Module 03 - Microbial Growth and Genetics Flashcards
microbial growth
refers to an increase in number of cells rather than an increase of cell size
binary fission
most common mechanism of cell replication in bacteria
- before dividing, the cell grows and increases its number of cellular components
- replication of DNA as the cell elongates
generation time
(doubling time) the time it takes for the population to double through one round of binary fission, can vary
example of generation time
E. coli can double in 20 mins in the lab, but in harsh environements it might take several days to double
growth curve
microorganisms grown in closed culture (batch culture) in which no nutriens are added and most waste isnt removed, follow a reproducible growth pattern
- infections in the body dont always follow the growth curve
lag phase (1)
no increase in number of living bacterial cells, small number of cells called inoculum, that are added ot a fresh culture medium, a nutritional broth that supports growth, cells are gearing up to go into next phase of growth, cell grow larger and are metabolically active, repairs happen in this phase, if cells where damages/shocked
log phase (2)
exponential increase in number of living bacterial cells (logarithmic phase) , cells are actively dividing by binary fission and numbers increase exponentially, cells have a constant growth rate and uniform metabolic activity , bacteria are most susceptible to action of disinfectants and common antibiotics that affect protein, DNA and cell wall synthesis
stationary phase (3)
plateau in number of living batcerial cells; rate of cell division and death roughly equal, waste products accumulate and nutrients are gradually used
decline (death) phase (4)
exponential decrease in number of living bacterial cells, number of dying cells exceeds the number of diving cells
- cells lyse and release nutrient to medium, allowing surviving cells to maintain viability and form endospores
direct methods of quantifying microbial growth
counting of number of bacteria, by counting colonies after growth in nutrient medium, or counting stained cells microscopically
indirect method of quantifying microbial growth
estimate culture density by measuring turbidity of culture/live cell density by measuring metabolic activity, another technique is electronic cell counting device to detect and count the changes in electrical resistance in a saline solution
biofilm
complex and dynamic ecosystems that form a variety of environmental surfaces, from industrial conduits and water treatment pipelines to rock in river beds
obligate anaerobe
microorganisms that are killed by normal concentrations of oxygen
aerotolerant anaerobe
are indifferent to the presence of oxygen, they dont use oxygen because they usually have a fermentative metabolism, arent harmed in the presence of oxygen
microaerophiles
bacteria that require a minimum level of oxygen for growth, about 1%-10%, well below 21% found in the atmosphere
obligate aerobe
bacteria that cant grow without an abundant supply of oxygen
facultative anaerobes
heavy growth at the top of a test tube and growth throughout the tube, organisms that thrive in the presence of oxygen but also grow in the absence of oxygen by relying on fermentation/anaerobic respiration, if there is a suitable electron acceptor other than oxygen and the organism is able to perform anaerobic respiration
optimum oxygen concentration
ideal concentration of oxygen for a particular microorganism
minimum permissive oxygen concentration
lowest concentration of oxygen that allows growth
maximum permissive oxygen concentration
highest tolerated concentration of oxygen
- organisms will not grow outside the range of oxygen levels found between the min and max permissive oxygen concentration
neutrophile
(most bacteria) they grow optimally at a pH within one or two pH units of the neutral pH of 7
examples of neutrophiles
E. coli, Staphylococci, and Salmonella
acidophile
microorganisms that grow optimally at pH less than 5.55
examples of acidophiles
sulfur oxidizing Sulfolobus spp.
