7.2 and 7.3 Flashcards
Nucleosomes & regulation of gene expression
Nucleosomes at the promoters of genes regulate the accessibility of the transcription machinery to DNA. Nucleosome is DNA and histones together. The tighter the DNA is wrapped around histones, the less likely transcription will occur.
Overall Outline of transcription- including enzymes and regulatory factors, direction of elongation, location, promoter vs. terminator
**This process occurs in the nucleus of the cell
An Enzyme called RNA Polymerase separates the two DNA strands. This enzyme allows polymerization of RNA nucleotides and base pairing along the DNA Template. To provide these functions, RNA polymerase must combine with a region of the DNA strand called a promoter. RNA polymerase allows assembly only in the 5’to 3’ direction like in DNA replication. The 5’ end of the free RNA nucleotide is added to the 3’ end of the RNA molecule being synthesized.
Once RNA polymerase has attached to the promoter region for a particular gene, the process of transcription begins. The DNA opens and a transcription bubble forms. This bubble contains the antisense DNA strand, the RNA polymerase, and the growing RNA transcript.
The promoter in the transcription process is a prime example of a non-coding section of DNA with a function.
The sense strand has the same base sequence as the new messenger mRNA. The antisense strand is the template for transcription, so the new mRNA has a base sequence that is complementary to it.
The transcription bubble moves from the DNA promoter region towards the terminator. The terminator is a sequence of nucleotides that, when transcribed, causes the RNA polymerase to detach from DNA. Once this happens, transcription stops, and the RNA transcript is detached from the DNA. The transcript carries the code of the DNA and is referred to as the messenger RNA.
roles of rna polymerase during transcription
RNA polymerase separates the two DNA strands
This enzyme allows polymerization of RNA nucleotides base pairing along the DNA Template.
Pre-mRNA editing/splicing- Introns vs. Exons, rearrangement, methyl cap & poly-A tail
Eukaryotic cell DNA is different from prokaryotic DNA in that within the protein-coding regions, there are stretches of noncoding DNA. These stretches of noncoding DNA are called introns.
As the complete region of a DNA molecule is transcribed to form mRNA, the first RNA formed is called pre-mRNA or the primary RNA transcript. It contains exons and introns. To make a functional mRNA strand in Eukaryotes, the introns are removed.
The process by which introns are removed is referred to as splicing. Those sequences of mRNA remaining after splicing are called Exons
Spliceosomes are composed of small nuclear RNAs. When they remove the introns, the exons may be rearranged, resulting in different possible proteins, this increases the number of possible proteins produced by one gene.
On one end (5’ end) of the final mRNA transcript (mature RNA) there is a cap made of modified guanine nucleotide with three phosphates (5’ cap). The other end (the 3’ end) is fitted with a poly-A tail, which is composed of 50-250 adenine nucleotides. The cap and poly-A tail seem to protect the mature mRNA from degradation in the cytoplasm and to enhance the translation process that occurs at the ribosome.
Sense vs. Antisense DNA strand during Transcription- study Diagram Sheet!
The promoter region for a particular gene determines which DNA strand is the antisense strand
The antisense strand (or the template stand) is the strand that is being copied during transcription
The DNA strand that carries the genetic code is called the sense strand (or coding strand)
Methylation and Gene expression:
It is apparent that inactive DNA is usually highly methylated compared with DNA that is actively being transcribed. A methyl group is an organic functional group with the formula CH3.
Genes that are more heavily methylated are not usually transcribed or expressed. Once a gene has been methylated, it will stay that way even through many cell divisions.
The methyl group appears to cause a section of DNA to wrap more tightly around histones, thus preventing transcription of that particular allele.
Unique methylation patterns have been associated with a large number of human cancers. These patterns include both hypermethylation (many methyl groups present compared with normal tissue) and hypomethylation (very few methyl groups present compared with normal tissue.
Proteins and Gene expression:
Gene expression is regulated by proteins. Every cell appears to have many different types of transcription factors. These are proteins that regulate transcription by assisting the binding of RNA polymerase at the promoter region of a gene. Another type of protein that has an effect on gene expression is called transcription activator.
