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Chemical Components of the Cells CB3 pp. 39-48, 50-59, 62-63, 78, 119-127, 130, 140-142 CB4 pp. 39-49, 50-59, 62-65, 121-130, 141-144 Figures reproduced from: 1. Alberts et al. Essential Cell Biology. Garland Science. 2. Despopoulos A., Silbernagl S. Color Atlas of Physiology. 5th edition. Thieme, 2003. Lecture Outline - atoms and molecules - chemical bonds - molecules in cells: 1) carbohydrates 2) nucleic acids 3) lipids 4) proteins - protein structure and function 2 Atoms and Molecules - atom: nucleus + electrons - nucleus contains proton(s) and neutron(s) 3 Atoms and Molecules (cont.) - molecule: 2 atoms or more - molecules are formed by sharing or transfer of electrons - this produces covalent and ionic bonds, respectively 4 Covalent Bonds - single: 2 electrons shared, allows rotation - double: 4 electrons shared, does not allow rotation, rigid - triple: 6 electrons shared, does not allow rotation, rigid and very strong H2, hydrogen 5 (C) ethyne (acetylene) N2, nitrogen Sharing of Electrons is Often Unequal - this produces polar covalent bonds - polar covalent bonds make water molecules polar - each water molecule is a dipole Electron sharing is equal only between atoms of the same kind carbons in organic compounds H2, hydrogen O2, oxygen 6 Water Molecule Polarity - 7 allows water molecules to form hydrogen bonds with each other (non-covalent bonds between H and O from different water molecules) note: hydrogen bonds are formed not only between water molecules, but also between water and other molecules, and between H and O within other molecules (e.g. in proteins, see further) Water Molecule Polarity (cont.) - consequences: 1) water is liquid at room temperature 2) water creates a solvent shield around charged and polar molecules (ions, membrane lipid polar heads, proteins). This causes dissociation of molecules with ionic bonds into ions (NaCl ↔ Na+ + Cl-) 3) water "repulses" non-polar parts of other molecules, forcing them together (helps hydrophobic interactions) 8 Van der Waal's Attraction - attraction of any atoms to each other - caused by vibrations of the nucleus within the electron cloud, which creates temporary dipoles - plays a role in hydrophobic interactions 9 Strength of Chemical Bonds 10 Molecules in Cells - four major families of small molecules - present as individual molecules, but also as parts of macromolecules - besides beeing building blocks, can serve as energy source and as signaling compounds 11 Molecules in Cells (cont.) - macromolecules are often polymers made of monomers - polymerization = adding monomers to an end of a polymer (condensation reaction); the reverse is hydrolysis 12 Sugars (Carbohydrates) - simple sugars, monosaccharides (e.g. glucose): energy source and building blocks - pentose: 5 carbons; hexose: 6 carbons glucose hexose 13 hexose too ! Isomers - have the same atom composition, but different spatial position of atoms - these small differences are recognized by proteins (e.g. by enzymes and transporters) D-glucose L-glucose optical isomers (mirror-image pairs) 14 Polysaccharides - - when combined by condensation reactions, monosaccharides give disaccharides (e.g. sucrose), oligosaccharides (3-50 sugar monomers) and polysaccharides (hundreds or thousands of sugar monomers) polysaccharides are formed to store the monosaccharides; when needed, polysaccharides are broken down and monosaccharides are used as energy source a polysaccharide 15 Carbohydrates as Parts of Other Molecules - monosaccharides in phosphatidylinositol and glycolipids - oligo- and polysaccharides in glycocalyx (parts of glycosylated proteins and glycolipids) - monosaccharides in nucleic acids (see further) phosphatidylinositol 16 Nucleic Acids - DNA, RNA - polymers made of nucleotide monomers: di-, oligo-, polynucleotides - DNA (deoxyribonucleic acids) are made of deoxyribonucleotides - RNA (ribonucleic acids) are made of ribonucleotides 17 Sugars in Nucleic Acids - pentoses (5 carbons, each is given a number with a prime mark) β α 18 DNA, RNA - formed by condensation reaction, phosphate group is linking the nucleotides - polynucleotides have chemical polarity (the ends are functionally different); not to be mixed up with electrical polarity! - the next nucleotide is attached to the 3' end of the growing polynucleotide H2O 19 Bases in Nucleic Acids - 5 types falling in 2 classes (used in RNA) 20 (used in DNA) Other Nucleotide-Containing Molecules - ATP: 1) building block for RNA 2) energy storage 3) source of phosphate groups for protein phosphorylation - ADP: product of degradation of ATP, re-usable ATP (adenosine-5’-triphosphate) 21 ADP (adenosine-5’-diphosphate) Other Nucleotide-Containing Molecules (cont.) - cAMP: signaling molecule cAMP (cyclic adenosine-3’,5’-monophosphate) 22 Lipids - fatty acids, triacylglycerols, phospholipids, glycolipids, cholesterol, steroids etc - often long molecules, but not always polymers - water-insoluble, soluble in organic solvents (for example, in the cell membranes!) - fatty acids: carboxyl group and hydrocarbon tail 23 Fatty Acids - saturated (all bonds in the tail are single) and unsaturated (some bonds in the tail are double; rigid, but give ”bended” structures) - unsaturated and polyunsaturated fatty acids are necessary in cell membranes, increase the membrane fluidity 24 Fatty Acids (cont.) - stored as triacylglycerols (esters with glycerol) 25 Triacylglycerols - animal fat (e.g. butter) mostly contain triacylglycerols with saturated fatty acids: pack tightly, solid at room temperature - plant oils contain much more triacylglycerols with unsaturated fatty acids: do not pack tightly, liquid at room temperature 26 Phospholipids, Glycolipids - components of the membrane lipid bilayer - some are precursors of signaling molecules (IP3, DAG) - some serve as docking sites at the membrane for certain proteins (DAG, PIP3) 27 