Microbiology Core Concepts

Title: URL Source: blob://pdf/e903f732-85d2-4062-ad0d-6c5c2448bf47 Markdown Content: Biology 303 General Microbiology Biology 303 General Microbiology I. Introduction: Course learning outcomes: Demonstrate an understanding of core concepts of microbiology . Demonstrate an understanding of hypotheses testing and experimental design . Display proficiency in basic microbiological laboratory skills . Record, interpret and evaluate scientific data . Communicate the fundamental concepts of microbiology , both in written and in oral format. Analyze, interpret and evaluate a range of scientific literature in microbiology. Loading BIOLOGY 303 General Microbiology Fall 2024 Dr. Juliette K. Tinker [email protected] > Lectures Tues/Thurs 1:30-2:45 Math BIDG113 > Labs Wed/Fri > Sections A-D Assessment: Lecture 3 lecture exams (multiple choice, Canvas testing center) (100pts) 1 final lecture exam (multiple choice, Canvas testing center) (100pts) Weekly lecture assignments (LA) (50 pts) iClicker lecture questions (50 pts) Laboratory 2 laboratory practical exams (100pts) 1 written laboratory report (30pts) 1 laboratory unknown presentation (40pts) 1 laboratory notebook (30pts) 700 total The Laboratory. Will learn the essentials of microbiology here: sterile technique plating/culturing isolation., characterization and idenfitication microorganims DNA extraction and molecular analysis quantification of bacteria biochemical assays phage quantification food and water microbiology bacterial physiology Loading ## Expectations Your time! Your work: https://www.boisestate.edu/online/admitted/time-management/ https://deanofstudents.boisestate.edu/student-code-of-conduct/ Academic Integrity Guidelines for AI DO Use AI For Brainstorming and ideation Understanding complex concepts Organizing your thoughts Getting feedback on your work Research and source discovery Study strategies and planning Use Caution With Direct answers to homework questions Complete essay or paper writing Take-home exams or quizzes Group project individual contributions Always check your professor's AI policy Best Practices Always cite AI assistance when required Use AI to enhance, not replace, your learning Verify information from AI responses Use AI responsibly and ethically !! boisestate.ai Chapter 1. The Microbial World Introduction to Microbiology 1.1 Exploring the Microbial World Classification and cell structure 1.4 Molecular Biology and the Unity and Diversity of Life Some history 1.3 Microbial Cultivation Expands the Horizon of Microbiology Introduction to Microbiology Microbes changed the world. so we could live here > Micro organisms 2015 Pearson Education, Inc. Figure 1.5 Mammals Humans Vascular plants Shelly invertebrates ~20% O 2 Algal diversity O 2 Modern eukaryotes Origin of cyanobacteria Earth is slowly oxygenated Anoxic Earth Present Origin of cellular life Anoxygenic phototrophic bacteria Origin of Earth (4.6 bya) 1 4 32 bya bya bya bya LUCA bya Bacteria Archaea Eukarya 4 3 2 1 0Loading Bacteria are the oldest living things on the planet 3.5 to 4 billion years ago Fossilized cyanobacteria Modern day stromatolites Cyanobacteria: perform oxygenic photosynthesis > Fossilized Matts > Phosphoriization ## Microorganisms live everywhere ## that life is possible . > ???? NH4+ for plants NH4+ for proteins N fixation ( N2 NH4+) Microorganisms are essential for life www.bbc.co.uk Figure 1.7 > Microorganisms can pull out carbon& nitrogen > and insert Microbial decomposition: all things must break down Microorganisms are essential for death. > Break down organic. materials (fungi) Where most of the microbes are: 2015 Pearson Education, Inc. Figure 1.9 Soyb ean plant Rumen Grass Cellulose Glucose Microbial fermentation Fatty acids (Nutrition for animal) CO 2 + CH 4 (Waste products) ## Microorganisms and agriculture 2015 Pearson Education, Inc. Figure 1.11 GLUCOSE Propionic acid + Acetic acid + CO 2 2 Lactic acid 2 Ethanol + 2 CO 2 2 Acetic acid Fermentations Fermented foods Microorganisms make food Microorganisms ## live in ## communities > Figure 1.1 Dynamic interaction between host/bacteria: Can result in: 1) transient colonization 2) long-term symbiotic relationship 3) disease What? Microbial cells outnumber our own cells in body 10:1 well not really, more like 1:1 BUT STILL pretty shocking > Some links: Bonnie Bassler, > Yale More like a 1:1 ratio - ## Impact of microorganisms on humans.. Nearly 2,000 different microbes cause disease 10 B infections/year worldwide 13 M deaths from infections/year worldwide > Figure 1.8 ## iClicker Question Lecture 1 Which of the following is NOT a reason why microbiology is important.for everyone? A. microorganisms live everywhere that life is possible B. microorganisms are the oldest forms of life C. microbiology is required for the MCAT D. microorganisms cause significant disease and death E. microorganisms break down organic material and make food Classification and Basic Cell Structure The Tree of Life ARCHAEA BACTERIA EUKARYA Green nonsulfur bacteria Mitochondrion Gram- positive bacteria Proteobacteria Chloroplast Cyanobacteria Green sulfur bacteria Thermotoga Thermodesulfobacterium Aquifex Crenarchaeota Thermoproteus Pyrodictium Thermococcus Nitrosopumilus Pyrolobus Methano- bacterium Euryarchaeota Methanosarcina Thermoplasma Methanopyrus Extreme halophiles Entamoebae Slime molds Animals Fungi Plants Ciliates Flagellates Trichomonads Microsporidia Diplomonads Macroorganisms Figure 1.5 Figure 1.36 Aren't looking under microscope Procaryotes Microbes classified into 7 main groups: 1) Archaea- prokaryotic 2) Protozoa eukaryotic 3) Algae-eukaryotic 4) Bacteria - prokaryotic 5) Fungi- eukaryotic, larger more complicated 6) Small invertebrates eukaryotic, most complex 7) Viruses what??? Prions???? Prokaryotic = single cell organism, no nucleus, no mitochondria, no Golgi, outer cell wall, typically smaller (1 mm in diameter) Bacteria and Archaea Eukaryotic = unicellular or multicellular, nucleus, mitochondria, Golgi, typically larger (10-100 mm diameter) Classification > protein ## Characteristics of microbes Microorganisms vary greatly in size ## and shape.. https://learn.genetics.utah.edu/content/cells/scale/ > Figure 1.38 2015 Pearson Education, Inc. Figure 1.3 Cell wall Cytoplasmic membrane Nucleoid Cytoplasm Plasmid Ribosomes Bacteria Archaea Prokaryote Eukaryote Eukarya Cell wall Cytoplasmic membrane Mitochondrion Nuclear membrane Ribosomes Endoplasmic reticulum Cytoplasm Golgi complex Nucleus Loading 2015 Pearson Education, Inc. Figure 1.4 Properties of all cells: Metabolism Cells take up nutrients, transform them, and expel wastes. 1. Genetic (replication, transcription, translation) 2. Catalytic (energy, biosyntheses) Properties of some cells: Cell Environment Some cells can form new cell structures such as a spore. Spore Cells interact with each other by ehemical messengers. Differentiation Communication Growth Nutrients from the environment are converted into new cell materials to form new cells. Evolution Genetic exchange Motility Cells can exchange genes by several mechanisms. Cells evolve to display new properties. Phylogenetic trees capture evolutionary relationships. Donor cell Recipient cell DNA Some cells are capable of self-propulsion. Flagellum Distinct species Distinct species Ancestral cell All cells bateria , Fungi > ~ exchange horizontal give transfer mutate & change iClicker Question Lecture 1 Which of the following is smaller than a bacterial cell ? A. a red blood cell B. a yeast cell C. a photoreceptor in the eye D. a grain of salt E. an HIV virus particle Some History. Antoni van Leeuwenhoek (16321723): the first to describe bacteria (Figure 1.14) > First to discover microorganisms and made microscope Founding microbiologists : Louis Pasteur (1822-1895) Robert Koch (1843-1910) > $^% > @$#& > ! *&!$# !! Louis Pasteur Father of Microbiology Showed microbes caused fermentation & spoilage. Disproved spontaneous generation. Developed aseptic techniques. Developed a rabies vaccine. (1822-1895) > (Mold goes on bread for no reason) > Initiated germ theory disease > - disease can be caused by microorganisms disproved 2015 Pearson Education, Inc. Dust and microorganisms trapped in bend Steam forced out open end Open end Nonsterile liquid poured into flask Neck of flask drawn out in flame Liquid sterilized by extensive heating Flask tipped such that microorganism-laden dust contacts sterile liquid Liquid putrefies Liquid cooled slowly Liquid remains sterile indefinitely Long time Short time Figure 1.26 Robert Koch Established a sequence of experimental steps to show that a specific microorganism causes a particular disease. Developed pure culture methods. Identified cause of anthrax, TB, & cholera. > (1843-1910) 2015 Pearson Education, Inc. KOCH'S POSTULATES Theoretical aspects Postulates: Laboratory tools: Microscopy, staining 1. The suspected pathogen must be present in all cases of the disease and absent from healthy animals. 2. The suspected pathogen must be grown in pure culture. Laboratory cultures Experimental animals 3. Cells from a pure culture of the suspected pathogen must cause disease in a healthy animal. 4. The suspected pathogen must be reisolated and shown to be the same as the original. Laboratory reisolation and culture Suspected pathogen Colonies of suspected pathogen Suspected pathogen Red blood cell Diseased animal Healthy animal Red blood cell No organisms present Observe blood/tissue under the microscope. Streak agar plate with sample from either a diseased or a healthy animal. Inoculate healthy animal with cells of suspected pathogen. Remove blood or tissue sample and observe by microscopy. Diseased animal Laboratory culture Pure culture (must be same organism as before) Experimental aspects Figure 1.29 how determine how a geri causes acertain disease Martinus Beijerinck (18511931) Sergei Winogradsky (18561953) Figure 1.32 Figure 1.33 > Isolated pure environmental Microbiology bacterial cultures from so :1 > o first to Identify > a vimscobar ) > discovered nitrogen cycling in soil > discovered microbes are the source of utilizable nitrogen Other pioneering microbiologists Angelina Fanny Hesse Lydia Villa-Komaroff Susumu Tonegawa Harold Amos Esther Lederberg Reyes Tamez > esse Guerra ## Modern Microbiology Applied and Basic EXAMPLES: Virology : the study of viruses Bacteriology : the study of bacteria Medical microbiology : infectious diseases Immunology : immune system Industrial microbiology : production of antibiotics, alcohols, and other chemicals Biotechnology : products of genetically engineered microorganisms Microbial systematics: the science of grouping and classifying microorganisms Microbial physiology : Study of the nutrients that microbes require for metabolism and growth and the products that microorganisms generate Microbial ecology: Study of microbial diversity and activity in natural habitats Lecture 2 : Chapters 1 and 2. Microscopy and Microbial Cell Structure and Function: Microscopy, cell size and shape, cell membranes and transport, cell walls.. Chapter 1 II. Microscopy and the origins of microbiology Compound light microscope uses visible light to illuminate cells Many different types of light microscopy: Bright-field Phase-contrast Dark-field Fluorescence (bright back , organism dark for staining) (Loading Bright-field scope (Figure 1.2) Specimens are visualized because of differences in contrast (density) between specimen and surroundings Two sets of lenses form the image Objective lens and ocular lens Total magnification = objective magnification ocular magnification Maximum magnification is ~2,000 > 10 X highest > - > 4X 100X(01) x10 x = 1000 X > - > 10X > 48x resolution :dependent upon Waveleng th of light using 100X0i1) R =0. 52/NA Figure 1.2 Ocular lenses Objective lens Stage Condenser Focusing knobs Light source Specimen on glass slide Loading Figure 1.2 Visualized image Ey e Ocular lens Intermediate image (inverted from that of the specimen) Objective lens Specimen Condenser lens Light source None 10X, 40X or 100X(oil) 10 X Magnification 100X, 400X, 1000X Light path Magnification : the ability to make an object larger Resolution : the ability to distinguish two adjacent objects as separate and distinct Contrast: diference in intensity between two objects or backgound Wavelength : difference between two corresponding parts of a wave > dependent on in of light used Figure 1.23 Procedure Result 1. Flood the heat-fixed smear with crystal violet for 1 min 2. Add iodine solution for 1 min 3. Decolorize with alcohol briefly about 20 sec 4. Counterstain with safranin for 12 min All cells purple All cells remain purple Gram-positive cells are purple; gram-negative cells are colorless Gram-positive (G +) cells are purple; gram-negative (G ) cells are pink to red G G + The Gram Stain contrast of specimen Via Stain > & differential > Simple-1 due > differential Stain - 2 or more > ex : gram stain kinds : Acidic : bind to pos charges ## - basic : bind to neg charges most structures of cells Ba of differences in cell Wall & cell membrane Structure Figures 1.24 and 1.27 Phase-contrast microscopy Dark-field microscopy Confocal scanning laser microscopy (CSLM) z # &Figure 1.29 electron microscopy uses electrons & higher > X a) proteins Loading Chapter 1: 1.3 Cell size and morphology Morphology = cell shape Major cell morphologies (Figure 2.11) Coccus (pl. cocci) : spherical or ovoid Rod : cylindrical shape Spirillum : spiral shape Figure 1.8 Morphology: cell shape Cocci:sphere (circle) Bracili: rod Spirochete: spiral Spirillum: thin hair spiral Helicol/vibrio Pleiomorphic Aggregate: binding to each other Cocci:. strepto stophylo tetrads Sardinia diplo Bacilli corynebacterium palisades > E Size range for prokaryotes: 0.2 m to >700 m in diameter Most cultured rod-shaped bacteria are between 0.5 and 4.0 m wide and < 15 m long Examples of very large prokaryotes Epulopiscium fishelsoni (Figure 1.6) Thiomargarita namibiensis (Figure 1.6 ) Size range for eukaryotic cells: 10 to >200 m in diameter The Small World > Advantages of being small: > -More surface area to volume ratio > supports more efficient nutrient exchange > can grow/replicate faster Figure 1.6 Thiomargarita namibiensis : WORLDS LARGEST BACTERIA The Small World Surface-to-volume ratios, growth rates, and evolution Advantages to being small (Figure 1.7) Small cells have more surface area relative to cell volume than large cells (i.e., higher S/V) Support greater nutrient exchange per unit cell volume Tend to grow faster than larger cells > Volume of a coccus > Function of the cube of the radius > Surface area of coccus > Function of the square of the radius > I want a small radius for a large s/v ratio > - want large s/v ratio to grow fast EX : 2 1011 S/ = 4. 5 macrophage SN : 2 myroplasm /=22 Figure 1.7 I. The Cell Envelope Chapter 2: Microbial Cell Structure and Function 2.1 Membrane Structure Cytoplasmic membrane Thin structure that surrounds the cell Vital barrier that separates cytoplasm from environment Highly selective permeable barrier; enables concentration of specific metabolites and excretion of waste products 2.1 Membrane Structure Composition of membranes General structure is phospholipid bilayer (Figure 2.14) Contain both hydrophobic and hydrophilic components Can exist in many different chemical forms as a result of variation in the groups attached to the glycerol backbone Fatty acids point inward to form hydrophobic environment; hydrophilic portions remain exposed to external environment or the cytoplasm R "head group" > I > 10 Phosphate glycerol Phospholipid bilayer hydrophobic 1 fatty acid & tructure for all # & U fatty acids > membraces obacteria > Phosphate glycerol tI &"head group - Eukarya > NOT Archaea Figure 2.1 Fatty acids Phosphate Ethanolamine Fatty acids Hydrophilic region Hydrophobic region Hydrophilic region Glycerophosphates Fatty acids Glycerol 2.1 Membrane Structure Cytoplasmic membrane (Figure 2.2) 810 nm wide Embedded proteins Stabilized by hydrogen bonds and hydrophobic interactions Mg 2+ and Ca 2+ help stabilize membrane by forming ionic bonds with negative charges on the phospholipids Somewhat fluid Figure 2.2 Phospholipids 68 nm Integral membrane proteins Hydrophilic groups Hydrophobic groups Phospholipid molecule Out In Membrane Structure Membrane proteins Integral membrane proteins Firmly embedded in the membrane Peripheral membrane proteins One portion anchored in the membran e Di ff erences between archael membranes and bacterial/eukaryot membrane 1) ether link instead of ester link between phosphate and fatty acid, 2) archaea have short carbon chains called isoprenes instead of fatty acids 3) archea can have monolayers instead of bilayers 4) archaea often have more unsaturated lipids Membrane Structure Archaeal membranes Ether linkages in phospholipids of Archaea (Figure 2.3) Bacteria and Eukarya that have ester linkages in phospholipids Archaeal lipids lack fatty acids; have isoprenes instead Major lipids are glycerol diethers and tetraethers Can exist as lipid monolayers, bilayers, or mixture Ester Ether Bacteria Eukarya Archaea # reduc aturation a Isoprene tFigure 2.3 Phytanyl Glycerol diether CH 3 groups Isoprene unit Biphytanyl Diglycerol tetraethers Crenarchaeol Out Out In In Glycerophosphates Phytanyl Membrane protein Lipid monolayer Biphytanyl or crenarchaeol Lipid bilayer Membrane Function Permeability barrier Protein anchor Energy conservation Functions of the cytoplasmic membrane Permeability barrier: Prevents leakage and functions as a gateway for transport of nutrients into, and wastes out of, the cell Protein anchor: Site of many proteins that participate in transport, bioenergetics, and chemotaxis Energy conservation: Site of generation and dissipation of the proton motive force Figure 2.4 Loading 2.2 Transporting nutrients into the cell http:// what-when-how.com/neuroscience/electrophysiology-of-neurons-the-neuron-part-1/ Nutrient Transport Active transport systems Show saturation effect Highly specific Three major classes All require energy in some form - usually ATP Figure 2.5 Types of solutions /external chemical environments isotonic: concentration of solutes (dissolved chemicals) Hypotonic: solute concentration is lower on outside of cell t > I > + )Phospholipid membrane : esther & ether Eukaryotic Cell membranes batteria Larchard - same as bacteria membranes Eukaved except :- have sterols (cholestera) to stabilize T perform unique functions endocytosis : creation of Vesicles to take In nutrients exocytosis : export of wastes in Vesicles prokaryotic all wall/all membrance structure gram pos regate Archaea gram ,all wall (PEP) thin Ch wall # a Ins T thick S Amino acid DAP # SCn aare cell wall : peptidoglycan (PEP) teichoid acids charged fatty acid 2.3 Cell Walls of Bacteria and Archaea Peptidoglycan Figure 2.7 > 2membranes 2. 