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Biochemistry > Metabolism > Flashcards

Metabolism Flashcards

1
Q

Functions of protein-bound oligosaccharides

A
  • Assist in chaperone folding
 (recognition sites for chaperones)
  • Provides specific oligosaccharide “tags” for protein binding
    • Prevents mislocalization of lysosomal enzymes
    • Controls rate of degradation for certain peptide hormones
    • Mediates binding of pathogens to cellular targets
  • Provides blood group specificity
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2
Q

What mediates hormonal regulation of glycolysis and gluconeogensis?

A

Fructose 2,6 bisphospate

  • F26BP activates PFK-1 allosterically, increasing its affinity for its substrate (Fructose 6-phosphate)
  • F26BP inactivates FBPase 1, decreasing its affinity for its substrate F1, 6 bisphosphate
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3
Q

Is Sucrose a Reducing Sugar?

A

No, both anomeric carbons are bonded.

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4
Q

What is Reduction potential, ε?

A

Τhe affinity of a substance for electrons. The greater the ε (reduction potential), the greater the tendency of an oxidized substance to accept electrons and become reduced.

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5
Q

What happens to the ETC when the ratio of ATP/ADP ratio increases?

A

Drop in glycolysis (ATP inhibition of PFK-1)

Drop in CAC (ATP inhibition via pyruvate dehydrogenase)

Drop in ETC as a result of decrease in NADH and FADH2

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6
Q

Proton Motive Force - Chemiosmotic theory

A
  • In ETC, the transport of H+ from low [H+] to high [H+] requires energy (endergonic) and generates a proton gradient (electrochemical and pH gradient).
  • Discharge of proton is exergonic. Free energy of discharge of proton gradient is harnessed by ATP synthase, driving ATP synthesis.
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7
Q

How is NAD+ regenerated?

A
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8
Q

What are glycoproteins?

A
  • Proteins that contain 1 or more oligosaccharides
  • Carbohydrate content of proteins from <1% to >70% of mass
  • Most secreted and membrane-associated proteins are glycosylated
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9
Q

F1 F0 ATP synthase (Complex V)

A
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10
Q

What is the final step of glycogen synthesis?

A

A branching enzyme cleaves off a growing glycogen segment and reattaches it to a glucose C6-OH group to create an α(1-6) branch point.

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11
Q

Pyranose vs Furanose

A

Pyranose is a 6 membered ring.

Furanose is a 5 membered ring.

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12
Q

Why would you want to remove OAA from the high energy yielding CAC to make glucose which just needs to be metabolized again through glycolysis and the CAC?

A

During gluconeogenesis, amino acids and pyruvate can be used to replenish oxaloacetate, which is then converted to malate to leave the mitochondria and regenerate glucose.

This would be crucial in the kidneys or liver, which buffers blood glucose levels. The process of removing OAA from the CAC does not occur in the muscles or anywhere else, except in the liver and kidneys.

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13
Q

D vs. L carbohydrates stereochemistry

A

Identify farthest carbon atom from the carbonyl group (=C=O)

D: –OH is to the right of the reference carbon

L: –OH is to the left of the reference carbon

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14
Q

Ribose vs. Deoxyribose?

A
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15
Q

Protein Kinase A (PKA)

A

activated by cAMP, phosphorylates Ser/Thr residues

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16
Q

Hormonal regulation of PFK-2 / FBPase-2 redux

A
  • Glucagon stimulates phosphorylation of PFK-2/FBPase 2
    • Activation of FBPase-2 activity (phosphatase)
    • Reduction of F26BP
    • ↓ Glycolysis
    • ↑ Gluconeogenesis
  • Insulin stimulates dephosphorylation of PFK-2/FBPase 2
    • Activation of PFK2 activity (Kinase)
    • Increase in F26BP
    • ↑ Glycolysis
    • ↓ Gluconeogenesis
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17
Q

Glycerophospholipids

A
  • Glycerol backbone
  • Fatty acid group at positions 1 and 2
  • Polar or charged head group in a
 phosphodiester linkage to position 3
  • The name of each glycerophospholipid
 comes from the specific head group
  • Amphiphilic/amphipathic molecules
  • Prominent in membrane bilayers
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18
Q

What are the two purines and what are the differences between them?

