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Advanced Cell Bio > Exam 1- Chapter 14- Cellular metabolism > Flashcards

Exam 1- Chapter 14- Cellular metabolism Flashcards

1
Q

Oxidation

A

Removal of electrons (e-) from 1 atom to another. An example is ferrous iron (Fe 2+) becoming ferric iron (Fe 3+) due to oxidation

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2
Q

Reduction

A

Addition of e- from 1 atom to another. An example is Cl gaining an electron to become Cl- due to reduction

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3
Q

How do enzymes work?

A

Lower activation energy for reactions. All reactions can occur spontaneously, but enzymes help them to occur much more quickly

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4
Q

Free energy (G) definition

A

Increase in disorder of the universe

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5
Q

Decrease in G

A

There is a negative ΔG, disorder increases, and the reaction is favorable. Energy is released. If the initial G is 2 and the final G is 6, the ΔG would be minus 4.

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6
Q

Increase in G

A

There is a positive ΔG, disorder decreases, the reaction is unfavorable. Requires energy, and therefore needs to be coupled to negative ΔG reactions

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7
Q

Food sources of energy (3)

A
  1. Carbohydrates- sugars
  2. Fats
  3. Proteins
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8
Q

Coupled reactions

A

Reactions that gave a positive ΔG are powered by a coupled reaction, and are paired with a reaction that produces negative ΔG. The negative ΔG reaction produces energy that is used to power the second reaction, which requires an energy input

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9
Q

Which macromolecules are the primary energy source?

A

Carbohydrates are the primary energy source, fats will be metabolized if sugars are limited, and proteins are metabolized when fats are limited

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10
Q

How do cells obtain energy?

A

From the oxidation (breakdown) of food molecules. Energy released from food breakdown may need to be stored prior to use

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11
Q

How is energy from the oxidation of food molecules stored?

A

The energy is captured in activated carrier molecules. The energy can be stored as a readily transferable chemical group (like a phosphate group). Energy can also be stored as high energy electrons. Energy is released when the bond breaks or when the electrons are lost

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12
Q

How are activated carrier molecules formed?

A

Their formation is energetically unfavorable, so they are formed via a coupled reaction. In this case, the energetically favorable breakdown of food molecules drives the subsequent unfavorable formation of activated carrier molecules

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13
Q

Adenosine triphosphate (ATP)

A

The most important and versatile activated carrier molecule. The phosphorylation of ADP to ATP is energetically unfavorable, so it is driven by the favorable oxidation of food molecules. ATP hydrolysis is used for other coupled reactions. The hydrolysis of ATP’s phosphate bond to ADP releases this energy (favorable) and drives coupled reactions for cellular processes (unfavorable)

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14
Q

Phosphoanhydride bonds

A

The bonds between the phosphate groups of ATP. They are very high energy, and energy is released when these bonds are broken.

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15
Q

ATP hydrolysis

A

If water is added, the phosphoanhydride bonds can be broken and energy is released. This results in ADP and Pi (inorganic phosphate) products

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16
Q

Phosphate transfer

A

Energy can also be released if the phosphate is transferred to another molecule. This is driven by kinases. In this case, the phosphoanhydride bond is broken and converted to a phosphodiester bond. This process requires much less energy, so energy is released.

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17
Q

2 step ATP hydrolysis

A

First hydrolysis reaction creates AMP and pyrophosphate (2 inorganic phosphates bound to each other). That pyrophosphate also hydrolyzes. In this reaction, 2 phosphoanhydride bonds are broken. Therefore, this reaction yields about twice as much energy as the previous single hydrolysis reaction

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18
Q

NADH and NADPH

A

Activated carrier molecules generated from nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+). Each of these pick up a packet of energy in the form of 2 high energy electrons bound to one H+ ion. They are responsible for providing energy (e-) and H+ necessary to create an H+ gradient in the mitochondria for oxidative phosphorylation.

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19
Q

NADH function

A

Responsible for providing the electrons necessary for the ETC

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20
Q

Hydride ion

A

In the reduced form, NADPH has the extra hydrogen. This hydrogen is carrying 2 electrons and is therefore referred to as a hydride ion. The hydride ion is not a standard hydrogen molecule because it contains the 2 high energy electrons from sugar oxidation. It loses the hydride ion in the oxidized form and becomes NADP+. This process releases energy

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21
Q

Differences between NADH and NADPH (2)

A
  1. The extra phosphate in NADPH gives it a different shape
  2. Different functions- NADPH supplies high energy electrons needed to synthesize energy rich biological molecules, mainly used in photosynthetic reactions. NADH supplies high energy electrons to the ETC
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22
Q

