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

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

Flashcards in Exam #4: Transcription, RNA Processing & Control of Gene Expression Deck (48):
1

3 Ways RNA Differs from DNA

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

2

What is the significance of the DNA template in transcription?

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

3

2 Differences Between DNA & RNA Polymerase

1) RNA Polymerase initiates RNA synthesis without a primer
2) RNA Polymerase is much more error prone

4

RNA Class Translated into Protein

mRNA

5

DNA Sequence that Specifies Start

- Promoter
- TATA box, CAAT box, & GC rich regions

6

DNA Sequence that Specifies End

- Terminator
- Polyadenylation

7

Typical "Layout of a Gene"

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

8

Alpha-Amanitin

-Toxin found in the "Death Cap" Mushroom
- inhibits Pol II & blocks synthesis of mRNA
-Results in liver failure

9

How does Rifampicin kill bacteria and not harm human cells?

- Potent antibiotic
- Inhibits bacterial RNA polymerase but not human Pol II

10

Capping

- 5' methylguanosine cap is put on pre-mRNA
- Distinguishes mRNA from other forms of RNA

11

Exon

Gene region that codes for protein

12

Intron

Gene region that is non-coding & spliced out

13

pre-mRNA splicing

- Removing introns from pre-mRNA
- Spliceosomes: recognize boundaries, cleave, & rejoin

14

Outline the Process of Splicing

- 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

15

How are the boundaries of introns and exons defined?

- 5' splice site
- 3' splice site
- branch point in middle
- AGG consensus sequence

16

Alternative Splicing

- Splicing different combinations of exons together to generate different proteins

17

Polyadenylation

- Tail of roughly 200 adenine nucleotides added to mRNA
- unique to mRNA

18

B-Thalassemia & Splice Errors

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

19

PKU & Splice Errors

- 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

20

HAT

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

21

HDAC

-Histone deacetylases
-Remove acetyl grouops
-INHIBIT transcription

22

DNA Methylation

-DNA can be methylated on cytosine
-Attracts HDACs
- INHIBITS transcription

23

Helix-turn-Helix Protein

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

24

Zinc Finger Protein

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

25

Leucine Zipper Proteins

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

26

How do DNA-binding proteins regulate transcription?

- Act as nucleation sites for more proteins
- Recruit HATs, HDACs or chromatin remodeling complexes to DNA

27

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

-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

How does cortisol regulate transcription?

See Diagram

29

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

See Diagram

30

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

See Diagram

31

Rubenstein-Taybi Syndrome

- Intellectual Disability
- Caused by mutations in CBP or EP300

32

Tamoxifen

-Competitive inhibitor of the estrogen receptor
- Tamoxifen + ER bind DNA but don't recruit proteins to activate transcription

33

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

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

34

Pol I

- rRNA (ribosomal)
- 28S, 18S, 5.8S, all come from one large rRNA
- NOT 5S rRNA

35

Pol III

-tRNA(adapter between mRNA & amino acid)
- 5S rRNA

36

Pol II

mRNA (messenger)

37

Consensus sequence

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

38

General Transcription Factors

- Required by Pol II to start transcription
- TFIID Complex (Transcription Factor for Pol II)

39

TBP

-Major component of TFIID complex
-Directs TFIIE, F, H & Pol II to promoter

40

Transcriptional Initiation Complex/ Basal Transcription Complex

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

41

Why are promoter regions rich in AT bases?

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

42

What catalyzes the separation of DNA for transcription?

DNA Helicase activity of TFIIH

43

Additional transcription factors for high rate transcription

SP-1 & NF 1

44

SP-1

-high rate transcription factor
-binds GC-rich sequences

45

NF1

-high rate transcription factor
-binds CAAT box

46

mRNA degradation

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

47

Chromatin Remodeling Complexes

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

48

Where do regulatory proteins typically bind DNA & why?

- Major Groove
- Where the exposed portion of the bases is located