Chapter 13 pt.1 Flashcards
Ribozymes
These catalytic RNA molecules can cut out part of their won sequences, connect some RNA molecules together, replicate others, and catalyze the formation of peptide bonds between amino acids
What was the RNA hypothesis?
Early in the history of life, RNA probably served both as the original genetic material and as biological catalyst
What is the difference between RNA and DNA?
- RNA has ribose and DNA has deoxyribose
(The difference arose from the presence/absence of an hydroxyl group) - RNA is sensitive alkaline hydrolysis and DNA is more resistant to alkaline hydrolysis
- RNA is normally found as single-stranded and DNA is normally found as double stranded
Explain what RNA secondary strictures are?
They are often hairpin loop/stem-loop structure
They are antiparallel
These secondary structures are formed from hydrogen bonding interactions
Ribosomal RNA
Ribosomal protein subunits make up the ribosome
Messenger RNA
Carries the coding region for a polypeptide chain from DNA to a ribosome
pre-messenger RNA
Intermediate product of transcription and is unique to Eukaryotes only
Transfer RNA
serves as the link between the coding sequence of nucleotides in an mRNA molecular and attaches to one particular type of amino acid and helps incorporate that amino acid into a polypeptide chain
CRISPER RNAs
It assists in the destruction of foreign DNA molecules and prokaryotes only
What are the three things that RNA transcription need?
- A DNA template
- The raw material – rNTPs – needed to build a new RNA molecules
- The transcription apparatus consisting of proteins necessary for catalyzing the synthesis of RNA
How does transcription appear under a microscope?
The transcription apparatus appears as a Christmas Tree, where the tree Trunk is equal to DNA and the branches represent RNA, and as the branches increase, it is indicative of transcription completing or going on
Explain Transcription
An RNA molecule that is complementary and antiparallel to the DNA template strand is synthesized; the RNA transcript has the same polarity and base sequence as the non-template strand expect that it contains U rather than T; in most organisms, each gene is transcribed from a single DNA strand, but different genes may be transcribed from different strands
Template strand
The nucleotide used for transcription
Non-template strand
The nucleotide that is not transcribed but is similar in sequence to the transcribed RNA with the U and T replaced
Transcription Unit
Is a stretch of DNA that encodes an RNA molecule and the sequences necessary for its transcription
What are the three components that make up the transcription unit?
The promoter, an RNA coding-sequence, and a terminator
Promoter
Is a DNA sequence that the transcription apparatus recognizes and binds, it indicates which of two DNA strands are the template, direction of transcription, transcription start site, and the first nucleotide to be transcribed
RNA coding sequence
A sequence of DNA nucleotides that is copied into an RNA molecule
Terminator
A sequence of nucleotides that signal where transcription is to end and part of the RNA coding sequence
Describe Transcription Elongation
RNA is synthesized from rNTPs, nucleotides are added one at a time to the 3’-OH group of the growing RNA molecule, two phosphate groups are cleaved from the incoming nucleotide to the growing RNA molecule
PPi
Pyrophosphate
What are the similarities between replication and transcription?
Nucleotides are always added to the 3’-OH end of the RNA molecule, like DNA molecule in replication, the direction of transcription is from the 5’ to 3’ end, just like DNA replication
What are the differences between replication and transcription?
Unlike DNA synthesis, RNA synthesis does not require a primer
RNA polymerase
They carry out all required steps in transcription
Explain Bacterial RNA polymerase
- One type of RNA polymerase that catalyzes the syntheses of mRNA, tRNA, rRNA, and Crisper
- Multimeric protein – multiple protein subunits
- Made up of 5 subunits: 2 alpha subunits, 1 beta subunit, 1 beta prime subunit, and 1 omega subunit
- Omega subunit does not participate in transcription, it stabilizes the enzyme
- The sigma factor directs the binding of the polymerase
The sigma factor
It controls the binding of RNA polymerase to the promoter, without sigma, RNA polymerase initiates transcription at random point along the DNA, when it binds to the subunit to forms a holoenzyme
The sigma factor is required only for the promoter binding and initiation; after a few RNA nucleotides have been joined together, sigma usually detaches from the core protein
Rifamycin
An antibiotic that targets the RNA polymerase in bacteria
RNA polymerase I
Eukaryotic; large rRNAs
RNA polymerase II
Eukaryotic; pre-mRNAs, mRNAs
RNA polymerase III
Eukaryotic; tRNAs
What steps are involved in RNA transcription initiation?
- The promoter recognition site
- Formation of a transcription bubble
- The creation of first bond between rNTPs
- Escape of the transcription apparatus from the promoter
Consensus Sequence
Is the set of the commonly encountered nucleotides usually implies that the sequence that posses considerable similarity; similar location with respect to start site
-10 consensus sequence
Pribnow box is often written simply as
5’-TATAAT-3’
3’-ATATTA-5’
-35 consensus sequence
5’-TTGACA-3’ , which lies approximately 35 nucleotides upstream of the start site
Explain Transcription Process
- The sigma factor associates with the core enzyme to form a holoenzyme
- This binds to the -35 and -10 consensus sequences in the promoter
- The holoenzyme binds to the promoter tightly and unwinds the double-stranded DNA
- An rNTP complementary to the base at the start site serves as the first nucleotide in the RNA molecule
- Two phosphate groups are cleared from each subsequent rNTP, creating an RNA nucleotide that is added to the 3’ end of the growing RNA molecule
- The sigma factor is released as the RNA polymerase moves beyond the promoter
What happens at the 5’end?
The RNA molecule contains three phosphate groups
Abortive initiation
- Occurs in both prokaryotes and eukaryotes
- Often in the course of initiation, the polymerase repeatedly generates and releases short transcripts, from 2 to 6 nucleotides in length, while still bound to the promoter
- After several abortive attempts, the RNA molecule synthesizes 9 to 12 nucleotides in length, which allows the polymerase to transition to the elongation stage
How is the accuracy of transcription maintained?
Rho-dependent Termination Process
Rho-independent termination Process
