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Exam 2_Concepts Flashcards

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1
Q

Metabolism

What is METABOLISM?

A

A network of molecules (NODES) and the reactions (LINKS) that interconvert them

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2
Q

Metabolism

What are the 2 FUNCTIONS of METABOLISM?

A
  1. Make and interconvert biomolecules

2. Store or extract energy

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3
Q

Metabolism

What are the 2 CATEGORIES of METABOLISM?

A
  1. Anabolism

2. Catabolism

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4
Q

Metabolism

What is ANABOLISM?

A

Type of metabolism that USES ENERGY to make biomolecules that can be used to construct cells and store energy as fuel molecules.

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5
Q

Metabolism

What is CATABOLISM?

A

Type of metabolism that RELEASES ENERGY by consuming fuel molecules.

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6
Q

Metabolism

What are the 2 CATEGORIES of ENERGY-PRODUCING CELLS?

A
  1. Phototrophs

2. Chemotrophs

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7
Q

Metabolism

How do phototrophic cells make energy?

A

Use energy from sunlight to make an energy rich ion-gradient that’s used to make energy-rich molecules, initially ATP

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8
Q

Metabolism

How do chemotrophic cells make energy?

A

By oxidating organic molecules to make energy rich molecules, ultimately ATP.

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9
Q

Metabolism

What are 3 ways organisms use chemical energy?

A
  1. To drive anabolism
  2. To perform mechanical work (i.e. MOVEMENT)
  3. To power contrathermodynamic concentration of molecules/ions (i.e. ACTIVE TRANSPORT)
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10
Q

Metabolism

What are 2 characteristics of metabolic pathways?

A
  1. Made up of a linked series of chemical reactions

2. Has common motifs

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11
Q

Metabolism

What are the 5 common motifs found in metabolic pathways?

A
  1. Small set of activated intermediates
  2. Use of an energy currency (ATP)
  3. Small number of reaction types
  4. Common regulatory mechanisms
  5. Small key set of molecules (~100)
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12
Q

Metabolism

What are the common regulatory mechanisms found in metabolic pathways?

A
  1. Allosteric enzymes & covalent modification
  2. Gene expression & protein degradation
  3. Responses to energy change ( [ATP] vs. [ADP] vs. [AMP].
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13
Q

Metabolism

Is it possible to drive an endergonic (unfavorable) rxn with a exergonic (favorable) rxn? If yes, how?

A

YES

HOW:
METHOD 1: By coupling the two reactions so that the change in free energy (ΔG) is negative (i.e. phosphoryl transfer)

*Hydrolysis of ATP is a very common exergonic process used to drive endergonic rxns

METHOD 2: increase concentration of reactants which changes the Keq to the point where Keq><1 in which rxn will be driven forward (Le Chatliers principle)

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14
Q

Metabolism

What is ΔG and what does it tell us about a reaction?

A

ΔG = free energy change for a rxn

Tells Us: The spontaneity of a rxn
ΔG>0= not spontaneous (unfavorable; endergonic)
ΔG<0= spontaneous (favorable; exergonic)
ΔG=0 rxn at equilibrium

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15
Q

Metabolism

What are the 3 reasons why PHOSPHOANHYDRIDE BONDS are energy rich?

A
  1. Charges are more delocalized (b/c products are stabilized by more resonance forms).
  2. Electrostatic repulsions between neighboring oxyanions are relieved.
  3. Increased hydration of ADP + P relative to ATP (i.e. water binds more effectively to ADP+P than to the phosphoanhydride part of ATP)
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16
Q

Metabolism

What compound serves as a reservoir of high potential phosphoryl groups in muscle cells?

A

Creatine phosphate

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17
Q

Metabolism

Is the transfer from higher to lower phosphoryl transfer potential compounds endergonic or exergonic?

A

Exergonic

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18
Q

Metabolism

Which is a richer source of energy? SUGARS or FATS?

A

Fats

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19
Q

Metabolism

What is SUBSTRATE LEVEL PHOSPHORYLATION?

A

A phosphorylated reactive intermediate donates/transfers a phosphoryl group to ADP to directly from ATP

*Involves the coupling of ATP forming rxn with a rxn where the product contains a donateable phosphoryl group

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20
Q

Metabolism

What is OXIDATIVE PHOSPHORYLATION?

A

Use of ion gradients across membranes created as a result of oxidation rxns to drive ATP formation

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21
Q

Metabolism

What is one enzyme that’s used in a lot of metabolic pathways?

A

Acetyl Coenzyme A (Acetyl CoA)

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22
Q

Metabolism

How is enzymatic control of metabolic pathsways possible when enzymes have such high group transfer potentials?

