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• Half Title
• Title Page
• Copyright Page
• Contents
• How Do We Understand Life?
• PART I: BIOLOGICAL MOLECULES
  • Chapter 1 From Genes to RNA and Proteins
    • A. INTERACTIONS BETWEEN MOLECULES
      • 1.1 The energy of interaction between two molecules is determined by noncovalent interactions
      • 1.2 Neutral atoms attract and repel each other at close distances through van der Waals interactions
      • 1.3 Ionic interactions between charged atoms can be very strong, but are attenuated by water
      • 1.4 Hydrogen bonds are very common in biological macromolecules
    • B. INTRODUCTION TO NUCLEIC ACIDS AND PROTEINS
      • 1.5 Nucleotides have pentose sugars attached to nitrogenous bases and phosphate groups
      • 1.6 The nucleotide bases in RNA and DNA are substituted pyrimidines or purines
      • 1.7 DNA and RNA are formed by sequential reactions that utilize nucleotide triphosphates
      • 1.8 DNA forms a double helix with antiparallel strands
      • 1.9 The double helix is stabilized by the stacking of base pairs
      • 1.10 Proteins are polymers of amino acids
      • 1.11 Proteins are formed by connecting amino acids by peptide bonds
      • 1.12 Amino acids are classified based on the properties of their sidechains
      • 1.13 Proteins appear irregular in shape
      • 1.14 Protein chains fold up to form hydrophobic cores
      • 1.15 α helices and β sheets are the architectural elements of protein structure
    • C. REPLICATION, TRANSCRIPTION, AND TRANSLATION
      • 1.16 DNA replication is a complex process involving many protein machines
      • 1.17 Transcription generates RNAs whose sequences are dictated by the sequence of nucleotides in gen
      • 1.18 Splicing of RNA in eukaryotic cells can generate a diversity of RNAs from a single gene
      • 1.19 The genetic code relates triplets of nucleotides in a gene sequence to each amino acid in a pro
      • 1.20 Transfer RNAs work with the ribosome to translate mRNA sequences into proteins
      • 1.21 The mechanism for the transfer of genetic information is highly conserved
      • 1.22 The discovery of retroviruses showed that information stored in RNA can be transferred to DNA
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 2 Nucleic Acid Structure
    • A. DOUBLE-HELICAL STRUCTURES OF RNA AND DNA
      • 2.1 The double helix is the principal secondary structure of DNA and RNA
      • 2.2 Hydrogen bonding between bases is important for the formation of double helices, but its effect
      • 2.3 The electronic polarization of the bases contributes to strong stacking interactions between bas
      • 2.4 Metal ions help shield electrostatic repulsions between the phosphate groups
      • 2.5 There are two common relative orientations of the base and the sugar
      • 2.6 The ribose ring has alternate conformations defined by the sugar pucker
      • 2.7 RNA cannot adopt the standard Watson-Crick double-helical structure because of constraints on it
      • 2.8 The standard Watson-Crick model of double-helical DNA is the B-form
      • 2.9 B-form DNA allows sequence-specific recognition of the major groove, which has a greater informa
      • 2.10 RNA adopts the A-form double-helical conformation
      • 2.11 The major groove of A-form double helices is less accessible to proteins than that of B-form DN
      • 2.12 Z-form DNA is a left-handed double-helical structure
      • 2.13 The DNA double helix is quite deformable
      • 2.14 DNA supercoiling can occur when the ends of double helices are constrained
      • 2.15 Writhe, linking number, and twist are mathematical parameters that describe the supercoiling of
      • 2.16 The writhe, twist, and linking number are related to each other in a simple way
      • 2.17 The DNA in cells is supercoiled
      • 2.18 Local conformational changes in the DNA also affect supercoiling
    • B. THE FUNCTIONAL VERSATILITY OF RNA
      • 2.19 Wobble base pairs are often seen in RNA
      • 2.20 Nonstandard base-pairing is common in RNA
      • 2.21 Some RNA molecules contain modified nucleotides
      • 2.22 A tetraloop is a common secondary structural motif that caps RNA hairpins
      • 2.23 Interactions with metal ions help RNAs to fold
      • 2.24 RNA tertiary structure involves interactions between secondary structural elements
      • 2.25 Helices in RNA often interact through coaxial base stacking or the formation of pseudoknots
      • 2.26 Various interactions between nucleotides stabilize RNA tertiary structure
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 3 Glycans and Lipids
    • A. GLYCANS
      • 3.1 Simple sugars are comprised primarily of hydroxylated carbons
      • 3.2 Many cyclic sugar molecules can exist in alternative anomeric forms
      • 3.3 Sugar rings often have many low energy conformations
      • 3.4 Many sugars are structural isomers of identical composition, but with different stereochemistry
      • 3.5 Some sugars have other chemical functionalities in addition to alcohol groups
      • 3.6 Glycans form polymeric structures that can have branched linkages
      • 3.7 Differences in anomeric linkages lead to dramatic differences in polymeric forms of glucose
      • 3.8 Acetylation or other chemical modification leads to diversity in sugar polymer properties
      • 3.9 Glycans may be attached to proteins or lipids
      • 3.10 The decoration of proteins with glycans is not templated
      • 3.11 Glycan modifications alter the properties of proteins
      • 3.12 Protein-glycan interactions are important in cellular recognition
    • B. LIPIDS AND MEMBRANES
      • 3.13 The most abundant lipids are glycerophospholipids
      • 3.14 Other classes of lipids have different molecular frameworks
      • 3.15 Lipids form organized structures spontaneously
      • 3.16 The shapes of lipid molecules affect the structures they form
      • 3.17 Detergents are amphiphilic molecules that tend to form micelles rather than bilayers
      • 3.18 Lipids in bilayers move freely in two dimensions
      • 3.19 Lipid composition affects the physical properties of membranes
      • 3.20 Proteins can be associated with membranes by attachment to lipid anchors
      • 3.21 Lipid molecules can be sequestered and transported by proteins
      • 3.22 Different kinds of cells and organelles have different membrane compositions
      • 3.23 Cell walls are reinforced membranes
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 4 Protein Structure
    • A. GENERAL PRINCIPLES
      • 4.1 Protein structures display a hierarchical organization
      • 4.2 Protein domains are the fundamental units of tertiary structure
      • 4.3 Protein folding is driven by the formation of a hydrophobic core
