Chapter 10 Gene Action: From DNA to Protein

Post transcriptional control is also exercised it the nucleus

*When* RNA leave the nucleus: some mature RNA leave the nucleus more quickly *How* the RNA leave the nucleus, a variety of mature mRNA can be produced due to alternative splicying patterns

Quaternary (4°) structure

A protein that has more than one polypeptide sub-unit.

Differential gene expression

-E.g. some cells make proteins prenatally and never post-natally *4 Levels of control* Transcription control in the nucleus is the 1st place to control(mechanism of transcription can either be stimulated or repressed) -Organization of chromatin: condensed vs. relaxed chromatin 1.heterochromatin vs. euchromatin (RNA polymerase complexes, are able to bind with the DNA sequence due to the unfolded structure of the euchromatin, not so much to the highly condensed heterochromatin). 2. Methylation- primarily in promoter region, silences gene expression (methylation competes for the promoter binding area) 3. Absence or presence of transcription factors control Frequency of transcription .

open reading frame

A sequence of DNA that does not include a stop codon.

The immediate product of transcription is mRNA, it is called a primary transcript or heterogeneous RNA. It undergoes three post-transcriptional modifications before it leaves the nucleus:

1) Its 5' end is capped with a modified guanine nucleotide. The cap tells the ribosome where to begin protein synthesis. 2) The 3' end is capped with a "poly-A" tail, an attachment of about 50-250 Adenine nucleotides. The tail facilitates transport of the transcript from the nucleus and protects the transcript from degradation during transition through the nuclear pore into the cytoplasm. 3) Genes contain some nucleotide sequences that do not express themselves in the protein product (noncoding sequences), and other nucleotide sequences that do express themselves in the protein product (coding sequences). Coding sequences are called exons, and noncoding sequences are called introns. Last and 3rd post-transcriptional modification involves removing the introns from the primary transcript and splicing the exons together. This is performed by a unit called a spliceosome, a complex of protein, RNA and the relevant intron. After processing, the now mature mRNA is ready to leave the nucleus and into the cytoplasm ready for translation.

Transcription (RNA Synthesis)

1) Transcription starts at a promoter, which is a stretch of DNA at 5' area in front of a gene to be transcribed and is often referred to as upstream. 2) Proteins called transcription factors recognize the promoter sequence and bind. First transcription factor to bind is TATA box -binding protein. 3) An enzyme called DNA-dependent RNA polymerase binds to the promoter and the transcription factors initiating transcription process.(Initiation) 4) This catalyzes the temporary unwinding of a segment of the DNA helix by breaking of hydrogen bonds between the bases of that segment, and binding of free RNA nucleotides to their complementary bases on the DNA template strand. 5) RNA polymerase does not need a primer. It strings RNA nucleotides together in the 5' to 3' direction, forming the backbone of the RNA strand. 6) The growing RNA strand does not fully associate with the DNA template, so most of it dangles off to one side. (Elongation) 7) The process continues until RNA polymerase reaches a DNA sequence called a terminator. 8) The terminator causes RNA polymerase to stop transcription and to release the RNA molecule. (Termination) 9) The DNA double helix comes back together and is ready to be transcribed again.

Translation (protein synthesis) 2.Elongation

1. Elongation factors are the proteins that facilitate binding of next t-RNA to the "A" site of the ribosome. Only t-RNA with the anticodon for the next amino acid codon is able to bind there. 2. Ribozyme catalyze formation of a peptide bond between amino acid at the "P"site and the amino acid at the "A" site. 3. Ribosome moves one codon down the mRNA in the 5'to3' direction to the next triplet /codon. This releases the discharged tRNA freeing "P' site on the ribosome and the entire ribosome complex now shifts over so that the part of mRNA that was the "A" site now is the "P" site. As a result of this shift , termed translocation, "A" site is now available to accept the next tRNA . 3. Elongation repeats extending growing polypeptide by one amino acid per each translocation and as instructed by the mRNA code.

Translation (protein synthesis) 3. Termination

1. Elongation halts once the ribosome reaches the stop codon. 2. Protein release factor binds the stop codon releasing polypeptide from tRNA and ribosome. Complex dissociates and is free to begin the process again or gets recycled.

Levels of Protein structure

1º sequence of amino acids 2 º Alpha-Helix, Beta-pleated sheet 3º Overall 3-d shape/conformation of a protein 4 º Multi-unit protein, where each unit individually with its own 3-d shape e.g. Hemoglobin

nonsynonymous codons

A codon that encodes a different amino acid from another codon

codons

A continuous triple of the mRNA that specifies a particular amino acid.

promoter

A control sequence near the start of a gene.

Messenger RNA (mRNA)

A molecule of RNA complementary in sequence to the template strand of a gene that specifies a protein product.

proteasomes

A multiprotein structure in a cell shaped like a barrel through which misfolded proteins pass and are refolded or dismantled.

exons

A part of a genes that encodes amino acids.

Transcription factors

A protein that activates the transcription of certain genes.

Chaperone proteins

A protein that binds a polypeptide and guides folding.

anticodon

A three-based sequence on one loop of a transfer RNA molecule that is complementary to an mRNA codon, and joins the appropriate amino acid and its mRNA.

Transfer RNA (tRNA)

A type of RNA that connects mRNA to amino acids during protein synthesis.

RNA polymerase (RNAP)

AN enzyme that adds RNA nucleotides to a growing RNA chain.

Alternate splicing

Building different proteins by combining exons of a gene in different ways.

Synonymous codons

DNA triples that specify the same amino acid.

Post- tanslational control

Delay of folding of the polypeptide into a functional protein. Feed-back inhibition, used by cells to decrease or halt synthesis of a product already abundant in the cell.

Translational control

Delay of protein synthesis temporarily, until the cell receives a signal from the environment e.g. molecule, or a change in the internal/external conditions Degradation of mRNA, before translation can occur.

secondary (2°) structure

Folds in a polypeptide caused by attractions between amino acids close together in the primary structure.

tertiary (3°) structure

Folds in the polypeptides caused by interactions between amino acids and water. This draws together amino acids that are far apart in the primary structure.

Translation is 3 step process of converting mRNA message into polypeptide/protein.

Initiation 1.Proteins called initiation factors bind to a tRNA carrying methionine which is called the initiator tRNA. This initiation complex guided by Cap binding protein and other initiation factors bind to mRNA and small ribosomal subunit, once all align the AUG-start codon is recognized by the anticodon of methionine carrying tRNA. 2. t-RNA with methionine will bind to the "P" site of the large ribosomal subunit.

introns

Part of a gene that is transcribed but is excised from the mRNA before translation into protein.

Ribosomal RNA (rRNA)

RNA that, with protein, comprises ribosomes.

template strand

The DNA strand carrying the information to be transcribed.

primary (1°) structure

The amino acid sequence of a protein.

Genetic Code

The correspondence between specific mRNA triplets and the amino acids the specify.

reading frame

The point in a DNA sequence from which contiguous triplets encode amino acids of a protein. A DNA sequence has three reading frames.

coding strand

The side of the DNA double helix for a particular gene from which RNA is note transcribed.

conformation

The three-dimensional shape of a molecule.

differemce b/t DNA and RNA

*DNA* -Double stranded -Deoxyribose -Thymine *RNA* -Single stranded -Ribose -Uracil

Translation

Assembly of an amino acid chain according to the sequence of base triplets in a molecule of mRNA.

Transcription

Manufacturing RNA from DNA.

3 types of RNA

mRNA- messenger RNA rRNA- ribosomal RNA tRNA- transfer RNA