Istanbul Aydin University MED108-1 Medical Biology and Genetics Lecture PDF

MED 108-1 MEDICAL BIOLOGY AND GENETICS EUKARYOTIC GENOME ORGANIZATION Assist. Prof. Meltem ERCAN, PhD. IAU Faculty of Medicine (Eng.) Medical Biology & Genetics 21/11/2024 [email protected] ...

MED 108-1 MEDICAL BIOLOGY AND GENETICS EUKARYOTIC GENOME ORGANIZATION Assist. Prof. Meltem ERCAN, PhD. IAU Faculty of Medicine (Eng.) Medical Biology & Genetics 21/11/2024 [email protected]  MED108-1 oLecture slides are responsibility. oLecture books for study. oLecture books’ pdf can be downloaded from Ubis. 1  OUTLINE Introduction to Prokaryotic Basic Genetic and Eukaryotic Terms Genome Configuration of Eukaryotic Genome 2 INTRODUCTION The most fundamental property of all living things is the ability to reproduce. All organisms inherit the genetic information specifying their structure and function from their parents. The classical principles of genetics were deduced by Gregor Mendel in 1865, based on the results of breeding experiments with peas. 3 Mendel studied inheritance of well-defined traits, like seed color, and deduced general transmission rules. He correctly interpreted inheritance patterns by assuming each trait is determined by a pair of inherited factors, now known as genes. 4  What is a gene? The basic physical and functional unit of BASIC heredity. GENETIC Made up of DNA. TERMS Passed from parents to offspring. Determine many of the traits. Some genes code for proteins while many genes do not. 5 What is a gene? 6  DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. What is a Nearly every cell in a person’s body has the same DNA? DNA. Most DNA is in the nucleus (nuclear DNA), but a small amount is found in mitochondria (mitochondrial DNA or mtDNA). 7  What is a DNA? DNA stores information as a code of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Human DNA has about 3 billion bases, with over 99% being the same in all people. 8 What is a chromosome? In each cell's nucleus, DNA is packaged into thread-like structures called chromosomes. Each chromosome consists of DNA tightly coiled around proteins called histones, which support its structure. Chromosomes are not visible in the cell’s nucleus — not even under a microscope — when the cell is not dividing. Becomes more tightly packed during cell division and is then visible under a microscope. 9 What is a chromosome? Each chromosome has a constriction point called the centromere, which divides the chromosome into two sections, or “arms.” The short arm ➔“p arm.” The long arm ➔“q arm.” The location of the centromere gives the chromosome its characteristic shape. 10  A karyotype is an individual's complete set of chromosomes. It is used to look for abnormalities in chromosome number or structure. 11  From Chromosomes to Genes Genes are segments of DNA that contain the code for a specific protein that functions in one or more types of cells in the body. Chromosomes are structures within cells that contain a person's genes. Genes are contained in chromosomes, which are in the cell nucleus. 12  What is a genome? A genome is an organism's complete set of genetic instructions, containing all the information needed for its growth and development. It consists of DNA (or RNA in RNA viruses). The genome includes both the genes (the coding regions) and the noncoding DNA, as well as mtDNA and chloroplast DNA. The study of the genome is called genomics. 13  Human Genome Project An international research effort called the Human Genome Project, which worked to determine the sequence of the human genome and identify the genes that it contains, estimated that humans have between 20,000 and 25,000 genes. 14  ▪ An allele is a variant form of a gene. ▪ Different alleles can produce variations in What is an the inherited characteristics of an allele? organism. ▪ For example, different alleles of a gene might result in different hair colors. 15 What is Genotype and Phenotype? ▪ The genotype is the genetic makeup of an organism, including all its genes and alleles. ▪ The genotype is the set of instructions encoded in DNA that contributes to the organism's traits. ▪ The phenotype is the observable physical or biochemical characteristics of an organism, which result from the interaction of its genotype with the environment. Examples include height, eye color, and blood type. 16 What are Dominant and Recessive Traits? Dominant Trait: A trait that is Recessive Trait: A trait that is expressed when at least one expressed only when two dominant allele is present. It recessive alleles are present, "masks" the expression of a meaning no dominant allele recessive trait. is present to mask it. 17 What is Homozygous and Heterozygous? Homozygous: An Heterozygous: An organism is homozygous organism is heterozygous for a trait if it has two for a trait if it has two identical alleles for a different alleles for a gene (e.g., AA or aa). gene (e.g., Aa). 