Category: Education

Presentation Description

No description available.


Presentation Transcript

Slide 1: 

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

Slide 2: 

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

Slide 3: 

-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

Slide 4: 

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

Slide 5: 

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

Slide 6: 

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

Slide 7: 

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

Slide 8: 

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

Slide 9: 

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

Slide 10: 

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

Slide 11: 

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

Slide 12: 

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

Slide 13: 

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

Slide 14: 

+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]

Slide 15: 

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

Slide 16: 

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

Slide 17: 

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

Slide 18: 

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

Slide 19: 

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

Slide 20: 

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

Slide 21: 

DNA RNA Transcription

Slide 22: 

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

Slide 23: 


Slide 24: 

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

Slide 25: 

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

Slide 26: 

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

Slide 27: 

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

Slide 28: 

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

Slide 29: 

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

Slide 30: 

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

Slide 31: 

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

Slide 32: 

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

Slide 33: 

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

Slide 34: 

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

Slide 35: 

+ 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

Slide 36: 

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

Slide 37: 

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

Slide 38: 

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

authorStream Live Help