Human Genome Project (HGP) Handout - Long Quiz 2 PDF

**Human Genome Project (HGP)** - The **Human Genome Project (HGP)** was an international scientific research project that aimed to determine the **complete sequence of nucleotide base pairs** that make up human DNA and all the genes it contains. - It remains the world\'s largest co...

**Human Genome Project (HGP)** - The **Human Genome Project (HGP)** was an international scientific research project that aimed to determine the **complete sequence of nucleotide base pairs** that make up human DNA and all the genes it contains. - It remains the world\'s largest collaborative biological project. - The idea was picked up in **1984** by the US government when the planning started, the project was formally launched in **1990** and was declared complete in **2003**. - **Genes** = specific sequences on DNA that can be expressed into proteins and other molecules. - **Genomes** = all DNA in nucleus of  the  cell. **Goals of HGP** - **Obtain physical map of genome**- Allows rough location of genetic fragments - **Develop sequencing technology**- Increase throughput and reduce cost - **Obtain human DNA sequence**- Achieve high accuracy, make freely accessible - **Analyze human sequence variation**- Identify SNPs, develop theory - **Create bioinformatics tools**- Develop databases and analysis algorithms - **Identify genes and coding regions**- Develop efficient in-*vitro or in-silico methods* - **Sequence other model organisms-** Bacteria, yeast, fruit fly, worm, mouse - **Ethical, legal and social issues**- Develop policies and public awareness ----------------------- --------------------------------------------------------------------------------------------- **Level of Analysis** **Definition** Genome Complete set of genes of an organism or its organelles Transcirptome Complete set of messenger RNA molecules present in a cell, tissue or organ Proteome Complete set of protein molecules present in a cell tissue or organ Metabolome Complete set of metabolites (low-molecular-weight intermediates in a cell, tissue or organ) ----------------------- --------------------------------------------------------------------------------------------- - The process of determining the human genome first involves genome mapping, or characterizing the chromosomes. This is called a **genetic map.** - The next step is DNA sequencing ,or determining the order of DNA bases on a chromosome. These are **physical maps.** **Genetic markers** - **Genetic markers** are invaluable for genome mapping. - Markers are any inherited physical or molecular characteristics that are different among individuals of a population (polymorphic) - A **genetic map** shows the relative locations of these specific markers on the chromosomes. **Restriction fragment length polymorphisms (RFLP)** - Used in **RFLP** markers are restriction enzymes. These enzymes recognize short sequences of DNA and cut them at specific sites, therefore, DNA can be cut into many different fragments. These fragments are the DNA pieces used in physical maps - RFLPs reflect sequence differences in DNA sites which are cleaved by restriction enzymes. **Single-nucleotide polymorphism (SNP)** - One-nucleotide difference in sequence of two organisms - Found by sequencing - Example: Between any two humans, on average one  **Sequencing Strategies** - To sequence DNA, it must be first be **amplified**, or increased in quantity. - Two types of DNA amplifications are **cloning** and Polymerase Chain Reactions **(PCR).** - Now that the DNA has been amplified, sequencing can begin. - Sequencing techniques used in HGP are:- **1)Shotgun sequencing method** -. Shotgun sequencing is a laboratory technique for determining the DNA sequence of an organism\'s genome. The method involves randomly breaking up the genome into small DNA fragments that are sequenced individually. **2)Sanger sequencing method** - Sanger sequencing, also known as the chain termination method, is a technique for DNA sequencing based upon the selective incorporation of chain-terminating dideoxynucleotides (ddNTPs) by DNA polymerase during in vitro DNA replication. **Outcomes of HGP** - There are approximately **22,300** protein-coding genes in human beings, the same range as in other mammals. **Mouse -- 23,000 genes (approx.)** **Drosophila -- 17,000 genes (approx.),** **C.elegans - \< 22,000 genes (approx.),** - We share many homologous genes (called \"orthologs\") with both these animals. - However :many of our protein-encoding genes produce more than one protein product (e.g., by alternative splicing of the primary transcript of the gene). On average, each of our ORFs produces 2 to 3 different proteins. - A larger proportion of our genome : encodes transcription factors is dedicated to control elements (e.g., enhancers) to which these transcription factors bind - The combinatorial use of these elements provides much greater flexibility of gene expression than is found in *Drosophila* and *C. elegans.* **Gene density** - 23 genes per million base pairs on chromosome 19 - 5 genes per million base pairs on chromosome 13. - Humans, and presumably most vertebrates, have genes not found in invertebrate animals like *Drosophila* and *C. elegans*. - Human genome comprises of 2% of exons (coding regions) and 98% of introns (non-coding regions). **Applications of HGP** - The sequencing of the human genome holds benefits for many fields, from molecular **[medicine to human evolution.]** - Helps in **[identifying] [disease causing gene.]** - **[Identification of mutations]** linked to different forms of cancer. - The sequence of the **[DNA is stored in databases]** available to anyone on the Internet. - Allow **[advances in agriculture]** through genetic modification to yield healthier, more disease-resistant crops. Benefitted the advancement of **[forensic science.]