Worksheet 9 - Protein structure PDF

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Protein structure...

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Worksheet 9 Protein Structure Learning Objective. This activity will help you dissect the multi-level structure of proteins. (10 points) Instructions. Answer the questions below. When you’re finished, upload your assignment into Blackboard as a .docx or .pdf (no .pages because I can’t view those). Drawings can be done in many different ways such as using the features in Word, using the Paint app on your computer and drawing with your mouse or touchpad, taking a picture of a hand-drawing and pasting that into the box below, or using a stylus/touch screen to draw in the structures. Pasted images taken from online will not be accepted. Part 1. Monomer: Amino Acid 1. Draw one generic amino acid molecule. Make the amino acid generic by having “R” as the side chain.

2. On your amino acid above, indicate the parts present in all amino acids by:   

Denoting the alpha carbon by placing an “α” as a subscript to that carbon Drawing a triangle around the amino group Drawing a circle around the carboxyl group

3. What type of bond is present between the atoms of your amino acid (in question 1)? Peptide bonds 4. How many different amino acids can be incorporated during translation? 20 1 WS-Proteins, BIOS 208, Dr. Bergan-Roller, Spring 2021 Online

5. What makes amino acids different from one another? Each amino acid is structurally and functionally different due to these R groups. 6. List the categories of amino acids.

7. Identify one example (e.g., histidine) for each category of amino acids. (match a with a, etc.)

a. Non-polar

a. Glycine

b. Polar

b. Tyrosine

c. Acidic

c. Glutamic acid

d. Basic

d. Lysine

Part 2. Primary Structure 8. Draw a string of three generic amino acids (include all of the atoms) with the amino end on the left and the carboxyl end on the right. This represents the backbone of the protein.

9. On your drawing above (for question 8), place boxes around each amino acid. 10. On your drawing above (for question 8), circle the bonds that connect each amino acid. 11.What type of bond connects each amino acid? Covalent bond 12. What is the name of the bond that connects each amino acid? 2 WS-Proteins, BIOS 208, Dr. Bergan-Roller, Spring 2021 Online

Peptide bond Part 3. Secondary Structure 13. List the two major categories of secondary structure.

14. Draw a simple representation of each of the two major categories of secondary structure.

a. Alpha helices

b. Beta pleated sheets

15. Choose one kind of secondary structure. Draw a detailed representation of that secondary structure. Alpha helices Be sure to:  

Identify the individual atoms (e.g., Carbons, Hydrogens, Oxygens, Nitrogens) Orient/align the backbone atoms of non-adjacent atoms to allow for hydrogen interactions (see question 16-19 for further guidance).

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16. Hydrogen interactions facilitate secondary structure. Define hydrogen interactions. Type of attractive (dipole-dipole) interaction between an electronegative atom and a hydrogen atom bonded to another atom. 17. What atoms do hydrogen interactions occur between? Oxygen and Hydrogen 18. Draw in at least three sets of hydrogen interactions to your drawing above (in question 15) with dotted lines (- - - -). 19. What part of the secondary structure do these hydrogen interactions (in question 15) occur between? (Select one) a. Backbone atoms b. Side chains/R groups Part 4. Tertiary Structure 20. How many polypeptide chains are present in the tertiary structure of a protein? 1 polypeptide 21. Tertiary structure is the irregular loops and folds of a polypeptide chain. Draw a representation of tertiary structure.

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22. The irregular loops and folds of tertiary structure form because of interactions between which portions of the polypeptide chain? (Select one) a. Backbone atoms b. Side chains/R groups In the Table below, 23. List the different types of interactions that can occur at the level of tertiary protein structure. 24. Provide a description for each of these interactions as they apply to proteins. a.

23. Interaction name Hydrophobic Interactions

24. Description These are non-covalent interactions between hydrophobic amino acid R chains which surround each other to reduce the net surface area.

b.

Hydrogen bonds

Type of attractive (dipole-dipole) interaction between an electronegative atom and a hydrogen atom bonded to another atom.

c.

Waals force of In teraction

These are weak forces of interaction between atoms of neutral molecules. It’s an attractive force between polar and non-polar molecules in large distances.

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d.

Covalent bonds

These are disulphide bonds. The amino acid cysteine forms a bond with another cysteine through its R group.

Part 5. Quaternary Structure Quaternary structure represents the three-dimensional (3D) structure of one functional protein. 25. The 3D quaternary structure is facilitated by interactions between which portions of the polypeptide chain? (Select one) a. Backbone atoms b. Side chains/R groups

26. List the different types of interactions that can occur at the level of quaternary protein structure. a. Ionic bonds

b. Hydrogen bonds

c. Hydrophobic bonds

d. Disulfide bridges 27. How many polypeptide chains are present in the quaternary structure of a protein?

2 polypeptide chains

28. When proteins have multiple polypeptide chains, what are the individual polypeptide chains called? Subunits

29. Find an example of a functional protein that is composed of multiple polypeptide chains (other than the example given in class). Provide the name of the protein below. Insulin

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30. Draw a representation of the protein named above (in question 29). Be sure to decipher the different subunits.

Academic Integrity Statement I have completed this assignment with academic integrity, as defined in the syllabus and according to NIU policy (https://www.niu.edu/academic-integrity/index.shtml), including creating my own novel work and not sharing my work with others to reuse in the future. All participation in scholarly discussions and brainstorming of ideas with peers were done in an ethical manner, enabling creative thought without jeopardizing academic integrity. A missing signature will result in a score of 0.

Signature: Bianca Uhuka

Z ID 18880

Evaluation. The worksheet will be graded as: Needs Improvement Answers are missing or mostly incorrect. 0-5 points

Fair All answers are present, but many are incorrect. 6-7 points

Good Answers are mostly correct but superficial. 8-9 points

Exceptional Answers are 100% accurate, thorough, and creative. 10 points

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