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Biology 241 > Classification of Organisms & Carbon and Energy Sources > Flashcards

Classification of Organisms & Carbon and Energy Sources Flashcards

1
Q

What were the originally (but wrong) 5 Kingdoms of Life and how were they organized?

A

Monera, protista, fungi, plantae, animalia and they were classified by their morphology (looks) and nutrition (metabolism).

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2
Q

What are the Three Domains of Life and how are they classified?

A

Bacteria, Archaea, Eukaryota and they are classified by molecular information (ribosomal RNA gene sequences).

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3
Q

Which type of cell has a higher surface area to volume ratio?

A

Prokaryotes have a greater surface-area to volume ratio.

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4
Q

As cell size increases, what happens to surface area to volume ratio?

A

It decreases and thus the cell becomes less efficient.

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5
Q

How do Eukaryotic cells survive although having a much lower surface area to volume ratio than prokaryotes?

A

They have separate membranes that carry out specific function like energy production.

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6
Q

What organelles are present in prokaryotic cells?

A

Plasma membrane, ribosome, cytoplasm and nucleoid

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7
Q

What is the nucleoid?

A

It is DNA or genetic information that is not bound in a membrane.

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8
Q

Where did the mitochondria and chloroplast orginate from?

A

They came from prokaryote organisms that most likely were engulfed by the ancestor of eukaryotes.

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9
Q

What is definite proof that the mitochondria and chloroplast originate from an eukaryote engulfing or combining with a prokaryote?

A

The DNA of these organelles are unique and different from our DNA.

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10
Q

What is the Endosymbiotic Theory?

A

The theory that some eukaroyte organelles, mainly the chloroplast and mitochondria, originated from prokaryotes.

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11
Q

How are bacteria and archaea different from eukaroytes?

A

They lack a membrane bound nuclei, have no energy-producing organelles and have no true sexual reproduction.

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12
Q

What are the special features of a bacteria cell?

A

They have circular DNA, have a plasmid, have no nucleus, no membrane, no energy-producing organelles and a cell wall made of peptidoglycan.

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13
Q

What is the bacteria cell wall made of?

A

Peptidoglycan

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14
Q

Why are bacteria cells so small?

A

In order to make diffusion to be as efficient as possible.

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15
Q

What is diffusion?

A

The movement of particles from a high area of concentration to an area of low concentration.

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16
Q

What is horizontal gene transfer?

A

It is the major source of bacterial diversity. It is the transfer or exchange of genes between bacteria.

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17
Q

How do bacteria reproduce?

A

By binary fission.

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18
Q

What is the pilus?

A

A structure that connects bacteria and allows them to exchange and transfer genes generally from the plasmid.

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19
Q

What is the plasmid?

A

It is an extra set of circular genetic material that most bacteria have. They are usually not essential to survival but they give the bacteria adaptive advantages.

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20
Q

What is conjugation?

A

The method of DNA transfer from bacteria cell to bacteria cell through the pilus. (Mainly from plasmid)

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21
Q

What is transformation?

A

When cells take up DNA released from cell breakdown, it generally requires large amounts of heat.

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22
Q

What is transduction?

A

The process in which a virus incorporates its genetic material into its host.

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23
Q

What distinguishes archaea from bacteria?

A

They have a unique ribosomal RNA structure, cell wall that is not peptidoglycan and they can live in extreme conditions.

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24
Q

How does intestinal bacteria help the human body?

A

They can help with digestion, secretion of vitamins, absorbance of biomolecules and guide development of our intestine lining.

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25
Q

How does bacteria help us in general?

A

They protect us against pathogens and strengthen our immune system.

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26
Q

What are harmful bacteria called?

A

Pathogens

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27
Q

What organism did the chloroplast originate from?

A

Cyanobacteria

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28
Q

What is a symbiont?

A

An organism that lives in closely evolved association with another organism.

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29
Q

How has does chloroplast differ from its ancestor?

A

It has lost many genes but still functions properly. These “lost” genes have migrated to the nuclues.

