Cytogenetics PDF

WEEK 1: Introduction Chapter 1 Generalized Animal Cells Bioethics deals with issues of privacy, discrimination,  Surrounded by the plasma membrane. and justice that arise from the use and misuse of  Contains: genetic information....

WEEK 1: Introduction Chapter 1 Generalized Animal Cells Bioethics deals with issues of privacy, discrimination,  Surrounded by the plasma membrane. and justice that arise from the use and misuse of  Contains: genetic information. o Intracellular organelles o Cytoplasm DNA, genes, chromosomes, exomes, and genomes o Stored proteins are the levels of genetic information, and they impact o Carbohydrates biology at the cell, tissue, organ, individual, family, and o Lipids population levels. o Pigment molecules o Other small chemicals Genes encode proteins, and the exome is the small part of the genome that does so. Most traits arise from Organelles interactions of genes and environmental factors. In  Divide labor by partitioning certain areas or addition to health care applications, DNA analysis is serving specific functions. useful in studying endangered species, establishing  Keep related biochemical and structures close identity, and illuminating history. to one another to interact efficiently.  Functions: The Precision Medicine Initiative is examining genome o Enable a cell to retain and use its information, the micro-biome, environmental genetic instructions. exposures, physiological measurements, and other o Acquire energy, secrete substances, data to better understand health. and dismantle debris. Cells The Cell Nucleus  Somatic (body) cells have two copies of the  Cell is a fundamental component of life genome and are said to be diploid. containing different organelles.  Sperm and egg cells have one copy of the  Nucleus genome and are haploid. o Prominent organelle of the cell.  Stem cells can divide to give rise to o Nerve center or control center of cell. differentiated cells and replicate themselves Surrounded by a layer of Nuclear Envelope. through self-renewal.  Contains: o Nuclear pores that allow movement Domains of Life of biochemical.  Biologists recognize three broad categories of o Nuclear lamina provides mechanical organisms: support and holds nuclear pores in o Achaea and Bacteria — Unicellular place. prokaryotes. o Nucleolus produces ribosomes. o Eukaryote — Includes both unicellular  Other contents — and multicellular eukaryotes. Chromosomes, RNA and  Cells of domains contain globular assemblies nucleoplasm. of RNA and protein called ribosomes. o Essential for protein synthesis. Endoplasmic Reticulum (ER)  Interconnected membranous tubules & sacs. Cell Chemical Constituents  Winds from the nuclear envelope to the  The major macromolecules that make up cells plasma membrane. are carbohydrates(sugars and starches),  Rough ER contains ribosomes and is involved lipids (fats and oils), proteins, and nucleic in protein synthesis. acids (DNA and RNA).  Smooth ER does not contain ribosomes and is  Carbohydrates provide energy and contribute important in lipid synthesis. to cell structure.  Proteins exit the ER in membrane-bounded,  Lipids form the basis of some hormones, form saclike organelles called Vesicles. membranes, provide insulation, and store energy. Golgi Apparatus  Proteins have many diverse functions such as  Stack of interconnected flat, membrane- forming the contractile fibers of muscle cells, enclosed sacs. enabling blood to clot, and forming the bulk of connective tissues.  Processing center that adds sugars forming glycoproteins and glycolipids.  Enzymes are especially important proteins because they facilitate, or catalyze,  Products are released into vesicles that bud biochemical reactions. off to the plasma membrane.  Nucleic acids (DNA and RNA) are most the most important macromolecules to the study of genetics. [Cytogen] 1 of 72 Peroxisomes The development of multicellular organisms requires  Sacs with outer membranes studded with Cell growth and division (Mitosis), as well as Cell several types of enzymes. death (Apoptosis).  Break down lipids, rare biochemical.  Synthesize bile acids. The Cell membrane controls what enters and leaves a cell.  Detoxify compounds from exposure to oxygen free radicals. Stem cells are crucial in the formation of specialized  Abundant in liver and kidney cells. (differentiated) cells during embryonic development and in the repair and replacement of tissues to Lysosomes maintain health.  Membrane-bound sacs containing 43 types of digestive enzymes. Stem cells persist in many adult tissues and have the  Dismantle bacterial remnants, worn-out potential to replace injured or diseased tissue. organelles, and excess cholesterol.  Engages in Autophagy. The human body also includes many bacterial cells, which are collectively called the Microbiome. Mitochondria  Surrounded by two membranes. Cells  Provide energy by breaking chemical bonds  Basic cell types that hold together nutrient molecules in food.  Somatic and Stem Cells  Freed energy is stored in adenosine  Four specialized type of cells triphosphate (ATP). o Connective o Epithelium Biological Membrane o Nervous  Proteins aboard lipids. o Muscle o Contribute to cell’s identity.  Chemical constituents o Transport molecules. o Lipids o Keep out toxins and pathogens. o Carbohydrates  Some membrane proteins form channels for o Proteins ions. o Nucleic Acids Plasma Membrane Stem Cells  Cell-to-Cell Communication.  Stem cell divides by Mitosis.  Molecules that extend from the plasma o Produces two daughter cells or a stem membrane are receptors. cell and a progenitor cell, which may  Signal Transduction be partially specialized o Molecules form pathways that detect  Progenitor cells do not have the capacity of signals from outside the cell and self-renewal. transmit them inward.  Cellular Adhesion o Plasma membrane helps cells attach to certain other cells. Cytoskeleton  Meshwork of protein rods and tubules.  Includes 3 major types of proteins. o Microtubules o Microfilaments o Intermediate filaments Introduction Chapter 2 Organelles are compartments that establish microenvironments for specific functions and may sequester enzymes that might otherwise damage the cell.  It forms from aggregates of macromolecules (proteins, lipids, carbohydrates, and nucleic acids. The Cytoskeleton, built of tubes and rods of proteins, provides distinctive cell shapes and the ability of a cell to move. [Cytogen] 2 of 72 Stem Cell Applications Mitosis “mitos”  Stem cells are being used in four basic ways:  Walther Flemming described the motion of o Discovery and development of drugs. what he saw under microscope as “threads” o Observing the earliest sign of disease. moving in an actively dividing cell. o Create tissues and organs, for use in  Karyokinesis implants and transplants, or to study. o Nuclear Division o Stimulating stem cells in the body via  Only occurs in Eukaryotes. the introduction of reprogramming  Produces 2 new cells that are both genetically proteins. identical to the original cell. Cell Division  Growth, development, maintaining health, and healing from disease or injury require an intricate interplay between the rates of: o Mitosis and Cytokinesis — Division of DNA and rest of the cell. o Apoptosis — Cell death.  Precise, genetically programmed sequence of events. Cell Division  Results in genetically identical daughter cells.  Cells duplicate their genetic material. The Cell Cycle Somatic Cells Germ Cells Mitosis Meiosis Diploid Haploid Interphase Prophase  Chromosomes are uncondensed.  Condensed chromosomes take up stain.  Microscopically – cells are quiet.  