Module 9 Flashcards
- are the monomeric units that make up the nucleic acids DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid)
Nucleotides
- are responsible for the storage and passage of the information needed for the production of proteins
Nucleic acids
Each nucleotide consists of __
a pentose sugar, a nitrogenous base, and a phosphate group
Result from linking one or more phosphates with a nucleoside onto the 5’ end of the molecule through esterification
Nucleotides
A __ is a 5-carbon sugar in a pentose ring form
pentose sugar
__ contains ribose, which has a hydroxyl group in both the 2’ and 3’ positions (prime refers to the carbon of the sugar)
RNA
__ has only a single hydroxyl group in the 3’ position
DNA
A __ is attached by a glycosidic bond to the 1’ carbon of the nucleotide’s sugar
nitrogenous base
__ consist of linked 5-membered and 6-membered rings (Adenine and Guanine, A and G) which can be found in DNA or RNA
Purines
__ consist of 6-membered rings Cytosine, Thymine, and Uracil (C, T, and U)
Pyrimidines
(pyrimidines)
__ is found in DNA or RNA, T is found in DNA, while U is found in RNA
Cytosine
- Planar, aromatic, and heterocyclic
- Derived from purine or pyrimidine
- Numbering of bases is “unprimed”
Nitrogenous Bases
The sugar derivatives
__ participate in sugar interconversions and in the biosynthesis of starch and glycogen
UDP-glucose and UDP-galactose
nucleoside-lipid derivatives such as __ are intermediates in lipid biosynthesis.
CDP-acylglycerol
The __ serve
as the second messengers in hormonally regulated events, and GTP and GDP play key roles in the cascade of events that characterize signal transduction pathways.
cyclic nucleotides cAMP and cGMP
__ are nitrogen-containing heterocycles, cyclic structures that contain, in addition to carbon, other (hetero) atoms such as nitrogen.
Purines and pyrimidines
Pyrimidine vs Purine
Note that the SMALLER
PYRIMIDINE MOLECULE has the longer name and the LARGER PURINE MOLECULE the shorter name, and that their six-atom rings are numbered in opposite directions.
__ are weak bases (pKa values 3-4), although the proton present at low pH is associated, not as one might expect with the exocyclic amino group, but with a ring nitrogen, typically N1 of adenine, N7 of guanine, and N3 of cytosine.
Purines or pyrimidines with an ´NH2 group
The sugar in ribonucleosides is D-ribose, and in deoxyribonucleosides is
2-deoxy-D-ribose. Both sugars are linked to the heterocycle by a __, almost always to the N-1 of a pyrimidine
or to N-9 of a purine
B-N-glycosidic bond
__ are nucleosides with a phosphoryl group esterified to a hydroxyl group of the sugar.
Mononucleotides
Additional phosphoryl groups, ligated by __ to the phosphoryl group of a mononucleotide, form nucleoside diphosphates and triphosphates.
acid anhydride bonds
Steric hindrance by the heterocycle dictates that there is no freedom
of rotation about the β-N-glycosidic bond of nucleosides or nucleotides. Both therefore exist as noninterconvertible __. While both syn and anti
conformers occur in nature, the anti conformers predominate.
syn or anti conformers
The conjugated double bonds of __ absorb ultraviolet light.
purine and pyrimidine derivatives
__ serves as an allosteric regulator and as an
energy source for protein synthesis.
GTP
__ serves as a second messenger in response to nitric oxide (NO)
during relaxation of smooth muscle
cGMP
__ forms the urinary glucuronide conjugates of bilirubin and of many drugs, including aspirin.
UDP-glucuronic acid
__ participates
in biosynthesis of phosphoglycerides, sphingomyelin, and other substituted sphingosines
CTP
__ have two acid anhydride bonds and one ester bond.
Nucleotide triphosphates
The purine analog __, used in treatment of hyperuricemia and gout, inhibits purine biosynthesis and xanthine oxidase activity.
allopurinol
__ is used in chemotherapy of cancer
Cytarabine
__ which is catabolized to 6-mercaptopurine, is employed during organ transplantation to suppress immunologic
rejection
azathioprine
The 5′-phosphoryl group of a mononucleotide can esterify a second hydroxyl group, forming a __. Most commonly, this second hydroxyl group is the 3′-OH of the pentose of a second nucleotide.
