Chapter 2 Summary (3 Edition)
Gene: Section of DNA for the synthesis of mRNA and proteins
Transcription: Using DNA to make RNA using the same nucleotide language
Messenger RNA (mRNA): RNA that carries the genetic message to ribosomes
Translation: Ribosome translates the language from nucleotides to amino acids.
Every 3 nucleotides becomes 1 codon for 1 protein.
Aminoacyl transerases transfers amino acid to transfer RNA (tRNA).
tRNA base pairs with the codon on mRNA via a anti codon.
Base pairing is antiparallel and has Uracil (U) instead of thymine (T).
Types of RNA:
There are many different types of RNA in the cell. mRNA and tRNA are an example.
RNA and DNA both contain a chain of nucleotides however RNA has a ribose sugar
instead of a deoxyribose sugar in DNA. Ribose sugar has a hydroxyl (OH) on the
The nucleotides are held together by phosphates that join the 5’ end of one sugar to
the 3’ end of another sugar.
The convection is that bases are read from 5’ to 3’. Bases closer to 5’ end are
‘upstream’ and those closer to the 3’ end are ‘downstream’.
All RNA is the same. Only difference is the sequence of nucleotides and length are
RNA is usually single stranded.
Primary structure of mRNA is just the sequences. Secondary the structure is caused
by some complementary bases within the sequence pairing up (going for a movie,
getting married and living long ever after. Jk.) and folding on itself.
Example of secondary structure is the hairpin. Antiparallel pairing and forms a helix.
Here G can pair with U or C. More base pairs, more stability.
Tertiary structure that is given is the pseudoknot which is when the unpaired region
of a hairpin (top part) pairs with a single strand of RNA.
RNA processing and modification:
The folding mentioned above are non-covalent changes. Only hydrogen bonds occur.
During RNA processing and modification, covalent changes take place.
RNA processing: Breaking and making phosphate bonds. Extreme but this can
involve adding or removing nucleotides. RNA modification: Altering bases and sugars. Eg. Methylating rRNA or enzymatic
alteration of tRNA.
Transcription: Synthesis of RNA from a DNA template.
Structure of Bacteria RNA Polymerase:
RNA polymerase makes all RNA except for Okazaki fragments.
About 2000 in a cell, one of the largest and has 6 subunits.
The core enzyme has 5 subunits: 2 aplha, 1 beta, 1 beta’ and 1 omega. Beta are
Sixth subunit is the sigma factor. Need for initiation of transcription and leaves after.
With the sigma factor, the RNA polymerase is known as a holoenzyme.
The sigma 2 region of the sigma factor bind to the -10 region of the promoter while
sigma 4 contacts the -35 region.
Overview of transcription:
RNA polymerase binds the 5’ phosphate group of the nucleotide to the 3’ hydroxyl of
the nucleotide before it.
RNA polymerases do not need primers to initiate synthesis of RNA.
RNA polymerase binds to the promoter sequence and separates the stands by itself
(no helicase needed).
Complementary nucleotides start binding to template. RNA polymerase catalyzes
the reaction of attaching the alpha phosphate of the new nucleotide to the 3’
hydroxyl group of the recently added nucleotide.
The strand of DNA that is being used in the process is called the template strand
while the other DNA strand is called the coding strand, as it is identical to the new
RNA polymerase does not transcribe the whole molecule in one go and therefore
starts at certain sites called promoters.
RNA polymerase recognizes a T or C in the promoter called the transcriptional start
site. Sequences 5’ of the site are upstream and 3’ of the site are downstream.
RNA polymerase recognizes different promoters depending on which sigma factor it
has attached. Most com