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30
Q

What organism did the mitochondria orginiate from?

A

Proteobacteria

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31
Q

How does mitochondria differ from its ancestor?

A

It has lost many of its genes but still functions properly. These genes have migrated to the nuclues.

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32
Q

What are the two main endosymbiotic theories?

A

That a prokaryote evolved into an eukaryote then it engulfed a proteobacterium in order to form an heterotrophic eukaryote. The other theory is that an archaeon hosted a proteobacterium and then proceeded to evolve into a heterotrophic eukaryote.

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33
Q

What are other names for the plasma membrane?

A

Cell membrane, cytoplasmic membrane and semi-permeable barriers.

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34
Q

What is the plasma membrane?

A

The structure that separates the contents of the cell from the surroundings.

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35
Q

What is the plasma membrane composed of?

A

Lipids, carbohydrates, proteins, steroids

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36
Q

What is the main component of the cell membrane and what are its properties?

A

Phospholipids make up the majority of the cell membrane. They have both a hydrophobic and hydrophilic end which are responsible for the unique structure of the membrane.

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37
Q

What is the fluid mosaic model?

A

The belief that the cell membrane is a mosaic or large variety of molecules that range from lipids, proteins and carbohydrates. It also states that the molecules in the membrane and the membrane itself is everchanging, dynamic and free to move.

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38
Q

What are the roles of proteins within the cell membrane?

A

They can act as transporters, channels, carriers, receptors, enzymes and anchors.

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39
Q

What are amphipathic molecules?

A

Molecules that have both hydrophobic and hydrophilic components such as phospholipids.

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40
Q

What are saturated lipids?

A

Lipids that have no double bonds and contain the largest amount of bonds as possible.

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41
Q

What are unsaturated lipids?

A

Lipids that have double bonds and do not have the maximum amount of bonds as possible.

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42
Q

Which type of lipid is more favourable in the cell membrane?

A

Unsaturated lipids because they have “looser” packing and thus are more “fluid.”

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43
Q

What are the three types of lipids that can form when lipids are placed in water?

A

Micelles, bilayers and liposomes

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44
Q

What are micelles?

A

They are a lipid type that takes a sphere like structure when placed in water.

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45
Q

What are bilayers?

A

A type of lipid has its hydrophobic ends facing towards the inside of the cell while having its hydrophilic ends facing outwards.

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46
Q

What are liposomes?

A

A type of lipid that is made of phospholipids that have formed a large enclosed bilayer structure (shaped like a cell).

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47
Q

Why do bilayers repair themselves effectively?

A

They change constantly and are able to surround damage areas with new, undamaged areas.

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48
Q

What is cholesterol?

A

An amphipathic membrane lipid that increases or decrease the membrane’s fluidity depending on temperature.

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49
Q

What does cholesterol do to the membrane at low temperatures?

A

It prevents the membrane from packing tightly thus maintaining the fluidity of the cell.

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50
Q

What type of organisms is cholesterol present in?

A

Only some eukaryotes like mammals NOT PLANTS.

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51
Q

How do the membranes of arachea differ from bacteria/eukaryotes?

A

Archea have an ether linkage while bacteria/eukaryote have an ester link.

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52
Q

Do phospholipids spontaneously form bilayers in water?

A

Yes

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53
Q

What is the goal of the lipid bilayer?

A

To transfer nutrients into the cell and waste out of the cell.

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54
Q

What water pass through the membrane?

A

Yes, it passes through due to a concentration gradient and the aquaporin transporters. However, it passes through slowly.

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55
Q

What molecules can pass through the cell membrane through passive diffusion?

A

Small uncharged molecules, small hydrophobic molecules and water

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56
Q

What cannot pass through the membrane through passive diffusion?

A

Charged molecules or large molecules

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57
Q

What is passive diffusion/transport?

A

The movement of molecules down their concentration gradient without the use of energy.

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58
Q

What is facilitated diffusion/transport?

