Bio 110 Impulitti Notes

Chapter 9: Cellular Respiration

Key Concepts:

1. Redox Reactions in Metabolism:

   • Oxidation: Loss of electrons or hydrogen atoms from a molecule. In cellular respiration, this typically involves the transfer of electrons from glucose (C—C or C—H bonds) to oxygen.

   • Reduction: Gain of electrons or hydrogen atoms. Oxygen is reduced during respiration when it gains electrons to form water.

   • Importance in Cellular Respiration: Redox reactions allow energy to be released in small, controlled amounts as electrons are transferred from molecules like glucose to electron carriers (NAD+ and FAD), which later donate these electrons to the electron transport chain (ETC).

2. Glycolysis:

   • Location: Cytoplasm

   • Function: The first stage of cellular respiration, glycolysis breaks down 1 molecule of glucose (6-carbons) into 2 molecules of pyruvate (3-carbons each).

   • Products: Produces 2 ATP (net gain), 2 NADH (electron carrier), and 2 pyruvate.

   • Detailed Steps:

     • Energy Investment Phase: 2 ATP molecules are used to phosphorylate glucose, creating an unstable sugar molecule that eventually splits into two 3-carbon molecules (glyceraldehyde-3-phosphate).

     • Energy Payoff Phase: Each glyceraldehyde-3-phosphate is oxidized, transferring electrons to NAD+ (forming NADH). Additionally, substrate-level phosphorylation produces 4 ATP (2 ATP per glyceraldehyde-3-phosphate), resulting in a net gain of 2 ATP.

   • Anaerobic and Aerobic Conditions: Glycolysis occurs whether oxygen is present (aerobic) or absent (anaerobic), making it an ancient, conserved metabolic pathway.

3. Pyruvate Oxidation:

   • Location: Mitochondrial matrix (in eukaryotes)

   • Function: Converts pyruvate into Acetyl-CoA, linking glycolysis to the Citric Acid Cycle.

   • Key Products: 2 pyruvate molecules are converted into 2 Acetyl-CoA, 2 NADH, and 2 CO2.

   • Process: Each pyruvate (3-carbon) loses one carbon in the form of CO2. The remaining 2-carbon molecule is oxidized, forming Acetyl-CoA, and the electrons are transferred to NAD+, forming NADH.

4. Citric Acid Cycle (Krebs Cycle):

   • Location: Mitochondrial matrix

   • Function: Completes the oxidation of glucose derivatives, transferring high-energy electrons to NAD+ and FAD for use in the ETC.

   • Products: For each Acetyl-CoA (2 per glucose molecule), the cycle produces 3 NADH, 1 FADH2, 1 ATP (via substrate-level phosphorylation), and releases 2 CO2. Since the cycle runs twice for each glucose, the total yield per glucose is 6 NADH, 2 FADH2, 2 ATP, and 4 CO2.

   • Key Steps:

     • Citrate Formation: Acetyl-CoA (2-carbon) combines with oxaloacetate (4-carbon) to form citrate (6-carbon).

     • Decarboxylation: Citrate undergoes a series of reactions, releasing 2 CO2 molecules.

     • Regeneration of Oxaloacetate: The cycle regenerates oxaloacetate to combine with another Acetyl-CoA.

5. Electron Transport Chain (ETC) and Chemiosmosis:

   • Location: Inner mitochondrial membrane

   • Function: The ETC uses electrons from NADH and FADH2 to pump protons (H+) across the inner membrane, creating a proton gradient. This gradient drives the synthesis of ATP via chemiosmosis, where protons flow back through the enzyme ATP synthase, producing ATP.

   • Oxygen’s Role: Oxygen is the final electron acceptor in the ETC. It combines with electrons and protons to form water. Without oxygen, the ETC cannot function, stopping ATP production.

   • ATP Yield: This process produces the majority of the cell’s ATP (~32-34 ATP molecules per glucose).

6. Aerobic vs. Anaerobic Respiration:

   • Aerobic Respiration: Requires oxygen and produces up to 38 ATP per glucose (glycolysis, Citric Acid Cycle, and oxidative phosphorylation combined).

   • Anaerobic Respiration: Occurs without oxygen, and organisms rely on fermentation to regenerate NAD+, yielding only 2 ATP per glucose through glycolysis.

7. Fermentation:

   • Alcoholic Fermentation: In yeast, pyruvate is converted to ethanol and CO2, regenerating NAD+ to keep glycolysis going.

   • Lactic Acid Fermentation: In muscle cells during oxygen depletion, pyruvate is reduced to lactate to regenerate NAD+ for glycolysis. This process allows ATP production in the absence of oxygen, but lactate accumulation can lead to muscle fatigue.

Important Reactions:

• Overall Cellular Respiration Equation:
  C6H12O6+6O2→6CO2+6H2O+ATP\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + \text{ATP}C6​H12​O6​+6O2​→6CO2​+6H2​O+ATP

• Glycolysis:
  Glucose → 2 Pyruvate, 2 ATP, 2 NADH

• Citric Acid Cycle:
  Acetyl-CoA → 2 CO2, 3 NADH, 1 FADH2, 1 ATP (per cycle)

Chapter 10: Photosynthesis

Key Concepts:

1. Photosynthesis Overview:

   • Photosynthesis converts light energy into chemical energy stored in glucose.

