Haploid only, asexual

• Binary fission (most common)
• Budding
• Filamentous

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

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

• 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

: 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

:Similar to cocci divisome but elongate prior to septation

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

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

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

- Cell synthesizing new components

- Varies in length

- 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

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

Possible reasons: no resources, waste, no more space

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

2 Hypotheses

-cells are viable but not culturable (VBNC)

- Programmed cell death

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

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

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

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

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)

- O₂ is ultimate e^- acceptor

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

- 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)

- 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

- Boiling will not destroy spores and does not sterilize

- Destroys viruses, fungi, and bacteria

- Degrades nucleic acids, denatures proteins, and disrupts membranes

-Carried out using an autoclave (heat + pressure)

- Effective against all types of microorganisms including spores

- Quality control - includes strips with Geobacillus stearothermophilus

Deoxyribonucleic acid

:genetic instructions to carry 0ut metabolism and reproduction

Ribonucleic acid

:expresses the information in DNA

:build cellular structures and do cellular work

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

- 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

- 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

- 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

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

- 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

-Synthesis of proteins using mRNA as template

-Occurs at the ribosomes

- tRNA and rRNA are essential in this process

Tertiary structure

Contains the anticodon

Complementary to the codon

binds the codon

3' end of tRNA binds amino acid

- 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)

- 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)

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

-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

-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

-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

Protein Folding

Bacteria vs. Eukaryotes

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

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

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

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

-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"

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

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

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

-Integration of donor DNA

-Donor DNA self-replicates - plasmid 

-Donor DNA cannot self-replicate

-Heat restriction

: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

: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

:the process of importing free DNA into bacterial cells

Cells must be "competent" - can be induced

Viruses - protein and nucleic acid

Viroids - only RNA

Virusoids- only RNA

Prions - proteins only

: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

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

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

-Can be enveloped or naked viruses

-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

-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

-Diverse nature of genomes

-May have single or double stranded DNA or RNA

-Size of nucleic acid varies

-Genomes can be segmented or circular

-Mechanism used depends on viral structure and genome

-Steps similar

-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

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

-Genome composition

-Capsid symmetry

-Envelope

-Size of the virion

-Host range