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Ali Microbiology > Chapter 3 Molecular basics of Life > Flashcards

Chapter 3 Molecular basics of Life Flashcards

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1
Q

What are the parts of a Gram Negative microbial cell?

A

Capsule, Peptidoglycan layer, Cell membrane (inner membrane), Periplasm

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2
Q

S-Layer

A

Found in most archaea, some bacteria have

Can prevent phagocytosis

Consists of thick Protein or glycoprotein (protein + sugar) subunits

General functions: proctive coats, cell adhesion and surface recognition, molecular sieves; molecular/ion trap, a scaffolding for enzymes and virulence factors (in bacteria)

Archaeal S layers can: determine cell shape and direct cell division - serves purpose of cell wall

S layer is rigid but also flexes to allow substances to pass in either direction

Closely associated with the LPS of the outer membrane

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3
Q

What are bacteria composed of?

A

Nucleic acids, proteins, phospholipids, and other organic and inorganic chemicals

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4
Q

Describe the type of membrane lipids that archaeal cells have

A

Glycerol linked to fatty acid through ether link (C-O-C) instead of ester link

THis allows them to grow at higher temperatures because ethers hydrolize more easily in water

Archaeal hydrocarbon chains are branched terpenoids - every fourth carbon extends a methyl branch –> this strengthens the membrane by limiting the movement of the hydrocarbon chains

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5
Q

What type of molecules can cross the membrane?

A

Small uncharged molecules

Polar molecules and charged molecules require membrane proteins to mediate transport

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6
Q

What does the archaeal envelope consist of?

A

Protein S layer (red)

Pseudo-murein cell wall (some have no cell wall, just S-layer) aka pseudo-peptidoglycan (grey)

Plasma/Cytoplasmic membrane (yellow lipids)

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7
Q

What kind of cells are these?

What kind of microscopy was used?

A
  1. an archaeon
  2. gram negative
  3. gram positive

TEM

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8
Q

Glycocalyx

A

External layer of the cell

Polysaccharide or protein coating surrounding the organism

Also called the capsule or slime layer

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9
Q

What is the function of the capsule?

A

Attachment, prevention of dissication (drying), evasion of immune system

-Noncapsulated cells of S. pneumoniae are relatively harmless

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10
Q

Lipopolysaccharide (LPS)

A

Found in Gram - cells

LPS = main outward facing phospholipids

Have shorter fatty acid chains than those of the inner membrane, some are branched

Can act as an endotoxin = Lipid A in picture

Bacteroidetes (GRAM -)10-1,000 less toxic but is still stoxic

Lipoteichoic acids from Gram + Lactobacilli help mitigate the endotoxic effect of LPS

Several lipid A species exhibit low or no endotoxicity

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11
Q

Endotoxin

A

cell component that is harmless as long as the pathogen remains inact, but when lysed it will overstimulates host defenses and possibly lead to lethal endotoxic shock

Ex. salmonella food poisoning

Lipid A is endotoxin

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12
Q

Treating/Preventing Endotoxic Shock

A

Glucocorticoids: immunosuppressant and anti-inflammatory steroid

Lazoroids: synthetic nonglucocorticoid steroid analogues

Anti-inflammatory drugs such as NSAIDS, ex. ibuprofen

Nitric oxide inhibitors

Summary: it is easier to prevent than to treat

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13
Q

The Bacterial Peptidoglycan

A

Also known as the Cell Wall

Sugar chains circle the cell (“glyco=sweet”)

(peptide-linked chains of amino sugars)

Linked by amino acids “peptide”

Prevent cell rupture

IMPORTANT: the cell wall provides structure but is not a permeablity layer

Polysaccharide backbone shown below in picture

Maintains turgor pressure

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14
Q

Thick Cell Wall will lead to…+ or - gram stain? How?

A

Positive Gram Stain

Gram + cluster phylogenetically (evoluntionary divergence among species)

Gram + cell, cells are fixed to slide surface, crystal violet stains cells reversibly, crystal violet stain binds to Gram + cells or gets trapped, Gram + cells remain purple

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15
Q

What are the steps of a Gram - stain?

A

Add methanol to fix cells to surface

Add crystal violet stain - cells are stained violet

Add iodine (which binds stain to Gram + cells)

Gram - has thin peptidoglycan so the stain washes away through the holes

Wash with ethanol - Stain is removed from the gram - cells

Add safranin counterstain (stains gram - cells pink)

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16
Q

Why do Gram positives retain the dye but not Gram negatives?

