Lecture in Biochemistry

Prof. Dr. Karl-Heinz van Pe

Technische Universitt Dresden
Solo
9th 22nd September 2016

This lecture is based on the textbook

Lehninger
PRINCIPLES OF
BIOCHEMISTRY
Fourth Edition
David L. Nelson (University of WisconsinMadison)
Michael M. Cox (University of WisconsinMadison)
2

Outline of the lecture

1. The Foundations of Biochemistry
1.1 Cellular Foundations
1.2 Chemical Foundations
1.3 Physical Foundations
1.4 Genetic Foundations
1.5 Evolutionary Foundations

Outline of the lecture

PART I. STRUCTURE AND CATALYSIS
2. Water
2.1 Weak Interactions in Aqueous Systems
2.2 Ionization of Water, Weak Acids, and Weak Bases
2.3 Buffering against pH Changes in Biological Systems
2.4 Water as a Reactant
2.5 The Fitness of the Aqueous Environment for Living Organisms
4

Outline of the lecture

3. Amino Acids, Peptides, and Proteins
3.1 Amino Acids
3.2 Peptides and Proteins
3.3 Working with Proteins
3.4 The Covalent Structure of Proteins
3.5 Protein Sequences and Evolution

Outline of the lecture

4. The Three-Dimensional Structure of Proteins
4.1 Overview of Protein Structure
4.2 Protein Secondary Structure
4.3 Protein Tertiary and Quaternary Structures
4.4 Protein Denaturation and Folding

Outline of the lecture

5. Protein Function
5.1 Reversible Binding of a Protein to a Ligand: Oxygen-Binding
Proteins
5.2 Complementary Interactions between Proteins and Ligands:
The Immune System and Immunoglobulins
5.3 Protein Interactions Modulated by Chemical Energy: Actin,
Myosin, and Molecular Motors
7

Outline of the lecture

6. Enzymes
6.1 An Introduction to Enzymes
6.2 How Enzymes Work
6.3 Enzyme Kinetics as An Approach to Understanding Mechanism
6.4 Examples of Enzymatic Reactions
6.5 Regulatory Enzymes

Outline of the lecture

7. Carbohydrates and Glycobiology
7.1 Monosaccharides and Disaccharides
7.2 Polysaccharides
7.3 Glycoconjugates: Proteoglycans, Glycoproteins, and Glycolipids
7.4 Carbohydrates as Informational Molecules: The Sugar Code
7.5 Working with Carbohydrates

Outline of the lecture

8. Nucleotides and Nucleic Acids

8.1 Some Basics
8.2 Nucleic Acid Structure
8.3 Nucleic Acid Chemistry
8.4 Other Functions of Nucleotides

10

Outline of the lecture

9. DNA-Based Information Technologies
9.1 DNA Cloning: The Basics
9.2 From Genes to Genomes
9.3 From Genomes to Proteomes
9.4 Genome Alterations and New Products of Biotechnology

11

Outline of the lecture

10. Lipids
10.1 Storage Lipids
10.2 Structural Lipids in Membranes
10.3 Lipids as Signals, Cofactors, and Pigments
10.4 Working with Lipids

