Genetics, DNA, Replication, Transcription, and Translation

1. Genetics, DNA, Replication, Transcription, and Translation Objectives: Describe the structure of DNA and chromosomes. List the 5 bases and the 2 categories they belong to. Discuss the processes of replication, transcription, and translation. Research/Investigate chromosome structure and genetic composition. Analyze the roles of mRNA, tRNA, and rRNA. Explain protein structure/folding. Predict the implications nutrient deficiencies might have on any of the above processes or structures. Describe the types of genetic mutations possible. Evaluate the pros and cons of current genetic technology Vocabulary: nucleotide * purine * pyrimidine * replication * replication forks * uracil * antiparallelism * histone * dimers * transcription * translation * codon * ribosomes * point mutation * promoter * anticodon * mRNA * tRNA * rRNA * genes * introns * exons * junk genes * methionine * R groups * complement * polypeptide * conformation * disulfide bonds * mutagen * carcinogen * substitution * deletion * insertion * frameshift * translocation * nonsense mutation * transposons * jumping genes * inversion * trisomy * monosomy * genetic engineering * GMO * restriction enzymes * electrophoresis * nondisjunction

2. DNA (deoxyribonucleic acid) consists of monomer nucleotides made of a 5 carbon sugar (deoxyribose), a nitrogenous base, and phosphate. The nitrogenous base can be either a double carbon and nitrogen ring called a purine or a single carbon and nitrogen ring called a pyrimidine. Adenine and guanine are purines and thymine and cytosine are pyrimidines. Adenine always binds to its complementary base, thymine, and guanine always binds to its complement, (partner) cytosine, via hydrogen bonds. These form the “rungs” of the DNA double helix “ladder”. The “rungs” are bound to deoxyribose on each side. Completing the sides of the ladder are phosphates. These alternate with the deoxyribose sugars. Chromosome Structure: PO4 PO4 Sugar -- purine* *pyrimidine -- Sugar PO4 PO4 (**hydrogen bonds)

3. Before a cell can divide, the DNA containing chromatin needs to double. This doubling process is called replication. For replication to proceed, the double helix of DNA strands must unwind (break hydrogen bonds between complementary base pairs) in many locations at once. These unzipped areas are called replication forks. Each DNA strand of the double helix has a 5’ (5 prime) and a 3’ end. The two DNA strands align in opposite directions. This head to tail alignment is called antiparallelism. Additional bases to form the new DNA strand are added from the 5’ end toward the 3’ direction. When replication is complete, 2 complete double helixes of DNA exist BUT each one contains 1 old strand and 1 new strand of DNA. It is only after replication that chromatin can condense around histone proteins to form chromosomes and complete the cell cycle. Unfortunately, if copying errors were made and not caught by proofreading polymerases, mutations can occur. Thymine dimers are the most common cause. This happens when 2 adjacent thymines on the same strand covalently bind to each other causing a kink. This makes it easier to insert the wrong base in the new DNA strand.

4. Transcription Since DNA can’t leave the nucleus, its information for protein synthesis has to be carried to the ribosomes (site of protein synthesis) in the cytoplasm by RNA (same basic structure as DNA but with a 5 carbon ribose sugar instead of deoxyribose). To do this, DNA unzips and nucleotides form the RNA complement to the DNA template. This process is called transcription. Only a single strand of RNA is formed. This RNA is called messenger RNA (mRNA) because it carries DNA’s message for protein synthesis. RNA will not normally contain thymine bases. Instead, every adenine on the DNA will be paired with a uracil base (pyrimidine) on the RNA strand. So, RNA can contain A, U, C, and G, but not T. A combination of a 3 base triplet on RNA that codes for an amino acid is called a codon. Only DNA sequences that code for amino acids or RNA parts (genes) need to reach the ribosomes. These sections of DNA are called exons. However, DNA contains many “non-gene” sequences too. These are called introns. When DNA is transcribed, the introns are cut away and the exons are re-assembled into mRNA. At one time, introns were considered genetic “junk”, or “junk genes”. Today we realize these segments probably control the when, where, etc. of DNA replication and transcription.

5. The cell knows where to start the transcription process because a promoter region on DNA attracts the transcription factors and RNA polymerase. There are many different factors controlling transcription. Some of these factors contain nutrients such as zinc, the amino acid leucine, etc. So, a deficiency in a particular nutrient could stop the transcription of information for an important protein. And, proteins are what give us our shape (morphology) and appearance (phenotype), so a missing or abnormal protein could cause disease or mutations. Finally, the cell knows when to stop transcribing DNA when a sequence of bases called the “terminator” region is reached. Imagine what might happen if the terminator region was not correctly replicated or read during transcription. Fortunately, our bodies have many “proofreading” enzymes doing their best to make sure all goes well.

6. Protein Synthesis The mRNA exits the nucleus and travels to the ribosomes (site of protein synthesis). Some ribosomes are attached to endoplasmic reticulum and will make mostly proteins for export out of the cell. Other ribosomes are loose in the cell and make proteins likely to stay in the cell and be used for growth, repair, etc. The ribosomes are composed of a protein sub-unit and an RNA sub- unit called ribosomal RNA (rRNA). It is at the ribosomes that mRNA will be translated. Translation is the process where mRNA is read in order to synthesize a new protein. mRNA contains triplets of nitrogenous bases. Each triplet codes for an amino acid (except the “stop” triplet). These triplets are called codons. The first mRNA codon is usually “AUG”. It signals the transfer RNA (tRNA) to start translation by bringing the amino acid “methionine”. tRNA carries amino acids to the ribosome to form a polypeptide. tRNA has anti-codons that are the triplet complement to the mRNA codons.

