Microbio 1

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Microbiology

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Study of microscopic organisms including fungi, protists and viruses

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What two themes does microbiology revolve around?

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1. Understanding basic life processes. 2. Applying that knowledge to benefit humans

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Why are microorganisms important?

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They are the oldest form of life, the largest mass of living material on earth, they carry out biogeochemical cycles, can live in Environments unsuitable for others and other life forms require microbes to survive.

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Cytoplasmic (cell) membrane

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Barrier that separates the inside of the cell from the outside Environment.

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Cytoplasm

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Aqueous mixture of macromolecules, ions and ribosome

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Ribosomes

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Protein synthesizing structures

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Cell wall

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Present in most microbes; confers structural strength

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What are the three domains?

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Eukarya, Bacteria and Archaea

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Archaea are more closely related to..

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Eukarya

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How are prokaryotes different from eukaryotes?

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There organelles are not membrane enclosed, they have no nucleus, and they are generally smaller than most eukaryotes

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How are eukaryotes different from prokaryotes?

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They have their DNA enclosed in a membrane bound nucleus and their cells are generally larger and more complex. They contain organelles.

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Genome

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A cells full complement of genes; includes chromosomes, epigenome, and plasmids

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Prokaryotic cells dna

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Single, circular DNa (called a chromosome), DNA aggregates to form the nucleoid region, they have small amounts of extra groomsman DNA (plasmids) that confer special properties.

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Escherichia coli genome vs human cells

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4.63 m BPs, 4300 genes; 1000x more DNA per cell than E. Coli, 7 X more genes than E. Coli

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What are the six characteristics of living cells?

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Metabolism, reproduction, differentiation, communication, movement (some cells are known with no form of movement) and evolution

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Age of the earth

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4.6billion

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First cells appear

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3.8-3.9 bya

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Anoxic until

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~2 bya

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Oxygen producing phototrophs that made the earth oxic

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Cyanobacteria; blue-green algae

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Life was exclusively microbial until

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~1 bya

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Evolution

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The process of change over time that results in new varieties and species of organisms

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Phylogeny

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Evolutionary relationships between organisms, relationships can be deduced by comparing genetic info in different specimens. rRNA can help determine phylogeny

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The three distinct domains were determined by comparison of

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rRNA

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Microbial communities

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Populations of interacting assemblages. This is how microorganisms exist in nature.

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Ecosystem

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All living organisms plus physical and chemical constituents in their environment.

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Microbial ecology

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The study of microbes in their natural environment.

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Diversity and abundance of microbes are controlled by

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Resources (nutrients) and Environmental conditions (temp, pH, O2,etc)

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Extremeophiles

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Bacteria and archaea that grow in extremely harsh environments (very hot or cold, acidic or caustic, salty or osmotically stressful, high pressure)

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What two cycles are microbes involved in?

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Nitrogen and sulfur ki

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Where in humans can microbes be found?

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Stomach, small intestine, large intestine

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What (beneficial) function do microbes serve in humans?

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Vitamins and nutrients, and keeping pathogens at bay; mouth has the greatest diversity

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How can microorganisms be used in food?

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Preservation, spoilage and food-safety

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What are some forms of glucose breakdown that can be used in foods?

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Robert Hooke (1635-1703)

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The first to describe microbes; illustrated the fruiting structures of molds

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Antoni von Leewenhoek (1632-1723)

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The first to describe bacteria; further progress required development of more powerful microscopes.

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Ferdinand Cohn (1828-1898)

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Founded the field of bacterial classification and discovered bacterial endospores

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Louis Pasteur (1822-1895)

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Discovered that living organisms discriminate between optical isomers. Discovered that alcoholic fermentation was a biologically mediated process. Disproved theory of spontaneous generation; led to the development of methods for controlling the growth of microorganisms (aseptic technique). Developed vaccines for anthrax, fowl cholera, and rabies

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Theory of spontaneous generation

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Robert Koch (1843-1910)

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Demonstrated the link between microbes and infectious diseases, identified causative agents of anthrax and tuberculosis. Koch's postulates. Developed techniques for obtaining pure cultures of microbes. Awarded Nobel piece prize for physiology and medicine in 1905.

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Koch's postulates

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Martinis Beijerinck (1851-1931)

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Developed enrichment culture technique.

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Enrichment culture technique

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Microbes can be isolated from natural samples in a highly selective fashion by manipulating nutrient and incubation conditions.

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Sergei Winogradsky (1856-1953)

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Demonstrated that specific bacteria are linked to specific biogeochemical transformations. Proposed concept of chemolithotrophy

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Chemolithotrophy

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Oxidation of inorganic compounds linked to energy conservation.

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Genomics

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Study of all of the genetic material in living cells

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Transcriptomics

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Study of RNA patterns

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Proteomics

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Study of all the protiens produced by a cell

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Metabolically

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Study of metabolic expression in cells

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Coccus

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Spherical or ovoid or nearly spherical

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Rod

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Cylindrical shape; vaccilus or vacili

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Spirillum

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Spiral shape

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Coccobaccili

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Short rod shaped

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Vibrio

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Comma or crescent shape

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What are cells with unusual shapes

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Spirochetes, appendaged bacteria, and filamentous bacteria

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Spirochete

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Budding and appendaged bacteria

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Filamentous bacteria

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What does bacterias small size and large surface area allow for?

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Fast replication, support a greater nutrient exchange per unit cell volume and they tend to grow faster than larger cells

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Cytoplasmic membrane

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Structure that surrounds the cell, vital barrier that separates cytoplasm from environment, highly selective permeable barrier which enables concentration of specific metabolites and excretion of waste products.

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Mycelles

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Sphere with 1 layer or bilayer membrane.

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What are the parts of membranes?

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1. Hydrophobic region (includes the fatty acids) 2. Hydrophilic region (includes a phosphate with a functional group)

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Cytoplasmic membrane

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Semifluid 8-10nm membrane with embedded proteins, that is stabilized with hydrogen bonds and hydrophobic interactions. They use Mg++ and CA++ to help stabilize by forming ionic bonds with neg charges on the phospholipids.

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What are the two types of membrane proteins?

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Integral and peripheral

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Integral membrane proteins

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Firmly embedded in the membrane

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Peripheral membrane proteins

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One portion anchored in the membrane

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What types of linkages do eukarya and bacteria have linking phospholipids?

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Ester

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What linkages do archaea have in phospholipids?

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Ether

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Archaea membranes

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Lack fatty acids, have isoprenes instead. Major lipids are glycerol dieters and tetraethyl. Can exist as lipid monolayers, bilayers or both

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Permeability barrier

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Polar and charged molecules must be transported which requires energy. Transport proteins accumulate solutes against the concentration gradient.

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Protein anchor

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Holds transport proteins in place

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Energy conservation

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Proton motive force

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Functions of the membrane

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Permeability barrier, protein anchor and energy conservation

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What are the three major classes of transport systems in prokaryotes?

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Simple transport, group translocation, and the ABC system *All require energy in some form, usually proton motive force

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Simple transport

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Driven by the energy in the proton motive Force

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Group translocation

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Chemical modification of the transported substance driven by phosphoenolpyruvate

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ABC transporter

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Periplasmic binding proteins are involved in energy comes from ATP; Texans can be delivered this way

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Peptidoglycan

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In bacteria that have cell walls, this is the main cell wall material

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LPS

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Lipidpolysaccharides; they are present in all gram-negatives

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Gram-negative cell

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They have one thin cell wall, in two phospholipid bilayers: the cytoplasmic and outer membrane.