alkaliphiles
microorganisms that grow best at pH between 8.0 - 10.5
- they adapt to harsh environments through evolutionary modifications of lipid and protein structure, and mechanisms to maintain the proton motive force in an alkaline environment
optimum growth pH
most favourable pH for growth of an organism
minimum growth pH
lowest pH value that an organism can tolerate
maximum growth pH
highest pH
optimum growth temp
growth rates at their highest for the organism
minimum growth temp
lowest temp at which an organism can survive and replicate
maximum growth temp
highest temp at which an organism can occur
psyotrophs
(psychrotolerant) prefer cooler environments from a high temp of 25 degrees to refrigeration temp of 4 degrees
mesophiles
(“middle loving”) are adapted to moderate temps, with optimal growth temps ranging from room temp (20 degrees) to about 45 degrees
- human body temp is 37, normal human microbiota and pathogens
thermophiles
organisms that grow at optimum temps of 50 degrees to a max of 60 degrees (“heat loving”)
- they are disrupted in hot springs, geothermal soils and man-made environements, such as garden compost piles
hyperthermophiles
(higher extreme temps) characterized by growth ranges from 80 degrees to a max of 110, with some extreme examples that survive temps about 121
examples of physiological adaptations to temperature extremes
- membranes lose their fluidity and are damaged by ice crystal formation
- heat denatures proteins and nucleic acids
- proteins in psychrophiles are rich in hydrophobic residues, displaying an increase in flexbility
- antifreeze proteins and solutes that decrease the freezing temps of the cytoplasm are common
halophiles
(“salt loving”) microorganisms that require high salt concentration for growth
- found in marine environments, salt concentration hover at 3.5%
halotolerant
dont need high concentration of salt for growth, they survive and divide in the presence of high salt
- cause of foodborne illnesses because they survive and multiply in salty foods
barophiles
microorganisms that require high atmospheric pressure for growth
- bacteria that live at the bottom of the ocean must be able to withstand great pressures
photoautotrophs/photoheterotrophs
(green sulfur bacteria/ purple sulfur bacteria) depend on sufficient light intensity at the wavelengths absorbed by their pigments to grow and multiply
enriched media
contains growth factors, vitamins, other essential nutrients to promote the growth of fastidious organisms, organisms that cannot make certain nutrients and require them to be added to the medium
chemically defined media
complete chemical composition of a medium is known
- ex. in EZ medium, all individual chemical components are identified and the exact amounts of each is known
selective media
media that inhibit growth of unwanted microorganisms and support the growth of the organism of interest by supplying nutrients and reducing competition
differential media
makes it each to distinguish colonies of different bacteria by a change in colour of the colonies/colour of medium
base sequence
each nucleic acid strand contains certain nucleotides that appear in certain order within a strand
DNA strand
responsible for carrying and retaining the hereditary information in a cell
deoxyribonucleotide
nucleotide that compose DNA, 3 components are a five-carbon sugar called deoxyribose, phosphate group, and a nitrogenous base
nitrogenous base
a nitrogen containing ring structure responsible for complementary base pairing between nucleic acid strands
deoxyribose
carbon atoms of the five-carbon deoxyribose are numbered 1’, 2’, 3’, 4’, and 5’
- a nucleoside comprises the five-C sugar and phosphate group
purines
they have a double-ring structure with a six-carbon ring fused to a five carbon ring (adenine - A and guanine - G)
pyrimidines
only have a six-carbon ring structure (smaller) (cytosine - C and thymine - T)
Chargaff’s rules
A=T and C=G, they have equal amounts
DNA denaturation
exposing two DNA strands of the double helix to high temperature/certain chemicals can break the H-bonds between complementary bases, thus seperating the strands into 2 seperate single strands of DNA
vertical gene transfer
transmission of info from mother to daughter cells, occurs through the process of DNA replication
- DNA stores info needed to build and control the cell
ribonucleic acid (RNA)
similar to DNA, but DNA molecules are long and double stranded, RNA molecules are much shorter and are single stranded
ribonucleotide
contain ribose (pentose sugar), one of four nitrogenous bases (A, U, G and C) and a phosphate group
