A0_ANIMASI_DNA

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Slide 1: 

R group Amino group Carboxylic group L-Form Amino Acid Structure H = Glycine CH3 = Alanine Juang RH (2004) BCbasics

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Mirror Images of Amino Acid Mirror image Same chemical properties Stereo isomers Juang RH (2004) BCbasics

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-C-C-CONH2 -C-CONH2 -C-COOH -C-C-COOH -H -CH3 -C-OH -C-SH -C-C-S-C -C-C-C-C-NH3+ South line Circular line Central line Nan-Kan line Chung-San line Northwest line Aliphatic Amide Acidic Imino, Circular Basic Sulfur Hydroxy Aromatic Amino Acid Subway Map Juang RH (2004) BCbasics

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POLAR NON- POLAR Tyr His Gly Acidic Neutral Basic Asp Glu Gln Cys Asn Ser Thr Lys Arg Ala Val Ile Leu Met Phe Trp Pro Classification of Amino Acids by Polarity Polar or non-polar, it is the bases of the amino acid properties. Juang RH (2003) Biochemistry

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Amino acids are connected head to tail Formation of Peptide Bonds by Dehydration Dehydration -H2O Carbodiimide Juang RH (2004) BCbasics

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Peptide Bond Is Rigid and Planar Juang RH (2004) BCbasics

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hydride - Hydrogen atom Hydride, Hydrogen and Proton Juang RH (2004) BCbasics

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Proton: abundant and small, affects the charge of a molecule H+ lone pair electrons Ampholyte contains both positive and negative groups on its molecule Proton Is Adsorbed or Desorbed pKa Juang RH (2004) BCbasics pKa

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COOH NH2 H+ Acidic environment Neutral environment Alkaline environment +1 -1 0 Isoelectric point 5.5 Juang RH (2004) BCbasics

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[OH] ? ? ? pK1 pK2 pH pI Isoelectric point = Amino Acids Have Buffering Effect Juang RH (2004) BCbasics

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Environment pH vs Protein Charge + Net Charge of a Protein Buffer pH Isoelectric point, pI - 0 - Juang RH (2004) BCbasics

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pKa = 1.8~2.4 pKa = 3.9~4.3 pKa = 6.0 pKa = 8.3 pKa = 10 pKa = 8.8~11 pKa = 10~12.5 Smaller pKa releases proton easier Residues on amino acids can release or accept protons pKa of Amino Acid Residues Only His has the residue with a neutral pKa (imidazole) pKa of a carboxylic or amino groups is lower than pKa of the R residues Juang RH (2004) BCbasics

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Amino acids -COOH -NH2 -R Gly G 2.34 9.60 Ala A 2.34 9.69 Val V 2.32 9.62 Leu L 2.36 9.68 Ile I 2.36 9.68 Ser S 2.21 9.15 Thr T 2.63 10.4 Met M 2.28 9.21 Phe F 1.83 9.13 Trp W 2.38 9.39 Asn N 2.02 8.80 Gln Q 2.17 9.13 Pro P 1.99 10.6 Asp D 2.09 9.82 3.86 Glu E 2.19 9.67 4.25 His H 1.82 9.17 6.0 Cys C 1.71 10.8 8.33 Tyr Y 2.20 9.11 10.07 Lys K 2.18 8.95 10.53 Arg R 2.17 9.04 12.48 pK1 pK1 pK2 pK2 pK3 pI pI ? three pKa two pKa ? ? pKa of Amino Acids Juang RH (2004) BCbasics

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+1 0 -1 -2 pK1 = 2.1 pK2 = 3.9 pK3 = 9.8 = 3.0 first second third Isoelectric point Isoelectric point is the average of the two pKa flanking the zero net-charged form Aspartic acid Juang RH (2004) BCbasics [OH]

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Trick 1 A U C G Ligation U C G A U C G A U C G Replication Mechanism of Nucleic Acid Juang RH (2004) BCbasics Two tricks to make copies from one molecule

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X Trick 2 RNA C G A T DNA Pairing Juang RH (2004) BCbasics 1.08 nm 1.08 nm

