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Exam 2 Flashcards

1
Q

Steps for binary fission

A

1.a cell at ealry phase of cycle
2.a cell prepares for division by enlarging it cell wall plasma membrane and overall volume DNA replication starts
3.the septum grows inward as the chromosomes move toward opposite ends of the cell other cytoplasmic components are ditributed to the two daughter cells.
4.the septum is synthesized completely throught the cell center creating two seperate cells
5. at this point the cells are divdied and some species completely seperate while some remain attached with lots of varitety.

quick summary
cell growth
DNA replication( semi conserv)
cytokinesis

this is not mitosis

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2
Q

Where does replication starts and end for bacteria?

A

-origin (ori)
-terminus

ori and terminus are away from each other

visually the nucleoid has a lose strand that contains the terminus

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3
Q

In a replisome what is involved

A

4 DNA polymerases
addition of daughter strand in the 3’ end
synthesis occurs in 5’-3’

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4
Q

Cytokinesis or Septation

A

Determine by FtsZ
location may vary

not all bacteria split right down the middle

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5
Q

Doubling time

A

-Generation time required for the population to double in size

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6
Q

how does doubling time lead to exponential growth

A

growth occurs via a log base 2 growth per generation bacteria can grow up to 32 cells after 5 generations.

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7
Q

Chemicaly defined media

A

Media when we know the exact mols of each chemical componet present

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8
Q

complex media

A

-beef broth
-yeast extract
-brain heart infusion (BHI)

we dont have exact control of mol of each componet

these broths are more nutrious

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9
Q

Growing microbes in the lab

A
  • Culture media
    Nutrition
    Macro/micronutrients
    Growth factors
  • Abiotic (environmental) factors
    Permissive growth temperature
    pH, pressure, and osmotic balance
    Oxygen
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10
Q

Culture media classifications

A

-state of matter
-ingredients (chem or complex)
-function

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11
Q

States of matter of media

A

Liquid: study growth patters of pure cultures
solid media: isolate pure cultures and quantify CFU
semi-solid: study motility and oxygen relationships

Fannie Hesse 1882: added agar to plates

state matter is dictated by the precense of agar content

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12
Q

Differential media vs Selective media

A

-Differential medium all 3 species grow but may show different reactions
-Selective medium one species grows

gen purpose diff -all species have similar apperance
gen purpose selc- all species grow

if something does not grow its selective

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13
Q

Bacterial Growth Curve

A

Lag Phase- Adapting to enviroment
Exponetial Growth Phase (log phase)-All bacteria is engaging in binary fission ( most uniform state)
Stationary phase- the start to run out of nutriets, oxygen and accumulation of waste product( acid waste lowering the pH) the rate of death is equal to replication
Death Phase- most cell will die as enviroment is no longer ideal but few cell may remain.

antibiotics work best when cells are dividing at log phase

antibiotics arent ideal in stationary phase as they turn on survival genes

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14
Q

Practical importance of the growth Curve

A
  • Cells express different genes at the
    different stages.
  • Actively growing cells are more
    vulnerable to conditions that disrupt
    cell metabolism and binary fission.
  • Growth patterns can correspond
    with the stages of infection.
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15
Q

Nutrients for microorganisms

A

-Macronutrients
CHONPS
Organic or Inorganic
growth factors
-Micronnutrients
trace elements

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16
Q

What are factors that affect microbial growth

A

tempature
pH
gases( O2/CO2)
Osmolarity( water avail.)
Light
Pressure
Radiation

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17
Q

Normal Growth Condition ( what humans like)

A
  • Temp 20-40 C
  • neutral pH
  • sea level
  • isotonic/hypotonic
  • ampel nutrients

anything outside these ranges are considered extremophiles

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18
Q

pH groups of microbes at optimum

A

acidophile pH 3
neutrophile pH 7
alkaliphile pH 10

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19
Q

What do extreme pH enviorments look like.

A
  • Rivers affected by acid mine
    drainage, pH as low as -3.4
  • Soda lakes, pH range from 9-12.
  • Soda lakes occur naturally
    throughout the world, typically in
    arid and semi-arid areas
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20
Q

How do microbes adapt to extreme pH changes?