The spindle assembles o Active protein synthesis. o Centrioles appear. o Chromosomes –not visible. o The nuclear envelope breaks down. o Consist of 3 parts: G1, G2 and S.  Gap 1- protein synthesis,  Cell prepares to divide by tightly condensing lipids and carbohydrates. its chromosomes.  Asters - pair of centrioles surrounded by halo  S phase- Replication of of microtubules. chromosomes.  Initiate mitotic spindle formation.  Chromosomes appear as long, thin threads.  G2- DNA replication and mitosis. Metaphase  Chromosomes align.  Attachment of chromosomes to spindle fiber forming a metaphase plate. o Align along the cell’s equator.  Chromosomes are at maximum contraction. [Cytogen] 3 of 72 Anaphase Hormones and Growth Factors  Centromeres part and chromatids separate.  Hormone is made in a gland and transported  Centromeres divide. in the bloodstream to another part of the body.  Sister chromatids are pulled apart to opposite o Exerts a specific effect. poles of the cell by kinetochore fibers  A growth factor acts locally. becoming independent chromosomes o Epidermal growth factor (EGF)  By the end of anaphase, the two ends of the stimulates cell division in the skin cell have equivalent and complete collections beneath a scab. of chromosomes.  Two types of proteins, the cyclins and kinases, interact inside cells, activating the genes Telophase whose products carry out mitosis.  The spindle disassembles and the nuclear envelope re-forms. Telomeres  Furrowing occurs.  Lose 50–200 endmost bases after each cell  Spindle falls apart. division.  Two daughter nuclei begin to form in the cell.  After 50 divisions, shortened telomeres  Nucleolus reappears. signal the cell to stop dividing. o Nuclear membranes form around the  Sperm, eggs, bone marrow, and cancer cells two sets of chromosomes. produce telomerase that prevent shortening of  Chromosomes become less condensed. telomeres.  Cytokinesis occurs. Failure of the Checkpoints 1. Mutations → cancer Mitosis-Cytokinesis 2. Genomic instability → birth defects  Organelles and macromolecules are distributed between the two daughter cells.  Microfilament band contracts, separating the Meiosis two cells.  Mixes up trait combinations.  Takes place in the Gametes, which are haploid and somatic cells that are diploid for each chromosome.  Humans normally contains 23 pairs of chromosomes.  Cell division that halves the chromosome number, homologous pairs have the same genes in the same order but carry different alleles, or variants, of the same gene.  Absence of meiosis could lead to genetically overloaded cells. Provides genetic diversity which can enable a population to survive an environmental challenge. Control of the Cell Cycle During Meiosis gamete (sex) cells undergo a “Double  Cell cycle checkpoints. Division” o Ensure that critical events in the DNA  Maintaining the DNA but reducing the replication and chromosome chromosomal count to 23. segregation. o 23 (sperm) + 23 (egg) = 46 (fertilized o Respond to damage by arresting cell cell). cycle.  Proteins as Checkpoints Meiosis reduces the number of chromosome sets from o Cyclin dependent kinases complexes diploid to haploid. o Ensures that all phases of cell cycle  Meiosis takes place in two sets of divisions: are executed in the correct order o Meiosis I reduces the number of  Cdk4 & Cdk6 – G1 chromosomes from diploid to haploid  Cdk2 – S-phase Cdk o Meiosis II produces four haploid  Cdk1 – M-phase Cdk daughter cells [Cytogen] 4 of 72 Meiosis I Special Events in Meiosis  Prophase I (early)  Pairing of homologous chromosomes o Synapsis and crossing over occurs. lengthwise is called synapsis.  Prophase I (late)  Cross overs or interchange of chromatid o Chromosomes condense and become segments between paired homologous visible. chromosomes o Spindle forms.  As homologous chromosomes separate points o Nuclear envelope fragments. of interchange are temporarily united and form o Spindle fibers attach to each an X like structure called Chiasma. chromosome.  Metaphase I Meiosis II o Paired homologous chromosomes Prophase II align along the equator of the cell.  Nuclear envelope fragments.  Anaphase I  Spindle forms and fibers attach to both o Homologous chromosomes separate chromosomes. to opposite poles of the cell. Metaphase II  Telophase I  Chromosomes align along the equator of the o Nuclear envelopes partially assemble cell. around chromosomes. Spindle Anaphase II disappears. Cytokinesis divides cells  Sister chromatids separate to opposite poles into two. of the cell. Telophase II Prophase I  Nuclear envelopes assemble around two  A spindle forms. daughter nuclei.  Chromosomes condense.  Chromosomes decondense.  Homologs pair-up and undergo crossing  Spindle disappears. over.  Cytokinesis divides cells.  Synapsed chromosomes separate but remain Results in: 4 NON-identical haploid daughter cells. attached at a few points. o Prophase I (early) - Synapsis and Significance of Meiosis crossing over occurs.  Provides constancy of the chromosome o Prophase I (late) - Chromosomes number from generation to generation by condense, become visible. Spindle reducing the chromosome number from diploid forms. to haploid, thereby producing haploid  Nuclear envelope fragments. gametes. Spindle fibers attach to each  Allows random assortment of maternal and chromosome. paternal chromosomes between the gametes.  Homologous chromosomes in a tetrad cross  Relocates segments of maternal and paternal over each other. chromosomes by crossing over of  Each tetrad usually has one or more chromosome segments, which "shuffles'' the chiasmata genes and produces a recombination of o X-shaped regions where crossing over genetic material. occurred  Pieces of chromosomes or genes are Fertilization exchanged  Structures that support and protect the embryo  Produces Genetic recombination in the include: offspring o Chorionic villi o Yolk sac Metaphase I o Allantois  Homologous pairs align along the equator of o Umbilical cord the cell. o Amniotic sac  Random alignment of chromosomes causes  By 10 weeks the placenta is fully formed. independent assortment of the genes that they  Copulations deposit sperm in the vagina. carry.  Fertilization can occur within 12 to 24 hours of ovulation. Anaphase I and Telophase I  When a sperm cell meets an oocyte, enzymes  Homologs separate in Anaphase I. are released to help the sperm in penetration  Move to opposite poles by Telophase I. in the oocyte's protective layer.  Centromeres of each homologous in Meiosis I  Once a sperm enters the oocyte, it will now remain together. trigger the blockage so other sperm cannot enter.  The two sets of chromosomes now meet and merge, forming a zygote [Cytogen] 5 of 72 Birth Defects  After puberty, meiosis I continues in one or  Time when genetic abnormalities, toxic several oocytes each month but halts again at substances, or viruses can alter a specific Metaphase II. structure is Critical period.  Most birth defects develop during the  Meiosis is only completed if the ovum is embryonic period. fertilized. o More severe than those that arise during the fetal period. Origin and Importance of Genetics  Some defects can be attributed to an abnormal gene. Old Ideas 1. All life comes from other life. Living organisms Teratogens are not spontaneously generated from non-living  Chemical or other agents that cause birth defects material.  Cause of birth defects due to exposure to a drug 2. Species concept: offspring arise only when two depend upon a woman’s genes members of the same species mate. Monstrous hybrids don’t exist.  