study of inheritance and inheritable traits as expressed in an organism's genetic material
genetics
Bacteria have ____ but ___ is the only genetic martial that is passed on
RNA
DNA
the entire genetic complement of an organism, includes its genes and nucleotide sequences
genome
True/False Virus can have RNA or DNA and they can pass either on to their offspring
TRUE
a rare event that is almost always deleterious and results in a change in the nucleotide base sequence of a genome
mutation
true/false: mutations provide diversification and without them life would have stopped however they can cause problems in the individuals
true
True/False: mutations rarely leads to a protein that improves ability of organism to survive
TRUE
Bacteria reproduces to make a new organism asexually (cell turn over). Bacterial sex is not involved in _____ BUT IS INVOLVED in ____ the DNA (horizontal gene transfer)
reproduction
diversifying
____ phage caries random DNA segments from donor to recipient is referred to as:
transduction
generalized transduction
transduction where only certain donor DNA sequences are transferred
specialized transduction
True/False: humans engage in transduction
FALSE
steps of transduction:
1. bacteriophage injects _____
2. phage ____ degrade host DNA
3. Cell synthesizes new _____ that incorporate phage DNA and mistakenly, some ____ DNA and they break out of the cell
4. Transducing phage injects ____ DNA
1. DNA
2. enzymes
3. phages, host
4. donor
in bacterial conjugation which cell creates the pilus?
the donor cell
DNA in bacteria conjugation is known as a
plasmid
True/False: the plasmid provides genes for essential nutrients and enzymes in the cell
FALSE
True/ False: a plasmid can give a cell all kinds of additional genes and could make a difference
TRUE
Bacterial Conjugation Steps:
1. donor cell attaches tot a recipient cell with its _____
2. pilus ____________
3. one strange of _____ DNA transfers over to the recipient
4. the recipient synthesizes a ______ strand and the donor synthesizes a ______ strand, restoring its complete plasmid
1. pilus
2. draws the cells together
3. plasmid
4. complementary, complementary
The piece of plasmid DNA is independent of the host chromosome—has an____ ____ _____ and a degree of _____ because it can replicate on its own
origin of replication
autonomy
segments of DNA that move from one location to another in the same or different molecule
transposons
True/False: transposons result in a kind of frameshift insertion
True
True/False: humans have transposons in their genes
TRUE
True/False: transposons can jump from one place to another on a DNA molecule and may replicate while moving resulting in a greater number of transposons in the cell
True
True/False: transposons can jump to plasmids and be transferred to another cell
True
True/False: in transduction, the bacteria and phage contribute sequences
FALSE
ONLY looking at BACTERIAL sequences, the phage doesn't contributed any sequence
presence of the phage establishing lysogeny and contributing a phage gene
Lysogenic conversion
True/False: If a virus infects a bacteria that virus can cause human disease directly
FALSE
it cannot cause human disease
it wont effect us
can cause problems indirectly but not directly
donor cell contributes part of genome to recipient cell
Horizontal Gene Transfer
What are the three types of horizontal gene transfer
Transformation
Transduction
Bacterial Conjugation (associated to pilli)
result of microbial growth on a plate is _____ _____
discrete colony
bacterial production is ______ (asexual)
uni-parental
starts with a single cell--it is asexual
True/False: organisms have enzymes to build and breakdown molecules that they need and it is encoded in their DNA
TRUE
most common nutrients contain necessary elements such as (4):
carbon
oxygen
nitrogen
hydrogen
True/False: Nutrition goes beyond energy for bacteria just like it does for us
TRUE
example: cant survive on sugar alone, does provide energy but doesn’t have necessary nutrients
microbes obtain nutrients from a _____ of sources
VARIETY
two groups of organisms based on source of carbon
autotrophs
heretrophs
self-feeding and make their own sources of carbon
autotrophs
True/False: every autotroph is photosynthetic
FALSE
get their source of carbon from other sources (not themselves)
heterotrophs
two groups of organisms based on source of energy
chemotrophs
phototrophs
organisms that get their source of energy from chemicals
chemotrophs
get their source of energy from light
phototrophs
___ and ____ complementary of each other
____ create sugar and give off oxygen
______ (humans) take in oxygen and eat the sugar and give off CO2 for the autos
heterotrophs, autotrophs
auto
hetero
which chemoheterotrophs participate in aerobic respiration (4)
most animals
fungi
protozoa
many bacteria
which chemoheterotrophs participate in anaerobic respiration (4)
some animals
protozoa
bacteria
archaea
which chemoheterotrophs participate in fermentation
some bacteria
yeasts
archaea
oxygen is essential for _____ _____, but oxygen is deadly for _____ _____
obligate aerobes
obligate anaerobes
Parts of the body with rich anaerobic normal microflora (3)
mouth
GI tract
female genital tract
True/False: We are obligate aerobes but some cells in our body are anaerobic
TRUE
RBC—carry it but don’t use it, are sensitive to O2 but are not equipped to use it
Why are free radicals/ROS very dangerous to obligate anaerobes but not as much to facultative anaerobes?
