Microbiology: A Systems Approach, 2 ed.instructors.butlercc.edu/sforrest/mcch2fa08.pdf · 2.1...
Transcript of Microbiology: A Systems Approach, 2 ed.instructors.butlercc.edu/sforrest/mcch2fa08.pdf · 2.1...
2.1 Atoms, Bonds, and Molecules: Fundamental Building Blocks
• Matter: anything that occupies space and has mass
• Can be liquid, solid, or gaseous state• Building blocks of matter‐ atoms
– Subatomic particles of atoms‐ protons (p+), neutrons(n0), and electrons (e‐)
– Protons and neutrons make up the nucleus, electrons surround the nucleus
– Held together by the attraction of positive protons to negative electrons
Different Types of Atoms: Elements and Their Properties
• Different numbers of protons, neutrons, and electrons in atoms create different elements
• Each element has a characteristic atomic structure and predictable chemical behavior
• Each assigned a distinctive name with an abbreviated shorthand symbol
The Major Elements of Life and Their Primary Characteristics
• Isotopes‐ variant forms of the same element that differ in the number of neutrons
• Radioactive isotopes used in research and medical applications and in dating fossils and ancient materials
• Electron orbitals and shells
Electron Orbitals and Shells
• An atom can be envisioned as a central nucleus surrounded by a “cloud” of electrons
• Electrons rotate about the nucleus in pathways called orbitals‐ volumes of space in which an electron is likely to be found
• Electrons occupy energy shells, from lower‐energy to higher‐energy as they move away from the nucleus
• Electrons fill the orbitals and shells in pairs starting with the shell nearest the nucleus
• Each element, then, has a unuiqe pattern of orbitalsand shells
Bonds and Molecules
• Most elements do not exist naturally in pure form• Molecule‐ a distinct chemical substance that results from the combination of two or more atoms (can be two of the same element, such as O2)
• Compounds‐molecules that are combinations of two or more different elements (such as CO2)
• Chemical Bonds‐When two or more atoms share, donate, or accept electrons
• Types of bonds formed and to which atoms and element bonds are determined by the atom’s valence
Covalent Bonds and Polarity: Molecules with Shared Electrons
• Covalent bonds‐ between atoms that share electrons (such as H2).
• The majority of molecules associated with living things are composed of single and double covalent bonds between C, H, O, N, S, and P.
Polar vs. Nonpolar Molecules
• Some covalent bonds result in a polarmolecule‐ an unequal distribution of charge (ex. H2O).– Polarity is a significant property of many large molecules, influences both reactivity and structure
• An electrically neutral molecule is nonpolar –share electrons equally
Ionic Bonds: Electron Transfer Among Atoms
• Electrons transferred completely from one atom to another, without sharing, results in an ionic bond (ex. NaCl)
• Molecules with ionic bonds, when dissolved in a solvent, can separate in to charged particles called ions in a process called ionization
• Cations‐ positively charged ions• Anions‐ negatively charged ions• These ionic molecules that dissolve to form ions are called electrolytes
Hydrogen Bonding
• Weak bond between a H covalently bonded to one molecule and an O or N atom on the same or different molecule (such as between water molecules)
Figure 2.8
Chemical Shorthand: Formulas, Models, and Equations
• Molecular formula‐ gives atomic symbols and the number of elements involved in subscript (H2O, C6H12O6).