A

The movement of molecules down their concentration gradient with the use of a transporter but NOT energy. (Protein carriers/channels required)

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59
Q

What is active transport?

A

The movement of molecules against their concentration gradient, it requires the use of energy, mainly ATP.

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60
Q

What is primary active transport?

A

The movement of molecules against their concentration gradient with the direct use of energy (ATP, NADH, FADH2).

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61
Q

What is secondary active transport?

A

The movement of molecules against their concentration gradient with the indirect use of energy (ATP, NADH, FADH2).

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62
Q

What are hypertonic solutions?

A

Solutions with a higher concentration of solute than the cell.

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63
Q

What are hypotonic solutions?

A

Solutions with less solute concentration than the cell.

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64
Q

What does it mean to salvate a molecule?

A
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65
Q

What molecules can pass through the cell membrane with passive diffusion?

A

Small hydrophobic and small polar molecules (CO2, H2O, O2)

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66
Q

What is an aquaporin channel?

A

A protein channel that allows for the diffusion of water into the cell (faciliated).

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67
Q

What molecules can pass through the cell membrane with facilitated diffusion?

A

Charged ions such as Na, K, Ca and also water.

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68
Q

Can ion channels transport any ion?

A

No, similar to enzymes, they are very specific to which ions they transfer because of the protein structure.

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69
Q

How does secondary active transport work?

A

Protons/ions are initially pumped out of the cell or against their concentration gradient with ATP (primary active transport). As a result, a large concentration/electrochemical gradient is built. This causes the protons to move down their concentration gradient back into the cell which supply energy so that another molecule can be transferred against its concentration gradient. (Similar to coupled reaction)

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70
Q

What is a symport transport?

A

Secondary active transport in which the coupled molecules move in the same direction.

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71
Q

What is antiport transport?

A

Secondary active transport in which the coupled molecules move in opposite directions.

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72
Q

What are integral membrane proteins?

A

Proteins that are permanently bound to the cell membrane.

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73
Q

What are peripheral membrane proteins?

A

Proteins that are bound to the membrane through weak covalent bonds and thus can be removed.

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74
Q

Most integral membranes are…

A

Transmembrane proteins

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75
Q

What are transmembrane proteins?

A

Integral proteins that span the entire lipid bilayer.

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76
Q

What is a cell wall?

A

An cell organelle that protects and maintains the structure of the cell.

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77
Q

What is osmosis?

A

The diffusion of water from an area of high water concentration or low solute concentration to an area of low water concentration or high solute concentration.

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78
Q

What happens when cells are placed in a hypertonic solution?

A

The water from their cells move to the solution and they proceed to shrink/shrivel up.

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79
Q

What happens to cells that are placed in a hypotonic solution?

A

The water from the solution moves into the cell and the cell swells or bursts.

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80
Q

What does it mean for a cell to lyses?

A

To burst

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81
Q

What is an isotonic solution?

A

A solution that has the same solute concentration as the solute concentration in the cell.

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82
Q

What type of solution is the extracellular fluid?

A

It is isotonic so there is no net movement of H2O and thus no damage to the cell.

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83
Q

What are plant cell walls made of?

A

Cellulose

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84
Q

What are fungi cell walls made of?

A

Chitin

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85
Q

What are contractile vacuoles?

A

Organelles in many single cellular organisms that takes up exess water from the cell and expels it to the environment.

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86
Q

What is turgor pressure?

A

The force exerted by waer against an object resulting in hydorstatic pressure. It is the reason why hydrated plants have rigid cell walls.

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87
Q

What is a vacuole?

A

An organelle that takes up water and contributes to the turgor pressure of the cell.

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88
Q

What is glycolysis?

A

The conversion of glucose into useful forms of energy such as ATP.

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89
Q

Why does glycolysis occur in many different reactions?

A

It is more effective and efficient to break glycolysis into smaller sub reactions in order to store the released energy into molecules such as ATP. If it was a single reaction, all of the chemical energy in glucose would be wasted.

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90
Q

What are catabolic reactions used for?

