Chap 2 micro bio lecture
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Contain membrane-bound organelles Larger and more complex cells found in plants, animals, fungi, and protists Prokaryotic cells Lack membrane-bound organelles Smaller and simpler cells found in bacteria and archaea 1. The chapter discusses the fundamental building blocks of matter including atoms, bonds, and molecules. It describes the basic atomic structure of elements and how different types of chemical bonds form compounds and molecules. 2. The chapter then examines macromolecules that are essential to life, including carbohydrates, lipids, proteins, and nucleic acids. It explains how each macromolecule is formed
![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+]](https://image.slidesharecdn.com/chapt02lecture-140113081244-phpapp01/85/Chap-2-micro-bio-lecture-27-320.jpg)
Chap 2 micro bio lecture
- 1. Microbiology: A nd Systems Approach, 2 ed. Chapter 2: The Chemistry of Biology
- 2. 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
- 3. Figure 2.1
- 4. 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
- 5. 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
- 6. 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 orbitals and shells
- 7. Figure 2.2
- 8. Bonds and Molecules Most elements do not exist naturally in pure form Molecule- the smallest particle of matter that can have independent existence; a distinct chemical substance that results from one atom of a noble gas (Ne) or the combination of two or more atoms (can be two atoms of the same element, such as O2). Compounds- are combinations of two or more different elements joined by chemical bonds. 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
- 9. Figure 2.3
- 10. 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.
- 11. Figure 2.4
- 12. Polar vs. Nonpolar Molecules Some covalent bonds result in a polar molecule- an unequal distribution of charge (ex. H2O). Polarity is a significant property of many large molecules, influencing both reactivity and structure. An electrically neutral molecule is nonpolar Van der Waals forces- weak attractions between molecules with low levels of polarity
- 13. Figure 2.5
- 14. Ionic Bonds: Electron Transfer Among Atoms • Electrons transferred completely from one atom to another, without sharing, results in an ionic bond (ex. NaCl) Crystals 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
- 15. Figure 2.6
- 16. Figure 2.7
- 17. 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
- 18. Chemical Shorthand: Formulas, Models, and Equations Molecular formula- gives atomic symbols and the number of atoms of the 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
- 19. Figure 2.9
- 20. Chemical Equations Equations are used to illustrate chemical reactions Reactants- Molecules entering the reaction Products- the substances left by a reaction
- 21. 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
- 22. Types of Reactions: Exchange: The reactants trade places between each other and release products that are combinations of the two AB + XY AX + BY (reversible reaction)
- 23. CATALYSTS Catalysts- increase the rate of the reaction Catalysts lower the energy required to get reactions started Enzymes are biological catalysts Most enzymes are proteins, but other substances, e.g. RNA can occasionally serve as enzymes
- 24. 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 Hydrophilic molecules- attract water to their surface (polar) Hydrophobic molecules- repel water (nonpolar) Amphipathic molecules- have both hydrophilic and hydrophobic properties
- 25. 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
- 26. Figure 2.11
- 27. 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+]
- 28. Figure 2.12
- 30. Neutralization Reactions Neutralization reactions- occur in aqueous solutions containing both acids and bases Give rise to water and other neutral byproducts HCl + NaOH H2O + NaCl
- 31. The Chemistry of Carbon and Organic Compounds Inorganic chemicals- usually do not contain both C and H (ex. NaCl, CaCO 3) 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
- 32. 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 chains Can form single, double, or triple bonds Most often associates with H, O, N, S, and P
- 33. Figure 2.13
- 34. Functional Groups of Organic Compounds Special molecular groups or accessory molecules that bind to organic compoundsfunctional 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
- 36. 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)
- 37. 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
- 38. Figure 2.14
- 39. 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
- 40. The Nature of Carbohydrate Bonds Figure 2.15
- 41. 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
- 42. Other Important Polysaccharides Include agar, peptidoglycan, chitin, lipopolysaccharide, glycocalyx, and glycogen Figure 2.16b
- 43. 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
- 44. Figure 2.17
- 45. Phospholipids PhospholipidsContain two fatty acids attached to the glycerol with a phosphate group on the third glycerol binding site Important membrane molecules Figure 2.18
- 46. Miscellaneous Lipids Steroids- complex ringed compounds commonly found in cell membranes and animal hormones Best known- cholesterol • Waxes- esters formed between a longchain alcohol and a saturated fatty acid
- 47. Figure 2.19
- 48. 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.
- 50. Figure 2.20
- 51. 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
- 52. Figure 2.21
- 53. 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
- 54. 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
- 55. Figure 2.22
- 56. Figure 2.23
- 57. 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
- 58. Figure 2.24
- 59. 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
- 60. 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.
- 61. Figure 2.25
- 62. 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
- 63. 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 Cell