Chapter%203%20(part%202)%20

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Chapter 3 (part 2) Protein Function
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Test Your Knowledge

• (True/False) All proteins bind to other
  molecules. Explain.
• What sort chemical interactions create the
  binding between the ligand and its protein
  partner? Name at least two.
• (True/False) A ligand binding site can be kept
  dry from surrounding water molecules. Explain.
• Explain two different ways (structural) that
  proteins typically bind to other proteins.
• What is Km? What does having a low Km say about
  the binding between a protein and its ligand?
• What are some of the major functions of proteins
  in a cell? Name at least 3 categories.

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Protein-Protein Binding Three major mechanisms

• surface string interaction
• helix-helix or coiled coil interaction
• surface-surface interaction

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SH2 domain (example of surface string
interaction) Central antiparallel bsheet
surrounded by two alpha helices
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Coiled coil regions of Rad50 molecules bind
together to form a complex of molecules that help
repair DNA
Surface-to-surface interaction between trypsin
and trypsin inhibitor protein
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Protein-Ligand Interactions
Protein Binding Sites Sterically and chemically
fit the ligand Examples are antibodies and
enzymes

• Water is typically excluded from the binding
  site, but is important to overall structure.
  Why?

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• Clustering of polar amino acid side chains can
  alter their reactivity and increase the
  attraction of the ligand for the binding site

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cAMP bound to a binding site on a protein
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• Enzymes and bound ligand go through a number of
  intermediate forms of different geometry. They
  are all called transition states.
• The energy that it takes to get to the most
  unstable transition state is called the
  activation energy.
• Enzymes speed reactions by selectively
  stabilizing the transition state (ES) and
  actually have a much higher affinity for the
  ligand in its transition state than the stable
  form of the ligand.

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• Enzymes not only bind to the substrate, but the
  nature of the amino acids and their side chains
  within the binding site alter chemical bonds in
  the substrate.
• Many enzymes can perform both acid and base
  catalysis because of the different side chains in
  their binding site. This allows increased speed
  of catalysis.

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Many Enzymes Require Tightly Bound Small
Molecules to Function
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• Enzymes sometimes form complexes that also
  improve efficiency of reactions that may
  otherwise be diffusion-limited.
• Examples pyruvate dehydrogenase, tryptophan
  synthase, aminoacyl t-RNA synthetase

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