12

Outline of the lecture

11. Biological Membranes and Transport

11.1 The Composition and Architecture of Membranes
11.2 Membrane Dynamics
11.3 Solute Transport across Membranes

13

1 THE FOUNDATIONS OF BIOCHEMISTRY

14

1.1 Cellular Foundations

15

The universal features of living cells

16

Phylogeny of the three domains of life

17

Classification of organisms according to their source

of energy

18

Common structural features of bacterial cells

19

Eukaryotic cell structure

Macht nichts

20

Structural hierachy in the molecular organization of cells

21

Energies of some covalent bonds and noncovalent

interactions

22

1.2 Chemical Foundations

23

Chemical elements which are essential for living organisms

most important elements

99.0 % in humans

for bacteria, plants or animals

essential trace elements

possibly essential trace

elements for some
24
species

Chemical differences between a living organism and

the earth

25

Versatility of carbon bonding

26

Geometry of carbon bonding

27

Some common functional groups of biomolecules

28

Some common functional groups of biomolecules

29

Several common functional groups in a single biomolecule

30

Molecular components in an E. coli cell

31

Representation of molecules

32

Configuration of geometric isomers

33

Molecular asymmetry: chiral and achiral molecules

34

Two types of stereoisomers

35

Naming systems for stereoisomers

36

Conformations

37

Some stereoisomers are distinguishable by smell

and taste in humans
Das macht nicht

38

1.3 Physical Foundations

39

Energy conversion in living organisms

Light-driven formation of glucose

40

Adenosine triphosphate (ATP)

41

The standard (Gibbs) free energy

G=HTS
G = H T S
G > 0: reaction is energy-requiring (endergonic)
G < 0: reaction liberates free energy (exergonic)
G: standard (Gibbs) free energy
H: enthalpy (reflects the number and kinds of bonds)
S: entropy (disorder)
42

Energy coupling in mechanical and chemical processes

43

The equilibrium constant Keq and the standard freeenergy change G

Reaction: aA + bB

cC + dD

Equilibrium constant:

Free-energy change:

When equilibrium is reached:

and G = 0
substitution results in: G = - RT ln Keq (given in joules per mole)

44

Energy changes during a chemical reaction

45

The central role of ATP in metabolism

46

Regulation: feedback regulation

47

1.4 Genetic Foundations

48

Complementation between the two strands of DNA

49

DNA to RNA to protein

50

1.5 Evolutionary Foundations

51

Role of mutations in evolution

Das macht

52

Abiotic formation of biomolecules

53

The RNA world

54

Landmarks of the evolution of life on Earth

55

Evolution of eukaryotes through endosymbiosis

56

Comparison of prokaryotic and eukaryotic cells

57

Generation of genetic diversity by mutation and gene

duplication

58

Part I
Structure and catalysis

59

Water

60

Water as a solvent

61

Melting point, boiling point, and heat of evaporation

of some common solvents

62

Structure of the water molecule

63

Hydrogen bonding in ice

64

Hydrogen bonds

65

Hydrogen bonding of water and some biologically

relevant molecules

66

Examples of polar, nonpolar, and amphipathic biomolecules

67

Water as a solvent

68

Water as a solvent

69

Amphipathic compounds in aqueous solution

70

Amphipathic compounds in aqueous solution

71

Release of ordered water favors formation of an

enzyme-substrate complex

72

van der Waals radii and covalent (single bond) radii

of some elements

73

Noncovalent interactions among biomolecules in

aqueous solvent

74

Example of water in an enzyme molecule

75

Effect of extracellular osmolarity on water movement

across a plasma membrane

76

Proton hopping

77

The ionization of water is expressed by an

equilibrium constant

Kw: ion product of water

with Keq (measured) = 1.8 x 10-16
With equal concentrations of OH- and H+, the solution is at neutral pH

78

The pH scale designates the H+ and OHconcentrations

79

Some practical considerations of everyday life

80

Dissociation constants (Ka)

81

Titration curve

82

Comparison of the titration curves of three weak

acids

83

The acetic acid acetate pair as a buffer system

84

The Henderson Hasselbalch equation

Macht nichts

at the midpoint of the titration we have:

85

The amino acid histidine has a side chain which is a

weak acid

86

Very important buffer systems are the phosphate

(cytoplasm) and the bicarbonate (blood plasma)
buffer systems

CO2 (d): dissolved CO2

CO2 (g): CO2 in the gas phase
leads to a pH around 6.9 7.4

leads to a pH close to 7.4

87

The pH optima of enzymes can differ quite substantially

88

Water as a reactant

89

Condensation and hydrolysis reactions

90

Amino Acids

91

General structure of an amino acid and numbering of

carbon atoms

92

Stereoisomerism in -amino acids

93

Steric relationship of the stereoisomers of alanine to the

absolute configuration of L- and D-glyceraldehyde

94

Properties and conventios associated with the

common amino acids found in proteins

95

Nonpolar, aliphatic R groups

96

Polar, uncharged R groups

COO +
H3N C H
CH2
SeH
Seleno-Cystein
Selenoysteine

97

Aromatic R groups

98

Positively charged R groups

99

Negatively charged R groups

100

Absorption of ultraviolet (UV) light by aromatic amino acids

101

Reversible formation of a disulfide bond

102

Uncommon amino acids

103

Amino acids can act as acid and bases (ampholytes)

