Exam 1 Learning Objectives PDF

Week 1 Learning Objectives 1.​ Explore and Outline the Symptoms of Cystic Fibrosis (CF): ○​ Persistent coughing with thick mucus ○​ Frequent lung infections ○​ Wheezing or shortness of breath ○​ Poor growth despite a good appetite ○​ Difficulty w...

Week 1 Learning Objectives 1.​ Explore and Outline the Symptoms of Cystic Fibrosis (CF): ○​ Persistent coughing with thick mucus ○​ Frequent lung infections ○​ Wheezing or shortness of breath ○​ Poor growth despite a good appetite ○​ Difficulty with bowel movements 2.​ Hypothesize the Mechanism Behind CF Symptoms: ○​ Caused by mutations in the CFTR gene affecting the CFTR protein, which regulates chloride ion transport across epithelial cells. ○​ Defective ion transport leads to thick, sticky mucus buildup in organs, primarily the lungs and digestive system. 3.​ Identify the Different Parts of a Phospholipid: ○​ Fatty Acid Tails: Hydrophobic (water-repelling) ○​ Glycerol Backbone ○​ Phosphate Group: Hydrophilic (water-attracting) 4.​ Relate Amphipathic Nature of Phospholipids to Bilayer Formation: ○​ Amphipathic: Contains both hydrophobic and hydrophilic regions. ○​ In aqueous environments, hydrophobic tails face inward, and hydrophilic heads face outward, forming a phospholipid bilayer. 5.​ Determine Molecules That Can Diffuse Through the Membrane: ○​ Small, nonpolar molecules (e.g., O2, CO2) and some small polar molecules (e.g., H2O) diffuse easily. ○​ Large or charged molecules require transport proteins. 6.​ Discuss Membrane Selective Permeability: ○​ Selective Permeability: Allows certain substances to pass while restricting others. ○​ Based on size, polarity, and charge of molecules. 7.​ Define Osmosis: ○​ The passive movement of water molecules across a selectively permeable membrane from areas of low solute concentration to high solute concentration. 8.​ Define Three Major Categories of Organelles: ○​ Membrane-bound (Endomembrane System): Nucleus, ER, Golgi apparatus ○​ Proteinaceous Organelles: Ribosomes ○​ Endosymbiotic Organelles: Mitochondria, Chloroplasts 9.​ Evolution of the Nucleus and Endomembrane System (FECA vs. LECA): ○​ FECA (First Eukaryotic Common Ancestor): Simple membrane systems, precursor to eukaryotes.  ○​ LECA (Last Eukaryotic Common Ancestor): Fully developed nucleus, mitochondria, complex organelles. 10.​Major Functions of the Endomembrane System: ○​ Nucleus: Houses genetic material ○​ Rough ER: Protein synthesis ○​ Smooth ER: Lipid synthesis ○​ Golgi Apparatus: Modifies, sorts, and packages proteins ○​ Lysosomes: Breakdown of waste 11.​Gene Expression and Endomembrane System: ○​ Transcription: Occurs in the nucleus (DNA → mRNA) ○​ Translation: Occurs in the cytoplasm or on the rough ER (mRNA → Protein) 12.​Analyze Micrographs Related to the Endomembrane System: ○​ Identify structures such as the nucleus, ER, Golgi apparatus, and vesicles using transmission electron microscopy (TEM). Key Terms ​ Epithelial Tissue: Tissues covering body surfaces and lining cavities. ​ Transmission Electron Microscopy (TEM): Technique for visualizing ultrastructures of cells. ​ Phospholipid: Composed of fatty acids, glycerol, phosphate group; forms cell membranes. ​ Hydrophobic: Repels water. ​ Hydrophilic: Attracts water. ​ Amphipathic: Molecule with both hydrophobic and hydrophilic parts. ​ Lipid Bilayer: Double layer of phospholipids forming cell membranes. ​ Selectively Permeable: Allows specific molecules to cross the membrane. ​ Osmosis: Diffusion of water across a membrane. ​ Hypertonic vs. Hypotonic: Conditions describing solute concentration differences across membranes. ​ Membrane-bound Organelles: Part of the endomembrane system. ​ Proteinaceous Organelles: Composed primarily of proteins (e.g., ribosomes). ​ Endosymbiotic Organelles: Originating from symbiotic relationships (e.g., mitochondria). ​ FECA vs. LECA: Stages in the evolution of eukaryotic cells. Week 2 Learning Objectives 1. Evidence Supporting RNA as the Early Information-Storing Molecule ​ RNA World Hypothesis: Suggests RNA was the first genetic material because it can both store information and catalyze