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Biochemistry > Exam #4: Transcription, RNA Processing & Control of Gene Expression > Flashcards

Exam #4: Transcription, RNA Processing & Control of Gene Expression Flashcards

1
Q

3 Ways RNA Differs from DNA

A

1) Ribose sugar instead of Deoxyribose
2) No thyamine, Uracil instead
3) Single stranded instead of double stranded

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2
Q

What is the significance of the DNA template in transcription?

A

DNA is the template for the synthesis of the complimentary RNA molecule

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3
Q

2 Differences Between DNA & RNA Polymerase

A

1) RNA Polymerase initiates RNA synthesis without a primer

2) RNA Polymerase is much more error prone

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4
Q

RNA Class Translated into Protein

A

mRNA

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5
Q

DNA Sequence that Specifies Start

A
  • Promoter

- TATA box, CAAT box, & GC rich regions

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6
Q

DNA Sequence that Specifies End

A
  • Terminator

- Polyadenylation

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7
Q

Typical “Layout of a Gene”

A
  • Enhancer elements far upstream of start site
  • Gene-specific (regulatory elements)
  • CAAT or GC rich region
  • TATA box
  • Transcription start point
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8
Q

Alpha-Amanitin

A
  • Toxin found in the “Death Cap” Mushroom
  • inhibits Pol II & blocks synthesis of mRNA
  • Results in liver failure
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9
Q

How does Rifampicin kill bacteria and not harm human cells?

A
  • Potent antibiotic

- Inhibits bacterial RNA polymerase but not human Pol II

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10
Q

Capping

A
  • 5’ methylguanosine cap is put on pre-mRNA

- Distinguishes mRNA from other forms of RNA

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11
Q

Exon

A

Gene region that codes for protein

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12
Q

Intron

A

Gene region that is non-coding & spliced out

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13
Q

pre-mRNA splicing

A
  • Removing introns from pre-mRNA

- Spliceosomes: recognize boundaries, cleave, & rejoin

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14
Q

Outline the Process of Splicing

A
  • Adenine residue attacks the 5’ splice site & cuts backbone
  • 5’ end becomes covalently attached to adenine, forming a loop
  • Newly generated free 3’ end reacts with the next 5’ end to join the exons together
  • Lariat intron structure is released
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15
Q

How are the boundaries of introns and exons defined?

A
  • 5’ splice site
  • 3’ splice site
  • branch point in middle
  • AGG consensus sequence
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16
Q

Alternative Splicing

A
  • Splicing different combinations of exons together to generate different proteins
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17
Q

Polyadenylation

A
  • Tail of roughly 200 adenine nucleotides added to mRNA

- unique to mRNA

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18
Q

B-Thalassemia & Splice Errors

A
  • Incorrect splicing leads to reduced synthesis of the B-chain of Hb
  • Less B chain= less Hb & profound anemia
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19
Q

PKU & Splice Errors

A
  • Lack of phenylalanine hydroxylase activity results in an inability to convert phenylalanine to tyrosine
  • Arises from a single base change in 5’ splice site of phenylalanine hydroxylase gene
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20
Q

HAT

A
  • Histone acetyltranferases= acetylate lysine residues in histones
  • decreases net positive charge of histone & loosens interaction with negatively charged DNA
  • ACTIVATE transcription
21
Q

HDAC

A
  • Histone deacetylases
  • Remove acetyl grouops
  • INHIBIT transcription
22
Q

DNA Methylation

A
  • DNA can be methylated on cytosine
  • Attracts HDACs
  • INHIBITS transcription
23
Q

Helix-turn-Helix Protein

A
  • Alpha helix, short amino acid chain, alpha-helix
  • Side chains close to the C-terminal of helices binds DNA
  • E.g. Homeobox proteins
24
Q

Zinc Finger Protein

A
  • Contain zinc as a structural element
  • Alpha-helices bind DNA
  • E.g. glucocorticoid receptor
25
Q

Leucine Zipper Proteins

A
  • Form dimers with two alpha-helices joined to form a coiled coil
  • E.g. Fos & Jun
26
Q

How do DNA-binding proteins regulate transcription?

A
  • Act as nucleation sites for more proteins

- Recruit HATs, HDACs or chromatin remodeling complexes to DNA

27
Q

How is transcription of the LDL-receptor gene enhanced in response to low cholesterol?

A
  • Promoter region for LDL receptor gene contains SRE-1 (sterol responsive element-1)
  • low cholesterol, SREBP-1a (sterol responsive element binding protein-1a) enter the nucleus and binds SRE-1
  • Recurits HAT
  • Chromatin relaxes and transcription of LDL-receptor increased
28
Q

How does cortisol regulate transcription?

A

See Diagram

29
Q

How do the thyroid hormone receptor and retinoid X receptor (RXR) act together to regulate transcription in response to thyroid hormomne?

A

See Diagram

30
Q

What are the roles of CREB & CBP in protein kinase A mediated transcriptional control?

A

See Diagram

31
Q

Rubenstein-Taybi Syndrome

A
  • Intellectual Disability

- Caused by mutations in CBP or EP300

32
Q

Tamoxifen

A
  • Competitive inhibitor of the estrogen receptor

- Tamoxifen + ER bind DNA but don’t recruit proteins to activate transcription

33
Q

Why is it acceptable for RNA polymerase to be much more error prone than DNA polymerase?

A

RNA is not the permanent repository of genetic information; DNA is

34
Q

Pol I

A
  • rRNA (ribosomal)
  • 28S, 18S, 5.8S, all come from one large rRNA
  • NOT 5S rRNA
35
Q

Pol III

A
  • tRNA(adapter between mRNA & amino acid)

- 5S rRNA

36
Q

Pol II

A

mRNA (messenger)

37
Q

Consensus sequence

A

Similar sequences of DNA found between different genes examined (promoters & terminators)

38
Q

General Transcription Factors

A
  • Required by Pol II to start transcription

- TFIID Complex (Transcription Factor for Pol II)

39
Q

TBP

A
  • Major component of TFIID complex

- Directs TFIIE, F, H & Pol II to promoter

40
Q

Transcriptional Initiation Complex/ Basal Transcription Complex

A

TFIID, E, F, H & Pol II assembled at the promoter

41
Q

Why are promoter regions rich in AT bases?

A

Easier to pull apart b/c they only contain two hydrogen bonds

42
Q

What catalyzes the separation of DNA for transcription?

A

DNA Helicase activity of TFIIH

43
Q

Additional transcription factors for high rate transcription

A

SP-1 & NF 1

44
Q

SP-1

A
  • high rate transcription factor

- binds GC-rich sequences

45
Q

NF1

A
  • high rate transcription factor

- binds CAAT box

46
Q

mRNA degradation

A

1) shortening of the poly-A tail
2) removal of the 5’ cap (triggered by shortening of tail)
3) Degradation by ribonucleases

47
Q

Chromatin Remodeling Complexes

A

Use the energy of ATP hydrolysis to change the structure of nucleosomes so that DNA is less tightly bound

48
Q

Where do regulatory proteins typically bind DNA & why?

A
  • Major Groove

- Where the exposed portion of the bases is located

Biochemistry (17 decks)

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