Chapter 13: DNA-RNA-protein

--Central Dogma of Molecular Biology: information in the cell flows from DNA to RNA to protein. Can't go back up the chain: RNA and proteins get thrown away, and only DNA is passed between generations

--DNA replication makes more DNA

--DNA --> RNA (RNA copy of genes) is transcription

--RNA --> protein is translation

--RNA: like DNA in having nucleotides consisting of base, sugar, phosphate but: key differences:

--RNA uses uracil (U) instead of thymine (T) to pair with A

--sugar in RNA is ribose, not deoxyribose (has an extra oxygen)

--RNA is single stranded--no double helix

--RNA is short: 1 gene long, not multiple genes

--3 basic types of RNA

1. messenger RNA: copy of genes that code for protein--get translated into protein

2. ribosomal RNA: part of the ribosomes, does the actual translation

3. transfer RNA: small molecules that deliver amino acids to ribosome one by one

--transcription. Making an RNA copy of a single gene (part of the DNA chromosome), in the nucleus. Done by the enzyme RNA polymerase, with triphisphate nucleotides as precursors, just like DNA replication. Starts at a promoter: signals gene start point and binds to RNA polymerase. Need to unwind DNA double helix to get at the DNA bases: the RNA bases match the DNA bases of teh template, and the RNA polymerase attaches them together with covalent bonds. The begining of the gene is the 5' end, an dthe end is the 3' end (based on the orientation of the sugars). The new RNA grows from 5' to 3'. RNA polymerase makes a copy until the end of the gene, then it falls off.

--the new RNA molecule needs to be processed: add a cap to the 5' end and a poly A tail to 3' end. These things protect the RNA from degradation. Other big procesing event: removal of introns. The DNA of a gene has the instructions for coding the protein, but coding regions are separated by areas of junk DNA, areas that don't code for the protein and have no apparent use. The coding areas are exons and the non-coding areas are introns. Introns must be removed from the RNA before it can be translated into proteins. Thus, after processing messenger RNA is a copy of only the exons of a gene, not the whole gene. Introns are spliced out of the RNA. After RNA processing: sdding 5' cap, 3' poly A tail, and intron removal, the RNA is a mature messenger RNA (mRNA) and it gets sent to the cytoplasm.

--genetic code. There are 4 bases in RNA (and DNA), and 20 different amino acids in proteins. How to get these to match up: each group of 3 bases is a codon and codes for 1 amino acid. There are 64 possible codons. 3 codons are used for STOP signals, they don't code for any amino acid. The other 61 code for the 20 amino acids, with a lot of duplication: several codons code for the same amino acid.

--transfer RNA. Has 2 ends: one end is the anticodon, 3 bases that match up with the codons on the mRNA. The other end holds the amino acid that corresponds to that codon. A whole group of enzymes attache the proper tRNAs to teh proper amino acids

--ribosomes: 2 subunits, small and large. Each contains a different rRNA molecule as well as a number of polypeptides (proteins). Ribosomes are RNA/protein hybrids. They are made in the nucleus, but do their work in the cytoplasm. They cause mRNA to be translated into proteins.

--the process of translation. Occurs in the cytoplasm, after the mRNA has been processed and exported from the nucleus. 3 steps: initiation, elongation, termination.

--initiation. Ribosme starts out separted into small and large subunits. Small subunit binds to initiator tRNA, a special tRNA that starts every protein and uses teh AUG codon (for methionine). Then this complex binds to mRNA at 5' end (the begining) and moves along it to the first AUG. This is how it knows where to start translation--there is untranslated RNA before and after the protein-coding part. Then, teh large subunit binds: now you have the mRNA, the complete ribosome, and teh initiator tRNA all together in one complex.

--elongation. 2 sites on teh ribosome next to each other for 2 tRNAs. First one holds initiator tRNA, then next one gets filled with the next tRNA (based on the codon-anitcodon pairing). he ribosome transfers the amino acid from the first tRNA onto the amino acid for the second tRNA, giving a polypeptide that is 2 amino acids long. then, the first tRNA leaves, the ribosome slides down one codon, and waht used to be the second tRNA is now in the first position on the ribosome. A new tRNA then comes in to match the third codon. the first 2 amino acids, attached together and attached to the second tRNA, get transferrred to the third tRNA, giving a 3 amino acid protein. The process repeats as the ribosome moves down the mRNA.

--termination. A stop codon on the mRNA has no tRNA corresponding to it. The ribosome senses this and releases teh new protein from the final tRNA. The protein floats away, and the ribosome releases from the mRNA. The ribosome splits back into its 2 subunits. The mRNA can be translated many times by different ribosomes.

--waht happens next to the protein. It folds spontaneously into its active configuration. Some proteins are synthesized into the membrane of the ER, so they are membrane-bound proteins. Others sythesized into interior of the ER: get secreted. Others just free in the cytoplasm.

--mutations. Any change in the DNA (change in the base sequence) is a mutation. General types: base-pair substitution (change one base for another--can give altered amino acid in a protein) , insertions or deletions: add or remove a group of bases (sometimes a lot), sometimes splice together 2 unrelated genes, sometimes split a gene in half. Lots of strange possibilities. Transposable elements: short DNA sequences taht have the abiilty to move to new positions within the genome, more or less under their own power--like a separate intra-nuclear parasite--can land in genes and cause mutations also.

--effects of mutations: usually only matters if a protein is affected, the protein that is made by the gene that has been mutated.

--If it occurs in a body cell not involved with sperm/egg production, it will only affect the individual, not future generations. Happens all the time: you have lots of cells so a defective one rarely makes a difference. However, cancer is caused by mutations that allow the cell to keep dividing without limits.

--most DNA cahnges have no real effect: lots of junk DNA whose seqeunce doesnt' matter: between geens, in introns. Also, several codons for 1 amino acid means that some changes in DNA will not affect teh resultsing protein. Also, a lot of the protein's amino acids aren't very critical: proteins can tolerate a fair amount of change without harm. neutral mutations

--but, some mutations do affect the action of a protein: usually destroy it, whcih is generally a bad thing. Sometimes just alter its specificty or optimum conditions. This kind of mutation can somtimes be advantageous: allow life in different environments, for example.

--other kinds of mutation can cause different regulation of the gene involved: change the time, cells, or conditions when the gene is on. Lots of strange things can happen, and these mutations that alter gene regulation are the main cause of differences between species.

--causes of mutation:

--high energy (ionizing) radiation can break DNA and also create high energy compounds (free radicals) that attack DNA. X-rays, gamma rays, radioactive material, cosmic rays: no escaping this, but of course minimizing medical x-rays helps. Average dose of radiation form cosmic rays in Denver is twice that of Chicago. Radioactive material in many rocks too.

--UV light (non-inoizing radiation): DNA absorbs it and causes bases to link together. Enzymes usually repair this, but not always: casue of skin cancer.

--some chemicals (carcinogens) attack DNA and cause breaks or base changes. Food and medicines are tested for this. Can be naturally occurring chemicals too: aflatoxin in peanuts causes liver cancer.