18  What is a Mutation? A mutation is a change in the DNA sequence of a gene. Mutations can be harmless, beneficial, or harmful, and they can result in new traits or diseases. Mutations can lead to various genetic disorders, such as cystic fibrosis, Huntington's disease, and sickle cell anaemia. 19 What is Gene Expression? Gene expression is the process by which the information in a gene is used to synthesize a functional gene product, typically a protein. Gene expression can be regulated at multiple levels, including transcription, RNA processing, and translation. 20  PROKARYOTIC AND EUKARYOTIC GENOME Prokaryotic Cell and Genome Eukaryotic Genome 21 22 EUKARYOTIC GENOME Larger size of eukaryotic genomes is not inherently surprising, since one would expect to find more genes in organisms that are more complex. The genome size of many eukaryotes does not appear to be related to genetic complexity. For example, the genomes of salamanders and lilies contain more than ten times the amount of DNA that is in the human genome, yet these organisms are clearly not ten times more complex than humans. 23 EUKARYOTIC GENOME Most eukaryotic genomes are larger and more complex than those of prokaryotes. This is due to the presence of not only protein-coding sequences but also large amounts of noncoding DNA in eukaryotic cells. 24 EUKARYOTIC GENOME Eukaryotic genome is linear and conforms the Watson-Crick Double Helix structural model. Chromosomes are composed of DNA tightly-wound around histones. These are positively-charged proteins that strongly adhere to negatively-charged DNA and form complexes called nucleosomes. 25  There are two molecules of each of four types of Histones namely H2A, H2B, H3 & H4. This give rise to a complex of 8 proteins named as HISTONES “Histone octomer” The H1 protein is present only in single set. These nucleosomes are attached to each other by means of a thin naked DNA which is known as Linker DNA. 26  CHROMATIN Chromatin is the complex basis of DNA and protein that makes up chromosomes consists of Linear unbroken double stranded DNA. Euchromatin : It is genetically active. It consists of all functional genes which are expressive, stains very lightly. Heterochromatin: It is genetically inactive, the genes are not expressive. Heterochromatin stains darkly because the chromatin region here is highly condensed. 27  CHROMATIN In interphase (nondividing) cells, most of the chromatin (called euchromatin) is relatively decondensed and distributed throughout the nucleus. About 10% of interphase chromatin (called heterochromatin) is in a highly condensed state that resembles the chromatin of cells undergoing mitosis. Heterochromatin is transcriptionally inactive and contains highly repeated DNA sequences, such as those present at 28 centromeres and telomeres.  DNA Content of Human Chromosomes Total amount of Amount of Total amount of Amount of Chromosome Chromosome DNA (Mb) heterochromatin (Mb) DNA (Mb) heterochromatin (Mb) 1 279 30 13 118 16 2 251 3 14 107 16 3 221 3 15 100 17 4 197 3 16 104 15 5 198 3 17 88 3 6 176 3 18 86 3 7 163 3 19 72 3 8 148 3 20 66 3 9 140 22 21 45 11 10 143 3 22 48 13 11 148 3 X 163 3 12 142 3 Y 51 27 29 One megabase (Mb) is equal to 1 million bases. CONFIGURATION of EUKARYOTIC GENOME ❑A genome is an organism’s complete set of DNA, comprising of nuclear and mitochondrialDNA. ❑A human haploid cell, consist of 23 nuclear chromosome and one mitochondrial chromosome, contains more than 3.2 billion DNA base pairs. 