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Transcript
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 DNA RNA Protein 1.2 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 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) Fig 1.2 (a) General formulas Fig 1.2(b) General Formulas Fig 1.2 (c) General Formulas 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 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 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 Fig 1.4 Egg white lysozyme (a) Free enzyme (b) Enzyme, bound substrate in active site cleft 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 Fig 1.5 Representations of the structure of ribose (a) Glucose, (b) Cellulose Glycosidic bonds connecting glucose residues are in red 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) Fig 1.7 Deoxyribose • Deoxyribose lacks a hydroxyl group at C-2. It is the sugar found in DNA. Nitrogenous bases • Major Purines: Adenine (A) Guanine (G) • Major Pyrimidines Cytosine (C) Thymine (T) Uracil (U) Fig 1.8 Adenosine Triphosphate (ATP) • Nitrogenous base (adenine), sugar (ribose) Structure of a dinucleotide • Residues are joined by a phosphodiester linkage Short segment of a DNA molecule • Two polynucleotides associate to form a double helix • Genetic information is carried by the sequence of base pairs 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 Structures of (a) glycerol 3-phosphate, (b) a glycerophospholipid Model of a membrane lipid • Hydrophilic (water-loving) head interacts with H2O • Hydrophobic (waterfearing) tail Fig 1.13 Structure of a biological membrane • A lipid bilayer with associated proteins 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 Prokaryotic Cells: Structural Features • Prokaryotes, or bacteria are usually singlecelled 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 ~0.5µm diameter, 1.5µm long E. coli cell 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 (a) Eukaryotic cell (animal) Fig 1.15(b) Eukaryotic cell (plant) A. The Nucleus Nuclear envelope and endoplasmic reticulum of a eukaryotic cell 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. Golgi apparatus C. Mitochondria and Chloroplasts • Mitochondria are the main sites of energy transduction in aerobic cells. Chloroplasts - sites of photosynthesis in plants, green algae 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 Fig 1.16 Fluorescently labeled: (a) Actin filaments (b) Microtubules Ionic and Polar Substances Dissolve in Water • Hydrophilic (water-loving) substances (polar and ionic (electrolytes)) readily dissolve in H2O • Polar water molecules align themselves around ions or other polar molecules • A molecule or ion surrounded by solvent molecules is solvated • When the solvent is water the molecules or ions are hydrated Solubilities of molecules in water • Solubility in water depends upon the ratio of polar to nonpolar groups in a molecule • The larger the portion of nonpolar groups the less soluble the molecule is in water • The larger the portion of polar groups (e.g. hydroxyl groups (-OH)) the more soluble the molecule is in water Fig. 2.7 Structure of glucose • Glucose has five hydroxyl groups and a ring oxygen which can hydrogen bond • Glucose is very soluble in water Nonpolar Substances Are Insoluble in Water • Hydrophobic (water-fearing) molecules are nonpolar • Hydrophobic effect - the exclusion of nonpolar substances by water (critical for protein folding and self-assembly of biological membranes) • Amphipathic molecules have hydrophobic chains and ionic or polar ends. Detergents (surfactants) are examples. Sodium dodecyl sulfate (SDS) • A synthetic detergent • A 12-carbon tail • Polar sulfate group Detergents in water • Monolayers can form on the surface • At higher concentrations detergents can form micelles Noncovalent Interactions in Biomolecules Weak noncovalent interactions are important in: • Stabilization of proteins and nucleic acids • Recognition of one biopolymer by another • Binding of reactants to enzymes Noncovalent forces There are four major types of noncovalent forces: (1) Charge-charge interactions (2) Hydrogen bonds (3) Van der Waals forces (4) Hydrophobic interactions A. Charge-Charge Interactions (Ion Pairing) • Electrostatic interactions between two charged particles • Can be the strongest type of noncovalent forces • Can extend over greater distances than other forces • Charge repulsion occurs between similarly charged groups Types of attractive