reactions (unlike DNA). ​ Key Evidence: ○​ Ribozymes: RNA molecules that act as enzymes, supporting the idea that RNA could catalyze its own replication. ○​ 3-D Structure: RNA folds into complex shapes necessary for catalytic functions, similar to proteins. ○​ RNA can self-replicate under certain conditions, a key feature for early life. 2. Why DNA is Better for Information Storage Than RNA ​ Stability: DNA is double-stranded and has a deoxyribose sugar, making it more chemically stable than RNA. ​ Repair Mechanisms: DNA’s double helix allows for error correction during replication. ​ Longevity: DNA is less reactive because it lacks the 2'-hydroxyl group found in RNA, reducing degradation. 3. Benefits of a Nucleus ​ Separation of Processes: Transcription (making RNA) occurs in the nucleus, while translation (making proteins) occurs in the cytoplasm, allowing regulation of gene expression. ​ DNA Protection: Shields DNA from harmful cytoplasmic reactions. ​ Efficient Regulation: Facilitates complex control over which genes are active. 4. Monomeric & Polymeric Forms of DNA ​ Monomer: Nucleotide—consists of: 1.​ Nitrogenous Base: Purines (Adenine, Guanine) & Pyrimidines (Thymine, Cytosine) 2.​ Sugar: Deoxyribose 3.​ Phosphate Group ​ Polymer: DNA is a polynucleotide chain formed by linking nucleotides through phosphodiester bonds between the 3' carbon of one sugar and the 5' carbon of the next. 5. DNA Polymer Formation & Base Pairing Rules ​ Phosphodiester Bonds: Link the sugar-phosphate backbone. ​ Base Pairing Rules: ○​ Adenine (A) pairs with Thymine (T) via 2 hydrogen bonds. ○​ Guanine (G) pairs with Cytosine (C) via 3 hydrogen bonds. ​ These rules ensure accurate DNA replication and structure. 6. Role of Hydrogen Bonds in DNA Structure ​ Hydrogen Bonds: Hold the two DNA strands together, enabling the double helix structure. ​ Strand Separation: During replication or transcription, hydrogen bonds break easily under heat or enzyme action, allowing the strands to separate while maintaining the overall structure. 7. How Changes in DNA Structure Impact Function ​ Mutations: Changes in base sequence can alter protein function (e.g., causing diseases like cystic fibrosis). ​ Structural Alterations: Damage to the sugar-phosphate backbone or improper folding can impair replication and gene expression. 8. Major DNA Modifying Enzymes ​ DNA Helicase: Unwinds the double helix. ​ DNA Polymerase: Synthesizes new DNA strands. ​ DNA Ligase: Seals nicks in the DNA backbone. ​ Topoisomerase: Relieves supercoiling during replication. ​ Nucleases: Cut DNA strands. ​ Methyltransferases: Add methyl groups to modify gene expression. 9. DNA Melting & Temperature (Tm) Analysis ​ DNA Melting: The process where double-stranded DNA separates into single strands upon heating. ​ Tm (Melting Temperature): The temperature at which 50% of the DNA is denatured. ○​ Higher Tm = More G-C pairs (since G-C has 3 hydrogen bonds, requiring more energy to break). ​ UV Absorbance Chart: Measures DNA melting by tracking changes in absorbance at 260 nm as DNA denatures. 10. Relationship Between DNA, Chromosomes, Genes, and Alleles (Example: Cystic Fibrosis) ​ DNA: The molecule that carries genetic instructions. ​ Chromosome: A long DNA molecule containing many genes. ​ Gene: A segment of DNA coding for a specific protein (e.g., the CFTR gene in cystic fibrosis). ​ Allele: Different versions of a gene (e.g., the mutant vs. normal CFTR allele). 11. Nucleosome Structure ​ Nucleosome: The basic unit of DNA packaging. ○​ Core Proteins: 8 histone proteins (H2A, H2B, H3, H4—two of each). ○​ DNA: About 147 base pairs wrapped around the histone core. ○​ Linker DNA: Connects nucleosomes, with H1 histone stabilizing the structure. 