Biology Week 1: Cystic Fibrosis and Phospholipids

Week 1 Learning Objectives

• Explore and outline the symptoms of Cystic Fibrosis (CF): persistent coughing with thick mucus, frequent lung infections, wheezing, shortness of breath, and poor growth despite a good appetite. Difficulty with bowel movements.
• Hypothesize the mechanism behind CF symptoms: Mutations in the CFTR gene affecting the CFTR protein, which regulates chloride ion transport. Defective ion transport leads to thick, sticky mucus buildup primarily in the lungs and digestive system.
• Identify the different parts of a phospholipid: Fatty acid tails (hydrophobic), glycerol backbone, and phosphate group (hydrophilic).
• Relate the amphipathic nature of phospholipids to bilayer formation: Amphipathic means possessing both hydrophobic and hydrophilic regions. In aqueous environments, hydrophobic tails face inward, and hydrophilic heads face outward, creating a phospholipid bilayer.
• 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, whereas large or charged molecules require transport proteins.
• Discuss membrane selective permeability: Allows certain substances to pass while restricting others, based on the molecule's size, polarity, and charge.
• Define osmosis: The passive movement of water molecules across a selectively permeable membrane from areas of low solute concentration to high solute concentration.
• Define three major categories of organelles: membrane-bound (e.g., nucleus, ER, Golgi apparatus), proteinaceous (e.g., ribosomes), and endosymbiotic (e.g., mitochondria, chloroplasts).
• Evolution of the nucleus and endomembrane system (FECA vs. LECA): FECA (First Eukaryotic Common Ancestor) possessed simple membrane systems as precursors to eukaryotes.

Week 2 Learning Objectives

• Evidence supporting RNA as the early information- storing molecule: RNA World Hypothesis suggesting RNA was the first genetic material, able to store information and catalyze reactions. Key evidence includes ribozymes (RNA molecules acting as enzymes), 3-D structure necessary for catalytic functions, and RNA self-replication.
• Why DNA is better for information storage than RNA: DNA's double-stranded structure and deoxyribose sugar offer greater stability. DNA has repair mechanisms and longevity due to its lack of a 2'-hydroxyl group, making it less reactive and less prone to degradation.
• Benefits of a Nucleus: Separation of processes (transcription in nucleus, translation in cytoplasm), protection of DNA from harmful cytoplasmic reactions, and efficient regulation of gene expression.

Week 2 Learning Objectives--Continued

• Monomeric & Polymeric forms of DNA: Monomer: Nucleotide (nitrogenous base, deoxyribose sugar, phosphate group). Polymer: DNA, linking nucleotides through phosphodiester bonds.
• DNA polymer formation & base pairing rules: Phosphodiester bonds link the sugar-phosphate backbone. Base pairing rules ensure accurate DNA replication, Adenine (A) pairs with Thymine (T) via 2 hydrogen bonds and Guanine (G) pairs with Cytosine (C) via 3 hydrogen bonds.
• Role of hydrogen bonds in DNA structure: Hydrogen bonds hold the two DNA strands together, creating the double helix. They break easily for strand separation in replication or transcription.
• How changes in DNA structure impact function: Mutations alter protein function and structural alterations can impair replication and gene expression.

Week 2 Learning Objectives--Continued

• 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, and Methyltransferases add methyl groups to modify gene expression.
• DNA melting & temperature (Tm) analysis: DNA melting is the process of double-stranded DNA separating into single strands upon heating. Tm is the temperature at which 50% of the DNA is denatured, higher Tm means more G-C pairs due to three hydrogen bonds. Measures DNA melting by tracking absorbance change at 260nm
• Relationship between DNA, chromosome, genes, and alleles (example: cystic fibrosis). DNA carries genetic instructions, Chromosomes are long DNA molecules containing many genes, Genes are segments of DNA coding for a specific protein & alleles are different versions of a gene. For example, CFTR gene in cystic fibrosis with mutant vs normal alleles.
• Nucleosome structure: Nucleosome is a basic unit of DNA packaging, containing core proteins (H2A, H2B, H3, H4) and DNA tightly wrapped around it for efficient packaging. Linker DNA connects nucleosomes with H1 histone for stabilization.
• Euchromatin vs. Heterochromatin: Euchromatin is loosely packed, actively transcribed, light-staining. Heterochromatin is tightly packed, transcriptionally inactive, dark-staining, concentrated at nuclear periphery.