30  CONFIGURATION of EUKARYOTIC GENOME 1) 2) A. B. C. A. B. ❑The configuration of eukaryotic genome includes protein coding region, gene regulating region, gene related sequence and intergenic/extra a. b. genic DNA which includes low copy a. number and moderate/high copy a. a. number repetitive sequence. b. b. c. b. c. d. c. d. e. d. 31  1. GENES AND GENE RELATED SEQUENCES A. PROTEIN CODING REGION (EXONS) Most eukaryotic genes also include large amounts of noncoding DNA. Such genes have a split structure in which segments of coding sequence (called exons) are separated by noncoding sequences (intervening sequences, or introns). The entire gene is transcribed to yield a long RNA molecule and the introns are then removed by splicing, so only exons are included in the mRNA. 32  1. GENES AND GENE RELATED SEQUENCES ❑The amount of DNA in the intron sequences is often greater than that in the exons. ❑For example, an average human gene contains about 10 exons (totaling 4.3 kb), interrupted by introns (totaling 52 kb), resulting in ~56 kb of genomic DNA. ❑The exons include regions at both the 5′ and 3′ ends of the mRNA that are not translated into protein (3′ and 5′ untranslated regions or UTRs). ❑These noncoding exons average about 2.6 kb and protein-coding sequences about 1.7 kb per gene. 33  1. GENES AND GENE RELATED SEQUENCES ❑Protein coding sequences account for only about 3% and introns make up approximately 93% of the average human gene. ❑Introns also contain regulatory sequences that control gene expression, which is critical to cell behavior. ❑Since all cells in an organism contain the same genes, regulated differences in gene expression determine the difference between one type of cell and another. 34  1. GENES AND GENE RELATED SEQUENCES B. GENE REGULATING SEQUENCES Promoters are combinations of short sequence elements (usually located in the immediate upstream region of the gene often within 200 bp of the transcription start site) which serve to initiate transcription. They can be subdivided into different components. 35  1. GENES AND GENE RELATED SEQUENCES B. GENE REGULATING SEQUENCES The core promoter directs the basal transcription complex to initiate transcription of the gene. The proximal promoter region is the sequence located immediately upstream of the core promoter, usually from -50 to -200 bp. 36  1. GENES AND GENE RELATED SEQUENCES B. GENE REGULATING SEQUENCES ENHANCERS are positive transcriptional control elements which are particularly prevalent in the cells of complex eukaryotes such as mammals but which are absent or very poorly represented in simple eukaryotes such as yeast. They serve to increase the basal level of transcription which is initiated through the core promoter elements. 37  1. GENES AND GENE RELATED SEQUENCES B. GENE REGULATING SEQUENCES SILENCERS serve to reduce transcription levels. Two classes have been distinguished: o classical silencers (also called silencer elements) are position independent elements that direct an active transcriptional repression mechanism; o negative regulatory elements are position-dependent elements that result in a passive repression mechanism. 38  1. GENES AND GENE RELATED SEQUENCES B. GENE REGULATING SEQUENCES BOUNDARY ELEMENTS (INSULATORS) are regions of DNA, often spanning from 0.5 kb to 3 kb, which function to block the spreading of the influence of agents that have a positive effect on transcription (enhancers) or negative one (silencers, heterochromatinlike repressive effects). (A) A barrier insulator is able to block the spread of heterochromatin and thus renders the downstream gene in an ‘on’ state. (B) An enhancer-blocking insulator complex limits the activity of an enhancer in an orientation-dependent manner. 39 Promoters that are shielded by the insulator are in an ‘off’ state.  1. GENES AND GENE RELATED SEQUENCES B. GENE REGULATING SEQUENCES RESPONSE ELEMENTS modulate transcription in response to specific external stimuli. They are usually located a short distance upstream of the promoter elements (often within 1kb of the transcription start site). A variety of such elements respond to specific hormones or to intracellular second messengers such as cyclic AMP. 40 1) 2) A. B. C. A. B. a. b. a. a. a. b. b. c. b. c. d. c. d. e. d. 41  1. GENES AND GENE RELATED SEQUENCES C. RELATED SEQUENCES a. NON-CODING RNA A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein. 42 43  1. GENES AND GENE RELATED SEQUENCES 1. GENES AND GENE RELATED SEQUENCES C. RELATED SEQUENCES - MicroRNAs (miRNAs) ❑The precursors of miRNAs are longer RNAs that fold into hairpin structures, which are then cleaved sequentially by the nucleases Drosha and Dicer. ❑One strand of a miRNA is incorporated into the RNA induced silencing complex (RISC), and the miRNA targets RISC to complementary mRNAs, where they inhibit translation and stimulate mRNA degradation. 44  - MicroRNAs (miRNAs) ❑ It is estimated that each miRNA can target up to 100 different mRNAs, so up to half of our protein-coding genes may be targets for regulation by miRNAs. ❑ miRNAs have been found to function in a variety of developmental processes, including development of early embryos, the nervous system, muscle, heart, lungs, and the immune system. ❑ miRNAs have also been shown to regulate cell proliferation and survival, and abnormal expression of miRNAs has been found to contribute to heart disease and several kinds of cancer. 