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Pairing Ligation U C G A U C G A U C G A G C U A G C U A G C Original Trick 1 2 Make template from the original molecule

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U C G A U C G A U C G Duplicate 1 Now make copies from the template

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U C G A U C G A U C G A G C U A G C U A G C Original Template Duplicate 2

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U C G A U C G A U C G A G C U A G C U A G C Original Template Duplicate 3 U C G A U C G A U C G Duplicate 1 Juang RH (2004) BCbasics

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DNA RNA Transcription

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T C A A T C G A T C G DNA mRNA Met Translation messenger Ribosome

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U A G C U A G C DNA mRNA tRNA Met Ile T C A A T C G A T C G A G U

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A T C G A T C G U A G C U A G C DNA mRNA Protein T C A A G U

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A T C G A T C G U A G C U A G C DNA mRNA Destroyed T C A A G U Juang RH (2004) BCbasics

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DNA DNA replaced RNA becoming the major genetic material RNA shifted its role to protein biosynthesis Final Version of Cellular Genetic Mechanism Prokaryote Eukaryote Student dormitory Furnished apartment Juang RH (2004) BCbasics

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23 paternal directories 23 maternal equivalents Total 35,000 files Replication Nucleus 23 x 2 In 46 chromosomes Homologous chromosomes Before cell division 3,000 MB Juang RH (2004) BCbasics

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Genome Sequence and Its Annotation ???? ???????? (annotation) ????????? ????? (bioinformatics) ????????????? Ancient Map Detailed Map Functional Map Juang RH (2004) BCbasics

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sp3 Life prefers lighter atoms (1) More abundant on Earth (2) Stronger bonding between small atoms From Atoms to Biological Molecules Chemical properties Atomic sizes The atomic composition of living organism is more complex than others The tetrahedral structure of carbon orbital has rigid steric strain which makes the basic building unit of protein conformation Electrons on the outer shell 1H 6C 7N 8O sp3 1s 2s 2p H C N O Juang RH (2004) BCbasics

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Review the structure of water Permanent dipole Electro-negativity O 3.5 N 3.0 C 2.5 H 2.1 If atoms in a functional group have notable difference in electronegativity, then this functional group will express high polarity and will be highly active ? High polarity ? High dielectric constant ? H-bond formation ? pH influence C-C Organic compound Functional group Juang RH (2004) BCbasics

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Exaggerated Model for Water Molecule Adapted from Zubay (1988) Biochemistry (2e) p.57 - + sp3

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Water 80.4 Methanol 33.6 Ethanol 24.3 Ammonia 17.3 Acetic acid 6.15 Chloroform 4.81 Ethyl ether 4.43 Benzene 2.28 Carbon tetrachloride 2.24 Dielectric Constant Adapted from Bohinski (1987) Modern Concepts in Biochemistry (5e) p.37 Molecules with asymmetrical distribution of electronegativity have higher polarity

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Ionic Bond Is Not Stable in Water Solution Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.115 - + + - ? + - + + + + + - - - - - - + Adapted from Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.87 Solvation ? But enzyme forms stable binding with its substrate in water

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Bond Energy in Water Might Be Different Bond length In vacuum Water solution Covalent bond Ionic bond Hydrogen bond Van der Waal force 0.15 nm 0.25 nm 0.30 nm 0.35 nm 90 80 4 0.1 90 3 1 0.1 kcal/mole Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.57

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+ Hydrogen Bond (H-Bond) The linearity is important for a perfect H-bond Weaker H-bond Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.58

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Polar ? Polar Nonpolar ? Nonpolar Like Dissolves Like Affinity between Two Molecules Juang RH (2004) BCbasics Molecules having similar polarity will attract each other

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Energy of Chemical Bonds in Cells kcal/mole Secondary bond Hydrogen bond Ionic bond Hydrophobic bond 90 kcal/mole 3 kcal/mole 1 kcal/mole 1 kcal/mole 0.1 kcal/mole Covalent bond Van der Waal force Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.53 Juang RH (2004) BCbasics

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Secondary Bonds Contribute to Molecular Affinity Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.161 Reversible non-covalent binding x

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