Chapter 4 review (notes + lectures + exam review)

Cell Structure and Membrane Organization

• The cell membrane is composed primarily of lipids and proteins, forming a flexible, selectively permeable boundary that encloses the cytoplasm.

• Phospholipid Bilayer:

  • Consists of two layers of phospholipid molecules.

  • Polar (Hydrophilic) Regions: Phosphate heads face the outer and inner surfaces, interacting with extracellular and intracellular fluids.

  • Nonpolar (Hydrophobic) Regions: Fatty acid tails orient inward, forming a hydrophobic interior that acts as a barrier to water-soluble substances.

• Membrane Proteins:

  • Transmembrane Proteins (Integral Proteins): Span the entire membrane thickness, possessing both hydrophilic (polar) regions interacting with fluid environments and hydrophobic (nonpolar) regions embedded within the interior bilayer.

  • Peripheral Proteins: Associated with only one side of the membrane surface.

  • Functional Types:

  • Channel Proteins: Form pores allowing specific ions or molecules to cross.

  • Receptor Proteins: Bind specific extracellular molecules (e.g., hormones) to trigger intracellular responses.

  • Cell Identity Markers: Glycoproteins that identify cells as self.

• Cholesterol: Embedded within the phospholipid bilayer to stabilize the membrane structure and maintain appropriate fluidity.

• Glycocalyx: Carbohydrate chains extending from membrane proteins and lipids on the outer membrane surface that mark cells of an individual as "self" and distinguish differentiated cell types.

• Cytoskeleton: A structural network of microfilaments and microtubules attached to the inner membrane surface supporting cell shape and intracellular transport.

Cell Division: Mitosis and Cytokinesis

• Chromatids: Replicated chromosomes distinct during cell division. Each chromosome consists of two sister chromatids joined together at a single centromere.

• Phases of the Cell Cycle:

  • Early Interphase: Period of normal cell growth and metabolic function in daughter cells following division.

  • Restriction Checkpoint: Critical decision point in $G_1$ phase determining whether a cell proceeds to division, remains specialized, or undergoes apoptosis.

  • Late Interphase ($S$ and $G_2$ Phases): Cell passes restriction checkpoint, replicates genetic material ($S$ phase), replicates centrioles and mitochondria, and synthesizes additional membrane components.

  • Prophase: Chromosomes condense and become visible under microscopic examination. Nuclear envelope and nucleolus disperse. Spindle apparatus begins forming.

  • Late Prophase: Centrioles migrate to opposite sides of the cytoplasm. Microtubules assemble and associate with centrioles and centromeres of sister chromatids.

  • Metaphase: Chromosomes line up single file along the cell equator (metaphase plate). Spindle fibers from centrioles attach directly to centromeres of sister chromatids. Critical Note: Chromosomes will not separate properly if centrioles fail to attach to centromeres.

  • Anaphase: Spindle fibers shorten, breaking centromeres and pulling sister chromatids apart. Individual chromosomes move toward opposite centrioles at poles.

  • Telophase and Cytokinesis: Nuclear envelopes reassemble around daughter nuclei. Chromosomes decondense into threadlike chromatin. Spindle apparatus disperses. Division of cytoplasm occurs via a cleavage furrow, yielding two distinct daughter cells.

Cellular Metabolism: Anabolism and Catabolism

• Metabolism: The sum of all chemical reactions occurring within the body.

• Cellular Metabolism: The sum of all chemical reactions taking place inside individual cells. Metabolic reactions typically occur in structured pathways or cycles.

• Anabolism:

  • Process where small molecules are built into larger ones.

  • Requires input of energy ($ATP$) generated during catabolism.

  • Provides materials necessary for cellular growth, maintenance, and structural repair.

  • Dehydration Synthesis:

  • Anabolic reaction mechanism where smaller precursor molecules are joined together to form a larger complex molecule.

  • A molecule of water ($H_2O$) is produced as a byproduct in each reaction link.

