Understand steps of transcription - AP Biology

Transcription factors bind to the TATA box (found only in eukaryotes and archaea). The TATA box is a promoter region of a gene on the DNA. If the transcription factor that binds it is an activator, then it will interact with RNA polymerase II to form a transcription initiation complex and begin transcription of mRNA. DNA polymerases I and III are involved in DNA replication, and do not interact with the TATA box. RNA polymerase I is responsible for transcribing rRNA genes in the nucleolus.

DNA is a nucleic acid, made up of the nucleotides, which contain a deoxyribose sugar, a phosphate group, and one of four nitrogenous bases. These bases are adenine, cytosine, guanine, and thymine. DNA is double-stranded, but transiently single-stranded during DNA replication and transcription.

Simply create a complementary strand of RNA with matching base pairs, but substitute uracil (U) for thymine (T), since RNA does not use thymine base pairs.

The answer choice starting with AUG might seem appropriate since it is the start codon, however, realize that the rest of the base pairs do not match up to the DNA template. Further, RNA templates do not begin right at the start codon; there are promotoer and enhancer regions of DNA that are transcribed well before the first exon is transcribed with its AUG start codon.

Histones are associated with DNA packed in chromatin. Acetylation of these histones allows for DNA transcription. Other proteins mentioned play no part in DNA chromatin structure.

Polymerases are active during DNA repair and transcription. Collagen is a fibrous protein associated with the extracellular matrix. Actin and myosin are myofilaments active in muscle contraction.

When finding the mRNA transcript from a template, there are two things to keep in mind:

1. The template strand will be complementary to the transcript, so it will be read in the opposite direction

2. Since the template strand is made from DNA, it will have thymine bases instead of uracil (which is found in RNA in place of thymine).

First, we can reverse the direction of our given DNA sequence.

5'-TACGCATT-3'

3'-TTACGCAT-5'

Then, complete each base pair. Guanine (G) and cytosine (C) always pair, and adenine (A) and thymine (T) always pair. In this case, since we are dealing with RNA, uracil (U) will have an adenine complement.

5'-AAUGCGUA-3'

Transcription is the process of synthesizing RNA from a DNA template. In eukaryotic cells, chromosomal DNA is contained within the nucleus. Transcription requires access to this DNA, and therefore must occur in the nucleus. Resulting RNA molecules are then shuttled out of the nucleus to be used in other processes.

The DNA gets transcribed into RNA inside the nucleus. This is where DNA is housed; DNA never leaves the nucleus (except during mitosis, during which the nuclear envelope will briefly disappear so that two cells can be formed). After DNA gets transcribed into RNA, the RNA is modified and eventually transported out of the nucleus as mRNA, which is now ready for translation.

Translation occurs on ribosomes, which can either be bound to the rough endoplasmic reticulum or free-floating in the cytoplasm. The nucleolus is a structure within the nucleus where ribosomal RNA (rRNA) is produced and ribosomal subunits are assembled. Mitochondria are essential for cellular respiration and ATP synthesis. Lysosomes are responsible for digesting wastes and defective proteins.

When RNA polymerase binds to a template strand of DNA, it recruits complementary ribonucleotides to form a strand of RNA. This strand of RNA, however, is incomplete and must undergo post-transcriptional modification to become a mature mRNA product. The initial RNA transcript is known as heteronuclear RNA, or htRNA.

Introns are removed for the htRNA and a 5'cap and poly-A tail are added to convert it to mRNA.

RNA polymerase is the protein that synthesizes an RNA complement to a gene. RNA polymerase binds the template DNA strand and recruits ribonucleotides to build a strand of heteronuclear RNA (htRNA). The htRNA then undergoes modification to become mature mRNA before exiting the nucleus into the cytosol for translation.

DNA polymerase and primase are essential for the replication of DNA. DNA polymerase recruits nucleotides to synthesize the daughter strand of DNA, and primase creates small RNA primers to recruit DNA polymerase to the replication fork. Trypsin is a protease that is not involved in transcription; it helps to digest proteins in the small intestine.