A

To break down macromolecules into subunits. This stores energy in molecules such as ATP.

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91
Q

What are anabolic reactions used for?

A

To build macromolecules from subunits. This requires energy which is obtained from molecules such as ATP.

92
Q

What are the three processes in which chemoorganotrophs produce energy?

A

Aerobic respiration, Fermentation and Anaerobic respiration

93
Q

What is aerobic respiration?

A

A metabolic process in which carbohydrates, lipids and proteins are broken down into useful forms of energy such as ATP. It requires oxygen however. (Mainly involves glucose)

94
Q

Which step of aerobic respiration requires oxygen?

A

The oxidative phosphorylation stage or electron transport chain.

95
Q

What are the four main stages of aerobic respiration?

A

Glycolysis, Acetyl-CoA synthesis (transport stage), Kreb Cycle/Citric Acid Cycle and Oxidative Phosphorylation (ETC).

96
Q

What are the important energy carriers in ATP synthesis?

A

NADH and FADH2

97
Q

What is the purpose of NADH and FADH2?

A

To carry protons and produced electrons to the electron transport chain where the majority of ATP is made.

98
Q

What kind of a reaction is aerobic respiration?

A

A redox reaction

99
Q

What is oxidation?

A

Loss of electrons (LEO)

100
Q

What is reduction?

A

Gaining of electrons (GER)

101
Q

What is the reducing agent?

A

The reactant that is oxidized in order to reduce another reactant.

102
Q

What is the oxidizing agent?

A

The reactant that is reduced order to oxidize another reactant.

103
Q

What is the enzyme for the redox reaction of NAD+?

A

Dehydrogenase

104
Q

What is the redox reaction between NAD+ and NADH?

A

NAD+ + 2e- + 2H+ <=> NADH+ + H+

105
Q

What are the three phases in glycolysis?

A

The Preparation/priming phase (-2ATP), Cleavage phase (Cut 6-carbon glucose into 2 x 3 carbon molecule), Payoff phase (+4ATP and 2NADH).

106
Q

What are the products of glycolysis?

A

Net 2 ATP, 2 NADH and 2 pyruvate (3C) molecules

107
Q

What is substrate level phosphorylation?

A

The process in which a phosphate group is taken off of the substrate to phosphorylate a ADP into an ATP molecule. (Coupled reaction)

OR

The process in which ATP is produced in an enzymatic reaction.

108
Q

What is the product made after the cleavage phase in glycolysis?

A

G3P or Glyceraldehyde 3-phosphate

109
Q

Is glycolysis always done regardless of the presence of oxygen?

A

Yes, if there is oxygen present aerobic respiration continutes, if not then fermentation is performed.

110
Q

How is glycolysis kept running?

A

By having the reduced electron carriers (NADH) being continually reoxidized into NAD+. (Recycle)

111
Q

Where are reduced electron carriers reoxidized in aerobic respiration?

A

In the electron transport chain

112
Q

Where are reduced electron carriers reoxidized in fermentation?

A

In the fermentation reaction (either lactic acid or ethanol production in most cases).

113
Q

What is produced in ethanol fermentation?

A

2 CO2, 2 ethanol molecules (2C) and 2 NAD+ molecules (NADH was oxidized)

114
Q

What is produced in lactic acid fermentation?

A

2 lactic acid molecules (3C) and 2 NAD+ (NADH is oxidized)

115
Q

What is ABE fermentation used for?

A

It is used to produce bio fuels in the present and was used to produce gun powder in the past.

116
Q

Where does glycolysis occur?

A

In the cytoplasm

117
Q

What is the purpose of fermentation?

A

To oxidize NADH and allow glycolysis to continue when no oxygen is present.

118
Q

Is glycolysis anaerobic or aerboic?

A

Anaerobic because it does not require oxygen.

119
Q

Which form of a molecule has more energy and why? (Oxidized vs Reduced)

A

The reduced form has more energy because it carries more electrons which can be transferred to oxygen in order to create ATP (oxidative phosphorylation).