phosphodiester
This forms a __ in which the pentose moieties are linked by a 3′,5′-phosphodiester bond to form the “backbone” of RNA and DNA.
dinucleotide
Posttranslational modification of preformed polynucleotides can generate additional structures such as __, a nucleoside in which D-ribose is linked to C-5 of uracil by a carbon-to-carbon bond rather than by the usual β-Nglycosidic
bond.
pseudouridine
- contains a single phosphate group, which is a strong acid
- can be attached through the oxygen of a hydroxyl at either the 5’ or 3’ position of the sugar
- It is more commonly attached to the 5’ position.
phosphate
A __ is the term for a sugar and a base
nucleoside
From __ can be attached to nucleosides to from nucleoside mono, di, or triphosphates
1 to 3 phosphates
A __ can also be called a nucleotide
nucleoside monophosphate
(Naming Conventions)
Nucleosides
Purine nucleosides end in “-sine”
- Adenosine, Guanosine
Pyrimidine nucleosides end in “-dine”
- Thymidine, Cytidine, Uridine
(Naming Conventions)
Nucleotides
Start with the nucleoside name from above and add “mono-”, “di-”, or “triphosphate”
- Adenosine Monophosphate, Cytidine Triphosphate, Deoxythymidine Diphosphate
__ are linked together by phosphodiester bonds between the 3’ hydroxyl on the sugar of one nucleotide through a phosphate molecule to the 5’ hydroxyl on the sugar of another nucleotide
Nucleotides
Nucleotide bonds are broken by __
phophodiesterases
Adenine nucleotides are components of 3 major coenzymes:
NAD+, FAD, COENZYME A
__ are activated precursors in nucleic acid synthesis.
Nucleoside triphosphates
(PURINE NUCLEOTIDE SYNTHESIS)
First purine derivative formed is __
Inosine Mono-phosphate (IMP)
SOURCES OF ATOMS IN PURINE BIOSYNTHESIS
N1 - Aspartate C2, C8 - 10-Formyl-THF N3, N9 - Glutamine C6 - CO2 C4, C5, N7 - Glycine
The activated sugar used is __
- is generated by the action of PRPP synthetase and requires energy in the form of ATP
- This reaction releases AMP. Therefore, 2 high energy phosphate equivalents are consumed during the reaction.
- First committed step of purine synthesis (Regulated)
5-phosphoribosyl-1-pyrophosphate, PRPP
5-phosphoribosyl-1-pyrophosphate, PRPP is inhibited by __
ADP and GDP
The major site of purine synthesis is in the __.
liver
Synthesis of the purine nucleotides begins with PRPP and leads to the first fully formed nucleotide, __.
inosine 5’-monophosphate (IMP)
The synthesis of IMP requires __
five moles of ATP, two moles of glutamine, one mole of glycine, one mole of CO2, one mole of aspartate and two moles of formate
The formyl moieties are carried on tetrahydrofolate (THF) in the form of __.
N5,N10-methenyl-THF and N10-formyl-THF
(SYNTHESIS OF AMP OR GMP)
__ represents a branch point for purine biosynthesis, because it can be converted into either AMP or GMP through two distinct reaction pathways.
IMP
The pathway leading to AMP requires energy in the form of GTP; that leading to GMP requires energy in the form of __
ATP
The accumulation of excess __ will lead to accelerated AMP synthesis from IMP instead, at the expense of GMP synthesis.
GTP
the conversion of IMP to GMP requires ATP, the accumulation of excess __ leads to accelerated synthesis of GMP over that of AMP.
ATP
The synthesis of PRPP by PRPP synthetase is feed-back inhibited by __ (predominantly AMP and GMP).
purine-5’-nucleotides
The amidotransferase reaction (2nd step) catalyzed by __ is also feed-back inhibited allosterically by binding ATP, ADP and AMP at one inhibitory site and GTP, GDP and GMP at another.
