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Microbio > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

Define growth in microbio

A

Growing of cell

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2
Q

Define replication/multiplication in microbio

A

Growing in numbers

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3
Q

Describe what binary fission is

A

This process is how cells replicate
- no genetic variability

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4
Q

What are the steps in binary fission

A
  1. Cell growth: this increase in size will initiate the replication cycle where DNA will replicate
    - ideal conditions need to be met to multiply
  2. DNA replication
    - initiates septation
  3. Septation: proteins accumulate which tells cell where they will septate into progeny cells
  4. Cytokinesis: process where 2 cells separate to give us the progeny cells

Result: 2 identical cells

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5
Q

What is the problem with binary fission

A

Little opportunity for genetic variability hen they’re reproducing because they’re making exact copies of themselves

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6
Q

How do microbes reproduce

A

Asexual reproduction
- by themselves (no partner)

Need:
- proper environment conditions
- proper food

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7
Q

What occurs during step 2 in DNA replication

A

Origin:
Where replication of DNA chromosome begins (particular DNA sequence that tells cell where to initiate)
- only have 1 origin (simple process)
- eukaryote and archaea have multiple

Replication forks:
Replication proceeds in both directions

Termination of replication:
Process of replication has more fidelity than eukaryotes replicate their DNA
- ends are not replicated in linear DNA (lose some sequence when replicating)

Results:
2 copies of that chromosome with semi-conservative replication

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8
Q

Describe replisome

A

4 DNA polymerase = 2 replication forks

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9
Q

How fast do replisomes act

A

Happens so fast that as soon as replisome leaves the point of origin, another 1 goes in and continues
- haven’t finished replicating and already started the process again

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10
Q

Describe what septation is

A

Imitated by DNA replication and separation
- tell cell it’s time to create 2 progeny cells

Determined by FtsZ
- cytoskeleton protein
- important in determining shape of cocci cells
- important for all bacterial cells in the septation process

Location may vary
- know where to separate
- don’t divide in the middle for all cells

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11
Q

Describe exponential growth

A

Every time they replicate, getting 2 more cells
- doubling the number of cells every time

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12
Q

Why aren’t we swimming in bacteria

A

Not enough resources to sustain exponential growth

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13
Q

Define generation (doubling time)

A

Time required for population to double in size
- quantify how long or fast they can multiply into a new generation

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14
Q

Describe growth in lab under ideal conditions

A

Different from growth in nature/person
- slower

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15
Q

What does growth time affect

A

Growth time affects how effective antibiotics will be
- work best when bacteria is actively dividing

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16
Q

Describe 3 factors that microbes need to grow in the lab

A

Culture media

Nutrition
- macro/micronutrients
- growth factors

Abiotic (environmental) factors
- permissive growth temp
- pH, pressure, and osmotic balance
- oxygen
*control environmental factors

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17
Q

Why do we add growth factors

A

Add something special for microbes to grow

Add for the picky eaters
- specific nutrients for them to grow

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18
Q

What can the culture media be classified via

A

State of matter

Ingredients

Function

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19
Q

What causes the changes in state of matter in culture media

A

Percent of agar

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20
Q

Why do we use liquid culture media

A

Study growth patterns of pure cultures

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21
Q

Why do we use solid culture media

A

Isolate pure cultures

Quantify CFU

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22
Q

Why do we use semi-solid culture media

A

Study motility

Oxygen relationships
- diff microbes prefer different concentration

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23
Q

Who is Fannie Hesse

A

1882

Gave the idea to use agar as solidifying agent for media
- reasons why we can make pure cultures

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24
Q

Define chemically defined media

A

Know exactly how many moles of every element in the media
- each chemical component in detail

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25
Q

Define complex media

A

Don’t know exactly to the mole
Each batch is different

  • beef broth
  • yeast extract
  • brain heart infusion (bhi)
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26
Q

