Principles of BIOCHEMISTRY Third Edition

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Principles of BIOCHEMISTRYThird Edition

• HORTON MORAN OCHS RAWN SCRIMGEOUR

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Chapter 1 Introduction to Biochemistry

• Adenovirus Viruses consist of a nucleic acid
  molecule surrounded by a protein coat

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1.1 Biochemistry Is a Modern Science

• Urea 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

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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
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1.2 The Chemical Elements of Life

• Only six nonmetallic elements oxygen, carbon,
  hydrogen, nitrogen, phosphorous, and sulfur
  account for gt97 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

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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)

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Functional groups in biochemistry

• Functional groups - 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 (CH3CH2)n-)

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Fig 1.2 (a) General formulas
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Fig 1.2(b) General Formulas
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Fig 1.2 (c) General Formulas
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1.3 Many Important Biomolecules are Polymers

• Biopolymers - macromolecules created by joining
  many smaller organic molecules (monomers)
• Condensation reactions join monomers (H2O is
  removed in the process)
• Residue - each monomer in a chain

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Molecular mass

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

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A. Proteins

• Proteins are composed of 20 common amino acids
• Each amino acid contains
• (1) Carboxylate group (-COO-)
• (2) Amino group (-NH2)
• (3) Side chain (R) unique to each amino acid

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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
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Polypeptides

• Polypeptides - amino acids joined end to end
• Conformation - 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

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Fig 1.4 Egg white lysozyme
(a) Free enzyme (b) Enzyme, bound substrate in
active site cleft
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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

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Fig 1.5 Representations of the structure of
ribose
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Fig 1.6 (a) Glucose, (b) Cellulose
Glycosidic bonds connecting glucose residues are
in red
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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)

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Fig 1.7 Deoxyribose

• Deoxyribose lacks a hydroxyl group at C-2. It is
  the sugar found in DNA.

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Nitrogenous bases

• Major Purines
• Adenine (A)
• Guanine (G)
• Major Pyrimidines
• Cytosine (C)
• Thymine (T)
• Uracil (U)

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Fig 1.8 Adenosine Triphosphate (ATP)

• Nitrogenous base (adenine), sugar (ribose)

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Fig 1.9 Structure of a dinucleotide

• Residues are joined by a phosphodiester linkage

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Fig 1.10 Short segment of a DNA molecule

• Two polynucleotides associate to form a double
  helix
• Genetic information is carried by the sequence of
  base pairs

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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

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Fig 1.11 Structures of (a) glycerol 3-phosphate,
(b) a glycerophospholipid
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Fig 1.12 Model of a membrane lipid

• Hydrophilic (water-loving) head interacts with
  H2O
• Hydrophobic (water-fearing) tail

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Fig 1.13 Structure of a biological membrane

• A lipid bilayer with associated proteins

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1.4 The Energetics of Life

• Photosynthetic organisms capture sunlight energy
  and use it to synthesize organic compounds
• Organic compounds provide energy for all
  organisms

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Energy Flow
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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

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Free energy (DG)

• Free energy change (DG) can predict the
  equilibrium concentrations and direction of a
  reaction whereDH enthalpy change, DS
  entropy change, T temp
• When DGlt0, the reaction will proceed
  spontaneously in the direction written
• When DGgt0, the reaction requires energy to
  proceed

DG DH - TDS
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1.5 Biochemistry and Evolution

• Prokaryotes - do not have a membrane-bounded
  nucleus
• Eukaryotes - possess nucleus and other complex
  internal structures
• Prokaryotes and eukaryotes appear to have evolved
  from a common ancestor over three billion years
  ago

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1.6 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

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1.7 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 0.5mm diameter, 1.5mm long

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Fig. 1.14 E. coli cell
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1.8 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

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Fig 1.15 (a) Eukaryotic cell (animal)
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Fig 1.15(b) Eukaryotic cell (plant)
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A. The Nucleus
Nuclear envelope and endoplasmic reticulum of a
eukaryotic cell
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B. Endoplasmic Reticulum and Golgi Apparatus

• Endoplasmic reticulum - network of membrane
  sheets and tubules extending from the nucleus
• Golgi apparatus - responsible for modification
  and sorting of some biomolecules.

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Golgi apparatus
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C. Mitochondria and Chloroplasts

• Mitochondria are the main sites of energy
  transduction in aerobic cells.

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Chloroplasts - sites of photosynthesis in plants,
green algae
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D. Specialized Vesicles

• Lysosomes - contain specialized digestive enzymes
• Peroxisomes - carry out oxidative reactions in
  animal and plant cells
• Vacuoles - fluid-filled vesicles, used as storage
  sites for water, ions and nutrients such as
  glucose

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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)

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Fig 1.16
Fluorescently labeled(a) Actin filaments (b)
Microtubules
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1.9 A Picture of Living Cell
Fig 1.17 Cytosol of an E. coli cell.
Magnification Top 106X Bottom 107X (shows
water, other small molecules)
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1.10 Biochemistry is Multidisciplinary

• Various disciplines contribute to understanding
  biochemistry
• Physics Genetics
• Chemistry Physiology
• Cell biology Evolution

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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