These are VERY dangerous to obligate anaerobes bc they cannot live with oxygen but are not very dangerous to falcultative anaerobes bc they can live with oxygen if need be
True/False: every part of the human body is saturated with oxygen
FALSE
We have anaerobic bacteria living in us and they need anaerobic conditions
What are the two environments that anaerobic bacteria can live in in our bodies
May be living in an environment present with aerobic bacteria (they are taking in all of the oxygen)
May be living in an environment where the O2 is hidden by something or by a fluid (oxygen has LOW solubility in fluid—must be carried in the RBCs)
True/False: there is a lot of indigenous anaerobic flora in the human body
TRUE
Anaerobic bacteria in the human mouth out number the aerobic bacteria ___:___
10: 1
True/False: Tooth surfaces also have more anaerobic bacteria
TRUE
In the gums, anaerobic bacteria out number the aerobes _____:____
1000: 1
what are the four toxic forms of oxygen and which is the most dangerous?
singlet oxygen
superoxide radicals
peroxide anion
hydroxyl radical (MOST dangerous)
do anaerobes possess superoxide dismutase?
NO! because it catalyzes a reaction that produces oxygen and it will kill them
do anaerobes possess catalase?
NO! because it catalyzes a reaction that produces oxygen and it will kill them
____ ___ is molecular oxygen with electrons that have even boosted to a higher energy state. It is a very reactive oxidizing agent
Singlet oxygen
____ ____ can be formed during the incomplete reduction of O2 during electron transport in aerobic organisms and during metabolism by anaerobes with the presence of oxygen.
___ ___ is a highly creative oxidant. IT is what makes hydrogen peroxide an antimicrobial agent.
Peroxide anion
____ converts peroxide into water and oxygen (safe products)
2H2O2--> 2H2O + O2
catalase
______ breaks down hydrogen peroxide
H2O2 + NADH + H+ --> 2H2O + NAD+
peroxidase
_____ ____ either lack both catalase and peroxidase or have a small amount of them
obligate anaerobes
_____ ____ is a product of ionizing radiation and the incomplete reduction of H2O2 : H2O2 + O- + H+ --> H2O + OH
hydroxyl radical
MOST reactive of the 4 toxic forms of oxygen
in the catalase test what will indicate a positive presences of catalase?
bubbles in the solution--since catalase breaks down H2O2 and produces water and O2 the O2 gas will form bubbles so you know catalase is working
The catalase test is very ____
fast
5 types of bacteria with varying oxygen requirements
Aerobes
Anaerobes
Facultative Anaerobes
Aerotolerant Anaerobes
Microaerophiles--live in about 2-10% oxygen
where are obligate aerobes in a test tube?
towards the top
where are obligate anaerobes in a test tube?
at the bottom
where are facultative anaerobes in a test tube?
throughout but mostly towards the top
where are aerotolerant anaerobes in a test tube?
pretty even throughout but kinda more towards the top
where are microaerophiles in a test tube?
they are scrunched in the middle
for the test tube experiment you cannot use a normal broth, you need to add what?
a reducing agent!