   • Formula:
     6CO2+6H2O+light energy→C6H12O6+6O26CO_2 + 6H_2O + \text{light energy} \rightarrow C_6H_{12}O_6 + 6O_26CO2​+6H2​O+light energy→C6​H12​O6​+6O2​
     (Carbon dioxide + water + light energy → glucose + oxygen).

   • Occurs in the chloroplasts of plant cells, mainly in mesophyll cells.

2. Structure of the Chloroplast:

   • Chloroplast Anatomy:

     • Stroma: Fluid inside the chloroplast where the Calvin Cycle occurs.

     • Thylakoids: Membrane-bound structures that house the light-dependent reactions.

     • Grana: Stacks of thylakoids.

     • Chlorophyll: A pigment located in the thylakoid membranes that absorbs light for photosynthesis (primarily absorbs blue and red light, reflects green).

3. Two Stages of Photosynthesis:

   • Light Reactions (in the thylakoid membranes):

     • Purpose: Convert solar energy into chemical energy (ATP and NADPH).

     • Process:

       • Photosystem II (PS II): Absorbs light, exciting electrons which are passed down the electron transport chain (ETC). Water is split, releasing oxygen, protons, and electrons.

       • Photosystem I (PS I): Absorbs light, re-exciting electrons that are used to reduce NADP+ to NADPH.

       • Chemiosmosis: As electrons move through the ETC, protons are pumped into the thylakoid space, creating a gradient. Protons flow back into the stroma through ATP synthase, generating ATP.

     • Outputs: ATP, NADPH, and O₂.

   • Calvin Cycle (in the stroma):

     • Purpose: Use ATP and NADPH to fix CO₂ and produce sugar.

     • Steps:

       • Carbon Fixation: CO₂ is fixed to a 5-carbon sugar, RuBP, by the enzyme Rubisco. This produces a 6-carbon intermediate that immediately splits into two 3-carbon molecules.

       • Reduction: ATP and NADPH are used to reduce the 3-carbon molecules into G3P.

       • Regeneration: Most G3P is used to regenerate RuBP, while some is used to form glucose.

     • Outputs: 1 G3P molecule (for glucose) for every 3 CO₂ molecules fixed.

4. Photorespiration and Adaptations in Plants:

   • Photorespiration: Occurs when Rubisco fixes O₂ instead of CO₂, leading to the consumption of energy without producing sugar. This happens under hot, dry conditions when plants close their stomata to conserve water, reducing CO₂ availability.

   • C4 Plants: Adapted to minimize photorespiration by separating carbon fixation and the Calvin cycle into different cells (e.g., maize).

   • CAM Plants: Open their stomata at night to take in CO₂ and store it as an organic acid for use during the day when the stomata are closed (e.g., cacti).

Chapter 11: Cell Communication

Key Concepts:

1. Cellular Messaging:

   • Purpose: Cells need to communicate with each other to regulate processes like growth, immune responses, and homeostasis. Communication is vital for maintaining the complex activities of multicellular organisms.

   • Types of Signals:

     • Autocrine Signaling: A cell targets itself by releasing signaling molecules that bind to its own receptors.

     • Paracrine Signaling: Cells release signals to nearby cells (e.g., growth factors that stimulate neighboring cells to divide).

     • Endocrine Signaling: Hormones travel through the bloodstream to target distant cells (e.g., insulin regulating blood sugar levels).

     • Synaptic Signaling: Neurons release neurotransmitters to communicate with adjacent nerve cells or muscles, as seen in the nervous system.

2. Quorum Sensing in Bacteria:

   • In the microbial world, bacteria release signaling molecules to monitor their population density (quorum sensing). When a sufficient concentration of signaling molecules is detected, it triggers behaviors like biofilm formation or virulence factor production.

3. Signal Transduction Pathway:

   • Reception: A signaling molecule (ligand) binds to a receptor on the cell surface (or inside the cell, in the case of intracellular receptors).

   • Transduction: The receptor undergoes a conformational change, initiating a cascade of intracellular events (e.g., phosphorylation). This amplification of the signal allows a small number of signaling molecules to produce a large cellular response.

   • Response: The final stage in which the cell responds to the signal by activating specific enzymes, changing gene expression, or altering cellular behavior (e.g., cell division, secretion of hormones).

4. G-Protein-Coupled Receptors (GPCRs):

   • Structure: GPCRs are membrane proteins that detect extracellular molecules and activate G-proteins inside the cell.

   • Function: Once a ligand binds, the GPCR activates the G-protein, which in turn activates enzymes or ion channels, triggering further intracellular signaling pathways (e.g., production of cyclic AMP (cAMP), a second messenger).

   • Examples: Many hormones, neurotransmitters, and sensory signals (e.g., vision and smell) are mediated by GPCRs.

5. Apoptosis (Programmed Cell Death):

   • Purpose: Apoptosis is essential for development (e.g., shaping fingers and toes) and for removing damaged cells.

   • Molecular Mechanism: Apoptosis is initiated by internal signals (e.g., DNA damage) or external signals (death ligands). These signals activate caspases (proteolytic enzymes) that degrade cellular components, leading to cell death.

   • Regulation: In worms (C. elegans), the protein Ced-9 inhibits apoptosis. When Ced-9 is inactivated by apoptotic signals, Ced-4 and Ced-3 are activated, initiating cell death.

Key Processes:

• Reception: Ligands (e.g., hormones) bind to specific receptors. Without the correct receptor, the cell cannot respond to the

Chapter 12: Mitosis

Key Concepts:

1. Cell Division and Its Importance:

   • Growth and Development: Organisms grow from a single fertilized cell to a multicellular organism through mitosis.

