Genetics Lecture Notes PDF

Genetics Génétique Dr. Ibrahim elkhalil BEHMENE  Training Objectives: Students of nature and life science must distinguish between prokaryotic and eukaryotic organisms in genetics. DNA is an easily maneuverable working tool in different molecular biology techniques,...

Genetics Génétique Dr. Ibrahim elkhalil BEHMENE  Training Objectives: Students of nature and life science must distinguish between prokaryotic and eukaryotic organisms in genetics. DNA is an easily maneuverable working tool in different molecular biology techniques, in, transgenesis and cloning without neglecting bacterial genetics.  Training Objectives: It is important to note that in nature there are certain anomalies due to different mutations in different products that detect and detect a cariological pattern for the organisms’ vegetables or animals. Through practical work the student will realize that it is possible to observe DNA.  Training Objectives: As for Mendel's main laws, they are treated in the form of exercises highlighting the prerequisites in terms of fundamental animal genetics.  Objectifs de la formation : Les étudiants en science de la nature et de la vie doivent en génétique distinguer les organismes procaryotes, des organismes eucaryotes. L’ADN est un outil de travail facilement maniable dans différentes techniques de biologie moléculaire, en, la transgénèse et le clonage sans négliger pour autant la génétique bactérienne.  Objectifs de la formation : Il faut noter également que dans la nature certaines anomalie dues à des mutations à différents échelle peuvent être produites et détecter par une étude caryologie pour les organismes végétaux ou animaux. Par le biais de travaux pratique l’étudiant prendra conscience qu’il est possible d’observer une méduse d’ADN à l’œil nu  Objectifs de la formation : Quant aux principales lois de Mendel elles sont traitées sous forme d’exercices mettant en lumière les prérequis en matière de génétiques fondamentale. Chapter 1: General on the cell (genetic approach) Prokaryotes - Bacteria Eukaryote Mushrooms (haploids) Mammals (diploid) Chapter 2: Structure of DNA Chromatin Chromosome Gene DNA Chapter 3: DNA Replication and Repair Replication DNA Repair Chapter 4: The cell cycle Mitosis Meiosis Chapter 5 : Mutations and their consequences Gene mutations Chromosomal mutations Genomic mutations  Chapter 6: Bacterial genetics Bacterial genotypic variations Concepts of phototrophic and auxotrophic bacteria Transfer of genetic material (bacterial conjugation) - Concepts of crossing over (genetic recombination) Genetic regulation (inducible and repressible regulatory pathways)  Chapter 7: karyotype The technique for obtaining a human karyotype The technique for obtaining a karyotype in plants Chromosome mapping Chapter 8: Sex chromosomes or gonosomes Sex determination in humans The human x chromosome The x chromosome (Lyon hypothesis) The human y chromosome The different sex chromosome systems  Chapter 9: Genetic engineering technique In situ hybridization or molecular hybridization Cloning Transgenesis  Genetics Chapter 1: General on the cell (Genetic approach) Dr. Ibrahim elkhalil BEHMENE 1 Chapter 1 Prokaryotes Chapter 1: General on the cell (genetic approach) Prokaryotes - Bacteria Eukaryote Mushrooms (haploids) Mammals (diploid) 2 Chapter 1 Prokaryotes Prokaryotes are single-celled organisms that lack a nucleus and other membrane-bound organelles. They are divided into two distinct groups: bacteria and archaea. 3 Chapter 1 Prokaryotes Most prokaryotes are small, single-celled organisms that have a relatively simple structure. Prokaryotic cells are surrounded by a plasma membrane, but they have no internal membrane-bound organelles within their cytoplasm. 4 Chapter 1 Prokaryotes The absence of a nucleus and other membrane-bound organelles differentiates prokaryotes from another class of organisms called eukaryotes. 5 Chapter 1 Prokaryotes Prokaryotes lack mitochondria and chloroplasts, and instead, processes such as oxidative phosphorylation and photosynthesis take place across the prokaryotic cell membrane. However, prokaryotes do possess some internal structures, such as prokaryotic cytoskeletons. 6 Chapter 1 Prokaryotes Here are some key features of prokaryotes: 1. Size: Most prokaryotes are between 1 µm and 10 µm, but they can vary in size from 0.2 µm to 750 µm. 2. Nucleus: Prokaryotes lack a distinct nucleus. 3. Organelles: Prokaryotes lack membrane-bound organelles. 7 Chapter 1 Prokaryotes 4. DNA: Most prokaryotes carry a small amount of genetic material in the form of a single molecule, or chromosome, of circular DNA. The DNA in prokaryotes is contained in a central area of the cell called the nucleoid, which is not surrounded by a nuclear membrane. Many prokaryotes also carry small, circular DNA molecules called plasmids, which are distinct from the chromosome. 8 Chapter 1 Prokaryotes 5. Cell wall: The cell wall provides structure and protection from the outside environment. Most bacteria have a rigid cell wall made from carbohydrates and proteins called peptidoglycans. 6. Flagella: Flagella are thin, tail-like structures that assist in movement. 9 Chapter 1 Prokaryotes Prokaryotes are important in many ways, including their roles in nutrient cycling, bioremediation, and disease 10 Chapter 1 Bacteria Bacteria are single-celled organisms that are classified as prokaryotes. They lack a nucleus and other membrane-bound organelles. Bacteria come in many different shapes, including spherical (cocci), rod-shaped (bacilli), and spiral-shaped (spirochetes). 11 Chapter 1 Bacteria 12 Bacterial morphology diagram Chapter 1 Bacteria Some bacteria are harmful, but many serve useful purposes, such as nutrient cycling and bioremediation. Bacteria are also important in the fields of medicine and biotechnology. Here are some key characteristics of bacteria: 1) Lack of membrane-bound organelles 2) Unicellular 3) Small size 4) Cell wall 5) Flagella 13 Chapter 1 Bacteria Bacteria are incredibly diverse, and there are many different types with unique characteristics. Some bacteria are beneficial, such as those that live in the human gut and aid in digestion. Others can cause disease, such as Streptococcus, which is responsible for strep throat. Understanding the characteristics and diversity of bacteria is important for many fields of study, including microbiology, medicine, and environmental science. 14 Chapter 1 Bacteria Quiz 1. How do bacteria reproduce? A. Sexual reproduction B. Horizontal gene transfer C. Binary fission D. Mitosis 2. Which is not one of the three main shapes of bacteria? A. Coccus B. Bacillus C. Spiral D. Star 3. When did bacteria first begin to exist on Earth? A. 4 billion years ago B. 2 billion years ago C. 1.6 billion years ago 15 D. 1 billion years ago Chapter 1 Bacteria Quiz 1. How do bacteria reproduce? C is correct. Bacteria reproduce asexually through binary fission. They can also exchange genes with other bacteria through horizontal gene transfer, but this is not reproduction since it does not involve creating offspring. Mitosis is similar to binary fission, but mitosis only occurs in eukaryotic cells. 