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Microbiology Exam 2
Martha Smith-Caldas Micro. Kansas State
72
Microbiology
Undergraduate 2
03/12/2013

Additional Microbiology Flashcards

 


 

Cards

Term
Reproductive Strategies: Bacteria and Archaea
Definition

Haploid only, asexual

  • Binary fission (most common)
  • Budding
  • Filamentous
Term
Multiple Fission
Definition

 

 

:in cyabacterium where cells are held within the cell wall of the parent cell until they are released

Term
Bacterial Cell Cycle
Definition

Includes DNA replication/partition and cytokinesis

  • Single origin of replication
  • Proteins needed for DNA synthesis (Replisome)
  • Origins separate - move in both directions
  • Cell elongates as replication continues
  • Chromosomes separate (septum form.) - cells divide
Term
Cytokinesis - Septation
Definition
  • Selection of site for septum
  • Assembly of Z ring (Z = a motor protein)
  • Linkage of Z ring to plasma membrane (cell wall)
  • Assembly of cell wall
  • Constriction of cell and septum formation
Term
Cocci Divisome
Definition



: new peptidoglycan forms only at the central septum

- FtsZ determines site of cell wall growth

-FtsZ may recruit PBPs (penicillin binding protein) for synthesis of septum

Term
Rod Divisome
Definition

 

:Similar to cocci divisome but elongate prior to septation

-MreB determines cell diameter and elongation as Z ring forms in center

Term
Plasmid Segregation
Definition

1. Single copy plasmid R1 replicates

2. ParM is anchored to ParC and ParR, which attach to the origin of each plasmid

3. ParM elongates, thereby pushing each plasmid to opposite poles of the dividing cell

4. Newly replicated cells with plasmid; the Par proteins will not be synthesized until the cell readies for division

Term
Growth/Growth Curve
Definition

Increase in cellular constituents

Growth refers to population growth rather than individual cells


Growth curve observed when microorganisms are cultivated in batch culture

Usually ploteed as a logarithm of cell number vs. time

1. Lag phase

2. Exponential (log) phase

3. Stationary phase

4. Death phase

Term
Lag Phase
Definition

 

 

- Cell synthesizing new components

- Varies in length

Term
Exponential Phase
Definition



- Rate of growth and division is constant and maximal


- Population is most uniform in terms of chemical and physical properties during this phase.


-Growth can be balanced or unbalanced due to change in nutrient levels or change in environmental conditions

Term
Stationary Phase
Definition

 

Bactive cells stop reproducing or reproductive rate is balanced by death rate

 

Possible reasons: no resources, waste, no more space

Term
Stationary Phase and Starvation Response
Definition

Entry into stationary phase due to starvation and other stressful conditions activates survival strategy


- morphological changes (endospore formation)

- decrease in size, protoplast shrinkage, and nucleoid condensation

- RpoS protein assists RNA polymerase in transcribing genes for starvation proteins

Term
Senescence and Death Phase
Definition

2 Hypotheses

-cells are viable but not culturable (VBNC)

 

- Programmed cell death

:fraction of the population genetically programmed to die (commit suicide)

Term
Halophiles
Definition

 

:grow optimally in the presence of NaCl or other salts at a concentration above or about 0.2M.

Term
Extreme halophiles
Definition

 

:cell wall, proteins, and plasma membrane require high salt to maintain stability and activity

Term
pH homeostasis
Definition

When exposed to acidic conditions: when inernal pH gets low, the cells can exchange extracellular K+ for intracellular protons


When exposed to alkaline conditions: 

-Modification of cell wall to protect cytoplasmic enzymes

-Use Na+ motive force in addition to proton motive force

-Secreted enzymes are able to work alkaline environment

Term
Adaptations of thermophiles
Definition

Protein structure stabilized by a variety of means:

- more H bonds

- more proline

- chaperones

Histone-like proteins stabilize DNA

Membrane stabilized by variety of means

-more saturated, more branched and higher molecular weight lipids

- ether linkages (archaeal membranes)

