Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIO 315 > Module 3 - Archaea > Flashcards

Module 3 - Archaea Flashcards

You may prefer our related Brainscape-certified flashcards:
Biology 101 flashcards
1
Q

How were archaea first characterized?

A

As bacteria (Archaebacteria)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

How come archaea were first characterized as bacteria?

A

Because they look very similar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

True or false: classification of archaea is simple

A

False: it is very difficult

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

How come classification of archaea is difficult?

A

A majority of them have not been isolated in the lab

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How are archaea discovered if most of them are not easy to culture?

A

Detection of nucleic acids from samples of their environment

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are archaea?

A

Single celled prokaryotes that have distinct characteristics from bacteria (and eukarya)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

True or false: many archaea can survive in the most inhospitable environments

A

True: many archaea are extremophiles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Where were the first archeons found?

A

In extreme environments (high saline, acidic, alkaline, temperature, etc.)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Where are a large amount of archaea found?

A

In the plankton community

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are plankton?

A

Small, microscopic organisms that live in large bodies of water

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

How many of the microbial cells in the ocean are archaea?

A

1/5 (20%)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

True or false: all archaea live in extreme environments

A

False: some live in very mild environments

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Why are rRNA genes used to establish evolutionary relationships?

A

Ribosomes are needed in all organisms to produce polypeptides

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is the structure of a ribosome?

A

A large subunit and a small subunit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What does the large subunit of the ribosome do?

A

Acts as a ribozyme to catalyze peptide bond formation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What rRNA gene is used for phylogeny?

A

16S

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Where is the 16S rRNA found?

A

In the small subunit of the ribosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What was the first group of archeons discovered?

A

The methanogens

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What are methanogens?

A

A group of microbes that can produce methane as a byproduct in anoxic conditions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

True or false: all methanogens are archaea

A

True: there are no methanogens in bacteria or eukarya

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Where are methanogens usually found?

A

In the GI track of mammals

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

How do methanogens help mammals?

A

By digesting food

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

How much does methane impact the environment?

A

Methane is the 2nd highest greenhouse gas emitted from humans in the US

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

How does methane impact climate change compared to carbon dioxide?

A

It is more efficient at trapping radiation, and it has a bigger impact on climate change than carbon dioxide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

True or false: only animals release methane

A

False: industries also release methane

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

How come methane released from animals is considered human related?

A

Because humans raise animals for food

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What are the largest sources of methane from industry?

A

Natural gas and petroleum systems

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What are extremophiles?

A

Organisms that live in extreme environments (salt, temperature, acidity, etc.)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

True or false: if two archeons have similar 16S sequences, they have similar growth requirements

A

False: the growth requirements can vary drastically, even if the 16S sequences are similar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What type of environment do Halobacterium salinarum grow in?

A

High salt concentrations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What type of environment do Pyrococcus furiosus grow in?

A

High temperature

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What type of environment do Picrophilus oshimae grow in?

A

Acidic conditions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What type of environment do Methanogenium frigidum grow in?

A

Low temperature

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

How did all cells start on Earth?

A

From a universal cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What does sequencing data suggest about how bacteria, eukarya, and archaea evolved?

A

Archaea and eukarya branched off from bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What was a branching point for when archaea became different from bacteria?

A

The presence of histones

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

How does the plasma membrane of archaea compare to bacteria and eukarya?

A

It is significantly different

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What is a possible function of the unique plasma membrane of archaea?

A

It may provide thermal stability

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What are some issues with the function of the unique plasma membrane being for thermal stability?

A
  1. Not all archaea thrive in high temperatures

2. Some bacteria can grow in high temperatures without this plasma membrane

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

What is the general size of archaea?

A

0.5 - 5 um

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

What is the smallest archeon?

A

Nanoarchaeum equitans (0.4 um)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

How big is Nanoarchaeum equitans?

A

0.4 um

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

What is the largest archeon?

A

Those in the Thermoproteus species

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

How big is Thermoproteus?

A

100 um

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

What is special about Ignicoccus?

A

It grows together with Nanoarchaeum

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

How does Nanoarchaeum grow?

A

Connected to Ignicoccus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

What shape are most archaeons?

