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Biochem 6200 > Leys Study Guide #3 > Flashcards

Leys Study Guide #3 Flashcards

1
Q

Cells acquire nucleotides through 2 processes: ____________ and __________

A

Cells acquire nucleotides through two processes: DE NOVO SYNTHESIS and SALVAGE PATHWAYS

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2
Q

De novo synthesis of purines results in the synthesis of ______ that can be converted to ______ and ___________

A

De novo synthesis of purines results in the synthesis of INOSINE that can be
converted into ADENOSINE and GUANINE

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3
Q

Atoms in newly synthesized purine are derived from several sources, name these 4 sources

A

Atoms in newly synthesized purine are derived from….

  1. Aspartate
  2. Glutamine
  3. Glycine
  4. Methyl Groups supplied by folic acid and carbon dioxide
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4
Q

_______ and _______ regulate de novo synthesis of purines at multiple points in the pathway.

A

ADP and GDP regulate de novo synthesis of purines at multiple points in the pathway.
(in other words, ADP and GDP => regulator of de novo synthesis.)

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5
Q

________ and _______ can be recycled through the __________ with (HGPRT) hypoxanthine guanine phosphoribosyl transferase.

A

HYPOXANTHINE and GUANINE can be recycled through the SALVAGE PATHWAY with (HGPRT) hypoxanthine guanine phosphoribosyl transferase.

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6
Q

__________ catalzyes a ____________ type reaction leading to the formation of __________ that can be excreted

A

XANTHINE OXIDASE catalyzes a HYDROXYLASE type reaction leading to the formation of URIC ACID that can be excreted.

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7
Q

Excess ________ is the cause of gout

A

Excess URIC ACID is the cause of gout

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8
Q

Gout is most often caused by ______________, but can also be caused by __________.

A

Gout is most often caused by LOW LEVELS OF SECRETION OF URIC ACID, but can also be caused by EXCESS PRODUCTION

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9
Q

Crystallization of ____________ in the joints leads to a localized ______ response

A

Crystallization of SODIUM URATE in the joints leads to a localized INFLAMMATORY response.

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10
Q

__________, a purine analog, is used to treat gout

A

ALLOPURINAL, a purine analog, is used to treat gout

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11
Q

Allopurinol inhibits ____________ preventing the formation of uric acid

A

Allopuriol inhibits XANTHINE OXIDASE preventing the formation of uric acid

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12
Q

A HGPRT deficiency causes _______ that results in severe retardation, crippling gouty arthritis and self-mutilation

A

A HGPRT deficiency casues LESCH-NYHAN SYNDROME that results in severe retardation, crippling gouty arthritis and self mutilation

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13
Q

Lesch-Nyhan syndrome occurs in males only because ___________

A

Lesch-Nyhan occurs in males only because the HGPRT GENE is located on the X CHROMOSOME

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14
Q

The breakdown of ______ can replenish TCA cycle intermediates through the production of _______

A

The breakdown of PURINES can replenish TCA cycle intermediates through the production of FUMERATE

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15
Q

Atoms in the pyrimidine ring are derived from ______ and ________.

A

The atoms in a pyrimidine ring are derived from ASPARTATE and CARBAMOYL PHOSPHATE

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16
Q

The ________ in the synthesis of pyrimidines are located of the same protein, ___________

A

The FIRST 3 ENZYMES in the synthesis of pyrimidines are located on the same protein, CAD PROTEIN

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17
Q

The pyrimidines _____ and _______ can be interconverted

A

The pyrimidines U and C can be interconverted

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18
Q

dUMP is converted to TMP by _________, an enzyme requiring the transfer of a methyl group from ___________

A

dUMP is converted to TMP by THYMIDYLATE SYNTHASE, an enzyme requiring the transfer of a methyl group from TETRAHYDROFOLATE.

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19
Q

Inhibitors of tetrahydrofolate production are used as therapeutic agents for _______ and _________

A

Inhibitors of tetrahydrofolate production are used as therapeutic agents for TREATING CANCER and BACTERIAL INFECTIONS

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20
Q

_________ that inhibit thymidylate synthase are used as anticancer agents

A

FLURO SUBSTITUTED PYRIMIDINE ANALOGS that inhibit thymidylate synthase are used as anticancer agents

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21
Q

Ribunucleotide reductase converts ______________ to ___________

A

Ribunucleotide reductase converts RIBONUCLEOTIDES to DEOXYRIBONUCLEOTIDES

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22
Q

Base-pairing in DNA is ____-____ and ____-____. In RNA it’s _____-____ and ____-____.

A

Base-pairing in DNA is A-T and G-C. In RNA it’s A-U and G-C.

