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Prentice Hall c2002Chapter 11 Principles of Biochemistry Fourth Edition Chapter 1: Introduction to Biochemistry Copyright © 2006 Pearson Prentice Hall,

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Presentation on theme: "Prentice Hall c2002Chapter 11 Principles of Biochemistry Fourth Edition Chapter 1: Introduction to Biochemistry Copyright © 2006 Pearson Prentice Hall,"— Presentation transcript:

1 Prentice Hall c2002Chapter 11 Principles of Biochemistry Fourth Edition Chapter 1: Introduction to Biochemistry Copyright © 2006 Pearson Prentice Hall, Inc. Horton Moran Scrimgeour Perry Rawn

2 Prentice Hall c2002Chapter 12 Chapter 1 Introduction to Biochemistry Adenovirus: Viruses consist of a nucleic acid molecule surrounded by a protein coat

3 Prentice Hall c2002Chapter Biochemistry Is a Modern Science Urea ( 尿素 ) was synthesized by heating the inorganic compound ammonium cyanate (1828) This showed that compounds found exclusively in living organisms could be synthesized from common inorganic substances

4 Prentice Hall c2002Chapter 14 In 1897 Eduard Buchner showed that extracts of yeast cells could catalyze the fermentation of the sugar glucose to alcohol and carbon dioxide. Fischer described enzymes as rigid templates, or locks, and substrates as matching keys. The last half of the 20th century saw tremendous advances in the area of structural biology, especially the structure of proteins.

5 Prentice Hall c2002Chapter 15 Two notable breakthroughs in the history of biochemistry (1) Discovery of the role of enzymes as catalysts (2) Identification of nucleic acids as information molecules Flow of information: from nucleic acids to proteins DNARNAProtein

6 Prentice Hall c2002Chapter 16 In 1944 Oswald Avery et al. provided the first conclusive evidence that DNA is the genetic material. In 1953 Watson and Crick deduced the three-dimensional structure of DNA In 1958, Crick proposed the Central Dogmal of molecular biology.

7 Prentice Hall c2002Chapter The Chemical Elements of Life Only six nonmetallic elements: oxygen, carbon, hydrogen, nitrogen, phosphorous, and sulfur account for >97% of the weight of most organisms These elements can form stable covalent bonds Water is a major component of cells Carbon is more abundant in living organisms than it is in the rest of the universe

8 Prentice Hall c2002Chapter 18 Fig 1.1 Periodic Table of the elements Important elements found in living cells are shown in color The six abundant elements are in red (CHNOPS) Five essential ions are in purple Trace elements are in dark blue (more common) and light blue (less common)

9 Prentice Hall c2002Chapter 19

10 Prentice Hall c2002Chapter 110 Functional groups in biochemistry Functional groups ( 官能基 )- specific parts of molecules involved in biochemical reactions Figure 1.2 shows the general formulas of: (a) Organic compounds (b) Functional groups (c) Linkages common in biochemistry (R represents an alkyl group (CH 3 CH 2 ) n -)

11 Prentice Hall c2002Chapter 111 Fig 1.2 (a) General formulas

12 Prentice Hall c2002Chapter 112 Fig 1.2(b) General Formulas

13 Prentice Hall c2002Chapter 113 Fig 1.2 (c) General Formulas

14 Prentice Hall c2002Chapter Many Important Biomolecules are Polymers Biopolymers - macromolecules created by joining many smaller organic molecules (monomers) Condensation reactions ( 縮合反應 ) join monomers (H 2 O is removed in the process) Residue ( 殘基 )- each monomer in a chain

15 Prentice Hall c2002Chapter 115 Molecular mass Molecular weight is more correctly termed the relative molecular mass (M r ) - the molecular mass relative to 1/12 mass of a carbon atom ( 12 C) M r is a relative quantity and is dimensionless A typical protein may have an M r = 38,000 The absolute molecular mass of this protein = 38,000 daltons (1 dalton = 1 atomic mass unit)

