Biokemi - Begreber + Opsummeringer PDF

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Biokemi – begreber + opsummeringer1 What Is Biochemistry?  Biochemistry aims to explain biological processes acellular levels. t the molecular and first experiments demonstrating the chemical basis oIn vitro alcoholic fermentation using yeast cell-free extracf life. ts was one of the  Biochemical...

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Biokemi 2019

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Casey Xiangyou Meng

Biokemi – begreber + opsummeringer 1.1 What Is Biochemistry? 

Biochemistry aims to explain biological processes at the molecular and cellular levels.

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In vitro alcoholic fermentation using yeast cell-free extracts was one of the first experiments demonstrating the chemical basis of life.

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Biochemical applications have led to the development of new pharmaceutical drugs, advances in medical diagnostics, the rise of the biotechnology industry, and improvements in agricultural and environmental sciences.

1.2 The Chemical Basis of Life: A Hierarchical Perspective 

The six elements that predominate in nature are H, O, C, N, P, and S, which together form the common chemical groups NH2, OH, SH, PO32−, COOH, and CH3.

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The four major classes of small biomolecules are amino acids, nucleotides, simple sugars, and fatty acids.

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The most abundant macromolecules in nature are polymers of nucleotides (DNA, RNA), amino acids (proteins), and the simple sugar glucose (cellulose, amylose, glycogen).

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Metabolic pathways consist of linked biochemical reactions in which the product of one reaction is the reactant for another.

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Living cells are highly ordered structures surrounded by a lipid membrane; they obtain energy from the Sun or from oxidation–reduction reactions to support metabolic processes.

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Organisms consist of many types of specialized cells that respond to changes in the environment by communicating with each other using a biochemical process called signal transduction, which involves the binding of molecules to receptor proteins, thus affecting the signaling activity of the receptors.

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Within ecosystems, organisms undergo complex interactions with one another, which can only be understood by studying key biochemical processes.

1.3 Storage and Processing of Genetic Information 

Deoxyribonucleotide base pairs in DNA consist of guanine hydrogen-bonded to cytosine (G-C and C-G) and adenine hydrogen-bonded to thymine (A-T and

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T-A). RNA lacks the nucleotide base thymine and instead contains the nucleotide base uracil, which forms hydrogen bonds with adenine (A-U and UA). 

The right-handed DNA double helix contains two antiparallel strands stabilized by the formation of hydrogen bonds between G-C and A-T base pairs and by base stacking in the interior of the DNA helix.

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DNA replication makes faithful copies of DNA using G-C and A-T base pairing. DNA transcription makes complementary RNA copies of protein-coding sequences called mRNA molecules, which are translated into proteins by tRNA and ribosomes.

1.4 Determinants of Biomolecular Structure and Function 

Biological structure and function are governed by evolutionary processes that affect function. This general principle holds true for macromolecules, cells, and organisms and can be seen in both the simplicity of the DNA double helix and the complexity of proteins.

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The evolutionary driving force for creating diverse protein structures is nucleotide changes in the coding sequences of genes, resulting from random mutation and natural selection.

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Orthologous genes are functionally related genes that have been evolutionarily conserved between species. Paralogous genes are functionally related genes present in the same species that have arisen from gene duplication.

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Proteins with high sequence conservation at the amino acid level usually have similar three-dimensional structures and biochemical functions. However, proteins with very different amino acid sequences can also have similar overall structures, which may or may not correspond to similar biochemical functions.

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Proteins in solution are in constant motion as a result of the formation and disruption of noncovalent interactions; therefore, molecular models of protein structures reveal very little about dynamic changes in protein structure that are likely to be involved in regulating protein function.