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Gram positive cell

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They have one thing cell wall which is about five to 10 times thicker than in a gram-negative cell and they have one phospholipid bilayer, the cytoplasmic membrane

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When is LPS released?

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Anytime the cell dies which can cause septic shock and lower the blood pressure.

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Peptidoglycan

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A rigid layer that provides strength to a cell wall. It has a polysaccharide composed of n-acetylglucosamine and n-acetylmuremic acid as well as amino acids and lysine or diaminopimelic acid (DAP). The polysaccharide is Crosslink differently in gram-negative bacteria and gram-positive bacteria

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What type of amino acids are common in nature?

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L; D forms may be used to stop enzymes from breaking them down but they're still are enzymes like lysozyme that have evolved to be able to break down the D form.

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Gram positive cell walls

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They can contain up to 90% peptidoglycan, And it is common for them to have teichoic acids embedded in their cell wall including lipoteichoic acids which are teichoic acids that are covalently bound to membrane lipids

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Give two examples of prokaryotes that lack cell walls

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Mycoplasmas ( a group of pathogenic bacteria including atypical pneumonia and walking pneumonia) and thermalplasma ( species of archaea)

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LPS

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Present in gram-negative pictorial only. It consists of core polysaccharides and O polysaccharides. It replaces most of the phospholipids in the outer half of the outer membrane and it is an endotoxin.

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EPS

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Extracellular polysaccharide. It can be present as a slime layer to form a capsule or slime around the cell outside of the LPS

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Label the different parts

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Periplasm

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The space located between the cytoplasmic in the outer membranes which is about 50 nanometers wide. The contents have a gel-like consistency and houses many proteins where initial digestion occurs.

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Porins

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Channels for movement of hydrophilic low-molecular-weight substances which of the involved in facilitated diffusion

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Archaeal cell walls

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They have no peptidoglycan in typically no outer membrane. Some contain pseudomurein.

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Pseudomurein

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Polysaccharide similar to peptidoglycan which is composed of N- acetylglucosamine and n-acetylalosaminuonic acid. it is found in the cell walls of certain methanogenic archaea.

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S-layers

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Most common cell wall type of archaea which consist of protein or glycoprotein and has a paracrystalline structure.

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Fimbriae/pili

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Short, rigid protein structures that are hairlike and involved in attachment to which can be seen around the outside of a cell

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Inclusions

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Granular or crystalline structures often involved in energy storage

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Gas vesicles

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Membrane-bound which can be proteinaceous and can hold gas or very low density proteins and also can be used for buoyancy in aquatic environments which allows the bacteria to dive deeper to block some of the UV light.

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Endospores

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when nutrients are scarce bacteria sacrifice themselves and form a small hard spore and when conditions are right they germinate and Form 1 cell

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Flagella

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Long tail like structures about two to three times the length of the cell made up of proteins called flagellins. They are attached to a motor which spans the cytoplasmic membrane cell wall and expands into the cytoplasm. Energy from ATP from the motive Force Powers it

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What is occurring when bacteria are mating?

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They are transferring genetic material that is not in the chromosome but in a plasmid the donor is f+ and the recipient is f minus

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Describe the shape and different arrangements of the flagella

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They are helical in shape and can be peritrichous (flagella all over), polar (flagella only at the ends) or lophotrichous (tuft of flagella at one or both ends)

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Describe the movement of flagella

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Move in runs (straight) and tumbles (turn by rotating flagella opposite direction)

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Flagellar structure of archaea

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They're half the diameter of bacterial flagella and composed of several different proteins and move by rotation

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Chemotaxis

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Movement in response to a chemical stimulus usually toward food or away from a chemical toxin

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Mot protein

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Involved in PH difference and obtains energy from the proton motive Force it works similarly to an electric motor and powered by the positive and negative charges.

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Describe the swimming motion of peritrichous flagella

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They move slowly and a straight line

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Describe the swimming and motility of Polarly flagellated cells

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They move more rapidly and typically spin around

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Gliding motility

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This is for flagella-independant motility which is slower and smoother than swimming. Movement typically occurs along the long axis of a cell and require surface contact the mechanisms used are by the excretion of polysaccharide slime, Type 4 pili or gliding specific proteins.

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What are the different types of Taxis

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Chemotaxis, phototaxis, Aerotaxis, osmotaxis and Hydrotaxis

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What is the function of smooth ER

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Lipid production

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In prokaryote what is the order of transcription and translation?

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They occur simultaneously

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Nutrients

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Supply of monomers or precursors required by cells for growth

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Macronutrients

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Nutrients required in large amounts including CNNaPCaFeMg

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Micronutrients

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Nutrients required in Trace Amounts

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Growth factors

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Organic compounds required in small amounts by certain organisms such as vitamins amino acids, purines, andpyrimidines

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Vitamins

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Most commonly required growth factors most function as coenzymes

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Culture media

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Nutrient Solutions used to grow microbes in the laboratory

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What are the two broad classes of culture media

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Defined media which has a precise chemical composition and complex media which is composed of digestive chemically undefined substances

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Enriched media

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Contain complex sometimes defined media plus additional nutrients which enrich for certain types of organisms over others

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Differential media

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Contain an indicator usually die that detects particular chemical reactions occurring during growth and allows you to differentiate between different microbes

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Pure culture

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Culture containing only a single kind of microbe

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Contaminants

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Unwanted organisms in a culture

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Solid culture media

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Prepared by addition of a gelling agent such as agar or gellatin and when grown and solid media cells form isolated misses called colonies

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Metabolism

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The sum total of all the chemical reactions that occur in a cell or associated with a cell

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Catabolism

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Breaking down chemicals

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Anabolism

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Building a chemical or molecule

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What energy classes are microorganisms grouped into

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Chemo organotrophs chemolithotrophs phototrophs heterotrophs and autotrophs

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Energy

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Measured in units of kilojoules which is a measure of heat energy

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Free energy (G)

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Energy released that is available to do work

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Change in free energy during reaction is referred to as

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Activation energy

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Energy required to bring all the molecules in a chemical reaction into the reactive state. catalysis is usually required to bridge activation energy barrier

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Catalyst

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Lowers the activation energy of a reaction increases the reaction rate and does not affect energetics or equilibrium of reaction

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Enzymes

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They are biological catalyst which are typically proteins (some RNAs), they are highly specific and generally larger than the substrate or product. They typically rely and weak bonds such as hydrogen bonds Van Der waals forces or hydrophobic interactions. They contain an active site and they increase the rate of a chemical reaction.

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Prosthetic group

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Bind tightly to enzymes usually bind covalently and permanently or at least her tightly associated

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Coenzymes

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Loosely bound to enzymes most are derivatives of vitamins

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Co-factors

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They're even smaller than a coenzyme and almost always and inorganic ions such as sodium magnesium calcium. Etc

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Redox reactions

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Energy from the misuse didn't synthesis of energy rich compounds such as ATP. They occur in pairs of two half reactions. There is an electron donor and an electron acceptor

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Carriers

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Intermediates usually involved in redox reactions

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What are the two classes that are electron carriers are divided into

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Prosthetic groups and coenzymes

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Give an example of a coenzyme

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NAD Plus or nadh

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NAD+/NADH cycling

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Where is the chemical energy that is released in redox reactions primarily stored?