involved in protein synthesis
mRNA, rRNA and tRNA
messanger RNA (mRNA)
existence of an intermediary between DNA and protein products
- mRNA carries the message from the DNA, which controls all of the cellular activities in a cell
- cell requires a certain protein to be synthesized, in the synthesized through the process of transcription
- interacts with ribosomes and other cellular machinery to direct the synthesis of protein it encodes during the process of translation
transfer RNA (tRNA) and ribosomal RNA (rRNA)
enconded in DNA, then copied into long RNA molecules that are cut to release smaller fragments containing the individual mature RNA species
rRNA
major constituent of ribosomes, composing up to 60% of ribosome by mass and providing the location where the mRNA binds
- rRNA of ribosome has enzyme activity and catalyzes the formation of peptide bonds between two aligned amino acids during protein synthesis
tRNA
one of the smallest, only 70-90 nucleotides long, carries the correct amino acid to the site of protein synthesis in the ribosome
- base pairing between tRNA and mRNA that allows for the correct amino acid to be inserted in polypeptide chain being synthesized
Example of RNA functioning as the storage material for genetic information
- RNA has the capability to serve as genetic info
- RNA is typically single stranded within cells but viruses are diverse
- Rhinoviruses; cause influenza viruses; Ebola virus are single stranded RNA viruses
- Rotaviruses are doubles stranded RNA viruses
gene
segments of DNA molecules
genome
complete set of genes/genetic material of a cell or organism
phenotypes
the set of genes being expressed at any given point in time determines the cells activities and its observable characteristics
- phenotypes may change in response to environmental signals that affect which nonconstitutive genes are expressed
chromosomes
discrete DNA structures within cells that control cellular activity
- eukaryotic chromosomes are housed in membrane-bound nucleus
- prokaryotic chromosomes contain single, circular chromosomes that is found in an area of the cytoplasm called the nucleoid
eukaryotic chromosomes
linear, have multiple distinct chromosomes, contain two copies of each chromosome = diploid
- some eukaryotic genomes are many times larger than human genomes
prokaryotic chromosomes
chromosomes in bacteria/archaea are circular, contain one single chromosome within the nucleoid
- has only one copy of each gene = haploid
- DNA gyrase that prevent overwinding of DNA
extrachromosomal DNA
most DNA is contained within a cells chromosomes, many cells have additional molecules of DNA outside the chromosome, part of its genome
- genomes of eukaryotes include chromosomes from any organelle like mitochondria/chloroplasts that these cells maintain
plasmids
a small circular DNA molecule found in bacteria and some other microscopic organism
describe different forms of viral genomes
they are diverse in structure, some viruses have genomes that have DNA as genetic material
form of viral genomes (DNA single stranded)
human parvoviruses
form of viral genomes (DNA double stranded)
herpesviruses and poxviruses
viral genomes
are small, encoded only a few genes because they rely on hosts to carry out many functions required for replication
describe two major functions of the genome
storage, propagation, transmission of genetic material rely on the use of genetic info encoded in a DNA sequence
central dogma
genetic info that goes from the RNA and DNA to proteins (translation and transcription)
genotype
full collection of genes
phenotype
set of observable characteristics that result from those genes
- product of proteins being produced by the cell at any given time, thats influenced by cells genotype and interactions with the cells environment
semiconservative replication
two strands of double helix seperate during DNA replication, each strand serves as a template from which the new complimentary strand is copied
- after replication, double stranded DNA includes a parental/”old” strand and one “new” strand
rolling circle replication
bacterial plasmids replicate by a process similar to that used to copy the bacterial chromosome, other plasmids, bacteriophages, and some viruses of eukaryotes
- bacteria –> DNA polymerase III binds to the 3’-OH group of the nicked strand and begins to unidirectionally replicate the DNA using the unnicked strand as a template
DNA polymerase
is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create two identical DNA duplexes from a single original DNA duplex.