Extra phosphate in NADPH

A

The extra phosphate in NADPH gives it a different shape from NADH. This means that NADPH and NADH bind as substrates to completely different sets of enzymes and mediate completely different sets of reactions. Used to transfer electrons between 2 different sets of molecules

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23
Q

Acetyl coenzyme A (acetyl CoA)

A

An activated carrier molecule that carries an acetyl group in a high energy bond. The breaking of this bond releases energy. The remainder of the molecule acts as a “handle” where enzymes and other proteins can bind. It allows specific enzymes to recognize acetyl CoA. The handle contains a nucleotide (usually adenine)

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24
Q

Main activated carrier molecules (4)

A
  1. ATP
  2. NADH
  3. NADPH
  4. Acetyl CoA
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25
Q

Glycolysis

A

If sugar molecules are present in the cell, metabolism will always start with glycolysis. Glycolysis is a central ATP producing pathway that does not involve oxygen. Occurs in all cells throughout evolution, including bacteria and animal cells. It even occurs in the more unusual cells in our bodies, like erythrocytes- they don’t have mitochondria but are still capable of glycolysis. Glycolysis is the breakdown of glucose over a 10 step reaction

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26
Q

General glycolysis pathway

A

Glucose (6 carbons) is broken down in 10 steps to 2 molecules of pyruvate (3 carbons each). 2 ATPs hydrolyzed to provide energy in early steps. 4 ATPs generated in later steps, resulting in a net gain of 2 ATP

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27
Q

Glycolysis products (3)

A
  1. Net gain of 2 ATP molecules
  2. The original glucose molecule becomes 2 pyruvate molecules
  3. 2 NADH molecules produced
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28
Q

First step of glycolysis

A

Glucose is phosphorylated by hexokinase via ATP hydrolysis. It forms glucose 6-phosphate. The phosphate is obtained from ATP and therefore one ATP molecule is used in this step

29
Q

Steps of glycolysis (10)

A
  1. One ATP is used, glucose is phosphorylated to make glucose 6-phosphate
  2. Bond rearrangements
  3. Fructose 6-phosphate is phosphorylated via ATP hydrolysis to form fructose 1,6 bisphosphate. This is the second input of ATP into the pathway.
  4. Breakdown reactions
  5. The pathway breaks down into 2 parallel tracks. Forms 2 glyceraldehyde 3-phosphate molecules
  6. The 2 glyceraldehyde 3-phosphate molecules are oxidized by NAD+ and inorganic phosphate is added, forming 1,6 bisphosphoglycerate
  7. 1,6 bisphosphoglycerate is dephosphorylated. The phosphate is added to an ADP molecule, creating ATP. This happens twice due to the 2 parallel tracks
  8. Breakdown reactions
  9. Breakdown reactions
  10. Phosphoenolpyruvate is dephosphorylated. The phosphate is added to ADP, creating 2 more ATP. Pyruvate is formed
30
Q

Uses of the products of glycolysis

A

ATP is an activated carrier molecule used in other reactions. NADH is used later, in the ETC. Pyruvate is utilized in the next metabolic pathway, the citric acid cycle, to generate more NADH.

31
Q

Enolase

A

An enzyme that catalyzes the bond rearrangements in the final steps of glycolysis. 2 phosphoglycerate is turned into phosphoenolpyruvate and water

32
Q

Pyruvate kinase

A

An enzyme that phosphorylates ADP in the final steps of glycolysis. Phosphoenolpyruvate is dephosphorylated and the phosphate is transferred to ADP, forming pyruvate and ATP. This final step is also important because this is where the net gain of ATP occurs

33
Q

Pentose phosphate pathway

A

An offshoot pathway of glycolysis, using glucose 6-phosphate as the initial molecule. The pathway produces pentose phosphates, which are precursors to ribose and deoxyribose (for RNA and DNA). It also produces erythrose phosphate, which is a precursor to aromatic amino acids (phenylalanine, tyrosine, and tryptophan). This pathway also produces NADPH, which is a major source of electrons in biosynthetic pathways.

34
Q

Where does glycolysis occur?

A

The cytoplasm- this is why all cells, including bacteria, are able to do it

35
Q

Production of acetyl CoA

A

Occurs in the mitochondria. Pyruvate is decarboxylated by the an enzyme called pyruvate dehydrogenase complex in the mitochondria. Products of the decarboxylation reaction are carbon dioxide (a waste product), NADH, and acetyl CoA. Acetyl CoA is the activated carrier molecule that will kick off the citric acid cycle.