A

Enzymes have a high enough activation energy barrier that prevents spontaneous reaction.

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23
Q

Metabolism

What group do NAD+ and FAD carry?

A

They both carry ELECTRONS

NAD+ can carry ONE ELECTRON

FAD can carry TWO ELECTRONS

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24
Q

Metabolism

When is NADPH used and when is NADH?

A

NADPH: used for REDUCTIVE BIOSYNTHESES

NADH: used for ATP GENERATION

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25
Q

Metabolism

How is rxn selectivity accomplished in nature and in eukaryotes?

A

In Nature: Substrate specificity of particular enzymes

In Eukaryotes: Compartmentalization of organelles

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26
Q

Metabolism

What are the 6 most common rxn types used in metabolism?

A

“add image; from ch 15 pg 443 of txtbook”

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27
Q

Metabolism

What are the 3 main ways metabolic processes are regulated?

A

By controlling the…

  1. Amount/Concentration of enzymes
  2. Catalytic activity of enzymes
  3. Accessibility of substrates
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28
Q

Metabolism

What are the 3 speculations Streyer gives to explain why glucose was chosen evolutionarily as the most common fuel source?

A
  1. Pyranose (hemiacetal) form is favored over open (α-hydroxy aldehyde) form b/c of its hydroxyl groups are equatorial to the compound
  2. Open form of aldoses react nonenzymatically w/ protein amino groups to give α-amino ketone derivative of proteins
  3. Glucose, compared to other aldoses, has a low tendency to modify/damage proteins
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29
Q

Metabolism

What is GLYCOLOSIS? what does it produce? is it anaerobic or aerobic?

A

Break down of glucose in conjunction with generating ATP.

Produces: 2 pyruvate molecules and 2 ATP

Anaerobic process

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30
Q

Metabolism

What is GLUCONEOGENESIS?

A

Production of glucose.

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31
Q

Metabolism

What is FERMENTATION?

A

Process that generates ATP anaerobically and organic compounds act as both electron donors and acceptors.

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32
Q

Metabolism

What is an ANAEROBIC PROCESS?

A

Process that does NOT require O2.

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33
Q

Metabolism

What is an AEROBIC PROCESS?

A

Process that DOES require O2.

34
Q

Metabolism

What are OBLIGATE ANAEROBES?

A

Organisms that can only live in anaerobic (no O2) environments b/c O2 is toxic to them.

35
Q

Metabolism

What are FACULTATIVE ANAEROBES?

A

Organisms that can live in both anaerobic (no O2) and aerobic (has O2) environments.

36
Q

Metabolism

What are the 9 mechanisms used in glycolysis?

A
  1. Phosphorylation (by ATP)
  2. Retroaldol Cleavage
  3. Keto-Enol Tautomerization
  4. Oxidation of aldehyde to thioester
  5. Acylation of phosphate (by thioester)
  6. Phosphorylation (by phosphoglyderate)
  7. Transphosphorylation
  8. β-elimination (of phosphoric acid)
  9. Phosphorylation (by phosphoenolpyruvate)
37
Q

Metabolism

Describe the 3 stages of glycolysis.

A

Stage 1-Trapping and Preparation Phase:
-trap glucose in the cell and form a compound
that can be readily cleaved into phosphorylated 3-
carbon units

Stage 2: Isomerization of 3-carbon compound
-3-carbon phosphorylated sugar is isomerized
into G3P
-Sugar ring gets opened via cleavage of a C-C
bond

Stage 3: ATP Harvesting
-3-carbon fragments are oxidized to pyruvate and
2 ATP are harvested from 1 molecule of glucose

38
Q

Metabolism

What are KINASES?

A

Enzymes that catalyze the transfer of a phosphoryl group from ATP to an acceptor.

39
Q

Metabolism

What is the role of HEXOKINASE?

A

Role: TRAPS GLUCOSE IN THE CELL

How: Catalyzes the phosphorylation of glucose into Glucose-6-Phosphate

Why works: Binding of glucose to hexokinase induces a major conformational change (INDUCED FIT) that PREVENTS THE RXN OF WATER (instead of glucose) WITH ATP.

40
Q

Metabolism

What does HEXOKINASE require to be active?

A

Mg2+

Why: Mg2+ helps to neutralize the negative charge of the phosphate groups on ATP which makes ATP more an electrophile thus making it more appealing to bond to for glucose.

41
Q

Metabolism

What is an ELECTROPHILE?