16 Prentice Hall c2002Chapter 116 A. Proteins Proteins are composed of 20 common amino acids Each amino acid contains: (1) Carboxylate group (-COO - ) (2) Amino group (-NH 2 ) (3) Side chain (R) unique to each amino acid

17 Prentice Hall c2002Chapter 117 Fig 1.3 Structure of an amino acid and a dipeptide (a) Amino group (blue), carboxylate group (red) (b) Dipeptides are connected by peptide bonds

18 Prentice Hall c2002Chapter 118 Polypeptides Polypeptides - amino acids joined end to end Conformation ( 構形 )- the three dimensional shape of a protein which is determined by its sequence Active site - a cleft or groove in an enzyme that binds the substrates of a reaction

19 Prentice Hall c2002Chapter 119 Fig 1.4 Egg white lysozyme (a) Free enzyme (b) Enzyme, bound substrate in active site cleft

20 Prentice Hall c2002Chapter 120 B. Polysaccharides Carbohydrates, or saccharides, are composed primarily of C,H and O Polysaccharides are composed of saccharide monomers Most sugar structures can be represented as either linear (Fischer projection) or cyclic

21 Prentice Hall c2002Chapter 121 Fig 1.5 Representations of the structure of ribose

22 Prentice Hall c2002Chapter 122 Fig 1.6 (a) Glucose, (b) Cellulose Glycosidic bonds connecting glucose residues are in red

23 Prentice Hall c2002Chapter 123 C. Nucleic Acids Polynucleotides - nucleic acid biopolymers are composed of nucleotide monomers Nucleotide monomers are composed of: (1) A five-carbon sugar (2) A heterocyclic nitrogenous base (3) Phosphate group(s)

24 Prentice Hall c2002Chapter 124 Fig 1.7 Deoxyribose Deoxyribose lacks a hydroxyl group at C-2. It is the sugar found in DNA.

25 Prentice Hall c2002Chapter 125 Nitrogenous bases Major Purines: Adenine (A) Guanine (G) Major Pyrimidines Cytosine (C) Thymine (T) Uracil (U)

26 Prentice Hall c2002Chapter 126 Fig 1.8 Adenosine Triphosphate (ATP) Nitrogenous base (adenine), sugar (ribose)

27 Prentice Hall c2002Chapter 127 Fig 1.9 Structure of a dinucleotide Residues are joined by a phosphodiester linkage

28 Prentice Hall c2002Chapter 128 Fig 1.10 Short segment of a DNA molecule Two polynucleotides associate to form a double helix ( 雙螺旋 ) Genetic information is carried by the sequence of base pairs

29 Prentice Hall c2002Chapter 129 D. Lipids and Membranes Lipids are rich in carbon and hydrogen, but contain little oxygen Lipids are not soluble in water Fatty acids are the simplest lipids: long chain hydrocarbons, a carboxylate group at one end Fatty acids are often components of glycerophospholipids

30 Prentice Hall c2002Chapter 130 Fig 1.11 Structures of (a) glycerol 3- phosphate, (b) a glycerophospholipid

31 Prentice Hall c2002Chapter 131 Fig 1.12 Model of a membrane lipid Hydrophilic (water-loving 親水性 ) head interacts with H 2 O Hydrophobic (water- fearing 忌 水性 ) tail

32 Prentice Hall c2002Chapter 132 Fig 1.13 Structure of a biological membrane A lipid bilayer with associated proteins

33 Prentice Hall c2002Chapter The Energetics of Life Photosynthetic organisms capture sunlight energy and use it to synthesize organic compounds Organic compounds provide energy for all organisms

34 Prentice Hall c2002Chapter 134 Energy Flow

35 Prentice Hall c2002Chapter 135 Metabolism and energy Metabolism - collection of reactions by which organic compounds are synthesized and degraded Bioenergetics - study of the changes in energy during metabolic reactions

36 Prentice Hall c2002Chapter 136 Free energy (  G) Free energy change (  G ) can predict the equilibrium concentrations and direction of a reaction where:  H = enthalpy change,  S = entropy change, T = temp When  G<0, the reaction will proceed spontaneously in the direction written When  G>0, the reaction requires energy to proceed  G =  H - T  S

