Exam 3 Review - TY Flashcards
1
Q
T/F: Euk. and prokaryotes share a very similiar system of binary fission
A
FALSE
1
Q
BLANK is the division of one cell to two cells
A
Binary fission
2
Q
What are some key things that happen in Binary fission?
A
- DNA replication
- Cell elongation
- Septum Formation
- Completion of Septum formation
3
Q
BLANK shares a similar system to the spindles of Euk. They are found in BLANK environments, and (ARE/ARE NOT) our normal pathogenic bacteria.
A
- Caulobacter (stalked bacteria)
- Soil environments
- ARE NOT
4
Q
Caulobacter use a BLANK system (partitioning system)
A
Par
5
Q
At replication initiation, we see anchoring of what? And where?
A
- anchoring of parent chromosome to one pole of cell
6
Q
BLANK proteins localized to the stalked pole
A
PopZ
7
Q
BLANK bind to a BLANK sequence within original chromosome
A
- ParB
- ParS
8
Q
Once ParB is bound to ParS, a conformational change occurs and BLANK binds, anchoring them to one side
A
- PopZ
9
Q
As replication goes on, BLANK will be able to find another BLANK sequence. If PopZ is already taken up, ParB will bind to BLANK, using energy to move ParB to the other pole
A
- Par B
- ParS
- Par A
10
Q
What is ParA?
A
ATPase, motor protein that binds to ParB and uses energy to move ParB to the other pole
11
Q
What is our “pathogenic” Bacteria that exhibits replication toward the end?
A
E. coli
12
Q
E.coli (pathogenic) exhibit seperation toward the end of replication. How do they unlink/separate chromosomes that are intertwined in the rings? (Structural maintenance of chromosome complex)
A
- Topoisomerase IV (cuts/unlinks)
- MukBEF proteins
(grab onto chromosomes and separates them as they gravitate to poles)
13
Q
BLANK cuts/unlinks chromosomes
A
Topoisomerase IV
14
Q
BLANK grab chromosomes and seperate them as they gravitate toward poles
A
MukBEF proteins
15
Q
What are the steps of Septation?
A
- Select Site
- Formation of FtsZ ring and Divisome formation
- Anchor FtsZ to plasma membrane
- Assemble cell wall
synthesizing machinery - Constriction of cell and septum
16
Q
Where is the location of Septation?
A
- exact midpoint of the cell
17
Q
Septation at the midpoint occurs in BLANK shaped bacteria, BLANK work slightly different.
A
Rod
Cocci
18
Q
What 3 proteins are used in the selection of site (septum)
A
- MinC + D
- MinE
19
Q
What proteins oscillate on an intracellular track? Where is the lowest and highest concentrations of these?
A
MinC + D
- Highest concentration at the poles, lowest at the exact midpoint
20
Q
What proteins makes up the intracellular track for the selection of site (septum)?
A
MinE
21
Q
In the exact midpoint, BLANK molecules are inserted, and the FtsZ ring is formed.
A
- FtsZ
22
Q
The Divisome includes other proteins, list them (4).
A
- FtsA
- ZipA
- FtsK
- FtsI
23
Q
T/F: In terms of elongation, we have multiple sites
A
True
24
(Divisome): Blank and BLANK are cell membrane anchors
FtsA and ZipA
25
(Divisome): BLANK binds to chromosomes, holding them in place
FtsK
26
(Divisome): BLANK is involved in peptidoglycan synthesis
FtsI
27
Note on Fts proteins:
Z =
A =
I =
K =
FtsZ = Midpoint
FtsA = Anchor
FtsI = Pep synth.
FtsK = Holds chromosomes together
28
BLANK is the site of cell wall synthesis and contains BLANK
MreB sites
Elongasomes
29
BLANK associates with the plasma membrane, holds the cell in the right shape, and has additional sites of peptidoglycan synthesis.
Elongasomes
30
MreB is homologous to BLANK
Actin
31
For cell wall synthesis, we should be thinking what?
