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Chapter 12: Gene Expression at the Molecular Level - Coggle Diagram
Chapter 12: Gene Expression at the Molecular Level
Central dogma
transcription
produces an RNA copy of a gene, mRNA which functions to carry information from the DNA to cellular components called ribosomes
Initiation
a protein called sigma factor binds to RNA polymerase, the enzyme that synthesizes strands of RNA
sigma factor recognizes the base sequence of a promoter and binds there - sigma factor causes RNA polymerase to bind to the promoter
the initiation stage is completed when the DNA strands are separated near the promoter to form an open complex that is approximately 10–15 bp long.
Elongation
RNA polymerase synthesizes the RNA transcript
sigma factor is released and RNA polymerase slides along the DNA in a way that maintains an open complex as it goes
DNA strand that is used as a template for RNA synthesis is called the template strand
for protein-encoding genes, the opposite DNA strand is called the coding strand
coding strand has the same sequence of bases as the resulting mRNA, except that the RNA has uracil instead of the thymine found in the DNA
the coding strand is so named because, like mRNA, it carries the information that codes for a polypeptide
nucleotides bind to the template strand and are covalently connected in the 5′ to 3′ direction
the complementarity rule used in this process is similar to the AT/GC rule of DNA replication, except that uracil (U) in RNA substitutes for thymine (T) in DNA
in bacteria, the rate of RNA synthesis is about 40 nucleotides per second, behind the open complex, the DNA rewinds back into a double helix
Termination
RNA polymerase reaches a terminator
newly made RNA transcript to dissociate from the DNA
when multiple genes within a chromosome are transcribed, the DNA strand that is used as the template strand varies among the genes
translation
process of synthesizing a specific polypeptide on a ribosome
initiation
elongation
termination
ribosome reaches a stop codon, and all of the components disassemble, releasing a completed polypeptide- occurs when the binding of a release factor to a stop codon causes the release of the completed polypeptide from the tRNA and the disassembly of the mRNA, ribosomal subunits, and the release factor
ribosome travels in the 5ʹ to 3ʹ direction and synthesizes a polypeptide- amino acids are added one at a time to a growing polypeptide
mRNA, tRNA, and the ribosomal subunits form a complex- mRNA assembles with the ribosomal subunits and an initiator tRNA molecule, which carries methionine, the first amino acid
In eukaryotes
transcription occurs in the nucleus
the mRNA then exits the nucleus through a nuclear pore
translation occurs in the cytosol
additional step occurs between transcription and translation
during RNA modification, the RNA transcript, pre-mRNA, is modified in ways that make it a functionally active mRNA
have 3 forms of RNA polymerase
I
transcribes rRNA
II
responsible for transcribing the mRNA from eukaryotic protein encoding genes
always requires 5 transcription factors to initiate transcription
transcription factors are proteins that influence the ability of RNA polymerase to transcribe genes
binding of RNA polymerase II to the promoter is an assembly process in which RNA polymerase II and the five transcription factors form a pre initiation complex
the complex then unwinds the DNA to initiate transcription
III
transcribes tRNA
pre-mRNA undergoes certain modifications before it exits the nucleus
final product is called a mature mRNA, or mRNA
tailing
3′ end, most mature eukaryotic mRNAs have a string of adenine nucleotides, typically 100 to 200 nucleotides in length, referred to as a poly A tail
poly A tail is not encoded in the gene sequence
tail is added enzymatically after a pre-mRNA has been completely transcribed
aids in the export of mRNA from the nucleus
stabilizes a eukaryotic mRNA so it can exist for a longer period of time in the cytosol
bacterial mRNAs also have poly A tails attached to them. However, the poly A tail has an opposite effect in bacteria, where it causes the mRNA to be rapidly degraded.
splicing
removes introns (transcribed but not translated)
connects remaining exons
introns are precisely removed from eukaryotic pre-mRNA by a large complex called a spliceosome that is composed of several different snRNPs
each snRNP contains small nuclear RNA and a set of proteins
the first 2 snRNPs bind to the 5ʹ splice site and branch site
additional snRNPs bind to the 3ʹ splice site and other locations to create a loop
the 5ʹ splice site is cut
the 5ʹ end of intron is covalently attached to the branch site
two snRNPs are released
3ʹ splice site is
cut
exon 1 is covalently attached to exon 2
the intron (in the form of a loop) is released along with the rest of the snRNPs and degraded
capping
modified form of guanine covalently attached at the 5′ end
occurs while a pre-mRNA is being made by RNA polymerase
needed for the proper exit of mRNAs from the nucleus
after an mRNA is in the cytosol, the cap structure helps to prevent its degradation
cap structure is recognized by cap-binding proteins that enable the mRNA to bind to a ribosome for translation
In bacteria
both events occur in the same location, the cytoplasm
1 form of RNA polymerase that transcribes all RNAs
have many sigma factors that recognize different promoters
mRNA
start codon
codon that specifies the first amino acid in a polypeptide sequence
stop codon
specifies the end of translation
ribosomal binding site
site for ribosome binding.
coding sequence
series of codons from the start codon to the stop codon that determine the sequence of amino acids of a polypeptide
RNA
protein encoding RNA
mRNA
never translated
non coding RNA
rRNA
forms part of ribosomes, which provide the site where translation occurs
tRNA
translates the language of mRNA into that of amino acids
has a 2D structure resembling a cloverleaf- two important sites are the amino acid attachment site at the 3′ end and the anticodon, which forms base pairs with a codon in mRNA
an organized unit of base sequences that enables a segment of DNA to be transcribed into RNA and ultimately results in the formation of a functional product
Gene
regulatory sequence
site for the binding of regulatory proteins
the role of regulatory proteins is to influence the rate of transcription
transcribed region
part of this region contains the information that specifies an amino acid sequence
terminator
signals the end of transcription.
promoter
a sequence of DNA that controls when and where transcription will begin
Ribosome
P site
peptide bond is formed between the amino acid at the A site and the growing polypeptide
lengthening the polypeptide by one amino acid
polypeptide is removed from the tRNA in the P site and transferred to the amino acid at the A site, an event termed a peptidyl transfer reaction
reaction is catalyzed by a region of the 50S subunit known as the peptidyltransferase center, which is composed of several proteins and rRNA
tRNA is then released
E site
mRNA, ribosomal subunits, and release factor dissociate
A site
charged tRNA carrying an amino acid binds to aminoacyl site
energy provided by hydrolysis of GTP proteins that function as elongation factors