2. Which is not one of the three main shapes of bacteria? D is correct. Star-shaped bacteria, such as those in the genus Stella, are not as common as cocci, bacilli, and spiral bacteria. 3. When did bacteria first begin to exist on Earth? A is correct. Bacteria first arose around 4 billion years ago. They are the oldest forms of life on the planet. Eukaryotes started to appear much later, around 1.6-2 billion years ago. 16 Chapter 1 Eukaryotes Eukaryotes are organisms whose cells have a nucleus and other membrane-bound organelles. All animals, plants, fungi, and many unicellular organisms are eukaryotes. Eukaryotic cell 17 Chapter 1 Eukaryotes 18 Chapter 1 Eukaryotes 19 Chapter 1 Eukaryotes Eukaryotes are a diverse group of organisms that range in size from microscopic single cells, such as picozoans under 3 micrometres across, to animals like the blue whale, weighing up to 190 tonnes and measuring up to 33.6 metres (110 ft) long, or plants like the coast redwood, up to 120 metres (390 ft) tall. 20 Chapter 1 Eukaryotes Here are some key characteristics of eukaryotes: 1) Nucleus: Eukaryotes have a distinct nucleus that contains their genetic material. 2) Membrane-bound organelles: Eukaryotes have membrane-bound organelles, such as mitochondria, chloroplasts, and the endoplasmic reticulum. 3) Cellular structure: Eukaryotic cells are larger and more complex than prokaryotic cells. 21 Chapter 1 Eukaryotes 4) Linear DNA: Eukaryotic DNA is linear and bound up with special proteins called histones to make chromosomes. 5) Flagella: Eukaryotes may have flagella, which are long, threadlike structures that propel the organism through liquid. The eukaryotic flagellum is completely different in structure from that of a bacterium. 22 Chapter 1 Eukaryotes Eukaryotes are incredibly diverse and play important roles in many ecosystems. They are the basis for both unicellular and multicellular organisms and are important in fields such as medicine, biotechnology, and environmental science. Understanding the characteristics and diversity of eukaryotes is important for many fields of study, including biology, genetics, and ecology. 23 Chapter 1 Mushrooms Mushrooms have a haploid life cycle, meaning that all structures are haploid except the zygote. In the life cycle of a sexually reproducing mushroom, a haploid phase alternates with a diploid phase. 24 Chapter 1 Mushrooms The haploid phase ends with nuclear fusion, and the diploid phase begins with the formation of the zygote (the diploid cell resulting from fusion of two haploid sex cells. Meiosis (cell division that reduces the chromosome number to one set per cell) restores the haploid number of chromosomes and initiates the haploid phase, which produces the spores. 25 Chapter 1 Mushrooms In the majority of fungi, all structures are haploid except the zygote. Nuclear fusion takes place at the time of zygote formation, and meiosis follows immediately. The haploid nuclei that result from meiosis are generally incorporated in spores called meiospores. 26 Chapter 1 Mushrooms Life Cycle of Fungi 27 Chapter 1 Mammals (diploid) Mammals have a diploid life cycle, meaning that the organism is diploid and the only haploid cells are the gametes. In mammals, specialized diploid cells called germ cells are produced within the gonads, which are the testes in males and ovaries in females. 28 Chapter 1 Mammals (diploid) These germ cells undergo meiosis to produce haploid gametes, which are the sperm in males and the eggs in females. Fertilization of a haploid female egg by a haploid male sperm results in a diploid zygote, which develops into a multicellular diploid organism. 29 Chapter 1 Mammals (diploid) Although mammals have haploid stages in the form of eggs and sperm, their life cycles are not considered alternation of generations because their development is different from that of plants and algae. 30 Quiz 31 Chapter 2: Structure of DNA Chromatin Chromosome Gene DNA Chapter 2: Chromatin  Chromatin is a complex of DNA and proteins found in eukaryotic cells, including the cells of humans and other higher organisms.  The primary function of chromatin is to package long DNA molecules into more compact and denser structures, allowing them to fit inside the cell nucleus. Chapter 2: Chromatin This packaging prevents the DNA strands from becoming tangled and helps regulate gene expression and DNA replication. Chapter 2: Chromatin The basic structural unit of chromatin is the nucleosome, which was described by Roger Kornberg in 1974. A nucleosome consists of DNA wrapped around a core of eight histone proteins, with an additional histone (H1) sealing the structure. Fig. 1 The organization of chromatin in nucleosomes Chapter 2: Chromatin  This packaging of DNA with histones forms a chromatin fiber approximately 10 nm in diameter, composed of chromatosomes separated by linker DNA segments.  The 10-nm fiber has a beaded appearance, which is the basis of the nucleosome model.  The chromatin fiber can further condense by coiling into 30-nm fibers. Chapter 2: Chromatin Chapter 2: Chromosome  Chromosomes are thread-like structures found in the nucleus of animal and plant cells.  They are composed of protein and a single molecule of deoxyribonucleic acid (DNA).  The term "chromosome" comes from the Greek words for color (chroma) and body (soma), as they are strongly stained by some colorful dyes used in research. Chapter 2: Chromosome The main functions of chromosomes are to carry the genomic information from cell to cell and to ensure the proper distribution of genetic material during cell division. Chapter 2: Chromosome Chapter 2: Chromosome Key points about chromosomes include: 1. Humans have 23 pairs of chromosomes, for a total of 46, in most cells of their body. Chapter 2: Chromosome  These include 22 pairs of autosomes (numbered chromosomes) and one pair of sex chromosomes (XX for females and XY for males).  Each pair of chromosomes contains two chromosomes, one inherited from each parent. Chapter 2: Chromosome 2. The only human cells that do not contain pairs of chromosomes are reproductive cells, or gametes, which carry just one copy of each chromosome. When two gametes unite during fertilization, they form a single cell with two copies of each chromosome, which then divides and produces a mature individual with a full set of paired chromosomes in virtually all of its cells. Chapter 2: Chromosome Chapter 2: Chromosome 3. The constricted region of a linear chromosome is known as the centromere, which divides the chromosome into two sections called "arms". Chapter 2: Chromosome The short arm is labelled the "p arm," and the long arm is labelled the "q arm". The location of the centromere on each chromosome gives the chromosome its characteristic shape and can be used to help describe the location of specific genes. DNA and histone proteins are packaged into structures called chromosomes. Chapter 2: Chromosome Diagram of a replicated and condensed metaphase eukaryotic chromosome: 1. Chromatid / 2. Centromere /3. Short arm /4. Long arm  Quiz The thread-like fine structures found in the nucleus carrying genetic instructions that are passed from one to another generation during the process of reproduction are chromosomes. These chromosomes have a critical role to play in the process of cell division, variation, heredity, repair, mutation and also regeneration. 