   • Repair: Mitosis replaces damaged or dead cells.

   • Reproduction: In unicellular organisms, mitosis is the method of reproduction (e.g., binary fission in prokaryotes).

2. The Cell Cycle:

   • Interphase: The cell grows, replicates its DNA, and prepares for division.

     • G1 Phase: Cell grows and synthesizes proteins.

     • S Phase: DNA is replicated.

     • G2 Phase: Cell continues to grow and produces proteins needed for mitosis.

   • Mitotic (M) Phase: Includes Mitosis and Cytokinesis.

     • Mitosis: Division of the nucleus into two genetically identical daughter nuclei.

     • Cytokinesis: Division of the cytoplasm, resulting in two daughter cells.

3. Stages of Mitosis:

   • Prophase:

     • Chromatin fibers condense into visible chromosomes.

     • The mitotic spindle forms, and centrosomes move to opposite poles.

   • Prometaphase:

     • The nuclear envelope breaks down.

     • Microtubules attach to kinetochores on the chromosomes.

   • Metaphase:

     • Chromosomes align at the cell’s equator, known as the metaphase plate.

   • Anaphase:

     • Sister chromatids separate at the centromeres, and are pulled toward opposite poles by the spindle fibers.

   • Telophase:

     • Chromatids reach the poles and begin to de-condense.

     • Nuclear envelopes reform around the two sets of chromosomes.

   • Cytokinesis:

     • The cytoplasm divides, forming two identical daughter cells.

4. Regulation of the Cell Cycle:

   • Checkpoints ensure that the cell only divides when conditions are appropriate.

   • G1 Checkpoint: The cell decides whether to divide based on environmental signals (nutrients, growth factors).

   • G2 Checkpoint: Ensures DNA has been replicated properly.

   • M Checkpoint: Ensures all chromosomes are attached to the spindle before progressing with division.

   • Cancer: Results from mutations that cause cells to bypass these checkpoints, leading to uncontrolled cell division. Cancer cells often have mutations in oncogenes (promote cell division) or tumor suppressor genes (prevent cell division).

5. Binary Fission in Prokaryotes:

   • Binary Fission is a simpler form of cell division in prokaryotes:

     • The bacterial chromosome is duplicated.

     • Each copy attaches to the plasma membrane, and as the cell grows, the copies are pulled apart.

     • The cell pinches in the middle to form two new cells.

Review Questions

1. Photosynthesis:

   • What are the two main stages of photosynthesis, and where do they occur?

   • Explain the role of chlorophyll in photosynthesis.

   • Compare and contrast C4 and CAM plants. How are they adapted to dry environments?

2. Mitosis:

   • Describe the stages of mitosis and the events that occur in each stage.

   • How does the cell cycle regulate cell division? What happens when regulation fails?

   • Explain the difference between mitosis in eukaryotes and binary fission in prokaryotes.

Chapter 13: Meiosis

Key Concepts:

1. Purpose of Meiosis:

   • Meiosis is a form of cell division that reduces the chromosome number by half, producing haploid gametes (sperm and egg) from a diploid organism.

   • It ensures genetic diversity through recombination and independent assortment.

2. Chromosomal Organization:

   • Diploid cells (2n): Contain two sets of chromosomes—one from each parent. For humans, 2n = 46 chromosomes.

   • Haploid cells (n): Gametes (sperm and eggs) contain only one set of chromosomes, n = 23.

   • Homologous chromosomes: Pairs of chromosomes that carry the same genes, one inherited from each parent.

3. Meiosis and Sexual Reproduction:

   • Meiosis alternates with fertilization in sexual reproduction. Fertilization restores diploidy by fusing two haploid gametes (sperm and egg), forming a zygote (2n).

   • This creates genetic variation in offspring, which is crucial for evolution.

4. Phases of Meiosis:

   • Meiosis I (Reductional Division):

     • Prophase I: Homologous chromosomes pair up (synapsis), and crossing-over occurs, where genetic material is exchanged between non-sister chromatids, creating recombinant chromosomes.

     • Metaphase I: Homologous pairs align at the metaphase plate.

     • Anaphase I: Homologous chromosomes are pulled apart to opposite poles.

     • Telophase I and Cytokinesis: Two haploid cells form, each with half the chromosome number, but still containing sister chromatids.

   • Meiosis II (Similar to Mitosis):

     • Prophase II: Spindle apparatus forms again in each of the two haploid cells.

     • Metaphase II: Chromosomes (sister chromatids) align at the metaphase plate.

     • Anaphase II: Sister chromatids separate and are pulled to opposite poles.

     • Telophase II and Cytokinesis: Four haploid daughter cells are produced, each genetically unique due to crossing-over and independent assortment.

5. Genetic Variation in Meiosis:

   • Crossing-over: Exchange of genetic material between homologous chromosomes during Prophase I, leading to recombinant chromosomes.

   • Independent Assortment: Random orientation of homologous pairs during Metaphase I allows for different combinations of maternal and paternal chromosomes in gametes.

6. Comparison to Mitosis:

   • Mitosis: Produces two genetically identical diploid daughter cells, used for growth, repair, and asexual reproduction.

   • Meiosis: Produces four genetically unique haploid cells, used for sexual reproduction.