A

Coccus or rod shaped

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

What are some other less common shapes of archaeons?

A

Unusual thin, flat, square, or irregular shapes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

What is the shape of Sulfolobus species?

A

Irregular

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

Which archaeons are irregularly shaped?

A

Sulfolobus species

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

What is the shape of Thermoproteus species?

A

Rectangular

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

Which archaeons are rectangularly shaped?

A

Thermoproteus species

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

What is the purpose of the special shapes of archeons?

A

It is not clear currently

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

What is the cytoplasm of archeons composed of?

A

Several molecules, such as the nucleoid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

What is the structure of the nucleoid in archaeal cells?

A

A singular, circular chromosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

What do the archaeal DNA replication enzymes resemble?

A

The eukaryal versions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

True or false: gas vesicles have been found in archaeal cells

A

True: some complex structures have been found in archaeal cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

True or false: archaea have plasmids

A

True: they may be able to pass them in a process similar to conjugation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

In general, what is similar between archaea and bacteria?

A

The types of molecules and the overall functions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

In general, what is different between archaea and bacteria?

A

The biochemical nature of the molecules

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

True or false: archaeons have histones

A

True: some can have histones

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

What are histones and what do they do?

A

Proteins that compact DNA to fit more in the nucleoid area

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

What is the structure of a histone in eukaryotic cells?

A

An octomeric complex, with 2 each of H1A, H2B, H3 and H4

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

How many bp of DNA wraps each histone octomer (in eukaryotic cells)?

A

160 bp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

What does histone H1 do (in eukaryotes)?

A

Interacts with the DNA and the histone complex

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

What is the structure of a histone in archaeal cells?

A

A tetrameric complex, with 2 each of H3 and H4

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

How many bp of DNA wraps each histone tetramer (in archaeal cells)?

A

60 bp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

What does the presence of histones in archaeons suggest?

A

Histones evolved early in the history of life

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

What would having histones be a prerequisite for (in terms of evolution)?

A

Increase genome size (as seen in eukaryotic cells)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

What is Ta0583?

A

An actin homolog found in archaea

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

What is an actin homolog found in archaea?

A

Ta0583

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

In what species is Ta0583 found?

A

In Thermoplasma acidophilum

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

What is Ta0583 closer to: eukaryotic actin or bacterial ParM/MreB?

A

Eukaryotic actin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

What is the actin found in Methanogenic bacteria closer to (eukaryotic or bacterial actin)?

A

Bacterial actin (MreB/ParM)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

True or false: all archaeons have a plasma membrane

A

True: it is required for life, although it is structured differently

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
76
Q

True or false: all archaeons have a cell wall

A

False: most, but not all, archaeons have a cell wall

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
77
Q

What is the structure of a bacterial/eukaryal plasma membrane?

A

A phospholipid bilayer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
78
Q

What is the structure of a phospholipid?

A

Fatty acids connected to a glycerol-3-phosphate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
79
Q

What molecule do the fatty acids bind to in a phospholipid?

A

Glycerol-3-phosphate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
80
Q

What type of bond is found between a fatty acid and the glycerol-3-phosphate in a phospholipid?

A

Ester linkages (O-C==O)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
81
Q

What is the structure of an archaeal plasma membrane?

A

Isoprenoids attached to glycerol-1-phosphate in a monolayer or bilayer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
82
Q

What molecule do the isoprenoids bind in an archaeal plasma membrane?

A

Glycerol-1-phosphate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
83
Q

What type of bound is found between an isoprenoid and the glycerol-1-phosphate?

A

Ether linkages (O-C)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
84
Q

What is the subunit of an isoprenoid?

A

Isoprene units

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
85
Q

What is the most common isoprene unit in archaeal plasma membranes?

A

Phytanyl

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
86
Q

What is phytanyl?

A

A 20-carbon hydrocarbon used to make up isoprenoids in the archaeal plasma membrane

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
87
Q

True or false: all archaeons have a plasma membrane monolayer

A

False: some have a bilayer, while others have a monolayer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
88
Q

What is the structure of a bilayer plasma membrane in archaeons?

A

Two isoprenoids attach to the glycerol-1-phosphate, and two of these complexes forms a bilayer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
89
Q

What is the structure of a monolayer plasma membrane in archaeons?

