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Bmsc 210 > Midterm #1 > Flashcards

Midterm #1 Flashcards

1
Q

What are the 3 domains of life?

A

Bacteria
Archaea
Eukarya

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2
Q

How did diversity of life arise?

A

Evolution

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3
Q

What is LUCA?

A

Last Universal Common Ancestor

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4
Q

How do we know when O2 appeared in our biosphere?

A

Oxygen interacting with iron which precipitates into sediments

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5
Q

Robert Hooke

A

1665- first book devoted to microscopic observations

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6
Q

Antoin Van Leeuwenhoek

A

1676- first to see bacteria

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7
Q

Ferdinand Cohn

A

~1850’s - first to see bacterial endospores

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8
Q

Louis Pasteur

A

1864- disproved spontaneous generation theory

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9
Q

Robert Koch

A

germ theory of infectious disease

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10
Q

Light microscopy

A

compound light microscope uses light to illuminate cells

- many different kinds

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11
Q

What are the two sets of lenses that form an image?

A

objective and ocular

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12
Q

Phase-Contrast Microscopy

A
  • invented by Fritz Zernike in 1936
  • phase ring amplifies difference in refractive index of cell and surroundings
  • improves contrast
  • allows visuals of live samples
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13
Q

Dark-Field Microscopy

A
  • light reaches the specimen from the sides

- image appears light on a dark background

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14
Q

Fluorescence Microscopy

A

-used to visualize specimens that fluoresce (emit light) whether they do so naturally or with a stain

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15
Q

Differential Interference Contrast (DIC) Microscopy

A
  • uses polarizer to make two distinct beams of polarized light
  • gives structures a 3-D appearance
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16
Q

Atomic Force Microscopy (AFM)

A

a stylus helps to generate an image by measuring weak repulsive forces b/w stylus and specimen

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17
Q

Confocal Scanning Laser Microscopy (CSLM)

A

uses computerized fluorescence microscope coupled with a laser source to generate 3-D image

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18
Q

Transmission electron microscopes

A

electromagnets function as lenses

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19
Q

Electron microscopes

A

uses electrons instead of photons to image cells and structures

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20
Q

Scanning electron microscopes

A

scattered electrons are collected by a detector and an image is producedx

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21
Q

Which two microbials do not live next to each other?

A

cyanobacteria and clostridium

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22
Q

Why is seeing images of microbial cells important?

A

to be able to look at structure-function relationship since seeing is believing

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23
Q

What are the major cell morphologies?

A

coccus (spherical)
rod (cylindrical)
spirillum (spiral)

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24
Q

What cells have unusual shapes?

A

spiroschetes
appendaged bacteria
filamentous bacteria

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25
Q

What does morphology not predict?

A

physiology, ecology, phylogeny of prokaryotic cells

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26
Q

Advantages of small cells?

A
  • more surface area
  • support greater nutrient exchange
  • grow faster
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27
Q

Cytoplasmic membrane

A

thin structure that surrounds the cell and a barrier that separates the cytoplasm from the environment

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28
Q

What functions do membranes perform for the cell?

A
  • permeability barrier
  • anchor for proteins
  • sire for energy conservation (ETC)
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29
Q

Integral membrane proteins

A

membrane proteins that are firmly embedded in the membrane

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30
Q

peripheral membrane proteins

A

membrane proteins where one portion is anchored in the membrane

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31
Q

archaeal membranes

A

ether linkages in phospholipids of archaea

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32
Q

What kind of linkages do bacteria and archaea have in phospholipids?

A

ester

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33
Q

What are the three classes of nutrient transport?

A

simple transport
group translocation
ABC system

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34
Q

Simple transport

A

the nutrient is simply transported by a transporter

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35
Q

Group translocation

A

substance transported is chemically modified during transport across the membrane and requires 5 proteins

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36
Q

ABC system

A

often involved in uptake of organic compounds, inorganic nutrients and trace metals

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37
Q

Peptidoglycan

A

a classification of bacteria

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38
Q

Gram-negative

A

two layers: peptidoglycan and outer membrane

- appear red

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39
Q

Gram-positive

A

one layer: peptidoglycan

- appear purple

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40
Q

Gram-stain

A

differential stains separate bacteria into groups (gram positive or negative)

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41
Q

What prokaryotes lack cell walls?