7. Polypeptides are long chains of amino acids that individually, or in combination, become a protein. Proteins are very complex and can fold into a 3 dimensional shape, called its conformation. The simplest “chain” of amino acids is called the “primary” conformation. Some folding occurs due to hydrogen bonds between non-adjacent carboxyl and amino groups (due to their polarity). This is called the secondary structure. Then more folding occurs as ionic bonds form between the side groups (R-groups) of the amino acids and as disulfide bonds form between sulfurs. This is the final, tertiary structure of individual polypeptides and many proteins. However, sometimes individual polypeptides must bond together to make a functional protein. For example, 4 polypeptide chains interact to make the blood protein hemoglobin. This interaction creates the quaternary structure of some proteins.

8. Mutations There are several copying errors that can be made during replication or transcription. Occasionally, these are induced by environmental hazards like ultraviolet light, X-rays, chemical exposure, etc. Anything that can cause a mutation is called a mutagen. (“Teratogens” is also used and refers to substances that cause structural birth defects.) Some mutations can actually be beneficial. However, if exposure to a mutagen causes cancer, the mutagen is known as a carcinogen. When a single base is incorrectly complemented, inserted or deleted, in a gene, it is called a point mutation. When the wrong base is substituted for the correct complement (Ex: an “A” partners with a “C” instead of a “T”), it’s called substitution. If this codes for a different amino acid than normally found here, it is sometimes called a missense mutation. When a complementary base is left out in the copying process, it’s a deletion. And, when an extra base is put in, it’s an addition. Usually, a substitution is the least serious because it sometimes allows the same amino acid to form or the new amino acid has little effect on the overall function of the protein formed. If the substitution causes the codon to read “stop”, it’s a “nonsense mutation”.

9. Additions or deletions are usually VERY serious problems for protein synthesis. That’s because they cause a reading frameshift mutation. Remember, each triplet (codon) of bases codes for a different amino acid. Think of these as words in a sentence. Ex: The Cat And Dog Ran. If I insert an “A” in the middle of “The”, the new triplets are read as . . . Tah Eca Tan Ddo Gra . . . If I delete the “H” from “The” in the original codon string, I get . . . Tec Ata Ndd Ogr An . . . A substitution is usually far less traumatic. Ex: Substitute “A” for “e” in “The” from the original triplet string. Tha Cat And Dog Ran HOWEVER, in sickle cell anemia only one base is wrong due to a substitution that caused valine (CAC at the DNA level - complements to GUG on mRNA)) to replace glutamic acid (CTC on DNA, but GAG on mRNA). Valine is a polar amino acid, that causes hemoglobin to fold incorrectly.

10. Chromosomal mutations can also occur. Pieces of chromosome can break off and be lost (deletion) in the copying process. They can break off and reconnect to a nonhomologous chromosome (Ex: break off chromosome #1 and reattach to chromosome #3). This is called translocation. There are certain genes (about 10% of them) in humans that fairly easily move to different chromosome locations. These are called “transposons” or “jumping genes”. Occasionally, a piece of chromosome breaks off and reattaches upside down to the same chromosome. This is called an “inversion”. And, of course, nondisjunction of chromosomes can cause trisomy (3 copies of a chromosome in the genome) or monosomy (a single chromosome, no homolog).

11. Gene Technology Genetic engineering involves cutting genes from one organism and splicing them into the genes of another. The combination DNA from the 2 organisms is called recombinant DNA. In order to create recombinant DNA, enzyme “knives” (restriction enzymes) that recognize certain base sequences are used to cut them away from the rest of the DNA. Once the selected DNA is isolated, it must be inserted into the DNA of the second organism. Very often a virus is used because these can easily enter cells. Bacterial plasmids (DNA rings) also work in some cases. Genetic engineering has been used to cheaply make insulin and other human hormones using human DNA inserted in bacteria. It has also been used in plants to make crops resistant to herbicides used to kill weeds in the fields As a result, GMO {genetically modified organisms} soybeans are more heavily sprayed than ever! It has also been used to insert the gene for BT (bacillus thurengis?) in corn to kill corn borers BUT it kills other caterpillars too! So, its use is quite controversial.

12. Gene splicing has also been used in vaccine production. For example, the vaccine for Hepatitis B involves splicing a gene from the virus with a fungus. Similar crosses are being used in plants to create rice, for example, that makes beta-carotene in levels similar to a carrot. Unfortunately, these combinations can cause allergic reactions that might not occur to the single organism’s DNA. Once these crosses are made, they are in the gene pool to stay and will be carried in future generations. So, if you are allergic to carrots, but not rice, GMO rice using carrot genes may now also cause an allergic reaction in you. In order to see gene sequences of nitrogenous bases, we can use gel electrophoresis. This allows us to take pieces of the human genome and display them as bands based on their molecular weight and their attraction to an electric current. The same technique can be used on other polar/charged molecules as well.