Chemistry Of Life PDF

Chemistry of life What is Matter? Matter consists of chemical elements in pure form and in combinations Physical Properties: ü Mass Chemical Properties: ü Reactivity ü Volume ü Flammability ü Boling point/Melting point ü Toxicity Figure 1.13 Energy is not matter What is a chemical element? An elemen...

Chemistry of life What is Matter? Matter consists of chemical elements in pure form and in combinations Physical Properties: ü Mass Chemical Properties: ü Reactivity ü Volume ü Flammability ü Boling point/Melting point ü Toxicity Figure 1.13 Energy is not matter What is a chemical element? An element is a substance that cannot be broken down to other substances by chemical reactions What is a compound? A compound is a substance consisting of two or more elements in a fixed ratio A compound has characteristics different from those of its elements Give an example of a compound + Sodium Figure 1.13 Chloride Sodium Chloride Essential Elements of Life Organisms are composed of matter, which consists of chemical elements in pure form or in compounds. Therefore, organisms are composed of different chemical elements and compounds. Figure 1.13 Essential Elements of Life Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter. A few other elements make up the remaining 4% of living matter. o Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur. Trace elements are required by an organism in only minute quantities. Figure 1.13 What is an atom? Each element consists of unique atoms. o An atom is the smallest unit of matter that still retains the properties of an element Atoms are composed of subatomic particles. Name the three major subatomic particles. What is the charge of each? Where in an atom is each located? Figure 1.13 Subatomic Particles Figure 1.13 Atoms The atomic number (Z) of an element o Represent the number of protons. o It is unique to each element. o Non-charged atoms have the same number of protons and electrons. The atomic mass (A) of an element o It is the sum of protons and neutrons in the nucleus of an atom. o Electrons have a mass, but it is extremely small compared to protons and neutrons If… A = Z + Nº of neutrons (N) so … N=A-Z Atoms Atoms of a given element may occur in different forms Carbon-14 is unstable and subject to radioactive decay Isotopes of a given element differ in the number of neutrons in the atomic nucleus (different N, so different A) but have the same number of protons (same Z, so all are carbons) Electron Distribution and Chemical Properties Electrons move around atomic nuclei in specific regions called orbitals. Orbitals are grouped into levels called electron shells. First shell holds up to 2 electrons Second shell holds up to 8 electrons Third shell holds up to 8 electrons Electron Distribution and Chemical Properties Valence electrons are those in the outermost shell, or valence shell. o The chemical behavior of an atom is mostly determined by the valence electrons. Elements with a full valence shell are chemically inert. Atoms in which the outermost electron shell is not completely filled with electrons tend to be chemically reactive. Chemical Bonds Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms. o These interactions usually result in atoms staying close together, held by attractions called chemical bonds. Types of chemical bonds: o Covalent bonds (polar vs. non-polar) o Ionic bonds o Hydrogen bonds Covalent Bonds An atom’s valence is the number of unpaired electrons in the valence shell. A covalent bond results from the sharing of a pair of valence electrons by two atoms. o In a covalent bond, the shared electrons count as part of each atom’s valence shell. o A molecule consists of two or more atoms held together by covalent bonds. Covalent Bond Single covalent bond = sharing of one pair of valence electrons Double covalent bond = sharing of two pairs of valence electrons Triple covalent bond = sharing of three pairs of valence electrons Covalent bonds can form between atoms of the same element or atoms of different elements Figure 1.13 Ionic Bonds Atoms sometimes strip electrons from their bonding partners o After the transfer of an electron, both atoms have charges. o A charged atom (or molecule) is called an ion. Ionic Bonds A cation is a positively charged ion. An anion is a negatively charged ion. cation An ionic bond is an attraction between an anion and a cation. o Compounds formed by ionic bonds are called ionic compounds or salts. § Salts, such as sodium chloride (table salt), are often found in nature as crystals. anion Comparison of Bonds Hydrogen Bonds A hydrogen bond forms when a partial positive charge in one polar molecule is attracted to the partial negative charge in another polar molecule. o In living cells, the electronegative partners are usually oxygen or nitrogen atoms. Would