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How is dna packaged?

How is dna packaged?

Description

Chapter 1


How is dna package?



∙ Genetics – the study of heredity and the variation of inherited  characteristics

∙ Molecular Biology – the study of the formation, structure, and  function of macromolecules essential to life, such as nucleic  acids and proteins  

∙ Protein as the molecule of heredity  

o Very diverse and on chromosomes  

o DNA was not…

 Chemically diverse (only on chromosomes)  

 Scientists thought DNA just provided structural  

stability to chromosomes  

o Early experiments had to show that DNA was the molecule  of heredity and prove that protein was not  

∙ Evidence that DNA was the molecule of heredity

o R (rough) colonies do not cause pneumonia  


What is an example of molecular biology?



Don't forget about the age old question of What is scientific ecological knowledge?
We also discuss several other topics like What was jean baptiste lamarck's theory of evolution?

 They are not protected from the host immune system o S (smooth) colonies are protected by a gelatinous capsule  and cause pneumonia in hosts  Don't forget about the age old question of Why is having a pet a good thing?

o “Something” passed from the S to the R strain confers  virulence to R  

o An experiment was conducted to determine what was  passed from S to R  

 Three Treatments  

 1. RNA Removed  

 2. Protein Removed  

 3. DNA Removed  

 In 1 and 2, R and S colonies were found, but in 3 only R was found in the dish  

o Determined that DNA is the molecule of heredity ∙ DNA Structure  

o DNA has a structure called a double-stranded helix   Sugar phosphate backbone  

 Paired nucleotides  


What are the active regions on chromosomes?



o Four nucleotides (or bases) Don't forget about the age old question of What are the roles of marketing in strategic planning?

 Adenine  

 Thymine  

 Guanine

 Cytosine  

o Complementary Base Pairing or Watson-Crick Base Pairing   Adenine and Thymine  Don't forget about the age old question of Identify the four major ocean basins.

 Guanine and Cytosine  

∙ Genotypes produce Phenotypes

o Genotype – the DNA sequence  

o Phenotype – the observed trait or characteristic  o DNA to Proteins is the central dogma of molecular biology  o Path from DNA to Population Characteristics

 DNA  

 RNA  

 Proteins

 Protein Interactions

 Cell Phenotypes

 Organism Phenotypes  

 Population Characteristics  

∙ Genes code for proteins 

o Genetic information contained in the nucleotide sequence  of DNA specify genes for particular types of proteins  o Proteins control the physical, chemical, and mechanical  properties of cells  

o Enzymes are proteins that are biological catalysts essential for metabolic activities in the cell  

o In 1908, Archibald Garrod proposed that enzyme defects  result in inborn errors of metabolism are hereditary  diseases  

∙ Inborn Errors of Metabolism  

o Metabolic Pathway

o Don't forget about the age old question of What technique uses an injection?

o Alkaptonuria (example)

 The symptom was black urine  

 Excess of homogentisic acid  

 Defect was homogentistic acid 1,2 dioxygenase

∙ Metabolic enzymes work in pathways or series of biochemical  reactions  

o Enzymes catalyze the conversion of substrate (metabolite)  to product  

o If an enzyme is inactive or defective, the pathway gets  blocked  

∙ Central Dogma (DNA to RNA to Protein)

o DNA to RNA - Transcription

o RNA to Protein – Translation  

∙ Genotypes produce phenotypes but environment makes a big  difference in the final outcome  

o Environmental factors affect all stages  

∙ Genes and Environment  

o Almost every trait has a genetic and an environmental  component 

 Ex. Height, hair color, eye color  

o Most complex traits are affected by multiple genetic and  environmental factors

 Ex. PKU mutants + diet = phenotype  

o Often several genes are involved in genetic disorders and  the severity of diseases often depend upon genetics and  the environment  

∙ The basics of genetics and molecular biology are shared by all  organisms  

o All organisms on earth share many features of the genetic  apparatus and many aspects of metabolism  

