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Flashcards in Nucleotides Deck (139):
1

Medical compounds that are foreign to the body

Xenobiotics

2

Metabolism of Xenobiotics: Phase 1 Reaction

Hydroxylation reactionsEnzyme: monooxygenases of cytochrome P450s

3

Metabolism of Xenobiotics: Phase 2 Reaction

Conjugation reactionsEnzymes: Glucoronosyltransferases, sulfotransferases, glutathione S-transferases

4

The monomer units or building blocks of nucleic acids

Nucleotides

5

Nitrogen-containing heterocycles, cyclic compounds whose rings contain both carbon and other elements

Purines and Pyrimidines

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Sugar + Purine or Pyrimidine; the link is a ring nitrogen

Nucleoside

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Nucleosides with a phosphoryl group esterified to a hydroxyl group of the sugar

Nucleotides

8

5'-phosphoryl group forms a phosphodiester bond with the 3'-OH of another nucleotide; Pgosphodiesterases catalyze the hydrolysis of phosphodiester bonds

Polynucleotides

9

Purine ring is constructed by adding carbons and nitrogens to a preformed ribose-5-phosphate

Purine Synthesis

10

Purine Synthesis: Sources of atoms

Aspartic acidGlycine GlutamineCarbon dioxideN10-formyltetrahydrofolate and N5, N10-methenyltetrahydrofolate

11

In contrast, the pyrimidine ring is synthesized before being attached to ribose 5-phosphate

Pyrimidine Synthesis

12

Pyrimidine Synthesis: Sources of atoms

GlutamineAspartic acidCarbon dioxide

13

What are the 2 compounds used in Purine Synthesis but not used in Pyrimidine Synthesis?

GlycineN10-formyltetrahydrofolate and N5, N10-methenyltetrahydrofolate

14

An activated pentose that participates in the synthesis of purines and pyrimidines, and in the salvage of purine bases

Synthesis of 5-phosphoribosyl-1-pyrophosphate (PRPP)Substrates: ATP and ribose 5-phosphateEnzyme: PRPP synthetase

15

This is a committed step in purine nucleotide biosynthesisEnzyme: glutamyl PRPP amidotransferase

Synthesis of 5'-phosphoribosylamine

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9 steps that lead to the synthesis of IMP; "Parent" purine nucleotide

Synthesis of inosine monophosphate

17

Requires a two-step energy-requiring pathway; AMP synthesis requires GTP, while GMP synthesis requires ATP

Conversion of IMP to AMP and GMP

18

Purines that result from the normal turnover of cellular nucleic acids or that are obtained from the diet and not degraded, can be reconverted into nucleoside triphosphates and used by the body

Salvage Pathways for Purines

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Salvage Pathways for Purines: Irreversible Enzymes

Adenine phosphoribosyltransferase (APRT)Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)

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Steps in De Novo Pyrimidine Synthesis: Regulated and Rate limiting stepEnzyme: Carbamoyl phosphate synthetase IIInhibited by UTPActivated by ATP and PRPP

Synthesis of Carbamoyl phosphate

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Steps in De Novo Pyrimidine Synthesis: Dihydroorotate reductase is located inside the mitochondria; All the rest are cystosolic

Synthesis of Orotic Acid

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Steps in De Novo Pyrimidine Synthesis: The "parent" pyrimidine nucleotide is Orotidine monophosphate (OMP)

Formation of Pyrimidine nucleotide

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Steps in De Novo Pyrimidine Synthesis: Enzyme: CTP synthetase

Synthesis of UTP and CTP

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Steps in De Novo Pyrimidine Synthesis: Enzyme: Thymidylate synthase; N5N10-methyltetrahydrofolate is the source of the methyl group

Synthesis of dTMP from dUMP

25

Few pyrimidine bases are salvaged in human cells

Salvage Pathway for Pyrimidines

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Nucleoside diphosphates are synthesized from the corresponding nucleoside monophosphates using base-specific nucleoside monophosphate kinases

Conversion of nucleoside monophosphate to nucleoside diphosphates and triphosphates

27

Enzyme: Ribonucleotide reductase; It is multisubunit enzyme that is specific for the reduction of necleoside diphosphates to their deoxy forms

Synthesis of Deoxyribonucleosides

28

Degradation of dietary nucleic acids occurs in the small intestines where a family of pancreatic enzymes hydrolyze the nucleotides to nucleosides and free bases