charged interactions • Salt bridges - attractions between oppositelycharged functional groups in proteins • Ion pairing - a salt bridge buried in the hydrophobic interior of a protein is stronger than one on the surface B. Hydrogen Bonds • Among the strongest of noncovalent interactions • H atom bonded to N, O, S can hydrogen bond to another electronegative atom (~0.2 nm distance) • Total distance between the two electronegative atoms is ~0.27 to 0.30 nm • In aqueous solution, water can H-bond to exposed functional groups on biological molecules Fig. 2.10 (a) Hydrogen bonding between A-H and B (b) Some biologically important H-bonds Hydrogen bonding between complementary bases in DNA C. Van der Waals Forces • Weak short range forces between: (a) Permanent dipoles of two uncharged molecules (b) Permanent dipole and an induced dipole in a neighboring molecule • Although individually weak, many van der Waals interactions occur in biological macromolecules and participate in stabilizing molecular structures D. Hydrophobic Interactions • Association of a relatively nonpolar molecule or group with other nonpolar molecules • Depends upon the increased entropy (+∆S) which occurs when water molecules surrounding a nonpolar molecule are freed to interact with each other in solution • The cumulative effects of many hydrophobic interactions can have a significant effect on the stability of a macromolecule Noncovalent interactions in biomolecules • Charge-charge interactions • Hydrogen bonds • Van der Waals interactions • Hydrophobic interactions Water Is Nucleophilic • Nucleophiles - electron-rich atoms or groups • Electrophiles - electron-deficient atoms or groups • Water is a relatively weak nucleophile • Due to its high cellular concentration, hydrolysis reactions in water are thermodynamically favored Hydrolysis of a peptide Condensation reactions can be favorable in cells • ATP chemical energy can be used to drive reactions • Glutamine synthetase catalyzes a condensation reaction 2.7 Ionization of Water • Pure water consists of a low concentration of hydronium ions (H3O+) and an equal concentration of hydroxide ions (OH-) • Acids are proton donors (e.g. H3O+) and bases are proton acceptors (e.g. OH-) 2.8 The pH Scale • pH is defined as the negative logarithm of the concentration of H+ Table 2.3 pH values for some fluids • Lower values are acidic fluids • Higher values are basic fluids Acid Dissociation Constants of Weak Acids • Strong acids and bases dissociate completely in water HCl + H2O Cl- + H3O+ • Cl- is the conjugate base of HCl • H3O+ is the conjugate acid of H2O Acetic acid is a weak acid • Weak acids and bases do not dissociate completely in H2O The Henderson-Hasselbalch Equation • Defines the pH of a solution in terms of: (1) The pKa of the weak acid (2) Concentrations of the weak acid (HA) and conjugate base (A-) Table 2.4 Buffered Solutions Resist Changes in pH • Buffer capacity is the ability of a solution to resist changes in pH • Most effective buffering occurs where: solution pH = buffer pKa • At this point: [weak acid] = [conjugate base] • Effective buffering range is usually at pH values equal to the pKa ± 1 pH unit Regulation of pH in the blood of animals • Blood plasma of mammals has a constant pH which is regulated by a buffer system of: carbon dioxide /carbonic acid /bicarbonate • Buffer capacity depends upon equilibria between: (1) Gaseous CO2 (air spaces of the lungs) (2) Aqueous CO2 (dissolved in the blood) (3) Carbonic acid (4) Bicarbonate Percentages of carbonic acid and its conjugate bases as a function of pH Fig. 2.21 Regulation of the pH of blood in mammals 3.1 General Structure of Amino Acids • Twenty common α-amino acids have carboxyl and amino groups bonded to the α-carbon atom • A hydrogen atom and a side chain (R) are also attached to the α-carbon atom Zwitterionic form of amino acids • Under normal cellular conditions amino acids are zwitterions (dipolar ions): Amino group = Carboxyl group = -NH3+ -COO- A. Aliphatic R Groups • Glycine (Gly, G) - the α-carbon is not chiral since there are two H’s attached (R=H) • Four amino acids have saturated side chains: Alanine (Ala, A) Valine (Val, V) Leucine (Leu, L) Isoleucine (Ile, I) • Proline (Pro, P) 3-carbon chain connects α-C and N Four aliphatic amino acid structures Proline has a nitrogen in the aliphatic ring system • Proline (Pro, P) - has a three carbon side chain bonded to the α-amino nitrogen • The heterocyclic pyrrolidine ring restricts