A

A POSITIVELY CHARGED species that are ATTRACTED TO ELECTRONS

They ACCEPT ELECTRON PAIRS in order to bond with a NUCLEOPHILE

  • usually positively charged BUT can also be neutral and have an atom w/out a full octet of electrons
  • get attacked by the most electron dense part of a nucleophile
42
Q

Metabolism

What is a NUCELOPHILE?

A

Chemical species that DONATES A PAIR OF ELECTRONS to an electrophile in order to form a bond

*ALL molecules with a FREE ELECTRON PAIR can act as a nucleophile.

43
Q

Metabolism

What is the ENZYME THAT ISOMERIZES Glucose-6-Phosphate into Fructose-6-Phosphate?

A

Phosphoglucose Isomerase

44
Q

Metabolism

What is the role of PHOSPHOFRUCTOKINASE (PFK)?

A

Catalyze the 2nd phosphorylation step of glycolysis to trap the ketone

  • Fructose-6-Phosphate becomes Fructose 1,6-biphosphate
  • This step is a KEY CONTROL POINT for metabolism
45
Q

Metabolism

What is the role of ALDOLASE?

A

Role: Catalyze the net retroaldol cleavage of Fructose 1,6-biphosphate into Glyceraldehyde 3-phosphate.

46
Q

Metabolism

What are the 5 things that the enzymatic mechanism of aldolase involve?

A
  1. Substrate binding
  2. Schiff base formation b/w the enzyme’s active site Lys residue and the open-chain form of F-1,6-BP
  3. Retroaldol cleavage to form an enamine intermediate of the enzyme and DHAP, with release of GAP (G3P)
  4. Tautomerization and protonation to the iminium form of the Schiff base
  5. Hydrolysis of the Schiff base w/ the release of DHAP
47
Q

Metabolism

What is the role of TIM (Triose Phosphate Isomerase)?

A

Role: Catalyze the isomerization which converts DHAP (dihydroxyacetone phosphate) into GAP (i.e. G3P, Glyceraldehyde 3-phosphate).

*this rxn is reversible

48
Q

Metabolism

Describe the structure of TIM and what happens when it binds to a substrate.

A

Structure: αβ barrel= a 7-strand β barrel inside a 7-helix array

When bound to a substrate:

  1. Loop closes the active site
  2. Forces intermediate enediol to undergo confirmation change causing it to get trapped in the active site of TIM
  3. Confirmation change makes intermediate unfavorable for an elimination rxn that produces toxic compound, methyl glyoxal.
49
Q

Metabolism

What is STEREOELECTRONIC CONTROL?

A

Control over the nature or rate of the products of a chemical rxn through control of the orientation of electron orbitals.

50
Q

Metabolism

Explain why TIM exhibits stereoelectronic control over the isomerization of DHAP.

A

IT’S ALL ABOUT THE O-H AND C-OPO3 BONDS:

When DHAP is in a confirmation where O-H and/or C-OPO3 bonds are PERPENDICULAR to the plane of the π-bond –> elimination is DISFAVORED –>leads to formation of methyl glyoxal (i.e. TOXIC)

When DHAP is in a confirmation where O-H and C-OPO3 bonds are COPLANAR with 1 of the p-orbitals of the π-bond–> elimination is FAVORED–> allows for simultaneous generation of new π-bonds and cleavage of σ-bonds.

51
Q

Metabolism

The isomerization of DHAP to G3P/GAP by TIM is a readily reversible rxn. How does it prevent the rxn from proceeding in a backwards manner from G3P/GAP to DHAP?

A

Since G3P can be used in glycolysis to form ATP, as DHAP is converted into G3P, G3P is removed and used in subsequent rxns in glycolysis.

This creates a constant conversion of DHAP into G3P (i.e. Le Chatlier’s Principle).

52
Q

Metabolism

Which residues are used in TIM-catalyzed isomerization and what purpose do they serve?

A

Used to pull the proton away from a carbon atom adjacent to a carbonyl group

Glu residue=acts as a general acid-base catalyst–>takes a proton (H+) from carbon 1 and gives it to carbon 2

His residue=proton donor which helps to stabilize neg charge that develops on the C-2 carbonyl group

53
Q

Metabolism

What group must TIM avoid eliminating?

A

Phosphate group because if the enediol intermediate lost its phosphate group, it would become methyl glyoxal (i.e. TOXIC compound)

54
Q

Metabolism

How efficient is TIM?

A

It has achieved CATALYTIC PERFECTION b/c it’s close to the DIFFUSION CONTROLLED RATE.

55
Q

Metabolism

What is CATALYTIC PERFECTION?

A

Describes enzymes whose rates of catalyzation occurs as quickly as the substrate diffuses to the enzyme (i.e. diffusion limited)–> basically every time substrate and enzyme meet, rxn is catalyzed.