120
Q

What is the net reaction for glycolysis?

A

Glucose + 2NAD+ + 2ADP + 2Pi -> 2 pyruvate + 2ATP + 2NADH + 2H20

121
Q

Are mitochondria and chloroplast still considered prokaryotes?

A

Yes, although they are found in eukaryote cells they are indeed prokaryote.

122
Q

How do the phospholipid in membranes move?

A

From side to side along the membrane

123
Q

What is the difference between primary active transport and secodnary active transport?

A

Primary active transport always occurs first (NOT IT USES ATP DIRECTLY, as there are cases where it doesn’t)

124
Q

What is facilitated diffusion most dependent on?

A

The concentration of solutes (not ions)

125
Q

How many membranes does the mitochondria have?

A

It is a double membraned strucutre. It is composed of the outermembrane, intermenbrane space, inner membrane and matrix.

126
Q

Where does the citric acid cycle or Kreb cycle occur?

A

In the matrix of the mitochondria.

127
Q

Where do the respiratory pathways occur in prokaryotes?

A

In the cytoplasm (as they do not have mitochondria)

128
Q

What type of transport is used to move pyruvate across the outer mitochondrial membrane?

A

Facilitated diffusion because the cytoplasm produces a large concentration of pyruvate.

129
Q

What type of transport is used to move pyruvate across the inter mitochondrial membrane?

A

Secondary active transport because the concentration of pyruvate inside the matrix is very high.

130
Q

Where does the bridge reaction or Acteyl-CoA Synthesis stage occur?

A

In the matrix of the mitochondria

131
Q

What is the reaction of the Acteyl-CoA synthesis stage?

A

2 pyruvate -> 2CO2 + 2NADH + 2 Acetyl-CoA (2C)

132
Q

What do coenzymes do?

A

They work with protein cataylst and add energy to compounds.

133
Q

What is produced in the Kreb Cycle per glucose?

A

6 NADH, 2 FADH2, 2 ATP and 4 CO2

134
Q

What happens to all of the carbons in glucose as aerobic respiration occurs?

A

They are all oxidized into CO2 and released into the environment.

135
Q

What is another function of the Kreb Cycle?

A

It can be used to synthesize intermediates of certain molecules like proteins. (The carbon is lost to cellular material instead of as carbon dioxide) Note this is when the Kreb cycle is reversed.

136
Q

How many ATPs are produced due to substrate level phosphorylation in cellular respiration?

A

4

137
Q

What are the final products produced after the Citric Acid Cycle?

A

10 NADH, 2 FADH2, 4 ATP, 6 CO2

138
Q

What are allosteric enzymes?

A

They are key regulatory enzymes that change their shape or binding pattern depending on the concentration of certain products or reactants. There are some enzymes that have both an active and allosteric site.

139
Q

How is PFK-1 activated during glycolysis?

A

High concentrations of AMP and ADP bind to the allosteric site of the enzyme and activates it.

140
Q

How is PFK-1 inhibited during glycolysis?

A

High concentrations of Citrate and ATP bind to the allosteric site and inhibit the enzyme.

141
Q

What are the other names for the Kreb cycle?

A

Citric acid cycle and tricarboxylic acid cycle

142
Q

What conditions indicate that the cell is in a low energy state?

A

High concentrations of ADP, AMP and NAD+

143
Q

What conditions indicate that the cell is in a high energy state?

A

High concentrations of ATP, NADH and Citrate

144
Q

Where does the Electron Transport Chain occur?

A

It happens in the inner mitochondrian membrane.

145
Q

Which molecule does Complex I oxidize? (Take electrons from)

A

NADH

146
Q

What happens at Complex I?

A

An NADH is oxidized into NAD+ and the electron is transferred to Coenzyme Q (To make CoQH2), while a H+ ion is pumped out of the matrix.

147
Q

What is Coenzyme Q or CoQ?