 Including a highly conversed genetic code  

o This is because all living organisms descended from a  common ancestor  

 Differences between similar genes in two organisms  are used to reconstruct relationships  

o Evolution occurs whether a population of organisms with a  common ancestry gradually changes in genetic  

composition over time  

∙ MAJOR CONCEPTS 

o DNA is the molecule of heredity  

o Chemical reactions in the cell, catalyzed by proteins,  contribute to phenotypes  

o Genotype + environment = phenotype  

Chapter 2  

∙ Mendel’s Genetic Hypothesis 

o 1. Each parent contributes to its progeny distinct elements  of heredity  

 Mendel referred to them as factors but they were just genes  

o 2. Factors (genes) remain unchanged (don’t blend) as they  pass through generations  

o Mendel quantified the outcome from his crosses to test his  hypothesis  

 He determined the numerical ratios of traits resulting from the crosses

∙ Pea Plant Importance

o There were many known varieties  

o They have easily distinguished traits

o The plants are self fertile  

o Artificial fertilization was possible  

o True-Breeding Varieties – self-fertilized plants produce only  progeny like themselves  

 Offspring would look exactly like the parents  

∙ Artificially Fertilizing Pea Plants  

o Take two true-breeding plants

 Ex. Round vs. Wrinkled Seeds

o Cut off male parts (anthers) of one parent plant

 Need to prevent self-fertilization  

o Brush with pollen of other parent plant  

o Now you have a first generation hybrid of the two parent  types  

 All F1 (first generation) offspring demonstrate one  parent trait (dominant trait)  

 The F2 (second generation) offspring demonstrate  both parent traits (dominant and recessive)  

o Reciprocal crosses produce the same offspring  

 Reciprocal cross – outcome of the cross is  

independent of whether the trait came from the male or female parent  

 Dominant – trait shown in hybrids  

 Recessive – trait masked in hybrids  

∙ Mendel’s Conclusions from his Pea Plant Experiment  o F1 hybrids only express the dominant trait 

o In the F2 generation, the recessive trait reappeared and  there were plants with the dominant trait and plants with  the recessive trait  

o In the F2 generation, the ratio of dominant to recessive  was 3:1 

∙ Self-Fertilization of the F1 generation

o All the dominant trait plants (3/4) that self-fertilized only  created dominant trait plants and their offspring also  created dominant trait plants  

o Of the recessive trait plants (1/3), 1/3 (of the 1/3)  produced recessive trait plants and the other 2/3 produced  a mix of recessive trait and dominant trait plants in the  ratio of 3:1  

∙ Explanation of Mendel’s Data  

o Genes come in pairs 

 Each parent has two copies of each gene  

o Gametes are reproductive cells that contain only one copy  of each gene  

o Principle of Segregation – genes separate into reproductive cells (one to each)  

o Gametes unite at random in fertilization  

∙ Important Terminology  

o Genes – the heredity determinant of the trait  

o Alleles – different forms of one particular gene (dominant  or recessive)  

o Heterozygous – the genotype in which the members of a  pair of alleles are different

o Homozygous – the genotype in which the members of a  pair of alleles are the same  

 Two Types – Homozygous dominant or homozygous  recessive

o Genotype – the genetic constitution of the individual  o Phenotype – the observable characteristic of the individual  ∙ Test Crosses

o A test cross is a cross between a dominant phenotype with  an unknown genotype and a recessive phenotype  

individual for the purpose of determining the genotype of  the dominant phenotype individual  

∙ Dihybrid Cross traits  

o Dihybrid is an F1 individual hybrid for two characteristics  o The phenotype ratio in dihybrids cross are 9:3:3:1  9 – dominant and dominant  

 3 – recessive and dominant  

 1 – recessive and recessive  

o Independent Segregation results in an equal frequency of  all four possible types of gametes  

 If given AaBb x AAbb separate the As and the Bs and  cross separately  

∙ Probability in Mendelian Genetics  

o Addition Rule – the probability of one or the other of two  mutually exclusive possibilities, A or B, is the sum of their  separate probabilities  

