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Principles of Biology I > Unit #2: Chapters 6-9 > Flashcards

Unit #2: Chapters 6-9 Flashcards

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1
Q

oxidation

A
  • loss of electrons

* results in positive charge

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2
Q

reduction

A
  • gain of electrons

* results in negative charge

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3
Q

reduced carbon

A

stores energy in chemical bonds of organic molecules

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4
Q

enzyme

A
  • globular protein with one or more active sites (“pockets”)
  • determines the course of metabolism by facilitating particular chemical reactions
  • almost every reaction has a corresponding enzyme to facilitate it
  • may also have inhibitors (competitive or non-competitive)
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5
Q

photosynthesis (defn and formula)

A
  • Formula: 6CO2 + 6H2O -> C6H12O6 + 6H2O + 6O2
  • Uses light energy to convert carbon dioxide and water to sugars and oxygen
  • occurs in the chloroplast
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6
Q

photon

A
  • a particle of light
  • acts as a discrete bundle of energy
  • energy content of a photon is inversely proportional to the wavelength of the light
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7
Q

proton

A

Positively-charged particle of an atom - H+

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8
Q

light-dependent reactions

A
  • capture energy from photons to make ATP and reduce NADP+ to NADPH
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9
Q

light-independent reactions

A
  • also called Calvin Cycle and carbon fixation reactions
  • If O2 is available, uses ATP and NADPH to synthesize organic molecules from CO2
  • If O2 is not available, side reactions store (?) as oxyloacetate when plant stomata are closed (C4 plants)
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10
Q

chlorophyll

A
  • green-colored pigment; absorbs red/blue light wavelengths, reflects green
  • chlorophyll a – primary pigment in plants and cyanobacteria that absorbs violet-blue and red light
  • chlorophyll b – secondary pigment absorbing light wavelengths that chlorophyll a does not absorb
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11
Q

absorption

A

atoms can only absorb photons with energy levels that correspond to the atom’s available energy levels. so each molecule has a specific range of photons it can absorb.

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12
Q

stroma

A

semiliquid substance surrounding thylakoid membranes

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13
Q

thylakoid

A
  • In the chloroplast
  • internal membrane arranged in flattened sacs
  • contains chlorophyll and other pigments
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14
Q

grana

A
  • stacks of thylakoid membranes

* includes a thylakoid space

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15
Q

chloroplast

A

An organelle in plant cells where photosynthesis takes place.

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16
Q

ATP (definition, function, structure)

A
  • adenosine triphosphate
  • the energy “currency” of cells - energy is released when PO4 is removed
  • portable and on-demand source of energy for endergonic reactions
  • ATP structure:
  • ribose, a 5-carbon sugar
  • adenine
  • three phosphates
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17
Q

NAD+

A
  • nicotinamide adenosine dinucleotide
  • one of the most important electron (e-) acceptor/carriers
  • a low-energy cofactor that accepts a pair of e- and a proton (H) to create NADH
  • composed of two nucleotides bound together by the phosphates
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18
Q

NADH

A
  • Reduced form of NAD+, that has accepted 2 e- and one proton
  • Reaction is reversible: can release 2 e- and 1 proton to become NAD+ again
  • Used in the mitochondrion in the e- transport chain
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19
Q

NADPH

A
  • Reduced NADP
  • synthesized in the chloroplast by light-dependent reactions
  • Used directly by the Calvin Cycle to synthesize organic molecules from CO2
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20
Q

FADH2

A
  • Reduced e- carrier (FAD that has accepted 2 e-)
  • Bound to its enzyme in the inner mitochondrial membrane, so only releases e- to the electron transport chain.
  • Worth 2 ATP
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21
Q

Calvin Cycle (defn and location)

A
  • biochemical pathway in photosynthesis that allows for carbon fixation
  • occurs in the stroma of chloroplast
  • uses ATP and NADPH as energy sources
  • incorporates CO2 into organic molecules
  • output is 2 molecules of G3P for every 6 molecules of CO2 (glucose is synthesized in a separate reaction)
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22
Q

ribulose biphosphate carboxylase

A

enzyme that carries out Phase 1 of the Calvin Cycle (the carbon fixation reaction), reacting RuBP (ribulose 1,5-biphosphate) with CO2 to produce 2 molecules of PGA

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23
Q

rubisco

A
  • nickname for ribulose biphosphate carboxylase

* the most prevalent enzyme in nature

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24
Q

CAM

A
  • alternative CO2 source for photosynthesis for tropical plants (like pineapple)
  • like C4 photosynthesis, fixes CO2 to PEP instead of PGA to form a C-4 molecule that stores CO2 until released to the Calvin Cycle
  • unlike C4 photosynthesis, these plants capture CO2 at night and decarboxylate (do the Calvin Cycle) during the day
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25
Q

