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Biology 2051 > Exam 3 > Flashcards

Exam 3 Flashcards

1
Q

Macronutrients/Macroelements are required in fairly large amounts. What are some examples?

A

Carbon, Oxygen, Nitrogen, Hydrogen, Phosphorus, Sulfur, Selenium
Potassium, Magnesium, Calcium, Sodium

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2
Q

Needed to make organic compounds such as amino acids, fatty acids, sugars, and nitrogenase bases

A

Carbon

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3
Q

How to Autotrophs and Heterotrophs get carbon?

A

Autotrophs: Use CO2
Heterotrophs: Use organic Compounds

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4
Q

How to autotrophs make carbon molecules?

A 
CO2 fixation: 
Calvin-Benson Cycle
Reverse Citric Acid pathway
Hydroxypropionate pathway
Acetyl-CoA pathway
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5
Q

How do heterotrophs make carbon molecules

A

They use part of the same pathways to make carbon molecules as autotrophs but with different entry into pathways

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6
Q

Biosynthesis pathway that required lots of ATP, CO2, and NADPH to produce sugars

A

Calvin-Benson Cycle

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7
Q

Where does the Calvin Benson Cycle occur

A

Phototrophic Eukaryotes: in the chloroplast stroma

Autotrophic Prokaryotes: in the carboxysomes

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8
Q

What is the main binding enzyme in the Calvin-Benson cycle and how does it work?

A

Rubisco

It binds Ribulose 1,5-Biphosphate (30 Carbons) to 6CO2. Carboxylated into 12 3-Phosphoglycerate (36 Carbons)

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9
Q

An example of a microbe that uses the Calvin-Benson cycle to generate carbon molecules (sugars)

A

Halothiobacillus neopolitans

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10
Q

How many times must a cell go through the Calvin Benson cycle to make a single molecule of sugar

A

6 times

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11
Q

Use the Acetyl-CoA pathway (acetogenesis) for autotrophic growth

A

Clostridium acetic - this is the only way this microbe can make ATP

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12
Q

What is created in Acetyl-CoA

A

Creates ATP and acetone. ATP created is equal to the ATP used.

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13
Q

Acetogens are chemo_____

A

Chemoorganotrophs

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14
Q

chemoorganotrophs that use CO2 for methanogenesis

A

Methanogens (Archaea)

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15
Q

How is methanogenesis coupled with autotrophy

A

Methyl created can go into the Acetyl-CoA pathway

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16
Q

A model Archaea organism for the study of methanogensis

A

Methanocaldoccus jannaschii

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17
Q

Obligate Aerobes

A

Require 20% oxygen for aerobic respiration

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18
Q

MIcroaerophilic Aerobes

A

Require oxygen but at levels lower than atmospheric (5-10%) for aerobic respiration

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19
Q

Facultative Aerobes

A

Oxygen is not required, but they grow better with oxygen. Can to Aerobic respiration, Anaerobic respiration, and fermentation

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20
Q

What is the first choice in metabolism and the last choice (in regards to oxygen)

A

Aerobic is the first choice, and Fermentation is the last choice

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21
Q

Aerotolerant Anaerobes

A

Oxygen is not required and grow no better when oxygen is present; fermentation

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22
Q

Obligate Anaerobes

A

oxygen is harmful or lethal; fermentation or anaerobic respiration

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23
Q

Reacts with oxygen to form water. Used to remove oxygen from broth

A

Reducing Agent

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24
Q

A reducing agent that converts oxygen present in air to water

A

Thyioglycolate broth

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25
Q

What is used to test an organism’s requirement for oxygen

A

thyioglycolate broth

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26
Q

Using Aerobes in lab

A

Need culture medium to be oxygenated (allow exposure to air, vigorous shaking, bubbling sterile air into the medium)

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27
Q

Using Anaerobes in lab

A

Need oxygen to be excluded form medium (bottles/tubes completely filled with media and sealed, use a reducing agent, anoxic jars and glove boxes)

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28
Q

An example of a toxic form of oxygen

A

singlet O2 produced by peroxides and others produces as byproducts during respirations

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29
Q

detoxifies hydrogen peroxide to release water and oxygen

A

catalase

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30
Q

uses NADH to detoxify hydrogen peroxide into water and NAD+

A

Peroxidase

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31
Q

detoxifies superoxide to produce hydrogen peroxide and oxygen

A

superoxide dismutase

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32
Q

Detoxification of superoxide that will create water and oxygen

A

superoxide dismutase and catalase in combination

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33
Q

detoxifies superoxide with cat c to produce peroxide

A

superoxide reductase

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34
Q

needed to make amino acids and nitrogenous bases

A

Nitrogen

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35
Q

Where do nitrogen fixing microbes get their nitrogen

A

atmospheric nitrogen (N2)