 A OR B

o Multiplication Rule – the probability of two independent  possibilities, A and B, occurring at the same time  

 A AND B

∙ Important Independent Events in Genetics

o Independent Segregation – Alleles segregate independently into gametes  

o Random Fertilization – gametes pair independently  therefore successive offspring are independent of each  other  

∙ Modern Molecular Genetic Analysis of the Pea

o The gene that determines the shape of a seed encodes an  enzyme, starch-branching enzyme I (SEBI), required to  synthesize a branched-chain form of starch known as  amylopectin  

 Round seeds contain amylopectin and shrink  

uniformly as they dry  

 Wrinkled seeds lack amylopectin and shrink  

irregularly

o Transposable Element – mobile DNA element that can  “hop” in and disrupt a gene  

 In the wrinkled peas, the SBEI gene is disrupted by a  transposable element  

o DNA gel electrophoresis – a method for separating DNA  molecules by size  

∙ Human Pedigree

o Pedigree is a family tree showing phenotypes of individuals o Pedigrees are used to determine individual genotypes and  to predict the mode of transmission of single gene traits 

o Important Symbols

 Shaded in circles are affected  

 Half-shaded circles have heterozygous genotypes  ∙ Autosomal Dominant Inheritance  

o Autosomal means that it is on a chromosome other than a  sex chromosome (X or Y)  

 The trait affects both sexes  

o Every affected person in autosomal dominant inheritance  has an affected parent 

o ½ of the offspring of an affected individual are affected   Can be shown in a punnett square  

o Example: Huntington’s Disease

∙ Autosomal Recessive Inheritance  

o Most affected people have parents who are not affected  Parents are carriers or heterozygous for recessive  allele  

o ¼ of the children of two carriers are affected  

o Example: Albinism

∙ Dominance

o Dominance is a property of a pair of alleles in relation to a  particular phenotype  

o It depends on the phenotype of the trait in question

o Incomplete dominance is when a phenotype of a  heterozygous genotype is intermediate between the  phenotypes of the homozygous genotypes  

 Incomplete dominance means intermediate  

phenotypes 

 It is often observed when the phenotype is  

quantitative rather than discrete  

∙ Multiple Alleles and Codominance  

o Codominance means that the heterozygous genotype  exhibits the traits associated with both homozygous  genotypes  

 Codominance is more frequent for molecular traits  than for morphological traits  

o Multiple alleles is the presence in a population of more  than two alleles of a gene  

∙ Human Blood  

o Blood types are determined by polysaccharides on the  surface of red blood cells  

o There are multiple alleles in human blood (3 alleles)  IA – type A polysaccharide and antigen  

 IB – type B polysaccharide and antigen  

 IO – type O polysaccharide and antigen  

o IA and IB are codominant to each other (AB blood type) o IA and IB are dominant to the recessive IO allele  

o ABO blood types are important for blood transfusions  because blood contains antibodies to the A and B  

polysaccharides  

 An antibody is a protein made by the immune system in response to a stimulating molecules called an  

antigen  

 Reaction of matching antibody and antigen causes  agglutination (clumping) of blood cells  

∙ Expressivity and Penetrance  

o Mutant genes aren’t always expressed in the same way   The effect could be modified by other genes or there  may be an environmental component  

o Variable expressivity means that the same mutant gene  can cause a sever defect in one individual, but a mild  defect in another  

 Variable expressivity is used when a range of  

phenotypes are produced by a single genotype 

 Same genotype  variable phenotype  

o Penetrance refers to the proportion of individuals whose  phenotype matches their genotype for a given trait

 A genotype that always results in a phenotype has a  penetrance of 100%

o Incomplete penetrance is used when discrete categories  are defined  

∙ Epistasis  

o Epistasis refers to any type of gene interaction that results  in the expected ratio from a dihybrid cross being modified  into some other ratio  

