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Flashcards in Biochem - Molecular Deck (178)
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1
Q

How many subunits make up a nucleosome core?

A

Eight; two of each of the four histone types

2
Q

What is the charge on DNA?

A

Negative

3
Q

The molecule shown here is synthesized from ____ and ____.

A

Carbamoyl phosphate and aspartate

4
Q

In this diagram, what enzyme is sealing the Okazaki fragment together with the lagging strand?

A

DNA ligase

5
Q

In this picture, what is the function of single-stranded binding proteins?

A

They prevent strands from reannealing

6
Q

How many times does the DNA loop around each octamer (nucleosome core)?

A

Two

7
Q

What histone type is found between the nucleosome cores (the histone octamers)?

A

H1

8
Q

What is the charge on histone octamer?

A

Positive; giving the histones affinity for negatively charged DNA

9
Q

Predominance of which two amino acids gives histones a positive charge?

A

Lysine and arginine

10
Q

What are the names of the four subunits of a nucleosome core?

A

Histones H2A, H2B, H3, and H4

11
Q

What is DNA called when it is condensed and transcriptionally inactive?

A

Heterochromatin

12
Q

Which histone is not part of the nucleosome core?

A

H1

13
Q

What is transcriptionally active DNA called?

A

Euchromatin; it is uncondensed and accessible to replication enzymes

14
Q

How many hydrogen bonds are there between adenine and thymine?

A

Two

15
Q

What are the two purines?

A

Adenine (A) and guanine (G) (remember: PURe As Gold: PURines)

16
Q

Which is stronger: a guanine-cytosine bond or an adenine-thymine bond?

A

A guanine-cytosine bond, because it has three hydrogen bonds; an adenine-thymine bond only has two

17
Q

What are the three pyrimidines?

A

Cytosine (C), thymine (T), and uracil (U) (remember: CUT the PY [pie]: PYrimidines)

18
Q

What physical property do nucleic acids with increasing proportions of guanine-cytosine bonds display?

A

Increasing melting temperatures due to the tighter binding of the strands

19
Q

How many rings do pyrimidine molecules have?

A

One

20
Q

How many rings do purine molecules have?

A

Two

21
Q

What molecule does deamination of cytosine yield?

A

Uracil

22
Q

Nucleoside = _____ + ribose

A

Base

23
Q

In what type of nucleic acid is uracil found?

A

RNA

24
Q

What type of bond links nucleotides?

A

3;-5; phosphodiester bond

25
Q

In what type of nucleic acid is thymine found?

A

DNA

26
Q

What nucleotide has a methyl group?

A

Thymine

27
Q

Nucleotide = _____ + phosphate

A

Nucleoside

28
Q

What are the two precursors to creating the pyrimidine ring?

A

Carbamoyl phosphate and aspartate

29
Q

In de novo nucleotide synthesis, _____ (purines/pyrimidines) are made from IMP precursors, while _____ (purines/pyrimidines) are made from orotate precursors.

A

Purines; pyrimidines

30
Q

What quality of trimethoprim makes it a good antibiotic?

A

Its target is bacterial dihydrofolate reductase, inhibiting DNA synthesis

31
Q

Pyrimidines are made from orotate precursor, with _____ added later.

A

Phosphoribosyl pyrophosphate

32
Q

What enzyme converts ribonucleotides to deoxyribonucleotides?

A

Ribonucleotide reductase

33
Q

Name four drugs that interfere with pyrimidine synthesis.

A

Hydroxyurea, 5-fluorouracil, methotrexate, trimethoprim

34
Q

Deoxyuridine monophosphate (dUMP) is converted to deoxythymidine monophosphate (dTMP) by which enzyme?

A

Thymidylate synthase

35
Q

What is the cofactor in the thymidylate synthase reaction?

A

The reaction requires N5N10 methylene tetrahydrofolate, which is generated by dihydrofolate reductase

36
Q

Converting carbamoyl phosphate into orotic acid requires _____.

A

Aspartate

37
Q

Converting phosphoribosyl pyrophosphate into inosinic acid requires ______,______,______, and ______.

A

Glycine, aspartate, glutamine, tetrahydrofolate

38
Q

What is the mechanism of the antineoplastic drug 6-mercaptopurine?

A

Blocks de novo purine synthesis

39
Q

What enzyme does hydroxyurea inhibit?

A

Ribonucleotide reductase

40
Q

5-fluorouracil inhibits ______, while methotrexate and trimethoprim both inhibit ______.

A

Thymidylate synthase; dihydrofolate reductase

41
Q

Deficiencies in what two enzymes will result in failure to convert orotic acid to uridine monophosphate?