A

mycoplasmas (bacteria) and thermoplasma (archaea)

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42
Q

Gram-positive cell wall

A

90% peptidoglycan

have teichoic acids embedded or lipoteichoic acids (have a lipid covalently bonded to it)

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43
Q

Gram-negative cell wall

A

~10% peptidoglycan

composed of outer membrane (LPS)

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44
Q

Lipopolysaccharide (LPS)

A

consists of core polysac and o-polysac

replaces most phospholipids in outer half of the membrane

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45
Q

Endotoxin

A

the toxic component of the LPS

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46
Q

Lipid A

A

endotoxin that is released when gram-negative cells are lysed

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47
Q

Periplasm

A

space located b/w cytoplasmic and outer membranes

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48
Q

porins

A

channels for movement of hydrophilic low-molecular-weight substances

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49
Q

What is different about archaea?

A

NO peptidoglycan or outer membrane

pseudomurein

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50
Q

pseudomurein

A

polysac similar to peptidoglycan that is composed of N-acetylglucosamine and N-acetyloamiuronic acid found in cells walls of certain archaea

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51
Q

S layer

A

found in both bacteria and archaea

made of protein and is present OUTSIDE other cell wall layers

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52
Q

Capsule and slime layer

A

layer of polysac made of carb polymers and assists with attaching to surfaces

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53
Q

Pili

A

filamentous protein structures, longer than fimbriae, assist with surface attachment, and facilitate with genetic exchange bw cells

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54
Q

fimbriae

A

filamentous protein structure that enables organisms to stick to surfaces or form pellicles

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55
Q

Carbon storage polymers

A

poly-B-hydroxybutyric acid and glycogen

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56
Q

sulfur globules

A

composed of elemental sulfur

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57
Q

polyphosphares

A

accumulations of inorganic material

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58
Q

carbonare minerals

A

composed of barium, strontium, and magnesium

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59
Q

Gas vesicles

A

decrease cell density causing buoyancy in planktonic cell composed of GvpA and GvpC

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60
Q

Endospores

A

contain dipicolinic acid and is rich in Ca2+

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61
Q

why do some species of bacteria make endospores?

A

bc highly differentiated cells are resistant to heat, harsh chemicals and radiation

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62
Q

flagella

A

structure that assists in swimming

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63
Q

flagella in bacteria

A

has several components, filament composed of flagellin, moved by rotation

64
Q

flagella in archaea

A

half the diameter of bacterial, composed of several different proteins, moved by rotation

65
Q

gliding motility

A

flagella independent, requires surface contact

66
Q

taxis

A

directed movement in response to chemical or physical gradients

67
Q

chemotaxis

A

response to chemicals

attractants and receptors are sensed by chemoreceptors

68
Q

phototaxis

A

response to light

69
Q

aerotaxis

A

response to oxygen

70
Q

asmotaxis

A

response to ionic strength

71
Q

hydrotaxis

A

response to water

72
Q

metabolism

A

the breaking down of ‘food’ for energy and building up of cell components

73
Q

catabolism

A

the breaking down and release of energy

74
Q

anabolism

A

the building up of cell components requiring energy

75
Q

What do you need to consider when growing a culture of microbes?