  • Used to synthesize major biomolecules:

    • Polysaccharides: Monosaccharide + Monosaccharide $\rightleftharpoons$ Disaccharide + $H_2O$

    • Triglycerides: Glycerol + 3 Fatty Acid Molecules $\rightleftharpoons$ Triglyceride (Fat) + 3 $H_2O$

    • Proteins: Amino Acid + Amino Acid $\rightleftharpoons$ Dipeptide + $H_2O$ (connected via a covalent peptide bond)

• Catabolism:

  • Process where larger molecules are broken down into smaller, simpler constituent molecules.

  • Releases chemical energy used to generate $ATP$.

  • Hydrolysis:

  • Catabolic reaction mechanism where water ($H_2O$) is used to split chemical bonds in larger molecules.

  • Directly reverses dehydration synthesis.

  • Used to decompose complex carbohydrates, proteins, and lipids.

• Control of Metabolic Reactions:

  • Every cell concurrently conducts anabolic and catabolic processes.

  • Rates of energy-releasing catabolic reactions must balance precisely with energy-utilizing anabolic reactions.

  • Metabolic imbalances can damage or kill a cell.

Enzyme Structure, Function, and Regulation

• Enzymes:

  • Globular protein catalysts that control and accelerate metabolic reaction rates without being consumed.

  • Lower the activation energy required to initiate chemical reactions.

  • Reusable repeatedly because they remain unaltered at the end of reactions.

• Enzyme-Substrate Interaction:

  • Each enzyme is specific to a particular target substrate molecule.

  • Specificity depends on the precise 3D shape and conformation of the enzyme's active site.

  • The active site binds the substrate to form a temporary enzyme-substrate complex, generating the product molecule and releasing the unaltered enzyme.

• Nomenclature:

  • Most enzyme names end with the suffix "-ase" and are named after their substrate (e.g., lipase breaks down lipids).

• Factors Affecting Enzyme Conformation and Function:

  • Enzyme activity depends on maintaining active 3D conformation.

  • Conformation can be altered or destroyed by:

  • Excess heat

  • Radiation

  • Electricity

  • Specific chemical exposures

  • Extreme pH values

  • Certain poisons

  • Denaturation: Inactivation of an enzyme caused by an irreversible alteration of its structural conformation, preventing substrate binding.

• Cofactors and Coenzymes:

  • Cofactor: A non-protein substance required by an enzyme to achieve full catalytic activity. Functions by helping fold the active site into proper conformation or assisting in substrate binding. Examples include inorganic ions or elements (e.g., copper ion, zinc ion).

  • Coenzyme: An organic molecule acting as a cofactor. Most coenzymes are vitamins (essential organic nutrients that humans cannot synthesize and must obtain from diet).

• Metabolic Pathways and Regulation:

  • A sequence of enzyme-controlled reactions leading to the formation of a specific end product.

  • Pathways can be stepwise (linear) or cyclical.

  • Each step is catalyzed by a distinct, specialized enzyme; each new intermediate substrate is the product of the preceding reaction.

  • Rate-Limiting Enzyme:

  • A regulatory enzyme that catalyzes one key step in a pathway, dictating the maximum speed of the overall reaction sequence.

  • Present in limited concentration and typically positioned as the first enzyme in a metabolic sequence.

  • Negative Feedback: Regulatory mechanism where accumulated end product inhibits the rate-limiting enzyme early in the pathway, preventing overproduction.

Metabolomics and Inborn Errors of Metabolism

• The Human Metabolome:

  • Metabolome: The entire set of small molecules (metabolites) involved in metabolic processes within a cell, tissue, organ, or organism.

  • Human Metabolome Database: Repository storing data on human metabolites (estimated at minimum 2,500 metabolites in human cells, with less than half currently fully identified).

  • Applications: Medical diagnostics, drug discovery, personalized nutrition, newborn screening, and organ transplant monitoring.

• Inborn Errors of Metabolism:

  • Genetic mutations causing deficient or nonfunctional enzymes, blocking specific metabolic steps.

  • Leads to toxic accumulation of the pathway's substrate and deficiency of its downstream products.

  • Phenylketonuria (PKU):

  • Caused by a missing or nonfunctional enzyme required to convert the essential amino acid phenylalanine into tyrosine.

  • Excess phenylalanine accumulates in the blood and body tissues, acting as a neurotoxin that causes severe brain damage and death.

  • Treatment requires a specialized low-phenylalanine diet initiated at birth and maintained lifelong.