Purine Degradation

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The pyrimidine ring can be opened and degraded to highly soluble structures

Pyrimidine Degradation

30

Sulfonamides are structural analogs of PABA that competitively inhibit bacterial synthesis of folic acid

PABA analogs

31

Methotrexate and TMP inhibit the reduction of dihydrofolate to tetrahydrofolate, catalyzed by dihydrofolate reductase

Folic Acid analogs

32

Hyperuricemia with recurrent attacks of acute arthritis caused by deposition of uric acid crystals

Gouty Arthritis

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X-linked recessive deficiency in HGPRT that causes a rise in intracellular PRPP and hyperuricemia; triad of hyperuricemia, mental retardation, self-mutilation

Lesch-Nyhan Syndrome

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Purine overproduction and hyperuricemia occurs secondary to enhanced generation of PRPP precursor ribose 5-phosphate

Von Gierke's Disease

35

Leads to severe combined immunodeficiency (both T and B lymphocytes affected)

Adenosine deaminase deficiency

36

Metabolically converted to 5-FdUMP which becomes permanently bound to the inactivated thymidylate synthase

5-Fluorouracil

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Low activities of orotidine phosphate decarboxylase and orotate phosphoribosyltransferase result in: Abnormal growth, megaloblastic anemia, excretion of large amounts of orotate in urine

Orotic Aciduria

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Deoxyribonucleic acid; A polymer composed of nucleotide building blocks

DNA

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5'-OH group attached to 3'-OH group; strands have directionality; bonds are cleaved hydrolytically by chemicals or hydrolyzed enzymatically by exonucleases or endonucleases

3'-5' Phosphodieters bonds

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Strands run in opposite directions

Antiparallel Strands

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Held together by hydrogen bonds and hydrophobic interactions

Complementary base pairing

42

In any sample of dsDNA, the amount of adenine equals the amount of thymine, the amount of guanine equals the amount of cytosine

Chargaff's Rules

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Temperature at which one half of the helical structure is lost;Under appropriate conditions, denaturation (annealing) may occur

Melting Temparature

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Most common; Right-handed helix with 10 residues per 360 turn of the helix

B-DNA

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Moderately dehydrated B form, also right-handed with about 11 base pairs per turn

A-DNA

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Left-handed helix that contains about 12 base pairs per turn, naturally in regions of alternating purines and pyrimidines

Z-DNA

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Five classes of small, positively charged proteins that form ionic bonds with negatively charged DNA

Histones

48

Further packing of DNA due to hydrophobic interactions and in association with other non-histone proteins compacts it into _____

Chromatin

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Densely packed and transcriptionally inactive chromatin during interphase, observe by electron microscopy

Heterochromatin

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Transcriptionally active chromatin that stains less densely

Euchromatin

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Also called a nucleofilament; nucleosomes that are packed more tightly; Organized into loops that are anchored by a nuclear scaffold containing several proteins

Polynucleosome

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Prokaryotic DNA Synthesis: Group of proteins that recognize the origin of replication

Step 1: DNA A protein

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Prokaryotic DNA Synthesis: unwind the double helix ahead of the advancing replication fork

Step 2: Helicase

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Prokaryotic DNA Synthesis: Maintain the separation of the parental strands

Step 3: Single-stranded DNA-binding proteins

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Prokaryotic DNA Synthesis: Remove supercoils that interfere with the further unwinding of the double helix

Step 4: DNA topoisomerases

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DNA Toposiomerase: Type I

Swivelase (cleaves one strand)

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DNA Toposiomerase: Type II

Gyrase (cleaves both strands; target of quinolone antibiotics)

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Prokaryotic DNA Synthesis: Synthesize short stretches of RNA called primers, needed by DNA polymerase to begin DNA chain elongation

Step 5: Primase

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Prokaryotic DNA Synthesis: Catalyzes chain elongation, using 5'-deoxyribonucleoside triphosphates as substrates

Step 6: DNA Polymerase III

60

Prokaryotic DNA Synthesis: Removes RNA primers using its 5'-3' exonuclease activity and fills in the resulting gaps

Step 7: DNA Polymerase I

61

Prokaryotic DNA Synthesis: Seals the nicks between Okazaki fragments and catalyzes the final phospholipid ester linkage