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In certain phosphorylated compounds such as ATP, phosphoenolpyruvate, glucose-6-phosphate and it can also be stored in coenzyme a

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How can energy be stored long-term

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An insoluble polymers that can be acted as to generate ATP. In prokaryotes this includes glycogen, poly- beta -hydroxybutyrate and other polyhydroxyalkanoates and elemental sulfur. In eukaryotes this is in the form of starch or lipids

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What are the two reaction series link to energy conservation in chemoorganotrophs with glycolysis?

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Fermentation and respiration

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Fermentation

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Substrate level phosphorylation. ATP is directly synthesized from an energy-rich intermediate. Recycles NAD plus produces no ATP

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Respiration

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Oxidative phosphorylation. ATP is produced from proton motive force from by transport of electrons

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Glycolysis

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Glucose is consumed it is an anaerobic process where two atp's are produced. Fermentation products are generated and some can be harnessed by humans for consumption.

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Saccharomyces cerevisiae

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Carry out fermentation or respiration. It uses the one that's most beneficial. Respiration generates ATP fermentation occurs when conditions are anoxic

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Aerobic respiration

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Oxidation using O2 is the terminal electron acceptor. It's a higher ATP yield then fermentations where ATP is produced at the expense of the proton motive Force which is generated by electron transport

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Electron transport systems

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It is membrane associated and it mediates the transfer of electrons. It can serve some of the energy released during transfer and used it to synthesize ATP. Many oxidation reduction enzymes are involved in electron transport such as nadh dehydrogenase is Flavorproteins, iron sulfur proteins and cytochromes

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NADH dehydrogenases

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Proteins found to the inside service of cytoplasmic membrane. Active site binds nadh and accept two electrons into protons that are passed to flavoproteins.

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Flavoproteins

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Contains Flavin prosthetic group that accept two electrons and two protons but donates electrons only to the next protein and the chain

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Cytochromes

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Proteins that contain heme prosthetic groups. They accept and donate a single electron via the iron atom in heme

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Iron-sulfur proteins

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Contain clusters of iron and sulfur. Reduction potentials vary depending on the number and position of iron and sulfur atoms

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Quinones

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Hydrophobic non protein containing molecules that participate in electron transport. They accept electrons and protons but pass along electrons only

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The proton motive Force

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The electron transport system is oriented in the cytoplasmic membrane allowing it to separate electrons from protons. Electron carriers are arranged in the membrane and Order of the reduction potential and the final carrier in the chain donates electrons and protons to the terminal acceptor.

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Where do protons in the electron transfer chain originate from

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Nadh in the dissociation of water

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What is the electrochemical potential across the membrane called

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The proton motive Force

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The inside of the three membrane becomes negative and

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Alkaline or basic. The outside is acidic

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ATP synthase

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Complex that converts proton motive Force into ATP using two components: F1( multi protein extra membrane complex which faces the cytoplasm) and F0 ( proton conducting intramembranous channel). This is reversible and dissipates the proton motive Force

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Citric acid cycle or Krebs cycle

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Pathway through which pyruvate is completely oxidized to carbon dioxide. The initial steps include glucose to pyruvate the same as glycolysis. Per glucose molecule six carbon dioxide molecules are released and nadh and fadh2 generated this plays a key role in catabolism and biosynthesis. There's an energetix advantage to aerobic respiration

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How many atp's can potentially be made from glycolysis + the Krebs cycle?

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38

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What is the 3 carbon compound that is a product of the Krebs cycle?

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Pyruvate or pyruvic acid

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What is the input for the Krebs cycle?

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Acetyl CoA

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alpha-Ketoglutarate and oxaloacetate (OAA)

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Compounds generated from the CAC; precursors of A.A.s; OAA is also converted to phosphoenolpyruvate, a precursor of glucose.

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Succinyl-CoA

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Generated from the CAC; required for synthesis of cytochromes, chlorophyll, and other tetrapyrrole compounds.

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Acetyl CoA

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Generated from the CAC; necessary for fatty acid biosynthesis

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What are some of the mechanisms microbes use to generate energy?

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Fermentation, aerobic respiration, anaerobic respiration, chemolithotrophy, and phototrophy.

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What types of organisms are use these processes?

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Chemolithotrophs

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What types of organisms are use these processes?

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Chemolithotrophs

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What types of organisms use these processes?

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Phototrophs

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In fermentation what is the electron donor?

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An organic compound

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What can beelectron acceptors in fermentation?

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S°, NO3-, SO4 2-, organic electron acceptors and O2

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What is the terminal electron acceptor in fermentation?

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O2

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In chemoorganotrophy what can be an electron donor?

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H2, H2S, Fe3+, NH4+, etc.

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In chemoorganotrophy, what can be electron acceptors?

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S°, SO4 2-, NO3-, O2

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What is the terminal electron acceptor in chemoorganotrophy?

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O2

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What type of compounds are used for a carbon source in photoheterotrophy?

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Organic compounds

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What is used for a carbon source in photoautotrophy?

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CO2

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What are prokaryotic polysaccharides synthesized from?

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Activated glucose

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Adenosine diphosphoglucose (ADPG)

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Precursor for glycogen biosynthesis

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Uridine diphosphoglucose (UDPG)

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Precursor of some glucose derivatives needed for biosynthesis of important polysaccharides; examples include N-acetylglucosamine, and N-acetylmuramic acid

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Gluconeogenesis

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Synthesis of glucose from phosphoenolpyruvate

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Phosphoenolpyruvate can be synthesized from what?

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Oxaloacetate

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What is the path from intermediates of the citric acid cycle to the first intermediate in glycolysis?

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What is required for the synthesis of nucleic acids?

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Pentoses (5 carbon sugars)

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If pentoses are unavailable in the environment how can organisms synthesize them?

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By the removal of one carbon from a hexose

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What is the path of using glucose to make DNA and RNA?

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How are carbon skeletons made during biosynthesis of amino acids and nucleotides?

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They come from intermediates of glycolysis or Krebs cycle.

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How is ammonia used during biosynthesis of AAs and nucleotides?

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It's Incorporated by glutamine dehydrogenase or glutamine synthetase.

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During biosynthesis of AAs and nucleotides what is the amino group transferred by?

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Transaminase and synthase

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During biosynthesis of AAs and nucleotides what is the amino group transferred by?

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Transaminase and synthase

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Oxitroph

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Deficient in 1 or more amino acids; used instead lab setting to manipulate bacteria.

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Haynes test

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Organisms lacking histodines are grown on media without histodines. If there are no mutagens present the BP can be changed so they no longer lack histodine.

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How many carbons at a time are fatty acids biosynthesized?

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2

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How is Acyl carrier protein (ACP) involved in fatty acid biosynthesis?

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It holds the growing fatty acid as it's being synthesized

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What is involved in the final assembly of lipids in bacteria and eukarya?

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The addition of fatty acids to glycerol

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Instead of fatty acids Archaea have lipids that contain what?

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Phytanyl side chains

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How can nitrogen fixing bacteria be found?

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Free living or symbiotic

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What is the nitrogen fixing reaction catalyzed by?

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Nitrogenase

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Nitrogenase is sensitive to the presence of what?

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Oxygen (only functional without it)

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Rhizobium

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Form nodules on the roots of legumes; symbiots with plants; convert N2 to ammonia

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Where does nitrogen fixation occur?

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In membrane bound organelles devoid of oxygen

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Where does nitrogen fixation occur?

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In membrane bound organelles devoid of oxygen

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Electron flow in nitrogen fixation

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What is involved in a redox reaction during nitrgen fixation?

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Dinitrogenase reductase/flavodioxin

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In nitrogen fixation for every N2 how many NH3- are made?