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36
Q

Where do non nitrogen fixing microbes get their nitrogen

A

use inorganic compounds such as ammonia (NH3) and nitrate (NO3)

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37
Q

Needed to make nucleic acids and phospholipids. Obtained form phosphate minerals and free peptides

A

Phosphorus

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38
Q

Needed to make amino acids cysteine and methionine and other vitamins, iron-sulfur proteins. Obtained from sulfates or sulfides

A

sulfur

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39
Q

Needed for some enzymes. Used to maintain solute concentrations. Obtained from free _ or _salts

A

potassium

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40
Q

stabilizes ribosomes, membranes, and nucleic acids and is required by many enzymes. Obtained from salts in various metals

A

magnesium

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41
Q

Stabilizes cell walls

A

calcium

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42
Q

calcium-dipicolinic acid complex

A

endospores

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43
Q

stabilizes cell walls in marine microorganisms; can power ATP synthase

A

sodium

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44
Q

elements needed in very small amounts (i.e. Iron needed for ETC proteins)

A

micronutrients (trace metals)

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45
Q

molecules that bind iron and transport it into the cell

A

siderophores

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46
Q

Sequester the limited iron supply in animal tissues to initiate infection (ex. E coli and Salmonella typhrium)

A

Enterobactins

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47
Q

Sequester the limited iron supply in animal tissues to initiate infection (ex. Marine bacteria)

A

Aquachelin

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48
Q

Organic compounds needed in very small amounts

A

Growth factors

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49
Q

Ex. of growth factors

A

Folic Acid, B vitamins, Nicotnic Acid (Niacin)

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50
Q

reduces spinabifida chance in babies; many bacteria have a biosynthetic pathway to make this

A

Folic Acid

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51
Q

precursor of NAD+

A

Niacin

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52
Q

sum of all catabolic and anabolic reactions

A

metabolism

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53
Q

energy producing reactions

A

catabolic

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54
Q

energy using (biosynthetic) reaction

A

anabolic

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55
Q

freely diffusible coenzymes that act as electron carriers

A

NAD+/ NADH

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56
Q

NAD+ Reduction

A

Enzyme 1 reacts with electron donor and oxidized form of coenzyme NAD+
Reaction is a part of the citric acid cycle

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57
Q

How is NAD+ reduced in the citric acid cycle

A

Isocitrate is an electron donor. A dehydrogenase oxidizes a substrate by transferring one of more protons and a pair of electrons to an acceptor (NAD/NADP, FAD, or FMN)

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58
Q

NADH oxidation

A

Enzyme II reacts with electron acceptor and reduced form of coenzyme NADH
Reaction is part of the biosynthesis of the amino acid glutamate

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59
Q

3 Classes of enzymes

A

Dehydrogenase, Kinase, Synthase

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60
Q

class of enzyme: oxidoreductase, sometimes coupled with phosphorylation

A

dehydrogenase

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61
Q

class of enzyme: phosphorylates

A

kinase

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62
Q

class of enzyme: joins together two molecules

A

synthase

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63
Q

What happens to energy in a redox reaction?

A

Energy is released and stored in molecules and transported where needed

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64
Q

Short term energy storage compounds

A

ATP (primary energy carrier in the cell that has high energy phosphate bonds)
Derivatives of Coenzyme A - thioester bonds

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65
Q

Long term energy storage compounds

A

Glycogen, Poly-beta-hydroxybutyrate, elemental sulfur

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66
Q

Source and process of energy production in chemoorganotrophs

A

Source: organic compound
Process: fermentation, aerobic respiration, or anaerobic respiration

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67
Q

Source and process of energy production in chemolithotrophs

A

Source: inorganic Compound
Process: primarily aerobic respiration but some are capable of anaerobic respiration

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68
Q

A phosphate group is removed form a substrate and added to ADP to make ATP

A

substrate level phosphorylation

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69
Q

inorganic phosphate is added onto ADP to make ATP by ATP synthase

A

oxidative phosphorylation

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70
Q

light-mediated oxidative phosphorylation

A

photophosphorylaiton

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71
Q

Glycolysis

A

Major pathway of glucose metabolism.

2 net ATP (2 in, 4 out) and 2 pyruvate generated per 1 glucose

72
Q

Where does glycolysis occur?