      • 4.4 The formation of α helices and β sheets satisfies the hydrogen-bonding requirements of the pro
    • B. BACKBONE CONFORMATION
      • 4.5 Protein folding involves conformational changes in the peptide backbone
      • 4.6 Amino acids are chiral and only the L form stereoisomer is found in genetically encoded proteins
      • 4.7 The peptide bond has partial double bond character, so rotations about it are hindered
      • 4.8 Peptide groups can be in cis or trans conformations
      • 4.9 The backbone torsion angles φ (phi) and ψ (psi) determine the conformation of the protein chai
      • 4.10 The Ramachandran diagram defines the restrictions on backbone conformation
      • 4.11 α helices and β strands are formed when consecutive residues adopt similar values of φ and
      • 4.12 Loop segments have residues with very different values of φ and ψ
      • 4.13 α helices and β strands are often amphipathic
      • 4.14 Some amino acids are preferred over others in α helices
    • C. STRUCTURAL MOTIFS AND DOMAINS IN SOLUBLE PROTEINS
      • 4.15 Secondary structure elements are connected to form simple motifs
      • 4.16 Amphipathic α helices can form dimeric structures called coiled coils
      • 4.17 Hydrophobic sidechains in coiled coils are repeated in a heptad pattern
      • 4.18 α helices that are integrated into complex protein structures do not usually form coiled coils
      • 4.19 The sidechains of α helices form ridges and grooves
      • 4.20 α helices pack against each other with a limited set of crossing angles
      • 4.21 Structures with alternating α helices and β strands are very common
      • 4.22 α/β barrels occur in many different enzymes
      • 4.23 α/β open-sheet structures contain α helices on both sides of the β sheet
      • 4.24 Proteins with antiparallel β sheets often form structures called β barrels
      • 4.25 Up-and-down β barrels have a simple topology
      • 4.26 Up-and-down β sheets can form repetitive structures
      • 4.27 Greek key motifs occur frequently in antiparallel β structures
      • 4.28 Certain structural motifs can be repeated almost endlessly to form elongated structures
      • 4.29 Catalytic sites are usually located within core elements of protein folds
      • 4.30 Binding sites are often located at the interfaces between domains
    • D. STRUCTURAL PRINCIPLES OF MEMBRANE PROTEINS
      • 4.31 Lipid bilayers form barriers that are nearly impermeable to polar molecules
      • 4.32 Membrane proteins have distinct regions that interact with the lipid bilayer
      • 4.33 The hydrophobicity of the lipid bilayer requires the formation of regular secondary structure w
      • 4.34 The more polar sidechains are rarely found within membrane-spanning α helices, except when the
      • 4.35 Transmembrane α helices can be predicted from amino acid sequences
      • 4.36 Hydrophobicity scales are used to identify transmembrane helices
      • 4.37 Integral membrane proteins are stabilized by van der Waals contacts and hydrogen bonds
      • 4.38 Porins contain β barrels that form transmembrane channels
      • 4.39 Pumps and transporters use energy to move molecules across the membrane
      • 4.40 Bacteriorhodopsin uses light energy to pump protons across the membrane
      • 4.41 A hydrogen-bonded chain of water molecules can serve as a proton conducting “wire”
      • 4.42 Conformational changes in retinal impose directionality to proton flow in bacteriorhodopsin
      • 4.43 Active transporters cycle between conformations that are open to the interior or the exterior o
      • 4.44 ATP binding and hydrolysis provides the driving force for the transport of sugars into the cell
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 5 Evolutionary Variation in Proteins
    • A. THE THERMODYNAMIC HYPOTHESIS
      • 5.1 The structure of a protein is determined by its sequence
      • 5.2 The thermodynamic hypothesis was first established for an enzyme known as ribonuclease-A, which
      • 5.3 By counting the number of possible rearrangements of disulfide bonds, we can confirm that ribonu
    • B. SEQUENCE COMPARISONS AND THE BLOSUM MATRIX
      • 5.4 Protein structure is conserved during evolution while amino acid sequences vary
      • 5.5 The globin fold is preserved in proteins that share very little sequence similarity
      • 5.6 Similarities in protein sequences can be quantified by considering the frequencies with which am
      • 5.7 The BLOSUM matrix is a commonly used set of amino acid substitution scores
      • 5.8 The first step in deriving substitution scores is to determine the frequencies of amino acid sub
      • 5.9 The substitution score is defined in terms of the logarithm of the substitution likelihood
      • 5.10 The BLOSUM substitution scores reflect the chemical properties of the amino acids
      • 5.11 Substitution scores are used to align sequences and to detect similarities between proteins
    • C. STRUCTURAL VARIATION IN PROTEINS
      • 5.12 Small but significant differences in protein structures arise from differences in sequences
      • 5.13 Proteins retain a common structural core as their sequences diverge
      • 5.14 Structural overlap within the common core decreases as the sequences of proteins diverge
      • 5.15 Sequence comparisons alone are insufficient to establish structural similarity between distantl
      • 5.16 The amino acids have preferences for different environments in folded proteins
      • 5.17 Fold-recognition algorithms evaluate the probability that the sequence of a protein is compatib
      • 5.18 The 3D-1D profile method maps three-dimensional structural information onto a one-dimensional s
      • 5.19 The database of known protein structures is used to generate a scoring matrix that gives the li
      • 5.20 The 3D-1D profile method matches sequences with structures
    • D. THE EVOLUTION OF MODULAR DOMAINS
      • 5.21 Domains are the fundamental unit of protein evolution
      • 5.22 Domains can be organized into families with similar folds
      • 5.23 The number of distinct fold families is likely to be limited
      • 5.24 Protein domains are remarkably tolerant of changes in amino acid sequence, even in the hydropho
      • 5.25 Structural plasticity in protein domains increases the tolerance to mutation
      • 5.26 The Rossmann fold is found in many nucleotide binding proteins
      • 5.27 Thioredoxin reductase and glutathione reductase are enzymes that diverged from a common ancesto
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
• PART II: ENERGY AND ENTROPY
  • Chapter 6 Energy and Intermolecular Forces
    • A. THERMODYNAMICS OF HEAT TRANSFER
