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BIOS 2210- self quiz review > module 2: metabolism, genetics, and environmental microbiology > Flashcards

module 2: metabolism, genetics, and environmental microbiology Flashcards

1
Q

are bacteria limited on how much they can replicate?

A

no, their only limit is their environment/resources

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2
Q

describe how bacteria grow as a species

A

they grow in size in their species (numbers). they do not grow as humans do in size

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3
Q

how do bacteria grow?

A

they double

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4
Q

describe the “surface area to volume ratio”

A

at a small size, the ratio is small and very efficient. cell exchanges with its world, gets gasses & nutrients, etc.
as the ratio gets bigger, the SA to V ratio gets worse and the diffusion isn’t as efficient

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5
Q

why cant you have huge bacteria?

A

there’s not enough surface area to volume exchange to efficiently get everything diffused out of/into the cell that it needs to survive

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6
Q

how do bacteria reproduce?

A

binary fission

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7
Q

describe the steps of binary fission

A
  • DNA has to get replicated
  • cell starts out with one circular chromosome
  • a whole other circle chromosome has to get produced
  • the two circles move to different ends of the cell
  • SEPTUM pierces off in the middle
  • pops apart into 2 separate cells
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8
Q

what is important about the septum?

A

the cell wall has to be re-established here

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9
Q

are bacteria clones?

A

yes. clones = exact replica

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10
Q

what doubles faster than any other bacteria?

A

E. coli

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11
Q

what is a closed growth system?

A

a flask or incubator. humans can also be considered a closed growth system.

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12
Q

describe the “standard closed system growth”

A
  • lag phase (bacteria have a period of time where they get used to their environment)
  • log phase (they grow rapidly… exponential growth)
  • stationary phase (dying cells = replicating cells)
  • death phase (more cells dying than are replicating)
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13
Q

describe mutations

A

when DNA is getting replicated, the cells will all be the same species but might have some small genetic differences as the population grows

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14
Q

describe what a “biofilm” is

A

a new hypothesis that some bacteria have the ability to live in a community. they are still single-celled, but live in a mass or clump

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15
Q

what is special about a biofilm? where are they commonly found?

A

they are very hard to kill. they are found in joint replacements (knee, hips, shoulder)… called a “biofilm infection”

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16
Q

how do biofilm infections grow?

A

they start as a little colony, then grow into a scaffold where they excrete protein so they can grow into a pod/film. the outside of the film take the brunt of the antibiotic

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17
Q

what are the 4 environmental factors of microbial growth?

A

oxygen, temperature, UV light, pH

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18
Q

describe oxygen in terms of microbial growth

A

oxygen is not required for all bacteria

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19
Q

what is aerobe

A

with oxygen

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20
Q

what is anaerobe

A

no oxygen

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21
Q

obligate aerobes…

A

do require oxygen

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22
Q

obligate anaerobes…

A

do NOT require oxygen. oxygen is harmful to them

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23
Q

facultative anaerobes…

A

flexible. can handle oxygen. some use it, but are fine without it as well

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24
Q

aerotolerant anaerobes…

A

don’t use/need oxygen, but are fine with it being around

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25
Q

microaerophiles…

A

use a very specific amount of oxygen. they live just under the surface of the ocean

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26
Q

describe temperature in terms of microbial growth

A

temperature ranges for bacteria can go from way below freezing to way near incineration levels. this means bacteria can live in any temperature range

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27
Q

describe UV light in terms of microbial growth

A

sunlight is the requirement for survival for some bacteria (photosynthetic). sunlight can also be the killer for others

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28
Q

describe pH terms of microbial growth

A

most bacteria like the middle range around 7. some thrive in either end.
neutrophil: prefer to grow around 7 pH
acidophiles: acid loving bacteria

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29
Q

describe the big picture concept of cellular respiration

A

taking glucose in, converting it, going through a cycle, the electrons go to the transport chain, converts it, makes ATP

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30
Q

what does “sequestered” mean for a cell?