1. The least level of chromosome organization is (a) 30nm fibre (b) solenoid (c) nucleosome (d) none of the above Chapter 2: Gene A gene is a fundamental unit of heredity and the basic physical and functional unit of genetic information. Chapter 2: Gene It is a sequence of nucleotides in DNA that carries the instructions for making a specific product, which can be a protein or a functional RNA molecule. Chapter 2: Gene A gene is a region of DNA that encodes function. A chromosome consists of a long strand of DNA containing many genes. A human chromosome can be up to 250 mega base pairs of DNA and contain thousands of genes. Chapter 2: Gene Here are some key points about genes: 1. Genes are made up of DNA, except in some viruses where they are composed of a closely related compound called RNA Chapter 2: Gene 2. A DNA molecule consists of two chains of nucleotides that form a twisted ladder, with the rungs formed by bonded pairs of nitrogenous bases (adenine, guanine, cytosine, and thymine). Chapter 2: Gene 3. The primary function of genes is to specify the production of proteins or RNA molecules that play various roles in the body. Protein-coding genes are responsible for producing proteins, while noncoding genes produce functional RNA molecules such as tRNA and rRNA. Chapter 2: Gene 4. Humans have approximately 20,000 protein-coding genes, which make up only about 1.5% of the entire human genome. The remaining portion of the genome includes noncoding DNA, which has regulatory functions and is involved in gene expression and other cellular processes. Chapter 2: Gene 5. Each person has two copies of each gene, one inherited from each parent. Most genes are the same in all people, but a small number of genes (less than 1% of the total) have slight differences between individuals, known as alleles. Chapter 2: Gene 6. Genes are located on chromosomes, which are thread-like structures in the nucleus of cells. Humans have 23 pairs of chromosomes, including 22 pairs of autosomes and one pair of sex chromosomes (XX for females and XY for males). The specific location of a gene on a chromosome is called its locus.  Quiz If Bb is a gene pair of an individual then the alleles for this gene pair are ………. (a) A and B (b) a and A (c) a and b (d) b and B Chapter 2: DNA DNA, or deoxyribonucleic acid, is a molecule that carries the genetic information responsible for the development and functioning of living organisms. Chapter 2: DNA DNA Types There are three different DNA types: A)A-DNA is a short, wide, right-handed helix. B) B-DNA, the structure proposed by Watson and Crick, is the most common conformation in most living cells. C) Z-DNA, unlike A- and B-DNA, is a left-handed helix. Chapter 2: DNA Gene Here are some key points about DNA structure: 1. DNA is a double-stranded helix, with the two strands connected by hydrogen bonds. Chapter 2: DNA 2. The structure is often compared to a twisted ladder, with the sugar-phosphate backbones forming the sides and the nitrogenous bases forming the rungs Chapter 2: DNA Gene 3. The two strands of DNA run in opposite directions, a property known as antiparallel. One strand runs from 5' to 3' (top to bottom), while the other runs from 3' to 5‘. Chapter 2: DNA 4. The nitrogenous bases in DNA include adenine (A), cytosine (C), guanine (G), and thymine (T). A always pairs with T, and C always pairs with G, forming the base pairs that hold the two strands of DNA together Chapter 2: DNA Gene 5. The order of the nitrogenous bases along the DNA molecule's backbone determines the genetic code or the instructions for making proteins or RNA molecules Chapter 2: DNA Gene 6. DNA is composed of nucleotides, which are made up of three components: a sugar (deoxyribose), a phosphate group, and a nitrogenous base. The sugar-phosphate backbones of the two DNA strands are on the outside of the double helix, while the nitrogenous bases are on the inside, forming the base pairs Chapter 2: DNA (A) A nucleotide (guanosine triphosphate). The nitrogenous base (guanine in this example) is linked to the 1′ carbon of the deoxyribose and the phosphate groups are linked to the 5′ carbon. Chapter 2: DNA A nucleoside is a base linked to a sugar. A nucleotide is a nucleoside with one or more phosphate groups. Chapter 2: DNA B) A DNA strand containing four nucleotides with the nitrogenous bases thymine (T), cytosine (C), adenine (A) and guanine (G) respectively.  Quiz I. DNA strands run _____ in relation to each other. a. antiparallel b. parallel c. perpendicular d. both a and b II. Between the two strands of a DNA segment the nitrogen bases are held together by _____. a. covalent bonds b. b. hydrogen bonds c. c. ionic bonds d. d. metallic bonds Chapter 2: DNA  Genetics Génétique Dr. Ibrahim elkhalil BEHMENE Chapter 3 Chapter 3: DNA Replication and Repair  DNA Replication  DNA Repair Chapter 3 DNA Replication DNA replication is the process by which a cell's DNA is copied during cell division. Chapter 3 DNA Replication It is a crucial part of biological inheritance, occurring in all living organisms. Chapter 3 DNA Replication The main steps of DNA replication are as follows: 1. Unzipping: The double helix structure of the DNA molecule is "unzipped" by an enzyme called helicase, which breaks the hydrogen bonds between the base pairs. Chapter 3 DNA Replication 2.Priming: A short piece of RNA called a primer, produced by an enzyme called primase, binds to the end of the leading strand. The primer acts as the starting point for DNA synthesis. Chapter 3 DNA Replication 3. Synthesis: DNA polymerase binds to the leading strand and "walks" along it, adding new complementary nucleotide bases (A, C, G, and T) to the strand of DNA in the 5' to 3' direction. This type of replication is called continuous. Chapter 3 DNA Replication 4. Lagging strand: The lagging strand is synthesized in short fragments called Okazaki fragments. DNA polymerase adds these fragments in the 5' to 3' direction away from the replication fork, and they are later joined together by DNA ligase. Chapter 3 DNA Replication Chapter 3 DNA Replication 5. Semi-conservative replication: The result of DNA replication is two DNA molecules consisting of one new and one old chain of nucleotides. This is why DNA replication is described as semi- conservative, with half of the chain being part of the original DNA molecule and half being brand