Monday 10 3 05

10/3/05 Lecture
Homework due is class. Next weeks homework is posted online.
To get the online program to view 3D proteins, go to the class website.
• Protein folding is very fast, 10^-13 sec.
• Loops are well defined in crystalline form.
• Proteins have a stable form but they are not locked to a confirmation. “they breath”
• Structures are form to keep out water.
• Online Program View of 1HOE : is a plant alpha-amylase. If water is in the molecule, then it plays a role in it function. Very rare but possible.
• Online Program View of 1EMA: bio-luminance from deep sea jelly fish. Has beta-barrel.
• Figure 4-18 cytochrom C is similar to myoglobin and hemoglobin. The red parts are the polar parts which are close to the surface.
• The four different types of bonds all help stabilize the protein.
• Figure 4-19 Troponin is used to bind calcium. Has two domains (dumbbell shape). Proteins don’t have to fold on top of themselves; they form domains and fold somewhat independently.
• Figure 4-20 Stable folding patterns in proteins. Beta-alpha-beta loop can be used to make beta barrels. Alpha-alpha corners are not beta turns because they do not have that H bonding.
• Online Program 1YPI
• Figure 4-22 Protein motifs. Similar 3-D function some times means similar function. Some are not from same gene family; they are different in primary amino acid sequencing.
• Tertiary structure- how a single polypeptide chain forms a complex structure.
• Proteins can combine with other proteins to create pathways. Higher level structures are called quaternary structure.
• Figure 4-23 Hemoglobin has four parts. 2 form the alpha chain and 2 from the beta chain (do not confuse this with alpha and beta structure.)
• Figure 4-25 viral particles make hallow shells.
• Figure 4-26 Denaturation: temperature affects different proteins. Another denaturizing agent is very powerful H agents.
• Figure 4-27 Exception to the denature rule. Ribonuclase can reform itself.