Review Questions for Meiosis:

1. Explain the difference between haploid and diploid cells.

2. List the stages of meiosis and describe what happens in each stage.

3. How does meiosis contribute to genetic diversity?

4. What are the key differences between meiosis and mitosis?

Chapter 14: Mendelian Inheritance

Key Concepts:

1. Mendel’s Experiments:

   • Monohybrid Crosses: Mendel crossed pea plants differing in a single trait (e.g., flower color). His work with true-breeding plants led to the 3:1 phenotypic ratio in the F2 generation, suggesting that traits are inherited as discrete units (genes), not blended.

2. Mendel's Model of Inheritance:

   • Genes: Heritable factors that determine traits.

   • Alleles: Different versions of a gene (e.g., purple or white flowers).

   • Law of Segregation: Each organism carries two alleles for each gene, which separate during gamete formation. Each gamete gets only one allele.

   • Law of Independent Assortment: Genes for different traits assort independently of one another during meiosis (only true for genes on different chromosomes or far apart on the same chromosome).

3. Mendelian Vocabulary:

   • Homozygous: Having two identical alleles for a gene (e.g., PP for purple flowers).

   • Heterozygous: Having two different alleles for a gene (e.g., Pp for purple flowers).

   • Genotype: The genetic makeup of an organism (e.g., Pp).

   • Phenotype: The physical expression of a trait (e.g., purple flowers).

   • Dominant allele: An allele that masks the effect of the recessive allele when present (e.g., P is dominant to p).

   • Recessive allele: An allele whose effects are masked in the presence of a dominant allele (e.g., p is recessive to P).

4. Punnett Squares and Probability:

   • Punnett Squares: A tool used to predict the genotypic and phenotypic ratios of offspring from genetic crosses.

   • Monohybrid Cross Example: Pp×PpPp \times PpPp×Pp Results in a 3:1 ratio of phenotypes (3 purple, 1 white) and a 1:2:1 ratio of genotypes (1 PP, 2 Pp, 1 pp).

   • Dihybrid Cross: Involves two traits (e.g., seed color and shape) and demonstrates the 9:3:3:1 ratio in the F2 generation, which led to the discovery of the Law of Independent Assortment.

5. Mendel’s Laws and Meiosis:

   • Law of Segregation is explained by the separation of homologous chromosomes during Anaphase I of meiosis.

   • Law of Independent Assortment is explained by the random alignment of homologous pairs during Metaphase I.

Review Questions for Mendelian Inheritance:

1. Explain Mendel’s Law of Segregation and how it applies to a monohybrid cross.

2. What is the Law of Independent Assortment, and how does it apply to a dihybrid cross?

3. How does meiosis support Mendel’s Laws of Segregation and Independent Assortment?

4. Define and distinguish between the terms homozygous, heterozygous, genotype, and phenotype.

5. Use a Punnett square to predict the outcome of a monohybrid or dihybrid cross.

Comparison of Mitosis and Meiosis

Study Guide: Chapter 15 - Chromosomal Inheritance

Key Concepts:

1. Chromosome Theory of Inheritance:

   • Gregor Mendel’s Findings: Mendel’s laws of inheritance (Segregation and Independent Assortment) suggested that “hereditary factors” are passed from parents to offspring. Modern science confirms that these hereditary factors are genes located on chromosomes.

   • Chromosome Theory: Genes have specific loci (locations) on chromosomes, and chromosomes undergo segregation and independent assortment during meiosis, leading to the distribution of genetic information across generations.

   • Thomas Hunt Morgan’s Contributions: Morgan’s work with fruit flies (Drosophila melanogaster) provided the first evidence that genes are located on chromosomes. He observed the link between eye color and sex in fruit flies, identifying that the gene for eye color is located on the X chromosome.

2. Linkage of Genes on Autosomal Chromosomes:

   • Linked Genes: Genes located close together on the same chromosome tend to be inherited together because they do not assort independently during meiosis.

   • Recombinant Chromosomes: Crossing-over between homologous chromosomes during meiosis can produce recombinant chromosomes with new allele combinations, breaking up linked genes. The closer two genes are on a chromosome, the less likely crossing-over will separate them.

   • Genetic Linkage Maps: Maps of chromosomes can be created based on the frequency of recombination (crossing-over). Map units (centimorgans, cM) represent a 1% recombination frequency, helping to approximate the physical distance between genes.

3. Sex Chromosomes and Inheritance:

   • Sex Chromosomes in Humans:

     • Humans have two sex chromosomes, X and Y. Females are XX, and males are XY.

     • Sex-determining region Y (SRY): A gene on the Y chromosome responsible for initiating male sex determination. In its absence, the default development is female.

   • Other Species: Sex determination varies across species. Some species may have Z and W chromosomes (e.g., birds, where males are ZZ, and females are ZW), while others use environmental factors for sex determination.

4. X-Linked Inheritance:

   • X-Linked Genes: Genes located on the X chromosome. Since males have only one X chromosome, they are hemizygous for X-linked traits, making recessive traits more common in males.

   • Examples of X-Linked Disorders:

     • Color blindness

     • Hemophilia

     • Duchenne Muscular Dystrophy

   • X Inactivation in Females:

     • Females have two X chromosomes, but one of them is randomly inactivated during early development. The inactivated X condenses into a structure called a Barr body.

     • Mosaic Phenotypes: In heterozygous females, X-inactivation leads to a mosaic of phenotypes, as different cells express different alleles. For example, calico cats have mosaic fur coloration due to X-inactivation, which is why most calico cats are female.