Commonly used: thioglycolate
True/False: aerotolerant anaerobes are strictly anaerobic but oxygen does NOT kill them
TRUE
Facultative anaerobes can go either way but you find more at the top (near more oxygen)—why?
They can use oxygen to grow faster—aerobic metabolism is much more efficient than anaerobic
anabolism often ceases due to insufficient _____
nitrogen
what would be the rate limiting factor in anabolism if you don't have N?
protein! you need protein for life
nitrogen is acquired from ____ and _____ nutrients
organic and inorganic
____ ____ by certain bacteria is essential to life on Earth
nitrogen fixation
Molecules with Nitrogen (3)
amino acids
nucleotides
Hb
If you don’t have N what would be causing more of a problem earlier—Nucleotides or proteins?
Nucleotides because they CODE for the amino acids
the effect of temperature on proteins and can be:
mild
it isn't all or nothing
effect of temperature on lipid-containing membranes of cells and organelles:
if too low:
if too high:
membranes become rigid and fragile
membranes become too fluid
True/False: in thermophiles and hypothermophiles, proteins are not denatured
TRUE
they have a variety of different mechanism that allows them to survive in High T environments
thermophiles and hypothermophiles are mostly ___ not ____ but some can be
archaea
bacteria
______ is a part of growth rate but not the only factor
denaturation
True/False: it doesn't take a lot of temp change to kill the bacteria
True
thats how fever works
How do human bacteria growth on plates in the following temperatures:
22*C--room T
30*C
37*C—body temperature
22*C-- don't grow well
30*C--grow a little bit better, getting closer to body T
37*C--grow the best at body temperature (this is optimal)
bacteria that have peak growth around 10*C
psychrophiles
bacteria that have peak growth around 35*C
mesophiles (found in our body)
bacteria that have peak growth around 65*C
thermophiles
bacteria that have peak growth around 90*C
hyperthermophiles
How do acidity changes affect bacterial proteins and DNA?
the H+ and OH- ratios interfere with hydrogen bonding and in proteins and DNA they have this bonding
grow best in a narrow range around neutral pH
neutrophiles
grow best in acidic habitats (found in yogurt and live in our digestive tracts)
acidophiles
live and grow best in alkaline soils and water
alkalinophiles
Microbes require ____ to dissolve enzymes and nutrients
water
most cells die in the absence of water-- but some cells have walls that retain water such as:
endospores
cysts (an aspiring endospore and found in many organisms)
two physical effects of water
osmotic pressure
hydrostatic pressure
the pressure exerted on a semipermeable membrane by a solution containing solutes that cannot freely cross membrane
osmotic pressure
complex relationships among numerous microorgaisms (could be members of the same species or extend to different species)
Biofilms
adering cells to one another, attaching to a substrate (bottom layer of something), and sequestering nutrients allow bacteria in a biofilm to
develop an extracellular matrix
sensing the population around them--how many other bacteria are present
quorum sensing
a critical number of individuals that need to be present
quorum
why are microorganisms more harmful (successful) as part of a biofilm
they develop partial multi-cellularity and are able to work in a team
comes from feel matter and by collecting it from the environment and growing it you can get information on what type of bacteria is there in the are that you collected and the numbers
Coliform Bacteria
clinical specimens come from
a person
environmental specimens come from
the environment
act of cultivating microorganisms or the microorganisms that are cultivated
culture
a culture with no strangers, what you are culturing is a specific bacteria and nothing else
axenic culture
what would it be good to culture a bacteria that is found in an HIV patient
It would be a good idea to culture a bacteria that is found in an HIV patient because they are so immunocompromised that other things can grow that may not normally grow
to introduce the bacteria to the medium and watch it grow
innoculate
cultures composed of cells arising from a single progenitor
pure cultures
what is a progenitor and how is it termed?
the parent that produces something (the progeny)
it is termed a CFU
what is CFU used to determine?
if something is alive
if it can form a colony, you assume it is dividing so it is alive
How can you check if a CFU is actually alive?
transfer the bacteria and it if grows it is alive
Why are visual or bacterial mass techniques to measure number of bacterial inaccurate
That is not a very accurate way to measure because some bacteria can be dead—may not look a whole lot different (after a while they will but freshly dead they won't) and freshly dead bacteria will still weight as much as much
why is it a good idea to have a flame when you are plating (2)
Easy to pass the loop through it to sterilize it if you need to
The hot air from the flame is rising and it helps minimize things from falling on your plate—less likely for air to fall and microbes to fall with the air (can also do it under a hood—will do the same effect)
___ technique prevents contamination of sterile substances or objects
aseptic (sterile)
two common isolation techniques
streak plates
pour plates
How do you execute the streak-plate method of isolation?