      • 6.1 In order to keep track of changes in energy, we define the region of interest as the “system
      • 6.2 Energy released by chemical reactions is converted to heat and work
      • 6.3 The first law of thermodynamics states that energy is conserved
      • 6.4 For a process occurring under constant pressure conditions, the heat transferred is equal to the
      • 6.5 Changes in energy do not always indicate the direction of spontaneous change
      • 6.6 The isothermal expansion of an ideal gas occurs spontaneously even though the energy of the gas
    • B. HEAT CAPACITIES AND THE BOLTZMANN DISTRIBUTION
      • 6.7 The heat capacity of an ideal monatomic gas is constant
      • 6.8 The heat capacity of a macromolecular solution increases and then decreases with temperature
      • 6.9 The potential energy of a molecular system is the energy stored in molecules and their interacti
      • 6.10 The Boltzmann distribution describes the population of molecules in different energy levels
      • 6.11 The energy required to break interatomic interactions in folded macromolecules gives rise to th
    • C. ENERGETICS OF INTERMOLECULAR INTERACTIONS
      • 6.12 Simplified energy functions are used to calculate molecular potential energies
      • 6.13 Empirical potential energy functions enable rapid calculation of molecular energies
      • 6.14 The energies of covalent bonds are approximated by functions such as the Morse potential
      • 6.15 Other terms in the energy function describe torsion angles and the deformations in the angles b
      • 6.16 The van der Waals energy term describes weak attractions and strong repulsions between atoms
      • 6.17 Atoms in proteins and nucleic acids are partially charged
      • 6.18 Electrostatic interactions are governed by Coulomb’s law
      • 6.19 Hydrogen bonds are an important class of electrostatic interactions
      • 6.20 Empirical energy functions are used in computer programs to calculate molecular energies
      • 6.21 Interactions with water weaken the effective strengths of hydrogen bonds in proteins
      • 6.22 The presence of hydrogen-bonding groups in a protein is important for solubility and specificit
      • 6.23 The water surrounding protein molecules strongly influences electrostatic interactions
      • 6.24 The shapes of proteins change the electrostatic fields generated by charges within the protein
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 7 Entropy
    • A. COUNTING STATISTICS AND MULTIPLICITY
      • 7.1 Different sequences of outcomes in a series of coin tosses have equal probabilities
      • 7.2 When considering aggregate outcomes, the most likely result is the one that has maximum multipli
      • 7.3 The multiplicity of an outcome of coin tosses can be calculated using a simple formula involving
      • 7.4 The concept of multiplicity is broadly applicable in biology because a series of coin flips is a
      • 7.5 The binding of ligands to a receptor can be monitored by fluorescence microscopy
      • 7.6 Pascal’s triangle describes the multiplicity of outcomes for a series of binary events
      • 7.7 The binomial distribution governs the probability of events with binary outcomes
      • 7.8 When the number of events is large, Stirling’s approximation simplifies the calculation of the
      • 7.9 The relative probability of two outcomes is given by the ratios of their multiplicities
      • 7.10 As the number of events increases, the less likely outcomes become increasingly rare
      • 7.11 For coin tosses, outcomes with equal numbers of heads and tails have maximal multiplicity
      • 7.12 When the number of events is very large, the probability distribution is well approximated by a
      • 7.13 The Gaussian distribution is centered at the mean value and has a width that is proportional to
      • 7.14 Application of the Gaussian distribution enables statistical analysis of a series of binary out
    • B. ENTROPY
      • 7.15 The logarithm of the multiplicity (ln W) is related to the entropy
      • 7.16 The multiplicity of a molecular system is the number of equivalent configurations of the molecu
      • 7.17 The multiplicity of a system increases as the volume increases
      • 7.18 For a large number of atoms, the state with maximal multiplicity is the state that is observed
      • 7.19 The Boltzmann constant, kB , is a proportionality constant linking entropy to the logarithm of
      • 7.20 The change in entropy is related to the heat transferred during a process
      • 7.21 The work done in a near-equilibrium process is greater than for a nonequilibrium process
      • 7.22 The work done in a near-equilibrium process is related to the change in entropy
      • 7.23 The statistical and thermodynamic definitions of entropy are equivalent
      • 7.24 The second law of thermodynamics states that spontaneous change occurs in the direction of incr
      • 7.25 Diffusion across a semipermeable membrane can lead to unequal numbers of molecules on the two s
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 8 Linking Energy and Entropy: The Boltzmann Distribution
    • A. ENERGY DISTRIBUTIONS AND ENTROPY
      • 8.1 The thermodynamic definition of the entropy provides a link to experimental observations
      • 8.2 The concept of temperature provides a connection between the statistical and thermodynamic defin
      • 8.3 Energy distributions describe the populations of molecules with different energies
      • 8.4 The multiplicity of an energy distribution is the number of equivalent configurations of molecul
      • 8.5 The multiplicity of a system with different energy levels can be calculated by counting the numb
    • B. THE BOLTZMANN DISTRIBUTION
      • 8.6 For large numbers of molecules, a probabilistic expression for the entropy is more convenient
      • 8.7 The multiplicity of a system changes when energy is transferred between systems
      • 8.8 Systems in thermal contact exchange heat until the combined entropy of the two systems is maxima
      • 8.9 Many energy distributions are consistent with the total energy of a system, but some have higher
      • 8.10 The energy distribution at equilibrium must have an exponential form
      • 8.11 The partition function indicates the accessibility of the higher energy levels of the system
      • 8.12 For large numbers of molecules, non-Boltzmann distributions of the energy are highly unlikely
    • C. ENTROPY AND TEMPERATURE
      • 8.13 The rate of change of entropy with respect to energy is related to the temperature
      • 8.14 The statistical and thermodynamic definitions of the entropy are equivalent
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
• PART III: FREE ENERGY
  • Chapter 9 Free Energy
    • A. FREE ENERGY