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fermentation (p. 5)

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enzyme (p. 5)

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biomolecule (p. 7)

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macromolecule (p. 7)

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metabolic pathway (p. 7)

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signal transduction (p. 7)

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ecosystem (p. 8)

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angstrom (A?) (p. 10)

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amino acid (p. 11)

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protein (p. 11)

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polypeptide (p. 11)

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nucleotide (p. 12)

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deoxyribonucleic acid (DNA) (p. 12)

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ribonucleic acid (RNA) (p. 12)

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simple sugar (p. 12)

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carbohydrate (p. 12

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fatty acid (p. 12)

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amphipathic (p. 12)

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phospholipid (p. 12)

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triacylglycerol (p. 13)

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polysaccharide (p. 13)

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phosphodiester bond (p. 13)

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peptide bond (p. 14)

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amylose (p. 14)

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chitin (p. 14)

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metabolite (p. 15)

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systems biology (p. 15)

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metabolic flux (p. 15)

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linear metabolic pathway (p. 17)

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forked pathway (p. 17)

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cyclic pathway (p. 17)

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prokaryote (p. 17)

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eukaryote (p. 17)

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capsule (p. 17)

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cytoplasm (p. 17)

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chromosome (p. 17)

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nucleoid (p. 17)

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flagella (p. 18)

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pilus (p. 18)

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plasmid (p. 18)

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genome (p. 18)

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chromatin (p. 18)

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nucleus (p. 18)

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nucleolus (p. 18)

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ribosome (p. 18)

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cytoskeleton (p. 19)

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mitochondria (p. 19)

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peroxisome (p. 19)

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lysosome (p. 19)

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chloroplast (p. 19)

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vacuole (p. 19)

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endoplasmic reticulum (p. 19)

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Golgi apparatus (p. 19)

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microtubule (p. 19)

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endosymbiotic theory (p. 19)

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ligand (p. 20)

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base pair (p. 24) base stacking (p. 25)

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central dogma (p. 25)

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DNA replication (p. 26)

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gene (p. 26)

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DNA transcription (p. 26)

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messenger RNA (mRNA) (p. 26)

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mRNA translation (p. 26)

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small nuclear RNA (snRNA) (p. 26)

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micro RNA (miRNA) (p. 26)

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ribosomal RNA (rRNA) (p. 26)

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transfer RNA (tRNA) (p. 26)

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reverse transcription (p. 27)

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transcriptome (p. 27)

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proteome (p. 27)

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template strand (p. 27)

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coding strand (p. 27)

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natural selection (p. 28)

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wild-type (p. 28)

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germ-line cell (p. 28)

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somatic cell (p. 28)

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bioinformatics (p. 29)

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orthologous gene (p. 31)

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gene duplication (p. 32)

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paralogous gene (p. 32)

2.1 Energy Conversion in Biological Systems 

Organisms use energy obtained from the environment to maintain homeostatic conditions that are far from equilibrium; reaching equilibrium with the environment is equivalent to death.

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Solar energy is converted to chemical energy through the processes of photosynthesis and carbon fixation; chemical energy is converted by cells into useful work (osmotic work, chemical work, and mechanical work).

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The primary energy conversion processes in cells are oxidation–reduction (redox) reactions that involve the transfer of electrons between molecules.

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All biological processes follow the laws of thermodynamics. The first law of thermodynamics states that energy cannot be created or destroyed, only converted from one form to another. The second law of thermodynamics states that entropy (S ), or the dispersion of energy, in the universe is always increasing.

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Enthalpy (H ) is defined as the heat content of a molecule and is reflected in the number and type of chemical bonds. Exothermic reactions give off heat, and the change in enthalpy (ΔH ) is negative; endothermic reactions absorb heat, and ΔH is positive.

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Changes in Gibbs free energy (ΔG ) describe the spontaneity of a reaction in terms of absolute temperature (T ) and changes in enthalpy (ΔH ) and entropy (ΔS ), using the relationship ΔG = ΔH − TΔS. Exergonic reactions (ΔG < 0) are favorable, whereas endergonic reactions (ΔG > 0) are unfavorable for the forward reaction.

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The equilibrium constant (Keq) can be used to determine the standard free energy (ΔG°) of a reaction using the equation ΔG° = −RT ln Keq, in which Keq is the ratio of the equilibrium concentrations of products over reactants, R is the gas constant, and T is the temperature in kelvins.

