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1
Q

what is transcription?

A

DNA to RNA

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2
Q

what is translation?

A

RNA to protein

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3
Q

what is the central dogma?

A

DNA->RNA->protein

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4
Q

amount of proteins depends on?

A

amount of transcription

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5
Q

what is RNA?

A

a polymer of 4 diff nucleotides linked together by phosphodiester bonds. (sugar, base, phosphate group) 5’-3’

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6
Q

how are RNA molecules bonded?

A

phosphate group to -OH group

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7
Q

what are 3 differences between DNA and RNA?

A

RNA contains ribose, DNA contains deoxyribose, RNA has uracil as appose to thymine, RNA is single stranded (does base pairing with itself, has a secondary structure) while DNA is double stranded

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8
Q

how does transcription occur?

A

DNA unwinds and one strand is used as a template. RNA chain is produced by adding 1 ribonucleotide at a time via complementary base pairing

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9
Q

what is a transcript?

A

the growing RNA chain off of a DNA

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10
Q

in what direction is the template strand read?

A

3’-5’

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11
Q

what is RNA polymerase?

A

an enzyme that zips down a DNA strand to construct transcript RNA

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12
Q

can many different RNA polymerases make RNA on the same DNA strand?

A

yes

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13
Q

what are some differences between RNA and DNA polymerase?

A

RNA polymerase catalyzes ribonucleotides, not deoxyribonucleotides
RNA polymerase can start a RNA chain without a primer
DNA polymerase has rare mistakes
DNA and RNA polymerase are not structurally related
RNA is much shorter than DNA
RNA strand does not remain H-bonded to DN template (DNA helix reforms)

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14
Q

what is a primer?

A

DNA polymerase needs primer to latch on DNA

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15
Q

what is the final product of noncoding RNA?

A

RNA as final product

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16
Q

what is the final product of mRNA?

A

protein

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17
Q

what is the function of mRNA?

A

used to ribosomes to make proteins

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18
Q

what is the function of rRNA?

A

form basic structure of ribosomes

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19
Q

ribosomes have how many subunits?

A

2

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20
Q

what rRNA does the small subunit have?

A

18S

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21
Q

what rRNA does the large subunit have?

A

5S, 28s, 5.8S rRNA

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22
Q

how do you make rRNA?

A

precursor rRNA undergoes chemical modification and then cleavage

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23
Q

what is tRNA?

A

transfer RNA, adaptors between mRNA and amino acids

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24
Q

what is snRNA?

A

small nuclear RNA, used for splicing

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25
what is snoRNA?
small nuclelor RNA, used when you want to modify the rRNA precursors
26
do different cell types have different genes?
no, cell "fate" is determined by with proteins get turned on, regulated by transcription
27
what is holoenzyme complex?
RNA polymerase and sigma factor
28
describe bacterial transcription
1. homoenzyme assembles and locates promoter 2. DNA starts unwinding 3. transcription begins 4. after 10 nucleotides, polymerase breaks off frfom sigma factor and promoter sequence 5. polymerase zooms down DNA 6. stops transcription at termination sequence 7. everything leaves
29
how does the RNA polymerase know when to start?
promoter sequence
30
what is RNA polymerase II?
transcribe all non-coding genes, mRNA, snoRNA, snRNA
31
what is DNA polymerase III?
tRNA genes transcribed, snRNA
32
what is RNA polymerase I?
rRNA genes transcribed
33
where is 5S rRNA transcribed?
encoded by rRNA polymerase III, not from precursor
34
what is a general transcription factor?
factors that work for every gene
35
what are activators/repressors?
only work for for some genes for differential gene
36
BRE and TATA box are found?
upstream, 30-35 nucleotides down
37
what is TBP?
TATA box bind protein, starting position of transcription
38
what is the order of the General TF?
TFIID, TDIIB, TDIIF, TDIIE, TDIIH
39
what is the role of TFIIF?
to bring TFIIE and TFIIH
40
what is the role of TFIIH?
unwinds DNA, phosphorylates CTD and releases polymerase II from promoter.
41
what is CTD?
part of RNA polymerase on c-terminus, the end of an AA chain. 7 repeated AA sequence 52 times.
42
what is phosphorylation?
last phosphate group of ATP attaches to a protein/lipid -OH group (serine, threonine, tyrosine)
43
what can reverse phosphorylation?
phosphatase
44
why would you phosphorylate CTD?
so proteins can interact with it. RNA processing proteins can interact with RNA
45
what is a cis regulatory element?
binds to gene regulators play a role in the start of transcription at a particular gene
46
what are cis regulatory sequences?
DNA sequences that transcription regulators bind to to turn off/on genes
47
if a mRNA is stable?
you can translate it many times
48
if a mRNA is unstable?
burst of protein expression and itll go away
49
what is a minor/major groove?
grooves in DNA that are smaller/larger
50
base pairings look _____ on a molecular level
different
51
amino acids can bond with specific base pairings because
each base pair has a substituents
52
what is transcriptional control?
controlling when and how often a given gene is transcribed
53
what is RNA processing control?
controlling the splicing and processing of RNA transcripts
54
what is RNA transport and localization control?
selecting which completed mRNAs are exported from the nucleus to the cytosol and determining where in the cytosol they are localized
55
what is translational control?
selecting which mRNAs in the cytoplasm are translated by ribosomes
56
what is mRNA degradation control?
selectively destabilizing certain mRNA molecules in the cytoplasm
57
what is protein activity control?
selectively in/activating degrading, localizing specific protein molecules after they have been made
58
chromatin is wrapped around
histones
59
what are histones made of?
8 proteins, H2A, H2B, H3, H4
60
how do you interact with DNA when it's wrapped around histone?
breathing, DNA has a small opening bc constantly moving, then regulatory elements can latch on
61
what is the role of transcription activators on histones?
DNA on histones open up
62
what are histone chaperone?
bring in a new variant or put in a different histone
63
many variants for all histones except for
h4
64
when are major histones synthesized?
during s phase, assembled into nucleosomes on daughter DNA behind replication fork
65
when are variant histones synthesized?
throughout interphase, inserted into already-formed nucleosomes with the help of histone remodeling complexes
66
what is the function of acetylation in histones?
removes positive charge of lysine and loosens chromatin structure
67
how do you get rid of acetylation?
histone deacetylase complex
68
what is the function of metyhlation?
adds methyl group, not clear as what it does, may or may not be packed
69
what is the job of the mediator?
assemble all components together onto polymerase
70
how do regulators (activors) open up the area?
1. activator bound to the enhancer promote another regulator 2. recruits rna polmyerase to promoter 3. releases rna polymerase to begin transcription 4. if polymerase gets stuck, activator helps release it
71
how to inhibitors work?
1. binds to activator that overlaps with enhancer region, competitive DNA binding 2. site where transcription factors is covered by repressor 3. directly interact with transcription factor so activators cant 4. recruit chromatin remodeling complex to pack up so area isnt available for transcription 5. recruit histone deactylase so acetylation is gone, DNA is packed more tightly 6. recruitment of histone methyl transferase puts methyl groups that make area unavailable for transcription
72
different binding partner can lead to _____ ____
different affects
73
how do you regulate transcription?
1. regulator needs to be made 2. regulator only works if it binds to something else 3. depends on it was modifed or not (phosphorylated or not) 4. inhibitor needs to be taken off 5. needs a second subunit 6. protein that blocks pathway out of nucleus is taken off 7. regulator needs to be cut out of membrane

bio 340 (13 decks)

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