Learning Objectives for Gene Regulation Lecture.by Dr. Ilya Ioshikhes,Department of Biomedical Informatics, 3017 Graves Hall,Tel. 292-6514, E-mail: [email protected] and prokaryotes.1. What is the meaning of these terms?2. Name some typical organisms that belong either to prokaryotes and eukaryotes.3. What is the main difference between the prokaryotes and eukaryotes?4. What is a cell hereditary substance?5. How is it organized in prokaryotes and eukaryotes?6. What is a chromosome? How many chromosomes are in Human? In E. coli?DNA, RNA and proteins – basics.7. What are the building blocks of DNA?8. What nucleotides are involved in DNA and RNA structure?9. How they are bound?10. What is a difference between the DNA and RNA?11. Name major functions of the DNA and RNA.12. How the information is transferred from DNA to proteins?13. What are the building blocks of proteins?14. How they are bound?15. What is the primary factor determining a protein’s shape and structure?16. Do the DNA, RNA and protein molecules have a beginning and an end? What are they?17. What is the major DNA structure?18. What are the rules of complementarity for the DNA?From DNA to proteins.19. What is the central dogma of molecular biology?20. What are genes?21. What are the main steps of gene expression in prokaryotes?22. – “ – in eukaryotes?23. What is the difference?Promoters and transcription.24. What is the DNA transcription?25. What is the promoter of a gene?26. What are its major elements in prokaryotes?27. –“– in eukaryotes?28. What is the TATA box and where it is located?29. What other core promoter elements do you know?30. What is RNA Polymerase and what are its functions?31. What types of the RNA Polymerase do you know? Which type participates in mRNA synthesis?32. What are general transcription factors and their function?33. What are cis- and trans-acting promoter elements? Examples?34. What are possible roles of transcription factors (TF)?35. Describe common bioinformatics methods for finding of TF binding sites.36. What are enhancers and how they act?Nucleosomes and chromatin.37. What is the chromatin?38. What are the nucleosomes?39. What is their primary role?40. Which basic levels of chromatin organization do you know?41. What is the role of nucleosomes in gene regulation?42. How the transcription is initiated if most of the promoters covered by the nucleosomes?DNA methylation and CpG islands.43. What is the DNA methylation?44. How it may transform the DNA sequence?45. How it may influence the gene expression?46. What are the CpG islands and where they are located?Splicing.47. What are exons and introns?48. What is primary RNA transcript?49. What is RNA splicing?50. What is alternative splicing?51. What are possible roles of the alternative splicing in a gene expression?Translation.52. What is the translation in molecular biology?53. Describe its major components.54. What is the role of RNA in protein synthesis?55. Which forms of RNA participate in it?56. Bring an example of a translational regulation.Key information elements.Eukaryotes and prokaryotes.1. Cells are the basic structural units of most of the living matter.2. Most of the organisms (excepting viruses) are a cell (single-celled organisms) or acomplex of multiple cells (multi-cellular organisms).3. The two major cell types are: eukaryotic cells (literally those with a true nucleus)and prokaryotic cells (those lacking a defined nucleus). All multi-cellularorganisms are eukaryotes.4. Eukaryotic cells contain a number of organelles.5. Prokaryotes and eukaryotes contain similar macromolecules. DNA is a hereditarysubstance of the both types.6. The organization of DNA differs greatly in prokaryotic and eukaryotic cells. In allprokaryotes studied to date, most or all of the cellular DNA is in the form of asingle circular molecule. The nuclear DNA of all eukaryotic cells, in contrast, isdivided between two or more different chromosomes. Human somatic cellscontain two sets of 23 chromosomes.7. Each chromosome contains a single linear double-stranded DNA molecule, boundto various proteins.DNA, RNA and proteins – basics.8. Nucleic acids (DNA and RNA) are linear polymers of nucleotides connected byphosphodiester bonds.9. A nucleotide has three parts: a phosphate group, a pentose (a five-carbon sugarmolecule), and an organic base. 10. In RNA, the pentose is always ribose, in DNA – deoxyribose.11. The name of the bases (and often of nucleotides) are adenine, guanine, cytosine(found in both DNA and RNA); thymine (found only in DNA); and uracil (foundonly in RNA) – abbreviated as A, G, C, T, and U, respectively.12. The bases are of two kinds: purines (A and G, their structure is two fused rings)and pyrimidines (C, T and U, with only one ring).13. In oligonucleotides, the nucleotide at one end has a free 3’ (deoxy)ribose hydroxylgroup, at the other end – a free 5’ phosphate or hydroxyl. They are related to the3’- and 5’-ends of the molecule, respectively.14. The native state of DNA is a double helix of two antiparallel chains that havecomplementary sequences of nucleotides. The bases on the opposite strands areheld together by hydrogen bonds: A is paired with T (2 bonds), G is paired with C(3 bonds).15. The building blocks of proteins are 20 amino acids. Each contains an aminogroup(-NH2) (imino group –NH- in proline), carboxyl group (-COOH) and a side chain(R group). The amino acids differ only in their side chains.16. Polypeptides are polymers composed of amino acids connected by peptide bonds.Proteins are polypeptides or complexes thereof.From DNA to proteins.17. Transcription of DNA to RNA to protein: This central dogma forms the backbone of molecular biology and is represented by four major stages. 1. The DNA replicates its information in a process that involves many enzymes: replication.2. The DNA codes for the production of messenger RNA (mRNA) during transcription. 3. In eukaryotic cells, the mRNA is processed (essentially by splicing) and migrates from the nucleus to the cytoplasm. 4. The messenger RNA carries coded information to ribosomes. The ribosomes "read" this information and use it for protein synthesis. This process is called translation. Proteins do notcode for the production of protein, RNA or DNA. They are involved in almost all biological activities, structural or enzymatic.18. Gene is a DNA segment responsible for a synthesis of