Cell Bio Final Flashcards
(38 cards)
Describe the role of noncovalent hydrogen bonds in protein and why pH changes influence these bonds.
Noncovalent hydrogen bonds play a critical role in maintaining the three-dimensional structure of a protein by forming connections between different amino acid residues, essentially acting as “molecular glue” that helps to hold the protein’s folded shape; however, pH changes can significantly influence these hydrogen bonds by altering the charge state of amino acid side chains, potentially disrupting the protein’s structure and function if the pH deviates too far from its optimal range
General functions of proteins
- Structure
- Enzymes
- Storage proteins
Describe how a mutation in the PAH gene can lead to nonfunctional protein.
A mutation in the PAH gene can lead to a nonfunctional protein by altering the genetic code, resulting in the production of an altered version of the phenylalanine hydroxylase enzyme that is unable to effectively break down the amino acid phenylalanine, causing it to accumulate in the body to potentially toxic levels; this malfunctioning enzyme can be caused by changes in the protein’s structure, stability, or active site due to the mutation, preventing it from performing its intended function properly.
Describe how the A300Q mutation may disrupt function
The PAH protein is an enzyme that exists to assist in catalyzing certain reactions to occur by lowering the the activation energy barrier. This turns a reaction from unfavorable to favorable. If this amino acid is found at the catalytic site of enzymes, the active site may not have the proper structure so that phenylalanine is not able to bind and undergo the transformation into tyrosine.
Explain the role of chaperone proteins in attempting to refold the mutant CFTR protein and why this is important
If an amino acid is missing or if an area is interfering with proper folding, chaperone proteins can bind to CFTR proteins which would then relax the protein chain. The CFTR protein could refold properly without interacting to the sites where chaperone proteins are present. Once complete, chaperone proteins can disengage for final folding saving the cell energy from what otherwise would have been a mutated protein needing to be degraded.
As mutant CFTR proteins accumulate in the cell, UPR is activated. What happens during UPR?
During the Unfolded Protein Response (UPR) cell process, when a high level of unfolded proteins accumulates in the endoplasmic reticulum (ER), the cell activates a signaling pathway to restore protein folding homeostasis by enlarging the ER, increasing the production of chaperone proteins, reducing protein synthesis, and promoting the degradation of misfolded proteins, essentially attempting to alleviate stress on the ER before resorting to cell death mechanisms if the stress is too severe. Some chaperone proteins may create hydrophobic chambers to refold proteins in isolated conditions. Once complete, normal ER function returns.
What happens when proteasomes degrade mutated CFTR proteins?
Mutated CFTR proteins are ubiqylated to be marked for degradation by ubiquitin chains. These chains guide the proteins to the proteasome and enter a channel where ubiquitin is removed and recycled. The mutated protein enters the main cavity where the protein is denatured into its primary sequence. The chain enters the center complex for final degradation into amino acids for reuse by the body.
Explain alternate mechanisms for the cell to degrade proteins by lysosomes.
Cells can degrade proteins through lysosomes via three primary mechanisms: endocytosis (including receptor-mediated endocytosis), phagocytosis, and autophagy; each involving the delivery of targeted proteins to the lysosome for degradation by fusing vesicles containing the proteins with the lysosomal membrane, allowing the lysosomal enzymes to break down the protein material within the acidic (ph 5) environment of the lysosome. Contained proteases break the protein down into amino acids for recycle by the body. This is energy intensive.
Describe the unique properties of membrane lipids into bilayers.
Lipids are made of nonpolar carbon chains that act as lipid tails and a polar head. Membrane lipids spontaneously fold in aqueous environments into two layers as the nonpolar carbon chains avoid interaction with the environment. The polar heads envelope the nonpolar tails and create the external structure. The nonpolar sides are still exposed so the bilayer structure extends so that a fully enclosed sphere forms where the nonpolar tails are fully protected by the polar heads. This leads to the amphetic nature of lipids, creating vesicles, organelles and cells.
Explain the adjustments a bacterium would take to make its membrane adapt to the environment.
