Intro To Microbiology Final Exam

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transcription

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Process of synthesizing RNA from DNA

the mRNA carries the coded strand to the ribosome.

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translation

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information encoded on the RNA is deciphered to synthesize proteins. with rRNA & tRNA. amino acid chains moving from site to site. is terminated by a stop codon & polypeptide chain released

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RNA Polymerase

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an enzyme at which synthesizes a complimentary strand of mRNA from unwound DNA

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promoter

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a specific protein or region that acts as an "on/off" switch

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nucleotides

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A:U, U:A, C:G, G:C Thymine is replaced with uracil in RNA

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Terminator

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a site on DNA that stops the production of nucleotide

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rRNA

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forms part of the ribosmal machinery used in protein syntesis

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tRNA

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Recognizes specific sequences of mRNA and transports the required amino acids a polypeptide chain

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Genetic Code

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deciphers information

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Codon

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a series of three nucleotides, 64 codons exist making up the 'alphabet' of proteins. 61 translate for the 20 amino acids the remaining 3 are stop codons

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Ribosomes

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direct the binding of tRNA to the correct codon on the mRNA.

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anticodon

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complimentary sequence to the specific codon in the mRNA

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translocate

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advancing a distance of codons

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Regulation of gene Expression

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microorganisms possess mechanisms to synthesize maximum amount of cell material from limited energy

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controlling synthesis of enzymes

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directed at making only what is required

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principles of regulation

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not all genes are subject to the same type of regulation. either routinely expressed or turned off and on by conditions

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constitutive enzymes

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constantly synthesized (enzymes of glycolysis)

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inducible enzymes

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not regularly produced, their synthesis is turned on in certain conditions ( B- galactosidase)

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Repressible enzymes

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routinely synthesized, but they can be turned off by certain conditions generally involved in biosynthetic pathways

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repressor

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blocks transcription by binding DNA at a region, the operator which is downstream of a promoter

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activator

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facilitates transcription

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operon

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a set of genes that includes an operator, promoter and structural genes. divided into 2 regions. control and structural.

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control region

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included operator and promoter. this region controls the transcription. the operator acts as the 'on/off' switch

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structural region

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included structural genes, this region contains the genes being transcribed

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lac operon

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when lactose is absent the repressor protein binds the operator gene, prevents polymerase from transcribing the structural gene no mRNA is made

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Lac operon

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when lactose is present the repressor binds to the lactose instead of operator. the RNA polymerase is then able to bind to the promoter. acts as inductor

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3 mechanisms to adapt to changing environments

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1. regulation of gene expression

2. mutation

3. gene transfer

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mutation

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nucleotides of DNA undergo changes in structure resulting in changes in the organisms properties. inherited vertically

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mutants

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the resultant organism after mutations

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gene transfer

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bacteria can acquire genes from another bacteria. usually occurs through plasmids, called horizontal gene transfer

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spontaneous mutation

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occurs in the natural environment

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rate of mutation

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probability that a mutation will be observed in a given gene each time it divides. generally 1/10,000 & 1/trillion. low rate is due to cellular repair mechanisms

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reasons why mutations occur

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base substitutions, removal or addition of nucleotides, transposable elements, base

substitutions, mistakes during DNA sequencing

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point mutations

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occur when one base pair is changed

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missense mutation

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a point mutation resulting in the substitution of an amino acid

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nonsense mutation

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mutation that changes a codon that normally encodes an amino acid to a stop codon

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frame shift mutation

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addition or removal of nucleotides resulting in the shift of translational reading and shifts the codon. premature stop codons so that the protein synthesis will be incomplete

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transposable elements

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special segments of DNA that can move from one site to another. disruption of proper function of gene

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induced mutations

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intentionally produced to demonstrate function of a particular gene or set of genes. via chemical mutagens, transposition, radiation

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chemical mutagens

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nitrous acid (changes C- U)

alkylating agents (alters H bonding)

transposition

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radiation

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UV light (forces T to distort)

Xrays (strands break to alter DNA)

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Processes of repair of DNA

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Proofreading DNA (excise incorrect base and replace with correct one)

mismatch (endonuclease enzymes removes short stretch of nucleotide DNA polymerase fills gap)

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Repair of Thymine dimers

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Light repair (uses visible light to break covalent bonds between bases)

Dark repair (excision repair, and new section is replicated and joined)

