Exam 1 Flashcards
1
Q
Fred Sanger
A
how nucleotides came together
2
Q
Walter Gilbert and Paul Burg
A
basic sequencing of genes
3
Q
Woese’s 3 domains of life
A
archaea, bacteria, eukarya
-based on 16s and rRna sequence
4
Q
Eubacteria
A
cyanobacteria, actinomycetes, Caulobacter spp, Myxococcus
5
Q
cyanobacteria
A
-blue green algae
-filamentous
-created oxygen env
6
Q
actinomycetes
A
-terrestrial bacteria
-form hyphae and stalks
-antibiotics
7
Q
Caulobacter spp
A
-sticky sessile bacteria or
-mobile free swimming flagellated bacteria
8
Q
Myxococcus
A
functions like slime mold by producing fruiting bodies
9
Q
what forces help stabilize protiens?
A
hydrogen and ionic bondings
10
Q
what are 3 main traits of archaea?
A
extremophiles (osmolarity), high temp, high pressure
11
Q
Robert Hooke
A
-first compound microscope
-firs to describe cells
12
Q
Francesco Redi
A
showed maggots didn’t spontaneously appear on decaying meat
-only when meat was exposed
13
Q
Lazzaro Spallanzani
A
-sealed flask of sterilized meat didn’t produce microbes
-disproved spontaneous generation of microbes
-but results were not valid because experiment didn’t have air
14
Q
Louis Pasteur
A
-boiled broth and placed in swan necked flasks
-flasks allowed air in, but not microbes
-proposed that the transmission of microbes cause disease
15
Q
Edward Jenner
A
-father of immunology (diseases not form karma)
-smallpox vaccine
-Variolation
-patient: James Phipps (given cowpox, protected from small pox)
-noted for saving millions of lives (attenuation of smallpox and given to people)
16
Q
John Tyndall
A
-discovered that organic matter can contain heat-resistant spores
-no spontaneous generation
17
Q
Joseph LIster
A
-antiseptic surgery
-phenol was used to sterilize surgical equipment
18
Q
Ignaz Semmelweis
A
-hand washing in hospitals
19
Q
Heat vs chemical fixation for specimen preparation
A
heat: preserves morphology but not internal structures
chemical: chemical penetrates cell to preserve internal structure
20
Q
what are 2 common features of dyes?
A
1) chromophore group- chemical groups with conjugated bonds (gives dyes its color)
2) able to bind to cells
21
Q
Gram + and - stain used
A
+ crystal violet, Gram’s iodine
- safarin counter stain
22
Q
Gram + examples
A
Bacillus, Streptococcus, Staphyloccus
23
Q
Gram - examples
A
Escherichia coli, Pseudomonas aeroginosa
24
Q
why is electron microscope better?
A
smaller wavelengths –> better resolution
25
Germ theory of disease
**Robert Kich proposed 4 criteria that must be met to determine if a microbe causes disease**
1) microbe always present in diseased organim
2) microbe is isolated from disease organism and grows in pure culture (get disease back)
3) microbe isolated must cause disease in healthy organism
4) re-isolate same microbe from now-sick individual
26
Barry Marshall 1984
Helicobacter pylori causes stomach ulcers
27
Prokaryotes vs eukaryotes
* size and simplicity
* most prokaryotes lack internal membrane systems and they are divided into bacteria and archaea
28
what are fimbrae/ pili functions?
attachment to surfaces, bacterial conjugation and transformation, twitching and gliding motility
29
what are the functions of the plasma membrane?
encompass cytoplasm
selectively permeable barrier
interacts with external environment (receptors for env. cues, transport systems, metabolic processes)
30
peripheral proteins
* loosely connected to membrane
* easily removed
* hydrophilic amino acids
31
integral proteins
* amphipathic (embedded within membrane)
* may exist as microdomains
32
hopanoids
-a type of bacterial lipid
-found in petroleum
-equivalent to cholesterol in eukaryotes (provide rigidity)
33
cell wall
* peptidoglycan (polymer = murein)
* rigid structure that lies outside cell membrane
* defines bacteria structure
* 2 types based on Gram stain
* maintains structure/ shape of bacterium
* helps protect cell from osmotic lysis and toxi materials
* may contribute to pathogenecity (attachment)
34
penicillin
-antibiotic that blocks peptidoglycan synthesis (prevents cell wall formation and cause bacteria to burst)
-inhibits transpeptadaze --> blocks cross-linking
35
peptidoglycan structure
* NAM and NAG alternating sugars
* alternating D and L amino acids
* strands have helical shape
* chains are crosslinked by peptides for strength (interbridges, peptidoglycan sacs)
36
why do variations in peptidoglycan structure exist?
want to disrupt other bacteria's cross links to gain their environment
37
LPS importance
-contributes to - charge on cell surface (protective barrier because many things trying to attach are +)
-helps stabilize outer membrane
-creates permeability barrier
-attachment to surfaces and biofilm formation
38
exoenzymes
-enzymes secreted by gram + bacteria
-outside the cell
-get energy from substrates (bonds built with energy)
-dont use ATP because ATP inside cell
-aid in degradation of large nutrients
39
LAL Assay
-endotoxic assay granules w clotting factor (coagulogen)
-horseshoe crabs w blue blood (hemocyanin assay substituted need for drugs w endotoxins)
-for endotoxin testing
40
porin proteins
form channels through which small molecules can pass (600-700 daltons ~7 a.a.)