A

nutrient, temp and atmosphere requirements and pH

76
Q

Microorganisms grouped into energy classes

A
  • chemoorganotrophs
  • chemolithotrophs
  • phototrophs
  • heterotrophs
  • autotrophs
77
Q

Exergonic

A

reactions with a negative G that RELEASE free energy

78
Q

Endergonic

A

reactions with a positive G that REQUIRE energy

79
Q

Free energy formation

A

how to calculate free energy yield of a reaction

80
Q

oxidation

A

removal of electrons from a substance

81
Q

reduction

A

addition of electrons to a substance

always works in pairs - donor or acceptor

82
Q

electron carriers

A

common link to diverse enzyme reactions

83
Q

prosthetic groups

A

electron carrier that is attached to enzymes

84
Q

coenzymes

A

electron carrier that is diffusible

- NAD+ and NADP

85
Q

Glycolysis

A

a common pathway for catabolism of glucose (anaerobic with 3 stages)

86
Q

Fermentation

A

substrate-level phosphorylation

ATP is directly synthesized from an energy-rich intermediate

87
Q

Respiration

A

oxidative phosphorylation

ATP is produced from PMF formed by transport of electrons

88
Q

Aerobic respiration

A

oxidation using O2 as the terminal electron acceptor and has higher ATP than fermentations

89
Q

NADH dehydrogenases

A

proteins bound to inside surface of cytoplasmic membrane

active site bind NADH and accepts 2 electrons and 2 protons that are passed to flavoproteins

90
Q

Flavoproteins

A

contains flavin prosthetic group (FMD, FAD) that accepts 2 electrons and protons but donates the electrons only to the next protein in the chain

91
Q

Cytochromes

A

proteins that contain heme prosthetic groups

accept and donate a single electron via the iron atom in heme

92
Q

Iron-sulfur proteins

A

contain clusters of iron and sulfur
reduction potentials vary depending on number and position of Fe and S atoms
carry electrons

93
Q

Quinones

A
  • hydrophobic non-protein containing molecules that participate in electron transport
  • accept electrons and protons but pass along electrons only
94
Q

Proton motive force

A

electron transport system in cytoplasmic membrane so that electrons are separated from protons

95
Q

ATP synthase

A

complex that converts PMF into ATP

96
Q

F1 of ATPase

A

multiprotein extramembrane complex that faces cytoplasm

97
Q

F0 of ATPase

A

proton-conducting intramembrane channel

98
Q

CAC and glyoxylate cycle

A

organic acids can be metabolized as electron donors and carbon sources by many microbes

99
Q

Anaerobic respiration

A

the use of electron acceptors other than oxygen (NO3-,Fe3+,SO42-, CO32-)
less energy released compared to aerobic

100
Q

Chemolithotrophy

A

uses inorganic chemicals as electron donors (H2S, H2, Fe2+, NH3) and is typically aerobic

101
Q

Phototrophy

A

uses light as energy source

102
Q

photophosphorylation

A

light-mediated ATP synthesis

103
Q

photoautotrophs

A

use ATP for assimilation of CO2 for biosynthesis

104
Q

Photoheterotrophs

A

use ATP for assimilation of organic carbon biosynthesis

105
Q

Adenosine diphosphoglucose (ADPG)

A

precursor for glycogen biosynthesis

106
Q

uridine diphosphoglucose (UDPG)

A

precursor for glucose biosynthesis

107
Q

Rho-dependent termination

A

rho protein recognizes specific DNA (RNA) sequences and causes a pause in the RNA polymerase

108
Q

Unit of Transcription

A

unit of chromosome bounded by sites where transcription of DNA to RNA is initiated and terminated

109
Q

Ending translation

A

translational termination occurs when the ribosome reaches a “stop” codon

110
Q

Signal sequences

A

found on proteins requiring transport from cell

111
Q

The Tat system

A

proteins to be exported, that fold in the cytoplasm, are exported by a transport system distinct from Sec, called the Tat protein export system (Fe-S proteins and redox proteins)

112
Q

Batch culture

A

a closed-system microbial culture of fixed culture of volume

113
Q

What are the 4 phases of the growth curve for a closed system of cells?