PRPP glutamyl amidotransferase
__ is regulated in the branch pathways from IMP to AMP and GMP. The accumulation of excess AMP leads to accelerated synthesis of GMP, and excess GMP leads to accelerated synthesis of AMP.
purine biosynthesis
Catabolism of the purine nucleotides leads ultimately to the production of __ which is insoluble and is excreted in the urine as sodium urate crystals.
uric acid
The synthesis of nucleotides from the purine bases and purine nucleosides takes place in a series of steps known as the __.
salvage pathways
The free purine bases, adenine, guanine, and hypoxanthine, can be reconverted to their corresponding nucleotides by __.
phosphoribosylation
Two key transferase enzymes are involved in the salvage of purines:
- adenosine phosphoribosyltransferase (APRT)
2. hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
A critically important enzyme of purine salvage in rapidly dividing cells is __ which catalyzes the deamination of adenosine to inosine.
adenosine deaminase (ADA)
Deficiency in adenosine deaminase (ADA) results in the disorder called __
severe combined immunodeficiency, SCID
__ can also contribute to the salvage of the bases through a reversal of the catabolism pathways. However, this pathway is less significant than those catalyzed by the phosphoribosyltransferases.
Purine nucleotide phosphorylases (PNPs)
- separate kinase for each nucleotide
Nucleoside Monophosphate kinases
- single enzyme with broad specificity
Nucleoside Diphosphate kinases
One genetic disorder of pyrimidine catabolism,
__, is due to total or partial deficiency of the enzyme dihydropyrimidine dehydrogenase.
β-hydroxybutyric aciduria
This disorder
of pyrimidine catabolism, also known as __, is also a disorder of β-amino acid biosynthesis, since the formation of β-alanine and of β-aminoisobutyrate is
impaired.
combined uraciluria-
thyminuria
The three processes that contribute to purine nucleotide biosynthesis are, in order of decreasing importance.
- Synthesis from amphibolic intermediates (synthesis de novo).
- Phosphoribosylation of purines.
- Phosphorylation of purine nucleosides.
__ has a low level of PRPP glutamyl amidotransferase, and hence depends in
part on exogenous purines.
Human brain tissue
__ cannot synthesize 5-phosphoribosylamine
and, therefore, also utilize exogenous
purines to form nucleotides.
Erythrocytes and polymorphonuclear
leukocytes
The rate of PRPP
synthesis depends on the availability of ribose 5-phosphate and on the activity of __, an enzyme whose activity is feedback inhibited
by AMP, ADP, GMP, and GDP
PRPP synthase
__ also inhibit hypoxanthine-guanine phosphoribosyltransferase,
which converts hypoxanthine and guanine to IMP and GMP, and GMP feedback inhibits PRPP glutamyl amidotransferase
AMP and GMP
Reduction of the 2′-hydroxyl of purine and pyrimidine ribonucleotides,
catalyzed by the complex that includes __, provides the deoxyribonucleoside diphosphates (dNDPs) needed for both the synthesis and repair of DNA
ribonucleotide
reductase
Five of the first six enzyme activities of pyrimidine biosynthesis
reside on __.
multifunctional polypeptides
For further pyrimidine synthesis to occur, dihydrofolate must be reduced
back to tetrahydrofolate. This reduction, catalyzed by dihydrofolate
reductase, is inhibited by __
methotrexate
- are alternate substrates for orotate phosphoribosyltransferase.
Both drugs are phosphoribosylated, and allopurinol is converted
to a nucleotide in which the ribosyl phosphate is
attached to N1 of the pyrimidine ring.
Allopurinol and 5-fluorouracil
Humans convert adenosine and guanosine to __. Adenosine is first converted to inosine by adenosine
deaminase.
uric acid
In mammals other than higher primates, __,converts uric acid to the watersoluble
product allantoin. However, since humans lack __, the end product of purine catabolism in humans is uric acid.
uricase
__ is a condition that results from the precipitation of urate (uric acid) as monosodium urate (MSU) or calcium pyrophosphate dihydrate (CPPD) crystals in the synovial fluid of the joints, leading to severe inflammation and arthritis.
Gout
Most forms of gout are the result of excess purine production or to a partial deficiency in the salvage enzyme, __
Hypoxanthine-guanine phosphorybosyl transferase (HGPRT)
increased activity of PRPP synthetase leads to excess PRPP leading to increased purine nucleotide production that can increase the rate of purine degradation and subsequently increase __
uric acid synthesis
Responsible for re-forming IMP and GMP from hypoxanthine and guanine
Hypoxanthine-guanine phosphorybosyl transferase (HGPRT) and the Salvage Pathway
Most forms of gout can be treated by administering the antimetabolite __ .
This compound is a structural analog of hypoxanthine that strongly inhibits xanthine oxidase.
allopurinol
- results from the loss of a functional HGPRT gene.