A

means that something is taken in and locked into a biomolecule inside the cell. for example. CO2 in a photosynthesizing microbe

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31
Q

what is the universal input for photosynthesis, regardless of the organism being oxygenic/not

A

carbon dioxide

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32
Q

describe what it means to be an “autotroph”

A

the organism makes their own food

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33
Q

describe what it means to be a “heterotroph”

A

the organism obtains food from an outside source

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34
Q

where do “phototrophs” get their energy from?

A

get energy from sunlight

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35
Q

where do “chemotrophs” get their energy from ?

A

get energy from chemical compounds

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36
Q

what does metabolism describe?

A

all the chemical exchanges going on inside the cell. all the break downs, build ups, transfers, chemical reactions, and energy transfers

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37
Q

what are the two different metabolic pathways?

A

anabolic & catabolic

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38
Q

what does “anabolic” mean?

A

DNA synthesis. it means to build up, with smaller substrates adding to each other to build big polymers

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39
Q

what does “catabolic” mean?

A

Glycolysis. it means to break down, and to release energy

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40
Q

define: rate limiting step

A

prevents a process from moving forward if the substrate is not present. in the instance of glycolysis, one example of a rate limiting step is whether NAD+ is present

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41
Q

what is “phosphprylation”

A

process of bacteria making ATP. specifically, when ADP adds another phosphate, this is called phosphorylation. there are now 3 phosphates

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42
Q

what is “dephosphorylation”?

A

breaking off a phosphate, making it into ADP. this releases some energy

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43
Q

what are enzymes?

A

they lower the activation energy. can be proteins, catalyze (to make faster) reactions, and be reusable. typically named “-ase” or “-zyme”

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44
Q

what are exoenzymes?

A

they harvest their own sugars from the outside world. they break down large particles so they can diffuse into the cell

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45
Q

what are endoenzymes?

A

enzymes found within the cell

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46
Q

in simple terms, describe glycolysis

A
  • glucose goes in
  • becomes G3P
  • becomes 2 separate pyruvate, 3 carbons in each
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47
Q

what is the first step of glycolysis?

A

a 6-carbon glucose molecule goes in

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48
Q

describe the “energy investment phase” of glycolysis

A

ATP is going in. to even get glycolysis going, we burn/use 2 ATP molecules

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49
Q

what would be considered the “middle” step of glycolysis?

A

when there are two “G3P” made… this is when the 6 carbon sugar from the first step is split in half

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50
Q

what is the “rate limiting step” of glycolysis?

A

NAD+ available to pick up an electron… this is called REDUCTION (LEO says GER)

51
Q

what is the final product of glycolysis?

A

you end with 2 pyruvate… each contains 3 carbon

52
Q

list the inputs of glycolysis:

A
  • glucose
  • 2 ATP
  • NAD+
53
Q

list the outputs of glycolysis:

A
  • 2 3-carbon pyruvate
  • a little ATP
  • NADH
54
Q

where does glycolysis occur in the cell?

A

cytoplasm

55
Q

is oxygen required for glycolysis?

A

no

56
Q

what occurs after glycolysis?

A

the 2 pyruvates are holding a lot of energy, stored in the strong covalent bonds between the carbons. to get that energy out, more metabolism has to happen.

57
Q

describe the transition step between glycolysis and the citric acid cycle

A

glycolysis –> pyruvate –> transition step –> CAC
pyruvate goes in, NAD+ is reduced to NADH (think energy that will be used later), and the output is acetyl CoA

58
Q

describe the big picture of the citric acid cycle:

A

the cycle turns twice, one per pyruvate. a bunch of enzymes do the work. acetyl CoA goes in, and ATP comes out, along with reduced forms of electron carriers

59
Q

what does it mean for an electron carrier to be “oxidized”?

A

oxidized = they lost an electron

60
Q

what does it mean for an electron carrier to be “reduced”?