phospholipid phosphatidylinositol (3,4,5)-trisphosphate (PIP3) Steroids - cholesterol: component of the membrane lipid bilayer, and precursor of other steroids: 1) sex hormones and other steroid hormones 2) bile acids (important in digestive tract) - vitamins D cholesterol 28 testosterone (male sex hormone) vitamin D2 Other Lipids - polyisoprenoids (polymers of isoprene) - precursors of vitamins A, E, K, coenzyme Q10 etc (all are lipid-soluble) retinol (vitamin A) 29 vitamin K Lipids as Parts of Other Molecules - can be bound to proteins to “anchor” them to membranes - examples of attaching of the lipids to the proteins: myristoylation, palmitoylation 30 Lipids as Parts of Other Molecules - can be bound to proteins to “anchor” them to membranes - examples of attaching of the lipids to the proteins: myristoylation, palmitoylation 31 Incorrect illustration! Heads of some phospholipids are used for docking of proteins (e.g. PIP3). Proteins - polymers made of amino acid monomers - short proteins can be called di-, tri-, oligo-, polypeptides, or just peptides - common features of amino acids: α-carbon, amino group, carboxyl group, side chain - 20 amino acids in proteins (differ by the side chains, see further); several more exist in cells as intermediates in metabolic reactions 32 L- and D- Amino Acid Isomers - optical isomers: L- and D-, all but glycine (R = H) - proteins consist exclusively of L-amino acids, but D-amino acids are present in the body (e.g. D-serine is a neurotransmitter) 33 Peptide Bonds - covalent bonds that are formed between amino acids within proteins (all bonds within individual amino acids are also covalent) - form rigid planar structures - peptide chains have chemical polarity (N-terminus and C-terminus) peptide bond amino terminus of the peptide (N-terminus, NH2-terminus) - the next amino acid is attached at the C-terminus of the growing peptide 34 carboxyl terminus of the peptide (C-terminus, COOH-terminus) Proteins Have Flexible Structures - despite the rigidity of the peptide bonds, since other bonds allow rotation amino terminus of the peptide (N-terminus, NH2-terminus) carboxyl terminus of the peptide (C-terminus, COOH-terminus) these bonds allow rotation 35 Amino Acids - depending on the side chain, are divided into four families: acidic (negatively charged side chain), basic (positively charged side chain), uncharged polar, nonpolar 36 Amino Acids (cont.) - acidic (negatively charged side chain) 37 Amino Acids (cont.) - basic (positively charged side chain) 38 Amino Acids (cont.) - uncharged polar can be glycosylated (a sugar added) 39 can be phosphorylated (phosphate group added) Amino Acids (cont.) - nonpolar (1) 40 Amino Acids (cont.) - nonpolar (2) 41 Amino Acids (cont.) - nonpolar (3) 42 Protein Structure - proteins have primary, secondary, tertiary and quaternary structure - primary structure: sequence of amino acid residues, atoms connected by covalent bonds histidine NH2 S 43 T cysteine A K P W valine G C V COOH Protein Structure (cont.) - secondary structure: α-helices 44 Protein Structure (cont.) - secondary structure: β-sheets 45 Protein Structure (cont.) - tertiary structure: the final 3-dimentional structure of an individual peptide chain 46 Protein Structure (cont.) - many proteins have structural and functional domains - transmembrane domains, catalytic domains, binding domains etc. domain 2 domain 1 47 Protein Structure (cont.) - quaternary structure: complex of 2 or more peptide chains (protein subunits) an antibody 48 Protein Structure (cont.) - secondary, tertiary and quaternary structure of proteins form due to interaction between amino acid side chains and between peptide bonds 49 Protein Structure (cont.) - other bonds stabilizing the higher structure of protein molecules: stacking interactions (technically covalent bond, sharing of electrons, but weak as van der Waals interaction) disulfide bonds (covalent bonds) an antibody 50 Protein Conformation - the final folded structure of a protein - proteins adopt conformation with the lowest energy - stable, but not rigid, the protein molecules are always in motion - can change due to interaction with other molecules (ions, lipids, other proteins etc) - can change due to phosphorylation (covalent binding of phosphate group) Ca2+- ATPase Ca2+- free 51 Ca2+- bound Protein Phosphorylation - covalent binding of phosphate group to serine, threonine, or tyrosine - the source of the phosphate groups is ATP - reversible - the most common way to regulate the function of proteins 52 ATP Protein Functions - transporters (transfer molecules through membranes) - receptors (membrane receptors bind signaling molecules on the outside of cells and transfer the signal to the inside of the cell; cytoplasmic receptors can bind signaling molecules within the cell) - attachment proteins (are exposed on the cell surface and bound to a surface, to the extracellular matrix, or to other cells; e.g. integrins) 53 can be an attachment protein Protein Functions (cont.) - structural proteins: cytoskeletal proteins, extracellular matrix proteins, scaffolding proteins (anchors) Cytoskeletal proteins can be an extracellular matrix protein can be an intracellular scaffolding protein 54 Protein Functions (cont.) - enzymes (catalyze chemical reactions) within a membrane within cytosol, or within an organelle, or outside the cell (like lysozyme below) lysozyme , cleaves polysaccharide chains on the surface of bacteria, decreasing their attachment ability 55 Protein Functions (cont.) - motor proteins (are able to move along other proteins and thereby to transport molecules, vesicles, organelles within the cells; to help cell migration, cell division, active cilia movement, muscle contraction etc) - antibodies (bind foreign molecules, help to protect the organism from molecular, bacterial, or viral invasion) motor protein (vehicle) a structural protein (road) an antibody 56