DNA and PROTEIN SYNTHESIS “ Cracking the Code ” The structure of DNA DNA replication and synthesis Making Proteins (protein synthesis) DNA and Mutations Oncogenes and cancer Biotechnology (mixing up the genes to make stuff)

The Structure of DNA ► During the 1940 ’ s, scientists accepted the idea that hereditary material existed in chromosomes, which are made up of proteins and nucleic acids (DNA). Originally, it was thought that the key component of the genetic code was the proteins, however, it was soon found that the key to the genetic code lie in the nucleic acids.

► DNA (deoxyribonucleic acid) is found in the cells of all organisms. DNA directs the activities of the cell, repairs and builds cell structures, and regulates all cell processes. DNA is the only molecule capable or replicating itself. DNA contains instructions that retain similar characteristics within a species. (That ’ s why people look like people and dogs look like dogs, but dogs don ’ t look like people.) DNA is also capable of mutation, which gives rise to diversity among individuals. ► DNA structure DNA structure DNA structure

► The DNA structure was first determined in the 1950 ’ s by James Watson and Francis Crick. They determined that DNA exists in a double helix, resembling a twisted ladder. Deoxyribose sugars and phosphates form the backbone and nitrogen base pairs form the rungs. These nitrogen bases are held together by hydrogen bonds, which cause the ladder structure to twist into a helix.

There are 4 DNA nucleotides found in all DNA. ► Purine base nucleotides have double rings.  Adenine  Guanine ► Pyrimidine base nucleotides have single ring structures.  Thymine  Cytosine

Complementary Pairing ► In DNA molecules, these hydrogen bonded nucleotides form specific complementary base pairs, consisting of 1 purine and 1 pyrimidine base. Adenine always binds with Thymine Guanine always pairs with Cytosine

► The “ genetic code ” is the sequence of these four DNA bases arranged along a strand of DNA. The code is read like letters that make up words, and words that make up sentences. Each genetic sentence produces a different protein. Combinations of sentences give rise to specific structures or characteristics. Different sequences and combinations give rise to different characteristics.

DNA Replication ► DNA is the only known molecule that is capable of self duplication. It undergoes a process called semi- conservative replication because one double stranded DNA produces two daughter strands that consist of one parent strand and a new, complementary strand.

The Steps for DNA Replication: 1. Unzipping of the double helix, and breaking the hydrogen bonds between the nucleotide bases.

2. Complementary pairing of free floating nucleotides to the bases on each of the separated parent template strands.

3. Nucleotides attach to the complementary parent bases, and fuse (hydrogen bond) with the help of polymerase enzymes. DNA makes DNA makes DNA

5’ vs 3’ ? ► =p835L4HWH68 =p835L4HWH68 =p835L4HWH68

DNA Editing ► Note: to prevent errors that might result from inappropriate pairing, cells contain special “ proof-reading enzymes ” that detect and correct mismatched base pairs along the newly synthesized DNA strands. If an error is detected, enzymes called exo-nucleases cut out the mismatched base, and replace it with the proper nucleotides. AMAZING!!! DNA has a spell check and correction function.

Protein Synthesis ► Proteins are composed of chains of only 20 different amino acids. Different sequences and numbers of amino acids give rise to different proteins with different functions. A protein can be as small as 8 amino acids, and as large as over 50,000 amino acids.

► One Gene One Protein Theory - states that the production of each protein is controlled by a separate gene. Since each gene is made up of many nucleic acid base pairs, a change in even one base pair could result in an incorrect protein being made.

How does DNA, made of only 4 nitrogen bases direct the construction of 20 different amino acids, which are sequenced together to produce thousands of different proteins? ► X1 base – 1 amino acid: ► X2 bases – 16 amino acids ► √ 3 bases – 64 amino acids!

Codons ► Are triplet codes, sequences of 3 nitrogen bases that code for a specific amino acid. Different codons can make the same amino acid. Some codons don ’ t code for amino acids, but tell the cell when to start or stop protein synthesis.

 Initiator codons – starts protein synthesis  Terminator codons – ends protein synthesis  Intron – non-coding sequences of DNA  Exon – coding sequences of DNA that make proteins

RNA (ribonucleic acid) is a long molecule made up of nucleotides that is similar to DNA, but different in 3 ways: ► 1. RNA is single stranded, DNA is double stranded ► 2. The sugar is ribose in RNA, deoxyribose in DNA ► 3. RNA uses the base uracil instead of thymine. Uracil binds with adenine.

There are 3 types of RNA, and each has a different role in protein synthesis. ► Messenger RNA (mRNA) – reads the DNA code and takes it to the ribosomes where proteins are made.

► Transfer RNA (tRNA) – brings the appropriate amino acids (forming anti- codons)from the cytoplasm to the ribosomes and strings them in order according to mRNA.

► Ribosomal RNA (rRNA) – is not directly involved with protein synthesis. It makes the ribosomes, so it is called structural RNA. DNA is transcribed into rRNA near the nucleolus, then the proteins migrate to the nucleolus where subunits are assembled into ribosomes. The ribosomes then migrate to the cytoplasm.