 Epistasis refers to gene interactions

o There must be more than one gene involved for epistasis  to occur  

o Epistatic interactions happen when the two genes both  contribute to a single trait being studied  

o In epistasis a change in the expected ratios of phenotypes  is observed  

 If there is a deviation from the expected 9:3:3:1,  check for epistasis 

∙ The Principle of Complementation  

o Complementation – if two recessive mutations are alleles of different genes, then the phenotype of an individual that  contains only one copy of each mutation will exhibit the  wildtype (normal) phenotype  

 Example: ppHH x PPhh

o Fail to complement: If two mutations occur on the same  gene, then the phenotype of an organism that contains one copy of each mutation has the mutant phenotype  

 Example: ppHH x ppHH

o Testing for complementation allows you to know if more  than one gene is needed for the observed phenotype   Can reveal whether two recessive mutations are  alleles of different genes  

 Can be repeated with many pure-breeding mutant  strains to determine how many genes are involved in the phenotype  

 Complementation groups contain genotypes that  have the same mutated gene

o Complementation relates to epistasis  

∙ Major Concepts 

o Inherited traits are determined by genes present in the  gametes

o Genes are inherited in pairs, one from each parent  o Alleles are forms of the same gene that differ in DNA  sequence  

o Dominant traits are expressed, recessive traits are masked

o Independent assortment of traits and independent  fertilization result in Mendel’s observed ratios

o Autosomal dominant inheritance is when only one mutant  allele is necessary to produce a phenotype  

o Autosomal recessive inheritance is when two mutant  alleles are necessary to produce a phenotype  

o Incomplete dominance relates to intermediate phenotypes  o Codominance means both traits are shown  

o Variable expressivity is how much of a phenotype shows up for a given genotype  

o Penetrance affects whether or not a phenotype shows up  for discrete traits, with a particular phenotype  

o Complementation tests are used to determine whether two strains with the same mutant phenotype have mutations in the same gene or different genes  

Chapter 3  

∙ Somatic Cells

o Somatic cells are cells of the body (basically everything  except gametes)

o Diploid means there are two copies of each chromosome in each diploid cell  

o Human somatic cells contain 23 pairs of chromosomes for  a total of 46

∙ Gametes

o Gametes are reproductive cells

 Ex: Sperm, oocytes, and pollen

o Haploid means there is one copy of each chromosome in  each haploid cell

o Haploid gametes unite in fertilization to produce a diploid  embryo  

∙ Mitosis  

o Mitosis is a process of chromosome segregation and cell  division that results in two genetically identical diploid  daughter cells  

∙ Cell Cycle

∙ Chromosomes during the cycle  

∙ Nomenclature in Chromosome Replication  

∙ Interphase (G1, S, G2)

o Everything except mitosis 

o Chromosome are not lined up and are not as condescend ∙ Stages of Mitosis  

o Prophase  

 Chromosomes condense  

 Chromatids are attached to each other at the

centromere

o Metaphase

Homologous 

 Mitotic spindle forms and attaches to the chromatids  near the centromere at a structure called a  

kinetochore  

 Chromosomes move to the metaphase plate  

 Proper chromosome alignment is essential  

o Anaphase

 Centromeres divide  

 Sister chromatids separate and move to opposite  

poles  

o Telophase and Cytokinesis  

 Nuclear membrane forms around each compact  

group of chromosomes  

 Chromosomes become de-condensed  

 In cytokinesis, the cell divides to form two daughter  cells

o Mitosis vs Meiosis 

 Mitosis produces duplicate somatic cells

 Meiosis produces haploid germ cells

∙ Meiosis  

o Meiosis is a process of chromosome segregation and cell  division that results in four haploid daughter cells  

 This requires two divisions, meiosis I and meiosis II,  and is known as reductional division

o Meiosis I  

 One cell duplicates its DNA, then divides, but the  chromosomes are handles differently from mitosis  