36
Q

Fatty acid metabolism

A

Fatty acids are oxidized to fatty acyl CoA, which is modified to acetyl CoA. The 3 products of this reaction are acetyl CoA, NADH, and FADH2.

37
Q

Citric acid cycle (Krebs cycle)

A

Acetyl group from acetyl CoA is transferred to oxaloacetate (4 carbons) to form 6-carbon tricarboxylic acid (citric acid). The breakage of the citric bond provides energy to power the cycle. Citrate is oxidized (loses electrons) over a period of 8 steps. Energy from the oxidation is harnessed to produce energy rich activated carrier molecules- these electrons are donated to NAD+ to make NADH. At the end of the cycle, oxaloacetate is regenerated and combines with acetyl CoA to begin the cycle over again. The electron carrier molecules will be important for the electron transport chain

38
Q

Net result of the citric acid cycle

A

One turn of the cycle produces 3 NADH, 1 GTP, and 1 FADH2. These are all activated carrier molecules

39
Q

FADH2

A

An important carrier of 2 electrons (2 hydride ions). When reduced, the hydride ions bind to the nitrogen molecules. It brings the total of electrons up to 5 in 1 turn of the cycle

40
Q

GTP

A

Important for creating ATP, it transfers phosphate to ADP in 1 turn of the cycle. This brings the total of ATP to 3 after 1 turn of the cycle

41
Q

Function of the intermediates in glycolysis and the citric acid cycle

A

All of the intermediate molecules in both of these processes serve as important starting points for important biological molecules. The creation of glucose 6-phosphate in the first step of glycolysis is important for the formation of nucleotides- necessary for DNA and RNA. Phosphoenolpyruvate is important for the formation of pyrimidines and amino acids. Citrate is important for cholesterol and fatty acids

42
Q

Protein metabolism

A

If sugars and fats are limited, proteins are broken down into amino acids. The amino acids then undergo deamination, which is the loss of their amine group (NH3).

43
Q

Which amino acids are broken down to form pyruvate?

A

Alanine, cysteine, glycine, threonine, and serine undergo deamination to form pyruvate. Pyruvate can then become acetyl CoA

44
Q

Which amino acids are broken down to form oxaloacetate?

A

Asparagine and aspartate undergo deamination to form oxaloacetate, which will feed into the citric acid cycle.

45
Q

Which amino acids are broken down to form succinyl-CoA?

A

Isoleucine, valine, and methionine undergo deamination to form succinyl CoA, which is also an intermediate of the citric acid cycle

46
Q

How many ATP are produced during metabolism?

A

30

47
Q

Structure of the mitochondria

A

The mitochondria has 2 membranes (outer and inner) and a space in between the membranes called the intermembrane space. The outer membrane contains porins that allows for the exchange of molecules, it is mostly permeable. The intermembrane space is chemically equivalent to the cytosol with respect to small molecules. The inner membrane has high levels of cardiolipin (high saturated double phospholipid) which makes the inner membrane very impermeable to ions. However, the inner membrane does contain transport proteins

48
Q

Cristae

A

Folds of the inner mitochondrial membrane that extend into the middle of the mitochondria. The cristae increases the surface area of the inner membrane. The ETC machinery is embedded in the inner mitochondrial membrane, so more surface area means that more ATP can be generated.

49
Q

Matrix

A

The “lumen” of the mitochondria, located inside the inner membrane

50
Q

Cardiolipin

A

“Double” phospholipid with 4 fatty acid tails. Makes up a great degree of the inner mitochondrial membrane and therefore allows the inner membrane to be an efficient permeability barrier

51
Q

Enzymes of the mitochondrial matrix

A

Pyruvate dehydrogenase complex- creates acetyl CoA. Includes enzymes that metabolize fatty acids to acetyl CoA and enzymes that oxidize acetyl CoA in the citric acid cycle

52
Q

Where does the citric acid cycle take place?

A

Completely takes place within the mitochondrial matrix

53
Q

Inner mitochondrial membrane

A

All of the machinery for the ETC, including enzymes for the ETC, is embedded here. Also contains ATP synthase, which is embedded in the membrane and creates a lot of ATP

54
Q

Oxidative phosphorylation

A

The electron transport chain is the first part, and it is made up of 3 respiratory complexes located in the inner membrane of the mitochondria. They have a high affinity for electrons and will strip the electrons from NADH. The electrons are then passed from one complex to the other, and they release energy each time they move. The energy that is released is used to pump protons out of the mitochondrial matrix into the intermembrane space. This creates a proton (H+) gradient that will be a source of energy for ATP synthase