Examples: 3. Organisms develop by expressing information o Thalidomide carried in their hereditary material. o Cigarettes and alcohol o Nutrients—Vitamins  Opposed to “preformation”: the idea that in o Occupational hazards each sperm (or egg) is a tiny, fully formed o Viral infections human that merely grows in size. 4. The environment can’t alter the hereditary Introduction Chapter 3 material in a directed fashion. There is no Genetic conditions may affect individuals at any stage “inheritance of acquired characteristics”. of existence. Mutations are random events. 5. Male and female parents contribute equally to Sexual reproduction (meiosis and fertilization) the offspring. maintains the diploid chromosome number and  Ancient Greek idea: male plants a “seed” recombines alleles from generation to generation, in the female “garden”. protecting against environmental change at the population and species levels. History of Genetics and Genomics The developing human is vulnerable to teratogens and  1859 Charles Darwin - Publication of “The detrimental environmental agents, which can lead to Origins of Species”, a treatise that formally birth defects. outlined the theory of evolution via natural selection Genome studies are revealing the genetic basis of longevity.  1865 Gregor Mendel - The concept of particulate (gene) inheritance was established. Gamete Maturation The laws of segregation and independent Spermatogenesis assortment were demonstrated. The publication  A diploid spermatogonium divides by mitosis to is entitled “Experiments in Plant Hybridization” produce a stem cell and another cell that and outlines the famous “pea experiments.” specializes into a mature sperm.  1866 Ernst Haeckel - Proposes the idea that the hereditary material resides in the nucleus.  In Meiosis I, the primary spermatocyte produces two haploid secondary spermatocytes.  1871 Friedrich Miescher - The term nuclein is used for the material found inside the nucleus of  In Meiosis II, each secondary spermatocyte a cell. Further experiments (1874) revealed produces two equal-sized spermatids. nuclein consisted of a nucleic acid and protein.  Spermatids then mature into a tadpole-shaped  1879 Walter Fleming - Described chromosome spermatozoa. behavior during animal cell division. He stains chromosomes to observe them clearly and Oogenesis describes the whole process of mitosis in 1882.  In Meiosis I, primary oocyte divides unequally forming a small polar body and a large  1899 William Bateson - The use of hybridization secondary oocyte. between two individuals is described as a tool of the scientific analysis of heredity. This again was  In Meiosis II, the secondary oocyte divides to discovered to be an important tenet of Mendel’s form another polar body and a mature ovum work.  Unlike spermatogenesis, oogenesis is a discontinuous process. Oocytes arrest at Prophase I until puberty. [Cytogen] 6 of 72  1900 Carl Correns, Hugo de Vries, Erich von  1952 Alfred Hershey, Martha Chase - The Tschermak - Mendel’s work is rediscovered classic “blender experiment” is reported that independently. De Vries and Correns were shows that phage DNA enters (along with a little experiments similar to those of Mendel and protein) and leads to the eventual rupture of the arrived at similar results. Once they read cell. This is often, and mistakenly, considered the Mendel’s paper, they recognized it’s pre- definitive experiment proving that DNA is the eminence and made the world aware of it. genetic material.  1900 Hugo de Vries - The term mutation is used  1953 James Watson, Francis Crick - A to describe the apparently spontaneous structural model of DNA is presented that states appearance of new traits in evening primrose. it consists of two anti-parallel chains held together by hydrogen bonds. The model  1902 Walter Sutton - Theodor Boveri, within a suggests a model of DNA replication. specific species, each chromosome is described as having unique physical characteristics. It is  1957 Francis Crick - The central dogma of shown that chromosomes occur in pairs, one molecular biology is proposed. This is a first parent contributes each member of the pair, and elucidation of the link between the sequences in the pairs separate during meiosis. Sutton the DNA molecule and the production of proteins. suggests chromosomes are a physical manifestation on which the unit of heredity  1961 Marshall Nirenberg - The concept that resides. This came to be known as the each amino acid corresponds to a triplet code chromosomal theory of inheritance. was developed. The first correspondence was found between the triplet AAA and the amino  1902 Archibald Garrod - The first human acid phenylalanine. disease is described that exhibits Mendelian inheritance. The disease is alkaptonuria. Later  1997 E. coli genome project E. coli (4.7 Mbp) is (1909) Garrod is the first to discuss the sequenced and shown to contain 4,500 genes. biochemical genetics of man.  2001 International Human Genome  1902 William Bateson - The terms genetics, Sequencing Consortium Celera Corp. – homozygote, heterozygote, epistasis, F1, F2, The human genome sequence (2900 Mbp) is and allelomorph (shortened later to allele) were published. It is estimated that the genome contains first used. between 35,000 and 40,000 genes. Later (2002) estimates place the number at 30,000 genes.  1903 Wilhelm Johannsen - The important concepts of phenotype, genotype, and selection  2002 Mosquito Sequencing Consortium - The were elucidated. The terms were actually coined malaria-parasite-carrying mosquito genome later (1909). sequence (278 Mbp) is published. It is shown to contain 13,600 genes, similar to the number  1910 Thomas Hunt Morgan - The first found in Drosophila demonstration of sex linkage in Drosophila is published. This suggested genes reside on  2003 British Columbia Cancer Agency The chromosomes. The era of fruit fly as a model SARS-associated coronavirus genome sequence organism begins. (30 Kbp) is released. The genome contains 16 open reading frames. The sequence is released  1928 Frederick Griffith - Transformation of less than five months after the disease began Pneumococci is obtained. This is the critical spreading worldwide. experiment that leads to the eventual discovery that DNA was the genetic material. Major Events in the 20th Century  1944 Oswald T. Avery, Colin M. MacLeod, Maclyn McCarty - Extending the experiments of 1900: Griffith (1929), it is first shown that DNA is the  Rediscovery of Mendel’s work by Robert Correns, genetic material. This fact is often lost, and this Hugo de Vries, and Erich von Tschermak. discovery is often afforded to Hershey and Chase (1953). 1902:  Archibald Garrod discovers that alkaptonuria, a  1950 Erwin Chargaff - Adenine=thymine and human disease, has a genetic basis. guanine=cytosine. It is demonstrate that within all DNA molecules, the number of adenines equals 1904: the number of thymine, and the number of  Gregory Bateson discovers linkage between guanine equals the number of cytosine. genes. Also coins the word “genetics”. [Cytogen] 7 of 72 1910: Genomics  Thomas Hunt Morgan proves that genes are  field that analyzes and compares genomes of located on the chromosomes (using Drosophila). different species 1918: Levels of Genetics and Genomics  R. A. Fisher begins the study of quantitative  Molecular > Cellular > Tissues > Organs > genetics by partitioning phenotypic variance into a Individuals > Families > Population > Evolution of genetic and an environmental component. species 1926: Deoxyribonucleic Acid Double Helix (DNA)  Hermann J. Muller shows that X-rays induce Components: mutations.  