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A.-F. Miller, 2008, pg
1
microreview
Primary structure of a protein: ADNLAVQRLNDYHVS
Secondary structure: α helical, β strands (↑↓ or ↑↑)
2er structure is stabilized by interactions of the backbone.
However the side chains do favour one or another (or
neither) 2er structure.
Tertiary structure arises from packing together of 2er
structural elements, and sequestration of hydrophobic side
chains away from water, to form a hydrophobic core.
A few motifs are particularly common (evolutionarily successful).
A.-F. Miller, 2008, pg
2
Extra Information on 1er str.
The amino acid sequence (1er str.) of one protein has been aligned with that of another by a “BLAST”
search. Thus we learn that the Fe-superoxide dismutase of E. coli is identical at most positions to that
of the chloroplast of B. unguicolata. Top line = E. coli, middle = identities, bottom = B. unguiculata.
Query= gi|169955|gb|AAA33960.1| Fe-superoxide dismutase
Length=248
>gi|29466958|dbj|BAC66946.1|
unguiculata]
Length=211
chloroplastic iron superoxide dismutase [Barbula
Score = 262 bits (669), Expect = 1e-68, Method: Composition-based stats.
Identities = 124/214 (57%), Positives = 158/214 (73%), Gaps = 18/214 (8%)
Query
28
Sbjct
12
Query
88
Sbjct
72
Query
148
Sbjct
132
Query
208
A.-F. Miller, 2008, pgSbjct
3
174
ELKPPPYPLNGLEPVMSQQTLEFHWGKHHKTYVENLKKQVVGTELDGKSLEEIIVTSYNK
+L+PPPY L+ LEP MS++TLE+HWGKHH+ YV+NLKKQ+ GTEL ++LE+I+ +YN
DLRPPPYALDALEPHMSKETLEYHWGKHHRAYVDNLKKQIEGTELASQTLEDIVRATYNN
87
GDILPAFNNAAQVWNHDFFWECMKPGGGGKPSGELLELIERDFGSFVKFLDEFKAAAATQ
G+
FNNAAQ WNH+FFW M P GG +P GEL+ L++RDFGS+ F+ EFK A ATQ
GEPTAPFNNAAQAWNHEFFWLSMSPHGGKQPDGELMSLLKRDFGSYDNFVKEFKQAGATQ
147
FGSGWAWLAYRARKFDGENVANPPSPDEDNKLVVLKSPNAVNPLVWGGYYPLLTIDVWEH
FGSGWAWL
D KL+V KSPNA+NPLV+ G+ P+L DVWEH
FGSGWAWLTV-----------------ADGKLMVEKSPNAINPLVF-GHVPILVADVWEH
207
AYYLDFQNRRPDYISVFMDKLVSWDAVSSRLEQA
AYYLD+QNRRPDY++ FM++LVSWDAV+ RL+ A
AYYLDYQNRRPDYLTTFMNELVSWDAVAKRLQLA
241
207
71
131
173
Tertiary structural models
4-helix bundle
β-sandwich
TIM barrel
Fatty Acid Binding
Protein.
Hemerythrin
A.-F. Miller, 2008, pg
4
Triose Phosphate
Isomerase
Quaternary
structure
Hemoglobin, G&G Fig 5.9
A.-F. Miller, 2008, pg
5
Hemerythrins from marine worms. Fig. 6.48 of Garrett & Grisham
Thermodynamic bases for
protein folding
Unfolding is highly cooperative.
A.-F. Miller, 2008, pg
6
Nucleobases: the variable
units of nucleic acids
For nucleotides, phosphate pK1 ≈ 1, pK2 ≈ 6
A.-F. Miller, 2008, pg
7
Nucleo bases Figs. 10.2, .3, .4 of Garrett & Grisham
RibonucleotiDes, (inc. 1 phosphate)
RNA: U and 2' OH
DNA: T and 2' deoxy
A.-F. Miller, 2008, pg
8
Fig. 10.13 of Garrett & Grisham
polynucleotide chains
DNA is
slightly more
labile.
Which one is RNA ?
A.-F. Miller, 2008, pg
9
5’-3’ phosphodiester linkages.
Polymer grows from 3’ OH (in general)
Watson-Crick base pairs
Major groove
Minor groove
Exposed functionalities differ for different base pairs.
Base stacking stabilizes double-helical secondary structure, Base pairing
provides fidelity in replication and transcription.
A.-F. Miller, 2008, pg
10
Fig. 10.20 of Garrett & Grisham
Antiparallel double helix
A.-F. Miller, 2008, pg
11
Different forms of NA
A.-F. Miller, 2008, pg
12
Fig. 11.10 of
Garrett & Grisham
A.-F. Miller, 2008, pg
13
Fig. 11.10 of Garrett & Grisham
A.-F. Miller, 2008, pg
14
Fig. 11.10 of Garrett & Grisham
A.-F. Miller, 2008, pg
15
Tertiary structure of RNA
Coaxial stacks of bases from the
bases of different stem-loops.
Pseudoknots: H-bonding between
loop bases and nearby SS-RNA.
Ribose zippers: H-bonds between
2’OH groups of ribose in
antiparallel SS strands.
Mg2+ binding, NEXT.
Three-base H-bonding.
11.34
A.-F.Fig.
Miller,
2008, pgof Garrett
16
& Grisham