Cell and Molecular chapters 13,14,15

this is about how cells obtain their energy.

What is the source of energy for cells to maintain biological order and stay alive?

Food

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\n What is the process that breaks down sugars into ATP, NADH, and other activated carrier molecules in cells?

catabolism

What is the main fuel molecule that cells use to generate energy?

sugar

where does the energy that is stored in food molecules come from?

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what is its purpose?

chemical bonds energy

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its fuel for cells

Where does Stage 1 of cellular metabolism occur?

Stage 1 mostly occurs outside cells, although special organelles called lysosomes can digest large molecules in the cell interior.

Where does Stage 2 of cellular metabolism occur?

Stage 2 occurs mainly in the cytosol, except for the final step of conversion of pyruvate to acetyl groups on acetyl CoA, which occurs in mitochondria.

Where does Stage 3 of cellular metabolism occur?

Stage 3 occurs entirely in mitochondria.

What is the process by which energy is preserved in cells?

The controlled oxidation of sugar in the cell preserves energy.

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What is the role of enzymes in oxidations that occur in cells?

Enzymes catalyze oxidations via a series of small steps in which free energy is transferred to carrier molecules - most often ATP and NADH.

How do enzymes control reactions in cells?

Enzymes control reactions by reducing the activation energy barrier at the temperature of cells.

What is the total free energy released by the controlled oxidation of glucose in cells?

The total free energy released by the controlled oxidation of glucose in cells is exactly the same as that released as heat during the direct burning of sugar.

What are the net products of glycolysis?

The net products of glycolysis are 2 pyruvate, 2 ATP, and 2 NADH.

How many enzymes catalyze the 10 steps of glycolysis?

10 steps of glycolysis is catalyzed by a different enzyme.

What happens in step 4 of glycolysis?

Step 4 cleaves a 6-carbon sugar into 2 three-carbon intermediates, so that the number of molecules at every stage after this doubles.

What is the name of the pathway that is sometimes referred to as glycolysis?

Embden-Meyerhof pathway.

hat is glucose converted to?

fructose 1,6-bisphosphate.

Are Step 1 and Step 3 reversible or irreversible reactions?

irreversible reactions

What is the enzyme that catalyzes Step 1?

Hexokinase

What is the enzyme that catalyzes Step 3?

PhosphofructokinaseWhat molecule is broken down to pyruvate during glycolysis?

What molecule is broken down into 2 pyruvates during glycolysis?

A fructose 1,6-bisphosphate is broken down to 2 molecules of pyruvate.

What are the net products of glycolysis?

2 pyruvates, 2 ATP, and 2 NADH.

What is the enzyme that catalyzes Step 6 of glycolysis?

glyceraldehyde 3-phosphate dehydrogenase.

What is the enzyme that catalyzes Step 7 of glycolysis?

phosphoglycerate kinase.

What is Step 10 of glycolysis and what is its significance? (2-part answer)

\-Step 10 of glycolysis is the final step, and it is irreversible.

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\-This step involves the transfer of a high-energy phosphate group to ADP, which forms ATP, completing glycolysis.

What is the enzyme that catalyzes Step 10 of glycolysis?

pyruvate kinase

What is substrate-level phosphorylation?

Substrate-level phosphorylation is the synthesis of ATP in glycolysis. It involves the transfer of a phosphate group directly from a substrate molecule.

What is the input of energy required for glycolysis?

form of ATP, at the start of the process.

What happens to pyruvate in the absence of oxygen?

Pyruvate is converted to lactate in the absence of oxygen.

Why is lactate produced in muscle cells undergoing vigorous contraction?

Lactate is produced in muscle cells undergoing vigorous contraction when there isn’t enough oxygen present.

What is the purpose of the lactate production in muscle cells?

to restore the NAD+ consumed in glycolysis.

What is fermentation?

an anaerobic energy-yielding pathway in which organic compounds are partially oxidized, and pyruvate is broken down in the absence of oxygen.

Why does fermentation yield less energy overall than complete oxidation?

The pathway is incomplete, and pyruvate is not fully oxidized.

In some organisms that can grow anaerobically, what is pyruvate converted into?

carbon dioxide and ethanol.