5. Alterations in Chromosome Number:

   • Nondisjunction: Occurs when chromosomes fail to separate properly during meiosis, leading to aneuploidy (abnormal chromosome number).

     • Aneuploidy Examples:

       • Trisomy 21 (Down syndrome): Caused by an extra chromosome 21.

       • Klinefelter Syndrome (XXY): Male with an extra X chromosome.

       • Turner Syndrome (X0): Female with a missing X chromosome.

     • Polyploidy: Having additional complete sets of chromosomes (e.g., 3n or 4n). This is more common in plants (e.g., bananas, wheat).

6. Alterations in Chromosome Structure:

   • Types of Structural Changes:

     • Deletion: Loss of a chromosome segment.

     • Duplication: Repetition of a chromosome segment.

     • Inversion: Reversal of a chromosome segment.

     • Translocation: Movement of a chromosome segment to a nonhomologous chromosome.

   • These alterations can lead to genetic disorders and impact an organism’s phenotype.

7. Inheritance of Organelle Genes:

   • Extranuclear Genes: Genes located in the mitochondria and chloroplasts (in plants) are inherited maternally because these organelles are transmitted via the egg.

   • Non-Mendelian Inheritance: Extranuclear genes follow a unique inheritance pattern, as they do not undergo meiosis. For instance, mutations in mitochondrial DNA can lead to metabolic disorders.

Important Vocabulary:

• Gene Linkage: Genes located close together on the same chromosome are inherited together.

• Recombinant Chromosomes: Chromosomes with new combinations of alleles due to crossing-over.

• Hemizygous: Having only one allele of a gene, as seen in males for X-linked genes.

• Barr Body: Condensed, inactive X chromosome in female cells.

• Nondisjunction: Failure of chromosomes to separate during meiosis.

• Aneuploidy: Abnormal chromosome number, such as trisomy or monosomy.

• Polyploidy: Having extra full sets of chromosomes (common in plants).

• Mosaic: Organism with two or more genetically distinct cell types due to X-inactivation in females.

Review Questions:

1. Explain the Chromosome Theory of Inheritance and how it relates to Mendel’s findings.

2. Describe the difference between linked and unlinked genes. How does crossing-over affect linked genes?

3. What is the role of the SRY gene in sex determination?

4. Why are recessive X-linked traits more common in males than in females?

5. How does X-inactivation lead to mosaic phenotypes in females? Provide an example.

6. List and describe types of chromosomal alterations and how they might lead to genetic disorders.

7. How are extranuclear genes inherited differently from nuclear genes?

Chapter 16: DNA Replication Study Guide

1. Structure of DNA Review

Basic Composition

• DNA (Deoxyribonucleic Acid): A double-stranded helical molecule carrying genetic information.

• Components of a Nucleotide:

  • Five-Carbon Sugar: Deoxyribose in DNA, lacking an oxygen atom compared to ribose in RNA.

  • Phosphate Group: Links the sugar molecules in a backbone via phosphodiester bonds.

  • Nitrogenous Base:

    • Purines: Adenine (A) and Guanine (G) – double-ring structures.

    • Pyrimidines: Cytosine (C) and Thymine (T) – single-ring structures.

• Base Pairing Rules:

  • A pairs with T (via 2 hydrogen bonds).

  • G pairs with C (via 3 hydrogen bonds).

• Double Helix Structure:

  • The two strands are antiparallel, meaning one strand runs 5′ to 3′, while the complementary strand runs 3′ to 5′.

  • The helix makes one complete turn every 10 base pairs, spaced 0.34 nm apart, with a diameter of 2 nm.

2. DNA Replication Overview

General Concept

• Semi-Conservative Replication: Each daughter DNA molecule consists of one parental strand and one newly synthesized strand.

• Origins of Replication:

  • Prokaryotes: Single origin, leading to a circular replication.

  • Eukaryotes: Multiple origins along linear chromosomes, increasing the efficiency of DNA replication.

Phases of the Cell Cycle

1. Interphase:

   • G1 Phase: Cell growth and preparation for DNA replication.

   • S Phase: DNA synthesis and replication, resulting in sister chromatids.

   • G2 Phase: Final preparations before cell division.

2. Mitotic Phase: Distribution of genetic material into two daughter cells.

3. Detailed Steps of DNA Replication

A. Initiation

1. Origin Recognition:

   • DNA replication begins at specific sequences called origins of replication.

   • Initiator Proteins: Bind to the origin, unwinding a short stretch of the DNA helix.

2. Formation of the Replication Fork:

   • Helicase: Enzyme that unwinds the DNA double helix by breaking hydrogen bonds between complementary bases, creating two single strands.

   • Single-Strand Binding Proteins (SSBs): Bind to and stabilize the separated single DNA strands, preventing them from re-annealing.

   • Topoisomerase: Alleviates the torsional strain caused by unwinding by inducing temporary nicks in the DNA backbone.

B. Elongation

1. Priming the Strands:

   • Primase: Synthesizes a short RNA primer (5-10 nucleotides long) on the single-stranded DNA to provide a starting point for DNA polymerase.

2. Synthesis by DNA Polymerase:

   • DNA Polymerase III (in prokaryotes) or DNA Polymerases (in eukaryotes): Adds nucleotides to the 3′ end of the primer, synthesizing the new DNA strand in a 5′ to 3′ direction.

   • Energy Source: The addition of nucleotides is powered by the hydrolysis of nucleoside triphosphates (e.g., dATP, dGTP), similar to ATP, releasing energy to drive the reaction.

