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Biochemistry > Nucleotides > Flashcards

Nucleotides Flashcards

0
Q

Metabolism of Xenobiotics: Phase 1 Reaction

A

Hydroxylation reactions

Enzyme: monooxygenases of cytochrome P450s

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1
Q

Medical compounds that are foreign to the body

A

Xenobiotics

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2
Q

Metabolism of Xenobiotics: Phase 2 Reaction

A

Conjugation reactions

Enzymes: Glucoronosyltransferases, sulfotransferases, glutathione S-transferases

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3
Q

The monomer units or building blocks of nucleic acids

A

Nucleotides

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4
Q

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

A

Purines and Pyrimidines

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5
Q

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

A

Nucleoside

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6
Q

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

A

Nucleotides

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7
Q

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

A

Polynucleotides

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8
Q

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

A

Purine Synthesis

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9
Q

Purine Synthesis: Sources of atoms

A 
Aspartic acid
Glycine 
Glutamine
Carbon dioxide
N10-formyltetrahydrofolate and N5, N10-methenyltetrahydrofolate
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10
Q

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

A

Pyrimidine Synthesis

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11
Q

Pyrimidine Synthesis: Sources of atoms

A

Glutamine
Aspartic acid
Carbon dioxide

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12
Q

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

A

Glycine

N10-formyltetrahydrofolate and N5, N10-methenyltetrahydrofolate

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13
Q

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

A

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

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14
Q

This is a committed step in purine nucleotide biosynthesis

Enzyme: glutamyl PRPP amidotransferase

A

Synthesis of 5’-phosphoribosylamine

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15
Q

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

A

Synthesis of inosine monophosphate

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16
Q

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

A

Conversion of IMP to AMP and GMP

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17
Q

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

A

Salvage Pathways for Purines

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18
Q

Salvage Pathways for Purines: Irreversible Enzymes

A 
Adenine phosphoribosyltransferase (APRT)
Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
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19
Q

Steps in De Novo Pyrimidine Synthesis: Regulated and Rate limiting step
Enzyme: Carbamoyl phosphate synthetase II
Inhibited by UTP
Activated by ATP and PRPP

A

Synthesis of Carbamoyl phosphate

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20
Q

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

A

Synthesis of Orotic Acid

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21
Q

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

A

Formation of Pyrimidine nucleotide

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22
Q

Steps in De Novo Pyrimidine Synthesis: Enzyme: CTP synthetase

A

Synthesis of UTP and CTP

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23
Q

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

A

Synthesis of dTMP from dUMP

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24
Q

Few pyrimidine bases are salvaged in human cells

A

Salvage Pathway for Pyrimidines

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25
Q

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

A

Conversion of nucleoside monophosphate to nucleoside diphosphates and triphosphates

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26
Q

Enzyme: Ribonucleotide reductase;

It is multisubunit enzyme that is specific for the reduction of necleoside diphosphates to their deoxy forms

A

Synthesis of Deoxyribonucleosides

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27
Q

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

A

Purine Degradation

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28
Q

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

A

Pyrimidine Degradation

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29
Q

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

A

PABA analogs

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30
Q

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

A

Folic Acid analogs

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31
Q

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

A

Gouty Arthritis

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32
Q

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

A

Lesch-Nyhan Syndrome

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33
Q

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

A

Von Gierke’s Disease

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34
Q

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

A

Adenosine deaminase deficiency

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35
Q

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

A

5-Fluorouracil

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36
Q

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

A

Orotic Aciduria

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37
Q

Deoxyribonucleic acid; A polymer composed of nucleotide building blocks

A

DNA

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38
Q

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

A

3’-5’ Phosphodieters bonds

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39
Q

Strands run in opposite directions

A

Antiparallel Strands

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40
Q

Held together by hydrogen bonds and hydrophobic interactions

A

Complementary base pairing

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41
Q

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

A

Chargaff’s Rules

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42
Q

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

A

Melting Temparature

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43
Q

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

A

B-DNA

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44
Q

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

A

A-DNA

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45
Q

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

A

Z-DNA

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46
Q

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

A

Histones

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47
Q

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

A

Chromatin

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48
Q

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

A

Heterochromatin

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49
Q

Transcriptionally active chromatin that stains less densely

A

Euchromatin

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50
Q

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

A

Polynucleosome

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51
Q

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

A

Step 1: DNA A protein

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52
Q

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

A

Step 2: Helicase

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53
Q

Prokaryotic DNA Synthesis: Maintain the separation of the parental strands

A

Step 3: Single-stranded DNA-binding proteins

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54
Q

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

A

Step 4: DNA topoisomerases

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55
Q

DNA Toposiomerase: Type I

A

Swivelase (cleaves one strand)

56
Q

DNA Toposiomerase: Type II

A

Gyrase (cleaves both strands; target of quinolone antibiotics)