• Molecular formulas might not be unique (glucose, galactose, and fructose, for example)
• Structural formulas illustrate the relationships of the atoms and the number and types of bonds
Chemical Equations
• Equations are used to illustrate chemical reactions– Reactants‐Molecules entering the reaction
– Products‐ the substances left by a reaction
Types of Reactions
• Synthesis: reactants bond together to form an entirely new molecule– A + B AB– S + O2 SO2– 2H2 + O2 2H2O (note that equations must be balanced)
• Decomposition: bonds on a single reactant molecule are permanently broken to release two or more product molecules– AB A + B– 2H2O2 2H2O + O2
• Exchange: The reactants trade places between each other and release products that are combinations of the two– AB + XY AX + BY (reversible reaction)
• Catalysts‐ increase the rate of the reaction
Solutions: Homogeneous Mixtures of Molecules
• Solution‐ a mixture of one or more solutes uniformly dispersed in a solvent
• The solute cannot be separated by filtration or settling• The rule of solubility‐ “like dissolves like”• Water‐ the most common solvent in natural systems because of its special characteristics– Hydrophilicmolecules‐ attract water to their surface (polar)
– Hydrophobicmolecules‐ repel water (nonpolar)– Amphipathicmolecules‐ have both hydrophilic and hydrophobic properties
Concentration of Solutions
• Concentration‐ the amount of solute dissolved in a certain amount of solvent– In biological solutions, commonly expressed as molar concentration or molarity (M)
• One mole dissolved in 1 L
• One mole is the molecular weight of the compound in grams
Acidity, Alkalinity, and the pH Scale
• Acidic solutions‐ when a component dissolved in water (acid) releases excess hydrogen ions (H+)
• Basic solutions‐ when a component releases excess hydroxide ions (OH‐)
• pH scale‐measures the acid and base concentrations of solutions– Ranges from 0 (most acidic) to 14 (most basic); 7 is neutral
– pH = ‐log[H+]
Neutralization Reactions
• Neutralization reactions‐ occur in aqueous solutions containing both acids and bases
• Give rise to water and other neutral by‐products
• HCl + NaOH H2O + NaCl
The Chemistry of Carbon and Organic Compounds
• Inorganic chemicals‐ usually does not contain both C and H (ex. NaCl, CaCO3)
• Organic chemicals‐ Carbon compounds with a basic framework of the element carbon bonded to other atoms– Most of the chemical reactions and structures of living things involve organic chemicals
Carbon‐ the Fundamental Element of Life
• Valence makes it an ideal atomic building block
• Forms stable chains containing thousands of C atoms, with bonding sites available
• Can form linear, branched, or ringed bonds
• Can form single, double, or triple bonds
• Most often associates with H, O, N, S, and P
Functional Groups of Organic Compounds
• Special molecular groups or accessory molecules that bind to organic compounds‐ functional groups
• Help define the chemical class of certain groups of organic compounds
• Give organic compounds unique reactive properties– Reactions of an organic compound can be predicted by knowing the kind of functional group or groups it carries
2.2 Macromolecules: Superstructures of Life
• Biochemistry‐ study of the compounds of life• Biochemicals‐ organic compounds produced by (or components of) living things– Four main families‐ carbohydrates, lipids, proteins, and nucleic acids
– Often very large, called macromolecules– All macromolecules except for lipids are formed by polymerization
• Repeating subunits (monomers) are bound in to chains of various lengths (polymers)
Carbohydrates
• Carbohydrates: Sugars and Polysaccharides– Most can be represented by the general formula (CH2O)n, where n = the number of units of this combination of atoms
Carbohydrates
• Exist in a variety of configurations– Sugar (saccharide)‐ a simple carbohydrate with a sweet taste
– Monosaccharide contains 3‐7 carbons– Disaccharide contains two monosaccharides– Polysaccharide contains five or more monosaccharides
• Monosaccharides and disaccharides are specified by combining a prefix that describes a characteristic of the sugar with the suffix –ose– Hexoses‐ six carbons– Pentoses‐ five carbons– Fructose‐ for fruit
The Functions of Polysacharides
• Structural support and protection
• Serve as nutrient and energy stores
• Cell walls in plants and many microscopic algae from cellulose
Figure 2.16a
Other Important Polysaccharides
• Include agar, peptidoglycan, chitin, lipopolysaccharide, glycocalyx, and glycogen
Figure 2.16b
Lipids: Fats, Phospholipids, and Waxes
• Lipids‐ a variety of substances that are not soluble in polar substances
• Will dissolve in nonpolar solvents
• Main groups of lipids– Triglycerides‐a single molecule of glycerol bound to three fatty acids
• Includes fats and oils
Phospholipids• Phospholipids‐ Contain two fatty acids attached to the glycerol with a phosphate group on the third glycerol binding site– Important membrane molecules
Figure 2.18
Miscellaneous Lipids
• Steroids‐ complex ringed compounds commonly found in cell membranes and animal hormones– Best known‐ cholesterol
• Waxes‐ esters formed between a long‐chain alcohol and a saturated fatty acid
Proteins: Shapers of Life
• Predominant organic molecules
• Building blocks‐ amino acids– 20 different naturally occurring forms
– Basic skeleton‐ a carbon (the α carbon) linked to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom (H), and a variable R group
– Peptide bond forms between the amino group on one amino acid and the carboxyl group on another.
