Ch. 3 Bacterial and Archaea Structure and Function Flashcards
1
Q
how do prokaryotes differ from eukaryotes?
A
in size and simplicity
2
Q
what are the most common shapes of bacteria?
A
cocci and rods
3
Q
what 2 things determine bacterial arrangement?
A
- plane of division
2. separation or not
4
Q
what is the average bacterial size?
A
varies
5
Q
what shape are cocci (S. Coccus)?
A
spheres
6
Q
list 3 types of cocci and their shape and arrangement
A
- diplococci (S. diplococcus): spheres in pairs
- streptococci: spheres in chains
- staphylococci: spheres in grape-like clusters
7
Q
what is a tetrad?
A
4 cocci in a square
8
Q
what is a sarcinae?
A
cubic configuration of 8 cocci
9
Q
what shape are Bacilli (S. bacillus)?
A
rods
10
Q
list 4 types of Bacilli and their shape
A
- coccobacilli: very short rods
- vibrios: resemble rods, comma shaped
- spirilla (S. spirillum): rigin helices
- spirochetes: flexible helices
11
Q
describe the shape and arrangement of mycelium
A
network of long, multinucleate filaments
12
Q
describe pleiomorphic organisms
A
organisms that are varibale in shape
13
Q
what is the size of the average bacterial rod?
A
6 um
14
Q
what is the size of viruses compared to bacteria?
A
MUCH MUCH smaller
15
Q
in a bacterial cell, what are flagella, and what is their purpose?
A
thin, rigid filaments sticking out of capsule; allow for movement
16
Q
in a bacterial cell what are fimbrae and what is their purpose?
A
the TALL structures sticking out of capsule, aid in adhesion and attachment
17
Q
in a bacterial cell what are pili and what is their function?
A
the SHORT structures sticking out of capsule, aid in adhesion and attachment like fimbrae, but ALSO function in conjugation
18
Q
in a bacterial cell, what is the capsule and what is its function?
A
the outer coating of the cell, functions in protection, binding, and avoiding phagocytosis
19
Q
in a bacterial cell, what is the plasma membrane and what is its function?
A
a semi-permeable membrane between the capsule and the cell wall that allows for transport of substances in and out of the cell
20
Q
in a bacterial cell what is the cell wall and what is its function?
A
the innermost layer, provides structure
21
Q
in a bacterial cell what are ribosomes and what is their function?
A
small, circular dots all around cell, function in protein synthesis
22
Q
in a bacterial cell, what is the cytoplasm and what is its function?
A
the goo inside the cell, contains water, enzymes, ribosomes, and circular DNA
23
Q
in a bacterial cell, what is circular DNA and what is its function?
A
super tightly coiled and only one per cell, holds genetic material
24
Q
in a bacterial cell, what is a plasmid and what is its function?
A
a little circle thing, contains extra genetic material, gives enhanced abilities like antibiotic resistance
25
what charge do both gram negative and gram positive bacteria usually carry?
negative
26
how are gram negatvie and gram positive bacteria named?
for how they stain
27
what are the big differences between gram negative and gram positive cell walls?
1. gram positive has a very thick layer of peptidoglycan
| 2. gram negative have an inner AND an outer plasma membrane
28
can a bacteria live without a plasma membrane?
no, it is an absolute requirement
29
what are the 3 functions of the bacterial plasma membrane?
1. encompasses the cytoplasm
2. selectively permeable barrier
3. interacts with external environment
30
list 3 ways the bacterial plasma membrane interacts with the external environment
1. has receptors for detection of and response to chemicals in surroundings
2. has transport systems
3. metabolic processes
31
what is the structure of the bacterial plasma membrane?
amphipathic lipid bilayers (polar head, nonpolar tail) with floating membrane proteins
32
what are the 2 types of membrane proteins?
1. integral
| 2. peripheral
33
describe peripheral plasma membrane proteins (2)
1. loosely conneected to membrane
| 2. easily removed
34
describe integral membrane proteins (2)
1. amphipathic- embedded within membrane
| 2. carry out important functions
35
what is peptidoglycan? (2)
1. rigid structure that lies just outside the bacterial cell plasma membrane
2. mesh-like polymer of two alternating sugars forming long strands
36
what are the two types of peptidoglycan/cell walls based on gram stain?
1. gram-positive: stains purple, thick peptidoglycan layer
| 2. gram-negative: stains pink or red; thin peptidoglycan and outer membrane
37
list the 4 functions of the bacterial cell wall
1. maintains shape of bacteria
2. helps protect from osmotic lysis
3. helps protect from toxic materials
4. may contribute to pathogenicity
38
do all bacteria have a cell wall?
ALMOST all
39
what are gram positive cell walls made of? (3)
composed primarily of peptidoglycan,
may contain teichoic and lipoteichoic acids,
and some will have a layer of proteins on the surface of the peptidoglycan
40
what charge do teichoic acids carry?
negatively charged
41
what are the 3 functions of teichoic acids?
1. help maintain cell envelope
2. protect from environmental substances
3. may bind to host cell
42
what are lipoteichoic acids? (2)
1. longer than teichoic acids
| 2. enter lipid bilayer
43
what do lysosomes target in peptidoglycan of bacterial cell walls?
sugar links
44
what do some antibodies target in the peptidoglycan of bacterial cell walls?
protein links
45
describe peptidoglycan structure (Studying Brooke: when you come to this card be able to draw it, I MEAN IT)
interlocking NAM and NAG sugars, held on top of each other by protein links/polypeptide bridges
46
what is NAM?
N-Acetylmuramic acid
47
what is NAG?
Acetylglucosamine
48
where is the periplasmic space located in gram-positive bactera? is it bigger of smaller than gram-negative?
lies between the plasma membrane and the cell wall; smaller space than gram-negative
49
does the periplasm have a lot of proteins in gram positive bacteria?
no; relatively few
50
describe gram-negative cell walls (4)
1. more complex than gram-positive
2. consist of a THIN layer of peptidoglycan surrounded by an outer membrane
3. outer membrane composed of lipids, lipoproteins, and LPS
4. no teichoic acids
51
what is the outer membrane of gram-negative cell walls composed of?
1. lipids
2. lipoproteins
3. lipopolysaccharides (LPS)
52
what is the peptidoglycan layer also called?
murein layer
53
how does the periplasmic space differ in gram negative bacteria from gram positive? (2)
1. more space taken up (20-40%) of cell volume
| 2. many enzmes present
54
list 3 enzymes/proteins that are present in the periplasmic space of gram negative bacteria
1. hydrolytic enzymes
2. transport proteins
3. other proteins
55
where does the outer membrane lie in gram negative bacteria?
outside the thin peptidoglycan layer
56
what connects the outer membrane of gram-negative bacteria to the peptidoglycan layer?
Braun's lipoproteins, also called lipoproteins
57
what is another outer membrane protein in gram negative cell walls and what is its function?
porin: transport in/out of cell
58
what lies on top of the outer membrane of gram-negative bacteria?
lipopolysaccharides (LPS)
59
what are the 3 parts of lipopolysaccharides from innermost to outermost?
1. lipid A (innermost, closest to outer membrane)
2. core polysaccharide
3. O side chain (O antigen)
60
how is lipid A of LPS attached to the cell?
embedded in the outer membrane
61
where are the core polysaccharide and O side chain of LPS found?
extend out from cell, lipid A anchors them to outer membrane
62
list the 6 functions of lipopolysaccharides (LPS)?
1. contribute to negative charge on cell surface
2. helps stabilize outer membrane structure
3. may contribute to attachment to surfaces and biofilm formation
4. creates a permeability barrier
5. protection from host defenses (O antigen)
6. can act as an endotoxin (lipid A)
63
describe how LPS can provide protection from host defenses
the O antigen is a unique sequence among/within bacterial cells, most host cells don't recognize or have defenses to it
64
what can the O antigen of LPS be used for?
to help identify types of bacteria
65
describe how LPS can act as an endotoxin
lipid A triggers the immune system; when the response of immune system is too big or there are too many bacteria, hosts can experience fever, chills, or another bad response
66
list the macroelements (macronutrients) that are found in organic molecules such as proteins, lipids, carbohydrates, and nucleic acids (6)
1. Carbon
2. Oxygen
3. Hydrogen
4. Nitrogen
5. Sulfur
6. Phosphorus
67
list the 4 macroelements (macronutrients) that are cations and serve in a variety of roles including enzymes and biosynthesis
1. Potassium (K)
2. Calcium
3. Magnesium
4. Iron (Fe)
68
are macroelements (macronutrients) required in large or small amounts?
required in relatively large amounts
69
what are micronutrients also called?
trace elements
70
what are the 6 micronutrients?
1. Manganese (Mn)
2. Zinc (Zn)
3. Cobalt (Co)
4. Molybdenum (Mo)
5. Nickel (Ni)
6. Copper (Cu)
71
describe micronutrients (trace elements) (4)
1. required in trace amounts
2. often supplied in water or media components
3. ubiquitous in nature
4. serve as enzymes and cofactors
72
what are growth factors? (3)
1. organic compounds
2. essential cell components (or their precursors) that the cell CANNOT SYNTHESIZE
3. must be supplied by environment if cell is to survive and reproduce
73
give 4 examples of growth factors
1. amino acids
2. purines
3. pyrimidines
4. vitamins
74
how do microbes accomplish nutrient uptake?
can only take in dissolved particles across a selectively permeable membrane
75
what are the 3 ways that microbes accomplish nutrient uptake?
1. some nutrients enter by passive diffusion
2. facilitated diffusion, a transport mechanism
3. active transport, a transport mechanism
76
compare and contrast nutrient uptake between gram positive and gram negative cells
gram-positive cells usually experience easier transport, can utilize passive diffusion more often; gram-negative cells usually require special transport mechanisms
77
how does the periplasmic space enzyme activity benefit gram-negative cells in nutrient uptake?
it begins digesting and breaking down nutrients to pass through the murein layer (peptidoglycan)
78
how does passive diffusion flow?
along concentration gradient
79
how does active transport flow?
against gradient, requires energy
80
what type of transport do bacteria have to use more often for nutrient uptake and why?
usually in environments with low nutrient availability = no gradient = have to use active transport more often
81
what is the outermost layer of a bacterial cell?
cell envelope
82
what are the 2 types of cell envelopes?
1. glycocalyx
| 2. S layers
83
what is a glycocalyx?
a network of polysaccharides that oozes out from the cell
84
give two types of glycocalyx found in bacterial cells
1. capsules
| 2. slime layers
85
what is the role of cell envelopes? give an example
aid in attachment to solid surfaces, ex.) biofilms in plants and animals
86
describe capsules (4)
1. usually composed of polysaccharides
2. well organized and NOT easily removed from the cell
3. visible in light microscopes
4. protective advantages
87
give 3 protective advantages of capsules
1. resistant to phagocytosis
2. protect from dessication
3. exclude viruses and detergents
88
what are capsules a predictor of? give 2 examples
predict if bacteria will be super harmful, like anthrax and penumonia which have capsules and fuck you up
89
describe slime layers (3)
1. similar to capsules except diffuse
2. unorganized and not easily removed
3. not as protective as a capsule
90
what is a possible role of slime layers?
may aid in motility
91
what are S layers?
regularly structured layers of protein or glycoprotein that self-assemble
92
where is the S layer in gram-negative bacteria?
adheres to outer membrane
93
where is the S layer in gram-positive bacteria?
associated with peptidoglycan surface
94
what are the 5 functions of the S layer?
1. protect from ion and pH fluctuations, osmotic stress, enzymes, and predation
2. maintains shape and rigidity
3. promotes adhesion to surfaces
4. protects from host defenses
5. potential use in nanotechnology
95
why do S layers have a potential use in nanotechnology?
the S layer spontaneously associates with bacteria
96
list the 4 bacterial cytoplasmis structures
1. cytoskeleton
2. inclusions
3. ribosomes
4. nucleoid and plasmids
97
what is protoplast?
the plasma membrane adn everything within it
98
what is cytoplasm?
the material bound by the plasma membrane
99
what is cytosol?
the liquid portion of cytoplasm
100
what does cytosol NOT include?
genetic material, ribosomes, etc. NOTHING but liquid
101
what are inclusions?
granules of organic or inorganic material that are stockpiled by the cell for future use; bacterial snack pouches!
102
when inclusions are enclosed by a single-layered membrane, what are they called?
vesicles
103
what are ribosomes? (2)
1. complex protein/RNA structures
| 2. sites of protein synthesis
104
what is the number designation for bacterial and archaea ribosomes?
70S
105
what is the number designation for eukaryotic ribosomes?
80S
106
what does the S stand for in the number designations in ribosomes?
Svedburg unit
107
describe bacterial ribosomal RNA in terms of its number designations and parts
16S small subunit
| 23S and 5S large subunit
108
is the bacterial nucleoid membrane bound?
not usually, but there are a few exceptions
109
what is the bacterial nuceloid?
the location of the chromosome and associated proteins
110
how many and what type of DNA molecules are found in the bacterial nucleoid?
usually one closed circular, double stranded DNA molecule
111
what aids in folding of the nuceloid to fit inside bacterial cells?
supercoiling and nucleoid proteins
112
are the nucleoid proteins that aid in fitting the bacterial nuceloid inside the cell the same as histones?
no, very different proteins
113
what are plasmids? (4)
1. extrachromosomal DNA found in bacteria, archaea, and some fungi
2. usually small, closed circular DNA molecules
3. exist and replicate independently of chromosome
4. contain a few genes that are non-essential
114
when are plasmids inherited?
during cell division
115
what do plasmids do?
confer selective advantage to the host
116
how are plasmids classified?
1. mode of existence
2. spread
3. function
117
list 2 examples of concerning plasmids and their functions
1. R plasmids: antibiotic resistance
| 2. virulence plasmids: contribute to virulence
118
what are external structures in bacteria?
extend beyond the cell envelope
119
what are the functions of external structures in bacteria? (4)
1. protection
2. attachment to surfaces
3. horizontal gene transfer
4. cell movement
120
list 3 types of bacterial external structures
1. pili
2. fimbriae
3. flagella
121
describe fimbriae and pili
1. fimbriae are longer and pili are shorter
2. short, thin, hairlike proteinaceous appendages
3. up to 1,000/cell
122
what are the functions of fimbriae and pili? (3)
1. can mediate attachment to surfaces
2. motility
3. DNA uptake
123
what are sex pili?
longer, thicker, and less numerous than fibriae and normal pili (1-10/cell)
124
what do sex pili contain?
genes for formation found on plasmids
125
what are sexpili required for?
conjugation
126
what are flagella?
threadlike, locomotor appendages extending outward from plasma membrane and cell wall
127
what are the functions of flagella? (3)
1. motility and swarming behavior
2. attachment to surfaces
3. may be virulence factors, trigger immume response like LPS does
128
what are specifically bacterial flagella?
thin, rigid protein structures that cannot be observed with bright-field microscopes unless specifically stained
129
what is the bacterial flagella ultrastructure composed of? (3)
1. filament/ long filament
2. basal body
3. hook
130
describe the basal body of bacterial flagella
4 rings, anchors to cell wall components and plasma
131
what is the role of the hook in bacteria flagella and how does it accomplish this?
gives motion by pumping protons through channels to provide the motion to move
132
what is the long filament of the bacterial flagella comprised of?
protein
133
why do gram-negative bacterial flagella basal bodies and hooks need more structures?
they have to anchor into a thicker cell wall
134
list the 5 patterns of flagella distrubution
1. monotrichous
2. polar flagellum
3. amphitrichous
4. lophotrichous
5. peritrichous
135
describe monotrichous flagellar distribution
one flagellum
136
describe polar flagellar distrubution
flagellum (any number) at one end of the cell
137
describe amphitrichous flagellar distribution?
one flagellum at each end of the cell
138
describe monotrichous polar flagellar distribution
one flagellum at one end of the cell
139
describe lophotrichous flagellar distribution
cluster of flagella at one or both ends of the cell
140
describe peritrichous flagellaar distribution
flagella spread over entire surface of the cell
141
list the 4 types of flagellar motility
1. flagellar movement
2. spirochete movement
3. twitching motility
4. gliding motility
142
what kind of movement do bacteria and archaea have?
directed movement
143
what is chemotaxis?
movement towards chemical attractants such as nutrients, and away from harmful substances
144
give 4 examples of taxis
move in response to
1. temperature
2. light
3. osmotic pressure
4. gravity
145
describe bacterial flagellar movement
1. flagella rotates like a propeller
| 2. very rapid rotation, up to 1100 revolutions/sec
146
what does kind of motion counterclockwise flagellar rotation cause?
forward motion, or a run
147
what kind of motion does clockwise flagellar motion cause?
disrupts run, causing cell to stop and tumble or change direction
148
describe spirochete motility
1. multiple flagella form axial fibirl which winds around the cell
2. flagella remain in periplasmic space inside outer sheath
3. corkscrew shape exhibits flexing and spinning movements
149
what might twitching and gliding motility involve?
pili and slime
150
describe twitching movement (3)
1. pili at ends of cell
2. short, intermittent, jerky motions
3. cells are in contact with each other and surface
151
describe gliding movement
smooth movement
152
what is the bacterial endospore?
a complex, dormant structure formed by some bacteria
153
where are endospores located?
various locations within the bacterial cell
154
list 4 environmental conditions that endospores are resistant to
1. heat
2. radiation
3. chemicals
4. desiccation
155
list a describe the 4 endospore layers from innermost to outermost
1. core: has nucleoid and ribosomes, perseved from cell
2. cortex: thick peptidoglycan beneath the coat
3. spore coat: thick layers of protein
4. exosporium: thin covering surrounding the spore
156
describe the water content of a spore
very low water content; just enough for some protein degradation, but tightly packed
157
what is sporulation?
the process of endospore formation; complex multistage process
158
how long does sporulation take?
is very quick, can take up to ten hours from when cell sensed danger
159
when does sporulation normally commence?
when growth ceases because of a lack of nutrients
160
how many stages of sporulation are there?
6
161
what are the 6 stages of sporulation?
1. DNA replication; plasma membrane pinches off extra DNA
2. membranes form around DNA
3. forespore (membrane) forms, taken from cell wall
4. protective cortex forms around the spore
5. protein coat forms around the cortex
6. spore is released
162
what is in an endospore? what does this mean?
a spore is just DNA and ribosomes, can't reproduce, can only survive until conditions are better, at which point the spore will acivate and start producing more genetic material
163
why are bacterial endospores of particular concern to the food industry?
canning food: need to get super hot to kill off potential bacteria; if not hot enough or if process not done right, can cause endospore formation
164
why are bacterial endospores of particular concern to the medical field?
1. bacteria are protected by spores from sanitation practices, people get exposed in process
2. colstridium tetani: sporulate, then activate when entering a wound, which is why you need a tetanus booster when you step on a rusty, shitty nail
165
What is the number of the unique subunit that is the target of sequencing in bacteria? (It’s sweet)
16S (sweet 16)