A

In the cytoplasm of cells capable of using glucose

73
Q

first enzyme used in glycolysis that requires ATP

A

hexokinase

74
Q

in glycolysis: transfers a phosphate from phosphoenolpyruvate to ADP to make ATP (substrate level phosphorylation)

A

pyruvate kinase

75
Q

If there is an electron acceptor present will respiration or fermentation occur

A

respiration

76
Q

If there is no exogenous electron acceptor, will respiration or fermentation occur?

A

fermentation

77
Q

anaerobic means of generating ATP; organic compounds serve as electron acceptors and donors; substrate level phosphorylation; redox cycling

A

fermentation

78
Q

creation of waste products regenerates NADH that is used in fermentation

A

redox cycling

79
Q

cooperative relationship in which the microbes work together to degrade a compound

80
Q

can ferment butyrate to acetate for energy if a methanogen is present to use the H2 generated; is not good at regenerating ETC but the methanogen makes ATP from the hydrogen

A

Synthrophomonas

81
Q

Alcoholic Fermentation in Yeast

A

Starts with Glycolysis; 2 Ethanol, 2 CO2 are waste products; purpose is to make more NAD+

82
Q

Homolactic fermentation (ex. Streptococcus and Lactococcus)

A

Converts pyruvate into lactate by lactate dehydrogenase to regenerate NAD+

83
Q

Heterolactic fermentation (ex. Leuconostoc)

A

No glycolysis at all.

Glucose goes in and the products are ethanol, lactate, and 1 net ATP (1 in, 2 out)

84
Q

some anaerobic eukaryotes (flagellated protozoan Trichomonas) have _____ that oxidize 1 pyruvate to generate 1 ATP by substrate level phosphorylation

A

hydrogenosomes

85
Q

What is generated in the oxidation of glucose to 2 pyruvate by glycolysis?

A

2 pyruvate, 2 NADH, 8 ATP

86
Q

What is generated in the oxidation of each pyruvate to CO2 by the citric acid cycle

A

1 GTP -> 1 ATP, 4NADH, 1 FADH, 30 ATP

87
Q

Why are NADH and FADH important to the ETC

A

They each donate protons and electrons creating the proton motive force used by ATP synthase to make ATP by oxidative phosphorylation

88
Q

Also known as the TCA cycle, Tricaroboxylic acid cycle, Kreb’s cycle

A

Citric Acid cycle

89
Q

Products of the Citric acid cycle

A

CO2 released
NADH and FADH generated for ETC
Organic intermediates used for biosynthesis
A small amount of GTP is made (1 per pyruvate)

90
Q

How can ATP be made from GTP

A

transferring a phosphate to ADP (substrate level phosphorylation)

91
Q

Terminal electron acceptor for an toxic and an anoxic environment

A

Oxic: O2
Anoxic: non-oxygen molecule

92
Q

commonly 1st enzyme of ETC; binds NADH, accepting 2 electrons and 2 protons: Releases NAD+, donates 2 electrons and 2 protons to next carrier

A

NADH dehydrogenases

93
Q

Receives 2 electrons and 2 protons; only donates 2 electrons to the next carrier (still releases the 2 protons)

A

Flavoproteins (FMN;FAD - flavin adenine dinucleotide)

94
Q

Receives and donates electrons; the amount of electrons transferred depends on the number of iron atoms

A

Iron-sulfur proteins

95
Q

Have a single iron atom that accepts/donates electrons

A

Cytochromes

96
Q

Non-protein electron carriers; receive 2 electrons and 2 protons; donates 2 electrons (still releases 2 protons)

97
Q

best primary electron donor

98
Q

best terminal electron acceptor

99
Q

Gram-negative proteobacteria that can oxidize hydrogen

A

Paracoccus denitrificans

100
Q

includes many quinones that move the electrons using protons in the ETC

A

Q-Cycle reactions

101
Q

Eukaryotic mitochondrial matrix or prokaryotic cytoplasm ETC

A

alkaline and electrically negative

102
Q

Environment outside the cell of mitochondrial inter membrane space

A

acidic and electrically positive

103
Q

ETC in E. coli - aerobic respiration

A

NADH donates to a flavoprotein, then a couple of quinones, then a pair of cytochromes

104
Q

ETC in E. coli - anaerobic respiration

A

Final electron acceptor is nitrate reductase

105
Q

Use of a proton motive force to generate ATP (ex. of oxidative phosphorylation)