Cell wall elongation, in terms of peptidoglycan
32
What are the four steps that occur at elongasomes for elongation to occur?
1. Autolysin Activity (CLEAVAGE)
2. Bactoprenol
(NEED TO FEED IN PEPTIDOGLYCAN PRECURSORS)
3. Glycosylase Activity
(GLUE)
4. Transpeptidation
(ENZYME THAT FACILITATES CROSSLINKING)
33
BLANK activity is cell lysis in a controlled manner. It cleaves at BLANK linkages between BLANK and BLANK
- Autolysin
- B1,4-glycosidic linkages
- NAG and NAM
34
BLANK facilitates precursor transport across the hydrophobic membrane. BLANK has 5 amino acids attached, list these.
- Bacteroprenol
- NAM
L-Alanine
D-Glutamic Acid
DAP
D-Alanine
D-Alanine
35
BLANK activity pastes in the BLANK and BLANK in the peptidoglycan into the cleavage point. (This is for sugars, not a protease)
- Glycosylase
- NAG and NAM
36
BLANK is an enzyme that crosslinks peptides between BLANK. This requires energy, which is obtained from the removal of an extra BLANK.
Transpeptidation
- NAM
- fuck u Brady
37
Give an example of a Transpeptidation enzyme.
Transpeptidase (FtsI)
38
What is a good target for antibiotics?
Peptidoglycan
39
Penicillin targets BLANK, specifically BLANK to prevent crosslinking. This lack of crosslinking keeps BLANK active.
- Transpeptidase
- FtsI
- Autolysin
40
With penicillin, where are mutations that help resistance usually observed?
FtsI since this is where penicillin targets
41
BLANK inhibits transpeptidase, but does not bind to BLANK, instead, targets Amino Acids, specifically BLANK to prevent extra energy.
- Vancomycin
- FtsI
- D-Alanine
42
Mutations that help resistance to Vancomycin, are usually observed in BLANK, which changes it to BLANK.
- D-Alanine
- D-Lactate
43
Rods have multiple sites of elongation, while Cocci do not. This is due to them lacking BLANK.
Absence of this allows FtsZ ring to become the BLANK and BLANK center.
- MreB
- Divisome
- Elongation center
44
What do antibiotics target?
Peptidoglycan synthesis
45
T/F: Cells must be actively growing or antibiotics will have no effect
True
46
Do antibiotics effect the existing peptidoglycan?
No
47
BLANK are big networks, mushroom like organizations of bacteria. The BLANK layer is usually growing, while the other is dormant.
- Biofilms
- Outer layer
48
Bacterial populations exhibit BLANK growth, rate is BLANK, and BLANK.
- Exponential growth
- Constant rate / Linear
49
What is the formula for Number of Bacteria
N = N0 x 2^n
50
What is the formula for mean growth rate / generation/Hr?
LogNt - LogN0 / Log2 (t)
51
What does log(2) = ?
0.301
52
Explain a Batch culture
- closed system
- specified amount of nutrients, air, media, etc.
- usually uses test tubes with a cap
**What they start with is all they get
53
What are the 4 phases of a batch culture growth curve?
1. Lag Phase
2. Exponential Phase
3. Stationary Phase
4. Death Phase
54
Which phase is the shortest?
Lag phase
55
What factors dictate the lag phase?
- length depends on the initial culture used to inoculate
- most primed vs. starving state
- most acclimated = faster
56
One bacteria are primed, they enter the BLANK phase.
Exponential phase
57
What phase are bacteria living at maximum potential? (Access to the most nutrients)
Exponential phase
58
Once bacteria hit their plateau, what phase do they leave and enter?
Leave Exponential phase
Enter Stationary phase
59
The stationary phase is where we have what in terms of growth and death rates?
They are equal rates for growth and death.
60
What factors accumulate in the stationary phase?
- Waste products build up (Acids, etc)
- Less space
- Less nutrients
61
What marks the end of the stationary phase?
Waste products become so high that growth is declining
62
What phase is the longest?
