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The Molecules of Life Chapter 2 Atoms and Elements Atoms Basic unit of all matter Made up of three major components Protons Positively charged Electrons Negatively charged Neutrons Uncharged Atoms and Elements Atom Protons and neutrons are found in the nucleus Account for the “weight” of the atom Atomic mass Electrons orbit the nucleus Have relatively little mass Do not contribute to the mass of the atom Approximately 2,000 electrons = 1 proton Protons and electrons are equal in a uncharged atom Atoms and Elements Elements Substance that consists of a single type of atom 92 naturally occurring elements 99% of all living matter by weight made up of four Carbon Hydrogen Oxygen Nitrogen Phosphorus and sulfur make up additional 0.5% Atoms and Elements Each element is identified by two numbers Atomic number Number of protons occupying the nucleus In an uncharged element this also equals the number of electrons Atomic mass Number of protons plus the number of neutrons Atoms and Elements Electrons of each element are arranged in orbitals Each orbital differs in energy Each orbital can contain a certain number of electrons The first orbital (closest to the nucleus) can hold a maximum of 2 electrons The next two orbital can have a maximum capacity of 8 electrons each Each orbital must be filled before electrons occupy the next Orbitals farthest from the nucleus have the highest energy Chemical Bonds and the Formation of Molecules Atoms are most stable when the outer orbital contains the maximum number of electrons 2, 8, 8 etc. To fill outer orbitals atoms form bonds with other atoms to fill outer orbitals Bonds are formed with the sharing or the gain or loss of electrons Molecules are formed when atoms bond together Chemical Bonds and the Formation of Molecules There are several types of chemical bonds They also vary in strength Chemical bonds include Covalent bonds Ionic bonds Hydrogen bonds Covalent Bonds Achieve stability through the sharing of electrons between atoms Creates a strong bond Difficult to break Requires significant energy usually in the form of heat Never break spontaneously at physiological temperatures Enzyme required to break at lower temperature Bonds can be polar or non-polar Covalent Bonds Non-polar and Polar Covalent bonds may have an equal or unequal attraction for the shared electrons Non-polar covalent Bonds formed between identical atoms or between atoms that have similar attraction H-H or C-H Covalent Bonds Non-polar and Polar Polar covalent One atom has a greater attraction to the electrons than the other Produces a slight charge within the molecule One part of the molecule with be slightly negatively charged and one molecule with by slightly positively charged O-H Ionic Bonds Formed by gaining or losing electrons Electrons completely leave first atoms and become part of outer orbital of second atom Loss and gain of electrons leads to charged atoms (ions) Atom that loses electrons becomes positively charged Atom that gains electron becomes negatively charged Charged atoms are attracted to each other and form a bond between ions Ionic bond Ionic Bonds Ionic bonds are weaker than covalent bonds Bonds dissociate in water Easily broken at room temperature Approximately 100 time weaker than covalent bonds Important among weak forces holding biological molecules together Hydrogen Bonds Weak bonds formed from the attraction of positively charged hydrogen atoms Hydrogen atoms in polar molecules are attracted to negatively charged atoms or molecules Most commonly oxygen or nitrogen Hydrogen bonds occur between molecules such as water and DNA Covalent bonds are formed within the molecules Hydrogen bonds hold molecules together Covalent bonds hold atoms together Hydrogen Bonds Weakest of the biological bonds Constantly being formed and broken at room temperature At room temperature the average lifetime of a single hydrogen bond is a fraction of a second Large numbers of hydrogen bonds can hold molecules together firmly Like numerous stitches in clothing One stitch won’t hold a shirt together but numerous stitches will Chemical Compounds of the Cell Most important molecule is water Makes up over 70% of all living organisms by weight Importance of water depends on it unusual bonding properties Bonding Properties of Water Bonding properties of water Hydrogen bonds form between positively charged hydrogen of one molecule and negatively charged oxygen of another Hydrogen bonding produces a polar molecule Bonding Properties of Water Polar nature accounts for ability to dissolve numerous compounds Water is known as universal solvent Molecules that dissolve in water must contain charged atoms NaCl readily dissolves in water forming Na+ ions and Cl- ions Ions become surrounded by water Na+ and Cl- ions no longer able to bond to each other pH Acidity is measured as pH Defined as concentration of H+ ions potential Hydrogen Measured on logarithmic scale of 0 to 14 0 highly acid 14 highly alkaline (basic) Acidity based on ionization of water to H+ and OH- ions When H+ and OH- ions are equal solution is neutral High H+ = acid High OH- = base Small Molecules in the Cell All cells contain small organic and inorganic molecules Approximately 1% of dry weight of bacteria composed of inorganic ions + + 2+ 2+ 2+ 3- and SO 2 Na , K , Mg , Ca , Fe , Cl , PO4 4 Certain enzymes require positively charged ions for proper functioning Negatively charged phosphate ions are essential in energy metabolism Small organic molecules act as precursor metabolites These are converted to the building blocks of macromolecules Macromolecules and Their Component Parts Macromolecules are very large Macro = large Biological macromolecules are divided into four classes Proteins Polysaccharides (carbohydrates) Lipids Nucleic acids Macromolecules and Their Component Parts All macromolecules are polymers Poly = many Large molecules formed by joining smaller subunits together Joining subunits together involves dehydration reaction H2O is removed during chemical reaction Reaction termed dehydration synthesis Macromolecules and Their Component Parts Macromolecules are broken down into smaller subunits Instead of removing H2O, a molecule of H2O is added Reaction termed hydrolytic