Genomic Organization at the DNA level! By: Caroline Fowle, Amanda Zink, Ben Whitfield, Farvah Khaja and Danielle Siegert

Transposons Transposons- ｷ stretches of DNA that can move from one location to another within a genome -enzymes used: transcriptase, reverse transcriptase, transposase Process: Copy and paste: transposon jumps from one location on the genome to another. Replicative: transposon replicates itself at the original site and the replication is then allowed to transpose Retrotransposons: transposable elements that move within a genome by means of an RNA intermediate. -enzymes used: transcriptase, reverse transcriptase, transposase

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Repetitive DNA -Nucleotide sequences that have many copies in the genome, but are not typically within genes. - ｷ Tandemly Repetitive DNA--short sequences repeated (GGTCAGGTCAGGTC) - ｷ Interspersed Repetitive DNA—Unlike tandemly repeated DNA, repeated sequence is scattered throughout the genome. (many are tranpsosons). - ｷ Alu elements are around 5% of DNA in primates and are around 300 nucleotides long.They are the exception to the rule that repeating DNA doesn’t code for RNA. Pseudogenes -have sequences very similar to real (functional) genes but lack the regulatory sequences (i.e. promoters) needed for gene expression. -Created through mutations/errors made when copying original, ancestral gene. Found in noncoding DNA. -Serves as evidence that mutated genes arose from one ancestral, working gene. Created gene families.

Multigene Families A multigene family is a set of several identical or similar genes that all evolved from one common ancestral gene. It is repetitive DNA with repeating gene-long units. Identical genes are usually clustered end-to-end and consist of genes for RNA products. Differences in genes in a multigene family are probably due to mutations in gene copies.

Gene Amplification- Selectively replicates certain genes -Causes multiple genes of a specific gene to be made so it enhances expression. Purpose- enables the developing egg cell to make huge numbers of ribosomes -Also in cancer cells. The resistant cells after chemotherapy have amplified segments of DNA which carry genes that are resistant to the drugs. Benefit- allows the egg to have a burst of protein synthesis once the egg is fertilized. Makes large amounts of growth possible (protein production) possible for the demanding egg. These extra copies cannot replicate and are broken down during early development.

Immunoglobulin Genes -genes that code for antibodies. Produces proteins that fight viruses, bacteria and other invaders of the body. -Immunoglobulins are antibodies which are made by B lymphocytes ( a type of white blood cells). -There are three regions in an antibody—the V (variable) region, the C (constant) region, and the J (junction) region. -There is lots of variation in the making of antibodies because of how many different combinations of V and C groups there can be, and since there are four different sections to the complete antibody molecule. Epitopes -part of the antigen that is recognized by antibodies/B cells/T cells in immune system AKA antigenic determinant. Types: -Conformational epitopes are discontinuous sections of the antigen’s amino acid sequence. -Linear epitopes are a continuous sequence of the amino acids. Red dots-epitopes

Review Questions! Q. What are the two types of transposition? What are the differences? A. Cut & paste (jumping from one location to another) and replicative (replicating itself at its original site and allowing the copy to transpose.) Q. What are the two types of repetitive DNA and what were the differences? What was the repetitive DNA that is found in primates that codes for RNA? A. Tandemly repeated and intersperesed DNA. Interspered repetition is scattered throughout the genome and tandemly repeated are short sequences repeated one after another.

…Questions (and answers) Continued… Q. Which region gives the antibody the ability to locate and bind to a certain foreign particle? A. Variable region Q.What do the genes in a multigene family have in common? A. they all evolved from a common ancestral gene, they have identical or very similar sequences Q. What is another name for an epitope? A. antigenic determinant Q. Why is it possible for there to be lots of variation in the antibodies that can be produced by the body? A. there are two different variable parts that can combine in many different ways to produce different antibodies

Relatable Words 1. Evolution 2. Amplification 3. Mutations 4. Locomotion/Transportation 5. Variation