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BMSC 240 > Midterm (lectures 1-12) > Flashcards

Midterm (lectures 1-12) Flashcards

1
Q

_____ controls are an experimental treatment which will give the desired result

A

Positive

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2
Q

_____ controls are an experimental treatment which will not give the desired result

A

Negative

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3
Q

False ____ can be detected by our negative control

A

positives

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4
Q

False ____ can be detected by our positive control

A

negatives

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5
Q

What is sensitivity in terms of limitations of lab measurements?

A

The minimum amount of X needed to record a positive result

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6
Q

What is specificity in terms of limitations of lab measurements?

A

A positive result only comes from a truly positive result

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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

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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

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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

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10
Q

pH = ?

A

-log[H+]

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11
Q

Buffered solutions reduce pH ______

A

fluctuations

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12
Q

What is the pKa?

A

the pH where there is 50% weak acid and 50% conjugate base

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13
Q

A buffer pair is only effective +/- __ unit from the pKa

A

1

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14
Q

What is the Henderson-Hasselbalch equation?

A

pH = pKa + log[base]/[acid]

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15
Q

Both the amino and carboxyl ends of an amino acid can act as an ____/____ ____ ____

A

acid, conjugate base pair

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16
Q

At a low pH, both ends are _____ and charge is ___

A

protonated, +1

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17
Q

At a high pH, both ends are _____ and charge is ___

A

deprotonated. -1

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18
Q

At a moderate pH the ___ end is protonated, the ____ end is deprotonated and the net charge is neutral

A

amino, carboxyl

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19
Q

An amino acid charge will change as the __ changes, therefore _____ _____ will be pH dependent

A

pH, protein stability

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20
Q

___ temperatures will denature proteins making them non-functional

A

high

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21
Q

The effectiveness of heat killing is altered by ?

A

Temperature, time, conductance

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22
Q

Boiling point can be increased by ?

A

pressure

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23
Q

What is the mechanism we use in the lab for steam sterilization?

A

Autoclave

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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

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25
Q

The quality of the image in a basic microscope is dependent on: ?

A

Thickness of section, lighting, quality/cleanliness of lenses, and staining

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26
Q

Oil immersion lenses increase resolution by increasing the _____ _____

A

numerical aperture

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27
Q

How would you calculate Absorbance with a spectrophotometer?

A

Abs = log [1/T]

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28
Q

What is the formula for resolution? And explain what each symbol represents

A

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

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29
Q

What is the formula for Beer-Lambert Law? And explain what each symbol represents

A

A = elc
e: molar absorptivity in L/molcm
l: path length in cm
c: concentration in mol/L

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30
Q

What is the Bradford Assay?

A

Measurement of color change when Coomassie Blue dye binds to protein. Unbound gives a reddish brown, whereas bound gives a blue color.

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31
Q

What are the pros/cons of the Bradford Assay?

A

it is quick and simple, but upper limit for linear detection of ~2mg/mL and dye and precipitate if detergents are present

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32
Q

What is the Biuret Assay?

A

Measurement of color change when Copper II Sulfate reacts with proteins under alkaline conditions. The solution turns purple

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33
Q

What is the spherical bacterial shape?

A

Coccus/cocci

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34
Q

What is the rod bacterial shape?

A

Bacillus/bacilli

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35
Q

What is the bent rod bacterial shape?

A

vibrios

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36
Q

What is the tight helical bacterial shape?

A

spirillas

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37
Q

What is the loose bendy bacterial shape?

A

spirochetes

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38
Q

What are pairs of bacterium called?

A

Diplo

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39
Q

What are clusters of bacterium called?

A

staphylo

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40
Q

What are chains of bacterium called?

A

strepto

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41
Q

Groupings of bacteria are related to the ____ of cell division

A

plane

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42
Q

Describe the cell wall structure (x3)

A
  • Threads of a repeating carbohydrate (NAG-NAM)
  • Glued together with proteins
  • These sugars and proteins form a compound called peptidoglycan
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43
Q

___-_____ makes the wall durable

A

cross-linking

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44
Q

Gram ____ cells have multiple layers of ______, with _____ _____ aiding in keeping the layers together that also help in increasing the ____ charge of the cell wall

A

positive, peptidoglycan, teichoic acids, negative

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45
Q

Gram ____ cells have a single layer of ______, a second ____ _____ outside the peptidoglycan which helps to block entry of ______, and can be ______

A

negative, peptidoglycan, phospholipid membrane, antibiotics, toxic

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46
Q

What are the 5 most common kinds of staining discussed in this class?