57
Q

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

A

Step 5: Primase

58
Q

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

A

Step 6: DNA Polymerase III

59
Q

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

A

Step 7: DNA Polymerase I

60
Q

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

A

Step 8: Ligase

61
Q

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

A

Telomeres

62
Q

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

A

Reverse transcriptase

63
Q

Mismatched strand, escaped proofreading

A

DNA Damage

64
Q

Identification of the mismatched strand

A

DNA Repair

65
Q

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

A

Mismatch Repair

66
Q

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

A

Base Excision Repair

67
Q

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

A

Nucleoside Excision Repair

68
Q

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

A

Double-Strand Break Repair

69
Q

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

A

RNA

70
Q

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

A

Ribosomal RNA or rRNA

71
Q

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

A

Transfer RNA or tRNA

72
Q

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

A

Messenger RNA or mRNA

73
Q

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

A

Small nuclear RNA or snRNA

74
Q

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

A

RNA polymerase

75
Q

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

A

Sigma factor

76
Q

Required for termination of transcription of some genes

A

Rho factor

77
Q

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

A

Step 1: Initiation

78
Q

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

A

Step 2: Elongation

79
Q

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

A

Step 3: Termination

80
Q

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

A

Pribnow Box

81
Q

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

A

-35 Sequence

82
Q

Classes of RNA polymerase: For large rRNAs in the nucleolus

A

RNA Polymerase I

83
Q

Classes of RNA polymerase: For mRNAs

A

RNA Polymerase II

84
Q

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

A

RNA Polymerase III

85
Q

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

A

Promoter Sequences

86
Q

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

A

Enhancers

87
Q

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

A

Primary transcript

88
Q

Synthesized from long precursor molecules called preribosomal RNAs

A

rRNAs

89
Q

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

A

tRNAs

90
Q

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

A

Genetic Regulation

91
Q

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

A

Operon

92
Q

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

A

Lactose Operon

93
Q

Encodes a β-galactosidase

A

Z gene

94
Q

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

A

Y gene

95
Q

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

A

i gene

96
Q

Encodes a thiogalactoside transacetylase enzyme, whose function is unknown

A

A gene

97
Q

Proteins translated on Ribosomes associated with RER

A

Secreted proteins
Proteins inserted into the cell membrane
Lysosomal enzymes

98
Q

Proteins translated on free cytoplasmic ribosomes

A

Cytoplasmic proteins

Mitochondrial proteins

99
Q

Consists of three bases (triplet)

A

Codon

100
Q

Total number of codons

A

64 codons

101
Q

Total codons that code for amino acids

A

61 codons

102
Q

Stop codons

A

Nonsense codons (UAA, UGA, UAG)

103
Q

Start codon

A

Initiation codon (AUG)

104
Q

A specific codon always codes from the same amino acid

A

Specific Genetic Code

105
Q

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

A

Universal Genetic Code

106
Q

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

A

Redundant Genetic Code

107
Q

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

A

Commaless Genetic Code

108
Q

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

A

tRNA wobble

109
Q

Binds an incoming aminoacyl-tRNA

A

A site codon

110
Q

Occupied by peptidyl-tRNA

A

P site codon

111
Q

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

A

E site codon

112
Q

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

A

Charging

113
Q

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

A

Step 1: Initiation

114
Q

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

A

Step 2: Elongation

115
Q

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

A

Step 3: Termination

116
Q

Energy Requirements of Translation

A

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

117
Q

Post-translational Modification

A

1) Trimming excess amino acids
2) Phosphorylation
3) Glycosylation
4) Hydroxylation
5) Destruction by Ubiquitin

118
Q

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

A

Mutation

119
Q

Point Mutation: Purine-Pyrimidine to Purine-Pyrimidine

A

Transition

120
Q

Point mutation: Purine-Pyrimidine to Pyrimidine-Purine

A

Transversion

121
Q

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

A

Silent Mutation

122
Q

New codon specifies a different amino acid

A

Missense Mutation

123
Q

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

A

Nonsense Mutation

124
Q

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

A

Frame shift Mutation

125
Q

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

A

Large segment deletion Mutation

126
Q

A splice site is lost through mutation

A

Splice donor or acceptor Mutation

127
Q

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

A

Triple repeat expansion Mutation

128
Q

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

A

Sanger DNA Sequencing

129
Q

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

A

Polymerase Chain Reaction

130
Q

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

A

Southern Blot

131
Q

Similar technique but involves radioactive DNA probe binding to sample RNA

A

Northern Blot

132
Q

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

A

Western Blot

133
Q

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

A

Microarrays

134
Q

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

A

ELISA

135
Q

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

A

FISH

136
Q

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

A

Restriction Fragment Length Polymorphism

137
Q

The production of recombinant DNA molecule that is self-perpetuating

A

Cloning

138
Q

Treatment option for diseases caused by deficiency of a gene product

A

Gene Treatment

Biochemistry (7 decks)

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