A

Gram +: Thick peptidoglycan with 9 amino acid crosslinks traps the dye

Gram -: thin peptidoglycan with 4 amino acid crosslinks allows dye to wash away

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17
Q

Escherichia coli

A

Gram negative proteobacteria

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18
Q

Thiomargarita

A

Gram negative proteobacteria

Thiomargarita namibiensis: reduced H2S is oxidized to S0 for energy

Why? to oxidize sulfur to SO4 2-

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19
Q

Bacillus

A

Gram positive

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20
Q

Epulopiscium

A

Gram positive

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21
Q

Staphylococcus

A

Gram positive firmicutes

Staphylococcus aureus: cocci, catalase positive, blood and chocolate agar to view

Can cause toxic shock syndrome

it is a super antigen toxin - activate immune system w/o being processed by antigen-presenting cells

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22
Q

Mycoplasma

A

Gram positive Firmicutes

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23
Q

Clostridium

A

Gram positive firmicute

C. difficile: commensual (living in a relationship in which one organism benefits, the other does not harm or help)

Treated by Vancomycin

  1. Can grow unabated post antibiotic
  2. Toxin can damage epithelial surface = exudative plaques
  3. Can cause pseudomembranous enterocolitis
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24
Q

Rosburia

A

Gram positive firmicutes

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25
Lactobacillus
Gram positive firmicutes
26
Streptomyces
Gram positive firmicutes **Streptomyces coelicolor**: found in soil, many antibiotics come from, may use the antibodies for signaling or to inhibit other soil bacteria Can be modified chemically (in lab) "Earth Smell" largest known genome - 9 mill + base pairs Can help decompose leaves
27
Prochlorococcus and Anabaena
28
Bacteroidetes
29
Cell Membrane: Structure and Function
Important: the membrane is the permeability layer Made of lipid bilayer (fatty) double layer of phospholipids, maintain proton motive force in ion gradient Proteins are embedded in membrane 1. Anchor lipids to wall, sense the outside 2. sense the outside world 3. transport to/from cell
30
Structure of Lipids
Polar phosphoryl head group Lipid tails
31
Bacterial Lipid Structure
Lipids are usually unbranched fatty acids Lipids are esther linked Almost always form a bi-layer Cis unsaturated fatty acids To stiffen their membranes: cyclopropane, saturated lipids, some branched-chain fatty acids Similar to butter
32
Archaeal Lipids
Most are not fatty acids (i.e. usually regular branching) Ether linked Maybe non polar May be Tetraether mono-layer Have a bilayer with no rings some unsaturations, still has branches and ether links and is better for extreme environments; not as fluid Cyclopentene ring Regularly branched lipids
33
Is this found in a bacterial or archaeal lipid?
Bacterial The picture below is found in an archaeal lipid!
34
Hopanoids
Found in bacteria, help stiffen membranes Pentacyclic (5 ring) hydrocarbon derivatives Provide useful data for petroleum exploration
35
Lipids are\_\_\_\_\_\_\_\_. A. Charged. B. Uncharged
Charged Polar head group Positively charged NH3+
36
Proton Motive Force
The hydrogen ion gradient + the electrochemical potential (charge difference across the membrane) Can be used to directly transport specific nutrients into the cell via transport proteins, to drive motors that rotate flagella, and to drive synthesis of ATP by a membrane embedded ATP synthase
37
Match these cell envelopes. Choices: Gram -, Gram +, Archaea
A. Gram - Archaea B. Gram + Archaea and Eubacteria In eubacteria, the cell wall is primarily composed of peptidoglycan C. Gram - eubacteria S-layer is closely associated with the LPS of the outer membrane
38
Does molecule diffusion change with pH?
Yes - for weak acids and bases
39
All cells (even acidophiles and alkaliphiles) try to keep a ______ cytoplasm
All cells (even acidophiles and alkaliphiles) try to keep a **pH neutral** cytoplasm
40
What is pH?
Power of hydrogen - measure of the hydrogen ion concentration in the body pH tells if it's protonated, charge tells you if it can cross the membrane
41
Can weak acids and weak bases cross the cell membrane?
Yes, because they exist partly in an uncharged form that can diffuse across the membrane and increase (acids) or decrease (bases) the hydrogen concentration within a cell
42
Membrane Transport: Passive and Active
Passive transport: small uncharged molecules can permeate the outer membrane through diffusion and porins (found in Gram -) Active transport: occurs in the cytoplasmic membrane, goes from low to high concentration, requires cells to spend energy ; may be powered by a coupled reaction