Define all purpose media

A

Let all microbes that can grow on the plate grow
- all species grow

All species have a similar appearance

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27
Q

Define selective medium

A

One species grows
- inhibit growth of some microbes and allow growth of others

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28
Q

Define differential medium

A

All 3 species grow but may show different reactions
- colonies will grow in different colors/appearances (identify different types of metabolisms)

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29
Q

Can selective medium also be differential medium

A

Can be both

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30
Q

Is the bacterial growth curve

A

Only happens when we grow bacteria in a lab, in a test tube, in a broth

  1. Lag phase
  2. Exponential phase
  3. Stationary phase
  4. Death phase
  • doesn’t happen in nature bc not enough resources to see this
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31
Q

Describe lag phase

A

Few cells are added to broth
No growth
Adapting to new environment
Activating necessary genes to consume available nutrients

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32
Q

Describe exponential growth phase

A

Cells at most uniform

Once they adapt, huge increase in growth that is almost linear

Bacteria living best life and happy
- multiplying really fast

Bacteria are even, doing same thing, expressing the same gene
- optimal phase for experiments

Antibiotics work best here

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33
Q

Describe stationary phase

A

Nutrient limitation

Limited oxygen available

Waste accumulation

Critical population density reached
- bacteria growth slows down, growth and death even out

Not even, not expressing all the same genes

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34
Q

Describe death phase

A

Some cells remain viable

So much waste accumulating
- acid is building up (acid is the waste product)

pH is dropping dramatically which is killing them

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35
Q

Practical importance of the growth curve

A
  1. Lag
    - microbe is multiplying, no symptoms
  2. Exponential
    - number of microbe is high enough to cause damage
    - start to feel “off”, not terrible
  3. Stag
    - highest number of microbes
    - feel it the worst, go to doctors
  4. Death
    - antibiotics/immune system kick in
    - start to feel better
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36
Q

What does length of the growth curve depend on

A

Pathogen and host

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37
Q

Define sequelae

A

Long term affect of damage

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38
Q

What are actively growing cells more vulnerable to

A

Conditions that disrupt cell metabolism and binary fission

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39
Q

What two aspects does binary fission need to happen

A

Nutrients

Environment

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40
Q

Describe the nutrients needed

A

Macronutrients
- chonps (organic or inorganic)
- growth factors

Micronutrients
- trace elements

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41
Q

What are the environmental factors affecting microbial growth

A

Temperature, pH, gases (o2 and co2), osmolarity (water avail), light, pressure, and radiation

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42
Q

Describe minimum, optimum, and maximum

A

Minimum: bacteria are barely holding on

Optimum: ideal living conditions, bacteria prefer this, bacteria are growing the best/fastest

Maximum: bacteria are barely holding on

Closer to optimum, bacterial living conditions are getting better

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43
Q

What are the groups for pH

A

Acidophile
- acid
- optimum is 3
- extremohpile

Neutrophile
- likely pH group for pathogenic microbe
- our body has a neutral pH
- optimum 7-7.5

Alkaliphile
- basic
- optimum 9.5
- extremophile

44
Q

When do we called microbes extremophiles

A

Anything outside our (human body) range

45
Q

Describe extreme pH locations

A

Rivers affected by acid mine drainage
- high heat
- acidophile

Soda lakes
- occur naturally throughout the world, typically in aids and semi-arid areas
- alkaliphile

46
Q

Describe adaptations to extreme pH

A

Maintain an internal pH near neutrality (cytoplasm)
- plasma membrane is impermeable to protons

Pump protons out/in of the cell
- transport proteins are essential to this
- to maintain the pH of the environment

Producing acidic or basic waste products
- this modifies their immediate environment

Proteins active at low or high pH

Some use chaperone proteins
- keep proteins functional for the cell
- secreted proteins need to tolerate the extreme pH and do this by using particular amino acid sequences in their proteins

47
Q

What is our body’s pH on average?