A

Each isoprenoid has a glycerol-1-phosphate on both ends, and one of these complexes forms a monolayer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
90
Q

Which archaeons typically have a monolayer?

A

Those that live in high temperatures

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
91
Q

How come archaeons that live in high temperatures typically have a monolayer?

A

A monolayer is more stable than a bilayer at high temperatures

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
92
Q

True or false: some archaeons look like Gram-negative bacteria

A

True: some, like Ignicoccus, have an outer membrane and a periplasm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
93
Q

What archaeon has an outer membrane and a periplasm?

A

Ignicoccus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
94
Q

In archaeons with an outer membrane, how are protons transported?

A

From the periplasm to the extracellular space (then back to the cell through ATP synthase)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
95
Q

Where is ATP synthase found in an archaeal cell with an outer membrane?

A

In the outer membrane

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
96
Q

Where is ATP synthase found in a bacterial cell with an outer membrane?

A

In the inner membrane

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
97
Q

What is the significance of the outer membrane in archaea?

A

It can be exploited for drug delivery and vaccine effectiveness

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
98
Q

What is the purpose of the cell wall?

A

To provide physical and osmotic protection

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
99
Q

What is the cell wall in archaea composed of?

A

Pseudopeptidoglycan (pseudomurein)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
100
Q

What is the structure of pseudomurein?

A

NAG and NAT linked to a small peptide chain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
101
Q

Where is NAG found?

A

In both bacterial and archaeal cell walls

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
102
Q

Where is NAM found?

A

Only in bacterial cell walls

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
103
Q

Where is NAT found?

A

Only in archaeal cell walls

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
104
Q

What does NAT stand for?

A

N-acetyltalosaminuronic acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
105
Q

What type of linkage is found between NAG and NAT?

A

Beta 1-3 linkage

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
106
Q

Where is the peptide found in the archaeal cell wall?

A

Attached to the NAT subunit only

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
107
Q

What types of amino acids are found in the short peptide attached to NAT?

A

L amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
108
Q

True or false: lysozyme is effective against archaeal cell walls

A

False: it cannot break the linkages

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
109
Q

How come lysozymes are not effective against archaeal cell walls?

A

They can only break down the beta 1-4 linkages in bacterial cell walls, not the beta 1-3 linkages in archaeal cell walls

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
110
Q

True or false: penicillins are effective against archaea

A

False: they are not effective

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
111
Q

True or false: all archaea have a cell wall

A

False: some archaea do not have a cell wall

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
112
Q

What is the appearance of an archaeon without a cell wall?

A

Non-spherical

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
113
Q

True or false: all archaea have flagella

A

False: some, not all, have flagella

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
114
Q

What is the function of flagella in archaea?

A

To provide movement

115
Q

In terms of size, how does archaeal flagella compare to bacterial flagella?

A

Archaeal flagella is usually thinner than bacterial flagella

116
Q

What is the composition of bacterial flagella?

A

A long filament composed of one type of flagellin protein

117
Q

What is the composition of archaeal flagella?

A

A variety of different flagellin protein species

118
Q

How do multiple bacterial flagella move?

A

They rotate independently

119
Q

How do multiple archaeal flagella move?

A

Together as a single assembly

120
Q

How are bacterial flagella motorized?

A

Through a proton (or sodium) gradient

121
Q

How are archaeal flagella motorized?

A

Through ATP hydrolysis

122
Q

True or false: the archaeal motor has been identified

A

False: it has not been identified yet

123
Q

How are bacterial flagella assembled?

A

By adding subunits to the tip

124
Q

How are archaeal flagella assembled?

A

By adding subunits to the base

125
Q

What is the overall summary of bacterial and archaeal flagella?

A

While the functions may be similar, the overall composition is very different

126
Q

What are archaeonics?

A

Antibiotics produced by archaea

127
Q

True or false: archaea produce antibiotics

A

True: they are called archaeonics

128
Q

Which species are thought to contain many archaeonics?

A

Haloarchaea and Sulfolobus

129
Q

What enzyme is needed for PCR?

A

DNA polymerase

130
Q

What DNA polymerase is commonly used for PCR?