104

Titration of an amino acid

105

Effect of the chemical environment on pKa

106

Isoelectric point and titration curves for glutamate (a)

and histidine (b)

107

Peptides and Proteins

108

Peptide bonds are formed by the condensation of

amino acids

109

A pentapeptide

110

Molecular data on some proteins

111

Amino acid composition of proteins and conjugated

proteins

112

Levels of structure in proteins

113

Column chromatography

114

Ion-exchange chromatography

115

Size-exclusion chromatograohy

116

Affinity chromatography

117

Electrophoresis
: electrophoretic mobility of the molecule
V: velocity of the molecule
E: electric potential
Z: net charge of the molecule
f: frictional coefficient (reflects in part the shape of the molecule)

118

Electrophoresis
Macht nichts

119

Estimation of the molecular weight of a protein

120

Isoelectric focusing

121

Two-dimensional electrophoresis

122

Steps in sequencing a polypeptide

123

Breaking disulfide bonds in proteins

124

The specificity of some common methods for

fragmenting polypeptide chains

125

Correspondence of DNA and amino acid sequences

126

The Three-Dimensional Structure of Proteins

127

The planar peptide group

Das macht nichts

128

Protein secondary structure: the -helix

129

Protein secondary structure: the -sheet

130

Protein secondary structure: the -turn

131

Relative probabilities of amino acids occuring in a

specific secondary structure

132

-Keratin: the structure of hair

133

Fibrous proteins

134

Collagen

135

4-Hydroxyproline is necessary for stable collagen and ascorbate

is required for restoring prolyl 4-hydroxylase activity

Without ascorbate reaction (b) would lead to inactive prolyl 4-hydroxylase due to the oxidation of Fe 2+ to Fe3+
136

-Sheet: silk

137

Tertiary structure of sperm whale myoglobin

138

The heme group

139

Three-dimensional structures of some small proteins

140

Protein denaturation measured by circular dichroism

141

Renaturing of unfolded, denatured ribonuclease

142

A simulated protein foding pathway

143

The thermodynamics of protein folding

144

Chaperones in protein folding

145

Chaperonins in protein folding

146

Protein function

147

The heme group

148

The heme group

149

Ligand binding

150

Steric effects on the binding of ligands

151

Structural change induced by ligand binding

152

Structural changes in a multisubunit protein

undergoing cooperative binding to ligand

153

Cooperative ligand-binding proteins

154

Sickle-cell anemia

155

Major histocampatibility complex (MHC) proteins

156

Structure of a human class I MHC protein

157

The structure of immunoglobulin G

158

Phagocytosis

159

Antibody techniques

160

The muscle protein myosin

161

Structure of skeletal muscle

162

Muscle contraction

163

Molecular mechanism of muscle contraction

164

Enzymes

165

Enzymes can contain metal ions as cofactors

166

Enzymes can contain small organic molecules which

are not amino acids

167

Classification of enzymes

168

Reaction coordinates for an uncatalysed chemical

and an enzyme-catalysed reaction

169

Equilibrium constant, free energy and rate equation

Equilibrium constant

Relationship between
the equilibrium constant
and the change in
standard free energy