Phosphate  Sugar 1944:  Base: Adenine (A) Thymine (T)  Oswald Avery, Colin MacLeod and Maclyn Cytosine (C) Guanine (G) McCarty show that DNA can transform bacteria, demonstrating that DNA is the hereditary material. Each consecutive three DNA bases is a code for a particular amino acid. 1953:  James Watson and Francis Crick determine the Ribonucleic Acid (RNA) structure of the DNA molecule, which leads directly Produced by transcription process to knowledge of how it replicates  Copies the sequence of part of one strand of a DNA molecule into a related molecule 1966:  Marshall Nirenberg solves the genetic code,  Three RNA bases in a row attract another showing that 3 DNA bases code for one amino RNA that functions as a connector, bringing in acid. a particular amino acid – Amino acids align to form a protein 1972:  Stanley Cohen and Herbert Boyer combine DNA From Gene to Protein to Person from two different species in-vitro, then transform it into bacterial cells: first DNA cloning.  DNA is transcribed into messenger RNA.  Messenger RNA is translated when three of its 2001: RNA bases attract another type of RNA that  Sequence of the entire human genome is functions as a connector, bringing in a particular announced. amino acid.  The amino acids align and link like snap beads, Gregor Mendel forming a protein.  Austrian Monk  Born 1822 in Czech Republic The Language of Life: DNA to RNA to Protein  Worked at monastery and taught high school Chromosomes  Tended the monastery garden  Composed of DNA and protein  Grew peas and became interested in the traits that  A human somatic cells have 23 pairs of were expressed in different generations of peas chromosomes  22 pairs of autosomes What Is Genetics?  A pair of sex chromosomes  It is the study of inherited traits and their variation.  Females have two X chromosomes  Males have one X and a Y  Certain difficult-to-define human characteristics might appear to be inherited if they affect several Mendelian Versus Multifactorial Traits family members but may reflect shared genetic  Multifactorial traits are determined by one or more and environmental influences. genes and environmental factors.  A human body contains approximately 37 trillion Genes cells. – All cells except RBCs contain the entire  Units of heredity genome.  Traits are produced by an interaction between  Use of different subsets of genes to manufacture genes and their environment proteins drives differentiation of distinctive cell types.  Stem cells are less specialized and provide a Genetic Information reserve supply of cells. Genome  The complete set of genetic instruction.  Human genome was completed in 2003 which started in 1990 [Cytogen] 8 of 72 Relationships: from Individuals to Families Health Care Allele: alternate or variant form of a gene  Diseases are viewed as the consequence of complex interactions among genes and Genotype: refers to the alleles present in an individual environmental factors that cause traits or disorders  Some people are more susceptible to contracting Phenotype: the expression of a gene in traits or certain infections than others due to inherited symptoms or the visible trait differences in immunity. Recessive: an allele whose expression is masked by  Genes affect how people respond to particular another allele drugs. Pharmacogenomics is a field that identifies individual drug reactions based on genetics. Dominant: a gene variant is expressed when present in just one copy.  Precision medicine is a medical approach that consults DNA information to select drugs that are most likely to work and have the least side effects Genotypes VS Phenotypes in a particular individual.  At each locus (except for sex chromosomes) there are 2 genes. These constitute the individual’s  This medical approach examines the individual’s genotype at the locus. genome, diet, exercise, environment, and microbiome.  The expression of a genotype is termed a phenotype. For example, hair color, weight, or the Genome Editing presence or absence of a disease  Genome editing is a newer technology that is used o Eb- dominant allele. to remove, replace, and or add specific genes into o Ew- recessive allele. the cells of any organism. The bigger picture: from populations to evolutions The Microbiome Population: group of interbreeding individuals  The microbiome is the symbiotic relationship between an individual’s genome, diet, lifestyle Gene pool: all the genes in a population factors, and the many microbes in the body. Pedigrees: are diagrams used to study traits in the family Exome Sequencing Applications of Genetics  It determines the order of DNA bases of all parts of the genome that encode proteins. DNA Profiling  The exome consists of approximately 20,325  Identification of victims of natural disasters or genes. terrorist attacks  The information is compared to databases that list  Matching the DNA of suspects to samples left at many variants (alleles) and their associations with the crime scene specific phenotypes, such as diseases.  Helping adopted individuals locate blood relatives Bioethics History and Ancestry  Addresses moral issues and controversies that arise in applying medical technology  DNA analysis can clarify details of history =  Concerned with issues of privacy, confidentiality, Revealing the offspring of Thomas Jefferson and and discrimination that arise from knowledge of Sally Hemmings our DNA sequences  Provide views into past epidemics by detecting genes of the pathogens = Revealed the presence of malaria in the analysis of DNA of king Tutankhamun’s mummy [Cytogen] 9 of 72  WEEK 2: INTRODUCTION CHAPTER 4 Mendel’s Experiments (3) Mendel’s laws of segregation and independent  True-breeding—Offspring have the same trait as assortment derive from events that occur as gametes parents. forms. o Example—Short parents produce all short offspring. Meiosis and fertilization produce greater genetic  The observed trait is dominant. variation in sexually reproducing organisms. Alleles  The masked trait is recessive. assort into gametes during anaphase I (segregation).  Monohybrid cross follows one trait.  Self-crossed plants are hybrids. New trait combinations arise from the random alignment of paired chromosomes during metaphase I (independent assortment) and from gamete Monohybrid Cross combinations at fertilization.  Experiments confirmed that hybrids hide one expression of a trait, which reappears when Mutations in single genes cause Mendelian diseases. hybrids are self-crossed.  Mendel speculated that each elementen was Pedigree charts track recessive and dominant packaged in a separate gamete. inheritance.  Law of segregation is Mendel’s idea that Exome sequencing helps to diagnose unknown elementen separate in the gametes. conditions or those with unusual presentations and can distinguish inheritance of recessive alleles from the appearance of a new dominant mutation Mendel’s First Law—Segregation (1)  Reflects the actions of chromosomes and the Characteristics of a Single-Gene Disease genes they carry during meiosis 1. In families the probability can be deduced by o Homozygous carry same alleles TT or tt knowing how the affected person is related to a o Heterozygous carry different alleles Tt family member.  Genotype = Organism’s alleles 2. Tests can sometimes predict the risk of developing  Phenotype = Outward expression of an allele symptoms. combination 3. The disease may be much more common in some  Wild Type = Most common phenotype populations than others. o Recessive or dominant 4. Some single-gene diseases have modes of inheritance, such as cystic fibrosis. Mendel’s First Law—Segregation (2)  Mutant phenotype = Variant of a gene’s The Inheritance of One Gene expression that arises when the gene undergoes  Modes of inheritance are the patterns in which mutation single-gene traits and disorders occur in families.  