A

Taq polymerase

131
Q

Where is Taq polymerase from?

A

The DNA polymerase of Thermus aquaticus

132
Q

Where is Pfu polymerase from?

A

The DNA polymerase of Pyrococcus furiosis

133
Q

What is the advantage of Pfu polymerase over Taq polymerase?

A

More thermostability, and has 3’ to 5’ exonuclease proofreading activity

134
Q

What is the significance of PCR?

A

Allowed for a simple and rapid technique for cloning DNA

135
Q

What does 3’ to 5’ exonuclease proofreading activity mean?

A

It can remove mismatched nucleotides from the growing DNA strand

136
Q

Are there pathogenic archaea?

A

There are no clear examples, but some may cause infections in the mouth

137
Q

What are the two main phyla of archaea?

A

Euryarchaeota and Crenarchaeota

138
Q

How have other phyla for archaea been proposed?

A

Through sequencing of the 16S rRNA gene

139
Q

What are some other phyla that have been proposed for archaea?

A

Nanoarchaeota and Korarchaeota

140
Q

What archeon has its own phylum?

A

Nanoarchaeum equitans (part of Nanoarchaeota)

141
Q

What types of species are part of Korarchaeota?

A

Unusual thermophilic species

142
Q

What is Korarchaeota more closely related to?

A

Crenarchaeota

143
Q

What does ARMAN stand for?

A

Archeal Richmond Mine Acidophilic Nanoorganisms

144
Q

What is ARMAN?

A

A new species of archaeons comprising microarchaeota and parvarchaeota (some of the smallest organisms known)

145
Q

What is special about ARMAN?

A

They are some of the smallest organisms known

146
Q

What were Crenarchaeota originally thought to be?

A

Sulfur extremophiles

147
Q

What has recent results concluded about Crenarchaeota (in terms of their members)?

A

They are the most abundant archaea in the marine environment

148
Q

What type of extremophiles are a majority of Crenarchaeota?

A

Thermophiles or hyperthermophiles

149
Q

What is a thermophile?

A

An organism that grows optimally in conditions greater than 55 C

150
Q

What is a hyperthermophile?

A

An organism that grows optimally in conditions greater than 80 C

151
Q

What is one of the most well studied Crenarchaeota?

A

Sulfolobus solfataricus

152
Q

Which organism is a model organism for studying hyperthermophiles?

A

Sulfolobus solfataricus

153
Q

In Crenarchaeota, what type of organism are many hyperthermophiles as well?

A

Acidophiles

154
Q

What is an acidophile?

A

An organism that grows optimally in a low pH environment

155
Q

What major phylum is majorly thermophiles and hyperthermophiles?

A

Crenarchaeota

156
Q

What major phylum contains acidophiles?

A

Crenarchaeota

157
Q

What is an example of an acidophile?

A

Sulfolobus solfataricus

158
Q

What are barophiles?

A

An organism that grows optimally under high pressure

159
Q

What type of organisms are found in deep sea thermal vents?

A

Organisms that are both thermophiles and barophiles

160
Q

What are some examples of adaptations that help Crenarchaeota survive in high temperature environments?

A

Tetraether lipids/lipid monolayers, more alpha-helixes in proteins, more salt bridges/side chain interactions, more arginine/tyrosine, less cysteine/serine, strong protein chaperones, thermostable DNA binding proteins, and reverse DNA gyrase

161
Q

What does high temperature lead to in most organisms?

A

Disruption of the plasma membrane

162
Q

What can be done to the plasma membrane to make it extra stable at high temperatures?

A

Have tetraether lipids or lipid monolayers

163
Q

What can be done to the proteins to make it extra stable at high temperatures?

A

More alpha helixes, salt bridges, side chain interactions, arginine, and tyrosine, and less cysteine and serine. Also having strong protein chaperones

164
Q

What can be done to the DNA to make it extra stable at high temperatures?

A

Have thermostable DNA binding proteins, and reverse DNA gyrase

165
Q

Why are alpha-helixes stable structures?

A

Interchain hydrogen bonds can help stabilize the structure

166
Q

Why would a protein want more alpha-helixes in a high temperature environment?

