Lecture 5 Web: pollev.com/ucibio Text: To: 37607

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Lecture 5 Web: pollev.com/ucibio Text: To: 37607 Type in: 169964 <your question>

Lecture 5 objectives Be able to design experiments to answer scientific questions Understand Anfinsen’s experiment; derive conclusions from data Understand why peptide bond angles are rotationally constrained Understand how rotational constraints lead to 2° structure Know the different interactions that stabilize structure

OK. What does this all have to do with enzymes? Need precise 3-D structure Protein made of amino acids R-groups have different interactions Connect R-groups/amino acids  Protein structure

The scientific method… I think “X” BECAUSE “Y” Design an experiment to PROVE “X” Experiment: Predict outcomes if “X” is TRUE Predict outcomes if “X” is FALSE Do experiment, observe results Results; Therefore “X” is TRUE/FALSE Unexpected results/observations = Discovery!

OK. What does this all have to do with enzymes? Anfinsen’s experiment Took a protein (AP) & forced it to unfold - Protein lost activity

OK. What does this all have to do with enzymes? Anfinsen’s experiment Took a protein (AP) & forced it to unfold - Protein lost activity Therefore:______________________________ Allowed protein to recover - Over time, activity returned

OK. What does this all have to do with enzymes? Anfinsen’s experiment Took a protein (AP) & forced it to unfold - Protein lost activity Therefore:______________________________ Allowed protein to recover - Over time, activity returned Therefore:______________________________

What does a protein need in order to fold? Protein folding information contained in OK. But how does amino acid sequence “fold?”

Peptide bond is planar…

…but not bonds on either side!

Rotation of bonds around peptide bond

Peptide backbone rotation

“Folding” proteins Amino acids have different properties Different preferred Psi and Phi angles Bonds can rotate and pivot

Secondary structure 3D structure H-bonds between ____ & ____ ____ & ____ of peptide bonds Close together in primary structure

Folding into secondary structures Bond rotation causes secondary structure

The a-helix: Annotate Different parameters define a-helix

b-Sheet: Annotate

b-Sheets Sheets can be twisted

Bends / Loops Bends or Loops: Important Structured/Unstructured

Tertiary structrue Bring secondary structure elements together _____________ interactions important Unstructured regions important

The a-helix Arrangement of side chains important

Tertiary structure

Tertiary structrue Take picture Upload to Canvas assignment “Barrel structure”