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repair of modified bases

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enzymes cuts DNA back bone and removes bases, DNA polymerase incorporates new base

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SOS repair

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last effort to by pass damage, induces system and produces new DNA polymerase

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techniques to detect mutants

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direct selection (inoculating medium which only mutants will grow on)

Indirection (requires isolate organisms that require growth factor that partent strain does not)

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mechanisms of gene transfer

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DNA mediated transformation

transduction

conjugation

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DNA- mediated transformation

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molecules passing through the cell walls and cytoplasmic membranes of the recipient cells and are then integrated into their chromosomes, replacing the hemolohous genes

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natural competence

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for natural transformation to occur in bacterial cells. a condition in which cells are capable of taking up and integrating donor DNA fragments

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stages of Natural transformation

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entry of DNA

integration of the donor DNA

Mismatch repair

cell multiplication

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intregration of the donor

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positioned by H bonding next to complimentary region, enzyme cleaves the recipients DNA on either side. then replaces the DNA.

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Homologous recombination

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Replacing recipient DNA with donor DNA

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breakage and reunion

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mechanism of replacing DNA

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Transduction

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short pieces of DNA being enclosed in a bacterial virus then transferred to recipient cells when virus invades these cells. the DNA is then integrated into recipient cell DNA

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Types of transduction

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generalized- any gene of donor can be transferred

specialized- only specific genes can be transferred

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conjugation

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only form of gene exchange in which donor survives. mediated by a plasmid. direct contact between cells. must be opposite mating types (F+/-) after transferred F- becomes F+

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Plasmids

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usually covalently closed, circular, double stranded DNA molecules, vary in size most prokaryotes contain more than one, non-essential. replicate using enzymes of cell

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Transposons

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mobile genetic elements.

ablility of multiple genes to move as a unit from a chromosome location to another site. also transferable to other cells

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taxonomy

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the science that studies organisms in otder to arrange them in to groups (taxa)

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identification

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process of charcaterizing in order to determin the group to which it belongs to

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nomenclature

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system of arranging names

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Bergeys manual of systematic bacteriology

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rely on this for reference text, names given according to the international code for the nomenclature of bacteria

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methods to identify prokaryotes

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morphology, metabolic capabilities, serology, gram stain, special stains

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biochemical tests

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rely on pH indicators, to see if a compound is degraded or not. can also be used to tract characteristics based on molecules

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ditchotomous key

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a flow chart of tests that give either a positive or negative result to identify bacteria based on a biochemical test

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serology

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technique relying on specific interaction between antibodies and antigens.

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type of serology

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FAME -fatty acid analysis (Fatty Acid Methyl Ester)

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identifying using genotypes

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nucleic acid probes (locating specific sequence) usally labeled with a radioisotope to detect a certain sequence

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serotype

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serological characteristics

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phage typing

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certain strains of given species susceptibe to various bacteriophages. identifies organism by the phage that infects them. been replace

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antibiograms

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identify organisms based on antibiotic susceptibility. Kirby bauer technique using antibiotic discs

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non living entities

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not considered organisms can infect organisms of any domain

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virion

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virus particle nucleic acid surrounded by a protein coat

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capsid

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protein coat composed of protein subunits

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capsomers

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protein subunits

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virus shapes

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isometric

helical

complex

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nucleocapsid

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viral capsid together with the nucleic acid

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types of virions

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naked viruses (no outter capsid)

enveloped viruses (double layer of lipid similiar to cell membrane)

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viral genome

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contains only single type of nucleic acid can be DNA or RNA

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taxanomic criteria for a virus

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genomic structure (single/double DNA/RNA strand)

virus particle structure (shape)

presence or absence of envelope

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coronaviridae

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family contains numerous genera names in in -virus

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enterovirus

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species name is the causes of the disease or virus

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respiratory viruses

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unuslly inhaled via infected respiratory droplets generally remained localized

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zoonotic viruses

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transmitted from animal to human or to another animal

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types of host relationships

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acute infections & persistent

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acute infections

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usually short in duration, long lasting immunity, may result in positive infections, large amount of viruses during replication

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steps of an acute infection

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attachment, entry into susceptible cell, targeting site of reproduction, uncoating of virion, synthesis of protein, maturation of viral particles, cell lysis, spreading within host, shedding of virions outside host, transmission to next host