A

The alpha-helix is a very stable structure

167
Q

How would a protein maintain its shape at higher temperatures?

A

By promoting more amino acid interactions

168
Q

How can a protein increase the amino acid interactions?

A

By having more arginine, tyrosine, salt bridges, and side chain interactions

169
Q

How come a protein in a high temperature would not have a lot of cysteine?

A

Cysteine is a temperature sensitive amino-acid, so it would denature easily

170
Q

What are chaperone proteins?

A

Proteins that help fold proteins or refold denatured proteins

171
Q

What do archaeal chaperone proteins more closely represent?

A

Eukaryotic chaperone proteins

172
Q

What do thermostable DNA binding proteins do?

A

Increase the melting temperature of DNA

173
Q

True or false: all hyperthermophiles have reverse DNA gyrase

A

True: they all have this enzyme to increase supercoiling

174
Q

What does reverse DNA gyrase do?

A

Increases supercoiling of the DNA

175
Q

What is the advantage of increasing the supercoiling of DNA?

A

It increases the temperature that DNA unwinds and denatures

176
Q

Besides supercoiling, what does reverse DNA gyrase do to the DNA?

A

Has heat protective DNA chaperone activity

177
Q

Besides thermophiles, what types of organisms are found in Crenarchaeota?

A

Mesophiles and psychrophiles

178
Q

What are mesophiles?

A

Organisms that grow in conditions between 15 C and 40 C

179
Q

What are psychrophiles?

A

Organisms that grow in conditions less than 15 C

180
Q

What is a possible role of the mesophiles and psychrophiles?

A

Important to biogeochemical cycling of carbon and nitogren in the ocean

181
Q

How are the mesophiles and psychrophiles usually detected?

A

Often through rRNA sequencing (not by cultivation)

182
Q

What is special about Cenarchaeum symbiosum?

A

It shares some genes with both Crenarchaeota and Euryarchaeotes, thus potenitally being part of a new phylum

183
Q

What groups are primarily found in Euryarchaeota?

A

Methanogens and halophiles

184
Q

Most methanogens are part of what phylum?

A

Euryarchaeota

185
Q

Most halophiles are part of what phylum?

A

Euryarchaeota

186
Q

How are Euryarchaeota similar and different within the phylum?

A

They are highly diverse based on morphology and biochemical properties, but they have similar 16S rRNA gene sequences

187
Q

What are halophiles?

A

Organisms that can survive extreme concentrations of salt (1.5 M)

188
Q

True or false: all methanogens are anarobes

A

True: they all live in anoxic environments

189
Q

What is an example of a methanogen?

A

Methanobrevibacter smithii

190
Q

Where is M. smithii found?

A

In the human gut

191
Q

What does M. smithii do?

A

Aids in the digestion of polysaccharides by consuming the end products of bacterial fermentation

192
Q

How does M. smithii aid in digestion?

A

By consuming the end products of bacterial fermentation

193
Q

What reaction do methanogens perform?

A

CO2 + 4H2 –> CH4 + 2H2O

194
Q

What is important about the methanogen reaction?

A

Enough energy is released to fix carbon

195
Q

What are the most well known high salt environments?

A

The Great Salt Lake in Utah, and the Dead Sea between Israel and Jordan

196
Q

What is the salt concentration in areas with high salinity?

A

Between 5-34%

197
Q

How much salinity does the ocean have?

A

3.5% (0.6 M)

198
Q

What happens if a cell is placed in an isotonic solution?

A

No net movement of water

199
Q

What happens if a cell is placed in a hypotonic solution?

A

The cell swells due to water influx

200
Q

What happens if a cell is placed in a hypertonic solution?

A

The cell shrinks due to water efflux

201
Q

What is a hypertonic solution?

A

The solution has more solute (salt) than the cell

202
Q

What is a hypotonic solution?

A

The solution has less solute (salt) than the cell

203
Q

What is an isotonic solution?

A

The solution has equal solute (salt) to the cell

204
Q

What is a model organism for studying halophiles?

A

Halobacterium salinarum

205
Q

How does H. salinarum offset the osmotic shock of high extracellular salt environments?

A

By maintaining high intracellular potassium levels

206
Q

What are the potential problems of having high intracellular potassium levels?