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2

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What is one way to assay nitrogenase activity?

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Acetylene reduction assay

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What occurs in a acetylene reduction assay?

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Nitrogen

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Typical bacterial cell is ≈13% nitrogen by dry weight; key element in proteins, nucleic acids, and many more cell constituents

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Phosphorus

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Synthesis of nucleic acids and phospolipids

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Sulphur

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Sulphur -chain amino acids (cysteine and methionine); vitamins and coenzyme-A

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Potassium

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Required by enzymes for activity

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Potassium

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Required by enzymes for activity

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Magnesium

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Stabilizes ribosomes, membranes, and nucleic acids; also required for many enzymes

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Calcium

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Helps stabilize cell walls in microbes; play key role in heat stability of endospores

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Sodium

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Required by some microbes

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Functional unit of the generic information

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Gene

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What are genes composed of?

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DNA

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What are the three informational macromolecules in a cell?

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DNA, RNA, and protein

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Three stages of genetic information flow?

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Replication, transcription and translation

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Replication

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DNA is duplicated

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Transcription

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Info from DNA is transferred to RNA

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Transcription

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Info from DNA is transferred to RNA

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mRNA

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Encodes polypeptides

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tRNA

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Plays role in protein synthesis

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rRNA

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Plays role in protein synthesis

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rRNA

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Plays role in protein synthesis

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Translation

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Info from RNA is used to build polypeptides

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Ribosomes

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Protein polymerases

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Why is DNA in a double helix

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More stable

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Central dogma

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DNA to RNA to protein

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Transcription in Eukaryotes

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Each gene is done individually; 1 gene/1 control region(transcriptional unit) which allows for more control but less efficiency.

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Transcription in prokaryotes

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Multiple genes may be done together in operons; multiple genes/1 control region(transcriptional unit) which allows efficiency and less energy; also don't have the luxury of space for more base pairs

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Operon

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What are the four nucleotides found in DNA?

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Adenine, Guanine, cytosine and thymine

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Describe the backbone of DNA

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It consists of alternating phosphates and the pentoses sugar, deoxyribose; phosphates connect 3'-carbon of one sugar to 5'-carbon of the adjacent sugar

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What bases are pyridimines?

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C,T and U

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What bases are purine bases?

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A and G

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What does it mean for DNA to have antiparallel strands?

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What are the complimentary base sequences in DNa?

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A and T, C and G

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How does the 3' and 5' ends get their name?

Back 241

Front 242

How does the 3' and 5' ends get their name?

Back 242

Front 243

1Mbp

Back 243

Mega base pair; 1 million

Front 244

How big is the E. coli genome?

Back 244

4.64Mbp

Front 245

How long is each BP?

Back 245

.34nm

Front 246

How many BP make up one turn of the helix?

Back 246

10

Front 247

Supercoiled DNA

Back 247

DNA is further twisted to save space

Front 248

Negative supercoiling

Back 248

Double helix is underwound

Front 249

Positive supercoiling

Back 249

Double helix is overwound

Front 250

Relaxed DNA

Back 250

DNA has number of turns predicted by number of bp

Front 251

DNA gyrase

Back 251

Introduces supercoils into DNA

Front 252

What are the benefits to DNA being wound?

Back 252

Protected and compact

Front 253

When is DNA unwound?

Back 253

Only when it needs to be read

Front 254

Genome

Back 254

Entire complement of genes in cell or virus

Front 255

Genome

Back 255

Entire complement of genes in cell or virus

Front 256

Chromosome

Back 256

Main genetic element in prokaryotes (other elements include virus genomes, plasmids, organelles genomes, and transposable elements)

Front 257

Extrachromosomal DNA

Back 257

DNA outside the chromosome; includes in plasmids, mitochondria and chloroplasts

Front 258

Describe virus genomes

Back 258

They contain either DNA or RNA; can be linear or circular; can be single or double stranded

Front 259

Plasmids

Back 259

Replicate separately from chromosomes, thought they may be in sync. The great majority are double stranded. Most are circular and they generally contain genes that are beneficial for the cell. Since it's costly to replicate the plasmids are only kept if they are needed. The smaller they are, the higher the copy number.

Front 260

Chromosome

Back 260

A genetic element with "housekeeping genes" (presence of essential genes is necessary to be considered a chromosome)

Front 261

What main way is a plasmid different from a chromosomal gene?

Back 261

It is expendable and rarely contains genes for growth under all conditions.

Front 262

Transposable elements

Back 262

Segment of DNA that can move from one site to another on the same or a different DNA molecule.

Front 263

What are the three main types of transposable elements?

Back 263

1. Insertion sequences 2. Transposons 3. Special Viruses

Front 264

Insertion sequences

Back 264

Usually smaller, found at the ends of most transposons

Front 265

Special viruses

Back 265

Some are associated with cancer because when they insert in the chromosome they can hit an essential gene.

Front 266

Random mutagenosis

Back 266

Old method

Front 267

Targeted mutagenosis

Back 267

Have the chromosomal DNA sequence. So construct a vector and swap out a targeted gene

Front 268

The Escherichia coli chromosome

Back 268

Because E. Coli is a useful model organism (biochemistry, genetics, and bacterial physiology) the genome (from the strain MG1655) has been mapped out using conjugation, transduction, molecular cloning, and sequencing

Front 269

How many minutes is the chromosome of E. Coli usually cut up into?

Back 269

100

Front 270

Conjugation

Back 270

Bacterial mating with sex/fertilization pilus; sometimes entire chromosomes can be transferred; process takes 100min.

Front 271

Features of the E. Coli chromosome

Back 271

Many genes encoding enzymes of a single biochemical pathway are clustered into operons. Operons are equally distributed on both strands (~5 MBP in size), about 40% of predicted proteins are of unknown function. The Ave protein contains about 300 AAs. Has insertion sequences.

Front 272

Describe plasmids

Back 272

Small circular or linear DNA, size: 1kbp to >1Mbp (typically less than 5% size of the chromosome). Carry non-essential but helpful genes. Abundance)copy number is variable.

Front 273

F plasmids

Back 273

Conjugated from cell to cell

Front 274

F plasmids

Back 274

Conjugated from cell to cell

Front 275

R plasmids

Back 275

Resistance plasmids; confer resistance to antibiotics and other growth inhibitors. Widespread and well-studied group of plasmids. Many are conjugative.

Front 276

tra genes

Back 276

Transfer; these genes are involved with the transfer of the plasmid

Front 277

Virulence factors

Back 277

In several pathogenic bacteria they are encoded by plasmid genes (on chromosome of those that require virulence for survival); enable pathogene to: colonize , cause additional host damage. Can contain hemolysin and/or enterotoxin

Front 278

Virulence

Back 278

A range which is determined by a virulence gene.

Front 279

Pathogenicity

Back 279

All or nothing (either is pathogenic or not)

Front 280

Hemolysin

Back 280

Lysing of cells, especially blood but also others

Front 281

Enterotoxin

Back 281

Often enzymes, effects the gut

Front 282

Bacteriocins

Back 282

Proteins produced by bacteria that inhibit or kill closely related species or even different strains of the same species; Colicin, nisin (sometimes used as anitmicrobials); genes are often carried on plasmids

Front 283

Semiconservative tendency of DNA replication

Back 283

Each of the two progeny double helices have one parental strand and one new strand.

Front 284

What is the precursor to each nucleotide?

Back 284

A deoxynucleoside 5'-triphosphate (dNTP)

Front 285

How does replication proceed?

