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Chapter 8 Flashcards

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Biology 101 flashcards
1
Q

How do you distinguish different nitrogenous bases

A
  • if purine (double ring), G is more decorated (think GO!)
  • if pyrimidine (single ring), T has more O’s (think TOO)
  • if ribose sugar and pyrimidine, U has the 2 O’s
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2
Q

What are the 3 parts of RNA ribonucleotides

A

1) ribose sugar
2) a nucleotide base
3) one or more phosphate groups

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3
Q

_______ catalyzes the addition of each ribonucleotide to the 3’ end of the growing RNA strand

A

RNA polymerase

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4
Q

What kind of bond does RNA polymerase make?

A

phosphodiester bond

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5
Q

_______ inhibits RNA synthesis in prokaryotes by inhibiting the formation of the _______ phosphodiester bond

A

Rifampicin
first

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6
Q

_______ is produced by protein-encoding genes and is a short-lived intermediary between DNA and protein

A

mRNA

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7
Q

mRNA is the only type of RNA that undergoes _______

A

translation

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8
Q

transcription of mRNA is often followed by _______

A

post-transcriptional processing

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9
Q

_______ are encoded in dozens of forms and are responsible for binding an amino acid and depositing it for inclusion into a growing protein chain

A

transfer RNA

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10
Q

_______ combines with numerous proteins to form ribosomes

A

ribosomal RNA

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11
Q

_______ of various types is found in the nucleus of eukaryotes and plays a role in mRNA processing

A

small nuclear RNA

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12
Q

_______ is active in plant and animal cells and is involved in post-transcriptional regulation of mRNA

A

micro RNA

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13
Q

_______ protects plant and animal cells from production of viruses and movement of transposons

A

small interfering RNA

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14
Q

Certain RNA’s in eukaryotic cells have catalytic activity; these are called _______

A

ribozymes

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15
Q

Transcription is the synthesis of a single-stranded RNA molecule by _______

A

RNA polymerase

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16
Q

RNA polymerase reads the _______ of the DNA to assemble a complementary, antiparallel strand of ribonucleotides

A

template strand

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17
Q

what is another name for the template strand

A

non-coding

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18
Q

what is another name for the coding strand

A

non-template

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19
Q

What are the 4 stages of transcription in bacteria?

A

1) promoter recognition
2) transcription initiation
3) chain elongation
4) chain termination

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20
Q

The _______ is immediately upstream (5’ of the coding strand) to the start of transcription

A

promoter

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21
Q

The _______ of the gene is the portion that contain the information needed to synthesize the protein product

A

coding region

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22
Q

the _______ of the gene regulates the cessation of transcription

A

termination region

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23
Q

The bacterial RNA polymerase holoenzyme is composed of a _______ and a _______ subunit

A

pentameric core
sigma

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24
Q

The large core enzyme of RNA polymerase holoenzyme is composed of _______, _______, _______, _______, _______

A

alpha 1
alpha 2
beta
beta’
w

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25
Q

several types of sigma subunits are available called _______

A

alternative sigma subunits

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26
Q

How do you make a consensus sequence

A

Take the most common letter in each column

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27
Q

a promoter is a _______-stranded DNA sequence that is the RNA polymerase binding site and is required for the initiation of transcription

A

double

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28
Q

_______ or ___ consensus sequnce and __ consensus sequence make up the promotor region in prokaryotes

A

pribnow box or -10
-35

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29
Q

What are the 2 steps in prokaryote transcription initiation

A

1) RNA polymerase holoenzyme makes the closed promoter complex
2) Then unwinds 18bp to make the open promotor complex

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30
Q

After how many bp polymerized does the sigma subunit disassociate?

A

8-10 RNA nucleotides

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31
Q

What are the two different types of transcription termination methods in prokaryotes? Explain each.

A

1) intrinsic termination (most common)
- invert repeat sequence makes hairpin and string of U’s unstablizes the polymerase allowing the hairpin to pull the RNA out
2) rho-dependent termination
- invert repeat makes hairpin however since there are no U’s, the rho protein binds to the RUT sequence (made of C’s) which pulls the RNA out

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32
Q

Eukaryotic genes carry _______ and_______ and require the process of removing _______

A

introns
exons
introns

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33
Q

Eukaryotic DNA is associated with proteins to form _______ which affects its transcription

A

chromatin

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34
Q

What does RNA polymerase I transcribe?

A

3 ribosomal RNA genes

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35
Q

What does RNA polymerase II transcribe?

A

mRNA and most snRNA genes

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36
Q

What does RNA polymerase III transcribe?