43
Porins are found in ____ cells and use _____ transport.
Porins are found in **Gram -** cells and use **passive** transport. They allow transport of molecules (\< .6 - 1.5 kda) but not \> 1.5 kda The outer membrane of porins is made up of beta sheets known as a beta barrel Channel Proteins
44
Facilitated Diffusion (Passive)
uses the concentration gradient of a compound to move it across a membrane from a compartment of high concentration to low concentration Some porins show substrate specificity (carrier proteins)
45
Antibiotics
low molecular weight chemicals that kill or inhibit growth of bacteria, some can be taken into the human body (ingested or injected) with minimal side effects
46
Antiseptics
antimicrobial compounds applied to the skin or mouth (mouthwash)
47
Disinfectants
antimicrobial compounds used to kill microorganisms on inanimate objects
48
Why is it difficult to find antifungal drugs that can be used systemically (taken internally)?
Fungi are also eukaryotes Small molecules that slow or kill fungi may hurt our cells as well
49
What do antibiotics target?
1. Translation: bind to the ribosomes and stop protein synthesis ex. Gentamicin, Erythromycin, Tetracycline, Streptomycin Streptomycin: binds to the ribosome 2. Bind to proteins that make peptidoglycan and stop cell wall synthesis ex. Pencillin and Ampicillin 3. Transcription: bind to RNA polymerase ex. Rifampicin/Rifampin Rifampicin bind to the Beta subunit of RNA polymerase
50
Aminoglycosides
Some prevent elongation Some cause misreads/interfere with proofreading ex. Streptomycin
51
Vancomycin
From soil bacterium Targets peptidoglycan in Gram + cells with thick cell wall Slightly toxic to people Large molecule \> 1 kda Cannot fit through porins Used as a drug of last resort to kill multi-drug resistant S. aureus (MRSA) Blocks transpeptidase enzymes from assembling the peptide cross links in peptidoglycan
52
How would a bacteria develop Vancomycin resistance?
It would need to change a peptide, which wouldnt be too difficult
53
Beta-lactams
ex. Penicillin and Cephalosporins Also block formation of peptide cross-links (by binding to transpeptidase) Contain beta-lactam rings that can be cleaved by beta-lactamases
54
What antibiotic is this? HINT: it is a beta-lactam (orange ring)
Penicillin
55
How do bacteria develop antibiotic resistance?
It is easily transferred from one bacterium to another on plasmids or small pieces of DNA The stress of being exposed to antibiotics encourages DNA exchange Particularly a problem if bacteria are exposed to non-lethal doses ex. over prescription of antibiotics and the use of antibacterial soaps
56
Are antibacterial drugs effective against viruses?
No because they only cure bacterial infections
57
List the four modes of antibiotic resistance. Which ones are broadspectrum (can impact more than on antibiotic)?
1. Limit access to the cell 2. Pump it out of the cell 3. Modifty (inactivate) the antibiotic (ex. beta-lactamases) 4. Modify the target Broadspectrum: limit access to the cell and pump it out of the cell
58
What are some examples of Beta-lactams antibiotics?
Penicillin, Cephalosporins, etc.. Can be combined with clavulanic acid to inhibit Beta lacatamase
59
Beta lactamase
common agent of resistance enzyme that cleaves the lactam ring of penicillin, rendering it ineffective as an inhibitor or transpeptidase
60
How do Beta lactamases work?
...? See slide 84
61
Carbapenemases
..? Slide 83
62
End of antibiotics for Gram negatives
...? see slide 88
63
Microbial Genomic DNA
= 1 + chromosome (s) + plasmid DNA Most bacteria and archaea have a single circular chromosome Single loop of double - stranded DNA - Average 4 x10^6 (4Mb = mega/millino bases) - 4,000,000 bp --\> 4,000 genes
64
How many copies of the bacterial genome do bacteria carry?
a single copy except when dividing EXCEPTION: Epulopiscium: 100s of thousands (up to 400,000 copies)
65
Plasmid DNA
Some bacteria have smaller extra-chromosomal DNA molecules 5kb to 20 kb (5000 - 20,000 bp) one of the major carriers of resistance genes these are non-essential - we know this because we have knocked them out and bacteria still grow
66
How many genes is 5kb to 20 kb (5000 - 20,000 bp)?
5-20 genes
67
DNA supercoiling - usually - or +?
DNA in bacteria is usually negatively supercoiled to facilitate unwinding
68
Why does - supercoiling facilitate unwinding?
Because when DNA supercoils start to pull apart or denature it creates spaces that make it easier to replicate and help facilitate central dogma
69
What kind of supercoiling do archaea use and why?
Positive supercoiling This helps them out b/c they usually live in extreme conditions which tend to denature DNA
70
What is the purpose of DNA
DNA carries the genetic info for life -for proteins, rRNA, basically all cell functions
71