Mendel observed the events of meiosis  Huntington’s disease is autosomal dominant.  Two copies of a gene separate with the homologs o Affects both sexes and appears in every that carry them when a gamete is produced generation  At fertilization, gametes combine at random o Cystic fibrosis is autosomal recessive. o Affects both sexes and can skip Mendel’s Experimentation Data generations through carriers 1. Seed form 2. Seed color Mendel’s Experiments (1) 3. Seed coat color  Described the units of inheritance and how they 4. Pod form pass from generation to generation 5. Pod color  Mendel had no knowledge of DNA, cells, or 6. Flower position chromosomes 7. Stem length o His laws of inheritance explain trait transmission in any diploid species Eye Color  Conducted experiments from 1857 to 1863 on  People differ in the amount of melanin and number traits in 24,034 plants of melanosomes. o Have the same number of melanocytes Mendel’s Experiments (2)  The surface of the back of the iris contributes to  Deduced that consistent ratios of traits in the the intensity of eye color. offspring indicated that plants transmitted distinct  OCA2confers eye color by controlling melanin units synthesis.  Analyzed genetic crosses of peas o HERC2 controls expression of the OCA2 o P1 Parental generation gene o F1 First filial generation o F2 Second filial generation [Cytogen] 10 of 72 Modes of Inheritance Mendel’s Second Law—Independent Assortment  Rules that explain the common patterns of single-  Considers two genes on different chromosomes gene transmission.  The inheritance of one does not influence the  Passing of a trait depends on whether chance of inheriting the other o Determining gene is on an autosome or on a  Two genes that are far apart on the same sex chromosome. chromosome appear to independently assort o Allele is recessive or dominant. o Numerous crossovers take place between  Autosomal inheritance can be dominant or them recessive. Probability Comparison of Autosomal Dominant and  The likelihood that an event will occur Autosomal Recessive Inheritance  Product rule—Probability of simultaneous independent events equals the product of their Autosomal Dominant individual probabilities  Males and females affected, with equal o Predicts the chance of parents with known frequency. genotypes to produce offspring of a  Successive generations affected until no one particular genotype inherits the mutation.  Example—Consider the probability  Affected individual has an affected parent, of obtaining a plant with wrinkled, unless he or she has a de novo mutation. green peas (genotype rryy) from dihybrid (RrYy) parents Autosomal Dominant Trait  Does not skip generations, can affect both sexes. Pedigree Analysis p.78-79 o Polydactyl - Extra fingers and/or toes. Pedigrees are symbolic representations of family relationships and the transmission of inherited traits. Look chart sa book p.78 Autosomal Recessive  Males and females affected, with equal An Unusual Pedigree frequency A partial pedigree of Egypt’s Ptolemy dynasty showing:  Can skip generations  Genealogy not traits  Affected individual has parents who are  Extensive inbreeding affected or are carriers (heterozygotes) Importance of Pedigrees Today Autosomal Recessive Trait  Helps families identify the risk of transmitting an  Albinism = Deficiency in melanin production inherited illness  Parents are inferred to be heterozygotes  Starting points for identifying and describing, or annotating, a gene from the human genome sequence Criteria for Autosomal Recessive Traits  Meticulous family records are helping researchers  Males and females can be affected. follow the inheritance of particular genes  Affected males and females can transmit the gene, unless it causes death before reproductive age. An Inconclusive Pedigree  Trait can skip generations.  This pedigree can account for either an autosomal  Parents of an affected individual are heterozygous dominant or an autosomal recessive trait or have the trait.  Passed in an autosomal dominant mode  Conditions likely to occur in families with consanguinity. Conditional Probability  Pedigrees and Punnett squares apply Mendel’s laws to predict the recurrence risks of inherited On the Meaning of Dominance and Recessiveness conditions  Knowing whether an allele is dominant or Punnett Square recessive is important in determining risk of inheriting a particular condition.  Represents how genes in gametes join if they are o Reflect the characteristics or abundance of on different chromosomes a protein  Recessive traits are due to “loss of function.” o Recessive disorders tend to be severe, produce symptoms earlier than dominant disorders o No protein made  Dominant traits arise from “gain of function.” o Different (toxic) form of protein made [Cytogen] 11 of 72  WEEK 3: INTRODUCTION CHAPTER 5 Discovering the Structure of DNA Early work of Phoebus Levene showed that DNA is Phoebus Levine composed of equal proportions of deoxyribose, ○ Russian-American biochemist nitrogenous bases, and phosphates. ○ Identified the 5-carbon sugars ribose in 1909 and deoxyribose in 1929 Erwin Chargaff’s experiments demonstrated that in ○ Revealed chemical distinction between RNA DNA the number of adenines (A) and thymine (T) are and DNA equal as are guanine (G) and cytosine (C). RNA has ribose DNA has deoxyribose Maurice Wilkins and Rosalind Franklin analyzed the ○ Discovered that the three parts of a structure of DNA using X-ray diffraction. Franklin’s nucleotide are found in equal proportions: photographs of B-form DNA revealed a helical Sugar structure. Phosphate Base Using Franklin’s X-ray diffraction patterns, Watson and ○ Deduced that a nucleic acid building block Crick deduced the double helix structure of DNA. They must contain one of each component published their work in the journal Nature in 1953. Erwin Chargaff, 1951 ○ Austrian-American biochemist History of DNA ○ Analyzed base composition of DNA from Friedrich Miescher, 1871 various species and observed regular ○ Swiss physician and biochemist relationships: A = T and C = G ○ Isolated nuclei from white blood cells in pus ○ Found an acid substance with nitrogen and Adenine(A) + Guanine(G) = Thymine(T) + Cytosine (C) phosphorus ○ He called it Nuclein ○ Later, it was called nucleic acid Rosalind Franklin and Maurice Wilkins, 1952 ○ English scientists ○ Used a technique called X-ray diffraction Archibald Garrod, 1902 Deduced the overall structure of the ○ English physician molecule from the patterns in which ○ Linked inheritance of inborn errors of the X rays were deflected metabolism with the lack of particular ○ Distinguished two forms of DNA enzymes “A” form, which is dry and crystalline “B” form, which is wet and cellular Frederick Griffith, 1928 ○ It took Franklin 100 hours to obtain “photo ○ English microbiologist 51” of the B-form of DNA ○ Worked with Streptococcus pneumoniae ○ Franklin reasoned that the DNA is a helix bacteria, which exists in two types: with symmetrically organized subunits. Type S (Smooth) = Enclosed in a polysaccharide capsule James Watson and Francis Crick Type R (Rough) = No capsule ○ Did not perform any experiments ○ Termed the conversion of one bacterial type Rather, they used the earlier into another as transformation research and inferences from model building with cardboard cutouts to solve the structure of