Chapter 1
What features of budding yeast make it valuable for modeling human cell biology compared to E. Coli?
Yeast such as S. Cerevisiae contain eukaryotic organelles similar to animal cells: nucleus, ER, mitochondria and Golgi are some of the conserved organelles that show us similar structure and function to the eukaryotic human cells.
Antibodies produced by an influenza vaccine strongly recognize viral antigens in one season but often fail to protect against strains circulating the next year. Explain why this happens at the molecular level and describe what scientists must do to ensure influenza vaccines remain effective.
Because influenza viruses undergo frequent mutations (antigenic drift) in the genes encoding their surface proteins, the antigenic epitopes change their structure and chemical properties. As a result, last year’s antibodies no longer fit the new epitopes. To maintain effectiveness, scientists must continually identify circulating strains and update the vaccine with antigens that match the new viral surface proteins.
Why might cells restrict the lateral mobility of certain membrane proteins, and what cellular consequences would arise if this restriction failed?
Cells restrict mobility using the underlying cortex, junctional complexes, or diffusion barriers to maintain polarity, localize signaling complexes, and create functional domains. Without restriction receptor clusters would diffuse around the cell leading to signaling collapse.
You find that a eukaryotic cell shows five defects:
It becomes fragile under stress
Proteins are not produced correctly
Vesicles fail to reach their targets within the cell
The cell has loss of polarity and motility
Finally core metabolic reactions in the fluid of the cell are failing to take place
Which cellular structures are most likely responsible for each of these failures.
Bonus Question: What could cause a single cell to exhibit all of these defects simultaneously?
Intermediate filaments
ER/Golgi
Microtubules
Microfilaments
Cytosol
A mutation in a protein changes one amino acid in the middle of its chain. The peptide bond backbone remains intact, but the folded protein becomes unstable and loses activity. Explain how a single amino acid substitution can disrupt multiple noncovalent interactions throughout the polypeptide chain, even if the overall peptide backbone is unchanged.
The linear sequence of amino acids determines how the chain folds and which residues interact. A single substitution can remove or introduce a charged, polar, or bulky side chain, disrupting local hydrogen bonds, ionic bridges, or hydrophobic packing. Because protein folding is highly cooperative, this local disturbance can cascade, weakening distant noncovalent interactions and destabilizing the entire threedimensional structure. This loss of folding precision explains why a mutation can abolish activity without breaking peptide bonds.
How could a researcher experimentally test whether a specific membrane protein is laterally mobile within the plasma membrane, and what results would indicate restricted versus free diffusion?
Use a laser to bleach an area of the plasma membrane containing GFP target labeled proteins. The speed of recovery is used to determine the lateral protein mobility
Why is it important that the amino acid sequence in the hypervariable loops of an antibody can change without disrupting the overall antibody structure?
Because the hypervariable loops (complementarity-determining regions, CDRs) are anchored on a stable β-sheet framework of the variable domains, their amino acid sequence can vary widely without destabilizing the antibody’s overall fold. This means the immune system can generate many different types of antibodies with unique antigen-binding sites while still preserving the conserved Y-shaped structure and effector functions needed for a coordinated immune response.
Phospholipids are synthesized in the endoplasmic reticulum (ER), yet certain phospholipids are asymmetrically distributed in the plasma membrane. What mechanisms establish and maintain this asymmetry, and what functional roles does it serve?
In the ER, phospholipids are evenly distributed due to scramblases, which result in symmetric growth of both halves of the bilayer. In the Golgi, flippases redistribute them, generating asymmetry. For example, phosphatidylserine is enriched on the cytosolic leaflet but externalized during apoptosis to signal phagocytosis.
Imagine a cell where all chaperone proteins are nonfunctional. A newly synthesized polypeptide has the correct amino acid sequence to form a multi-subunit protein. Predict how the absence of chaperones would affect each level of protein structure (primary, secondary, tertiary, quaternary) and explain the likely consequences for protein function. Propose one strategy the cell might use to minimize misfolding under these conditions.
Primary structure: The amino acid sequence remains intact because peptide bonds are unaffected.
Secondary structure: α-helices and β-sheets may form incorrectly or prematurely, as exposed backbone regions could form inappropriate hydrogen bonds.
Tertiary structure: Misfolding is likely because side chain interactions may lead to incorrect packing and aggregation without chaperone guidance.
Quaternary structure: Multi-subunit assembly may fail due to misfolded subunits, preventing functional complex formation.
Consequences: Loss of protein function, aggregation, and potential cellular toxicity.
Possible cellular strategy: Upregulate proteases to degrade misfolded proteins or induce heat shock response to produce compensatory chaperones once possible.
You are investigating a newly discovered DNA-binding protein suspected to regulate transcription. Design an experiment to determine whether this protein co-localizes with transcriptionally active DNA regions in the nucleus. You have access to:
-Microscopy techniques: SEM, TEM, confocal, super-resolution, and bright field
-Fluorescent dyes: DAPI, FITC, and rhodamine
Explain how you would use these tools to visualize the protein’s interaction with DNA and describe how dual labeling with FITC, and rhodamine could help confirm co-localization.
Finally, you discover that electrostatic interactions are disrupted within the tertiary structure of the protein, what amino acids may have been mutated to cause this.
1. Label DNA-binding protein with rhodamine
2. Label transcriptionally active DNA with FITC
Use super-resolution fluorescence microscopy
Amino Acids (Asp, Glu, Lys, Arg): possibly His