37 Prentice Hall c2002Chapter Biochemistry and Evolution Prokaryotes ( 原核生物 )- do not have a membrane-bounded nucleus Eukaryotes ( 真核生物 ) - possess nucleus and other complex internal structures Prokaryotes and eukaryotes appear to have evolved from a common ancestor over three billion years ago

38 Prentice Hall c2002Chapter The Cell is the Basic Unit of Life Plasma membrane - surrounds aqueous environment of the cell Cytoplasm - all materials enclosed by the plasma membrane (except the nucleus) Cytosol - aqueous portion of the cytoplasm minus subcellular structures Bacteriophage or phage - viruses that infect prokaryotic cells

39 Prentice Hall c2002Chapter Prokaryotic Cells: Structural Features Prokaryotes, or bacteria are usually single- celled organisms Prokaryotes lack a nucleus (their DNA is packed in a nucleoid region of the cytoplasm) Escherichia coli (E. coli) - one of the best studied of all living organisms E. coli cells are ~0.5  m diameter, 1.5  m long

40 Prentice Hall c2002Chapter 140 Fig E. coli cell

41 Prentice Hall c2002Chapter Eukaryotic Cells: Structural Features Eukaryotes: plants, animals, fungi, protists Have a membrane-enclosed nucleus containing the chromosomes Are commonly 1000-fold greater in volume than prokaryotic cells Have an intracellular membrane network that subdivides the interior of the cell

42 Prentice Hall c2002Chapter 142 Fig 1.15 (a) Eukaryotic cell (animal)

43 Prentice Hall c2002Chapter 143 Fig 1.15(b) Eukaryotic cell (plant)

44 Prentice Hall c2002Chapter 144 A. The Nucleus Nuclear envelope and endoplasmic reticulum of a eukaryotic cell

45 Prentice Hall c2002Chapter 145 B. Endoplasmic Reticulum and Golgi Apparatus Endoplasmic reticulum ( 內質網 )- network of membrane sheets and tubules extending from the nucleus Golgi apparatus ( 高氏體 )- responsible for modification and sorting of some biomolecules.

46 Prentice Hall c2002Chapter 146 Golgi apparatus

47 Prentice Hall c2002Chapter 147 C. Mitochondria and Chloroplasts Mitochondria ( 粒線體 ) are the main sites of energy transduction in aerobic cells.

48 Prentice Hall c2002Chapter 148 Chloroplasts ( 葉綠體 )- sites of photosynthesis in plants, green algae

49 Prentice Hall c2002Chapter 149 D. Specialized Vesicles Lysosomes ( 溶素體 )- contain specialized digestive enzymes Peroxisomes - carry out oxidative reactions in animal and plant cells Vacuoles ( 液泡 )- fluid-filled vesicles, used as storage sites for water, ions and nutrients such as glucose

50 Prentice Hall c2002Chapter 150 E. The Cytoskeleton A protein scaffold is required for support, internal organization and movement of a cell Actin filaments form ropelike threads Microtubules are rigid fibers packed into bundles - Serve as an internal skeleton - Form the mitotic spindle during mitosis - Form movement structures (e.g. cilia, flagella)

51 Prentice Hall c2002Chapter 151 Fig 1.16 Fluorescently labeled: (a) Actin filaments (b) Microtubules

52 Prentice Hall c2002Chapter A Picture of Living Cell Fig 1.17 Cytosol of an E. coli cell. Magnification: Top 10 6 X Bottom 10 7 X (shows water, other small molecules)

53 Prentice Hall c2002Chapter Biochemistry is Multidisciplinary Various disciplines contribute to understanding biochemistry: Physics Genetics Chemistry Physiology Cell biology Evolution

54 Prentice Hall c2002Chapter 154 Textbook organization Horton is organized into four sections: 1. PART ONE: Introduction 2. PART TWO: Structure and Function of Biomolecules 3. PART THREE: Metabolism and Bioenergetics 4. PART FOUR: Biological Information Flow

55 Prentice Hall c2002Chapter 155

56 Prentice Hall c2002Chapter 156


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