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