Step 8: Ligase

62

Stretches of highly repetitive DNA found at the ends of linear chromosomes; As cells divide and age, these sequences are shortened, contributing to cell death

Telomeres

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Make a DNA copy of their RNA, integrate that copy into host cells; lack of proof reading explains high mutation rate

Reverse transcriptase

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Mismatched strand, escaped proofreading

DNA Damage

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Identification of the mismatched strand

DNA Repair

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DNA Repair: Copying errors (single base or two to five base unpaired loops); Methyl-directed strand cutting, exonuclease digestion, and replacement

Mismatch Repair

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DNA Repair: Spontaneous, chemical, or radiation damage to a single base; Base removal by N-glycosylase, abasic sugar removal, replacement

Base Excision Repair

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DNA Repair: Spontaneous, chemical, or radiation damage to a DNA segment; Removal of an approximately 30-nucleotide oligomer and replacement

Nucleoside Excision Repair

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DNA Repair: Ionizing radiation, chemotherapy, oxidative free radicals; Synapsis, unwinding, alignment, ligation

Double-Strand Break Repair

70

Polymers of nucleotides, but differ from DNA by containing: Ribose instead of deoxyribose, Uracil instead of thymine

RNA

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"Rampant" because it is the most common type of RNA; Associated with several proteins as a component of the ribosomes

Ribosomal RNA or rRNA

72

"Tiny" because it is the smallest RNA; Adaptor molecule that carries a specific amino acid to the site of protein synthesis

Transfer RNA or tRNA

73

"Massive"; Carries genetic information from the nuclear DNA to the cytosol, where it is used as the template for protein synthesis

Messenger RNA or mRNA

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A subset of RNAs significantly involved in mRNA processing and gene regulation

Small nuclear RNA or snRNA

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4-subunit enzyme that synthesizes RNA; Possesses 5'-3' polymerase activity

RNA polymerase

76

Recognizes the nucleotide sequence (promoter region) at the beginning of the length of the DNA to be transcribed

Sigma factor

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Required for termination of transcription of some genes

Rho factor

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Prokaryotic DNA Transcription: RNA polymerase holoenzyme binds to the promoter region

Step 1: Initiation

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Prokaryotic DNA Transcription: RNA polymerase copying one strand of the DNA double helix, pairing Cs with Gs and As with Us

Step 2: Elongation

80

Prokaryotic DNA Transcription: Maybe accomplished by RNA polymerase alone or may require ρ factor

Step 3: Termination

81

Stretch of 6 nucleotides (5'-TATAAT-3') centered about 8 to 10 nucleotides to the left of the transcription start site

Pribnow Box

82

Second consensus nucleotide sequence (5'-TTGACA-3') about 35 bases to the left of the transcription start site

-35 Sequence

83

Classes of RNA polymerase: For large rRNAs in the nucleolus

RNA Polymerase I

84

Classes of RNA polymerase: For mRNAs

RNA Polymerase II

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Classes of RNA polymerase: For tRNAs and some other small rRNAs in the nucleoplasm

RNA Polymerase III

86

TATA or Hogness box, CAAT box and GC box; Serve as binding sites for proteins called general transcription factors

Promoter Sequences

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DNA sequences that increase the rate of initiation of transcription by binding to specific transcription factors called activators

Enhancers

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Linear copy of the transcriptional unit, the segment of DNA between specific initiation and termination sequences

Primary transcript

89

Synthesized from long precursor molecules called preribosomal RNAs

rRNAs

90

Also made from longer precursor molecules; these must have an intervening sequence removed and the 5' and 3' ends of the molecule are trimmed by ribonuclease

tRNAs

91

Regulation of gene expression in prokaryotes usually involves either initiation or termination of transcription

Genetic Regulation

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A set of structural genes coding for a group of proteins required for a particular metabolic function along with the regulatory region that controls the expression of the structural genes

Operon

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Portion of the bacterial chromosome that controls the synthesis of the enzymes involved in lactose metabolism

Lactose Operon

94

Encodes a β-galactosidase

Z gene

95

Encodes a galactosidase permease, the transport protein required for the entry of lactose into the cell

Y gene

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Encodes a lac repressor protein that is constitutively expressed and located at a distant site in the DNA

i gene

97

Encodes a thiogalactoside transacetylase enzyme, whose function is unknown

A gene

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Proteins translated on Ribosomes associated with RER