A
  1. Lag phase
  2. Exponential phase
  3. Stationary phase
  4. Death phase
114
Q

Continuous culture

A

an open-system microbial culture of fixed volume

115
Q

Chemostat

A

most common type of continuous culture

  • if dilution rate too HIGH = organism WASHED out
  • if dilution too LOW = organism DIE
116
Q

Dilution rate

A

rate at which fresh medium is pumped in and spent medium is pumped out (controls growth rate)

117
Q

Flow cytometer

A

a second method for enumerating cells in liquid reproducing population using laser beams, fluorescent dyes and electronics

118
Q

Viable counts

A

measurement of living, reproducing population

119
Q

Spectrophotometry

A

turbidity measurements are indirect, rapid, and useful methods of measuring microbial growth

120
Q

Optical density (OD)

A

measurement used for turbidity

121
Q

What conditions affect growth?

A
  • temp
  • pH
  • osmolarity
  • oxygen availability
122
Q

Cardinal temperatures

A

the minimum, optimum, and maximum temperatures at which an organism grows

123
Q

Extremophiles

A

organisms that grow under very hot and very cold conditions

124
Q

Psychrophiles

A

organisms with cold temperatures optima and inhabit permanently cold environment

125
Q

Psychrotolerant

A

organisms that can grow at O C but have optima of 20-40 C and more widely distributed in nature than psychrophiles

126
Q

Thermophiles

A

organisms with growth temperature optima b/w 45-80D

127
Q

Hyperthermophiles

A

organisms with optima greater than 80C

128
Q

Neutrophiles

A

organism that grow optimally at pH 5.5-7.9

129
Q

Acidophiles

A

organisms that grow best at low pH (<5.5)

130
Q

Alkaliphiles

A

organisms that grow best at high pH (>or = 8)

131
Q

Osmosis

A

water diffuses from high to low concentrations

132
Q

Aerobes

A

requires oxygen (respiration) and grow at full oxygen tension (~21%)

133
Q

Microaerophiles

A

can use oxygen only when it is present at levels reduced from that in air due to limited respiration or oxygen sensitivity

134
Q

Facultative organisms

A

can live with or without oxygen

135
Q

Anaerobes

A

cannot respire oxygen

136
Q

Aerotolerant anaerobes

A

tolerate oxygen and grow in its presence even though they cannot respire

137
Q

Obligate anaerobes

A

inhibited or killed by oxygen (ex: some bacteria and archaea, fungi, protozoa)

138
Q

Metabolic Regulation

A

metabolic activity of a cell = expressed proteins

139
Q

what are the different types of metabolic regulation?

A
  • degradation
  • modification
  • allosteric regulation
140
Q

Negative control

A

gene that are negatively controlled have a default of ON

141
Q

Positive control

A

genes that are positively controlled have a default of OFF

142
Q

induction

A

= loss of repression

143
Q

Repressor gene

A

a protein that binds the transcription start site of a negatively controlled gene

144
Q

Global control systems

A

regulate expression of many different genes simultaneously

145
Q

Catabolite repression

A

ex of global control and is the synthesis of unrelated catabolic enzymes is repressed if glucose is present in growth medium

146
Q

Diauxic growth

A

two exponential growth phases

147
Q

Cyclic AMP and CRP

A

in catabolite repression, transcription is controlled by an activator protein and is a form of positive control

148
Q

CRP

A

activator protein

149
Q

Cyclic AMP

A

is a key molecule in many metabolic control systems and is derived from a nucleic acid precursor

150
Q

Sensor kinase

A

detects environmental signal and autophosphoylates (in cytoplasmic membrane)

151
Q

Response regulator

A

DNA-binding protein that regulates transcription (in cytoplasm)

152
Q

Phototaxis

A

movement toward light, light sensor replaces MCP’s

153
Q

aerotaxis

A

movement toward oxygen, redox protein monitors oxygen level

154
Q

Quorum sensing

A

mechanism by which bacteria assess their population density and ensures that a sufficient number of cells are present before initiating a response that to be effective, requires a certain cell density

155
Q

Acyl homoserine lactone

A

the first autoinducer to be identified

156
Q

Heat shock response

A

largely controlled by alternative sigma factors

157
Q

Heat shock proteins

A

counteract damage of denatured proteins and help cell recover from temp stress

Bmsc 210 (1 decks)

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