BMB401 F10 T1 Crib Notes

BMB401 F10 T1 Crib Notes - Amino acids (at pH NH2 O H3 C -...

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Unformatted text preview: Amino acids (at pH NH2 O H3 C - H2 N O + + NH + NH2 - O O O O + - + O H3 N - O + CH3 NH3 NH3 Leu (L) 131 H3 C + Ser (S) 105 NH3 NH3 Ile (I) 131 O O NH3 Phe (F) 165 Pro (P) 115 O CH3 O - O + O - H3 C NH3 HO Trp (W) 204 Thr (T) 119 - O NH3 - NH O + O H2 + N - O + - O + His (H) 155 Met (M) 149 NH3 NH3 O + + O CH3 O H3 C - - - HO O Cys (C) 121 O S CH3 O - NH3 NH3 Lys (K) 146 O + O O + O Basic O Gly (G) 75 Basic + - HS NH3 N Gln (Q) 146 O H N - NH3 Glu (E) 147 HO H3 N O Asp (D) 133 O + O - + O Asn (N) 132 - + H3 C NH3 O NH3 O + O - Acid ic O - O NH3 O Acidic - H2 N O Arg (R) 174 Ala (A) 89 O O O Basic NH3 - Premed411.com 7.4 with most of the Carbon and Hydrogen atoms not labelled) Tyr (Y) 181 + O NH3 Val (V) 117 Sugars and Bases OH H OH H HO O OH HO O OH O NH2 NH H HO OH H OH OH OH OH NH N O O OH -D-Glucopyranose Deoxyribose Ribose Uracil O NH2 NH NH2 N N Adenine N NH O Cytosine NH OH 4' 1' N NH2 Guanine Henderson-Hasselbalch equation ATP NH NH 2' OH O H3 C NH N O 3' O N OH N N 5' HO P O P O P O OH N O O Thymine pH=pKa + log[A-]/[HA] Free energy change of a reaction ∆ G=∆ Go + RTln[C][D]/[A][B] Arrhenius equation: k=Ae- ∆ G‡/RT ∆ Go=-RtlnKeg -∆ G‡/RT [S‡]=[S] e ! Michaelis- Menten V=k2[ET][S]/(Km + [S]) or . ! Linweaver- Burk 1/V=Km/(Vmax [S]) + 1/Vmax ∆ G=∆ H - T∆ S V=k[S] e-∆ G‡/RT V=Vmax[S]/(Km + [S]) Km=(k2+k-1)/k1 Effects of inhibition on Km and Vmax Inhibition Rate equation Apparent Km ! None V=Vmax[S]/(Km+[S]) Km ! Competitive V=Vmax[S]/(Km(1+[I]/KI)+[S]) Km(1+[I]/KI) ! Non-competitive V=Vmax[S]/(1+[I]/KI)(Km+[S]) Km Apparent Vmax Vmax Vmax Vmax/(1+[I]/KI) Amino Acid α -Carboxyl Alanine (A) Arginine (R Asparagine (N) Aspartic acid (D) Cysteine (C) Glutamic acid ( E) Glutamine (Q) Glycine (G) Histidine (H) Isoleucine (I) Leucine ( L) Lysine (K) Methionine ( M) Phenylalanine ( F) Proline (P) Serine ( S) Threonine (T) Tryptophan (W) Tyrosine (Y) Valine (V) 2.3 1.8 2.0 2.0 1.8 2.2 2.2 2.3 1.8 2.4 2.4 2.2 2.3 1.8 2.1 2.1 2.6 2.4 2.2 2.3 Conversion Factors Physical quantity Length Mass Volume Temperature Energy Pressure α -N H 3 R g ro u p 9.9 9.0 8.8 9.8 10.8 9.7 9.1 9.8 9.2 9.7 9.6 9.0 9.2 9.1 10.6 9.2 10.4 9.4 9.1 9.6 12.5 pKas 3.9 8.3(SH) 4.3 6.0(IMI) 10.8 13(OH) 13(OH) PHYSICAL CONSTA NTS AND CONV ERSION O F UNITS Values of physical constants Physical constant Symbol Value Atomic mass unit (dalton) amu 1.661 x 10-24 g Avogadro’s number N 6.022 x 1023 mol-1 Boltzmann’ constant k 1.381 x 10-23 J deg-1 3,298 x 10-24 cal deg-1 Electron volt eV 1.602 x 10-19 J 3.828 x 10-20 cal Faraday constant F 9.649 x 104 C mol-1 2.306 x 104 cal volt-1 eq-1 Curie Ci 3.70 x 1010 disintegrations sec-1 Gas constant R 8.314 J mol-1 deg-1 1.987 cal mol-1 deg-1 Planck’s constant h 6.626 x 10-34 J sec 1.584 x 10-34 cal sec Speed of light in a vacuum c 2.998 x 1010 cm sec-1 _________ Abbreviations: C , coulo mb; cal, calorie; cm, centimeter; deg, degree Kelvin; eq, equivalent; g, gram; J, jo ule; mol, mole; sec, second 10.9(OH) ____________________________ ____________________________ Equivalent___________________ 1cm = 10 m = 10 mm = 104µm = 107 nm 1cm = 108 Å = 0.3937 inch 1g = 10-3 kg = 103 mg = 106 µg 1g = 3.527 x 10-2 ounce (avoirdupoir) 1 cm3 = 10-6m3 = 103 mm3 1 ml = 1 cm3 = 10-3l = 103 µl 1 cm3 = 6.1 x 10 –2 in3 = 3.53 x 10-5 ft3 K = °C + 273.15 °C = 5/9 (°F – 32) 1 J = 107 erg = 0.239 cal = 1 watt sec 1 torr = 1 mm Hg (0°C) = 1.333 x 102 newton/m2 = 1.333 x 102 pascal = 1.316 x 10-3 atmospheres ______________________________________ -2 ∆G'=RT1n([C2]/[C1])+ZF∆Ѱ E'=E°'+(RT/nF)1n([ox]/[red]) Molecular masses: H=1 Standard prefixes Prefix Symbol kilo k hecto h d eca da d eci d centi c milli m micro µ n an o n pico p ∆G°'=-nF∆E°' S=(4Dt)½ C=12 Y= pO2n/(pO2+P50)n Hill equation n=1 for myoglobin and 2.8 for hemoglobin To be N-glycosolated: N-X-(S/T) Asn—Anything—(Ser or Thr) Mathematical consta nts π = 3.14159 e = 2.71828 logex = 2.303 log10x N=14 Factor 103 102 101 1 0 -1 1 0 -2 1 0 -3 1 0 -6 1 0 -9 10-12 ∆G°'=-RTlnK O=16 Y/(1-Y)= pO2n/P50n P=31 S=32 log Y/(1-Y)= n log pO2 – n logP50 ...
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