Secreted proteinsProteins inserted into the cell membraneLysosomal enzymes

99

Proteins translated on free cytoplasmic ribosomes

Cytoplasmic proteinsMitochondrial proteins

100

Consists of three bases (triplet)

Codon

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Total number of codons

64 codons

102

Total codons that code for amino acids

61 codons

103

Stop codons

Nonsense codons (UAA, UGA, UAG)

104

Start codon

Initiation codon (AUG)

105

A specific codon always codes from the same amino acid

Specific Genetic Code

106

It has been conserved from very early stages of evolution with only slight differences in the manner in which the code translated

Universal Genetic Code

107

A given amino acid may have more than one triplet coding for it

Redundant Genetic Code

108

Code is read from a fixed starting point as a continuous sequence of bases, taken three at a time

Commaless Genetic Code

109

Accurate base pairing is required only in the first 2 nucleotide positions of an mRNA codon, so codon differing in the 3rd wobble position may code for the same tRNA/amino acid

tRNA wobble

110

Binds an incoming aminoacyl-tRNA

A site codon

111

Occupied by peptidyl-tRNA

P site codon

112

Occupied by the empty tRNA as it is about to exit the ribosome

E site codon

113

Amino-acetyl-tRNA synthetase (1perAA) uses an ATP scrutinizes an amino acid before and after it binds to tRNA

Charging

114

DNA Translation: Activated by GTP hydrolysis, initiation factors (eIFs) help assemble the 40s ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal unit assemble with the complex

Step 1: Initiation

115

DNA Translation: Aminoacyl-tRNA binds to A site; Elongation factors direct the binding of the appropriate tRNA to the codon in the empty A site

Step 2: Elongation

116

DNA Translation: Releasing factors are proteins that hydrolyze the peptidyl-tRNA bond when a stop codon occupies the A site

Step 3: Termination

117

Energy Requirements of Translation

1) tRNA aminoacylation (ATP➡️AMP)2) Loading tRNA onto ribosome (GTP➡️GDP)3) Translocation (GTP➡️GDP)

118

Post-translational Modification

1) Trimming excess amino acids2) Phosphorylation3) Glycosylation4) Hydroxylation5) Destruction by Ubiquitin

119

Any permanent heritable change in the DNA base sequence of an organism; Has the potential to change the base sequence of mRNA and the amino acid sequence of proteins

Mutation

120

Point Mutation: Purine-Pyrimidine to Purine-Pyrimidine

Transition

121

Point mutation: Purine-Pyrimidine to Pyrimidine-Purine

Transversion

122

New codon specifies same amino acid, often base change in 3rd position of codon

Silent Mutation

123

New codon specifies a different amino acid

Missense Mutation

124

New codon is a stop codon; Shorter than normal protein, usually nonfunctional

Nonsense Mutation

125

Deletion or addition of a base; Protein usually nonfunctional, often shorter than normal

Frame shift Mutation

126

Unequal crossover in meiosis; Loss of function, protein shorter than normal or entirely missing

Large segment deletion Mutation

127

A splice site is lost through mutation

Splice donor or acceptor Mutation

128

Expansions in coding regions cause protein product to be longer than normal and unstable

Triple repeat expansion Mutation

129

Used to deduce original sequence of DNA; Dideoxynucleotides halt DNA polymerization at each base, generating sequences of various lengths that encompass the entire sequence

Sanger DNA Sequencing

130

Molecular biology lab procedure that is used to synthesize many copies of a desired fragment of DNA

Polymerase Chain Reaction

131

A DNA sample is electrophoresed on a gel and then transferred to a filter

Southern Blot

132

Similar technique but involves radioactive DNA probe binding to sample RNA

Northern Blot

133

Sample protein is separated via gel electrophoresis and transferred to a filter

Western Blot

134

Thousands of nucleic acid sequences are arranged in grids on glass or silicon

Microarrays

135

Enzyme-linked immunosorbent assay; A rapid immunologic technique testing for antigen-antibody reactivity

ELISA

136

Flourescence in situ hybridization; Flourescence probe binds to specific gene site of interest

FISH

137

Inherited difference in the pattern of restriction; Important in understanding various single-gene and multigenic diseases

Restriction Fragment Length Polymorphism

138

The production of recombinant DNA molecule that is self-perpetuating

Cloning

139

Treatment option for diseases caused by deficiency of a gene product

Gene Treatment