A

reduced = they’re carrying an electron

61
Q

list the inputs of the citric acid cycle:

A
  • acetyl CoA
  • oxidized forms of electron carriers (NAD+ and FAD)
  • ADP
62
Q

list the outputs of the citric acid cycle:

A
  • reduced forms of electron carriers (3 NADH, 1 FADH2)
  • a little CO2
  • one ATP per cycle (so 2 in total)
63
Q

where does glycolysis occur?

A

cytoplasm

64
Q

after the citric acid cycle loads energy onto the electron carriers, where do they take it?

A

electron transport chain

65
Q

what is the overall purpose of the electron transport chain?

A

to take back electrons from the electron carriers

66
Q

what two things come to the ETC and start the process?

A

NADH and FADH2 come to the ETC and drop off their electrons

67
Q

after dropping off electrons, what happens to NADH and FADH2?

A

they become oxidized, and turn into NAD+ and FAD

68
Q

once the electrons are at the ETC, where do they go?

A

the electrons stimulate hydrogen protons inside the cell to be driven to the outside, across the membrane

69
Q

once hydrogen goes across the membrane, what is waiting outside?

A

a high concentration of hydrogen protons… aka “a proton storm”

70
Q

what is caused by the “proton storm” and how does it relate to ATP synthase?

A

the proton storm is referred to as “the proton motive force.” ATP synthase is an enzyme that is driven by the proton motive force

71
Q

what drives the production of ATP?

A

the hydrogen flowing back through the ATP synthase. as hydrogen flows through ATP synthase, it forces phosphorylation of ADP into ATP

72
Q

how does oxygen relate to the ETC?

A

oxygen comes into play at the end of the chain. when electrons come off the domino effect chain, they end up connecting to oxygen, and this creates water. this is also known as the “final electron acceptor”

73
Q

list the inputs of the ETC:

A
  • energy, in the form of reduced electron carriers (NADH & FADH2)
  • O2 gas
74
Q

list the outputs of the ETC:

A
  • NAD+, FAD
  • ATP
  • small amt of water
75
Q

describe the overview of fermentation:

A

fermentation is just glycolysis plus some weird byproduct, like lactate. the whole process follows glycolysis and involves regeneration of NAD+. fermentation is in no big rush.

76
Q

list the inputs of fermentation:

A

pyruvate

77
Q

list the possible outputs of fermentation:

A
  • lactic acid
  • alcohol
  • acetone
78
Q

is fermentation aerobic or anaerobic?

A

anaerobic

79
Q

are anaerobic cellular respiration the same as fermentation?

A

NO. anaerobic respiration is a whole different type of cell respiration… where at the end of the ETC, oxygen is not used

80
Q

describe the big picture of environmental microbiology

A

the study of microbes in the air, water, and soil & how elements cycle through the planet

81
Q

define “biogeochemical cycling”

A

how elements like water move through the living & non-living world

82
Q

what are the major microbial roles of biogeochemical cycling?

A
  1. decomposers
  2. primary producers (photosynthesizers)
83
Q

what is bioremediation?

A

use of organisms such as microbes & bacteria to decontaminate affected areas. it helps clean up pollution naturally

84
Q

give an example of how microbes play a role in the carbon cycle

A

prochlorococcus: cyanobacteria living in the oceans, sequesters CO2 from the atmosphere

85
Q

what are genes?

A

sections of base pairs in DNA that contain hereditary information

86
Q

describe what the “central dogma” is

A

gene –> DNA –> RNA –> protein

87
Q

what did Griffith discover?

A

he found that there was some compound or material within bacterial cells that allowed them to exchange information throughout the population. he discovered TRANSFORMATION through mice experiment

88
Q

describe transformation as seen in bacteria

A

living bacteria can take in little sections of DNA from dead cells and claim it to be their own, resulting in them exhibiting those characteristics

89
Q

what is the “dangling hydroxyl” end of DNA? what else is it referred to as?