A

Gram, Acid Fast, Negative, Flagella, Endospore

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47
Q

What is the point of aseptic technique?

A

Prevention of contamination

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48
Q

Which counterstain do you use with acid fast stains?

A

methylene blue

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49
Q

What is the difference between a capsule and a slime layer?

A

Capsule: neatly organized
Sime layer: unorganized and loose/diffused

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50
Q

The glycocalyx increases ______

A

pathogenicity

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51
Q

What is a negative stain?

A

Allows for the visualization of the glycocalyx, composed of nigrosin/congo red acidic dyes

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52
Q

What is the pro/con of the Negative stain?

A

Cells are not fixed, but additional staining is needed to visualize bacteria

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53
Q

Visualization with a light microscope requires the ______ of the flagellum

A

thickening

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54
Q

What are atrichous flagella patterns?

A

The complete absence of flagella

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55
Q

What are monotrichous flagella patterns?

A

singular flagella

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56
Q

What are amphitrichous flagella patterns?

A

flagellum on both ends

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57
Q

What are lophotrichous flagella patterns?

A

tufts from a single point

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58
Q

What are peritrichous flagella patterns?

A

surrounding the bacterium

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59
Q

Endospore producing bacteria are also known to produce ____

A

toxins

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60
Q

Which dye is used for an Endospore Stain, and what is used as a counterstain?

A

Malachite Green, safranin

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61
Q

Order these in context of coldest to hottest: mesophile, psychotroph, thermophile, psychrophile, hyperthermophile

A

Psychrophile, psychrotrophs, mesophile, thermophile, thermophile, hypertherophiles

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62
Q

Most bacteria need a salt salt concentration below __%

A

2

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63
Q

Extreme halophiles can live in __-__% salt

A

30-40

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64
Q

Rank these elements as most commonly found in living organisms to least common: phosphorus, calcium, carbon, sulfur, nitrogen, hydrogen & oxygen

A

Hydrogen & oxygen
Carbon
Nitrogen
Phosphorus
Sulfur
Calcium

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65
Q

Oxygen generates free radicals that damage ___, ____, and ___

A

DNA, proteins, lipids

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66
Q

Aerobically living organisms can produce a series of enzymes which ____ the oxygen free radicals

A

detoxify

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67
Q

Describe the Catalase test

A

Where we introduce hydrogen peroxide to a sample and if oxygen bubbles then it is positive

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68
Q

What are obligate aerobes?

A

Only grow and survive in the presence of oxygen

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69
Q

What are facultative anaerobes?

A

Can grow in the presence or absence of oxygen

70
Q

What are obligate anaerobes?

A

Cannot tolerate oxygen and grow in its complete absence

71
Q

What are aerotolerant anaerobes?

A

Can survive in the presence of oxygen, but do not use it

72
Q

What are microaerophiles?

A

Require oxygen, but only at reduced levels and lower concentrations

73
Q

What is a complex media?

A

Has fewer things, but are more complicated. We are not aware of every chemical in the media

74
Q

What is a defined media?

A

Usually has more things, but we know exactly what they are. Every chemical in the media is known. Can be tailored to requirements

75
Q

What conditions are created using a Candle Jar?

A

It will not create a completely anaerobic environment, just a much lower oxygen concentration

76
Q

What are the pros/cons of broth?

A

Grow large quantities of culture, but difficult to check for purity

77
Q

What are the pros/cons of plate?

A

Readily score and separate colonies, but does not score well

78
Q

What are the pros/cons of slants?

A

“Mini-plates” for storage with smaller volume, but difficult to check for purity

79
Q

What are the pros/cons of semi-solid deeps?

A

Can score motility and oxygen requirements, but difficult to check for purity

80
Q

What is agar?

A

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
Q

What is Nutrient Agar made of and who is it best suited for?

A

Peptone and beef extract, suitable for non-fastidious(non-picky eater) organisms

82
Q

____ media will encourage the growth of some bacteria while preventing the growth of others

A

Selective

83
Q

______ media will produce different visual cues as to the type of organism growing

A

Differential

84
Q

______ media is a type of selective media used to allow proliferation of rare bacteria in a mixed population while limiting other organisms

A

Enrichment

85
Q

What are MacConkey plates used for?

A

Selective and differential, selects against non-enteric gram +’s. Contains lactose and pH indicators: fermenters turn purple and non-fermenters stay creamy

86
Q

What are Mannitol Salt Agar (MSA) plates used for?

