Amino Acids and Proteins (an introduction)

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Amino Acids and Proteins (an introduction)

• Doug Raiford
• Lesson 14

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Dogmas

• Reminder
• Involved in virtually every chemical reaction
• Enzymes catalyze reactions
• Structure
• muscle, keratins (skin, fur, nails, etc), actin
  and myosin (muscle), collagens (tendons, hides),
  etc.

Sequence? Structure? Function
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Amino acids

• Translation
• Forms peptide bonds
• Dehydration process
• Residue
• N side amine
• C side acid
• Hence amino acid

Peptide bond
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Side chains

• Amino acids are differentiated by their side
  chains
• Chemical properties
• Hydrophobicity/hydrophilicity
• Polarity
• Acidity/Bassicity

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The Hydrophobic Amino Acids
Val
Phe
Ala
Leu
Ile
Met
Proline severely limits allowable conformations!
Pro
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The Charged Amino Acids
Lys
Asp
His
Glu
Arg
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The Polar Amino Acids
Tyr
Ser
Thr
Cys
Asn
Gln
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More Polar Amino Acids
Gly
Trp
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How do proteins fold?
R
? almost always 180?
?
?
?
R
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Planarity

• 4 atoms on same plane

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Doesnt just collapse into a wad

• Two common arrangements show-up over and over
• Alpha helix
• Beta sheet
• Constitute secondary structure

RNase P
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The alpha helix

• ? ? ? ? ?60
• Hydrogen bondsbetween CO ofresidue n, andNH
  of residuen4

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Functional roles

• Fit nicely in the grooves of DNA
• Globular proteins are often mostly helices
• Or coiled coils

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The beta strand ( sheet)

• ? ? -135, ? ? 135 stretched out
• R groups are above and below
• Form hydrogen bonds with the adjacent strands

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View from the side

• Pleated
• R groups above and below
• Means nature can dictate the chemical properties
  of the surface of the sheet
• BTW terminology C-terminus
• Similar to 5-3

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Goes both ways

• Can be parallel or anti-parallel

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Parallel and anti-parallel ?-sheets

• Anti-parallel is slightly energetically favored

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Beta tendancies

• In middle of sheet
• Large aromatic residues (Tyr, Phe and Trp) and
  ß-branched amino acids (Thr, Val, Ile) favored

• On edges, aas like proline, very non-reactive
• Prevents aggregation
• Mutations that cause aggregation prions
• Alzheimer's amaloid plaque

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Functional role

• Some of the coolest proteins
• Porins (aqua porins allow water into cells)

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Turns and Loops

• Secondary structure elements are connected by
  regions of turns and loops (or coils)
• Turns short regionsof non-?,
  non-?conformation
• Loops larger stretches with no secondary
  structure. Often disordered.

• Disordered loops
• Often
• Link domains
• Solvent exposed
• Vary greatly in length and composition from
• homolog to homolog
• Rich in polar and charged amino acids
• Why?

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The Ramachandran Plot
Observed (non-glycine)
Observed (glycine)
Calculated

• G. N. Ramachandran first calculations of
  sterically allowed regions of phi and psi
• Note the structural importance of glycine

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By far, the coolest

• Chaperone proteins
• Sucks in a protein into chamber
• Provides safe environment to fold
• Top closes like an iris
• Allosteric enzyme
• Termed "heat shock" proteins
• Heat destabilizes proteins

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Wait, wait, this is by far the coolest

• Active transport (pumps)
• ATPase pumps (ATP provides energy to transport
  solutes across membrane)
• Calcium
• ATP synthase
• Proton gradient provides energy for ATP synthesis
• http//www.youtube.com/v/J6VyKPeORHIhlenfs1re
  l0

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OK, OK, this is the coolest

• No really!
• http//www.youtube.com/watch?featureplayer_detail
  pagev4jtmOZaIvS0

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