4 Peptidoglycan Species of Bacteria separated into two groups based on Gram stain Gram-positives and gram-negatives have different cell wall structure (Figure 2.7) Gram-negative cell wall > Two layers: LPS and peptidoglycan Gram-positive cell wall > One layer: peptidoglycan Peptidoglycan Rigid layer that provides strength to cell wall Polysaccharide composed of: N-acetylglucosamine and N-acetylmuramic acid Amino acids Lysine or diaminopimelic acid (DAP) Cross-linked differently in gram-negative bacteria and gram- positive bacteria (Figure 2.26) peptidoglycan (PEP) -LyjD-don Differences of Archael all wali - -trampos all No peptidoglycan B(1 ,4) link can have pserdouve in #N PNAG-NAT) Laconive - B(1-3) link some have protein layer D-glutemine (D-Glu -NH2) > Stayer I 2 - Lysine I Ddonine IS - 45 glycine bridge Differences - # am neak i-girtemic acid () direct link () N - archive & L-aconive gram pos thicker I L-glutamic adid L-glutanic acid () L-glutamic acid -DA --donine DAP - D-Glenie direct link Figure 2.9 Polysaccharide backbone Peptides Interbridge Escherichia coli (gram-negative) Staphylococcus aureus (gram-positive) Peptidoglycan Gram-positive cell walls (Figure 2.10) thick, have teichoic acid and lipoteichoic acid, contain glycine bridge and L-lys Gram-negative cell walls thin, do not have teichoic acid, contained in periplasmic space, no glycine bridge and DAP Figure 2.10 Peptidoglycan cable Teichoic acid Peptidoglycan Lipoteichoic acid Cytoplasmic membrane Wall-associated protein Chapter 2: Microbial Cell Structure and Function: Archaeal cell walls, LPS, cell surface structures, vesicles, endospores, flagella, eukaryotic surface structures . > http://www.bif.kit.edu/58.php 2.3 Archaeal Cell Walls No peptidoglycan Typically no outer membrane Pseudomurein found in some methanogens > Polysaccharide similar to peptidoglycan > Composed of N-acetylglucosamine and N- > acetylalosaminuronic acid (Figure 2.11) Cell walls of some Archaea lack pseudomurein S-layers are most common cell wall type in Archaea Loading Figure 2.14 Loading 2.4 LPS: The Outer Membrane in GRAM NEGATIVE BACTERIA Total cell wall contains ~10% peptidoglycan Most of cell MEMBRANE composed of outer membrane , aka lipopolysaccharide (LPS) layer LPS consists of core polysaccharide and O-polysaccharide (Figure 2.13) LPS replaces most of phospholipids in outer half of outer membrane (Figure 2.12) Endotoxin : the toxic component of LPS Figure 2.13 O-specific polysaccharide Core polysaccharide Lipid A Protein Lipopolysaccharide (LPS) Phospholipid Porin Porin Lipoprotein Outer membrane Periplasm Cytoplasmic membrane 8 nm Out Cell wall Outer membrane Periplasm Cytoplasmic membrane Peptidoglycan Peptidoglycan In Figure 2.12 2.4 LPS: The Outer Membrane Structural differences between cell walls of gram-positive and gram-negative Bacteria are responsible for differences in the Gram stain reaction Chapter 2. II. Other Cell Surface Structures and Inclusions 2.6 Cell Surface Structures 2.7 Cell Inclusions and gas vesicles 2.8 Endospores Loading 2.7 Cell Surface Structures Capsules and slime layers Polysaccharide layers (Figure 2.16) May be thick or thin, rigid or flexible Assist in attachment to surfaces Protect against phagocytosis Resist desiccation Figure 2.16 2.6 Cell Surface Structures Fimbriae Filamentous protein structures (Figure 2.17) Enable organisms to stick to surfaces or form pellicles > Flage > lla > Fimbr > iae Figure 2.17 Cell Surface Structures Pili Filamentous and longer than fimbriae Assist in surface attachment Facilitate genetic exchange between cells (conjugation) Type IV pili involved in twitching motility > Virus- > covered > pilus Figure 2.18 2.7 Cell Inclusions Carbon storage polymers Poly--hydroxybutyric acid (PHB) : lipid Glycogen : glucose polymer Polyphosphates : accumulations of inorganic phosphate Sulfur globules : composed of elemental sulfur Carbonate minerals : composed of barium, strontium, and magnesium Magnetosomes : magnetic storage inclusions (Figure 2.24) Figure 2.24 https://phys.org/news/2018-09-magnetic-bacteria-unique- superpower.html Gas Vesicles Gas vesicles Confer buoyancy in planktonic cells Spindle-shaped, gas-filled structures made of protein Impermeable to water Figure 2.23 2.8 Endospores Endospores Highly differentiated cells resistant to heat, harsh chemicals, and radiation Dormant stage of bacterial life cycle Ideal for dispersal via wind, water, or animal gut Present only in some gram- positive bacteria > Exos > poriu > m > Spo > re > coat > Cor > e > wall > C > or > te > x > D > N > A Figure 2.28 Figure 2.26 III. 2.9 Flagella and Swimming Motility Flagella : structure that assists in swimming Different arrangements: peritrichous , polar , lophotrichous (Figure 2.30) Helical in shape Figure 2.30 2.11 Flagella and Motility Flagellar structure of Bacteria Consists of several components Filament composed of flagellin Move by rotation Flagellar structure of Archaea Half the diameter of bacterial flagella Composed of several different proteins Move by rotation > 1520 nm > Filament > Flagellin > L > P > MS > Hook > Outer > membrane > (LPS) > L Ring > P Ring > Rod > Peptidoglycan > Periplasm > MS Ring > Basal > body > C Ring > Cytoplasmic > membrane > Fli proteins > (motor switch) > Mot protein Mot protein > 45 nm > Rod > MS Ring > C Ring > Mot > protein > ++++++++ > Figure 2.34 Figure 2.33 Bundled flagella (CCW rotation) Tumble flagella pushed apart (CW rotation) Flagella bundled (CCW rotation) CCW rotation Unidirectional flagella Reversible flagella CW rotation CW rotation Cell stops, reorients CW rotation Peritrichous Polar 2.11 Chemotaxis and Other Taxes Taxis : directed movement in response to chemical or physical gradients Chemotaxis : response to chemicals Phototaxis : response to light Aerotaxis : response to oxygen Osmotaxis : response to ionic strength Hydrotaxis : response to water Income Taxes: (just kidding) Figure 2.39 Tumble Run Run Attractant No attractant present: Random movement Attractant present: Directed movement Tumble Barbara Irene Kazmierczak , PhD, MD Professor of Medicine (Infectious Diseases); Director, MD-PhD Program, Yale University; Professor of Microbial Pathogenesis Avraham Beer Physics Department Ben-Gurion University of the Negev https://www.nature.com/articles/s41598-022-20644-3#Sec17 Mixed species swarming Chapter 2. IV. Eukaryotic Microbial Cells 2.13 The Nucleus and Cell Division 2.15 Mitochondria, Hydrogenosomes, and Chloroplast 2.16 Other Major Eukaryotic Cell Structures Smooth endoplasmic reticulum Rough endoplasmic reticulum Cytoplasmic membrane Mitochondrion Microfilaments Ribosomes Flagellum Mitochondrion Microtubules Figure 2.42 Microfilaments Lysosome Chloroplast Nuclear envelope Nuclear pores Nucleolus Nucleus Golgi complex Loading 2.14 The Nucleus and Cell Division Nucleus : contains the chromosomes (Figure 2.46) DNA is wound around histones (Figure 2.46b) Enclosed by two membranes Within the nucleus is the nucleolus Site of ribosomal RNA synthesis > Nucle > us Nucl > ear > pores > Vacu > ole Lipid > vacuo > le > Mitochon > dria > Double- > stranded > DNA > Nucleoso > me core Histo > ne H1 > Core > histone Figure 2.43 2.13 The Nucleus and Cell Division Cell division Mitosis Normal form of nuclear division in eukaryotic cells Chromosomes are replicated and partitioned into two nuclei (Figure 2.44) Results in two diploid daughter cells Meiosis Specialized form of nuclear division Halves the diploid number to the haploid number Results in four haploid gametes 2.14 Mitochondria and Chloroplast Mitochondria (Figure 2.45) Respiration and oxidative phosphorylation Chloroplast (Figure 2.46) Chlorophyll-containing organelle found in phototrophic eukaryotes > membrane bound in Eukaryotic Cell (photo Synthetic) Figure 2.45 Inner membrane Matrix Cristae Porous outer membrane -Figure 2.46 Chloroplast Thylakoid Stroma THE Endosymbiotic Theory Chloroplasts and mitochondria suggested as descendants of ancient prokaryotic cells (endosymbiosis ) Evidence that supports idea of endosymbiosis Mitochondria and chloroplasts contain DNA DNA is circular Mitochondria and chloroplasts contain own ribosomes Eukaryotic nuclei contain genes derived from bacteria > https://www.khanacademy.org/science/ap-biology/cell-structure-and-function/cell-compartmentalization- > and-its-origins/v/endosymbiosis-theory * able to do aerobic Evidence for endosymbiosis Isize of Mitochondria + Chloroplasts > ~ of a prokaryotic 2) Mitochondria all > + Chloroplast have double membrane > 3) Mitochondria + chloroplasts have own DNA 4) Mitochondria can divide into two by binary fission (now Eukaryotic cells duplicate) 5) Mitochondria have ribosomes like bacterial ribosomes > I 6) energy is made at membrane like prokaryotic cells The Endosymbiotic Theory Chloroplasts and mitochondria suggested as descendants of ancient prokaryotic cells (endosymbiosis ) Evidence that supports idea of endosymbiosis.. > Dr. Lynn Margulis 2.16 Other Major Eukaryotic Cell Structures Endoplasmic reticulum (ER) Golgi complex Lysosomes Microtubules , microfilaments, and intermediate filaments Flagella > Flag > ella > Ci > lia Figure 2.53 > proteins fold > proteins transport Chapter 3: Microbial Metabolism : microbial cell chemistry, nutrition, energy, electron transfer, fermentation, respiration, glycolysis, the citric acid cycle and oxidative phosphorlyation Figure 3.1 > reactants break down into products I. Fundamentals of Metabolism Metabolism The sum total of all of the chemical reactions that occur in a cell Catabolic reactions (catabolism) Energy-releasing metabolic reactions Anabolic reactions (anabolism) Energy-using metabolic reactions > - > exergon > - > Indogonic # Loading Metabolic types based on energy sources > Figure 3.3 3.1 Defining the requirements of life Energy from oxidationreduction ( redox ) reactions is used in synthesis of energy-rich compounds (e.g., ATP) Redox reactions occur in pairs (two half reactions ; Figure 3.2) Electron donor : the substance oxidized in a redox reaction Electron acceptor : the substance reduced in a redox reaction Bio energetics =All Chemical reactions that are accompanied by changes in energy in a all compounds can use energy or release energy during formation G : change in free energy (reaction between products & reactants) 1G = G[c +D] - G[A + B] products reactants exergonic-release (Catabolism) (- -G] endergonic-use of free energy (++ G) - Redox-reactions - transfer electrons Oxidation = involves loss (e-) reduction = gain (e-) (gain H) electron acceptor - electron carrier Co-enzymes > - Oxidized reduced > -- > NAD - NADH NADPt > NADPH F AD + - FADH2 Selectron acceptors Selection donors) Loading Free Energy Energy is defined in units of kilojoules (kJ), a measure of heat energy In any chemical reaction, some energy is lost as heat Free energy (G) : energy released that is available to do work The change in free energy during a reaction is referred to as G0Figure 3.2 Electron Donors and Electron Acceptors Redox couples are arranged from strongest electron donor to strongest acceptor at the bottom (Figure 3.4) Redox reactions usually involve reactions between intermediates ( electron carriers ) These are divided into two classes > Prosthetic groups (attached to enzymes) > Coenzymes (diffusible) > Examples: NAD +, NADP (Figure 3.10 ) > prote portion The redox tower > Figure 3.4 Figure 3.6 NAD + reduction NAD + binding site Product Enzyme I l Enzymesubstrate complex NAD + + NADH oxidation NADH binding site Active site Product NADH + + Substrate (e acceptor) Enzymesubstrate complex Substrate (e donor ) Enzyme I Enzyme I reacts with e donor and oxidized form of coenzyme, NAD +. 1. Enzyme II reacts with e acceptor and reduced form of coenzyme, NADH. 3. NADH and reaction product are formed. 2. 4. NAD + is released. Active site NADH dehydrogenases : Flavoproteins : Electron Carriers and NAD+/ NADH cycling 3.4 Cellular Energy Conservation Chemical energy released in redox reactions is primarily stored in certain phosphorylated compounds (Figure 3.12) > ATP; the prime energy currency > Phosphoenolpyruvate > Glucose 6-phosphate Chemical energy also stored in coenzyme A Loading Anhydride bonds Ester bond Ester bond Anhydride bond Acetyl Thioester bond Coenzyme A Anhydride bond Phosphoenolpyruvate Adenosine triphosphate (ATP) Glucose 6-phosphate Acetyl phosphate Acetyl-CoA Compound G0kJ/mol G0< 30kJ G0< 30kJ Phosphoenolpyruvate 1,3-Bisphosphoglycerate Acetyl phosphate ATP ADP AMP 51.6 52.0 44.8 31.8 31.8 35.7 14.2 13.8 Acetyl-CoA Glucose 6-phosphate Figure 3.8 3.5 Catalysis and Enzymes Enzymes Biological catalysts Typically proteins ( some RNAs) Highly specific Generally larger than substrate Typically rely on weak bonds Examples: hydrogen bonds, van der Waals forces, hydrophobic interactions Active site : region of enzyme that binds substrate helps lower activation energy > - 2015 Pearson Education, Inc. Figure 3.9 3.5 Catalysis and Enzymes II. Catabolism: Chemoorganotrophs 3.6 Respiration 3.6 Respiration: Citric Acid and Glyoxylate Cycle3 3.7 3.7 Fermentative Diversity and the Respiratory Option 3.8 Respiration: The Proton Motive Force and the Electron Transport Chain metabolic strategies base upon final election acceptor : Definition : Aerobic .Occurs in presence of 02) anaerobic : (occurs in absence of 02) 1) cellular respiration > anaerobic - final electron acceptor is element other than Oxygen (fe ,+,s -acrobie : Final electron acceptor is 02 (best , most ATP) 2) fermentation : Final election acceptor is an internal Organi compound (NAD production of Waste products like lactic acid in humans or pyrovate 3) photosynthesis metabolic to conserve energy > - final electron receptor NABP 3.6 Chemoorganotrophs Two reaction series are linked to energy conservation in chemoorganotrophs: fermentation and respiration (Figure 3.11) Differ in mechanism of ATP synthesis Fermentation : substrate-level phosphorylation; ATP is directly synthesized from an energy-rich intermediate Respiration : oxidative phosphorylation; ATP is produced from proton motive force formed by transport of electrons metabolic Strategies based on find electron acceptor Cellular respiration : utilizes glycolysis Civil acid cycle electron transport chain -Oxidative Phospholation (nowcel makes a fermentation utilizes glycosis Internal final electron acceptor compond substrate level phosphorylation not much ATp is mad photosynthes is uses light as energy uses electron transport Chain photophosphorylation to make ATP Catabolism : break down molecules to mak ATP > - & In put (ex : glucose] energy carbon electron sources -tabolic Rxn * diversity in microbes Glycolysis Citric ad aaent # Afind electron recept diversit in microbes ->energy storage ATP 3.6 Respiration: Glycolysis Glycolysis (EmbdenMeyerhof pathway) : a common pathway for catabolism of glucose (Figure 3.14) Anaerobic process Three stages Glucose is consumed Two ATPs are produced Fermentation products are generated Some harnessed by humans for consumption > https://www.youtube.com/watch?v=EfGlznwfu9U > - dosen't need 02 # Summary of glycolysis Inorganic phosphorous glucose + 2 ADP + Pj + 2 NAD + 2 pyruvate + 2 ATP + 2NADH + H20 Estages 1) 6 carbon Sugar -> 2 - 3 carbon sugars (ATPs Input 2) 3 carbon molecules dephosphorylate -> ATP made > 4AtPS made ->2 ATPs NET 3) recycling of electron carriers NAIH NADT After glycosis D) synthesis of Acetyl-CoA pyruvate arbot Acetate (Acetyl-DOA ## S 02-carbon) 02 NAD NADH 2) citill acid cycle For each Acetyl-CoA : make : 2 molences of Co 2 > - ## 3 Moews of NASA 1 GTP -ATP 2015 Pearson Education, Inc. Figure 3.11 3.6 Respiration: Citric Acid and Glyoxylate Cycle Citric acid cycle (CAC) : pathway through which pyruvate is completely oxidized to CO 2 (Figure 3.12) Per glucose molecule, 6 CO 2 molecules released and NADH and FADH generated Plays a key role in catabolism AND biosynthesis Energetics advantage to aerobic respiration > transfer elections from glycolysis to (Act More ATP made 2015 Pearson Education, Inc. Figure 3.12 Other pathways for chemoorganotropy Glyoxylate cycle Catabolism of C2-C3 organic acids typically involves production of oxaloacetate through the glyoxylate cycle (Figure 3.13) A variation of the citric acid cycle Glyoxylate is a key intermediate Rhodobacter sphaeroides Microorganism (Eukaryotic) helps all to make molecules that help W/cell structure 2015 Pearson Education, Inc. 3.7 Fermentation Figure 3.14 3.7 Fermentative Diversity Fermentations classified by products formed Ethanol Lactic acid Propionic acid Mixed acids Butyric acid Butanol 3.0 Respiration: Oxidative Phosphorylation Aerobic respiration Oxidation using O 2 as the terminal electron acceptor Higher ATP yield than fermentations ATP is produced at the expense of the proton motive force, which is generated by electron transport 3.11 Respiration: Electron Transport Chain Electron transport systems Membrane-associated Mediate transfer of electrons Conserve some of the energy released during transfer and use it to synthesize ATP Many oxidationreduction enzymes are involved in electron transport (e.g., NADH dehydrogenases, flavoproteins, iron sulfur proteins, cytochromes) > mitochondria 2015 Pearson Education, Inc. Figure 3.19 3.9 Respiration: Electron Transport Chain categories of large protein carries in membrane : electron transport chain -flavprotins (FAv) eNADH > - Ubigunones & FADH , # X imput - metol-containing (e) e NADH -Cytochromes(oxidoses) * NADI arranged In order of reduction potential strong donors -Strong, eptors Loading 3.9 Respiration: The Proton Motive Force During electron transfer, several protons are released on outside of the membrane Protons originate from NADH and the dissociation of water Results in generation of pH gradient and an electrochemical potential across the membrane (the proton motive force ) The inside becomes electrically negative and alkaline The outside becomes electrically positive and acidic 3.9 Respiration: The Proton Motive Force ATP synthase (ATPase) : complex that converts proton motive force into ATP; two components (Figure 3.20) F1: multiprotein extramembrane complex; faces cytoplasm Fo: proton-conducting intramembrane channel Reversible; dissipates proton motive force Figure 3.20 ADP + P i ATP Membrane F 1 Out Out In In F 1 b 2 F 0 F 0 b 2 c1 2 a a c 2015 Pearson Education, Inc. Figure 3.21 glycosis - carbon : glocse -> Pyrovi acid 6 3( ATP : 2ATP (per glocosel e-caries : 2 NABH (per glucose) -yrvic acid & Acetol CoA carbon : pyrvic acid & Acetyl-CoA )+ loseca) 3L 2 e carries : 2NADH (per glucose) HAcid Cycle carbon : 2c + 6195C + 4c (Close (02) ATP : 2ATP (GTP] (per glucose) ecaWies :GNADY per gos He ETC : Selectron transport chain) - glycolysis , CAC , pyrvat acid 10 NADH = 30 ATP CAC 2 WADH2 = (Citric acid cycl) 4 ATPs > = 34 ATPs #HATP Gr glucose For prokaryotes ! 