C3

A
  • most plants use this form of photosynthesis

* called C3 because the first intermediate of the Calvin Cycle is phosphoglycerate (PGA), with 3 C atoms

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26
Q

C4

A
  • alternative photosynthesis plants (like grasses, corn)
  • fixes CO2 to PEP instead of PGA to form a 4-C molecule which stores the CO2 until it is released to the Calvin Cycle
  • reduces photorespiration (which reduces the yield of carbohydrates)
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27
Q

Krebs Cycle (summary description and location)

A
  • 9-step process to reduce the acetyl group from Pyruvate Oxidation
  • Occurs in the matrix of the mitochondria
  • Otherwise known as the citric acid cycle or TCA cycle
  • When the cell’s ATP concentration is high, the process shuts down and acetyl-CoA is channeled into fat synthesis.
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28
Q

Glycolysis (definition/description)

A
  • The break-down of glucose in a cell for metabolism
  • E- of C-H bonds are stripped off in a series of reactions
  • Occurs in the cytoplasm
  • Results in net gain of 2 ATP
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29
Q

cytoplasm

A

Material inside a cell, not including the nucleus.

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30
Q

oxyloacetate

A
  • “Feeder” molecule (4-carbon) that reacts with acetyl-CoA to start the Krebs Cycle
  • Also the Step 9 product of the Krebs Cycle
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31
Q

carbon dioxide

A

CO2 - feeds photosynthesis and is an output of respiration

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32
Q

cis-aconitate

A

an intermediate in the isomerization of citrate to isocitrate in the citric acid cycle

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33
Q

alpha-ketoglutarate

A

Step 4 product of the Krebs Cycle, a 5-carbon molecule

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34
Q

acetyl-CoA

A
  • The end product of Pyruvate Oxidation
  • Feeds the Krebs Cycle
  • consists of 2 carbons from pyruvate attached to coenzyme A
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35
Q

citric acid

A
  • Step 1 product of the Krebs Cycle, a 6-carbon molecule
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36
Q

isocitrate

A

in isomer of citrate where on OH group is repositioned

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37
Q

fermentation

A
  • Occurs when oxygen is not available
  • ATP must be produced by glycolysis
  • Final electron acceptor is an organic molecule
  • ex: yeast grows in O2, then runs out and ferments pyruvate to alcohol
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38
Q

lactate

A

Ionized form of lactic acid

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39
Q

alcohol

A

A reduced organic compound through fermentation.

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40
Q

electron transport system

A
  • Series of e- carriers to store energy from oxidation reactions
  • Located in the inner membrane of the mitochondrion.
  • Electrons from NADH and FADH2 are transferred from complex to complex, with some e- energy lost at each transfer, used to pump H+ out of matrix to inter-membrane space.
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41
Q

catabolism

A
  • chemical reactions that harvest energy when bonds are broken (respiration)
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42
Q

anabolism

A
  • chemical reactions that expend energy to make new chemical bonds (photosynthesis)
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43
Q

metabolism

A

all chemical reactions occurring in an organism (anabolism + catabolism)

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44
Q

fumarate

A

Step 7 product of the Krebs Cycle, a 4-carbon molecule

45
Q

malate

A

Step 8 product of the Krebs Cycle, a 4-carbon molecule

46
Q

succinate

A

Step 6 product of the Krebs Cycle, a 4-carbon molecule

47
Q

succinyl-CoA

A

Step 5 product of the Krebs Cycle, a 4-carbon molecule

48
Q

isocitrate

A

Step 2/3 product of the Krebs Cycle, a 6-carbon molecule

49
Q

matrix

A

The inner-mitochondrial space, inside the inner membrane.

50
Q

cristae

A

The folds of the inner membrane layer of the mitochondrion, creating many layers to pack lots of e- transfer enzymes

51
Q

aerobic

A

involving oxygen (final electron acceptor is O)

52
Q

anaerobic

A
  • not involving oxygen (final electron acceptor is an inorganic molecule other than O)
  • in respiration, won’t go to Pyruvate Oxidation, only glycolysis
53
Q

autotroph

A

organism that makes its own food (plants that photosynthesize sugars)

54
Q

heterotroph

A

organisms that do not make their own food and so eat autotrophs or other heterotrophs

55
Q

potential energy

A

stored energy (put into chemical bonds)

