Midterm (lectures 1-12) Flashcards
(170 cards)
1
Q
_____ controls are an experimental treatment which will give the desired result
A
Positive
2
Q
_____ controls are an experimental treatment which will not give the desired result
A
Negative
3
Q
False ____ can be detected by our negative control
A
positives
4
Q
False ____ can be detected by our positive control
A
negatives
5
Q
What is sensitivity in terms of limitations of lab measurements?
A
The minimum amount of X needed to record a positive result
6
Q
What is specificity in terms of limitations of lab measurements?
A
A positive result only comes from a truly positive result
7
Q
What is the difference between random error and systematic error?
A
Random: new error introduced with each measurement
Systematic: error that is consistently present
8
Q
What is the difference between accuracy and precision?
A
Accuracy: how close a recorded value is to the true value
Precision: how reliably you can measure a value
9
Q
A dye solution for DNA is made at 5mg/mL but the working concentration should be 50µg/mL. How much is needed to make 300µL of a DNA solution?
A
C1 = 5mg/mL -> 5000µg/mL
C2 = 50µg/mL
V2 = 300µL
C1V1 = C2V2; V1 = C2V2/C1; ANS = 3mL
10
Q
pH = ?
A
-log[H+]
11
Q
Buffered solutions reduce pH ______
A
fluctuations
12
Q
What is the pKa?
A
the pH where there is 50% weak acid and 50% conjugate base
13
Q
A buffer pair is only effective +/- __ unit from the pKa
A
1
14
Q
What is the Henderson-Hasselbalch equation?
A
pH = pKa + log[base]/[acid]
15
Q
Both the amino and carboxyl ends of an amino acid can act as an ____/____ ____ ____
A
acid, conjugate base pair
16
Q
At a low pH, both ends are _____ and charge is ___
A
protonated, +1
17
Q
At a high pH, both ends are _____ and charge is ___
A
deprotonated. -1
18
Q
At a moderate pH the ___ end is protonated, the ____ end is deprotonated and the net charge is neutral
A
amino, carboxyl
19
Q
An amino acid charge will change as the __ changes, therefore _____ _____ will be pH dependent
A
pH, protein stability
20
Q
___ temperatures will denature proteins making them non-functional
A
high
21
Q
The effectiveness of heat killing is altered by ?
A
Temperature, time, conductance
22
Q
Boiling point can be increased by ?
A
pressure
23
Q
What is the mechanism we use in the lab for steam sterilization?
A
Autoclave
24
Q
What is the solution for solutions that cannot be heated?
A
Filtration. Liquids can be passed through filters which contain holes too small for bacteria to pass
25
The quality of the image in a basic microscope is dependent on: ?
Thickness of section, lighting, quality/cleanliness of lenses, and staining
26
Oil immersion lenses increase resolution by increasing the _____ _____
numerical aperture
27
How would you calculate Absorbance with a spectrophotometer?
Abs = log [1/T]
28
What is the formula for resolution? And explain what each symbol represents
R = 0.61λ /NA, where NA = nsinθ
λ: wavelength of light
NA: numerical aperture of the lens
n: refractive index
θ: 1/2 the angle the light can enter the lens
29
What is the formula for Beer-Lambert Law? And explain what each symbol represents
A = elc
e: molar absorptivity in L/molcm
l: path length in cm
c: concentration in mol/L
30
What is the Bradford Assay?
Measurement of color change when Coomassie Blue dye binds to protein. Unbound gives a reddish brown, whereas bound gives a blue color.
31
What are the pros/cons of the Bradford Assay?
it is quick and simple, but upper limit for linear detection of ~2mg/mL and dye and precipitate if detergents are present
32
What is the Biuret Assay?
Measurement of color change when Copper II Sulfate reacts with proteins under alkaline conditions. The solution turns purple
33
What is the spherical bacterial shape?
Coccus/cocci
34
What is the rod bacterial shape?
Bacillus/bacilli
35
What is the bent rod bacterial shape?
vibrios
36
What is the tight helical bacterial shape?
spirillas
37
What is the loose bendy bacterial shape?
spirochetes
38
What are pairs of bacterium called?