DNA Avery, MacLeod, and McCarty, 1944 ○ American physicians DNA Structure ○ Treated lysed S bacteria with protease and A gene is a segment of DNA containing the DNase information to specify a sequence of amino acids ○ On DNa prevented transformation in a protein, which is very diverse. ○ Thus, DNA is the transforming principle Can convert type R bacteria into S Nucleotide Building Blocks ○ A building block of DNA is a nucleotide, which consists of one deoxyribose, one Alfred Hershey and Martha Chase, 1953 phosphate group, and one nitrogenous ○ American microbiologists base. ○ Used E.coli bacteria infected with a virus that ○ Adenine and guanine are purine bases; consisted of a protein head surrounding DNA cytosine and thymine are pyrimidine bases. ○ Grew a batch of virus in a medium containing ○ A kilobase is a thousand DNA bases, and a 35S and 32P megabase is a million. ○ Blender experiments showed that the virus transfers DNA, not protein, into a bacterial cell Thus, DNA is the genetic material [Cytogen] 12 of 72  Gene is a section of a DNA molecule. The Directional Flow of Genetic Information ○ Sequence of building blocks specifies the ○ Production of protein from instructions on the sequence of amino acids in a particular DNA protein. A single building block is a Nucleotide. ○ Gene expression requires ○ Each nucleotide is composed of: The transcription that synthesizes an RNA A deoxyribose sugar molecule. A phosphate group A nitrogenous base; one of four The translation that uses the information in types: the RNA to manufacture a protein by Adenine (A), Guanine (G) = aligning and joining specified amino acids. Purines Cytosine (C), Thymine (T) = Then Folding of the protein into a specific 3- Pyrimidines D form. Nucleotides are joined into chains. Nucleic Acids ○ Phosphodiester bonds form between the ○ The DNA strand from which RNA is copied is the deoxyribose sugars and the phosphates. template strand, and the other strand of DNA is This creates a continuous sugar- the coding strand. phosphate backbone. ○ RNA polymerase catalyzes the synthesis of DNA Consists of Two Chains of Nucleotides in an RNA. Antiparallel Configuration ○ RNA differs from DNA in that it is generally Two polynucleotide chains align forming a Double single-stranded, has uracil instead of thymine, Helix. and has the sugar ribose instead of deoxyribose. ○ The opposing orientation (head-to-toe) is called antiparallelism. ○ These differences enable RNA to fold into three- Antiparallel nature of the DNA double dimensional conformations. helix becomes apparent when the carbons in the sugar are numbered. DNA Is Highly Condensed Scaffold proteins form frameworks that guide DNA The key to the constant width of the double helix is strands. the specific pairing of purines and pyrimidine via hydrogen bonds The DNA coils around proteins called Histones, forming a bead-on-a-string-like structure. The complementary base pairs are: ○ The bead part is called the Nucleosome. ○ Adenine and guanine ○ Cytosine and thymine DNA wraps at several levels, until it is compacted into a chromatid. DNA Is Directional Chromosome substance is called Chromatin. Note that one strand of the double helix runs in a 5’ to 3’ direction, and the other strand runs in a 3’ When chromatin is loose (not condensed into to 5’ direction. chromosomes that are visible upon staining), it forms loops at about 10,000 places in the genome. Polynucleotide Chains Are Antiparallel An “anchor” protein called CTCF brings together ○ The antiparallel nature of the DNA double helix parts of the DNA sequence within the same long becomes apparent when the carbons in the sugar DNA molecule to form the overall “loop-ome” are numbered. Carbons are numbered from 1 to 5. structure. ○ Phosphodiester bonds join DNA nucleotides via RNA Structure and Types the alternating deoxyribose and phosphate groups RNA is the bridge between gene and protein. that compose the sugar-phosphate backbone. Bases of an RNA sequence are complementary to ○ The two polynucleotide chains run head-to-toe, those of one strand of the double helix, called the exhibiting anti-parallelism based on the relative Template Strand. locations of the carbons in the sugars (5' to 3' and 3' to 5'). RNA Polymerase builds an RNA molecule. Nontemplate strand of the DNA double helix is called the Coding Strand. Messenger RNA (mRNA) carries the information that specifies a particular amino acid sequence. [Cytogen] 13 of 72  Each three mRNA bases in a row form a codon. Ribosomal RNA (rRNA) joins with certain proteins to form ribosomes. Ribosomes physically support the other structures involved in protein synthesis, and some rRNA catalyzes the formation of peptide bonds. Transfer RNA (tRNA) folds into a cloverleaf shape. It carries a specific amino acid at one end. One loop forms an anticodon, which is complementary to a specific mRNA codon. Polymerase Chain Reaction (PCR) DNA amplification is biotechnology that conducts DNA replication outside of cells. Techniques for nucleic acid amplification were developed in the 1970s and 1980s. The polymerase chain reaction (PCR) was the first such technology. It can amplify selected sequences of DNA in a manner similar to DNA replication in the nucleus. Types of RNA There are three major types of RNA: PCR is repeated cycles of denaturation of double- ○ Messenger RNA or mRNA - 500 to 4,500+ -- stranded DNA, annealing of primers, and DNA Encodes amino acid sequence synthesis using heat-stable DNA polymerases. ○ Ribosomal RNA or rRNA - 100 to 3,000 -- Associates with proteins to form ribosomes, which Nucleic Acids structurally support and catalyze protein synthesis There are two types of nucleic acids: ○ RNA ○ Transfer RNA or tRNA - 75to 80 -- Transports ○ DNA specific amino acids to the ribosome for protein synthesis Both consist of sequences of nitrogen-containing bases joined by sugar-phosphate backbones. DNA 1. Usually double-stranded 2. Thymine as a base 3. Deoxyribose as the sugar 4. Maintains protein-encoding information 5. Cannot function as an enzyme 6. Persists mRNA 7. Stores RNA-and protein-encoding information, Carries information that specifies a particular and transfers information to daughter cells protein Three mRNA bases in a row form a codon which RNA specifies a particular amino acid 1. Usually single-stranded Most mRNAs are 500–4500 bases long 2. Uracil as a base Differentiated cells produce certain mRNA 3. Ribose as the sugar molecules called transcripts 4. Carries protein-encoding information and ○ Information in the transcripts is used to controls how information is used manufacture the encoded proteins 5. Can function as an enzyme 6. Short-lived rRNA 7. Carries protein-encoding information, and helps Most rRNAsare from 100–3000 nucleotides long to make proteins Associate with proteins to form ribosomes Ribosomes consist of two subunits that join during protein synthesis rRNAs provide structural support ○ Some are catalysts (ribozymes) and others help align the ribosome and mRNA [Cytogen] 14 of 72  WEEK 4: CHAPTER 5 Overview of DNA Replication 1. Parent DNA molecule. 2. Parental strands unwind and separate at several points. 