- is inherited as a sex-linked trait, with the HGPRT gene on the X chromosome (Xq26-q27.2).
- Patients with this defect exhibit not only severe symptoms of gout but also a severe malfunction of the nervous system.
- In the most serious cases, patients resort to self-mutilation.
Lesch-Nyhan syndrome
- is most often (90%) caused by a deficiency in the enzyme adenosine deaminase (ADA).
- This is the enzyme responsible for converting adenosine to inosine in the catabolism of the purines
SCID (Severe Combined Immunodeficiency Disease)
- selectively leads to a destruction of B and T lymphocytes, the cells that mount immune responses.
- deoxyadenosine is phosphorylated to yield levels of dATP that are 50-fold higher than normal
ADA deficiency
A less severe immunodeficiency results when there is a lack of __, another purine-degradative enzyme.
purine nucleoside phosphorylase (PNP)
- One of the many glycogen storage diseases __ also leads to excessive uric acid production.
- results from a deficiency in glucose 6-phosphatase activity.
- The increased availability of glucose-6-phosphate increases the rate of flux through the pentose phosphate pathway, yielding an elevation in the level of ribose-5-phosphate and consequently PRPP
- The increases in PRPP then result in excess purine biosynthesis.
von Gierke disease
3 different enzyme defects can lead to gout:
- PRPP synthetas elevated
- HGPRT deficiency
- glucose-6-phosphatase deficiency
APRT lacking
Renal lithiasis
PNP lacking
Immunodeficiency
Xanthine oxidase absent
Xanthinuria
(Pyrimidine Nucleotide Biosynthesis)
The first completed base is derived from __
1 mole of glutamine, one mole of ATP and one mole of CO2 (which form carbamoyl phosphate) and one mole of aspartate.
The carbamoyl phosphate used for pyrimidine nucleotide synthesis is derived from __, within the cytosol
glutamine and bicarbonate
Carbamoyl phosphate is then condensed with aspartate in a reaction catalyzed by the rate limiting enzyme of pyrimidine nucleotide biosynthesis, __.
aspartate transcarbamoylase (ATCase)
UMP Synthesis Overview
- 2 ATPs needed: both used in first step
- One transfers phosphate, the other is hydrolyzed to ADP and Pi
- 2 condensation reactions: form carbamoyl aspartate and OMP
Pyrimidine ring is synthesized from __
Carbamoyl phosphate and Aspartate
Carbamoyl-P for pyrimidine synthesis:
a. Formed in cytosol
b. Formed by a cytosolic form of the carbamoyl-P-synthetase II
c. Uses Glutamine as N-donor
d. Pyrimidine are attached to PRPP after synthesis
(DIFFERENCES IN PURINE AND PYRIMIDINE BIOSYNTHESIS) 1
- The ring structure is assembled as a free base, not built upon PRPP.
* PRPP is added to the first fully formed pyrimidine base (orotic acid), forming orotate monophosphate (OMP), which is subsequently decarboxylated to UMP.
(DIFFERENCES IN PURINE AND PYRIMIDINE BIOSYNTHESIS) 2
- There is no branch in the pyrimidine synthesis pathway. UMP is phosphorylated twice to yield UTP (ATP is the phosphate donor).
* The first phosphorylation is catalyzed by uridylate kinase and the second by ubiquitous nucleoside diphosphate kinase.
(DIFFERENCES IN PURINE AND PYRIMIDINE BIOSYNTHESIS) 3
- UTP is aminated by the action of CTP synthase, generating CTP.
* The thymine nucleotides are in turn derived by de novo synthesis from dUMP or by salvage pathways from deoxyuridine or deoxythymidine.
- is a multifunctional enzyme that contains redox-active thiol groups for the transfer of electrons during the reduction reactions.
Ribonucleotide reductase (RR)
- is reduced in turn, by either thioredoxin or glutaredoxin.
- The ultimate source of the electrons is NADPH.
- The electrons are shuttled through a complex series of steps involving enzymes that regenerate the reduced forms of thioredoxin or glutaredoxin.