How do bacterial cells undergo cell division?
Binary Fission Steps: 1. Cell size doubles 2. DNA replicates (2 chromosomes) 3. Replication origins (green) move to opposite poles of the cell (compartmentalize genetic material) 4. Cytoplasm is cleaved in two (septation), usually at equator
72
What is the final culminating event in cell division called?
Septation
73
Replisome
complex of DNA polymerase and other accessory molecules that performs DNA replication bidirectional replication
74
What proteins are involved in cell division and cell shape?
FtsZ --\> Z ring Polymerizes around the circumference of the cell division plane to form a Z ring that determines cell diameter Like a big rubberband around the cell Homologus to tubulin (component of mitotic apparatus in eukaryotes) Cytoskeleton homolog (shared ancestry)
75
Do bacteria have a cytoskeleton?
Eukaryotic Cytoskeleton: - Actin, intermediate filaments, tubulin - Help maitain shapre MreB protein (actin like) - helps with elongation of rod shaped bacteria, localizes in arc-shaped patches just beneath the mebrane CreS - crescentin (intermediate filament like), appears in curved rod shaped bacteria and polymerizes along the inner curve of the crescent
76
nucleoid
Contains loops of DNA, supercoiled and bound to DNA binding proteins
77
Where is DNA transcribed?
DNA is transcribed in the cytoplasm, often at the same time it is being replicated It is replicated bidirectionally by the replisome
78
Gas Vesicles
water impermeable/gas permeable protein coat Used for bouyancy to stay close to the surface/light
79
Why would Methanothrix (a strict anaerobe) produce gas vesicles?
They are used to move up and down to get closer to bacteria produceing sediment they need
80
What types of compounds are stored in storage granules?
Glycogen (sugar) for energy Polyphosphate PHB (fatty acid polymer) for energy Sulfur
81
Magnetosomes
microscopic membrane-embedded crystals of the magentic mineral megnetite (Fe3O4) - ferrimagnetic iron oxide Helps cells detect which way is up/down and aid in movement in low O2 zones enclosed by a lipid bilayer
82
magnetotaxis
the ability to sense and respond to magnetism
83
Some strains of bacteria grow stalks of iron..which ones?
Gallionellea (in picture): form twisted stalk from secreted iron oxide aids in waste removal and movement toward oxygen Leptothrix: leaves empty sheath behind as cells move forward
84
Stalks
appendage that helps attach cells to surfaces Extension of cell cytoplasma
85
Fimbriae
aka pili Filamentous structures extending from the cell surface that help attach cells to surfaces Made of protein "pilin" Singular: pilus, fimbria
86
What kind of surfaces can fimbriae attach to?
Aka pili Can attach to abiotic surfaces (teeth, rocks, catheters) Can also attach to biotic surfaces (cells) Ex. neiserria gonorrhoeae attaches to epithelial cells in cervix or urethra via its pili
87
What are the different ways a fimbriae/pili can help a cell move?
Twitching motility - extension and contraction of the pili Walking Conjugation
88
Flagellum
Appendage for Cell Motility Helical tube made up of protein Much longer and wider than pili (usually) Can propel bacteria 170 mm/hr or 60 body length/second DIfferent numbers and locations 1. Monotrichious - one flagellum 2. Polar (amphitrichous) - both poles 3. Lophotrichous - strategically located (one pole) 4. Peritrichous - all over
89
What is the structure/funciton of flagella?
Swimming - roll and rumble Rotary movement - similar to propellar in motor boat but driven by protons Very powerful and complex
90
Chemotaxis
an elaborate sensory system present in most cells w/ flagella that allows them to swim towards favorable environmentsand away from inferior environments Use a polar array of chemoreceptors to detect attractants and repellants Requires mechanism for bacteria to propel towards/away - biased random walk
91
Phototrophs
Possess thylakoid membrane organelles packed with photosynthetic apparatus and carboxysomes for CO2 fixation
92
Opportunistic Pathogens
Don't typically cause disease unless the opportunity presents itself
93
Microbes in Indoor Environments look most like those from A. Gut B. Urine C. Soil D. Skin E. Mouth
D. Skin
94
Obese individuals have a lower percentage of bacteriodetes in their gut microbiome compared to lean individuals. TRUE OR FALSE?
TRUE
95
Microbes in the home are introduced by what?
People (skin, hands, mouths, saliva, feces,shoes) Food Water Pets Air, dust, dirt
96
Two locations in the kitchen where bacteria diversity is low but load is high
Sponges and sink drain
97
Hygene hypothesis?
lifestyle changes have led to a decrease in exposure to microorganisms that are important to the development of the immune system
98
Immuniological equilibrium

Ali Microbiology (8 decks)

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