Bio Final Cards

***CHECK HOW WELL YOU HAVE TO KNOW THIS! Citric acid cycle has 8 steps, order of intermediates formed is (list the 8 intermediates starting with citrate ending with oxaloacetate)

(1) Citrate → (2) Isocitrate → (3) α-Ketoglutarate → (4) Succinyl CoA → (5) Succinate → (6) Fumarate → (7) Malate → (8) Oxaloacetate.

The next step of Cell Respiration is the CITRIC ACID CYCLE, but before the pyruvate can enter this cycle, it must do these 2 things

(1) Enter the Mitochondria (2) be oxidized to Acetyl Co-A.

Two Stages of Photosynthesis (what are they, where does each take place, and generally what does each do)

(1) Light Reaction—in thylakoids, light energy→chemical energy (NADPH and ATP) (2) Calvin Cycle—in stroma (makes sugar from CO2 + ATP and NADPH)

Excited Electrons in the Photosystems can generate ATP through 2 different routes

(1) Linear Electron Flow, (2) Cyclic electron flow.

Steps of pyruvate oxidation

(1) transport protein takes pyruvate from cytoplasm into mitochondria (2) releases CO2 (2) remaining 2-carbon molecule oxidized, NAD+ reduced to NADH (gains electron) (3) coenzyme-A added on to form Acetyl Co-A.

CO2 is then released from the 4-carbon molecule and re-incorprated by rubisco and the calvin cycle (no flip):

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Excited electrons in the Photosystems can generate ATP through two different routes (Linear Electron Flow, Cyclic Electron Flow).

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For the net synthesis of one molecule of G30, cycle must take place 3 times (3 CO2s required) (no flip):

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Glucose metabolism as the center of the cell's metabolic pathways—we are rarely consuming only glucose (no flip):

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Glycolysis occurs in both aerobic respiration and fermentation

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LECTURE 9, PHOTOSYNETHESIS AND CELL RESPIRATION:

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PHOTOSYNTHESIS:

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Photorespiration performs the Calvin cycle by rubisco incorporating O2 instead of CO2, yields two carbon product that is further split to form CO2...Consumes ATP, produces no sugar, wastes organic material...bad all around!:

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Sun→PHOTOSYNTHESIS→glucose→GLYCOLYSIS→pyruvate→CELLULAR RESPIRATION or →FERMENTATION (no oxygen present), no flip:

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Which steps are CO2 released?

1 CO2 released during each of the following steps, Isocitrate→ a-Ketoglutarate, a-Ketoglutarate→ Succinyl CoA. ATP generate during Succinyl coA→ Succinate.

3 NADH formed, say the steps where its formed

1 NADH formed from each of the following steps Isocitrate→α-Ketoglutarate, α-Ketoglutarate→ Succinyl CoA, malate→ oxaloacetate. generate during Succinyl coA→ Succinate.

Glycolysis, overall reaction, starts at glucose, becomes these three products ___ (3rd product is final product)

1 glucose→ 2 pyruvate. Starts as glucose → fructose 1,6-biphosphate → 2 glyceraldehyde 3-phosphate → 2 pyruvate.

From 3 CO2s there will be 6 G3Ps, but only __ output, the other __ will continue in the cycle

1 output, the other 5 continue in the cycle.

If there is no Oxygen present, one of these 2 paths may be followed (instead of aerobic cellular respiration)

1. Anaerobic respiration—uses ETC (uses a different molecule than oxygen as the electron acceptor, i.e. sulfate) 2. Fermentation—does NOT use ETC.

3 Things that occur in the Calvin Cycle

1. Carbon fixation—incorporate CO2 from air into organic molecules 2. Electrons added to the fixed carbon to make a carbohydrate 3. Requires input of NADPH and ATP.

Cell can use glucose to make ATP through 2 different pathways (what are they, and what determines which one is used)

1. Cellular respiration (aerobic) 2. Fermentation (anaerobic). Which one is used dependent upon whether or not OXYGEN is PRESENT. If present, goes through cellular respiration.

The 3 main components of Cellular Respiration (in the order they happen) are

1. Glycolysis 2. Citric Acid Cycle 3. Oxidative Phosphorylation.

Locations for the different components of cellular respiration (1. glylocolysis and fermentation, 2. electron transport chain, 3. citric acid cycle, 4. pyruvate oxidation)

1. Glycolysis and fermentation located external to mitochondria 2. Electron transport chain, inner membrane of mitochondria 3. Citric acid cycle, mitochondrial matrix 4. Pyruvate oxidation, mitochondrial matrix.

