On Page 9 of your comp book (after your enzyme notes) make a bell-ringer page that looks like this, divided into three rows. In the first row write today’s date and answer the following question. BELL-RINGER 10/4/17 List three things that can affect an enzyme’s activity (not all environmental) and say WHY / HOW it would affect the chemical reaction. Do you know what the dress up day is today? What do you notice about me and this bell-ringer??? First Optional Homework (more to come) Complete corrections of missed questions on all Quizzes during this six weeks (we’ll have at least 2). The corrections for this first quiz will be due by Friday Oct. 13th (yikes) If you made a 100, just give an explanation for any one answer.

Take your two pipe-cleaners and spiral them together on one end, so you end up with one long pipe-cleaner ~23 inches/ 58 cm in length.

• The ‘straight’ part of your pipe-cleaner represents the backbone Using your assigned amino acid sequence and the back of your protein notes (where you will find the 20 different amino acids and the characteristics of their side R group), you are going to turn your pipe-cleaner into a simulated 8-amino acid polypeptide chain. • The ‘straight’ part of your pipe-cleaner represents the backbone (the repeated amino, carboxyl, central carbon, & lone hydrogens of your 8 amino acids.) • The beaded loops will represent the side R groups of each amino acid. Amino Acid # 1 Amino Acid # 2 Amino Acid # 3 Amino Acid # 4 Amino Acid # 5

KEY Cysteine EXCEPTION Negatively-charged Acids Even though Cysteine is hydrophilic and polar, it typically forms a disulfide covalent bond with another Cysteine. They get a loop with a white bead. Negatively-charged Acids get a loop with a red bead. Hydrophobic get a loop with a yellow bead. Positively-charged Bases get a loop with a green bead. All polar, hydrophilic amino acids, EXCEPT CYSTEINE, get a loop with a blue bead.

your amino acids. My example is below. Use the correct beads in the key and twist your wire to simulate all eight of your amino acids. My example is below. • Use two finger-widths of space untwisted at the starting end of your pipe-cleaner. • Use 2 to 3 finger-widths of space in between each amino acid side R group. The first amino acid in my sequence is Methionine. When I look at the back of my protein notes, I see that Methionine has a nonpolar, hydrophobic side R group. When I look at the key I see that Hydrophobic side R groups need to have a loop containing a yellow bead. So for my first amino acid, I make a loop containing a yellow bead to represent hydrophobic Methionine.

Join up with another person at your table and using the two finger-width at the beginning of your chains, combine your polypeptide chains to create a 16-amino acid chain. Now you have finished the first degree of protein structure: a sequence of amino acids.

4. To simulate the 2˚ of protein structure add small pleats and/or spirals to the length of your polypeptide chain.

5. Now comes the 3˚ of protein structure- caused by interactions of the side R groups TO EITHER EACH OTHER OR THE OUTSIDE ENVIRONMENT (WATER). Charged R groups (Red and green beads) will be more towards the outer surface and neutralize each other by forming an electric bond. Hydrophobic R groups (Yellow beads) will be buried in the core of the globular protein where they are hidden away from the polar water molecules of the outside environment.

Polar Hydrophilic R groups Cysteine amino acids (white beads) form covalent disulfide bonds with each other and stabilize the protein structure. Polar Hydrophilic R groups (Blue beads) will be on the outside surface of the protein where they interact with water by forming hydrogen bonds.

6. For 4° structure, combine your protein with a neighbor making sure that the hydrophobic side R groups are in contact with each other in the center.

Next we are going to simulate thermal denaturation. - When heat increases, it increases the energy of a molecule and causes it to vibrate. This movement causes the interactions of the side R groups and hydrogen bonds to break, resulting in a loss of native structure. (FYI, this is what happens when you cook an egg) - Simulate this thermal denaturation by shaking your protein until it loses its shape.