A

Chemiosmosis

106
Q

Environment of chemiosmosis

A

Gram Neg - periplasm

Gram Pos - space between cytoplasmic membrane and cell wall

107
Q

Ex of Chemoorganotrophs

A

E. coli & Paracoccus denitrificans

108
Q

Ex. of Chemolithotrophs

A

Hydrogen oxidation by Ralston eutropha
Sulfur chemolithotroph like beggiatoa
Iron-Oxidizing chemolithorophic Acidithiobacillus ferrooxidans

109
Q

Functions of a pigment in photosynthesis

A

absorb light energy; transfer light energy to photosynthetic reaction center

110
Q

Location of photosynthetic pigments

A

Eukaryotes - chloroplasts (thylakoid membrane)

Prokaryotes - chlorosomes, cytoplasmic membrane, thylakoid membranes

111
Q

What are the thylakoid membranes in a photosynthetic cyanobacterial cell like Cyanothece

A

the white lines

112
Q

Structure containing antenna bacteriochlorophyll; used by some photosynthetic gram-neg bacteria like the green sulfur Chlorobaculum tepidum and green non-sulfur Chloroflexus; embedded on the membrane

A

Chlorosome

113
Q

Central pigments of photosynthesis embedded in photosynthetic membranes

A

Chlorophylls/ Bacteriochlorophylls

114
Q

Chlorophyll is used in ___ phototrophs like Chlamydomonas

115
Q

Bacteriochlorophyll is used in ____ phototrophs like Rhodopseudomonas

A

anoxygenic

116
Q

Absorbs light energy and transfers it to the reaction center

117
Q

Accumulate energy here to initiate photosynthetic electron transport

A

Reaction Center

118
Q

Antenna pigments; widespread; absorb blue light; give wide array of colors

A

carotenoids

119
Q

PHotoprotective role of carotenoids

A

quench toxic oxygen species

120
Q

Cyanobacteria thylakoid membranes and red algal chloroplasts; Absorb yellow or red light (they look blue/green); act as antenna pigments

A

phycobilins

121
Q

Phycobilins are found in groups attached to _____

A

photosynthetic membranes

122
Q

ETC in anoxygenic photosynthesis is _____

A

cyclic
Light energy converts weak donor into strong donor. Cyclic electron flow generates a proton motive force which excites a poor electron donor and makes it a strong one.

123
Q

a green sulfur bacterium also capable of using hydrogen sulfide as an electron donor

A

Chlorobium

124
Q

How is a proton motive force created in anoxygenic photosynthesis

A

the quinones are pushing protons out as the pass electrons and the ATPsynthase pushes the protons back in

125
Q

How is ATP made in anoxygenic photosynthesis

A

Oxidative Phosphorylation, but because it is light driven we call is photo-phosphorylation

126
Q

Purple sulfur proteobacterium used for studying anoxygenic photosynthesis

A

Rhodobacter capsulatus

127
Q

ETC in oxygenic photosynthesis is ____

A 
Not cyclic (Z scheme)
PSII:A poor electron donor (but excellent electron acceptor) becomes an extremely good electron donor when noncyclic electron flow generates a proton motive force. 
PSI: cyclic electron flow generates proton motive force
128
Q

Example of a microbe that has the ability to do anoxygenic photosynthesis using PSI

A

Oscillatoria

129
Q

Microbes used to study oxygenic photosynthesis

A

Prokaryotic cyanobacterium Synechocystis & eukaryotic green alga Chlorella

130
Q

Substrates to Products. Makes ATP by a proton motive force

A

Catabolism: energy generation

131
Q

Monomers to macromolecules and other cellular constituents by biosynthesis. Uses ATP.

A

Anabolism: energy consumption

132
Q

Glucose and its derivatives. Obtained from the growth medium or made by gluconeogenesis

133
Q

Ribose and deoxyribose. Made by removing CO2 from hexose.

134
Q

Glycogen, Starch, Peptidoglycan subunits, lipopolysaccharide. Made from activated glucose - UDPG or ADPG

A

Polysaccharides

135
Q

How are polysaccharides made

A

From activated Glucose (UDPG or ADPG)
When the UDP on UDPG is cleaved off, the energy released allows of the attachment of the glucose molecule in the cell to create the growing chain of glucose that is glycogen

136
Q

Carbon skeletons from intermediates in glycolysis or citric acid cycle. Derived from inorganic nitrogen source

A

Amino Acids

137
Q

Gets:

Carbon from several sources; nitrogen from amino acids

A

Nucleotides

138
Q

Precursor for purines (A, G)

A

Inosinic Acid

139
Q

Precursor for pyrimidines (C, T, U)

140
Q

Synthesized 2 carbons (acetyl unit) at a time.

