G6P NADPH Ru5P DNA, RNA R5P Xu5P ATP G3P Su7P F6P E4P Xu5P...

NADPH

G6P

Ru5P

Xu5P

G3P Su7P

F6P E4P Xu5P

G3P

R5P

F6P

Pentose Phosphate Pathway

Glycolysis

DNA, RNAATP

Coordinate Regulation of Glycolysis and Gluconeogenesis

O P OO

O

OOPO

O

OH OH

OH

O

OOPO

O

OH OH

OH

O

OH

OOPO

O

OH OH

OH

O

OH

OOPO

O

OH OH

O

OH

O PO

O

O

OOPO

O

OH OH

O

OH

O PO

O

O

Glycolysis Gluconeogensis

ATP ADP

Pi

PFK2-bPase

complex

phosphatase

kinase

PFKF-1,6-bPase

F2,6bP glucose

ATP F2,6bPglucose

ATP

Glycogen Phosphorylase Regulation

ab

ATP ADP

ActiveR

Conformationalchange

InactiveT

Muscle; b state responds to energy charge

bR

bT aT

aRbR

bT aT

aR

High [ATP], [G6P] High [AMP]

Liver; a state responds to glucose levels

bR

bT aT

aRbR

bT aT

aR

Low [glucose]High [glucose]

Pancreatic β cell glucose sensing mechanism.

(portal vein)

ATP

GlucoseGlucose

K+

Ca2+

K +

Ca2+

glycolysis, TCA cycle and ox-phos

Hi ATP:ADP ratio inhibits K+ efflux pump, depolarizes cell.

Depolarization induces Ca2+ influx

Ca2+ spike causes exocytosis of insulin

cAMP ATP

O N

N

NO

OP

O

O

OH

NH2

+ +

Adenylate cyclase

Glucagonreceptor and G-coupled protein

PKAi PKAaATP ADP

PKAi PKAa

ATP ADP

Phosphorylasekinase

Glycogen phosphorylase

b a

Protein Kinase A

Glycogenbreakdown

+

++

+ PKA exists as C2R2tetramer in inactive form. cAMP binding causes dissociation into two active C monomers that phosphorylate other proteins.

Glucagon activates cAMP cascade in the liver

PKA coordinately regulates carbohydrate metabolism

PKAa

glycogen

Glc

G1P

G6P F6P F1,6bP

pyruvate

Phosphorylate PFK2-F2,6bPase complex;stimulates F-2,6-bPase activity and inactivates the kinase; activates gluconeogenesis

Phosphorylateglycogen

phosphorylase:stimulates glycogen

breakdown; phosphorylate

glycogen synthase: inhibits

glycogen synthesis.

Glucose is secreted into the blood.

Liver cell

TCA cycle and related metabolism

Ala,Val,Leu,IlePhe,Tyr,

Pyr

AcCoA

Succ-CoA

OAA

Fatty acids

Asp,Asn citrate

isocit

α-kg

Succ

fum

mal

PEPGlycolysisGluconeogenesis

NADH + H+NADH + H+

Glu, Gln

NADH + H+

FADH2Part of Ox-Phos

ATP

Redox Shuttling in Mitochondria

NAD+

NADH+ H+

NAD+

NADH+ H+

Q

2e- 2e-

2e- 2e-

Succ

FumOH OPO3

OH

OH OPO3

O

Glycerol 3-phosphate

DHAP

Glycerol 3-phosphate dehydrogenase

Succinatedehydrogenase

Complex 1; NADH

Dehydrogenase

NAD+

NADH+ H+

CytosolicNADH

dehydrogenase

matrix cytoplasm

FADH2 FADH2

Inner mitochondrial membrane

Mal-Asp Shuttle in Mitochondria

matrix cytoplasm

αkg αkg

Asp

Mal

NADH+ H+

Asp

MalNAD+

Inner mitochondrial membrane

Glu

OAA

Glu

OAA

NAD+

NADH+ H+

Aspartate-glutamate

carrier

α-kg –malatecarrier

β-Oxidation of fatty acids.