A

7.5

48
Q

What are the groups for temperature

A

Psychrophiles
- ice
- 8-10

Psychotolerants (some of this can be pathogenic)
- fridge
- 20

Mesophiles (only these can be pathogenic)
- humans/ mammals
- 37

Thermophiles
- hot springs, geysers
- 60

Hyperthermophiles
- acid mine drainage
- 90-100

49
Q

Describe adaptations of thermophiles

A

Protein structure is stabilized by a variety of means (and protein sequence need to protect to prevent protein denaturation )
- more H bonds
- more proline (r groups look like a hook, maintain bends in proteins without having desaturation happen)
- chaperones (proteins that help proteins resold back to the original configuration)

Histone- like proteins stabilize DNA (Histones help refold DNA so it’s compacted inside the cell)

Membrane stabilized by a variety of means (become extreme,y fluid under high heat)
- more saturated, more branched, and longer lipids (help maintain proper fluidity at high temp)
- ether linkages

50
Q

Describe osmolarity

A

Isotonic
- ideal
- equilibrium between what’s outside the cell and inside the cell

Hypertonic
- more solute out than in
- water moves out
- cell shrivels up
(cure meats, preserve meat by adding a bunch of salt, creating this environment and killing them)

Hypotonic
- more solute in than out
- water moves in
- cell wall protects cell from osmolysis
- cell is okay here

51
Q

What are the three groups of osmolarity

A

Halotolerant
- no definitive peak
- 1

Halophile
- .2M

Extreme Halophile
- 3.5M

52
Q

Describe the osmophile adaptations

A
  1. Accumulate K and Cl in the cytoplasm
  2. Keep salt ions outside of the cell
  • 1&2 moving protons in and out of cell is key to microbe survival
  1. Synthesize compatible solutes that do not interfere with growth
    - produce molecules that serve as solutes to maintain that balance to the solid conc. I’m and out of cell
53
Q

What are “normal” growth conditions

A
  • temp 20-40 C
  • near neutral pH
  • sea level
  • isotonic/hypotonic
  • ample nutrients

*pathogenic microbe needs to meet the criteria, all of it

54
Q

Describe oxygen and growth

A

Has the greatest impact on microbial growth
- oxygen can become a toxic product inside cells and cause damage, damaging proteins, DNA, and membranes
- use oxygen to generate ATP

Microbes fall into one of the three categories
- those that use oxygen and can detoxify it
- those that do not use oxygen but can detoxify it
- those that can neither use oxygen nor detoxify it

55
Q

What are the toxic oxygen byproducts

A

Oxygen
Superoxide anion
Peroxide
Hydrogen peroxide
Hydroxyl radical
Hydroxyl ion

56
Q

What are the two enzymes used to remove toxic oxygen

A

Superoxide dismutase

Catalase

57
Q

Which microbes use oxygen and can detoxify it

A

Obligate areobe
- strict aerobe
- only grow at top of tube b/c this is where O2 is present
- can detoxify byproducts

Facultative anaerobe
- optional anaerobe
- grow in presence or absence of oxygen
- prefers to grow with oxygen present (more at top, but turbidity throughout)

Microaerophile
- little bit of oxygen needed to grow
- towards topish/middle
- have 1 enzyme or the other, can’t completely detoxify

58
Q

Do not use oxygen but can detoxify it

A

Aerotolerant
- tolerate oxygen but don’t need it
- turbid throughout is equal
- 1 enzyme

59
Q

Cannot use oxygen nor detoxify it

A

Strict anaerobe
- obligate anaerobe
- only at bottom where oxygen is absent
- no enzymes, can’t detoxify it

60
Q

Describe the growth of microbes in the lab

A

Microbes in nature exist in complex, multi species communities
- diverse communities

Pure culture for detailed studies
- this is artificial, done in lab

We have succeeded in culturing less than 1%
- plate shows less than 1%

61
Q

Define great plate count anomaly

A

the difference in abundance between the numbers of cells from natural environments that form colonies on agar media and the numbers countable by pure cultures

Microscope = saw tons of bacterial cells
Petri dish = 1 colony when placed in a Petri dish

62
Q

Why does the great plate count anomaly happen

A

Living cells
- some

Dead cells
- some

Viable but not culturable cells (VNBC)
- alive, but not growing in media that they are in

63
Q

Why does VNBC happen?