3. Leading and Lagging Strands:

   • Leading Strand: Synthesized continuously in the direction of the replication fork (5′ to 3′).

   • Lagging Strand: Synthesized discontinuously in fragments called Okazaki fragments, each requiring a new primer.

   • Okazaki Fragments: Short DNA segments that are later joined together.

4. DNA Polymerase I (in prokaryotes): Removes RNA primers and replaces them with DNA nucleotides.

5. DNA Ligase: Seals the gaps between Okazaki fragments, forming a continuous DNA strand.

C. Termination

• Replication concludes when the replication machinery encounters specific sequences or when replication forks meet.

• Eukaryotic Considerations: Special structures called telomeres at chromosome ends are replicated using the enzyme telomerase to prevent loss of essential genetic material.

4. Mechanisms and Key Players in Replication

Enzymes and Their Functions

1. Helicase: Unzips the DNA strands by disrupting hydrogen bonds.

2. Single-Strand Binding Proteins (SSBs): Stabilize single strands of DNA.

3. Topoisomerase: Relieves tension ahead of the replication fork.

4. Primase: Synthesizes RNA primers to initiate DNA synthesis.

5. DNA Polymerase:

   • DNA Polymerase III: Main enzyme for synthesizing new DNA in prokaryotes.

   • DNA Polymerase I: Replaces RNA primers with DNA.

   • Eukaryotic Polymerases: Include Pol α, Pol δ, and Pol ε, with specific roles in replication and proofreading.

6. DNA Ligase: Connects Okazaki fragments on the lagging strand.

7. Telomerase: Extends telomeres to protect chromosome ends in eukaryotic cells.

5. Understanding DNA Synthesis Directionality

• 5′ to 3′ Synthesis: DNA polymerase can only add nucleotides to the free 3′ hydroxyl group of the growing DNA strand.

• Antiparallel Nature: The opposite orientation of the DNA strands dictates the continuous and discontinuous replication process.

6. Summary of Differences Between DNA and RNA

• DNA: Double-stranded, deoxyribose sugar, thymine as a base.

• RNA: Single-stranded, ribose sugar, uracil replaces thymine.

7. Critical Review Questions

1. What are the structural differences between purines and pyrimidines, and how do they affect base pairing?

2. Describe how the antiparallel structure of DNA affects replication.

3. What roles do helicase, primase, and DNA polymerase play in unwinding and synthesizing DNA?

4. Why is the replication of the lagging strand more complex than the leading strand?

5. Explain the significance of telomerase in eukaryotic DNA replication and aging.

6. Illustrate the steps of DNA replication with a diagram, including key enzymes and the replication fork.

Chapter 17: The Central Dogma Study Guide

1. Understanding the Central Dogma

• Definition: The Central Dogma describes the flow of genetic information:

  • Pathway: DNA → RNA → Protein

• Key Points:

  • Transcription: The process where mRNA is synthesized from a DNA template.

  • Translation: The process where a polypeptide (protein) is created using mRNA information.

• Relation to Cell Function:

  • Different cell types (e.g., cheek cells vs. muscle cells) have distinct phenotypes because of the different proteins they express, even though all somatic cells share the same genome (46 chromosomes).

  • Proteins play roles such as:

    • Catalytic: Enzymes that facilitate biochemical reactions.

    • Structural: Components like the cytoskeleton.

2. Gene Expression and Protein Synthesis

• Gene Expression: How genetic information leads to protein synthesis.

  • "Proteins are the link between genotype and phenotype."

  • Gene: A sequence of DNA that codes for a specific protein.

• One Gene, One Polypeptide: Each gene codes for a single polypeptide chain, emphasizing the specificity of genetic coding.

3. Structure of Proteins

• Primary Structure: Sequence of amino acids.

• Secondary Structure: Formation of helices and sheets through hydrogen bonding.

• Tertiary Structure: 3D shape of a protein determined by interactions among side chains.

• Quaternary Structure: Assembly of multiple polypeptide subunits.

4. Genetic Information in DNA

• DNA Structure:

  • Consists of nucleotide sequences that store genetic information.

• Replication and Transcription:

  • DNA replication uses a template strand to synthesize new DNA.

  • DNA also serves as a template for RNA synthesis during transcription.

• Concept of Translation:

  • Converting nucleotide language (DNA/RNA) into amino acid sequences (proteins).

5. Transcription Process

• Overview: DNA to mRNA occurs in the nucleus.

Key Elements:

• RNA Polymerase: Enzyme responsible for synthesizing RNA from DNA.

  • Operates in the 5' to 3' direction and does not require a primer.

• Nontemplate vs. Template Strand:

  • Nontemplate Strand: Complementary to the RNA produced.

  • Template Strand: Directly guides the RNA sequence.

Initiation of Transcription:

• Promoter: The DNA region where RNA polymerase binds to begin transcription.

  • In Prokaryotes: RNA polymerase recognizes and binds directly to the promoter.

  • In Eukaryotes: Multiple transcription factors assist RNA polymerase binding.

Elongation:

• RNA polymerase unwinds DNA and pairs RNA nucleotides with DNA bases.

• Elongation speed: ~40 nucleotides per second.

Termination:

• Prokaryotes: RNA polymerase detaches upon reaching a terminator sequence.

• Eukaryotes: Polyadenylation signal (AAUAAA) signals transcript release downstream.

