Nucleotides Flashcards
Define nucleoside.
composed of ribose and a heterocyclic base
Define nucleotide.
composed of ribose, heterocyclic base, and 1 or more phosphates
Define deoxynucleotide.
nucleotide lacking a 2’-hydroxyl group on ribose ring, replaced by a hydrogen
How many rings do purines have?
2 fused heterocyclic rings
How many rings do pyrimidines have?
one heterocyclic ring
True or false genes are DNA.
True
What does DNA stand for?
deoxyribonucleic acid
Where does DNA come from?
nucleotides
What is the process going from DNA to RNA?
transcription
What is the process going from RNA to DNA, and what utilizes this process?
reverse transcription; viruses
What is the process going from RNA to proteins?
translation
What are the repeating units of DNA?
nucleotides, sugar, bases
What is the difference between RNA and DNA?
OH group on sugars, T in DNA, U in RNA
What is the molecule of heredity in all prokaryotic and eukaryotic organisms?
DNA
True or false, viruses can contain RNA or DNA.
True
All cellular DNA consists of ____ very long ____ polynucleotide strands _____ around a common ____.
2; helical; coiled; axis
What is the DNA backbone and how is it oriented?
sugar-phosphate; to the outside
How are the bases oriented?
to the inside
What forces stabilize the bases?
stacking
How are the bases connected?
Hydrogen bonding
How do the 2 strands run compared to each other?
in opposite directions
True or false, the 2 strands of the double helix of DNA compliment each other.
True
Adenine is paired with ____ and they form ___ H-bonds.
thymine; 2
Cytosine is paired with ____ and they form ___ H-bonds.
guanine; 3
List the forms of DNA and their handedness.
Z (L), A (R), B (R)
What are the effects of super coiling of DNA?
compacts the DNA
Makes DNA more accessible for interactions with other biomolecules
_____ give rise to ____ _____ _____ regions in complicated ____ structures of single stranded nucleic acids (___).
hairpin turns; extensive double helical; 3-D; RNA
Describe semi-conservative replication.
- strands of helix separate
- new strand complimentary to each original strand is synthesized
- 2 new helices are generated with 1 original and 1 new strand each
True or false the sequence of bases in one strand determines the sequence of bases in the other strand of DNA.
True
Define melting.
heating a solution of double helical DNA to separate the strands
Define cooling.
lowering the temperature of the melted/heated strands so they can reanneal and reform the double helix
True or false, in the cell special proteins temporarily separate the strands in replication.
True
True or false pyrimidine is first assembled and then linked to they ribose phosphate to form a pyrimidine nucleotide.
True
What is the donor of the ribose phosphate moiety?
5-phosphoribosyl-1-pyrophosphate
What is the salvage pathway of pyrimidine synthesis?
thymine to thymidine to TMP
From what precursors is the purine ring assembled?
glutamine, glycine, aspartate, , N10-THF, CO2
True or false the purine ring is synthesized directly on the ribose phosphate.
True
What is the committed step in purine ring synthesis?
formation of 5-phophoribosylamine from PRPP & glutamine
What is the salvage pathway of purine synthesis?
preformed bases reacts directly with PRPP
What is the basic DNA structure?
sugar-phosphate backbone with bases attached
True or false, a DNA strand is read 5’ to 3’.
true
How is a DNA strand synthesized?
each new group is added to the phosphate of the 3’C on the chain (5’ to 3’)
What are the two types of grooves of the double helix of DNA?
major, minor
How condensed are mitotic DNA compared to interphase DNA?
500 times
How many nucleotides are in our geonome?
300 billion
What distance could our stretched out genome cover?
to the moon and back
Explain what is the dynamic situation of our genome.
must allow rapid localized access to DNA for gene expression
What DNA binding proteins are involved in forming chromosomes?
histones and non-histone chromosomal proteins
What is chromatin?
protein + nuclear DNA
Nucleotides are the ____ ____ of nucleosides.
phosphate esters
What do nucleotides contain?
base, sugar, phosphate
base sugar = ?
nucleoside
base + sugar + phosphate = ?
nucleotide
nucleoside + phosphate = ?
nucleotide
nucleotide - phosphate = ?
nucleoside
connected nucleotides
polynucleotides = nucleic acids = DNA or RNA
List the purines.
Adenine & guannin
List the pyrimidines.
cytosine, uracil, & thymine
What is the structure of Adenosine triphosphate (ATP)?
Adenine + ribose + 3 phosphates
List the hydrolysis reactions.
ATP to ADP + Pi
ATP to AMP + PPi
PPi to Pi + Pi
Of the hydrolysis reactions which yields the highest energy?
ATP to AMP + PPi
-10.9 kcal/mol
Of the hydrolysis reactions which yields the second highest energy?
ATP to ADP + Pi
-7.3 kcal/mol
Of the hydrolysis reactions which yields the lowest energy?
