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Gene Action and Expression

10.1 Transcription-The Link Between Gene and Protein
1. In a cell, transcription is the process that copies the information stored in DNA into RNA.
2. Translation uses the RNA's information to construct amino acid chains that comprise proteins.
3. The directional flow of genetic information from DNA to RNA to protein is known as the central dogma of molecular biology.
4. Gene regulation controls the pattern of gene expression and cellular differentiation.

RNA Structure and Types
1. RNA is copied from one strand of the double helix called the template strand.
2. RNA differs from DNA in that it is single-stranded, has uracil instead of thymine, and has ribose instead of deoxyribose.
3. Messenger RNA (mRNA) carries the information that specifies a particular amino acid sequence of a protein product. Each three mRNA bases in a row form a codon.
4. Ribosomal RNA joins certain proteins to form ribosomes. Ribosomes physically support the other structures involved in protein synthesis, and some rRNA catalyzes formation of peptide bonds.
5. Transfer RNA is cloverleaf-shaped and connects an mRNA codon to an amino acid.

Transcription Factors
1. Bacterial genes are organized into operons and coordinately regulated.
2. Operon organization is rare in eucaryotes, but has been found in the roundworm Caenorhabditis elegans.
3. Most eucaryotic genes are controlled by a complex set of transcription factors.
4. A few human diseases are due to defects in transcriptional factors.

Steps of Transcription
1. Transcription factors and RNA polymerase recognize sequences in the DNA near a gene. This region is called a promoter.
2. The binding of transcription factors to the promoter attracts and binds RNA polymerase, which begins transcription.
3. Transcription proceeds as RNA polymerase inserts complementary RNA bases opposite the template strand of the DNA double helix.

RNA Processing
1. In prokaryotes, RNA is translated as soon as it is transcribed.
2. In eukaryotes, RNA is often altered (or modified) before it is active.
3. Messenger RNA gains a modified nucleotide cap and a poly A tail.
4. Many genes have intervening sequences called introns, which are transcribed and cut from the mRNA. The protein encoding sequences in mRNA, exons, are then reattached.
5. The function of introns is still a mystery.
6. Ribozymes are small RNAs with catalytic activity that can splice introns. They join proteins to form snurps, which associate to form spliceosomes.
7. RNA editing changes the size of the protein product in different cell types.
8. After being processed, the RNA must be exported from the nucleus before it is translated.

10.2 Translating a Protein

Deciphering the Genetic Code
1. Crick and coworkers confirmed the triplet nature of the genetic code.
2. The reading frame of a gene is the particular sequence of amino acids in a protein that is encoded from a certain point in a gene. Adding or subtracting 1 or 2 DNA bases to a gene disrupts the reading frame. Adding or deleting 3 contiguous bases, adds or deletes one amino acid to the protein product but does not disrupt the reading frame.
3. The genetic code is nonoverlapping, continuous, virtually universal, and degenerate.
4. Crick hypothesized the existence of an adaptor molecule necessary for translation. This was later discovered and called transfer RNA (tRNA).

Building a Protein
1. As translation begins, mRNA, tRNA with bound amino acids, ribosomes, energy molecules, and protein factors assemble.
2. To initiate translation, the mRNA leader sequence binds to rRNA in the small subunit of a ribosome, and the first codon attracts a tRNA to form the initiation complex.
3. In elongation, the large ribosomal subunit attaches to the initiation complex. Peptide bonds form between the amino acids attached to the aligned tRNAs, building a polypeptide.
4. Protein synthesis halts when a stop codon is reached.
5. Translation is efficient and economical, as RNA, ribosomes, enzymes, and key proteins are recycled.

Protein Folding
1. The protein folds as translation proceeds, with enzymes and chaperone proteins assisting the amino acid chain in assuming its final functional (three-dimensional) shape.
2. In addition to folding properly certain proteins must be modified before they are functional.
3. Errors in protein folding may be the basis of some diseases.

10.3 The Human Genome Sequence Reveals Unexpected Complexity
1. The genomes of an increasing number of organisms have been and are being sequenced.
2. Proteomics, based on genome analysis, is the study of the collection of proteins produced by a particular cell.

Genome Economy: Reconciling Gene and Protein Number
1. Differential intron splicing and exon shuffling explain how one gene can produce more than one protein.
2. Intron sequences of one gene may contain the coding sequences for another protein.
3. Trans-splicing involves the splicing together of two different RNAs (from separate genes) to form a translatable message.

What Does the Other 98.5 Percent of the Human Genome Do?
1. Ninety eight percent of the human genome does not code for protein. What is its function?
2. About 1/3 of the human genome produces non-coding RNAs (i.e. rRNA, tRNA, snRNA, snoRNA, etc.).
3. Part of the human genome is composed of pseudogenes. These may or may not be transcribe, and are never translated into protein.
4. A large part of the human genome is composed of repeat sequences such as SINEs and LINEs.

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