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23
Q

___________ can be compared among different species to determine phylogenetic relationships

A

HOMOLOGOUS REGIONS OF DNA can be compared among different species to determine phylogenetic relationships

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24
Q

Closely related organisms contain similar _________, however they are often arranged differently on the __________ of each species

A

Closely related organisms contain similar DNA COMPLIMENTS, however they are often arranged differently on the CHROMOSOMES of each species

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25
Q

The living world is made up of 3 divisions, or domains: ______, ________, & _________.

A

The living world is made up of 3 divisions, or domains: BACTERIA, ARCHEA, and EUKARYOTES

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26
Q

There are 4 main processes for generating change in a genome, name all 4.

A

There are 4 main processes for generating change in a genome:

  1. INTRAGENIC MUTATION (single base change), 2. GENE DUPLICATION
  2. DNA SEGMENT SHUFFLING
  3. HORIZONTAL TRANSFER (from one cell to another).
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27
Q

___________ are usually clustered into groups of operons that are ________ as a single unit

A

BACTERIAL GENES are usually clustered into groups of operons that are TRANSCRIBED as a single unit

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28
Q

Eukaryotic genes are often broken up with regions of ________ between regions of ________

A

Eukaryotic genes are often broken up with regions of NONCODING DNA (INTRONS) between regions of CODING DNA (EXONS)

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29
Q

In comparison of the same gene is several closely related species, the _____ will generally be very similar (conserved), while the _______ will vary in size and content

A

In a comparison of the same gene in several closely related species, the EXONS will generally be very similar (conserved), while the INTRONS will vary in size and content.

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30
Q

Most of the DNA in higher eukaryotes including humans does not _____ for ______

A

Most of the DNA in higher eukaryotes including humans does not CODE for PROTEINS

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31
Q

Most of the human genome is made up of repeated sequences, many of which are ______________________

A

Most of the human genome is made up of repeated sequences. Many of those sequences are MOBILE ELEMENTS THAT CAN MOVE AROUND IN THE GENOME

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32
Q

____________ chromosomes are linear and __________ chromosomes are _________

A

EUKARYOTIC chromosomes are linear and BACTERIAL chromosomes are circular

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33
Q

In addition to the human genome, the entire genomes of a large number organisms have been completed including _________

A

In addition to the human genome, the entire genomes of a large number organisms have been completed including SEVERAL BACTERIA THAT ARE FOUND IN THE ORAL CAVITY

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34
Q

It is possible to construct __________ and compare them with other organisms by examining their entire ________ content

A

It is possible to construct METABOLIC PATHWAYS and compare them with other organisms by examining their entire GENOME content

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35
Q

Genes can be grouped into families bases on ____________________

A

Genes can be grouped into families bases on SIMILAR SEQUENCES (HOMOLOGOUS) FOUND IN DIFFERENT ORGANISMS

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36
Q

Homologous sequences can be found in genes of the same organism that carry out ________

A

Homologous sequences can be found in genes of the same organism that carry out DIFFERENT BUT SIMILAR FUNCTIONS

37
Q

Genes that have similar functions in ___________ can have similar sequences (homology)

A

Genes that have similar functions in VERY DISTANTLY RELATED ORGANISMS can have similar sequences (homology)

38
Q

The Phylogenetic relationship of different organisms can be compared by comparing _______________

A

The phylogenetic relationship of different organisms can be compared by comparing DNA SEQUENCES of SIMILAR GENES in the TWO ORGANISMS

39
Q

DNA polymerase is a ______________ enzyme

A

DNA polymerase is a DNA DEPENDENT (uses DNA as a template) DNA SYNTHESIZING enzyme

40
Q

RNA polymerase is a _____________ enzyme

A

RNA polymerase is a DNA DEPENDENT RNA SYNTHESIZING enzyme

41
Q

Reverse transcriptase is a __________________ enzyme

A

Reverse transcriptase is a RNA DEPENDENT DNA SYNTHESIZING enzyme

42
Q

Primase is a ___________ polymerase

A

Primases is a DNA DEPENDENT RNA polymerase

43
Q

Primase synthesizes a small RNA primer that can be ___________

A

Primase synthesizes a small RNA primer that can be USED BY DNA POLYMERASE TO ELONGATE THE CHAIN

44
Q

DNA polymerase minimizes the __________ by using a 3’-5’ ________ activity that is part of the same protein

A

DNA polymerase minimizes the NUMBER OF MISTAKES by using a 3’ to 5’ EXONUCLEASE activity (proofreading activity) that is part of the same protein

45
Q

DNA polymerase as well as all other nucleic acid polymerases synthesize DNA in the _______ direction only