Back 285

From the 5' end to the 3' end

Front 286

DNA polymerases catalyze what?

Back 286

the addition of dNTPs

Front 287

How many different DNA polymerases are there in E. Coli?

Back 287

5

Front 288

What is the primary enzyme replicating chromosomal DNA in E. Coli?

Back 288

DNA polymerase III

Front 289

What do DNA Polymerases require to attach?

Back 289

A primer

Front 290

What are primers made from?

Back 290

RNA by primase

Front 291

Polymerase

Back 291

Anything that takes small monomers and turns them into polymers

Front 292

Where does DNA synthesis begin?

Back 292

At the origin of replication in prokaryotes

Front 293

Replication fork

Back 293

Zone of unwound DNA where replication occurs; bidirectional

Front 294

How is the leading strand synthesized

Back 294

Continuously

Front 295

How is the lagging strand synthesized?

Back 295

In fragments (okazaki)

Front 296

DNA helicase

Back 296

Unwinds the DNA

Front 297

DNA polymerase I

Back 297

Removes the RNA primer and replaced it with DNA

Front 298

DNA ligase

Back 298

Seals Nick's in the DNA

Front 299

DNA ligase

Back 299

Seals Nick's in the DNA

Front 300

DNA synthesis in prokaryotes

Back 300

Bidirectional in the chromosome; two replication forks moving in opposite directions

Front 301

Hiw many BP can DNA Polymerase III add per second?

Back 301

1000 / 1 kbp

Front 302

Replisome

Back 302

Complex of multiple proteins involved in replication; area of synthesis; DNA is pulled through the replisome

Front 303

What helps DNA replication to be extremely accurate?

Back 303

Proofreading

Front 304

Mutation rates during replication

Back 304

10^-8 – 10^-11 errors per base inserted

Front 305

What can detect mismatch through incorrect hydrogen bonding during DNA synthesis?

Back 305

Polymerase

Front 306

What types of organisms have a proofreading mechanism?

Back 306

Prokaryotes, eukaryotes and viral DNA replication systems

Front 307

How can you obtain a pure culture easily?

Back 307

Using Koch's method of streaking

Front 308

What is almost always involved in metabolic reactions?

Back 308

Enzymes

Front 309

Selective medium

Back 309

Inhibits some types of organisms while promoting others

Front 310

Selective medium

Back 310

Inhibits some types of organisms while promoting others

Front 311

Who was considered the father of infectious disease?

Back 311

Koch

Front 312

What type of microscopy are we using in the lab?

Back 312

Bright field

Front 313

What is the most simple type of organism?

Back 313

Bacteria

Front 314

What type of translocation involves a chemical modification of the delivered material?

Back 314

Group translocation

Front 315

What type of bacteria has teichoic acids?

Back 315

Gram positive; they are embedded in the cell wall

Front 316

Does aseptic technique include turning the plates upside down?

Back 316

No

Front 317

Enriched medium

Back 317

Favors the growth of one over all others

Front 318

Who disproved spontaneous generation?

Back 318

Louis Pasteur

Front 319

Transcription (DNA to RNA) is carried out by what enzyme?

Back 319

RNA polymerase

Front 320

In transcription RNA polymerase uses what as a template?

Back 320

DNA

Front 321

In transcription what are the RNA precursors?

Back 321

ATP, GTP, CTP, and UTP

Front 322

In transcription how does chain growth take place?

Back 322

5'-3'

Front 323

For any gene what is transcribed by RNA polymerase?

Back 323

Only one of two strands of DNA

Front 324

How many different subunits does RNA polymerase have?

Back 324

Five

Front 325

Promotors

Back 325

Sites on DNA recognized by RNA Polymerase

Front 326

Promotors

Back 326

Sites on DNA recognized by RNA Polymerase; site of initiation of transcription, recognized by sigma factor of RNA polymerase

Front 327

Transcription terminators

Back 327

Specific sites where Transcription stops

Front 328

Transcription terminators

Back 328

Specific sites where Transcription stops

Front 329

Why does transcription involve smaller units of DNA (as small as a single gene) unlike with DNA replication?

Back 329

It allows the cell to transcribe different genes at different rates

Front 330

How is sigma factor used in transcription?

Back 330

It works with DNA polymerase and recognizes two highly conserved regions of the promotor and initiation site. When transcription begins it is released to be used for another RNA polymerase.

Front 331

Simultaneous Transcription-Translation

Back 331

Only occurs in prokaryotes

Front 332

Simultaneous Transcription-Translation

Back 332

Only occurs in prokaryotes

Front 333

What are the two highly conserved regions of the promotors?

Back 333

Pribnow box and -35 region

Front 334

Pribnow box

Back 334

Located ten bases before the start of transcription (-10 region); TATA box

Front 335

-35 region

Back 335

Located ~35 bases upstream from transcription

Front 336

What is termination of RNA synthesis governed by?

Back 336

A specific RNA sequence

Front 337

Intrinsic terminators

Back 337

Transcription is terminated without any additional factors

Front 338

Rho-dependent termination

Back 338

Rho protein recognizes specific DNA sequences and causes a pause in the RNA polymerase

Front 339

Unit of transcription

Back 339

Unit of chromosome bounded by sites where transcription of DNA to RNA is initiated and terminated

Front 340

What are some types of RNA that are not translated and are very stable?

Back 340

rRNA, tRNA, etc.

Front 341

What are the three types of rRNA?

Back 341

16s, 23s, and 5s

Front 342

What is tRNA cotranscribed with?

Back 342

rRNA or other tRNA

Front 343

What type of RNAs have short half lives of a few minutes?

Back 343

mRNAs

Front 344

Polycistronic mRNA

Back 344

A mRNA encoding group of cotranscribed genes

Front 345

Operon

Back 345

A group of related genes cotranscribed on a polycistronic mRNA which allows for expression of multiple genes to be coordinated

Front 346

Describe RNA polymerase in archaea.

Back 346

There is only one, which resembles eukaryotic polymerase II.

Front 347

Transcription in Archaea

Back 347

It is a simplified version of the eukaryotic transcription apparatus including promoters and RNA polymerase similar to eukaryotes. However, the regulation of transcription has major similarities with Bacteria.

Front 348

Exons

Back 348

Coding sequences in Eukaryotic genes

Front 349

Introns

Back 349

The intervening sequences in Eukaryotic genes; they are rare in Archaea but found in their tRNA and rRNA genes

Front 350

What are archaeal introns excised by?

Back 350

Special endonucleases

Front 351

Eukaryotic RNA processing

Back 351

Many RNA molecules are altered before they carry out their role in the cell.

Front 352

Eukaryotic RNA processing

Back 352

Many RNA molecules are altered before they carry out their role in the cell. Includes RNA splicing, RNA capping, and a Poly(A) tail.

Front 353

RNA splicing

Back 353

Takes place in the nucleus; removes introns from RNA transcripts; performed by the spliceosome

Front 354

Spliceosome

Back 354

Bends transcripts so RNA can be spliced out

Front 355

RNA capping

Back 355

Addition of methylated Guanine to 5' end of mRNA

Front 356

Poly(A) tail

Back 356

Addition of 100-200 adenylate residues; stabilizes mRNA and is required for translation; can isolate mRNA from other RNA in the cell.

Front 357

Proteins

Back 357

Play a major role in cell function

Front 358

Proteins

Back 358

Play a major role in cell function; polymers of AAs; they are linked by peptide bonds form a polypeptide

Front 359

What are some different types of proteins?