      • 9.1 The combined entropy of the system and the surroundings increases for a spontaneous process
      • 9.2 The change in entropy of the surroundings is related to the change in energy and volume of the s
      • 9.3 The Gibbs free energy (G) of the system always decreases in a spontaneous process occurring at c
      • 9.4 The Helmholtz free energy (A) determines the direction of spontaneous change when the volume is
    • B. STANDARD FREE-ENERGY CHANGES
      • 9.5 Standard free-energy changes are defined with reference to defined standard states
      • 9.6 The zero point of the free-energy scale is set by the free energy of the elements in their most
      • 9.7 Thermodynamic cycles allow the determination of the free energies of formation of complex molecu
      • 9.8 The free energy of formation of glucose is obtained by considering three combustion reactions
      • 9.9 Enthalpies and entropies of formation can be combined to give the free energy of formation
      • 9.10 Calorimetric measurements yield the standard enthalpy changes associated with combustion reacti
      • 9.11 The entropy of formation of a compound is derived from heat capacity measurements
    • C. FREE ENERGY AND WORK
      • 9.12 Expansion work is not the only kind of work that can be done by a system
      • 9.13 Chemical work involves changes in the numbers of molecules
      • 9.14 The decrease in the Gibbs free energy for a process is the maximum amount of non-expansion work
      • 9.15 The coupling of ATP hydrolysis to work underlies many processes in biology
      • 9.16 The synthesis of ATP is coupled to the movement of ions across the membrane, down a concentrati
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 10 Chemical Potential and the Drive to Equilibrium
    • A. CHEMICAL POTENTIAL
      • 10.1 The chemical potential of a molecular species is the molar free energy of that species
      • 10.2 Molecules move spontaneously from regions of high chemical potential to regions of low chemical
      • 10.3 Biochemical reactions are assumed to occur in ideal and dilute solutions, which simplifies the
      • 10.4 The chemical potential is proportional to the logarithm of the concentration
      • 10.5 Chemical potentials at arbitrary concentrations are calculated with reference to standard conce
    • B. EQUILIBRIUM CONSTANTS
      • 10.6 The chemical potentials of the reactants and products are balanced at equilibrium
      • 10.7 The concentrations of reactants and products at equilibrium define the equilibrium constant (K)
      • 10.8 Equilibrium constants can be used to calculate the extent of reaction at equilibrium
      • 10.9 The free-energy change for the reaction (ΔG), not the standard free-energy change (ΔGº), det
      • 10.10 The ratio of the reaction quotient (Q) to the equilibrium constant (K) determines the thermody
      • 10.11 ATP concentrations are maintained at high levels in cells, thereby increasing the driving forc
    • C. ACID-BASE EQUILIBRIA
      • 10.12 The Henderson–Hasselbalch equation relates the pH of a solution of a weak acid to the c
      • 10.13 The proton concentration ([H+]) in pure water at room temperature corresponds to a pH value of
      • 10.14 The temperature dependence of the equilibrium constant allows us to determine the values of Δ
      • 10.15 Weak acids, such as acetic acid, dissociate very little in water
      • 10.16 Solutions of weak acids and their conjugate bases act as buffers
      • 10.17 The charges on biological macromolecules are affected by the pH
      • 10.18 The charge on an amino acid sidechain can be altered by interactions in the folded protein
    • D. FREE-ENERGY CHANGES IN PROTEIN FOLDING
      • 10.19 The protein folding reaction is simplified by ignoring intermediate conformations
      • 10.20 Protein folding results from a balance between energy and entropy
      • 10.21 The entropy of the unfolded protein chain is proportional to the logarithm of the number of co
      • 10.22 The number of conformations of the unfolded chain can be estimated by counting the number of l
      • 10.23 The free-energy change opposes protein folding if the entropy of water molecules is not consid
      • 10.24 Protein folding is driven by an increase in water entropy
      • 10.25 Calorimetric measurements allow the experimental determination of the free energy of protein f
      • 10.26 The heat capacity of a protein solution depends on the relative population of folded and unfol
      • 10.27 The area under the peak in the melting curve is the enthalpy change for unfolding at the melti
      • 10.28 The heat capacities of the folded and unfolded protein allow the determination of ΔHº and Δ
      • 10.29 Folded proteins become unstable at very low temperature because of changes in ΔHº and ΔSº
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 11 Voltages and Free Energy
    • A. OXIDATION-REDUCTION REACTIONS IN BIOLOGY
      • 11.1 Reactions involving the transfer of electrons are referred to as oxidation-reduction reactions
      • 11.2 Biologically important redox-active metals are bound to proteins
      • 11.3 Nicotinamide adenine dinucleotide (NAD+) is an important mediator of redox reactions in biology
      • 11.4 Flavins and quinones can undergo oxidation or reduction in two steps of one electron each
      • 11.5 The oxidation of glucose is coupled to the generation of NADH and FADH 2
      • 11.6 Mitochondria are cellular compartments in which NADH and FADH 2 are used to generate ATP
      • 11.7 Absorption of light creates molecules with high reducing power in photosynthesis
    • B. REDUCTION POTENTIALS AND FREE ENERGY
      • 11.8 Electrochemical cells can be constructed by linking two redox couples
      • 11.9 The voltage generated by an electrochemical cell with the reactants at standard conditions is k
      • 11.10 The electric potential difference (voltage) between two points is the work done in moving a un
      • 11.11 Standard reduction potentials are related to the standard free-energy change of the redox reac
      • 11.12 Electrode potentials are measured relative to a standard hydrogen electrode
      • 11.13 Tabulated values of standard electrode potentials allow ready calculation of the standard pote
      • 11.14 The Nernst equation describes how the potential changes with the concentrations of the redox r
      • 11.15 The standard state for reduction potentials in biochemistry is pH 7
    • C. ION PUMPS AND CHANNELS IN NEURONS
      • 11.16 Neuronal cells use electrical signals to transmit information
      • 11.17 An electrical potential difference across the membrane is essential for the functioning of all