6. RNA Processing in Eukaryotes

• Difference from Prokaryotes:

  • Prokaryotic mRNA: Immediately ready for translation.

  • Eukaryotic mRNA: Requires extensive processing.

• mRNA Modifications:

  • Capping: A modified guanine nucleotide is added to the 5' end.

  • Poly-A Tail: A string of adenine nucleotides added to the 3' end to stabilize mRNA.

  • Splicing: Removal of introns (non-coding regions); exons are spliced together.

    • Human Example: An initial transcript averages 27,000 nucleotides, reduced to ~1,200 in the final form.

Study/Review Questions

1. Explain the concept of the Central Dogma and its significance in molecular biology.

2. Describe how transcription differs in prokaryotes and eukaryotes.

3. Outline the roles of RNA polymerase in transcription.

4. What are the steps involved in eukaryotic mRNA processing?

5. How does the structure of proteins relate to their function?

 Chapter 18: Regulation of Bacterial Gene Expression

 1. Overview of Gene Expression Regulation

- Definition: Gene expression regulation refers to the mechanisms that turn genes on or off as needed. This ensures that:

  - Different types of cells (e.g., muscle vs. cheek cells in humans) express different sets of genes.

  - Cells express genes based on environmental needs (e.g., E. coli synthesizes tryptophan only if it's not available in the environment).

 2. Differential Gene Expression

- Differential Expression: Different cells or conditions require specific transcription factors, leading to unique gene expression patterns.

  - Example: Pancreas cells produce insulin when blood glucose is high.

 3. Mechanisms of Transcriptional Regulation in Prokaryotes

- Operons: An operon is a group of genes controlled by a single on-off switch (operator), which enables coordinated control of gene expression.

- Two Levels of Metabolic Control:

  1. Feedback Inhibition: Directly inhibits enzymes to control metabolic activity.

  2. Gene Transcription Control: Regulates the synthesis of mRNA, thereby controlling enzyme production.

 4. Types of Operons in Bacteria

   - Repressible Operons:

      - Default state is on, but they can be repressed when a specific molecule is abundant.

      - Example: Trp Operon (for tryptophan synthesis)

        - Function: Encodes enzymes required for synthesizing tryptophan in E. coli.

        - Mechanism:

            - When tryptophan levels are low, the trp repressor (inactive state) does not bind to the operator, allowing transcription.

            - When tryptophan levels are high, tryptophan binds to the trp repressor, activating it. This active repressor binds to the operator, blocking RNA polymerase and stopping transcription.

   - Inducible Operons:

      - Default state is off, but can be turned on (induced) when needed.

      - Example: Lac Operon (for lactose metabolism in E. coli)

        - Function: Encodes enzymes like β-galactosidase that break down lactose into glucose and galactose.

        - Mechanism:

            - In the absence of lactose, the lac repressor binds to the operator, preventing transcription.

            - When lactose is present, an isomer (allolactose) binds to the lac repressor, inactivating it, allowing transcription to proceed.

 5. Key Components of Operons

- Promoter: DNA sequence where RNA polymerase binds to initiate transcription.

- Operator: DNA region that acts as an on-off switch for gene transcription.

- Repressor: Protein that can bind to the operator to inhibit transcription.

- Regulatory Gene: Produces repressor proteins that control operon activity.

- Inducers and Corepressors:

  - Inducers: Small molecules that inactivate repressors (e.g., allolactose for the lac operon).

  - Corepressors: Small molecules that activate repressors (e.g., tryptophan for the trp operon).

 6. Comparison of Trp and Lac Operons

 7. Positive Control: The Role of CRP and cAMP in Lac Operon

- cAMP (cyclic AMP) and CRP (cAMP receptor protein) play an activator role when glucose levels are low.

  - High cAMP (low glucose): CRP-cAMP complex binds to the lac promoter, enhancing transcription of the lac operon when lactose is present.

  - Low cAMP (high glucose): CRP does not bind, thus transcription is reduced even if lactose is present, as glucose is the preferred energy source.

 8. Key Vocabulary

- Differential Gene Expression: Cells express different genes based on their function and environment.

- Feedback Inhibition: A method of metabolic control that prevents excess enzyme activity.

- Transcriptional Control: Regulation of gene transcription as a means to control protein synthesis.

 9. Study/Review Questions

1. Define the following key terms: promoter, operator, operon, repressor, regulatory gene.

2. What is differential gene expression? Explain using E. coli and tryptophan synthesis as an example.

3. Describe two primary mechanisms of metabolic control in bacterial cells.

4. Explain how a repressible operon like the trp operon can be turned off.

5. Distinguish between inducible and repressible operons. Give an example of each.

Chapter 19: Viruses

What Are Viruses?

• Definition:

  • Viruses are not living organisms. They lack cellular structure, metabolism, and independent reproduction but hijack host cells for replication, leading a "borrowed life."

• Key Features:

  • Genome: DNA or RNA; can be double-stranded (ds) or single-stranded (ss).

    • Examples:

      • dsDNA: Adenoviruses (cold-like symptoms)

      • ssRNA: Influenza virus

  • Capsid: Protein coat made of subunits called capsomeres; determines shape.

  • Envelopes (in some viruses): Derived from the host’s cell membrane; aids entry and evasion of host immune systems.

Virus Structure and Diversity

1. Shapes of Capsids:

   • Helical (e.g., Tobacco Mosaic Virus): Rod-shaped.

   • Icosahedral (e.g., Adenovirus): 20-sided shape.