Cellular Energy and ATP Dynamics

• Energy: The capacity to produce change or perform physical/chemical work. Common forms include heat, light, sound, electrical, mechanical, and chemical energy.

• First Law of Thermodynamics: Energy cannot be created or destroyed, but can be converted from one physical/chemical form to another.

• Chemical Energy and Oxidation:

  • Cellular work relies primarily on chemical energy stored in molecular bonds.

  • Oxidation: Process releasing chemical energy from glucose and nutrient molecules through loss of hydrogen atoms and their electrons.

  • Enzymes lower the activation energy necessary for cellular oxidation reactions.

• Energy Distribution in Respiration:

  • $40\%$ of released chemical energy is captured and stored in $ATP$ bonds.

  • $60\%$ of released energy escapes as heat, maintaining homeostatic body temperature.

• Adenosine Triphosphate ($ATP$):

  • Primary energy-carrying molecule within cells.

  • Structure:

  • Adenosine: Composed of the nitrogenous base Adenine bound to a 5-carbon Ribose sugar.

  • Phosphate Chain: Three linked phosphate groups ($P \sim P \sim P$).

  • Second and third phosphate bonds are high-energy bonds that release transferable energy upon cleavage.

• ATP-ADP Energy Cycle:

  • Energy Release: Cleavage of the terminal phosphate bond converts $ATP$ into Adenosine Diphosphate ($ADP$) and inorganic phosphate ($P_i$), releasing energy for cellular work.

  • Phosphorylation: Reattaching a phosphate group to $ADP$ requires energy input derived from cellular respiration ($ADP + P_i \rightarrow ATP$).

Cellular Respiration and Energy Production

• Cellular Respiration: Metabolic process transferring chemical energy from nutrient molecules (glucose) to $ATP$ for cellular utilization.

• Overall Process Equation & Products:

  • Glucose + O_2 \rightarrow CO_2 + H_2O + ATP (40\%) + \text{Heat } (60\%)$\n - Maximum Yield: Up to 36 ATP per glucose molecule.\n\n- **Respiration Pathways Overview**:\n - **Anaerobic Reactions**: Do not require oxygen (O_2); occur in cytoplasm.\n - **Aerobic Reactions**: Require oxygen (O_2); occur within mitochondria.\n\n## Stage 1: Glycolysis\n\n- **Location**: Cytosol / Cytoplasm.\n- **Oxygen Requirement**: Anaerobic.\n- **Sequence**: A stepwise series of 10 enzyme-catalyzed reactions breaking 1 6-carbon glucose molecule into 2 3-carbon pyruvic acid molecules.\n\n- **Three Phases of Glycolysis**:\n - **Phase 1: Phosphorylation (Priming)**: Glucose is phosphorylated twice using 2 ATP molecules, forming fructose-1,6-diphosphate.\n - **Phase 2: Cleavage**: The 6-carbon intermediate is cleaved into two 3-carbon molecules: dihydroxyacetone phosphate and glyceraldehyde phosphate (G3P).\n - **Phase 3: Oxidation and ATP Formation**: G3P is rearranged; hydrogen atoms/electrons are transferred to 2 NAD^+$(nicotinamide adenine dinucleotide) to form 2$NADH + H^+$; 4$ADP$are phosphorylated to yield 4$ATP.\n\n- **Net Yield of Glycolysis**:\n - 2 Pyruvic acid molecules\n - 2 Net ATP$(4 produced$-$ 2 invested)

  • 2 $NADH + H^+$

Stage 2: Synthesis of Acetyl-CoA and Anaerobic Fermentation

• Anaerobic Pathway (Lactic Acid Fermentation):

  • In the absence of $O_2$, electron transport stops, leaving no terminal electron acceptor.

  • $NADH$ unloads high-energy electrons and hydrogen atoms back onto pyruvic acid, converting it into lactic acid ($2\text{ pyruvic acid} + 2\text{ NADH} + 2H^+ \rightarrow 2\text{ lactic acid} + 2\text{ NAD}^+$).

  • Lactic acid accumulates in tissues, inhibiting glycolysis and limiting energy yield to a net of 2 $ATP$ per glucose.

