Discussion 7 protein folding and targeting key
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Bio 151 Rounds
Discussion 7
fall 2023
Discussion 7 Protein Trafficking and folding
Names, day and time:
Team portion:
Please note that the team portion is worth 7 points this week and the individual is only
worth 3.
1.
Receptors for intercellular signals (like insulin) are proteins and must be trafficked to the
cell surface through the endomembrane system. If the extracellular portion (which binds the
signal) of the protein is folded from the first 150 amino acids (N-terminus) of the protein that are
translated (the protein is 800 amino acids long) and there is a single transmembrane domain
between amino acid 150 and 300, draw how the protein would be configured in the endoplasmic
reticulum
AND
at the plasma membrane. Be sure to indicate the N and C termini.
(1.5 points)
1
Bio 151 Rounds
Discussion 7
fall 2023
2. A protein (the squiggles below) is inserted into ER microsomes
(little isolated balls of ER). The proteins are either untreated (in the
first lane) or have had a non-membrane permeant protease outside
the microsome (just like in class) added (all the other lanes). Which
lane represents which microsome (
1.5 point
)
3. There’s a 100 kD protein (1000 amino acids ~10 a.a. per kD). Place the following bands on
the gel. (kD is a measure of protein mass). (2 points)
lane 1 -- wt
Lane 2 MT1-- an in frame mutation from UCG → UAG U=nucleotide 1500 (3 nt’s per codon).
Lane 3 MT2-- a deletion of the final nucleotide in this codon: UGA → UG__ at the final codon.
Lane 4 MT3 -- a mutation of the codon CAC → CAU at nucleotide 1000
4. In the peptide below:
Put a square around a hydrophobic R-group. (1 point)
2
Bio 151 Rounds
Discussion 7
fall 2023
Circle a group that could participate in hydrogen bonding in a beta sheet. (1 point)
¾ credit for N or C terminus
Discussion 7 Protein Trafficking and form
Name, day and time:
Individual portion:
1.
Put a square around a hydrophobic R-group. (1 point)
2.
Circle a group that could participate in hydrogen bonding in a beta sheet. (1 point)
3. Receptors for intercellular signals (like insulin) are proteins and must be trafficked to the cell
membrane through the endomembrane system. If the extracellular signal binding portion of the
3
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Related Questions
Further discussion questions:
a) What is the wavelength of UV light with maximal absorbance by purified protein? Which amino acid(s) in protein has/ have the highest absorbance at this wavelength? b) Name and briefly describe two methods (other than UV absorbance) to detect proteins in a sample.
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Question for protein crystallography-
1. While performing a routine protein crystallization screening, you observe that one of your well drops has doubled in size compared to the remaining wells. Note: the drop in question was set up by taking 1 µL of the protein solution (10 mg/mL LDH in 20 mM TRIS pH 7.5, 0.5 M NaCl and 10% PEG 4000K) and adding it to 1 µL of the crystallization solution (10% PEG 4000K, 50 mM NaCl and 20 mM TRIS pH 8.0). Why did this drop grow larger in size compared to when you initially set it up?
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UPVOTE WILL BE GIVEN! ANSWER IN 3-5 PARAGRAPHS (TYPEWRITTEN)
a. What are the applications of modern biological membranes in the field of engineering?
b. What are the implications of these applications?
c. How do you think these applications will change the world in the future?
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Need help, please.
Answer choices are provided below for drop-down questions.
1. The overall charge of this protein at pH 7 is Drop-down answer choices are [positive, negative, or neutral]
2. In the first dimension of 2-D PAGE, this protein's isoelectric focusing point is Drop-down answer choices are [between 4 and 6, between 6 and 8, or between 8 and 10]
5.
A mole of the above protein weighs ____ g. For 1 mL of a 5 mM solution of the above protein, you would need to weigh out ____ Drop-down answer choices are [g, mg, mcg, ng, or pg] (number and unit, at least one non-zero integer to the left of the decimal point, don't round)
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[Ten - Biomolecules]
INSTRUCTIONS
— Answer the following multiple-choice questions and EXPLAIN in 3-5 sentences why you chose that answer.