A

tRNA
1 snRNA
1 rRNA

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37
Q

Most common eukaryotic promoter consensus sequence? What is its position?

A

TATA box or Goldberg-Hogness box
Position -25

38
Q

Which consensus sequence is found near the -80 position in eukaryotes?

A

CAAT box

39
Q

Which consensus sequence is found near -90 position in eukaryotes?

A

GC-rich box

40
Q

RNA pol II recognizes and binds to promoter sequences with the aid of proteins called _______

A

Transcription Factors (TFs)

41
Q

TFs bind to nearby _______ sequences and interact with _______

A

Regulatory
RNA Polymerase

42
Q

TF’s that interact with pol II are called _______ factors

A

TF II

43
Q

What is TFIID composed of

A

Multisubunit protein containing TBP (TATA-binding protein) (2x) and TAF (TBP -associated factor)

44
Q

What is the initial committed complex composed of?

A

TFIID binded to the TATA box

45
Q

What makes up the minimal initiation complex?

A

TFIID, with the addition of TFIIB, TFIIF, and RNA pol II (image adds TFIIA)

46
Q

What makes up the complete initiation complex?

A

the minimal initiation complex + TFIIE and TFIIH

47
Q

The complete initiation complex contains multiple proteins commonly referred to as _______

A

General Transcription Factors (GTFs)

48
Q

How do we experimentally determine what DNA sequences are binding sites for RNA Polymerase and/or other Transcription factors? (2)

A

Using Band Shift Assay and DNA Footprint Protection Assay

49
Q

How does the Band Shift Assay work? What does it allow us to do?

A

1) Fragments of DNA are isolated and mixed with RNA Polymerase
2) The Fragments that bind to pol will have slower electrophoretic migration
- allows us to determine which DNA fragments are bound by transcriptional proteins

50
Q

How does the Footprint Protection Assay work? What does it allow us to do?

A

1) Fragments are end-labeled with 32P
2) Fragments of DNA are isolated and mixed with RNA polymerase
3) Dnase 1 is added and cleaves DNA not protected by proteins
- Allows us to determine where within fragments a transcriptional protein binds

51
Q

Describe what each variable is in the hardy weinberg equations: p+q = 1 and p^2 + 2pq + q^2 = 1

A

p is frequency of dominant allele
q is frequency of recessive allele

52
Q

Describe what each variable is in the binomial probability equation: (n!/s!t!)p^s q^t

A

n is the total number
s is outcome 1
t is outcome 2
p is the probability of outcome 1
q is the probability of outcome 2

53
Q

What happens if mutations occur inside the consensus region?

A

Reduce levels of transcription

54
Q

What happens if mutations occur outside the consensus region?

A

Nonsignificant effects on transcription

55
Q

What do enhancer sequences do?

A

Increase the level of transcription of specific gene

56
Q

How do enhancer sequences form protein bridges?

A

Bind activator proteins and co-activators that link to the promoter

57
Q

The enhancer and silencer proteins make a bridge that _____ the DNA so that proteins are close enough to interact

A

bends

58
Q

What do silencer sequences do?

A

Repress transcription by using repressor proteins that induce bends in DNA
(These bends reduce transcription of the target gene)

59
Q

How do silencer sequences form their protein bridges?

A

Bind repressor proteins and co-repressors that link to the promoter

60
Q

Ribosomal genes are found in the _______

A

nucleolus

61
Q

What are the 2 functional sequences near the transcription start for RNA Pol I promoters? And what binds to each?

A

1) core element (sigma like factor 1)
2) upstream control element (upstream binding factor 1)

62
Q

Most RNA pol III promoters have an _______

A

Internal Control Region (ICR)

63
Q

What are the 2 scenarios of short DNA sequences for ICR

A

1) box A + box B
2) box A + box C

64
Q

Describe archaeal promoters sequence (2)

A

1) TATA_binding protein (TBP) binds to the TATA box and Transcription factor B (TFB) binds to TFB-recognition element (BRE)
2) RNA polymerase binds

65
Q

What are the 3 steps in eukaryotic post-transcriptional processing?

A

1) 5’ capping
2) 3’ adenylation
3) intron splicing

66
Q

A special enzyme, _______, adds a guanine to the 5’ end of the pre-mRNA

A

guanylyl transferase

67
Q

What kind of bond does guanylyl transferase make?

