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BioMedChem Midterm 1 > 1 - Basic Concepts in Metabolism > Flashcards

1 - Basic Concepts in Metabolism Flashcards

1
Q

Typical Enzymes

A
  • Not a Drug Target:
    • ​Lysosyme
      • ​hydrolyzes bacterial cell wall
  • ​​Drug Targets
    • Lactate Dehydrogenase
      • ​Lactate -> Pyruvate
    • Carbonic Anhydrase
      • CO2 -> Bicarbonate
    • Orotidine Decarboxylase
      • ​Greatest Rate of ACCELERATION/enhancement
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2
Q

6 Main Enzyme Classes

A
  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases
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3
Q

Oxidoreductases

A

Redox Reactions

Lactate dehydrogenase

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4
Q

Transferases

A

Move Chemical Group

Creatine KINASE

Alanine aminotransferase

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5
Q

Hydrolases

A

Hydrolysis

Bond cleavage w/ xfer of

fxn group –> Water

Lysosyme

Chymotrypsin

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6
Q

Lyases

A

Non-hydrolytic bond cleavage

Addition of groups across a DOUBLE BOND

Fumerase

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7
Q

Isomerases

A

Intramolecular group transfer

–> change in spatial geometry

Triose Phospate isomerase

Methylmalonyl CoA mutase

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8
Q

Ligases

A

formation of New covalent bond

between substrates using NTP Hydrolysis

RNA polymerase

Pyruvate carboxylase

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9
Q

Enzyme Sub-Classes

A

Used to describe the different

Enzyme-catalyzed rxns

Amoung the PROTEINS catalyzing them

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10
Q

Isozyme

A

Catalyze the SAME rxn but differ in AA Sequence

Allows for FLEXIBILITY & CONTROl

  • Differ in catalytic activity / cofactor / regulation
    • ​Encoded by diff genes
    • Expressed at different stages of development / tissue
    • Across components
  • Lactate Dehydrogenase
    • 5 different Isozymes
      *
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11
Q

Cofactors

A

Small organic/inorganic molecule or ions

to ASSIST IN CATALYSIS

  • Dietary intake of vitamins & Minerals (IRON)​​
    • _​_most can be synthesized by humans
      • tetrapyrrole ring of heme groups
    • but many need to be chemically modified first
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12
Q

CoEnzymes

Type of Cofactor

A
  • Held LOOSELY by enzymes
  • Rxn –> Release –> Recycled (by a different set of enzymes)
  • NADH / CoA
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13
Q

Prosthetic Groups

​Type of Cofactor

A
  • Held “TIGHTLY” by enzymes
  • Recycled when IN PLACE
  • Heme / Flavin / Fe-S centers
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14
Q

Catabolic Pathway

A

Break DOWN complex precursors –> simple products

Make Energy

Can occur in the same or different place as anabolism

  • Proteins -> AA
  • FA -> Acetyl-CoA
  • Carbs -> CO2 + H2O
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15
Q

Anabolic / Biosynthetic

A

BUILD UP –> Complex Products

USE ENERGY

Can occur in the same or different place as catabolism​

  • AA -> Protein
  • Acetyl-CoA -> Lipids
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16
Q