What is the function of the pathway that converts pyruvate to carbon dioxide and ethanol?

converts pyruvate to carbon dioxide and ethanol regenerates NAD+ from NADH, as required to enable glycolysis to continue.

What enzyme converts pyruvate to acetyl CoA and CO2?

pyruvate dehydrogenase.

Where does the pyruvate dehydrogenase complex convert pyruvate to acetyl CoA?

in the mitochondrial matrix.

What molecules are generated from 2 molecules of pyruvate? ( 2 part answer)

\-2 lactates,

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\-or 2 molecules of CO2 and 2 ethanol, plus 2 molecules of NAD+.

How many enzymes and polypeptides does Pyruvate dehydrogenase complex contain ?

3 enzymes

60 polypeptides

How are fatty acids derived from fats converted to acetyl CoA?

Fatty acids derived from fats are also converted to acetyl CoA in the mitochondrial matrix.

What is the structure of triacylglycerol?

glycerol portion, 3 fatty acid chains linked to it through ester bonds.

What are lipases and what do they do?

Lipases are enzymes that can hydrolyze ester bonds in triacylglycerol, releasing fatty acids that can be used for energy.

How are fatty acids coupled to coenzyme A?

Fatty acids are coupled to coenzyme A in a reaction requiring ATP.

What happens to the fatty acyl CoA molecule in the breakdown cycle?

Each turn of the cycle shortens the fatty acyl CoA molecule by 2 carbons.

and generates one molecule each of FADH2, NADH, and acetyl CoA.

Why do many metabolic pathways proceed in cycles?

Enzymatic pathways proceed in cycles to constantly regenerate the substrate, creating an abundant supply of substrate material.

How does this compare to non-cyclical pathways like glycolysis?

Non-cyclical pathways like glycolysis require the organism to physically replenish the substrate through various macromolecular sources.

How do predatory animals with high protein, low carb diets regulate carbohydrate breakdown?

\- ketogenesis

these pathways breakdown proteins

\-also, less efficient pathway

Where is acetyl CoA produced in eukaryotic cells?

mitochondria from molecules derived from sugars and fats.

Where do most of the cell's oxidation reactions occur and where is most of its ATP generated?

cell's oxidation reactions occur in mitochondria, and most of its ATP is generated here.

Where does the citric acid cycle take place in eukaryotes and what is directed for acetyl CoA production?

in mitochondria, in which pyruvate and fatty acids are directed for acetyl CoA production.

What happens in the presence of oxygen during the citric acid cycle?

pyruvate is converted to acetyl CoA plus CO2.

What converts the acetyl group in acetyl CoA to CO2 and H2O in the citric acid cycle?

The citric acid cycle

How is ATP produced using the high-energy electrons stored in NADH and FADH2?

using the high-energy electrons stored in NADH and FADH2 through a process called oxidative phosphorylation in the electron transport chain (ETC)

Who discovered the citric acid cycle and what did he receive for his discovery?

Dr. Hans Krebs discovered the citric acid cycle and he received the Nobel Prize in Medicine in 1953.

What are the 3 names for the Cycle established by Dr. Hans Krebs?

citric acid cycle

* Krebs cycle
* Tricarboxylic acid (TCA) cycle

What is gluconeogenesis, and what molecules are used to synthesize glucose during this process?

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\-Gluconeogenesis is a process in which blood glucose is synthesized from small non-carbohydrate organic molecules

\- lactate, pyruvate, or amino acids.

Are the synthetic reactions carried out in gluconeogenesis energetically favorable or unfavorable?

The synthetic reactions carried out in gluconeogenesis require an input of energy, whereas glycolysis as a whole is an energetically favorable set of reactions.

Where does gluconeogenesis occur mainly, and why?

occurs mainly in liver cells to keep the blood supplied with glucose by using different molecules.

How is the balance between glycolysis and gluconeogenesis regulated?

glucose is broken down rapidly when energy reserves run low, but is synthesized and exported to other tissues when the liver cell has sufficient energy reserves in the form of pyruvate, citrate, or ATP.

What is the key control point in the breakdown of glucose, and how is it regulated?

