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Dental Biochemistry Review. CHO and N Metabolism; Molecular Biology. Free energy of a reaction. The free energy change ( D G ) of a reaction determines its spontaneity. A reaction is spontaneous if D G is negative (if the free energy of products is less than that of reactants). .

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dental biochemistry review

Dental Biochemistry Review

CHO and N Metabolism; Molecular Biology

free energy of a reaction
Free energy of a reaction

The free energy change (DG) of a reaction determines its spontaneity. A reaction is spontaneous if DG is negative (if the free energy of products is less than that of reactants).

DGo' = standard free energy change (at pH 7, 1M reactants & products); R = gas constant; T = temp.

high energy bonds
“High energy” bonds

Phosphoanhydride bonds (formed by splitting out H2O between 2 phosphoric acids or between carboxylic & phosphoric acids) have a large negative DG of hydrolysis.

slide5

BIOENERGETICS SUMMARY

  • Actual (NOT Standard) Free Energy Change determines reaction spontaneity
  • Enzyme reactions may be coupled to promote reaction spontaneity
  • Free energy is released by hydrolysis of “high energy” molecules (e.g. ATP)
  • Reduced coenzymes (e.g. NADH, FADH) are energy-rich compounds
slide6

Metabolism of Glucose

Catabolic Pathways:

Glycolysis (Glucose  Pyruvate + ATP)

Citric Acid (TCA) (+ oxidative phosphorylation)

Pentose Phosphate Shunt

Glycogenolysis

Anabolic Pathways:

Gluconeogenesis

Glycogenesis

slide10
Phosphofructokinase is usually the rate-limiting step of the Glycolysis pathway.

Phosphofructokinase is allosterically inhibited byATP.

  • At low concentration, the substrate ATP binds only at the active site.
  • At high concentration, ATP binds also at a low-affinity regulatory site, promoting the tense conformation.
slide16

Glycogen Synthesis

  • Ingestion of abundant carbohydrates
  • Blood [glucose] increase
  • Secretion of insulin
  • GLUT 4 translocation
  • Activation of Glycogen Synthase
  • Inactivation of Glycogen Phosphorylase
slide20

Glycogen Degradation

Precondition: Low blood glucose

Epinephrine (immediate energy need)

Glucagon (need for glucose homeostasis)

Liver exports glucose

Muscle metabolizes Glucose-6-P

slide26

Actions of Insulin and Glucagon

Metabolic Pathway InsulinGlucagon

Glucose Uptake Increased

Glycolysis Increased Decreased

Gluconeogenesis Decrease Increased

Glycogenesis Increased Decreased

Glycogenolysis Decreased Increased

slide27

Citric Acid (TCA) Cycle and Electron Transport

Complete oxidation of glucose to CO2 + H2O

Oxidative Phosphorylation (ATP generation)

slide33

Biosynthetic “Families” of Amino Acids and their Metabolic Precursors

PrecursorAmino Acid(s)

α-ketoglutarate Glu (E), Gln (Q), Pro (P), Arg (R)

Oxaloacetate Asp (D), Asn (B), Met (M),Thr (T), Ile (I), Lys (K)

3-phosphoglycerate Ser (S), Cys (C), Gly (G)

PEP + Erythrose-4-P Phe (F), Tyr (Y), Trp (W)

Pyruvate Ala (A), Val (V), Leu (L)

Ribose-5-P His (H)

slide38

Urea Cycle Purpose: Disposal of Nitrogen (ammonia)

Urea: the main nitrogenous end product in mammals

A source of amino acid (Arginine)

slide42

Amino Acid Derivatives

Amino AcidDerivativeFunction

Histamine Histidine Vasodilation

Tyrosine Thyroxine Iodine carrier

Nor/Epinephrine Hormone(s)

DOPA Neurotransmitter

Dopamine Neurotransmitter

Tryptophan Serotonin Neurotransmitter

Melatonin Pigment

slide49

Purine Nucleotide Biosynthesis: PRPP to Inosine monophosphate

Inosine monophosphate

(IMP)

H2O

formyl-THF

fumarate

ATP

glycine

Ring closure

asp

formyl-THF

ATP

ATP

gln

CO2

ATP

ATP

Ring closure

slide53

De Novo Pyrimidine Synthesis

HCO3 + Gln

+ 2ATP

Carbamoyl phosphate synthetase II

Aspartate transcarbamoylase

Dihydroorotase

UMP

dihydroorotate

Orotate

Phosphoribosyltransferase

OMP decarboxylase

UMP

Synthase

Dihydrorotate

dehydrogenase

orotate

PRPP

slide54

Nomenclature of bases, nucleosides, and nucleotides

Pyrimidine

BaseRibonucleosideRibonucleotide

Uracil Uridine Uridylate (UMP, UDP, UTP)

Cytosine Cytidine Cytidylate (CMP, CDP, CTP)

Thymine Thymidine Thymidylate (TMP, TDP, TTP)

Purine

BaseRibonucleoside Ribonucleotide

Adenine Adenosine Adenylate (AMP, ADP, ATP)

Guanine Guanosine Guanylate (GMP, GDP, GTP)

slide60

Nucleic Acid Structure and Function

DNA

RNA

Enzyme activities

Replication & Transcription

slide66

DNA Polymerase

  • Successive addition of nucleotides to the end of a growing chain is catalyzed by DNA polymerases.
  • E. coli has 5 DNA polymerases, only three of which are considered here:
    • DNA Pol I: repairs DNA and participates in synthesis of lagging strand during replication
    • DNA Pol II: DNA repair.
    • DNA Pol III: major replication enzyme: responsible for chain elongation during replication; largest of polymerases; key component of replisome.
      • contains 10 different subunits; genes have been isolated.
      • Holoenzyme is an asymmetric dimer consisting of two copies of each polypeptide consisting of a core complex, sliding clamp, and single γ(gamma) complex.
slide79

Catabolite Repression

high

No CAP/lac operon complex

[Glucose]

[cAMP]

No lac operon activation,

i.e. catabolite repression

low

[cAMP]

cAMP-CAP lac operon complex

high

low

CAP activation of lac operon

[Glucose]

Lac operon expression stimulated