45  1. GENES AND GENE RELATED SEQUENCES 1. GENES AND GENE RELATED SEQUENCES C. RELATED SEQUENCES - short interfering RNAs (siRNAs) ❑ RNA interference (RNAi) has more recently emerged as an extremely effective and widely used method for interfering with gene expression at the mRNA level. ❑ RNA interference (RNAi) mediated by short double-stranded RNAs is widely used as an experimental tool to block gene expression at the level of translation. ▪ Double-stranded RNA molecules are cleaved by the enzyme Dicer into siRNAs. ▪ The siRNAs associate with the RISC and are unwound. ▪ The antisense strand of siRNA then targets RISC to a homologous mRNA, which is cleaved by one of the RISC proteins. ▪ The RISC–siRNA complex is released and can participate in further cycles of mRNA degradation 46  1. GENES AND GENE RELATED SEQUENCES C. RELATED SEQUENCES ❑ A major advance in our understanding of the functional elements of the human genome was made in 2012 by a large- scale project called ENCODE (Encyclopedia of DNA Elements). ❑ The goal of the ENCODE project was to define the functions of the different types of sequences in the human genome. ❑ The results of ENCODE suggest that the extent to which noncoding RNAs regulate gene expression is much greater than previously appreciated. 47  C. RELATED SEQUENCES b. INTRONS, UTRS ❑Sequences within introns regulate splicing, which is critical to the formation of functional mRNAs. ❑The presence of introns allows the exons of a gene to be joined in different combinations, resulting in the synthesis of different proteins from the same gene. ❑This process, called alternative splicing occurs frequently in the genes of complex eukaryotes. Animation 6.1 Alternative Splicing - The Cell 8e Student Resources - Oxford Learning Link ❑An untranslated region (or UTR) refers to either of two sections, one on each side of a coding sequence on a strand of mRNA. 5' UTR (or leader sequence) and 3' UTR (or trailer sequence) 48  C. RELATED SEQUENCES c. GENE FRAGMENTS ❑ Pieces of genes containing only the exons (those parts of the gene which actually encode the protein sequence). They are composed of cDNA. d. PSEUDOGENES ❑ Dysfunctional relatives of genes that have lost their gene expression in the cell or their ability to code protein. Pseudogenes often result from the accumulation of multiple mutations within a gene whose product is not required for the survival of the organism. e. LONG NON-CODING RNA (LNC RNA) ❑ A type of non-coding RNAs (ncRNAs) longer than 200 nucleotides. They are abundant in the mammalian transcriptome and play roles in various cellular functions, including regulation of gene transcription by recruiting chromatin-modifying enzymes. 49  1. GENES AND GENE RELATED SEQUENCES C. RELATED1. GENES AND GENE RELATED SEQUENCES SEQUENCES e. Long noncoding RNAs (lncRNAs) ❑They have recently become recognized as major regulators of gene expression in eukaryotic cells. ❑The phenomenon of X chromosome inactivation provides one of the first examples of the role of a lncRNA. 50  e. Long noncoding RNAs (lncRNAs) ❑In many animals; including humans, females have two X chromosomes, and males have one X and one Y chromosome. ❑The X chromosome contains approximately 1000 genes that are not present on the much smaller Y chromosome. ❑Thus females have twice as many copies of most X chromosome genes as males have. ❑Despite this difference, female and male cells contain equal amounts of the proteins encoded by the majority of X chromosome genes. ❑This results from a dosage compensation mechanism in which most of the genes on one of the two X chromosomes in female cells are silenced early in development. ❑Consequently, only one copy of most genes located on the X chromosome is available for transcription in either female or male cells. ❑The key element in X chromosome inactivation is a lncRNA called Xist, which is 17 kb in length. ❑Xist RNA binds to the inactive X, blocking its transcription. 51 1) 2) A. B. C. A. B. I. II. a. a. a. b. b. c. b. c. d. c. d. e. d. 52  2. INTERGENIC /EXTRAGENIC DNA An Intergenic region is a stretch of DNA sequences located between genes. Intergenic regions are a subset of Noncoding DNA. Occasionally some intergenic DNA acts to control genes nearby, but most of it has no currently known function. It is sometimes referred to as junk DNA. Extragenic DNA: Located outside the boundaries of genes, encompassing both intergenic regions and other non-coding elements like satellite DNA or transposable elements. A. UNIQUE/LOW COPY NUMBER Low Copy Number (LCN) is a DNA profiling or DNA testing technique developed by the Forensic Science Service (FSS) which has been in use since 1999. 