Free response questions
what is the RNA world hypothesis? what is one piece of evidence that supports this idea? what problem does this hypothesis solve?
The RNA world hypothesis proposes that early life was based on RNA, which served as both the genetic material and a catalyst for biochemical reactions, before DNA and proteins evolved.
Evidence: Ribozymes, RNA molecules with catalytic properties, demonstrate that RNA can both store information and facilitate chemical reactions, supporting its dual role in early life.
Problem solved: It addresses how life could have originated by explaining a plausible precursor to the DNA-protein system, which requires complex interdependence
describe the differences among primary, secondary, tertiary, and quaternary structure of proteins
Primary structure: The linear sequence of amino acids in a protein.
Secondary structure: Local folding patterns (e.g., α-helices, β-sheets) stabilized by hydrogen bonds.
Tertiary structure: The overall 3D shape of a single polypeptide, determined by interactions like hydrophobic interactions, hydrogen bonds, and disulfide bridges.
Quaternary structure: The assembly of multiple polypeptide chains into a functional protein complex
what are the big advantages to using RNAi to study biological processes in C. elegans? Describe the advantages of RNAi, as well as why C. elegans is particularly well suited to this technique
RNAi (RNA interference) is advantageous for studying biological processes because it enables precise, sequence-specific gene silencing, allowing researchers to investigate gene function effectively.
Advantages of RNAi:
High specificity in targeting genes.
Simple and scalable, enabling high-throughput studies.
Reversible, avoiding permanent genetic changes.
Why C. elegans is well-suited:
RNAi is efficiently taken up by feeding, injection, or soaking.
Its transparent body and short lifecycle facilitate rapid phenotypic analysis.
A fully mapped genome and conserved pathways enhance relevance to other organisms.
compare the rate of lateral diffusion of a lipid with that of flip-flop. what is the reason for difference? how is flippase involved?
Lateral diffusion of lipids within the same leaflet is very fast, occurring on the scale of microseconds, while flip-flop (movement of lipids between leaflets) is very slow, taking hours or longer.
Reason for difference: Lateral diffusion is energetically favorable since it doesn't involve crossing the hydrophobic core of the membrane, whereas flip-flop requires overcoming a significant energy barrier due to the polar head group passing through the hydrophobic bilayer.
Flippase role: Flippases are enzymes that facilitate the flip-flop of specific lipids by lowering the energy barrier, enabling rapid and selective movement between leaflets.
describe the steps from an impulse arriving at aa terminal knob of a presynaptic neuron to action potential initiation in a postsynaptic cell
Impulse Arrival: An action potential reaches the terminal knob of the presynaptic neuron.
Calcium Influx: Voltage-gated calcium channels open, allowing calcium ions to enter the terminal.
Neurotransmitter Release: Calcium triggers synaptic vesicles to fuse with the membrane, releasing neurotransmitters into the synaptic cleft.
Neurotransmitter Binding: Neurotransmitters bind to receptors on the postsynaptic cell membrane.
Ion Channel Opening: Receptor activation opens ion channels, leading to ion flow (e.g., Na⁺ influx).
Depolarization: If the membrane potential reaches the threshold, an action potential is initiated in the postsynaptic cell.
How does the fact that the G domain is conserved give Ras-like proteins their identity? How do the non-conserved regions create diversity among Ras-like protein? What impact does this have on interacting proteins such as GEFs, GAPs, and effectors?
The conserved G domain in Ras-like proteins defines their identity by providing a shared structure and mechanism for binding and hydrolyzing GTP. The non-conserved regions create diversity by enabling specific interactions with distinct regulators and effectors, such as GEFs, GAPs, and effectors. This diversity ensures that each Ras-like protein can engage in unique signaling pathways, allowing for precise cellular functions.
compare and contrast mitochondria and chloroplasts in structure and explain how these structures aid in their functions
Similarities: Both mitochondria and chloroplasts are double-membraned organelles with their own DNA and ribosomes. They have highly folded inner membranes (cristae in mitochondria, thylakoid membranes in chloroplasts) to increase surface area for chemical reactions.
Differences: Mitochondria have cristae for the electron transport chain and ATP production during cellular respiration. Chloroplasts have thylakoid membranes containing chlorophyll for light absorption and photosynthesis.
Functional relevance: The increased surface area in both organelles enhances their ability to generate energy efficiently—ATP in mitochondria and glucose in chloroplasts.
How are plasmodesmata and gap junctions similar? how are they dissimilar? would you expect a moderately sized protein to pass through a plasmodesma?
Similarity: Plasmodesmata in plants and gap junctions in animals both allow direct communication and material exchange between adjacent cells.
Dissimilarity: Plasmodesmata are larger and can transport larger molecules, including RNA and proteins, whereas gap junctions are smaller and typically allow the passage of ions and small molecules.
Protein passage: Yes, a moderately sized protein can pass through a plasmodesma, as these structures are capable of accommodating larger molecules compared to gap junctions.
Describe the two earlier models for the dynamics of transport through the golgi complex. What is the current model?
The two earlier models for transport dynamics through the Golgi complex are the "Cisternal Maturation Model" and the "Vesicular Transport Model."
Cisternal Maturation Model: Proposes that Golgi cisternae mature from one type to another, facilitating transport as they progress through the stack, with enzymes being added or removed as necessary.
