Unit #2: Chapters 6-9 Flashcards
oxidation
- loss of electrons
* results in positive charge
reduction
- gain of electrons
* results in negative charge
reduced carbon
stores energy in chemical bonds of organic molecules
enzyme
- 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)
photosynthesis (defn and formula)
- Formula: 6CO2 + 6H2O -> C6H12O6 + 6H2O + 6O2
- Uses light energy to convert carbon dioxide and water to sugars and oxygen
- occurs in the chloroplast
photon
- 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
proton
Positively-charged particle of an atom - H+
light-dependent reactions
- capture energy from photons to make ATP and reduce NADP+ to NADPH
light-independent reactions
- 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)
chlorophyll
- 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
absorption
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.
stroma
semiliquid substance surrounding thylakoid membranes
thylakoid
- In the chloroplast
- internal membrane arranged in flattened sacs
- contains chlorophyll and other pigments
grana
- stacks of thylakoid membranes
* includes a thylakoid space
chloroplast
An organelle in plant cells where photosynthesis takes place.
ATP (definition, function, structure)
- 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
NAD+
- 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
NADH
- 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
NADPH
- Reduced NADP
- synthesized in the chloroplast by light-dependent reactions
- Used directly by the Calvin Cycle to synthesize organic molecules from CO2
FADH2
- 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
Calvin Cycle (defn and location)
- 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)
ribulose biphosphate carboxylase
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
rubisco
- nickname for ribulose biphosphate carboxylase
* the most prevalent enzyme in nature
CAM
- 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
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
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)
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.
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
cytoplasm
Material inside a cell, not including the nucleus.
oxyloacetate
- “Feeder” molecule (4-carbon) that reacts with acetyl-CoA to start the Krebs Cycle
- Also the Step 9 product of the Krebs Cycle
carbon dioxide
CO2 - feeds photosynthesis and is an output of respiration
cis-aconitate
an intermediate in the isomerization of citrate to isocitrate in the citric acid cycle
alpha-ketoglutarate
Step 4 product of the Krebs Cycle, a 5-carbon molecule
acetyl-CoA
- The end product of Pyruvate Oxidation
- Feeds the Krebs Cycle
- consists of 2 carbons from pyruvate attached to coenzyme A
citric acid
- Step 1 product of the Krebs Cycle, a 6-carbon molecule
isocitrate
in isomer of citrate where on OH group is repositioned
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
lactate
Ionized form of lactic acid
alcohol
A reduced organic compound through fermentation.
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.
catabolism
- chemical reactions that harvest energy when bonds are broken (respiration)
anabolism
- chemical reactions that expend energy to make new chemical bonds (photosynthesis)
metabolism
all chemical reactions occurring in an organism (anabolism + catabolism)
fumarate
Step 7 product of the Krebs Cycle, a 4-carbon molecule
malate
Step 8 product of the Krebs Cycle, a 4-carbon molecule
succinate
Step 6 product of the Krebs Cycle, a 4-carbon molecule
succinyl-CoA
Step 5 product of the Krebs Cycle, a 4-carbon molecule
isocitrate
Step 2/3 product of the Krebs Cycle, a 6-carbon molecule
matrix
The inner-mitochondrial space, inside the inner membrane.
cristae
The folds of the inner membrane layer of the mitochondrion, creating many layers to pack lots of e- transfer enzymes
aerobic
involving oxygen (final electron acceptor is O)
anaerobic
- not involving oxygen (final electron acceptor is an inorganic molecule other than O)
- in respiration, won’t go to Pyruvate Oxidation, only glycolysis
autotroph
organism that makes its own food (plants that photosynthesize sugars)
heterotroph
organisms that do not make their own food and so eat autotrophs or other heterotrophs
potential energy
stored energy (put into chemical bonds)
kinetic energy
energy of motion, much wasted as heat
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+
glucose-6-phosphate
- Step 1 product of glycolysis
glucose has gained a phosphate from ATP
fructose-6-phosphate
- Step 2 product of glycolysis
glucose 6-phosphate has been reorganized
cyanide
a poison that stops the e- transport system, and consequently ATP generation
cyclic photophosphorylation
bacterial cycles, with one photosystem
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)
citric acid cycle
Also known as the Krebs Cycle, or TCA cycle
TCA cycle
Also known as the Krebs Cycle, or citric acid cycle
fructose-1,6-biphosphate
- Step 3 product of glycolysis
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.)
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
proton motive force
the proton gradient that drives oxidative phosphorylation via the ATP synthase enzyme
phospho-gluco isomerase
the enzyme that turns glucose-6-phosphate into fructose-6-phosphate
PEP carboxylase
enzyme used in C4 metabolism
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
photosystem 1
- protein-bound bundle on the thylakoid membrane with pigments
- collects energy output from photosystem II
photosystem 2
- protein-bound bundle on the thylakoid membrane with pigments
- collects energy from protons and outputs an e-
end product inhibition
- competitive & non-competitive
* final product of a reaction feeds back and shuts it down
ligand
- signaling molecule
- when signal reaches a receptor protein, this initiates signal transduction which converts the signaled information into a cellular response
desmosome
- junctions between cells
* glycoproteins that paste cells together
hemidesmosome
- half a desmosome
* faces a basal lamina
gap junction
- connects cytoplasms of cells
* facilitates diffusion between them
tight junction
- water-proof seal that attaches cells together
adherens junction
will stick cells together
cAMP
- cyclic adenosine monophosphate
- reacts with own hydroxyl end to form a circle
- a 2nd messenger
- primitive signal molecule (used by slime molds)
kinase
anything that attaches PO4 to something else
chemiosmosis
the proton pump/ATP synthase process to produce ATP
proton pump
see ATP synthase
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
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
Calvin Cycle (steps)
- Phase I - carbon fixation
- Phase 2 - reduction
- Phase 3 - regeneration of RuBP
carbon fixation
the conversion of inorganic carbon as CO2 into organic carbon in the form of carbohydrates
glyceraldehyde-3-phosphate (G-3-P)
- 3-carbon sugar
- can link together to form glucose
- Step 4/5 product in glycolysis.
endocrine
- hormonal cell signalling
* sent throughout system; target cells have receptors
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
autocrine
- signals itself
* secretes signals that bind to specific receptors on a cell’s own plasma membrane
exocrine
- sends molecules outside self, or even the organism (such as sweat or digestive stuff)
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.
1st law of thermodynamics
energy is neither created nor destroyed by natural processes, just converted between kinetic and potential
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)
action spectrum
plant growth vs. wavelengths of light
absorption spectrum
wavelengths absorbed where plants grow best
evolution
- chloroplasts and mitochondria evolved by endosymbiosis (double membranes, DNA)
- photosynthesis likely developed first
- metabolism may have developed to remove toxic O2
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.
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.
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.
Krebs Cycle output
- 2 CO2
- 1 ATP
- 3 NADH (3 pairs of e-)
- 1 FADH2 (1 pair of e-)
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)
competitive inhibitors
a molecule that binds to the same active site as an enzyme’s substrate, competing with the substrate
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
respiration ATP generation
36 for eukaryotes
ATP usage to make one glucose
54