the geometry of polypeptides B. Aromatic R Groups • Side chains have aromatic groups Phenylalanine (Phe, F) - benzene ring Tyrosine (Tyr, Y) - phenol ring Tryptophan (Trp, W) - bicyclic indole group Aromatic amino acid structures C. Sulfur-Containing R Groups • Methionine (Met, M) - (-CH2CH2SCH3) • Cysteine (Cys, C) - (-CH2SH) • Two cysteine side chains can be cross-linked by forming a disulfide bridge (-CH2-S-S-CH2-) • Disulfide bridges may stabilize the threedimensional structures of proteins Methionine and cysteine Proteins: Three Dimensional Structure and Function • Conformation - three dimensional shape • Native conformation - each protein folds into a single stable shape (physiological conditions) • Biological function of a protein depends completely on its native conformation • A protein may be a single polypeptide chain or composed of several chains D. Side Chains with Alcohol Groups • Serine (Ser, S) and Threonine (Thr, T) have uncharged polar side chains E. Basic R Groups • Histidine (His, R) - imidazole • Lysine (Lys, K) - alkylamino group • Arginine (Arg, R) - guanidino group • Side chains are nitrogenous bases which are substantially positively charged at pH 7 Structures of histidine, lysine and arginine F. Acidic R Groups and Amide Derivatives • Aspartate (Asp, D) and Glutamate (Glu, E) are dicarboxylic acids, and are negatively charged at pH 7 • Asparagine (Asn, N) and Glutamine (Gln, Q) are uncharged but highly polar Structures of aspartate, glutamate, asparagine and glutamine Compounds derived from common amino acids Column Chromatography (a) Separation of a protein mixture (b) Detection of eluting protein peaks Electrophoresis • Polyacrylamide gel electrophoresis (PAGE) Separates molecules on a polyacrylamide gel matrix when an electric field is applied • SDS-PAGE. Sodium dodecyl sulfate (SDS) coats proteins with negative charges. Coated polypeptide chains then separate by molecular mass (method to determine molecular weight) (a) SDS-PAGE Electrophoresis (b) Protein banding pattern after run Types of proteins • Proteomics - study of large sets of proteins, such as the entire complement of proteins produced by a cell • E. coli has about 4000 different polypeptides (average size 300 amino acids, Mr 33,000) • Fruit fly (Drosophila melanogaster) about 16,000, humans, other mammals about 40,000 different polypeptides E. coli proteins on 2D gel electrophoresis Globular proteins • Usually water soluble, compact, roughly spherical • Hydrophobic interior, hydrophilic surface • Globular proteins include enzymes,carrier and regulatory proteins Fibrous proteins • Provide mechanical support • Often assembled into large cables or threads • α-Keratins: major components of hair and nails • Collagen: major component of tendons, skin, bones and teeth Antibodies Bind Specific Antigens • Vertebrate immune systems synthesize protein antibodies (immunoglobulins) to eliminate bacteria, viruses, other foreign substances • Antibodies specifically recognize and bind antigens • Antibodies are synthesized by lymphocytes (white blood cells) Fig 4.52 (a) Human antibody structure Fig. 4.52 (b) • Heavy chains (blue) and light chains (red) • Disulfide bonds (yellow) • Variable domains colored darker Structural and Functional Diversity of Lipids • Fatty acids - R-COOH (R=hydrocarbon chain) are components of triacylglycerols, glycerophospholipids, sphingolipids • Phospholipids - contain phosphate moieties • Glycosphingolipids - contain both sphingosine and carbohydrate groups • Isoprenoids - (related to the 5 carbon isoprene) include steroids, lipid vitamins and terpenes Structure and nomenclature of fatty acids Glycerophospholipids • The most abundant lipids in membranes • Possess a glycerol backbone • A phosphate is esterified to both glycerol and another compound bearing an -OH group • Phosphatidates are glycerophospholipids with two fatty acid groups esterified to C-1 and C-2 of glycerol 3-phosphate (a) Glycerol 3-P and (b) phosphatidate Structures of glycerophospholipids (next slide) (a) Phosphatidyl ethanolamine (b) Phosphatidyl serine (c) Phosphatidylcholine • Functional groups from esterified alcohols are shown in blue • General names refer to a family of compounds Fig 9.9 Phospholipases hydrolyze phospholipids Structure of an ethanolamine plasmalogen • Plasmalogens - C-1 hydrocarbon substituent attached by a vinyl ether linkage (not ester linkage) Structure of a typical eukaryotic plasma membrane Characteristics of membrane transport