      • 11.18 The sodium–potassium pump hydrolyzes ATP to move Na+ ions out of the cell with the coupled m
      • 11.19 Sodium and potassium channels allow ions to move quickly across the membrane
      • 11.20 Sodium and potassium channels contain a conserved tetrameric pore domain
      • 11.21 A large vestibule within the channel reduces the distance over which ions have to move without
      • 11.22 Carbonyl groups in the selectivity filter provide specificity for K+ ions by substituting for
      • 11.23 Rapid transit of K+ ions through the channel is facilitated by hopping between isoenergetic bi
    • D. THE TRANSMISSION OF ACTION POTENTIALS IN NEURONS
      • 11.24 The asymmetric distribution of ions across the cell membrane generates an equilibrium membrane
      • 11.25 The Nernst equation relates the equilibrium membrane potential to the concentrations of ions i
      • 11.26 Cell membranes act as electrical capacitors
      • 11.27 The depolarization of the membrane is a key step in initiating a neuronal signal
      • 11.28 Membrane potentials are altered by the movement of relatively few ions, enabling rapid axonal
      • 11.29 The propagation of voltage changes can be understood by treating the axon as an electrical cir
      • 11.30 The propagation of changes in membrane potential in the axon are described by the cable equati
      • 11.31 The resting membrane potential is determined by a combination of the basal conductances of pot
      • 11.32 The propagation of a voltage spike without triggering voltage-gated ion channels is known as p
      • 11.33 If membrane currents are neglected, then the cable equation is analogous to a diffusion equati
      • 11.34 Leakage through open ion channels limits the spread of a voltage perturbation
      • 11.35 The time taken to develop a membrane potential is determined by the conductance of the membran
      • 11.36 Myelination of mammalian neurons facilitates the transmission of action potentials
      • 11.37 Action potentials are regenerated periodically as they travel down the axon
      • 11.38 A positively charged sensor in voltage-gated ion channels moves across the membrane upon depol
      • 11.39 The structures of voltage-gated K+ channels show that the voltage sensors form paddle-like str
      • 11.40 The crystal structure of a voltage-gated K+ channel suggests how the voltage sensor opens and
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
• PART IV: MOLECULAR INTERACTIONS
  • Chapter 12 Molecular Recognition: The Thermodynamics of Binding
    • A. THERMODYNAMICS OF MOLECULAR INTERACTIONS
      • 12.1 The affinity of a protein for a ligand is characterized by the dissociation constant, KD
      • 12.2 The value of KD corresponds to the concentration of free ligand at which the protein is half sa
      • 12.3 The dissociation constant is a dimensionless number, but is commonly referred to in concentrati
      • 12.4 Dissociation constants are determined experimentally using binding assays
      • 12.5 Binding isotherms plotted with logarithmic axes are commonly used to determine the dissociation
      • 12.6 When the ligand is in great excess over the protein, the free ligand concentration, [L], is ess
      • 12.7 Scatchard analysis makes it possible to estimate the value of KD when the concentration of the
      • 12.8 Scatchard analysis can be applied to unpurified proteins
      • 12.9 Saturable binding is a hallmark of specific binding interactions
      • 12.10 The value of the dissociation constant, KD , defines the ligand concentration range over which
      • 12.11 The dissociation constant for a physiological ligand is usually close to the natural concentra
    • B. DRUG BINDING BY PROTEINS
      • 12.12 Most drugs are developed by optimizing the inhibition of protein targets
      • 12.13 Signaling molecules are protein targets in cancer drug development
      • 12.14 Most small molecule drugs work by displacing a natural ligand for a protein
      • 12.15 The binding of drugs to their target proteins often results in conformational changes in the p
      • 12.16 Induced-fit binding occurs through selection by the ligand of one among many preexisting confo
      • 12.17 Conformational changes in the protein underlie the specificity of a cancer drug known as imati
      • 12.18 Conformational changes in the target protein can weaken the affinity of an inhibitor
      • 12.19 The strength of noncovalent interactions usually correlates with hydrophobic interactions
      • 12.20 Cholesterol-lowering drugs known as statins take advantage of hydrophobic interactions to bloc
      • 12.21 The apparent affinity of a competitive inhibitor for a protein is reduced by the presence of t
      • 12.22 Entropy lost by drug molecules upon binding is regained through the hydrophobic effect and the
      • 12.23 Isothermal titration calorimetry allows us to determine the enthalpic and entropic components
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 13 specificity of Macromolecular Recognition
    • A. AFFINITY AND SPECIFICITY
      • 13.1 Both affinity and specificity are important in intermolecular interactions
      • 13.2 Proteins often have to choose between several closely related targets
      • 13.3 specificity is defined in terms of ratios of dissociation constants
      • 13.4 The specificity of binding depends on the concentration of ligand
      • 13.5 Fractional occupancy and specificity are important for activities resulting from binding
      • 13.6 Most macromolecular interactions are a compromise between affinity and specificity
      • 13.7 Fibroblast growth factors vary considerably in their affinities for receptors
      • 13.8 The recognition of DNA by transcription factors involves discrimination between a very large nu
      • 13.9 Lowering the affinity of lac repressor for the operator switches on transcription
    • B. PROTEIN-PROTEIN INTERACTIONS
      • 13.10 Protein-protein complexes involve interfaces between two folded domains or between a domain an
      • 13.11 SH2 domains are specific for peptides containing phosphotyrosine
      • 13.12 Individual SH2 domains cannot discriminate sharply between different phosphotyrosine-containin
      • 13.13 Combinations of peptide recognition domains have higher specificity than individual domains
      • 13.14 Protein-protein interfaces usually have a small hydrophobic core
      • 13.15 A typical protein–protein interface buries about 700 to 800 Å2 of surface area on each prot
      • 13.16 Water molecules form hydrogen-bonded networks at protein-protein interfaces
      • 13.17 The interaction between growth hormone and its receptor is a model for understanding protein-p
      • 13.18 The major growth hormone-receptor interface contains many types of interactions