reaction or hydrolysis Proteins and Their Functions Constitute over 50% of cell dry weight Made up of amino acid subunits Most versatile Some responsibilities include Catalyzing reactions Composition and shape of certain bacterial structures Gene regulation Nutrient procurement Amino Acid Subunits Proteins are composed of numerous combinations of 20 amino acids Protein function depends on the shape of the protein Protein shape depends on the sequence of amino acids Amino Acid Subunits All amino acids have the following shared features A carboxyl group (COO-) An amino group (NH2+) A central carbon A side chain The side chain differentiates the amino acids • Amino acids are subdivided based on similarities of the side chain Peptide Bonds and Their Synthesis The amino acids that form proteins are held together by peptide bonds Unique type of covalent bond Formed between the interaction of the carboxyl group of one amino acid and the amino group of the following amino acid Reaction causes the release of water and the formation of a peptide bond Protein Structure Proteins have four structures Primary Secondary Tertiary Quaternary Protein Structure Primary structure Sequence of amino acids In large part determines other protein features Protein Structure Secondary structure Primary structure folds into new configuration Helical structure Alpha (α) helix Pleated structure Beta (β) sheet New configuration results from weak bonds formed between amino acids Protein Structure Tertiary structure 3 dimensional structure 2 major shapes Globular Fibrous Becomes functional protein Protein Denaturation Proteins must have specific shape to have proper function Environmental conditions can break bonds within the protein Causes shape change Shape change causes protein to stop functioning Called denaturation Denaturation can be reversible or irreversible Environment determines reversibility Carbohydrates Carbohydrates are diverse group of molecules with various sizes Play important roles in all organisms including Common source of food and energy Form part of nucleic acids Form part of bacterial cell wall Carbohydrates Carbohydrates contain carbon, hydrogen and oxygen in 1:2:1 ratio Each carbon atom is bound to two hydrogen atoms and one oxygen atom CH2O Polysaccharide large molecules made of carbohydrate molecules Oligosaccharide short chains of carbohydrates Monosaccharide Single carbohydrate molecule Carbohydrates Monosaccharide Classified by number of carbons in molecule Most common monosaccharides 5 and 6 carbon sugars 5 carbon sugars = pentose Ribose and deoxyribose 6 carbon sugars = hexose Glucose, fructose and galactose Carbohydrates Disaccharides Produced by joining two monosaccharides through dehydration synthesis Lactose and sucrose most common in nature Glucose + galactose = lactose Glucose + fructose = sucrose Maltose less common Glucose + glucose = maltose Carbohydrates Polysaccharides Serve different function Cellulose most abundant organic molecule on earth Polymer of glucose molecules Principle constituent in plant cell wall Glycogen is carbohydrate storage molecule of animals and some bacteria Polymer of glucose subunits Dextran storage molecule for carbon and energy for some bacteria Polymer of glucose subunits Nucleic Acids Two types of nucleic acid DNA RNA Carrie genetic code in all cells Decodes sequence of amino acids to produce proteins Sub units of nucleic acids are nucleotides DNA Master molecule Determines specific properties of the cell Nucleotides are composed of three units Nitrogen containing ring compound Nitrogenous base Purine Adenine and guanine Pyrimidine Thymine and cytosine Five carbon sugar molecule Deoxyribose Phosphate molecule DNA Nucleotides are joined through covalent bonding Bond created between phosphate of one nucleotide and sugar of the adjacent through dehydration synthesis Phosphate molecule acts as a bridge between the number 3 (3’) carbon of one sugar and the number 5 (5’) carbon of the adjacent Results in a sugar phosphate backbone DNA DNA in living organisms is a double stranded helical molecule Strands are held together by hydrogen bonding between the nitrogen bases Specific pairing between bases Adenine binds to thymine A-T or T-A Guanine binds to cytosine G-C or C-G Bases are complementary RNA Involved in decoding DNA Structure is similar to DNA Differs in a number of ways Thymine is replaced by uracil There is no thymine base in RNA The sugar is ribose in place deoxyribose RNA is generally shorter Exists as a single stranded molecule not double stranded Lipids Critical component of the cell membrane Membranes act a gatekeepers to the cell Often determines what enters or leaves the cell Heterogeneous group of molecules Made up of different subunits Defining feature Insoluble in water Smallest of the four macromolecules Can be divided into two general classes Simple lipids Compound lipids Simple Lipids Contain only carbon, hydrogen and oxygen Most common are called fats Solid at room temperature Made of glycerol and fatty acids Fatty acids are long hydrocarbon chains plus an acid group (COOH) at the end Glycerol is carbon hydrogen chain with three hydroxyl (OH) groups attached Allows for the binding of three fatty acids to one glycerol Triglyceride • Fatty acids bond to glycerol covalently through dehydration synthesis Simple Lipids Steroids are also considered simple lipids Differ from fats in structure and function Structure consists of fourmembered ring Classified as lipid because steroids are insoluble in water If one of the rings has a hydroxyl (OH) group attached it is classified as a sterol Example: cholesterol Compound Lipids Contain fatty acids, glycerol and other elements Phospholipid most important compound lipid Phospholipid is made up of a phosphate and two fatty acids attached to a glycerol molecule Phosphate head is polar and soluble in water Hydrophilic Fatty acids are non polar and insoluble in water Hydrophobic Compound Lipids Phospholipids Major component in lipid cell membrane Membrane is a double or bilayer of phospholipids Hydrophilic heads orient towards internal and external environments Hydrophobic tails orient themselves away from aqueous environment towards each other Membrane acts as a barrier to the entry and exit of cellular substances