Brock Biology of Microorganisms

Bacteriocins

plasmids may also allow code for genes that produce proteins that allow bacteria to kill or inhibit related or unrelated strains of bacteria

Conjugation

involves cell to cell contacta replicative process whereby both cells end up with copies of the plasmidprocess of genetic transfer

Episome

it can integrate into the host chromosome

Examples of short wavelength

1) X-rays2) Cosmic Rays3) Gamma Rays

Generalized transduction

virus incorporates random fragments of the host bacteria cell's chromosomal DNA into the viral genomeefficiency is low

Insertional Activation

foreign DNA is inserted into one of these restriction sites contained within an antibiotic resistant gene, antibiotic resistance will be lost. can be used as a means of selecting transformed bacterial clones that have picked up the insert

Pilus

produced by the donor cell. allows for direct contact between the cells

RecA

allows homologous recombination to occur which allows transforming DNA to be integrated into the genome of the recipient

Specialized transduction

DNA from a specific region of the host bactera chromosome is integrated directly into the virus genome and ususally replaces some of the virus genesefficiency may be very highonly occurs in some temperate viruses

Spontaneous Mutations can occur because of this

1) exposure to nautral forms of radiation2) oxygen radicals3) base pairing errors during DNA replication

Transduction

bacterial DNA is transferred from cell to cell by a bacterial virusoccurs by generalized transduction or specialized transduction

Transfection

introduces bacteriophage lambda into host cellallows DNA fragments up to 20 kb to be clones into lambda

Why are bacteriophages like lambda advantageous?

1) transfection rate is greater than the transformation rate of plasmid vectors 2) can hold larger amounts of DNA than most plasmid vectors

Allostery

property that makes the process of feedback inhibition possible

Catabolite repression

ensures that cells always use glucose first. prevents the expression of all other catabolic operons affected by this control mechanism when cells are grown in a medium containing glucose

Global Control System

used by cell to make most efficient use of the available carbon source.scell always uses glucose first

Glucose Effect

1) best energy source is chosen 2) cell does not waste energy making enzymes for catabolizing the other sugars3) if glucose is exhausted, next best sugar taken

Quorum Sensing

sensing mechanism involving signaling molecules that allows cells to survey their environment for cells of their own speciesensures that sufficient cell numbers of a given species are present before eliciting a particular biolgoical responsewidespread in gram (-) bacteria

Sigma factors can also be used for these three different circumstances

1) Nitrogen assimilation2) iron transport3) heat shock

Three examples of Quorum Sensing bacteria

1) V. Fischeri (bioluminescent ability)2) P. Aeruginosa (produce a biofilm that can prevent antibioltic penetration)3) S. Aureus (produce peptides that damange host cells and disrupt immune system)

Two components of regulatory systems

1) Specific sensor kinase protein2) Partner response regulator protein

Why does attenuation occur?

because a portion of the newly formed mRNA folds into a unique stem-loop taht causes cessation of RNA polymerase activity

3 Key sites on the ribosome

1) Acceptor Site2) Peptide Site3) Exit Site

Borrelia burgdorferi

rare instance of prokaryotes with linear DNA

composition of 30S subunit

consists of 16S rRNA and ~21 proteins

composition of 50S subunit

consists of 5S and 23S rRNA and ~34 proteins

DNA gyrase

produces negative supercoiling in bacteria and Archae. belongs to group of enzymes called "topoisomerases"classified as topoisomerase II

how do antibiotics inhibit protein synthesis

do so by inhibiting the activity of bacterial ribosomes

How do prokaryotes protect their own DNA

they do so by modifying through methylation

How long are prokaryotic subunits

30S and 50S subunits

How many different types of tRNAs are in bacteria cells and mammalian cells respectively?

60 in bacteria100-110 in mammalian cells

Hybridization

invovles putting together two DNA strands from different sources. annealing can be used to do this

Inverted Repeats

Short repeated sequences in DNA molecules

methylation

specific bases within the recognition sequence have methyl groups attached to them

RNA Longevity

1) in prokaryotes, mRNA's have short "half lives" (usually only minutes)2) rRNAs and t RNAs are more stable because of their highly folded structures3) RNAs are degraded by cellular ribonucleases

Structure of tRNAs (4 facts)

1) short single stranded molecules with extensive secondary structure2) have lengths of 73-93 nucleotides3) have conserved and variable regions4) have cloverleaf structure

Supercoiling

very long DNA molecule can be packaged into the cell because it is further twisted. Can occur in a positive or negative direction

the four steps of protein synthesis

1) Initiation2) Elongation3) Termination4) Release

The three types of RNA

1) Messenger RNA (mRNA)2) Transfer RNA (tRNA)3) Ribosomal RNA (rRNA)

Three characteristics of Eukaryotic Genetics

1) linear DNA2) chromosomes inside nucleus and ribosomes in the cytoplasm3) all have introns between exons

Three characteristics of Prokaryotic Genetics

1) circular DNA2) no membrane separating the chromosome and cytoplasm3) vast majority have no introns

Three facts about plasmids

1) replicate separately from chromosomes2) Double Stranded DNA that is usually circular but can be linear3) Do not cause dammage and do not have extracellular forms

Three facts about viruses

1) Consist of either RNA or DNA2) control their own replication3) viral chromosome may be linear or circular

What method is preferred for DNA sequencing and what does this method entail?