Linear Electron Flow (PSII→PSI)

1. Light excites PSII, causing an electron to be transferred to the Primary Electron Acceptor. 2. Water is split → 2 electrons supplied to each of the two chlorophyll a P680 pair, protons released into thylakoid lumen, O2 released. 3. Photoexcited electrons pass from PSII to PSI via an electron transport chain (ETC), The fall of electrons → H+ pumped into thylakoid lumen, provides energy for ATP synthesis. 4. Meanwhile light has excited PSI, electron from P700 chlorophyl has transferred electron to primary electron acceptor → 5. Electrons passed down a SECOND ETC. → Enzyme NADP+ reducatse catalyzes transfer of electrons to NADP+ (electron acceptor) to make NADPH.

Pyruvate is a fork in the catabolic pathways, depending on presence of oxygen, those two paths in the fork are

1. O2 present→ aerobic cellular respiration 2. No O2 present→ Fermentation.

3 Things that occur in the Light Reaction

1. Splits water into electrons, protons, and O2 (byproduct) 2. NADP+ serves as electron carrier and is reduced to NADPH 3. Generate ATP (photophosphorylation).

Glycolysis, Initial energy investment, net energy yield. Which steps are energy-investing reactions, which are energy harvesting (generating) reactions

2 ATP = initial energy investment, 2 ATP & 2 NADH = net energy yield. Glucose→ fructose 1,6-biphosphate = energy-investing reactions, fructose 1,6-biphosphate→ 2 glyceraldehyde 3-phosphate = energy-harvesting (generating), 2 glyceraldehyde 3-phosphate → 2 pyruvate = energy harvesting.

Summary of Pyruvate Oxidation Yields (per glucose molecule, or 2 pyruvate)

2 NADH, 2 CO2.

But one glucose actually yields___ acetyl Co-A, since __ pyruvate were formed from glycolysis

2 acetyl co-A, 2 pyruvate were formed. So the yields that will from Citric acid cycle should actually be double from one glucose molecule (since were doing the Citric acid cycle for 1 acetyl co-A molecule).

Overall Yield from Citric Acid Cycle (Krebs), from 1 Acetyl co-A entering! (# of CO2, ATP (how is it produced), NADH, FADH2

2 carbons enter each cycle, generates 2 CO2 molecules, 1 ATP (indirectly through production of GTP), 3 NADH, 1 FADH2 (similar electron carrier).

To summarize, based on glycolysis, each GLUCOSE MOLECULE GENERATES

2 pyruvate, 2 ATP, 2 NADH + 2H+

By driving ATP Synthase, Chemiosmosis makes ___ ATP's per glucose, with each NADH being worth ~ ___ ATPs

26-28 ATP's, with each NADH being worth ~ 2.5-3 ATP.

Cellular respiration can generate __ molecules of ATP

32.

Summary of glucose oxidation—TOTAL YIELDS ENDING CITRIC ACID CYCLE (including glycolysis & pyruvate oxidation) (# ATP, NADH, FADH2, and CO2)

4 ATP, 10 NADH, 2 FADH2, 6 CO2.

During Phase II of Calvin Cycle, ATP donates a phosphate group to each sugar (1 CO2 → 2 3-carbon sugars, so 3 CO2s → 6 3-carbon sugars), so __ ATPs are used at this point, also NADPH donates a pair of electrons to each sugar so __NADPHs are also needed

6 ATPs, 6 NADPHS.

Summary of Citric Acid Cycle yields (per glucose molecule, or 2 acetyl co-A)

6 NADH + H+, 4 CO2, 2 ATP, 2 FADH2.

which step is the ATP produced?

ATP generate during Succinyl coA→ Succinate (and as a result of GDP forming GTP (and then the formation of ATP regenerates the GDP).

Two main types of Fermentation

Alcohol and Ethanol Fermentation.

In Linear Electron Flow, sunlight is taken in by ___

BOTH PSII and PSI

Mechanisms of carbon fixation (3 main ones)

C3 pathway (normal one we've discussed); the C4 pathway (sugarcane corn), and the CAM plants.

Cellular Respiration, Rxn (formula)

C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy (ATP and heat).

Calvin Cycle, Phase I =____, Phase II = ______

Carbon Fixation, then Reduction.

ATP Synthesis drive by___

Chemiosmisis.

