Question

6. What is the basic difference between general transcription factors and specific transcription factors?

7. How is DNA opened up along a prokaryotic promoter. How does this occur along a eukaryotic promoter?

8. Describe the functions of Transcription factors: TFIID(TBP,TAFs),TFIIA, TFIIB, TFIIE, TFIIF, TFIIH.

9. What is ELL(negativeelongationfactor) and pTEFb?

10.What is the CTD tail? What are some of the functions of it? What are the phosphorylation states and what do they signify?

Answer 1

6. Before we see the difference in both, the simple definition we need to know that the transcription factors are proteins that help turn specific genes "on" or "off" by binding to nearby DNA.

General transcription factors (GTFs) first bind to the promoter, then start transcription. GTFs are also intimately involved in the process of gene regulation, and most are required for life.

Specific transcription factors act on INDIVIDUAL genes, rather than all of them. They can interact directly with the general factors to help them or inhibit them in forming the initiation complex.

General transcription factors (GTFs), also known as basal transcriptional factors, are a class of protein transcription that bind to specific sites (promoter) on DNA to activate transcription of genetic information from DNA to messenger RNA.

7. Prokaryotic transcription is the process by which messenger RNA transcripts of genetic material in bacteria are produced, to be translated for the production of proteins. Unlike in eukaryotes, bacterial transcription and translation can occur simultaneously in the cytoplasm. This is impossible in eukaryotes, where transcription occurs in a membrane-bound nucleus while translation occurs outside the nucleus in the cytoplasm. In bacteria, genetic material is not enclosed in a membrane-enclosed nucleus and has access to ribosomes in the cytoplasm

Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells. Unlike prokaryotic RNA polymerase that initiates the transcription of all different types of RNA, RNA polymerase in eukaryotes (including humans) comes in three variations, each encoding a different type of gene. A eukaryotic cell has a nucleus that separates the processes of transcription and translation. Eukaryotic transcription occurs within the nucleus where DNA is packaged into nucleosomes and higher-order chromatin structures.

8. Transcription factor II Human (Transcription Factor II H; TFIIH) is an important protein complex, having roles in transcription of various protein-coding genes and DNA nucleotide excision repair (NER) pathways.

Transcription factor IIF (TFIIF) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex.

Transcription factor IIF is encoded by the GTF2F1, GTF2F2, and GTF2F2L genes.

TFIIF binds to RNA Pol II when the enzyme is already unbound to any other transcription factor, thus avoiding it from contacting DNA outside the promoter. Also, it stabilizes the RNA polymerase II while it's contacting TBP and TFIIB.

Transcription factor TFIIA is a nuclear protein involved in the RNA polymerase II-dependent transcription of DNA. TFIIA is one of several general (basal) transcription factors (GTFs) that are required for all transcription events that use RNA polymerase II.

Transcription factor II B (TFIIB) is a general transcription factor that is involved in the formation of the RNA polymerase II preinitiation complex (PIC) and aids in stimulating transcription initiation.

9. 9. In molecular biology, NELF (negative elongation factor) is a four-subunit protein (NELF-A, NELF-B, NELF-C/NELF-D, and NELF-E) that negatively impacts transcription by RNA polymerase II (Pol II) by pausing about 20-60 nucleotides downstream from the transcription start site (TSS).

P-TEFb complex: The positive transcription elongation factor, P-TEFb, plays an essential role in the regulation of transcription by RNA polymerase II (Pol II) in eukaryotes. Immediately following initiation Pol II becomes trapped in promoter-proximal paused positions on the majority of human genes.

TEFb is a cyclin-dependent kinase. P-TEFb is regulated in part by a reversible association with the 7SK snRNP.

10. The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH).

When the protein is translated from messenger RNA, it is created from N-terminus to C-terminus. The convention for writing peptide sequences is to put the C-terminal end on the right and write the sequence from N- to C-terminus.

Protein phosphorylation is a post-translational modification of proteins in which an amino acid residue is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Phosphorylation alters the structural conformation of a protein, causing it to become activated, deactivated, or modifying its function.