Chapter 7

binary fission

how most bacterial and archaeal cells reproduce

cell cycle

the complete sequence of events extending from formation of a new cell through the next cell division; has three phases

origin of replication

site at which replication begins

terminus

site at which replication is terminated; located opposite to the origin

replisome

DNA synthesis machinery

partitioning system

has three components: ParA protein, ParB protein, and parS region on chromosome

cytokinesis

formation of two daughter cells following cell division

septation

formation of cross wall between two daughter cells

septation steps

1. selection of site for septum formation

2. assembly of Z-ring (composed of protein FtsZ)

3. assembly of cell wall synthesizing machinery

4. constriction of cell and septum formation

FtsZ

involved in assembly of Z-ring, first protein to localize to the future division site, monomers polymerize, localize with Min system to establish division site at midcell

importance of Z-ring timing

location of PtsZ polymerization mist coordinate with timing; if occurs too early, Z-ring could constrict preventing proper partitioning

nucleoid occlusion

coordinates chromosome movement and cell separation; SlmA coats chromosome except at the replication termination region (Z-ring can form when SlmA-tagged chromosome has moved away)

divisome formation

Process in bacterial cell division where a protein complex called the divisome assembles at the midcell, leading to the formation of a septum that divides the cell into two daughter cells. Essential for successful cell division and involves multiple proteins and regulatory factors.

peptidoglycan synthesis scheme

Process in which N-acetylglucosamine and N-acetylmuramic acid are cross-linked by peptide bridges to form a mesh-like structure in bacterial cell walls. Inhibited by antibiotics like penicillin.

cell shape determination

cellular location of peptidoglycan synthesis plays role in determining cell shape

coccus shape

peptidoglycan only forms at central septum, FtsZ localization placement involved

rod shape

elongasome (rod complex) is used; MreB is scaffold by creating filaments along cytoplasmic face of plasma membrane; growth occurs in numerous bands around cell, not at the poles

curved shape

crescentin localizes to one side of the cell, resulting in asymmetric cell wall and vibroid shape

sulfolobus cell cycle

similar to mitotic cell cycle; growth phase (G1) followed by DNA replication (S phase), then G2 phase, segregation of chromosomes, and cytokinesis

segregation in sulfolobus cell cycle

occurs via use of SegA/SegB protein system that is similar to bacterial partitioning systems

SegA

similar in structure and function to ParA

SegB

unique to archaea but thought to function similarly to ParB

does archaea have DNA sequences similar to parS?

there is no evidence that has been found yet

CdvA

binds the membrane and forms a non-contractile ring at midcell

CdvB

ring constricts to separate the daughter cells

CdvC

recruited with CdvB to the site of division

FtsZ

Z-ring associates with new S-layer

is growth referring to individual cell growth or population growth?

population growth

batch culture

incubated in a closed vessel with a single batch of medium

lag phase

cell synthesizing new components; replenishes ribosomes and ATP, adapts to new medium/conditions, cells replicate DNA, increase in mass, and divide; first phase

exponential phase

rate of growth and division is constant and maximal; population is most uniform in terms of chemical and physical properties during this phase; second phase

exponential growth phase depends on…

nutrient availability; final net growth increases with the initial amount of the limiting nutrient present, then growth rate increases with nutrient concentration but saturates over time

stationary phase

when growth eventually ceases and the total number of viable cells remains constant (balance between cell division and death); happens due to nutrient limitation, limited oxygen availability, toxic waste accumulation, or critical population density has been reached; third phase

death phase

number of viable cells declines exponentially, with cells dying at constant rate; nutrient deprivation and buildup of toxic wastes causes irreparable harm to cells; fourth phase

long-term stationary phase

bacterial population continually evolves; process marked by successive waves of genetically distinct variants; natural selection occurs within a single culture; fifth phase

generation/doubling time

time required for population to double in size; varies depending on species of microorganism and environment

growth rate constant (k)

number of generations per unit time; formula: g=1/k

extremophiles

grow under harsh conditions that would kill most other organisms

most microbes live in a…

hypotonic environment

mechanosensitive (MS) channel

in plasma membrane, allows solutes to leave

protists expel excess water via…

contractile vacuoles

halophiles

require NaCl at a concentration above about 0.2M

extreme halophiles

require salt concentrations between 3M and 6.2M

osmotolerant

microorganisms that can grow over wide ranges of water activity but optimally at higher levels

xerotolerant

microbes that withstand high solute concntrations

acidophiles

grow best between pH 0 and 5.5

alkaliphiles

grow best between pH 8 and 11.5

fungi prefer an environment…

with a pH 4-6

psychrophiles

grow best in 0-20 degrees C

psychotrophs

grow best in 0-35 degrees C

mesophiles

grow best in 20-45 degrees C

thermophiles

grow best in 45-85 degrees C

hyperthermophiles

grow best in 85-100 degrees C

protein structure of thermophiles

stabilized by more H bonds, more proline and less flexible peptides, and chaperones aid in folding

