymatic activity.

Membrane Transport Overview

• Three Classes of Membrane Transporter Proteins:

  • Pumps: Active transport mechanisms that require energy to move substances from low to high concentration.

  • Carriers: Facilitate movement of molecules across the membrane without direct energy use, taking advantage of high to low concentration gradients.

  • Channels: Facilitate ion or water transport, moving substances from high to low concentration.

Active vs. Passive Transport

• Active Transport: Movement against a concentration gradient, requiring energy (e.g., ATP).

  • Positive change in Gibbs free energy (ΔG > 0).

• Passive Transport: Movement down a concentration gradient without energy input.

  • Negative change in Gibbs free energy (ΔG < 0).

  • Examples: Simple diffusion (lipophilic molecules), facilitated diffusion (polar molecules).

Free Energy Change for Charged Species

• Electrochemical Potential: Defined as the sum of concentration and electric terms.

• Free energy change for moving a charged species: ΔG = RT ln(c2/c1) + ZFΔV where:

  • Z = charge of the species

  • ΔV = voltage across the membrane

  • F = Faraday's constant (96.5 kJ V⁻¹ mol⁻¹)

Na⁺–K⁺ ATPase

• Function: Maintains K⁺ and Na⁺ gradients across the plasma membrane.

• Mechanism: Catalyzes the hydrolysis of ATP to transport 3 Na⁺ out and 2 K⁺ in per cycle, requiring magnesium (Mg²⁺).

  • Standard Gibbs energy change: ΔG = 41.7 ext{ kJ mol}^{-1}.

Multidrug Resistance (MDR) Proteins

• Function: ATP-dependent transporters that expel toxins and drugs, allowing cancer cells to remove toxic drugs that enter the cell.

• Structure: Contain multiple membrane-spanning and ATP-binding domains.

Secondary Active Transport: Lactose Permease

• Definition: Coupled transport that uses the gradient of one ion (usually proton) to drive the transport of another substrate.

• Types:

  • Symporters: Transport substrates in the same direction.

  • Antiporters: Transport substrates in opposite directions.

  • Uniporters: Transport one substrate based on its concentration.

Ion Channels

• Function: Facilitate passive transport of ions rapidly across membranes.

• Mechanism of Action Potentials:

  • Depolarization occurs when Na⁺ flows into the cell; repolarization happens as K⁺ flows out.

  • Channels are voltage-gated (Na⁺ and K⁺ channels) and open in response to changes in membrane potential.

  • The ball and chain mechanism explains why channels remain inactive for a period of time (refractory period) after activation.

Nernst Equation

• The equilibrium potential for a given ion can be calculated as: V{eq} = -\frac{RT}{zF} ln\frac{[X]{in}}{[X]_{out}}

  • Where [X]{in} and [X]{out} are the intracellular and extracellular concentrations, respectively.

Gap Junctions and Aquaporins

• Gap Junctions: Facilitate intercellular communication, allowing small molecules and ions to pass between cells.

  • Composed of connexins.

• Aquaporins: Water channels that facilitate rapid transport of water across membranes while preventing the conduction of protons and other charged ions.

  • Their structure allows for selective permeability, ensuring that only water pass through rapidly while

Nomenclature of Fatty Acids

• Fatty acids are named based on the length of the carbon chain and the location of double bonds.

  • The naming convention involves replacing the final 'e' of the parent hydrocarbon with 'oic'.

  • The first number indicates carbon atoms, and the second indicates double bonds (e.g., 18:1 indicates 18 carbons and 1 double bond).

Functions of Lipids

• Energy Sources: Lipids serve as rich fuel sources and storage for energy.

• Hormonal Signaling: They act as signaling molecules that facilitate communication within and between cells.

• Membrane Composition: Membranes are made primarily of lipids, supporting their structural integrity and functionality.

Attributes of Membranes

• Membranes are composed of lipid bilayers that are sheet-like structures, two molecules thick.

• They are asymmetric and fluidic, allowing dynamic interactions between different lipid and protein components.

Basic Components of a Phospholipid

• Composed of:

  • A glycerol (or sphingosine) backbone.

  • Two fatty acids attached via ester bonds.

  • A phosphate group linked to an alcohol.

Glycerol Backbone vs Sphingosine Backbone

• Glycerol Backbone: Found in phosphoglycerides; it has three hydroxyl groups.

• Sphingosine Backbone: Found in sphingolipids; it has a long hydrocarbon chain with a single hydroxyl group and an amine group.

Basic Components of a Glycolipid

• Composed of:

  • A carbohydrate moiety attached to a backbone (glycerol or sphingosine).

  • One or two fatty acid tails.

Structure of Cholesterol

• Cholesterol has a steroid structure consisting of four fused hydrocarbon rings, with a hydroxyl group that is small compared to the bulk.

Formation of Micelles and Liposomes

• Amphipathic Nature of Phospholipids: The hydrophilic heads interact with water while hydrophobic tails avoid water, leading to the spontaneous formation of micelles and liposomes.

