Intro Biophysics

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},. protein amino acids nucleic acids (DNA, etc.) ... only four classes of biomolecules! protein lipid 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 2nd letter of codon 1st letter of codon adapted from Lehninger, Nelson & Cox – Principles of Biochemistry and from Alberts et al. – Molecular Biology of the Cell 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.

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