41
hypotonic vs hypertonic environments
**hypotonic:** [solute] larger inside cell and cell swells w water; cell wall protects from lysis
**hypertonic**: [solute] larger OUTSIDE cell and plasmolysis occurs as cell shrinks
42
lysozyme
* breaks bond bw NAM and NAG
* degrades bacterial cell wall
* made by phage
43
what happens if cell is in a hypotonic solution and treated with lysozyme or penicllin?
cell will because cell wall destroyed
44
glycocalyx
* made of: glycoprotein/ glycosaccharide
* capsules and slime layers
* S layers
* aid in attachment to solid surfaces
45
capsules
* protective barrier for cell made of polysaccharides
* well organized and not easily removed from cell
* resistant to phagocytes, protect from desiccation, exclude viruses and detergents
* ex: C-diff in hospitals hard to get rid of
46
S layers
* -in all bacteria & archaea
* -made in cytoplasm -> leaves cytoplasm -> spontaneously forms
* -**in gram -** attaches to outer membrane
* -**in gram +** attaches to peptidoglycan surface
* -**functions**: protective barrier
maintains shape and rigidity, promtoes adhesion to surfaces, protects from host defesnses, ion and pH fluctitaions
47
slime layer
-move around in environment and can provide protection (stiff to get through)
-similar to capsules, except diffuse, unorganized, and easily removed
48
what is virulance factor
-anything that can help cause disease
-tissue specific
-toxin production
49
endospores
-nonreproductive and dormant state (waits for right conditions to reactivate)
-normally initiated due to a lack of nutrients
-protection for DNA (packaged into a cortex)
-resistant to heat and radiation
-521 year half-life of DNA
DPA
50
DPA
dipicolinic acid
-in endospores
-removes water around DNA and puts DPA in its palce
51
are archaea single or multicellular?
single
52
archaeal cell envelopes
-some lack cell wall
-S layer may be only component outside plasma membrane
-capsules and slime layers are RARE
53
archaeal membrane composition
-isoprene units (5 carbon, branched -> slow movement, more rigidity in bilayer)
-ether linkages (instead of ester)
-some have monolayer structure (more stable for high rpessure/ temp env)
54
archaeal cell walls
-lack peptidoglycan (dont use NAM)
-S layer is most common cell wall, separated from membrane by pseudomurein
-may have protein sheath external to S layer
55
reason for diversity in archaea cell envelopes
phage were a major selective force and archaea had to evolve to survive that
56
difference between pseudomurein and peptidoglycan
**pseudomurein**: 1->3 glycosidic bond, L-aa, n-acetyltalosaminuronic acid (instead of NAG) (NAM &NAT)
**peptidoglycan**: 1->4 glycosidic bond, D-aa, NAM & NAG
57
protoplast
plasma membrane and everything in it
58
cytoplasm
material bounded by plasmid membrane
59
cytoskeleton functions
role in cell division
protein localization
determination of cell shape
60
FtsZ
-forms rings during septum formation in cell wall
-assemble in center of bacteria and coordinate all other enzymes involved in cell division
61
MreB
-maintains shape by positioning peptidoglycan synthesis machinery (to get rod shape)
-will form from 1 pole to other, scaffolding-based protein
62
CreS
-maintains curve
-block cell wall synthesis on one side of cell
-block MrB components
63
plasma membrane infoldings
-increase SA to pack more things and for metabolic process
-in many photosynthetic bacteria (analogous to thylakoids in chloroplasts & rxns are center for ATP formation)
-anammoxosome in Planctomycetes
-global nitrogen cycles/ anaerobic ammonium oxidation
64
inclusions
granules of organic/inorganic material that are stockpiled by the cell for future use
-some enclosed by a single-layered membrane
-**ex**: microcompartments: not bound by membranes but compartmentalized for a specific function
65
what do inclusions storage?
nutrients, glucogen, carbon (PHB), phosphate (volutin), amino acids (R/D)
66
carboxysomes
-type of inclusion
-CO2 fixing bacteria, contain Rubisco enzyme, found in cyanobacteria
67
gas vacuoles
-type of inclusion
-to hold gas inside the cell
-found in aquatic photosynthetic bacteria and archaea to stay within surface of water
-provide bouyancy in gas vesicles
68
magnetosomes
-type of inclusion
-found in aquatic bacteria
-magnetite particles for orientation (reach certain parts) in Earth's magnetic field
-mineralized iron oxide
69
MamK
-type of inclusion
-cytoskeleton protein
-helps form magnetosome chain
70
ribosomes
-sites of protein synthesis
bacterial and archaeal: 70S
eukaryotic: 80s
71
bacterial & archaeal rRNA
-16S (small subunit)
-23S and 5S in large
-archaea has additional 5.8 S
72
nucleoid
-no nucleus in bacteria & archaea
-not membrane bound (no separation of functionality)
-irregularly shaped region w chromosome and associated proteins
-usually 1 chromosome (closed circular, double stranded DNA molecule)
-supercoiling (making more compact) and nucleoid proteins (HV)
-aid in folding to hold DNA
73
Carbs, lipids, proteins, and nucleic acid composition
CHO, CHOP, CHONS, CHONPS
74
what are micronutrients
required in trace amounts
Mn, Zn, Co, Mo, Ni, and Cu
often supplied in water or media
75
what nutritional types do the majority of microorganisms have?
1.) photolithoautotrophs (photoautotrophs)
2.) chemoorganoheterotrophs (chemoheterotrophs majority of pathogens)
76
Beggiatoa
type of chemolithoheterotrauph
oxidized hydrogen sulfide (H2S)
77
Nitrobacteria
uses nitrite oxidation to nitrate for carbon fixation
78
growth factors
essential organic cell components that the cell cannot synthesize
1.) amino acids (for protein synthesis)
2.) purines & pyrimidines (for nucleic acid synthesis)
3.) vitamins (function as enzyme cofactors)
4.) heme (iron constrained in the center of a heterocyclic organic ring)
79
what is anaerobic respiration
reducing sufate to hydrogen sulfide
(getting rid of it)
SO4 2- --> H2S
80
how is sulfur usually supplied?
via assimilatory sulfate reduction
reduce sulfate to sulfide
81
how is phosphorous usually supplied?
inorganic phosphate
82
facilitated diffusion
uses carrier molecule permeases
smaller [] gradient needed
glycerol, sugars, and amino acids
83
what molecules do passive diffusion
H2O, O2, CO2
84
what are permeases and when are they used?
membrane bound carrier molecules
facilitated and active transport
85
ABC transporters
primary active transporters (ATP)
bind to ATP -> energy released -> move things out of cell against [ ] gradient
86
secondary active transport
uses energy already built up
major facilitator superfamily (MFS)
uses ion gradients to co-transport substances
protons, antiport, symport
87
antiport vs symport
anti: 2 substances move in opposite directions
sym: 2 substance move in same direction
88
group translocation
transport that chemically modifies bacteria as it is brought into the cell
so it cant be recognized by permease -> cant interfere and keep [ ] gradients
energy dependent
phosphotransferase system (PTS)- transport of sugars while phosphorylating using PEP
89
how can diffusion get better when we have protein to help?
protein has affinity to what is helping pass, so it is no longer that passive
90
when does rate of facilitated diffusion increase more rapidly?
at lower concentration and reaches plateaue when carrier becomes saturated
91
iron uptake
siderophores bind to iron
92
culture media
complex vs defined
nutrients for organism to grow
complex: dont know everything that is there
defined: pick things specifically
93
who is attributed to types of media?
Koch
94
what is the environment inside the cell like?
reductive-based
95
how do some microorganisms change pH of habitat?
producing acidic/ basic waste
cant regulate internal temp
96
what is protein structure stabilized by?
proline, chaperons, and more hydrogen bonds
97
what is membrane stabilized by?
more saturated and branched
higher molecular weight of lipids
ether linkages (resistant to heat and pH levels)
98
superoxide dismutase
catalyzes/ neutralizes superoxide into oxygen and hydrogen
99
catalase
catalyses H2O2 into oxygen and water
100
what do superoxide and dismutase do together?
detoxify products with oxygen
101
barolotolerant organisms
adversely affected by high pressure
102
barophilic (peizophilic) organisms
require/grow more rapidly when pressure is high
change membrane fatty acids to adapt to high pressure
103
French Pressure Cell
change in pressure used to break bacteria cell wall
104
cell-cell communication
1) biofilms- bacteria communicate using quorum sensing
2) produce small proteins that increase [ ] as microbes replicate and convert microbe to a competent state (DNA uptake as bacteriocins released)
105
Acylhomoserine lactone (AHL)
autoinducer molecule produced by many gram - org
diffuses across plasma membrane and once inside induces exprssion of target genes
can prevent virulance
106
quorum sensing systems
host-microbe interactions
symbiosis: Vibrio fischeri and bioluminescence in squid
pathogenicity and increased virulence factor production
DNA uptake (competent state) for antibiotic resistant genes
107
quorum quenching
mess with sensing and get rid of quorum-sensing molecule -> cant communicate
108
sanitization
reduction of microbial population to levels deemed safe
109
antisepsis
prevention of infection of living tissue by microorganisms
pathogens still present
110