A

Competition
- some eat faster than others (leave no nutrients for others)

Stress
- changing environment is too much (switch from soil to media is stressful)

Siderophores
- taking up all the iron (none left for others)
- too much iron kills cells (can’t add more)

Cooperativism & Mutualism
- need to be together to grow, if 1 doesn’t grow, other won’t either

Predation
- eat other microbes

Antagonism
- create antibiotics

64
Q

Describe what is needed for biofilms and what they are

A

Community behavior

Components:
1. Microbes (any microbe can be part of biofilm)
2. Surface (for attachment, top of water, medical devices)
3. “Slime” - Extra Polymeric Substance
- glycocalyx (secreted by microbes, slime provides microbes protection)
- DNA (found dead microbes)
- proteins (found dead microbes)
- organic and inorganic compounds

  • once slime is produced, the biofilm is forever
  • really important virulence factors
  • help attach to surfaces, spread to other areas, and evade/escape our immune system
65
Q

Describe the development of biofilm

A
  1. Primary adhesion
    - pioneer bacteria fall and attach to surfaces via weak bonds
    - reversible (electrostatic and hydrophobic interactions)
    - this is the only step where we can prevent biofilm from forming
  2. Secondary adhesion
    - irreversible, mediated by appendages (pili, fimbriae, flagella)
    - used to attach to surface, once this happens, game over
  3. Pioneer bacteria is going to start multiplying, dividing, and start producing that slime in the surface
    - quorum sensing
  4. Mature biofilm, microbes play diff roles
    - quorum sensing
    - diffusion of nutrients
  5. Dispersal, chunks break off and spread out to initiate new biofilm
66
Q

Define quorum sensing

A

Definition: Bacterial communication via secreted small molecules

Function: Coordinate behaviors at high populations
- differential gene expression
- conjugation (happening a lot in biofilm, genetic variability)
- production of virulence factors
* production of bioluminescence

67
Q

Describe mature biofilm

A

Complex, heterogenous and dynamic community

Differences in gene expression, metabolic activity, and locations of microbes
- bc of quorum sensing

Interactions occur among the attached organisms

  • nutrient gradient: border of film is going to receive more nutrients than the middle
  • cells closer to border are multiplying faster
  • antibiotics will be more effective at border bc they are multiplying compared to middle
  • slime has - charge, anything we add that has + charge will not penetrate and just become a part of the biofilm
  • get trapped with electrostatic forces
  • unlikely to penetrate all the way to bottom
68
Q

Describe the benefit for microbes in biofilm

A

Protection from
-UV
- predation
- antibiotics
- Chimal treatments

Organization

Cooperation (synotropy)
- metabolic
- attachment
- more efficient at using whatever little nutrient is found
- take advantage of the little bit of nutrient that’s available

69
Q

What is the relationship between gum disease and heart disease

A

Correlation between gum disease and heart disease
Dental plaque -> gets into circulatory system -> heart disease

70
Q

List the beneficial biofilms

A

Human microbiota
- providing protection from other diseases
- digest food
- helps our behavior

Waste water treatment facilities
- remove organic material to clean water for reuse

Aquariums (biological filter)

Biogeochemical cycles

71
Q

Why are we all the same

A

A lot of evidence that suggests all living organisms come from one cell
- phylogenetic tree

Can use DNA sequences to observe that we have a common ancestor

At basic level, we are all the same bc we are made out of cells that have the have the same chemical structure

All cells do central dogma

72
Q

Explain similarities within central dogma

A

Although the central dogma is universal in all cells, the processes of replication, transcription, and translation differs in bacteria, archaea, and eukaryotes
* all cells do all of this, but do it differently

73
Q

Differences in the organization and structure of DNA between eukaryotes and prokaryotes