3. Each parental strand provides a template for DNA polymerase to bind complementary bases, A with T and G with C. 4. Sugar-phosphate backbones of daughter strands close. tRNA Matthew Meselsonand Franklin Stahl, 1957 Binds an mRNA codon and a specific amino acid Demonstrated the semiconservative mechanism of Only 75–80 nucleotides long DNA replication with a series of density shift ○ The 2-D shape is a cloverleaf shape experiments ○ The 3-D shape is an inverted L Labeled replicating DNA from bacteria with a Has two ends: heavy form of nitrogen and traced its pattern of ○ The anticodon is complementary to an distribution mRNA codon ○ Higher-density nitrogen was incorporated ○ The opposite end strongly bonds to a specific into one strand of each daughter double amino acid helix DNA Replication DNA replication is semiconservative. Two identical double helices are formed from one original, parental double helix. ○ Each new DNA double helix conserves half of the original. DNA Replication is Semiconservative DNA replication is semiconservative in that the two parental strands separate and each is a template for assembling new daughter strands. Semiconservative means that each new DNA double helix conserves half of the parental one. Meselson and Stahl in 1957 showed that DNA replication is semiconservative by labeling batches of dividing bacteria with heavy or light nitrogen and observing the pattern of distribution of the heavy nitrogen in subsequent generations. THE CENTRAL DOGMA The experiments ruled out a conservative The Central Dogma states that the pattern of mechanism (labeling all new DNA heavy) and information that occurs most frequently in our cells dispersive (mixing up old and new DNA). is: ○ From existing DNA to make new DNA (DNA replication) ○ From DNA to make new RNA (transcription) Steps of DNA Replication (Overview) ○ From RNA to make new proteins (translation) DNA replication occurs during the S phase of the Sequencing DNA cell cycle, prior to cell division. When DNA is replicated, it separates and The Sanger method of DNA sequencing was hydrogen bonds holding the base pairs together invented in 1977 and is still used to sequence break. genes and to check accuracy of other techniques. ○ Two identical nucleotide chains are built from one, as the bases form pairs. Next-generation sequencing yields many copies of A site where DNA is locally opened is called a every contiguous section of bases. The more often replication fork. a particular sequence appears among the pieces, the more accurate the sequencing of that section. [Cytogen] 15 of 72 Steps of DNA Replication (Legit) Gene Expression requires several steps: 1. DNA replication occurs during the S phase of the 1. Transcription = Synthesizes an RNA molecule cell cycle. 2. At each replication fork, helicase unwinds the DNA 2. Translation = Uses the information in the RNA to and primase builds a short RNA primer. manufacture a protein by aligning and joining 3. DNA polymerase adds bases to the RNA primer, specified amino acids and hydrogen bonds hold them together, stabilizing the structure. 3. Folding of the protein into specific 3-D form 4. DNA polymerase can only add DNA in a 5' to 3' direction. 5. Bases in the parental and new strand hydrogen Transcription Factors bond to form the new double helix. Interact and form an apparatus that binds DNA at 6. The new strand is checked for errors and the RNA certain sequences primers are replaced with DNA. Initiates transcription at specific sites on 7. Ligase joins the sugar-phosphate backbone. chromosomes 8. DNA replication is discontinuous because DNA Respond to signals from outside the cell polymerase can’t readily replicate strands that run Link the genome to the environment in opposite directions. Mutations in transcription factors may cause a 9. DNA replication occurs simultaneously at several wide range of effects points on each human chromosome called Replication Bubbles. Steps of Transcription Transcription is described in three steps: ○ Initiation Enzymes in DNA replication ○ Elongation Helicase unwinds parental double helix. ○ Termination Binding proteins stabilize separate strands. In transcription initiation, transcription factors and RNA polymerase are attracted to a Promoter Primase adds a short primer to the template RNA polymerase joins the complex, binding in strand. front of the start of the gene sequence In transcription elongation, enzymes unwind the DNA polymerase binds nucleotides to form new DNA double helix. strands. ○ Free RNA nucleotides bond with exposed complementary bases on the DNA template Ligase joins Okazaki fragments and seals other strand. nicks in the sugar-phosphate backbone. ○ RNA polymerase adds the RNA nucleotides, in the sequence the DNA specifies. A terminator sequence in the DNA indicates where Activities at the Replication Fork the gene’s RNA-encoding region ends. 1. Helicase binds to origin and separates strands. ○ DNA template strand - 3´ C C T A G C T A C 5´ 2. Binding proteins keep strands apart. ○ Transcribed RNA 5´G G A U C G A U G 3´ 3. Primase makes a short stretch of RNA on the DNA ○ Coding DNA sequence - 5´ G G A T C G A T G 3´ template. 4. DNA polymerase adds DNA nucleotides to the RNA primer. RNA Processing 5. DNA polymerase proofreading activity checks and In eukaryotes, mRNA must exit the nucleus to replaces incorrect bases. enter the cytoplasm. 6. Continuous strand synthesis continues in a 5’ to 3’ Several steps process pre-mRNA into mature direction. mRNA. 7. Discontinuous synthesis produces Okazaki ○ A methylated cap is added to the 5’ end. fragments on the 5’ to 3’ template. Recognition site for protein synthesis 8. Enzymes remove RNA primers. Ligase seals ○ A poly A tail is added to the 3’ end. sugar-phosphate backbone. Necessary for protein synthesis to beginand stabilizes the mRNA Splicing occurs. Gene Expression ○ Introns (“intervening sequences”) are DNA of the human genome which encodes protein removed. is called the Exome. ○ Ends of the remaining molecule are spliced ○ However, this represents only a small part of together. the genome. ○ Exons are parts of mRNA that remain, Much of the human genome controls protein translated into amino acid sequences. synthesis. ○ Note that introns may outnumber and ○ Including the time, speed, and location outsize exons. Genes encode 20,325 types of proteins. mRNA is proofread and the mature mRNA is sent Production of protein from instructions on the DNA out of the nucleus. [Cytogen] 16 of 72 Alternate Splicing Elongation Mechanism of combining exons of a gene in  The large ribosomal subunit joins. different ways: ○ Cell types can use versions of the same  GGA bonds to its complementary anticodon, which protein in slightly different ways in different is part of a free tRNA that carries the amino acid tissues glycine. o Two amino acids attached to their tRNAs Translation align. Assembles a protein using the information in the mRNA sequence  Positions of the sites on the ribosome remain the ○ Particular mRNA codons correspond to same, cover different parts of the mRNA as the particular amino acids ribosome moves. Occurs on the ribosome o The P site bears growing amino acid chains. o The A site holds the next amino acid to be The Genetic Code (p.182-184 table) added to the chain. The correspondence between the chemical languages of mRNA and proteins  Amino acids link by a peptide bond, with the help In the 1960s, researchers used logic and clever of rRNA that functions as a ribozyme. experiments on simple genetic systems to decipher the genetic code  The polypeptide builds one amino acid at a time. o Each piece is brought in by a tRNAwhose It is a triplet code. anticodon corresponds to a consecutive ○ Three successive mRNA bases form a codon. mRNA codon as the ribosome moves down ○ There are 64 codons. the mRNA. ○ Altering the DNA sequence by one or two bases produced a different amino acid Termination sequence due to disruption in the reading  Occurs when a stop codon enters the A site of the frame. ribosome Adding a base at one point and deleting a  A protein release factor frees the polypeptide base at another point disrupted the  The ribosomal subunits separate and are recycled reading frame between the sites.  