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\-The key control point in the breakdown of glucose lies in step 3 of glycolysis, the production of **fructose** **1,6-bisphosphate** by the enzyme **phosphofructokinase**

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\-phosphofructokinase is activated by **AMP, ADP**, and inorganic phosphate (the byproducts of ATP hydrolysis), and inhibited by **ATP**, citrate, and fatty acids

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\-other enzyme that catalyzes the reverse reaction, fructose **1,6-bisphosphatase,** is regulated in the opposite direction

What is the purpose of animal cells storing glycogen?

\-Animal cells store glycogen to provide energy in times of fasting

\- when more ATP is needed than can be generated from food molecules taken from the bloodstream.

2. What is the structure of glycogen in animal cells and how does it compare to starch in plants?

\-glycogen in animal cells is a branched polymer of glucose

\- glycogen has many more branch points than starch.

How is glycogen broken down to provide energy?

\-Glycogen is broken down to glucose 1-phosphate by the enzyme glycogen phosphorylase in liver cells,

\-hen converted to glucose 6-phosphate and fed into the glycolytic pathway to produce ATP.

How are the glycogen synthetic and degradation pathways regulated?

\- **Glycogen synthetic** and degradation pathways are regulated by **glucose 6-phosphat**e, but in opposite directions

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\-Glycogen synthase in the synthetic pathway is **activated by glucose 6-phosphate**

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\-**glycogen phosphorylase** that **catalyzes** the breakdown of **glycogen i**s inhibited by **both glucose 6-phosphate and ATP.**

5. Where does natural uncoupling occur in some specialized fat cells, and why is it important?

* Natural uncoupling occurs in brown fat cells, and it is important for protecting sensitive areas of newborn human babies from the cold. Most of the energy from oxidation in brown fat cells is dissipated as heat rather than converted into ATP.

4. What was the effect of DNP on patients who took it?

* Patients who took DNP experienced an elevated temperature and sweated profusely during the treatment.

3. What was the historical use of DNP in medicine?

* In the 1940s, small amounts of DNP were given to patients to induce weight loss.

1. What are uncoupling agents?

* Uncoupling agents are H+ carriers that can insert into the mitochondrial inner membrane.

1. What are uncoupling agents and what do they do in the mitochondria?

Uncoupling agents are H+ carriers that can insert into the mitochondrial inner membrane. They make the inner membrane permeable to protons, allowing H+ to flow into the mitochondrion without passing though ATP synthase so that ATP can no longer be made

2. What is the effect of 2,4-dinitrophenol (DNP) on ATP production?

* DNP prevents ATP from being made by making the inner membrane permeable to protons, which allows H+ to flow into the mitochondrion without passing though ATP synthase.

What happens to fatty acids in mitochondria?

Fatty acids are converted to acetyl CoA in mitochondria.

What is generated in each turn of the fatty acid breakdown cycle?

Each turn of the cycle generates 1 Acetyl CoA, 1 NADH, and 1 FADH2.

What is produced in each turn of the citric acid cycle?

Each turn of the citric acid cycle produces one molecule of GTP and one molecule of FADH2.

What is GTP and how is it related to ATP?

\-GTP is produced in the citric acid cycle

\-close relative of ATP

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-ATP is the substitution of the base guanine for adenine.

What is GDP and how is it related to ADP?

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\-is a close relative of ADP

GDP and ADP is the substitution of the base guanine for adenine.

What is the difference between GTP and GDP?

The presence of an additional phosphate group in GTP.

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What is produced during each turn of the citric acid cycle?

Each turn of the citric acid cycle produces 1 GTP and 1 FADH2.

What is the role of FADH2 and NADH?

FADH2 and NADH are carriers of hydrogens and high-energy electrons.

How is ATP produced from the high-energy electrons of NADH and FADH2?

oxidative phosphorylation

What is the structure of FADH2? (Hint: FAD is the oxidized form)

\- in its oxidized form (FAD)

\-FAD can accept two hydrogen atoms, along with their electrons, to form the reduced FADH2.

What are the steps of the complete citric acid cycle? (in dashed points)

* 2 carbons from acetyl CoA enter

When fatty acids are in the form “fatty acetyl CoA “ are broken down by a cycle of reactions ,

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What do the reactions do to “fatty acetyl CoA ?

