Genetics Notes PDF - HIGHER SCHOOL OF SAHARIAN AGRICULTURE - ELOUED

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