membrane structure of thermophiles

stabilized by more saturation, more branched and higher molecular weight, and ether linkages resistant to hydrolysis

obligate aerobe

requires oxygen

obligate anaerobe

usually killed in presence of oxygen

microaerophile

requires 2-10% oxygen

facultative anaerobes

does not require oxygen but grows better in its presence

aerotolerant anaerobes

can grow with or without oxygen

reactive oxygen species (ROS)

superoxide radical, hydrogen peroxide, hydroxyl radical

how microorganisms protect against ROS

aerobes produce protective enzymes like superoxide dismutase (SOD), catalase, or peroxidase

barotolerant

adversely affected by increased pressure, but not as severely as nontolerant organisms

peizophilic (barophilic)

requires high pressure for growth; change membrane fatty acids to adapt to increasing pressure (lipids become more unsaturated and shorter)

ionizing radiation

X-rays and gamma rays that cause mutations that indirectly result in death; disrupts structure of many molecules (breaks H bonds and destroys ring structures)

Deinococcus radiodurans

endospores are resistant to ionizing radiation

UV radiation

most lethal wavelength is 260nm because it is absorbed by DNA

visible light

at high intensities generates singlet oxygen, a powerful oxidizing agent; carotenoid pigments protect many light-exposed microorganisms from photooxidation

microbial environments

are complex and constantly changing; expose a microorganism to overlapping gradients of nutrients and environmental factors; contain micro-and macro-organisms

eutrophic

nutrient rich environments

oligotrophic

low nutrient environments

growth arrest

when a microbe enters a stationary phase in response to starvation or stress

sessile

microbes that grow attached to surfaces

planktonic

microbes that grow free floating

biofilm

complex, slime enclosed communities of microbes; ubiquitous in nature in water; can be formed on any conditioned surface

extracellular polymeric substance (EPS)

microbes reversibly attach to conditioned surface and release polysaccharides, proteins, and DNA; additional polymers are produced as microbes reproduce and biofilm matures

quorum sensing

bacterial cells communicate via small molecules that diffuse in the environment; requires sufficient number of microbes participating

N-acylhomoserine lactone (AHL)

autoinducer; moves across plasma membrane from the cytoplasm to the outside of the cell; when cell population is high, AHL diffuses into the cell which induces specific gene expression

autoinducing peptides (AIP)

in gram-positive bacteria, autoinducing short peptides

culture medium

solid or liquid mixture of nutrients and other components; used to grow, transport, and store microorganisms in the lab; must contain all growth factors microorganisms require

defined/synthetic medium

each ingredient can be defined with a chemical formula

complex media

contain some ingredients of nonspecific chemical composition

agar

sulfated polymer solidifying agent; most microorganisms cannot degrade it

peptones

partial proteolytic digestion of protein sources

extracts

aqueous extracts that contain amino acids, peptides, nucleotides, organic acids, vitamins, and minerals (usually beef or yeast)

supportive media

sustain growth of many microorganisms (can be made up of tryptic soy broth and agar)

enriched media

supportive media supplemented with special nutrients (like blood agar)

selective media

allow growth of particular microorganisms, while inhibiting the growth of others; gram-negative bacteria can grow on bile salts while gram-positive cannot

differential media

distinguish among different groups of microbes and even permit tentative identification of microbes based on their biological characteristics

blood agar

distinguish between hemolytic versus nonhemolytic bacteria

MacConkey agar

distinguish between lactose fermenters versus non-fermenters

what are candle jars used for?

anaerobic microbe cultivation

pure or axenic culture

population of cells arising from a single cell; allows for study of single type of microorganism in mixed culture

enrichment culture

encourages growth of microbes with a particular characteristic, while inhibiting growth of others

three factors considered in enrichment culture

a suitable source of microbes, nutrients that should and should not be included in the culture medium, and environmental conditions

streak plate

technique of spreading a mixture of cells on an agar surface using an inoculating loop or swab; goal is to obtain individual cells that are separated from each other (each cell can reproduce to form a separate colony)

spread plate

small volume of diluted mixture is transferred to center of an agar plate and spread evenly over surfaces with a sterile bend rod (dilution made by serial dilution)

pour plate

sample is serially diluted and mixed with liquid agar which is the poured into sterile culture dishes; used when sampling heterogenous populations of microbes that might produce overgrown colonies

culturomics

use miniature cultures and incubate in many different conditions to find the best one

direct counts

counting chambers (special slides and cover slips with grids to facilitate counting), membrane filter technique (microbes are filtered then stained), flow cytometry (stream of cells so narrow that one cell at a time passes through the laser beam), and electronic counters (like the Coulter counter)