Histones are the packaging proteins on which long DNA molecules are coiled before mitosis. In this respect they are involved in cell division, but they are most closely linked to chromosome condensation. During interphase DNA is mostly packaged as euchromatin. Euchromatin is loosely packed and is capable of being transcribed, making it essential for protein synthesis and cell growth during the G1 and G2 phases. During mitosis the DNA condenses into tightly-packed heterochromatin in the form of chromosomes, which allow for cell division. The difference in packaging between euchromatin and heterochromatin comes from histone proteins. During chromosome formation, DNA becomes tightly wound around the histones to create the chromosome structure.

PABP (poly-A-binding protein) binds to the poly-A tail in the 3' UTR of eukaryotic mRNA. It is likely that this species would not have a PABP homolog because it does not have a poly-A tail.

eIF4E binds to the 5' cap. eIF2 is responsible for bringing the first tRNA to the initiation complex. eEF1 is an elongation factor that helps bring tRNAs to the ribosome.

To help remember which bases are purines and which are pyrimidines, there are two acronyms. Pure As Gold. Adenine and guanine are purines because of their structure. Also, pyrimidines, like pyramids, are "sharp". Sharp things CUT (cytosine, uracil and thymine).

Following DNA transcription, the resulting RNA molecule must be modified before leaving the nucleus. Proteins in the nucleus add a 5' cap to the 5' end of the RNA strand, and a poly-A tail to the 3' end. These additions help prevent degradation of the transcript by any hydrolytic enzymes in the cytosol. Protein complexes called spliceosomes interact with the transcript to remove segments of non-coding RNA called introns. The remaining transcript following the excision of introns is composed only of coding segments of RNA, known as exons.

Though introns are removed during post-transcriptional modification, exons are not inserted. Rather, they are simply the remaining RNA sequences after the introns have been spliced out.

Proteins are coded for by RNA, which is coded for by DNA. The central dogma of molecular biology is the general sequence for the flow of information in coding for a protein. An mRNA strand is created using the DNA strand as a template. This new strand of mRNA then leaves the nucleus and is used as a template for 3-pronged tRNA molecules carrying amino acids to create a chain, which will eventually create a protein.

The central dogma of molecular biology is the general sequence of DNA to RNA to protein.

A coding sequence is the sequence of DNA that will code for a particular protein. In this process an messenger or mRNA molecule is transcribed from DNA and later translated into a protein by ribosomes. Messenger or mRNA is flanked by an upstream 5’ UTR untranslated leader sequence and a downstream 3’ UTR untranslated region that follows the termination codon of the synthesized protein.

The term “directionality” refers to the chemical orientation of a molecule. In DNA and RNA, directionality is described as 3’ (three prime) or 5’ (five prime). 3’ refers to the third carbon group in a sugar ring, which terminates in a hydroxyl group, and 5’ refers to the fifth carbon in the sugar ring. In transcription, RNA polymerase reads the template DNA strand in a 3’ to 5’ direction. Reading the template DNA strand in this direction allows transcription to proceed without primers and Okazaki fragments. This yields an RNA molecule that is formed in a mirrored 5’ to 3’ direction.

Promoter sequences are regions of DNA located upstream of transcription start sites. Transcription factors bind to the promoter sequence, which promotes the binding of RNA polymerase and initiation of transcription. Together, along with activators and repressors, these make up the pre-initiation complex. A well-characterized promoter sequence is called the TATA box, which is present within promoters of of human genes.

Activators are proteins that increase transcription of a specific gene. Activators bind to promoters and often coactivators to facilitate binding of the pre-activation complex and initiation complexes; therefore, they stimulate the transcription of a given gene.

During transcription, RNA polymerase enzymes bind to DNA promoter sequences. This binding is facilitated by the pre-initiation complex (composed of transcription factors, the promoter sequence, activators, and repressors) as well as RNA polymerase. In eukaryotic cells, certain transcription factors must bind to the promoter sequence before RNA polymerase can. This is due to an inability of RNA polymerase to independently recognize the promoter sequence. Once RNA polymerase does bind, transcription can be initiated.