Diplo
39
What are clusters of bacterium called?
staphylo
40
What are chains of bacterium called?
strepto
41
Groupings of bacteria are related to the ____ of cell division
plane
42
Describe the cell wall structure (x3)
- Threads of a repeating carbohydrate (NAG-NAM)
- Glued together with proteins
- These sugars and proteins form a compound called peptidoglycan
43
___-_____ makes the wall durable
cross-linking
44
Gram ____ cells have multiple layers of ______, with _____ _____ aiding in keeping the layers together that also help in increasing the ____ charge of the cell wall
positive, peptidoglycan, teichoic acids, negative
45
Gram ____ cells have a single layer of ______, a second ____ _____ outside the peptidoglycan which helps to block entry of ______, and can be ______
negative, peptidoglycan, phospholipid membrane, antibiotics, toxic
46
What are the 5 most common kinds of staining discussed in this class?
Gram, Acid Fast, Negative, Flagella, Endospore
47
What is the point of aseptic technique?
Prevention of contamination
48
Which counterstain do you use with acid fast stains?
methylene blue
49
What is the difference between a capsule and a slime layer?
Capsule: neatly organized
Sime layer: unorganized and loose/diffused
50
The glycocalyx increases ______
pathogenicity
51
What is a negative stain?
Allows for the visualization of the glycocalyx, composed of nigrosin/congo red acidic dyes
52
What is the pro/con of the Negative stain?
Cells are not fixed, but additional staining is needed to visualize bacteria
53
Visualization with a light microscope requires the ______ of the flagellum
thickening
54
What are atrichous flagella patterns?
The complete absence of flagella
55
What are monotrichous flagella patterns?
singular flagella
56
What are amphitrichous flagella patterns?
flagellum on both ends
57
What are lophotrichous flagella patterns?
tufts from a single point
58
What are peritrichous flagella patterns?
surrounding the bacterium
59
Endospore producing bacteria are also known to produce ____
toxins
60
Which dye is used for an Endospore Stain, and what is used as a counterstain?
Malachite Green, safranin
61
Order these in context of coldest to hottest: mesophile, psychotroph, thermophile, psychrophile, hyperthermophile
Psychrophile, psychrotrophs, mesophile, thermophile, thermophile, hypertherophiles
62
Most bacteria need a salt salt concentration below __%
2
63
Extreme halophiles can live in __-__% salt
30-40
64
Rank these elements as most commonly found in living organisms to least common: phosphorus, calcium, carbon, sulfur, nitrogen, hydrogen & oxygen
Hydrogen & oxygen
Carbon
Nitrogen
Phosphorus
Sulfur
Calcium
65
Oxygen generates free radicals that damage ___, ____, and ___
DNA, proteins, lipids
66
Aerobically living organisms can produce a series of enzymes which ____ the oxygen free radicals
detoxify
67
Describe the Catalase test
Where we introduce hydrogen peroxide to a sample and if oxygen bubbles then it is positive
68
What are obligate aerobes?
Only grow and survive in the presence of oxygen
69
What are facultative anaerobes?
Can grow in the presence or absence of oxygen
70
What are obligate anaerobes?
Cannot tolerate oxygen and grow in its complete absence
71
What are aerotolerant anaerobes?
Can survive in the presence of oxygen, but do not use it
72
What are microaerophiles?
Require oxygen, but only at reduced levels and lower concentrations
73
What is a complex media?
Has fewer things, but are more complicated. We are not aware of every chemical in the media
74
What is a defined media?
Usually has more things, but we know exactly what they are. Every chemical in the media is known. Can be tailored to requirements
75
What conditions are created using a Candle Jar?
It will not create a completely anaerobic environment, just a much lower oxygen concentration
76
What are the pros/cons of broth?
Grow large quantities of culture, but difficult to check for purity
77
What are the pros/cons of plate?
Readily score and separate colonies, but does not score well
78
What are the pros/cons of slants?
"Mini-plates" for storage with smaller volume, but difficult to check for purity
79
What are the pros/cons of semi-solid deeps?
Can score motility and oxygen requirements, but difficult to check for purity
80
What is agar?
Carbohydrates, it melts at 85 degrees. It has thermal hysteresis: after it comes down from 85 degrees and solidifies, you can go all the way back up close to 85 degrees without it melting again
81
What is Nutrient Agar made of and who is it best suited for?
Peptone and beef extract, suitable for non-fastidious(non-picky eater) organisms
82
____ media will encourage the growth of some bacteria while preventing the growth of others
Selective
83
______ media will produce different visual cues as to the type of organism growing
Differential
84
______ media is a type of selective media used to allow proliferation of rare bacteria in a mixed population while limiting other organisms
Enrichment
85
What are MacConkey plates used for?
Selective and differential, selects against non-enteric gram +'s. Contains lactose and pH indicators: fermenters turn purple and non-fermenters stay creamy
86
What are Mannitol Salt Agar (MSA) plates used for?
