Unit #2: Chapters 6-9 Flashcards
(108 cards)
1
Q
oxidation
A
- loss of electrons
* results in positive charge
2
Q
reduction
A
- gain of electrons
* results in negative charge
3
Q
reduced carbon
A
stores energy in chemical bonds of organic molecules
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)
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
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
7
Q
proton
A
Positively-charged particle of an atom - H+
8
Q
light-dependent reactions
A
- capture energy from photons to make ATP and reduce NADP+ to NADPH
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)
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
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.
12
Q
stroma
A
semiliquid substance surrounding thylakoid membranes
13
Q
thylakoid
A
- In the chloroplast
- internal membrane arranged in flattened sacs
- contains chlorophyll and other pigments
14
Q
grana
A
- stacks of thylakoid membranes
* includes a thylakoid space
15
Q
chloroplast
A
An organelle in plant cells where photosynthesis takes place.
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
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
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
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
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
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)
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
23
Q
rubisco
A
- nickname for ribulose biphosphate carboxylase
* the most prevalent enzyme in nature
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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C3
* 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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C4
* 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)
27
Krebs Cycle (summary description and location)
* 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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Glycolysis (definition/description)
* 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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cytoplasm
Material inside a cell, not including the nucleus.
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oxyloacetate
* "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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carbon dioxide
CO2 - feeds photosynthesis and is an output of respiration
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cis-aconitate
an intermediate in the isomerization of citrate to isocitrate in the citric acid cycle
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alpha-ketoglutarate
Step 4 product of the Krebs Cycle, a 5-carbon molecule
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acetyl-CoA
* The end product of Pyruvate Oxidation
* Feeds the Krebs Cycle
* consists of 2 carbons from pyruvate attached to coenzyme A
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citric acid
* Step 1 product of the Krebs Cycle, a 6-carbon molecule
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isocitrate
in isomer of citrate where on OH group is repositioned
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fermentation
* 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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lactate
Ionized form of lactic acid
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alcohol
A reduced organic compound through fermentation.
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electron transport system
* 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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catabolism
* chemical reactions that harvest energy when bonds are broken (respiration)
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anabolism
* chemical reactions that expend energy to make new chemical bonds (photosynthesis)
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metabolism
all chemical reactions occurring in an organism (anabolism + catabolism)
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fumarate
Step 7 product of the Krebs Cycle, a 4-carbon molecule
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malate
Step 8 product of the Krebs Cycle, a 4-carbon molecule
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succinate
Step 6 product of the Krebs Cycle, a 4-carbon molecule
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succinyl-CoA
Step 5 product of the Krebs Cycle, a 4-carbon molecule
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isocitrate
Step 2/3 product of the Krebs Cycle, a 6-carbon molecule
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matrix
The inner-mitochondrial space, inside the inner membrane.
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cristae
The folds of the inner membrane layer of the mitochondrion, creating many layers to pack lots of e- transfer enzymes
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aerobic
involving oxygen (final electron acceptor is O)
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anaerobic
* not involving oxygen (final electron acceptor is an inorganic molecule other than O)
* in respiration, won't go to Pyruvate Oxidation, only glycolysis
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autotroph
organism that makes its own food (plants that photosynthesize sugars)
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heterotroph
organisms that do not make their own food and so eat autotrophs or other heterotrophs
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potential energy
stored energy (put into chemical bonds)
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kinetic energy
energy of motion, much wasted as heat
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pyruvate
* 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+
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glucose-6-phosphate
* Step 1 product of glycolysis
| glucose has gained a phosphate from ATP
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fructose-6-phosphate
* Step 2 product of glycolysis
| glucose 6-phosphate has been reorganized
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cyanide
a poison that stops the e- transport system, and consequently ATP generation
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cyclic photophosphorylation
bacterial cycles, with one photosystem
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non-cyclic photophosphorylation
e- are boosted from photosystem II to photosystem I and absorbed by NADP to NADPH which is used in Calvin Cycle (not cycled back)
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citric acid cycle
Also known as the Krebs Cycle, or TCA cycle
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TCA cycle
Also known as the Krebs Cycle, or citric acid cycle
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fructose-1,6-biphosphate
* Step 3 product of glycolysis
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substrate level phosphorylation
* 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.)
