Chapter 5 Flashcards
Similarities between DNA and RNA
Similarities
- uses A, C, G
- has sugar phosphate backbone
- both have phosphodiester bond
- A-U and A-T
Differences between DNA and RNA
RNA
- ribose sugar (5C ) that has an extra O on the second carbon therefore has (OH) on the second carbon
- uses Uracil not Thymine
- single stranded
- complementary nature - can fold into specific 3-D structure
DNA
- deoxyribose
- uses Thymine
- Double stranded
- anti parallel
- cant fold into itself
What is transcription
It is the process that produces RNA strand that is complementary (opposite) to one of the strand of DNA
describe the process of transcription
- RNA polymerase binds to the promoter gene on the template strand (antisense strand)
- RNA Polymerase unwinds the double helix of just that gene region
- the RNA strand synthesize in the direction of 5’ ——> 3’ therefore the template strand is being copied in 3’ ——-> 5’ direction
- the RNA copies the strand using ribose sugar and uracil
- RNA polymerase stops once it reaches the terminator gene
- the mRNA strand is formed ( complementary/opposite to template strand)
- many RNA polymerase can transcribe a gene at the same time.
- also RNA is transcribe gene by gene, when gene is transcribed it then goes to form the protein instead of transcribing the second gene
Describe the three types of RNA and its function
1- mRNA : Messenger RNA, an intermediate of gene and a polypeptide
- codes for protein
2- ribosomal RNA
- Forms the core of the ribosome structure
- Catalyze protein synthesis
- MicroRNA
- regulate gene expression
3- TransferRNA
- serves as adaptors between mRNA and amino acids during protein synthesis
- Other noncoding enzymes eg: snRNA , snoRNA, miRNA, incRNA.
- gene regulation, telomere maintenance, RNA splicing
What is a gene
Segment of DNA thats contains instruction/information ( sequence of nucleotide bases/ nucleotide code) to produce an RNA molecule and protein
FLOW OF INFORMATION
Describe briefly, the overview of the flow of information in a cell
1- TRANSCRIPTION copies a segment of DNA gene into a pre mRNA
2- the pre- mRNA is PROCESSED into a mature mRNA( only in eukaryotes)
3- the mature mRNA is EXPORTED out of nucleus to the cytoplasm
4- the mRNA is TRANSLATED by ribosomes using tRNA
The mRNA is read out in codon by————-
Ribosome
What is ribosomes made of
rRNA and proteins
Similarities between mRNA and tRNA and ribosomes sub units
Both are made in nucleus and then translocate to the cytoplasm
Every gene isn’t transcribed at the same rate - T/F?
True
The codon/anticodon of mRNA is transcribed to the anticodon/codon of tRNA
Codon
Anticodon
One anticodon is specific to 1 tRNA T/F
True
TRANSCRIPTION IN GENERAL
What is a tata box
A tata box is a sequence of TATA nucleotides that acts as the promoter gene for RNA polymerase II
Where does RNA polymerase bind on a template gene
Between the TATA box and + 1
Describe the promotor region
The promotor region is a specific sequence of nucleotides , usually AT rich
RNA polymerase binds to this region to initiate transcription however the enzyme requires the help of transcription factors to recognize the promotor region
Describe the terminator region
A specific region on the template strand with GC rich nucleotide. This can cause the RNA POLYMERASE II to stop transcribing
Describe in detail the gene transcription initiation by RNA POLYMERASE II
1- the TBD region on TFIID ( TATA binding protein) binds to the TATA box
2- this causes a conformal change in DNA ,it bends
3- TFIIA and TFIIB binds to the PROMOTER
4- the TFIIF on RNA POLYMERASE to the promotor
5- the TFIIE and then the TFIIH binds to the promotor completing PIC
Function of TFIID, TFIIA , TFIIB
TFIID – binds to DNA at the core promoter and bends DNA which is important for recruiting other tfs (eg: TFII A and B)
TFIID TFIIA and TFIIB forms protein - protein interactions to recruit RNA pol II
Function of TFIIH
- it pries apart the DNA double helix at +1 exposing the template strand
- also acts as protein Kinase ( together with other kinase ) to phosphorylate RNA pol II to activate it
Overall the function of GTS is (6gtfs + other)
6GTs - recruit RNA Pol II and initiate transcription
Other gts - Regulate the rate of transcription , to allow transcription further bcz the 6GTFs only allow minimal trancription
What happens After all 6 GTFS bind ( after complete initiation complex forms)
TFIIH and other kinase phosphorylates RNA POL II by THIIF also acting as protein kinase to catalyze the phosphorylation
GTFS dissociate
Why are additional transcription factors needed
Because the 6 GTPS only allow for minimal transcription.
If DNA sequence is an enhancer, ———- binds , which ——— the rate of transcription
Activator binds
Increses
If DNA sequence is a silencer, ———— binds , the rate of transcription ———
Repressor
Decreases
Sites at which activator or repressor bind is same - T/F
False
Difference and similarities between eukaryotes and prokaryotes transcription
Differences
1 Transcription mechanism
Different factors used in both cells
2 RNA POLYMERASE
Only 1 type in prokaryotes
Three types in eukaryotes
SIMILARITIES
Both have similar promotor and terminator with only slight differences
How many upstream and downstream do each GTF occur
TFIIB= -35
TBP subunit of TFIID= -30
TFIID = starting site of transcription
TFIID = +35
Types of RNApolymerase and gene transcribed
RNA POLYMERASE I - Most rRNA genes
RNA POLYMERASE II. - All protein coding genes, miRNA, genes of non coding RNAs
RNA POLYMERASE III - tRNA genes, 5SRNA genes, genes of other small RNAs
Precursor of pre- mRNA
heterogeneous nuclear RNA - hnRNA
Describe hnRNA
hnRNA is same as pre mRNA - precursor of mature mRNA
Found in nucleus
Has large molecular weight - exons +introns
Processed to make mRNA ( mature)
Where does processing of pre mRNA occur
Factories within the nucleus
What are the steps in the processing of the RNA
7-Methylated guanosine + 5’5 triphosphate bridge - 5’ cap
Polyadenilation - poly A tail
5’ CAP - explain the steps
1- capping ENZYME recruits a methylated guanosine to the 5’UTR / noncoding end = 7-methylated guanosine ( ribose + sugar - CH3 )
2- a 5’5 triphosphate bridge forms between 5’ of methylated guanosine and 5’ of nucleotide
3- the previously first 1st nucleotide becomes the 2nd after addition of 5’ cap
4- the 2nd nucleotide becomes methylated - 2’ - O - methyl-ribonucleoside ( phosphate + base + ribose - OCH3 )
Functions of 5’ cap
- protects RNA from exonuclease
- helps in transportation from nucleus to cytoplasm
- plays a role in initiation of translation
Describe Polyadenilation
- endonuclease ENZYME binds to the 3’ UTR
- adds 250 - 500 adenosines forming a tail
- tail starts 20 bases downstream from the AAUAAA Polyadenilation signal
Function of Polyadenilation
1 - protects the RNA from exonuclease
2 - Allows mRNA purification by affinity chromatography
By removing mRNAs from rest of the soultion
Function of endonuclease
Cleaves pre - mRNA downstream from the signal
Function of C terminal RNA POL II
serves as a scaffold for other factors involved in RNA processing
Pre-initiation complex ……….
Complete initiation complex …………
Pre-initiation complex = DNA + TFII D
Complete initiation complex = DNA + RNA poly + 6 GTFs