Back 359

Catalytic (enzymes), structural and regulatory

Front 360

Primary structure

Back 360

linear array of AAs in a polypeptide

Front 361

What are the chemical properties of the amino acid related to?

Back 361

Their side chain

Front 362

Secondary structure

Back 362

Adjacent nucleotides or nearly adjacent; interactions of the R groups force the molecule to twist and fold in a certain way.

Front 363

Tertiary structure

Back 363

3-D shape of polypeptide

Front 364

Quaternary structure

Back 364

Number and types of polypeptides that make a protein; >1 polypeptide involved

Front 365

Translation

Back 365

The synthesis of proteins from RNA

Front 366

Genetic code

Back 366

A triplet of nucleic acid bases (codon) encodes a single amino acid; there are specific codons for starting and stopping translation

Front 367

Degenerate code

Back 367

Multiple codons encode a single AA

Front 368

Anticodon

Back 368

On tRNA, recognizes codon

Front 369

Anticodon

Back 369

On tRNA, recognizes codon

Front 370

Wobble

Back 370

Irregular base pairing allowed at third position of tRNA

Front 371

Stop codons

Back 371

Terminate transaction (UAA, UAG, and UGA)

Front 372

Start codon

Back 372

Translation begins with AUG (methionine)

Front 373

Reading frame

Back 373

Triplet code requires translation to begin at the correct nucleotide

Front 374

Shine-Dalgarno sequence

Back 374

Ensures proper reading frame

Front 375

Open reading frame (ORF)

Back 375

AUG followed by a number of codons and a stop codon in the same reading frame

Front 376

Codon bias

Back 376

Multiple codons for the same AA are not used easily; varies with organism; correlated with tRNA availability; Cloned genes from one organism may not be translated by recipient organism because of codon bias.

Front 377

Transfer RNA

Back 377

At least one tRNA per AA; bacterial cells have 60 different tRNAs; Mammalian cells have 100-110 different tRNAs; specific for both a codon and it's cognate AA

Front 378

What are tRNA and AA brought together by?

Back 378

aminoacyl-tRNA synthetases; ATP is required to attach AA to tRNA

Front 379

What is the shape of tRNA?

Back 379

Cloverleaf

Front 380

Anticodon

Back 380

Three bases of tRNA that recognize three complementary bases on mRNA

Front 381

Anticodon

Back 381

Three bases of tRNA that recognize three complementary bases on mRNA

Front 382

Why is fidelity of recognition process between tRNA and aminoacyl-tRNA synthetase critical?

Back 382

Incorrect AA could result in a faulty or nonfunctioning protein.

Front 383

Ribosomes

Back 383

Sites of protein synthesis; thousand per cell; composed of 30s and 50s in prokaryotes to form a 70s (Svedberg units) ribosome in bacteria (40+60=80 in eukaryotes); combination of rRNA and protein

Front 384

How many different distinct ribosomal proteins does E. Coli have?

Back 384

52

Front 385

What are the three main steps that translation is broken down into?

Back 385

1. Initiation 2. Elongation 3. Termination

Front 386

Initiation

Back 386

Two ribosomal subunits assemble with mRNA; Begins at an AUG start codon

Front 387

Elongation

Back 387

AAs are brought to the ribosome and are added to the growing polypeptide. Occurs in the A and P sites of a ribosome. Translocation occurs

Front 388

Translocation

Back 388

Movement of the tRNA holding the polypeptide from the A to the P site

Front 389

Termination

Back 389

Occurs when ribosome reaches a stop codon. Release factors are involved. Ribosome subunits then dissociate. Subunits free to form new initiation complex and repeat process.

Front 390

Release factors

Back 390

Recognize stop codon and cleave polypeptide from tRNA

Front 391

Polysomes

Back 391

A complex formed by ribosome simultaneously translating one mRNA

Front 392

What is the advantage to having the ribosomes packed together?

Back 392

Process occurs faster

Front 393

Denaturation

Back 393

Occurs when proteins are exposed to extremes of heat, pH, or certain chemicals; causes the polypeptide chain to unfold; destroys the 2°, 3°, and/or 4° structure of the protein

Front 394

Renaturation

Back 394

Bring back function to protek; may or may not occur when brought back to normal conditions

Front 395

Molecular Chaperones or chaperonins

Back 395

Assist in folding, not Incorporated into protein; can also aid in refolding partially denatured proteins.

Front 396

Signal sequences

Back 396

Found on proteins requiring transport from cell; 15-20 residues long; found at the beginning of a protein molecule. Signal the cells secretory system; prevent protein from completely folding; needed for exportation

Front 397

SecA

Back 397

Helps feed linear protein through cytoplasmic membrane

Front 398

Sec system

Back 398

Main secretory system

Front 399

Translational apparatus

Back 399

Front 400

The Tat system

Back 400

Secretion of folded proteins; proteins that fold in the cytoplasm are exported by a transport system distinct from SEC, called the Tat protein export system (iron-sulfur proteins and redox proteins)

Front 401

Secretion of proteins types I - VI

Back 401

All are a large complex of proteins that form channels through membranes; types 2 and 4 depend on Sec or Tat; types 1, 3, 4 and 6 do not require SEC or Tat

Front 402

Secretion of proteins types I - VI

Back 402

All are a large complex of proteins that form channels through membranes; types 2 and 4 depend on Sec or Tat; types 1, 3, 4 and 6 do not require SEC or Tat

Front 403

Injectisome

Back 403

Front 404

Growth

Back 404

Increase in the number of cells

Front 405

Binary fission

Back 405

Cell division following enlargement of a cell to twice it's minimum size.

Front 406

Generation time

Back 406

Time required for microbial cells to double in number (varies by organism and their environment); most prokaryotes have a shorter gen time than Eukaryotes; dependent on growth medium and incubation conditions

Front 407

What does each daughter cell recieves during division in prokaryotes?

Back 407

A chromosome and sufficient copies of all other cell constituents to exist as an independent cell.

Front 408

Cell growth for one generation

Back 408

Front 409

Fts proteins

Back 409

Filamentous temperature-sensitive proteins; they are essential for cell division in all prokaryotes. They interact to form the divisome.

Front 410

FtsZ

Back 410

Forms ring around center of the cell; related to tubulin

Front 411

ZipA

Back 411

Anchor that connects FtsZ ring to cytoplasmic membrane.

Front 412

FtsA

Back 412

Helps connect FtsZ ring to membrane and also recruits other divisome proteins; related to actin

Front 413

Divisome complex

Back 413

Front 414

Where is the nucleoid region present in the cell?

Back 414

Almost always up against the side

Front 415

Where is the nucleoid region present in the cell?

Back 415

Almost always up against the side

Front 416

How are cell walls formed in cocci?

Back 416

They grow in opposite directions outward from the FtsZ ring

Front 417

How are cell walls formed in cocci?

Back 417

They grow in opposite directions outward from the FtsZ ring

Front 418

How are cell walls formed in rod-shaped cells?

Back 418

Growth occurs at several points along the length of the cell.

Front 419

Bactoprenol

Back 419

Carrier molecule that plays major role in insertion of peptidoglycan precursors. C55 alcohol. Bonds to N-acetylglucosamine/N-acetylmuramic acid/pentaprism peptidoglycan precursor

Front 420

Glycolases

Back 420

Enzymes that interact with bactoprenol; they listen the rigid cell wall up for growth; insert wall precursors into growing points of cell wall; catalyze glycosidic bind formation

Front 421

What has to be broke in the growth site of peptidoglycan?

