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HEAL1500 > UNIT 3 - DNA AND GENE EXPRESSION > Flashcards

UNIT 3 - DNA AND GENE EXPRESSION Flashcards

1
Q

what is DNA?

A

-deoxyribonucleic acid
-genetic material
-short segments of DNA code for specific traits (genes)

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2
Q

where is DNA found in eukaryotic cells?

A

-in the nucleus mainly
-small amount in the mitochondria

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3
Q

what are the 2 forms of chromatin?

A

-euchromatin
-heterochromatin

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4
Q

what is euchromatin?

A

-open and loose
-usually transcriptionally active
-appears lighter under the microscope

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5
Q

what is heterochromatin?

A

-more compact
-not transcriptionally active
-appears darker under the microscope

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6
Q

what are nucelosomes?

A

-DNA rolled around a bunch of 8 histones

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7
Q

when does heterochromatin condense to a chromosome?

A

-when cells are dividing

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8
Q

what are the different stages of chromatin hierarchy?

A

-euchromatin
-nucleosomes
-heterochromatin
-chromosomes

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9
Q

what is the structure of DNA?

A

-double helix
-each strand has a series of nucleotides

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10
Q

what are DNA nucleotides made of?

A

-3 subunits
-phosphate
-pentose sugar (deoxyribose)
-nitrogen containing base

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11
Q

what are the 4 nitrogen containing bases in DNA?

A

-adenine
-guanine
-cytosine
-thymine

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12
Q

which of the 4 bases in DNA are purines? what makes them a purine?

A

-adenine
-guanine
-2 carbon rings

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13
Q

which of the 4 bases in DNA are pyrimidines? what makes them a pyrimidine?

A

-cytosine
-thymine
-1 carbon rings

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14
Q

how many hydrogen bonds pair the complementary bases together?

A

-A pairs with T using 2 H-bonds
-G pairs with C using 3 H-bonds

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15
Q

what is specific about how the DNA strands are joined together?

A

-they run antiparallel (opposite directions)
-because of the position of carbon molecules on the deoxyribose sugar
-5’ carbon at one end
-3’ carbon at the other end

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16
Q

When does DNA replication occur?

A

-during the S phase of interphase

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17
Q

what is special about DNA replication?

A

-semi- conservative
-each double helix has one original strand and one new strand
-original strand serves as a template

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18
Q

which direction is DNA replicated in?

A

-5’ to 3’
-new nucleotides are added on the 3’ end

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19
Q

what are the 3 stages of DNA replication?

A

-initiation
-elongation
-termination

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20
Q

what occurs during initiation of DNA replication?

A

-proteins bind to the origin
-helicase unwinds DNA
-2 replication forks are formed

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21
Q

what occurs during elongation of DNA replication?

A

-primase adds an RNA primer
-DNA polymerase adds DNA nucleotides to the 3’ end of each strand

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22
Q

what occurs during termination of DNA replication?

A

-RNA primers are removed and replaced with DNA nucleotides
-backbone + okazaki fragments are sealed by ligase

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23
Q

what is the leading strand?

A

-DNA strand that gets made continuously
-OG strand in the 3’ to 5’ direction
-new strand in the 5’ to 3’ direction
-follows the helicase enzyme

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24
Q

what is the lagging strand?

A

-DNA strand made in fragments called okazaki fragments
-OG strand in the 5’ to 3’ direction
-new strand in the 3’ to 5’ direction
-primers need to be placed multiple times

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25
Q

what is the role of topoisomerase?

A

-prepares DNA for helicase
-stops DNA from supercoiling

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26
Q

what is the role of helicase?

A

-unwinds DNA by breaking hydrogen bonds between bases

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27
Q

what is the role of DNA polymerase?

A

-adds new DNA nucleotides

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28
Q

what is the purpose of Single Strand Binding proteins (SSBs)?

A

-stabilize DNA strands (keep them seperate)

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29
Q

what is the role of primase?

A

-puts RNA primers on each strand to allow DNA polymerase to begin
-replaced at the end by DNA nucleotides

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30
Q

what is the role of DNA polymerase delta and flap endonuclease?

A

-remove RNA from the okazaki fragments

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31
Q

what is a mutation? how is this taken care of?

A

-error in replication
-sequence of bases in new strand is not identical to template strand
-repair enzymes usually fix it

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32
Q

what happens when repair enzymes cannot fix a mutation?

A

-genetic variability is introduced
-new allele that alters the phenotype

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33
Q

does only one origin exist in a DNA strand?