   • Complex (e.g., Bacteriophage T4): Combines icosahedral head and tail fibers.

2. Viral Genomes:

   • Can be DNA or RNA:

     • DNA viruses often use host replication machinery.

     • RNA viruses may require viral enzymes to replicate.

   • RNA viruses are further categorized:

     • Positive-sense RNA: Acts as mRNA directly.

     • Negative-sense RNA: Serves as a template for mRNA synthesis.

     • Retroviruses: Use reverse transcription (e.g., HIV).

Virus Life Cycles

1. General Replicative Cycle:

   • Attachment: Virus binds to host receptors via glycoproteins.

   • Entry: Viral genome enters the host.

     • Methods: Membrane fusion, endocytosis, injection.

   • Replication:

     • Host cell machinery is reprogrammed to produce viral components.

   • Assembly: Capsid proteins and genomes assemble into new virions.

   • Release: Viruses exit the host, often killing it.

2. Specific Cycles in Phages:

   • Lytic Cycle:

     • Virus replicates rapidly, causing host cell lysis.

     • E.g., T4 bacteriophage.

   • Lysogenic Cycle:

     • Viral DNA integrates into host genome as a prophage.

     • May switch to the lytic cycle under stress.

Animal Viruses

• Enveloped Viruses:

  • Enter via fusion with host cell membranes (e.g., Influenza).

  • Viral envelope derived from the host aids immune evasion.

• Retroviruses:

  • Use reverse transcriptase to convert RNA into DNA, integrating into the host genome.

  • E.g., HIV, which targets specific immune cells.

Impact of Viruses

1. Human Health:

   • Influenza, HIV, COVID-19.

2. Plant Viruses:

   • Impact agriculture, causing billions in losses annually.

   • Spread via horizontal transmission (insects, wounds) or vertical transmission (seeds, cuttings).

3. Evolutionary Role:

   • Likely evolved from mobile genetic elements (e.g., plasmids, transposons).

   • Provide insight into gene transfer and molecular biology.

Prions

• Infectious proteins that cause diseases such as:

  • Mad cow disease, scrapie, chronic wasting disease, and Creutzfeldt-Jakob disease.

• Unique Features:

  • Catalyze the misfolding of normal proteins into prions.

  • Form indestructible plaques that disrupt cellular function.

Study Questions

1. Define a virus. How is it different from living organisms?

2. Compare and contrast the lytic and lysogenic cycles.

3. Explain how retroviruses replicate and why they are unique.

4. What are prions, and how do they cause disease?

Chapter 20: Biotechnology

Key Techniques

1. Polymerase Chain Reaction (PCR):

   • Purpose: Amplify specific DNA sequences in large quantities.

   • Process:

     • Denaturation (95°C): DNA strands separate.

     • Annealing (45-55°C): Primers bind complementary sequences.

     • Extension (72°C): DNA polymerase (Taq polymerase) synthesizes new strands.

   • Ingredients:

     • Template DNA.

     • Primers (short, complementary sequences).

     • DNA polymerase (heat-stable).

     • Free nucleotides.

   • Applications:

     • Forensics: DNA fingerprinting.

     • Genetic testing: Identify mutations.

     • Disease diagnosis: Detect pathogens.

     • Research: Amplify genes for cloning or sequencing.

2. DNA Cloning:

   • Purpose: Isolate and replicate specific genes.

   • Steps:

     1. Restriction Enzymes: Cut DNA at specific sequences, leaving "sticky ends."

     2. Cloning Vectors (e.g., plasmids): Carry the gene of interest.

     3. Ligation: DNA ligase seals fragments into the vector.

     4. Transformation: Introduce recombinant plasmid into bacteria.

     5. Selection: Identify bacteria with the plasmid using markers (e.g., antibiotic resistance).

   • Applications:

2. Produce proteins (e.g., insulin).

3. Study gene function.

4. Genetically modify organisms (GMOs).

3. Gel Electrophoresis:

   • Purpose: Separate DNA or proteins by size.

   • Method:

     • DNA samples loaded into a gel matrix.

     • Electric current moves DNA toward the positive electrode (due to DNA’s negative charge).

     • Shorter fragments travel faster, separating by size.

   • Uses:

     • Analyze restriction fragments.

     • Verify PCR results.

     • DNA fingerprinting.

4. Sanger Sequencing:

   • Purpose: Determine the exact sequence of DNA.

   • Process:

     • PCR amplifies DNA with fluorescently labeled dideoxynucleotides (ddNTPs) that terminate synthesis.

     • Fragments of varying lengths are separated via electrophoresis.

     • Laser detects fluorescent tags, revealing the sequence.

   • Applications:

     • Genome sequencing.

     • Detect mutations.

Applications of Biotechnology

1. Medicine:

   • Human growth hormone, insulin production.

   • Gene therapy for genetic disorders.

2. Agriculture:

   • Pest-resistant crops (e.g., Bt corn).

   • Enhanced nutritional content.

3. Environmental:

   • Bioremediation using bacteria to clean oil spills or toxins.

4. Forensics:

   • Solve crimes via DNA fingerprinting.

Study Questions

1. Outline the steps and ingredients needed for PCR. How does it amplify DNA?

2. What are restriction enzymes, and how do they create recombinant DNA?

3. Describe the purpose and procedure of gel electrophoresis.

4. How does Sanger sequencing determine a DNA sequence?

Comparative Analysis of Chapters