36 ATD for Eukaryote So energy can get out of mitochondria 2 net ATP in fermentation Chapter 3: Microbial Metabolism Chapter 14: Metabolic Diversity The ISME Journal (2011) 5, 17351747 Loading Microbes have diverse options of sources and methods of energy conservation: Microorganisms demonstrate a wide range of FI NAL ELECTRO N ACCEPTORS (metabolic strategies ) > Aerobic respiration > Anaerobic respiration > Fermentation > Photosynthesis Microorganisms also demonstrate wide range of sources of ENERGY, ELECTRO NS and CARBO N(Figure 3.22) (primary nutritional groups ) > Figure 3.22 # Loading I. Microbial Types of metabolism based on FI NAL ELECTRO N ACCEPTOR (metabolic strategies) 1) Cellular respiration: Aerobic Anaerobic 2) Fermentation 3) Photosynthesis * 3.10 Catabolic Diversity :Anaerobic respiration Anaerobic respiration The use of electron acceptors other than oxygen Examples include nitrate (NO 3), ferric iron (Fe 3+ ), sulfate (SO 42 ), carbonate (CO 32 ), certain organic compounds Less energy released compared to aerobic respiration Dependent on electron transport, generation of a proton motive force, and ATPase activity > no 02 (fermination) microorganisms E > marobical > - > - > - > electron transport chains -14. IV. Respiratory Processes Defined by Electron Acceptor * Final electron acceptor not oxygen= anaerobic 14.11 Nitrate Reduction and Denitrification 14.13 Other Electron Acceptors Principles of Anaerobic Respiration In anaerobic respiration, electron acceptors other than O 2 are used Anaerobic and aerobic respiratory systems are similar But anaerobic respiration yields less energy than aerobic respiration Energy released from redox reactions can be determined by comparing reduction potentials (Figure 14.39 ) > - eless energy > moving electrons > - > > different Waste Figure 13.39 Figure 14.1 good final -- receptor > - averbo resp. > - > +free energy Respiration and nitrate-based anaerobic respiration in Escherichia coli . Figure 3.23 > - > can do both > acrolis # Loading 14.13 Other Electron Acceptors Fe 3+ , Mn 4+ , ClO 3, and various organic compounds can serve as electron acceptors for bacteria (Figure 14.52) Fe 3+ is abundant in nature, and its reduction is a major form of anaerobic respiration > not much detail Question II. Microbial metabolism based on sources : Microbial PRIMARY NUTRITIO NAL GROUPS 1) Source of ENERGY CHEMO PHOTO 2) Source of ELECTRONS (i.e. ELECTRON DONOR) ORGANO LITHO 3) Source of CARBON AUTO HETERO > important > diversity In beginning Microbial Primary nutritional groups > - source of energy , elections , carbon gets] Ever chemotroph-chemical source of energy - #totroph-light (photosynthesis Elections Lithotroph-Morganic chemical ganotroph-organi Chemical > H+ carbon #tenotroph-organic Chemical Structure Autotroph-CO2 6.101 % > - Chemo , organo heterotroph > -- energy elections carbon gorse ralstonia chemo litho , autotroph -a #2 H2 We IIA. Chapt 3.11 Chemotrophy * source of energy = chemicals Figure 3.3 IIB. Chapt 14. Phototrophy *source of energy = light Photosynthesis and Chlorophylls Anoxygenic Photosynthesis Oxygenic Photosynthesis > T 14.3 Photosynthesis and Chlorophylls Photosynthesis is the conversion of light energy to chemical energy Phototrophs carry out photosynthesis Most phototrophs are also autotrophs Photosynthesis requires light-sensitive pigments called chlorophylls Photoautotrophy requires ATP production and CO 2 reduction > microorganism > help capture light Prokaryotic phototrophs Purple and green bacteria Cyanobacteria Anoxygenic Light ADP ATP Reducing power Carbon Energy Oxygenic Reducing power Carbon Energy electrons electrons electrons ADP Light ATP Figure 14.5 don't need Need 02 82 microbial photosynthesis - oxygenic : > - uses tho as source of elelations > - make 02 > - 2 photosystems - electron transport chains Z-scheme > - Anoxygenic : > - using inorganic molecule other than H20 as election donor > - make gas as waste ex :sulfur > - 1photosystem - electron transport > - lessATP is made Figure 14.8 14.6 Oxygenic Photosynthesis Oxygenic phototrophs use light to generate ATP and NADPH The two light reactions are called photosystem I and photosystem II "Z scheme " of photosynthesis (Figure 14.14) > Photosystem II transfers energy to photosystem I ATP can also be produced by cyclic photophosphorylation Figure 14.14 A comparison of electron flow in anoxygenic and oxygenic phototrophs. > Figure 14.16 II.C. 3.11 and 3.12 Phototrophy and Autotrophy * source of energy = light * source of carbon = CO 2 The Calvin cycle (Figure 3.27) Named for its discoverer, Melvin Calvin Fixes CO 2 into cellular material for autotrophic growth Requires NADPH, ATP, ribulose bisphophate carboxylase (RubisCO), and phosphoribulokinase 6 molecules of CO 2 are required to make 1 molecule of glucose (Figure 14.17) plants torn into > glucose etc . #y enzyme allows CO2 to go into sugars Calvin cycle > - used by Autotrophs to fix CO2 to organic carbon > - A lot of ATP is required to make Carbohydrates > - CO2 is source of carbon > - uses enzyme RUBISCO > = summary : > - take CO2 + 12 NADPH + 18 ATP &CH ,200 # > t reduced electron 12 NADB + > CaWiers t 18 ADP + Pi Figure 3.27 Don't need to know Chapt 14.V. One carbon metabolism 14.15 Methanogenesis *source of carbon = CO 2 Methanogenesis Involves a complex series of biochemical reactions that use novel coenzymes (Figure 14.37) > autotroph methogenesis - production of methane gas CHy by microorganism - mostly archate > - Anaerobic respiration z final electron acceptor is co2-Strategy > - primary nutiction groups > - energy - H, chemotroph elections - He lithotroph Carbon - CO2 Autotroph > - Important waste product - met have gas > - II.D. Chapt 3.11 Lithotrophy * source of electrons = chemicals Energy conservation in Ralstonia eutropha , an autotrophic chemolithotroph that oxidizes H2 Figure 3.24 Chapt 14. III. Respiratory Processes Defined by Electron Donor : lithotrophy 14.7 Oxidation of Sulfur compounds *source of electrons = sulfur 14.9 Nitrification 14.9 Nitrification *source of electrons = nitrogen 14.7 Oxidation of Sulfur Compounds Figure 14.20 Loading 14.9 Nitrification NH 3 and NO 2 are oxidized by nitrifying bacteria during the process of nitrification Two groups of bacteria work in concert to fully oxidize ammonia to nitrate Key enzymes are ammonia monooxygenase , hydroxylamine oxidoreductase , and nitrite oxidoreductase Only small energy yields from this reaction Growth of nitrifying bacteria is very slow good final a - > receptor > & > Can be source of e-[Ncuck) Electron transport generates a proton motive force. Oxidation of hydroxylamine Oxidation of ammonia Reduction of oxygen 4 e 2 e 2 e 2 e 2 e HAO AMO Reverse e flow to make NADH Cyt aa 3 Out ADP + P i Q ATP Cyt c Cyt c Figure 14.24 Figure 14.25 Ralstonia eutropha Dr. Min Zhang NREL Golden CO > 1 itno troph &biL coegetting fixed auto troph Calvin Cycle Pause.and question III. BIOS NTHESIS PATHWAY that ties it all together: 3.12 Nitrogen Fixation Only certain prokaryotes can fix nitrogen Some nitrogen fixers are free-living, and others are symbiotic Reaction is catalyzed by nitrogenase > Sensitive to the presence of oxygen A wide variety of nitrogenases use different metal cofactors 3.12 Nitrogen Fixation Electron flow in nitrogen fixation electron donor dinitrogenase reductase dinitrogenase N2 Ammonia is the final product Figure 3.28 Electrons for nitrogenase Nitrogenase activity 4 Dinitrogenase reductase (Red) Dinitrogenase (Red) 4 Flavodoxin (Red) 4 Pyruvate 4 Flavodoxin (Ox) 2 e (4) 16 ATP 16 ADP + 16 P i Dinitrogenase (Ox) 4 Dinitrogenase reductase (Ox) Pyruvate donates electrons to flavodoxin. Flavodoxin reduces dinitrogenase reductase. Electrons transferred to dinitrogenase one at a time. 2 ATP are consumed per electron. Sum: (16 ATP 16 ADP + 16 P i)14.11 Nitrate Reduction and Denitrification Inorganic nitrogen compounds are the most common electron acceptors in anaerobic respiration https://www.researchgate.net/figure/258060211_fig1_FIG-1-The-nitrogen- cycle-Denitrification-consists-of-the-sequential-reduction-of IV. Microbial partnerships :14.22 Syntrophy Syntrophy Process whereby two or more microbes degrade a substance neither can degrade alone Most syntrophic reactions are secondary fermentations Most reactions are based on interspecies hydrogen transfer H2 production by one partner is linked to H 2 consumption by the other (Figure 14.51) Syntrophic reactions are important for the anoxic portion of the carbon cycle Figure 14.51 LA Lecture s 4 and 5 Due 9-21 -2 5 (5pts) Names of people worked with (or worked alone ) _________________________ _________________________ _________________________ _________________________ 1) Answer the following: Photorhabdus luminescens lives inside the digestive tract of soil nematodes and also produces a toxin to kill insects. There is much interest in the metabolism and nutrient requirements of this species to study it as a natural insecticide. This organism lives mostly in the absence of oxygen, and uses the endogenous organic molecule fumarate as a final electron acceptor. However, it can also live in the presence of oxygen and it as a final electron acceptor. Organic molecules obtained from the nematode are used as a source of energy, electrons and carbon. Name the three primary nutritional groups of this microorganism: 2) Answer the following about photosynthesis: Describe the difference between ANOXIGENIC and OXIGENIC photosynthesis. What is the final electron acceptor for photosynthesis? What does the CALVIN CYCLE do? 3) Using the paper this week by Wei et al. (2023) https://www.sciencedirect.com/science/article/pii/S2667370323000061 Name the three primary nutritional groups of Ralstonia eutropha : Sydney > - > - fermentation Chemo , organo , heterotroph Ton Anoxigenic : Inorganic molecle breaks carbon at to make glucose oxigenic : uses H2o + makes 02 lithotroph > chemotroph -energy) aerobic Autotroph lecture I Chapter microbiology is the study of organism you can't see with the unaided eye > - Microbiology is Important because it is the cause of death & disease ,production of food , oldest living thing > - archala , Eukamotic ,bacteria > - Archaca , protozoa ,algae , bacteria ,fugi , small Invertebrates , Virus > - prokaryotes have cell wall ,no organelles . smaller Eukaryotes have nuclus ,Miltocondra > - All alls : cell Membrane , DN A ,vibosomes cy to plasm , metablism , response to enviro 1) Van leuwenhoek > - first person to describe microbiology LOUIS pastur > ~ mach frist vactim(vabies] > - disproved spontaneus generation bacteria can grow from nothing . > Is bottle experiment > - artain geoms are associated with particular disease Koch discovered viruses a made scientific method to pure culturing bacterich > - why microorganism cause Certain a Beigernick > - pure cultured bacteria from soil Intentified viruses Winogradsky > - N fixation modern mich > - pathology ,virology , biothnology ,Immunology Chapter 2 (lecture 223) magnification : making something bigger Contrast : the difference in color resolution : ability to identify two adjacent items #breant : cuts organism to see Inside zD electron & outside 3D > - gram Stain (stiferential) purple = + llarge paptioglycan cell wall) pink = > - ILDS , > small PED , 2 cell membranes] B? > - acidic(pos] basic (neg) > - simple 1 dye mo or Bhology = Shape movi II oc[I * vachili N Pirillium - pirochste - # elico # iy 0use in etrad 800 00 Sardinin 0000 d iplo 8 > - 0. 2-700Nm 1 >200 on Yuka mote > - thio margarita Le vesicles energy product > - DNA & ribosomes compartment les Into membrane like vasisles more surface area = thore absorption , smaller als large all-lower surface area : less absorption III Cytoplasmic : thin Structure Surrounding all separates cytoplam from environment > - Phospholipid bilayer I &pop )() hydrophobic racias) hydrophilic head > - embeded proteins ester - > 200 - > in membraned integral proteins : firmly embedded In me inbrare peripheral : One portion is anchored archeal membranes > - ether link Instead of ester G O + 2C - 0- > - ssoprens instead of fatty acids short a chains > - monolayers not bilayers plasma membrans > - permeable barrier = > ~ preserves energy (passive transport) > - protein anchor nutrient transport : active trasport- Use of ATP ISO to Mic hyper tonic hypotonic endocytosis : creation of vesicles to take In nutrients exocytosis : export waste in Vesicles aud membrane tequoid grampos Guter neg dirct link # Fran > - ## glycine wall dea -lyE Pam bran Archea Archea differences D - No PEP > - DAP > - slayer has > - gram neg ~10 % PEP most outer membrane IS LPS LipS = 0-specific polysacchavide , sore polysacavide , l pid A lipid A: Fatty acids endotoxin-stimulate immune system Cove polysaclavides :repeated Sugars Attached to Lipid A *Specific polySallavida : repeated sugars attached to Love .different amost species capsule/slime layer prevents drying out Allows Attachment to surface biofilm : community of microorganism that adhere to each other & a surface Aids in resistance to chemicals , antibiotics e immune > alls fibria > - fillment made of protein helps attach microorganism Pt longer + helps DNA exchanse gas vesicles > - brancy to planktonic cells > - Impermeable to H, o > - Spindle shape gas chambers Made of Protein Endospores > - > now reproductive ,non meta bolically active > - helps all survive hargh conditions > - makes all resistant to radiation > disacotiation > heat > chemicals flagella help cell move bacteria : long made of flagelin Arshea : shorter made of protein Chemotaxis : movement In response to Chemicals nucleus holds BNA In a Sokaryotic call nucleolus Mitosis :Makes daughter diploid chromosomes > & body celes melosis makes haploid daughter cells gameetes , specialized Mitochondria :makes ATP cellular respiration Chloroplast : plant cells photosynthetic hydrogenosomes anacrobic generate ATP Endosymbiosis Theory > - Chlorplasts + Mitochondria are decendants of prokaryoti all > size -Similar remembrane - have own INA > - Mitochondria can divide via binary fission > & have vibosomes like bacterial Vibosomes > energy made at membrane election donor : Oxidation Close e-7 electron Acceptor = reduction (gaine bio energetics : All chemical reactions accompanied by a change of energy in a cell redox : Oxidation + reduction happening together strongest electron donor - >strongest e- Acceptor enzymes carry out chemical reactions (proteins) Catalysts : Speed up reaction > cellular respiration Gutilizes glycolysis Oxidative phosphoritation makes a lot of ATP > fermentation utilizes glycolysis Internal final electron acceptor substrate leve phosphorilation not much ATP > photosynthesis light-energy electron transport chain to make ATt Catabolism :break down modules input a catabolic vxn > glycolysis ,citull acid , elefron transport chain butput-energy ATP > glycolysis :Catabolism of glucose > - anderbil 1. glucose consumed > 2. 2 ATP produced > 3. fermentation generated Synthesis of Aceytl-CoA pyruvate ->Acetated ->Acetyl-CoA 3 Eco 2[ > ~ Citric and Cycle from glycolysis to make more ATP pylvate oxidized > - glyoxylate > - oxaloacetate > - helps all make molecules that help u/ structure > - Fermentation produces > & thano Lactic acid propionic acid mixed acids butyvic did butano