A

A coenzyme that takes up electrons from the reduced electron carriers produced in aerobic respiration. It transports electrons along the ETC to Cytochrome C. (Electron taxi) It is EVERYWHERE in the membrane, a fluid.

148
Q

What is the reduced form of CoQ?

A

CoQH2

149
Q

In the ETC, protons are always pumped __ of the matrix?

A

Out into the innermembrane space of the mitochondria.

150
Q

Which Complex in the ETC does not pump a proton out of the matrix?

A

II

151
Q

What happens at Complex II?

A

FADH2 is oxidized into FAD and the electron is transferred to CoQ (to make CoQH2). Succinate is changed into Fumerate. THERE IS NOT PROTON TRANSFER OUT OF MATRIX.

152
Q

Which part of the ETC is directly linked to the Kreb Cycle?

A

The oxidation of FADH2 which was made ONLY in the Kreb Cycle.

153
Q

What happens at Complex III?

A

Electrons from CoQH2 are transfered to a soluble electron carrier, Cytochrome C (it is reduced). Meanwhile, a proton is pumped out of the matrix.

154
Q

Does CoQH2 from Complex I jump over Complex II in order to reach Complex III?

A

NO, CoQ can be thought of as a pool that transcends the membrane. (Cannot be removed from membrane and thus not soluble) The electrons take a direct route from I to III and II to III. (Two separate paths)

155
Q

What is Cytochrome C?

A

An electron carrier that takes electrons from CoQH2 at Complex II (is reduced) and takes these electrons to Complex IV where it is oxidized. It is soluable and able to move outside of the membrane unlike CoQ.

156
Q

What happens at Complex IV?

A

Cytochrome C (reduced form) docks onto Complex IV and transfers its electrons to oxygen (reduced into water). Meanwhile, a proton is pumped out of the matrix.

157
Q

What is the purpose of the ETC?

A

To build an electrochemical gradient (proton) in order to provide energy in order to create ATP. (All steps contribute)

158
Q

What is an electrochemical gradient?

A

A gradient that is composed of both a charge gradient and chemical/concentration gradient. This is the driving force in the production of ATP in the ETC.

159
Q

How does ATP Synthase work?

A

The electrochemical gradient built from Complex I to Complex IV allows for the movement of the protons back into the matrix (down their concentration gradient). This energy spins ATP Synthase and creates ATP from ADP and Pi. (A coupled reaction occurs with the movement of the proton and the production of ATP)

160
Q

Why is the ETC broken into so many steps?

A

In order to conserve or extract more energy into ATP and to build the proton gradient.

161
Q

Generally, for each electron moved how many protons are moved outside of the matrix in the ETC?

A

1 (The electron and proton follow each other)

162
Q

Where does all of the NADH in the ETC come from?

A

All of the prior steps within aerobic respiration… Glycolysis (2), Bridge (2) and Kreb Cycle (6)

163
Q

Where does all of the FADH2 in the ETC come from?

A

From the Kreb Cycle ONLY!

164
Q

Why is oxygen required in aerobic respiration?

A

It is the final electron acceptor within the ETC. If there is nothing to accept the electron, then NADH must be oxidized back into NAD+ in order to keep glycolysis going.

165
Q

What is ATP Synthase made of?

A

F0 and F1

166
Q

What is the function of F0 in ATP Synthase?

A

It is the proton channel that allows protons to pass through it down the electrochemical gradient. It spins as it does so, which provides energy for the production of ATP.

167
Q

What is the function of F1 in ATP Synthase?

A

It is the part of ATP Synthase that harnesses the rotational energy in order to produce ATP from ADP and Pi.

168
Q

Does osmosis increase entropy?

A

Yes, the movement of the water from the area of low solute to high solute increases the entropy of that area MORE than the water that left the low solute area. (Thus net entropy increases, plus it is sponataneous)

169
Q

How many ATP is made within aerobic respiration?

A

Approximately 32

170
Q

How many ATP is made due to substrate level phosphorylation?

A

4, 2 within glycolysis and 2 within the Kreb Cycle

171
Q

How many ATP is made due to oxidative phosphorylation?