new. Chapter 3 DNA Replication 6. Winding up: Following replication, the new DNA automatically winds up into a double helix. Chapter 3 DNA Replication  DNA Replication https://youtube.com/watch?v=TNKWgcFPHqw Chapter 3 Chapter 3: DNA Replication and Repair  DNA Replication  DNA Repair Chapter 3 DNA Repair DNA Repair Cells use DNA repair mechanisms to correct mistakes in the base sequence of DNA molecules. Mistakes can occur spontaneously during normal cellular activities, or be induced. Chapter 3 DNA Repair Mutations in your DNA can be repaired in four major ways: 1. Mismatch repair: Incorrect bases are found, removed, and replaced with the correct, complementary base. Most of the time, DNA polymerase, the enzyme that helps make new DNA, immediately detects mismatched bases put in by mistake during replication. Chapter 3 DNA Repair Chapter 3 DNA Repair The mismatch repair enzymes can detect any differences between the template and the newly synthesized strand, so they clip out the wrong base and, using the template strand as a guide, insert the correct base. Chapter 3 DNA Repair 2. Direct repair: Bases that are modified in some way are converted back to their original states. Instead of using a cut-and-paste mechanism, the enzymes clip off the atoms that don’t belong, converting the base back to its original form. Chapter 3 DNA Repair 3. Base-excision repair: Base-excisions occur when an unwanted base is found. Specialized enzymes recognize the damage, and the base is snipped out and replaced with the correct one. Chapter 3 DNA Repair 4. Nucleotide-excision repair: Nucleotide-excision means that the entire nucleotide gets removed all at once. Chapter 3 DNA Repair When intercalating agents or dimers distort the double helix, nucleotide- excision repair mechanisms step in to snip part of the strand, remove the damage, and synthesize fresh DNA to replace the damaged section.  Genetics Génétique Dr. Ibrahim elkhalil BEHMENE Chapter 4 Chapter 4: the cell cycle Mitosis Meiosis Chapter 4 Mitosis The cell cycle, also known as the cell-division cycle, is a series of events that take place in a cell, leading to its division into two daughter cells In eukaryotic cells the cell cycle is divided into two main stages: interphase and the mitotic (M) phase, which includes mitosis and cytokinesis Chapter 4 Mitosis Interphase can be further divided into three phases: G1 phase : The cell prepares to divide by growing and synthesizing the proteins necessary for DNA replication Chapter 4 Mitosis S phase (Synthesis): The cell copies all of its DNA, ensuring that each daughter cell will receive a complete set of genetic material Chapter 4 Mitosis G2 phase : The cell continues to grow and prepares for cell division by organizing and condensing its genetic material Chapter 4 Mitosis After interphase, the cell enters the mitotic phase, which consists of mitosis and cytokinesis: - Mitosis: The replicated chromosomes, organelles, and cytoplasm separate into two new daughter cells. - Cytokinesis: The division of the cytoplasm and the formation of two distinct daughter cells. Chapter 4 Chapter 4 Mitosis The four stages of mitosis are prophase, metaphase, anaphase, and telophase Chapter 4 Mitosis Prophase: Chromatin condenses into chromosomes, the nuclear envelope breaks down, and chromosomes attach to spindle fibers by their centromeres Chapter 4 Mitosis Metaphase: Chromosomes line up along the metaphase plate (center of the cell). Chapter 4 Mitosis Anaphase: Sister chromatids are pulled to opposite poles of the cell Chapter 4 Mitosis Telophase: Nuclear envelope reforms, chromosomes unfold into chromatin, and cytokinesis can begin Chapter 4 Chapter 4: the cell cycle Meiosis Chapter 4 What are the stages of meiosis? Meiosis can be divided into two rounds of division, meiosis I and meiosis II, each of which consists of several stages Chapter 4 The stages of meiosis I are: 1. Interphase: The DNA in the cell is copied resulting in two identical full sets of chromosomes. Outside of the nucleus are two centrosomes, each containing a pair of centrioles, which are critical for the process of cell division. Chapter 4 1. Prophase I: Chromosomes condense, nuclear membrane dissolves, homologous chromosomes form bivalents, and crossing over occurs. Chapter 4 1. Metaphase I: The chromosome pairs line up next to each other along the center (equator) of the cell. Chapter 4 1. Anaphase I: Spindle fibers contract and split the bivalent, homologous chromosomes move to opposite poles of the cell. Chapter 4 1. Telophase I and cytokinesis: Chromosomes reach the poles of the cell, and the cell divides into two daughter cells. Chapter 4 The stages of meiosis II are: 1. Prophase II: Chromosomes condense, and the nuclear membrane dissolves.  Metaphase II: Chromosomes line up along the center (equator) of the cell.  Anaphase II: Sister chromatids separate and move to opposite poles of the cell. 1. Telophase II and cytokinesis: Chromosomes reach the poles of the cell, and the cell divides into two daughter cells. Chapter 4 Chapter 4: the cell cycle Mitosis Meiosis  1 Genetics Génétique Dr. Ibrahim elkhalil BEHMENE 21/12/2023 Chapter 5 2 Chapter 5: Mutations and their consequences Gene mutations Chromosomal mutations 21/12/2023 Chapter 5 Gene mutations 3 Gene mutations : are changes in the DNA sequence of a gene that can occur during cell division when cells make copies of themselves. Types of Mutations : Mutations fall into two major categories 21/12/2023 Chapter 5 Gene mutations 4 I. Somatic mutations: Mutations that occur in the somatic cells aren't heritable that is, the changes can’t be passed from parent to offspring , but they do affect the person with the mutation. 21/12/2023 Chapter 5 Gene mutations 5 II.Germ-cell mutations: Mutations in the sex cells (germ cells like eggs and sperm) that lead to embryo formation. Instead, they affect the offspring of the person with the mutation and are heritable from then on. 21/12/2023 Chapter 5 What are the different types of genetic mutations? 