The light reaction generates ATP Through ____ in the ETC, ETC pump protons across __ membrane and into the ____, and as they diffuse back down theire gradient they create a ___ that drives ____, causing ADP to be phosphorylated to ATP

Chemiosmosis. ETC pumps protons across the Thylakoid Membrane (from the stroma) into the Thylakoid Space, as they diffuse back into the stroma, they create a PROTON MOTIVE FORCE, which drives ATP SYNTHASE.

In Linear Electron Flow, ATP is produced during ETC _, NADPH produced during ETC __

ETC I produces ATP, ETC II produces NADPH, with help of NADP+ reductase which catalyzes the reduction to NADPH.

These electron transfers require ___, such as ___, which receive electrons from glucose to become ___, and electron donor

Electron Carriers, such as NAD+, receives electron from glucose → NADH (an electron donor).

We only have 4 molecules of ATP so far...where do we get the rest of the energy?

Electrons being carried by NADH and FADH2.

Which step is the FADH2 formed?

FADH2 formed from Succinate → Fumarate.

Cell Respiration (gen rxn)

Glucose + O2 → CO2 + H2O + Energy(ATP), Turns organic molecules → ATP

The Thylakoid space is like the ____ in the mitochondria (for cell respiration), and the Stroma is like the ___

Intermembrane space; mitochondrial matrix.

Photosynthesis (gen rxn)

Light + H20 + CO2 → Glucose + O2, Turns sunlight into organic molecules

Photosynthesis General Reaction

Light Energy + 6CO2 + 6H2O → C6H12O6 + 6O2, chloroplast capture light energy and convert it into chemical energy (sugar).

Linear Electron Flow

Light excites PSII causing an electron to be transferred to Primary Electron Acceptor. Water is split—Two electrons are supplied to each of the two chlorophyll, a P680 pair.

Electrons go from glucose to NAD+, which becomes NADH, which is what enters the ETC and shuttles those electrons to Oxygen via ____, so oxygen is the ultimate ____

NADH shuttles those electrons to oxygen via an ELECTRON TRANSPORT CHAIN to oxygen, the ULTIMATE ELECTRON ACCEPTOR.

Cyclic Electron Flow does NOT result in the production of___ or the release of___, but does generate ___

No NADPH produced, No oxygen released. ATP IS GENERATE THOUGH.

Continues to the Citric acid (from glycolysis and pyruvate oxidation) if this is present...

O2.

____ pulls electrons down the ETC, and energy released drives ___across membrane

OXYGEN pulls electrons down, and the energy released drives PROTONS across the membrane.

The final step of Cellular Respiration (if oxygen is present) is___ (made up of these 2 processes)

Oxidative Phosphorylation, consisting of electron transport and chemiosmosis.

To clarify, the reaction center for Photosystem II is ___, for Photosystem of I__

P680, P700.

In C4 plants, PEP Carboxylase adds CO2 to ___ to form ___ , its more efficient at binding CO2 than ___

PEP to form Oxaloacetate (note ATP needed to make PEP). More efficient at binding CO2 than rubisco.

Calvin Cycle Summary (phases, what is synthesized, from how many CO2s, how many ATPs and NADPHs are consumed in total

Phase I is carbon fixation (3 CO2 fixed→ 3 6-carbon sugars→ 6 3-carbon sugars), Phase II is reduction where 6 ATPs used and 6 NADPH, Phase III is regeneration of RuBP, where 5 G3Ps rearranged to regenerate 3 RuBP. ULTIMATELY: 1 G3P sugar is synthesized, 9 ATPs spent, and 6 NADPH.

Two types of photosystems in the Thylakoid membrane, containing different reaction centers (say what each is for each photosystem), excited electrons in the Photosystems can generate ATP through 2 different routes

Photosystem II (functions first, contains Reaction Center Chlorophyll a: P680), Photosystem I (Reaction Center Chlorophyll a: P700).

Ethanol Fermentation (pyruvate become___ by losing__, which is then reduced to ___, regenerating __ NAD+

Pyruvate becomes ACETALDEHYDE by losing CO2, the Acetaldehyde then gets reduced to Ethanol. Per glucose molecule, 2 ATP are formed, and 2 NAD+ are regenerated to enter glycolysis again.

Lactic Acid Fermentation (produces __ ATP, regenerates __ NAD+, pyruvate reduced directly to__)

Pyruvate is reduced directly to lactate, regenerating NAD+ and allowing it to go back to glycolysis to make more ATP. LA Fermentation produces 2 ATP total, regenerating 2 NAD+ (to go back into glycolysis), per glucose molecule!