A

It can denature proteins and split dsDNA

207
Q

How does Halobacterium overcome the problem of splitting dsDNA?

A

By having a high GC content

208
Q

How does having high GC content protect the dsDNA from splitting in high salt conditions?

A

GC are stronger bonds (3 H bonds) compared to AT (2 H bonds)

209
Q

How does Halobacterium overcome the problem of denaturing proteins?

A

By having highly acidic proteins

210
Q

Which amino acids are acidic?

A

Aspartic acid and glutamic acid

211
Q

How does having acidic proteins protect it from denaturing in high salt conditions?

A

The negatively charged acids are more stable in a high (positive) salt (potassium) environment

212
Q

True or false: Halobacterium gets energy from sunlight

A

True: while it does not use photosynthesis, it can get energy from sunlight

213
Q

True or false: Halobacterium uses photosynthesis

A

False: while they can get energy from sunlight, they do not use photosynthesis

214
Q

What does Halobacterium not use for producing energy from sunlight?

A

Chlorophyll or an ETC

215
Q

How does Halobacterium harvest energy from sunlight?

A

Through bacteriorhodopsin

216
Q

What is bacteriorhodopsin?

A

An integral protein that can harvest energy from sunlight

217
Q

How much of the surface area of Halobacterium is bacteriorhodopsin?

A

~50%

218
Q

What light is bacteriorhodopsin best at absorbing?

A

Green light

219
Q

What is the appearance of bacteriorhodopsin?

A

Reddish/purplish hue

220
Q

How does bacteriorhodopsin work?

A

It acts as a proton pump, using the light energy to pump protons across the cell membrane out of the cell

221
Q

What happens once the proton gradient is established by bacteriorhodopsin?

A

They flow back into the cell through ATP synthase to generate ATP

222
Q

True or false: methanogens and halophiles are the only members of Euryarchaeota

A

False: while those two groups are the most well studied, other types of organisms exist

223
Q

What are the other species of Euryarchaeota (besides methanogens and halophiles)?

A

Thermophiles, hyperthermophiles, and acidophiles

224
Q

What is an example of an archeon from Euryarchaeota that is a theromphile and acidophile?

A

Picrophilus species

225
Q

What happens to Picrophilus species when pH increases?

A

The plasma membrane becomes destabilized

226
Q

What species are part of Nanoarchaeota?

A

Nanoarchaeum equitans

227
Q

How was N. equitans decided to be its own phylum?

A

Based on the differences in 16S rRNA sequences from both Crenarchaeota and Euryarchaeota

228
Q

How big is N. equitans?

A

One of the smallest organisms on Earth

229
Q

How does N. equitans survive?

A

Through symbiosis with other organisms

230
Q

How was archaea first distinguished from bacteria?

A

Through 16S rRNA sequencing by Carl Woese of the methanogens

231
Q

True or false: the plasma membrane of archaea is required to live in high temperature environments

A

False: some bacteria can also live in high temperature environments without this membrane

232
Q

What shape is Sulfolobus?

A

Irregular

233
Q

What shape is Thermoproteus and Pyrobaculum?

A

Rectangular

234
Q

What shape is Haloquadratum walsbyi?

A

Thin and flat squares

235
Q

When did histones evolve?

A

After bacteria but before eukarya (during archaea)

236
Q

What is the importance of histones?

A

It allows for larger genome size through DNA packaging

237
Q

How many carbons are in an isoprene?

A

5

238
Q

What is the relationship between glycerol-3-phosphate and glycerol-1-phosphate?

A

They are stereoisomers

239
Q

What is biphytanyl?

A

A 40 carbon hydrocarbon found in archaeal monolayers

240
Q

Where is biphytanyl found?

A

In archaeal monolayers

241
Q

True or false: monolayer liposomes are more stable than bilayer liposomes

A

True: this is seen in archaea that live in high temperature environments

242
Q

What is the advantage of an ether linkage over an ester linkage?

A

They are more resistant to high temperatures, oxidation, and alkaline degradation

243
Q

Since T. acidophilum does not have a cell wall, how does it maintain its shape?