A

Eukaryotes
- chromosomes = linear, and way more
- nucleus = store DNA, protects it from other processes

Prokaryotes
- chromosomes = circular, much smaller and much less, DNA in cytoplasm (no compartmentalization of DNA sequence)
- plasmids = fairly unique, replicate independently, small circular pieces of DNA

74
Q

Differences in the DNA replication across domains

A

Bacteria
- 1-2 chromosome
1 origin per chromosome

Archaea
- 1-2 chromosomes
- 2-4 origins on each chromosome (many)

Eukaryotes
- many chromosomes
- tens of thousands of origins (many)

75
Q

Describe the relationship of DNA replication and antibiotics

A

A process that is unique to bacteria gives us a beautiful target for an antibiotic
- selectively toxic

Cell wall
- blocks production of peptidoglycan, inhibiting cell wall biosynthesis

DNA synthesis
- inhibits DNA synthesis, blocking cell replication
- targets enzymes in DNA replication

RNA synthesis
- blocks transcription

Ribosomes
- binds to 70s ribosome, blocking protein synthesis

Metabolic pathways
- compete with bacterial metabolic enzymes, stops synthesis of production

76
Q

How are species defined in biology and why is this hard for bacteria

A

2 organisms that can produce and have fertile progeny
- requires sexual reproduction which microbes do not do

Problems:
- Microbes exchange DNA with other microbes
- Using different genes to sequence

77
Q

How do bacterial gain genetic variation

A

Sexual reproduction and recombination (wrong)

Spontaneous mutations (happens randomly)
- errors during RNA replication (low frequency)
- transposons

Horizontal gene transfer

78
Q

Describe transposons

A

Discovered by Barbara McClintock

Piece of DNA that jumps from one part of the chromosome to another

Mobile genetic elements or jumping genes
- if inside the transposon we have a new gene, bacteria will gain a new piece of DNA in that process

79
Q

Describe mutations

A

DNA replication mistakes
- frequency of mutation in bacteria is 10^5 to 10^9 through pure culture

Won’t see change in 1st generation

See change in second generation
- 3:1 ratio (few will have mutation, majority will be wt)
- fosters antibiotic resistance

80
Q

Describe horizontal gene transfer in terms of genetic variability

A

Not parent to progeny (vertical gene transfer)

Prokaryotes are very promiscuous
- side to side

Traditional concept of species is not readily application to microbes due to asexual reproduction and the frequent occurrence of horizontal gene transfer

81
Q

Name three ways horizontal gene transfer can occur

A

Transformation

Conjugation

Transduction

82
Q

Describe transformation of free DNA

A

Observed by the Griffith experiment (1928)
- proved DNA carries the genetic info for organisms
- showed transformation

Defined: bacteria can take up that free/naked DNA and incorporate it into their genome
- free dna can be a fragment or a plasmid

83
Q

Describe transformation with dna fragment

A

Cannot self replicate
- integrate into the chromosome through homologous recombination or it will be degraded
- less chance to be incorporated bc if it doesn’t recombine to the chromosome, doesn’t have ability to self replicate

84
Q

Describe transformation with plasmid

A

All plasmid just need to replicate
- plasmids self replicate

85
Q

What is a requirement that bacteria need up free DNA

A

Bacteria must be competent to take up free DNA
- not all bacteria are naturally competent

86
Q

Describe conjugation in terms of genetic variability

A

Requires physical contact

One of the cells have to encode for genes for a pilus
- bacteria can only pass DNA to bacteria that has no pilus, but needs a pilus to pass DNA

Happens all the time, esp in biofilm

Plasmids are easily passed bc they’re small, chromosomes will be harder bc it’s longer

87
Q

What are the two groups in transduction

A

Generalized (lytic cycle)

Specialized (lysogenic cycle)