Death phase
63
Explain some features of the death phase
- longest phase
- more death than reproduction
- Exponential rate but not nearly as steep as exponential growth phase
64
As the environment degrades in the stationary phase, what type of cells do we see forming?
Persister cells
65
What two features do the pesister cells exhibit that contribute to their lifespan?
1. Starvation mode (protection)
2. Cryptic growth (maintainence)
66
Persister cells go into a starvation mode, where they upregulate proteins. What does this cause and what proteins are observed? What do these proteins do?
Increase crosslinking in peptidoglycan
- Chaperone proteins
(protect DNA and bind enzymes to prevent denaturing)
67
How do persister cells "Maintain"?
- go into a cryptic growth
- Some cells go into a programmed cell death to provide energy for others
68
Persister cells can also go into what state? Can they come out of this?
- Viable but Non-culturable State (VBNC)
- they can come out of this if nutrients become available again
69
When using the viable count method, what is needed? How are they counted at the end?
- Known number of organisms (start)
- Counted using serial dilutions
70
Instead of bacteria/ml, what do we use?
cfu/ml
71
cfu/ml = ?
cfu/ml = plate count x DF x 1/ amount plated
72
What are some negatives of Viable cell count (plating method)?
- limited in what we can grow
- count colonies not individual bacteria
- Takes more time
73
What does the Direct (total) cell count use?
- Microscopes
- Hemocytometer
74
Are dilutions still needed in the Direct cell count method?
Yes
75
In the Direct (total) cell count, microscopes and BLANK are used. The sample is placed in a 4x4 square, observed and individual BLANK are counted, taking the average. The last step is to use BLANK as they are still needed.
- Hemocytometer
- bacteria
- Dilutions
76
What method counts individual bacteria?
Direct (total) cell count
77
What method is easier to count, and counts both dead and alive cells?
Direct (total) cell count method
78
Which method would likely give a smaller cell count? Why?
Viable count method would give a smaller number since its counting colonies, rather than individual bacteria in the Direct (total) cell count. Direct also count alive and dead.
79
An indirect measurement of growth, BLANK, uses a BLANK to determine bacterial concentrations. TO achieve this, a BLANK is needed to compare numbers. What is a negative for this?
Turbidity
- spectrophotometer
- Standard curve
- The negative is, we need a standard curve, which means we cannot use this method for new bacteria
80
What is a new method for cell counting?
Flow Cytometer
81
The Flow cytometer uses BLANK focusing, and creates very thin samples to go in front of a detector, BLANK cell at a time.
- Hydrodynamic focusing
- one cell at a time
82
T/F: You can use several types of cells with a flow cytometer
True
83
In flow cytometer, what gives us cell size?
- Forward light scatter
84
In flow cytometer, BLANK light scatter gives us Cell BLANK (density inside the cell).
- Side light scatter
- Granularity
85
Cell granularity is often measured in BLANK cells. This is used to see highly granulated vs. non-granulated cells.
Immune cells
86
What are the Four biggest features of Flow Cytometer?
1. Cell Size
2. Cell Granularity
3. Cell Sorting
4. Immunofloresence
87
A chemostat is used to examine BLANK interests.
Metabolic
87
BLANK is a continuous culture system.
Chemostat
88
What factors can we control in a Chemostat?
- Specific growth rate
- Cell density
89
What controls the specific growth rate in the chemostat?
Dilution rate: Rate at which new media is added and old media is removed
89
What controls cell density in the Chemostat?
Use of a limiting nutrient
- keep one nutrient at a specific level to make sure population does not get out of hand
90
4 environmental factors that effect microbial growth
1. Temperature
2. pH
3. Osmolarity
4. Oxygen
91
Can bacteria thermoregulate?
No
92
BLANK is the range (min, opt, max) of temperatures for bacteria.
Cardinal range
93
The Cardinal range is usually what?
15-40 degrees
94
What factors dictate cardinal range?
1. Enzymes (more max range)
2. Cell membrane (more min range)
95
Cell membrane is involved with BLANK of the cell.
Fluidity
96
The minimum temperature is defined what?