New polypeptide is released It is non overlapping. The closer to the end of the gene, the longer the ○ In an overlapping DNA sequence, certain polypeptide amino acids would follow others, constraining protein structure Protein Structure It includes controls. Proteins fold into one or more 3-D shapes or ○ Includes directions for starting and stopping Conformations translation  Based on attraction and repulsion between An open reading frame does not include atoms of proteins, and interactions of proteins a stop codon with chemicals in the environment It is universal. There are four levels for protein structure: ○ Evidence that all life evolved from a common  Primary(1°) structure ancestor the sequence of amino acids in a Different codons that specify the same polypeptide chain amino acid are termed synonymous codons  Secondary(2°) structure Nonsynonymous codons encode loops, coils, sheets, or other shapes different amino acids formed by hydrogen bonds between neighboring carboxyl and amino groups Translation—Building a Protein Requires mRNA, tRNAs with amino acids, ribosomes,  Tertiary(3°) structure energy molecules (ATP, GTP) and protein factors three dimensional forms shaped by bonds between R groups, interaction between R Initiation groups and water  The leader sequence of the mRNA forms H bonds with the small ribosomal subunit.  Quaternary(4°) structure protein complexes formed by bonds  The start codon (AUG) attracts an initiator tRNA between separate polypeptides that carries methionine.  This completes the Initiation Complex. [Cytogen] 17 of 72  Protein Folding WEEK 5: CHAPTER 5 Proteins begin to fold after the amino acid chain Mutations may occur spontaneously or by exposure to winds away from the ribosome. a chemical or radiation. First few amino acids in a protein secreted in a membrane form a “signal sequence.” An agent that causes a mutation is called a Mutagen. o Leads it and the ribosome into a pore in the ER membrane A mutation is a change in a DNA sequence that is rare o Not found on proteins synthesized on free in a population and affects the phenotype. It includes ribosomes single base changes, deletions, additions, or moved sequences in genes that encode proteins or in Chaperone proteins regulatory genes. They can involve entire chromosomes.  Stabilize partially folded regions in their correct form Loss-of-function mutations are typically recessive  Prevent a protein from getting stuck in an and decrease the abundance of the encoded protein. intermediate form  Developed into drugs to treat diseases that result Gain-of-function mutations tend to be dominant and from misfolded proteins alter the encoded protein. Protein Misfolding (table p.189) A mutation refers to genotype; mutant refers to Misfolded proteins are tagged with ubiquitin. phenotype. Protein with more than one tag is taken to a Proteasome (a tunnel-like multiprotein structure) Identifying how a mutation causes symptoms has ○ As the protein moves through the tunnel, it is clinical applications straightened and dismantled. Examples of mutations that cause disease: ○ Proteasomes also destroy properly folded o Beta globin gene proteins that are in excess or no longer o Collagen genes needed. Proteins misfold from a mutation, or by having Causes of Mutation more than one conformation. ○ A mutation alters the attractions and repulsions A Spontaneous Mutation occurs during normal between parts of the protein. genetic and metabolic functions in the cell resulting ○ Prion protein can fold into any of several from internal factors such as an error in replication, conformations. mistakes in recombination, misrepair of damaged Moreover, it can be passed on to other DNA, and base modification. proteins upon contact, propagating like an infectious agent. It may occur when rare tautomers of bases are incorporated into replicating DNA, causing a base In several disorders that affect the brain, the mismatch. The spontaneous mutation occurs at misfolded proteins aggregate. low frequency but is more likely in or near ○ The protein masses that form clog the repetitive or symmetrical DNA sequences. proteasomes and inhibit their function. Different proteins are affected in different disorders. An Induced Mutation is caused by mutagens, many are also carcinogens and cause cancer. Researchers The Importance of Proteins use mutagens, such as chemicals or radiation, to Genes encode proteins, which are synthesized using cause mutations in genes, which they study to shed amino acids that come from the diet. Biological light on normal gene function. proteins are long molecules consisting of 20 types of amino acids. Can be accidental when exposure to mutagens comes from nuclear accidents, radiological An adult can synthesize 12 of the 20 amino acids, the weapons, and medical treatments. Whereas, other 8 are essential which can come from the diet. natural environmental mutagens include ionizing radiation such as cosmic rays, chemicals, and An amino acid has a central carbon atom bound to an radioactive isotopes in rocks. amino (NH2) group, an acid (COOH) group, a hydrogen atom (H), and an “R” group that is different in The Ames test evaluates the mutagenicity of a the 20 amino acid types. substance. Chains of amino acids are polypeptides. Proteins Site-directed mutagenesis is a PCR-based serve many vital functions; some of these functions are technique using primers with intentional contractile, regulatory, enzymatic, structural, transport, mismatches to engineer and amplify DNA immunity, and clotting. Deficiency or absence of a sequences containing specific mutations. protein devastates health. [Cytogen] 18 of 72 Types of Mutation  High levels of oxidants occur when eating 1. Missense mutation - replaces one amino acid fava beans or taking certain antimalarial with another drugs. 2. Nonsense mutation - changes a codon for an DNA Repair amino acid into a stop codon Errors in DNA replication or damage to DNA creates truncated proteins that are often create mutations. nonfunctional ○ May result in cancer stop codon that is changed to a coding Fortunately, most errors and damage are repaired. codon lengthens the protein Organisms vary in their ability to repair DNA. 3. Deletion - removes genetic material– Male infertility: Tiny deletions in the Y Types of DNA 1. Photoreactivation Repair 4. Insertion - adds genetic material– Gaucher  Enzymes called photolyases use light energy to disease: Insertion of one base break the extra bonds in a pyrimidine dimer.  Enables UV-damaged fungi to recover from 5. Frame shift - the disruptions of the reading frame exposure to sunlight when nucleotides change not in multiples of 3.  Humans do not have this type of repair 6. Duplication - insertion of identical sequences side by side 2. Excision Repair  Pyrimidine dimers and surrounding bases are 7. Expanding Repeats - insertion of triplet repeats removed and replaced. leads to extra amino acids. It can explain “anticipation,” a disease that worsens with each  Humans have two types of excision repair generation. The number of repeats correlates with  Nucleotide excision repair replaces up to earlier onset and more severe phenotype. 30 nucleotides that have undergone Different types of mutations can cause the chemical, ultraviolet, or oxidative same single-gene disorder. damage ○ Ex: Hypercholesterolemia  Base excision repair replaces one to five nucleotides that have had oxidative The Importance of Position