Back 421

Front 422

Transpeptidation

Back 422

Final step in cell wall synthesis; forms the peptide cross-links between muramic acid residues in adjacent glycan chains; inhibited by the antibiotic penicillin (and others)

Front 423

What form of amino acids are not very common in nature? What one are?

Back 423

D; L

Front 424

Asynchronous growth

Back 424

Bacteria grow exponentially but daughter cells do not divide at the same exact moment

Front 425

Exponential growth

Back 425

Growth of a microbial population in which cell numbers double within a specific time interval

Front 426

Cell replication over time

Back 426

Front 427

Batch culture

Back 427

A closed-system microbial culture of fixed volume.

Front 428

What are the four phases of a typical growth curve for a population of cells grown in a closed system?

Back 428

Lag, exponential, stationary, and death

Front 429

Lag phase

Back 429

No growth, increase in cell size

Front 430

Exponential phase

Back 430

Log phase; exponential growth

Front 431

Stationary phase

Back 431

Exponential growth stops; horizontal line; still division but cell growth= cell death

Front 432

Death phase

Back 432

"decline phase"; exponential decrease, death outnumbers cell division

Front 433

Survival phase

Back 433

5th phase, not always mentioned; horizontal line near zero, but above zero then finally complete death

Front 434

What are two ways to count colonies and determine their phase?

Back 434

Viable count and turbidity

Front 435

Turbidity

Back 435

Measured with a spectrophotometer; it counts both live and dead cells that haven't lysed; these measurements are indirect, rapid, and are useful for measuring microbial growth. Most often measured with a spectrophotometer. Measurement referred to as optical density (OD)

Front 436

Continuos culture

Back 436

An open system microbial culture of fixed volume. There is fresh broth and culture brought in at a constant rate; want growth to be locked in late log

Front 437

Batch culture

Back 437

Adding new O2 with shaking, but not adding new nutrients

Front 438

Chemostat

Back 438

Most common type of continuous culture device which allows control of growth rate and pop density independently and simultaneously.

Front 439

Dilution rate

Back 439

Rate at which fresh medium is pumped in and spent medium is pumped out.

Front 440

In a chemostat what is growth rate controlled by?

Back 440

Dilution rate

Front 441

In a chemist the growth yield (cell #/ml) is controlled by what?

Back 441

The concentration of the limiting nutrient

Front 442

Since in a batch culture growth conditions are constantly changing its impossible to independently control what?

Back 442

Both growth parameters

Front 443

What are chemostat cultures sensitive to?

Back 443

The dilution rate and limiting nutrient concentration

Front 444

What happens when chemostat cultures are at too high a dilution rate?

Back 444

The organism is washed out

Front 445

What happens when cultures in a chemostat are at too low of a dilution rate?

Back 445

The cells may die from starvation

Front 446

In a chemist, increasing concentration of a limiting nutrient results in what?

Back 446

Greater biomass but the same rate

Front 447

Hemacytometer

Back 447

A way to enumerate cells with microscopic observations which can have unreliable results. By picking cells at midlog phase most cells will be viable.

Front 448

Viable cell counts (plate counts)

Back 448

Measurement of living, reproducing population. Can be highly unreliable when used to assess total cell numbers of natural samples. By using selective culture media and growth conditions you can target only a particular species. These are viable but non culturable.

Front 449

What are the two main ways to perform plate counts?

Back 449

Spread plate method and pour plate method (incorporate bacteria into agar)

Front 450

What are some limitations to performing viable cell counts?

Back 450

They have to incubate and need time to grow. They may be hard to grow in a lab setting.

Front 451

Serial dilutions

Back 451

Front 452

To relate a direct cell count to a turbidity value, what must first be established?

Back 452

A standard curve

Front 453

When does turbidity work best?

Back 453

For low ODs; >5.0 OD may need further dilution

Front 454

Turbidity measurements

Back 454

They are quick and easy to perform, they typically do not require destruction or significant disturbance of sample. This is sometimes problematic (clumps or biofilm forms), not accurate at high ODs.

Front 455

qPCR

Back 455

Type of real time PCR but for more quantitative studies. Standard PCR but with dye Incorporated into the product; detection for fluorescence over time.

Front 456

Real time PCR

Back 456

Amp is in real time; more qualitative analysis. RNA is less stable than DNA so if it's present then there are live samples.

Front 457

PCR

Back 457

Contains 2 primers, forward and reverse, (complementary to the targeted DNA sequence), dNTPs (DNA), polymerase Taq (thermistor aquatis), there is DNA/template, fluorescent dye, and a buffer (ions that Pol needs as a cofactor)

Front 458

Cardinal temperatures

Back 458

The minimum, optimum, and maximum temperatures at which an organism grows.

Front 459

What occurs at the minimum growth temp?

Back 459

Membrane gelling; transport processes are so slow that growth cannot occur

Front 460

What occurs in between the minimum and optimum temp of growth?

Back 460

Enzymatic reactions are occurring at increasingly rapid rates

Front 461

What is occurring at the optimum temp of growth?

Back 461

Enzymatic reactions are occurring at a maximal possible rate.

Front 462

What is occurring at the maximum temperature of growth?

Back 462

Protein denaturation; collapse of the cytoplasmic membrane; thermal lysis

Front 463

Cardinal temp growth curve

Back 463

Front 464

Psychrophile

Back 464

Low temp optima; below freezing point of water

Front 465

Mesophile

Back 465

Midrange temp optima; human assoc organisms 25-40°C

Front 466

Thermophile

Back 466

High temp optima; above 45 or 50°C to 80°C

Front 467

Hyperthermophile

Back 467

Very high temp optima above 80°C; "extreme thermophiles" can go above 100°C and still grow

Front 468

What adaption support psychrophily?

Back 468

1.Production of enzymes that function optimally in the cold and features that may provide more flexibility of proteins so they don't freeze at colder temperatures. 2. Transport processes that function optimally at low temperatures

Front 469

What are some features that allow for more flexibility of proteins seen psychrophily?

Back 469

More alpha helices than beta sheets, more polar and less hydrophobic amino acids, fewer weak bonds and decreased interactions between protein domains.

Front 470

What are some modifications in transport processes in psychrophily which allows them to operate optimally at low temps?

Back 470

Modified cytoplasmic membranes, and high unsaturated fatty acid content

Front 471

At temps higher than about what can only prokaryotic life forms exist?

Back 471

~65°C

Front 472

At temps higher than about what can only prokaryotic life forms exist?

Back 472

~65°C

Front 473

Hyperthermophiles in hot springs

Back 473

Chemoorganotrophs and Chemolithotrophs present; high prokaryotic diversity of archaea and bacteria are represented

Front 474

Which organisms have the highest temperature optima?

Back 474

Archarea

Front 475

Which can grow at higher temps phototrophic or nonphototrophic organisms?

Back 475

Nonphototrophic

Front 476

What are some molecular adaptions to thermophily?

Back 476

1. Enzyme and proteins function Optimally at high temperatures; features that provide thermal stability. 2. Modifications in cytoplasmic membranes to ensure heat stability

Front 477

What are some features that provide thermal stability in thermophiles?

Back 477

Critical amino acid substituents in a few locations provide more heat folds, an increased number of ionic bonds between basic and acidic amino acids resist unfolding in the aqueous cytoplasm, and production of solutes

Front 478

What are the modifications seen in thermophiles cytoplasmic membranes that ensures heat stability?

Back 478

Bacteria have lipids rich in saturated fatty acids and archaea have a lipid monolayer rather than a bilayer.