• Lipid bilayers form due to hydrophobic interactions, with self-sealing capabilities to minimize energetically unfavorable edges.

Permeability of Lipid Bilayers

• Impermeable Features: Lipid bilayers are impermeable to most polar and ionic substances due to their hydrophobic core.

• What Can Cross: Small nonpolar molecules (e.g., O₂, CO₂) can diffuse freely across.

• What Cannot Cross: Large polar molecules and ions usually cannot pass freely without aid.

Integral vs Peripheral Membrane Proteins

• Integral Proteins: Span the lipid bilayer and are often involved in transport.

• Peripheral Proteins: Attracted to membranes by weaker interactions and do not penetrate significant depths of the bilayer.

Typical Motifs Seen in Integral Membrane Proteins

• Specific structural motifs such as alpha-helices or beta-barrels that facilitate their integration into the lipid bilayer.

Prostaglandin H2 Synthase Example

• Review of its structure and function in membrane dynamics, showcasing the operation of integral membrane proteins in catalyzing reactions.

Lateral vs Transverse Diffusion

• Lateral diffusion: Movement of lipids within the same layer of the bilayer.

• Transverse (flip-flop): Movement of lipids from one layer to another, which occurs much less frequently due to the energy barrier.

FRAP Technique

• Fluorescence Recovery After Photobleaching: A technique used to study the fluidity and dynamics of membranes by observing the recovery of fluorescence in a bleached region of the membrane.

Factors Influencing Tm of Fluid Membranes

• Transition temperature (Tm) is influenced by fatty acid composition (chain length and degree of saturation).

  • Shorter and more unsaturated fatty acids lower Tm, while longer and saturated chains increase Tm.

Lipid Rafts

• Dynamic domains within the membrane enriched in cholesterol and specific lipids; play important roles in signaling and protein sorting.

Gram Positive vs Gram Negative Bacteria

• Gram Positive: Thick peptidoglycan layer retains crystal violet stain during Gram staining.

• Gram Negative: Thin peptidoglycan layer surrounded by an outer membrane; does not retain the crystal violet stain effectively.

Receptor-Mediated Endocytosis

• Specific uptake of molecules triggered by receptor binding, leading to internalization via vesicles.

• Membrane Budding and Fusion: Critical processes in intracellular transport and signaling.

SNAREs

• Proteins that mediate the fusion of vesicles with target membranes, facilitating the transport of cargo within cells.

• Formula of a Monosaccharide: The empirical formula for monosaccharides is $(CH2O)n$, where $n$ is typically between 3 to 7. They consist of carbon backbone with hydroxyl groups and may include additional functional groups.

• Structure of Glucose:

  • Flat Form: The flat structure of glucose, also known as its Fischer projection, shows the carbon atoms arranged in a linear chain with the aldehyde group at one end.

  • Ring Form: Glucose can cyclize into a ring form through a reaction between the carbonyl group and a hydroxyl group, leading to the formation of either $α-D$-glucopyranose or $β-D$-glucopyranose, depending on the orientation of the hydroxyl group on the anomeric carbon (C-1).

• Types of Isomers:

  • Constitutional Isomers: These have identical molecular formulas but differ in the connectivity of their atoms.

  • Stereoisomers: These have the same bonding sequence but differ in their spatial arrangement (e.g., D and L configurations;

    • Enantiomers: A type of stereoisomer that are mirror images of each other.

    • Diastereoisomers: Stereoisomers that are not mirror images of each other.

• Boat vs. Chair Formation of Glucose: The chair conformation is more stable than the boat conformation due to less steric hindrance between bulky groups, allowing for more favorable interactions between atoms.

• Importance of D-Glucose: D-Glucose is essential for most organisms as it serves as a primary source of energy for cellular processes through cellular respiration, and is a crucial building block for other carbohydrates.

• Reducing Sugar: Reducing sugars are those that can donate electrons to oxidizing agents, hence they can reduce substances such as Fehling's or Benedict's solutions. A test for reducing sugars involves heating a sugar solution with Fehling's solution, leading to the formation of a brick-red precipitate if reducing sugars are present.

• Glycation Importance in Diabetes: Glycation refers to the non-enzymatic addition of sugars to proteins, leading to the formation of advanced glycation end products (AGEs). Increased levels of AGEs in the body are linked to diabetic complications, as they can contribute to insulin resistance and vascular damage.

• Glycosidic Linkage:

  • O-Glycosidic Linkage: This type of bond forms between the anomeric carbon of a monosaccharide and the hydroxyl group of an alcohol.

  • N-Glycosidic Linkage: This bond forms between the anomeric carbon of a monosaccharide and the nitrogen of an amine.

• Phosphorylation of Sugars: The addition of phosphate groups to sugars is relevant for cellular metabolism as it helps in the regulation of sugar metabolism, promotes activation of sugars for further enzymatic reactions, and facilitates the retention of sugars within cells.