A

-No!
-more than 1 origin is necessary for efficiency

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34
Q

what is RNA?

A

-ribonucleic acid
-assists in processing genetic information
-gene regulation + producing proteins

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35
Q

what is the structure of RNA?

A

-single strand of nucleotides

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36
Q

what are RNA nucleotides made of?

A

-3 subunits
-phosphate
-pentose sugar (ribose sugar)
-nitrogen containing base

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37
Q

what are the 4 nitrogen containing bases in RNA?

A

-adenine
-uracil
-cytosine
-thymine

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38
Q

is uracil a pyrimidine or a purine?

A

-pyrimidine like thymine

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39
Q

what are the types of RNA?

A

-mRNA (messenger)
-rRNA (ribosomal)
-tRNA (transfer)
-small non coding RNAs

40
Q

when and where is mRNA produced?

A

-during transcription
-in the nucleus
-DNA is used as a template

41
Q

what is mRNA’s purpose?

A

-carry genetic info from DNA to ribosomes in the cytoplasm (for protein synthesis)

42
Q

where and how is rRNA produced?

A

-in the nucleolus
-using a DNA template

43
Q

what will rRNA eventually form? how is this done?

A

-ribosomal subunits
-4 sizes of rRNA join with proteins to form the large ribosomal subunit and the small ribosomal subunit

44
Q

what happens after ribosomal subunits are formed?

A

-leave the nucleus
-attach to the endoplasmic reticulum or remain free in the cytoplasm
-will combine to form a ribosome during protein synthesis

45
Q

where and how is tRNA produced?

A

-in the nucleus
-using DNA as a template

46
Q

what is the purpose of tRNA?

A

-transfer amino acids to the ribosomes during protein synthesis
-each tRNA will carry a different amino acid

47
Q

how many types of amino acids are there?

A

-20/21

48
Q

what is the 3 base sequence that is present on tRNA?

A

-anticodon

49
Q

what are the 4 classes of small non coding RNAs?

A

-small nuclear RNAs (snRNAs)
-small nucleolar RNAs (snoRNAs)
-microRNAs (miRNAs)
-small interfering RNAs (siRNAs)

50
Q

what are small nuclear RNAs purpose?

A

-splicing mRNA before it leaves the nucleus

51
Q

what are small nucleolar RNAs purpose?

A

-modify the ribosomal RNAs within the nucleolus

52
Q

what are microRNAs purpose?

A

-attach to mRNAs in the cytoplasm
-prevents unnecessary translation
-when the cell is down regulating the production of specific proteins

53
Q

what are small interfering RNAs purpose?

A

-attach to mRNAs
-prepare them for degradation

54
Q

what is the basic overview of gene expression?

A

-transcription (1st step)
-copies DNA to RNA (mRNA)
-translation (2nd step)
-makes a protein from the mRNA (mRNA > amino acids)

55
Q

what can be said about each different cells genetic template?

A

-they are all the same
-express different RNAs which lead to cell specific proteins

56
Q

what is the importance of cell specific proteins?

A

-basis of cell differentiation
-basis of cell function

57
Q

what are proteins composed of? how do proteins differ?

A

-subunits called amino acids
-differ b/c of the number and order of amino acids

58
Q

what type of structure is the sequence of amino acids? what type of structure does this lead to?

A

-sequence is primary structure
-leads to tertiary structure (proteins particular shape)

59
Q

what is a codon? what does it represent?

A

-three base sequence in mRNA
-different amino acids

60
Q

how many possible codons are there?

A

-64

61
Q

how many codons correspond to a specific amino acid? what are the remaining codons?

A

-61
-remaining 3 are stop codons

62
Q

what is the purpose of stop codons?

A

-polypeptide termination

63
Q

which codon/amino acid acts as the start codon?

A

-methionine (AUG)

64
Q

what differs in the transcription of different RNA molecules?

A

-the RNA polymerase involved
-RNA poly 1 (rRNA)
-RNA poly 2 (mRNA)
-RNA poly 3 (tRNA)

65
Q

what is RNA polymerase?

A

-large complex that adds RNA nucleotides using base pairing rules
-always add on the 3’ end

66
Q

what is the only coding mRNA?

A

-mRNA

67
Q

what does it mean to be a coding RNA?

A

-leading to/coding for a protein

68
Q

how is mRNA first processed before it leaves the nucleus?

A

-process primary mRNA into mature mRNA
-primary mRNA contains introns and exons
-introns are removed leaving only exons in the mature mRNA

69
Q

what are introns?

