exam 1 Flashcards
(125 cards)
1
Q
What is the result of small organisms having a very large surface : volume ratio?
A
Rapid uptake of nutrients & elimination of waste
2
Q
What are disadvantages of being unicellular?
A
Influenced by environment easily, cannot stabilize conditions like multicellular organisms such as temperature regulation
3
Q
What types of compounds make up most of the cell?
A
Water, carbon, oxygen, nitrogen
4
Q
Which macromolecule makes up most of the cell?
A
Protein (55%) followed by RNA (20.5%)
5
Q
What are the basic 3 cellular structures of all prokaryotes?
A
- Protein 50% 2. RNA 25% 3. DNA 3%
6
Q
How to identify an organism by genus, species, and strain?
A
Example: Escherichia coli strain B
Species: Coli, Genus: Escherichia, Strain: B
7
Q
When bacteria switch from minimal to rich media, what happens to metabolism?
A
Increases, more RNA in fast growing cells to produce more protein & enzymes
8
Q
What constitutes the majority of cell dry mass?
A
Macromolecules
9
Q
What are the 2 substances unique to bacteria?
A
LPS in G- bacteria, and murein
10
Q
When cells are fractionated into classes of molecules and measured by radioactivity, what graph do we see?
A
1: Small organic molecules or precursors (building blocks: amino acids, nucleic acids)
2: Macromolecules, labeled slowly and more stable (ex: NADP, proteins)
3: Small pool, labeled quickly & continuously degrades mRNA
11
Q
How much does the average protein weigh?
A
40,000 g/mol = average weight
12
Q
How much does an average protein molecule weigh?
A
40,000 g/mol / 6.022 x 10^23 = 6.6 x 10^-20 g/molecule
13
Q
How many protein molecules are in 155 femtograms?
A
155 femtograms (155 x 10^-15) / weight of protein = 2.36 million molecules (2.36 x 10^6)
14
Q
What is rRNA composed of and how much is made up in dry mass?
A
16s RNA, 23s, 5s - 1/5 of dry mass
15
Q
How many ribosomes are there per cell?
A
18,700
16
Q
Why do cell compositions change when grown in different media?
A
To adapt to its environment to survive
17
Q
What components of the cell would change and why?
A
Metabolism due to change in nutrients (ex: media) more RNA, protein & DNA to metabolize media
18
Q
What does tRNA do and how much does it make up of RNA content?
A
Transfer RNA for protein synthesis ~15% of RNA content
19
Q
What does murein do (peptidoglycan)?
A
Responsible for structural rigidity of cell, teichoic acids with murein in G+ cell
20
Q
How many femtograms of carbohydrates are there and what are 2 features?
A
7 femtograms
PHB - poly hydroxylbutyrate, no storage
21
Q
How many femtograms of low molecular weight organic molecules are there and what are these?
A
8 femtograms
- Amino acids, nucleotides, sugars
- Metabolic intermediates
- Cofactors
22
Q
What is the difference between prokaryotes, eukaryotes & archaea in terms of peptidoglycan?
A
Bacteria has it; archaea & eukarya do not
23
Q
What is the difference between prokaryotes, eukaryotes & archaea in terms of lipids?
A
Bacteria & eukarya - ester linked; archaea - ether linked
24
Q
What is the difference between prokaryotes, eukaryotes & archaea in terms of ribosomes?
A
Bacteria - 70s; archaea - 70s; eukarya - 80s
25
What is the difference between prokaryotes, eukaryotes & archaea in terms of introns?
Bacteria does not have it; archaea & eukarya have it
26
What are the differences between prokaryotes and eukaryotes in terms of organelles or electron transport?
Prokaryotes have no nucleus or organelles; eukaryotes - ET happens in mitochondria, bacteria - ET happens in plasma membrane
27
What is the function of subcellular structures / layers?
1. Adhesion + mobility
2. Protection from phagocytosis
3. Protect from physical injury + dehydration
28
Why do bacteria lose surface layers when cultured in the lab?
Does not have the same stresses as outside environment
29
What happens when there is no cell wall?
Bacteria becomes coccus shape
30
What is the role of D-amino acid lysozymes?
To break cell wall
31
What is the role of lipoteichoic acids?