88
Q

What is a phage

A

Viruses that specifically infect bacteria

Aka bacteriophages

Only infect bacteria, not other organisms

89
Q

What is the general transduction lytic cycle

A
  1. Bacteriophage attaches to cell
  2. Phage deposits viral dna in cell
  3. Cell becomes a factory for virus, makes the components
  4. Cell assembles components, packages bacterial dna
  5. Cell explodes, releases virus that has bacterial dna from other cell and deposits it
  6. Integrated via homologous recombination
90
Q

Describe generalized transduction lytic cycle

A

High risk, high reward

Any random piece of bacterial DNA gets packaged

Some viruses take up bacteria instead of phage DNA

No viral infection, so cell doesn’t die, and gains new bacterial DNA

91
Q

Describe specialized transduction lysogenic cycle

A

Phage dna gets integrated into bacterial DNA

Homologous recombination (aka prophage)
- have phage DNA in chromosome of bacteria
- can live like this forever, multiplying

Piece of phage DNA gets cut out, so,e chromosomal DNA gets accidentally cut

Every single progeny of the virus will have that phage and bacterial DNA packaged inside
- infect other bacteria and go through lysogenic cycle (gain phage dna and bacterial dna)

92
Q

Who found out about transduction

A

Esther Lederberg

93
Q

Why do we use DNA replication machinery as a target for antibiotics?

A

Bacteria has a unique process compared to eukaryotes

94
Q

What’s another word for transcription and what does it signal

A

Gene expression

When to express certain genes

95
Q

Compare central dogma in archaea to central dogma in eukaryotes and bacteria

A

Similar to bacteria
- 1-2 circular chromosomes
- organization of genes similar to bacteria
- may have plasmids
- all in cytoplasm
- translation process more like bacteria
- 70s ribosomes

Similar to eukaryotes
- 2-4 origins of replication
- dna replication and transcription processes (polymerases, transcriptional factors, introns, promoter sequences)
* enzymes in dna replication and transcription are more similar to eukaryotes

96
Q

What is the gene organization in prokaryotes

A

1 promoter for multiple genes
- unique to bacteria
- eukaryotes have 1 pro,other for 1 gene

Need these genes at the same time, makes sense to do transcription once

1 long mRNA sequence that has 3 different proteins aka polystronic mRNA
- Results in three separate proteins

97
Q

Compare where central dogma happens in bacteria and eukarya

A

Eukaryotes
- DNA replication and transcription happen in nucleus
- processes so it doesn’t get degraded when leaves the nucleus

Bacteria:
- transcription, translation, and dna replication happen at the same time and place
- no processing so no degradation worries
- protein synthesis happens faster (time not number)

98
Q

What influences gene expression

A

External and internal molecular cues and/or signals

99
Q

Define constituye genes

A

Genes that are always on because they need these to survive

100
Q

Define inducicble genes and reprensible genes

A

Genes that are turned on

Genes that are turned off

*ways cells regulate which genes are expressed

101
Q

Define promoter

A

DNA sequence that tells cell when to transcribe the gene next to it
-promoter is not transcribed

Prokaryotes: promoter is right next to the gene
Eukaryotes: promoter is far from gene

102
Q

Define gene

A

Encode for the protein

103
Q

Define induced and corepressor

A

Both molecules

Inducer: signal to tell cell to express a gene
Co-repressor: signal ti tell cell not to express a gene

Can come from environment or inside the cell

104
Q

Define transcriptional regulator; activator and repressor

A

Protein

Transcriptional activator: binds to activating site, help rna polymerase

Transcriptional repressor: binds to operator, inhibit the rna polymerase

RNA polymerase can’t transcribe genes on its own

105
Q

Describe process of gene regulation

A

Gene regulation: when to transcribe and when not to transcribe

More mrna -> inducer -> transcriptional activator or repressor

Less mrna -> co repressor -> transcriptional activator or repressor

106
Q

Describe quorum sensing part 2

A

Take census of how many of them are around to coordinate behavior
- need many to be harmful to us

*regulation of gene expression based on population density
- virulence factors
- conjugation
- sporulation
- bioluminescence

Microbio (4 decks)

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