A
  • Most microbes maintain an internal pH near neutrality
    -the plasma membrane is impermeable to protons
  • Pump protons out/in of the cell
  • Producing acidic or basic waste products
  • Proteins active at low or high pH
  • Some use chaperone proteins
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21
Q

tempature groups of microbes at optimum

A

Psychrophiles ( 10 C ) artic
psychrotolerants ( 20 C) fridge not as extreme
mesophiles ( 37 C) at ricky martin temp
thermophiles ( 60 C)
hyperthermophiles (100 C)

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22
Q

What does adaptations in thermophiles look like.

A

Protein structure is stabilized by a variety of means
* e.g., more H bonds
* e.g., more proline
* e.g., chaperones

Histone-like proteins stabilize DNA

Membrane stabilized by a variety of means
* e.g., more saturated, more branched, and longer lipids
* e.g., ether linkages

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23
Q

Osmophiles

A

Adaptations:
* Accumulate K and Cl in the
cytoplasm.
* Keep salt ions outside of the
cell.
* Synthesize compatible
solutes that do not interfere
with growth.

Halotolerant ( 1M of NaCl)
Halophile (2 M of NaCl)
Exteme Halophiles ( 5M of NaCl)

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24
Q

Oxygen and Growth

A

Has the greatest impact on
microbial growth

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

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25
Use oxygen and detoxify
- Obligate aerobe - Faculatative anerobe - microaerophile
26
Obligate aerobe
These guys need oxygen to make energy, They tend to grow in areas near oxygen. They will have the enzymes SOD and Catalase
27
Faculatative Anerobe
Can grow if oxygen is around to make energy but if there is no oxygen can figure out ways to grow without it. It does prefer to have the oxygen. It does have the enzymes SOD and Catalase. In test tube frow all over it but slighlty more conc. in the top for oxygen
28
microaerophile
These guys need a little bit of oxygen to grow. They cannot grow in the absnece of oxygen. But they also dont have all the enzymes to detoxify the oxygen. Meaning they will remain in areas with low oxygen conc. as they need it but only a bit. Have SOD but low levels of Catalase
29
Do not use oxygen but can detoxify it
- Aerotolerant anaerobe these guys dont need oxygen to produce energy they can surive with out it but have the enzymes SOD and catalase which allows them to detoxify it. They will grow in equal portions of the test tube as they dont care for oxygen conc.
30
Cannot use oxygen and Cannot detoxify it
- strict anaerobe these are guys that cannot use oxygen to make energy but at the same time they lack the enzymes of SOD and Catalase. they tend to grow at the bottom of the test tube.
31
Describe the great count anomlay.
* Microbes in nature exist in complex, multispecies communities * Pure culture for detailed studies * We have succeeded in culturing < 1% * when looking at an enviromental sample we have tons of bactereia growing but trying to grow this in a petri dish not all cell will grow.
32
Explain why most microbes cannot be cultured in the lab
* some cells will be dead. * some cell that are living but there are a chunk of them that are viable but not culturable cells * This all comes down to their nutrional needs temp,pH , gases , osmolarity , nutrients (these factors fluctuate heavily in their enviroments) * Stress such as oxidative stess ( free radicals) * Competition for nutrients with other microbes * Cooperativism mutualism ( microbes need other microbes to grow) * predation ( microbes that will eat other microbes * Antagonism ( one microbes produces a chemical that inhibts another microbes growth
33
Define biofilms and their componets
-Community behavior that provide protection Components * Microbes * Surface * ”Slime” – Extra polymeric substance (EPS)  Glycocalyx  DNA  Proteins  Organic and inorganic compounds
34
Biofilm development
1. Primary adhesion * Reversible - electrostatic and hydrophobic interactions 2. Secondary Adhesion Irreversible - Mediated by appendages * Pili * Fimbriae * Flagella 3. Pioneers secrete extracelluar material that helps keep them on the surface as attachment point for later colonizers quorum-sensing chemical are released by bacteria 4. In many but not all biofilms other speceis join and may contribute to the extracelluar matrix and /or particpate in quorum sensing with their own chemicals or ones released by other species
35
Recall the role of quorum sensing
* Bacterial communication via secreted small molecules * Coordinate behaviors at high populations -Differential gene expression -Conjugation -Production of virulence factors - Dispersal can occur once the biofilm has grown large enough which leads to spreading of this biofilm. | Big lego city
