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Biochem > Module 8 - Cell-Cell Interactions Pt1 > Flashcards

Module 8 - Cell-Cell Interactions Pt1 Flashcards

1
Q

What is aerobic respiration and what process does it involve

A

Most important process to produce energy for a cell
Involves: glycolysis, pyruvate oxidation, the citric acid cycle and electron transport
○Sugars, fats and protein enter these pathways and can break down to produce ATP energy for an cell

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1
Q

What is the citric acid cycle and where does it happen,

A
  • aka the tricarboxylic acid cycle
  • takes place in the matrix or fluid of the mitochondria where mitochondrial DNA is found and where fatty acid breakdown takes place
  • a series of eight rxns break down the two-carbon acetylCoA to the one-carbon molecule of CO2, while at the same generating three molecules of NADH, one molecule of FADH2 and GTP
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2
Q

How many chemical reactions take place in citric acid cycle, what are the products and reactants

A

Involves eight chemical reactions that use acetyl coA and oxaloacetate to produce carbon dioxide, NADH, GTP and FADH2

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3
Q

Give a quick overview of Citric acid cycle

A

Step 1: 2C molecule and 4C molecule combine to form 6C molecule which undergoes biochemical changes an at end original 4C molecule is produced

  • Each time C is lost CO2 is released
  • 2 CO2 are formed during conversion of 6C to 4C
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4
Q

What is the 2C molecule and how is it formed. Where is it formed? What are the products?

A

● The 2-carbon molecules come from pyruvate (product of glycolysis in the cell, transported into the mitochondrial matrix where it is oxidized to acetyl CoA by pyruvate dehydrogenase → produces one NADH and one CO2 for each of the two pyruvate molecules made from glucose.)

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5
Q

What does the citic acid cycle start w/

A

●Acetyl CoA is the starting point of the cycle, the acetyl group from acetyl CoA is transferred to oxaloacetate from citrate

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6
Q

What step is succinate formed and what does it produce by then

A

●5 different rxns lead to the formation of succinate

○Produce two co2, two NADHS and one ATP

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7
Q

hat is Succinate recycles back into and how many rxns does that take and what does it produce during that time

A

● Succinate is then recycled back to oxaloacetate through three more reactions = produce FADH2 and one more NADH = important for fully functioning cells

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8
Q

What are the two stages by which pyruvate is oxidized

A

○1st the conversion of the three-carbon pyruvate to a two-carbon molecule of acetylCoA,
○2nd the oxidation of acetylCoA to carbon dioxide through the citric acid cycle

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9
Q

How does pryruvate become acetylCoA and where

A

● The oxidation of pyruvate to acetylCoA is catalyzed by the enzyme, pyruvate dehydrogenase (PDH) which is located in the mitochondrion

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10
Q

What happens to NADH and FADH2. What does this do to the energy

A

● All reducing equivalents NADH and FADH2 will go on to the final stage of metabolism which is the electron transport chain which reduces the potential energy

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11
Q

What is the strucutre of the mitochondria

A
  • has double membrane, outer mitochondrial membrane surrounds the entire structure while the inner mitochondrial membrane is invaginated to increase the surface area of the membrane
  • invaginations are called cristae and the inner compartment is called matrix
  • Space bwn the inner and outer membrane is called intermembrane space
  • outer mitochondrial membrane is highly permeable with large channels that span the membrane are called porins which allow compounds less than approx 5000 daltons in size to pass
  • the inner mitochondrial membrane is relatively impermeable, allowing only small uncharged compounds like CO2 and water to cross the membrane
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12
Q

How do larger or charged molecules cross the inner membrane

A

○Larger or charged molecules like pyruvate, protons or ATP will cross with transport proteins

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13
Q

Describe the inner membrane compared to the outer membrane of the mitochondria

A
  • inner contains a much higher concentration of proteins as it contains these specific transport proteins as well as the protein complex involved in the electron transport chain,
    ○the relative permeability of the inner mitochondrial membrane allows a proton gradient to be established for the electron transport chain
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14
Q

Where are enzymes for citric acid cycle located

A

Inner membrane, Matrix

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15
Q

What does the Matrix of the mitochondria contan

A 
-PDH pyruvate dehydrogenase complex
Citric acid cycle enzymes
- Fatty B oxidation enzymes
-AA oxidation enzymes
-Many other enzymes
-ATP, ADP, PI, Mg, Ca, K
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16
Q

What is Coenzyme A.

