Protein Structures (Angelica Zapata)

Title: Protein Structures

Principle(s) Investigated:

• How protein structures are formed
• The uses of proteins
• Interactions/Bonding

Standards:

HS-LS1-6. Construct and revise an explanation based on evidence for how carbon, hydrogen, and oxygen from sugar molecules may combine with other elements to form amino acids and/or other large carbon-based molecules.

Materials:

• Amino Acids Key Chart
• Pipe cleaners
• Many colored beads
• DNA Sequence Worksheet
• PowerPoint

Procedure:

1. You have been provided with a DNA sequence below. Transcribe and translate the template DNA.
2. Once you have translated the DNA, build the primary structure of the protein using the correct colored beads and same color pipe cleaners (Look at Amino Acid Chart for bead colors).
   • When building your structure:
     • Use two 12 inch pipe cleaners (of the same color) and tie one end of one pipe cleaner to the other end of the second pipe cleaner, forming a long 24 inch piece.
     • Then add your amino acids (beads) 2-inches apart on the long strand you just made.
3. Once you have built your primary structure, raise your hand to get it checked by the teacher.
4. Decide which secondary structure would the protein be: alpha-helix or beta-sheet.
5. Now, extend your learning by predicting how the protein will fold into a tertiary structure. Get it checked by the teacher once you think you got it.
6. After it has been checked, find someone else who is done and form the quaternary structure.

Student prior knowledge: Students need to understand that DNA determines a protein's structure and function and that the folding of the primary structure of the protein is determined by different interactions, such as hydrophobic interactions and ionic bonds. They need to have knowledge about the cell’s environment and how it may affect the structure of biomolecules. They need to be able to identify when something is hydrophobic and hydrophilic.

Explanation: The activity is to give a better understanding to students about the different protein structures, because many students may not fully understand the difference between the secondary, tertiary, and quaternary structures. This allows them to physically see the different possible structures proteins can form. On the fifth and sixth step, students should be able to figure out that they should connect the same colored beads to form its structures. As students get to the third structure, example how they can function at this stage without sometimes going to the quaternary structure.

Questions & Answers:

1. Translate the RNA to protein below. If the second codon was changed from CGA to CGC, how would this change the protein structure?

• RNA: A U G C G A A C U G U U U U C G A A G A G A A A A U C G C G U A G
• Protein: Met Arg Thr Val Phe Glu Gly Lys Ile Ala Stop
• The protein structure will not change because it will still be the same amino acid, Arginine, although the codon is different.

1. Is it necessary to go to the quaternary structure?

• No, the protein can function when it is at the tertiary structure. Not all proteins need to bind together to form the quaternary structure to function.

1. Proteins are pH sensitive in order to function. If the normal pH for a protein to function was 6.5-6.8 and the pH was changed to 7.0, how would this affect the protein? Would the protein function work again if the pH was changed back to its functional pH range.

• The protein structure will denature and it will no longer function. If the pH was changed back, the protein will fold back but it may not fold back the same way. If it does not change the same way, its function may no longer work or it will have a different function.

Applications to Everyday Life:

1. Antibiotics affect ribosomes, the cell’s protein-building components. Ribosomes are in all living things from bacteria to eukaryotic cells, with some differences. Antibiotics are made to specifically block ribosomes from bacteria and prevent them from building proteins to function.
2. Crime Investigators use a combination of substances to cut through proteins. These proteins are cut to make a mixture of peptides (short amino acid sequences), which will be analyzed through a liquid chromatography mass spectrometer, to separate the proteins by mass alone to identify them. Through this identification, one can pin down protein markers to determine the sequence.
3. GMOs use protein modification to enhance specific activity. Proteins are used to produce high productivity or expression of something. GMOs can be used to alter the proteins of parasites and are used to increase the number of chromosomes on fruit, which creates bigger fruit.

Photographs:

Primary Structure