Fluidity of a lipid membrane is determined by the length of the carbon chain on nonpolar tails and the number of unsaturated carbon to carbon bonds on the tail. A bacterium in a cold environment might adapt to cold weather so that they have more unsaturated carbon bonds or shorter chains to be more fluid for survival. In warmer temperatures, a bacterium could utilize sterols, or cholesterol, to stiffen up its membrane to be less fluid. Sterols typically fit between unsaturated bonds without having to rebuild or shorten carbon chains.
Pick the amino acid sequence below that represents sequences of transmembrane helices. Justify your answer and how it is different than channels.
a-helices form so that the outside of the helix is nonpolar to interact with the nonpolar interior membrane while the internal structures of the helix are polar. This allows a-helices to be inserted through the lipid bilayer of the membrane. For a single transmembrane, the domain would need to be without any charges so as not to affect the cell membrane. The answer would not have charged amino acid groups.
Identify the molecules that are more likely to diffuse through the lipid bilayer.
Amino acid or steroids
Cl- or ethanol
Glycerol or RNA
H2O or O2
Amino acid or steroids*
Cl- or ethanol*
Glycerol* or RNA
H2O or O2*
3 proteins related to glucose transport:
Glucose transporter allowing glucose to travel from high to low concentrations without energy (passive). Transporter is either open or closed and if concentration allows for movement into cell, glucose will bind to transformer.
Glucose pumps allows glucose to travel from low to high concentrations even when gradient is unfavorable. Energy is required. Glucose binds to pump and pump conforms to allow glucose to enter cell.
Sodium-glucose pump: Na+ exits the cell from high to low concentrations and glucose and glucose enters the cell as the protein conforms its shape. Passive
Describe the normal function of CFTR protein in airway epithelial cells
The CFTR protein functions as a chloride ion channel, actively transporting chloride ions out of the cell, which in turn draws water to the cell surface, helping to maintain a hydrated mucus layer crucial for normal mucociliary clearance and healthy airway function
Explain how mutations in the CFTR gene affects protein function
The protein is not properly able to form as as a result of incorrect amino acid sequences. As a result, chlorine cannot bind to the CFTR protein to be removed from the cell. Chlorine builds up.
Discuss the consequences of impaired CFTR function on ion transport and mucus consistency
As chlorine cannot be removed from the cell or being removed at a reduced rate, the charge in the cell tends to be more positive. As a result, sodium enters the cell to equalize the electrochemical gradient. As a result, this affects water levels as the cell then has to bring in water to correct sodium levels, though this dehydrates the aqueous environment leaving a mucus. This impacts cilia movement, sperm movement that requires a thinner consistency to move.
Describe the structure and function of a voltage-gated sodium ion channel, including all four domains of the channel proteins.
Pore Region: The domain forms the central pore through which sodium ions pass. The selectivity filter within this loop ensures high specificity for sodium ions over other cations.
Voltage-Sensing Domain: The voltage sensor. When the membrane potential changes, a conformational change occurs that opens or closes the channel.
Activation Gate: The activation gate opens first during depolarization, enabling sodium ion flow.
Inactivation Proteins: The inactivation gate, which plugs the pore during the refractory period after activation.
Describe what is happening to the membrane potential of a neuron during action potential. Be sure to include the membrane potential changes of the squid Axon and what is responsible for those changes.
In the squid neuron, there are sodium and potassium channels that are steadily allowing the flow of ions to increase the membrane potential to -40 millivolts. At this point an action potential signals for the sodium voltage gate to open which floods the cell with sodium depolarizing the membrane to 40 millivolts. The sodium voltage gates is inactivated and the potassium voltage gate opens allowing the cell to repolarize the membrane with potassium moving into the cell. At -70 millivolts the potassium voltage gate closes. The sodium gates are officially closing at -60 millivolts. The membrane potential slowly depolarizes back to -40 millivolts with leak channels.