12. Euchromatin vs. Heterochromatin Euchromatin Heterochromatin Loosely packed Tightly packed Actively transcribed (gene-rich) Transcriptionally inactive (gene-poor) Light-staining in microscopy Dark-staining in microscopy Found throughout the nucleus Concentrated at nuclear periphery 📚 Key Terms to Remember ​ Ribozyme: Catalytic RNA molecule. ​ Polymer vs. Monomer: Long chain vs. single unit (nucleotide = monomer; DNA = polymer). ​ Nucleotide: Nitrogenous base + sugar + phosphate group. ​ Purines vs. Pyrimidines: Double-ring (A, G) vs. single-ring (T, C). ​ 3’ and 5’ Ends: Directionality of DNA strands. ​ Phosphodiester Bond: Links nucleotides. ​ Hydrogen Bonds: Stabilize base pairs. ​ Major vs. Minor Groove: Grooves in the DNA helix where proteins bind. ​ DNA Melting (Tm): Temperature where DNA strands separate. ​ Chromosome vs. Chromatid vs. Gene vs. Allele: Levels of genetic structure. ​ Chromatin: DNA + proteins (histones). ​ Nucleosome: DNA wrapped around histone proteins. ​ Euchromatin vs. Heterochromatin: Active vs. inactive chromatin forms. Week 3 Learning Objectives 1. Genome ​ Definition: The complete set of an organism's genetic material, including all genes and non-coding regions. ​ Variation between organisms: Genome size and structure vary across organisms. For example, humans have about 3 billion base pairs, while some organisms, like bacteria, have much smaller genomes. Larger, multicellular organisms tend to have more complex genomes due to the need to regulate a higher number of genes. 2. Regulatory and Structural Components of a Eukaryotic Genome ​ Regulatory components: Include promoters, enhancers, silencers, and other DNA sequences that control gene expression. ​ Structural components: Composed of genes (exons and introns) and non-coding regions that maintain genome integrity. 3. Connection between Multicellularity and Genome Size ​ Multicellular organisms typically have larger and more complex genomes to accommodate the regulation of gene expression across different cell types, tissues, and developmental stages. 4. Differential Gene Expression ​ The process where different cells in an organism express different genes based on cell type, developmental stage, and environmental factors, leading to cellular specialization. 5. DNA-Binding Proteins in the Transcription Initiation Complex (TIC) ​ Basal Transcription Factors: Essential for the basic transcription machinery to assemble and initiate transcription. ​ Co-activators: Proteins that enhance transcription by interacting with activators, but do not bind directly to DNA. ​ Activators: Transcription factors that increase gene expression by helping to form the transcription complex. ​ Repressors: Transcription factors that decrease gene expression by preventing transcription complex formation. 6. Relationship of DNA-Binding Proteins to Target DNA Sequences ​ Enhancers: DNA sequences where activators bind to increase transcription. ​ Silencers: DNA sequences where repressors bind to decrease transcription. ​ TATA Box: A specific DNA sequence where basal transcription factors bind to start transcription. 7. Formation of the TIC and Effects of Alterations ​ The TIC assembles at the promoter region of a gene. If any protein or DNA sequence is altered (e.g., mutation in the TATA box), it could disrupt transcription initiation and result in reduced or absent gene expression. 8. RNA Polymerase Positioning at the Start of Transcription ​ RNA polymerase binds to the promoter region with the help of transcription factors. The polymerase is positioned to start transcription after the pre-initiation complex is formed. 9. How the Transcription Rate is Altered ​ Transcription rate is influenced by the efficiency with which the TIC forms. More rapid formation leads to higher transcription rates, while slower assembly results in reduced transcription. 10. DNA Ends (5' and 3') in Transcription ​ 5' end: The starting point of transcription. RNA is synthesized in the 5' to 3' direction. ​ 3' end: The end of the newly synthesized RNA. 11. Coding vs. Template Strands ​ Coding strand: The DNA strand that has the same sequence as the RNA (with T instead of U). ​ Template strand: The DNA strand used by RNA polymerase to synthesize the RNA. 12. Pre-mRNA to Mature mRNA Formation ​ Splicing: Introns are removed, and exons are joined together to form a continuous coding sequence. ​ 5' capping: A methylated guanine cap is added to the 5' end of pre-mRNA for protection and recognition. ​ Poly-A tail: A polyadenine sequence added to the 3' end of pre-mRNA to stabilize the mRNA. 13. RNA and Protein Components of snRNPs ​ snRNPs (small nuclear ribonucleoproteins) are complexes of snRNAs and proteins that play a crucial role in splicing. They recognize splice sites at exon-intron boundaries and catalyze the removal of introns. 