Download Lesson16AminoAcids+Proteins

Doug Raiford
Lesson 14

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.
transcription
translation
DNA  RNA  Protein
Sequence Structure Function
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Proteins
2
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Translation
 Forms peptide
bonds
 Dehydration
process
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Residue
N side: amine
C side: acid
Hence: amino
acid
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Proteins
Peptide
bond
3
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Amino acids are differentiated by their side
chains
Chemical properties
 Hydrophobicity/hydrophilicity
 Polarity
 Acidity/Bassicity
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Proteins
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Ala
Ile
Val
Met
Phe
Proline severely
limits allowable
conformations!
Pro
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Leu
Proteins
5
Lys
Asp
His
Glu
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Arg
Proteins
6
Ser
Cys
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Tyr
Thr
Proteins
Asn
Gln
7
Gly
Trp
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Proteins
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 almost
always
180
 

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9
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4 atoms on same plane
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Two common arrangements show-up over
and over
 Alpha helix
 Beta sheet
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Constitute secondary structure
RNase P
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    60°
Hydrogen bonds
between C=O of
residue n, and
NH of residue
n+4
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Fit nicely in the grooves of DNA
Globular proteins are often
mostly helices
Or coiled coils
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  -135,   +135°; stretched out
R groups are above and below
Form hydrogen bonds with the adjacent strands
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Proteins
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Pleated
R groups above and below
 Means nature can dictate the chemical properties
of the surface of the sheet
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BTW: terminology — C-terminus
 Similar to 5’-3’
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Can be parallel or anti-parallel
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Anti-parallel is slightly energetically favored
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In middle of sheet
 Large aromatic
residues (Tyr, Phe and
Trp) and β-branched
amino acids (Thr, Val,
Ile) favored
On edges, aa’s like proline,
very non-reactive
 Prevents aggregation
 Mutations that cause
aggregation: prions
 Alzheimer's: amaloid plaque

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Some of the coolest proteins
Porins (aqua porins allow water into cells)
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Secondary
structure
Disordered
loops
Oftenare connected
elements
•Link
by regions
ofdomains
turns and
exposed
loops (or •Solvent
coils)
•Vary greatly in length and composition from
Turns – short
regions
homolog
to homolog
of non-,•Rich
non-
in polar and charged amino acids
conformation
Loops – larger stretches
with no secondary
Why?
structure. Often disordered.
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Proteins
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Observed
(non-glycine)
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
Calculated
Observed
(glycine)
G. N. Ramachandran – first calculations of
sterically allowed regions of phi and psi
Note the structural importance of glycine
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Proteins
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Chaperone proteins
Sucks in a protein into chamber
Provides safe environment to
fold
Top closes like an iris
 Allosteric enzyme
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Termed "heat shock" proteins
Heat destabilizes proteins
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Proteins
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Active transport (pumps)
ATPase pumps (ATP provides energy to
transport solutes across membrane)
 Calcium
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ATP synthase
 Proton gradient provides energy for ATP synthesis

http://www.youtube.com/v/J6VyKPeORHI&hl
=en&fs=1&rel=0
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No really!
http://www.youtube.com/watch?feature=pla
yer_detailpage&v=4jtmOZaIvS0
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Proteins
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Proteins
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