Vesicular Transport Model: Suggests that cargo is transported between Golgi cisternae via vesicles that bud off from one and fuse with another.
The current model integrates aspects of both, recognizing that while vesicular transport occurs, cisternae also undergo maturation as they move through the stack.
In the paper we read by Reeve et al. they reviewed mitochondrial disease. Why did they argue this paper was important? What was the “so what” factor?
This paper was important because it determined the connection between mtDNA with aging and neurodegeneration. By recognizing this relationship, they were able to identify a similar cause among people that were affected by the mutation, and the conditions that improved or worsened its effects.
In the paper we read by Akhavan et al. they investigated the role of loss of function in the LARGE gene (LARGE-) on cell proliferation. What is the effect of LARGE- on cell proliferation? What was the main effect on the cell cycle that they found in LARGE- cells? How does this promote tumor growth?
In this paper, LARGE- was found to increase cell proliferation. The S phase of the cell cycle, the division of cells, occurred more rapidly with the presence of LARGE-. This promotes tumor growth because these cancerous cells are being generated quickly. The defective laminin anchoring were a result of LARGE-, and these effects are linked to brain and breast cancer cells.
Outline the steps involved in the breakdown of glycogen to glucose by the liver. Include in your answer: Glucagon, GPCR, ATP, GaS, cAMP, Adenylate cyclase, PKA, and regulators.
The breakdown of glycogen to glucose in the liver begins when glucagon, a hormone released during fasting, binds to a G protein-coupled receptor (GPCR) on liver cells. This initiates a signaling cascade that involves the following steps:
Glucagon Binding: Glucagon binds to the GPCR, resulting in a conformational change in the receptor.
G Protein Activation: The activated GPCR interacts with the G protein, activating the GaS subunit.
cAMP Production: GaS stimulates adenylate cyclase, leading to the conversion of ATP to cyclic AMP (cAMP).
PKA Activation: Increased levels of cAMP activate protein kinase A (PKA).
Glycogen Breakdown: Activated PKA then phosphorylates key enzymes involved in glycogen breakdown, leading to the activation of glycogen phosphorylase and inhibition of glycogen synthase.
Glucose Release: Glycogen phosphorylase catalyzes the cleavage of glycogen into glucose-1-phosphate, which is then converted to glucose-6-phosphate. If required, glucose-6-phosphate can be dephosphorylated to form free glucose, which is released into the bloodstream.
Regulation: The process is tightly regulated by various factors including the concentration of glucose, energy status of the cell, and the feedback mechanisms that inhibit or stimulate further glycogen breakdown depending on the organism’s metabolic needs.
Describe the steps leading to the cell cycle checkpoint resulting from UV damage. Include in your answer: ATR, Chk1, Cdc25, and the relevant stages of the cell cycle.
UV Damage Detection: UV damage induces DNA lesions, activating ATR (Ataxia Telangiectasia and Rad3-related protein).
Chk1 Activation: ATR phosphorylates and activates Chk1 (Checkpoint Kinase 1).
Cdc25 Inhibition: Chk1 phosphorylates Cdc25, inhibiting its activity.
Cell Cycle Arrest: Inhibition of Cdc25 prevents dephosphorylation of CDK complexes, halting the cell cycle at the G1/S or G2/M checkpoint to allow DNA repair.
Describe the multiple levels of organization that comprise the structure of an intermediate filament.
Intermediate filaments are composed of a diverse group of proteins that assemble into a complex structure, organized at multiple levels:
Monomeric Units: The basic building blocks of intermediate filaments are individual polypeptide chains, which can vary widely in sequence and structure depending on the specific type of intermediate filament (e.g., keratins, vimentin, neurofilaments).
Dimer Formation: These monomers form coiled-coil dimers through interactions between their helical regions, creating a stable unit that serves as the foundation for filament assembly.
Tetramer Assembly: Two dimers align in an antiparallel orientation, resulting in a tetramer that is crucial for the filament's structural integrity and mechanical resilience.
Protofilament Formation: Multiple tetramers then associate laterally to form protofilaments, which further aggregate to create the thicker intermediate filament structure.
Filament Organization: Finally, the protofilaments intertwine and stabilize through non-covalent interactions, resulting in the mature intermediate filament that provides structural support and resilience to cells.
Kinesin-5 was described as having two heads. How does this play a role in spindle fiber dynamics? What direction does each motor move?
Kinesin-5, facilitates the sliding of interpolar microtubules apart during mitosis, which is essential for the separation of spindle poles. Each motor head moves towards the plus end of the microtubules, allowing the kinesin-5 molecules to push the spindle fibers apart, thereby contributing to the elongation of the spindle.
Describe how wee1 and cdc25 control the cell cycle in yeast. Describe how knockout mutations of each impact yeast cells.
wee1 makes Cdk inactive by inhibiting mitotic cyclins from allowing passage from G2 to mitosis. cdc25 causes cdk to remain active. knockout mutations impact yeast cells as seen in the figure. the WT depicts an ideal process from G2 to mitosis. When wee1 becomes knocked out, the process is shortened and proliferation occurs regardless and at a faster rate because there is no inhibition. When cdc is knocked out, there are no synthesis stages and the cell does not split, it is inhibited.