— Answer properly
Questions;
Thomas was purifying an enzyme from a homogenate of muscle cells. He went through seven steps of purification and found that the enzyme activity was the same as the homogenate value. On the eighth step, when the protein washighly pure, the enzyme activity rose to five times that of the homogenate value. Can you suggest a possible reason?
A. the homogenate assay was wrong
B. step eight has co-purified an activator of the enzyme.
C. the enzyme has an inhibitor present in the muscle cell homogenate
D. the temperature at step eight was just right for the enzyme activity.
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GABA (B)
Need help answering these questions about the GABA(B) protein.
What class (globular, fibrous, membrane) protein is the protein Identify the organism (or organisms that have this protein) Identify the cellular location of this protein Describe the function Find the primary structure (list it on a slide) Describe secondary structure (alpha-helix, beta sheet, and how many of each and what percent of the total protein) Find a picture of the tertiary structure (which should also show secondary structure) Does the protein have a quaternary structure, if so what is it?
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Question:-
How can we determine trans-membrane domains of proteins in the absence of crystal structure?
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Topic:?? Experiment Protein Estimation
What color change occurs when proteins combine with Coomassie dye under acidic conditions?
detailed answer
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Q3, What are the structural features of 7N7H (Viperin-like enzyme)?
a) Must show 3D structure and brief description
b) Primary structure – how many aa in the protein Viperin-like enzyme?
c) Describe secondary and tertiary structure.
d) Does Viperin-like enzyme have quaternary structure?
appreciate any help
thanks
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384
Functional Classes of Proteins
Q4.3- For each of the five major protein types in eukaryotic cells 1) provide a specific example of a protein in each class, 2) describe its primary function, and 3) identify cellular locations where you would find this specific protein (nucleus, cytosol, membranes).
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Question:-
Given the very complex lipid composition of cell membranes, what variations exist within the different membranes of organelles in an animal cell? What are the functional consequences of these differences?
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Problem 1
Which one of the following will have the least difficulty in crossing the plasma membrane?
small charged molecules such as sugars
"small, polar, hydrophilic molecules such as water "
"small, nonpolar, hydrophobic molecules such as fatty acids"
large nonpolar hydrophobic molecules
large polar hydrophilic molecule
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PROBLEM 3-1 Sentence InterpretationWhen scientists submit papers for publication, they often dread the re-sponse of reviewers. Here are four sentences that could have been writ-ten in different structural arrangements by reviewers to deliver the same news. Which statement is the one most likely resulting in the paper being accepted, and which is most likely the one resulting in rejection? Explain why.1. Overall, although this manuscript is of interest for structural biologists, a more detailed analysis of ABC should be provided. 2. Although a more detailed analysis of ABC should be provided, this manuscript is of interest for structural biologists.3. This manuscript is of interest for structural biologists, but a more detailed analysis of ABC should be provided.4. A more detailed analysis of ABC should be provided, but overall, this manuscript is of interest for structural biologists.
PROBLEM 3-2 Word Placement and Flow Rewrite the following paragraph. Place words such that the reader…
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Text:QUESTION 16 Protein maturation in the ER includes.
A Disulfide bond formation
B. proteolytic cleavage
C attachment of oligosaccharide
d. Prolyl isomertzation
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Question:
Explain: Lipids supply more than twice as many calories as carbohydrates. Based on the results of the Sudan dye III experiment, which will supply more lipids, honey, or vegetable oil? Why?
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Question:-
What is an example of a heterotrimeric G protein and what role does it play?
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Paper link - https://www.jneurosci.org/content/40/8/1756.long
Neuronal Mitochondria Modulation of LPS-Induced Neuroinflammation
What is LPS (not just what does it stand for)? Why is it used as a model for neuroinflammation?
Describe microglia: where are they found, what role do they play, why can't that role be carried out the same way it is in the rest of the body?