Selective and differential, and has high salt content. Fermenters turn yellow, non-fermenters stay red
87
What are Blood Agar (BAP) plates used for?
Enrichment and differential, test for hemolytic activity (cells which can bursts red blood cells).. Alpha is (greening), beta is (clearing, making it look yellow), gamma is (none)
88
What are Saboraud Dextrose Agar (SDA) plates used for?
Similar to nutrient agar but with a high amount of glucose (4%). Selects for acid and high sugar, mostly molds, and inhibits most bacteria
89
What are SIM Deep tubes used for?
All differential:
Sulfur Reduction: positive reaction turns black
Indole Production: if tryptophan is metabolized, it produces indole, which can be detected by dripping Kovak's reagent on top (red = positive)
Motility: if cells grow away from the stab they are motile
90
What is an oxidase test?
Test for cytochrome 3, if positive will turn the paper purple
91
Order these phases into the proper order for a growth curve: Log/exponential phase, death phase, lag phase, stationary phase
Lag phase, Log/exponential phase, stationary phase, death phase
92
What is the lag phase of a growth curve?
Initial inoculation, the bacteria are getting used to and optimizing their machinery to take advantage of the environment around them
93
What is the log/exponential phase of a growth curve?
More cells are dividing than dying, some are still dying but cannot keep up. The increase is exponential
94
What is the stationary phase of a growth curve?
At some point something becomes limited. Is a plateau, not the absence of cell division, some are still dividing, but those cells are balanced by the equal number of cells that are dying off
95
What is the death phase of a growth curve?
More cells are dying than dividing, but some are still dividing, but cannot keep up, the decrease is also exponential
96
What is turbidity?
The cloudiness of a solution
97
What is the difference between a viable count and a whole count?
Viable: Proof of life
Whole: living or dead
98
Plates with __-__ colonies are a good dilution to back-calculate to CFU
25-250
99
What method can be used to calculate the proper amount of concentrate needed on a plate for a good CFU count?
Serial dilution
100
What is an antibiotic?
Prevent the growth of bacteria while keeping the host healthy
101
There are two kinds of antibiotics, what are they?
Bactericidal: kills bacteria
Bacteriostatic: stops proliferation
102
What is the effective dose?
The concentration that kills the bacteria
103
What is the toxic dose?
The concentration with side effects/causes host toxicity
104
What is the optimal T/E (therapeutic index) value?
T/E should always be > 1, because if its < 1, it is host killing
105
Compare and contrast natural, semi-synthetic, and synthetic
Natural: Found in a living source
Semi-Synthetic: modified version of the natural compound
Synthetic: not living sourced at all
106
The closer an organism is to us, the ___ it is to treat as drugs must be more specific
harder
107
Cell inhibitors come in both ____ and ___-____ forms
natural, semi-synthetic
108
What are the 2 most common cell wall inhibitors?
Penicillins and cephalosporins
109
All cell wall inhibitors contain a __-____ ___
β-lactam ring
110
Natural penicillin works only against ___ __
gram +
111
For cell wall inhibitors, semisynthetic modifications can..?
- Make it more resistant to acid breakdown
- Make it more stable
- Broaden the activity spectrum
112
Are cell wall inhibitors lytic or static?
lytic
113
Protein synthesis are generally more ____ spectrum but more ___
broad, toxic
114
What are the two kinds of Plasma Membrane Damaging antibiotics?
Polymyxins, and Daptomycin
115
What are polymyxins?
Damage gram - membranes, they are poorly absorbed and toxic to neurons and kidneys
116
What is daptomycin?
Depolarizes gram + membranes
117
What kind of antibiotic is tetracycline?
Protein synthesis inhibitor
118
What kind of antibiotic is ampicillin?
A kind of penicillin, which is a cell wall inhibitor
119
What are nucleic acid synthesis inhibitor antibiotics?
Impair transcription or replication
120
_____ are metabolic inhibitors
Sulfonamides
121
Metabolic inhibitors are completely ____
synthetic
122
Metabolic inhibitors competitively inhibit ____ needed to generate ___, which is used to produce thymine and uracil and humans are unable to synthesize it
PABA, folate
123
No folic acid = ?
no life
124
What is sensitivity testing?
Use disk diffusion assays to determine what drugs are useful against a bacteria. It is non-quantitative and distance ranges
125
What are Epsilometer tests (E tests)?
Use a strip of antibiotic to determine a therapeutic dose
126
What is MIC?
Minimal inhibitory concentration
127
What are the 5 ways to increase antibiotic resistance?
