Chapter Six: DNA, RNA, and Protein Synthesis

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Chapter outline

1. Early hypotheses regarding the genetic material
   1. Genetic material is the substance in a cell which passes information from the parent cell to the daughter cell.
   2. Biologists realized that it was likely that chromosomes contain the genetic information because of the care a cell takes to provide each daughter cell with a full set of chromosomes.
   3. Chromosomes are made of protein and DNA, and scientists initially believed that protein was the genetic material because it comes in many varieties.
2. The famous DNA experiments
   1. Fred Griffith's experiment
      1. Griffith injected one group of mice with live virulent bacteria, another with live non-virulent bacteria, another with heat-killed virulent bacteria, and another with both heat-killed virulent bacteria and live non-virulent bacteria.
      2. Some of the mice which received heat-killed virulent bacteria and live non-virulent bacteria died, and live virulent bacteria was found in their blood.
      3. Griffith concluded that the genetic information in the heat-killed virulent bacteria was not destroyed by the heating and was taken in by some of the live non-virulent bacteria.
      4. Since heat denatures proteins, the genetic information had to be some other material.
   2. Oswald Avery's experiment
      1. Avery used heat to kill virulent bacteria and then extracted RNA, DNA, carbohydrates, lipids, and proteins from them.
      2. He placed each of these substances into different cultures of live non-virulent bacteria.
      3. Only the non-virulent bacteria which received DNA became virulent. This suggested that DNA is the genetic material.
3. DNA's chemical composition and structure
   1. Composition of DNA
      1. Nucleic acids (DNA and RNA) are composed of nucleotides: a phosphate group, a five-carbon sugar, and a nitrogenous base.
      2. The four bases in DNA are adenine, cytosine, guanine, and thymine. RNA has uracil in place of thymine.
      3. Adenine and guanine are called the purine bases; their structure has two rings of atoms.
      4. Cytosine, thymine, and uracil are the pyrimidine bases; their atoms are arranged in a single ring.
   2. Structure of DNA
      1. In the 1940s, Erwin Chargaff found that a DNA molecule has about the same amount of adenine as thymine, and of cytosine as guanine.
      2. In 1953, James Watson and Francis Crick published a paper suggesting that DNA is a double helix.
      3. The rungs of this twisted ladder are the nitrogenous bases, adenine bonding only with thymine and cytosine bonding only with guanine.
      4. The opposite sides of the helix are antiparallel, meaning that if one side ends in the phosphate group (the 5' end), then the other side ends with the sugar molecule (the 3' end).
4. The packing of DNA in eukaryotes
   1. A single molecule of DNA from a human cell is actually about two meters long.
   2. A stretch of the DNA molecule is wrapped twice around a cluster of proteins called histones.
   3. A cluster of histones and the two loops of DNA around it is called a nucleosome.
   4. The nucleosomes are coiled together, and then this coil is packed into tight loops.
   5. This mass of loops is the chromatin seen in a eukaryotic cell's nucleus.
5. DNA replication
   1. The three hypothesis for DNA replication were called conservative replication, semiconservative replication, and dispersive replication.
   2. Scientists Matthew Meselson and Franklin Stahl rules out conservative and dispersive replication is possibilities, and semiconservative replication has since been proven to be correct.
   3. Steps in DNA replication
      1. The enzyme DNA helicase begins at the replication origin and runs down the DNA molecule, separating the bonds between the nitrogenous bases.
      2. DNA polymerase attaches new bases to each of the exposed bases as the DNA molecule is unzipped.
      3. In constructing a new strand of DNA, DNA polymerase can only work from the new strand's 5' end to its 3' end. On one side of the replication origin, the DNA polymerase follows the DNA helicase, but on the other side, it must move backwards for short intervals, creating small pieces of DNA called Okazaki fragments.
      4. The Okazaki fragments are linked together by the enzyme DNA ligase.
6. Transcription of RNA
   1. Research by George Beadle and Edward Tatum suggested that DNA determines which proteins a cell produces.
   2. Steps in RNA transcription
      1. The DNA molecule is unzipped as in DNA replication.
      2. The enzyme RNA polymerase attaches to a sequence of bases on the DNA molecule called the promoter, moves down the strand, and bonds the appropriate base to each exposed base on the DNA molecule.
      3. Instead of thymine, RNA polymerase bonds uracil to adenine.
      4. Transcription ends when the RNA polymerase reaches a sequence of bases called the termination signal.
   3. In order to dictate the production of proteins, a molecule of messenger RNA must be transcribed. This molecule is then translated at the ribosomes into a protein molecule.
7. Types of RNA and the mRNA code
   1. Messenger RNA (mRNA)
      1. The mRNA molecule is the longest of the three types of RNA; it takes a copy of the DNA code to the ribosome for translation into a protein molecule.
      2. After exiting the nucleus, a 7-methylguanosine "head" is added which helps it attach to the ribosome.
      3. A poly-A "tail" consisting of adenosine residues is also added, which protects the mRNA molecule from enzymes in the cytoplasm.
   2. Transfer RNA (tRNA)
      1. tRNA attaches to an amino acid and brings it to the ribosome when the mRNA code requires it in the construction of a protein molecule.
      2. One side of the tRNA molecule bonds to a specific amino acid, and the other side contains a sequence of bases which is complimentary to the sequence on the mRNA molecule which codes for the amino acid.
   3. Ribosomal RNA (rRNA)
      1. Ribosomes have two components: proteins and rRNA.
      2. The large subunit of a ribosome contains an rRNA molecule 2904 nucleotides long, and the small subunit has an rRNA molecule 1542 nucleotides long.
   4. The mRNA code
      1. Each triplet of bases on the mRNA molecule (and the DNA molecule) codes for a single amino acid.
      2. Many amino acids are associated with several codons.
      3. There are also special "stop" codons which end the process of translation.
8. Translation
   1. Translation is the synthesis of a protein molecule based on the sequence of nitrogenous bases in an mRNA molecule.
   2. The small ribosomal subunit attaches to the 5' end of the mRNA molecule. The first codon there is always AUG.
   3. The tRNA molecule with the anticodon which matches AUG attaches to it. This tRNA molecule is bonded to the amino acid methionine.
   4. The large ribosomal subunit attaches on top of the tRNA molecule, aligning it in the subunit's A site (the second site, called the P site, is used later).
   5. The ribosome moves along the mRNA molecule so that the next codon is aligned in the A site. The previous codon and the tRNA attached to it are now in the P site.
   6. A tRNA with the anticodon complimentary to the codon in the A site attaches there, lining up its amino acid with the one being held in the P site.
   7. A peptide bond forms between the two amino acids, the tRNA molecule in the P site releases its bond to its amino acid, and the process repeats until the ribosome reaches a "stop" codon.
9. Mutations
   1. A mutation is a change in a cell's DNA.
   2. Point mutations
      1. A point mutation occurs when one base is substituted for another.
      2. Point mutations affect only the codon in which they occur.
      3. Proteins produced based on a code containing a point mutation are usually still functional, since they are only one amino acid different from what they should be.
   3. Frame shift mutations
      1. A frame-shift mutation occurs when a base is either added to or deleted from a sequence of bases.
      2. Frame-shift mutations affect all of the codons after the mutation.
      3. Proteins produced from a sequence of bases containing a frame-shift mutation are rarely functional, since all of the amino acids after the mutation are different than normal.