A

28

172
Q

How many ATP does each NADH molecule yield?

A

2.5

173
Q

How many ATP does each FADH2 molecule yield?

A

1.5

174
Q

What is chemiosmosis?

A

The movement of ions (protons) down its concentration gradient through a selective membrane in order to provide energy to produce ATP.

175
Q

What is another type of gradient created within the ETC?

A

In addition to the electrochemical gradient, a pH gradient is also formed. (Goes from low pH or high protons to high pH or low protons)

176
Q

What happens in the ETC when there is excess ATP?

A

ATP synthase is a reversible enzyme, so it will hydrolize ATP into ADP + Pi while pumping hydrogen ions out of the matrix.

177
Q

What happens to the ETC when there is a blocked electron transport chain?

A

Electrons are unable to be transferred thus a proton gradient is unable to be established and fermentation will occur instead of the ETC.

178
Q

Is ATP synthase a reversible enzyme?

A

Yes, if there is high levels of ATP, it can work in reverse. (Hydrolysis of ATP and pumping H+ out of the matrix)

179
Q

Where does oxygen come from in photosynthesis?

A

The water molecule is oxidized into oxygen

180
Q

Where is the proton gradient built in photosynthesis?

A

It is built in the lumen of the chloroplast. (Protons are pumped into the lumen from the stroma)

181
Q

What are features of a chloroplast cell?

A

It is a double membraned organelle like the mitochondria. (Has an inner and outer membrane) Inside of the inner membrane, there is the stroma and stacks of thylakoids called granas. The thylakoids also have membranes which are called the thylakoid membrane. Inside oft these stacks is lumen.

182
Q

Why are leaves generally green?

A

Because green is the least absorbable wavelength of light and thus it is reflected thus making leaves appear to be green.

183
Q

What is a photic zone?

A

A surface layer in the ocean that is about 100 m deep where photosynthesis can still occur/

184
Q

What is the thylakoid membrane?

A

The area of the chlorophyll where the photosynthetic electron transport chain occurs.

185
Q

What are grana?

A

Stacks of thylakoids

186
Q

What is lumen?

A

The fluid within the thylakoid membrane.

187
Q

What is the stroma?

A

The region surrounding the thylakoid membrane.

188
Q

Where does carbon fixation occur?

A

In the stroma

189
Q

What are photosystems?

A

A complex of proteins and pigments that are embedded into the thylakoid membrane.

190
Q

What is chlorophyll?

A

The major photosynthetic pigment within plants.

191
Q

What are accessory pigments?

A

Photosynthetic pigments that allow photosynthetic cells to absorb broader ranges of visible light than would be possible with only chlorophyll.

192
Q

Where does ATP synthase and PSI operate?

A

In the thylakoid membrane however primarily when there is good contact with the stroma.

193
Q

Where does PSII operate?

A

In the thylakoid membrane but predominately on in the grana.

194
Q

What are the antennae chlorophyll/complexes?

A

The energy transfer sites that randomly transfer absorbed photons/energy until it reaches the reaction center.

195
Q

What happens to the energy when it reaches PSII?

A

It uses the energy to oxidize water (into oxygen) and strip the water of its electron.

196
Q

What is PSII?

A

Photosystem II is a complex or reaction center within the thylakoid membrane which absorbs energy to oxidize water into oxygen and hydrogen atoms. An electron is then transferred to plastoquinone. (Pq)

197
Q

What is Pq?

A

Plastoquione is a eletron taxi within the thylakoid membrane that takes electrons from PSII and transfers it to cytochrome. It also pumps a proton across the thylakoid membrane (stroma to lumen).

198
Q

What is Cytochrome?

A

A complex within the thylakoid membrane that takes electrons from plastoquinone and transfers them to a soluble electron taxi, Pc.

199
Q

What is Pc?

A

Plastocyanin is a soluble electron taxi or carrier in the lumen that takes electrons from cytochrome and transfers them to photosystem II.

200
Q

What is PSI?

