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Ali Microbiology > Chapter 3 Molecular basics of Life > Flashcards

Chapter 3 Molecular basics of Life Flashcards

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Biology 101 flashcards
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
Q

Lactobacillus

A

Gram positive firmicutes

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26
Q

Streptomyces

A

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

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27
Q

Prochlorococcus and Anabaena

A
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28
Q

Bacteroidetes

A
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29
Q

Cell Membrane: Structure and Function

A

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
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30
Q

Structure of Lipids

A

Polar phosphoryl head group

Lipid tails

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31
Q

Bacterial Lipid Structure

A

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

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32
Q

Archaeal Lipids

A

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

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33
Q

Is this found in a bacterial or archaeal lipid?

A

Bacterial

The picture below is found in an archaeal lipid!

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34
Q

Hopanoids

A

Found in bacteria, help stiffen membranes

Pentacyclic (5 ring) hydrocarbon derivatives

Provide useful data for petroleum exploration

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35
Q

Lipids are________.

A. Charged.

B. Uncharged

A

Charged

Polar head group

Positively charged NH3+

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36
Q

Proton Motive Force

A

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

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37
Q

Match these cell envelopes.

Choices: Gram -, Gram +, Archaea

A

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

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38
Q

Does molecule diffusion change with pH?

A

Yes - for weak acids and bases

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39
Q

All cells (even acidophiles and alkaliphiles) try to keep a ______ cytoplasm

A

All cells (even acidophiles and alkaliphiles) try to keep a pH neutral cytoplasm

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40
Q

What is pH?

A

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
Q

Can weak acids and weak bases cross the cell membrane?

A

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
Q

Membrane Transport: Passive and Active

A

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
Q

Porins are found in ____ cells and use _____ transport.

A

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
Q

Facilitated Diffusion (Passive)

A

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
Q

Antibiotics

A

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
Q

Antiseptics

A

antimicrobial compounds applied to the skin or mouth (mouthwash)

47
Q

Disinfectants

A

antimicrobial compounds used to kill microorganisms on inanimate objects

48
Q

Why is it difficult to find antifungal drugs that can be used systemically (taken internally)?

A

Fungi are also eukaryotes

Small molecules that slow or kill fungi may hurt our cells as well

49
Q

What do antibiotics target?

A
  1. Translation: bind to the ribosomes and stop protein synthesis
    ex. Gentamicin, Erythromycin, Tetracycline, Streptomycin

Streptomycin: binds to the ribosome

  1. Bind to proteins that make peptidoglycan and stop cell wall synthesis
    ex. Pencillin and Ampicillin
  2. Transcription: bind to RNA polymerase
    ex. Rifampicin/Rifampin

Rifampicin bind to the Beta subunit of RNA polymerase

50
Q

Aminoglycosides

A

Some prevent elongation

Some cause misreads/interfere with proofreading

ex. Streptomycin

51
Q

Vancomycin

A

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
Q

How would a bacteria develop Vancomycin resistance?

A

It would need to change a peptide, which wouldnt be too difficult

53
Q

Beta-lactams

A

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
Q

What antibiotic is this?

HINT: it is a beta-lactam (orange ring)

A

Penicillin

55
Q

How do bacteria develop antibiotic resistance?

A

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
Q

Are antibacterial drugs effective against viruses?

A

No because they only cure bacterial infections

57
Q

List the four modes of antibiotic resistance.

Which ones are broadspectrum (can impact more than on antibiotic)?

A
  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
Q

What are some examples of Beta-lactams antibiotics?

A

Penicillin, Cephalosporins, etc..

Can be combined with clavulanic acid to inhibit Beta lacatamase

59
Q

Beta lactamase

A

common agent of resistance

enzyme that cleaves the lactam ring of penicillin, rendering it ineffective as an inhibitor or transpeptidase

60
Q

How do Beta lactamases work?

A

…?

See slide 84

61
Q

Carbapenemases

A

..?