56
Q

Metabolism

What is DIFFUSION CONTROLLED RATE?

A

Rate of rxn is limited by the rate of encounter of the substrate with the enzyme.

57
Q

Metabolism

By the end of stage 2 of glycolysis, what has been used and what has been created?

A

Used:

  • 2 ATP
  • 1 molecule Glucose

Created:
-2 molecules of G3P/GAP (Glyceraldehyde 3-phosphate)

58
Q

Metabolism

What is the role of GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE (GAPDH)?

A

To catalyze the conversion of G3P/GAP into 1, 3-BPG (1,3-bisphosphoglycerate)

  • this is the 1st step of stage 3
  • rxn involves coupling the oxidation and phosphorylation processes to avoid a high energy activation step

Oxidation rxn= oxidation of the aldehyde to a carboxylic acid by NAD+

Phosphorylation rxn= carboxylic acid and orthophosphate are joined together to form the acyl-phosphate product.

59
Q

Metabolism

What are the steps of the GAPDH catalyzed coupled phosphorylation-oxidized rxn of G3P?

A
  1. Aldehyde substrate reacts with the sulfhydryl group of cystein to form a hemithioacetal
  2. A hydride ion (H-) is transferred to a molecule of NAD+ that’s tightly bound to the enzyme and adjacent to the cystein residue
    -creates a favorable compound for deprotonation
    of hemithioacetal by histidine
  3. Deprotonation produces the products: NADH and a thioester intermediate
    *note: thioester intermediate’s free energy is
    close to that of the reactants
  4. NADH leaves the enzyme and gets replaced by a 2nd NAD+
    -IMPORTANT step b/c (+) charge of NAD+
    polarizes the thioester intermediate to facilitate
    the attack by orthophosphate
  5. Orthophosphate attacks the thioester to form 1,3-BPG and the cysteine residue is freed
60
Q

Metabolism

Why can 1,3-BPG be used to power the synthesis of ATP from ADP?

A

Because 1,3-BPG has a greater phosphoryl-transfer potential than ATP.

61
Q

Metabolism

What is the enzyme used to catalyze the formation of ATP from 1,3-BPG? What kind of phosphorylation is this?

A

PHOSPHOGLYCERATE KINASE

  • it catalyzes the TRANSFER of the phosphoryl group from the acyl phosphate of 1,3-BPG to ADP.
  • 1,3-BPG becomes 3PG (3-PHOSPHOGLYCERATE)

Type of Phosphorylation: Substrate-Level Phosphorylation

62
Q

Metabolism

What is a MUTASE?

A

Mutase is an enzyme that catalyzes the intramolecular shift (i.e. within same molecule) of a chemical group.

63
Q

Metabolism

Explain the function of PHOSPHOGLYCERATE MUTASE (PGM).

A

Role: Move phosphate group from oxygen 3 to oxygen 2 (i.e. CONVERTS 3-Phosphoglycerate into 2-Phosphoglycerate)

How:
1. 2,3-BPG is needed to activate Phosphoglycerate Mutase by phorylation of a histidine residue.

64
Q

Metabolism

Where does the 2,3-BPG needed to activate phosphoglycerate mutase come from?

A

From isomerization of 1,3-BPG (an intermediate in glycolysis) which is catalyzed by 1. bisphosphoglycerate mutase and then 2. 2,3-biphosphoglycerate phosphatase (a Pi is removed here)

This is done by ERYTHROCYTES (red blood cells).

65
Q

Metabolism

Name 2 functions of 2,3-BPG.

A
  1. Activate phosphoglycerate mutase (PGM)

2. Regulate oxygen binding affinity of hemoglobin.

66
Q

Metabolism

What is the function of ENOLASE.

A

Catalyzes the dehydration of 2PG which adds a C-C double bond to form PEP (phosphenolpyruvate).

67
Q

Metabolism

Is the phosphoryl group-transfer potential of PEP high or low? Why?

A

HIGH

Why: Due to enol-keto tautomerization.
-phosphoryl group traps molecule in its UNSTABLE enol form

-when phosphoryl group is transferred to ADP, the enol (PEP) converts into a more stable ketone (Pyruvate)

68
Q

Metabolism

What is ENOL-KETO TAUTOMERIZATION?

A

Molecule switches back and forth between enol and keto form.

By moving a H atom from an adjacent carbon atom to a carbonyl group of a keto compound= becomes enol form

By moving a H atom from a carbonyl group to an adjacent carbon atom of a enol compound= becomes keto form.

69
Q

Metabolism

What enzyme is responsible for the transfer of a phosphoryl group from PEP to ADP? How many ATP are generated?

