Exam 1

Ch. 1-6

catalase and peroxidase

-convert H2O2 to O2 and H2O

microorganisms

-oldest forms of life

-major fraction of Earth's biomass

microbial applications

-animal health, human health, ecosystem health, water and waste, agriculture, natural resources, food, biotechnology, industry, bioenergy

common structure of all cells

-cytoplasmic membrane: barrier that separates the inside of the cell from the outside environment

-cytoplasm: aqueous mixture of macromolecules, small organics, ions, and ribosomes inside the cell

-ribosomes: protein-synthesizing structures

-cell wall: present in some microbes: confers to structural strength

prokaryotes

-bacteria and archaea

-no organelles and nucleus

eukaryotes

-plants, animals, algae, protozoa, fungi

-contain organelles

-DNA in nucleus (membrane bound)

-mitochondria and chloroplasts

properties of all cells

-structure, metabolism, growth, evolution

properties of some cells

-differentiation, communication, motility, horizontal gene transfer

prokaryotes size

-0.2-600+ μm range

-

eukaryote size

- 5- 100 μm

surface area and volume

-the smaller you are then the relatively larger your surface area is

-larger surface area encourages the highest diffusion efficiency

-greater nutrient and waste product exchange per unit cell

-surface area: 4pi x r^2

-volume: (4/3) pi x r^3

-surface/volume = 3r

Cell morphologies

-coccus: spherical or ovoid

-rod/bacillus: cylindrical

-spirillum: flexible spiral

Bacteria

-prokaryotes

-undifferentiated single cells

-80+ phylogenetic lineages

Archaea

-prokaryotes

-associated with extreme environments (extremophiles)

-lack parasites or pathogens for plants/animals

Eukarya

-plants, animals, fungi

-first were unicellular

-vary dramatically

viruses

-obligate parasites that only replicate within host cells

-not cells

-small genomes

-do not carry out metabolism

percent global biomass

-70-80% of all P and N concentrated within microbial biomass

-80% C is in plants biomass

extremophiles

-cellsthat live in extreme environments.

Death rates for leading causes of death in the United States

Industrial Microbiology

-wastewater treatment: microbes are used to clean wastewater

-bioremediation: microbes are used to clean contaminated environments

-biofilms: microbes grow on surfaces and can foul pipes and pipelines

-biotechnology: microbes can be genetically modified to produce high-value products such as pharmaceuticals and enzymes

-fermentation: microbes are used at industrial scale to make chemicals, solvents, enzymes, and pharmaceuticals

-biofuels: microbes are used to convert biomass into ethanol and wastes into natural gas

Robert Hooke

-first to observe microbes

-illustrated the fruiting structures of molds

Antoni can Leeuwenhoek

-first to see bacteria

-used a light microscope

Bright field scope

-Specimens are visualized because of differences in contrast (density) between specimen and surroundings

-pigments add contrast

basic dyes

-positively charged , bind strongly to negatively charged cell components

differential stains

-render different kinds of cells different colors

Procedure for gram staining

gram positive

-appear purple-violet

gram negative

-appear pink

phase contrast microscopy

-improves image contrast of unstained live cells

-phase ring amplifies differences in the refractive index of cell and surroundings

dark field microscopy

-light reaches specimen from the sides

-only light scattered by specimen reaches the lens

-image appears light on a dark background

-better resolution than light microscopy and better for motility

fluorescence microscopy

-used to visualize specimens that fluoresce

-cells appear to glow on black background

-dye: DAPI

-used in clinical diagnostic microbiology and microbial ecology

transmission electron microscopy

-much greater resolving power than light microscopy

-visualization of structures at the molecular level

-needs to be stained with high atomic weight substances that scatter e-

Scanning Electron Microscope (SEM)

-specimen coated with a thin film of heavy metal

-electron beam scans the object

-scattered electrons collected to project the image

-very large specimens

-only surface

confocal laser scanning microscope

-uses computerized fluorescent microscope coupled with a laser source to generate a 3D image

-can focus the laser of single layers

-different layers compiled for 3D image

Pasteur

-disproved spontaneous generation

-led to sterilization methods and food preservation

-vaccines for anthrax, fowl cholera, and rabies

Koch

-demonstrated a link between microbes and infectious diseases

-developed solid media for obtaining pure cultures of microbes

microbial diversity

-focuses on nonmedical aspects of microbiology in soil and water

Sergei Winogradsky

-demonstrated that specific bacteria are linked to specific biogeochemical transformations

-Beggiatoa (sulfur oxidizers)

-concept of chemolithotrophy: oxidation of only inorganic compounds to yield energy

-first to demonstrate nitrogen fixation (Clostridium pasteurianum) and nitrification

Martinus Beijerinck

-developed enrichment culture technique which selectively encourages growth of specific bacterium