Term
Aerobes
Definition

- O2 is ultimate e- acceptor

 

- In the presence of O2 organisms will be doing aerobic respiration

Term
Anaerobes
Definition

- NO3- (nitrate) or NO2- (nitrite) are final e- acceptors

- Reactive oxygen species (ROS), are produced by metabolic reactions when the cell is exposed to O2 (toxic to cell)

Term
Conditions Influencing the Effective Antimicrobial Agent Activity
Definition

- Population size

- Population composition

- Concentration or intensity of an antimicrobial agent

- Duration of exposure

- Temperature

- Local environment

>pH, viscosity, and concentration of organic matter

>biofilms


 

Term
Moist Heat
Definition

- Boiling will not destroy spores and does not sterilize

- Destroys viruses, fungi, and bacteria

- Degrades nucleic acids, denatures proteins, and disrupts membranes

Term
Steam Sterilization
Definition

-Carried out using an autoclave (heat + pressure)

- Effective against all types of microorganisms including spores

- Quality control - includes strips with Geobacillus stearothermophilus

Term
DNA
Definition

Deoxyribonucleic acid

 

:genetic instructions to carry 0ut metabolism and reproduction

Term
RNA
Definition

Ribonucleic acid

 

:expresses the information in DNA

Term
Proteins and enzymes
Definition

 

:build cellular structures and do cellular work

Term
The Flow of Genetic Information
Definition

- Central Dogma
the pathway from DNA ro RNA to protein is gene expression
-From one generation to the next
DNA stores genetic information
information is duplicated by replication and is passed on to the next generation
- DNA divided into genes
transcription yields RNA. Copy of specific genes
translation uses information in mRNA to synthesize a polypeptide
Term
Helicase
Definition
unwind DNA strands
Term
Single stranded binding proteins (SSB)
Definition
keep strands apart for replication to occur
Term
Topoisomerases
Definition
breaks one strands of DNA to relieve tension / prevents supercoiling
Term
DNA gyrase (topoisomerase)
Definition
also introduces negatie supercoiling to help compact bacterial chromosome
Term
Primase
Definition

 

synthesizes short complementary strands of RNA (~10 nucleotides) to serve as primers needed by DNA polymerase

Term
Ligase
Definition
join the Okasaki fragments
Term
Events at the replication fork in E. coli
Definition

- DnaA proteins bind oriC (origin of replication) causing

bending and separation of strands

- Helicase separates strands, SBB attach

- Primerase synthesis RNA primer

- Lagging and leading strand is synthesized

- DNA polymerase I removes RNA primers

- Okazaki fragments are joined by DNA ligase


Term
Linking the fragments
Definition
DNA ligase forms a phosphodiester bond between 3'-hydroxyl of the gorwing strand and the 5'-phosphate of an Okazaki fragment
Term
Proofreading
Definition



- Carried out by DNA polymerase III


- Removal of mismatched base from 3 end of growing strand

by exonuclease activity of enzyme


- This activity is not 100% efficient

Term
Gene Structure
Definition

- Defined as a polynucleotide sequence that codes for a functional product, e.g. polypeptide, tRNA, rRNA

- Has a fixed start point and end point

- Codons are found in mRNA and code for single amino acids

- Promoter is located at the start of the gene

>the recognition/binding site for RNA polymerase

>functions to orient polymerase

-Leader sequence is transcribed into mRNA but it's not

translated into amino acids

Term
Transcription occurs in 3 phases:
Definition

1. Initiation: RNA pol holoenzyme binds to the promoter

2. Elongation: the RNA chain is extended

3. Termination: RNA pol detaches from the DNA, after the transcript is made

Term
The genetic code
Definition

- Final step in expression of protein encoding genes

- mRNA sequence is translated into amino acid sequence of polypeptide chain (process = translation)