A

Guanine - Gooooooo - has an “O”

Adenine - topped with an “N”

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19
Q

What are the ΔG’s at key points of regulation within a pathway?

A

The substrate cycles are the key points of regulation. They are not reversible, and require whole different enzymes. Their ΔG’s would be large and negative.

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20
Q

What are the two families of monosaccharides?

A
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21
Q

Summary of the Citric Acid Cycle

A

2 C acetyl groups combine with a 4 C oxaloacetate to yield a 6 C citrate

2 C’s are lost in the pathway as CO2

OAA consumed in the 1 st step is regenerated in the last.

Energy-rich electrons are transferred to NAD+ or to FAD+

1 round of Cycle yields:

2 CO 2 , 3 NADH, 1 FADH 2 , and 1 GTP

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22
Q

Name the glycosidic bond

A

Cellulose is a polymer of glucose linked by an (β1→4) glycosidic bond

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23
Q

What is pyruvate dehydrogenase?

A

The enzyme that catalyzes the decarboxylation of pyruvate to produce Acetyl-CoA

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24
Q

What is the role of Glycogen Synthase?

A

It’s the main enzyme for glycogen synthesis. It takes the activated glucose (UDP-Glucose) and attaches it to the nonreducing end to the glycogen polymer.

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25
Q

Second messenger

A

Small molecules that are generated intracellularly when a signaling molecule activates a receptor.

Transmits signals to downstream targets within a cell.

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26
Q

What are the steps in glycogenolysis?

A
  1. Glycogen phosphorylase phosphorylizes a glucose at a glycogen nonreducing end to yield glucose-1-phosphate.
  2. G1P is converted to G6P, which can enter glycolysis, skipping the hexokinase step.
  3. In the liver only, Glucose-6-phosphotase removes the phosphate from G6P and glucose can leave the cell.
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27
Q

What are the most important regulatory points in glycolysis and gluconeogenesis?

A
  • PFK-1 and FBPase-1
    • reciprocally regulated
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28
Q

Kd

A

dissociation constant: ligand concentration at which half of the receptors are bound.

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29
Q

Receptor Tyrosine Kinases

A
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30
Q

Intracellular Receptors

A

Steroid hormones (examples: estrogen and cortisol) - readily cross membranes and bind to intracellular receptors.

Following ligand binding, the receptor-ligand complex moves to the nucleus and binds DNA sequences called hormone response elements (HRE) adjacent to specific genes.

Receptors regulate transcription ↓ or ↑

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31
Q

What does phosphogluco-mutase do?

A

In the first step of glycolysis, it converts G6P to G1P.

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32
Q

Liposome vs Micelle vs Bilayer

A
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33
Q

What is the Citric Acid Cycle?

A
  • It’s a metabolic hub, a gateway to the metabolism of any molecule that can be converted to acetyl-CoA
    • glucose, fatty acids, amino acids
  • It’s an important source of oxaloacetate, which serves as a precursor to glucose.
  • And it’s a source for amino acid precursors.
  • CAC alone does not generate a large amount of ATP.
  • Through oxidation–reduction reactions, the CAC generates high-energy electrons used to power ATP synthesis in the electron transport chain.
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34
Q

malate-aspartate shuttle system

A

Cytosolic reducing equivalents from glycolysis must enter the matrix through the malate-aspartate shuttle system.

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35
Q

Adenine nucleotide translocase and the H+ symporter.

A

(a) Adenine nucleotide translocase exports ATP and imports ADP
(b) P<em>i</em> is imported from the cytosol in symport with H+

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36
Q

Flow of electrons in mitochondria

A

The greater the Δε the greater the ΔG.

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37
Q

In what direction are DNA/RNA sequences read?

A

DNA/RNA sequences are read 5’ to 3’.

Phosphate groups link the 3’ C of one sugar to the 5’ C of another

5’ end has a free P group on the C5’ carbon

3’ end has a free OH on the C3’ carbon

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38
Q

What is Polymerase Chain Reaction (PCR)?

A
  • Thermo-cycling technique to amplify specific DNA sequences
  • Generates thousands to millions of copies
  • Utilizes Tm to denature DNA and anneal DNA primers
  • Heat-stable DNA-polymerase replicates DNA
39
Q

Describe the hormonal regulation of PFK-2 / FBPase-2

A

Low blood glucose → Glucagon → G-coupled protein signalling → cAMP-dependent protein kinase phosphorylates PFK-2 / FBPase-2.