56
Q

kinetic energy

A

energy of motion, much wasted as heat

57
Q

pyruvate

A
  • Step 10 product of glycolysis.
  • The further fate of pyruvate depends on oxygen availability:
    • When oxygen is present, pyruvate is oxidized in Pyruvate Oxidation to acetyl-CoA, which enters the Krebs cycle
    • Without oxygen, pyruvate is reduced in order to oxidize NADH back to NAD+
58
Q

glucose-6-phosphate

A
  • Step 1 product of glycolysis

glucose has gained a phosphate from ATP

59
Q

fructose-6-phosphate

A
  • Step 2 product of glycolysis

glucose 6-phosphate has been reorganized

60
Q

cyanide

A

a poison that stops the e- transport system, and consequently ATP generation

61
Q

cyclic photophosphorylation

A

bacterial cycles, with one photosystem

62
Q

non-cyclic photophosphorylation

A

e- are boosted from photosystem II to photosystem I and absorbed by NADP to NADPH which is used in Calvin Cycle (not cycled back)

63
Q

citric acid cycle

A

Also known as the Krebs Cycle, or TCA cycle

64
Q

TCA cycle

A

Also known as the Krebs Cycle, or citric acid cycle

65
Q

fructose-1,6-biphosphate

A
  • Step 3 product of glycolysis
66
Q

substrate level phosphorylation

A
  • The creation of ATP from ADP by transferring a phosphate group from another molecule
    (Endergonic, enzyme-facilitated reaction where PEP and ADP bind to an enzyme’s active sites and a phosphate group is transferred from PEP to ADP.)
67
Q

ATP synthase

A
  • An enzyme that facilitates the synthesis of ATP through oxidative phosphorylation (a second method to substrate-level - energy to transfer the phosphate comes from a proton gradient).
  • A membrane-bound enzyme that uses the energy of the proton gradient to synthesize ATP from ADP + Pi
  • 1 proton results in 1 ATP
  • process is called chemiosmosis
68
Q

proton motive force

A

the proton gradient that drives oxidative phosphorylation via the ATP synthase enzyme

69
Q

phospho-gluco isomerase

A

the enzyme that turns glucose-6-phosphate into fructose-6-phosphate

70
Q

PEP carboxylase

A

enzyme used in C4 metabolism

71
Q

G protein

A
  • cell surface (membrane) receptor
  • a go-between for the receptor and the enzyme the signal is intended for
  • causes signal to 2nd messenger, etc. on signal transduction system
72
Q

photosystem 1

A
  • protein-bound bundle on the thylakoid membrane with pigments
  • collects energy output from photosystem II
73
Q

photosystem 2

A
  • protein-bound bundle on the thylakoid membrane with pigments
  • collects energy from protons and outputs an e-
74
Q

end product inhibition

A
  • competitive & non-competitive

* final product of a reaction feeds back and shuts it down

75
Q

ligand

A
  • signaling molecule
  • when signal reaches a receptor protein, this initiates signal transduction which converts the signaled information into a cellular response
76
Q

desmosome

A
  • junctions between cells

* glycoproteins that paste cells together

77
Q

hemidesmosome

A
  • half a desmosome

* faces a basal lamina

78
Q

gap junction

A
  • connects cytoplasms of cells

* facilitates diffusion between them

79
Q

tight junction

A
  • water-proof seal that attaches cells together
80
Q

adherens junction

A

will stick cells together

81
Q

cAMP

A
  • cyclic adenosine monophosphate
  • reacts with own hydroxyl end to form a circle
  • a 2nd messenger
  • primitive signal molecule (used by slime molds)
82
Q

kinase

A

anything that attaches PO4 to something else

83
Q

chemiosmosis

A

the proton pump/ATP synthase process to produce ATP

84
Q

proton pump

A

see ATP synthase

85
Q

NADH dehydrogenase

A
  • the first membrane-embedded enzyme to receive e- in the e- transport chain
  • oxidizes NADH to NAD+ and releases a proton (H+) to the intermembrane space
86
Q

cytochrome b-c complex

A
  • bc complex is the second enzyme in the e- transport chain which uses energy from e- to pump a proton to the intermembrane space
  • cytochrome oxidase complex does the same thing, pumping another proton
87
Q

Calvin Cycle (steps)

A
  • Phase I - carbon fixation
  • Phase 2 - reduction
  • Phase 3 - regeneration of RuBP
88
Q

carbon fixation

A

the conversion of inorganic carbon as CO2 into organic carbon in the form of carbohydrates

89
Q

glyceraldehyde-3-phosphate (G-3-P)

