Lecture 1/19 - Central Dogma Flashcards
Does DNA polymerase require a primer
Yes it requires an RNA primer. It can’t get started de novo
Joining of Okazaki fragments
ligase
Requirements for DNA transcription
RNAP, template DNA, UTP, ATP, GTP, CTP and Mg++ or Mn++ ion
How many different tRNAs
61 (3/64 are stop codons)
CAP (catabolic activator protein)
CRP (c-AMP Response Protein)
Name the site where RNA Polymerase II (RNAPII) would bind in order to transcribe this gene
into mRNA
Promoter region
Name the two possible sites where the transcription factor, SREBP, might bind
promotor or enhancer region
What must be loosened or moved out of the way for effective RNAPII binding?
Histones
When cholesterol levels drop, the SREBP moves to the Golgi. Describe what happens that
enables SREBP to activate transcription
Protease clips SREBP to free it from transmembrane domain and it diffuses to nucleus to find its target DNA element
The 45 S pre-rRNA of eukaryotes
a.
Is transcribed by RNA Polymerase I from DNA in the nucleolus region of the nucleus
b. FALSE (not translated) Is processed into 28 S, 18 S, and 5.8 S rRNA pieces that are translated into proteins by
existing ribosomes in the cytoplasm
c.
Provides part of ribosomal structure after it is processed and combined with ribosomal
proteins
d. Is the source of the enzymatic activity for peptidyl transferase present in ribosomes
The synthesis of mRNA in eukaryotes requires…
a.
RNA polymerase II
b. General (basal) transcription factors such as TFIID, TFIIB
c.
DOES NOT need An RNA primer
d. A free 3’ hydroxyl group to which the incoming nucleotide will be attached
Histone acetylases
a.
Loosen the binding of histones to DNA by adding acetyl groups to histones
b. Are recruited by coactivators that may be bound to transcription factors
c. FALSE
Repress transcription until the acetyl group is removed by Histone deacetylases
d. FALSE Are enzymes that are part of the histone H2a, H2b, H3, and H4 structures
Single strand binding proteins
Keep the strands apart
DNA polymerase adds to which end
3’
Which ways does replication proceed in the transcription bubble
Both ways
Topoisomerase (gyrase)
Responsible for straightening out the helixes (unwinds)
Single strand binding proteins
Keep the strands apart
DNA polymerase adds to which end?
3’
Which ways does replication proceed in the transcription bubble?
Both ways
Helicase
The enzyme responsible for separating DNA strands
How many DNA polymerase III’s are in replication bubble
2
Removal of okazaki RNA primers
RNase H and DNA polymerase I
Differences between DNA and RNA polymerase
- RNA polymerase only copies template strand (anti-sense strand)
- Doesn’t require primer
- Doesn’t have editing function
- w/ sigma - holoenzyme; w/o sigma - core enzyme
Function of A site in ribosome
Where we bring in a new amino acid
Function of P site
Holding polypedide site
Function of E site
Let go of polypeptide site
peptidyl transferase
moves polypetide chain off of middle chain onto amino acid
where will methionine be
It will always be at the amino end (N-site) of polypeptide chain (will be sticking up from ribosome)
How many RNA polymerases do eurkaryotes have? Why?
many. Because different polymerases recognize different promoter sequences. Need to be able to regulate mRNA more.
Transcription factors
- Basal transcription factors (need for any transcription)
2. Specific transcription factors
Promoter sequences
DNA that RNA polymerase recognize; will cause RNAP to stop at the right place. In E. Coli, two promoter sequences are -10 and -35 (from +1 start site)/ They are upstream from the gene.
Consensus sequences
The sequences at the promoter site
Initiation
- Finding promoter
- binding
- initiation
What does an element refer to?
a section of DNA, not RNA
RNAP transcription bubble
Appears to move because RNAP does the unwinding job itself and RNA closes on its own
Methods for RNA transcription termination
Rho protein (pull strand off), or hairpin (requires palindromic sequence)
How do you tell the difference between a weak and strong promoter
By their difference in distance from the transcription start point. Will change the rate of transcription
TATA-box-binding-protein (TBP)
Binds to DNA first, then attracts other binding factors
Purpose of the phosphorylation of mRNA tail
Causes RNAP to leave (start transcription)
Where are enhancer sequences located along the DNA
They are a distance away from gene. Can be upstream/downstream/on another stand (trans). They bind other activators
What are silencer elements
Like an enhancer element, but it binds other repressors than promoter’s
cis-acting elements
They are on the same strand. This is the only one prokaryotes have.
trans-acting elements
Possible with eukaryotes where the enhancer/silencer element is present on a different strand (chromosome)
How do coactivators activate transcription?
They modify or remove histones with acetyltransferases (HATS)
Histone acetylase (HATS)
adds acetyl to R group of lysine on histone tails
Histone deacetlyase (HDAC)
removes acetyl, which represses transcription
What is the effect of acetylation?
Enhances transcription by removing histones
