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BIOL 228 > Module 03 - Microbial Growth and Genetics > Flashcards

Module 03 - Microbial Growth and Genetics Flashcards

1
Q

microbial growth

A

refers to an increase in number of cells rather than an increase of cell size

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2
Q

binary fission

A

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

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3
Q

generation time

A

(doubling time) the time it takes for the population to double through one round of binary fission, can vary

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4
Q

example of generation time

A

E. coli can double in 20 mins in the lab, but in harsh environements it might take several days to double

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5
Q

growth curve

A

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

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6
Q

lag phase (1)

A

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

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7
Q

log phase (2)

A

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

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8
Q

stationary phase (3)

A

plateau in number of living batcerial cells; rate of cell division and death roughly equal, waste products accumulate and nutrients are gradually used

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9
Q

decline (death) phase (4)

A

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

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10
Q

direct methods of quantifying microbial growth

A

counting of number of bacteria, by counting colonies after growth in nutrient medium, or counting stained cells microscopically

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11
Q

indirect method of quantifying microbial growth

A

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

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12
Q

biofilm

A

complex and dynamic ecosystems that form a variety of environmental surfaces, from industrial conduits and water treatment pipelines to rock in river beds

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13
Q

obligate anaerobe

A

microorganisms that are killed by normal concentrations of oxygen

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14
Q

aerotolerant anaerobe

A

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

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15
Q

microaerophiles

A

bacteria that require a minimum level of oxygen for growth, about 1%-10%, well below 21% found in the atmosphere

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16
Q

obligate aerobe

A

bacteria that cant grow without an abundant supply of oxygen

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17
Q

facultative anaerobes

A

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

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18
Q

optimum oxygen concentration

A

ideal concentration of oxygen for a particular microorganism

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19
Q

minimum permissive oxygen concentration

A

lowest concentration of oxygen that allows growth

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20
Q

maximum permissive oxygen concentration

A

highest tolerated concentration of oxygen
- organisms will not grow outside the range of oxygen levels found between the min and max permissive oxygen concentration

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21
Q

neutrophile

A

(most bacteria) they grow optimally at a pH within one or two pH units of the neutral pH of 7

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22
Q

examples of neutrophiles

A

E. coli, Staphylococci, and Salmonella

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23
Q

acidophile

A

microorganisms that grow optimally at pH less than 5.55

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24
Q

examples of acidophiles

A

sulfur oxidizing Sulfolobus spp.

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25
Q

alkaliphiles

A

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

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26
Q

optimum growth pH

A

most favourable pH for growth of an organism

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27
Q

minimum growth pH

A

lowest pH value that an organism can tolerate

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28
Q

maximum growth pH

A

highest pH

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29
Q

optimum growth temp

A

growth rates at their highest for the organism

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30
Q

minimum growth temp

A

lowest temp at which an organism can survive and replicate

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31
Q

maximum growth temp

A

highest temp at which an organism can occur

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32
Q

psyotrophs

A

(psychrotolerant) prefer cooler environments from a high temp of 25 degrees to refrigeration temp of 4 degrees

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33
Q

mesophiles

A

(“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

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34
Q

thermophiles

A

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

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35
Q

hyperthermophiles

A

(higher extreme temps) characterized by growth ranges from 80 degrees to a max of 110, with some extreme examples that survive temps about 121

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36
Q

examples of physiological adaptations to temperature extremes

A
  • 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
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37
Q

halophiles

A

(“salt loving”) microorganisms that require high salt concentration for growth
- found in marine environments, salt concentration hover at 3.5%

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38
Q

halotolerant

A

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

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39
Q

barophiles

A

microorganisms that require high atmospheric pressure for growth
- bacteria that live at the bottom of the ocean must be able to withstand great pressures

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40
Q

photoautotrophs/photoheterotrophs

A

(green sulfur bacteria/ purple sulfur bacteria) depend on sufficient light intensity at the wavelengths absorbed by their pigments to grow and multiply

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41
Q

enriched media

A

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

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42
Q

chemically defined media

A

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

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43
Q

selective media

A

media that inhibit growth of unwanted microorganisms and support the growth of the organism of interest by supplying nutrients and reducing competition

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44
Q

differential media

A

makes it each to distinguish colonies of different bacteria by a change in colour of the colonies/colour of medium

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45
Q

base sequence

A

each nucleic acid strand contains certain nucleotides that appear in certain order within a strand

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46
Q

DNA strand

A

responsible for carrying and retaining the hereditary information in a cell

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47
Q

deoxyribonucleotide

A

nucleotide that compose DNA, 3 components are a five-carbon sugar called deoxyribose, phosphate group, and a nitrogenous base

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48
Q

nitrogenous base

A

a nitrogen containing ring structure responsible for complementary base pairing between nucleic acid strands

49
Q

deoxyribose

A

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

50
Q

purines

A

they have a double-ring structure with a six-carbon ring fused to a five carbon ring (adenine - A and guanine - G)

51
Q

pyrimidines

A

only have a six-carbon ring structure (smaller) (cytosine - C and thymine - T)

52
Q

Chargaff’s rules

A

A=T and C=G, they have equal amounts

53
Q

DNA denaturation

A

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

54
Q

vertical gene transfer

A

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

55
Q

ribonucleic acid (RNA)

A

similar to DNA, but DNA molecules are long and double stranded, RNA molecules are much shorter and are single stranded