Steps in Protein Synthesis ► 1. Transcription – double stranded DNA opens up (unzips) so that mRNA subunits can bind to it, creating a complementary single strand. RNA polymerase attaches the subunits together, and the complementary strand detaches from the DNA and moves out of the nucleus to the ribosome. ► DNA-RNA-Protein DNA-RNA-Protein

► 2. Translation – as mRNA is fed through the ribosomes, tRNA brings amino acids from the cytoplasm to the ribosome. A complementary tRNA anti-codon matches up with a mRNA codon to drop off the amino acids in the correct order. When a stop codon is reached, the protein is completed. The tRNA returns to the cytoplasm and the mRNA is broken down. ► DNA-RNA-Protein DNA-RNA-Protein

Summary of Protein Synthesis DNA Transcription TranscriptionmRNAtRNATranslationProtein A Science Odyssey: You Try It: DNA Workshop Activity A Science Odyssey: You Try It: DNA Workshop Activity

DNA and Mutations ► Mutations are inheritable changes in the genetic code that can be caused by mutagenic agents. These are substances that alter DNA such as radiation and chemicals. Not all mutations are bad. Some mutations produce variation that improves functioning, but most have adverse side effects.

There are 4 basic sources of mutations: 1. Substitution of nitrogen bases 2. Translocation of a gene 3. Deletion of a nucleotide or gene sequence 4. Addition of extra nucleotide(s) Mutations in body cells often have little consequences compared to mutations of the germ cells (sperm or egg). A single mistake in the DNA of a sperm or egg cell would be repeated billions of times if that cell underwent fertilization to become a complete individual.

Transposons ► are “ jumping genes ”, DNA sequences that have the ability to move in / out of chromosomes, changing their location. These sequences usually act to enhance or suppress gene expression.

Control of Gene Expression The expression of genes (and ultimately the production of proteins) is constantly regulated. Not all genes are actively making proteins all the time. ► ► There are 4 levels of gene regulation in eukaryotic cells:

Control of Gene Expression Transcriptional control – determines which genes will be transcribed and how fast

► ► Post-Transcriptional control – speed at which mRNA leaves the nucleus and is processed

► ► Translational control – how soon / long mRNA is active in the cytoplasm determines whether or not the protein will be made

► ► Post-Translational control – how soon proteins become active of functional (some need activating enzymes)

Oncogenes and Cancer ► Cancer is characterized by uncontrolled cell division. Evidence suggests that cancer may result from changes to the genetic code. This is supported by 3 lines of evidence: 1. Cancerous cells often display nitrogen base substitutions 2. Many known mutagens, are also known to cause cancer 3. In 1982, segments of chromosomes extracted from cancerous mice transformed normal mouse cells into cancerous cells. It is believed that these chromosomal segments contained cancer-causing genes called oncogenes.

Oncogenes ► It has been found that oncogenes are present in normal cells, and do not always result in cancer. In order for a cell to become cancerous, it is believed that these oncogenes must be transposed to another site on the chromosome. When the oncogene binds to this alternate site, it disrupts the normal regulator sequences that prevent the cell from dividing, and uncontrolled division occurs.

The Ames Test ► To test for potential mutagens, scientists have developed the Ames Test. ► The bacterial Salmonella typhimurium is unable to make histidine, so this amino acid must be supplied for the bacteria to survive. After the bacteria is exposed to a potential mutagen, it is grown in a culture without histidine. If no mutation took place, the bacteria will die due to the lack of histidine. If the bacteria survives, it is because a mutation has taken place, and the bacteria is now able to produce histidine. This will result in the substance being labeled as mutagenic and dangerous for humans.

Biotechnology

► Biotechnology – is the use of natural biological systems to produce a product. ► Genetic engineering – is the process of producing cells that are transgenic. Such cells have foreign DNA (from other species) inserted into their own DNA, and are thus able to produce foreign proteins.

► Recombinant DNA – is DNA that comes from 2 or more sources. Usually, the DNA is specifically chosen, and introduced into the host cell by a vector. ► Vector – is an organism (bacteria or virus) that carries and leaves its genetic material (DNA or RNA) in a host cell. The host then replicates the vector ’ s genetic material. ► Plasmid – is circular DNA found in bacteria. This is often used as a vector in DNA recombination.

The process of creating recombinant DNA involves 2 types of enzymes: ► Restriction Enzymes – cut the DNA strand at specific sites (palindromes). (i.e. a strand may be cut between G and A GAATTCCTTAAG ► DNA ligase – is genetic glue that puts DNA strands back together.

► Diabetic patients rely on daily insulin injections. Insulin used to be harvested from pigs, but some individuals did not tolerate non-human insulin. With the help of genetics, we are able to use bacteria to produce human insulin in large quantities. This is tolerated much better by patients. This procedure was first marketed in Canada in 1983!

Other Aspects of Biotechnology ► Gene sequencing – is the process of determining the location and composition of specific genes. A huge international collaboration called The Human Genome Project has identified the general sequences in the human genome. Scientists still do not know what each gene does, but they are well on their way to identifying many genes that cause diseases such as cancer. ► NOVA Online | Cracking the Code of Life | Sequence for Yourself NOVA Online | Cracking the Code of Life | Sequence for Yourself NOVA Online | Cracking the Code of Life | Sequence for Yourself

► RFLP – restriction fragment length polymorphism is a procedure used to identify the gene sequence. Restriction enzymes are used to cut DNA into segments, resulting in many segments of different lengths. The patterns of genes in these segments is unique to each individual, thus making genetic fingerprinting possible.

► DNA fingerprinting – is the procedure developed by Alec Jeffries used to identify an individual based on their unique genetic code. Jeffries found that homologous segments of DNA are similar but contain unique patterns of nitrogen bases. These unique patterns can be used to identify an individuals involved in crimes, and to establish paternity with a high degree of certainty.

DNA Fingerprinting

Misc. Technology ► PCR - PCR Animation (link no good) PCR AnimationPCR Animation ► Gel Electrophoresis - Biology I Interactive Animations (link no good) Biology I Interactive AnimationsBiology I Interactive Animations ► Paternity Testing - Paternity Testing Paternity TestingPaternity Testing ► Gene Gun - Genegun1 (link no good) Genegun1