Dental Biochemistry Review

CHO and N Metabolism; Molecular Biology

Free energy of a reaction

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

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

For a reaction A + B C + D

G = Go' + RT ln[C] [D][A] [B]

“High energy” bonds

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

N

NN

N

NH 2

O

OHOH

HH

H

CH 2

H

OPOPOP-O

O

O- O-

O O

O-

adenine

ribose

ATP adenosine triphosphate

phosphoanhydride bonds (~)

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

Metabolism of GlucoseCatabolic Pathways:

Glycolysis (Glucose Pyruvate + ATP)

Citric Acid (TCA) (+ oxidative phosphorylation)

Pentose Phosphate Shunt

Glycogenolysis

Anabolic Pathways:

Gluconeogenesis

Glycogenesis

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

Phosphofructokinase is allosterically inhibited by ATP.

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.

CH 2 O PO 32

O H

CH 2 O H

H

O H H

H HO

O6

5

4 3

2

1 CH 2 O PO 32

O H

CH 2 O PO 32

H

O H H

H HO

O6

5

4 3

2

1

A T P A D P

M g 2 +

f r u c t o s e - 6 - p h o s p h a t e f r u c t o s e - 1 , 6 - b i s p h o s p h a t e

P h o s p h o f r u c t o k i n a s e

Glycogen Synthesis

•Ingestion of abundant carbohydrates

•Blood [glucose] increase

•Secretion of insulin

•GLUT 4 translocation

•Activation of Glycogen Synthase

•Inactivation of Glycogen Phosphorylase

Glycogen Degradation

Precondition: Low blood glucose

Epinephrine (immediate energy need)

Glucagon (need for glucose homeostasis)

Liver exports glucose

Muscle metabolizes Glucose-6-P

Actions of Insulin and Glucagon

Metabolic Pathway Insulin Glucagon

Glucose Uptake Increased

Glycolysis Increased Decreased

Gluconeogenesis Decrease Increased

Glycogenesis Increased Decreased

Glycogenolysis Decreased Increased

Citric Acid (TCA) Cycle and Electron Transport

Complete oxidation of glucose to CO2 + H2O

Oxidative Phosphorylation (ATP generation)

Biosynthetic “Families” of Amino Acids and their Metabolic Precursors

Precursor Amino 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)

Urea Cycle Purpose: Disposal of Nitrogen (ammonia)

Urea: the main nitrogenous end product in mammals

A source of amino acid (Arginine)

Amino Acid Derivatives

Amino Acid Derivative Function

Histamine Histidine Vasodilation

Tyrosine Thyroxine Iodine carrier

Nor/Epinephrine Hormone(s)

DOPA Neurotransmitter

Dopamine Neurotransmitter

Tryptophan Serotonin Neurotransmitter

Melatonin Pigment

Synthesis of Heme and Hemoglobin

Purine Nucleotide Biosynthesis: PRPP to Inosine monophosphate

glycine

formyl-THF

gln

ATP

ATP

ATPRing closure

CO2

ATP

aspATP

fumarate

Ring closure

formyl-THFH2O

Inosine monophosphate(IMP)

http://courses.cm.utexas.edu/archive/Spring1999/CH369/LEC23/pur9.gif

Carbamoyl phosphate synthetase II

Aspartate transcarbamoylase

Dihydroorotase

Dihydrorotatedehydrogenase

OrotatePhosphoribosyltransferase

OMP decarboxylase

PRPP

orotateUMP

Synthase

dihydroorotate

UMP

HCO3 + Gln+ 2ATP

De Novo Pyrimidine Synthesis

Nomenclature of bases, nucleosides, and nucleotides

Pyrimidine

Base Ribonucleoside Ribonucleotide

Uracil Uridine Uridylate (UMP, UDP, UTP)

Cytosine Cytidine Cytidylate (CMP, CDP, CTP)

Thymine Thymidine Thymidylate (TMP, TDP, TTP)

Purine

Base Ribonucleoside Ribonucleotide

Adenine Adenosine Adenylate (AMP, ADP, ATP)

Guanine Guanosine Guanylate (GMP, GDP, GTP)

Nucleic Acid Structure and Function

DNA

RNA

Enzyme activities

Replication & Transcription

DNA PolymeraseSuccessive 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.

Catabolite Repression

[Glucose]

[cAMP]

[Glucose]

[cAMP] cAMP-CAP lac operon complex

CAP activation of lac operon

Lac operon expression stimulated

No CAP/lac operon complex

No lac operon activation,i.e. catabolite repression

low

high

lowhigh

Termination step of protein synthesis