Glycolysis

A

Glucose -> Pyruvate

Cytosol

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17
Q

Fatty Acid Oxidation

A

FFA -> Acetyl-CoA

MITO

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18
Q

Amino Acid Catabolism

A

AA -> Ketoacids + Urea

MITO

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19
Q

TCA Cycle

A

Pyruvate -> Acetyl-CoA -> NADPH

Mitochondrial MATRIX

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20
Q

Oxidative Phosphorylation

A

ATP Synthase

NADH -> ATP

Mitochondrial MEMBRANE

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21
Q

Urea Cycle

A

AA -> Ammonia -> UREA

Cytosol->MITO

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22
Q

Glycogenesis

A

Glycogen Synthesis

Glucose –> GLYCOGEN

CYTO of muscle/liver/adipose

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23
Q

Glycogenolysis

A

Glycogen Breakdown

Glycogen -> GLUCOSE

CYTO of muscle/liver/adipose

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24
Q

Gluconeogenesis

A

AA / TG / Glycerol -> GLUCOSE

Production of GLUCOSE by non-carbohydrates

Cytosol + Mitochondria

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25
Q

Lipogenesis

A

Fatty Acid Synthesis

Acetyl-CoA –> FFA

CYTOSOL

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26
Q

Triglyceride Synthesis

A

FFA + Glycerol –> TG’s

Cytosol

27
Q

Amino Acid Synthesis

A

Nitrogenous Molecoles -> AA

Mitochondria

28
Q

Porphyrin Synthesis

A

Heme Synthesis

Glycine + Succinyl-CoA -> HEME

Mito + Cyto

29
Q

Mevalonate Pathway

A

Cholesterol + Steroid Synthesis

Acetyl-CoA -> Cholesterol

CYTOSOL

30
Q

Nucleotide Synthesis

A

Phosphate + Sugar + N-Base -> NUCLEOTIDE

Both Cyto/mito

31
Q

Catabolic Funnel Stages

A
  1. ​Complex Molecules -> Monomers
    1. ​Fats / Polysacchrides / Proteins
  2. Monomers -> Simple Intermediates
    1. ​–> Acetyl-CoA
  3. Produce Energy
    1. ​TCA Cycle + Oxidative phosporylation
      1. Recycles cofactors
32
Q

Committing Step

A

First Unique Step

Typically the natural choice for a point of REGULATION

PFK-1 = first unique step in Glycolysis

33
Q

How to decide on which step we should regulate

A
  • Target the MOST EFFICIENT SITE (typically most unique)
    • Junctions of metabolic/signaling paths
      • Not just the start or the unique step
      • Glycolysis - G6K step is also used in
        • ​spinal/sensory neurons outide of the cell
34
Q

PFK-1

A

Committing Step of Glycolysis

NOT used in any other pathways

F6K -> F1,6Bisphosphate

35
Q

Sites of Glycolysis Regulation

A

PFK-1 = commiting step

HEXOKINASE (Start)

Glucose -> G6P

PYRUVATE KINASE (end)

-> Pyruvate

36
Q

3 (6) Basic Ideas for

Maintaining Metabolic Homeostasis

A
  1. Feedback
  2. Crossover Theorem
  3. Energy Charge
  4. Compartmentalization
  5. Tissue Communication / signal transduction
  6. Energy Regulation
37
Q

Tisssue Communication / Signal Transduction

Maintaining Metabolic Homeostasis

A

Hormones / Cytokines / Nervous System

used to Maintain Metabolic Homeostasis

38
Q

Feedback

Maintaining Metabolic Homeostasis

A

Returns a portion of the Output of a system as an INPUT

Typically is NEGATIVE FEEDBACK

39
Q

Negative Feedback

A

Returns the system to the STATUS QUO

MAINTAIN HOMEOSTASIS​

ATP -/-> Glycolysis

UTP + CTP -/-> Pyrimidine synthesis

Contraction of iris in eye in bright light

40
Q

Positive Feedback

A

Can be DANGEROUS -> Runaway reactions

relatively rare in metabolism

Microphone shriek

Cancer

41
Q

Crossover Theorem

A
  • Activating or inhibiting an enzyme in a pathway will result in:
    • Changes in the metabolite concentrations before & after that step
    • Changes occur in opposite directions
  • PKU
    • MORE PKU -> Drop in TYR production
      • but also a rise in the metabolites of PHE
42
Q

Phenylalanine Hydroxylase

A

Phe + BH4 -> Tyr

BH4 is a COFACTOR for the enzyme

43
Q

Dihydrobiopterin Reductase

A

BH2 + NADPH -> BH4

BH4 is a needed cofactor for Phenylalanine Hydroxylase

( Phe -> Tyr )

44
Q

Phenylketouria

PKU

A

Lack of Phenylalanine Hydroxylase

Phe -/-> Tyr

  • Tyrosine becomes Essential
    • used for Catacholamines (hormones + NTs)
      • ​-> Mental Retardation / Neurological Upsets
  • ​​Build up of Phe & its unusual metabolites
    • ​“Cross over Theorem”
      • phenylacetate
45
Q

Varient PKU

A

Defects in metabolism of BH4

Treated with BH4 supplement

BH4 needed for Phenylalanine Hydroxylase

+ L-Dopa & 5 hydroxytryptophan for NT synthesis

46
Q

PKU Diagnosis + Treatment

A

Lab Test on blood / Urine (Mass Spec)

  • Dietary Interventions:
    • Supplement Tyrosine
    • Restrict intake of Phe
    • Avoid protein rich foods, Aspartame
47
Q