14. Alternative RNA Splicing ​ A process that allows a single gene to produce multiple mRNA isoforms by including or excluding certain exons. This increases protein diversity. 15. Cellular Locations and Functions ​ Transcription: Occurs in the nucleus. ​ Pre-mRNA processing: Occurs in the nucleus, where splicing, capping, and polyadenylation take place. ​ Translation: Occurs in the cytoplasm. 16. Mutation vs. Epigenetic Regulation ​ Mutation: A permanent change in the DNA sequence. ​ Epigenetic regulation: Changes in gene expression that do not involve changes to the DNA sequence, often through mechanisms like DNA methylation and histone modification. 17. Three Types of Single Nucleotide Mutations ​ Silent mutation: No change in the protein sequence. ​ Missense mutation: Changes one amino acid in the protein sequence.  ​ Nonsense mutation: Introduces a premature stop codon, truncating the protein. 18. Role of Epigenetics in Gene Expression ​ Epigenetic mechanisms, such as DNA methylation and histone modification, regulate gene expression by altering chromatin structure or the accessibility of DNA without changing the genetic code. 19. DNA Methylation vs. Histone Modification ​ DNA methylation: Addition of a methyl group to cytosine residues, typically silencing gene expression. ​ Histone modification: Chemical changes to histone proteins (e.g., acetylation, methylation), influencing chromatin structure and gene accessibility. 20. Methylation-Sensitive Restriction Enzymes ​ These enzymes are used to detect methylation patterns in DNA. They cleave DNA only when a specific methylation pattern is absent, allowing researchers to determine methylation status. Key Terms and Definitions: 1.​ Genome: Complete set of genetic material in an organism. 2.​ Non-coding RNAs: RNA molecules that do not code for proteins but have regulatory functions. 3.​ Differential gene expression: The expression of different genes in different cells or under different conditions. 4.​ Transcription factors: Proteins that bind to DNA and regulate gene transcription (activators, repressors, coactivators, basal transcription factors). 5.​ DNA regulatory regions: Sequences of DNA that control gene expression (promoters, enhancers, silencers). 6.​ Structural regions (exons): Coding regions of DNA that are transcribed into RNA and translated into proteins. 7.​ Pre-initiation complex: The assembly of transcription factors and RNA polymerase at the promoter before transcription begins. 8.​ RNA polymerase: The enzyme that synthesizes RNA from the DNA template. 9.​ Helicase: An enzyme that unwinds the DNA double helix during transcription. 10.​Transcription bubble: The region of unwound DNA where transcription occurs. 11.​Coding vs. Template: The coding strand has the same sequence as the RNA, while the template strand is used by RNA polymerase to create RNA. 12.​mRNA processing: Modifications to pre-mRNA that include capping, splicing, and polyadenylation to produce mature mRNA. 13.​Spliceosome: Complex responsible for removing introns from pre-mRNA. 14.​Alternative RNA splicing: The process by which different proteins are produced from the same gene by varying the exons included in the mRNA. 15.​Mutation vs. Epigenetics: Mutation refers to permanent changes in DNA, while epigenetics refers to heritable changes in gene expression that do not involve changes in DNA sequence. 16.​CpG Island: Regions of DNA with a high frequency of CG dinucleotides, often found in gene promoters. 17.​Methylation: The addition of methyl groups to DNA or histones, often repressing gene expression. 18.​Post-translational modifications: Chemical modifications made to proteins after they are translated, affecting their function. 19.​RNAi (miRNA): Small RNA molecules that regulate gene expression by degrading mRNA or inhibiting translation.