Week 3 Learning Objectives

• Genome definition: The complete set of an organism's genetic material, including genes and non-coding regions.
• Variation between organisms: Genome size and structure vary across organisms. Larger, multicellular organisms generally have more complex genomes to regulate a higher number of genes.
• Regulatory and structural components of a eukaryotic genome: Regulatory components include promoters, enhancers, silencers, which control gene expression. Structural components consist of genes (exons and introns) and non-coding regions to maintain genome integrity.
• Connection between multicellularity and genome size: Multicellular organisms typically have larger, more complex genomes to regulate gene expression across different cell types, tissues, and developmental stages.

Week 3 Learning Objectives--Continued

• 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.
• DNA-binding proteins in the transcription initiation complex (TIC): Basal transcription factors are essential for the basic transcription machinery. Co-activators, activators, and repressors impact transcription by binding and enhancing or preventing gene expression.
• Relationship between DNA-binding proteins and target DNA sequences: Enhancers increase, silencers decrease transcription. Specific DNA sequences such as the TATA box act as binding sites for basal transcription factors.
• Formation of the TIC and effects of alterations: The TIC assembles at the promoter. Alterations can disrupt transcription initiation and result in reduced or absent expression.
• RNA polymerase positioning at the start of transcription: RNA Polymerase binds to promoter region with the help of transcription factors to start transcription.
• How the transcription rate is altered: Transcription rate depends on the efficiency of the TIC formation. More efficient TIC assembly results in more rapid transcription.
• DNA ends (5' and 3') in transcription: 5' end is the start point, and RNA is synthesized from 5' to 3’. The 3' end is the end of the synthesized RNA.

Week 3 Learning Objectives--Continued

• Coding vs. template strand: Coding strand has the same sequence as the RNA. Template strand is used by RNA polymerase to synthesize RNA, substituting Thymine (T) for Uracil (U).
• Pre-mRNA to mature mRNA formation: Splicing removes introns, 5' capping protects and signals. Addition of a Poly-A tail at the 3' end helps with stability.
• RNA and protein components of snRNPs: snRNPs (small nuclear ribonucleoproteins) play a role in splicing, identifying splice sites, and catalyzing intron removal.
• Alternative RNA splicing: A process enabling one gene to produce multiple mRNA isoforms leading to diverse proteins.
• Cellular locations and functions of transcription, pre-mRNA processing, and translation. Transcription occurs in the nucleus. Pre-mRNA processing and splicing also occur in the nucleus. Translation occurs in the cytoplasm..
• Mutation vs. epigenetic regulation. A mutation is a permanent change in DNA sequence. Epigenetic modification regulates gene expression without changing the DNA sequence.
• Three types of single nucleotide mutations. Silent, missense and nonsense.
• Role of Epigenetics in Gene Expression: Epigenetic mechanisms regulate gene expression by altering chromatin, without changing the DNA sequence.
• DNA methylation vs. histone modification: DNA methylation is the addition of a methyl group to cytosine residues which typically silences gene expression. Histone modification (e.g., acetylation, methylation) affects chromatin structure and gene accessibility.
• Methylation-sensitive restriction enzymes used to detect methylation patterns in DNA.
• mRNA processing: Modifications such as capping, splicing, and polyadenylation to produce mature mRNA. Spliceosome processes removal of introns. Alternative splicing enables creation of different proteins from the same gene through different mRNA isoforms. Mutations differ from epigenetics as mutations are permanent DNA changes while epigenetics are heritable changes in gene expression without changing the DNA sequence, e.g., methylation.
• Post-translational modifications affect proteins' function after translation, impacting their function. RNAi and miRNA are small RNA molecules.