A

Selective and differential, and has high salt content. Fermenters turn yellow, non-fermenters stay red

87
Q

What are Blood Agar (BAP) plates used for?

A

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
Q

What are Saboraud Dextrose Agar (SDA) plates used for?

A

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
Q

What are SIM Deep tubes used for?

A

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
Q

What is an oxidase test?

A

Test for cytochrome 3, if positive will turn the paper purple

91
Q

Order these phases into the proper order for a growth curve: Log/exponential phase, death phase, lag phase, stationary phase

A

Lag phase, Log/exponential phase, stationary phase, death phase

92
Q

What is the lag phase of a growth curve?

A

Initial inoculation, the bacteria are getting used to and optimizing their machinery to take advantage of the environment around them

93
Q

What is the log/exponential phase of a growth curve?

A

More cells are dividing than dying, some are still dying but cannot keep up. The increase is exponential

94
Q

What is the stationary phase of a growth curve?

A

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
Q

What is the death phase of a growth curve?

A

More cells are dying than dividing, but some are still dividing, but cannot keep up, the decrease is also exponential

96
Q

What is turbidity?

A

The cloudiness of a solution

97
Q

What is the difference between a viable count and a whole count?

A

Viable: Proof of life
Whole: living or dead

98
Q

Plates with __-__ colonies are a good dilution to back-calculate to CFU

A

25-250

99
Q

What method can be used to calculate the proper amount of concentrate needed on a plate for a good CFU count?

A

Serial dilution

100
Q

What is an antibiotic?

A

Prevent the growth of bacteria while keeping the host healthy

101
Q

There are two kinds of antibiotics, what are they?

A

Bactericidal: kills bacteria
Bacteriostatic: stops proliferation

102
Q

What is the effective dose?

A

The concentration that kills the bacteria

103
Q

What is the toxic dose?

A

The concentration with side effects/causes host toxicity

104
Q

What is the optimal T/E (therapeutic index) value?

A

T/E should always be > 1, because if its < 1, it is host killing

105
Q

Compare and contrast natural, semi-synthetic, and synthetic

A

Natural: Found in a living source
Semi-Synthetic: modified version of the natural compound
Synthetic: not living sourced at all

106
Q

The closer an organism is to us, the ___ it is to treat as drugs must be more specific

A

harder

107
Q

Cell inhibitors come in both ____ and ___-____ forms

A

natural, semi-synthetic

108
Q

What are the 2 most common cell wall inhibitors?

A

Penicillins and cephalosporins

109
Q

All cell wall inhibitors contain a __-____ ___

A

β-lactam ring

110
Q

Natural penicillin works only against ___ __

A

gram +

111
Q

For cell wall inhibitors, semisynthetic modifications can..?

A
  • Make it more resistant to acid breakdown
  • Make it more stable
  • Broaden the activity spectrum
112
Q

Are cell wall inhibitors lytic or static?

A

lytic

113
Q

Protein synthesis are generally more ____ spectrum but more ___

A

broad, toxic

114
Q

What are the two kinds of Plasma Membrane Damaging antibiotics?

A

Polymyxins, and Daptomycin

115
Q

What are polymyxins?

A

Damage gram - membranes, they are poorly absorbed and toxic to neurons and kidneys

116
Q

What is daptomycin?

A

Depolarizes gram + membranes

117
Q

What kind of antibiotic is tetracycline?

A

Protein synthesis inhibitor

118
Q

What kind of antibiotic is ampicillin?

A

A kind of penicillin, which is a cell wall inhibitor

119
Q

What are nucleic acid synthesis inhibitor antibiotics?

A

Impair transcription or replication

120
Q

_____ are metabolic inhibitors

A

Sulfonamides

121
Q

Metabolic inhibitors are completely ____

A

synthetic

122
Q

Metabolic inhibitors competitively inhibit ____ needed to generate ___, which is used to produce thymine and uracil and humans are unable to synthesize it

A

PABA, folate

123
Q

No folic acid = ?

A

no life

124
Q

What is sensitivity testing?

A

Use disk diffusion assays to determine what drugs are useful against a bacteria. It is non-quantitative and distance ranges

125
Q

What are Epsilometer tests (E tests)?

A

Use a strip of antibiotic to determine a therapeutic dose

126
Q

What is MIC?

A

Minimal inhibitory concentration

127
Q

What are the 5 ways to increase antibiotic resistance?