• Disaccharides: There are reducing and non-reducing disaccharides:

  • Reducing: Lactose (glucose + galactose), Maltose (glucose + glucose)

  • Non-reducing: Sucrose (glucose + fructose). The reducing end refers to the capability of one of the monosaccharide units to undergo oxidation/reduction.

• Glycogen, Starch, and Chitin:

  • Glycogen: Animal storage form of glucose, branched structure with $α-1,4$ and $α-1,6$ linkages.

  • Starch: Plant storage form of glucose; consists of amylose (unbranched) and amylopectin (branched).

  • Chitin: A structural polysaccharide found in the cell walls of fungi and exoskeletons of arthropods, composed of N-acetylglucosamine linked by $β-1,4$ linkages.

• Insoluble vs. Soluble Fiber:

  • Insoluble Fiber: Provides bulk, aiding in digestive health and preventing constipation.

  • Soluble Fiber: Can lower blood cholesterol and glucose levels, contributing to heart health.

• Glycoproteins:

  • Classes:

  • Glycoproteins: Have carbohydrate moieties influencing cell recognition and signaling.

  • Proteoglycans: Composed mainly of carbohydrate; provide structural support.

  • Mucins: Help in lubrication and protection of epithelial surfaces.

• N-linkage vs. O-linkage:

  • N-linkage: Involves attachment of carbohydrates to nitrogen on asparagine.

  • O-linkage: Involves attachment of carbohydrates to oxygen on serine or threonine.

• Post-translational Modification: Primarily occurs in the rough endoplasmic reticulum (RER) and Golgi apparatus, which are responsible for folding and processing proteins after protein synthesis, facilitating their functional maturation.

• Blood Group Antigens and Glycosylation: Various blood types arise from specific glycosylation patterns on red blood cells, modified by glycosyltransferases. Enzyme expression determines which sugars are added and thus influences a person’s blood type.

• I-Cell Disease: This lysosomal storage disease is caused by defective glycosylation, preventing lysosomal enzymes from reaching their intended location. Normally, lysosomal proteins have a mannose 6-phosphate tag that directs them to lysosomes, and this process is disrupted in I-Cell disease.

• Lectins: Focus on C-type lectins, which are important for cell-cell recognition and selectin function in the immune response.

• Influenza Virus: The influenza virus exploits glycoproteins on the host cell surface to attach and enter the cells. Viral particles exit by budding from the host cell membrane, where they also acquire a lipid bilayer that includes host glycoproteins essential for infectivity.

STEPS OF ACETYLCHOLINE

Acetylcholine (ACh) is a neurotransmitter that plays a critical role in neurotransmission. Here are the key steps involved in the synthesis, release, and degradation of acetylcholine:

1. Synthesis of Acetylcholine:

   • ACh is synthesized in the cytoplasm of the presynaptic terminal from acetyl-CoA and choline.

   • The enzyme choline acetyltransferase (ChAT) catalyzes this reaction, producing acetylcholine and CoA.

2. Packaging into Vesicles:

   • Once synthesized, acetylcholine is transported into vesicles by the vesicular ACh transporter (VAChT), where it is stored until release.

3. Release into Synaptic Cleft:

   • Upon an action potential reaching the presynaptic terminal, voltage-gated calcium (Ca²⁺) channels open, allowing calcium ions to enter the neuron.

   • Increased intracellular calcium concentration triggers the fusion of ACh-containing vesicles with the presynaptic membrane, releasing ACh into the synaptic cleft through exocytosis.

4. Binding to Receptors:

   • Acetylcholine diffuses across the synaptic cleft and binds to specific receptors on the postsynaptic membrane, such as nicotinic or muscarinic receptors.

   • This binding triggers a response in the postsynaptic neuron, leading to excitation or inhibition depending on the receptor type.

5. Degradation of Acetylcholine:

   • Acetylcholine in the synaptic cleft is rapidly degraded by the enzyme acetylcholinesterase (AChE), which hydrolyzes ACh into acetate and choline.

   • The breakdown products are taken back up into the presynaptic terminal for recycling, with choline being reused in the synthesis of new acetylcholine.

Understanding the complete cycle of acetylcholine from synthesis to degradation is essential for grasping neurotransmission mechanisms and their importance in the nervous system.

1. Synthesis: Acetylcholine is made from acetyl-CoA and choline in the presynaptic terminal by the enzyme choline acetyltransferase (ChAT).

2. Packaging: It is stored in vesicles via the vesicular ACh transporter (VAChT).

3. Release: When an action potential arrives, calcium ions enter the neuron, causing vesicles to fuse with the membrane and release ACh into the synaptic cleft.

4. Binding: ACh binds to nicotinic or muscarinic receptors on the postsynaptic neuron, leading to a response.

5. Degradation: Acetylcholine is broken down by acetylcholinesterase (AChE) into acetate and choline, which can be recycled for future synthesis.