Transcriptional activators can cause looping of DNA, which results in a shorter distance between the activator and the promoter region of the gene. This will bring about gene expression. There are also repressor proteins that bind to segments of DNA called silencers. This prevents transcription of the segment of that particular region.
mRNA
(messenger RNA): Produced during transcription. Carries the genetic instructions of a gene from the nucleus to the ribosome in the cytoplasm.
rRNA
(ribosomal RNA): Together with proteins, composes the ribosome, the organelles that are the site of protein synthesis.
tRNA
(transfer RNA): Brings the correct amino acid to the ribosome during translation.
Overall process of translation- including Initiation, Elongation, Translocation & Termination
The translation process involves several phases: initiation, elongation, translocation, and termination
The initiation phase:
The start codon (AUG) is on the 5’ end of all mRNAs. Each codon, other than the three stop codons, attaches to a particular tRNA.
The tRNa has a 5’ and a 3’ end, like all other nucleic acid strands.
The 3’ end of tRNA is free and has the base sequence of CCA. This is the site of amino acid attachment. Because there are complementary bases in the single-stranded tRNA, hydrogen bonds form in four areas. This causes the tRNA to fold and take on a three dimensional structure. One of the tips of the clover leaf contains an exposed anticodon. This is unique to each type of tRNA and it is this anticodon that pairs with a specific codon of mRNA.
Each of the 20 different amino acids will bind to the appropriate tNRA because of the action of a particular enzyme. Because there are 20 amino acids, there are 20 enzymes, collectively called tRNA- activating enzymes). The active site of each enzyme allows a fit only between a specific amino acid and a specific tRNA.
The attachment of the amino acid and the tRNA requires energy supplied by ATP. The structure is referred to as an activated amino acid- tRNA can now deliver the amino acid to a ribosome to make polypeptide chain
The first step in initiation is when an activated amino acid- Methionine is attached to a tRNA with the anticodon UAC, and combines with a mRNA strand and a small ribosomal subunit. The triplet bases of the mRNA codon form complementary base pairs with the triplet anticodon of tNRA.
The small subunit moves down the mRNA unit until it contacts the start codon (AUG). This contact starts the translation process. Hydrogen bonds form between the initiator tRNA and the start codon. Next, the large ribosomal subunit combines with these parts to form the translation initiation complex. Joining the initiation complex are proteins called initiation factors that require energy from guanosine triphosphate (GTP)
The Elongation Phase:
Once the initiation phase is complete, elongation occurs. This phase involves tRNAs bringing amino acids to the mRNA-ribosome complex in the order specified by the codons of the mRNA.
Proteins called elongation factors assist in binding the tRNAs to the exposed mRNA codons at the A site.
The initiator tRNA moves to the P site. The ribosomes catalyze the formation of peptide bonds between adjacent amino acids that are brought to the polypeptide assembling area.
The Translocation phase (during Elongation):
Translocation involves the movement of the tRNAs from one site of the mRNA to another. First the tRNA binds with the A site. Its amino acid is then added to the growing polypeptide chain by a peptide bond (the anticodon that moves into the A site is specific for the codon of the mRNA at that position.
This causes the polypeptide chain to be attached to the tRNA at the A site. tRNA then moves to the P site, it transfers its polypeptide chain to the new tRNA, which moves into the now exposed A site. The now empty tRNA is transferred to the E site, where it is released. This whole process occurs in the 5’ to 3’ direction, moving along the mRNA towards the 3’ end.
Termination Phase: End
The termination phase begins when one of the three stop codons appear at the open A site. A protein called a release factor then fills the A site. The release factor does not carry an amino acid, but catalyzes hydrolysis of the bond linking the tRNA in the P side with the polypeptide chain. This frees the polypeptide releasing it from the ribosome, and from then, separates from the mRNA and splits into its subunits.
The termination phase completes the process of translation and at this point, the disassembly process occurs in which the mRNa detaches from the ribosome, all tRNAs detach from the mRNA-ribisomal complex and the protein is released from the ribosome.