HMG-CoA Reductase

A

Comitting step in Cholesterol Synthesis

  • Statin Inhibition exploits the Cross Over Theorem
    • ​Leads to less cholesterol
    • HMG-CoA -> Mevalonic Acid ->->-> Cholesterol
48
Q

Energy Charge

EC

Maintaining Metabolic Homeostasis

A

Ratio of Available Phosphoanhydrade Linkages

ATP + 1/2 ADP

—————-

ATP + ADP + AMP

Entire pool of adenine nucleotides

Higher when MORE ENERGY is available for Work

49
Q

Energy Charge Graph

A
  • Steepest Parts = Most sensative to changes in EC
    • ​0.80 - 0.95 for most cells
  • ​HIGH EC
    • ​inhibits pathways GENERATING ENERGY
    • STIMULATES pathways that consume energy
50
Q

Glycolysis Regulation @ PFK-1

A
  • Stimulated by:
    • ​ADP / AMP / cAMP / Fructose 2,6-bisP
      • ​PFK-2 forms F26BP but is not in glycolysis
      • This is a rare example of POSITIVE FEEDBACK
  • ​Inhibited by:
    • ​ATP & Citrate
      • NEGATIVE FEEDBACK​​
51
Q

Compatmentalization

Maintaining Metabolic Homeostasis

A

Major OPPOSING pathways are often located in DIFFERENT intracellular compartments

membrane barriers / special transport systems

  • Compartments allow for control of:
    • Concentrations
    • Seperation of competting processes
  • ​Fatty Acid Oxidation in MITO__​__​
  • Fatty Acid Syntheis in CYTO
52
Q

Regulation of Enzymes

Maintaining Metabolic Homeostasis

A

Control Concentration of Materials W/

Enzymes / Substrates / Cofactors / Products

Isozymes for flexibility

Enzymes Activation/deactivation

53
Q

Covalent Modification

Ways to Activate / Deactivate Enzymes

A

Often used in Signaling Cascades

Can be Reversible or Not

  1. Phosphorylation
  2. Acetylation
  3. Proteolytic Processing
  4. Glycosylation
  5. Adenylation
  6. Methylation
54
Q

Reversible Non-Covalent Modifications

Ways to Activate / Deactivate Enzymes

A

Allosteric Effectors

Often the effector concentation is connected to overall metabolic state of cell

55
Q

Phosphorylation

Covalent Modification

A

Sensitive to EC

Phosphate -> OH

of Ser Thr Tyr

56
Q

Acetylation / Acylation

Covalent Modification

A

Sensitive to Metabolic State of Cell

Acetyl -> OH

of Ser / Thr

Fatty Acid (Acyl) -> Direct protein

like inserrtion in a membrane

57
Q

Proteolysis / Proteolytic Cleavage

Covalent Modification

A

Activate Proenzymes / Pro-hormones

Deactivate / Recycle Mature proteins / peptides / enzymes

INSULIN needs to be proteolytically activated

58
Q

Glycosylation

Covalent Modification

A

Sugar -> Protein Site

Used in TARGETING the protein to a cell location

or in PROTECTION in cleavage / denaturing agents

59
Q

Allosterism

A

Change Shape & Activity

R Form = Active

  • ATCase
    • ​key enzyme in PYRIMIDINE Synthesis
    • responds to effectors & contraolled by allosterism
  • Hemogloblin
    • ​Oxygen transporter
    • Changes shape upon Oxygen uptake/release
60
Q

R Form

Allosterism

A

Active & Open

conformation

61
Q

T Form

Allosterism

A

LESS Active

conformation

62
Q

Reciprocal Regulation

A

Cell will contain enzymes for both

Synthysizing & Breaking down

the same set of biochemical compounds

  • Leads to PROBLEMS if in SAME COMPARTMENT
    • ​Waste of energy / resources
    • Loss of time
  • ​–> subcellular organelles w/ specialization
63
Q

How to Achieve Homeostasis

A
  • Use Two of the main control mechanisms
    • Covalent Modification
    • NonCovalent binding of small efector molecules
  • ​To alter activity
    • Can be employed at the SAME TIME
    • –> Regulate a PAIR of competing pathways
  • Ex.
    • Glycogen synthesis & breakdown
    • AA synth/breakdown

BioMedChem Midterm 1 (9 decks)

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