When phosphorylated, the bifunctional enzyme’s phosphatase is actived → it removes phosphate group from F26BP and decreases F26BP.

  • low F26BP inhibits glycolysis, stimulates gluconeogenesis
  • high F26BP stimulates glycolysis, inhibits gluconeogenesis.
40
Q

Pyruvate Carboxylase and Phosphoenolpyruvate Carboxykinase

A
  • These enzymes are unique to gluconeogenesis
  • PC and PEPCK are energetically undoing the highly exergonic activity of pyruvate kinase.
41
Q

What is the tissue specific regulation of hexokinase in muscle?

A

Hexokinase I and II is present in muscle

  • High affinity for glucose (Km of 0.1 mM)
  • Permits initiation of glycolysis even when glucose is low
  • Blood glucose levels entering the muscle saturate hexokinase
  • Allosterically inhibited by its own product, glucose 6-phosphate, which prevents the consumption of too much ATP when glucose concentrations are not limiting
42
Q

Why must blood glucose be maintained within strict parameters?

A

Because of the brain. Blood glucose is buffered by the liver.

43
Q

Regulation of the CAC redux

A
  • Substrate availability
    • e.g., availability of OAA and acetyl CoA varies with cellular conditions.
  • Product inhibition
    • e.g., NADH inhibits each of the regulatory proteins.
  • Allosteric Activation
    • e.g., activation by ADP
  • Competitive feedback inhibition
    • a product than feeds back to its production farther up in the pathway and competes with the substrate.
      • e.g., Succinyl-CoA competes with acetyl-CoA for citrate synthesis.
44
Q

What kind of enzymes catalyze oxidation-reduction reactions?

A

Dehydrogenases (e.g. lactate dehydrogenase, pyruvate dehydrogenase)

45
Q

Is gylcogen degraded from reducing or nonreducing ends?

A

Glycogen is degraded from its nonreducing ends, allowing the release of glucose from all branches simultaneously. Glycogen only has a single reducing end.

46
Q

How do you identify a reducing sugar?

A

Sugars with free aldehydes (anomeric carbon) are reducing sugars.

To identify the anomeric carbon:

Linear form: carbonyl carbon (either aldose or ketose)

Cyclic form: carbon bonded to both the ring O and a hydroxyl group.

47
Q

Mitochondrial Structure

A
  • Outer membrane
    • relatively porous up to 10kD
  • Inner membrane
    • nonporous
  • Intermembrane space
    • ionically similar to cytosol.
  • Matrix
    • unique composition, different from the intermembrane space.
  • Cristae
    • invaginated inner membrane.
48
Q

How is glycogenolysis upregulated?

A

Allosterically

  1. Phosphorylase - activated by AMP, inhibited by ATP and G6P
  2. Synthase - activated by G6P

Hormonally

  1. Glucagon (at the liver only) and epinephrine (at the muscle and liver) use G-protein receptors to start a signal cascade.
  2. Protein Kinase A phosphorylates glycogen synthase (deactivating it) and Glycogen Phosphorylase (activating it)
49
Q

What is the effect of cholesterol on a lipid?

A

It broadens the phase transition

  • Cholesterol makes membrane fluidity less sensitive to temperature changes (gradual change from solid to liquid).
  • Stabilizes membrane fluidity by preventing sharp transitions.
  • Protein function depends on the proper fluidity of the membrane.
  • Cholesterol maintains the proper environment for membrane-protein function
50
Q

What are nucleic acids and what’s the difference between a nucleoside and a nucleotide?

A
51
Q

Major features of the DNA alpha helix

A
  • The 2 strands of DNA are antiparallel
  • DNA is a right-handed helix
  • The sugar phosphate backbones run along the exterior and are exposed to solvent
  • The base pairs are in the interior of the helix; each base is H-bonded to the base on the opposite strand
  • The helix completes a turn about every 10th base pair
  • The twisting of the DNA creates 2 grooves of unequal width - major and minor grooves
  • The base pairs stack on top of each other creating a solid core
52
Q

What is the glucose transporter isoform present in myocytes and adiposites?

A

GLUT4

  • Glucose is imported into cells through a passive glucose transporter. Whereas in the absence of insulin transporters are sequestered within the cell, elevated blood glucose and insulin levels lead to an increased number of GLUT4 transporters at the plasma membrane.
  • The liver and brain have insulin-insensitive transporters
53
Q

Hydrogen bonding between bases

A

G≡C

A=T

Bases are stacked on top of each other with the planes of their rings parallel and stabilized by Van der Waals forces and Hydrophobic interactions, which are much stronger in G:C pairs.

54
Q

Purine vs. Pyrimidine

A
55
Q

What are the reactions that drain Citric Acid Cycle intermediates?

A
  1. Gluconeogenesis: oxaloacetate from Pyruvate must be converted to malate for transport to cytoplasm.
  2. FA biosynthesis: Acetyl CoA must be converted to citrate for transport, reforming acetyl-CoA in cytoplasm.
  3. Amino acid biosynthesis: α-ketoglutarate and OAA are starting materials.
56
Q

To what extent is gluconeogenesis a reversal of glycolysis?

A

Some enzymes that are part of near-term equillibrium reactions are reversable, but there are 4 unique enzymes in gluconeogenesis:

  1. Pyruvate Carboxylase
  2. Phosphoenolpyruvate carboxykinase
  3. Fructose bisphosphatase
  4. Glucose-6-phsophatase
57
Q

Summary of electron transport and oxidative phosphorylation

A
  • 4 Protein complexes shuttle electrons using prosthetic groups that participate in electron transfer (redox centers). Chains of redox centers have increasing reduction potentials.
  • Starting from NADH, electrons travel a path of increasing reduction potential with the final reduction being the reduction of O2 to H2O.
  • 2 shuttles pass electrons between complexes:
    • Coenzyme Q in the inner membrane
    • Cytochrome C – peripheral protein.
  • As electrons move through the complexes (I, III, and IV), protons are pumped from the matrix to the intermembrane space generating a proton gradient.
58
Q

What happens to the ETC when ATP consumption is increased?

A
  • The ratio of ATP/ADP drops, which upregulates glycolysis (ADP activation of PFK-1);
  • Upregulation in CAC (ADP activation of regulatory enzymes)
  • Upregulation in ETC
59
Q

The Binding Change Mechanism

A

Rotation driven conformational changes alter the affinity of the catalytic β-subunits.

  1. ADP and Pi bind to β in loose conformation (L)
  2. γ subunit rotates (120 °) causing β to move to tight conformation (T) -ATP is produced
  3. γ subunit rotates (120 °) causing β to move to open conformation (O) -ATP is released
60
Q

Define substrate-level phsphorylation

A

Substrate level phosphorylation: the enzymatic transfer of phosphoryl group to a nucleoside diphosphate.

ATP synthesis via kinases, vs. oxidative phosphorylation involves the electron transport chain and ATP synthase.

61
Q

What is thermogenin?

A

An uncoupling protein in the mitochondria of brown fat that allows the generation of heat.

62
Q

What are the Pyrimidines?

A

Cytosine - has an “N”

Uracil - Oooo - has an “O”

Thymine also has an “O”, among other things, like a methyl group.

63
Q

Energy yields in cellular respiration

A

32 ATP total. NADH and FADH2 supply electrons to electron transport chain and are used to generate ATP.

  • 1 NADH yields ~ 2.5 ATP
  • 1 FADH 2 yields ~ 1.5 ATP
64
Q

Where does Fructose 2,6-bisphosphate come from?

A

Phosphofructokinase-2/Fructose bisphosphatase-2 (PFK-2/FBPase-2)

Hormonal activity regulates the bifunctional enzyme PFK-2/FBPase-2 which produces F2,6-bisphosphate. It has a Kinase and Phosphatase domain.

65
Q

The mitochondrial expression of pyruvate carboxylase

A

The majority of gluconeogensis occurs in the cytosol. Pyruvate Carboxylase uses the substrates in the mitochondria that lead to pyruvate to make oxaloacetate. So, oxaloacetate is converted to Malate so it can be shuttled across the mitochondrial membrane to the cytosol, where it’s reconverted back to Oxaloacetate and eventually to glucose.

66
Q

What is the Pentose Phosphate Pathway?

A

Mainly active in tissue with high demand for lipid biosynthesis (liver and adipose tissue) or in rapidly dividing cells, which have a high depand for nucleotides.