- An understanding of the genetic code is necessary before translation is studied

- Codon: genetic code word, 3 bp long

specifies amino acid

anticodon on tRNA is complementary

Start codon/Stop codon

Term
Translation
Definition

-Synthesis of proteins using mRNA as template

-Occurs at the ribosomes

- tRNA and rRNA are essential in this process

Term
Transfer RNA
Definition

Tertiary structure

Contains the anticodon

Complementary to the codon

binds the codon

3' end of tRNA binds amino acid

Term
Amino Acid Activation
Definition

- Attachment of amino acid to tRNA

- Catalyzed by aminoacyl-tRNA synthetases

- at least 20 each specific for single amino acid and for all the tRNAs to which each may be properly attached (cognate tRNAs)

Term
Elongation Cycle (transpeptidation)
Definition

- Sequential addition of amino acids to growing polypeptide

- Consists of 3 phases:

1. aminoacyl-tRNA binding

2. transpeptidation reaction

3. translocation

-involves several elongation factors (EFs)


Term
Final stage in elongation: Translocation
Definition

3 simultaneous events

-peptidyl-tRNA moves from A site to P site

-ribosome moves down one codon

-empty tRNA leaves P site

requires GTP hydrolysis

Term
Termination of protein synthesis
Definition

-takes place at any one of three stop codons

-release factors (RFs)

aid in recognition of stop codons

3 RFs function in prokaryotes

-GTP hydrolysis required

Term
Protein Maturation and Secretion
Definition

-Protein function depends on 3-D shape

-Occurs as post translational event

>requires folding

>association with other proteins

>delivered to proper subcellular or

      extracellular site

Term
Protein Folding and Molecular Chaperones
Definition

-Molecular chaperones

>proteins that aid the folding of nascent  

      polypeptides

>protect cells from thermal damage

    heat-shock proteins

>aid in transport of proteins across    

    membranes

Term

Protein Folding

Bacteria vs. Eukaryotes

Definition

Domains:

- Structurally independent regions of polypeptide

- Separated from each other by less structured portions of

polypeptide 

In eukaryotes:

- domains fold independently right after being synthesized

-molecular chaperones not as important

In bacteria:

- polypeptide does not fold until after synthesis of entire polypeptide

-molecular chaperones play important role


Term
Mutations
Definition

Stable, heritable changes in sequence of bases in DNA

-point mutations most common

>from alteration of single pairs of nucleotide

-larger mutations are less common

>insertions, deletions, inversions, duplication, and  

     translocations

Mutations can be spontaneous or induced

Term
Mutations in Protein Coding Genes
Definition

Point Mutations

- in protein-coding genes can affect protein structure


-Are named according to if and how they change the encoded protein


-The most common types are: silent, missense, nonsense, and

         frameshift mutations



Term
DNA Repair
Definition

Proofreading

-correction of errors in base pairing made during replication

-errors corrected by DNA polymerase

Other DNA repair mechanisms also exist


Excision Repair

-corrects damage that causes distortions in double helix

-two types of repair systems are known

>nucleotide excision repair

>base excision repair

>both remove the damaged portion of the DNA strand

Term
The SOS Response
Definition

-Extensive DNA damage leads to initiation of the SOS response

-This system is not a single repair mechanisms but a set of different mechanisms that collaborate to rescue the cell.

-In order to save the cell, the SOS repair can introduce  mutations into severly damaged DNA 

-"Repair" refers to saving the integrity of the circular chromosome even if incorrect bases are introduced

- "Mutate or die"


Term
Creating Genetic Variability
Definition

Mutations are subject to selective pressure 

-each mutant form that survive becomes an allele, an alternate form of a gene


Recombination is the process in which a donor DNA molecule replaces a segment of a host genome or is inserted into a host genome


Term
Horizontal Gene Transfer in Bacteria and Archaea creates recombinants
Definition