      • 13.19 The interface between growth hormone and its receptor contains hot spots of binding affinity,
      • 13.20 Residues that do not contribute to binding affinity may be important for specificity
      • 13.21 The desolvation of polar groups at interfaces makes a large contribution to the free energy of
    • C. RECOGNITION OF NUCLEIC ACIDS BY PROTEINS
      • 13.22 Complementarity in both electrostatics and shape is an important aspect of the recognition of
      • 13.23 Proteins distinguish between DNA and RNA double helices by recognizing differences in the geom
      • 13.24 Proteins recognize DNA sequences by both direct contacts and induced conformational changes in
      • 13.25 Hydrogen bonding is a key determinant of specificity at DNA-protein interfaces
      • 13.26 Water molecules can form specific hydrogen-bond bridges between protein and DNA
      • 13.27 Arginine interactions with the minor groove can provide sequence specificity through shape rec
      • 13.28 DNA structural changes induced by binding vary widely
      • 13.29 Proteins that bind DNA as dimers do so with higher affinity than if they were monomers
      • 13.30 Linked DNA binding modules can increase binding affinity and specificity
      • 13.31 Cooperative binding of proteins also enhances specificity
      • 13.32 Proteins that recognize single-stranded RNA interact extensively with the bases
      • 13.33 Stacking interactions between amino acid sidechains and nucleotide bases are an important aspe
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 14 Allostery
    • A. ULTRASENSITIVITY OF MOLECULAR RESPONSES
      • 14.1 Molecular outputs that depend on independent binding events switch from on to off over a 100-fo
      • 14.2 The response of many biological systems is ultrasensitive, with the switch from off to on occur
      • 14.3 Cooperativity and allostery are features of many ultrasensitive systems
      • 14.4 Bacterial movement towards attractants and away from repellants is governed by signaling protei
      • 14.5 The flagellar motor switches to clockwise rotation when the concentration of CheY increases ove
      • 14.6 The response of the flagellar motor to concentrations of CheY is ultrasensitive
      • 14.7 The MAP kinase pathway involves the sequential activation of a set of three protein kinases
      • 14.8 Phosphorylation controls the activity of protein kinases by allosteric modulation of the struct
      • 14.9 The sequential phosphorylation of the MAP kinases leads to an ultrasensitive signaling switch
    • B. ALLOSTERY IN HEMOGLOBIN
      • 14.10 Allosteric proteins exhibit positive or negative cooperativity
      • 14.11 The heme group in hemoglobin binds oxygen reversibly
      • 14.12 Hemoglobin increases the solubility of oxygen in blood and makes its transport to the tissues
      • 14.13 Hemoglobin undergoes conformational changes as it binds to and releases oxygen
      • 14.14 The sigmoid binding isotherm for an allosteric protein arises from switching between low-and h
      • 14.15 The degree of cooperativity between binding sites in an allosteric protein is characterized by
      • 14.16 The tertiary structure of each hemoglobin subunit changes upon oxygen binding
      • 14.17 Changes in the tertiary structure of each subunit are coupled to a change in the quaternary st
      • 14.18 The hemoglobin tetramer is always in equilibrium between R and T states, and oxygen binding bi
      • 14.19 Bisphosphoglycerate (BPG) stabilizes the T-state quaternary structure of hemoglobin
      • 14.20 The low pH in venous blood stabilizes the T-state quaternary structure of hemoglobin
      • 14.21 Hemoglobins across evolution have acquired distinct allosteric mechanisms for achieving ultras
      • 14.22 Allosteric mechanisms are likely to evolve by the accretion of random mutations in colocalized
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
• PART V: KINETICS AND CATALYSIS
  • Chapter 15 The Rates of Molecular Processes
    • A. GENERAL KINETIC PRINCIPLES
      • 15.1 The rate of reaction describes how fast concentrations change with time
      • 15.2 The rates of intermolecular reactions depend on the concentrations of the reactants
      • 15.3 Rate laws define the relationship between the reaction rates and concentrations
      • 15.4 The dependence of the rate law on the concentrations of reactants defines the order of the reac
      • 15.5 The integration of rate equations predicts the time dependence of concentrations
      • 15.6 Reactants disappear linearly with time for a zero-order reaction
      • 15.7 The concentration of reactant decreases exponentially with time for a first-order reaction
      • 15.8 The reactants decay more slowly in second-order reactions than in first-order reactions, but th
      • 15.9 The half-life for a reaction provides a measure of the speed of the reaction
      • 15.10 For reactions with intermediate steps, the slowest step determines the overall rate
    • B. REVERSIBLE REACTIONS, STEADY STATES, AND EQUILIBRIUM
      • 15.11 The forward and reverse rates must both be considered for a reversible reaction
      • 15.12 The on and off rates of ligand binding can be measured by monitoring the approach to equilibri
      • 15.13 Steady-state reactions are important in metabolism
      • 15.14 For reactions with alternative products, the relative values of rate constants determine the d
      • 15.15 Measuring fluorescence provides an easy way to monitor kinetics
      • 15.16 Fluorescence measurements can be carried out under steady-state conditions
      • 15.17 Fluorescence quenchers provide a way to detect whether a fluorophore on a protein is accessibl
      • 15.18 The combination of forward and reverse rate constants is related to the equilibrium constant
      • 15.19 Relaxation methods provide a way to obtain rate constants for reversible reactions
      • 15.20 Temperature jump experiments can be used to determine the association and dissociation rate co
      • 15.21 The rate constants for a cyclic set of reactions are coupled
    • C. FACTORS THAT AFFECT THE RATE CONSTANT
      • 15.22 Catalysts accelerate the rates of chemical reactions without being consumed in the process
      • 15.23 Rate laws for reactions usually must be determined experimentally
      • 15.24 The hydrolysis of sucrose provides an example of how a reaction mechanism is analyzed
      • 15.25 The fastest possible reaction rate is determined by the diffusion-limited rate of collision
      • 15.26 Most reactions occur more slowly than the diffusion-limited rate
      • 15.27 The activation energy is the minimum energy required to convert reactants to products during a