A

DNA polymerase as well as all other nucleic acid polymerases synthesize DNA in the 5’ TO 3’ direction only

46
Q

During replication, each new nucleotide is added to the ________________

A

During replication, each new nucleotide is added to the 3’ CARBON ON THE LAST NUCLEOTIDE of the NEW DNA CHAIN

47
Q

The ___________ is connected to the sugar at the 1’ carbon, and the adjacent nucleotides in a DNA chain are attached at ____________

A

The BASE COMPONENT OF EACH NUCLEOTIDE is connected to the sugan at the 1’ carbon, and adjacent nucleotied in a DNA chain are attached at THE 5’ and 3’ CARBONS

48
Q

The _____ carbon differs between RNA and DNA

A

The 2’ carbon differs between RNA and DNA

49
Q

DNA polymerase is an __________ enzyme; it cannot ___________

A

DNA polymerase is an ELONGATING enzyme; it cannot INITIATE SYNTHESIS

50
Q

Because DNA polymerase is only an elongating enzyme, a ______ is required for elongation of a ___________ using the DNA polymerase

A

A PRIMER is required from the elongation of a NEW STRAND using the DNA polymerase

51
Q

Bacterial chromosomes contain only one _____ of _________

A

Bacterial chromosomes contain only one ORIGIN of REPLICATION

52
Q

In bacteria, DNA synthesis proceeds in ____ direction away from the origin until the _____________

A

In bacteria, DNA synthesis proceeds in BOTH directions away from the origin until the TWO REPLICATION FORKS MEET AT A SPECIFIC SEQUENCE ON THE OTHER SIDE OF THE CHROMOSOME

53
Q

In bacteria, new rounds of DNA replication can begin ____________

A

In bacteria, new rounds of DNA replication can begin BEFORE THE PREVIOUS ROUND IS COMPLETED

54
Q

Eukaryotic chromosomes contain many ________ that may change during the development of the organism

A

Eukaryotic chromosomes contain many ORIGINS OF REPLICATION that may change during the development of the organism

55
Q

In eukaryotes, each entire chromosome is replicated __________, and new rounds of replication do not start until _________

A

In Eukaryotes, each entire chromosome is replicated ONLY ONCE EACH CELL DIVISION and new rounds of replication do NOT start until AFTER THE CELL DIVIDES.

56
Q

Eukaryotic chromosomes are ________ in organization, and special structures called ________ are placed on each end

A

Eukaryotic organisms are LINEAR in organization, and special structures called TELOMERES are placed on each end.

57
Q

Telomeres are constructed with the enzyme __________ that uses a _______ template to synthesize a ___________ at the ends of chromosomes

A

Telomeres are constructed with the enzyme TELOMERASE that uses an RNA template to synthesize a SHORT REPEATED DNA SEQUENCE at the ends of chromosomes

58
Q

Because the polymerase in eukaryotes must synthesize new DNA in a ________ direction, the two polymerase molecules must move __________

A

Because the polymerase in eukaryotes must synthesize DNA in a 5’-3’ direction, the two polymerase molecules must move AWAY FROM EACH OTHER

59
Q

The enzyme _________ unwinds the 2 DNA strands _______ polymerization of the new strands

A

The enzyme HELICASE unwinds the 2 DNA strands BEFORE polymerization of the new strands

60
Q

______________ keep the 2 complementary strands from reforming a double helix

A

SINGLE-STRANDED BINDING PROTEINS keep the two complementary strands from reforming a double helix

61
Q

The polymerase on the leading strand move toward the __________ and the polymerase on the lagging strand move away from it

A

The polymerase on the leading strand moves toward the REPLICATION FORK and the polymerase on the lagging strand moves away from it.

62
Q

The lagging strand is synthesized in _______ fragments

A

The lagging strand is synthesized in SHORT (OKIZAKI) fragments

63
Q

Primase initiates synthesis of each Okazaki fragment by __________

A

Primase initiates synthesis of each Okazaki fragment by MAKING A SHORT RNA PRIMER

64
Q

The leading strand is synthesized by the _____________

A

The leading strand is synthesized by the CONTINUOUS MOVEMENT OF THE DNA POLYMERASE ALONG THE TEMPLATE

65
Q

__________ signals that the DNA is unreplicated and is ready to be used as a template for the next round of synthesis

A

METHYLATION OF THE DNA signals that the DNA us unreplicated and is ready to be used as a template for the next round of synthesis

66
Q

New or modified genes can be generated by one or a combination of 4 events, name these events.