-isolated Azotobacter (aerobic nitrogen fixing)

-first to observe a virus (tobacco mosaic virus)

Frederick Griffith

-Discovered transformation in pneumonia-causing bacteria

James Watson, Francis Crick, Rosalind Franklin

-discovered the structure of DNA

Emile Zuckerland and Linus Pauling

-scientists that discovered molecular sequences and evolutionary relationships

Carl Woese

-three domain based on r RNA (eukarya, bacteria, archaea)

-found evolutionary relationships between all living cells could be revealed with RNA analysis to create a tree of life

-16 S in prokaryotes or 18 S / 23 S RNA in eukaryotes

-not viruses

-discovered archaea when studying methanogens

E. Haeckel

-first to attempt to put all the living organisms on the same tree of life

-5 kingdoms

Gram Positive

-large layer of peptidoglycan

-have Teichoic acid and Lipoteichoic acid

-glycosidic bonds on the outside

-dark purple when stained

Gram Negative

-second lipid bilayer external to the cell wall

-outer membrane contains polysaccharides covalently bound to lipids

-contains porins (transmembrane transport proteins)

-small layer of peptidoglycan

-pink when stained

Capsule cell surface

-if tightly attached, tight matrix; visible if treated with India ink

-assist in attachment to surfaces

-role in development and maintenance of biofilms

-contribute to infectivity

-prevent dehydration/desiccation

Slime layer surface

-loosely attached, easily deformed

-sticky polysaccharide coat outside cell envelope

-assist in attachment to surfaces

-role in development and maintenance of biofilms

-contribute to infectivity

-prevent dehydration/desiccation

Fimbriae

-extensions of the cell surface

-pili: thin long filamentous protein structures; shorter than flagellum; longer than a fimbria

-made by all gram-negative and many gram-positives

-sex pili: facilitate genetic exchange between cells through conjugation

Endospores

-malachite green to stain

-highly specialized spores

-highly differentiated, dormant cells resistant to heat, radiation, chemical exposure, drying, lack of nutrients

-only present in some gram positive bacteria (Bacillales and Clostridiales)

-Vegetative->Endospore->Vegetative

-many layers: core, inner membrane, cortex, outer membrane, endospore coat, exosporium

-dipicolinic acid with Ca2+

-small acid-soluble spore proteins which bind and protect DNA and function as carbon and energy source for growth

Structure of endospores

Difference between endospores and vegetative cells

Formation of endospores

Flagella/archaella

-structure that assists in swimming in Bacteria and Archaea

-long, thin appendages anchored in a cell at one end

-peritrichous, polar, lophotrichous

-powered by proton motive force

-filament, book, basal body

Movement in peritrichously and polarly flagellated prokaryotic cells

Twitching motility

- requires type IV pili

- extend from one cell pole, attach to surface, retract to pull cell forward

- energy from ATP hydrolysis

-e.g. Pseudomonas and myxobacteria

Gliding motility

-smooth, continuous motion along long axis without external structures

-only bacteria so far (e.g. Myxococcus)

-helical intracellular protein track + gliding motors and adhesion proteins

Chemotaxis

-cell movement in response to chemicals

-run: smooth forward motion, flagellar motor rotates counterclockwise

-tumble: bacteria stops and jiggles because flagellar motor rotates

-run and tumble caused by different types of rotation of the flagella

-measured with capillary tube that has decreasing concentration far from tip

Other forms of taxis

-osmotaxis: response to ionic strength

-hydrotaxis: response to water

-aerotaxis: response to O2

-phototaxis: response to light

Nucleus

-contains the chromosomes

-DNA wound around histones forming nucleosomes that are organized into chromosomes

-archaea contain histones and nucleosomes

-nucleolus: inside nucleus and site of ribosomal RNA synthesis

Mitosis

-results in two diploid (two copies of each chromosome) daughter cells

Meiosis

-converts diploid into haploid cells

Mitochondria

-respiration and oxidative phosphorylation for aerobic eukaryotes

-cristae: folded internal membranes

-matrix: innermost area of mitochondrion

Chloroplasts

-chlorophyll containing organelle found in phototrophic eukaryotes

-site of photosynthesis with two membranes

-inner membrane surrounds stroma

-stroma contains large amounts of RuBisCO which is the key enzyme for the Calvin cycle

-thylakoids: flattened membrane discs contain chlorophyll and ATP synthetic components, form proton motive force

Cytoskeleton

-microtubules: maintain cell shape, facilitate motility; move chromosomes and organelles

-microfilaments: maintain and change cell shape; involved in amoeboid motility and cell division