You want to be able to dilute each time
Inoculate one—sterilize loop—streak some of one and make two—sterilize—streak some of three and make four
why do you want to make a dilute colony when doing the streak plate method
Want to make it more dilute so you can look at an individual isolate colony
Why is not having nutrients in agar a good thing?
by not having nutrients it allows you to add what you need to add
if it did you would not know what nutrients are in it and it would be confusing to see what nutrients the bacteria needs
T/F: all media has agar or another gelling agent to it
False: not every media has agar in it– some media are liquid broths—in the pic above the test tubes have liquid broth and things are still growing!– add agar after
Why don’t you fill the container completely up of broth (1 L of broth for a 4 L flask)
The bacteria need oxygen—the 3 L of empty space is full of air for the bacteria
what is serial dilution (pour plate method of isolation)
you start with an initial sample and then add 1 mL of initial sample to 9mL of broth and then add 1ml of that to another 9mL of broth
Add 1 mL of the current solution to a petri dish and add 9 mL of warm agar and mix gently
Take current 10 mL broth and take 1 mL of this and add to another 9 mL broth and then add 1 mL to another petri dish and add warm agar
why have the majority of prokaryotes have not been grown in culture medium?
we haven't gotten around to it or they can't be grown?
why?--we don't know what they need (nutritional requirements) and what they can't tolerate
medium where you know exactly what you are adding to the agar and simply follow the protocol
Defined media (aka minimal media)
what do you use defined media for?
fastidious organisms (requiring very specific things)
a media that we don't know exactly what is in it
example:
complex media
example: ground up yeast, beed or hydrolyzed proteins
when would you use a complex media?
when you want to grow something and you don't care what the nutritional requirements are and you just want to grow the bacteria and want it to work
environment that will select for/against certain species of bacteria and that uses a marker to select
example:
selective media
example: add antibiotic to media to see what is resistant
a medium where anything can grow there (not selective) but that is something that will differentiate what you are looking for
Differential Media
add a reducing factor or heat up the medium before using this type of media
anaerobic media
will cause the gaseous O2 to leave
use this media when you don't want the bacteria to grow, you just want everything to stay the same and stay alive (very minimal media)
transport media
want to say stable while transporting it--if there is growth you will get a distorted profile on the number of bacteria and the type (due to competition)
if you can't culture a bacteria what do you do
they isolate it and then they do PCR to amplify DNA and then try to read from DNA what it might be
If you cant grow a bacteria in culture media there is another way to grow it without using any culture, how?
You can grow it in an animal that the bacteria infects
slant in a tube shows evidence of what?
growth
Durham tube is used for what?
to trap gas which indicates production of gas and growth (or fermentation)
the GasPak is used for what?
to create an anaerobic system and you are trying to remove the oxygen from the system
two special techniques developed for culturing microorganisms
animal and cell culture
low-oxygen culture
in a candle jar what bacteria are you trying to an environment for?
capnophiles (CO2 loving)
what is a way to preserve cultures for a short period of time
refrigeration
temptures:
Room T:
Body T:
Refrigerator:
Room T: low to mid 20s (22-25*C)
Body T: 37*C
Refrigerator: 4*C (40*F)
preservation method that stores culture for years but must have certain chemicals in the dish before you do this
deep-freezing
what chemicals need to be added before deep-freezing
glycerol is often used (this prevents it being frozen solid and it will be like a slurry)
a way of preserving bacteria that is known as freeze drying and stores things for decades
lyophilization
what is a problem with freezing and defrosting?