The process by which Pyruvate is oxidized to Acetyl Co-A is called____, and takes place in the ___

Pyruvate oxidation, takes place in the mitochondrial matrix.

Calvin Cycle, Phase 3 (How much of what is regenerated (and from what), and how many more ATPs are needed)

Regeneration of RuBP, from the 5 G3Ps which are rearranged into 3 RuBPs. Need 3 additional ATPs.

However, sometimes photoexcited electrons can take a "shortcut," use photosytem I but not Photosytem II...so instead of going through ETC II, they cylce back through the ___complex of ___, this is known as CYCLIC ELECTRON FLOW

They cycle back through the cytochrome complex of ETC I. (so it uses the SECOND PHOTOSYSTEM (PSI), with the FIRST ELECTRON TRANSPROT CHAIN (connecting PSII and PSI)).

Electron Transport Chain (components, where it is located, what electrons are initially transferred to and from what)

a collection of molecules, proteins and prosthetic groups like Heme, embedded in the inner membrane of the mitochondria (in the CRISTAE, lots of surface area for oxidative phosphorylation). Electrons are initiall transferred from NADH to complex I (a multiprotein complex like the others). FADH2 adds electrons in to complex II, provides less energy. Passed along to subsequent molecules in each complex, ultimately getting to oxygen, which also picks up a pair of H+ to form water.

The immediate product of CO2 being fixed on RuBP is ____, which is very unstable so immediately splits into 2 molecules of the 3-carbon sugar ___

a very unstable 6-carbon intermediate, split into 2 molecules of 3-phosphoglycerate.

Photosynthesis is an ____ reaction, consuming ____ to build____

an ENDERGONIC reaction, consuming sunlight to build a more complex molecule (glucose).

Photoexcited electron passes from PSII to PSI via___, causes ___ to be pumped into___, providing energy for___

an electron transport chain—the fall of electrons to lower energy level causes H+ to be pumped into thylakoid lumen, providing energy for ATP synthesis.

Light excites PSII, then what happens...

causing an electron to be transferred to the primary acceptor, splitting of water replaces (I think?) the two electrons in P680, and O2 is released.

The electron flow down the ETC between PSII and PSI is what provides the energy for the ___synthesis of ATP

chemiosmotic.

Light Reaction—Excitation of Chlorophyll by Light (where can the chlorophyll transfer the energy given off by the excited electrons (2 options)

chlorophyll is the molecule that absorbs a photon of light, energy from the photon boosts an electron into an outer orbital, when the excited electron returns to its normal orbital it gives off energy, when this happens the chlorophyll can transfer the energy to (1) nearby surrounding molecules or (2) an electron acceptor (like NADP+).

Fermentation (defining characteristics, it consists of glycolysis + reactions that regenerate __ by transferring electrons from ___ to ___, main end products)

does NOT use ETC, undergoes glycolysis, and more substrate-level phosphorylation, 2 main end products are Lactic Acid, and Alcohol. It is glycolysis plus reactions that regenerate NAD+ by transferring electrons from NADH to pyruvate (or its derivatives).

But NADH→NAD+ is a big energy difference so needs to be done in ___, and in the process ___ is formed

done in a series of smaller-step reaction, water forms in the process. Energy is released in this process.

In cell respiration, energy ultimately comes from ____, which releases energy stored in___ (an example of such a transfer___), and ultimately this energy is used to synthesize ___

energy ultimately comes from the transfer of electrons, which releases energy stored in organic molecules, such as when electrons are transferred from glucose to oxygen. Ultimately the energy from these transfers of electrons is used to synthesize ATP.

After Acetyl coA, the first intermediate product is ___, which is ultimately broken down to ____, which combines with ___ from ____ to produce ____...and so the cycle begins again

first intermediate is CITRATE, broken down to ultimately form OXALOACETATE, which combines with the ACETYL Group from Acetyl co-A to produce Citrate, allowing the cycle to start again.

CO2 is fixed onto a 5-carbon sugar ___, and the enzyme that catalyzes this is ___

fixed onto RuBP (ribulose biphosphate), Rubisco is the enzyme that catalyzes this.

C4 Plants = alternate mode of carbon fixation

forms a four-carbon compound as its first product.

Summary of Electron travel (4 things)

glucose→NADH→electron transport chain→Oxygen.

In terms of a change in free energy diagram, the energy-investing reaction you would see delta G (y-axis), going ___, while it would be going ___ for the energy-harvesting reactions

going up, going down.