Rate equation

170

Relationship between the rate constant k and the

activation energy

k is the rate constant

k is the Boltzmann constant

and h is Plancks constant

A lower activation energy means a faster reaction rate

171

Some rate enhancements produced by enzymes

172

A reaction catalysed by an imaginary enzyme

173

Role of binding energy in catalysis

174

Avoiding unfavorable charge development

175

Acid-base catalysis

176

Substrate saturation curve

rectangular hyperbola

177

The Michaelis-Menten equation

since the breakdown of ES is the rate limiting step

Steady-state: [ES] is constant

Et is the total enzyme concentration

with (k2 + k-1)/k1 = Km
Km is the Michaelis constant
This is the Michealis-Menten equation
178

Dependence of initial velocity on substrate

concentration

179

The Michaelis constant Km and the dissociation

constant Kd

Das mach t nichts

Under theses conditions, Km reflects the affinity of the enzyme to its substrate in the ES complex

180

The Lineweaver-Burk plot

This is the Lineweaver-Burk equation

describing a straight line
181

The turnover number kcat

182

The specificity constant or enzyme efficiency kcat/Km

183

Enzyme inhibition

184

pH Dependence of an enzyme-catalysed reaction

185

Allosteric enzymes

186

Feed back inhibition

187

Regulation of enzyme activity by covalent

modification

188

Carbohydrates and Glycobiology

189

Representative monosaccharides

190

Representation of stereoisomers of glyceraldehyde

191

D-Aldoses

192

D-Ketoses

abcde

193

Epimers

194

Hemiacetals, acetals, hemiketals, and ketals

195

Straight-chain and cyclic forms of D-glucose

196

Pyranoses and furanoses

197

Important hexose derivatives

198

Sugars as reducing agents

199

Formation of maltose

200

Some common disaccarides

201

Monosaccharides and polysaccharides

202

Starch consists of amylose and amylopectin

203

Cellulose has 1

4 linkages

204

Cellulose can be broken down by most bacteria and

fungi, but not by animals and humans

205

Chitin, the second most abundant polysaccharide

206

Conformation at the glycosidic bonds

207

The structure of starch

208

Peptidoglycan

209

Agarose

210

Repeating units of some common

glycosaminoglycans of extracellular matrix

211

Structures and roles of some polysaccharides

212

Proteoglycans

213

Proteoglycan structure of an integral membrane

protein

214

Proteoglycan aggregate of the extracellular matrix

215

Glycoproteins

216

Roles of oligosaccharides in recognition and

adhesion at the cell surface

217

Nucleotides and Nucleic Acids

218

Desoxyribonucleotides of nucleic acids

219

Ribonucleotides of nucleic acids

220

Nucleotide and nucleic acid nomenclature

221

Adenosine monophosphates
Adenine
Adenine

Adenosine 5-monophosphate Adenosine 2-monophosphate

Adenine

Adenine

Adenosine 3-monophosphate cyclic Adenosine 2,3-monophosphate

222

Phosphodiester linkages in the covalent backbone of

DNA and RNA

223

Hydrolysis of RNA under alkaline conditions

224

Hydrogen-bonding patterns

225

Complementarity of strands in the DNA double helix

226

Base-paired helical structures in an RNA

Nur zum fllen

227

Nonenzymatic reactions of nucleotides

228

Formation of pyrimidine dimers induced by UV light

229

Nucleotide phosphates

230

Coenzymes containing adenosine

231

Coenzymes containing adenosine

232

Coenzymes containing adenosine

233

Cleavage of DNA by restriction endonucleases

234

Joining (ligation) of DNA by DNA ligase

235

Lipids

236

Some naturally occuring fatty acids

237

The packing of fatty acids into stable aggregates

238

239

Biological wax

240

Some common types of storage and membrane

lipids

241

L-Glycerol 3-phosphate, the backbone of

phospholipids

242

Glycophospholipid

243

Glycerophospholipids

244

Cholesterol

245

Arachidonic acid and some eicosanoid derivatives

246

247

Vitamin A1 and ist precursor and derivatives

248

Some other biologically active isoprenoid

compounds and derivatives

249

Some other biologically active isoprenoid

compounds and derivatives

250

251

252