** **Gene Structure and Function** Function of Genes On the basis of behavior, the genes are categorized into the following types. - **[Basic Genes]** - **[Lethal Genes]** - **[Multiple Gene]** - **[Cumulative Gene]** - **[Pleiotropic Gene]** - **[Modifying Gene ]** - **[Inhibitory Gene]** **Gene Interaction** **Gene interactions can be classified as** - **Allelic/ non epistatic gene interaction -** This type of interaction gives the classical ratio of 3:1 or 9:3:3:1 - **Non-allelic/ epistatic gene interaction-** In this type of gene interaction genes located on same or different chromosome interact with each other for their expression The key difference between allelic and non allelic gene is that in allelic genes, the alleles are present at the same location of the homologous chromosome while in non-allelic gene, the alleles are present at different locations of the same homologous chromosome to express a particular character.  **Allelic Interaction** -- one gene controlling one trait 1. **Complete Dominance (3:1)** 2. **Incomplete Dominance (1:2:1)** 3. **Co-dominance (1:2:1)** 4. **Dominant Lethal (0:2:1) or (0:1)** 5. **Recessive Lethal (1:2:0) or (3:0)** **Non-Allelic** **A. Epistatic Gene** - a gene or locus which suppress or mask the phenotypic expression of another gene at another 1. **Dominant Epistasis (12:3:1) or (13:3)** 2. **Recessive Epistasis (9:3:4)** 3. **Duplicate Gene Action (15:1)** 4. **Complementary Gene Action (9:7)** **B. Novel Phenotypes --** Complete dominance at both gene pairs, new phenotypes are produced from interaction between dominants and between both homozygous recessives. (A dominant to a; B dominant to b; a interacts with B producing new phenotype; aabb also produces a new phenotype) (i.e pepper color and Mutant alleles associated with novel eye phenotypes of fruit fly)  **Gene Expressions** - Eukaryotic genes also are regulated in units of protein-coding sequences and adjacent controlling sites, but operons are not known to occur. - Eukaryotic gene regulation is more complex because eukaryotes possess a nucleus. (transcription and translation are not coupled). - Two "categories" of eukaryotic gene regulation exist: **[Short-term]** - genes are quickly turned on or off in response to the environment and demands of the cell. **[Long-term]** - genes for development and differentiation. **[Eukaryote gene expression is ]** **[regulated at six levels]:** 1. **Transcription** - **Promoters** - Occur upstream of the transcription start site. - Some determine [where] transcription begins (e.g., TATA), whereas others determine [if] transcription begins. - Promoters are activated by specialized transcription factor (TF) proteins (specific TFs bind specific promoters). - One or many promoters (each with specific TF proteins) may occur for any given gene. - Promoters may be positively or negatively regulated - **Enhancers** - Occur upstream or downstream of the transcription start site. - Regulatory proteins bind specific enhancer sequences; binding is determined by the DNA sequence. - Loops may form in DNA bound to TFs and make contact with upstream enhancer elements. - Interactions of regulatory proteins determine if transcription is activated or repressed (positively or negatively regulated). No description available. - RNA Polymerase -- enzyme that transcribes gene into RNA - Promoter -- DNA sequence that RNA polymerase binds to initiate transcription of gene - Enhancer -- DNA sequence, often far from the gene that transcription factors bind - Transcription Factors- regulatory proteins that bind enhancer and help RNA polymerase bind the promoter 2. **RNA processing** - RNA processing regulates mRNA production from precursor RNAs. - Two independent regulatory mechanisms occur: - [Alternative polyadenylation] = where the polyA tail is added - [Alternative splicing] = which exons are spliced - Alternative polyadenylation and splicing can occur together. - Examples: - Human calcitonin (CALC) gene in thyroid and neuronal cells 3. **mRNA transport** - Eukaryote mRNA transport is regulated. - Some experiments show \~1/2 of primary transcripts never leave the nucleus and are degraded. - Mature mRNAs exit through the [nuclear pores]. 4. **mRNA translation** - Unfertilized eggs are an example, in which mRNAs (stored in the egg/no new mRNA synthesis) show increased translation after fertilization). - Presence or absence of the 5' cap and the length of the poly-A tail at the 3' end can determine whether translation takes place and how long the mRNA is active. - Conditions that affect the length of the poly-A tail or leads to the removal of the cap may trigger the destruction of an mRNA. 5. **mRNA degradation** - All RNAs in the cytoplasm are subject to degradation. - tRNAs and rRNAs usually are very stable; mRNAs vary considerably (minutes to months). - Stability may change in response to regulatory signals and is thought to be a major regulatory control point. - The life span of mRNA molecules in the cytoplasm is a key to determining protein synthesis - The longer the mRNA last, the more protein can be made - Eukaryotic mRNA is more long lived than prokaryotic mRNA 6. **Protein degradation** - Proteins can be [short-lived] (e.g., steroid receptors) or [long-lived] (e.g., lens proteins in your eyes). - This is a cells last change to affect gene expression. - Protease, enzymes that break down proteins, are confined to lysosomes and proteasomes. - When a protein is tagged by a signaling protein, it enters a proteasome to be degraded. - Proteasomes are giant protein complexes that bind protein molecules and degrade them