A

Orotic acid phosphoribosyltransferase or orotidine 5-phosphate decarboxylase

42
Q

Which synthetic pathway utilizes the conversion of orotic acid to uridine monophosphate?

A

The de novo pyrimidine synthesis pathway

43
Q

What is the inheritance pattern of orotic aciduria?

A

Autosomal recessive

44
Q

What diagnosis would you suspect in a child with megaloblastic anemia not responsive to B12 or folate administration, failure to thrive, and a normal ammonia level?

A

Orotic aciduria

45
Q

Serum studies show increased orotic acid and hyperammonemia; this is consistent with _____ (orotic aciduria/ornithine transcarbamylase deficiency).

A

Ornithine transcarbamylase deficiency; orotic aciduria does not have hyperammonemia

46
Q

What is the treatment for orotic aciduria?

A

Oral uridine administration

47
Q

What is the end product of guanosine and adenosine degradation?

A

Uric acid; uric acid is eventually renally excreted

48
Q

What enzyme in the purine salvage pathway catalyzes the formation of guanosine monophosphate from guanine?

A

Hypoxanthine-guanine phosphoribosyl transferase

49
Q

What enzyme in the purine salvage pathway catalyzes the formation of inosinic acid from hypoxanthine?

A

Hypoxanthine-guanine phosphoribosyl transferase

50
Q

What enzyme in the purine salvage pathway catalyzes both the conversion of hypoxanthine into xanthine and the conversion of xanthine into uric acid?

A

Xanthine oxidase

51
Q

What enzyme catalyzes the formation of adenosine monophosphate from adenine?

A

Adenine phosphoribosyl transferase

52
Q

Severe combined immunodeficiency disease may be caused by a deficiency of what enzyme of the purine salvage pathway?

A

Adenosine deaminase

53
Q

Inhibition of which enzyme occurs due to adenosine triphosphate and deoxyadenosine triphosphate accumulation in severe combined immunodeficiency?

A

Ribonucleotide reductase

54
Q

Lesch-Nyhan syndrome is the result of an absence of what enzyme?

A

Hypoxanthine-guanine phosphoribosyl transferase; remember the mnemonic, He's Got Purine Recovery Trouble

55
Q

The enzyme hypoxanthine-guanine phosphoribosyl transferase is responsible for the formation of what two products in the purine salvage pathway?

A

Inosinic acid and guanylic acid

56
Q

What type of inheritance does Lesch-Nyhan syndrome demonstrate?

A

X-linked recessive

57
Q

A patient has hyperuricemia, gout, and choreoathetosis. He has mental retardation and signs of self-mutilation. What is the underlying metabolic disorder?

A

Lesch-Nyhan syndrome

58
Q

What is called when a purine is substituted for a pyrimidine or when a pyrimidine is substituted for a purine?

A

Transversion

59
Q

What is it called when one purine is substituted for the other purine or when one pyrimidine is substituted for the other pyrimidine?

A

Transition

60
Q

Where might you see a genetic code that has overlapping genes?

A

Some viruses do not adhere to the commaless, nonoverlapping genetic code rule

61
Q

What is the significance of the genetic code being unambiguous and yet redundant?

A

Whereas each codon specifies a single amino acid, an amino acid can be coded for by multiple codons

62
Q

What does a commaless, nonoverlapping genetic code entail?

A

The entire genome is read from a fixed starting point as a continuous string of bases

63
Q

How many codons code for methionine?

A

One (AUG)

64
Q

Rank the following types of mutations in order of severity: missense, silent, nonsense.

A

Nonsense (a stop codon) missense silent

65
Q

What is it called when a mutation in DNA results in no change to the amino acid that is being coded for?

A

Silent mutation

66
Q

Silent mutations are often the result of changes in what position of a codon?

A

The third position (due to tRNA wobble)

67
Q

What is it called when a DNA mutation yields a single changed amino acid?

A

Missense mutation; the severity of the mutation depends on the location of the change and the chemical similarity of the new amino acid to the old

68
Q

What kind of mutation is a DNA change that results in the misreading of all nucleotides downstream of it?

A

Frameshift

69
Q

A frameshift mutation tends to yield what?

A

A truncated or nonfunctional protein

70
Q

What is a nonsense mutation?

A

A DNA change that results in an early-stop codon

71
Q

What is the purpose of DNA topoisomerases creating a nick in the DNA helix?

A

To relieve supercoils

72
Q

How many origins of replication do prokaryotes use in DNA replication?

A

One (single)

73
Q

What is the function of primase?