Protein Structure and Diversity
• Primary (1°) structure‐ the type, number, and order of amino acids in the chain
• Secondary (2°) structure‐ when various functional groups exposed on the outer surface of the molecule interact by forming hydrogen bonds– Coiled configuration‐ α helix– Accordion pattern‐ β‐pleated sheet
• Tertiary (3°) structure‐ created by additional bonds between functional groups
• Quarternary (4°) structure‐more than one polypeptide forms a large, multiunit protein
Protein Shape
• Each different type of protein develops a unique shape, so it can only react with molecules that fit its particular surface features– Ex. enzymes and antibodies
– Native state‐ the functional three‐dimensional form of a protein
– Denatured‐ when the protein’s native state has been disrupted
The Nucleic Acids: A Cell Computer and Its Programs
• DNA‐ specially coded genetic program• DNA transfers its program to RNA• Both are polymers of repeating units called nucleotides
– Nucleotides‐ composed of three smaller units: a nitrogen base, a pentose sugar, and a phosphate.
– The nitrogen base can be one of two forms‐ a purine (two rings) or a pyrimidine (one ring)
• Two types of purines: adenine (A) and guanine (G)• Three types of pyrimidines: thymine (T), cytosine (C), and uracil (U)• DNA contains all of the nitrogen bases except uracil• RNA contains all of the nitrogen bases except thymine
• The nitrogen base is covalently bonded to ribose in RNA and deoxyribose in DNA
• Phosphate (PO43‐) covalently bonds the sugars in series
The Double Helix of DNA
• Formed by two long polynucleotide strands
• Linked along their length by hydrogen bonds between complimentary pairs of nitrogen bases– Adenine pairs with thymine
– Cytosine pairs with guanine
RNA: Organizers of Protein Synthesis
• Also consists of a long chain of nucleotides• It is single stranded and contains ribose instead of deoxyribose anduracil instead of thymine
• Several functional types of RNA formed using the DNA template– Messenger RNA (mRNA)‐ a copy of a gene that provides the order and type of amino acids in a protein
– Transfer RNA (tRNA)‐ a carrier that delivers the correct amino acids for protein assembly
– Ribosomal RNA (rRNA)‐ a major component of ribosomes
ATP: The Energy Molecule of Cells
• Adenosine triphosphate (ATP)‐ a nucleotide containing adenine, ribose, and three phosphates
• High‐energy compound that gives off energy when the bond is broken between the outermost phosphates
• Releases and stores energy for cellular chemical reactions
• When the terminal phosphate bond is broken to release energy, adenosine diphosphate (ADP) is formed
• ADP can be converted back to ATP when the third phosphate is restored.
2.3 Cells: Where Chemicals Come to Life
• The fundamental unit of life‐ cell
• Fundamental characteristics of cells– Tend to be spherical, polygonal, cubical, or cylindrical
– Their protoplasm is encased in a cell or cytoplasmic membrane
– Chromosomes containing DNA
– Ribosomes for protein synthesis
Eukaryotic and Prokaryotic Cells
• Eukaryotic cells– Found in animals, plants, fungi, and protists
– Contain organelles that perform cell functions (such as the nucleus, Golgi apparatus, endoplasmic reticulum, vacuoles, and mitochondria)
• Prokaryotic cells– Only found n bacteria and archae
– No nucleus or other organelles