A

Likely through a cytoskeleton

244
Q

How come archaeosomes may be useful clinically?

A

They are more stable, so they may be more effective in vaccine delivery

245
Q

True or false: archaea can have an S-layer

A

True: this may help to protect the cell

246
Q

What is special about Pyrodictium?

A

They have cannulae

247
Q

What species features cannulae?

A

Pyrodictium?

248
Q

What are cannulae, and what do they do?

A

Hollow glycoprotein tubes that connect individual cells together

249
Q

Where are cannulae located?

A

In the periplasm, but not cytoplasm, of cells

250
Q

What is the archaellum?

A

The archaeal flagella

251
Q

How thick are archaeal flagella?

A

10-14 nm

252
Q

How thick are bacterial flagella?

A

20-24 nm

253
Q

What type of glycosylation is found in archaeal flagella?

A

N-linked glycosylation

254
Q

What type of glycosylation is found in bacterial flagella?

A

O-linked glycosylation

255
Q

Through what pathway are bacterial flagella assembled?

A

Through the type III secretory pathway

256
Q

How do flagellin monomers reach the tip of the filament (in bacteria)?

A

By traveling through the developing filament

257
Q

What is the assembly of archaeal flagella similar to?

A

The assembly of bacterial pili

258
Q

What are the links between bacterial pili and archaeal flagella?

A
  1. They exhibit some amino acid similarity

2. Homologous assembly proteins have been identified

259
Q

True or false: homologous assembly proteins have been found for bacterial flagella in archaea

A

False: no such proteins have been found

260
Q

True or false: homologous assembly proteins have been found for archaeal flagella in bacteria

A

False: no such proteins have been found

261
Q

True or false: bacterial and archaeal flagella may have similar chemotaxis pathways

A

True: similar genes have been found for this in both bacteria and archaea

262
Q

What proteins are involved in chemotaxis?

A

CheA, CheB, and CheY

263
Q

What three other phyla have been proposed alongside Crenarchaeota and Euryarchaeota?

A

Thaumarchaeota, Korarchaeota, and Nanoarchaeota

264
Q

What is a thermosome?

A

A complex of protein chaperons found in hyperthermophiles

265
Q

What is the importance of proteins that function under high temperatures?

A

They could have important industrial uses

266
Q

What phyla were Thaumarchaeota thought to be a part of?

A

Crenarchaeota

267
Q

What types of organisms are part of Thaumarchaeota?

A

Mesophiles and psychrophiles

268
Q

Where are Thaumarchaeota commonly found?

A

In marine environments, such as near hydrothermal vents

269
Q

What is the importance of organisms in Thaumarchaeota?

A

They may function in carbon cycling and biogeochemical cycles in the oceans

270
Q

What does AOA stand for?

A

Ammonia-oxidizing archaea

271
Q

What does AOB stand for?

A

Ammonia-oxidizing bacteria

272
Q

What is the signifance of AOAs?

A

They function in the first step of the nitrification process

273
Q

True or false: methanogens are autotrophs

A

True: they can incorporate inorganic carbon into organic molecules

274
Q

True or false: all methanogens are thermophiles

A

False: they can also be mesophiles or psychrophiles

275
Q

If an environment has high sodium carbonate, what environment is created?

A

An alkaline environment

276
Q

What is phototrophy?

A

The acquisition of energy from sunlight

277
Q

Which organism undergoes an unusual method of phototrophy?

A

Halobacterium salinarum

278
Q

What molecule in bacteriorhodopsin captures the light energy?

A

Retinal

279
Q

True or false: Korarchaeota has been cultured

A

False: no archaea in this phylum have been cultured

280
Q

If no Korarchaeota has been cultured, how has its genome been sequenced?

A

Through enrichment culture

281
Q

How come Korarchaeota has been proposed as a separate phylum?

A

It has genes similar to both Crenarchaeota and Euryarchaeota

282
Q

Why does N. equitans grow with Ignicoccus?

A

It depends on the host for survival

283
Q

What evidence shows that N. equitans needs a host for survival?

A
  1. All attempts to grow N. equitans independently have failed
  2. Its genome lacks genes to synthesize nucleotides, lipids, cofactors, and amino acids

BIO 315 (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions