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Biochem exam 3 > Lecture 36: Transcription > Flashcards

Lecture 36: Transcription Flashcards

1
Q

**3 steps of making proteins from DNA

A
  1. Transcription
  2. mRNA editing (ONLY EUKARYOTES)
  3. Translation
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2
Q

**In transcription, the info from DNA is copied into a complimentary strand of RNA. This RNA copy is called __________.

A

mRNA

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3
Q

What are segments of DNA that encode information from our genome?

A

Genes

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4
Q

**What are the DNA sequences that get translated? What typically separates them?

A
  1. Exons
  2. Introns

Genes include DNA sequences that encode for all exons and introns and those sequences at the beginning and end of the RNA that are not translated into a protein.

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5
Q

** What is the DNA sequences that does not get translated because it is spliced out during RNA processing?

A

Intron

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6
Q
  1. What introns cut themselves out?
  2. What introns need the spliceosome to get cut out Spliceosomes are made up of other non-coding RNAs
  3. What introns need enzymes to get cut out?
A
  1. Group I and II
  2. Nuclear pre-mRNA
  3. tRNA
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7
Q

What are the sequences at the beginning and end of the RNA that are not translated into a protein called?

A

Normally called the 5’ and 3’ UTR (untranslated region) in the mRNA.

5’ UTR: “Pre mRNA”
3’ UTR ”poly(A) tail”

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8
Q

**What does the 5’ UTR contain in DNA? vs mRNA?

**What does the 3’ UTR contain in DNA? vs mRNA?

A
  1. DNA: the promoter for transcription; RNA: promoter for translation and expression regulatory elements
  2. DNA: the terminator sequence for transcription; mRNA: contains the signal for the addition of the Poly(A) tail and expression regulatory elements.
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9
Q

***Transcription is gene specific, what does this mean?

A

Each gene provides instructions for a SINGLE protein (If on = only ONE gene is transcribed)

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10
Q

What is it called when genes are transcribe CONTINUOUSLY independent of cell health/environment?

A

Constituitive expression: - Usually seen for those proteins that are needed 100% of the time - Example: ATP synthase, actin, tubulin

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11
Q

**What type of expression typically involves ONE OF MORE SIGNAL TRANSDUCTION PATHWAYS that signal the cell from the outside or inside to start transcription? What is the purpose?

A
  1. Regulated expression
  2. allows for much tighter control of gene expression
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12
Q

What are the 2 main ways DNA is freed from histones? What is targeted in each?

*HY: know the types, details not as impt

A
  1. Histone acetylation: histone acetyl transferases (HATs) add an acetyl group (CH3CO) to the histone —> neutralizes the positive charge of the histone
  2. Histone methylation: a methyl group is transferred to either lysine (K) or arginine (R) ONLY on the histone protein —> weakens histone attraction to DNA
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13
Q

All genes (eukaryotic and prokaryotic) have a unique region of DNA sequence upstream of the transcriptional start site, what is this called? What binds here?

A
  1. PROMOTERS
    **2. binding site for RNA polymerase enzymes
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14
Q

**Functions of promoters (3) in transcription?

A
  1. Provides specificity (tells cell WHERE the gene of interest is)
  2. Tells RNA polymerase where to start (***No promoter (or mutated promoter) ->no transcription)
  3. Indicates WHICH strand will be transcribed and the direction of transcription
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15
Q

What is the consensus sequence of a promoter? If its mutated, what will happen?

A
  1. It is the few common sequence elements that are evolutionarily conserved and part of most promoters
  2. NO TRANSCRIPTION
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16
Q

**What are the 3 major consensus sequences of promoters? Where are they located?

A

1) TATA box (TATAAA): located -25 to -30
2) CAAT/CCAAT box: Located -70 to -80
3) GC box (typically GGGcGG): found ~ -110 bps.

***The #s equal the number of nucleotides they are located away from the start of the 1st EXON (ATG/AUG)

17
Q

**Mutation of WHICH consensus sequence of a promoter typically lowers the rate of transcription significantly?

A

***CAAT/CCAAT box

18
Q

What type of cells have THREE RNA polymerases and none of them recognize the promoter sequences directly?

A

Eukaryotic cells

19
Q

**1. What does RNA polymerase I produce?
**2. What does RNA polymerase II produce?
3. What does RNA polymerase III produce?

A
  1. Ribosomal RNA (rRNA)
  2. Messenger RNA (mRNA)
    **ALLLLL mRNA is made by RNA pol II
  3. Some types of rRNA and tRNA
20
Q

What are the class of proteins that bind to DNA and help to recruit RNA polymerase enzymes to promoters?

A

Transcription factors

21
Q

What is the common set of transcription factors used by all promoters to get transcription started (give low levels of transcription)?

A

Basal transcription factors

22
Q

What are the transcription factors that provide more specific transcriptional control by activating or repressing transcription above/below basal levels?

A

Regulatory transcription factors

Regulation of eukaryotic genes is usually positively regulated

23
Q

Steps of basal transcription factor binding to the promoter and RNA pol II (mRNA) recruitment?

A
  1. TBP subunit of TFIID binds to TATA box —> alters DNA shape
  2. TFIIA/TFIIB can bind to the new shape
    TFIIA: stabilizes intxn between TBP/DNA
    TFIIB: helps find start site of transcription
  3. TFIIF brings in RNA pol II to interact with complex and other factors help it interact
  4. TFIIH serves as Helicase to help separate strands
24
Q

How does RNA pol II stop transcribing in eukaryotic cells vs prokaryotic?

A

Eukaryotic: have characteristic termination sequences that are rich in As and Ts but no CLEAR term signal, termination is coupled to mRNA processing

Prokaryotic: RNA pol II transcribes a terminator signal (spike in the road) to slow does RNA pol II and weaken DNA/RNA intxn

25
Q

Where does RNA processing occur?

A

In the nucleus BEFORE the mRNA leave to go to the cytosol

26
Q

RNA processing: 5’ capping of the mRNA

A
  1. GUANINE is added to 5’ end via 5’-5’ linkage to 1st nucleotide
  2. Guanine is methylated to 7-methyl guanosine
    ***3. Cap-binding proteins attach to the cap
27
Q

***Purpose of cap-binding proteins in mRNA capping?

A
  1. protects mRNA from RNases in cytoplasm
  2. Indirectly allows mRNA to attach to small ribosomal subunit for translation
28
Q

RNA processing: addition of poly-A tail to 3’ (back) end

A
  1. poly(A) polymerase detects a consensus sequence AAUAAA near mRNA end and cuts it ~25 nucleotides downstream
  2. Then it adds 50-200 ADENINES to the cut end
29
Q

***Purpose of the poly A tail?

A

**1. Protects the 3’ end of the mRNA from RNases
**2. Allows cell to regulate mRNA stability (Longer tail = longer life span)
3. Helps in mRNA ribosome binding

30
Q

What are the stretches of noncoding sequences that MUST be removed from mRNA (MC in eukaryotes)?

A

INTRONS

31
Q

How are group I/II introns removed (found in rRNA and some bacterial genes)?

A
  1. They use guanosine to excise themselves out and “glue” the remaining exons together
32
Q

What type of introns from lariats when removed that are degraded by lysosomes in the cytosol?

A

Nuclear pre-mRNA introns

Biochem exam 3 (11 decks)

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