bchm 4116 test 2

metabolism

converting food into energy

catabolism

breaking down molecules for energy

de novo

from scratch

de novo synthesis for purines and pyrimidines

needed cus purines and pyrimidines don’t come from diet

relationship between antibiotics/anticancer drugs and nucleotide synthesis

many antibiotics/anticancer drugs are inhibitors of nucleotide synthesis cus nucleotide synthesis is the core of proliferation

purine biosynthesis step number

11 steps

purine biosynthesis ATP requirenments

6 ATP

purine biosynthesis location

liver

purine biosynthesis goal

make inosine monophosphate

precursors of purine ring

N1: Asp

C2: N10 formyl FH4

N3: Gln

C4:,5, and N7: Gly

C6: CO2

C8: N10 formyl FH4

N9: Gln

5-phosphoribosyl-1-pyrophosphate synthase (purine biosynthesis)

synthesizes 5-phosphoribosyl-1-pyrophosphate (PRPP)

prep step of purine synthesis (uncommitted)

REQUIRES ATP

R5P + ATP —> PRPP + AMP

5-phosphoribosyl-1-pyrophosphate is the activated form of ribose

5-phosphoribosyl-1-pyrophosphate synthase regulators

activators: inorganic phosphate

inhibitors: ADP and GDP (end product inhibition)

glutamine phosphoribosyl amidotransferase (purine biosynthesis)

5-phosphoribosyl 1-amine synthesis

PRPP + Gln + H2O —> 5-phosphoribosyl 1-amine + Glu + PPi

glutamine phosphoribosyl amidotransferase regulation

inhibitors: A[M,D,T]P and G[M,D,T]P (end product inhibition)

phosphoribosylglycinamide synthase (purine biosynthesis)

glycinamide ribosyl 5-phosphate synthesis

REQUIRES ATP

5-ribosyl 1-amide + Gly + ATP —> glycinamide ribosyl 5-phosephate + ADP + Pi

steps to make IMP (R5P to IMP)

0.) R5P activated to make PRPP (REQUIRES 1 ATP)

1.) Gln provides N9

2.) Gyl provides C4,5, and N7 (REQUIRES 1 ATP)

3.) N10 formyl FH4 provides C8

4.) Gln provides N3 (REQUIRES 2 ATP)

5.) CO2 provides C6

6.) Asp provides N1 (REQUIRES 1 ATP)

7.) N10 formyl FH4 provides C2 (results in IMP)

adenylosuccinate synthetase (purine biosynthesis)

adenylosuccinate synthesis

REQUIRES GTP

IMP + Asp + GTP —> adenylosuccinate + GDP + Pi

adenylosuccinate synthetase regulation

inhibitors: AMP

IMP dehydrogenase (purine biosynthesis)

xanthosine monophosphate synthesis

IMP + NAD+ + H20 —> xanthosine monophosphate + NADH + H+

IMP dehydrogenase regulation

inhibitors: GMP

adenylosuccinase (purine biosynthesis)

AMP synthesis

adenylosuccinate —> AMP + fumarate

GMP synthase (purine biosynthesis)

GMP synthesis

REQUIRES ATP

xanthosine monophosphate + Gln + ATP —> GMP + Glu + AMP + Pi

reciprocity of regulation

synthesis of AMP requires GTP and synthesis of GMP requires ATP

they help regulate each other

adenylate kinase (purine biosynthesis)

base specific ATP dependent kinase

ADP synthesis

AMP + ATP —> 2 ADP

guanylate kinase (purine biosynthesis)

base specific ATP dependent kinase

GDP synthesis

GMP + ATP —> GDP + ADP

nucleoside diphosphate kinase (purine biosynthesis)

non base specific kinase

nucleotide (purine) triphosphate synthesis

NDP + ATP —> NTP +ADP

steps for ATP starting from IMP

1.) adenylosuccinate synthase (forms adenylosuccinate) (REQUIRES GTP)

2.) adenylosuccinate (forms AMP)

3.) adenylate kinase (forms ADP) (REQUIRES ATP)

4.) nucleoside diphosphate kinase (forms ATP) (REQUIRES ATP)

steps for GTP starting from IMP

1.) IMP dehydrogenase (forms xanthosine monophosphate)

2.) GMP synthase (forms GMP) (REQUIRES ATP)

3.) guanylate kinase (forms GDP) (REQUIRES ATP)