R

O

CoA

O

CoA

R

O

CoA

R

O

CoA

OH

R

O

CoA

O

R

O

CoA

FADH2

NADH

Citrate – Malate – Pyruvate Transport System

Mito Cyto

Cit Cit

PiPi

MalMal

CoASH

OAA Ac-CoA

Pyr

ATP ADP

NADH + H+

NAD+

NADPH + H+

Ac-CoA

OAA

NADP+NAD+

NADH + H+

ATP

ADP

Pyr

1

2

3

45

6

FattyAcids

Enzymes:1. Citrate synthase2. ATP-citrate lysase3. Malate dehydrogenase4. Malic enzyme5. Pyruvate carboxylase6. Malate dehydrogenase

Carriers:Citrate transported by two pumps, both are co-transporters. One co-transports orthophosphate, the other malate. Pyruvate transported by a separate pump.

CO2

Regulating Fatty Acid Synthesis and Degradation

cAMP

Insulin receptorGlucagon receptor

PKAactive PKAinactive

ACCaseACCase

FA FANADH, FADH2

β-Ox TCAFAS

AcCoAPyrCitCit

AcCoAMalCoA

AMP Glucose

Pyr

PPP

NADPH

triglycerides

FA

+

+

+

+

mitochondria

Cytochrome Oxidase Cycle

O=OO2

Fe Cu

2 H2O

OH

-OH

O-OOH

=O

H+

F1F0 ATPase structure

From the ATPase Group at Univeristat Freiburg: http://www.atpase.de/

Ion binding and rotary motion in ATPase

This particular figure is drawn for a Na-ATPasewith a geometry that differs from that of the F1F0ATPase in ox-phos, but the phyisico-chemical principles are very similar. In fact, since this protein is much easier to work with, it is generally used as a model system for the more complex F1F0 ATPase.

Ions enter channel from one side of rotor and are forced to the “bottom” by low dielectric environment. Once the cation is at the bottom of the channel, it interacts electrostaticallywith an Arg sidechain. The electrostatic repulsion drives the charges apart, leading to rotational motion.

Copyright ©1999 by the National Academy of Sciences

Dimroth, Peter et al. (1999) Proc. Natl. Acad. Sci. USA 96, 4924-4929

Z-scheme in Photosynthesis

Photophosphorylation

Oxidative metabolism of arachidonic acid

O

CO2-

OH

O

O

O

CO2-

OH

O

O

CO2-

OOH

CO2-

2O2

Other PG’s

PGG2

PGH2

TXA2

Thromboxane synthase

cyclooxygenase

peroxidase

Inhibited by NSAIDs

CO2-OOH

OCO2-

lipoxygenase

O2

Cyclooxygenase and peroxidase activities in one enzyme called prostaglandin synthase

5-HPETE

LTA4

Other LT’s

Lipoproteins : lipid and cholesterol transport in the blood.

• Lipids transported– Triglycerides, phospholipids, cholesterol, and

cholesteryl esters• Proteins in lipoproteins

– Structural proteins– enzymes

• Nomenclature of lipoproteins– Electrophoretic mobility

α: highest mobility; HDL particlesβ: lowest mobility; LDL particlesPre−β: intermediate mobility; VLDL

– Density, size Protein Particle Function

C=chylomicron; H=HDL; VL=VLDL; L=LDL; I=IDL

A-I C,H Ligand for HDL receptor; activates LCAT

A-II C,H Inhibitor of A-I

A-IV C,H ???

B-100 L,VL,I VL synthesis; Ligand for receptor

B-48 C C synthesis

C-I VL,H,C Activator of LCAT?

C-II VL,H,C Activate lipoprotein lipase

C-III VL,H,C Inhibit C-II

D Some H Lipid transfer protein?