6 Here are some of the most common types of genetic mutations: I. Small-scale mutations: II. Large-scale mutations: 21/12/2023 Chapter 5 I. Small-scale mutations: 7 a. Point mutation: A change in one base in the DNA sequence 21/12/2023 Chapter 5 I. Small-scale mutations: 8 b. Substitution: When one or more bases in the sequence is replaced by the same number of bases 21/12/2023 Chapter 5 I. Small-scale mutations: 9 C. Inversion: When a segment of a chromosome is reversed end to end. 21/12/2023 Chapter 5 I. Small-scale mutations: D. Insertion: When a base is added to the sequence 10 21/12/2023 Chapter 5 I. Small-scale mutations: 11 E. Deletion: When a base is deleted from the sequence 21/12/2023 Chapter 5 II. Large-scale mutations: 12 1. Copy number variation (CNV): A type of mutation where large chunks of DNA are inserted, repeated, or lost. 21/12/2023 Chapter 5 II. Large-scale mutations: 13 2.Duplication of genes: When there is an increase in the number of copies of a gene 21/12/2023 Chapter 5 II. Large-scale mutations: 14 3. Loss of one copy of a gene in an organism that previously had two copies 4. Loss of both copies of the same gene 21/12/2023 Chapter 5 II. Large-scale mutations: 15 5. Movement of sections of DNA from one location to another 21/12/2023 16 21/12/2023 Chapter 5 17 Chromosomal mutations 21/12/2023 Chapter 5 Chromosomal mutations 18 Chromosomal mutations are changes in the structure or number of chromosomes that can occur during cell division There are two broad categories of chromosomal mutations: a) Chromosomal Mutations I b) Chromosomal Mutations II 21/12/2023 Chapter 5 a) Chromosomal Mutations I 19 Chromosomal Mutations I: involve structural mutations that arise as a result of alterations in the structure of the chromosomes 21/12/2023 Chapter 5 a) Chromosomal Mutations I 20 1. Inversion occurs when a segment of a chromosome is reversed end to end 21/12/2023 Chapter 5 a) Chromosomal Mutations I 21 2. Deletion involves the loss of all or part of a chromosome 21/12/2023 Chapter 5 a) Chromosomal Mutations I 22 3.Duplication occurs when the mutant genes are displayed twice on the same chromosome due to duplication of these genes 21/12/2023 Chapter 5 a) Chromosomal Mutations I 23 4.Translocation occurs when a segment of one chromosome breaks off and attaches to another chromosome 21/12/2023 24 21/12/2023 Chapter 5 b) Chromosomal Mutations II 25 Chromosomal Mutations II : include mutations that are caused by the alterations in the number of chromosomes in a cell, including aneuploidy and polyploidy 1.Aneuploidy: is the loss or gain of one or more chromosomes 2. polyploidy : is the gain of one or more complete sets of chromosomes 21/12/2023 Chapter 5 b) Chromosomal Mutations II Examples of Aneuploidy 26 Down syndrome. It is caused by the ​trisomy is the nondisjunction of chromosome 21. It usually causes mental retardation that can be mild or even severe. 21/12/2023 Chapter 5 b) Chromosomal Mutations II Examples of Polyploidy 27 The “Doob” plant in South Asia undergoes this type of mutation being triploid and sterile. It can, however, be cultivated vegetatively. Fig : Cynodon dactylon 21/12/2023 Chapter 5 Harmful Effects 28 a. Some of the most harmful mutations are those that dramatically change protein structure or gene activity. b. The defective proteins produced by these mutations can disrupt normal biological activities, and result in genetic disorders. c. Some cancers, for example, are the product of mutations that cause the uncontrolled growth of cells. 21/12/2023 Chapter 5 Beneficial Effects 29 Some of the variation produced by mutations can be highly advantageous to an organism or species. For example: mutations have helped many insects resist chemical pesticides. Some mutations have enabled microorganisms to adapt to new chemicals in the environment. 21/12/2023  Genetics Génétique Dr. Ibrahim elkhalil BEHMENE Chapter 6 Chapter 6: Bacterial genetics I. Bacterial genotypic variations Chapter 6 I. Bacterial genotypic variations Bacterial genotypic variations : refer to changes in the genetic makeup of bacteria, which can lead to differences in their characteristics and traits. Here are some key points about bacterial genotypic variations Chapter 6 I. Bacterial genotypic variations 1. Genotypic Variation: Any change in the genotype of a bacterium or its phenotype is known as variation Genotypic variation can occur as a result of changes in the genes by way of mutation, loss, or acquisition of new genetic elements These variations are heritable, meaning they can be passed on to future generations of bacteria Chapter 6 I. Bacterial genotypic variations 2. Mechanisms of Genetic Variation There are three major natural strategies in the spontaneous generation of genetic variations in bacteria:  Small local changes in the nucleotide sequence of the genome  Intragenomic reshuffling of segments of genomic sequences  The acquisition of DNA sequences from another organism Chapter 6 I. Bacterial genotypic variations 3. Heritable Variations a) Conjugation: transfer of genetic material (usually plasmid) from one bacterium to another through the mediation of sex pili is known as conjugation. Chapter 6 I. Bacterial genotypic variations 3. Heritable Variations b) Mutation: A gene can mutate spontaneously , Some mutants can adapt more readily to the environment, leading to the emergence of new bacterial variants Chapter 6 I. Bacterial genotypic variations 3. Heritable Variations c) Transformation: Some bacteria have the ability to uptake naked DNA fragments from the surrounding environment, conferring new properties to the bacterium Chapter 6 I. Bacterial genotypic variations 3. Heritable Variations d)Transduction: Transfer of genetic material through the mediation of bacteriophage is known as transduction Chapter 6 Bacterial genotypic variations 3. Heritable Variations e) Transposition: Variations in bacterial antigens can occur due to transposons Chapter 6 Bacterial genotypic variations 4. Impact of Genetic Variation Genetic variation makes it possible for individual members of huge populations of bacteria to quickly evolve new traits Mutation and gene transfer work together to accelerate the rate of bacterial evolution  Chapter 6: bacterial genetics II. CONCEPT OF PROTOTROPHIC AND AUXOTROPHIC BACTERIA  PROTOTROPHIC AND AUXOTROPHIC Prototrophic and auxotrophic bacteria are two groups of microorganisms that differ based on their ability to produce organic compounds for their grow  PROTOTROPHIC AND AUXOTROPHIC Prototrophs are wild-type microorganisms that are capable of producing all required organic compounds  PROTOTROPHIC AND AUXOTROPHIC Auxotrophs are mutant microorganisms that have lost the ability to produce a particular organic compound required for their growth Chapter 6 Chapter 6: Bacterial genetics III. Transfer of genetic material (Bacterial conjugation) Chapter 6 Bacterial conjugation Bacterial conjugation : is the process by which one bacterium transfers genetic material to another through direct contact. Here are the key points about bacterial conjugation: 1. Process of Conjugation Chapter 6 Bacterial conjugation During conjugation, one bacterium serves as the donor, transferring genetic material to another bacterium through a structure called a pilus Process of Conjugation Chapter 6 Bacterial conjugation The donor bacterium pulls itself close to the recipient using the pilus, and DNA is transferred between the cells Process of Conjugation Chapter 6 Bacterial conjugation The genetic material transferred during conjugation can be in the form of a plasmid, which can be copied in the receiving cell and passed on to its descendants Process of Conjugation  Bacterial conjugation 2. Importance of Bacterial Conjugation Conjugation is an essential mechanism for the transfer of genetic material from one bacterium to another, allowing for the spread of genetic traits and adaptation to changing environments