A

Photosystem I is a reaction center or complex where energy is absorbed in order to energize the electron it receives from plastocyanin. It transfers this energized electron to Fd.

201
Q

What is Fd?

A

Ferridoxin is a soluble electron taxi or carrier in the stroma that takes energized electrons from PSI to the NADP reductase where NADP+ is reduced into NADPH.

202
Q

What is NADP reductase?

A

An enzyme within the stroma that takes electrons from Fd in order to reduce NADP+ into NADPH.

203
Q

Where is NADPH produced from the light-dependent reaction?

A

In the stroma

204
Q

Where is ATP produced in the light-depedent reaction?

A

In the stroma

205
Q

What is the electron flow within the light-dependent reaction?

A

Electrons are donated from water to PSII, then it goes to Pq, to Cyt, to Pc, energized at PSI, to Fd, to NADH reductase and finally to NADP+ in order to make NADPH.

206
Q

Which parts of the thylakoid membrane pump build the electrochemical gradient within the lumen?

A

ONLY the plastoquinone

207
Q

What is the final electron acceptor in the light-dependent reaction?

A

NADP+

208
Q

What is the cyclic electron transport system?

A

When the light dependent reaction inhibits the transfer of electrons from Fd to NADP reductase. Instead, Fd cycles the electron back to Pq in order to pump even more protons into the lumen. As a result, more ATP is produced due to the greater electrochemical gradient.

209
Q

What is carbon fixation most dependent on?

A

ATP not NADPH, hence why the cyclic ETC occurs.

210
Q

What is anaerobic respiration?

A

The conversion of glucose into useful forms of energy using a different final electron acceptor than oxygen. (Hence anaerobic)

211
Q

Does the electron transport chain DIRECTLY produce ATP?

A

No, it just builds a electrochemical gradient that is used to drive ATP synthesis with ATP synthase.

212
Q

What is the most abundunt enzyme on the planet?

A

Rubisco

213
Q

Is carbon fixation a fast or slow process?

A

It a very slow reaction even with a catalyst because it requires a LARGE amouunt of energy.

214
Q

What are the three steps of the Calvin cycle?

A

Carbon Fixation (RuBP + CO2), Reduction (3 phosphoglycerate > triose phosphate), Regeneration (triose phosphate > RuBP)

215
Q

How many ATP and NADPH are used per Calvin cycle (6CO2)?

A

12 ATP and 6 NADPH (6 ATP and 6 NADH in reduction and 6 ATP in regeneration)

216
Q

What is the 5 carbon compound that is used to fix carbon dioxide?

A

RuBP, Ribulose-1,5-bisphosphate

217
Q

What is CO2 fixed into?

A

3-Phosphoglycerate (3PGA)

218
Q

What is 3PGA reduced into?

A

Triose phosphate

219
Q

What is the rate limiting step of the Calvin cycle?

A

The regeneration phase slows the reaction down substantially.

220
Q

How is glucose created from the Calvin cycle?

A

When 3PGA is reduced into triose phosphate, two of these exit the Calvin cycle and forms glucose.

221
Q

What is the stoichiometric summary of the Calvin cycle?

A

6 RuBP (5C) + 6 CO2 (1C) => 12 3PGA (2C) => 12 Triose Phosphate (3C) => 2 Triose Phosphates leave to form glucose => 10 Triose Phosphate (3C) => 6 RuBP (5C)

222
Q

Is the ATP made in the light reaction used for energy?

A

NO, it is only used for carbon fixation!

223
Q

What is the photosynthetic pigment in prokaryotic cells?

A

Bacterio chlorophyll

224
Q

Which PS do most bacteria lack?

A

PSI

225
Q

What is the only bacteria that fixes carbon?

A

Cyanobacteria

226
Q

What is bacteriorhodopsin?

A

A light energized proton pump that pumps protons out of the cell in order to build a concentration gradient. This gradient can either produce ATP or act as symport or antiport to move material against their concentration gradient.

Biology 241 (2 decks)

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