      • 15.28 The reaction rate depends exponentially on the activation energy
      • 15.29 Transition state theory links kinetics to thermodynamic concepts
      • 15.30 Catalysts can work by decreasing the activation energy, by increasing the preexponential facto
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 16 Principles of Enzyme Catalysis
    • A. MICHAELIS-MENTEN KINETICS
      • 16.1 Enzyme-catalyzed reactions can be described as a binding step followed by a catalytic step
      • 16.2 The Michaelis-Menten equation describes the kinetics of the simplest enzyme-catalyzed reactions
      • 16.3 The value of the Michaelis constant, KM , is related to how much enzyme has substrate bound
      • 16.4 Enzymes are characterized by their turnover numbers and their catalytic efficiencies
      • 16.5 A “perfect” enzyme is one that catalyzes the chemical step of the reaction as fast as the s
      • 16.6 In some cases the release of the product from the enzyme affects the rate of the reaction
      • 16.7 The specificity of enzymes arises from both the rate of the chemical step and the value of KM
      • 16.8 Graphical analysis of enzyme kinetic data facilitates the estimation of kinetic parameters
    • B. INHIBITORS AND MORE COMPLEX REACTION SCHEMES
      • 16.9 Competitive inhibitors block the active site of the enzyme in a reversible way
      • 16.10 A competitive inhibitor does not affect the maximum velocity of the reaction, Vmax , but it in
      • 16.11 Reversible noncompetitive inhibitors decrease the maximum velocity, Vmax , without affecting t
      • 16.12 Substrate-dependent noncompetitive inhibitors only bind to the enzyme when the substrate is pr
      • 16.13 Some noncompetitive inhibitors are linked irreversibly to the enzyme
      • 16.14 In a ping-pong mechanism the enzyme becomes modified temporarily during the reaction
      • 16.15 For a reaction with multiple substrates, the order of binding can be random or sequential
      • 16.16 Enzymes with multiple binding sites can display allosteric (cooperative) behavior
      • 16.17 Product inhibition is a mechanism for regulating metabolite levels in cells
    • C. PROTEIN ENZYMES
      • 16.18 Enzymes can accelerate reactions by large amounts
      • 16.19 Transition state stabilization is a major contributor to rate enhancement by enzymes
      • 16.20 Enzymes can act as acids or bases to enhance reaction rates
      • 16.21 Proximity effects are important for many reactions
      • 16.22 The serine proteases are a large family of enzymes that contain a conserved Ser-His-Asp cataly
      • 16.23 Sidechain recognition positions the catalytic triad next to the peptide bond that is cleaved
      • 16.24 The specificities of serine proteases vary considerably, but the catalytic triad is conserved
      • 16.25 Peptide cleavage in serine proteases proceeds via a ping-pong mechanism
      • 16.26 Angiotensin-converting enzyme is a zinc-containing protease that is an important drug target
      • 16.27 Creatine kinase catalyzes phosphate transfer by stabilizing a planar phosphate intermediate
      • 16.28 Some enzymes work by populating disfavored conformations
      • 16.29 Antibodies that bind transition state analogs can have catalytic activity
    • D. RNA ENZYMES
      • 16.30 Small self-cleaving ribozymes and ribonuclease proteins catalyze the same reaction
      • 16.31 Self-cleaving ribozymes use nucleotide bases for catalysis, even though these do not have pK a
      • 16.32 Hairpin ribozymes optimize hydrogen bonds to the transition state rather than to the initial o
      • 16.33 There are at least two possible mechanisms for bond cleavage by the hairpin ribozyme
      • 16.34 The splicing reaction catalyzed by group I introns occurs in two steps
      • 16.35 Metal ions facilitate catalysis by group I introns
      • 16.36 Substitution of oxygen by sulfur in RNA helps identify metals that participate in catalysis
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 17 Diffusion and Transport
    • A. RANDOM WALKS
      • 17.1 Microscopic motion is well described by trajectories called random walks
      • 17.2 The analysis of bacterial movement is simplified by considering one-dimensional random walks wi
      • 17.3 The probability distribution for the number of moves in one direction is given by a Gaussian fu
      • 17.4 The probability of moving a certain distance in a one-dimensional random walk is also given by
      • 17.5 The width of the distribution of displacements increases with the square root of time for rando
      • 17.6 Random walks in two dimensions can be analyzed by combining two orthogonal one-dimensional rand
      • 17.7 A two-dimensional random walk is described by two one-dimensional walks, but the effective step
      • 17.8 The assumption of uniform step lengths along each axis means that the random walk occurs on a g
      • 17.9 A three-dimensional random walk is described by three orthogonal one-dimensional walks, and the
      • 17.10 The movement of bacteria in the presence of attractants or repellents is described by biased r
    • B. MACROSCOPIC DESCRIPTION OF DIFFUSION
      • 17.11 Fick’s first law states that the flux of molecules is proportional to the concentration grad
      • 17.12 Fick’s second law describes the rate of change in concentration with time
      • 17.13 Integration of the diffusion equation allows us to calculate the change in concentration with
      • 17.14 The diffusion constant is related to the mean square displacement of molecules
      • 17.15 Diffusion constants depend on molecular properties such as size and shape
      • 17.16 The diffusion constant is inversely related to the friction factor
      • 17.17 Viscosity is a measure of the resistance to flow
      • 17.18 Liquids with strong interactions between molecules have high viscosity
      • 17.19 The Stokes-Einstein equation allows us to calculate the diffusion coefficients of molecules
      • 17.20 The diffusion constants for nonspherical molecules are only slightly different from those calc
      • 17.21 Diffusion-limited reaction rate constants can be calculated from the diffusion constants of mo
      • 17.22 One-dimensional searches on DNA increase the rate at which transcription factors find their ta
      • 17.23 Restricting diffusion to two-dimensional membranes can slow down the rate of encounter but sti
      • 17.24 Concentration gradients determine the outcomes of many biological processes
      • 17.25 Cells use motor proteins to transport cargo over long distances and to specificlocations
      • 17.26 Vesicles are transported by kinesin motors that move along microtubule tracks
      • 17.27 ATP hydrolysis provides a powerful driving force for kinesin movement