53  2. INTERGENIC /EXTRAGENIC DNA B. MODERATE/HIGHLY REPETITIVE Genome contain some repetitive DNA sequences, including repetitive coding DNA. However, the majority of highly repetitive DNA sequences occur outside genes. 54 2. INTERGENIC /EXTRAGENIC DNA B. MODERATE/HIGHLY REPETITIVE I) TANDEMLY REPETITIVE REGION: Highly repeated noncoding human DNA often occurs in arrays (or blocks) of tandem repeats of sequence which may be a simple one (1-10 nucleotides), or a moderately complex one (tens to hundreds of nucleotides). (a) Satellite DNA: Satellite DNA is transcriptionally inactive as is the vast majority of minisatellite DNA, but in the case of microsatellite DNA a significant percentage is located in coding DNA. 55 (a) Satellite DNA: 56  2. INTERGENIC /EXTRAGENIC DNA B. MODERATE/HIGHLY REPETITIVE (b) Minisatellites DNA: It comprises of a collection of moderately sized arrays of tandemly repeated DNA sequence which are dispersed over considerable portions of nuclear genome. (c) Microsatellites DNA: Also called simple sequence repeats (SSR), are small arrays of tandem repeats of a simple sequence (usually less than 10 bp). 57  2. INTERGENIC /EXTRAGENIC DNA B. MODERATE/HIGHLY REPETITIVE (d) STRs: Short tandem repeat is a microsatellite, consisting of a unit of two to thirteen nucleotides repeated hundreds of times in a row on the DNA strand. 58 2. INTERGENIC /EXTRAGENIC DNA B. MODERATE/HIGHLY REPETITIVE II) INTERSPERSED REPEAT: are repetitive DNA sequences scattered throughout the genome. They originate from transposable elements (TEs), which can move or replicate within the genome. These sequences play roles in genome evolution, structure, and regulation. 59 60  2. INTERGENIC /EXTRAGENIC DNA B. MODERATE/HIGHLY REPETITIVE (a) LINES: (long interspersed nuclear elements) have been very successful transposons. As autonomous transposons, they can make all the products needed for retro transposition, including the essential reverse transcriptase. 61  2. INTERGENIC /EXTRAGENIC DNA B. MODERATE/HIGHLY REPETITIVE (b) SINES: (short interspersed nuclear elements) are retrotransposons about 100– 400 bp in length. Unlike LINEs, SINEs do not encode any proteins and they cannot transpose independently. Key Difference: LINEs are autonomous retrotransposons—they encode the proteins required for their own mobilization. SINEs are non-autonomous—they depend on LINE-encoded proteins for their transposition. 62  2. INTERGENIC /EXTRAGENIC DNA B. MODERATE/HIGHLY REPETITIVE (c) LTR ELEMENTS: LTR transposons include autonomous and non-autonomous retrovirus-like elements that are flanked by long terminal repeats (LTRs) containing necessary transcriptional regulatory elements. The above structure of retrotransposons showed two genes— “gag” and “pol” that encode protein integrase, RNase H, reverse transcriptase and help in autonomous transposition. 63  Both SINEs and LINEs are examples of transposable elements, which are capable of moving to different sites in genomic DNA. SINEs and LINEs are retrotransposons, meaning that their transposition is mediated by reverse transcription 64  2. INTERGENIC /EXTRAGENIC DNA B. MODERATE/HIGHLY REPETITIVE (d) DNA TRANSPOSONS: Some transposable elements, known as DNA transposons, move by a simple 'cut-and-paste' mechanism removing DNA from one site and inserting it into a new target site. They have terminal inverted repeats and encode a transposase that regulates transposition. They account for close to 3% of the human genome. DR, direct repeat (in the host-cell DNA); ITR, inverted terminal repeat. 65 66 67  What is the defining characteristic of SINES compared to LINES? A. SINES are autonomous transposons, while LINEs are not. B. SINES are retrotransposons that encode Study Question-1 reverse transcriptase. C. SINES depend on LINE-encoded proteins for their transposition. D. SINES are not found in the eukaryotic genome. E. SINES can independently move within the genome. 68  Which of the following sequences is primarily responsible for increasing the basal level of transcription in eukaryotic cells? Study Question-2 A. Promoters B. Enhancers C. Silencers D. Boundary Elements E. Response Elements 69  70 Thank you for your attention.