Title:

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Markdown Content:
Biology 303

General

Microbiology Biology 303

General Microbiology

I. Introduction:

Course learning outcomes:

Demonstrate an understanding of core concepts of

microbiology .

Demonstrate an understanding of hypotheses testing and

experimental design .

Display proficiency in basic microbiological laboratory skills .

Record, interpret and evaluate scientific data .

Communicate the fundamental concepts of microbiology ,

both in written and in oral format.

Analyze, interpret and evaluate a range of scientific literature

in microbiology. Loading

BIOLOGY 303 General Microbiology

Fall 2024

Dr. Juliette K. Tinker

juliettetinker@boisestate.edu

> Lectures Tues/Thurs 1:30-2:45 Math BIDG113
> Labs Wed/Fri
> Sections A-D

Assessment:

Lecture

3 lecture exams (multiple choice, Canvas testing center) (100pts)

1 final lecture exam (multiple choice, Canvas testing center)

(100pts)

Weekly lecture assignments (LA) (50 pts)

iClicker lecture questions (50 pts)

Laboratory

2 laboratory practical exams (100pts)

1 written laboratory report (30pts)

1 laboratory unknown presentation (40pts)

1 laboratory notebook (30pts)

700 total The Laboratory.

Will learn the essentials of

microbiology here:

sterile technique

plating/culturing

isolation., characterization and

idenfitication microorganims

DNA extraction and molecular

analysis

quantification of bacteria

biochemical assays

phage quantification

food and water microbiology

bacterial physiology Loading

## Expectations

Your time!