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persistent infections

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viruses continually present in hose releasr from infected cell. divided into 3 catagories; latent, chronic, slow

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latent infections

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followed by symptomless period, then reactivation, particles not detected until reactivation, intial disease may differ

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chronic infections

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virus can be detected at all times, disease may be present or absent during extended times or may develop late (hepitis)

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slow infections

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agent gradually increases in amount over long periods of time, no significant symptoms apparent during this time (HIV)

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plant viruses

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can be of major economic importance, recognized by pigment loss, marks on leaves and fruit, tumors, stunted growth. do not generally recover

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spread of plant viruses

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through wound sites in cell wall, do not attach to specific cell receptors, through plasmodesmata, many viruses resistant to inactivation, through contaminated soil.

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Prions

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proteinaceous infectious agents. only proteins, no nucleic acid. causes brain degeneration, develops sponge like holes, resistant to UV

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prion mutation

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arose from gene encoding normal prion protein (PrPc) causes different folding properties

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viroids

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replicating autonomously in susceptible cells. capable of infecting cells, circular, resistant to nuclease digestion, all infect plants.

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immunity

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protection against infectious agents and other substances.

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innate immunity

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not affected by prior contact with the infection agent or other material involved and is not mediated by lymphocytes

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adaptive immunity

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host defenses that develop throughout life, involves B cells and T cells

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first line of defense

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barriers that shield interior of body from external surroundings. ie skin or mucous

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sensor system

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signals when first line barriers have been breached 2 groups of receptors

gr 1- tool like receptors & NOD proteins

gr2- complement system proteins

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Phagocytes

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specialized cells that engulf and digest microbes and cellular debris. altered to signs of invation. can be recruited from bloodstream

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cytokines

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proteins that act as chemical messengers. difuse from one cell to another, transmits signal and induces changes

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inflammation

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initiated by microbial invasion or tissue damage. blood cells allow certain changes to get certain immune particles to leak out of the cell

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fever

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bodys innate defense mechanisms to discourage infection

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mucous membrane

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lines digestive tract, respiratory tract and genitourinary tract, protects surfaces from infection

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lysozyme

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enzymes that degrade peptidoglycan, found in tears, siliva, blood

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peroxidase enzymes

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found in saliva, body tissues, breaks down hydrogen peroxide to produce oxygen

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lactoferrin

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found in silvia blood and tissue fluids, produces iron which is essential for microbial growth

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defensins

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found on mucous membranes, short antimicrobial peptides, these get inserted into microbial membrane

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normal flora

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microorganisms that are found growing on body surfaces of healthy individuals. covers binding sites, competes for nutrients.

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cells of the immune system

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always found in the normal blood, numbers increasing during infection. originate in stem cells in bone marrow and blood.

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hematopoiesis

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formation of blood cells

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categories of blood cells

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red blood- carry oxygen

platelets- blood clotting

white blood- host defenses (4 subcategories)

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granulocytes

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cytoplasmic granules, neutrophils, basophils, eosinophils

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monocytes

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circulate in the blood

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lymphocytes

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involved in adaptive immunity, B cells and T cells

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surface receptors

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membrane proteins to which signal molecules bind specific to molecule which it bonds

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adhesion molecules

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allows cells to stick to each other, responsible for phagocytes to injury

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sensor system

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dectects signs of tissue damage or microbial invasion. responds to patters associated with danger by destroying microbes

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process of phagocytosis

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chemotaxis, recognition, engulfment, phagosome lysosome fusion, destruction and digestion, exocyctosis

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diapedesis

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leakage of phagocytes from blood vessels

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out comes of inflammation

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to contain site of damage, localize response and restore function

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apoptosis

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controlled death that surpasess the inflamitory response

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pyrogens

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temperature regulation center of body responds to fever-inducing substances. inhibits growth of pathogens.

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adaptive immunity categories

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Humoral immunity- eliminates antigens that are extracellular (toxins ect)

Cellular- eliminates antigens residing within a host cell

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plasma cells

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function as antibody-producing. intresponse to extracellular antigens

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indirect effects of plasma cells

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phagocytosis may enhance the process of destruction of antigens when it is bound by antibodies

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T Cells

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They mature in thymus, response to extracellular antigens. 2 subsets.

cytotoxic cells- poliferate & differentiate to induce self cells

Helper- orchestrate responses of humoral immunity

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autoimmune diseases

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when the immune system cant distinguish and destroy only the self cells that are infected

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naturally acquired immunity

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through natural events such as exposure to an infectious agent

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artificially acquired immunity

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created by immunizations

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active immunity

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results from immune response during exposure develops after illness or immunization

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passive immunity

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occurs during pregnancy protects baby, occurs from breast feeding. or from antibodies produced from another person or animal.