What partof it is reactive

A
  • a coenzyme that participates in the pyruvate dehydrogenase rxn, it is a derivative of pantothenic acid, which is a B vitamin
  • Free thiol group is the reactive part of coenzyme A which will form an energy-rich thioester bond with the two-carbon acetyl group that will be derived from pyruvate
  • In reduced form it is also called CoASH
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17
Q

What is Coenzyme A

A

a coenzyme that participates in the pyruvate dehydrogenase rxn, it is a derivative of pantothenic acid, which is a vitamin B

  • Free thiol group is the reactive part of coenzyme A which will form an energy-rich thioester bond with the two-carbon acetyl group that will be derived from pyruvate
  • In reduced form it is also called CoASH
  • functions as a carrier that serves to activate the two-carbon acetyl group through the formation of that high-energy thioester bond
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18
Q

What is Pyruvate Dehydragenase,

What does it do

A
  • Stage 1
  • Catalzyes the irreversible oxidative decarboxylation of pyruvate to acetyl-CoA
  • Oxidative: because electrons are reducing NAD+ to NADH
  • decarboxylation reaction because a one-carbon carbon dioxide molecule is removed from the three carbon pyruvate.
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19
Q

What is the leaving group in pyruvate that makes it a 2C acetyl group

A

carboxyl group of pyruvate is good ‘leaving group’ which leaves in the form of carbon dioxide

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20
Q

What does CoASH attach itself to and what is its fxn

A

● Free thiol group from CoASH is forming that energy-rich thioester bond (in red) with two-carbon acetyl group derived from pyruvate
- effectively activating the 2C acetyl group

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21
Q

What is the structure of Pyruvate Dehydrogenase and what else does it require

A
  • multi-enzyme complex Consists of 3 Core enzymes and 2 Regulatory enzymes
  • three core enzyme subunits, named E1, E2 and E3, which participated in the oxidative decarboxylation of pyruvate
  • Two regulatory enzymes: PDH kinase (inactives PDH by phosphorylation) and PDH phosphase (activates PDH by dephosphorylation)
  • ALSO REQUIRES: 5 Co-factors
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22
Q

Whats so important about the E2 enzymes-

A

Contains Lipoic acid which is an important coenzyme that is covalently attached to E2 enzyme that serves as a ‘swinging arm’ for the acetyl group as it goes from one enzymatic rxn to the next in the overall rxn of the pyruvate dehydrogenase complex.

23
Q

What are the names of the 3 core enzymes

A

E1: Pyruvate dehydrongenase
E2: Dihydrolipoamide transacetlase
E3: Duhydrolipoamide dehydrogenase

24
Q

What are the 5 Coenzymes required for PDH and what are their functions

A

○NAD+ electron carrier
○FAD+ electron carrier
○Thiamine pyrophosphate (TPP) coenzyme of pyruvate decarboxylase has two thiol groups that can undergo reversible oxidation to a disulfide bond
○Lipoic acid: serves as electron (H) carrier and acyl carrier
○CoA serves as a carrier of the activated acyl group

25
Q

What are the advantages of Multienzymes complex

A
  1. Increased rate or efficency of rxn due to minimized diffusion distance for intermediates between enzymes
  2. Minimized side reactions between successive enzymes in the pathway (In PDH this is lipoic acid)
  3. Rxns catalyzed by multienzyme complexes can be coordinately regulated
26
Q

What does PDH kinase and PDH phophatase do

A

Kinase phosphorylated - bring PDH to its inactive PDH-b form

Kinase phosphatase - bring PDh to its active PDH-a form

27
Q

PDH kinase is allosterically regulated by:

A

Acetyl-CoA, ATP, and NADH which activated PDH kinase and promotes phosphorylation
-●Elevated level of acetylCoA and NADH signal to PDH that they have accumulated in the call and therefore, there is no need to further breakdown pyruvate until they can be utilized further downstream.
●Elevated levels of ATP signal that the energy status of the cell is high and that no further pyruvate breakdown is necessary.
- Negactive allosteric regulator

28
Q

PDH phosphatase is allosterically regulated by:

A

Insulin and Ca2+, activates PDH phosphatase to promote dephosphorylation
- insulin is released following the consumption of a meal, signals that glucose is abundant and can be broken down for energy and any excess glucose can be converted to acetylCoA which is the precursor for fat synthesis.
○Through this mechanism, excess glucose will be converted to fat for longer-term storage
●Ca2+ is released during exercise to signal muscle contraction
●By activating PDH phosphatase, it will promote activation of PDH to its active form to increase flux of pyruvate into the citric acid cycle for the continued generation of ATP to support the exercising muscle.
●Balance of positive and negative factors will determine whether PDH exists in an active a-form or less active b-form

29
Q

What does elevated levels of pyruvate, ADP and NAH+ do

A

inhibit the kinase and therefore promote the active form of PDH and PDHa

30
Q

What does competitive inhibition look like in regards to PDH

A
  • regulated by feedback inhibition when concentrations of acetyl-CoA and NADH are elevated.
    ●These serve to feedback and inhibit PDH when they accumulate in the cell.
31
Q

What is the net reaction of the citric acid cycle and the equation

A

3 NADH, 1 FADH2, 1 GTP, 2 CO2m and free coenzyme A

2NAH+ + FAD + GDP +Pi + acetyl CoA ~ 3NADH + FADH2 + GTP + CoA + CO2

32
Q

How many enzymes are used in the citric acid cycle

A

● Are 8 eight enzymes in the citric acid cycle and all of these are compartmentalized in the mitochondria

33
Q

What about all the enzymes of the citric acid cycle and what are the exceptions

A

●All citric acid cycle enzymes are soluble within the matrix, with exception of the enzyme, succinate dehydrogenase, which is a member of protein that is contained in the inner mitochondrial membrane

34
Q

What is the origin of the name citric acid cycle

A

●Named after the product of the first reaction, citrate
●Citrate is a tricarboxylic acid
●cycle because it begins and ends with oxaloacetate

35
Q

How are NADH, FADH2 and pyruvate regenerated

A

though the electron transport chain

36
Q

What are the three ways regulatory enzymes of the citric acid cycle are regulated:

A

○Availability of substrates, oxalate and acetylCoA must be available in 1:1 ratio for this first rxn also there must be an adequate supply of NAD+ to allow the cycle to continue
○Competitive inhibition by-products: accumulation of products such as NADH will inhibit some of the key enzymes in the pathway such as the dehydrogenases that are responsible for generating these reducing equivalents
○Allosteric regulation, some key enzymes are subject to positive and or negative allosteric regulation.
- Ex. Ca+ positive regulation, ATP negative regulation, ADP positive regulation

37
Q

What are common themes in metabolic regulation

A

1) Energy status of the cell, reflected by the relative concentrations of ADP and ATP
2) Redox state of the cell, reflected by the relative concentrations of NADH and NAD+ are important regulators of metabolism
3) Regulatory enzymes upstream in pathway to be subjected to feedback inhibition by products, serves as a fine-tune flux through the pathway overall
○ Not every enzyme in a pathway is regulated, but there are normally two or three key enzymes in a pathway that represents points of regulation

38
Q

What does it mean for the citric acid cycle to be AMphibolic

A

it is both catabolic and anabolic

39
Q

What happens during the catabolic process of the citric acid cycle

A
  • : oxidavely breaks down glucose fat and amino acids, producing energy & break down produces starting material for the biosynthesis of some compounds
  • Citrate is siphoned off to produce fatty acids and steroids
  • succinylCoA is siphoned off for the synthesis of heme and chlorophyll.
  • Alpha-ketogluarate and oxaloacetate are siphoned off for the synthesis of some amino acids as well as purines and pyrimidines, respectively
40
Q