Cell membrane
- Slower / less movement in cytoplasm
97
The optimum temperature is closer to the BLANK temperature. Why?
Maximum
We need fluidity in the membrane, higher temps things move more
98
Maximum temperature is defined by what?
Enzymes
- higher temps cause denaturing, which these help to prevent
99
Eukaryotic, Prokaryotic, and Archaea max temps
E = 65C
P = 95C
A = Over 95C
100
BLANK live in colder temperatures, with smaller ranges
Psychrophile
101
BLANK live in the optimal temp of 37C (our temp), and are often BLANK organisms.
Mesophiles
- pathogenic
102
What is in the middle between mesophile and hyperthermophile
thermophile
103
What (higher) range are bacteria a part of ?
Hyperthermophile
104
What (higher) range are archaea a part of ?
Hyperthermophile
105
Psychrophiles have an optima of 15C or less. What changes do we see in their enzymes?
1.) More Alpha helices (increases flexibility) in Beta sheets
2.) More polar/less hydrophobic interactions (increases flexibility).
--> Hydrophobic interactions are very strong and cause rigidity, so decreasing is essential
3.) Cold shock proteins --> Chaperone proteins
--> Constitutive expression (always on)
106
Psychrophiles have an optima of 15C or less. What changes do we see in their cell membrane?
Fatty acids are unsaturated and have shorter chains
107
Psychrophiles have an optima of 15C or less. What changes do we see past enzymes and cell membrane?
1. Cryoprotectants
--> specific solutes like glycerol and sugars (offset freezing point)
2. Exopolysaccharide
--> layer on the outside to add insulation
108
Psychrophiles have an optima of 15C or less. What changes do we see?
1. Enzymes (Alpha helices, polar, cold-shock proteins)
2. Cell membrane (FA)
3. Cryoprotectants (solutes)
4. Exopolysaccharide (insulation)
109
BLANK grow in cooler temps like the fridge. Give an example.
- Psychrotolerants
- Listeria monocytogenes
110
BLANK are commonly pathogenic
Mesophiles
111
BLANK are found in direct sunlight, often in soil. Ranges 50-70C.
Thermophiles
112
What changes do we observe in the enzymes of thermophiles?
- highly hydrophobic interiors (adds rigidity)
- Stabilizing solutes
--> Di-inositolphosphate
--> Diglyceride Phosphate
113
What are the two stabalizing solutes used in thermophiles?
- Di-inositolphosphate
- Diglyceride Phosphate
114
What changes to we observe in the cell membrane of thermophiles?
- Fatty acids are saturated and have long chains
(increases melting point and hydrophobic interactions)
115
BLANK are found in Hot springs, steam vents, range 100 - 500C and often contain Archaea. BLANK are expressed, creating what?
Hyperthermophiles
Biphatanol is expressed, creating a monolayer instead of a bilayer
116
When talking about pH, is it external or internal that we focus on?
External, internal pH does not have alot of room to change.
117
What pH range do we see inside the cell?
5-9
118
Mesophiles are nutraphiles with a pH around BLANK. What two buffers do we commonly see, used in tissue culture?
pH = 7
1. Sodium Bicarbonate
2. Potassium Phosphate
119
Blank are found in more acidic environment, having (MORE / LESS) Archaea than bacteria and a lower pH, usually below BLANK externally.
Acidophiles
- More archaea than bacteria
- external pH usually lower than 5.5
120
How do Acidophiles deal with a low external pH ? (concentration gradient)
- Transport cations into the cell to balance out (K+)
- Proton transporters (pump protons back out)
- Highly impermeable membranes (barrier)
121
BLANK are in more basic/alkalinity environments that have a high pH. How do they deal with this?
Alkaphiles
- Sodium motive force
122
In basic environments, the concentration of H is BLANK. In acidic environments, the concentration of H is BLANK.
Low
High
123
BLANK = lots of solutes inside
Hypotonic
124
BLANK = lots of solutes outside
Hypertonic
125
How do bacteria deal with hypotonic conditions?