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attenuated vaccines

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weakened from pathogens and generally not able to cause disease. replicated in recipient for long lasting immunity.

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inactivated vaccines

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unable to replicate in recipient, not pathogenic, contains killed or inactive virus, or contains portions of the toxins.

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seronegative

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person not yet exposed to antigen has no specific antibodies

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seropositive

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person with exposure and actively producing antibody

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titer

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concentration of antibodies in the serum, rise indicated active infection, small and steady indicated previous exposure

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precipitation reactions

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immunodiffusion tests where an antigen and an antibody is placed in separate wells in gell, they diffuse and meet between causing a line of precipitation in zone of optimal proportion

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agglutination reactions

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large insoluble particles makes antigens easier to see. direct (clumping) and indirect (beads)

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hypersensitivities

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immune responses that cause tissue damages

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immunodeficiency

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immunologic disorder occurs when the immune system responds too little

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allergens

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antigens that cause allergic reactions

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categories of hypersensitivities

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type I- immediate Ig E (mediated)

type II- cytotoxic

type III- immune complex (mediated)

type IV- delayed cell (mediated)

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Rejection of transplant tissues

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the transplant of organs and other tissues between genetically non-identical humans. causes rejections

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Primary or congenital Immunodeficiency disorders

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inborn as result of genetic defect or developmental abnormality

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secondary or acquired immunodeficiency

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result of infection or other stresses on the immune system

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symbiosis

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intimate interaction between microorganisms and the human body. there are a variety of types and forms of relationships.

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types of symbiosis

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Mutualism- both partners benefit

commensalism- one partner benefits and other is unharmed

parasitism- one parner benefits at the expense of the host

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resident flora

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extended inhabitation of an organism

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Transient flora

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temperary inhabitation of an organism

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pathogenicity

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organisms that can cause disease in healthy people. only when body's innate and adaptive defenses are compromised

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virulence

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the degree of pathogenicity. more likely to cause diseases

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communicable/ contagious diseases

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spreads from one host to another

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infectious dose

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number of organisms needed to establish an infection. small doses are easily spread

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course of infectious diseases

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incubation period (time between intro and symptoms)

illness (symptoms of disease)

convalescence (recuperation & recovery)

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distribution of pathogens

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localized, systemic/generalized, bacteremia, toxemia, viremia, septicemia

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Robert Koch

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specific organisms cause specific diseases, microbe present in every case, pure culture from hosts, must be reproduced, must be recovered

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molecular postulates

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virulence factor should be found in all strains of suspected pathogen, intro of clones virulence will reverse pathogenicity, must be expressed during disease process, antibodies must be protective

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Epidemiology

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combines diverse disciplines of ecology microbiology sociology statistics and psychology

used to determine agents reservoirs transmissions

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reservoir

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natural habitat, pathogen must leave to be transmitted

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rate of disease

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Rate = portion of a given population infected

100/10,000,000 vs 100/1000

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attack rate

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number of cases developing in a group of exposed people to an infectious agent

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morbidity rate

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number of cases of illness in a given time period/population at risk

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mortality rate

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% of population that dies from the disease

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incidence

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reflects the number of new cases in a specific time period in a given population at risk

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prevalence

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reflects total existing both old and new in a population at risk

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endemic

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diseases that are constantly present in a given population

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epidemic

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unusually large number of cases in a population

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pandemic

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epidemics spreading worldwide

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outbreak

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cluster of cases occuring in a breif time interval and affecting a specific population

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reservoirs of infection

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affect the extent and distribution of the disease, human animal environmental

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portals of exit

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microbes path out of one host in order to be transmitted to another host.

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horizontal transmission

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transmission of a pathogen from person to person through contact, ingestion of food or water

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vertical transmission

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from a pregnant woman to the fetus or mother to child during child birth or breast feeding

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indirect contact

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transmission through inanimate objects.