RNA transcript
info encoded within the DNA sequence of one/more genes is transcribed into a strand RNA
- transcription require DNA double helix to partially unwind in the region of RNA synthesis
transcription bubble
unwounded region
antisense strand
transcription of a gene proceeds from one of two DNA strands that act as a template
transcription in prokaryotes
difference between DNA and RNA polymerase is a requirement for a 3’-OH onto which to add nucleotides
- transcription takes place in the nucleus
transcription in eukaryotes
transcription takes place in the nucleus, proteins are needed
5’ cap
primary transcript is being synthesized; a special 7-methylguanosine nulceotide, added to 5’ end of growing transcript
poly-A tail
enzyme adds a string of 200 adenine nucleotides to the 3’ end
genetic code
relationship between an mRNA codon and its corresponding amino acid
codon
each amino acid is defined within mRNA by a triplet of nucleotides
- 3 nucleotide codes = 64 possible combinations
stop codons
61 of 64 possible triplet code for animo acids, three of 64 codons do not code for an amino acid; terminate protein synthesis, releasing the polypeptide from translation machinery
start codon
AUG, initiate translation
explain why the genetic code is (almost) universal
a few exceptions, virtually all species use the same genetic code for protein synthesis, powerful evidence that all extant life on earth shares a common origin
process of translation as it occurs in prokaryotic cells
translation occurs in the cytosol, where large and small subunits of the ribosome bind to mRNA
mutation
heritable change in DNA sequence of an organism
point mutation
affects a single base and most commonly occurs when one base s substituted/replaces by another
insertion
addition of one or more bases
deletion
removal of one or more bases
silent mutation
change has no effect on proteins structure
missense mutation
results in different amino acids being incorporated into the resulting polypeptide
- depends on how chemically different the new amino acids is from the wild-type amino acid
nonsense mutation
(type of point mutation) converts codon encoding an amino acid into a stop codon
- result in protein synthesis that are shorter than the wild type/not functional
frameshift mutations
caused by insertion/deletions of a number of nucleotides that arent a multiple of 3 are extremely problematic because a shift in the reading frame result
- can change every amino acid after the point of mutation
nucleoside analogs (chemical mutagens)
chemical that are structurally similar to normal nucleotide bases and can be incorporated into DNA during replication
- others can result in modifiying normal DNA bases, resulting in different base-pairing rules
intercalating agents
molecules slide between stacked nitrogenous bases of DNA double helix, distorting the molecule and creating atypical spacing between nucleotide base pairs
Ames test
Bruce Ames, methods that uses bacteria for rapid, inexpensive screening for carcinogenic potential of a new chemical compound
- measures mutation rates associated with exposure to compound
- chemicals that are more mutagenic will bring about for mutants with restored histidine synthesis in the test
HGT in prokaryotes - 3 primary mechanisms
- transformation: naked DNA is taken up from environment
- transduction: genes are transfered between cells in a virus
- conjugation: use of a hollow tube called a conjugation pilus to transfer genes between cells
transformation
prokaryotes take up naked DNA found in environments that is derived from other cells that have lysed on death and release their contents, including genome into the environment
transduction
viruses that infect bacteria may also move short pieces of chromosomal DNA from one bacterium to another
conjugation
DNA is directly transferred from one prokaryote to another using conjugation pilus, which brings the organisms into contact with one another
horizontal gene transfer (HGT)
intro of genetic material from one organism to another organism within the same generation, important for genetic diversity
transposon
(genetic elements) “jumping genes” are molecules of DNA that include special inverted repeat sequences at their ends and a gene encoding the enzyme transposase
- they carry additional genes, moving them from one location to another
transposition
transposon allow the entire sequence to independently excise from one location in DNA molecules and integrate into the DNA elsewhere
operon
structural proteins with related function are usually encoded together within the genome in a block, transcribed together under the control of a single promoter, resulting in formation of polycistronic transcript
repressor
a transcription factor that supresses transcription of a gene in response to an external stimulus by binding to a DNA sequence within a regulatory region
inducer
regulatory molecule, small molecule that activates or represses transcription by interacting with a repressor/activator
repressible operons
have gene encoding enzymes required for a biosynthetic pathway - trp operon
inducible operons
contain gene encoding enzymes in a pathway involved in the metabolism of specific substrates like lactose - lac operon
describe why regulation of operons is important
allows protein synthesis to be controlled coordinately in response to the needs of the cell
