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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
what is the role of topoisomerase?
-prepares DNA for helicase -stops DNA from supercoiling
26
what is the role of helicase?
-unwinds DNA by breaking hydrogen bonds between bases
27
what is the role of DNA polymerase?
-adds new DNA nucleotides
28
what is the purpose of Single Strand Binding proteins (SSBs)?
-stabilize DNA strands (keep them seperate)
29
what is the role of primase?
-puts RNA primers on each strand to allow DNA polymerase to begin -replaced at the end by DNA nucleotides
30
what is the role of DNA polymerase delta and flap endonuclease?
-remove RNA from the okazaki fragments
31
what is a mutation? how is this taken care of?
-error in replication -sequence of bases in new strand is not identical to template strand -repair enzymes usually fix it
32
what happens when repair enzymes cannot fix a mutation?
-genetic variability is introduced -new allele that alters the phenotype
33
does only one origin exist in a DNA strand?
-No! -more than 1 origin is necessary for efficiency
34
what is RNA?
-ribonucleic acid -assists in processing genetic information -gene regulation + producing proteins
35
what is the structure of RNA?
-single strand of nucleotides
36
what are RNA nucleotides made of?
-3 subunits -phosphate -pentose sugar (ribose sugar) -nitrogen containing base
37
what are the 4 nitrogen containing bases in RNA?
-adenine -uracil -cytosine -thymine
38
is uracil a pyrimidine or a purine?
-pyrimidine like thymine
39
what are the types of RNA?
-mRNA (messenger) -rRNA (ribosomal) -tRNA (transfer) -small non coding RNAs
40
when and where is mRNA produced?
-during transcription -in the nucleus -DNA is used as a template
41
what is mRNA's purpose?
-carry genetic info from DNA to ribosomes in the cytoplasm (for protein synthesis)
42
where and how is rRNA produced?
-in the nucleolus -using a DNA template
43
what will rRNA eventually form? how is this done?
-ribosomal subunits -4 sizes of rRNA join with proteins to form the large ribosomal subunit and the small ribosomal subunit
44
what happens after ribosomal subunits are formed?
-leave the nucleus -attach to the endoplasmic reticulum or remain free in the cytoplasm -will combine to form a ribosome during protein synthesis
45
where and how is tRNA produced?
-in the nucleus -using DNA as a template
46
what is the purpose of tRNA?
-transfer amino acids to the ribosomes during protein synthesis -each tRNA will carry a different amino acid
47
how many types of amino acids are there?
-20/21
48
what is the 3 base sequence that is present on tRNA?
-anticodon
49
what are the 4 classes of small non coding RNAs?
-small nuclear RNAs (snRNAs) -small nucleolar RNAs (snoRNAs) -microRNAs (miRNAs) -small interfering RNAs (siRNAs)
50
what are small nuclear RNAs purpose?
-splicing mRNA before it leaves the nucleus
51
what are small nucleolar RNAs purpose?
-modify the ribosomal RNAs within the nucleolus
52
what are microRNAs purpose?
-attach to mRNAs in the cytoplasm -prevents unnecessary translation -when the cell is down regulating the production of specific proteins
53
what are small interfering RNAs purpose?
-attach to mRNAs -prepare them for degradation
54
what is the basic overview of gene expression?
-transcription (1st step) -copies DNA to RNA (mRNA) -translation (2nd step) -makes a protein from the mRNA (mRNA > amino acids)
55
what can be said about each different cells genetic template?
-they are all the same -express different RNAs which lead to cell specific proteins
56
what is the importance of cell specific proteins?
-basis of cell differentiation -basis of cell function
57
what are proteins composed of? how do proteins differ?
-subunits called amino acids -differ b/c of the number and order of amino acids
58
what type of structure is the sequence of amino acids? what type of structure does this lead to?
-sequence is primary structure -leads to tertiary structure (proteins particular shape)
59
what is a codon? what does it represent?
-three base sequence in mRNA -different amino acids
60
how many possible codons are there?
-64
61
how many codons correspond to a specific amino acid? what are the remaining codons?
-61 -remaining 3 are stop codons
62
what is the purpose of stop codons?
-polypeptide termination
63
which codon/amino acid acts as the start codon?
-methionine (AUG)
64
what differs in the transcription of different RNA molecules?
-the RNA polymerase involved -RNA poly 1 (rRNA) -RNA poly 2 (mRNA) -RNA poly 3 (tRNA)
65
what is RNA polymerase?
-large complex that adds RNA nucleotides using base pairing rules -always add on the 3' end
66
what is the only coding mRNA?
-mRNA
67
what does it mean to be a coding RNA?
-leading to/coding for a protein
68
how is mRNA first processed before it leaves the nucleus?
-process primary mRNA into mature mRNA -primary mRNA contains introns and exons -introns are removed leaving only exons in the mature mRNA
69
what are introns?
-segments of DNA that do not code for any part of a protein
70
what are exons?
-segments of DNA that will potentially be translated to produce a protein
71
how are the introns removed from primary mRNA?
-mRNA is spliced -completed by a complex called a spliceosome
72
what is a spliceosome composed of?
-RNA protein complexes (small nuclear ribonucleic proteins) -other various proteins
73
what is alternative mRNA splicing? what does this result in?
-cells only will use certain exons (some exons are removed as well as introns) -different proteins from a single gene
74
what occurs during the final processing of mRNA?
-5' end is capped by an altered guanine nucleotide -3' end is given a tail (addition of multiple adenosine nucleotides)
75
what is the 3' ends tail often referred to as? what is the purpose for this tail?
-polyA tail -increases stability
76
does every mature mRNA molecule that leaves the nucleus result in a protein?
-NO -a portion go to the cytoplasm and are decayed
77
what is the translation complex? how does it work?
-small and large ribosomal subunit joined together (ribosome) -reads the mRNA and elongates the protein by adding amino acids
78
what are the 3 sites of the ribosome involved in translation?
-A site (enters) -P site (elongated) -E site (exits)
79
what are the 3 stages of translation?
-initiation -elongation -termination
80
what occurs during the initiation stage of translation?
-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
what is a reading frame?
-way to divide DNA or RNA into a set of consecutive non-overlapping triplets (codons)
82
how many possible reading frames does each nucleic acid have?
-DNA (6) -RNA (3)
83
what occurs during the elongation stage of translation?
-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
can more that one tRNA occupy the ribosomes different sites?
-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
what occurs during the termination stage of translation?
-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
what does the release factor do?
-binds to the stop codon and cleaves the polypeptide from the last tRNA
87
what is a polyribosome? what does this allow for?
-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
what are the different levels of control of gene expression?
-pre-transcriptional -transcriptional -post-transcriptional -translational -post-translational
89
what is the pre-transcriptional mechanism of control?
-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
what is the transcriptional mechanism of control?
-several mechanisms -regulate which genes are transcribed and the rate of transcription -called transcription factors
91
what are transcription factors?
-DNA-binding proteins -once binded to DNA, recruit RNA polymerase
92
what controls which genes are active on a cell?
-the specialization of a cell
93
what is the post-transcriptional mechanism of control?
-occurs in the nucleus -splicing + RNA degradation
94
what is the translational mechanism of control?
-occurs in the cytoplasm -microRNAs bind to mRNAs to inhibit translation -small interfering RNAs mark the mRNA for destruction by nucleases
95
what is the post-translational mechanism of control?
-occurs in the cytoplasm -phosphorylations of proteins -folding modifications -glycosylations
96
what is epigenetics?
-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
what are examples of epigenetic mechanism?
-DNA methylation -histones modifications -non-coding RNAs

HEAL1500 (12 decks)

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