The two major products of PPP are

  1. NADPH, necessary for reductive biosynthesis of fatty acids and cholesterol and not interchangable with NADH
  2. Ribose 5 phosphate, which is a precursor for ribose units of nucleotide biosynthesis.
67
Q

Sphingolipids

A
  • Sphingosine backbone
  • Fatty acid derivatives of sphingosine are ceramides
  • Different sphingolipids are derived from ceramide
  • Different head group at C-1
68
Q

The Cori Cycle

A
69
Q

Which of the following CAC enzymes are subject to regulation?

A

The ones with large negative ΔG’s, so:

  • Citrate synthase,
  • Isocitrate dehydrogenase, and
  • α-Ketoglutarate dehydrogenase multienzyme complex.
70
Q

How is glycogenolysis downregulated?

A

Allosterically

  1. Phosphorylase - activated by AMP, inhibited by ATP and G6P
  2. Synthase - activated by G6P

Hormonally

  1. Insulin uses G-protein signal transduction to activate PP1 (Phosphoprotein Phosphatase-1), which dephosphorylates glycogen phosphorylase (inactivating it) and glycogen synthase (activating it).
71
Q

What’s the transition phase of the CAC?

A
  • Oxidative decarboxylation of pyruvate to CO2
  • Transfer of acetyl units to Coenzyme A
72
Q

What is the first regulatory step of glycolysis?

What is the first committed step?

A
  • Hexokinase is the first regulatory step of glycolysis, but it’s not committed.
  • Phosphofructokinase is the first committed step, whose products are unique to glycolysis.
  • In the brain, which doesn’t store glycogen, hexokinase is both the first regulatory and first committed step.
73
Q

Regulation of the Citric Acid Cycle

A
74
Q

Which complex in the ETC does not contribute to the proton gradient?

A

Complex II

It ultimately supplies electrons to the electron transport chain via the FAD → FADH2 cycle, giving Q electrons to make QH2. It’s an enzyme bound prosthetic group.

75
Q

Membrane Transport

Non-mediated vs. Mediated

Channel vs. Carrier

Uniport vs. Symport vs. Antiport

A
  • Non-mediated is simple diffusion.
  • Mediated is passive or active
    • active uses energy
      • primary - requires ATP directly
      • secondary - relies on something else (a gradient, for instance)
  • Channel
    • cannot be saturated
    • can be gated
  • Carrier
    • can be saturated
    • undergoes conformational change
  • Uniport transports one molecule one way
  • Symport transports two molecules one way
  • Antiport transports two molecules two ways
76
Q

What is lactate dehydrogenase?

A

Lactate dehydrogenase is an enzyme found in nearly all living cells. LDH catalyzes the conversion of lactate to pyruvic acid and back, as it converts NAD to NADH and back. A dehydrogenase is an enzyme that transfers a hydride from one molecule to another.

77
Q

What are epimers?

A

Epimers: sugars that differ only in the configuration around one carbon.

78
Q

Is glucose oxidized or reduced during glycolysis?

A
  • Glucose is oxidized reducing 2 NAD+ to 2 NADH
  • NADH must be oxidized to regenerate NAD+
    • Reoxidation of NADH occurs through aerobic (electron transport chain and oxidative phosphorylation) and anaerobic pathways (fermentaion)
79
Q

When oxaloacetate is depleted from TCA cycle because of gluconeogenesis or amino acid sytnehsis, how is it replenished?

A

If there’s no oxaloacetate, the CAC flow slows down and Acetyl-CoA builds up, since there’s no OAA for it to combine with.

Acetyl-CoA then activates pyruvate carboxylase, which is a key enzyme for gluconeogenesis. In this case, it converts pyruvate to oxaloacetate for the citric acid cycle.

80
Q

What are Proteoglycans?

A

A type of glycoprotein with very large polysaccharides called glycosaminoglycans, which are very numerous repeating units of disaccharides.

Membrane Proteoglycans

Structure: Core membrane protein with covalently attached glycosaminoglycans on the outer surface of the cell.

Glycosylated domains in the extracellular space bind to proteins and signaling molecules to alter their activity.

81
Q

What is an Amphibolic Pathway?

A

The CAC is an amphibolic pathway, meaning that it has intermediates that are entering and leaving the citric acid cycle - so its a cycle that involves both anabolism and catabolism.