A

New or modified genes can be generated by one or a combination of 4 events:

1) point mutations in the coding region that change the amino acid composition of the protein. 2) duplication of the entire gene.
3) Mixing of segments of one gene with segments of another gene – segment shuffling.
4) Acquisition of new activities by transfer of genes between two organisms – horizontal gene transfer.

67
Q

Many genes belong to gene families that share homologous regions. These regions usually _____________________

A

Many genes belong to gene families that share homologous regions. These regions usually CODE FOR PROTEINS THAT CARRY OUT SIMILAR FUNCTIONS

68
Q

Breaks in the DNA (especially double-stranded breaks) facilitate ______________

A

Breaks in the DNA (especially double-stranded breaks) facilitate the INITIATION OF RECOMBINATION

69
Q

A defect in ______, that affects joining together of adjacent segments of DNA on a chromosome, can cause abnormal amounts of recombination

A

A defect in DNA LIGASE, that affects joining together of adjacent segments of DNA on a chromosome, can cause abnormal amounts of recombination

70
Q

Define recombination

A

Recombination is the reciprocal exchange of genetic information

71
Q

Recombination can result from 4 “things”….what are they?

A

Recombination can result from…

  1. Reciprocal exchange during cell division
  2. DNA damage (eg X-ray damage)
  3. Introduction of foreign DNA
  4. Programmed recombination during the development or maturation of a cell type (eg antibody producing genes during B-cell maturation)
72
Q

Define gene conversion

A

Gene conversion is the non-reciprocal exchange of genetic information

73
Q

Recombination between direct repeated sequences on the same chromosome causes the loss of _______________

A

Recombination between direct repeated sequences on the same chromosome causes the loss of DNA THAT WAS BETWEEN THE TWO REPEATED SEGMENTS

74
Q

Circular DNA can be inserted in a chromosome by recombination between a region of ________ and an _______________

A

Circular DNA can be inserted in a chromosome by recombination between a REGION ON A CIRCULAR MOLECULE and an HOMOLOGOUS REION ON THE CHROMOSOME

75
Q

X-rays and other agents that cause breaks in DNA induce ______

A

X-rays and other agents that cause breaks in DNA induce RECOMBINATION

76
Q

T/F: Transposable elements are found only in eukaryotes

A

FALSE!! Transposable elements are found in all species from bacteria to human

77
Q

Transposable elements move from one location in the _______ to another location within that _____

A

Transposable elements move from one location in the DNA to another location within that CELL.

78
Q

_______ can cause changes in the DNA at the site of insertion.

A

TRANSPOSABLE ELEMENTS can cause changes in the DNA at the site of insertion

79
Q

There are two major types of transposable elements, one type that contains inverted repeated sequences at the ends and causes ___________ and a second type that is structurally similar to a retrovirus and transposes through _________.

A

There are two major types of transposable elements, one type that contains inverted repeated sequences at the ends and causes A SHORT REGION OF THE GENOME TO BE DUPLICATED AT THE SITE OF INSERTION and a second type that is structurally similar to a retrovirus and transposes through AN RNA INTERMEDIATE.

80
Q

Unequal crossing over is recombination that resulted from imprecise pairing of _________.

A

Unequal crossing over is recombination that resulted from imprecise pairing of TANDEMLY REPEATED SEQUENCES

81
Q

There are 2 general types of mutations, name them.

A

There are two types of mutations:

  1. DNA rearrangements
  2. Base substitutions.
82
Q

T/F: There are many mechanisms in each cell for repairing DNA

A

TRUE!

83
Q

Damage to a nucleotide (eg deamination) can either be _______ or lead to a ________.

A

Damage to a nucleotide (eg deamination) can either be REPAIRED or lead to a PERMANENT MUTATION

84
Q

Mutations can be cause be either errors _________ or by injury to the DNA from _____ or ______

A

Mutations can be caused by either errors DURING REPLICATION or by injury to the DNA from CHEMICALS or RADIATION.

85
Q

A small fraction of every genome (about 3% in humans) is made up of ____________ or large regions that are present in ______ copy.

A

A small fraction of every genome (about 3% in humans) is made up of SEGMENTAL DUPLICATIONS or large regions that are present in MORE THAN ONE copy.

86
Q

The duplicated DNA is generated by a process called _________

A

The duplicated DNA is generated by a process called GENE AMPLIFICATION

87
Q

Gene amplification can result in _______, transformation into ______, or other changes in the cell phenotype.

A

Gene amplification can result in RESISTANCE TO DRUGS, transformation into CANCEROUS CELLS, or other changes in the cell phenotype.

88
Q

Several human diseases are due to defects in _______ enzymes

A

Several human diseases are due to defects in DNA REPAIR enzymes

Biochem 6200 (4 decks)

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