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droplet transmission

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droplet when dropped release the pathogen people in close proximity inhale infected droplets. can suspend indefinately as long as food and light occur

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portals of entry

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route pathogen must enter to colonize new host

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factors that effect epidemiology

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dose, incubation period, population characteristics

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acts of prevention

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infectious disease surveillance

public health agency of canada

centre for infectious disease prevention & control

world health organization

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reduction of disease

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sanitation, vector control, vaccination, antiobiotic treatment

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microenvironment

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environment immediately surrounding the individual microorganism

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microbial competition

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results of competition evident among organisms ability to compete related to rate of growth

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bacteriocins

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produced by certain species kill other strainsusually grow in biofilms

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polymerase chain reaction

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used to detect certain organisms and assessment of population charcteristics

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denaturing gradient gel elecrophoresis

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used to separate and examine a set of amplified

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biogeochemical cycles

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cyclical paths that elements take as they flow through living and nonliving components of the ecosystem

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prokaryotes

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use nitrogen as the final electron acceptor

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ammonification

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decomposition process that converts organic nitrogen into ammonia

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nitrification

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process that oxidizes ammonium nitrate

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denitrification

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process that converts nitrate into a gaseous nitrogen

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phosphorus cycle and others

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most plants and microorganisms readily take up phosphorus as orthophosphate and assimilate it into the biomass

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rhizobia

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significant relationships with plants and crop growth.

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leguminous plants

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agriculturally important nitrogen fixers

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rumen

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ruminants in herbivores,located in front of true stomach, allows for digestion of cellulose and hemicellulose

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sewage treatment

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all materials of household plumbing systems. used to eliminate potential pathogens

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Biochemical oxygen demand

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amount of oxygen required for microbial decomposition of matter in a sample. proportional to amount of organic material. raw sewage= 300-400mg/litr

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effluent

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liquid portion of treated waste water

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sludge

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solid portion of waste, further treated in anaerobic digestion

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primary treatment

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physical process designed to remove materials, passes through a series of screens that remove large objects. skimmers remove scum. sludge is then removed after settling is complete.

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secondary treatment

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chemical process, to convert suspended solids to compounds for removal, eliminates 95% of BOD. growth. aerobic organisms degrade organic material to CO2 +H2O

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methods of secondary treatment

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activated sludge, trickling filter, lagoons, artificial wetlands,

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flocs

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system employs mixed aerobes and grow in biofilms. they convert the waste water as they use it, and then settle in easily cleaned sludge at the bottom

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trickiling filter

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used in smaller treatment plants. rotating arm sprays sewage over bed of rocks, they become coated with biofilms. consists of bacteria fungi algae protozoa and nematodes.

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lagoons

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sweages is channeled into a shallow pond or lagoon. remains there for a period of time. algae and cyanobacteria grow on surface for oxygen, allowing for aerobic degredation of sewage

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artificial wetlands

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employ same principles as lagoons, offers means to treat waste water. provides habitat for other species. is cleaned as it runs down through the stages of wetland.

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advanced treatment

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any purification process beyond secondary treatment. included tertiary treatment, chemical or physical, expensive. to remove ammonia, nitrates, & phosphates.

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disinfection

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effluent is disinfected with one or a combination of both chlorine, ozone, UV light. decreases amount of organisms & viruses

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anaerobic digestion processes

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acts on solids removed through sedimentation

organic matter- organic acids & CO2+H2

acids- acetate & CO2+H2

acetate- methane

remaining sludge is dehydrated to form stable sludge

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nutrient rich product

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can be incinerated, placed in a landfill or fertilizer

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water treatment process

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water flows into reservoir, allows particulates to settle, water is transferred to tank and mixed with floc chemicals, causes suspended material to coagulate & sink, water is filtered, organic chemicals removed by additional filtration, disinfected as final step

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coliforms

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gastrointestinal pathogens ie e.coli

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bioremediation

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use of biological agents to degrade pollutants in a given environment. most organic compounds can be degrade by at least 1 or more species

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xenobiotics

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biotics that presist for long periods of time

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biostimulation

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speed up growth of indigenous microbes in contaminated site by addition of nutrients

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bioaugmentation

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relies on activities of microorganisms added to contaminated materials. helps resident flora

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co-metabolism

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pollutants that only degrade when specific stubstrates are available

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offsite processes

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rely on and may be preformed in bioreactor to accelerate microbial processes