Chapter Two: The Chemistry of Biology. The molecules of life make up the structure of cells Chemistry of biological molecule

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1 Chapter Two: The Chemistry of Biology The molecules of life make up the structure of cells Chemistry of biological molecule Atoms and Elements: Atoms: The basic units of all matter, containing three major components: 1. Electrons: negatively charged electrons e- 2. Protons: positively charged p+ 3. Neutrons: uncharged Protons and neutrons heaviest components are found in the nucleus of the atom. The electrons orbit the nucleus The number of protons normally equals the number of electrons, atoms is uncharged Elements: A substance that consists of a single type of atom 92 natural occurring elements and only four (4) that make up 99% of all living material by weight: 1. Carbon C 25% 2. Hydrogen H 49% 3. Oxygen O 25% 4. Nitrogen N 0.5% P (phosphorous ) and S (sulfur) makeup another 0.5% All other elements account for less than 0.5% To date 115 elements: both naturally and artificially Each element is unique in its number of protons, neutrons, and electrons 1 H Element: Atomic number: Atomic mass: Hydrogen # of p+ = # of electrons the sum of the number of protons and neutrons Hydrogen is unique in that it is the only element that has one proton, one electron, and no neutron Same atomic number and mass number 22

2 Electrons are arranged in Orbitals of different levels. Electrons can move from orbital to another as they gain or lose electrons. Each orbital contain a certain number of electrons 1. First orbital, closest to the nucleus contains maximum of 2 electrons, the second 8, the third can hold up to 18, fourth can hold up to 32 The Stability of an atom depends upon its outer orbital containing the maximum number of electrons. If outer orbital is not filled, then it will fill by bonding with others. To fill their outer orbital, atoms can either gain or lose electrons to others. To gain or lose electrons, atoms bonds with other atoms to form molecules. A molecule: consists of two or more atoms held together by chemical bonds. The atoms that make up a molecule may be the same or different elements. H 2, N 2 two of the same atoms. H 2 0 two different atoms. A compound: consist of two or more different elements The molecular weight of a molecule or compound is the sum of the atomic weights of the atom. Water is =18 The three chemical bonds that hold atoms together are: 1. Covalent bonds 2. Ionic bonds 3. Hydrogen bonds 23

3 Bonds: Covalent bonds: Strong bonds formed by atoms sharing electrons with other atoms, filling the outer orbital of both atoms simultaneously. Carbon - single most important atom in biology Carbon has four electrons but requires a total of eight to fill its outer orbital. Hydrogen has one electron and requires two to fill its outer orbital H 2 CH 4 - Methane Organic compounds: Inorganic compounds: C to C or C to H bonds do not contain C-C bond C-H: A single covalent bond, two atoms sharing electrons O=C=O: double covalent bond two pair of electrons shared between atoms to fill the outer orbitals All covalent bonds are strong Two types of covalent bonds: 1. Non-polar: identical or different atoms have equal attraction for a shared electrons H-H, C-H 2. Polar: One atoms has a much greater attraction for electrons than the other, electron are shared unequally. Slightly positive and slightly negative charge Water: H 2 0 Ionic Bonds: Electron Transfer Among Atoms Join ions together If electrons from one atom are attracted very strongly by another nearby atom, the e- completely leave the first atom and becomes part of the outer orbital of the 2 nd, without sharing electrons are transferred completely from one atom to another and are not shared. The loss or gain of the electrons leads to an atom that is electrically charged The attraction of the + charged to the charged atoms forms the ionic bond. Ionization: Ionic bond is broken and atoms dissociate (separate) into unattached charged particles which are called ions. NaCl: Na + Cl - (charged particles) NaCl electrically neutral Ions: Atom gains e- becomes (negatively) charged -- Anions Cl - Atoms that losses becomes + (positively) charged -- Cations Na + 24