ice crystals can mess up the viability of the cells
can't talk about this with bacteria because they have NO nucleus
fusion turns ____ bacteria into ____
2
1
fission turns ___ bacteria into ____
1
2
True/False: bacteria undergo mitosis
FALSE
Don’t talk about mitosis with bacteria bc it is a part of the cell cycle and bacterial do NOT have a cell cycle
what is the difference between logarithmic ad arithmetic growth
logarithmic is multiplying by 2--doubling
arithmetic--adding 2
2^10=
2^20=
2^30=
2^40=
2^10= ~ 1000
2^20= ~1 million
2^30= ~ 1 billion
2^40= ~1 trillion
time required for a bacterial cell to grow and divide and is dependent on chemical and physical conditions
generation time
what are the two chemical and physical conditions in which generation time is dependet
biochemical
genetics of the bacteria
5 direct methods for measuring microbial reproduction
serial dilution and viable plate counts
membrane filtration
most probably number
microscopic counts
electron encounters
indirect methods of microbial growth (3)
metabolic activity--creation of CO2 or utilization of O2
dry weight--dry bacteria on a filter
turbidity--cloudiness=growth of bacteria
what can be used to quantify the amount of bacteria based on turbidity?
spectrophotometer
True/False: the numbers that come from a spectrophotometer are the number of bacteria present
FALSE!
the numbers themselves don't mean anything unless you can compare it to other empirical results
LOOK AT THE DIRECT METHODS OF MEASURING BACTERIA IN NOTES
DONE
genetic methods of measuring microbial growth include
isolating DNA sequence of unculturable prokaryotes and use to estimate the number of these microbes
phase where bacteria is synthesizing what it needs for reproduction (ribosomes, nucleic acid, enzymes, ATP)
Very little to no growth
lag phase
where will the lag phase be longer: nutrient rich media or a nutrient poor media
nutrient poor media because it needs to synthesize more things itself--in a nutrient rich media the things they need are in the media
phase where there is exponential growth in numbers (NOT SIZE)
log phase
phase where bacteria stop growth and die
stationary phase
why do bacteria die during the stationary phase (2)
lack of resources (space, oxygen, nutrients)
waste build up from dying bacteria (more bacteria, more waste)--includes CO2 (unless they are capnophiles) and acidity--when bacteria die both of these seep from the bacterial carcass
what is a way to prevent death in the stationary phase?
use a chemostat--it will take away the waste and provide fresh media (nutrients)
how to some bacteria get out of dying in the stationary phase (2)
they form spores
they produce antibiotics and can fend themselves against other bacteria and out survive
why is the stationary phase flatjQuery110106855092255864292_1509366932754
the death rate is balancing the growth rate so no net growth or death--it is flat
phase where the number of bacteria decline
death (decline) phase
True/False: the death phase is exponential
TRUE
two indicators of growth in a flask (physical)
turbidity
foul smell
true/false: after bacteria growth a lot bacteria will be dead so you need to filter them out
TRUE
how?
with a centrifuge or a filter
what is the chemical that is needed by organisms and is found in ATP, DNA and RNA
phosphorus
a chemical that is required that is found in cysteine, methionine, and di-sulfide bonds
sulfur
True/False: We require a tiny amount of trace elements—too many can be toxic
True!!
we need some, but too much are very toxic to us
necessary organic chemicals that cannot be synthesized by certain organisms
growth factors
True/False: humans get their growth factors from the environment
FALSE
we do not need them from the environment
True/False: in most bacteria, growth factors must come from the environment
TRUE
what is an example of a bacteria that doesn't require growth factors
E. Coli
what is an example of a bacteria synthesizing a vitamin growth factor
synthesis of folic acid from forming
certain antibiotics: sulfadrugs in bacteria and methotrexate in humans inhibit this formation and therefore kill the bacteria (or cancerous cells)
T/F: Some bacteria must import growth factors and others can make it but depends on the vitamin and the bacteria
True
what is an example of growth factors that humans can't make and must take in from the environment
essential amino acids (essential in the diet)
Growth factors depend on the bacteria we are looking at but could include (4)