Mitofusin2 (Mfn2) is a mitochondrial protein. What is its apparent role? Can you think of a reason why overexpression could be protective against a stress? Is it reasonable that overexpression of this gene could also cause problems (if so, how)?
How did the authors arrange that Mfn2 was only upregulated in the brain and spinal cord of TMFN mice, and not in other tissues of the mice? How do they demonstrate this?
Briefly describe the roles of these molecules in immunity/inflammation:IL-1βIL-6IL-10TNFα They all belong to a class of molecules; what is that class called?
What evidence do the authors provide that…
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Need correct answer with explanation
Don't give spam
Will give Positive rating for good answer.
Answer all.
1.Which is the correct statement:
Speed of protein synthesis > speed of protein folding
Speed of protein synthesis < speed of protein folding
Explain your answer.
2. a. How do the majority of proteins that exist outside cells get outside cells? Explain the pathway. b. Explain at least three major exceptions to your answer in part a.
(HINTs: Curr. Opin. Biotechnol. 21, 621; Nature 496, 243.)
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Question:-
Some bacteria secrete enzymes capable of digesting collagen and other extracellular matrix molecules. Why did such a property evolve? What is the benefit of bacteria?
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384
Peptides & X-ray/NMR Methods
Q4.2- Describe one advantage and one disadvantage of trying to solve molecular protein structures by 1) X-ray crystallography and by 2) Nuclear Magnetic Resonance (NMR) spectroscopy.
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IX - BIOMOLECULES
Instructions :
- Answer the question properly.
- Please do not copy here in Bartleby
- Explain why did you choose that answer in 3-5 sentences.
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Seven [BIOMOLECULES]
Instructions;
— Answer the questions properly.
— Do not copy in Google or Bartleby.
— Plase make sure the answer are correct.
Failed to follow the Instructions will report directly to Bartleby. THANK YOU!
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Learning Objectives
Identify a peptide bond, the N-terminus (amino-terminus) and C- terminus (carboxyl-terminus) of a polypeptide in a series of linked amino acids.
Describe the four levels of protein structure (primary, secondary, tertiary, and quaternary), what types of bonding interactions hold each level together, and how a protein’s structure relates to its cellular function.
Link the chemical structures of amino acid R groups to the types of interactions they could form in the folded structure of a protein.
Hypothesize the likely consequence of environmental conditions on the folded structure.
Recognize secondary structure elements when proteins are represented in different ways (e.g. ball-and-stick structures, ribbon diagrams).
Define these terms: enzyme, enzyme activity, active site, substrate, enzyme substrate complex, product, denature.
Explain with molecular detail how some conditions affect enzyme activity.
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Q8: The primary structural components of the cell membrane areO proteins and cellulose.O glycoproteins and cholesterol.O cholesterol and proteins.O phospholipids and cellulose.O phospholipids and proteins.
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Cell Membrane Coloring WorksheetComposition of the Cell Membrane & FunctionsThe cell membrane is also called the ___PlasmaMembrane____________ membrane and is made of a phospholipid_____________. The phospholipids have a hydrophilic (waterattracting) __________ and two hydrophobic (water repelling) ____________. The head of a phospholipid is made of an alcohol and__________ group, while the tails are chains of ____________.Phospholipids can move _______________ and allow water and other_________ molecules to pass through into or out of the cell. This isknown as simple ____________ because it does not require__________ and the water or molecules are moving __________ theconcentration gradient. SKETCH AND LABEL a phospholipid coloringthe heads red and the tails blue.PHOSPHOLIPID
Another type of lipid in the cell membrane is ______________that makes the membrane more fluid. Embedded in the phospholipidbilayer are __________ that also aid in diffusion and in cellrecognition. Proteins…
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VIII - BIOMOLECULES
Instructions :
- Answer the question properly.
- Please do not copy here in Bartleby
- Explain why did you choose that answer in 3-5 sentences.
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V - BIOMOLECULES
Instructions :
- Answer the question properly.
- Please do not copy here in Bartleby
- Explain why did you choose that answer in 3-5 sentences.