Bound to membrane, glycerol backbone
32
What is the role of porins?
Channels that help transport molecules in/out of cell, such as hydrophilic molecules
33
What is the function of LPS?
Endotoxin, produce antibody response causing immune response / antigenic
34
What is the function of braun lipoprotein?
Stabilize cell wall by attaching outer membrane to cell wall
35
What are the 5 components of periplasmic space?
1. Oligosaccharides & osmotic regulation
2. Solute binding proteins
3. Cytochrome C
4. Hydrolytic enzymes
5. Detoxifying enzymes
36
How is osmosis regulated in periplasmic space?
Increased osmolarity and decreased oligosaccharides
37
What do solute binding proteins do?
Assist transport of sugars, ions, molybdate
38
What are the roles of cytochrome C?
Involved in ETC, oxidize carbon or inorganic compounds
39
What is the role of hydrolytic enzymes?
Amylase -> cleaves oligosaccharides
40
Where are pili located and what are their 3 functions?
Located on surface of prokaryotic cells (G-)
## Footnote
1. Adhesion pili facilitate colonization of mucoid surface
2. Important factor in infection
3. Contain adhesions in tips = proteins bind to oligosaccharides in cell receptors
41
How do flagella differ in eukaryotic vs prokaryotic?
Prokaryotic simpler and composed of three parts
42
What are the three parts of flagella?
1. Filament
2. Hook
3. Basal body
43
What is the filament of flagella?
Most distal / outermost region, hollow tube composed of flagellum
44
What is the hook of flagella?
Next region, composed of hook protein or product of flgE gene, universal joint that rotates
45
What is the basal body of flagella?
Connected to hook and located in cell wall or envelope
46
What is the difference between G+ and G- basal body?
G+ has 2 rings; G- has 4 rings
47
What is rotation powered by and by what proteins?
Proton gradient through MotA and MotB, if mutated then flagella cannot rotate; Fil proteins = switch proteins (change direction of rotation)
48
What is the order of synthesis of flagella?
1. Insert M & S ring into cytoplasmic membrane
2. Attachment of hollow rod
3. Addition of P & L rings
4. Synthesis of hook & filament
5. Addition of motility proteins
49
What is the periplasmic flagella and where is it found?
Flagella found in spiral shaped bacteria located in periplasmic surrounded by membranous sheath
## Footnote
Rotational motility, able to move through high viscosity medium & supports pathogenicity
50
What is the mechanism of swarming motility?
Organisms run out of nutrients -> moves through flagella by making more flagella
51
What are the 4 features of intracytoplasmic membranes and their functions?
1. Methanotrophs: place for methane oxidation
2. Nitrogen fixers: N2 + nitrogenase -> NH3
3. Nitrifiers: place for ammonia & oxidation enzymes
4. Phototrophs: site of photosynthesis
52
What is the composition of 70s ribosome?
Small unit 30s -> 16s + 21 proteins; large subunit: 50s -> 5s + 23s + 31 proteins
53
What is the function of ribosomes and its mechanism?
Protein synthesis
## Footnote
1. Ribosome attaches to mRNA
2. Recognize tRNA
3. Join amino acid by peptide bonds
54
What is needed for bacteria to grow?
1. Synthesize subunits (make molecules to make large components like amino acids -> proteins)
2. Polymerization of subunit
3. Synthesize structure
55
What is yield, and what letter represents it?
Amount of growth (Y)
56
What is g?
Generation time, time for population to double
57
What is k and in what units?
Speed of growth
58
What is balanced growth?
Log phase, exponential growth
59
What are the 2 theories as to why division is obligatory for microbial cells?
1. Allows microbes to maintain S:V ratio
2. Certain amount of genetic material is required to control a certain amount of protoplasm
60
What are the 3 ways microorganisms can grow & divide?
1. Binary fission = 2 equal daughter cells
2. Budding = yeast + small daughter cell
3. Fragmentation
61
Explain the process of binary fission.
1. Parent cells prepare for division, cells enlarge including cell wall, membrane, & volume - DNA synthesis initiated
2. Septum grows inwards, chromosomes move to opposite ends
3. Septum synthesized, separates cells
4. Daughter cells separated
62
How are sister chromosomes separated?