\-Trims 2 carbons at a time from the carboxyl end

What is an overview of the complete “Krebs cycle”? (dashes used)

1. 2 carbons from Acetyl-CoA enter and combine with oxaloacetate to form citrate.

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2. Citrate is rearranged and oxidized to form isocitrate.

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3. Isocitrate is oxidized to form alpha-ketoglutarate, releasing one molecule of carbon dioxide and producing NADH.

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4. Alpha-ketoglutarate is oxidized to form succinyl-CoA, releasing one molecule of carbon dioxide and producing NADH.
5. Succinyl-CoA is converted into succinate, producing GTP, which is a molecule that can be used to produce ATP.


6. Succinate is oxidized to form fumarate, producing FADH2.
7. Fumarate is converted into malate.
8. Malate is oxidized to reform oxaloacetate, producing NADH.

What are the precursors provided by glycolysis and the citric acid cycle?

are needed to synthesize many important biological molecules.

What are some examples of biological molecules that are synthesized using intermediates from glycolysis and the citric acid cycle?

amino acids, nucleotides, lipids, and other small organic molecules.

What happens to the intermediates formed in the glycolysis and the citric acid cycle?

are used for **biosynthetic (anabolic**) **pathways,** where they are converted into other molecules.

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Why is regulation of metabolism important in a cell?

\-to ensure that the cell can survive and respond to its environment.

\- The choice of which pathway each metabolite will follow must be carefully regulated at every branch point to maintain order in cells.

How do organisms replenish their ATP pools?

through sugar or fat oxidation.

Why do animals and plants synthesize food reserves?

\-Animals have only periodic access to food

\-plants need to survive overnight without sunlight.

\-This ensures that energy is available when other energy sources are scarce to synthesize food reserves in times of plenty that can be consumed later.

What is the difference between anabolic and catabolic pathways?

\-**Anabolic pathways** : build molecules

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\-**Catabolic pathways : build molecules** break molecules down to provide energy

What is used to control whether the correct pathway throughout cell (**anabolic or catabolic pathways)?**

Key metabolites

What are the "reverse" reactions that occur during glycolysis?

Gluconeogenesis

Why are bypass reactions needed in gluconeogenesis?

Bypass reactions are needed in gluconeogenesis to get around the steps 1, 3, and 10 in glycolysis, which are essentially irreversible.

What is the role of ATP synthase in oxidative phosphorylation?

1\.    ATP synthase is an enzyme located in the inner mitochondrial membrane that uses the energy from the transmembrane proton gradient to convert ADP and Pi into ATP.



 

What is the function of the respiratory enzyme complexes embedded in the inner mitochondrial membrane?

1\.    The respiratory enzyme complexes embedded in the inner mitochondrial membrane pump H+ out of the matrix to create a transmembrane proton (H+) gradient.

What is the role of NADH and FADH2 in oxidative phosphorylation?

1\.    NADH and FADH2 donate high-energy electrons to the electron-transport chain in the inner mitochondrial membrane, which eventually combine with molecular oxygen (O2) to generate ATP through oxidative phosphorylation.

What is the function of the inner mitochondrial membrane?

1\.    The inner mitochondrial membrane encloses the mitochondrial matrix, which contains many enzymes including those of the citric acid cycle, and serves as a barrier to maintain a transmembrane proton gradient.

What is the mechanism by which mitochondria produce ATP

1\.    Mitochondria produce ATP by a membrane-based mechanism called chemiosmotic coupling.

What is the role of ATP synthase in oxidative phosphorylation?

1\.    ATP synthase is an enzyme located in the inner mitochondrial membrane that uses the energy from the transmembrane proton gradient to convert ADP and Pi into ATP.

What is the function of the respiratory enzyme complexes embedded in the inner mitochondrial membrane?

The respiratory enzyme complexes embedded in the inner mitochondrial membrane pump H+ out of the matrix to create a transmembrane proton (H+) gradient.

What is the function of the inner mitochondrial membrane?

1\.    The inner mitochondrial membrane encloses the mitochondrial matrix, which contains many enzymes including those of the citric acid cycle, and serves as a barrier to maintain a transmembrane proton gradient.