A

5’ to 5’ triphosphate linkage

68
Q

5’ capping functions
- _______ of RNA from rapid degradation
- facilitating _______ of mRNA out of the nucleus
- facilitating subsequent intron _______
- enhancing _______ efficiency by orienting the ribosome on the mRNA

A

1) protections
2) transport
3) splicing
4) translation

69
Q

Functions of 3’ Polyadenylation
- facilitating _______ of mature mRNA across the nuclear membrane (through nuclear pore complex) to the cytoplasm
- _______ the mRNA from degradation
- Enhance _______ by enabling the ribosomal recognition of mRNA

A

1) transport
2) protect
3) translation

70
Q

Describe the steps to polyadenylation (6)

A

1) cleavage and polyadenylation specificity factor (CPSF) binds near the polyadenylation sequence
2) cleavage-stimulating factor (CstF) binds to U-rich region downstream of the polyadenylation sequence
3) CFI, CFII, and polyadenylate polymerase bind
4) The pre-mRNA is cleaved 15-30 nucleotides downstream of the polyadenylation sequence
5) Cleavage and polyadenylation specificity factor and polyadenylate polymerase add the A’s
6) after 10 adenines poly-A-binding protein (PABII) joins

71
Q

Polyadenylation and transcription termination are connected by the activity of a specialized _______

A

RNase (torpedo RNAse)

72
Q

Pre-mRNA transcript introns are the most common type of intron and are removed by a _______

A

spliceosome complex

73
Q

The presence of intron sequences can be demonstrated by a technique called _______

A

R-looping

74
Q

The 5’ splice site contains a consensus sequence with an invariant _____ dinucleotide at the 5’ most end of the intron

A

GU

75
Q

The 3’ splice site has a consensus with a pyrimidine region and a nearly invariant _______ dinucleotide at the most 3’ end

A

AG

76
Q

The _______ is 20-40 nucleotides upstream of the 3’ end of the intron and contains an invariant adenine called the _______ near the 3’ end of the consensus

A

branch site
branch point adenine

77
Q

Introns are removed from the pre-mRNA by an _______ complex called the spliceosome

A

snRNA-protein

78
Q

The 5’ splice site is cleaved first and a _______ intron structure is formed

A

lariat

79
Q

What does snRNP’s stand for?

A

small nuclear ribonucleoprotein particle (U1-U6)

80
Q

Spliceosome components are recruited to 5’ and 3’ splice sites by _______; these bind to sequences on the exons called _______ and ensure accurate splicing

A

SR proteins
exonic splicing enhancers (ESE’s)

81
Q

What is the difference between cis and trans splicing?

A

Cis: connects exons from single mRNA
Trans: connects exons from multiple mRNA’s

82
Q

What is the difference between intragenic and intergenic splicing? (both are examples of trans splicing)

A

intragenic: exons from a single TYPE of mRNA (can duplicate an exon)
intergenic: exons from more than one TYPE of mRNA fused together

83
Q

The _______ of RNA polymerase II functions as an assembly platform and regulator of pre-mRNA processing machinery

A

Carboxyl-terminal domain (CTD)

84
Q

What are the 3 mechanisms for alternative pre-mRNA processing

A

1) spliced in alternative patterns
2) alternative promoters
3) alternative sites for polyadenylation

85
Q

Group 1 intron SELF-splicing produces a _______ intron sequence, while group 2 intron SELF-splicing produces a _______ intron sequence

A

linear
lariat

86
Q

Some _______ tRNA’s are produced simultaneously with rRNA’s while each _______ tRNA gene is individually transcribed

A

bacterial
eukaryotic

87
Q

Bacterial tRNA processing
1) tRNA’s are _______ from their large precursor transcripts (several tRNA’s can be produced from one transcript)
2) _______ are trimmed from the 3’ and 5’ ends of the molecule
3) certain _______ nucleotides are chemically modified
4) tRNA’s _______ into a precise 3d structure
5) tRNA’s undergo posttranscriptional _______ of bases most commonly CCA at the 3’ end

A

1) cleaved
2) nucleotides
3) individual
4) fold
5) addition

88
Q

in one kind of RNA editing, uracils are added with the assistance of _______ which contains a sequence complementary to the RNA that it edits

A

guide RNA (gRNA)

89
Q

A second type of RNA editing is _______, the frequent replacement of cytosine with uracil

A

base substitution
(can make premature stop codon)

90
Q

Describe how each RNA pol (RNA pol I, II, and III) terminate

A

1) RNA pol I terminates by a string of uracils but no inverted repeat
2) RNA pol II terminates poly-A tail then by torpedo RNAse
3) RNA pol III terminates by Trancription Termination Factor 1

genetics (22 decks)

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