Biology M200 1st EditionExam # 1 Study Guide Lectures: 1 - 6Lecture 1 (January 13)Microbiology: Introduction IDefine Microbiology. It is a science that follows the scientific method.The study of small (microscopic) organisms:-All 6 organisms are considered microbes (bacteria, archaea, protists, algae, fungi, viruses). The first five are considered microorganisms and include: bacteria, archaea, protists, algae, and fungi.All living things are organized into one of three domains:- Bacteria- Archaea. - EucaryaProkaryotes include: Bacteria and ArchaeaEukaryotes include: Protists, algae, and fungi (small, yet incredibly diverse)Eukaryotes:-organelles-Nucleus (membrane-enclosed)-Multiple, linear chromosomes-80S ribosomesProkaryotes:-No organelles-“Nucleoid” (no membrane)-single, circular chromosomes-70S ribosomes- Viruses are not microorganisms, they are parasites! (considered microbes), and do not obtain or use nutrients and energy in the traditional sense. Lecture 2 (January 15) Microbiology: Introduction IIHow many kinds of microbes are there? It depends on how you name them.- Nomenclature- a system of naming- Taxonomy- placing organisms in groups (classification)Biological Nomenclature:- Domain- the highest taxonomic rank- There are only three domains: archaea, bacteria, and eucarya- The name always begins with the genus and the second name is the species.- Species- an interbreeding population that is reproductively isolated.- Bacteria do not sexually reproduce- This method fails!!!Numerical Taxonomy:- Name bacteria based on trait SIMILARITY.- If two microorganisms share enough “important” traits then they are the same species.- As you go up classes, they become more inclusive.- Disadvantages: Trait choice is arbitrary, all traits are weighted equally, some traits are simple while others very complex, and the same trait may arise through different mechanisms.Phylogenetics:- Taxonomy based on similarity of gene sequences.- As time passes, microorganisms evolve, and their gene sequences slowly change.- Organisms with fewer changes between their gene sequences are more closely related.- Gene sequences must meet the following criteriao Found in all representatives of the group studied.o Function must be the same in all representatives.o Sufficient similarity between genes so that the sequences can be aligned.o Sufficient differences such that each sequence has its own signature.- Disadvantage: universal but does NOT tell you about the properties of the organism.Naming by disease:- Pathogenic species are named based on the disease they cause.Overall complication to naming bacteria:- Characterization can be a long and difficult process- Some important traits can be hard to observe.- There are more bacteria than microbiologists.- Some bacteria can’t be grown in the lab.- Naming is dynamic, names change as we learn more. Lecture 3 (January 20)Microbes: What are they made of?Atoms:- The smallest chemical unit of matter.- Protons: positively charged- Neutrons: uncharged- Electrons: negatively charged subatomic particles.Chemical Bonds:- Atoms like to have a full outer shell - Covalent bond: sharing of a pair of electrons by two atoms.- Nonpolar Covalent bond: pair of electrons is nearly equally shared between two atoms.- Hydrogen bond: A weak ionic bond between hydrogen and an atom with a slightly negative charge.Polysaccharide function:- Energy source (carbohydrates)o Found out in the environment- Structural componento Cell wallo Capsules- Informationo Sugar pattern on cell surface can identify microorganisms.Capsules:- Extracellular polysaccharide coat- Capsules help Xanthomonas campestriso Prevent from drying outo Attach to its hostProteins:- Very complex structures/shapes- Enzymeso Do almost all of the work in a cello Catalyze reactionso Synthesize and assemble the cell parts.- Structureo Internal and externalNucleic Acids:- Information storageo Genetic material, DNA chromosomeo Information conversion (transcription, translation)- Structureo Ribosome- Energy intermediateo Energy “currency” (ATP/NADH)Lecture 4 (January 22)Cell structure- Cell membranes: separate the “inside” from the “outside”o Permeability barriero Prevents sugar from entering the cell.o Membranes are fragile- Thermal Damageo Heat speeds up molecular motion so cell compensates with saturated fatty acids.o Cold slows down molecular motion so cell compensates with unsaturated fatty acids.- Gram Positive cell architectureo Thick external wall of Peptidoglycano Cell membraneo Rigid external wall protects the cell membrane from osmotic pressure.o Teichoic acids: protect the cell membrane from chemicals.- Gram Negative Architecture:o Outer membraneo Peptidoglycano Cell membraneo Outer membrane shields peptidoglycan and cell membraneo Lipopolysaccharide (LPS): barrier against chemicalso Porin: channel through the outer membrane- Flagella (prokaryotes)o Corkscrew structures that extend beyond the cell surface o Rotates like a propellero Provide motility to the cell Made of proteins- Cell Interioro Cytoplasm:  70% water No empty space and very little “free” water Wide variety of proteins and chemicalso Nucleus Contains the chromosomes- Flagella and Cilia (eukaryotes)o Encased by the cell membraneo Both used for movemento Made of protein (tubulin)o Cilia are shorter and more numerous than flagella.- Endoplasmic Reticulumo Hollow, net-like, tubeso Transport system within a cello Rough ER: ribosomes on the surface make proteins, which are then transported around the cell.o Smooth ER: lipid synthesis and transport.Lecture 5 (January 27)Growth and Metabolism IMetabolism = catabolism + anabolism- Catabolism- reactions that breakdown larger molecules into smaller molecules and energy.- Anabolism- reactions that assemble small molecules into larger molecules and biomass. - Metabolic classeso Energy source: Chemo-troph and photo -tropho Electron source- organo- troph and litho -tropho Carbon source- hetero- troph and auto- troph- Glucose Metabolismo First step: glycolysis (chemical reactions catalyzed by an enzyme)o Second step: either respiration (Krebs cycle, electron transport chain) or fermentation.- Growth= population growth (increase in cell number, not necessarily size)- Exponential Growtho The time between generations is the same.o Cells double at the same rate. Lecture 6 (January 29)Growth and Metabolism IIWhat conditions influence bacterial growth?- Temperatureo Metabolism optimized