HGT is the transfer of genes from one independent, mature organism to another

-stable recombinant has characteristics of donor and recipient


Important in evolution of many species

-expansion of ecological niche, increased virulence


Term
Horizontal Gene Transfer Mechanisms
Definition

Occurs in the 3 mechanisms evolved by bacteria to create recombinants

-Conjugation

-Transformation

-Transduction

Genes can be transferred to the same or different species

The donor DNA has 4 possible fates in the recipient

Term
4 fates  of donor DNA
Definition

-Integration of donor DNA

-Donor DNA self-replicates - plasmid 



-Donor DNA cannot self-replicate

-Heat restriction

Term
Conjugation
Definition

:the transfer of DNA from one bacterium to another, following cell-to-cell contact

-Initiated by a special pilus protruding from the donor cell

-Conjugation requires the presence of special transferable plasmids

-A well-studied example in E. coli is the fertility factor (F factor)

contains 2 replication origins

oriV used in nonconjugating     

oriT used during DNA transfer

Term
Transduction
Definition

:the process in which bacteriophages carry host DNA from one cell to another

2 basic types

Generalized transduction: can transfer any gene from a donor to a recipient cell

Specialized transduction: can transfer only a few closely linked genes between cells

Term
Transformation
Definition

:the process of importing free DNA into bacterial cells

Cells must be "competent" - can be induced


Term
Acellular Agents
Definition

 

Viruses - protein and nucleic acid

Viroids - only RNA

Virusoids- only RNA

Prions - proteins only

Term
What is a Virus?
Definition

:a noncellular particle that must infect a host cell, where it reproduces

-Obligate intracellular parasites

-Subverts the cell's machinery and directs it to produce viral particles

-Single nucleic acid (DNA or RNA) contained within a protective protein capsid

-All life froms can be infected by a virus

-Tissue damage and cell death accounts for the destructive effects seen in many viral diseases

Term
Properties of Viruses
Definition

Virion:

-Complete virus particle (ready to infect)

-Consists of >1 molecule of DNA or RNA enclosed in a coat of protein

-may have additional layers

-Although cannot reproduce independent of living cells nor carry out cell division, can exist extracellularly

Term
The Structure of Viruses
Definition

-All virions contain a nucleocapsid which is composed of nucleic acid (DNA or RNA) and a protein coat

-Can be enveloped or naked viruses

Term
Capsids
Definition

-Large macromolecular structures which serve as protein coat of virus

-Protect viral genetic material and aids in its transfer between host cells

-Made of protein subunits called protomers

-Helical, icosahedral, or complex

Term
Viral Envelopes
Definition

-Many viruses bound by an outer, flexible, membranous layer called the envelope


Viral Envelope Proteins

-Envelope proteins, which are viral encoded, may project from the envelope surface as spikes or peplomers

>viral attachment

>identification

>enzymatic activity

>play a role in nucleic acid replication

Term
Viral Genome
Definition

-Diverse nature of genomes


-May have single or double stranded DNA or RNA


-Size of nucleic acid varies


-Genomes can be segmented or circular

Term
Viral Multiplication
Definition

-Mechanism used depends on viral structure and genome


-Steps similar

Term
Fusion
Definition

-Virus's envelope spikes bind to receptors on surface of host cell

-Lipid bilayer of viral envelope fuses with host cell membrane

-Nucleocapsid is released into the cytoplasm

Term
Endocytosis
Definition

Nonenveloped viruses and enveloped - different ways


Nonenveloped: virus's capsid proteins bind to receptors on cell surface and receptor mediated endocytosis- nucleic acid is extruded from the endosome into cytoplasm


Enveloped: virus's envelope spikes bind to receptors on cell's surface - increased acidity allows nucleocapsid to escape from the endosome into cytoplasm

Term
Injection
Definition
:compresses and injects nucleic acid directly in cell
Term
Classification of Viruses
Definition

-Genome composition

-Capsid symmetry

-Envelope

-Size of the virion

-Host range

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