Front 479

Give an example for how enzymes produced by hyperthermophiles can be used in industrial microbiology.

Back 479

Taq polymerase (from thermus aquatis. 96-97°C; used for PCR)

Front 480

Neutrophiles

Back 480

Organisms that grow best between pH of 6 and 8.

Front 481

Acidophiles

Back 481

Organisms that grow best at low pH (<6); some are obligate acidophiles (has to be in acidic ENV. To grow) and there membranes are destroyed at neutral pH; stability of the cytoplasmic membrane is critical

Front 482

Alkaliphiles

Back 482

Organisms that grow best at high pH (>9); some have sodium motive force rather than proton motive force

Front 483

Internal pH of a cell

Back 483

Has to stay relatively close to neutral even though the external pH is highly acidic or basic; *exceptions has been found to be as low as 4.6in acidophiles and as high as 9.5 in alkaliphiles.

Front 484

Positive water balance

Back 484

The tendency of water to move into the cell because of the higher internal conc of solute.

Front 485

Halite

Back 485

Mineral-> rock salt

Front 486

Halophiles

Back 486

Organisms that grow best at reduced water potential; have a specific requirement for NaCl

Front 487

Extreme halophiles

Back 487

Organisms that require high levels (15-30%) of NaCl for growth

Front 488

Halotolerant

Back 488

Organisms that can tolerate some reduction in water activity of environment but generally grow best in the absence of the added solute

Front 489

Nonhalophile

Back 489

Front 490

Osmophiles

Back 490

Organisms that live in environments high in sugar as solute ( or other non sodium solute)

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Xerophiles

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Organisms able to grow in very dry environments; they capture and hold onto Environments

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Aerobes

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Require oxygen to live

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Anaerobes

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Do not require oxygen and may even be killed with oxygen exposure

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Facultative orgsnisms

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Can live with or without oxygen, but prefer oxygen if it's available; some can utilize both at the same time

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Aerotolerant anaerobes

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Can tolerate oxygen and grow in its presence even though they cannot use it

Front 496

Microaerophiles

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Can use oxygen only when it is present at levels reduced from that in air.

Front 497

Reducing agents

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Chemicals that may be added to culture media to reduce oxygen

Front 498

What toxic forms of oxygen. Can be formed in the cell?

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Front 499

What enzymes are present to reduce most of the toxic species of oxygen?

Back 499

Catalase, peroxidase, superoxide dimutase, superoxide reductase

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Sterilization

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The killing or removal of all viable organisms within a growth medium.

Front 501

Satellite colonies

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Front 502

Bacteriostatic

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Inhibits growth; does not kill

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Bacteriocidal

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Kill bacteria

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Inhibition

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Effectively limiting microbial growth; not necessarily 100%. * Some antibiotics like penicillin and esp. Ampicillin

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Decontamination

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The treatment of an object to make it safe to handle; removing microbes from an object but not necessarily all of them, just to a safe level.

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Disinfection

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Directly targets the removal of all pathogens, not necessarily all microorganisms

Front 507

Heat sterilization

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The most widely used method of controlling microbial growth. High temps denature macromolecules.

Front 508

Decimal reduction time

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Amount of time required to reduce viability tenfild

Front 509

Endospores

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Resistant cells produced by bacteria that can survive heat that would rapidly kill vegetative cells.

Front 510

Autoclave

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Sealed device that uses steam at 121°C under pressure of 1.5 ATM (allows temp to go high) which kills microbes including endospores.

Front 511

Pasteurization

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The process of using precisely controlled heat to reduce the microbial load in heat-sensitive liquids; does not kill all organisms so it is different from sterilization

Front 512

What types of light waves can be used for sterilization?

Back 512

Microwaves, UV, X-rays, gamma rays, and electrons

Front 513

UV

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Has sufficient energy to cause modifications and breaks in DNA; useful for decontaminating surfaces, but cannot penetrate solid, opaque or light absorbing surfaces.

Front 514

Lamenter file hood

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Uses IV light in nonpathogenic labs

Front 515

Ionizing radiation

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Electromagnetic radiation that produces ions and other reactive molecules (ex. Ozone), generates electrons, hydroxyl radicals, and hydride radicals. Down microrganisms are more resistant to radiation than others

Front 516

Sources of radiation

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Cathode ray tubes, x-rays, and radioactive nuclides

Front 517

Radiation

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Used for sterilization in the medical field and food industry; it is approved by the WHO and is used in the USA for decontaminating foods particularly susceptible to microbial contamination such as hamburger, chicken and spices

Front 518

Filtration

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One of the most widely used forms of control. Avoids the use of heat on sensitive liquids and gases; pores of the filter are too small for organisms to pass through but allow liquids and gases to pass through.

Front 519

What are some times of filters used?

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Nylon, cellulose, and nitrocellulose

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Depth filters

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HEPA filters

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Depth filters

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HEPA filters

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Membrane Filters

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Function more like a sieve

Front 523

What is the standard pore size of filters?

Back 523

.45u - .2um

Front 524

How can antimicrobial agents be classified?

Back 524

Bacteriostatic, bacteriocidal, and bacteriolytic

Front 525

Bacteriostatic

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Inhibits cell growth does not kill

Front 526

Bacteriocidal

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Death of cells

Front 527

Bacteriolytic

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Cells lyse

Front 528

Minimum inhibitory concentration (MIC)

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The smallest amount of an agent needed to inhibit growth of a microorganism; varies with the organism used, inoculum size, temperature, pH, etc.

Front 529

Disc diffusion assay

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Uses solid media; antimicrobial agents is added to the filter paper disc (embedded in or on them) and mic is reached at some distance

Front 530

Zone of inhibition

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Area of no growth around disk

Front 531

What are the two categories that antimicrobial agents can be divided into?

Back 531

1. Products used to control microorganisms in commercial and industrial applications (chem in foods, air conditioning cooling towers, textile and paper products, fuel tanks) 2. Products designed to prevent growth of human pathogens in inanimate environments and on external body surfaces (sterilants, disinfectants, sanitizers, and antiseptics)

Front 532

Genome

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Entire complement of genetic information, includes genes, regulatory sequences, and noncoding DNA

Front 533

Genomics

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Study of the genome; discipline of mapping, sequences, analyzing, and comparing genomes

Front 534

What was the first genome sequenced (1976)

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RNA virus MS2; 3569 bp

Front 535

What was the first cellular genome sequenced in 1995?

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Haemophilus influenza; 1,830,137 bp

Front 536

Sequencing

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Determining the precise order of nucleotides in a DNA or RNA molecule

Front 537

Sanger dideoxy method

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Invented by Nobel prize winner Fred Sanger, dideoxy analogs of dNTPs used in conjunction with dNTPs, analog prevents further extension of DNA chain, bases are labeled with radioactivity, gel electrophoresis is then performed on products.

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Automated DNA sequencing systems

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Based on Sanger method, radioactivity replaced by fluorescent dye.

Front 539

Shotgun sequencing

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Entire genome is cloned, and resultant clones are sequenced, much of the sequencing is redundant, generally 7- to 10-fold coverage; computer algorithms are used to look for replicate sequences and assemble them.

Front 540

Second generation DNA sequencing

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Generated data 100x faster than Sanger method; massively parallel methods (lg # of samples sequenced side by side), uses increased computer power and miniaturization

Front 541

454 sequencing system

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DNA is broken into small segments, then is amplified using PCR, light is released each time a base is added to DNA strand. The instrument measures the release of light. It can handle only short stretches of DNA