A
  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
Q

What are the 5 modes of resistance that bacteria may develop to fight antibiotics?

A
  1. Drug modification
  2. Pathway protection
  3. Target alteration
  4. Rapid Efflux
  5. Alternative pathways
129
Q

What organelle contains the potential to create antibiotic resistance through genetic changes?

A

Plasmid

130
Q

What is a way modern medicine fights antibiotic resistance?

A

Using a combination of drugs greatly decreases the chance of developing drug resistance and reducing bacterial exposure

131
Q

The charge of some R groups is __ dependent

A

pH

132
Q

_____/__-___ R-groups tend to fold internally

A

hydrophobic non-polar

133
Q

_____/___ R-groups tend to fold externally

A

Hydrophillic, polar

134
Q

What is the reaction rate?

A

How fast substrate is converted into product

135
Q

What are the 2 possible formulas for reaction rate?

A

v = -Δ[S] / Δt
v = +Δ[P] / Δt

136
Q

What are the units of reaction rate?

A

Concentration over time

137
Q

Over time, reactions will slow down as ___ decreases and ___ increases and enzyme molecules are lost to _____ and _____

A

[R], [P], denaturation, oxidation

138
Q

_____ _____ ___ is used to get non-attenuated rates

A

Initial velocity (Vo)

139
Q

Initial velocity is ideally measured quickly and for a short period of time ( ?)

A

before 10% of the reactant is used up

140
Q

In a [P] vs t graph, what is the slope of the line?

A

Velocity

141
Q

Rate can be limited by 2 things, what are they?

A
  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
Q

Under ideal conditions, Vo is limited by ____ and _____

A

[S], enzyme

143
Q

Under optimal conditions, and with an excess of substrate, the limiting step is ?

A

How fast the enzyme can catalyze ES -> E + P

144
Q

What is the formula for Vo?

A

Vo = ([S] x Vmax)/([S] + Km)

145
Q

What is Km?

A

The Michaelis constant, the affinity of the enzyme to bind to its substrate

146
Q

What is the formula for Km?

A

Km = [S] when Vo = 0.5 Vmax

147
Q

What is an example of the importance of different Km values?

A

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
Q

How has the Michaelis Menten equation evolved to the Lineweaver-Burk plot?

A

The Lineweaver -Burk plot uses the double reciprocal of rate and concentration to place Vmax and Km on the X and Y intercepts

149
Q

The reciprocal of the Y-intercept is ___

A

Vmax

150
Q

The negative reciprocal of the X-intercept is ___

A

Km

151
Q

A _____ ____ reversibly binds to the active site and blocks substrate binding

A

competitive inhibitor

152
Q

How can the inhibition be overcome with competitive inhibitors?

A

Having a high [S]

153
Q

The ____ inhibitor has the same Vmax but an increased Km

A

competitive

154
Q

The ____ inhibitor has the same Km but a decreased Vmax

A

noncompetitive

155
Q

The ____ inhibitor has an increased Km but a decreased Vmax

A

uncompetitive

156
Q

The ______ inhibitor is a compound that binds to the ES complex and slows the transition to EP, but does not bind to E alone

A

uncompetitive

157
Q

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

A

uncompetitive, right

158
Q

______ 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

A

Noncompetitive, Vmax

159
Q

Unlike competitive inhibitors, in ___ inhibitors more substrate has no effect

A

noncompetitive

160
Q

Each preparation/isolation of enzymes that do the same reaction may be faster or slower depending on factors like ?

A

purity or source organism

161
Q

Different enzymes that complete the same reaction may have different values for ___ and ___

A

Vmax, Km

162
Q

Enzymes are quantified by comparing the ?

A

amount needed to compete a set amount of reaction in a set period of time

163
Q

What is 1 international unit (IU)?

A

Enzyme will catalyze 1µmol in 1 minute at an optimal temperature and pH, and high substrate concentration

164
Q

What is activity?

A

The concentration of a enzyme

165
Q

What are the units for activity?

A

U/mL or U/µL

166
Q

How is total activity calculated?

A

Activity x volume

167
Q

What is the formula for activity?

A

[(Δc/min)(reaction volume)]/(enzyme volume)

168
Q

What is specific activity?

A

The potency of an enzyme by weight of protein

169
Q

What is the formula for specific activity?

A

activity/[protein]

170
Q

What are the units for specific activity?

A

U/mg or U/µg

BMSC 240 (2 decks)

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