PHRD5025 Lecture 13 - Nucleic Acid Metabolism & DNA Replication
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What type of bond links nucleotides through sugar groups?
The 5’ end terminates in a ______group and the 3’ end terminates in a _______group.
Chargaff’s rules (4)
- •The base composition of DNA generally
- varies between species.
- •DNA isolated from different tissues of the same organism have the same base composition.
- •Base composition of DNA in a given species does not change with age, nutrition or environment.
- •In all DNAs, regardless of species, the # of A=T and G=C (or # purines = # pyrimidines, A+G = T+C)
classic characteristics of DNA structure from the Watson-Crick model (5)
- - right handed double helix
- - has major/minor grooves
- - hydrophilic backbone
- - phosphate backbone is on outside of
- - hydrophobic bases are inside the helix
How RNA is different from DNA (6)
- Thymidine (T) is replaced by Uridine (U)
- Pentose sugar is ribose
- complex tertiary structures
- Shorter half-life
- Shorter (in terms of length) than DNA
limiting factor in cell division
what Glutamine-PRPP amidotransferase is inhibited by (3)
AMP, GMP, IMP
During negative feedback regulation of purine
biosynthesis, the ___________ enzyme in the pathway is usually rate-limiting and the ___________.
first; most regulated
NMPs are converted to NDPs by ____ nucleoside _____ kinases.
NDPs are converted to NTPs by _____ nucleoside _____ kinases.
The cancer chemotherapeutic Gemcitabine is an irreversible inhibitor of _____. This enzyme helps to synthesize deoxyribonucleotides from ribonucleoside diphosphates.
Chemotherapy drug used to inhibit Thymidylate Synthase?
Chemotherapy drugs used to competitively inhibit Dihydrofolate Reductase?
Methotrexate or Aminopterin
(binds w/ 100X higher affinity than dihydrofolate)
Purines are degraded by Xanthine Oxidase into
Disease in which B and T lymphocytes do not fully develop.
Severe Combined Immunodeficiency Disease (SCID)
In Lesch-Nyhan Syndrome, what does the lack of HGPT ultimately result in?
Gout-like tissue damage (due to increased uric acid production)
Which DNA Polymerase has 5’ > 3’ exonuclease
DNA Polymerase I
3 stages of DNA replication
Requires primer to start, helicase unwinds DNA,Topoisomerase II relieves helical tension, stage can be regulated.
DNA Polymerases duplicate the lagging and leading strands.
Termination sequence encountered and stops
replication, Topoisomerase IV unlinks the two intertwined strands.
only stage of DNA replication that is regulated
_____________ relieves helical stress caused by unwinding of dsDNA during replication.
topoisomerase II (DNA gyrase)
Compared to prokaryotes, eukaryotes have DNA molecules which are (smaller / larger) and are (circular / not circular)
larger; not circular
DNA viruses such as Parvovirus, herpes virus pox viruses and HPV undergo _____ replication.
Retroviruses involve the +RNA virus being reverse transcribed by _____ specifically known as RNA-dependent DNA polymerase, (RDDP). This produces a RNA/DNA hybrid intermediate.
viral reverse transcription (RT)
_____ RNase activity removes the RNA strand while synthesizing a new DNA strand to produce _____.
RT; dsDNA intermediate
What must happen before “prodrugs” can become activated?
they must first be phosphorylated
3 components of a nucleotide
- nitrogenous base
- pentose (ribose or deoxyribose)
nucleotide without a phosphate
connects purine/pyrimidine to pentose
effect of cAMP as a secondary messenger
- "fight or flight"
- caffeine effects (inhibits phosphodiesterase)
effect of cGMP as a secondary messenger
- (Viagra inhibits cGMP PDE)
part of DNA that is constant
alternative pentose & phosphate backbone
part of DNA that is variable
what the 3' end of DNA terminates in
what the 5' end of DNA terminates in
orientation of 2 strands of DNA
type of bonding between base pairs
type of RNA that serves as an intermediate in gene expression
type of RNA that serves as adapters in protein synthesis
type of RNA that is an integral part of the structure of ribosomes that are involved in protein synthesis
RNAs that have catalytic activity
precursors for de novo nucleotide synthesis (4)
- 1) amino acids
- 2) ribose-5-phosphate
- 3) CO24) NH3
when does nucleotide synthesis occur?
during DNA replication
nucleic acid purines
nucleic acid pyrimidines
cytosine, thymine, uracil
committed step in de novo purine biosynthesis
PRPP -> 5-phospho-
-D-ribosylamine (by glutamine-PRPP amidotransferase)
primary regulatory enzyme in de novo pyrimidine synthesis
- aspartate transcarbamoylase (ATCase)
- **1st step
inhibits de novo pyrimidine synthesis
energy requirement for purine synthesis
energy requirement for pyrimidine synthesis
how CTP is formed
amination of UTP
2'-2' difluorodeoxycytidine (dFdC)
- cancer chemotherapeutic
- nucleoside analog prodrug
- irreversible inhibitor of ribonucleotide reductase (RNR)
- suicide inhibitor
how dUMP is converted to dTMP
methylation by thymidylate synthase
result of pyrimidine degradation
ammonia & succinyl-CoA (->CAC)
result of purine degradation
uric acid (by xanthine oxidase)
xanthine oxidase inhibitor
cause of Lesch-Nyhan Syndrome
defect in purine salvage pathway leading to deficiency in HGPT
when does mitochondrial DNA replicate?
during cell division
principle prokaryotic replication enzyme
DNA Pol III
cleanup and repair enzyme in prokaryotes
DNA Pol I
how leading strand begins during elongation (in prokaryotes)
DNA primase adds RNA primer
prokaryotic enzyme that separates catenated (interlinked circles) DNA
drug with selectivity for prokaryotic topoisomerase II and IV
enzyme that links DNA fragments
in eukaryotes, terminate replication and prevent premature shortening of chromosome ends
eukaryotic polymerase that synthesizes Okazako fragments
eukaryotic polymerase involved in DNA repair
viruses with contain mRNA and can be immediately translated into proteins
postive-strand RNA viruses
viruses that must first be converted by RDRP contained within the virion
negative strand RNA viruses
viruses that utilize classical semi-conservative replication
viruses that use RNA-dependent DNA polymerase (RDDP) to produce an RNA/DNA hybrid intermediate
MOA of AZT against HIV
inhibits reverse transcriptase (RDDP)
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