you expect to see water molecules lined up like this? The Structure of Water is Related to its Properties What type of bond holds the atoms of a water molecule together? Polar covalent bond What type of bond occurs between water molecules? Hydrogen bonds Life Requires Water Life is based on water because water is an excellent solvent. o A solute dissolved into a solvent makes a solution. o Substances are more likely to react when they are dissolved in a solvent like water. Why does water make such an excellent solvent? Water is a Versatile Solvent Hydrophilic (“water-loving”) atoms and molecules are ions and/or polar molecules that stay in solution because they interact with water’s partial charges. Hydrophobic vs. Hydrophilic Hydrophobic (“water-fearing”) molecules are uncharged and nonpolar compounds that do not dissolve in water. o Hydrophobic molecules interact with each other through hydrophobic interactions. Cohesion and Adhesion Cohesion: attraction of molecules of water to other molecules of water. Adhesion: attraction of molecules of water to another kind of molecules. Surface Tension Surface tension is the cohesive force caused by attraction between the molecules at the surface of a liquid. Water resists any force that increases its surface area. Water Expands Upon Freezing When water freezes, it expands and becomes less dense. As a result, ice floats on liquid water. When frozen, the water molecules form a highly ordered, open, and hexagonal structure. Water has a High Heat Capacity Water has a high heat capacity, meaning that a lot of heat energy is necessary to raise the temperature of a certain amount of water by one degree. It helps regulate temperature Vancouver humidity and excess of rain regulates Humans use sweat to cool down. The water absorbs the body’s excess heat. the temperature of the region allowing for a warmer winter and a cooler summer Chemical Reactions Chemical reactions involve the making and breaking of chemical bonds. Acids and Bases Water is in a state of dynamic equilibrium in which water molecules dissociate at the same rate at which they are being reformed. Acidic Basic More H+ = acidic; More OH- = basic pH = - log ([H+]) Buffers resist pH change by binding H+ or OH- Buffers Carbonic acid (H2CO3) – bicarbonate (HCO3-) buffer system Regulates pH of blood (pH 7.4) Below 7.35 = acidemia Above 7.45 = alkalemia CO2 + H2O = H2CO3 carbonic acid H2CO3 ↔ HCO3- + H+ carbonic acid bicarbonate Carbon Electron configuration is the key to an atom’s characteristics. Electron configuration determines the kinds and number of bonds an atom will form with other atoms. What types of bonds is carbon most likely to form? Covalent bonds How many covalent bonds carbon can do? 4 Carbon All life on earth is carbon-based Organisms are formed by macromolecules constituted of successive covalent bonds between carbon, hydrogen, and functional groups. Functional Groups Functional groups give organic molecules different chemical properties. A functional group can participate in specific chemical reactions. Functional groups are in many different biological molecules. Figure 1.13 Macromolecules Macromolecules are polymers built from monomers A polymer is a long molecule formed by many similar (similar is different from equal) building blocks called monomers o Monomers link together (polymerize) to form polymers Proteins, nucleic acids, and carbohydrates can be macromolecules. Polymer is like a chain, while the links within the chain are the monomers Macromolecules Monomers polymerize through condensation (dehydration) reactions, which results in the loss of a water molecule. Hydrolysis is the reverse reaction which breaks polymers apart by adding a water molecule. Proteins What is the general term for monomers of proteins? Amino acids What is the general term for polymers of proteins? Polypeptides What do proteins do? Catalysis: speed up chemical reactions Defence: antibodies attack pathogens Movement: move cells or molecules within cells Signalling: convey signals between cells Structure: shape cells and comprise body structures Transport: allow molecules to enter and exit cells or carry them throughout the body Amino Acids Amino acids are organic molecules with carboxyl and amino groups. o Amino acids differ in their properties due to differing side chains, called R groups. Amino Acids The 20 amino acids differ only in the unique R-group, or side chain, attached to the central carbon. Amino acids can be grouped into four types based on the properties of the side chains: 1. Nonpolar 2. Uncharged polar 3. Charged—includes both acidic (−) and basic (+) Peptide Bonds Amino acids polymerize when a bond forms between a carboxyl group of one amino acid and an amino group of another. oThe resulting C–N bond is called a peptide bond. Peptide Bonds Amino Acid Polymers