4 Weak bonds: weak forces holding ions, atoms and molecules together In aqueous solutions, weak bonds are easily broken at room temperature A large number of weak bonds are required t hold molecules together. In the absence of water, ionic bonds are strong and account for crystal formation, account for the strength. Hydrogen Bonds: Weak bonds resulting from the attraction of positively charged hydrogen atom in a polar molecule to a negatively charged atom ( O or N) in another polar molecule. Hydrogen bonds are important in biological systems, living organisms are composed of many molecules that contain Hydrogen atoms bonded to N or O in atoms. Weak bonds: holding molecules together Formed and broken at room temperature Average lifetime of a single H bond is only a fractions of a second at room temperature, enzymes are not necessary to break these bonds. Single H bond is weak, but number can hold DS DNA molecule together and can be broken at a temperature of 100 C. Water: The most single most important molecule in the cell as well as the world The life of all organisms depend on it. Makes up 70% of all living organism by weight. Hydrogen bonding is an important factor in water Universal solvent of life because it dissolves so many compounds. ph: potential Hydrogen: Degree of acidity Concentration of H+ in moles per liter Measure of logarithmic scale of 0 to 14 in which the lower the number, the more acidic the solution. Water can split into H+ (proton) -- acidic and OH- (basic or alkaline) When HOH H+ + OH-occurs H+ and OH are equal and the concentration of each is 10-7 The ph scale ranges from 0 to 14 b/c the concentrations of H+ and OH- varies. When the concentration of H+ and OH- are equal, the ph is neutral, ph 7 This is ph for which most bacteria live, near neutrality. Acidophiles: Very acidic conditions Alkalophines: Very alkaline conditions Buffers: added to growth mediums to maintain the Ph near neutrality. added to solutions because bacteia produce acids and bases when they degrade compounds. Which can halt the growth of the bacteria. EX. NAHPO4 25

5 Small Molecules in the Cell: All cells contain a variety of small organic and inorganic molecules: About 1% of the bacterial cell (dry weight) is composed of inorganic ions o NA+ Sodium Ions o K+ Potassium Ions o Mg2+ Magnesium o CA2+ Calcium o Fe2+ Iron o CL- Chloride o PO4 3- Phosphate o SO4 2- Sulfate Positively charged ions: required in minute amounts in order for certain enzymes to function. Negatively charged phosphate ions play a key role in energy metabolism Precursor metabolites: organic small molecules converted to the building blocks of larger molecules called macromolecules. ATP: Adenosine triphosphate: the storage form of energy in the cell. o Composed of the following: sugar ribose, purine adenine an three phosphate groups o Energy rich molecule because of the bonds that join the phosphate, when broken, there is much energy given off o When ATP is broken: inorganic phosphate and the release of energy Macromolecules: Superstructures of Life Biochemistry Biochemicals: Organic compounds produced by (or components of) living things. Macromolecules (Very large molecules) and Their Component Parts. Four major classes of biological importance: 1. Proteins 2. Carbohydrates/Polysaccharides 3. Nucleic acids 4. Lipids All macromolecules are polymers (many) : formed by joining together small molecules Synthesis: 1. Subunits are synthesized from different precursor metabolites 2. Joined together, one by one involving many different chemical reactions Overall process of joining two subunits involves a chemical reaction Dehydration synthesis: water is removed. 26

6 When Macromolecule is broken down into its subunits, reverse reaction occurs: Hydrolytic reaction or hydrolysis: water is added back Proteins: Shapers of Life and Their Functions: 50% of dry weight of cells and the predominant organic molecules in cells. Bacterial cells contain DIFFERNET KINDS OF PROTEINS AT ANY ONE TIME. Within the Bacterial World proteins function to: 1. Catalyze all reactions of the cell required for life 2. The structure and shape of certain structures as ribosomes: the protein-building machinery in all cells. 3. Cell movement by flagella 4. Taking nutrients in the cell 5. Turning genes on and off 6. Certain properties of various membranes in the cell Amino Acid Subunits: Proteins are composed of numerous combinations of 20 major amino acids. AA are building blocks of protein. The properties of a protein depend mainly on its shape, which in turns depends on the arrangement of the amino acid that make up the protein. All amino acids have at one end an alpha carbon atom to which a carboxyl group (COOH), a Hydrogen atom (H) and an amino group (NH 2 ) are bonded. This carbon atom also is bonded to a side chain or back-bone (labeled R), which gives each amino acid its unique characteristic properties. The amino acids are subdivided into several different groups based on similarities in their side chains. An important property of the side chains: polar or non-polar, determining the solubility properties of the protein, its shape, and how it interacts in the cell. AA contain methyl (CH3) non-polar and therefore do not interact with water molecules. o Not readily soluble in water (hydrophobic water fearing) o AA on the inside of the protein AA readily soluble in water: (hydrophilic water loving) 27