Chapter 6 Chapter 6: Bacterial genetics IV.Concepts of crossing over (genetic recombination) Chapter 6 crossing over Crossing over, also known as genetic recombination, is a fundamental genetic process that occurs during meiosis. Here are the key concepts related to crossing over Chapter 6 crossing over 1. Definition and Process Crossing over allows alleles on DNA molecules to change positions from one homologous chromosome segment to another, leading to the exchange of genetic material between paired homologous chromosomes Chapter 6 crossing over During prophase I of meiosis, homologous chromosomes align and exchange DNA sequences, resulting in the formation of chiasmata and the exchange of genetic material Chapter 6 crossing over 2. Genetic Diversity and Evolution Crossing over is a process that increases genetic diversity by creating new combinations of alleles in the gametes, ensuring genomic variation in offspring Chapter 6 crossing over This genetic variation contributes to the ability of species to respond to changing environments and evolve over time, strengthening their survival and adaptability Chapter 6 3. Significance and Impact The exchange of genetic material during crossing over results in recombinant chromosomes, leading to the production of genetically unique daughter cells after meiosis Chapter 6 Chapter 6: Bacterial genetics V.Genetic regulation (inducible and repressible regulatory pathways) Chapter 6 Genetic regulation Genetic regulation refers to the process by which cells control the expression of their genes. Inducible and repressible regulatory pathways are two types of gene regulation that occur in bacteria. Here are the key concepts related to these regulatory pathways : Chapter 6 Genetic regulation 1) Inducible Regulatory Pathways Inducible genes are normally turned off but can be turned on when needed. Inducible operons are controlled by inducers, which are small molecules that bind to regulatory proteins and activate transcription Chapter 6 Genetic regulation The lac operon is an example of an inducible operon that is activated in the presence of lactose Chapter 6 Genetic regulation 2. Repressible Regulatory Pathways Repressible genes are normally turned on but can be turned off when needed Repressible operons are controlled by repressors, which are regulatory proteins that bind to DNA and prevent transcription Chapter 6 Genetic regulation The trp operon is an example of a repressible operon that is turned off in the presence of tryptophan 3. Regulatory Proteins Repressors and activators are regulatory proteins that bind to DNA and control transcription Inhibitors and inducers are small molecules that bind to repressors or activators and regulate their activity The lac repressor is an example of a regulatory protein that binds to the operator region of the lac operon and prevents transcription in the absence of lactose 4. Importance and Impact Inducible and repressible regulatory pathways are essential for bacterial cells to respond to changes in their environment and optimize their metabolic activity These regulatory pathways contribute to the versatility and adaptability of bacterial cells, allowing them to express genes when needed and conserve energy when not needed  Genetics Génétique Dr. Ibrahim elkhalil BEHMENE Chapter 7 Chapter 7: karyotype The Technique for Obtaining a Human Karyotype Chapter 7 The Technique for Obtaining a Human Karyotype A human karyotype is obtained through a process called karyotyping, which involves examining the chromosomes in a sample of cells to identify genetic problems. Chapter 7 The Technique for Obtaining a Human Karyotype Procedure 1. Sample Collection: Mitotic cells are collected from various tissue types such as peripheral blood, skin biopsy, tumor biopsies, or bone marrow samples Chapter 7 The Technique for Obtaining a Human Karyotype 2. Cell Growth and Staining: The collected cells are allowed to grow in the laboratory and then stained using standardized staining procedures to reveal the characteristic structural features of each chromosome Chapter 7 The Technique for Obtaining a Human Karyotype 3. Examination and Photography: A laboratory specialist examines the stained sample under a microscope to analyze the size, shape, and number of chromosomes. The stained sample is then photographed to create a karyotype, which shows the arrangement of the chromosomes Chapter 7 The Technique for Obtaining a Human Karyotype Karyotyping is used : 1. Genetic Testing : Karyotyping is used to identify genetic disorders, birth defects, and even cancers by detecting gross genetic changes, changes in chromosome number, and more subtle structural changes such as deletions, duplications, translocations, or inversions. 2. Prenatal Testing : It can be used to check unborn babies for chromosome problems, such as Down syndrome, and to identify genetic disorders in unborn babies. The technique for obtaining a karyotype in plants  The technique for obtaining a karyotype in plants Karyotyping in plants involves several steps, including: 1. Root tip collection: actively growing root tips are collected from the plant. Meristematic cells in the root tips are dividing rapidly, making them ideal for karyotyping.  The technique for obtaining a karyotype in plants 2. Pre-treatment: root tips are treated with a colchicine solution to arrest mitosis at metaphase, where chromosomes are highly condensed and visible.  The technique for obtaining a karyotype in plants 3.Fixation: root tips are fixed in a solution like ethanol or methanol to preserve the cell morphology and prevent chromosome damage.  The technique for obtaining a karyotype in plants 4. Maceration: root tips are macerated in an enzyme solution to break down the cell walls and release the individual cells. 5. Slide preparation: the released cells are dropped onto a microscope slide and allowed to dry.  The technique for obtaining a karyotype in plants 6. Staining: the dried cells are stained with a dye, such as Giemsa or DAPI, to visualize the chromosomes. 7. Karyotyping: the stained chromosomes are arranged and photographed under a microscope to create a karyotype.  The technique for obtaining a karyotype in plants This information can be used for various purposes, such as: 1. Species identification and classification: different plant species have distinct karyotypes, making them useful for identification and classification.  The technique for obtaining a karyotype in plants 2. Ploidy level determination: karyotyping can determine if a plant is diploid, tetraploid, or has other ploidy levels.  The technique for obtaining a karyotype in plants 3. Genetic diversity assessment: karyotypes can be compared between individuals or populations to assess genetic diversity and identify potential hybridization events.  