These polymers range in length from a few to more than a thousand monomers. oAn oligopeptide is a polymer of less than 50 amino acids. oA polypeptide is a polymer of more than 50 amino acids. Protein can be used to refer to any amino acid chain. oMore formally refers to the complete, functional form of the molecule. Each protein has a unique linear sequence of amino acids. Proteins Proteins have unparalleled diversity of size, shape, and chemical properties. o The sequence of amino acids determines a protein’s threedimensional structure. o A protein’s structure determines its function. How does a protein acquire this unique three-dimensional shape? Four Levels of Protein Structure Primary structure is the unique sequence of amino acids in a protein. How is the primary structure of a protein determined? Primary structure is determined by inherited genetic information. Four Levels of Protein Structure Primary structure is fundamental to the higher levels of protein structure. The amino acid R-groups affect a polypeptide’s properties and function. o A single amino acid change can radically alter protein function. Four Levels of Protein Structure A protein’s secondary structure is formed by hydrogen bonds between the carboxyl group of one amino acid and the amino group of another amino acid. o Can occur only when a polypeptide bends so that C=O and N–H groups of the backbone are close together. Types of secondary structure: o a-helices o b-pleated sheets Four Levels of Protein Structure The tertiary structure of a polypeptide results from interactions between R-groups or between R-groups and the peptide backbone. These contacts cause the backbone to bend and fold, contributing to the distinctive three-dimensional shape of the polypeptide. Four Levels of Protein Structure Quaternary structure results when two or more polypeptide chains form one macromolecule. Four Levels of Protein Structure Protein Folding Each protein has a characteristic folded shape that is necessary for its function. Many proteins have a disordered shape when they are inactive. When the active protein is needed, it folds into an ordered, active conformation. Some proteins are regulated by controlling when or where they are folded into active shapes. Protein Denaturation Protein denaturation occurs when a protein unravels and loses its shape o Intermolecular bonds formed in the quaternary, tertiary and secondary structures of protein are broken o Peptide bonds between amino acids are not broken o A denatured protein is biologically inactive Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to denature. Why are proteins so important? Why does the shape (folding) of a protein matter so much? Enzymes What is a catalyst? An enzyme is a protein that functions as a catalyst. Substrates are the reactants in enzymecatalyzed reactions. The location on an enzyme where substrates bind and react is the active site. Antibodies Nucleic Acids What is the general term for monomers of nucleic acids? Nucleotides What is the general term for polymers of nucleic acids? Polynucleotides Nucleic Acids List the major types of nucleic acid. Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) Adenosine triphosphate (ATP) What major functions do nucleic acids perform? Nucleotides Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group. Nucleotide Monomers There are two families of nitrogenous bases: o Pyrimidines (cytosine, thymine, and uracil) have a single six-membered ring. o Purines (adenine and guanine) have a sixmembered ring fused to a five-membered ring. In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose. Lecture Outline 1. 2. 3. 4. Nucleotides Polynucleotides Complementary bases RNA Nucleotide Polymers Nucleotide monomers are linked together to build a polynucleotide. oAdjacent nucleotides are joined by covalent bonds that form between the –OH group on the 3¢ carbon of one nucleotide and the phosphate on the 5¢ carbon on the next. These covalent bonds are called phosphodiester linkages. Nucleotide Polymers These phosphodiester bonds create a backbone of sugar and phosphate units with nitrogenous bases as appendages. Complementary Bases The nitrogenous bases in DNA pair up and form hydrogen bonds. Because of their shapes, only certain nitrogenous bases can bond together. These are known as complementary bases. Complementary Bases DNA Double Helix A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix. o The two strands run antiparallel to each other. Nucleic Acids List the three major types of RNA. mRNA (messenger RNA) rRNA (ribosomal RNA) tRNA (transfer RNA) Why do you think DNA, rather than RNA, is used for long-term information storage in cells? List three structural differences between DNA and RNA. DNA is double stranded; RNA is single-stranded. The pentose sugar in DNA is deoxyribose and the