7 Peptide Bonds and Their Synthesis: AA that make up proteins are held together by peptide bonds: Peptide bonds: unique, covalent bond linkage formed when the carboxyl group of one AA reacts with the amino group of another amino acid with the dehydration of water. Polypeptide chain: the chain of AA formed when a large number of AA are joined by peptide bonds. A protein is a long polypeptide chain. o Proteins are always synthesized in cells from the N terminal end. Protein Structure and Diversity: Proteins have 4 levels of structure: 1. Primary structure of a protein is its type, number, and order of amino acids in the peptide chain which varies extensively from protein to protein. Determines the other features of the AA. 2. The secondary structure of a protein structure is determined by intermolecular bonding between AA twisted to form alpha helices and folded to from rhe beta sheets (resulting from weak bond formation with between each AA). 3. The tertiary structure of a protein describes the three dimensional shape of the protein, (where the protein folds). Hydrophilic AA: outside the protein molecule interacting with polar water molecules. Hydrophobic AA are pushed together and cluster inside the molecule to avoid water molecules. Explaining non-polar molecules of fat droplets in a aqueous environment. Hydrophobic interactions: NON-POLAR AA form weak interactions with each other 4. Quaternary structure describes the structure resulting from the interaction of several polypeptide chains. Proteins: Proteins develop unique shapes allowing its surfaces to display a distinctive pattern of pockets and bulges. Allowing proteins to react only with molecules that complement or fit its particular surface like lock and key. Providing the functional diversity required for many thousand of cellular reactions. Enzymes: serve as a catalyst for all chemical reactions in cells and nearly all reactions required a different enzyme. Protein Denaturation: In order to function the protein must have its proper shape. Denatured: bonds within the protein and the protein loses it shape and no longer functions. 28

8 Conditions that causes the protein to denature: High temperature - Heat High or low ph Acids and alcohols Certain solvents some disinfectants Bonds within the proteins Most bacteria cannot grow at very high temperatures b/c their enzymes are denatured at very high temperatures. Denaturation can be reversed in some cases: if a solvent is removed a protein may refold to its original shape. Carbohydrates: (CH 2 O) n Carbohydrates comprise a heterogenous group of compounds of various sizes that play a variety of important roles in the life of all organisms. These include: 1. Carbohydrates are a common food source from which organisms can obtain energy and make cellular material. 2. Metabolism 3. Two sugars form a part of the nucleic acids, DNA and RNA. 4. Certain carbohydrates serve as a reserve source of food in bacteria. 5. Nutrient and energy sources 6. Sugars form a part of the bacterial cell wall structural support and protection. Common Feature: Saccharide: simple (COH) mono. or diss. has a sweet taste. The one feature common to all diverse carbohydrates is that they contain carbon, hydrogen, and oxygen atoms in an approximate ratio of 1:2: 1. Polysaccharides are high molecular weight compounds and are linear or branched polymers of their subunits. Oligosaccharides are short chains. The term sugar is often applied to monosaccharides (a single molecule) and disaccharides -two monosaccharides joined together by covalent bonds. Monosaccharides: Classified by the number of carbon atoms they contain, most commonly 3-7 carbon atoms Ribose and deoxribose: sugars in nucleic acids Deoxyribose: is ribose away from oxygen Common 6 carbon sugars: glucose, galactose, and fructose Sugars can be drawn in two forms: linear and ring form 29