A

biosynthesis of fatty acids

141
Q

holds growing fatty acids as it is synthesized

A

acyl carrier protein

142
Q

Glycerol, phosphate, and various sugars are added

A

biosynthesis of lipids

143
Q

Source of electrons for phototrophs

A

Anoxygenic - inorganic compounds

Oxygenic - water

144
Q

describes the total number of difference species in a community

A

species richness

145
Q

the proportion of each species in a community

A

species abundance

146
Q

Microbial communities consist of ___ of metabolically related organisms

147
Q

Microbial communities and their natural environment make up an ____

148
Q

The place where the microbe actually lives

A

microenvironment

149
Q

Suboptimal Growth is due to

A

Suboptimal resources or growth conditions; distribution of nutrients not uniform in habitat; microbes growing in mixed populations where competition exists

150
Q

Most terrestrial microbial growth occurs on

A

the surface of soil particles around plant roots in the rhizosphere

151
Q

Hydrogen sulfide is ____ proportional to oxygen levels

152
Q

levels of organic carbon and oxygen are ____ related in a river

153
Q

Most abundant photosynthetic microbe

A

Prochlorococcus

154
Q

require high pressure

A

extreme piezophile

155
Q

Example of an extreme piezophile

A

Moritella (700-800 atm)

156
Q

Grow best under high pressure

A

Piezophile

157
Q

Tolerate elevated pressure but grow best at low pressure

A

Piezotolerant

158
Q

Chemolithotrophs in hydrothermal vents get there CO2 from this enzyme that helps with the conversion of bicarbonate to CO2 or backwards

A

Carbonicane Hydrase

159
Q

Example of a Mutualistic relationship in marine invertebrate/bacteria

A

Rift giant tube worm and sulfide-reducing bacteria.

Bacteria use sulfide as an electron donor and CO2 on floor to create organic compounds that the worm uses

160
Q

Bacterial assemblages that form on surfaces (can be other microbes besides bacteria)
Also includes waste

161
Q

Why do solid surfaces serve as microbial habitats

A

Nutrients adhere to surface; Surface itself is nutritious

162
Q

Why do biofilms form?

A

Defense in numbers; allow cells to stay in favorable niche; cells live in close association (metabolic cooperation between species)

163
Q

How do Biofilms form?

A

Attachment, Colonization (lawn of cells),Development, Active Dispersal (hipster cells leave)

164
Q

intercellular communication, growth, and polysaccharide formation

A

colonization

165
Q

triggered by environmental factors such as nutrient availibility

A

active dispersal

166
Q

biofilm mushroom; adhesive matrix holds the biofilm together

A

Pseudomonas aeruginosa

167
Q

How do biofilms affect cystic fibrosis

A

don’t have a way to clear microbes because of the mucus

168
Q

How do biofilms affect periodontal disease

A

Microbes on teeth; primarily Streptococcus that form lactic acid

169
Q

How doe biofilms affect infections associated with implants

A

Breast: Staphylococcus epidermis comes in because it is part of the normal flora on skin and breast glands.
Artificial Joints: Propionibacterium acnes and Staphylococcus species

170
Q

What mechanical issues have biofilms been implicated in?

A

Pipeline (oil, water) congestion and corrosion; Degradation submerged objects

171
Q

How does Squid-Allivibrio symbiosis work

A

Allivibrio fischeri bioluminesce in the light organ of the Hawaiian bobtail squid and helps the squid not make a shadow

172
Q

When enough cells assemble in a biofilm (quorum), the concentration of AHL increases which then changes the activity of many genes allowing the cells in the biofilm to

A

Recruit; Bioluminesce; Make Antibiotics; regulate virulence factors (release toxins)

173
Q

Recognize AHL that activate an activator protein to locate brother and sister cells

A

Quorum sensing

174
Q

extremely thick biofilms; layers are made of species from different guilds; most commonly found in hyper saline or geothermal habitats with little grazing by animals and competition

A

microbial mats

175
Q

During the DAY part of a diel cycle in a microbial mat

A

oxygenic phototrophs are producing oxygen and creating a surface environment in the surface layers; in the lower layers, sulfate reduction occurs

176
Q

During the NIGHT part of a diet cycle in a microbial mat

A

photosynthesis stops and the mat quickly become anoxic throughout hydrogen sulfide accumulates

Biology 2051 (7 decks)

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