By proteins, similarly to tubules & separates chromosomes
63
What are the 3 genes that regulate septum formation?
minC, minD, minE
64
What happens if the min genes are removed?
Cannot divide in the middle
65
What is FtsZ?
Cytoplasmic molecule - aggregates on inner surface of cell membrane; binds to molecule anchored in membrane
66
What is FtsA?
ATPase, interacts with FtsZ for septation
67
What is ZipA?
Cell membrane protein bound to FtsZ in septal ring; attaches to ring & anchors; needed for constriction
68
What is the septum formation process?
1. FtsZ forms ring with ZipA at center of cell, ZipA acts as anchor
2. FtsA joins ring, then FtsK
3. FtsQ, FtsI, FtsB added, then FtsW + FtsI and then FtsN
4. Constriction at septal site
5. EnvC + EnvA help with cell envelope synthesis
69
What happens when mutants lack FtsN?
Form filaments that have no constrictions
70
What is the role of MinCD?
(Prevents FtsZ ring formation) oscillates in the cell and blocks septum formation; high concentration of MinC at the poles
71
What is the role of MinE?
Controls minCDs oscillation; in the middle of the cell in order to push minCD to the poles; forms its own ring
72
What is the mechanism of minCD and minE together?
1. minCD forms cylinder coat in one half of a cell, ring of minE formed at end of cylinder
2. minE ring moves sideways towards pole, removes minCD from half through minD ATP hydrolysis
3. minCD reassembles on other half of cell & repeats
73
What are the early events in cell division?
1. minE forms ring, relieves FtsZ formation by MinCD. MinE keeps region free by moving proteins to pole
2. FtsZ assembles into ring, recruits proteins to form septal ring
3. Constriction, MinE disassembles
4. MinE forms ring at center of new cells. MinCD prevents FtsZ formation at other sites
74
What is the recap of events of binary fission?
1. DNA replication
2. Separation of bacterial chromosomes
3. Septum formation
4. Cell division
75
What are the 3 methods to measure cell growth?
1. Direct count
2. Flow cytometer
3. Viable count
76
What are the pros & cons of direct count of cells?
Pros: Quick; Disadvantage: Human error, bacteria motile
## Footnote
Done by determining cell number of living & dead cells by dilution and fill chamber, stain
77
What are the pros & cons of flow cytometer?
Detecting cells passing through a laser beam
## Footnote
Pros: Sensitive; Cons: Too sensitive
78
What are the pros & cons of viable count?
Measure cells that reproduce / alive
## Footnote
Done through serial dilutions and plating and counting; Pros: Easy to perform, sensitive; Cons: One cell does not equal to one quality
79
What are the 3 ways of measuring changes in cell mass?
1. Indirect measurement - measurement of turbidity/density
2. Use of spectrophotometer
3. Direct measurement - dry weight
80
What are the pros & cons of spectrophotometer?
Pro: Quick, does not destroy sample; Disadvantages: Not sensitive
81
What are the pros & cons of direct measurement?
Dry weight through centrifugation, washes, & dry at 70 C & weigh
## Footnote
Pro: More sensitive; Cons: Washing with non-isotonic liquid leads to lysis & loss of cells
82
What are the ways to change weight in part of cell mass?
1. Biuret
2. Folin reaction
3. Coomassie blue
83
What are the pros and cons of Biuret Assay?
Pros: Not biased in terms of amino acid content; Con: Large amount of protein needed for reading
84
What are the pros and cons of Folin reaction?
Pros: Depends on interaction of protein oxidized with Folin reagent - coupled with reduction of phosphotungstate & phosphomolybdate
## Footnote
Pro: More sensitive; Con: Interference
85
What are the pros and cons of Coomassie blue?
Bradford method dyes positively charged protein
## Footnote
Pros: Sensitive, rapid; Con: Less sensitive to interference
86
What are the 4 phases of growth?
1. Lag phase = bacteria adapting to environment
2. Log phase = bacterial growth
3. Stationary = new growth = death
4. Death = no growth
87
What does shift down mean?
Less nutrition in new culture than the inoculum
88
What does shift up mean?