-intermediate filaments: maintain cell shapes and position organelles

endoplasmic reticulum

-network of membranes continuous with nuclear membrane

-smooth: participates in the synthesis of lipids and carbohydrate metabolism

-rough: produces glycoproteins and new membrane material

golgi complex

-stacks of membrane-bound sacs modifying ER products

lysosomes

-membrane-enclosed compartments containing digestive enzymes and recycling cell components

first law of thermodynamics

-energy is neither created nor destroyed

free energy

-energy available to do work

reducing power

-an ability to donate electrons

-requires a compound that serves as a source of electrons

-reduction potential: tendency to donate electrons

exergonic reactions

-reactions with negative deltaG that release free energy

endergonic reactions

-reactions with positive deltaG that require energy

catabolic pathways

-generate free energy

-coupled to ATP synthesis to conserve free E

-breaking down of metabolic compounds

-degradation of glucose linked to production of ATP

anabolic pathways

-use up free energy

-coupled to ATP degradation reaction

-creating of different metabolic compounds

electron donor

-transfers electrons (oxidized)

electron acceptor

-adds electrons (reduced)

phototrophs

-obtain energy from light

-oxygenic (O2 produced) and anoxygenic (no O2 produced) photosynthesis

-oxidative phosphorylation

chemotrophs

-obtain energy from chemical reaction

-chemoautotrophs: energy source is inorganic

-chemoorganotrophs: energy source is organic (fatty acid e.g.)

-aerobic reactions require O2 as electron acceptor

-anaerobic reactions use anything other than O2 as electron acceptor

redox tower

-Represents the range of possible reduction potentials

-The reduced substance at the top of the tower donates electrons

-The oxidized substance at the bottom of the tower accepts electrons

-The farther the electrons "drop" the greater the amount of energy released

NAD+/NADH

-soluble electron carriers

-coenzymes

-coupled value is -0.32 V

-NADH good electron donor and can also donate hydrogens

-NAD+ weak electron acceptor

calculating deltaG

-Δ G0 = −n F Δ E0ʹ

-Δ E0ʹ : change in reduction potential

-can also be found by finding the difference between free energy of formation of products and reactants

substrate-level phosphorylation

-energy-rich substrate bond hydrolyzed directly to drive ATP formation (e.g., hydrolysis of phosphoenolpyruvate)

oxidative phosphorylation

-movement of electrons generates a proton motive force (electrochemical gradient) used to synthesize ATP

photophosphorylation

-light used to form proton motive force

enzymes

-prosthetic groups: tightly bound, usually covalently and permanently

-coenzymes: loose and transiently bound with most being derivatives of vitamins

Glycolysis

-stage 1: energy investing or preparatory, forming G3P intermediate

-stage 2: energy producing, redox, energy conserved, 2 pyruvates formed

-net is 2 ATPs, 2 NADHs, 2 pyruvates per glucose

Citric Acid Cycle

-2 CO2, 3 NADH, 1 FADH2, 1 ATP formed per each pyruvate being oxidized

-oxaloacetate is regenerated so the cycle is repeated

glyoxylate cycle

-plants and bacteria

-acetyl-coA --> carbohydrates

fermentation

-conserve energy (produce ATP)

-restore redox balance (regenerate NADH)

-need to produce compounds containing high energy bonds for ATP synthesis

respiration

-electrons transferred from reduced electron donors to external electron acceptors

-reoxidation occurs during the electron transport chain

-occurs in cytoplasmic membrane due to electrochemical gradient that conserves energy through ATP synthesis

-arranged with increasingly more positive reduction potential

NADH dehydrogenase

-active site binds NADH, accepts two electrons and two protons that are transferred to flavoproteins, regenerating NAD+

Flavoproteins

-contain derivative of riboflavin as prosthetic group that accepts two electrons and two protons but only donate electrons

cytochromes

-proteins that contain heme prosthetic groups

-oxidized or reduced by 1 electron via the iron atom

nonheme iron proteins

-contains cluster of iron and sulfur

quinones

-small hydrophobic nonprotein redox molecules

-can move within membrane

-ubiquinone (coenzyme Q) and menaquinone are the most common

ATP synthase

-oxidative phosphorylation from respiratory electrons

-photophosphorylation from light energy

-uses energy from proton motive force to form ATP

-38 ATP in aerobic respiration and 2 ATP in lactic acid fermentation

respiration in Escherichia coli

-versatile chemoorganotroph with electron transport similar to Paracoccus denitrificans

-grows by aerobic respiration, fermentation, anaerobic respiration (nitrate)

-no O2, then E. coli uses nitrate reductase as a terminal reductase

chemolithography

-use inorganic chemicals as inorganic electron donors

-use reverse electron transport for proton motive force

calvin cycle

-reactions of photosynthesis in which energy from ATP and NADPH is used to build high-energy compounds such as sugars

-requires CO2, a CO2 acceptor (RuBP), NADPH, ATP, ribulose bisphophate carboxylase (RubisCO), and phosphoribulokinase