E All Ligand for receptors

PL>>CE>>TG~PL30-50<20HDL

CE>>PL>TG~C21~20LDL

CE>TG~PL>CE10~25IDL

TG>PL~CE>C8~50VLDL

TG>>PL>CE>C1100’sChyl

Lipids% ProteinD, nmParticle

Lipoprotein Biochemistry: Generation of lipoprotein particles

Chylomicrons

VLDLs& LDLs

HDLs

Figures from Harper’s Biochemistry, 25th Edition

Regulation of Glutamine Synthetase

Metabolic fates of glutamine

From Purdue University: http://www.hort.purdue.edu/rhodcv/hort640c/hort640c.htm

PII PII

Glu Gln

ATPα-kg

ATP + NH4+ ADP

ADP

PPi Pi

UTP PPi

H2OUMP

PII

AT

PII

AT

GS

GS

UT

inactive

active

AT

Uridylylated PII binds to AT and

activates the deadenylylation of

GS

Non-uridylylated PII converts AT into an adenylylating form that inactivates GS

AT inhibited by α-kg; activated by Gln

Regulation of Glutamine Synthetase

AMP

De-adenylylationadenylylation

UT inhibited by Gln,Activated by α-kg and ATP

Self-mutiliation inLesch-Nyhan syndrome

Gout: excess uric acid

Folate and Purine Biosynthesis

N

N

NH

N

NHR

NH2

O

N

N

NH

N

NHR

NH2

O

HH

N

N

NH

N

NHR

NH2

O

HH

H

H

NADPH+ H+

NADP+

NADPH+ H+

NADP+

NADPH+ H+

NADP+

N

N

NH

N

NHR

NH2

O

H

CH3

Met

HCysDHFR catalyzes these reactions

N

N

NH

N

NR

NH2

O

H

H

O

Formate+

ATP

ADP +Pi

5

10

5

10

5

105

10

5

10

Ribonucleotide reductase mechanism.1. The free radical of ribonucleotide reductase

eliminates a hydrogen atom from carbon 3' of the substrate, generating a free radical.

2. One of the thiol groups of the enzyme donates a proton to oxygen on C2'.

3. A water molecule is eliminated. 4. The carbocation on C2' is reduced by the

second sufhydryl group. 5. The enzyme donates a hydrogen atom to C3'

to form the deoxyribonucleotide. The enzyme in converted in its radical form and must be reduced to its starting disulfhydryl form.

The initial free radical is generated via a dinuclearFe cluster in the enzyme. O2 is the oxidant that converts the Fe(II)-Fe(II) form into the Fe(III)-Fe(II) form.

Fe(II) Fe(II) Fe(III) Fe(II)

O2

From: http://www.med.unibs.it/~marchesi/ndp_reductase.html

Ribonucleotide reductase structural biology

R1 dimerR1 hexamer

http://opbs.okstate.edu/~leach/biochem203folder/bioch203%20classes/b203c19/dndp.htm

Model for Ribonucleotide Reductase Activity

Hexamer site• binds ATP, makes hexamer

Adenosine site• binds ATP (KM= 100 µM) or dATP (KM=0.3 µM)• dATP binding changes R1 to inactive tetramer

Specificity site

R1 R12 R14a R16

Low population states

Most active

R14bS site Reduced

ATP or dATP CDP UDP

dTTP GDP CDP UDP

dGTP ADP CDP GDP UDP

Inactive active

From: Cooperman & Kashlan (2003) Adv. Enzym. Regul. 43, 167-182.

Regulating Transcription

A. Negative Regulation: derepressionexample: lac repressor; ligand = galactose

C. Positive Regulation: inductionexample: CAP; ligand = cAMP

Regulation of lac operon

1. Glucose: well-fed state lowers [cAMP]means no induction; system C on left of equilibriumif low [Galactose], system A on left; lac genesrepressed; if high [Galactose], system A on right; lac gene expression de-repressed, i.e. express lac genes

2. Glucose: starvation raises [cAMP];system C shifted to right; express lac genessystem insensitive to whether Galactose hi or lo

B. Negative Regulation: repressionexample: trp repressor; ligand = tryptophannot involved in lac gene regulation.