    • C. EXPERIMENTAL MEASUREMENT OF DIFFUSION
      • 17.28 Diffusion constants can be measured experimentally in several ways
      • 17.29 Movement of molecules in solution can be driven by centrifugal forces
      • 17.30 Equilibrium centrifugation can be used to determine molecular weights
      • 17.31 Electrophoresis provides an alternative method for driving molecular motion
      • 17.32 The electrophoretic mobility of nucleic acids decreases with size
      • 17.33 Gel electrophoresis analysis of proteins is useful for size determination
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
• PART VI: ASSEMBLY AND ACTIVITIY
  • Chapter 18 Folding
    • A. HOW PROTEINS FOLD
      • 18.1 Protein folding is governed by thermodynamics
      • 18.2 The reversibility of protein folding can also be demonstrated by manipulating single molecules
      • 18.3 Unfolded states of proteins correspond to wide distributions of different conformations
      • 18.4 Protein folding cannot be explained by an exhaustive search of conformational space
      • 18.5 Many small proteins populate only fully unfolded and fully folded states
      • 18.6 The order in which secondary and tertiary interactions form can vary in different proteins
      • 18.7 Folding rates are faster when residues close in sequence end up close together in the folded st
      • 18.8 The folding of some proteins involves the formation of transiently stable intermediates
      • 18.9 Folding pathways can have multiple intermediates
      • 18.10 Changes in the sequence of a protein at certain positions can affect folding rates substantial
      • 18.11 The nature of the transition state can be identified by mapping the effect of mutations on the
      • 18.12 The process of protein folding can be described as funneled movement on a multidimensional fre
    • B. CHAPERONES FOR PROTEIN FOLDING
      • 18.13 Many proteins tend to aggregate rather than fold
      • 18.14 The high concentration of macromolecules inside the cell makes the problem of aggregation part
      • 18.15 Proteins inside the cell usually fold into a functional form rapidly
      • 18.16 Some proteins form irreversible aggregates that are toxic to cells
      • 18.17 Molecular chaperones are proteins that prevent protein aggregation
      • 18.18 Hsp70 recognizes short peptides with sequences that are characteristic of the interior segment
      • 18.19 Hsp70 binds and releases protein chains in a cycle that is coupled to ATP binding and hydrolys
      • 18.20 The GroEL chaperonin forms a hollow double-ring structure within which protein molecules can f
      • 18.21 GroEL works like a two-stroke engine, binding and releasing proteins
      • 18.22 GroEL-GroES can accelerate the folding of proteins through passive and active mechanisms
    • C. RNA FOLDING
      • 18.23 The electrostatic field around RNA leads to the diffuse localization of metal ions
      • 18.24 RNA folding can be driven by increasing the concentration of metal ions
      • 18.25 RNAs form stable secondary structural elements, which increases their tendency to misfold
      • 18.26 RNA folding is hierarchical with multiple stable intermediates
      • 18.27 Collapse is an early event in the folding of RNA
      • 18.28 RNA folding landscapes are highly rugged
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
  • Chapter 19 Fidelity in DNA and Protein Synthesis
    • A. MEASURING THE STABILITY OF DNA DUPLEXES
      • 19.1 The difference in free energy between matched and mismatched base pairs can be determined by me
      • 19.2 DNA melting can be studied by UV absorption spectroscopy
      • 19.3 The changes in enthalpy and entropy associated with DNA melting can be determined from the conc
      • 19.4 DNA duplexes containing a mismatched base pair at one end are only marginally less stable than
      • 19.5 The entropy of each DNA chain is reduced upon forming a duplex
      • 19.6 The stability of DNA depends on the pattern on base stacks in the duplex
      • 19.7 Base stacking is more important than hydrogen bonding in determining the stability of DNA helic
    • B. FIDELITY IN DNA REPLICATION
      • 19.8 The process of DNA replication is very accurate
      • 19.9 The energy of DNA base-pairing cannot explain the accuracy of DNA replication
      • 19.10 The overall process of DNA synthesis can be described as a series of kinetic steps
      • 19.11 Primer elongation by polymerase is quite rapid
      • 19.12 The rate-limiting step in the DNA synthesis reaction is a conformational change in DNA polymer
      • 19.13 Determination of the values of V max and K M for the incorporation of correct and incorrect ba
      • 19.14 DNA polymerase has a nuclease activity that can remove bases from the 3′ end of a DNA strand
      • 19.15 The structure of DNA polymerase has fingers, palm, and thumb subdomains
      • 19.16 DNA polymerase binds DNA using the “palm” and nearly encircles it
      • 19.17 The active site of polymerase contains two metals ions that catalyze nucleotide addition
      • 19.18 A conformational change in DNA polymerase upon binding dNTP contributes to replication fidelit
      • 19.19 DNA polymerases recognize DNA using the backbone and minor groove
      • 19.20 DNA polymerases sense the shapes of correctly paired bases
      • 19.21 The shape of a nucleotide is more important for its being incorporated into DNA than its abili
      • 19.22 The growing DNA strand can shuttle between the polymerase and exonuclease active sites
    • C. HOW RIBOSOMES ACHIEVE FIDELITY
      • 19.23 The ribosome has two subunits, each of which is a large complex of RNA and proteins
      • 19.24 Protein synthesis on the ribosome occurs as a repeated series of steps of tRNA and protein bin
      • 19.25 Selection of the correct A-site tRNA by base-pairing alone cannot explain ribosome fidelity
      • 19.26 A ribosome-induced bend in the EF-Tu•tRNA complex plays an important role in generating spec
      • 19.27 The ribosome undergoes conformational changes during the process of tRNA selection
      • 19.28 Tight interactions in the decoding center can only occur for correct codon–anticodon pairs
      • 19.29 Coupling of the decoding center and the GTPase active site of EF-Tu involves multiple conforma
      • 19.30 The active site of EF-Tu needs only a small rearrangement to be activated
      • 19.31 Release of EF-Tu allows the aminoacyl group of the A-site tRNA to move to the peptidyl transfe
      • 19.32 The ribosome catalyzes peptidyl transfer
    • Summary
    • Key Concepts
    • Problems
    • Further Reading
• Glossary
• Index

UM RAFBÆKUR Á HEIMKAUP.IS

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