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ATP synthase
* 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
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proton motive force
the proton gradient that drives oxidative phosphorylation via the ATP synthase enzyme
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phospho-gluco isomerase
the enzyme that turns glucose-6-phosphate into fructose-6-phosphate
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PEP carboxylase
enzyme used in C4 metabolism
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G protein
* 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
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photosystem 1
* protein-bound bundle on the thylakoid membrane with pigments
* collects energy output from photosystem II
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photosystem 2
* protein-bound bundle on the thylakoid membrane with pigments
* collects energy from protons and outputs an e-
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end product inhibition
* competitive & non-competitive
| * final product of a reaction feeds back and shuts it down
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ligand
* signaling molecule
* when signal reaches a receptor protein, this initiates signal transduction which converts the signaled information into a cellular response
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desmosome
* junctions between cells
| * glycoproteins that paste cells together
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hemidesmosome
* half a desmosome
| * faces a basal lamina
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gap junction
* connects cytoplasms of cells
| * facilitates diffusion between them
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tight junction
* water-proof seal that attaches cells together
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adherens junction
will stick cells together
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cAMP
* cyclic adenosine monophosphate
* reacts with own hydroxyl end to form a circle
* a 2nd messenger
* primitive signal molecule (used by slime molds)
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kinase
anything that attaches PO4 to something else
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chemiosmosis
the proton pump/ATP synthase process to produce ATP
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proton pump
see ATP synthase
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NADH dehydrogenase
* 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
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cytochrome b-c complex
* 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
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Calvin Cycle (steps)
* Phase I - carbon fixation
* Phase 2 - reduction
* Phase 3 - regeneration of RuBP
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carbon fixation
the conversion of inorganic carbon as CO2 into organic carbon in the form of carbohydrates
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glyceraldehyde-3-phosphate (G-3-P)
* 3-carbon sugar
* can link together to form glucose
* Step 4/5 product in glycolysis.
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endocrine
* hormonal cell signalling
| * sent throughout system; target cells have receptors
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paracrine
* 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
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autocrine
* signals itself
| * secretes signals that bind to specific receptors on a cell's own plasma membrane
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exocrine
* sends molecules outside self, or even the organism (such as sweat or digestive stuff)
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steroid hormones
* 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.
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1st law of thermodynamics
energy is neither created nor destroyed by natural processes, just converted between kinetic and potential
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2nd law of thermodynamics
disorder is always increasing in the universe - energy used to create order in one place creates disorder elsewhere (releases heat in the process)
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action spectrum
plant growth vs. wavelengths of light
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absorption spectrum
wavelengths absorbed where plants grow best
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evolution
* chloroplasts and mitochondria evolved by endosymbiosis (double membranes, DNA)
* photosynthesis likely developed first
* metabolism may have developed to remove toxic O2
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Glycolysis Steps
* 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.
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Glycolysis: summary of 1st 5 reactions and 2nd 5 reations
* 1st 5: Convert a molecule of glucose into two molecules of G3P.
* 2nd 5: Convert two molecules of G3P into two molecules of pyruvate.
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Krebs Cycle steps
* 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.
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Krebs Cycle output
* 2 CO2
* 1 ATP
* 3 NADH (3 pairs of e-)
* 1 FADH2 (1 pair of e-)
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photosynthesis (steps)
* 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)
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competitive inhibitors
a molecule that binds to the same active site as an enzyme's substrate, competing with the substrate
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non-competitive inhibitors
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
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respiration ATP generation
36 for eukaryotes
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ATP usage to make one glucose
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