- Mechanosensitive channels that put pressure on the membrane
- dump solutes out
126
How do bacteria deal with hypertonic conditions?
- Compatible solutes that are highly water-soluble solutes
Ex: Sugars (sucrose, trehalose), AA derivitaves
127
Are compatible solutes universal across species?
No, they are controlled genetically and range, which can be used to categorize species.
128
What is a consideration for hypertonic, specifically the compatible solutes and metabolism?
They cannot interfere with metabolism and reactions that take place in the cell
129
What are some compatible solutes?
- Sugars (Sucrose, trehalose)
- Amino acid derivatives
130
BLANK grow optimally when in the presence of NaCl.
Halophiles
131
The presence of BLANK dictates growth of halophiles
NaCl
132
Range for a Mild Halophile:
Compound type:
1-6%
Organic compounds
133
Range for a Moderate Halophile:
Compound type:
7-15%
Organic compounds
134
Range for a Extreme halophile:
Compound type:
15-30%
Inorganic compound: KCl
135
BLANK organisms grow best in the ABSENCE of NaCl but can withstand a small concentration in the environment
Halotolerant
136
What is tied directly with metabolism?
Oxygen
137
BLANK requires gaseous oxygen for metabolism
Aerobe
138
BLANK cannot withstand atmospheric oxygen levels but REQUIRE a low level of oxygen. What is this range>
Microaerophile
2-10% O2
139
BLANK do not use oxygen in metabolism. The first type, BLANK will not use oxygen, but can withstand its presence, the second, BLANK cannot be around it at all (deadly).
Anaerobes
- Aerotolerant
- Obligate/strict
140
BLANK use oxygen in respiration but can also live without it
Facultative anaerobes
141
With facultative anaerobes, do they prefer oxygen or another source for the for metabolism and why? What other pathways are available if O2 is not.
Oxygen is preferred as it releases more energy.
- Fermentation (No ETC)
- Anaerobic respiration (use ETC)
142
BLANK broth is whats used to detect types of metabolism in bacteria
Thioglycollate broth
143
What three factors are used Thioglycollate broth
1. Sodium thioglycolate
2. Redox indicator
3. Small amount of agar
144
BLANK is used to reduce oxygen
Sodium thioglycollate
145
With the redox indicator:
Pink =
Yellow =
Pink = O2 present
Yellow = no O2
146
Why is a small amount of agar used?
allows for fluidity but still limits O2
147
Where do aerobes grow?
Just at the top (pink layer only)
148
Where do facultative anaerobes grow?
Everywhere, but with bias to the top where oxygen is present
149
Where do obligae anaerobes grow?
Heavy growth at bottom where no oxygen is present
150
Where to aerotolerant grow?
No bias, even spread
151
Oxygen can be turned into toxic byproducts referred to as BLANK
Reactive oxygen species (ROS)
152
Why are reactive oxygen species harmful?
They are highly reactive and can react with proteins and everything around them, denaturing them
153
What are some examples of ROS
1. Singlet oxygen (O)
2. Superoxide anion (O2-)
3. Hydrogen Peroxide (H2O2)
4. Hydroxyl radical (OH)
154
What ROS species are usually the first to be produced?
- Superoxide anion (O2-)
- Hydrogen peroxide (H2O2)
155
What is the most potent ROS?
- Hydroxyl radical (OH)
156
How do bacteria protect themselves against ROS?
Enzymes to destroy toxic compounds
157
Give an enzyme used to destroy toxic ROS. What does this produce? And what fixes this ?
Superoxide dismutase (for superoxide anion)
- produces hydrogen peroxide
- Catalase or Peroxidase is needed to destroy hydrogen peroxide
158
What (3) components in the ETC react with oxygen to create ROS?
- Flavoproteins
- Quinones
- Iron-sulfur proteins
159
What do aerotolerant organisms use instead of enzymes against ROS?
Protein-free manganese complexes
160
What do strict anaerobes use against ROS?