A

3’ end. aka OH

90
Q

what is the “finished phosphate” end of DNA?

A

5’ end

91
Q

what are the nitrogen bases of DNA?

A

A,T,C,G

92
Q

what is the end of a nucleic strand with a free phosphate group called?

A

5’

93
Q

during denaturation of DNA, what happens?

A

the inside nitrogen bases become unbonded, allowing the complementary bases to open up. it does NOT mean the sugar phosphate backbone falls apart

94
Q

describe “haploid”

A

bacterial cells only have one copy of each chromosome

95
Q

what is DNA gyrase?

A

the unwinder enzyme. it helps DNA open up & unwind so it can be read. also referred to as “topoisomerase”

96
Q

describe NAPS

A

these keep the tightly bound supercoils of DNA bound down

97
Q

what are plasmids & describe them in bacterial cells

A

plasmids are “the bling”… or accessory genes.
F plasmids, R plasmids, and Toxins are found in bacterial cells. they code for something special beyond what species they are

98
Q

what’s the biggest structural difference between RNA and DNA

A

RNA has an OH (hydroxyl), DNA has H (hydrogen)

99
Q

who is credited with discovering genetic information?

A

George Beadle & Edward Tatum

100
Q

what is the goal of DNA Replication?

A

DNA making more DNA. to replicate and make an exact copy

101
Q

describe the main 3 steps of DNA replication

A
  1. initiation
  2. elongation
  3. termination
102
Q

describe the plasmids of bacteria

A

they are circle shaped and must double

103
Q

what is the role of DNA helicase?

A

enzyme involved in breaking hydrigen bonds & the unwinding of DNA

104
Q

what forms after the nitrogen bases are broken apart?

A

the replication fork forms

105
Q

describe what “bidirectional DNA synthesis” means

A

once the origin opens up, new DNA will be built in both directions

106
Q

what is DNA polymerase?

A

the enzyme used to build new nucleotides! DNA polymerase is the building enzyme of growing chains of nucleotides

107
Q

describe the directions of DNA polymerase

A

it can only read the template strand in the 3’ to 5’ direction.
it will only build to the 3’ OH end of the growing strand

108
Q

describe what “semiconservative replication” means

A

when new DNA is made, they contain old and new sides

109
Q

describe what the leading strand is:

A

the side growing TOWARDS the replication fork in one continuous path

110
Q

describe what the lagging strand is:

A

the antiparallel strand coming OUT of the replication fork. this means it has to build backward, resulting in Okazaki fragments

111
Q

what are the concepts attached to gene expression?

A
  • central dogma (gene to protein)
  • transcription/translation
112
Q

what is a gene?

A

section of DNA that codes for protein

113
Q

what is the main goal of transcription?

A

to make mRNA

114
Q

what does RNA polymerase do in transcription?

A

the builder of RNA

115
Q

what is the product of transcription?

A

mRNA

116
Q

once transcription occurs, where does the mRNA go?

A

goes to the ribosome

117
Q

what happens in translation?

A

mRNA is read by the ribosomes, and tRNA brings amino acids, as well as matching codons. tRNA plays a pivotal role in bringing the proper amino acid to the growing polypeptide chain

118
Q

what are codons?

A

located in the mRNA, they say which amino acid to bring

119
Q

what are anticodons?

A

on the tRNA, they are the key-shaped structures that match the pair of each amino acid to be brought to the building chain

120
Q

what are the 3 possibilities in horizontal gene transfer?

A
  1. conjugation
  2. transduction
  3. transformation
121
Q

describe conjugation (horizontal gene transfer)

A

sister cell moving DNA from one cell to another

122
Q

describe transduction (horizontal gene transfer)

A

involves bacateriophage. moves DNA out of bacteria

123
Q

describe transformation (horizontal gene transfer)

A

random DNA in the environment that is engulfed by bacteria

BIOS 2210- self quiz review (3 decks)

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