9 Disaccharides: Consist of two monosaccharide joined by a covalent bond between their hydroxyl group Most common: lactose and sucrose (table sugar) Polysaccharides: Macromolecules consisting of five or more monosaccharide subunits, Most abundant organic molecule one earth: cellulose polymer of glucose subunits and the principal constituent of plant cell walls. Synthesized by bacteria and attaches bacteria to various surfaces. Glycogen: COH storage product of animals and bacteria Dextran: synthesized by bacteria as a storage product Peptidoglycan source of structural support to the bacterial cell wall. Gram negative bacteria lipopolysaccharide symptoms of fever and shock. Nucleic Acids: Carry the genetic information in all cells. Information is decoded into the sequence of amino acids in protein molecules. Two types of nucleic acids: Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) and their nucleotides DNA Master molecule of the cell all of the cell's properties are determined by its DNA. This information is coded in the sequence of nucleotides. The code is then converted into a specific arrangement of amino acids that make up the protein molecules of the cell. Nucleotides: composed of three units 1. Nitrogen containing ring base Four different bases divided into two groups: o Two purines: adenine and guanine (two rings) o Two pyrimidines: cytosine and thymine (single ring) 2. Deoxyribose 3. Phosphate Nucleotides play additional roles: o Carry chemical energy in their bonds o Part of certain enzymes o Serve as a specific signaling molecules Nucleotides are joined by a covalent bond (sharing) between phosphate and sugar of the adjacent molecule. Phosphate joins the 3 end of the 3rd carbon atom to the 5 end which is the 5th carbon atom resulting in a backbone molecule alternating in sugar and phosphate. Two ends are different 30

10 5 end has a P molecule 3 end has an OH More nucleotides are added by adding to the 3 end. The DNA of a typical bacterium is a single molecule composed of nucleotides joined together and arranged in a double-stranded helix, with about 4 million nucleotides in each strand. This double-stranded helical molecule can be pictured as a spiral staircase with two railings and stairs split in half. The railings represent the sugar-phosphate backbone of the molecule The stairs attached to the railings are the bases. One half of each stair is strongly attached to one railing, and the other half is strongly attached to the other railing. Each pair of (bases) is held together by weak hydrogen bonds. Adenine (A) can only hydrogen bond to Thymine (T) Guanine (G) to Cytosine (C) Base pairs that bond are complementary to each other. G complimentary to C and A complimentary to T. Resulting in one strand of DNA being complementary to the other strand. In all DNA molecules, the total number of adenine molecules is equal to the total number of thymine molecules, as the total number of guanines equals the number of cytosines. Two strands of DNA differ: Sequence of bases Arranged in opposite directions. One goes in the 3' to the 5' direction and the other in the 5 to 3 direction RNA: RNA is involved in decoding the information in the DNA into a sequence of amino acids in protein molecules. Structure of RNA : RNA contains the pyrimidine uracil in place of thymine and the sugar ribose in place of deoxyribose RNA is considerably shorter and exists as a single chain of nucleotides that may form short double-stranded stretch as a result of hydrogen bonding between complementary bases in the single strand. Lipids: Heterogeneous group of molecules that are slightly soluble in water and very soluble in most organic solvents: Two groups: 31

11 1. Simple: contain carbon, hydrogen, and oxygen and maybe liquid or solid at room temperature o Fats: common simple lipids and consist of glycerol bound to a fatty acid molecule with long chains of C atoms bonded to H atoms with an COOH on one end. o Fatty acids are stored in the body as an energy reserve by forming triglycerides. 2. Compounds: contain fatty acids and glycerol and other elements other than C, H, & O o Phospholipids: phosphate molecule in addition to fatty acids and glycerol Further linked to other polar molecule such as alcohols, sugar, and one certain AA referred to as a polar head group and is soluble in water. Importance of Phospholipids: o Occur in double layers bilayer of unit membrane in the cytoplasmic membrane. The structure of the bilayer produces the essential properties of the cytoplasmic membrane. o Structure of phospholipids: 1. phosphate bonded to the polar head group is hydrophilic, soluble in water 2. long fatty acid chain of C & H, hydrophobic (water insoluble) Cell: Where Chemicals Come to Life a huge aggregate of carbon, hydrogen, oxygen, nitrogen, any many other atoms. The combination of these atoms produces characteristics, reactions, and products that can only be described as living. Fundamental Characteristics of Cells Processes That Define Life The biological activities or properties that help define and characterize cells as living entities are: growth; reproduction and heredity; metabolism, including cell cynthesis and the release of energy; movement and/or irritability; cell support, protection, and storage mechanisms; and the capacity to transport substances into and out of the cell 32