A

-segments of DNA that do not code for any part of a protein

70
Q

what are exons?

A

-segments of DNA that will potentially be translated to produce a protein

71
Q

how are the introns removed from primary mRNA?

A

-mRNA is spliced
-completed by a complex called a spliceosome

72
Q

what is a spliceosome composed of?

A

-RNA protein complexes (small nuclear ribonucleic proteins)
-other various proteins

73
Q

what is alternative mRNA splicing? what does this result in?

A

-cells only will use certain exons (some exons are removed as well as introns)
-different proteins from a single gene

74
Q

what occurs during the final processing of mRNA?

A

-5’ end is capped by an altered guanine nucleotide
-3’ end is given a tail (addition of multiple adenosine nucleotides)

75
Q

what is the 3’ ends tail often referred to as? what is the purpose for this tail?

A

-polyA tail
-increases stability

76
Q

does every mature mRNA molecule that leaves the nucleus result in a protein?

A

-NO
-a portion go to the cytoplasm and are decayed

77
Q

what is the translation complex? how does it work?

A

-small and large ribosomal subunit joined together (ribosome)
-reads the mRNA and elongates the protein by adding amino acids

78
Q

what are the 3 sites of the ribosome involved in translation?

A

-A site (enters)
-P site (elongated)
-E site (exits)

79
Q

what are the 3 stages of translation?

A

-initiation
-elongation
-termination

80
Q

what occurs during the initiation stage of translation?

A

-mRNA binds to the small ribosomal subunit (initiates translation complex)
-tRNA binds with AUG codon (methionine)
-sets the open reading frame
-large ribosomal subunit completes the complex (ribosome)

81
Q

what is a reading frame?

A

-way to divide DNA or RNA into a set of consecutive non-overlapping triplets (codons)

82
Q

how many possible reading frames does each nucleic acid have?

A

-DNA (6)
-RNA (3)

83
Q

what occurs during the elongation stage of translation?

A

-the polypeptide lengthens
-tRNA arrives at the A site
-ribosome “moves down” the mRNA strand one codon at a time
-P site now is filled by a tRNA peptide complex
-tRNA moves to the E site and exits the ribosome

84
Q

can more that one tRNA occupy the ribosomes different sites?

A

-YES
-one tRNA can be in the P site and another can be in the A site
-the polypeptide chain gets passed from the tRNA at the P site to the arriving tRNA at the A site

85
Q

what occurs during the termination stage of translation?

A

-protein synthesis is terminated once a stop codon has entered the A site
-a protein called a “release factor” is required for termination
-ribosomal subunits dissociate

86
Q

what does the release factor do?

A

-binds to the stop codon and cleaves the polypeptide from the last tRNA

87
Q

what is a polyribosome? what does this allow for?

A

-multiple ribosomes that can move along one mRNA at the same time
-allows for several polypeptides of the same type to be synthesized using 1 mRNA molecule

88
Q

what are the different levels of control of gene expression?

A

-pre-transcriptional
-transcriptional
-post-transcriptional
-translational
-post-translational

89
Q

what is the pre-transcriptional mechanism of control?

A

-occurs in the nucleus
-accessibility of DNA
-DNA must uncoil to give access for transcription
-proteins + chemical modifications that protect the DNA must be removed
-euchromatin (open) vs heterochromatin (compact)

90
Q

what is the transcriptional mechanism of control?

A

-several mechanisms
-regulate which genes are transcribed and the rate of transcription
-called transcription factors

91
Q

what are transcription factors?

A

-DNA-binding proteins
-once binded to DNA, recruit RNA polymerase

92
Q

what controls which genes are active on a cell?

A

-the specialization of a cell

93
Q

what is the post-transcriptional mechanism of control?

A

-occurs in the nucleus
-splicing + RNA degradation

94
Q

what is the translational mechanism of control?

A

-occurs in the cytoplasm
-microRNAs bind to mRNAs to inhibit translation
-small interfering RNAs mark the mRNA for destruction by nucleases

95
Q

what is the post-translational mechanism of control?

A

-occurs in the cytoplasm
-phosphorylations of proteins
-folding modifications
-glycosylations

96
Q

what is epigenetics?

A

-study of heritable and stable changes in gene expression
-occurring through alterations of the chromosome rather than DNA sequence
-modify DNA bases and change chromosome superstructure

97
Q

what are examples of epigenetic mechanism?

A

-DNA methylation
-histones modifications
-non-coding RNAs

HEAL1500 (12 decks)

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