What happens during the anabolic process of the citric acid cycle

A

-citric acid cycle generates reduced factors, such as NADH and FADH2.
-citric acid cycle intermediates can also be starting materials for biosynthetic pathways
○ Process of replenishing citric acid cycle intermediates that have been extracted for biosynthesis is anaplerosis
■ Always will have adequate amounts of oxaloacetate to begin the cycle again

41
Q

What is anaplerosis and what is the most important anaplerotic reaction

A

○The process of replenishing citric acid cycle intermediates that have been extracted for biosynthesis
- Most important anaplerotic rxn is Synthesis of oxaloacetate from pyruvate

42
Q

What are processes that are involved in the anaplerotic pathway in the citric acid cycle

A

●Pyruvate carboxylase catalyzes the following reaction: pyruvate + Co2 + ATP + H2O→ oxaloacetate + APP + P
oxaloacetate (a 4C molecule) and acetate (a 2C molecule) forming citrate (a 6C molecule)
Prruvate + malic enzyme → Malate

43
Q

What ensures a 1:1 ratio of oxaloacetate:acetylCoA

A

● If the supply of acetyl-CoA (form glycolysis or B-oxidation) is greater than the supply of oxaloacetate, then citrate synthase will not function maximally due to substrate limitation.
● Therefore, excess acetyl-CoA will inhibit PDH, diverting pyruvate to the pyruvate carboxylase rxn.

44
Q

What is the Kerbs cycle neumonic, what does each mean

A 
Can I Keep selling sex for money officers
The products of each step chronologically
-Citrate
-isocitrate
-a-ketoglutarate.
-succinyl CoA
-succinate
-fumarate
-malate
-oxaloacetate
45
Q

What happens in the first step of Kerbs cycle

A
  • aldol condensation
  • an enzyme called citrate synthase joins the two-carbon acetyl group from acetyl coA with the four-carbon oxaloacetate to form a six-carbon citrate
  • highly exergonic (negative delta G/standard free energy) due to the high-energy thioester intermediate
  • essential because oxaloacetate is normally very low (micromolar).
46
Q

What is the second step of the Kerbs cycle

A
  • dehydration and rehydration
  • an enzyme called aconitase converts citrate into isocitrate
  • Aconitase contains an iron-sulfur center which acts both in the binding of the substrate at the active site and in the catalytic addition or removal of H2O.
47
Q

What is the 3rd step in Kerbs Cycle

A
  • Oxidative Decarboxylation
  • isocitrate dehydrogenase enzyme oxidizes isocitrate, a six-carbon molecule to a five-carbon a-ketoglutarate.
  • The carbon that was lost is released as carbon dioxide and one NADH is also formed
  • Mn2+ in, active site stabilizes
48
Q

What is the 4th step in Kerbs Cycle

A
  • Oxidative decarboxylation
  • an enzyme called a-ketoglutarate dehydrogenase converts a-ketoglutarate into a four-carbon succinyl CoA
  • Produces 1 CO2 and 1 NADH
49
Q

What is 5th step in Kerbs Cycle

A
  • substrate level phosphorylation
  • succinyl coA synthase enzyme converts succinyl CoA into succinate, produces GTP which is converted to ATP (or vis-versa)
  • Like acetyl CoA has thioster bond w/ large negative free energy of hydrolysis. Energy released in breakage of bond used to make GTP. Succinate formed in process
50
Q

What is the 6th step in Kerbs Cycle

A
  • Dehydrogenation
  • an enzyme called succinate dehydrogenase converts succinate to fumarate
  • Makes one FADH2
51
Q

What is the 7th step

A
  • hydration

- a fumarate hydratase enzyme then converts fumarate to malate

52
Q

What is the last step in kerbs cycle

A
  • Dehydrogenation
  • malate dehydrogenase enzyme converts malate back to oxaloacetate
  • NADH is produced
53
Q

Where do we get fat from

A

from consuming too many calories from sugar, fat or protein

54
Q

WHat are sources of acetyCoA

A

Pyruvate breakdown, breakdown of fats (triacylglycerols), ketone bodies and some amino acids

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