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state transition diagram for home nursing during covid-19
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Q4: Describe the structure of plasma membrane. Suggest the mechanism(s) by which each of the following substances is transported across cell membranes: a. CO2 b. Glucose c. C1– d. K+ e. Fat molecules
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Topic?? Experiment Protein Estimation.
What is the standard curve equation for this BSA standard?
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QUESTION 13
What is the mechanism by which microtubules can rapidly shrink, or undergo â catastrophe?â
A
At low levels of ATP, tubulin subunits are not added to the + end of the microtubule.
B
At low levels of GTP, beta-tubulin subunits at the + end of the microtubule hydrolyze GTP, undergo a conformational change, and destabilize the filament so that the filament starts to disassemble from the + end.
C
At low levels of GTP, tau proteins are phosphorylated and bind to the microtubule to destabilize the + end.
D
At high levels of GTP, tubulin subunits are more quickly added to the â end than to the + end of the microtubule, resulting in a shrinking + end of the microtubule.
E
At low levels of ATP, the microtubules rapidly disassemble since ADP-bound tubulin subunits are lost at both the + and â ends of the filament.
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Q1)
-When an inhibitor is bound to the enzyme via a combination of (nonbonding interactions) electrostatic,
H-bonding, and hydrophobic Interactions.
This statement describes:a) reversible binder to an enzyme.b) irreversible binder to an enzyme.c) covalent binder to an enzyme.d) none of the choices
-In protein X-ray crystallography, one of the following atoms is not solved:
a. Hydrogen atoms.b. Carbon atoms.c. Nitrogen atomsd. Water molecules
-In HM, loop modeling is difficult because:
a) Surface loops tend to be involved in crystal contacts, leading to a significant conformational change.b) They are rigid bodies with low flexibility.c) They are less flexible than alpha helices.
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- Need help, please. Answer choices are provided below for drop-down questions. 1. The overall charge of this protein at pH 7 is Drop-down answer choices are [positive, negative, or neutral] 2. In the first dimension of 2-D PAGE, this protein's isoelectric focusing point is Drop-down answer choices are [between 4 and 6, between 6 and 8, or between 8 and 10] 5. A mole of the above protein weighs ____ g. For 1 mL of a 5 mM solution of the above protein, you would need to weigh out ____ Drop-down answer choices are [g, mg, mcg, ng, or pg] (number and unit, at least one non-zero integer to the left of the decimal point, don't round)arrow_forward[Ten - Biomolecules] INSTRUCTIONS — Answer the following multiple-choice questions and EXPLAIN in 3-5 sentences why you chose that answer. — Answer properly Questions; Thomas was purifying an enzyme from a homogenate of muscle cells. He went through seven steps of purification and found that the enzyme activity was the same as the homogenate value. On the eighth step, when the protein washighly pure, the enzyme activity rose to five times that of the homogenate value. Can you suggest a possible reason? A. the homogenate assay was wrong B. step eight has co-purified an activator of the enzyme. C. the enzyme has an inhibitor present in the muscle cell homogenate D. the temperature at step eight was just right for the enzyme activity.arrow_forwardGABA (B) Need help answering these questions about the GABA(B) protein. What class (globular, fibrous, membrane) protein is the protein Identify the organism (or organisms that have this protein) Identify the cellular location of this protein Describe the function Find the primary structure (list it on a slide) Describe secondary structure (alpha-helix, beta sheet, and how many of each and what percent of the total protein) Find a picture of the tertiary structure (which should also show secondary structure) Does the protein have a quaternary structure, if so what is it?arrow_forward
- Question:- How can we determine trans-membrane domains of proteins in the absence of crystal structure?arrow_forwardTopic:?? Experiment Protein Estimation What color change occurs when proteins combine with Coomassie dye under acidic conditions? detailed answerarrow_forwardQ3, What are the structural features of 7N7H (Viperin-like enzyme)? a) Must show 3D structure and brief description b) Primary structure – how many aa in the protein Viperin-like enzyme? c) Describe secondary and tertiary structure. d) Does Viperin-like enzyme have quaternary structure? appreciate any help thanksarrow_forward
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