Ribonucleotide reductase (RR)
ATP ACTIVATES REDUCTION OF
- CDP
- UDP
- induces GDP reduction
- inhibits reduction of CDP. UDP
dTTP
- inhibits reduction of all nucleotides
dATP
- stimulates ADP reduction
- inhibits CDP,UDP,GDP reduction
dGTP
(Synthesis of the Thymine Nucleotides)
The de novo pathway to __ first requires the use of dUMP from the metabolism of either UDP or CDP.
dTTP synthesis
(Synthesis of the Thymine Nucleotides)
The dUMP is converted to dTMP by the action of __.
thymidylate synthase
(Synthesis of dTMP from dUMP)
The unique property of the action of __ is that the THF is converted to dihydrofolate (DHF), the only such reaction yielding DHF from THF.
thymidylate synthase
(Synthesis of dTMP from dUMP)
In order for the thymidylate synthase reaction to continue, THF must be regenerated from DHF. This is accomplished through the action of __.
dihydrofolate reductase (DHFR)
(Synthesis of dTMP from dUMP)
THF is then converted to N5,N10-THF via the action of __.
serine hydroxymethyl transferase
__, unlike mammals, cannot use exogenous folate but must synthesize it from PABA. This pathway is thus essential for production of purines and nucleic acid synthesis in bacteria
Sulfonamide-susceptible organisms
__ is also useful as an antibacterial; it does not affect mammalian cells because it is about 50,000 times less efficient in inhibition of mammalian dihydrofolate reductase
Trimethoprim
The activity of __ (one of the various deoxyribonucleotide kinases) is unique in that it fluctuates with the cell cycle, rising to peak activity during the phase of DNA synthesis; it is inhibited by dTTP.
thymidine kinase
The regulation of pyrimidine synthesis occurs mainly at the first step which is catalyzed by __.
aspartate transcarbamoylase, ATCase
__ is inhibited by CTP, UDP, UTP, and dUTP; it is activated by ATP
ATCase
The role of glycine in ATCase regulation is to act as a competitive inhibitor of the __ binding site.
glutamine
Catabolism of the __ leads ultimately to β-alanine (when CMP and UMP are degraded) or β-aminoisobutyrate (when dTMP is degraded) and NH3 and CO2.
pyrimidine nucleotides
These deficiencies result in __ that causes retarded growth, and severe anemia caused by hypochromic erythrocytes and megaloblastic bone marrow.
- Leukopenia is also common in __
orotic aciduria
Orotic aciduria can be treated with __, which leads to increased UMP production via the action of nucleoside kinases.
uridine and/or cytidine
__ can also cause orotic aciduria because it can act as an alternate substrate and compete with orotic acid for degradation
Allopurinol
- Storage, transmission, and expression of genetic information
Nuclei Acids
- Lack nucleus
- Single chromosome
- Plasmids (nonchromosomal DNA)
Prokaryotes
- Nucleus
- Mitochodrion
- chloroplasts
Eukaryotes
The DNA Structure
- Deoxyribonucleoside monophosphate polymer
- 3’ → 5’ covalent phosphodiester bond
- Cleaved chemically (ONLY RNA cleaved by alkali)
- Enzymatically: deoxyribonucleases (DNAse) and ribonucleases (RNAse)
- Occur as double stranded (exception ssDNA viruses)
The DNA Structure (Prokaryotes vs Eukaryotes)
Prokaryotes: associated with nucleoid
Eukaryotes: nucleoproteins
- 2 chains coiled around the axis of symmetry
- Antiparallel chains/strands
- Deoxyribose-phosphate backbone: hydroPHILIC
- Base pairs: hydroPHOBIC
- “Twisted ladder”
- Proposed structure: 1953 by Watson and Crick
DNA
provide spatial access to DNA-binding proteins
Minor (narrow) and major (wide) grooves
__ intercalates into the minor groove
Dactinomycin (actinomycinD)
- In a dsDNA, amount of A is equal to T, amount of G is equal to C, amount of purines A and G = pyrimidines T and C
Chargaff Rule
Base Pairs are Complementary (1)
- The base of one strand is paired to the other
- Base pairs are perpendicular (900 ) to axis of symmetry
- A to a T (U), G to a C
- A to T (2 hydrogen bonds)
- G to C (3 hydrogen bonds)
- Strand separation: pH ionization and heat
Base Pairs are Complementary (2)
- NOTE: Phosphodiester bonds not broken down by pH and heat
- Denaturation: loss of helical DNA
- Measured at 260 nm absorbance
- ssDNA has higher relative absorbance
- Tm : melting temperature where there is loss of half of the DNA helical structure