• Aerobic Pathway (Acetyl-CoA Formation):

  • In the presence of $O_2$, pyruvic acid moves from cytoplasm into the mitochondrial matrix.

  • Each 3-carbon pyruvic acid loses 1 carbon atom as carbon dioxide ($CO_2$) and combines with Coenzyme A (CoA) to produce 2-carbon Acetyl Coenzyme A (Acetyl-CoA).

  • Generates 1 $NADH + H^+$ per pyruvic acid (total 2 $NADH$ per glucose).

Stage 3: Citric Acid Cycle (Krebs Cycle)

• Location: Mitochondrial matrix.

• Oxygen Requirement: Aerobic.

• Mechanism: A cyclical metabolic pathway where the final product reacts to replenish the initial substrate.

• Reaction Steps:

  1. 2-carbon Acetyl-CoA combines with 4-carbon oxaloacetic acid to form 6-carbon citric acid.

  2. Citric acid undergoes sequential enzymatic modifications, converting back into oxaloacetic acid.

  3. Each turn removes 2 carbon atoms as $2\text{ }CO_2$, synthesizes 1 $ATP$, and transfers hydrogen atoms to carrier molecules ($NAD^+$ and $FAD$).

• Yield per Glucose Molecule (2 turns of cycle):

  • 2 $ATP$

  • 6 $NADH + H^+$

  • 2 $FADH_2$

  • 4 $CO_2$

Stage 4: Electron Transport Chain and Oxidative Phosphorylation

• Location: Inner mitochondrial membrane (cristae).

• Oxygen Requirement: Aerobic.

• Mechanism:

  • $NADH$ and $FADH_2$ deliver high-energy electrons and hydrogen ions ($H^+$) to a series of membrane-bound enzyme complexes (electron carriers).

  • As electrons pass down the chain, released energy powers the enzyme ATP synthase to catalyze phosphorylation of $ADP$ into $ATP$.

  • Oxygen ($O_2$) serves as the final electron acceptor, combining with $2e^-$ and $2H^+$ to yield water ($H_2O$).

• ATP Yield Calculation in Electron Transport System (ETS):

  • Electron carriers entering ETS per glucose: 10 $NADH$ (2 from Glycolysis, 2 from Acetyl-CoA formation, 6 from Citric Acid Cycle) and 2 $FADH_2$ (from Citric Acid Cycle).

  • Standard calculation per slide notes:

  • 8 $NADH$ entering oxidative pathways $\times$ 3 $ATP$ = 24 $ATP$

  • 2 $FADH_2$ $\times$ 2 $ATP$ = 4 $ATP$

  • Total ETS Yield = 28 $ATP$ (or 26–28 $ATP$ depending on transport shuttle efficiency).

• Summary of Complete Glucose Oxidation Yield:

  • Glycolysis: 2 $ATP$

  • Citric Acid Cycle: 2 $ATP$

  • Electron Transport Chain: 28 $ATP$

  • Grand Total: Up to 36 $ATP$ per glucose molecule.

Carbohydrate Storage and Alternative Metabolic Pathways

• Monosaccharides derived from carbohydrate digestion can:

  • Enter catabolic pathways to yield energy, $CO_2$, and $H_2O$

  • Enter anabolic pathways to construct storage molecules

  • React to form certain non-essential amino acids

• Storage Forms:

  • Glycogen: Polysaccharide stored primarily in liver and muscle cells.

  • Fat (Triglycerides): Synthesized when excess glucose remains after glycogen reserves are saturated; stored in adipose tissue.

• Catabolism of Other Nutrient Biomolecules:

  • Proteins: Broken down into amino acids $\rightarrow$ deaminated (removal of $-NH_2$ amine group) $ ightarrow$ converted to pyruvic acid, Acetyl-CoA, or Citric Acid Cycle intermediates.

  • Fats: Hydrolyzed into glycerol (converted to pyruvic acid/G3P in glycolysis) and fatty acids (broken down into 2-carbon Acetyl-CoA fragments via beta-oxidation).

Nucleic Acids, DNA Structure, and Genome Organization

• Deoxyribonucleic Acid (DNA): Genetic material storing instructions for amino acid sequences required to construct structural proteins, blood proteins, enzymes, antibodies, and membrane transporters.