4.) nucleoside diphosphate kinase (forms GTP) (REQUIRES ATP)

purine salvage pathway steps

1.) free base reacts with PRPP to form nucleotides

2.) 5’ nucleotidase converts nucleotides to nucleosides

3.) purine nucleoside phosphorylase generates free bases from nucleosides

phosoribosyltransferase (PRT)

used in purine salvage pathways to make bases from nucleotides

hypoxanthine gaunine phosoribosyltransferase (HGPRT) (purine salvage)

makes gaunine/hypoxanthine in purine salvage pathway

adenine phosoribosyltransferase (APRT) (purine salvage)

make adenine in purine salvage pathway

Lesch-Nyhan syndrome overview

complete deficiency of hypoanthine gaunine phosphoribosyltransferase (HGPRT)

inability to salvage hypoxanthine or gaunine

X linked recessive

Lesch-Nyhan syndrome effects

increased PRPP and degradation of purines (excess uric acid)

decreased IMP and GMP

Lesch-Nyhan syndrome symptoms

self mutilation

mental retardation

purine degradation location

liver if purine was de novo

small intestine if purine was diet

AMP deaminase (purine degradation)

IMP synthesis

AMP —> IMP + NH4+

5’ nucleotidase (purine degradation)

gaunosine or inosine synthesis

GMP or IMP —> guanosine or inosine + Pi

purine nucleoside phosphorylase (purine degradation)

gaunine or hypoxanthine synthesis

gaunosine or inosine + Pi —> gaunine or hypoxanthine + ribose 1-phosphate

gaunase or xanthine oxidase (purine degradation)

xanthine synthesis

gaunine —> xantine + NH4+

hypoxanthine + O2 —> uric acid + H2O2

further xanthine oxidase (purine degradation)

uric acid synthesis

xanthine + O2 —> uric acid + H2O2

purine degradation steps

1.) AMP deaminase (IMP synthesis)

2.) 5’ nucleotidase (guanosine or inosine synthesis)

3.) purine nucleoside phosphorylase (gaunine or hypoxanthine synthesis)

4.) guanase or xanthine oxidase (xanthine synthesis)

4.) further xanthine oxidase (uric acid synthesis)

Gout overview

high level of uric acid

due to overproduction or inadequate excretion of uric acid

urate crytalizes in soft tissues

Gout treatment

allopurinol

allopurinol converts to oxypurinol that inhibits xanthine oxidase

due to inhibition, hypoxanthine and xanthine accumulate not uric acid

hypothxanthine and xanthine are more soluble than uric acid thus less inflammation

pyrimidine synthesis overview

goal of making UMP

pyrimidine ring is synthesized before PRPP attachment (unlike purine ring made in process)

precursors of pyrimidine ring

N1, C4,6: synthesized before

C2: CO2

N3: Gln

C5: Asp

carbamoyl phosphate synthase II (CPS II)

carbamoyl phosphate synthesis

also first step of urea cycle

carbamoyl phosphate synthase II (CPS II) regulation

activators: PRPP and ATP

inhibitors: UTP and UDP

apspartate transcarbmoylase

carbmoyl aspartate synthesis

carbmoyl phosphate + Asp —> carbmoyl aspartate + Pi

oxidation of carbmoyl aspartate

orotate synthesis

ring closes and is oxidized to make orotate synthesis

orotate phosphoribosyltransferase

orotidine 5’ phosphate (OMP) synthesis

orotate + PRPP —> OMP + PPi

orotidine 5’-phosphate decarboxylase

UMP synthesis

OMP —> UMP + CO2

nucleoside monophosphate kinase

UDP synthesis

REQUIRES ATP

UMP + ATP —> UDP + ADP

nucleoside diphosphate kinase

UTP synthesis

UDP —> UTP

CTP synthase

CTP synthesis

UTP + Gln —> CTP

ribonucleotide reductase

CDP synthesis

CTP —> CDP + Pi

pyrimidine synthesis

1.) carbamoyl phosphate synthesis

2.) carmoyl aspartate synthesis

3.) ring close and orotate synthesis

4.) orotindine 5’ phosphate synthesis

5.) UMP synthesis

6.) UDP synthesis

7.) UTP synthesis

8.) CTP synthesis

9.) CDP synthesis

hereditary orotic aciduria overview

increased orotate excreted in urine

caused by deficiency of one or both activities of single polypeptide chain UMP synthase

decreased levels of UMP

thus pyrimidines cannot be produced and no cell growth

hereditary orotic aciduria treatment

oral uridine

uridine converted to UMP to bypass blockage

thymidylate synthase

deoxythymidine monophosphate (dTMP) synthesis

dUMP + N N methylene FH4 —> dTMP + FH4

thymidylate synthase regulation

inhibitors: FdUMP

FdUMP formed by 5-fluorouracil (5-FU)