A

It makes an RNA primer on which DNA polymerase III can then initiate replication

74
Q

What enzyme has exonuclease activity in prokaryotic DNA replication?

A

DNA polymerase III has 3; to 5; exonuclease activity for proofreading

75
Q

What enzyme elongates the leading strand of DNA synthesis by building on an RNA primer?

A

DNA polymerase III

76
Q

What does DNA polymerase III require to initiate replication?

A

RNA primer

77
Q

What enzyme degrades the RNA primer and replaces it with DNA during prokaryotic DNA replication?

A

DNA polymerase I

78
Q

Onto which end of the newly synthesized DNA molecule does DNA polymerase III add the next subunit?

A

3;. This is 5; to 3; synthesis

79
Q

What enzyme seals pieces together during prokaryotic DNA replication?

A

DNA ligase

80
Q

When does DNA polymerase III stop adding deoxynucleotides to the 3; end?

A

When it reaches the primer of the preceding fragment

81
Q

Which drug category inhibits DNA gyrase (a specific prokaryotic topoisomerase)?

A

Fluoroquinolones; they impair bacterial DNA synthesis

82
Q

Which protein unwinds the DNA template at the replication fork?

A

Helicase

83
Q

Where does eukaryotic DNA replication begin?

A

At a consensus sequence of base pairs; this is AT-rich

84
Q

What is the function of single-stranded binding proteins?

A

Single-stranded binding proteins prevent strands from reannealing

85
Q

What are the pieces that are formed in discontinuously synthesized DNA called?

A

Okazaki fragments on the lagging strand

86
Q

DNA polymerase I and III are _____ (prokaryotic/eukaryotic) enzymes.

A

Prokaryotic

87
Q

What enzyme has 5; → 3; exonuclease activity?

A

DNA polymerase I (removes RNA primer)

88
Q

True or False? Eukaryotic DNA has more than one origin of replication.

A

TRUE

89
Q

During nucleotide excision DNA repair, what enzyme removes the damaged DNA?

A

Endonuclease

90
Q

What is the specific defective DNA repair mechanism in xeroderma pigmentosa?

A

Nucleotide excision repair

91
Q

Patients with xeroderma pigmentosum show excessive sensitivity to what? What organ is most affected?

A

Ultraviolet light; the skin

92
Q

What is the inheritance pattern of xeroderma pigmentosa?

A

Autosomal recessive

93
Q

Xeroderma pigmentosa results in an inability to repair what specific DNA error?

A

Thymidine dimers

94
Q

Xeroderma pigmentosum is associated with what cancer?

A

Melanoma

95
Q

What is the first step in the base excision repair of damaged DNA?

A

Specific glycosylases recognize and remove a single damaged base

96
Q

In base excision repair, what does the apurinic/apyrimidinic endonuclease do?

A

It cuts the DNA at a apyrimidinic site and removes the empty sugar

97
Q

In single-stranded DNA repair, how are nucleotide excision and base excision repair different?

A

During nucleotide repair, the entire nucleotide structure is removed and replaced; during base excision repair, the base is clipped off of the sugar and repaired without the whole backbone of the DNA being taken apart

98
Q

In DNA mismatch repair, how does the repair mechanism recognize the new strand (and thereby avoid replacing bases on the original template strand of DNA)?

A

The mismatch repair mechanism recognizes the template (and, therefore, the older strand) by its degree of methylation and excises the mismatched base from the new strand

99
Q

Hereditary nonpolyposis colon cancer results from loss of what DNA repair mechanism?

A

The mismatch repair system

100
Q

In what direction does protein synthesis proceed?

A

From N to C

101
Q

True or False? RNA is synthesized in the 3;-to-5; direction.

A

False; RNA is synthesized in the 5; to 3; direction

102
Q

During DNA and RNA synthesis, what is the target of the incoming nucleotide?

A

The 3;-hydroxyl of the nascent chain; the 5;-triphosphate provides the energy for the new bond

103
Q

What type of RNA is the largest?

A

mRNA

104
Q

What type of RNA is the most abundant?

A

rRNA

105
Q

What type of RNA is the smallest?

A

tRNA

106
Q

In prokaryotes, the initial AUG codes for what amino acid?

A

Formyl-methionine

107
Q

What codon is the mRNA initiation codon?

A

AUG (or, rarely, GUG) (remember, AUG inAUGurates protein synthesis)

108
Q

In eukaryotes, AUG codes for what amino acid?

A

Methionine

109
Q

List three stop codons.

A

UGA, UAA, UAG (remember, UGA = U Go Away; UAA = U Are Away; UAG = U Are Gone)

110
Q

What is the name of the DNA site at which RNA polymerase and multiple other transcription factors bind?