pentose sugar in RNA is ribose. In DNA, the nitrogenous bases are adenine, thymine, cytosine, and guanine. In RNA, the nitrogenous bases are adenine, uracil, cytosine, and guanine. In RNA, uracil replaces thymine. Carbohydrates What is the general term for monomers of carbohydrates? Monosaccharides What is the general term for polymers of carbohydrates? Polysaccharides Carbohydrates Carbohydrates include sugars and the polymers of sugars. What are the major functions of carbohydrates? Carbohydrates serve as fuel, building material, and cell identity markers. Monosaccharide Molecular Structure (one) (sweet) Number of carbons in the molecule Stoichiometric formular: (CH2O)n Carbon Water (hydrate) Glucose (C6H12O6) is the most common monosaccharide Monosaccharides Though often drawn as linear skeletons, in aqueous solutions many sugars form rings. Monosaccharide Polymerization Monosaccharides polymerize when a condensation reaction occurs between two hydroxyl groups. The covalent bond formed between two monosaccharides is called a glycosidic bond Two sugars linked together form a disaccharide. Disaccharides Examples (two) (sweet) Maltose syrup Polysaccharides (many) (sweet) Polysaccharides are large carbohydrates formed by a repeated sequence of monosaccharides. Polysaccharides can play two major functions in organisms: oEnergy storage oStructural support Polysaccharides (many) (sweet) oEnergy storage § Potential chemical energy storage in covalent bonds of the polysaccharide. § Animals store energy in a polysaccharide named glycogen. § Plants store energy in a polysaccharide named starch. Glycogen Mitochondria Starch Chloroplast Starch Glycogen granules 0.5 µm 1 µm Glycogen (b) Glycogen: an animal polysaccharide (a) Starch: a plant polysaccharide Polysaccharides (many) (sweet) oStructural support § Some polysaccharides, known as fibres, form rigid structures that provide physical structural support. § Cellulose is a polysaccharide found in plant cell walls that form fibres. § Fibres are undigestible but assist in the regulation of digestion. Cell Identity Carbohydrates indicate cell identity. Display information on the outer surface of cells. Play important role in: Cell-cell recognition: Identify cells as “self”. Cell-cell signalling: Communication between cells. Lipids Lipids are the one class of large biological molecules that do not form polymers. The unifying feature of lipids is having little or no affinity for water. oLipids are hydrophobic because they consist mostly of carbon-hydrogen bonds. Why are lipids hydrophobic? Non-polar covalent bonds Lipids Function: Fuel, building material and signaling Oils, waxes, fats and sterols The most biologically important lipids are fats, phospholipids and steroids. Oils and Fats Function: energy storage (fuel) Fats are constructed from two types of monomers: glycerol and fatty acids Glycerol is a three-carbon alcohol with a hydroxyl group (OH) attached to each carbon A fatty acid consists of a carboxyl group (COOH) attached to a long carbon skeleton Triglycerides Three fatty acids are joined to glycerol by ester linkages Oils and Fats Fatty acids vary in the length and number and locations of double bonds they contain Saturated No double bonds between carbons in a fatty acid chain More solid at room temperature Unsaturated Have one or more double bonds between carbons in fatty acid chain More liquid at room temperature Types of Fats Fats Name three functions of fat in an animal’s body. Insulation Cushioning and protection of organs Energy storage oA gram of fat stores more than twice as much energy as a gram of polysaccharide. Phospholipids Function: building blocks Consisted of two fatty acids and one phosphate group attached to glycerol Consist of a hydrophilic “head” and hydrophobic “tails” ü Hydrophobic fatty acid chains + hydrophilic head that is charged Building blocks of the cell's membranes Steroids Function: signaling Steroids are lipids characterized by a carbon chain consisting of four fused rings One steroid, cholesterol, is found in animal cell membranes and is a precursor for some hormones Amphipathic Molecules Molecules that contain both hydrophilic and hydrophobic elements Examples: cholesterol, phospholipids, soaps and detergents Cholesterol Phospholipid Soaps and Detergents Monomers Polymers Type of Linkage Proteins Amino acids Polypeptides Nucleic Acids Peptide bond Function Catalysis, structure, movements, signalling, defence, and transport Store and transmit important Phosphodiester information for grown. Nucleotides Polynucleotide Monosaccharides Polysaccharides Glycosidic linkage Energy storage Structural support It is not a polymer Ester linkage between glycerol and fatty acids Energy storage Cushioning Insulation Membranes Signalling Carbohydrates Lipids No monomers Glycerol + Fatty acids Questions?