• Key Definitions:

  • Gene: Sequence of DNA nucleotides containing genetic instructions to synthesize 1 functional protein.

  • Genome: Complete set of genetic material in a cell (human genome contains approximately 3.2 billion base pairs).

  • Exome: Small portion of the genome that directly codes for proteins.

  • Gene Expression: Control of which specific proteins are produced in each cell type, in what amounts, and under given physiological conditions.

• Molecular Structure of DNA:

  • Double-stranded molecule twisted into a double helix resembling a spiral ladder.

  • Building Blocks: Nucleotides, each consisting of:

  • A 5-carbon sugar: Deoxyribose

  • A phosphate group

  • A nitrogenous base: Adenine ($A$), Guanine ($G$), Cytosine ($C$), or Thymine ($T$)

  • Structural Components:

  • Backbone: Alternating covalent sugar-phosphate chain.

  • Antiparallel Orientation: The two nucleotide chains run in opposite directions.

  • Nitrogenous Base Classes: Purines (Adenine and Guanine) and Pyrimidines (Cytosine and Thymine).

  • Complementary Base Pairing: Nitrogenous bases pair across strands linked by hydrogen bonds. A purine always binds a specific pyrimidine:

    • Adenine pairs with Thymine ($A-T$)

    • Cytosine pairs with Guanine ($C-G$)

  • Chromatin & Chromosomes: DNA double helix wraps around globular histone proteins to condense into chromatin and highly coiled chromosomes.

• DNA Profiling (DNA Fingerprinting): Analytical technique comparing variable regions of the genome between individuals. Used in crime scene identification, paternity testing, and exonerating wrongfully convicted individuals.

DNA Replication

• Occurs prior to cell division during Interphase ($S$ phase) to ensure daughter cells receive identical genetic information.

• Steps of DNA Replication:

  1. Hydrogen bonds between complementary base pairs break.

  2. Double helix unwinds and the two strands separate.

  3. DNA Polymerase matches new complementary nucleotides with exposed bases on template strands ($A-T$, $C-G$).

  4. Ligating enzymes connect the new sugar-phosphate backbones, creating two identical double-stranded DNA molecules.

Protein Synthesis: Transcription and Translation

RNA Structure and Types

• Ribonucleic Acid (RNA) vs. DNA:

  • Single strand of nucleotides (vs. double-stranded DNA).

  • Contains Ribose sugar (vs. Deoxyribose).

  • Contains the pyrimidine base Uracil ($U$) instead of Thymine ($A-U$, $C-G$ base pairing).

  • Substantially shorter chain length than DNA.

• Types of RNA:

  • Messenger RNA (mRNA): Carries transcribed genetic code from DNA in nucleus out to cytoplasm.

  • Transfer RNA (tRNA): Reads mRNA codons and transfers specific amino acids to ribosome during translation.

  • Ribosomal RNA (rRNA): Structural and catalytic RNA component forming ribosome subunits along with proteins.

Stage 1: Transcription

• Definition: Synthesis of an mRNA molecule containing the complementary code of a specific DNA gene sequence.

• Location: Nucleus.

• Steps in Transcription:

  1. RNA Polymerase recognizes and binds to the Promoter (a specific DNA sequence signaling the start of a gene).

  2. RNA polymerase unwinds and separates a segment of the DNA double helix to expose gene bases.

  3. RNA polymerase moves down the template DNA strand, assembling complementary RNA nucleotides ($A \rightarrow U$, $T \rightarrow A$, $C \rightarrow G$, $G \rightarrow C$).

  4. Reaches a termination signal $\rightarrow$ newly synthesized mRNA strand is released.

  5. DNA rewinds back into a double helix.

  6. mRNA exits the nucleus through a nuclear pore to enter the cytoplasm.

Stage 2: Translation

• Definition: Conversion of genetic code carried by mRNA into a specific polypeptide chain of amino acids.

• Location: Cytoplasm at a ribosome.

• The Genetic Code:

  • Codon: A sequence of 3 consecutive mRNA nucleotides coding for a specific amino acid.

  • Total possible codons: $4^3 = 64$ combinations for 20 amino acids.