PPi to Pi + Pi
-4.0 kcal/mol
What is the universal currency of free energy in biological systems?
ATP
What are some specific roles of nucleotides?
Coenzyme A, NAD+, FAD
How many angstroms is a turn in a DNA helix?
34
How many base pairs per turn?
~10
What is the most common form of DNA?
B DNA
What is the limiting factor in DNA synthesis?
cytosine
What do ribonucleases do for RNA?
breaks up long chain RNA into short RNA segments
What do deoxyribonucleases do for RNA?
breaks up long chain DNA into short DNA segments
What do phosphodiesterase do?
Cuts the phosphodiester bond between nucleotides
creates NMPs and dNMPs
What do nucleotidase do?
cleaves phosphate off nucleotides = nucleosides
What do nucleosidase do?
cleaves the base off nucleosides = purines and pyrimidines
Describe xanthine oxidase
Catalyzes the oxidation of hypoxanthine to xanthine and xanthine to uric acid
has 2 flavin adenine dinucleotides (FADs), 2 Mo atoms, and 8 Fe atoms per molecule of enzyme
Drug target for the treatment of gout
What is the latin word for gout?
gutta (drop of discharge)
What is gout historically regarded as and why?
disease of the wealthy (excess wine, food, and sex)
What is the most commonly affected area for gout?
the big toe (metatarsal pharangeal joint)
Define gout.
Characterized by intensely painful and inflamed joints
Characterized by high levels of uric acid levels in blood resulting from over production of uric acid (primary hyperuricemia)
or under secretion of uric acid (secondary hyperuricemia)
Sodium urate crystals precipitate in synovial fluid of joints
deposits are very painful
in the kidneys can cause kidney damage
phagocytic cells engulf crystals and release factors that initiate acute inflammatory response
What type of diet may trigger episodes of gout?
rich in purines (beans, lentils, spinach) with meat, seafood, and alcohol
What is the treatment for gout?
colchicine (decreases movement of granulocutes to the affected area)
allopurinol (inhibits xanthine oxidase to form the more soluble hypoxanthine)
What are the normal serum uric acid levels for adult males and females?
males = 4-8.6 mg/dL
females = 3.0-5.9 mg/dL
Serum urate levels >9mg/dL increase ____ of ___.
risk, gout
What are normal urinary urate levels?
True or false, urinary urate levels vary day to day.
True
Dietary pyrimidines are readily converted to what in pyrimidine catabolism.
metabolized ketogenic or glucogenic water soluble compounds such as malonyl CoA, methyl malonyl CoA and succinyl CoA
What are the sources for ring atoms in purine synthesis?
CO2, Gln, Gly, Asp, N10-formylTHF
What are the sources for ring atoms in pyrimidine synthesis?
HCO32-, Gln, Asp, N5N10-methyleneTHF
True or false, inosinate monophosphate is not commonly found in DNA or RNA.
True
What is inosinate monophosphate converted into?
guanosin monophosphate (GMP) or adenosine monophosphate (AMP)
What are the 2 salvage enzymes for purine biosynthesis?
hypoxanthine guanine phosphoribosyl transferase
adenine phosphoribosyl transferase
What is a central constituent of nucleotide metabolism?
PRPP = phosphoribosyl pyrophosphate
What is PRPP synthesized from?
ribose phosphate and ATP
What does tetrahydrofolate do in purine synthesis?
closes the ring, makes IMP
Describe the role of methotrexate.
Antineoplastic agent
inhibits dihydrofolate reductase which disrupts DNA replication in rapidly dividing cells (cancer)
efficacy depends on selective drug uptake by cancer cells versus normal cells
How much more tightly does methotrexate bind dihydrofolate reductase?
100 fold
What controls the synthesis of purine nucleotides?
feedback regulation at several sites to balance the production
List the checkpoints of purine synthesis.
PRPP and PR-amine
AMP and GMP from IMP
AMP synthesis is stimulated by what?
GTP
GMP synthesis is stimulated by what?
ATP
True or false, nucleoside phosphates can be interconverted.
true
What is the committed step in pyrimidine synthesis?
formation of n-carbamoyl aspartate
How is orotic aciduria treated?
with oral uridine
What is the human hereditary disorder involving the synthesis of the pyrimidine nucleotides?
orotic aciduria
How are deoxyribonucleotides formed?
from the ribonucleotides by the reduction of ribonucleoside diphosphates
What is the hydrogen donor for the reduction of ribonucleoside diphosphates?
reduced thioredoxin or glutaredoxin
Where are the 2 major control points of pyrimidine biosynthesis?
- Carbamoyl phosphate synthetase is inhibited by UMP, purines, and stimulated PRPP
- Aspartate transcarbamoylase is feedback inhibited by CTP
What type of regulation are the control points of pyrimidine biosynthesis?
allosteric regulation
What is the limiting factor for DNA synthesis?
dTTP