Chlorophyll absorbs ____, and resides in the ____

light energy, resides in the Thylakoid membranes of chloroplasts.

Alternate modes of carbon fixation have developed in some plants to minimize___ and optimize ___ in hot dry climates

minimize photorespiration, optimize calvin cycle.

Photorespiration (when / why does it occur)

occurs in hot dry conditions, plants close pores to prevent water leaving, but it also prevents CO2 from entering...starves the calvin cycle...photorespiration initiated.

Chlorophyll is organized into complexes called ___, containing these 2 complexes ___ & ___

organized into Photosystems, contains the Light-Harvesting complex, and the Reaction Center complex.

Oxidative Phosphorylation vs. Substrate-Level Phosphorylation (what each uses to make their ATP, and what transfers the inorganic phosphate group to ADP)

oxidative phosphoyrlyation (which is responsible for 90% of the ATP generated) utilizes the electron transport chain and PROTON GRADIENT, inorganic phosphate added onto to ADP by ATP synthase. Substrate-Level Phosphorylation (used in glycolyis and citric acid cycle) makes smaller amount of ATP through DIRECT ENZYMATIC REACTION, phosphate groups transferred from a substrate.

Reaction Center Complex (what special pair of molecules it contains, what they can do, what other molecule in complex accepts the electrons from previous pair of molecules)

proteins holding a special pair of Chlorophyll a molecules, chlorophyll a pair are unique because they can not only boost their own electrons, but also transfer them! Rxn. Center contains a molecule capable of accepting electrons—the Primary Electron Acceptor.

ATP Synthase

protons move one by one into binding sites on "rotor" of the enzyme→ causes it to spin→ catalyzes ATP production from ADP and Pi (works like a waterwheel).

Pyruvate oxidation links these two components of cell respiration ___, releases ___ , resulting in a __-carbon molecule, __NADH generated, ___added on

pyruvate oxidation links glycolysis and citric acid cycle, releases CO2, generating a 2-carbon molecule, co-enzyme A is added on. Now, It is ready to go on to citric acid cycle for further oxidation.

STRUCTURE of PYRUVATE (be able to draw, and GLUCOSE!)

pyruvate, CH3—(C=O)—(C=O, --O-)

Cell respiration does not break down glucose in a single explosive step, rather it does so in a ___, each one catalyzed by ___. This ETC allows energy to be stored in a form ____

series of step, each one catalyzed by an enzyme. ETC allows energy to be stored in form that can be used to make ATP.

The Calvin Cycle is ANABOLIC (constructs larger molecule from smaller ones), it Spends ___ per 1 CO2, and Consumes ___ per 1 CO2, Carbon enters in the form of ___ and leaves in the form of a 3-carbon sugar ____

spends 3 ATP and consumes 2 NADPH per 1 CO2. Carbon enters in the form of CO2 and leaves in the form of G3P.

The light reaction has used sunlight and water to generate ATP and NADPH, the CALVIN CYLE will now use this ATP and NADPH to synthesize ___ from ___

synthesize sugar from CO2.

ETC does not generate ATP directly...so what does___

the H+ gradient = The proton motive force, which is created by the ETC. The ETC uses the energy released by the flow of electrons to drive H+ across the inner mitochondrial membrane, from the mitochondrial matrix into the intermembrane space.

Light-Harvesting complexes

the antenna for the reaction center complex contains various pigment molecules bound to proteins. When a pigment molecule in this complex absorbs a photon, the energy is transferred from pigment molecule to pigment molecule within the complex until it is finally passed to chlorophyll located in the reaction-center complex (in the middle).

The result of the input of 6 ATPs and 6 NADPHs (after 3 CO2 have been fixed to RuBP)

the result is the 3-carbon sugar G3P (glyceraldehyde 3-phosphate).

Chemiosmosis

uses energy of an existing H+ ion gradient across inner mitochondrial membrane (high concentration in intermembrane space, low in mitochon. Matrix—this exists due to the ETC pumping the H+ ions across the membrane originally), so chemiosmosis uses energy of H+ gradient to drive ATP Synthase, which makes ATP.

Oxidative Phosphorylation uses energy released by the ____ to drive ATP synthesis

uses energy released by the electron transport chain (ETC)

The waste materials of each reaction are the raw materials for the other (say what they are for each)

waste materials of photosynthesis is O2 which is a raw material for cell respiration. CO2 and H20 are raw materials are waste materials for cell respiration but are the raw materials for photosynthesis.