A

Promoter

111
Q

What are the elements that make up the promoter region?

A

The promoter region is an AT-rich sequence with TATA and CAAT boxes

112
Q

Is a promoter upstream or downstream of its gene locus?

A

Upstream

113
Q

What is the name for a DNA site where negative regulators (repressors) bind?

A

Silencer

114
Q

What commonly results from a mutation within a promoter?

A

A significant decrease in gene transcription

115
Q

What is the name for a stretch of DNA that alters gene expression by binding transcription factors?

A

Enhancer

116
Q

True or False? An enhancer that regulates expression can be located close to the gene it regulates, far from the gene it regulates, and within the gene that it regulates.

A

TRUE

117
Q

In eukaryotes, what enzyme makes rRNA?

A

RNA polymerase I

118
Q

True or False? In eukaryotes, RNA polymerases have a proofreading function.

A

False; RNA polymerases have no proofreading function in eukaryotes

119
Q

What poisonous protein, which inhibits RNA polymerase II, is found in death cap mushrooms?

A

-Amanitin; it causes liver failure when consumed

120
Q

In eukaryotes, what enzyme makes mRNA?

A

RNA polymerase II

121
Q

In eukaryotes, what enzyme makes tRNA?

A

RNA polymerase III

122
Q

In prokaryotes, what enzyme makes rRNA, mRNA, and tRNA?

A

RNA polymerase

123
Q

Where does eukaryotic RNA processing occur?

A

In the nucleus

124
Q

List the three parts of eukaryotic RNA processing.

A

Capping on the 5; end, polyadenylation on the 3; end, and splicing out of the introns

125
Q

What gets placed on the 5 end during the process of capping?

A

7-Methyl-guanosine

126
Q

Approximately how many adenosine monophosphates get added to the 3; end of mRNA during polyadenylation?

A

200

127
Q

What is the term for the initial (unprocessed) RNA transcript?

A

Heterogeneous nuclear RNA

128
Q

What series of bases encodes the polyadenylation signal?

A

AAUAAA

129
Q

True or False? Poly-A polymerase requires a template.

A

False; poly-A polymerase does not require a template

130
Q

What binds to a primary mRNA transcript and forms a spliceosome?

A

Small nuclear ribonucleoprotein particles and other proteins

131
Q

What is the shape of the intermediate that is formed during mRNA splicing?

A

Lariat

132
Q

Patients with which disease make antibodies to spliceosomal small nuclear ribonucleoproteins?

A

Lupus

133
Q

What is the name of the portions of a gene that contain the actual genetic information coding for the protein?

A

Exons (remember: EXons EXit and are EXposed)

134
Q

What is the name for the intervening noncoding segments of DNA within a gene?

A

Introns (remember: INtrons are INtervening sequences and stay IN the nucleus)

135
Q

-thalassemia is due to a mutation causing splicing defects in a process that combines different exons within a single gene. What mechanism allows the same gene to encode for multiple different proteins?

A

Alternative splicing; in this case the alternative splicing yields a pathological protein

136
Q

What mechanism allows the same gene to encode for multiple different proteins?

A

Alternative splicing of exons

137
Q

How many nucleotides make up the structure of an average tRNA?

A

Approximately 75 to 90

138
Q

What part of a tRNA lies opposite from its 3; aminoacyl end?

A

The anticodon end

139
Q

What three-nucleotide sequence do all eukaryotic and prokaryotic tRNAs have at their 3; ends?

A

CCA

140
Q

Where on a tRNA does the amino acid that will be incorporated into the protein bind?

A

The 3; end

141
Q

Does charging a tRNA molecule with an amino acid require energy?

A

Yes, adenosine triphosphate is hydrolyzed in the process

142
Q

If a tRNA had a methionine bound to it, what would the sequence of the codon it binds read? (Give this in order from the 5; end to the 3; end.) What would its anticodon sequence read? (Give this in the same order.)

A

Codon = AUG; anticodon = CAU

143
Q

What enzyme charges tRNA by adding an amino acid to it?

A

Aminoacyl-tRNA synthetase

144
Q

What are the substrates of the reaction that is catalyzed by aminoacyl-tRNA synthetase?

A

The uncharged tRNA, the appropriate amino acid, and ATP

145
Q

Name the enzyme that proofreads the match between a tRNA and its amino acid.

A

Aminoacyl-tRNA synthetase

146
Q

How does tetracycline interfere with protein translation?

