adapted from lehninger, nelson & cox – principles of ... i valine m cha cooh i ... adapted...
TRANSCRIPT
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adapted from Lehninger, Nelson & Cox – Principles of Biochemistry
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informationtransfer
Waste:molecules oflow energy/high entropy
Feed:molecules of highenergy/low entropy
proteins:molecular machines
assembly oforganisedstructures
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adapted from Nelson – Biological Physics
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order created via energy throughput in a dissipative system:sand ripples created by wind
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adapted from Nelson– Biological Physics
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A “simple” cell: E. coli(artist’s rendering after structural/microscopy data)
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adapted from Lehninger, Nelson & Cox – Principles of Biochemistry
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layer 4: cells and organelles
The Biological Cell j},.
layer 3: supra molecular
complexes
layer 2: macromolecules
layer 1: biomolecules
nucleotides N~
---- f o)y! -o-p-o-cko~
A si;-fil
protein
amino acids
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protein
nucleic acids(DNA, etc.)
lipid
polysaccharide
adapted from Phillips et al. – Physical Biology of the Cell
... only four classes ofbiomolecules!
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adapted from Phillips et al. – Physical Biology of the Cell
Two “polymer languages”are important in biology
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adapted from Phillips et al. Physical Biology of the Cell
Translationbetween the“polymer languages”:The Genetic Code
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adapted from Phillips / Kondev / Theriot – Physical Biology of the Cell
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adapted from Phillips et al. – Physical Biology of the Cell
model building in biophysics:biological cartoons representidealizations of different aspectsof relevance in different contexts
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cell volume VE coli 1 μm3
cell mass mE coli 1 pg
repl cycle time tE coli 3,000 s
surface area AE coli 6 μm2
genome length NE coli 5×106 bp
swimming speed vE coli 20 μm/s
E. coli adapted from Phillips et al. – Physical Biology of the Cell
biology by numbers:
order-of-magnitudeestimates are essentialfor model building!
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length per bp lbp 0.34 nm
volume per bp Vbp 1 nm3
charge density per unit length λDNA 2 e/0.34 nm
persistence length ξDNA 50 nm
double-stranded DNA
typical diameter dprotein 4–5 nm
typical volume Vprotein 25 nm3
avrg. mass of AA MAA 100 Da
typ. protein mass Mprotein 30 kDa
protein conc in cell cprotein 300 mg/mL
diffusion const in water Dprotein 100 μm2/s
amino acids and proteins
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dipole moment: e•r = 1.85 D (1 D = 3.33 x 10–30 Cm)→ water dielectric constant ε ~ 80 (room temp)→ boiling point: TB = 373 K (extraordinarily high!)
→
dipole moment: e•r = 0.97 D→ boiling point: TB = 213 K
→
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adapted from Nelson– Biological Physics
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COOH I
H2N- C- H I
alanine (A) CH3
COOH I
H2N-C-H I
CH3-CH I
valine M CHa
COOH I
H2N-C-H I
H-C-CHa I
isoleucine ?Hz (I) CH3
COOH proline (P) .... Jt!
H2C NH I I
HzC--CHz
COOH I
H2N- C-H
glycine (G) A
COOH I
H2N-C-H I
serine (S) CHzOH
COOH I
H2N-C-H I
H-C-OH I
threonine (T) CHa
COOH I
H2N-C-H I
cysteine (C) ?Hz SH
COOH I
H2N-C-H
tyrosine M ~~ y OH
COOH I
H2N-C- H I
tryptophane ?Hz 0/V) C=CH
b"
COOH I
H2N-C-H I
aspartic CHz
acid(D) booH
COOH I
H2N-C-H I
CH2 I
glutamic CHz
acid (E) booH
COOH I
H2N-C-H I
histidine (H) . b~~H II PH
HC..._Nor
COOH I
H2N-C-H . I
asparag1ne CH2
(N) I "'c.....___
0 "' NHz
COOH I
HzN-C- H I
phenylalanine
6CHz
(F) ~ I
'
COOH I
H2N-C-H I
arginine ?Hz (R) CHz
I CHz I
NH I C=NH I
NHz
COOH I
H2N-C-H
tHz I CH2 I
lysine (K) CHz I CHz I
NHz
COOH I
H2N-C-H
th. . I
me 1omne CH2
. (M) I CHz
~ I CHa
COOH I
H2N- C- H I
glutamine ?Hz
(Q) CHz I
"'c o"' NHz
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adapted from Nelson– Biological Physics
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hydrogen bond 0.177 nm
covalent bond 0.0965 nm
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adapted from Alberts et al. –Molecular Biology of the Cell
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limitations to dihedral angles: Ramachandran diagram
adapted from Jackson– Molecular & Cellular Biophysics
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example:bacteriorhodopsin, a membrane-bound converter for light into electrical energy
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“free” water:high disorder – tumbling motion, yet many H bondsH bonds may form in many mutual orientations – entropy large
water near hydrophilic headgroup:same structure as in “free “ water
water near hydrophobic tail:highly ordered water: low entropy
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lipid aggregation in water
entropy decrease for lipids,but larger entropy increase for water
entropy decrease for lipids,but larger entropy increase for water
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adapted from Alberts et al. –Molecular Biology of the Cell
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lipid molecule protein molecules
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adapted from Lehninger, Nelson & Cox – Principles of Biochemistry
lipid/proteinmembranes
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adapted from Alberts et al. –Molecular Biology of the Cell
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proteins with differentproperties (e.g., shorttransmembrane span)
can’t enter raft → selectivity!
adapted from Alberts et al. –Molecular Biology of the Cell
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MD simulation: D. Tobias, UC Irvineadapted from Nelson – Biological Physics
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adapted from Alberts et al. –Molecular Biology of the Cell
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o-o ...... , 0 'p-0
O~p- -\ _0/ \ , 0 o:R
/ 0 O =P-0-
\ hydrogen bond 5' end 3'end
0 \
P=O cf 'o- l
0.34 nm
phosphodiester bond
J
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adapted from Alberts et al. –Molecular Biology of the Cell
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H
0 IIIIH-N1
H
N ~ rN H
1N-H i1111 0 y
n,;no• g.ooVO /
T1'aior groove T1'aior groove
H I
CH3 0 111\IH-N N~
"-- n,;no, g.oo<'
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H I
/C~ /CH3 N C I I thymine
c c 0~ ""'-N/ ~0
I -H
II N"" ~c,
C N I // N // adenine -- c
"---H
"'
5'
cytosine
...-:::C t. _ Ac, 0/" ~ " N-H
I H H H
I I /N"-. / N '- -::/0\
H C C hydrogen 11 1 bond
sugar-phosphate backbone
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adapted from Alberts et al. –Molecular Biology of the Cell
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adapted from Lehninger, Nelson & CoxPrinciples of Biochemistry
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1st
lett
er
of
codon
2nd letter of codon
adapted from Lehninger, Nelson & Cox – Principles of Biochemistry and from Alberts et al. – Molecular Biology of the Cell
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tRNA
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phosphoanhydride bonds
~ ~ o- o- o -1 I I
-o-P-0-P-0-P
energy in ,.. photosynthesis,
food , ...
o-1
-o-P-OH + II 0
II II II 0 0 0
o- o-1 I -o-P -0-P - 0-CH II II 2
0 0
energy out ,.. chemical synthesis,
motility, ... (almost anything
that requires energy in the cell!)
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many isomers possible!
myriads of differentstructures possible!
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GlcNAc: N-acetyl glucosamineMurNAc: N-acetyl muraminic acid
adapted fromLehninger, Nelson & Cox
Principles of Biochemistry