Oxidative catabolism of carbs, fatty acids, and amino acids, providing CAC intermediates.

Synthesis of precursors for glucose, amino acids, fatty acids, and heme are siphoned off.

82
Q

Proton transport through F0

A
  • One proton binds a c-subunit in the intermembrane space
  • The c-ring rotates away from the a-subunit, positioning the adjacent c-subunit at the a-subunit
  • A proton is released into the matrix from the newly positioned c-subunit – proton is released down the concentration gradient into the matrix.
  • 12 protons = one complete rotation.
  • On the 4th proton binding, the gamma subunit (which has been straining during rotation) snaps into position, altering the conformation of the β subunit of F1.
83
Q

DNA Sequencing - Automated Sanger Method

A

Complementary Primers are annealed to DNA.

Dye labeled dideoxy nucleotides terminate chain when incorporated during DNA replication.

Results in labeled DNA fragments of varying length.

84
Q

Name the glycosidic bonds

A

Gal (β1→4) Glc

and

Glc (α1→1α) Glc

85
Q

What is the tissue specific regulation of hexokinase in the liver?

A
  • Hexokinase IV (a.k.a. glucokinase) is present in the liver
  • Low affinity for glucose (Km of 10 mM) - Km is higher than the concentration of blood glucose – rarely saturated
  • Direct regulation of enzyme by blood glucose
  • High glucose – metabolized by hex IV
  • Low glucose – not necessarily metabolized, allowing glucose from gluconeogenesis to leave the liver before being phosphorylated
  • Subject to (long term) regulation by transcription
    • high blood glucose causes increased transcription of glucokinase
    • low blood glucose causes greater transcription of glucose-6-phosphatase
86
Q
A

Electrons flow from the substance with lower reduction potential to the substance with high reduciton potential.

So, NADH + Q + H+ → NAD+ + QH2 is correct.

87
Q

Triacylglycerol

A

3 fatty acid chains linked to a glycerol backbone with ester linkages.

88
Q

How is glycolysis and gluconeogenesis regulated by energy state?

A
  • High ATP
  • Citrate (intermediate in CAC, FA, AA oxidation)
    • biosynthetic intermediates are abundant
  • Low ATP (AMP or ADP) signals that consumption of ATP outpaces its production, and a need for glycolysis.
89
Q

Oligosaccharide linkages in glycoproteins for

(a) Post-translational modification
(b) Co-translational modification

A
90
Q

G-protein Coupled Receptors

A
  1. GDP bound – inactive trimer
  2. Ligand binding induces a conformational change causing GDP to be replaced with GTP.
  3. α and βγ subunits dissociate and activate.
  4. Intrinsic GTPase activity of the α subunit hydrolyses GTP to GDP Inactivates α and reforms trimer.
91
Q

In order to replenish CAC intermediates, why is pyruvate converted to OAA rather than entering the CAC through acetyl-CoA?

A

Acetyl-CoA is not an intermediate of TCA cycle and pyruvate’s entering the pathway by combining with acetyl-CoA will not solve the reason for the reduced flux (e.g., lack of oxaloacetate, which may have been used up in gluconeogenesis).

92
Q

Anomer Stereochemistry

What is the difference between an α and β anomer?

What is a hemiacetal?

A

Anomers are monosaccharides that differ in configuration around the hemiacetal carbon, which is the one attached to two oxygens.

  • α anomer: the -OH attached to the hemiacetal C is trans (opposite) to the CH2OH of the reference carbon.
  • β anomer - the -OH attached to the hemiacetal C is cis (same side) to the CH2OH of the reference carbon.

Anomers freely interconvert between the α and β forms

93
Q

NADH + Q ⇌ NAD+ + QH2

Which products/reactants are reduced and which are oxidized?

A

Q = ubiquinone (coenzyme Q10, any of a class of compounds that act as electron-transfer agents in respiration.)

QH2 = ubiquinol (an electron-rich, reduced, form of the above)

94
Q

How and when is Glucose-1-Phosphate activated during Glycogen synthesis?

A

In step 2 of glycogen synthesis, G1P is activated with UTP (Uridine triphosphate), to produce UDP-glucose in a highly exergonic reaction that drives the process forward.

Biochemistry (3 decks)

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