Chapter 3: Chemistry of Life PDF

Chapter 3: Chemistry of Life Atoms, Molecules, Chemical Bonds Water – A Cradle of Life Organic Compounds  Atoms An atom is a smallest structure of matter that retains all properties of chemical element; the building blocks for all physical things Protons – positively charged partic...

Chapter 3: Chemistry of Life Atoms, Molecules, Chemical Bonds Water – A Cradle of Life Organic Compounds  Atoms An atom is a smallest structure of matter that retains all properties of chemical element; the building blocks for all physical things Protons – positively charged particles found within the nucleus of an atom Neutrons – particles with no charge found within the nucleus of an atom Electrons – negatively charged particles that rotate around the nucleus forming the electron shell of the atom  Atoms We measure the mass of an atom in subatomic units (au) Protons and neutrons = 1au Electrons = negligible The mass of an atom is concentrated in the nucleus of an atom Each element has a specific mass Chemical Bonds A lasting attraction between atoms that enables the formation of molecules Ionic bond – forms from the complete transfer of electrons from one atom to another, producing ions that are attract eachother Ions are atoms that have an irregular number of electrons making them positively or negatively charged Covalent bond – sharing of electrons between two atoms This occurs to make a more stable molecule Hydrogen bond: a weak electrical attraction between a partially positive hydrogen atom and a partially negative end of a polar molecule Ionic Bonds Ionic bonds form between two or more atoms by the transfer of one or more electrons between atoms. Electron transfer produces negative ions called anions and positive ions called cations. These ions attract each other, forming the ionic bond. Salt (NaCl) is an ionic bond Na donates an electron to Cl Na+ (lost electron) now bonds with Cl- (gained electron) Covalent Bonds Sharing of electrons between two atoms Valence electrons are the outer ring of electrons floating around the atom Elements tend to want a total of 8 valence electrons and will form covalent bonds with other elements to reach this state Carbon is the king of covalent bonds with 4 valence electrons it can make up to 4 bonds with other atoms Nitrogen and Oxygen also have high electronegativity (attract electrons) and easily form covalent bonds Review: Ordinary table salt (NaCl) is composed of one positive and one negative ion. Which of the following types of bonds holds these ions together? a. polar b. covalent c. ionic d. hydrogen  Water H2O is formed by a covalent bond between oxygen and two hydrogen atoms Oxygen is highly electronegative (pulls electrons close). This forms a polar covalent bond and the water molecule is polarized, or Dipole having a slight negative charge on one end and a slight positive charge on the other Review: How do the two hydrogens and oxygen in a water molecule interact to create a polar molecule? a. The oxygen nucleus pulls the negative electrons away from the hydrogen nuclei, creating a separation of charge in the entire molecule. b. The two hydrogen atoms pull the positive protons toward them, creating a separation of charge. c. The higher mass of the oxygen polarizes the molecule. d. all of the above  All life depends on water, and contains water Most abundant inorganic molecule in cells Dipolar molecules are subject to Van der Waals Water forces, or the attraction between positive and negative poles Van der Waals forces are the cause of water tension and solubility of salts and other molecules Review: Which of the following is the most abundant inorganic substance in cell? a. Oxygen b. Carbon dioxide c. Water d. Carbohydrates e. Proteins Water and Solutions Solution – a liquid water with dissolved molecules Solvent – water allows other molecules to dissolve into solution Solute – dissolved molecules Electrolytes – dissolved ions that make the solution conductive Hydrophilic – water loving, easily dissolved Hydrophobic – water repelling, do not mix in water (think oil/fats) States of Matter The physical state of water depends on temperature. Solid = ice Occurs at and below 0oC A stable network of hydrogen bonds emerges as a crystal structure. Liquid = fluid water Occurs between 0oC and 100oC Water bonds constantly break and re-form. Gas = water vapor or steam Occurs when water boils at 100oC  Carbon is the backbone of Biological Molecules Inorganic carbon (CO2) is transformed into organic Organic carbon by photosynthesis Organic Chemistry is the study of Carbon-based Compound molecules s Carbon generally makes FOUR covalent bonds (valence e- = 4) to fill its outer shell  An atom is the building blocks for all physical things A molecule is made of multiple atoms held together by chemical bonds Biomolecules (or macromolecules) are large organic molecules that are critical for living cells Polymer – a long molecule made of Biomolecul many small, similar, repeating units es connected in a chain by covalent bonds Monomer – the small building blocks of a polymer Carbohydrates Monomer: simple sugars Food source (glucose, starch..) Energy source Plant cell wall (cellulose) Examples: Starch, glycogen, polysaccharides Carbohydrates Monomers = monosaccharides Two-monomer sugars = disaccharides Complex carbohydrates = thousands of monosaccharides Vary in size and shape and, therefore, function Short-term energy storage Cell’s direct fuel to make ATP Review: The monomers of the carbohydrates are generally called: a. Fatty acids b. Amino acids c. Nucleotides d. Monosaccharides e. Glycerol. Review: Which term includes all others in the list? a. Monosaccharide. b. Disaccharide. c. Starch. d. Carbohydrate. e. Polysaccharide. Review: Select the simplest sugar: a. Sucrose b. Glycogen. c. Lactose d. Glucose e. Starch Proteins Monomer: amino acids Regulate chemical reactions in cells Make up the structural parts of cells The most diverse Macromolecule Examples: Hemoglobin, enzymes, collagen Proteins Monomers - amino acids Bond – covalent bond called peptide bonds link amino acids This polymer is called a polypeptide A protein is a polypeptide (or more than one) folded into a functional conformation. (Conformation = shape. Shape = function!) There are 20 amino acids that constitute structure of every protein molecule. Protein Structure Primary Structure: Polypeptide – string of amino acids Secondary Structure: hydrogen bonds Tertiary Structure: hydrogen bonds Quatenary Structure: bonds between polypeptide chains Protein Structure = Function Proteins that serve architectural and structural roles are often long and cable- like Proteins that act as enzymes are globular, having a special 3-D shape that fits precisely with another chemical they cause the chemical that they fit with to undergo a reaction Altering the amino acid sequence changes the quaternary shape of a protein and potentially it’s function Lipids (Triglycerols) Monomer: glycerol and fatty acids Energy source Hormones Make up cell membrane Examples: Triacylglycerol, cholesterol  Lipids Fatty acids have different chemical properties due to the number of hydrogens that are attached to chain of carbons Saturated fats: two hydrogens at each carbon Unsaturated: at one or more carbons they only have ONE attached hydrogen A double bond between these two carbons Review: Triglycerides (fats) are made of: a. Glucose and fructose b. Fatty acids and glycerol c. Glycogen and cholesterol d. Nucleotides and pentose e. Amino acids and glycerol  Plasma membrane: the barrier separating a The cell from it’s external environment Plasma Made of two layers of phospholipids Phospholipids: a molecule with BOTH an Membrane attraction to water, AND a water-repellent factor hydrophilic, or water-LOVING head hydrophobic or water-FEARING tail Nucleic Acids Monomer: nucleotides ATGCU Make up DNA Examples: DNA, RNA  Nucleotide s Nucleotides have 3 components Nitrogenous base Adenosine Guanine Thymine Cytosine Uracil (RNA only) 5 carbon sugar Phosphate group (PO4)  DNA provides living organisms with long- term, stable genetic information storage DNA in a form that is easily copied and passed on to future generations. Review: Substances that dissolve in water include all of the following except: a. Proteins. b. Salts. c. Glucose. d. Nucleic acids. e. Lipids. Review: Choose the pair of terms that correctly completes this sentence: “Glucose molecules are to _____________________ as _____________________ are to proteins.” a. Carbohydrates; amino acids b. Amino acids; fatty acids c. Amino acids; monosaccharides d. Lipids; cholesterol e. Nucleic acids; fatty acids Review: The building blocks of organic macromolecules are known as: a. Electrolytes b. Polymers c. Monomers d. Enzymes e. Functional groups  Biomolecules Examples Functions Monomer (building block) Carbohydrates Starch, glycogen Energy storage, cell Simple sugars (polysaccharides) surface marker, cell (glucose, galactose) signaling Proteins Hemoglobin, Catalyze reactions, Amino Acids Enzymes, Collagen physical structure, (glycine, cysteine) cell signaling Nucleic Acids DNA, RNA Store Genetic Nucleotides Information, Gene (A,C,G,T, U) expression Lipids Triacylglycerol, Energy Storage, Fatty Acids and cholesterol Cell Membranes, Glycerol Hormones Question s?