The sanger method is used. DNA is sequenced by making a copy of a single stranded DNA template strandpolymerase adds nucleotidesdideoxy analog acts as the specific chain termination reagent

Metabolism

Coordination of chemical reactions whereby molecules are organized into specific structures

Catabolic

energy releasing reactions

Anabolic

energy requiring reactions

Name 7 Micronutrients

1) Chromium2) Copper3) Selenium4) Zinc5) Vanadium6) Boron7) Iron

Name 7 Macronutrients

1) Carbon2) Nitrogen3) Oxygen4) Hydrogen5) Sulfur6) Phosphorous7) Manganese

Free Energy (G)

the energy released that is available to do useful work

Exergonic Reactions

release energy (negative deltaG)

Endergonic Reactions

requires energy (postive deltaG)

What two things does a catalyst do?

1) lowers the energy of activation of a reaction2) increases the rate of reaction

Prosthetic Groups

covalenty bonded very tightly to enzymes permanently

Cellulase

enzyme that break down cellulose

Glucose Oxidase

catalyzes the oxidation for glucose

What is the primary electron donor?

NAD+/NADH

What is the terminal electron acceptor?

O2

What are two mechanisms for energy conservation known in chemoorganotrophs?

1) Fermentation2) Respiration

Oxidative Phosphorylation

cytoplasmic membrane energized by the proton motive force dissipates energy that allows ADP and PO4 to form ATP

What three classes of protein electron carriers does aerobic respiration use?

NADH dehydrogenases (accept 2e- or 2H+)Flavoproteins (accept 2e- or 2H+)Cytochromes (accept single e-)

Quiniones

another type of e- carrier that are non-proteinaccept 2e- or 2H+

Proton Motive Force

When e- are transported through the e- transport chain, protons are extruded to the outside of the membrane

ATP Synthase (ATPase)

large membrane enzyme catalyst complex that is responsible for the conversion of the proton motive force (pmf) into the production of ATP

ATPase catalyzed ATP synthesis is referred to as what in respiratory systems?

oxidative phosphorylation

ATPase catalyzed ATP synthesis is referred to as what in phototropic systems?

Photo-phosphorylation

What is the primary difference between anaerobic and aerobic respiration?

Anaerobic respiration uses e- acceptors other than O2, such as NO3-, Fe3+, SO42-, and CO32-

Photoautotrophy

Use light as an energy source in the process of photosynthesis

Gram Stain

a differential staining technique that dvides bacteria into two groupsGram (+) stain purple and Gram (-) stain red

Phase Contrast Microscope

made it possible to see cells without staining them

Flourescence Microscope

used to visualize specimens that emit light of a given wavelength

Atomic Force Microscopy (AFM)

Contains a probe that establishes weak atomic forces between probe and the specimen generating digital information that produces an image

Confocal Scanning Laser Microscopy (CSLM)

Allows for 3-D images of microbes and other biological specimens

Transmission Electron Microscope (TEM)

Resovling power is much greater than a light microscope (1000x)

Scanning Electron Microscope (SEM)

Image produced when electron beam is directed onto the specimen

Four advantages that small microbes have

1) higher surface to volume ratio compared to large cells2) Nutrients and waste products pass in and out of the cell more easily3) Capable of more rapid growth4) Faster evolutionary change due to faster rate of mutation

How is the cytoplasmic membrane stabalized?

Stabilized by H-bonds, hydrophobic interactions, and some ionic bonds using Mg and Ca ions and cholesterol

Archae side chains are called these.

Isoprene Hydrocarbons

Translocases

Proteins that help export in prokaryotic cells

Three characteristics of the cell wall of prokaryotes

1) cell walls allow the cell to withstand pressure gradients2) give shape and supply rigidity to the cell3) Differences in cell wall structure are at the heart of gram staining

Peptidoglycan

A rigid polysaccharide layer composed of sugar derivatives and a small number of amino acids

How does cross linkage occur in Gram (-) Bacteria?

It occurs by peptide linkage of the amino group of DAP to the carboxyl group of the terminal D-alanine

DAP

Diaminopimelic AcidFound in all Gram (-) bacteria

What does the glycan backbone consist of?

Consists of glucosamine and muramic acid

How does cross linkage occur in Gram (+) bacteria?

It occurs by way of a peptide interbridge

Teichoic Acids

Found in cell walls of Gram (+) bacteria that help bind postively charged ions like Ca and Mg

LPS (Lipopolysaccharide Layer)

Outer wall found in Gram (-) bacteriaA second lipid bilayer composes of a phospholipid, protein, and polysaccharide

Functions of Outer Membrane

1) Major function is structural2) Secretes toxic substances called "endotoxins"3) Provides channels for passage of hydrophillic substances out of the cell using "porin structures"

Lysozyme

breaks bonds between glucosamine and muramic acid in the glycan backbone of peptidoglycan. found in body fluids like saliva and tears

What bacteria and archae groups both naturally lack cell walls?

Mycoplasms and Thermoplasma respectively

pseudo-peptidoglycan

very similar to peptidoglycansome cell walls of archae consist of this

What is pseudo-peptidoglycan made of?

Minuronic acid and glucosamine

What do some archae have instead of pseduo-peptidoglycan in their cell walls, and what is the most common cell wall type among archae?

They may have polysaccharide, glycoprotein or protein. most common is paracrystalline surface layer (S-Layer)

Fimbrae

Short, filamentous structures that enable the organism to stick to surfacesfound in many pathogens like salmonella and bordetella

Pilli

long filamentous structures taht are involved in conjugation which is a form of genetic exchange

PHB

carbon/energy storage polymer

Sulfur

accumulates as a result of sulfur metabolism from compounds like H2S

Lophotrichous flagella

multiple.. in group arrangement on cell

Peritrichous flagella

appearing at many locations around the cell surface

Shape and composition of flagella

helically shaped. composed of protein "flagellin"