  • Initiation Codon: AUG (codes for methionine and signals the start of protein synthesis).

  • Stop Codons: UAA, UAG, UGA (signal termination of translation; do not code for amino acids or bind tRNA).

  • Anticodon: A 3-base sequence on tRNA complementary to a specific mRNA codon.

• Steps in Translation:

  1. Ribosome binds to mRNA strand near the start codon (AUG).

  2. Initiator tRNA carrying Methionine binds via its anticodon (UAC) to the start codon (AUG).

  3. A second tRNA carrying its designated amino acid binds to the adjacent mRNA codon.

  4. A peptide bond forms between the adjacent amino acids.

  5. The first tRNA releases its amino acid and detaches from ribosome to return to cytoplasm (where it can bind another identical amino acid).

  6. Ribosome shifts down the mRNA strand by one codon.

  7. Process repeats sequentially, elongating the polypeptide chain.

  8. Ribosome reaches a Stop codon (UAA, UAG, or UGA) $\rightarrow$ completed protein releases $\rightarrow$ folds into functional conformation. mRNA, ribosome, and tRNAs are recycled.

Genetic Variations, Mutations, and DNA Repair

• Genome Similarity: All humans share $99.9\%$ of their DNA sequence. The $0.1\%$ variation accounts for individual differences in health, physical appearance, and benign sequence variations.

• Mutation: Any permanent alteration in a DNA base sequence (bases substituted, added, or deleted).

• Causes of Mutations:

  • Spontaneous Mutations: Arise naturally from rare errors during DNA replication (e.g., insertion of an unstable base).

  • Induced Mutations: Caused by exposure to mutagens (environmental agents such as chemical toxins or radiation).

• Consequences of Mutations:

  • Harmful Mutations: Alter amino acid sequences, producing nonfunctional or missing proteins.

  • Example: Sickle Cell Disease — A single nucleotide substitution alters the amino acid sequence of hemoglobin, causing red blood cells to deform into a sickle shape under low-oxygen conditions, producing severe pain and tissue ischemia.

  • Neutral Mutations: Do not alter protein function, often due to code degeneracy (where 2 to 4 codons code for the same amino acid).

  • Beneficial Mutations: Rare mutations providing functional advantages (e.g., a receptor mutation preventing HIV entry into host cells).

• Protection Against Mutations:

  • DNA Repair Systems: Repair enzymes scan DNA to detect and correct mismatched bases.

  • Code Degeneracy: Third-base codon changes often code for the identical amino acid.

  • Diploid Genome: Having two copies of each chromosome provides a normal backup gene copy if one allele is mutated.

Classroom Dialogue and Student Discussion

• Question: What occurs during a catabolic process?

  • Answer: A large, single substrate molecule is broken down into multiple smaller products or substances, releasing energy.

• Question: Is an enzyme specific to every single substrate?

  • Answer: No. Enzymes have specific active site shapes that fit only designated target substrate molecules, analogous to a lock and key.

• Question: What is the distinction between a cofactor and a coenzyme when classifying vitamins?

  • Answer: While a coenzyme is technically a specialized organic subtype of a cofactor, vitamins are explicitly categorized as coenzymes.

• Question: What occurs medically in individuals diagnosed with Phenylketonuria (PKU)?

  • Answer: Individuals with PKU lack the active enzyme required to process the amino acid phenylalanine into tyrosine. Unprocessed phenylalanine accumulates in body fluids, causing severe brain toxicity and death if untreated dietarily.

• Question: Can energy be destroyed according to physical laws?

  • Answer: No, chemical and physical energy cannot be created or destroyed; it is transformed from one physical state or molecular bond to another.

• Question: How is energy partitioned during glucose oxidation in cellular respiration?

  • Answer: $40\%$ of released energy is conserved as chemical energy in $ATP$ bonds, while the remaining $60\%$ is released as heat.

• Question: When a phosphate bond is broken from $ATP$, is energy released or absorbed?

  • Answer: Cleaving the terminal phosphate bond releases chemical energy for cellular work, forming $ADP$.

• Question: Does attaching a phosphate back to $ADP$ release or require energy?

  • Answer: Reattaching a phosphate group to $ADP$ requires energy input derived from nutrient oxidation during cellular respiration.