Explain the process of exocytosis in the context of neurotransmitter release at a synapse. 7 steps
–Neuronal Action Potential Arrival: An action potential propagates down the axon of the presynaptic neuron and reaches the axon terminal. The depolarization of the terminal membrane causes voltage-gated calcium channels to open.
–Calcium Influx: Calcium ions enter the axon terminal through these channels due to the electrochemical gradient. This initiates the neurotransmitter release process.
–Synaptic Vesicle Docking and Priming: Synaptic vesicles, which contain neurotransmitters, are docked at the active zone of the presynaptic membrane. Docking involves vesicle tethering to specific sites via protein complexes, such as the SNARE complex
–Vesicle Fusion: Ca2+ binds to a calcium-sensing protein called synaptotagmin, located on the synaptic vesicle membrane. This triggers the full assembly of SNARE proteins. This leads to the fusion of the vesicle membrane with the presynaptic plasma membrane.
–Neurotransmitter Release: The fusion creates a pore through which neurotransmitters (e.g., acetylcholine, dopamine, glutamate) are released into the synaptic cleft. Neurotransmitters diffuse across the cleft to bind to receptors on the postsynaptic membrane.
–Termination of Neurotransmitter Signal: After release, neurotransmitters are cleared from the synaptic cleft via reuptake into the presynaptic neuron, enzymatic degradation, or diffusion away from the synapse.
–Recycling of Synaptic Vesicles: The vesicle membrane is retrieved by endocytosis and refilled with neurotransmitters, readying it for another round of exocytosis.
Entry to the ER: explain how proteins destined for membrane bound organelles enter the endoplasmic reticulum.
An mRNA sequence is transcribed in the cytoplasm by a ribosome. If the correct ER signal sequence is transcribed, transcription stops and an SRP protein binds to the signal sequence. SRP pulls the sequence/ribosome to an SRP receptor on the ER membrane and the signal sequence is inserted into a protein translocator ER transprotein. SRP is cleaved and the SRP receptor is removed. The ribosome continues transcription, and the polypeptide is slowly fed through the transmembrane protein into the ER. Eventually at the stop sequence transcription stops. The signal sequence is cleaved from the polypeptide freeing the polypeptide from the ER membrane.
ER to Golgi Transport: what directs proteins to move from the ER to the golgi apparatus? Describe the tag involved in the process.
Proteins contain a specific signal sequence that directs which receptors it will bind to. Proteins meant for the golgi apparatus will have mannose binded to them. The mannose sugar is then able to bind with the correct receptors allowing movements to the golgi apparatus. This specific sequence contains arginine which binds to mannose.
Modification in the cis-Golgi: how are lysosomal proteins modified in the cis-Golgi
In the cis-Golgi, lysosomal proteins are primarily modified by the addition of a phosphate group to a mannose sugar residue, creating a “mannose 6-phosphate” (M6P) tag, which acts as a sorting signal to direct the protein to the lysosome; this modification is crucial for correctly targeting lysosomal enzymes to their proper destination.
Trans golgi to endosome transport: describe the process by which lysosomal proteins move from the trans-golgi network to the endosome. Be sure to include a description of vesicle budding in your answer.
Lysosomal proteins bind to a mannose-6-phosphates receptor which causes conformational changes to the receptor. Adaptin can now bind to the receptor and clathrin binds to the adaptin molecule. As more receptors bind it to adaptin and clathrin the triskelion nature of clathrin allows clathrin molecules to bind together distorting the plasma membrane. Eventually a budding vesicle forms which is then cut off by dynamin. Then another protein cleaves off the clathrin and adoptin coats so the naked vesicle can bind to the endosome.
Endosome sorting: describe the mechanisms by which endosomes sorts lysosomal proteins and receptors. What happens to the lysosomal protein? What happens to the receptor?
The pH of endosomes is roughly 6.5 which is too low for hydrogen bonds to stay bonded. The bond between the receptor breaks and the receptor remains in the endosome’s membrane for reuse in the golgi via vesicle transportation. The phosphate from mannose sugar is also broken off to ensure the protein does not accidentally return to the golgi. The protein and mannose sugar molecule continues to the lysosome.