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The ΔG° value for a given reaction is a constant and is determined experimentally from the Keq using standard conditions (298 K, 1 atm pressure) and an initial 1 M concentration of reactants and products.

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The ΔG° value of coupled reactions is equal to the sum of the ΔG° values for each individual reaction. Cleavage of a phosphoanhydride bond in ATP is often coupled to an otherwise unfavorable reaction to drive the reaction forward (overall ΔG° < 0).

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The energy charge (EC) of the cell reflects the relative concentrations of ATP, ADP, and AMP. When the EC is high, anabolic pathways (biosynthesis) are favored because ATP is plentiful; when the EC is low, catabolic pathways (degradation) are favored. 2.2 Water Is Critical for Life Processes 

Water has three properties that make it essential for life on Earth: (1) the solid form of water is less dense than the liquid form, which is why ice floats; (2) water is liquid over a wide range of temperatures; and (3) water is an excellent solvent because of its hydrogen-bonding abilities and polar properties.

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The molecular structure of H2O gives rise to a separation of charge, with two partial negative charges on the oxygen atom (2δ−) and one partial positive charge on each of the hydrogens (δ+ and δ+).

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Extensive hydrogen bonding between H2O molecules gives water its unusually high viscosity, boiling point, and melting protons at high pH. eukaryotic cells that contain membrane-embedded proteins,

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The Henderson–Hasselbalch equation relates pH and which carry out energy-converting reactions leading to the pKa and can be used to determine the ratio of HA (proton production of ATP.

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bioenergetics (p. 40)

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homeostasis (p. 40)

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equilibrium (p. 40)

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solar energy (p. 41)

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photosynthetic autotroph (p. 41)

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aerobic respiration (p. 41)

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heterotroph (p. 41)

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photosynthesis (p. 41)

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carbon fixation (p. 42)

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biosphere (p. 42)

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redox reaction (p. 42)

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photooxidation (p. 42)

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photophosphorylation (p. 42)

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oxidative phosphorylation (p. 42)

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first law of thermodynamics (p. 44)

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second law of thermodynamics (p. 44)

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entropy (p. 44)

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enthalpy (H ) (p. 44)

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bomb calorimeter (p. 44)

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exothermic (p. 45)

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endothermic (p. 45)

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calorie (cal) (p. 45)

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joule (J) (p. 45)

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Gibbs free energy (G ) (p. 48)

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exergonic (p. 48)

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endergonic (p. 48)

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standard free energy change (ΔG°) (p. 48)

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biochemical standard conditions (p. 48)

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equilibrium constant (Keq) (p. 49)

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hydrogen bond (p. 57)

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proton hopping (p. 58)

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ionic interaction (p. 61)

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van der Waals interaction (p. 61)

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van der Waals radius (p. 62)

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hydrophobic (p. 63)

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hydrophilic (p. 63)

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colligative properties (p. 67)

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osmotic pressure (p. 68)

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osmosis (p. 68)

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erythrocyte (p. 69)

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hypotonic (p. 69)

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hypertonic (p. 69)

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isotonic (p. 69)

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contractile vacuole (p. 69)

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hydrogen ion (H+) (p. 71)

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hydroxyl ion (OH−) (p. 71)

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hydronium ion (H3O+) (p. 71)

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water ionization constant (Kw) (p. 71)

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pH (p. 72)

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weak acid (p. 73)

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conjugate base (p. 73)

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acid dissociation constant (Ka) (p. 73)

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pKa (p. 73)

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Henderson–Hasselbalch equation (p. 74)

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titration curve (p. 75)

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equivalent (p. 76)

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buffer (p. 76)

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polyprotic acid (p. 76)

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Le ChaPtelier's principle (p. 78)

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acidosis (p. 78)

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alkalosis (p. 78)

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biological membrane (p. 79)

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phospholipid bilayer (p. 79)

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micelle (p. 80)

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liposome (p. 80)

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flippase (p. 82)

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endomembrane system (p. 83)

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