YIJC [H2] CI2.4 Gene Expression and Regulation I (N)(S) vetted (wo checkpoint answers)

2024 JC1 BIOLOGY LECTURE NOTES CORE IDEA 2: GENETICS AND INHERITANCE TOPIC 2.4: GENE EXPRESSION AND REGULATION (PART 1) Learning Outcomes: (c) Describe how the information on DNA is used to synthesize polypeptides in prokaryotes and eukaryotes (description of the processes of transcription, formation of mRNA from pre-mRNA and translation is required) (d) [modified] Describe the structure and organisation of eukaryotic genomes (including DNA / RNA, single- / double-stranded, number of nucleotides, packing of DNA, linearity/circularity and presence of introns). (i) Describe the structure and function of non-coding DNA in eukaryotes (i.e. portions that do not encode protein or RNA, including introns, centromeres, telomeres, promoters, enhancers and silencers) (Knowledge of transposons, satellite DNA, pseudo-genes and duplication of segments is not required) (j) explain how differential (i.e. spatial and temporal) gene expression in eukaryotes can be regulated at different levels: (i) chromatin level (histone modification and DNA methylation) (ii) transcriptional level (control elements, such as promoters, silencers and enhancers, and proteins, such as transcription factors, including activators and repressors) (iii) post-transcriptional level (processing of pre-mRNA in terms of splicing, polyadenylation and 5’ capping) Use the knowledge gained in this section in new situations or to solve related problems. References: Reece, J. B. et al. (2018). Campbell Biology (11th Ed). Chapter 18: Regulation of Gene Expression, pp. 368 – 385. Note: This textbook is available in our library. You may wish to borrow the book to supplement your reading when necessary. H2

2 Contents 1. Glossary of Terms ....................................................................................................................... 3 1.1 Organisation of DNA ................................................................................................................ 5 1.2 Definition of a Gene ................................................................................................................. 7 1.3 Structure and Organisation of Eukaryotic Genomes .......................................................... 8 1.4 Non-coding DNA ..................................................................................................................... 12 1.4.1 Introns ............................................................................................................... 12 1.4.2 Centromere ....................................................................................................... 13 1.4.3 Telomere ........................................................................................................... 14 1.4.4 Promoter ........................................................................................................... 19 1.4.5 Enhancer ........................................................................................................... 19 1.4.6 Silencer ............................................................................................................. 20 2. Central Dogma of Molecular Biology ..................................................................................... 22 3. Protein Synthesis (Part I) ......................................................................................................... 25 3.1 Transcription ...................................................................................................................... 25 3.2 Post-Transcriptional Modification ................................................................................... 32 4. Importance of regulatiing gene expression ........................................................................... 35 4.1 Regulation at Chromatin Level .................................................................................... 38 4.1.1 Histone modification ........................................................................................ 38 4.1.2 DNA Methylation ............................................................................................... 40 4.2 Regulation at Transcription Level ........................................................................................ 43 4.2.1 Control Elements .............................................................................................. 43 4.2.2 Transcription Factors ....................................................................................... 46 4.3 Regulation at Post-transcriptional Level ............................................................................. 51 4.3.1 Pre-mRNA Processing (Refer to Section 3.2 for details) .............................. 51 4.3.2 mRNA Transport ............................................................................................... 53

3 1. Glossary of Terms Retrieve knowledge from Topic 2.1 Structure and Function of Nucleic Acids: DNA is a long, double-stranded molecule that forms a double helix. Each strand is made up of deoxyribonucleotides, which are composed of a pentose sugar, a phosphate group, and one of four nitrogenous bases (adenine, thymine, guanine, and cytosine). The two strands are held together by hydrogen bonds between the complementary base pairs (adenine pairs with thymine, and guanine pairs with cytosine). Definition list 1. Genome: The complete set of genetic instructions or DNA present in an organism. It contains all the information needed for the development, growth, and functioning of that organism. 2. DNA (Deoxyribonucleic Acid): A long, double-stranded molecule that carries the genetic instructions for the development, functioning, and reproduction of living organisms. It is composed of four nucleotide bases: adenine (A), thymine (T), guanine (G), and cytosine (C). 3. Chromosome: A thread-like structure composed of DNA and proteins, found in the nucleus of cells. Chromosomes carry the genetic information in the form of genes 4. Coding Region: The portion of a gene's DNA or RNA sequence that provides instructions for the synthesis of a specific protein. It is the region that is translated into the amino acid sequence of a protein. 5. Non-coding Region: The portion of a gene's DNA or RNA sequence that does not code for a protein. These regions may have regulatory functions or may not have any known function. 6. Coding Sequence: The specific sequence of nucleotides in a gene's DNA or RNA that encodes the amino acid sequence of a protein. It is the same as the coding region. 7. Non-coding Sequence: The sequence of nucleotides in a gene's DNA or RNA that does not encode a protein. These sequences may have regulatory or structural roles. 8. Centromere: A constricted region of a chromosome that holds the two sister chromatids together during cell division. It is the attachment point for the spindle fibers that separate the chromosomes during cell division. 9. Telomere: A repetitive nucleotide sequence at the end of a chromosome that protects the chromosome from deterioration during cell division. 10. Promoter: A specific DNA sequence located near the beginning of a gene that serves as a binding site for RNA polymerase and other transcription factors, initiating the process of transcription. 11. Enhancer: A short DNA sequence that can increase the transcription of a gene by binding to specific proteins called transcription factors, even if the enhancer is located far away from the gene it regulates. 12. Silencer: A DNA sequence that binds to specific proteins and inhibits the transcription of a gene, effectively silencing or reducing its expression.

4 13. Intergenic Introns: Non-coding regions of DNA that are located between genes. 14. Intragenic Introns: Non-coding regions of DNA that are located within a gene, interrupting the