A

Enzyme responsible: PYRUVATE KINASE (PK)

Generates: 2 ATP

70
Q

Metabolism

What is the net amount of ATP generated in glycolysis?

A

2 ATP

71
Q

Metabolism

How is the NAD+ consumed by GAPDH regenerated and why is this necessary?

A

Necessary to keep glycolysis going.

Methods:

  1. Ethanolic fermentation
    • turns pyruvate into ethanol
  2. Homolactic fermentation
    • turns pyruvate into lactate
  3. Formation of acetyl CoA via oxidative decarboxylation of pyruvate
72
Q

Metabolism

What role does TPP (THIAMINE PYROPHOSPHATE) play in ethanolic fermentation?

A

Role: Acts as a coenzyme to pyruvate decarboxylase which decarboxylates pyruvate.

How: inverts the normal electron deficient polar reactivity of the ketone carbonyl thus allowing a carbanion to be formed on the carbon on pyruvate

73
Q

Metabolism

What are the 3 methods of controlling glycolysis and how fast are each of them?

A
  1. Allosteric Control: enzymes respond to small
    molecules
    -milliseconds
  2. Phosphorylation: controlled by kinases
    -seconds
  3. Transcriptional Control: control enzyme conc. by
    controlling rate of protein production
    -hours
74
Q

Metabolism

Which 3 enzymes are most often used as control points for metabolic pathways?

A
  1. PKF (Phosphofuctokinase)
  2. HX (Hexokinase)
  3. PK (Pyruvate Kinase)

Why: they catalyze “essentially” irreversible rxns

75
Q

Metabolism

Describe the allosteric control(s) of PKF in glycolysis.

A

*PKF structure has 4 allosteric sites: 2 are catalytic sites and 2 are regulatory sites. Catalytic and regulatory sites do not share the same structural shape.

  1. High [ATP] or High [citrate] inhibits PKF (*but AMP is the positive regulator of PKF)
    How: ATP binds to a specific regulatory site
    distinct from catalytic site which lowers PKF’s
    affinity for F6-P–>slows down glycolysis.
  2. Low [ATP] or Low [citrate] stimulates PKF activity
  3. Decrease in pH increases the inhibitory effect of ATP which results in inhibition of PKF
  4. PFK activity increases when ATP/AMP ratio is lowered
    Why: AMP reverses the inhibitory effect of ATP
  5. F-2, 6-BP activates PFK by increasing PFK’s affinity for F6P (substrate for PFK) and decreasing inhibitory effect of ATP
76
Q

Metabolism

Describe the regulatory mechanism of Hexokinase.

A

-Allosterically inhibited by high [G6-P] in muscle/brain (neg feedback)
-This causes glucose to be converted into G6-P in the liver by GLUCOKINASE
-The G6-P form in liver is used to store glucose
as glycogen

  • If Hexokinase is active it converts glucose into G6-P form used for glycolysis and synthesis of glycogen, ribose or NADPH–found in muscle or brain
  • PGI catalyzes rxn of G6-P to F6-P
  • F6-P can become F1,6P (via PFK catalysis) or F2,6BP (via FBPase2)
  • F2,6BP acts as positive feedback for PFK activity and the conversion of ATP to ADP coupled with F6-P to F1,6BP
  • F1,6BP converts into ATP or Citrate and acts as neg feedback for PFK activity
77
Q

Metabolism

What are ISOZYMES?

A

Enzymes that are almost identical to one another

ex. hexokinase and glucokinase

78
Q

Metabolism

What is the COMMITTED STEP (i.e. key control point) of glycolysis?

A

PFK catalyzed rxn of F6-P to F1,6-BP

*this is the first use of ATP: ATP is converted into ADP

79
Q

Metabolism

How is the location of where glycolysis generates ATP from PEP controlled?

A

Through use of PYRUVATE KINASE ISOFORMS
-these prevent glycolysis from occurring simultaneously in dif parts of the body which would cause them to compete for energy resources

Isoforms of pyruvate kinase:
L (liver) Isoform: deactivated by phosphorylation when blood [glucose] low

M (muscle, brain) Isoform: cannot be turned off by phosphorylation

80
Q

Metabolism

What regulates the distribution of glucose?

A

Family of glucose transporter isoforms

  • Regulate it through mediated passive diffusion
  • Transporters found on cell membrane will transport glucose along conc. gradient
  • Transporters found within the cell on membranous vesicles are inactive
  • Transporters are activated by INSULIN
81
Q

Metabolism

What is GLUCONEOGENESIS?

A

Formation of glucose from pyruvate

Chemistry of Living Systems (7 decks)

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