A

Tetracycline binds to the 30S subunit of the ribosome, blocking attachment of the aminoacyl tRNA

147
Q

Accuracy in which two nucleotide positions of an mRNA codon is required for proper protein synthesis.

A

First and second (tRNA wobble hypothesis)

148
Q

What are the sizes of the two subunits of the eukaryotic ribosome called?

A

The 60S subunit and the 40S subunit

149
Q

When referring the A site of a ribosome, what does the A stand for?

A

Aminoacyl; the incoming aminoacyl tRNA is accommodated in the A site

150
Q

_____ (Eukaryotes/prokaryotes) have ribosomes with 50S and 30S subunits.

A

Prokaryotes

151
Q

At the start of protein synthesis, methionine sits in which site on the ribosome?

A

In the P site

152
Q

At the start of protein synthesis, what process occurs at the same time as the hydrolysis of methionine's bond with its tRNA?

A

The formation of a peptidyl bond between methionine and the second amino acid in the polypeptide

153
Q

When referring the P site of a ribosome, what does the P stand for?

A

Peptidyl; the P site accommodates the growing polypeptide chain

154
Q

During protein synthesis, the incoming amino acid binds to which site on the ribosome?

A

The A site

155
Q

Which molecules are responsible for assembling the 40S subunit with the initiator tRNA?

A

Eukaryotic initiation factors

156
Q

In what direction relative to the mRNA does the ribosome shift after the formation of a peptidyl bond?

A

Toward the 3; end

157
Q

When the ribosome shifts after the formation of a peptidyl bond, in what position does the tRNA with the growing peptide chain end up?

A

The P site

158
Q

What molecule provides the energy for the charging of tRNA?

A

Adenosine triphosphate

159
Q

What molecule provides the energy for the binding of tRNA to the ribosome/mRNA complex?

A

Guanosine triphosphate

160
Q

What molecule provides the energy for the translocation of the ribosome along the mRNA?

A

Guanosine triphosphate

161
Q

When the ribosome shifts after the formation of a peptidyl bond, where is the uncharged tRNA found?

A

In the E position

162
Q

What is the order of the positions of the ribosome that the tRNA occupies during translation?

A

A, P, E (think of going APE)

163
Q

In protein synthesis, what is the role of initiation factors?

A

To assemble the 40S ribosomal subunit with the initiation tRNA

164
Q

In protein synthesis, what are the three steps of protein elongation?

A

(1) Aminoacyl-tRNA binds to the A site;

(2) peptidyltransferase adds a peptide to the amino acid chain at site A; and

(3) the ribosome advances three nucleotides in the 3 direction, thereby moving the peptidyl tRNA to the P site

165
Q

How do aminoglycosides interfere with protein synthesis?

A

They inhibit formation of the initiation complex, causing misreading of mRNA

166
Q

What enzyme is affected by chloramphenicol?

A

50S peptidyltransferase

167
Q

Where do macrolides and clindamycin bind?

A

The 50S subunit

168
Q

What is the result of clindamycin binding to the 50S subunit?

A

Translocation of the tRNA is blocked

169
Q

Why are antibiotics such as chloramphenicol, clindamycin, and macrolides selective for bacteria and not toxic to human cells?

A

They affect the 50S subunit of the ribosome, which is found in prokaryotic cells

170
Q

What is the total energy expenditure required in the addition of a single amino acid to a protein in translation?

A

Four high-energy phosphoanhydride bonds per amino acid added; two adenosine triphosphate bonds to load tRNA; one guanosine triphosphate bond to load the ribosome and one to translocate the polypeptide chain

171
Q

What is an example of proteins that are trimmed after translation?

A

The removal of N- or C-terminal propeptides from zymogens to generate mature proteins

172
Q

Covalent alterations involve what kinds of posttranslational protein modifications?

A

Phosphorylation, glycosylation, and hydroxylation

173
Q

How do cells handle defective proteins that are translated?

A

Attach ubiquitin to defective proteins to tag them for breakdown

174
Q

In this image, where does DNA synthesis start and end?

A

DNA is synthesized in the 5'-to-3' direction

175
Q

In this image, where does capping occur?

A

Capping occurs on the 5' end

176
Q

In this image, what are the light blue (A) and dark blue (B) segments?

A

Light blue (A) are introns and dark blue (B) are exons (EXons EXit and are EXposed)

177
Q

In this image, what enzyme charges tRNA by adding an amino acid to it?

A

Aminoacyl-tRNA synthetase

178
Q

Identify the E, A, and P sites in this diagram.

A

(E) holds Empty tRNA as it Exits; (P) accommodates growing Peptide; (A) incoming Aminoacyl-tRNA