36
Explain the complexity of mature biofilm
* Complex, heterogeneous, and dynamic community * Differences in gene expression, metabolic activity, and locations of microbes * Interactions occur among the attached organisms
37
benefits for microbes due to biofilm
Protection * UV * Predation * Antibiotics * Chemical treatments Organization Cooperation (syntropy) * Metabolic * Attachment
38
Biofilms and Health
Negative Health Impacts - Catheter contaminaiton - gum disease - implant contamination - bacteria rendering Beneficial Biofilms * Human Microbiota * Waste Water Treatment Facilities * Aquariums (Biological Filter) * Biogeochemical cycles
39
Describe how DNA is orgnaized within a prokaryotic cell?
-1-2 Chromosomes -shape is circular -DNA resides within the Cytoplasm -Additionaly pieces of DNA plasmids -Central Dogma followed with some variation -Have one ORI site | EUK have many ORI sites due to length
40
Central Dogma in Archae
1-2 circular chromosomes * 2-4 origins of replication Organization of genes similar to bacteria May have plasmids All in cytoplasm DNA replication and transcription processes * Polymerases * Transcriptional factors * Introns * Promoter sequences | Proteins are more like EUK proteins ## Footnote Bacteria dont have introns,
41
Understand how "prokaryoties gain genetic variability
Spontaneous mutations- - DNA replication mistakes every 10^5 - 10^9 Low frequency - Transpoons-Mobile Genetic elements or Jumping genes - Horizontal Gene Trasnfer ( most variability comes from here) ## Footnote Transpoons can move with in genome or movement to plasmid
42
HGT
* Not parent to progeny * Prokaryotes very promiscuous * The traditional concept of species is not readily applicable to microbes due to asexual reproduction and the frequent occurrence of horizontal gene transfer.
43
Different methods of HGT
Transformation- DNA picked up from enviorment Conjugation- Physical Contact between bacteria which passes DNA Transduction- Phages transfers DNA from one bacteria to another | Phage- only infects bacteria
44
DNA replicaiton and antibiotic targets
Cell wall DNA synthesis RNA synthesis membrane or LPS Ribosomes Metabolic Pathways
45
How does HGT advance bacterial evolution?
Genetic change (variation) Selection genetic traits taht provide advantage during selection survive and reproduce
46
Explain why the concept of species does not really apply to bacteria.
Usually relates to the idea of replication of and making a fertile progeny. But bacteria dont do sexual reproduciton and are very promiscuous.
47
Generalized transduction | Discovered by Dr.Esterh Lederberg
- phage that is doing the lytic cycle. And - a random piece of bacterial DNA. And there's not going to be phage DNA. - A few of the progeny of the phages will have this. The majority will be the normal phage. DNA. It's just a few are going to have a chunk of that bacterial DNA, and when those that have the bacterial DNA infect nothing is going to happen because they don't have phage DNA, they cannot kill the cell. But the whole cell that was infected - will receive more bacterial DNA | random DNA
48
Specialized Transduciton Lysogenic Cycle
- It's a lysogenic phage, so - integrate into the chromosome. - specific piece of bacterial DNA with the whole phage genome inside all of the phage progeny.and then all phage progeny will infect the cell and do the lysogenic cycle again. So here it's going to be more uniform because all the phages are going to do this, and they're going to give the same thing to all the host cells they infect
49
Describe how DNA is organized within a “prokaryotic” cell and how that affects the central dogma and infectious disease.
we're going to have one promoter regulating multiple genes elegant way to regulate transcription of genes. And also it's a way to save genetic sequence. Because if I need these 3 genes at the same time, they might as well transcribe them all together.
50
Describe how bacteria organize their genes and what advantages it provides them.
They have an operon The control region and the structural genes in prok one promoter with many genes euk has one to one promoter regions lies in the control region. This advantages becasue it saves time becasue it can express many genes in one go instead of having very vast DNA. The lack of a nucleus also means that trasncription and translaiton can occur at the same time. EUK dont have this abiliyt as they have to wait for the mRNA to enter the cytoplasm.
51
Identify targets of antibiotics and their mode of action.
Ribosomes where it bind to 70s blocking protein synthesis
52
Describe the roles of activators, repressors, inducers, and corepressors.
activators: promotes trasncription repressors: Prevents trasncripiton inducers: small molecule that leads to a final result of more transcription corepressors: small molecule that leads to a final result of less/no transcription