Your work:

https://www.boisestate.edu/online/admitted/time-management/

https://deanofstudents.boisestate.edu/student-code-of-conduct/ Academic Integrity Guidelines for AI

DO Use AI For

Brainstorming and ideation

Understanding complex concepts

Organizing your thoughts

Getting feedback on your work

Research and source discovery

Study strategies and planning

Use Caution With

Direct answers to homework questions

Complete essay or paper writing

Take-home exams or quizzes

Group project individual contributions

Always check your professor's AI policy

Best Practices

Always cite AI assistance when required

Use AI to enhance, not replace, your learning

Verify information from AI responses

Use AI responsibly and

ethically !!

boisestate.ai Chapter 1. The Microbial World

Introduction to Microbiology

1.1 Exploring the Microbial World

Classification and cell structure

1.4 Molecular Biology and the Unity and

Diversity of Life

Some history

1.3 Microbial Cultivation Expands the Horizon

of Microbiology Introduction to Microbiology Microbes changed the world.

so we could live here

> Micro organisms

2015 Pearson Education, Inc. Figure 1.5

Mammals Humans

Vascular

plants

Shelly

invertebrates

~20% O 2

Algal

diversity

Modern

eukaryotes Origin of

cyanobacteria

Earth

is slowly

oxygenated

Anoxic

Earth

Present

Origin of

cellular life

Anoxygenic

phototrophic

bacteria

Origin of

Earth

(4.6 bya)

1 4

bya

bya bya

bya

LUCA

bya

Bacteria

Archaea

Eukarya

4 3 2 1 0Loading

Bacteria are the oldest living things on the planet

3.5 to 4 billion years ago

Fossilized

cyanobacteria Modern day

stromatolites

Cyanobacteria: perform oxygenic photosynthesis

> Fossilized Matts
> Phosphoriization

## Microorganisms live everywhere

## that life is possible .

> ????

NH4+ for plants

NH4+ for proteins

N fixation ( N2  NH4+)

Microorganisms are essential for life

www.bbc.co.uk

Figure 1.7

> Microorganisms can pull out carbon& nitrogen
> and insert

Microbial decomposition:

all things must break down

Microorganisms are essential for death.

> Break down organic. materials (fungi)

Where most of the microbes are:  2015 Pearson

Education, Inc. Figure 1.9

Soyb

ean

plant

Rumen

Grass Cellulose Glucose Microbial fermentation

Fatty acids

(Nutrition for animal)

CO 2 + CH 4

(Waste products)

## Microorganisms and agriculture  2015 Pearson

Education, Inc. Figure 1.11

GLUCOSE

Propionic acid + Acetic

acid + CO 2

2 Lactic acid

2 Ethanol + 2 CO 2

2 Acetic acid

Fermentations Fermented foods

Microorganisms make food Microorganisms

## live in

## communities

> Figure 1.1

Dynamic interaction between host/bacteria:

Can result in:

1) transient colonization

2) long-term symbiotic relationship

3) disease

What? Microbial cells outnumber

our own cells in body 10:1  well

not really, more like 1:1  BUT

STILL pretty shocking

> Some links: Bonnie Bassler,
> Yale More like a 1:1 ratio -

## Impact of microorganisms on humans..

Nearly 2,000 different microbes cause disease

10 B infections/year worldwide

13 M deaths from infections/year worldwide

> Figure 1.8

## iClicker Question Lecture 1

Which of the following is  NOT  a reason why

microbiology is important.for everyone?

A. microorganisms live everywhere that life is

possible

B. microorganisms are the oldest forms of life

C. microbiology is required for the MCAT

D. microorganisms cause significant disease and

death

E. microorganisms break down organic material and

make food Classification and Basic Cell Structure The Tree of Life ARCHAEA BACTERIA EUKARYA

Green nonsulfur

bacteria

Mitochondrion

Gram-

positive

bacteria

Proteobacteria

Chloroplast

Cyanobacteria

Green sulfur

bacteria

Thermotoga

Thermodesulfobacterium

Aquifex

Crenarchaeota

Thermoproteus

Pyrodictium

Thermococcus

Nitrosopumilus Pyrolobus

Methano-

bacterium

Euryarchaeota

Methanosarcina

Thermoplasma

Methanopyrus

Extreme

halophiles

Entamoebae Slime

molds

Animals

Fungi

Plants

Ciliates

Flagellates

Trichomonads

Microsporidia

Diplomonads

Macroorganisms

Figure 1.5

Figure 1.36

Aren't looking under microscope

Procaryotes Microbes classified into 7 main groups:

1) Archaea- prokaryotic

2) Protozoa  eukaryotic

3) Algae-eukaryotic

4) Bacteria - prokaryotic

5) Fungi- eukaryotic, larger more complicated

6) Small invertebrates  eukaryotic, most complex

7) Viruses  what???

Prions????

Prokaryotic = single cell organism, no nucleus,

no mitochondria, no Golgi, outer cell wall, typically smaller

(1 mm in diameter) Bacteria and Archaea

Eukaryotic = unicellular or multicellular, nucleus,

mitochondria, Golgi, typically larger (10-100 mm diameter)

Classification

> protein

## Characteristics of microbes Microorganisms vary greatly in size

## and shape..

https://learn.genetics.utah.edu/content/cells/scale/

> Figure 1.38

2015 Pearson Education, Inc. Figure 1.3

Cell wall

Cytoplasmic

membrane

Nucleoid

Cytoplasm

Plasmid

Ribosomes

Bacteria

Archaea

Prokaryote

Eukaryote Eukarya

Cell wall

Cytoplasmic

membrane

Mitochondrion

Nuclear

membrane

Ribosomes

Endoplasmic

reticulum

Cytoplasm

Golgi

complex

Nucleus Loading

2015 Pearson Education, Inc. Figure 1.4

Properties of all cells:

Metabolism

Cells take up nutrients,

transform them, and expel

wastes.

1. Genetic (replication,

transcription, translation)

2. Catalytic (energy,

biosyntheses)

Properties of some cells:

Cell

Environment

Some cells can form new cell

structures such as a spore.

Spore

Cells interact with each other

by ehemical messengers.

Differentiation

Communication

Growth

Nutrients from the

environment are converted

into new cell materials to

form new cells.

Evolution

Genetic exchange

Motility

Cells can exchange genes by

several mechanisms.

Cells evolve to display new

properties. Phylogenetic

trees capture evolutionary

relationships.

Donor cell Recipient cell

DNA

Some cells are capable of

self-propulsion.

Flagellum

Distinct

species

Distinct

species

Ancestral

cell

All

cells bateria ,

Fungi

> ~

exchange

horizontal give transfer

mutate & change iClicker Question Lecture 1

Which of the following is  smaller  than a

bacterial cell ?

A. a red blood cell

B. a yeast cell

C. a photoreceptor in the eye

D. a grain of salt

E. an HIV virus particle Some History. Antoni van Leeuwenhoek (16321723): the

first to describe bacteria (Figure 1.14)

> First to discover microorganisms and made microscope

Founding microbiologists :

Louis Pasteur (1822-1895)

Robert Koch (1843-1910)

> $^%
> @$#&
> !

*&!$#

!! Louis Pasteur

Father of Microbiology

Showed microbes caused

fermentation & spoilage.

Disproved spontaneous

generation.

Developed aseptic

techniques.

Developed a rabies vaccine.

(1822-1895)

> (Mold goes on bread for no reason)
> Initiated germ theory disease
> - disease can be caused by microorganisms

disproved  2015 Pearson

Education, Inc.

Dust and microorganisms

trapped in bend

Steam forced

out open end

Open end

Nonsterile

liquid

poured into

flask

Neck of flask

drawn out in

flame

Liquid

sterilized

by extensive

heating Flask tipped such that

microorganism-laden dust

contacts sterile liquid

Liquid

putrefies

Liquid cooled slowly Liquid remains

sterile indefinitely

Long time

Short time

Figure 1.26 Robert Koch

Established a sequence of

experimental steps to show

that a specific

microorganism causes a

particular disease.

Developed pure culture

methods.

Identified cause of anthrax,

TB, & cholera.

> (1843-1910)

2015 Pearson

Education, Inc.

KOCH'S POSTULATES

Theoretical aspects

Postulates: Laboratory

tools:

Microscopy,

staining

1. The suspected pathogen

must be present in all

cases of the disease

and absent from healthy

animals.

2. The suspected pathogen

must be grown in pure

culture.

Laboratory

cultures

Experimental

animals

3. Cells from a pure culture

of the suspected

pathogen must cause

disease in a healthy

animal.

4. The suspected pathogen

must be reisolated and

shown to be the same

as the original.

Laboratory

reisolation

and culture

Suspected

pathogen

Colonies

of suspected

pathogen

Suspected

pathogen

Red

blood

cell

Diseased

animal

Healthy

animal

Red

blood

cell

organisms

present

Observe

blood/tissue

under the

microscope.

Streak agar plate

with sample

from either a

diseased or a

healthy animal.

Inoculate healthy animal with

cells of suspected pathogen.

Remove blood or tissue sample

and observe by microscopy.

Diseased animal

Laboratory

culture

Pure culture

(must be

same

organism

as before)

Experimental aspects

Figure 1.29

how determine how a geri causes

acertain disease Martinus Beijerinck

(18511931)

Sergei Winogradsky

(18561953)

Figure 1.32

Figure 1.33

Isolated pure environmental Microbiology

bacterial cultures

from so :1

> o

first to Identify

> a

vimscobar )

discovered nitrogen

cycling in soil

discovered microbes

are the source of

utilizable nitrogen Other pioneering microbiologists

Angelina Fanny Hesse

Lydia Villa-Komaroff

Susumu Tonegawa

Harold Amos

Esther

Lederberg

Reyes Tamez

> esse

Guerra

## Modern Microbiology

Applied and Basic EXAMPLES:

Virology : the study of viruses

Bacteriology : the study of bacteria

Medical microbiology : infectious diseases

Immunology : immune system

Industrial microbiology : production of antibiotics, alcohols, and other

chemicals

Biotechnology : products of genetically engineered microorganisms

Microbial systematics: the science of grouping and classifying

microorganisms

Microbial physiology : Study of the nutrients that microbes require for

metabolism and growth and the products that microorganisms generate

Microbial ecology: Study of microbial diversity and activity in natural

habitats Lecture 2 : Chapters 1 and 2.

Microscopy and Microbial Cell Structure and

Function:

Microscopy, cell size and shape, cell membranes and transport, cell

walls.. Chapter 1

II. Microscopy and the origins of microbiology

Compound light microscope uses visible light to

illuminate cells

Many different types of light microscopy:

Bright-field

Phase-contrast

Dark-field

Fluorescence

(bright back , organism dark for staining)

(Loading

Bright-field scope (Figure 1.2)

Specimens are visualized because of differences in contrast

(density) between specimen and surroundings

Two sets of lenses form the image

Objective lens and ocular lens

Total magnification = objective magnification  ocular

magnification

Maximum magnification is ~2,000

> 10 X

highest

> -
> 4X

100X(01) x10 x = 1000 X

> -
> 10X
> 48x resolution :dependent upon Waveleng th of light using

100X0i1) R =0.

52/NA Figure 1.2

Ocular

lenses

Objective lens

Stage

Condenser

Focusing knobs

Light source

Specimen on

glass slide Loading

Figure 1.2

Visualized

image

Ocular lens

Intermediate

image (inverted

from that of the

specimen)

Objective lens

Specimen

Condenser lens

Light source

None

10X, 40X or

100X(oil)

Magnification

100X, 400X,

1000X

Light path Magnification : the ability to make an object larger

Resolution : the ability to distinguish two adjacent objects

as separate and distinct

Contrast: diference in intensity between two objects or

backgound

Wavelength : difference between two corresponding parts

of a wave

> dependent on in of light used

Figure 1.23

Procedure Result

1. Flood the heat-fixed

smear with crystal

violet for 1 min

2. Add iodine solution

for 1 min

3. Decolorize with

alcohol briefly

about 20 sec

4. Counterstain with

safranin for 12 min

All cells purple

All cells remain purple

Gram-positive cells are

purple; gram-negative

cells are colorless

Gram-positive (G +) cells

are purple; gram-negative

(G ) cells are pink to red

The

Gram

Stain

contrast of specimen

Via Stain

> &

differential

Simple-1 due

differential Stain -

2 or more

> ex :

gram stain

kinds : Acidic : bind to pos charges

## - basic : bind to neg charges

most structures of cells

Ba of differences in cell Wall & cell membrane

Structure Figures 1.24 and 1.27

Phase-contrast microscopy

Dark-field microscopy

Confocal scanning laser

microscopy (CSLM)

# &Figure 1.29 electron microscopy

uses electrons & higher

> X

proteins Loading

Chapter 1:

1.3 Cell size and morphology

Morphology = cell shape

Major cell morphologies (Figure 2.11)

Coccus (pl. cocci) : spherical or ovoid

Rod : cylindrical shape

Spirillum : spiral shape

Figure 1.8

Morphology: cell shape

Cocci:sphere (circle)

Bracili: rod

Spirochete: spiral

Spirillum: thin hair

spiral

Helicol/vibrio

Pleiomorphic

Aggregate: binding to

each other

Cocci:.

strepto

stophylo

tetrads

Sardinia

diplo

Bacilli

corynebacterium

palisades

> E

Size range for prokaryotes: 0.2 m to >700 m in

diameter

Most cultured rod-shaped bacteria are between 0.5 and 4.0 m

wide and < 15 m long

Examples of very large prokaryotes

Epulopiscium fishelsoni (Figure 1.6)

Thiomargarita namibiensis (Figure 1.6 )

Size range for eukaryotic cells: 10 to >200 m in

diameter

The Small World

> Advantages of being small:
> -More surface area to volume ratio
> supports more efficient nutrient exchange
> can grow/replicate faster

Figure 1.6 Thiomargarita namibiensis :

WORLDS LARGEST BACTERIA The Small World

Surface-to-volume ratios, growth rates, and evolution

Advantages to being small (Figure 1.7)

Small cells have more surface area relative to cell volume than

large cells (i.e., higher S/V)

Support greater nutrient exchange per unit cell volume

Tend to grow faster than larger cells

> Volume of a coccus
> Function of the cube of the radius
> Surface area of coccus
> Function of the square of the radius
> I want a small radius for a large s/v ratio
> - want large s/v ratio to grow fast

EX :

2 1011 S/ = 4. 5

macrophage SN : 2

myroplasm /=22 Figure 1.7 I. The Cell Envelope

Chapter 2: Microbial Cell Structure and Function 2.1 Membrane Structure

Cytoplasmic membrane

Thin structure that surrounds the cell

Vital barrier that separates cytoplasm from environment

Highly selective permeable barrier; enables concentration of

specific metabolites and excretion of waste products 2.1 Membrane Structure

Composition of membranes

General structure is phospholipid bilayer (Figure 2.14)