Superoxide reductase
- oxygen is not released as a product
- organisms cannot live around oxygen
161
Eukaryotic chromosomes
Geometry:
Number of chromosomes:
Amount of chromosomes:
- linear
- more than one
- large number
162
Why do euk have a larger amount of chromosomes?
Lots of non-coding DNA
Sexual reproduction = 2 copies of every gene
163
What percent of euk genome is non-coding DNA?
90%
164
Prokaryotic chromosomes
Geometry:
Number of chromosomes:
Amount of chromosomes:
- circular
- usually only have one
- smaller numbers
165
why do prok have smaller numbers of DNA?
Binary fission = one copy of every gene
Small number of non-coding DNA
166
what percent of genome is non-coding DNA in prok
less than 10%
167
DNA =
Deoxyribonucleic Acid
168
DNA is a polymer of BLANK, which are composed of a BLANK, BLANK, and BLANK.
Nucleotides
Pentose sugar
Phosphate
Nitrogenous base
169
What gives DNA its negative charge
Phosphate
170
What are the two forms of Nitrogenous bases?
Purines (AG)
Pyrimidines (TC)
171
What are the purines?
Adenine
Guanine
172
What are the pyrimidines
Thymine
Cytosine
173
How many hydrogen bonds between C-G and A-T?
C-G = 3
A-T = 2
174
Vegetative cells are in the BLANK form DNA
B-form
175
One helical turn =
10 base pairs
176
One helical turn creates BLANK and BLANK grooves
Major and Minor
177
A-form DNA has BLANK base pairs per helical turn, making it more compact
11
178
What is the largest component in a bacterial cell? What is second?
Peptidoglycan
DNA
179
In Euk, DNA is stored within the BLANK, while Prok store it in BLANK.
Nucleus
Nucleoid region
180
Condensing of bacterial DNA is facilitated by BLANK DNA into BLANK.
Supercoiling
Domains
181
The BLANK manner twists in the opposite direction of the right-handed double helix, causing supercoiling
Negative
182
BLANK are enzymes that either insert or remove supercoiling
Topoisomerases
183
Topoisomerases are separated into two classes. Explain them.
Class 1: Nick one strand of the chromosome
--> Single protein, nicks single strand
Class 2: Nick both strands of chromosome
--> Multi-subunit complex, nick both strands
184
With class 2 topoisomerases, what is most common for insertion?
DNA Gyrase
185
Does Supercoiling require energy?
Yes
186
BLANK are positively-charged proteins that bind to DNA and stablize them into BLANK
Histone-like proteins
- Domains
187
What is similiar about Euk and Prok Histones / histone like proteins
The (+) charge associated, thats it
- this allows interaction with the (-) charged DNA
188
BLANK help with regulation and only expose what we need, when we need it
Domains
189
Eukarya: DNA is wound around clusters of histone (#), forming structures called BLANK
- 8 histones
- nucleosomes
190
Archaea: Histones form clusters of (#), and utalize BLANK with DNA gyrase being most common.
- 4
- Topoisomerase
191
BLANK contain reverse DNA gyrase
Hyperthermophiles- Archaeal
192
Are histone-fold present in Euk, Arch, and Bact?
- Euk: Present, including ends
- Archaea: Present, only center
- Bacteria: Not present
193
Histone clusters (#) in Euk and Archaea
Euk = 8
Arch = 4
194
Topoisomerase expression in Euk, Arch, and Bacteria
Euk: Not expressed = good target for anti-biotics
Archaea: Some do some don’t (Usually DNA gyrase)
Bacteria: Usually class 2 (DNA gyrase)
195
Hyperthermophiles contain reverse DNA gyrase (positive supercoiling instead of negative). How does this help them?
High heat can cause denaturing. Positive supercoiling makes it harder to open up (much tighter).
They also have biphatenol = monolayer
196
Topoisomerase is a good target for anti-biotics. What are two examples of Quinolones?
1. Ciprofloxacin
2. Nalidixic acid
197
What doe quinolones target?
Topoisomerase, specifically DNA gyrase (most common)
