Kami Export - Protein Virtual Folding Activity PDF

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Protein Virtual Folding Activity...

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Protein Folding Virtual Activity Learning Objective: Explain how a change in the subunits of a polymer may lead to changes in structure or function of the macromolecule. (protein) Website: https://learn.concord.org/resources/787/protein-folding (You will have to create a free account.)

Setup: Make sure 3-letter codes are checked. Click on the hydrophobicity section and click on Charge and Hydrophobicity. Click on solvent type as Water. Generate a random protein Push play (at bottom)

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Directions: Use Amino Acid Chart at the end of the handout to answer questions 1-4. 1. What properties do the brown amino acids exhibit? Non-polar, have a methyl group. 2. What properties do the purple amino acids exhibit? +Charge, have a carbonyl group. 3. What properties do the green amino acids exhibit? Polar, have a carboxyl group. 4. What properties do the pink amino acids exhibit? - Charge, have 2 methyl groups.

Use the simulation to answer the following questions. Brown amino acids tend to be found in the center of the

5. Where do most of the brown amino acids congregate? Why? molecule because they stabilize the structure. 6. Where do the green amino acids tend to be exhibited? Why?Green amino acids tend to be located on the protein surface because they are capable of interacting with water molecules. 7. Why do purple and pink amino acids attract each other?

Change in settings:

They are attracted to each other because of their unlike charges. Ionic bonds result from electrostatic attractions between positively and negatively charged side chains of amino acids.

Click on Generate random protein Click on All hydrophobic Push Play

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8.All of What happened? Why do you think this occurred? the amino acids are brown and this occurred because only non-polar amino acids are hydrophobic. When I pressed play all of them clustered in the middle shivered due to the fact they are hydrophobic.

Change in settings: •

9.

Change water to oil What happened? Why do you think this occurred? When I pressed play for this one all of the amino acids went and spread out and this is because the solvent was oil. The non-polar amino acids are not oil fearing, they are water fearing and oil doesn't contain any water either.

Change in settings: • • • •

Click Generate Random Protein. Click All Hydrophilic Click Water Push Play

chain of molecules spreads out again because all of them are hydrophilic 10. What happens? Why do you think this occurred? The which means they like water and bond with it. Although some still did cluster. 11. Why do some still cluster? The ones that did cluster were only when there was a - charged amino acid between 2 polar amino acids. This is because polar molecules contain polar bonds d a difference in electronegativity between the bonded atoms.

Further Thinking: 12. What causes amino acids to fold in different patterns to form different looking structures? Hydrogen bonding causes folding in different patterns of amino acids. This folding is responsible for the formation of different structures of proteins. This folding also helps in producin the secondary structure of protein. This hydrogen bond is present between amino groups and carboxyl groups which helps them in folding their structure in different patterns.

Research: 12. What would happen if you changed ONE amino acid in the primary chain?

A change in gene sequence can lead to a different amino acid being added to a polypeptide chain instead of the normal one. This causes a change in protein structure and function. The sequence and number of amino acids in a polypeptide chain is its primary structure.

13. How would this affect its function?

Amino acid substitutions at the interaction interface may result in binding affinity changes, and therefore affect the structure of the protein complex. This structural change may A covalent bond is formed between two significantly affect the binding energy, and make the protein complex unstable. cysteines of a protein in which the hydrogen

sulfhydryl group of the two cysteines is removed 14. What type of bond occurs between two cysteines? What is its purpose?ofandthea bond is formed between the two sulfurs. In order to function as a stabilizer for high-order structure of the 15. What type of bonds occurs between the amino acids? Peptide Bonds protein, or an active center for its bioactivity. 16. What type of bonds occurs between neighboring amino acids in a secondary structure in

creating alpha helices and beta pleats? Hydrogen Bonds 17. What type of bonds occurs in tertiary and quaternary structures to cause a “globular” look? A variety of weak bonds and disulfide bridges....