Slide 83

62
Q

End of antibiotics for Gram negatives

A

…?

see slide 88

63
Q

Microbial Genomic DNA

A

= 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
Q

How many copies of the bacterial genome do bacteria carry?

A

a single copy except when dividing

EXCEPTION: Epulopiscium: 100s of thousands (up to 400,000 copies)

65
Q

Plasmid DNA

A

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
Q

How many genes is

5kb to 20 kb (5000 - 20,000 bp)?

A

5-20 genes

67
Q

DNA supercoiling - usually - or +?

A

DNA in bacteria is usually negatively supercoiled to facilitate unwinding

68
Q

Why does - supercoiling facilitate unwinding?

A

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
Q

What kind of supercoiling do archaea use and why?

A

Positive supercoiling

This helps them out b/c they usually live in extreme conditions which tend to denature DNA

70
Q

What is the purpose of DNA

A

DNA carries the genetic info for life

-for proteins, rRNA, basically all cell functions

71
Q

How do bacterial cells undergo cell division?

A

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
Q

What is the final culminating event in cell division called?

A

Septation

73
Q

Replisome

A

complex of DNA polymerase and other accessory molecules that performs DNA replication

bidirectional replication

74
Q

What proteins are involved in cell division and cell shape?

A

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
Q

Do bacteria have a cytoskeleton?

A

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
Q

nucleoid

A

Contains loops of DNA, supercoiled and bound to DNA binding proteins

77
Q

Where is DNA transcribed?

A

DNA is transcribed in the cytoplasm, often at the same time it is being replicated

It is replicated bidirectionally by the replisome

78
Q

Gas Vesicles

A

water impermeable/gas permeable protein coat

Used for bouyancy to stay close to the surface/light

79
Q

Why would Methanothrix (a strict anaerobe) produce gas vesicles?

A

They are used to move up and down to get closer to bacteria produceing sediment they need

80
Q

What types of compounds are stored in storage granules?

A

Glycogen (sugar) for energy

Polyphosphate

PHB (fatty acid polymer) for energy

Sulfur

81
Q

Magnetosomes

A

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
Q

magnetotaxis

A

the ability to sense and respond to magnetism

83
Q

Some strains of bacteria grow stalks of iron..which ones?

A

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
Q

Stalks

A

appendage that helps attach cells to surfaces

Extension of cell cytoplasma

85
Q

Fimbriae

A

aka pili

Filamentous structures extending from the cell surface that help attach cells to surfaces

Made of protein “pilin”

Singular: pilus, fimbria

86
Q

What kind of surfaces can fimbriae attach to?

A

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
Q

What are the different ways a fimbriae/pili can help a cell move?

A

Twitching motility - extension and contraction of the pili

Walking

Conjugation

88
Q

Flagellum

A

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
Q

What is the structure/funciton of flagella?

A

Swimming - roll and rumble

Rotary movement - similar to propellar in motor boat but driven by protons

Very powerful and complex

90
Q

Chemotaxis

A

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
Q

Phototrophs

A

Possess thylakoid membrane organelles packed with photosynthetic apparatus and carboxysomes for CO2 fixation

92
Q

Opportunistic Pathogens

A

Don’t typically cause disease unless the opportunity presents itself

93
Q

Microbes in Indoor Environments look most like those from

A. Gut

B. Urine

C. Soil

D. Skin

E. Mouth

A

D. Skin

94
Q

Obese individuals have a lower percentage of bacteriodetes in their gut microbiome compared to lean individuals.

TRUE OR FALSE?

A

TRUE

95
Q

Microbes in the home are introduced by what?

A

People (skin, hands, mouths, saliva, feces,shoes)

Food

Water

Pets

Air, dust, dirt

96
Q

Two locations in the kitchen where bacteria diversity is low but load is high

A

Sponges and sink drain

97
Q

Hygene hypothesis?

A

lifestyle changes have led to a decrease in exposure to microorganisms that are important to the development of the immune system

98
Q

Immuniological equilibrium

A

Ali Microbiology (8 decks)

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