56
Q

ribonucleotide

A

contain ribose (pentose sugar), one of four nitrogenous bases (A, U, G and C) and a phosphate group

57
Q

involved in protein synthesis

A

mRNA, rRNA and tRNA

58
Q

messanger RNA (mRNA)

A

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

59
Q

transfer RNA (tRNA) and ribosomal RNA (rRNA)

A

enconded in DNA, then copied into long RNA molecules that are cut to release smaller fragments containing the individual mature RNA species

60
Q

rRNA

A

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

61
Q

tRNA

A

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

62
Q

Example of RNA functioning as the storage material for genetic information

A
  • 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
63
Q

gene

A

segments of DNA molecules

64
Q

genome

A

complete set of genes/genetic material of a cell or organism

65
Q

phenotypes

A

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

66
Q

chromosomes

A

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

67
Q

eukaryotic chromosomes

A

linear, have multiple distinct chromosomes, contain two copies of each chromosome = diploid
- some eukaryotic genomes are many times larger than human genomes

68
Q

prokaryotic chromosomes

A

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

69
Q

extrachromosomal DNA

A

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

70
Q

plasmids

A

a small circular DNA molecule found in bacteria and some other microscopic organism

71
Q

describe different forms of viral genomes

A

they are diverse in structure, some viruses have genomes that have DNA as genetic material

72
Q

form of viral genomes (DNA single stranded)

A

human parvoviruses

73
Q

form of viral genomes (DNA double stranded)

A

herpesviruses and poxviruses

74
Q

viral genomes

A

are small, encoded only a few genes because they rely on hosts to carry out many functions required for replication

75
Q

describe two major functions of the genome

A

storage, propagation, transmission of genetic material rely on the use of genetic info encoded in a DNA sequence

76
Q

central dogma

A

genetic info that goes from the RNA and DNA to proteins (translation and transcription)

77
Q

genotype

A

full collection of genes

78
Q

phenotype

A

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

79
Q

semiconservative replication

A

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

80
Q

rolling circle replication

A

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

81
Q

DNA polymerase

A

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.

82
Q

RNA transcript

A

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

83
Q

transcription bubble

A

unwounded region

84
Q

antisense strand

A

transcription of a gene proceeds from one of two DNA strands that act as a template

85
Q

transcription in prokaryotes

A

difference between DNA and RNA polymerase is a requirement for a 3’-OH onto which to add nucleotides
- transcription takes place in the nucleus

86
Q

transcription in eukaryotes

A

transcription takes place in the nucleus, proteins are needed

87
Q

5’ cap

A

primary transcript is being synthesized; a special 7-methylguanosine nulceotide, added to 5’ end of growing transcript

88
Q

poly-A tail

A

enzyme adds a string of 200 adenine nucleotides to the 3’ end

89
Q

genetic code

A

relationship between an mRNA codon and its corresponding amino acid

90
Q

codon

A

each amino acid is defined within mRNA by a triplet of nucleotides
- 3 nucleotide codes = 64 possible combinations

91
Q

stop codons

A

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

92
Q

start codon

A

AUG, initiate translation

93
Q

explain why the genetic code is (almost) universal

A

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

94
Q

process of translation as it occurs in prokaryotic cells

A

translation occurs in the cytosol, where large and small subunits of the ribosome bind to mRNA

95
Q

mutation

A

heritable change in DNA sequence of an organism

96
Q

point mutation

A

affects a single base and most commonly occurs when one base s substituted/replaces by another

97
Q

insertion

A

addition of one or more bases

98
Q

deletion

A

removal of one or more bases

99
Q

silent mutation

A

change has no effect on proteins structure

100
Q

missense mutation

A

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

101
Q

nonsense mutation

A

(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

102
Q

frameshift mutations

A

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

103
Q

nucleoside analogs (chemical mutagens)

A

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

104
Q

intercalating agents

A

molecules slide between stacked nitrogenous bases of DNA double helix, distorting the molecule and creating atypical spacing between nucleotide base pairs

105
Q

Ames test

A

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

106
Q

HGT in prokaryotes - 3 primary mechanisms

A
  1. transformation: naked DNA is taken up from environment
  2. transduction: genes are transfered between cells in a virus
  3. conjugation: use of a hollow tube called a conjugation pilus to transfer genes between cells
107
Q

transformation

A

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

108
Q

transduction

A

viruses that infect bacteria may also move short pieces of chromosomal DNA from one bacterium to another

109
Q

conjugation

A

DNA is directly transferred from one prokaryote to another using conjugation pilus, which brings the organisms into contact with one another

110
Q

horizontal gene transfer (HGT)

A

intro of genetic material from one organism to another organism within the same generation, important for genetic diversity

111
Q

transposon

A

(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

112
Q

transposition

A

transposon allow the entire sequence to independently excise from one location in DNA molecules and integrate into the DNA elsewhere

113
Q

operon

A

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

114
Q

repressor

A

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

115
Q

inducer

A

regulatory molecule, small molecule that activates or represses transcription by interacting with a repressor/activator

116
Q

repressible operons

A

have gene encoding enzymes required for a biosynthetic pathway - trp operon

117
Q

inducible operons

A

contain gene encoding enzymes in a pathway involved in the metabolism of specific substrates like lactose - lac operon

118
Q

describe why regulation of operons is important

A

allows protein synthesis to be controlled coordinately in response to the needs of the cell

BIOL 228 (3 decks)

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