1. Misuse of antibiotics
2. Discontinuing antibiotics before the pathogen is eradicated
3. Use a poorly chosen antibiotic
4. Use of antibiotics against viral infections
5. Preventative use of antibiotics
128
What are the 5 modes of resistance that bacteria may develop to fight antibiotics?
1. Drug modification
2. Pathway protection
3. Target alteration
4. Rapid Efflux
5. Alternative pathways
129
What organelle contains the potential to create antibiotic resistance through genetic changes?
Plasmid
130
What is a way modern medicine fights antibiotic resistance?
Using a combination of drugs greatly decreases the chance of developing drug resistance and reducing bacterial exposure
131
The charge of some R groups is __ dependent
pH
132
_____/__-___ R-groups tend to fold internally
hydrophobic non-polar
133
_____/___ R-groups tend to fold externally
Hydrophillic, polar
134
What is the reaction rate?
How fast substrate is converted into product
135
What are the 2 possible formulas for reaction rate?
v = -Δ[S] / Δt
v = +Δ[P] / Δt
136
What are the units of reaction rate?
Concentration over time
137
Over time, reactions will slow down as ___ decreases and ___ increases and enzyme molecules are lost to _____ and _____
[R], [P], denaturation, oxidation
138
_____ _____ ___ is used to get non-attenuated rates
Initial velocity (Vo)
139
Initial velocity is ideally measured quickly and for a short period of time ( ?)
before 10% of the reactant is used up
140
In a [P] vs t graph, what is the slope of the line?
Velocity
141
Rate can be limited by 2 things, what are they?
1. By the availability of substrate or enzyme ( the transition from E + S -> ES)
2. The time it takes for production of product (Transition from ES-> EP -> E + P)
142
Under ideal conditions, Vo is limited by ____ and _____
[S], enzyme
143
Under optimal conditions, and with an excess of substrate, the limiting step is ?
How fast the enzyme can catalyze ES -> E + P
144
What is the formula for Vo?
Vo = ([S] x Vmax)/([S] + Km)
145
What is Km?
The Michaelis constant, the affinity of the enzyme to bind to its substrate
146
What is the formula for Km?
Km = [S] when Vo = 0.5 Vmax
147
What is an example of the importance of different Km values?
Hexokinase initiates glycolysis and it has a Km of 30µM. Glucokinase can act as a sensor for glucose concentration by having a Km of 10mM
148
How has the Michaelis Menten equation evolved to the Lineweaver-Burk plot?
The Lineweaver -Burk plot uses the double reciprocal of rate and concentration to place Vmax and Km on the X and Y intercepts
149
The reciprocal of the Y-intercept is ___
Vmax
150
The negative reciprocal of the X-intercept is ___
Km
151
A _____ ____ reversibly binds to the active site and blocks substrate binding
competitive inhibitor
152
How can the inhibition be overcome with competitive inhibitors?
Having a high [S]
153
The ____ inhibitor has the same Vmax but an increased Km
competitive
154
The ____ inhibitor has the same Km but a decreased Vmax
noncompetitive
155
The ____ inhibitor has an increased Km but a decreased Vmax
uncompetitive
156
The ______ inhibitor is a compound that binds to the ES complex and slows the transition to EP, but does not bind to E alone
uncompetitive
157
In _____ inhibitors, as the ES complex is affected, but not E alone, the equilibrium for E + S -> ES shifts to the ___ to make the affinity appear higher
uncompetitive, right
158
______ inhibitors are compounds that bind to E and change the shape of the active site, so as there are fewer functional E proteins, the overall ____ will be reduced
Noncompetitive, Vmax
159
Unlike competitive inhibitors, in ___ inhibitors more substrate has no effect
noncompetitive
160
Each preparation/isolation of enzymes that do the same reaction may be faster or slower depending on factors like ?
purity or source organism
161
Different enzymes that complete the same reaction may have different values for ___ and ___
Vmax, Km
162
Enzymes are quantified by comparing the ?
amount needed to compete a set amount of reaction in a set period of time
163
What is 1 international unit (IU)?
Enzyme will catalyze 1µmol in 1 minute at an optimal temperature and pH, and high substrate concentration
164
What is activity?
The concentration of a enzyme
165
What are the units for activity?
U/mL or U/µL
166
How is total activity calculated?
Activity x volume
167
What is the formula for activity?
[(Δc/min)(reaction volume)]/(enzyme volume)
168
What is specific activity?
The potency of an enzyme by weight of protein
169
What is the formula for specific activity?
activity/[protein]
170
What are the units for specific activity?
U/mg or U/µg