5-fluorouracil (5-FU)

used to treat colon cancer cus cus it inhibits cell growth

pyrimidine salvage pathway overview

pyrimidine base CAN be recycled but free pyrimidine bases CANNOT be recycled

pyrimidine nucleoside phosphorylase

non specific

converts pyrimidine bases to respective nucleotides

nucleoside kinase

specific

react with nucleoside to form nucleotides

REQUIRES ATP

pyrimidine salvage pathway steps

1.) pyrimidine base converted to respective nucleosides

2.) nucleoside converted to nucleotide

pyrimidine degradation

pyrimidine ring is opened and degraded to HIGHLY soluble products

catabolism of pyrimidine bases don’t cause issues like gout cus they convert to such soluble products

pyrimidine degradation steps

1.) pyrimidines are hydrolyzed to their nucleosides and Pi

2.) nucleosides are cleaved to ribose-1 phosphate and the free pyrimidine bases (T,U,C)

3.) bases deaminated to CO2, NH3, and B alanine

4.) those are either excreted in urine or converted to CO2, H2O, NH3

ribonucleotide reductase (RR)

reduces ribose to deoxyribose

requires thioredoxin to create little redox cycle

ONLY occurs at the nucleotide DIPHOSPHATE level

ribonucleotide reductase (RR) regulation 2 forms

1.) overall activity turned on and off depending on need for dNTPs

2.) relative amounts of each NDP substrate are heavily controlled for balance

ribonucleotide reductase (RR) regulation allosteric sites

different than the substrate binding catalytic site

1.) overall activity site

2.) substrate specificty site

increased ATP = more dNTPs needed = increased RR activity

overall activity site (RR regulation)

ONLY ATP and dATP bind

activator: ATP

ATP binds = active

inhibitor: dATP

dATP binds = inactive

substrate specificity site (RR regulation)

ATP, dTTP, dGTP, or dATP binds

substrate specificity

APT binds UDP or CDP

dTTP binds GDP

dGTP binds ADP

Burkitt lymphoma

highly aggressive malignancy of B cells

too many B cells cause tumors

due to c-myc gene chromosome translocation leading to overproduction of myc in B cells where it shouldnt normally be made

Epstein Barr virus

first virus discovered to cause cancer

c-myc overview

protooncogene that drives cell growth

first found in avian retrovirus

commonly expressed in proliferating cells

higher levels when younger and more heavily regulated when older

turned on by growth factors or mutations

oncogene

cancer causing gene

protooncgene

gene that has potential for causing cancer

structure of c-myc gene

MB1 and MB2

NLS

Basic and HLH and LZ

MB1 and MB2

motifs unique to c-myc

nuclear localization sequence (NLS)

motif indicating location

Basic and helix loop helix (HLH) and leu zipper (LZ)

DNA binding protein

c-myc dimerization

c-myc + Max

myc-max heterodimer binds to DNA Ebox as a dimer

Max

dimerization partner of myc

purely for structure

DNA Ebox

a short palindrome thats the binding site on DNA for mcy-max

c-myc function

activates transcription of target genes

induction of the transcription factor myc promotes cell proliferation and apoptosis

THUS MYC IS ALSO A SAFETY MECH FOR PROGRAMED CELL DEATH thru c-myc and p53

also important for cell differentiation

acetylation of DNA

changes histone structure/unwinding for DNA binding proteins

p53

senses DNA damage; tumor suppressor

all cancer require reduction of p53 activity

activated when DNA damaging agents are introduced

c-myc indices p53 meditated apoptosis

DNA damaging agents and p53

DNA damaging agents are used to induce p53

eg Doxo and Etop

p53 regulation

regulated by Mdm2 which degrades p53 and keeps p53 at low levels when not activated

Mdm2 regulation

regulated by ARF with promotes degradation of Mdm2

increased myc = increased ARF = increased p53

anti apoptotic mutations

cause myc to be cancerous by blocking c-myc ability to apoptosis thus it only proliferates

RAS

when actived, cell proliferation increases

increased myc and increased RAS = no p53 activty thus proliferation

increased c-myc results in apoptosis

increased RAS results in senescence

when both are mutated, proliferation increases

omomyc

cancer treatment cus it promotes c-myc degradation

origin of replication (ori)

AT rich due to 2 H bonds

prokary have 1 and eukary have multiple

energy dependent strand separation to ssDNA for DNA rep

prepriming complex

helicase

SSB proteins

topoisomerases

helicase

ATP driven forcible strand separation

SSB proteins

prevent strands from reannealing

protects strands from enzymeatic cleavage

topoisomerase

removes supercoiling

DNA gyrase

type II topoisomerase

introduces (-) supercoiling to relive tension during replication and transcription