Contain both hydrophobic and hydrophilic components

Can exist in many different chemical forms as a result of

variation in the groups attached to the glycerol backbone

Fatty acids point inward to form hydrophobic environment;

hydrophilic portions remain exposed to external environment

or the cytoplasm R "head group"

> I
> 10 Phosphate glycerol

Phospholipid bilayer hydrophobic 1 fatty acid & tructure for all

# & U fatty acids

> membraces obacteria
> Phosphate glycerol tI

&"head group - Eukarya

> NOT Archaea

Figure 2.1

Fatty acids

Phosphate

Ethanolamine

Fatty acids

Hydrophilic

region

Hydrophobic

region

Hydrophilic

region

Glycerophosphates

Fatty acids

Glycerol 2.1 Membrane Structure

Cytoplasmic membrane (Figure 2.2)

810 nm wide

Embedded proteins

Stabilized by hydrogen bonds and hydrophobic interactions

Mg 2+ and Ca 2+ help stabilize membrane by forming ionic

bonds with negative charges on the phospholipids

Somewhat fluid Figure 2.2

Phospholipids

68 nm

Integral

membrane

proteins

Hydrophilic

groups

Hydrophobic

groups

Phospholipid

molecule

Out

In Membrane Structure

Membrane proteins

Integral membrane proteins

Firmly embedded in the membrane

Peripheral membrane proteins

One portion anchored in the membran e

Di ff erences between archael membranes and bacterial/eukaryot

membrane

1) ether link instead of ester link between phosphate and fatty

acid,

2) archaea have short carbon chains called isoprenes instead of

fatty acids

3) archea can have monolayers instead of bilayers

4) archaea often have more unsaturated lipids Membrane Structure

Archaeal membranes

Ether linkages in phospholipids of Archaea (Figure 2.3)

Bacteria and Eukarya that have ester linkages in

phospholipids

Archaeal lipids lack fatty acids; have isoprenes instead

Major lipids are glycerol diethers and tetraethers

Can exist as lipid monolayers, bilayers, or mixture Ester Ether

Bacteria

Eukarya

Archaea

# reduc aturation

Isoprene tFigure 2.3

Phytanyl

Glycerol diether

CH 3

groups Isoprene unit

Biphytanyl

Diglycerol tetraethers

Crenarchaeol

Out Out

In In

Glycerophosphates

Phytanyl

Membrane protein

Lipid monolayer

Biphytanyl or

crenarchaeol

Lipid bilayer Membrane Function

Permeability barrier

Protein anchor

Energy conservation

Functions of the cytoplasmic membrane

Permeability barrier:

Prevents leakage and functions as a

gateway for transport of nutrients into,

and wastes out of, the cell

Protein anchor:

Site of many proteins that participate in

transport, bioenergetics, and chemotaxis

Energy conservation:

Site of generation and dissipation of the

proton motive force

Figure 2.4 Loading

2.2 Transporting nutrients into the cell

http:// what-when-how.com/neuroscience/electrophysiology-of-neurons-the-neuron-part-1/ Nutrient Transport

Active transport systems

Show saturation effect

Highly specific

Three major classes

All require energy in

some form - usually ATP

Figure 2.5

Types of solutions /external chemical environments

isotonic: concentration of solutes (dissolved

chemicals)

Hypotonic: solute concentration is lower on outside

of cell t

> I
> +

)Phospholipid

membrane : esther & ether

Eukaryotic Cell membranes batteria Larchard

same as bacteria membranes Eukaved

except :- have sterols (cholestera) to stabilize

perform unique functions

endocytosis : creation of Vesicles to take In nutrients

exocytosis : export of wastes in Vesicles

prokaryotic all wall/all membrance structure

gram pos regate Archaea

gram ,all wall (PEP) thin

Ch wall

# a Ins T

thick S

Amino acid DAP

# SCn aare

cell wall :

peptidoglycan (PEP)

teichoid acids

charged fatty acid 2.3 Cell Walls of Bacteria and Archaea

Peptidoglycan Figure 2.7

> 2membranes

2. 4 Peptidoglycan

Species of Bacteria separated into two groups based

on Gram stain

Gram-positives and gram-negatives have different

cell wall structure (Figure 2.7)

Gram-negative cell wall

> Two layers: LPS and peptidoglycan

Gram-positive cell wall

> One layer: peptidoglycan

Peptidoglycan

Rigid layer that provides strength to cell wall

Polysaccharide composed of:

N-acetylglucosamine and N-acetylmuramic acid

Amino acids

Lysine or diaminopimelic acid (DAP)

Cross-linked differently in gram-negative bacteria and gram-

positive bacteria (Figure 2.26) peptidoglycan (PEP) -LyjD-don Differences of Archael all wali

-trampos all

No peptidoglycan

B(1 ,4) link

can have pserdouve in

#N PNAG-NAT)

Laconive -

B(1-3) link

some have protein layer

D-glutemine (D-Glu -NH2)

Stayer

2 -

Lysine

Ddonine

IS -

45 glycine bridge

Differences

# am neak

i-girtemic acid ()

direct link () N

- archive

& L-aconive

gram pos thicker

I L-glutamic adid  L-glutanic acid () L-glutamic acid -DA --donine

DAP -

D-Glenie direct link Figure 2.9

Polysaccharide

backbone

Peptides

Interbridge

Escherichia coli

(gram-negative)

Staphylococcus aureus

(gram-positive) Peptidoglycan

Gram-positive cell walls (Figure 2.10)

thick, have teichoic acid and lipoteichoic acid, contain

glycine bridge and L-lys

Gram-negative cell walls

thin, do not have teichoic acid, contained in

periplasmic space, no glycine bridge and DAP Figure 2.10

Peptidoglycan

cable

Teichoic acid Peptidoglycan

Lipoteichoic

acid

Cytoplasmic membrane

Wall-associated

protein Chapter 2:

Microbial Cell Structure and Function:

Archaeal cell walls, LPS, cell surface structures, vesicles,

endospores, flagella, eukaryotic surface structures .

> http://www.bif.kit.edu/58.php

2.3 Archaeal Cell Walls

No peptidoglycan

Typically no outer membrane

Pseudomurein  found in some methanogens

> Polysaccharide similar to peptidoglycan
> Composed of N-acetylglucosamine and N-
> acetylalosaminuronic acid (Figure 2.11)

Cell walls of some Archaea lack pseudomurein

S-layers are most common cell wall type in Archaea Loading

Figure 2.14 Loading

2.4 LPS: The Outer Membrane in GRAM

NEGATIVE BACTERIA

Total cell wall contains ~10% peptidoglycan

Most of cell MEMBRANE composed of outer

membrane , aka lipopolysaccharide (LPS) layer

LPS consists of core polysaccharide and O-polysaccharide

(Figure 2.13)

LPS replaces most of phospholipids in outer half of outer

membrane (Figure 2.12)

Endotoxin : the toxic component of LPS Figure 2.13 O-specific

polysaccharide

Core polysaccharide

Lipid A Protein

Lipopolysaccharide

(LPS)

Phospholipid

Porin Porin

Lipoprotein

Outer membrane

Periplasm

Cytoplasmic

membrane

8 nm

Out

Cell

wall

Outer

membrane

Periplasm

Cytoplasmic

membrane

Peptidoglycan Peptidoglycan

Figure 2.12 2.4 LPS: The Outer Membrane

Structural differences between cell walls of

gram-positive and gram-negative Bacteria are

responsible for differences in the Gram stain reaction Chapter 2. II. Other Cell Surface Structures and

Inclusions

2.6 Cell Surface Structures

2.7 Cell Inclusions and gas vesicles

2.8 Endospores Loading

2.7 Cell Surface Structures

Capsules and slime layers

Polysaccharide layers (Figure 2.16)

May be thick or thin, rigid or flexible

Assist in attachment to surfaces

Protect against phagocytosis

Resist desiccation

Figure 2.16 2.6 Cell Surface Structures

Fimbriae

Filamentous protein structures (Figure 2.17)

Enable organisms to stick to surfaces or form pellicles

> Flage
> lla
> Fimbr
> iae

Figure 2.17 Cell Surface Structures

Pili

Filamentous and longer than fimbriae

Assist in surface attachment

Facilitate genetic exchange between cells (conjugation)

Type IV pili involved in twitching motility

> Virus-
> covered
> pilus

Figure 2.18 2.7 Cell Inclusions

Carbon storage polymers

Poly--hydroxybutyric acid (PHB) : lipid

Glycogen : glucose polymer

Polyphosphates : accumulations of inorganic phosphate

Sulfur globules : composed of elemental sulfur

Carbonate minerals : composed of barium, strontium, and

magnesium

Magnetosomes : magnetic storage inclusions (Figure 2.24) Figure 2.24

https://phys.org/news/2018-09-magnetic-bacteria-unique-

superpower.html Gas Vesicles

Gas vesicles

Confer buoyancy in planktonic cells

Spindle-shaped, gas-filled structures

made of protein

Impermeable to water

Figure 2.23 2.8 Endospores

Endospores

Highly differentiated cells resistant

to heat, harsh chemicals, and

radiation

Dormant  stage of bacterial life

cycle

Ideal for dispersal via wind, water,

or animal gut

Present only in some gram-

positive bacteria

> Exos
> poriu
> m
> Spo
> re
> coat
> Cor
> e
> wall
> C
> or
> te
> x
> D
> N
> A

Figure 2.28 Figure 2.26 III. 2.9 Flagella and Swimming Motility

Flagella : structure that assists in swimming

Different arrangements: peritrichous , polar , lophotrichous

(Figure 2.30)

Helical in shape Figure 2.30 2.11 Flagella and Motility

Flagellar structure of Bacteria

Consists of several components

Filament composed of flagellin

Move by rotation

Flagellar structure of Archaea

Half the diameter of bacterial flagella

Composed of several different proteins

Move by rotation

> 1520 nm
> Filament
> Flagellin
> L
> P
> MS
> Hook
> Outer
> membrane
> (LPS)
> L Ring
> P Ring
> Rod
> Peptidoglycan
> Periplasm
> MS Ring
> Basal
> body
> C Ring
> Cytoplasmic
> membrane
> Fli proteins
> (motor switch)
> Mot protein Mot protein
> 45 nm
> Rod
> MS Ring
> C Ring
> Mot
> protein
> ++++++++
>

Figure 2.34 Figure 2.33

Bundled

flagella

(CCW rotation)

Tumble  flagella

pushed apart

(CW rotation)

Flagella bundled

(CCW rotation)

CCW rotation

Unidirectional flagella

Reversible flagella

CW rotation

Cell

stops,

reorients CW rotation

Peritrichous

Polar 2.11 Chemotaxis and Other Taxes

Taxis : directed movement in response to chemical or

physical gradients

Chemotaxis : response to chemicals

Phototaxis : response to light

Aerotaxis : response to oxygen

Osmotaxis : response to ionic strength

Hydrotaxis : response to water

Income Taxes: (just kidding) Figure 2.39

Tumble

Run

Attractant

No attractant present: Random

movement

Attractant present: Directed

movement

Tumble Barbara Irene Kazmierczak ,

PhD, MD

Professor of Medicine (Infectious

Diseases); Director, MD-PhD

Program, Yale University;

Professor of Microbial

Pathogenesis Avraham Beer

Physics Department

Ben-Gurion University

of the Negev

https://www.nature.com/articles/s41598-022-20644-3#Sec17

Mixed species swarming Chapter 2. IV. Eukaryotic Microbial Cells

2.13 The Nucleus and Cell Division

2.15 Mitochondria, Hydrogenosomes, and

Chloroplast

2.16 Other Major Eukaryotic Cell Structures Smooth endoplasmic reticulum

Rough endoplasmic

reticulum

Cytoplasmic

membrane

Mitochondrion

Microfilaments

Ribosomes

Flagellum

Mitochondrion Microtubules

Figure 2.42

Microfilaments

Lysosome

Chloroplast

Nuclear envelope

Nuclear pores Nucleolus

Nucleus

Golgi complex Loading

2.14 The Nucleus and Cell Division

Nucleus : contains the chromosomes (Figure 2.46)

DNA is wound around histones (Figure 2.46b)

Enclosed by two membranes

Within the nucleus is the nucleolus

Site of ribosomal RNA synthesis

> Nucle
> us Nucl
> ear
> pores
> Vacu
> ole Lipid
> vacuo
> le
> Mitochon
> dria
> Double-
> stranded
> DNA
> Nucleoso
> me core Histo
> ne H1
> Core
> histone

Figure 2.43 2.13 The Nucleus and Cell Division

Cell division

Mitosis

Normal form of nuclear division in eukaryotic cells

Chromosomes are replicated and partitioned into two nuclei

(Figure 2.44)

Results in two diploid daughter cells

Meiosis

Specialized form of nuclear division

Halves the diploid number to the haploid number

Results in four haploid gametes 2.14 Mitochondria and Chloroplast

Mitochondria (Figure 2.45)

Respiration and oxidative phosphorylation

Chloroplast (Figure 2.46)

Chlorophyll-containing organelle found in phototrophic

eukaryotes

> membrane bound in Eukaryotic Cell

(photo Synthetic) Figure 2.45

Inner membrane

Matrix

Cristae

Porous outer

membrane

-Figure 2.46

Chloroplast

Thylakoid

Stroma THE Endosymbiotic Theory

Chloroplasts and mitochondria suggested as

descendants of ancient prokaryotic cells

(endosymbiosis )

Evidence that supports idea of endosymbiosis

Mitochondria and chloroplasts contain DNA

DNA is circular

Mitochondria and chloroplasts contain own ribosomes

Eukaryotic nuclei contain genes derived from bacteria

> https://www.khanacademy.org/science/ap-biology/cell-structure-and-function/cell-compartmentalization-
> and-its-origins/v/endosymbiosis-theory

able to do aerobic Evidence for endosymbiosis

Isize of Mitochondria +

Chloroplasts

> ~

of a prokaryotic

2) Mitochondria all

> +

Chloroplast have double membrane

> 3)

Mitochondria + chloroplasts have own DNA

4) Mitochondria can divide into two by binary fission (now Eukaryotic cells duplicate)

5) Mitochondria have ribosomes like bacterial ribosomes

> I

6) energy is made at membrane

like prokaryotic cells The Endosymbiotic Theory

Chloroplasts and mitochondria suggested as

descendants of ancient prokaryotic cells

(endosymbiosis )

Evidence that supports idea of endosymbiosis..