More nutrition (min to rich)
89
What is lag phase?
Period of adjustment, influenced by conditions
90
How would you shift up a culture of bacteria? Would that process shorten lag phase? Why or why not?
Place bacteria in nutrient-rich broth
## Footnote
Would make lag phase longer because bacteria has to adapt to new conditions
91
What is k?
Growth rate, change of cell mass or number of generations/unit of time
92
What is Y?
Generation time, from plot x vs t
93
What is the response to limiting nutrients in terms of cell size?
No nutrients = smaller size
94
What is the response to limiting nutrients in terms of morphology?
Rod shape organisms become cocci
95
What is the response to limiting nutrients in terms of surface property?
Organism becomes more hydrophobic due to attachment to nutrients
96
What is the response to limiting nutrients in terms of metabolic activities?
Decrease in metabolism
97
What is the response to limiting nutrients in terms of protein composition?
Increase in variety of proteins (ex: increase in nitrogenase)
98
What is the response to limiting nutrients in terms of resistance to environmental stress?
Resistance to increased temperature, pH changes, & hydrogen peroxide
99
What are the 3 proteins synthesized due to resistance to environmental stress?
1. Catalase
2. Exonuclease
3. Acid phosphatase
100
What is the response to limiting nutrients in terms of control of rRNA synthesis?
Decreases rRNA synthesis due to amino acid starvation
101
How does cell composition change as a function of growth?
Increased ribosomes = increased growth rate
102
What is metabolism?
Response to limiting nutrients affects protein composition.
103
How does metabolism respond to limiting nutrients in terms of protein variety?
There is an increase in variety of proteins (ex: increase in nitrogenase).
104
How does metabolism respond to limiting nutrients regarding environmental stress?
Resistance to increased temperature, pH changes, & hydrogen peroxide.
105
What are the three proteins synthesized due to resistance to environmental stress?
1. Catalase
2. Exonuclease
3. Acid phosphatase
106
How does limiting nutrients affect rRNA synthesis?
Decreases rRNA synthesis due to amino acid starvation.
107
How does cell composition change as a function of growth?
Increased ribosomes = increased growth rate, increased RNA/protein ratio, increased DNA, increased mass.
108
What is diauxic growth?
Uses glucose first and then lactose.
109
In the formula Bf-B0 = Y(C0 - C), what does B, C, and Y represent?
B = biomass
C = limiting nutrient
Y = dry weight of bacteria/limiting nutrient.
110
What happens to yield when there is a small amount of limiting nutrient and a large amount of biomass?
Yield goes up.
111
What is continuous culture?
Unlimited log phase used by chemostat in a constant environment vs environment that is constantly changing.
112
How is bacterial diversity maintained in a chemostat?
Limit on nutrient such as glucose to maintain in log phase.
113
What is chemostat operation based on?
Variation of growth rate with limiting nutrient.
114
Explain the self-correcting system of a chemostat.
Increased fresh medium -> increased loss of cells -> decreases cell density -> increases growth rate -> loss of cells becomes equal to cells produced -> decreases growth rate.
115
What is MRT?
Mean residence time - average time of cell in culture vessel.
116
How to calculate the rate of cell loss from the outflow?
Multiply the number of cells by the dilution rate.
117
What is V/f?
V = volume of culture, f = flow rate (units of culture volume/hour).
118
How can growth rate be changed in relation to D = f/V?
By changing f, which determines dilution rate.
119
In steady state, what is the relationship between growth rate and dilution rate?
k = d.
120
What happens at higher growth rates?
Increased dilution rate = growth rate is faster = doubling time shortens until washout at high dilution.
121
How is the density of bacterial cells in the growth chamber manipulated?
By changing the concentration of limiting nutrient.
122
In the equation Y = x / Sr-S, what does each unit represent?
Y = growth yield
x = amount of bacteria
Sr = substrate in reservoir
S = substrate in vessel.
123
What conclusions can be made from the equation Y = x / Sr-S?
1. If you increase Sr, you increase X.
2. Only way to change K is to change D in chemostat (adding more media).
3. Only way to change X is to change S.
124
What is dilution rate?
Rate of medium is added.
125
What is steady-state?
Growth rate = dilution rate.