The technique for obtaining a karyotype in plants 4. Linkage group analysis: karyotypes can be used to study the arrangement of genes on chromosomes, known as linkage groups. Chromosome Mapping  Chromosome Mapping Chromosome mapping is a technique used to identify the location of genes on chromosomes. There are two main types of chromosome mapping: 1. Genetic linkage mapping: This type of mapping relies on the fact that genes that are located close together on a chromosome are more likely to be inherited together. By studying the patterns of inheritance of different genes, scientists can infer the relative positions of these genes on the chromosome. 2. Physical mapping: This type of mapping relies on techniques that can directly visualize the DNA on a chromosome. These techniques can be used to create a detailed "map" of the chromosome, showing the precise location of each gene.  Applications of chromosome mapping 1. Diagnosis of genetic disorders: Chromosome mapping can be used to diagnose genetic disorders by identifying the location of the gene responsible for the disorder. 2. Development of new therapies: Chromosome mapping can be used to identify the genes responsible for genetic disorders. This information can then be used to develop new therapies for these disorders. 3. Study of evolution: Chromosome mapping can be used to study the evolution of genes and chromosomes. This information can be used to understand how different species have evolved.  Quiz Which characteristic is not a piece of information obtained from a karyotype? A.Sex of the individual B. Number of autosomes C. Number of sex chromosomes D. Number of Giiemsa bands E. Placement of centromere Correct Answer D. Number of Giiemsa bands Explanation The sex of the individual, number of autosomes (non-sex chromosomes), number of sex chromosomes, and placement of the centromere can all be determined from a karyotype. However, the number of Giiemsa bands is not a piece of information obtained from a karyotype. Giiemsa bands refer to specific regions of chromosomes that can be stained and visualized under a microscope. The number of Giiemsa bands is not a standard or commonly used parameter for analyzing karyotypes.  Quiz What makes this person's karyotype abnormal? A. An extra autosome B. A missing sex chromosome C. An extra sex chromosome D. None of the above Correct Answer A. An extra autosome Explanation This person's karyotype is abnormal because they have an extra autosome. Karyotype refers to the number and appearance of chromosomes in an individual's cells. In a normal karyotype, there should be a specific number of autosomes (non- sex chromosomes) and sex chromosomes. However, in this case, there is an additional autosome present, which deviates from the typical karyotype and makes it abnormal.  Quiz The cooperative effort between Zooweb and the University of Wisconsin State Laboratory of Hygiene published each karyotype in three forms or formats. How many chromosomes does a patient have with Trisomy-18? A. 23 B.46 C.47 D.52 Correct Answer C. 47 Explanation Trisomy-18 is a genetic disorder where an individual has an extra copy of chromosome 18. Normally, humans have 46 chromosomes, but in the case of Trisomy-18, there is an additional copy of chromosome 18, resulting in a total of 47 chromosomes. Therefore, the correct answer is 47.  Genetics Génétique Dr. Ibrahim elkhalil BEHMENE Chapter 8 Chapter 8: Sex chromosomes or gonosomes  Sex determination in humans  The human x chromosome  The x chromosome (Lyon hypothesis)  The human y chromosome  The different sex chromosome systems Chapter 8 Sex determination in humans Sex determination in humans is the process that determines the biological sex of an offspring and, as a result, the sexual characteristics that they will develop Chapter 8 Sex determination in humans Chromosomal sex is determined at the time of fertilization, where a chromosome from the sperm cell, either X or Y, fuses with the X chromosome in the egg cell Chapter 8 Sex determination in humans Females typically have two X chromosomes, while males typically have a Y chromosome and an X chromosome Chapter 8 Sex determination in humans Chapter 8 Chapter 8 X chromosome The X chromosome is one of the two sex chromosomes in humans and many other mammals. Chapter 8 X chromosome The X chromosome contains about 900 genes, making it about three times larger than the Y chromosome, which has about 55 genes Chapter 8 X chromosome Here are some of the key functions of the X chromosome: 1. Sex determination: The presence or absence of an SRY gene on the Y chromosome determines whether an individual is male or female. Females have two X chromosomes, and males have one X and one Y chromosome. Chapter 8 X chromosome 2. Dosage compensation: In females, one of the two X chromosomes is randomly inactivated in each cell. This process is called X inactivation and ensures that females have only one active copy of each X-linked gene. Chapter 8 X chromosome 3.Gene expression: The X chromosome contains a variety of genes that are important for development and health. These genes include genes for intelligence, color vision, blood clotting, and many other traits. Chapter 8 X chromosome 3.Non-coding RNA: The X chromosome also contains a number of non-coding RNAs, which are RNA molecules that do not code for proteins. These RNAs play important roles in gene regulation and other cellular processes. Chapter 8 X chromosome Chapter 8 X-Chromosome Inactivation (The Lyon Hypothesis ) The Lyon Hypothesis was proposed by British geneticist Mary Lyon in 1961. The Lyon Hypothesis is a scientific hypothesis that states that one of the two X chromosomes in female cells is inactivated during early embryo development. Chapter 8 X-Chromosome Inactivation (The Lyon Hypothesis ) This process is called X inactivation and ensures that females have only one active copy of each X-linked gene. This inactivation occurs during early embryo development and is stably maintained throughout the lifetime of the animal Chapter 8 The human Y chromosome The human Y chromosome is one of the two sex chromosomes in humans, the other being the X chromosome. Chapter 8 The human Y chromosome The Y chromosome is responsible for important biological roles such as sex determination and male fertility, and it is always in the haploid state. Chapter 8 The human Y chromosome One of the genes on the Y chromosome is the SRY gene, which turns on a set of other genes that cause the embryo to develop certain sex characteristics, such as testes. Chapter 8 The human Y chromosome The Y chromosome is also a powerful tool to study human populations and evolutionary pathways, as it retains a record of the mutational events that have occurred along male lineages throughout evolution. Chapter 8 The different sex chromosome systems Sex determination systems vary across species and can be genetic or environmental. The most familiar system is the XX/XY system, found in most mammals, including humans, where females have two of the same kind of sex chromosome (XX), while males have two distinct sex chromosomes (XY). Chapter 8 The different