Terms to know

• codon - A sequence of three base pairs on the mRNA molecule which codes for a particular amino acid.
• conservative replication - A hypothesis for DNA replication whereby the original strand is unchanged and a completely new strand of DNA is synthesized.
• dispersive replication - A hypothesis for DNA replication whereby the DNA molecule is broken into many small segments alongside which new DNA strands are formed, after which the segments are reassembled into two molecules of DNA.
• DNA - Deoxyribonucleic acid. DNA is a long molecule composed of deoxyribose, phosphate groups, and nitrogenous bases which indirectly dictates the production of proteins in a cell.
• frame shift mutation - A mutation which occurs when a base is either added or deleted from the DNA molecule, resulting in a new reading of the triplet codons and a completely different amino acid being produced.
• histone - A protein molecule which exists in clusters around which DNA wraps so that it is condensed in the nucleus.
• mRNA - Messenger RNA. It carries large portions of the information contained in the DNA molecule to the ribosomes for protein synthesis.
• nucleosome - The fundamental packing unit of DNA. It consists of a cluster of histones with two loops of DNA around it.
• nucleotide - The unit of structure of a nucleic acid. It consists of a five carbon sugar, a phosphate group, and a nitrogenous base.
• Okazaki fragment - Small pieces of DNA which form during DNA replication since DNA polymerase must work backwards on some strands. The Okazaki fragments are joined together by the enzyme DNA ligase.
• point mutation - A mutation which occurs when one base in the DNA molecule is replaced by another. This results in the production of a protein only one amino acid different from normal, so it is usually not very harmful.
• promoter - A sequence of bases on the DNA molecule to which RNA polymerase must attach to begin the transcription of an RNA molecule.
• purine base - A nitrogenous base with two rings of atoms in its structure. This includes adenine and guanine.
• pyrimidine base - A nitrogenous base with one ring of atoms in its structure. This includes cytosine, thymine, and uracil.
• RNA - Ribonucleic acid. RNA is a molecule composed of ribose, phosphate groups, and nitrogenous bases used to transfer information from the DNA molecule to the ribosomes where proteins are produced.
• rRNA - Ribonucleic acid. RNA is a molecule composed of ribose, phosphate groups, and nitrogenous bases used to transfer information from the DNA molecule to the ribosomes where proteins are produced.
• semiconservative replication - A hypothesis for DNA replication whereby the DNA molecule "unzips" and a new strand of DNA is assembled on either side. The resulting DNA molecules are half from the original molecule and half newly synthesized.
• termination signal - A second sequence of bases on the DNA molecule which signals the RNA polymerase to end transcription.
• transcription - The process by which RNA is created off of a DNA template.
• translation - The process by which the code on an mRNA molecule is used to form a protein molecule at the ribosomes.
• tRNA - Transfer RNA. It transfers a specific amino acid to the ribosome when the appropriate codon on the mRNA molecule has been reached.