55
Q

Proton gradient

A

There are more protons in the intermembrane space than there are in the matrix. During oxidative phosphorylation, the gradient is used by ATP synthase in order to synthesize ATP

56
Q

Electron transport chain (ETC) respiratory complexes (3)

A
  1. NADH dehydrogenase
  2. Cytochrome bc1
  3. Cytochrome c oxidase- this is where the final electron acceptor (oxygen) is found
57
Q

NADH dehydrogenase complex

A

The largest complex, which is made of more than 40 polypeptide chains. Because it is the first complex, it takes/accepts the electrons from the NADH that was generated in the citric acid cycle. As the electron is moved, it releases energy that pumps protons into the intermembrane space. Within NADH dehydrogenase, electrons pass through 7 iron-sulfur centers to an electron carrier called ubiquinone (Q). The iron allows the electrons to be conducted throughout the complex. Q transfers the electrons to the second respiratory complex.

58
Q

Cytochrome b-C1

A

The second respiratory complex, which is made of around 11 polypeptide chains. Forms a dimer- each monomer has 3 heme groups bound to cytochrome proteins and an iron-sulfur protein. Heme also contains iron that allows for the electrons to be conducted through the complex. Cytochrome b-C1 accepts electrons from ubiquinone and passes them to a second carrier called cytochrome c (C), which carries electrons to the next complex

59
Q

Cytochrome C oxidase complex

A

The final respiratory complex, which forms a dimer. Each monomer has 13 different polypeptide chains. Includes 2 cytochromes and 2 copper atoms, which again allows for electrical conduction. The complex accepts 1 electron at a time from cytochrome C. It passes 4 electrons to oxygen and hydrogen, forming water

60
Q

Electron transport chain (ETC)

A

Contains 3 respiratory complexes embedded in the inner mitochondrial membrane. Electrons pass from 1 metal ion to another within the respiratory complexes. The energy released by the movement of electrons pumps protons, forming the proton gradient. NADH from the citric acid cycle is stripped of its electrons by the first complex. Electrons move through the NADH dehydrogenase complex and are picked up by ubiquinone, which moves through the hydrophobic interior of the membrane to bring the electrons to cytochrome b-c1. A second electron carrier, cytochrome C, brings the electrons to the cytochrome C oxidase complex. Cytochrome C leaves the membrane because it cannot travel in the hydrophobic interior of the membrane. The final complex must take up 4 electrons so oxygen can be safely released

61
Q

Oxygen reduction

A

In cytochrome C oxidase, oxygen accepts electrons as the final step. Cytochrome cannot release oxygen too early without the 4 electrons, or ROS will be produced. Oxygen takes 4 electrons, then 2 hydrogens reduce each oxygen to form 2 water molecules. Oxygen has a high affinity for electrons, which is good because a large amount of free energy is released when it forms water. This reaction accounts for around 90% of total oxygen uptake in all cells- this is why we breathe. Therefore, cytochrome oxidase is crucial for all aerobic life

62
Q

Cyanide function

A

Cyanide and azide bind cytochrome oxidase, which stops electron transport and compromises ATP production. This results in cell death. This is why these compounds are toxic and shows why cytochrome C oxidase is so important

63
Q

Cytochrome C oxidase prevention of ROS

A

Oxygen has a really high affinity for electrons, so once it takes up one oxygen, it becomes dangerously reactive and rapidly steals 3 electrons wherever it can. Cytochrome oxidase prevents this from happening by holding onto oxygen and not releasing it too early. It keeps the oxygen in place by clamping it between a heme-linked iron and a copper atom until it has picked up 4 electrons, and then the clamp will release. Then, oxygen can be combined with 4 hydrogens to be safely released as water.

64
Q

Pumping of protons by NADH dehydrogenase

A

Pumps out 2 protons per electron that passes

65
Q

Pumping of protons by ubiquinone

A

Ubiquinone is a hydrophobic molecule that is freely mobile in the membrane bilayer. It transfers 2 electrons to cytochrome b-C1 but also picks up a proton. It pumps one proton across the membrane after electron release

66
Q

Pumping of protons by Cytochrome b-c1

A

Pumps out 2 protons per electron. Quinones are similar in function to ubiquinone with respect to proton pumping

67
Q

Pumping of protons by cytochrome oxidase

A

Pumps out 1 proton per electron. Oxygen is the electron acceptor here

68
Q

How many total protons are pumped by the electron transport chain?

A

Transfer of electrons from complex to complex provides free energy for proton pumping and creates a proton gradient in the intermembrane space. After transfer of 4 electrons across the chain, 24 protons are pumped out. This contributes to the proton gradient

Advanced Cell Bio (17 decks)

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