> Dr. Lynn Margulis

2.16 Other Major Eukaryotic Cell Structures

Endoplasmic reticulum (ER)

Golgi complex

Lysosomes

Microtubules , microfilaments, and intermediate

filaments

Flagella

> Flag
> ella
> Ci
> lia

Figure 2.53

> proteins fold
> proteins transport

Chapter 3:

Microbial Metabolism : microbial cell chemistry,

nutrition, energy, electron transfer, fermentation,

respiration, glycolysis, the citric acid cycle and

oxidative phosphorlyation

Figure 3.1

> reactants break down into products

I. Fundamentals of Metabolism

Metabolism

The sum total of all of the chemical reactions that occur in a

cell

Catabolic reactions (catabolism)

Energy-releasing metabolic reactions

Anabolic reactions (anabolism)

Energy-using metabolic reactions

> -
> exergon
> -
> Indogonic

# Loading

Metabolic types based on energy sources

> Figure 3.3

3.1 Defining the requirements of life

Energy from oxidationreduction ( redox ) reactions is

used in synthesis of energy-rich compounds (e.g., ATP)

Redox reactions occur in pairs (two half reactions ;

Figure 3.2)

Electron donor : the substance oxidized in a redox

reaction

Electron acceptor : the substance reduced in a redox

reaction Bio energetics =All Chemical reactions

that are accompanied by

changes in energy in a all

compounds can use energy or release energy

during formation

G :

change in free energy (reaction between products & reactants)

1G = G[c +D] -

G[A + B]

products reactants

exergonic-release (Catabolism) (- -G]

endergonic-use of free energy (++ G)

Redox-reactions -

transfer electrons

Oxidation = involves loss (e-)

reduction = gain (e-) (gain H)

electron acceptor

electron carrier Co-enzymes

> -

Oxidized reduced

> --
>

NAD - NADH

NADPt > NADPH

F AD + - FADH2

Selectron acceptors Selection donors) Loading

Free Energy

Energy is defined in units of kilojoules (kJ), a measure

of heat energy

In any chemical reaction, some energy is lost

as heat

Free energy (G) : energy released that is available to do

work

The change in free energy during a reaction is referred

to as G0Figure 3.2 Electron Donors and Electron Acceptors

Redox couples are arranged from strongest electron

donor to strongest acceptor at the bottom (Figure 3.4)

Redox reactions usually involve reactions between

intermediates ( electron carriers )

These are divided into two classes

> Prosthetic groups (attached to enzymes)
> Coenzymes (diffusible)
> Examples: NAD +, NADP (Figure 3.10 )
> prote portion

The redox tower

> Figure 3.4

Figure 3.6

NAD + reduction

NAD +

binding

site

Product

Enzyme I l

Enzymesubstrate

complex

NAD + +

NADH oxidation

NADH

binding

site

Active

site

Product

NADH

Substrate

(e  acceptor)

Enzymesubstrate

complex

Substrate

(e  donor )

Enzyme I

Enzyme I reacts with e

donor and oxidized form of

coenzyme, NAD +.

Enzyme II reacts with e

acceptor and reduced

form of coenzyme, NADH.

NADH and

reaction

product are

formed.

4. NAD + is

released.

Active

site

NADH dehydrogenases :

Flavoproteins :

Electron Carriers and NAD+/ NADH cycling 3.4 Cellular Energy Conservation

Chemical energy released in redox reactions is primarily

stored in certain phosphorylated compounds (Figure

3.12)

> ATP; the prime energy currency
> Phosphoenolpyruvate
> Glucose 6-phosphate

Chemical energy also stored in coenzyme A Loading

Anhydride bonds Ester bond

Ester bond

Anhydride bond

Acetyl

Thioester

bond

Coenzyme A

Anhydride bond

Phosphoenolpyruvate Adenosine triphosphate (ATP) Glucose 6-phosphate

Acetyl phosphate

Acetyl-CoA

Compound G0kJ/mol

G0< 30kJ

Phosphoenolpyruvate

1,3-Bisphosphoglycerate

Acetyl phosphate

ATP

ADP

AMP

51.6

52.0

44.8

31.8

35.7

14.2

13.8

Acetyl-CoA

Glucose 6-phosphate

Figure 3.8 3.5 Catalysis and Enzymes

Enzymes

Biological catalysts

Typically proteins ( some RNAs)

Highly specific

Generally larger than substrate

Typically rely on weak bonds

Examples: hydrogen bonds, van der Waals

forces, hydrophobic interactions

Active site : region of enzyme that binds substrate

helps lower activation energy

> - 2015 Pearson Education, Inc.

Figure 3.9

3.5 Catalysis and Enzymes II. Catabolism: Chemoorganotrophs

3.6 Respiration

3.6 Respiration: Citric Acid and Glyoxylate Cycle3 3.7

3.7 Fermentative Diversity and the Respiratory

Option

3.8 Respiration: The Proton Motive Force and the

Electron Transport Chain metabolic strategies base upon final election acceptor :

Definition : Aerobic .Occurs in presence of 02)

anaerobic : (occurs in absence of 02)

1) cellular respiration

> anaerobic -

final electron acceptor is element other than Oxygen (fe ,+,s

-acrobie : Final electron acceptor is 02 (best , most ATP)

2) fermentation :

Final election acceptor is an internal Organi compound (NAD production of Waste products like lactic acid in humans or pyrovate

3) photosynthesis

metabolic to conserve energy

> -

final electron receptor

NABP 3.6 Chemoorganotrophs

Two reaction series are linked to energy conservation in

chemoorganotrophs: fermentation and respiration

(Figure 3.11)

Differ in mechanism of ATP synthesis

Fermentation : substrate-level phosphorylation; ATP is directly

synthesized from an energy-rich intermediate

Respiration : oxidative phosphorylation; ATP is produced from

proton motive force formed by transport of electrons metabolic Strategies based on find electron acceptor

Cellular respiration :

utilizes glycolysis

Civil acid cycle

electron transport chain

-Oxidative Phospholation (nowcel makes a

fermentation

utilizes glycosis

Internal final electron acceptor

compond

substrate level phosphorylation

not much ATp is mad

photosynthes is

uses light as energy

uses electron transport Chain

photophosphorylation to make ATP

Catabolism : break down molecules to mak ATP

> -

& In put (ex :

glucose]  energy carbon electron sources

-tabolic Rxn * diversity in microbes

Glycolysis

Citric ad aaent

# Afind electron recept diversit in

microbes

->energy storage ATP 3.6 Respiration: Glycolysis

Glycolysis (EmbdenMeyerhof pathway) : a common

pathway for catabolism of glucose (Figure 3.14)

Anaerobic process

Three stages

Glucose is consumed

Two ATPs are produced

Fermentation products are generated

Some harnessed by humans for consumption

> https://www.youtube.com/watch?v=EfGlznwfu9U
> -

dosen't need 02

# Summary of glycolysis

Inorganic phosphorous

glucose + 2 ADP +

Pj + 2 NAD +

2 pyruvate + 2 ATP + 2NADH + H20

Estages

1) 6 carbon Sugar -> 2 - 3 carbon sugars

(ATPs Input

2) 3 carbon molecules dephosphorylate -> ATP made

> 4AtPS made ->2

ATPs NET

3) recycling of electron carriers

NAIH NADT

After glycosis

D) synthesis of Acetyl-CoA

pyruvate arbot Acetate (Acetyl-DOA

## S 02-carbon)

02 NAD NADH

2) citill acid cycle

For each Acetyl-CoA :

make :

2 molences of Co 2

> -

## 3 Moews of NASA 1 GTP -ATP  2015 Pearson Education, Inc. Figure 3.11 3.6 Respiration: Citric Acid and Glyoxylate Cycle

Citric acid cycle (CAC) : pathway through which

pyruvate is completely oxidized to CO 2 (Figure 3.12)

Per glucose molecule, 6 CO 2 molecules released and NADH

and FADH generated

Plays a key role in catabolism AND biosynthesis

Energetics advantage to aerobic respiration

> transfer elections from glycolysis to (Act More ATP made

2015 Pearson Education, Inc. Figure 3.12 Other pathways for chemoorganotropy

Glyoxylate cycle

Catabolism of C2-C3 organic acids typically involves

production of oxaloacetate through the glyoxylate cycle

(Figure 3.13)

A variation of the citric acid cycle

Glyoxylate is a key intermediate

Rhodobacter sphaeroides

Microorganism (Eukaryotic)

helps all to make molecules that help

W/cell structure  2015 Pearson Education, Inc.

3.7 Fermentation

Figure 3.14 3.7 Fermentative Diversity

Fermentations classified by products formed

Ethanol

Lactic acid

Propionic acid

Mixed acids

Butyric acid

Butanol 3.0 Respiration: Oxidative Phosphorylation

Aerobic respiration

Oxidation using O 2 as the terminal electron acceptor

Higher ATP yield than fermentations

ATP is produced at the expense of the proton motive force,

which is generated by electron transport 3.11 Respiration: Electron Transport Chain

Electron transport systems

Membrane-associated

Mediate transfer of electrons

Conserve some of the energy released during transfer and use

it to synthesize ATP

Many oxidationreduction enzymes are involved in electron

transport (e.g., NADH dehydrogenases, flavoproteins, iron

sulfur proteins, cytochromes)

> mitochondria  2015 Pearson Education, Inc.

Figure 3.19

3.9 Respiration: Electron Transport Chain categories of large protein carries in

membrane : electron transport chain

-flavprotins (FAv) eNADH

> -

Ubigunones & FADH ,

# X imput -

metol-containing (e) e NADH

-Cytochromes(oxidoses) * NADI

arranged In order of reduction potential

strong donors -Strong, eptors Loading

3.9 Respiration: The Proton Motive Force

During electron transfer, several protons are released on

outside of the membrane

Protons originate from NADH and the dissociation of water

Results in generation of pH gradient and an

electrochemical potential across the membrane (the

proton motive force )

The inside becomes electrically negative and alkaline

The outside becomes electrically positive and acidic 3.9 Respiration: The Proton Motive Force

ATP synthase (ATPase) : complex that converts proton

motive force into ATP; two components (Figure 3.20)

F1: multiprotein extramembrane complex; faces cytoplasm

Fo: proton-conducting intramembrane channel

Reversible; dissipates proton motive force Figure 3.20

ADP + P i

ATP

Membrane

Out Out

In In

2015 Pearson Education, Inc.

Figure 3.21 glycosis -

carbon : glocse -> Pyrovi acid

6 3(

ATP : 2ATP (per glocosel

e-caries : 2 NABH (per glucose)

-yrvic acid & Acetol CoA

carbon : pyrvic acid & Acetyl-CoA )+ loseca) 3L 2

e carries : 2NADH (per glucose)

HAcid Cycle

carbon : 2c + 6195C + 4c (Close (02)

ATP : 2ATP (GTP] (per glucose)

ecaWies :GNADY per gos He

ETC : Selectron transport chain) -

glycolysis , CAC , pyrvat acid

10 NADH = 30 ATP

CAC

2 WADH2 = (Citric acid cycl) 4 ATPs

> =

34 ATPs

#HATP Gr glucose

For prokaryotes !

36 ATD for Eukaryote

So energy can get out of mitochondria

2 net ATP in fermentation Chapter 3:

Microbial Metabolism Chapter 14: Metabolic Diversity

The ISME Journal (2011) 5, 17351747 Loading

Microbes have diverse options of sources and

methods of energy conservation:

Microorganisms demonstrate a wide range of FI NAL

ELECTRO N ACCEPTORS (metabolic strategies )

> Aerobic respiration
> Anaerobic respiration
> Fermentation
> Photosynthesis

Microorganisms also demonstrate wide range of

sources of ENERGY, ELECTRO NS and CARBO N(Figure 3.22) (primary nutritional groups )

> Figure 3.22

# Loading

I. Microbial Types of metabolism based on

FI NAL ELECTRO N ACCEPTOR

(metabolic strategies)

1) Cellular respiration:

Aerobic

Anaerobic

2) Fermentation

3) Photosynthesis * 3.10 Catabolic Diversity :Anaerobic respiration

Anaerobic respiration

The use of electron acceptors other than oxygen

Examples include nitrate (NO 3), ferric iron (Fe 3+ ),

sulfate (SO 42 ), carbonate (CO 32 ), certain organic

compounds

Less energy released compared to aerobic

respiration

Dependent on electron transport, generation of a

proton motive force, and ATPase activity

> no 02

(fermination) microorganisms

> marobical
> -
> -
> -
> electron

transport chains -14. IV. Respiratory Processes Defined by Electron

Acceptor

* Final electron acceptor not oxygen= anaerobic

14.11 Nitrate Reduction and Denitrification

14.13 Other Electron Acceptors Principles of Anaerobic Respiration

In anaerobic respiration, electron acceptors other than O 2 are

used

Anaerobic and aerobic respiratory systems are similar

But anaerobic respiration yields less energy than aerobic respiration

Energy released from redox reactions can be determined by

comparing reduction potentials (Figure 14.39 )

> -

eless energy

> moving electrons
> -
> 
> different Waste

Figure

13.39

Figure 14.1

good final -- receptor

> -

averbo resp.

> -
> +free

energy Respiration and nitrate-based anaerobic

respiration in Escherichia coli .