53
Lux
Qurom sensing: inducible lux operon RNA polymerease Promoter: Lux promoter inducer: autoinducer corepressor: none Transcriptional regulator trasncritional activator: LuxR Transcriptional repressor: none
54
lac
RNA polymerase promoter: lac promoter gene: lac operon 3 genes inducer: lactose corepressor: none trasncritional regulator act: none rep: lac repressor | reps bind operator region
55
arg
RNA polymerase promoter: arg promoter gene: arg operon( 3 genes) inducer: none corepressor: arginine Transcriptional regulator act : none rep: ArgR
56
catobolite repression
* cAMP- inducer of lac operon * CAP- transcriptional activator of lac operon * cAMP– high levels indicate low/no glucose levels | both cAMP and lactose are inducer ## Footnote cAMP induces the CAP bidning to DNA CAP site. lactose bind repressor to allow transcription.
57
Diauxic Growth | refrence back to lac operon
A biphasic growth pattern— preferential use of one carbon source over another when both are available in the environment. Lag occurs—after the preferred substrate is exhausted, growth resumes using the second carbon source.
58
levels of lac operon mRNA
+lac : yes -lac : no -lac and +glu : no +lac and +glu : no
59
Inducer Transcriptional Activator
Activator protein will not bind the DNA so there will be no transcription. The addition of an inducer protein will then allow for transcription. | ex. Lux operon
60
Inducer transcriptional Repressor
Repressor protein will bind the DNA and block transcription. The precense of the inducer molecule will then bind the repressor protein allowing transcripiton to occur. | ex. Lac operon
61
Co-repressor Trancriptional Activator
The activator is bound to the DNA and transcripiton occurs. The corepressor molecule will then bind the activator protein and lead to stop of transcription.
62
Co-repressor Transcriptional repressor
The repressor protein is not bound to the DNA so transcription is occuring. When the corepressor molecule is present the repressor protein can bind the DNA and stop transcription. | ex. arg operon
63
Explain the endosymbiotic theory and state evidence to support it.
- Eukaryotic Cells May Have Originated as Predators - anerobic cell consumed a aerobic bacterium( formed the mitochondria) - early aerobic euk cell engulfed photosytetic baacterium( chloroplast) evidence supporting this ? - own dna - own ribosomes - double membranes | Dr.Lynn Margulis
64
Define the major categories of eukaryotic microbes.
Protist fungi
65
Define protists.
* Eukaryotic * Unicellular * Neither plant, animal, or fungi * Very diverse group of organisms
66
# Define protists. Describe the basic characteristics of Fungi cell types
* Found everywhere * Unicellular or multicellular * Sexual and asexual reproduction Haploid and diploid * Non-motile - Diverse morphology Yeasts Molds Mushrooms
67
Describe the basic characteristics of Fungi structures
* Cell wall - chitin * Do not have chloroplasts uni celluar - yeast multicellular- mold and mushrooms
68
Protist in the enviroment
* Photosynthesis * Produce oxygen ( produce majority of oxygen we breathe) * Essential for coral reefs * Part of the food chain in aquatic and soil systems * Decomposers * Pathogens of plants, animals, and humans * Irish potato famine
69
yeast
* Microscopic * Cell distinguished by its oval shape * It grows swellings on its surface called buds, which then become separate cells
70
mold
* Can be seen with the naked eye * Produce toxins, pharmaceuticals * Can cause food spoilage
71
mold structures
* Hyphae – one filament of cells * Mycelium – an aggregate of hyphae * Aerial hyphae (reproductive structures with spores)
72
aerial hyphae
* Fruiting body, sporangia * Reproductive structure with spores * Usually, different colors than hyphae
73
mushrooms
* Seen with the naked eye * Source of Food Toxins Psychedelics 17
74
Endospores vs fungal spores
fungal spores are different as endospores are meant for survival mechanisms. Fungal does not contain many layes for additonal protection. It will always make spores regardless of the enviroment in order to spread.
75
adverse impact due to fungi
* Food spoilage * Toxins –e.g. aflatoxin, ergot( salem witch trials) * Great plant pathogens; crop destruction, food storage * Pathogenic on amphibians, insects * Few true pathogens of mammals, most opportunistic pathogens ## Footnote take advantage of weak immune systems as they arent capable of handling our complex defenses
76
beneficial effects fungi
* Saprophytes (decomposers) * Used in food production (fermentation) * Secondary metabolites: sources of antibiotics, vitamins, cancer drugs, hallucinogens * Beneficial relationships with trees: mycorrhizae

Microbiology (4 decks)

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