A
  • 3-carbon sugar
  • can link together to form glucose
  • Step 4/5 product in glycolysis.
90
Q

endocrine

A
  • hormonal cell signalling

* sent throughout system; target cells have receptors

91
Q

paracrine

A
  • signals nearby cells by releasing its signal into the extracellular fluid between cells and sent by diffusion
  • concentration of signal is dependent on the distance from the signalling cell
92
Q

autocrine

A
  • signals itself

* secretes signals that bind to specific receptors on a cell’s own plasma membrane

93
Q

exocrine

A
  • sends molecules outside self, or even the organism (such as sweat or digestive stuff)
94
Q

steroid hormones

A
  • binds to an intracellular receptor, usually in the nucleus
  • have a nonpolar, lipid-soluble structure
  • can cross the plasma membrane to a steroid receptor
  • usually act as regulators of gene expression
  • An inhibitor blocks the receptor from binding to DNA until the hormone is present.
95
Q

1st law of thermodynamics

A

energy is neither created nor destroyed by natural processes, just converted between kinetic and potential

96
Q

2nd law of thermodynamics

A

disorder is always increasing in the universe - energy used to create order in one place creates disorder elsewhere (releases heat in the process)

97
Q

action spectrum

A

plant growth vs. wavelengths of light

98
Q

absorption spectrum

A

wavelengths absorbed where plants grow best

99
Q

evolution

A
  • chloroplasts and mitochondria evolved by endosymbiosis (double membranes, DNA)
  • photosynthesis likely developed first
  • metabolism may have developed to remove toxic O2
100
Q

Glycolysis Steps

A
  • Step 1: Phosphate group added to glucose by ATP (to ADP). Produces Glucose 6-phosphate
  • Step 2: Rearrange Glucose 6-phosphate into Fructose 6-phosphate. Produces Fructose 6-phosphate
  • Step 3: Phosphate group added to Fructose 6-phosphate by ATP (to ADP). Produces Fructose 1,6-biphosphate
  • Step 4/5: Fructose 1,6-biphosphate is split into two 3-carbon molecules. Produces one G3P and one that is converted into G3P in a second reaction.
  • Step 6: Two G3P molecules are each oxidized by NAD+ and a P-group added. Produces 2 NADH and 2 BPG.
  • Step 7: One phosphate group removed from each BPG by ADP. Produces two ATP and two 3PG.
  • Step 8: Two 3PG molecules rearranged into two 2PG.
  • Step 9: Dehydration reaction on two molecules of 2PG. Produces 2 molecules of water and two PEP.
  • Step 10: One phosphate group removed from each of two molecules of PEP by ADP. Produces two ATP and two Pyruvate.
101
Q

Glycolysis: summary of 1st 5 reactions and 2nd 5 reations

A
  • 1st 5: Convert a molecule of glucose into two molecules of G3P.
  • 2nd 5: Convert two molecules of G3P into two molecules of pyruvate.
102
Q

Krebs Cycle steps

A
  • Step 1: (Condensation) Oxaloacetate reacts with acetyl-CoA to produce citrate.
  • Steps 2/3: (Isomerization) 2-step process to rearrange citrate into an isomer isocitrate.
  • Step 4: (1st Oxidation) Isocitrate is oxidized, producing alpha-ketoglutarate, one CO2, and one NADH.
  • Step 5: (2nd Oxidation) alpha-ketoglutarate is oxidized, producing succinyl-CoA, one CO2, and one NADH.
  • Step 6: (Substrate-level Phosphorylation) Succinyl-CoA is cleaved into two molecules and the energy released bonds a phosphate to GDP, which releases it to ADP, producing succinate and one ATP.
  • Step 7 (3rd Oxidation) Succinate is oxidized, producing fumarate and one FADH2.
  • Step 8/9 (Regeneration of Oxaloacetate) Fumarate accepts a water molecule, turning into malate, which is then oxidized, producing oxaloacetate one NADH.
103
Q

Krebs Cycle output

A
  • 2 CO2
  • 1 ATP
  • 3 NADH (3 pairs of e-)
  • 1 FADH2 (1 pair of e-)
104
Q

photosynthesis (steps)

A
  • pigment molecules capture photons, passing the energy through the photosystem
  • the energy is passed as an excited e- to a protein and down an e- transport chain, producing ATP and NADPH
  • NADPH and ATP are then used in the Calvin Cycle to build organic molecules (carbohydrates)
105
Q

competitive inhibitors

A

a molecule that binds to the same active site as an enzyme’s substrate, competing with the substrate

106
Q

non-competitive inhibitors

A

a molecule that binds to a location other than the active site of an enzyme, changing the enzyme’s shape so that it cannot bind to its substrate

107
Q

respiration ATP generation

A

36 for eukaryotes

108
Q

ATP usage to make one glucose

A

54

Principles of Biology I (11 decks)

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