Figure 3.23

> -
> can

do both

> acrolis

# Loading

14.13 Other Electron Acceptors

Fe 3+ , Mn 4+ , ClO 3, and various organic compounds

can serve as electron acceptors for bacteria (Figure

14.52)

Fe 3+ is abundant in nature, and its reduction is a major

form of anaerobic respiration

> not much detail

Question II. Microbial metabolism based on sources :

Microbial PRIMARY NUTRITIO NAL GROUPS

1) Source of ENERGY

CHEMO

PHOTO

2) Source of ELECTRONS (i.e. ELECTRON DONOR)

ORGANO

LITHO

3) Source of CARBON

AUTO

HETERO

> important
> diversity In beginning

Microbial Primary nutritional groups

> -

source of energy , elections , carbon

gets]

Ever chemotroph-chemical source of energy -

#totroph-light (photosynthesis

Elections

Lithotroph-Morganic chemical

ganotroph-organi Chemical

> H+

carbon #tenotroph-organic

Chemical Structure

Autotroph-CO2

6.101 %

> -

Chemo , organo heterotroph

> --

energy elections carbon gorse

ralstonia chemo litho , autotroph -a #2 H2 We IIA. Chapt 3.11 Chemotrophy

* source of energy = chemicals

Figure 3.3 IIB. Chapt 14. Phototrophy

*source of energy = light

Photosynthesis and Chlorophylls

Anoxygenic Photosynthesis

Oxygenic Photosynthesis

> T

14.3 Photosynthesis and Chlorophylls

Photosynthesis is the conversion of light energy to

chemical energy

Phototrophs carry out photosynthesis

Most phototrophs are also autotrophs

Photosynthesis requires light-sensitive pigments called

chlorophylls

Photoautotrophy requires ATP production and CO 2

reduction

> microorganism
> help capture light

Prokaryotic phototrophs

Purple and green bacteria Cyanobacteria

Anoxygenic

Light

ADP

ATP

Reducing power Carbon Energy

Oxygenic

Reducing power Carbon Energy

electrons

ADP

Light

ATP

Figure 14.5

don't need Need 02

82 microbial photosynthesis -

oxygenic :

> -

uses tho as source of elelations

> -

make 02

> -

2 photosystems -

electron transport chains

Z-scheme

> -

Anoxygenic :

> -

using inorganic molecule

other than H20 as election donor

> -

make gas as waste

ex :sulfur

> -

1photosystem -

electron transport

> -

lessATP is made Figure 14.8 14.6 Oxygenic Photosynthesis

Oxygenic phototrophs use light to generate ATP and

NADPH

The two light reactions are called photosystem I and

photosystem II

"Z scheme " of photosynthesis (Figure 14.14)

> Photosystem II transfers energy to photosystem I

ATP can also be produced by cyclic

photophosphorylation Figure 14.14 A comparison of electron flow in anoxygenic

and oxygenic phototrophs.

> Figure 14.16

II.C. 3.11 and 3.12 Phototrophy and Autotrophy

* source of energy = light

* source of carbon = CO 2

The Calvin cycle (Figure 3.27)

Named for its discoverer, Melvin Calvin

Fixes CO 2 into cellular material for autotrophic growth

Requires NADPH, ATP, ribulose bisphophate carboxylase

(RubisCO), and phosphoribulokinase

6 molecules of CO 2 are required to make 1 molecule of

glucose (Figure 14.17)

plants torn into

> glucose etc .

#y enzyme allows CO2 to go into sugars Calvin cycle

> -

used by Autotrophs to fix CO2 to organic

carbon

> -

A lot of ATP is required to make Carbohydrates

> -

CO2 is source of carbon

> -

uses enzyme RUBISCO

> =

summary :

> -

take CO2 + 12 NADPH + 18 ATP &CH ,200 #

> t

reduced electron 12 NADB +

> CaWiers t

18 ADP +

Pi Figure 3.27

Don't need to know Chapt 14.V. One carbon metabolism

14.15 Methanogenesis

*source of carbon = CO 2

Methanogenesis

Involves a complex series of biochemical reactions that use

novel coenzymes (Figure 14.37)

> autotroph

methogenesis -

production of methane gas CHy by

microorganism -

mostly archate

> -

Anaerobic respiration z

final electron acceptor is

co2-Strategy

> -

primary nutiction groups

> -

energy - H, chemotroph

elections - He lithotroph

Carbon - CO2 Autotroph

> -

Important waste product -

met have gas

> -

II.D. Chapt 3.11 Lithotrophy

* source of electrons = chemicals

Energy conservation in Ralstonia

eutropha , an autotrophic

chemolithotroph that oxidizes H2

Figure 3.24 Chapt 14. III. Respiratory Processes Defined by

Electron Donor : lithotrophy

14.7 Oxidation of Sulfur compounds

*source of electrons = sulfur

14.9 Nitrification  14.9 Nitrification

*source of electrons = nitrogen 14.7

Oxidation of

Sulfur

Compounds

Figure 14.20 Loading

14.9 Nitrification

NH 3 and NO 2 are oxidized by nitrifying bacteria during the

process of nitrification

Two groups of bacteria work in concert to fully oxidize ammonia

to nitrate

Key enzymes are ammonia monooxygenase , hydroxylamine

oxidoreductase , and nitrite oxidoreductase

Only small energy yields from this reaction

Growth of nitrifying bacteria is very slow

good final a -

> receptor
> &
> Can be source of

e-[Ncuck) Electron transport

generates a proton

motive force.

Oxidation of

hydroxylamine

Oxidation of

ammonia

Reduction

of oxygen

4 e  2 e

2 e

HAO

AMO

Reverse e  flow

to make NADH

Cyt aa 3

Out

ADP

+ P i

ATP

Cyt c Cyt c

Figure 14.24 Figure 14.25 Ralstonia eutropha

Dr. Min Zhang

NREL

Golden CO

> 1

itno troph

&biL

coegetting fixed

auto troph

Calvin Cycle Pause.and question III. BIOS NTHESIS

PATHWAY that ties it all together:

3.12 Nitrogen Fixation

Only certain prokaryotes can fix nitrogen

Some nitrogen fixers are free-living, and others are

symbiotic

Reaction is catalyzed by nitrogenase

> Sensitive to the presence of oxygen

A wide variety of nitrogenases use different metal

cofactors 3.12 Nitrogen Fixation

Electron flow in nitrogen fixation

electron donor

dinitrogenase reductase

dinitrogenase  N2

Ammonia is the final product Figure 3.28

Electrons

for

nitrogenase

Nitrogenase

activity

4 Dinitrogenase

reductase

(Red)

Dinitrogenase

(Red)

4 Flavodoxin

(Red)

4 Pyruvate

4 Flavodoxin

(Ox)

2 e  (4)

16 ATP

16 ADP

+ 16 P i

Dinitrogenase

(Ox)

4 Dinitrogenase

reductase

(Ox)

Pyruvate donates

electrons to

flavodoxin.

Flavodoxin reduces

dinitrogenase

reductase.

Electrons transferred to

dinitrogenase one at a

time. 2 ATP are

consumed per electron.

Sum:

(16 ATP 16 ADP + 16 P i)14.11 Nitrate Reduction and Denitrification

Inorganic nitrogen compounds are the most common electron

acceptors in anaerobic respiration

https://www.researchgate.net/figure/258060211_fig1_FIG-1-The-nitrogen-

cycle-Denitrification-consists-of-the-sequential-reduction-of IV. Microbial partnerships :14.22 Syntrophy

Syntrophy

Process whereby two or more microbes degrade a substance neither

can degrade alone

Most syntrophic reactions are secondary fermentations

Most reactions are based on interspecies hydrogen transfer

H2 production by one partner is linked to H 2 consumption by the other

(Figure 14.51)

Syntrophic reactions are important for the anoxic portion of the

carbon cycle

Figure 14.51 LA Lecture s 4 and 5

Due 9-21 -2 5 (5pts)

Names of people worked with (or worked alone )

_________________________

1) Answer the following:

Photorhabdus luminescens lives inside the digestive tract of soil nematodes and also produces a

toxin to kill insects. There is much interest in the metabolism and nutrient requirements of this

species to study it as a natural insecticide. This organism lives mostly in the absence of oxygen,

and uses the endogenous organic molecule fumarate as a final electron acceptor. However, it can

also live in the presence of oxygen and it as a final electron acceptor. Organic molecules obtained

from the nematode are used as a source of energy, electrons and carbon.

Name the three primary nutritional groups of this microorganism:

2) Answer the following about photosynthesis:

Describe the difference between ANOXIGENIC and OXIGENIC photosynthesis. What is

the final electron acceptor for photosynthesis? What does the CALVIN CYCLE do?

3) Using the paper this week by Wei et al. (2023)

https://www.sciencedirect.com/science/article/pii/S2667370323000061

Name the three primary nutritional groups of Ralstonia eutropha :

Sydney

> -
> -

fermentation

Chemo ,

organo , heterotroph

Ton

Anoxigenic : Inorganic molecle breaks carbon

to make

glucose oxigenic : uses H2o + makes 02 lithotroph

> chemotroph

-energy)

aerobic

Autotroph lecture I Chapter

microbiology is the study of organism

you can't see with the unaided eye

> -

Microbiology is Important because it is

the cause of death & disease ,production of

food , oldest living thing

> -

archala , Eukamotic ,bacteria

> -

Archaca , protozoa ,algae , bacteria ,fugi ,

small Invertebrates , Virus

> -

prokaryotes have cell wall ,no organelles .

smaller

Eukaryotes have nuclus ,Miltocondra

> -

All alls : cell Membrane , DN A ,vibosomes

cy to plasm , metablism , response to enviro

1) Van leuwenhoek

> -

first person to describe microbiology

LOUIS pastur

> ~

mach frist vactim(vabies]

> -

disproved spontaneus generation

bacteria can grow from nothing .

> Is

bottle experiment

> -

artain geoms are associated with

particular disease

Koch

discovered viruses a made scientific method to pure culturing

bacterich

> -

why microorganism cause Certain a

Beigernick

> -

pure cultured bacteria from soil

Intentified viruses

Winogradsky

> -

N fixation

modern mich

> -

pathology ,virology , biothnology ,Immunology

Chapter 2 (lecture 223)

magnification : making something bigger

Contrast : the difference in color

resolution : ability to identify two adjacent

items

#breant : cuts organism to see Inside zD

electron & outside 3D

> -

gram Stain (stiferential)

purple = + llarge paptioglycan cell wall)

pink =

> -

ILDS ,

> small

PED , 2 cell membranes]

> -

acidic(pos] basic (neg)

> -

simple 1 dye mo or Bhology = Shape movi

II oc[I *

vachili N

Pirillium -

pirochste -

# elico

# iy 0use in

etrad 800 00

Sardinin 0000

d iplo 8

> -

0. 2-700Nm 1 >200 on Yuka mote

> -

thio margarita

Le vesicles energy product

> -

DNA & ribosomes compartment les Into membrane

like vasisles

more surface area = thore absorption , smaller als

large all-lower surface area : less absorption

III Cytoplasmic :

thin Structure Surrounding all

separates cytoplam from environment

> -

Phospholipid bilayer I

&pop

)() hydrophobic racias)

hydrophilic

head

> -

embeded proteins ester -

> 200 -
> in

membraned

integral proteins : firmly embedded In me inbrare

peripheral : One portion is anchored

archeal membranes

> -

ether link Instead of ester

G O + 2C - 0-

> -

ssoprens instead of fatty acids

short a chains

> -

monolayers not bilayers

plasma membrans

> -

permeable barrier =

> ~

preserves energy (passive transport)

> -

protein anchor

nutrient transport :

active trasport- Use of ATP

ISO to Mic

hyper tonic

hypotonic

endocytosis : creation of vesicles to take

In nutrients

exocytosis : export waste in Vesicles aud membrane

tequoid grampos Guter neg dirct link

# Fran

> -

## glycine wall dea -lyE Pam bran

Archea

Archea differences

D -

No PEP

> -

DAP

> -

slayer has

> -

gram neg ~10 % PEP

most outer membrane IS LPS

LipS = 0-specific polysacchavide ,

sore polysacavide , l pid A

lipid A: Fatty acids

endotoxin-stimulate immune system

Cove polysaclavides :repeated Sugars Attached to

Lipid A

*Specific polySallavida : repeated sugars attached to

Love .different amost species capsule/slime layer

prevents drying out

Allows Attachment to surface

biofilm : community of microorganism

that adhere to each other & a surface

Aids in resistance to chemicals , antibiotics e immune

> alls

fibria

> -

fillment made of protein

helps attach microorganism

Pt longer + helps DNA exchanse

gas vesicles

> -

brancy to planktonic cells

> -

Impermeable to H, o

> -

Spindle shape gas chambers Made of Protein

Endospores

> -
> now

reproductive ,non meta bolically active

> -

helps all survive hargh conditions

> -

makes all resistant to

radiation

disacotiation

heat

chemicals

flagella help cell move

bacteria :

long made of flagelin

Arshea : shorter made of protein Chemotaxis : movement In response to Chemicals

nucleus holds BNA In a Sokaryotic call

nucleolus

Mitosis :Makes daughter diploid chromosomes

> &

body celes

melosis makes haploid daughter cells

gameetes , specialized

Mitochondria :makes ATP cellular respiration

Chloroplast : plant cells photosynthetic

hydrogenosomes

anacrobic generate ATP

Endosymbiosis Theory

> -

Chlorplasts + Mitochondria are decendants of

prokaryoti all

> size

-Similar remembrane -

have own INA

> -

Mitochondria can divide via binary fission

> &

have vibosomes like bacterial Vibosomes

energy made at membrane

election donor : Oxidation Close e-7

electron Acceptor = reduction (gaine

bio energetics : All chemical reactions

accompanied by a change of

energy in a cell redox : Oxidation + reduction happening together

strongest electron donor - >strongest e-

Acceptor

enzymes carry out chemical reactions (proteins)

Catalysts : Speed up reaction

cellular respiration

Gutilizes glycolysis

Oxidative phosphoritation makes a lot of ATP

fermentation

utilizes glycolysis

Internal final electron acceptor

substrate leve phosphorilation  not much ATP

photosynthesis

light-energy

electron transport chain to make ATt

Catabolism :break down modules

input a

catabolic vxn

glycolysis ,citull acid , elefron transport chain

butput-energy ATP

glycolysis :Catabolism of glucose

> -

anderbil

1. glucose consumed

> 2.

2 ATP produced

> 3.

fermentation generated Synthesis of Aceytl-CoA

pyruvate ->Acetated ->Acetyl-CoA

3 Eco 2[

> ~

Citric and Cycle

from glycolysis to make more ATP

pylvate oxidized

> -

glyoxylate

> -

oxaloacetate

> -

helps all make molecules that

help u/ structure

> -

Fermentation produces

> &

thano

Lactic acid

propionic acid

mixed acids

butyvic did

butano

Transcript for:Microbiology Core Concepts

Transcript for:
Microbiology Core Concepts