sex chromosome systems Other systems include the ZW system found in birds, where the mother's sex chromosome determines the genetic sex of the offspring. Chapter 8 The different sex chromosome systems The X0 system found in some insects, where females have two copies of the sex chromosome (XX) but males have only one (X0). Chapter 8 The different sex chromosome systems There are also species where the two sexes are chromosomally indistinguishable, and sex is determined by a dominant male- determining factor. Chapter 8 Chapter 8 The different sex chromosome systems X0 system: In this variant of the XY system, females have two copies of the sex chromosome (XX) but males have only one (X0). The 0 denotes the absence of a second sex chromosome. This system is observed in a number of insects, including grasshoppers, crickets, and cockroaches, as well as some mammals. Chapter 8 The different sex chromosome systems ZW system: This system is opposite of the XY system in that the mother's sex chromosome determines the genetic sex of the offspring. Females have two different sex chromosomes (ZW), while males have two of the same kind of sex chromosome (ZZ). This system is found in birds, some reptiles, and some fish. Chapter 8 The different sex chromosome systems Haplodiploidy : This system is found in some insects, including bees and ants. Females develop from fertilized eggs and have two sets of chromosomes (diploid), while males develop from unfertilized eggs and have only one set of chromosomes (haploid).  Genetics Génétique Dr. Ibrahim elkhalil BEHMENE  Genetics Génétique Dr. Ibrahim elkhalil BEHMENE Chapter 9: Genetic engineering technique In situ hybridization Cloning Transgenesis Chapter 9 In situ hybridization Chapter 9 In situ hybridization In situ hybridization ISH is a technique that is used to detect and localize specific nucleic acid sequences in cells or tissues. The technique is based on the principle of hybridization, which is the pairing of complementary nucleic acid sequences. Chapter 9 In situ hybridization (ISH) In ISH, a labeled probe is used to hybridize to the target nucleic acid sequence in the cell or tissue. The probe can be either DNA or RNA, and it is labeled with a radioactive, fluorescent, or enzymatic marker. Chapter 9 In situ hybridization (ISH) Steps involved in ISH:  Sample preparation: The cells or tissues are fixed and prepared for hybridization.  Probe preparation: The probe is labeled with a marker. Chapter 9 In situ hybridization (ISH)  Hybridization: The probe is hybridized to the target nucleic acid sequence in the cell or tissue.  Detection: The marker is detected, and the location of the target nucleic acid sequence is determined. Chapter 9 In situ hybridization (ISH) Applications ISH and MH have a wide range of applications in research and diagnostics. Some of the most common applications include:  Identifying and characterizing new genes  Studying gene expression  Diagnosing genetic disorders  Monitoring the progression of diseases  Developing new therapies Chapter 9 Cloning Chapter 9 Cloning Cloning is the process of producing genetically identical copies of a biological entity Chapter 9 Cloning Types of Cloning There are two main types of cloning: 1. Therapeutic cloning: This type involves creating a cloned embryo for the sole purpose of producing embryonic stem cells with the same DNA as the donor cell. These stem cells are then used to generate new tissue or organs that could be transplanted into the patient without the risk of rejection. Chapter 9 Cloning 2. Reproductive cloning: This type of cloning involves creating a cloned animal that is genetically identical to its parent. Reproductive cloning has been achieved in a number of animals, including sheep, mice, and cows. Chapter 9 Cloning Applications of Cloning Cloning has a number of potential applications, including: 1. Medicine: Cloned stem cells could be used to generate new tissue or organs for transplant patients. This could help to alleviate the shortage of donor organs and tissues. 2. Agriculture: Cloned animals could be used to produce genetically identical offspring with desirable traits, such as increased milk or meat production. 3. Conservation: Cloned endangered animals could be used to increase their populations and help to prevent them from going extinct. Chapter 9 Transgenesis  Transgenesis Chapter 9 Transgenesis is a technique used to introduce foreign genetic material, known as a transgene, into the genome of an organism. This can be done for a variety of purposes, including:  Transgenesis Chapter 9 Studying gene function: By introducing a transgene into an organism, scientists can study how the gene affects the organism's development, physiology, or behavior. Producing therapeutic proteins: Transgenic animals can be used to produce large quantities of therapeutic proteins, such as human insulin or growth hormone.  Transgenesis Chapter 9 Developing new crops: Transgenic plants can be developed with desirable traits, such as resistance to pests or diseases, or improved nutritional value.  Transgenesis Chapter 9 Steps in Transgenesis : The steps involved in transgenesis typically include: 1. DNA isolation: The desired gene is isolated from the source organism. 2. Vector construction: The gene is inserted into a vector, which is a piece of DNA that can be used to deliver the gene to the target organism.  Transgenesis Chapter 9 3. Transfection: The vector is introduced into the target organism. 4. Selection: The target organism is screened for the presence of the transgene.  Transgenesis Chapter 9 Types of Transgenesis There are two main types of transgenesis: 1. Germline transgenesis: This type of transgenesis involves introducing the transgene into the germline cells of the target organism. This means that the transgene will be passed on to the organism's offspring.  Transgenesis Chapter 9 2. Somatic cell transgenesis: This type of transgenesis involves introducing the transgene into somatic cells, which are not involved in reproduction. This means that the transgene will not be passed on to the organism's offspring. Chapter 9 Applications of Transgenesis 1. 1. Medicine: Transgenic animals can be used to produce therapeutic proteins, such as human insulin or growth hormone. Transgenic plants can also be developed with improved nutritional value or with the ability to produce pharmaceuticals. 2. Agriculture: Transgenic plants can be developed with desirable traits, such as resistance to pests or diseases, or improved nutritional value. 3. Research: Transgenesis is a powerful tool for studying gene function and for developing new models of human disease.  Transgenesis Chapter 9 Conclusion Transgenesis is a powerful tool with the potential to benefit society in many ways. However, it is important to carefully consider the ethical implications of using this technology and to take steps to minimize the potential risks.  Genetics Génétique Dr. Ibrahim elkhalil BEHMENE