 Prophase I – chromosomes condense, pair, and cross  over

∙ Synapsis – pairing of homologous  

chromosomes  

∙ Chiasmata – connections between homologous  

chromosomes  

o Results from physical exchange of DNA  

between chromatids of homologous  

chromosomes  

o Two important purposes of chiasmata

 Stick the homologous  

chromosomes together so the  

chromosomes can align correctly at

the metaphase plate in Metaphase  

I  

 Exchange genetic information  

between homologs to increase  

genetic diversity  

∙ Crossing over (or recombination) is a genetic  

exchange between homologous chromosomes  

 Metaphase I – bivalents align at the center  

∙ Bivalents are a pair of homologous  

chromosomes (each consisting of two  

chromatids) associated with meiosis I  

∙ Alignment is random  

o Independent assortment of genes on  

separate chromosomes  

 Anaphase I – chromosomes separate to the poles

 Telophase I – cells get set up for Meiosis II  

∙ During telophase, the spindle breaks down  

∙ In some species, the nuclear envelope briefly  

forms around each group of chromosomes  

o Meiosis II  

 Two diploid cells will become four haploid cells  

 Because crossing over in meiosis I, the two sister  chromatids (still attached) are not identical along  

their entire lengths

∙ Individual cells received different homologous  

chromosomes

 Prophase II – spindle reforms  

 Metaphase II – chromosomes align  

 Anaphase II – centromeres split and chromatids  

separate

 Telophase II – cells divide and nuclei re-form  

∙ Four new cells are formed  

∙ Chromosomes are diverse

o Chromosome size and structure varies a lot between  organisms

o Circular or linear  

o Big (millions of base pairs) or small (thousands of base  pairs)

o Nuclear or in organelles (mitochondria and chloroplasts) ∙ Chromosome number varies between species

o Chromosome complement is the complete set of  chromosomes  

o Number of chromosomes doesn’t have anything to do with  species “complexity”

∙ Chromosomes are a compact way of packaging DNA  o Chromosomes are composed of DNA and protein o Chromatin is the term for the DNA and protein that the  chromosome consists of  

o There is about 2 meter of DNA in every cell  

∙ How DNA is packed  

o The major chromatin structures

∙ ∙ Metaphase chromosomes are very tightly condensed  o The process of chromosome condensation is not well  

understood  

o This compaction is necessary because otherwise the  

chromosomes would become entangled and break during  

mitosis  

∙ Histones are a major protein component of chromatin  

o Histones are the structural unit of the “bead” in a  

nucleosome  

o There are five major types of histones

 H1

 H2A

 H2B

 H3

 H4

o Positively charged amino acids in histones allow binding to  the negatively charged DNA  

o Histones from different organisms are very similar  

 Cow and pea H4 differ jn only 2/102 amino acids  

∙ Regions of chromosomes  

o Heterochromatin – in interphase, these regions are  

compact  

 Heterochromatin have few genes and long stretches  

of repeat sequences called satellite DNA  

o Euchromatin – condensed only during mitosis or meiosis   In interphase, contains many active genes  

o Telomere – essential for maintenance of chromosome ends

o Centromere – essential for proper chromosome segregation

∙ Chromatin Condensation Related to Function  

∙ Eukaryotic chromosomes exist in four major types based on the  

position of the centromere

∙ The centromere is essential for chromosome segregation

o Centromere – DNA region essential for aligning  

chromosomes during metaphase  

o Kinetochore – DNA and protein complex that includes the  

centromere  

 The spindle attaches at the kinetochore  

∙ Telomeres are essential for chromosomes stability 

o A telomere is a region of highly repetitive DNA at the end  

of each linear chromosome  

o During DNA replication, a short strand of single stranded  

DNA (ssDNA) is left over

o The enzyme telomere lengthens the telomere and allows  DNA polymerase to finish replicating the chromosome  o Telomeres are essential for chromosome stability   Prevent loss of genes from ends of chromosomes   Prevent ssDNA from sticking chromosomes together  ∙ Chromosomes Theory of Heredity

o Genes are located in chromosomes  

o After Mendel was rediscovered, it was assumed that genes  were physically located on chromosomes, based on the  mechanisms of segregation and independent assortment of chromosomes in meiosis  

o But, the first evidence that genes were on chromosomes  came from experiments looking at patterns of transmission in sex chromosomes  

o Basically, the sex of the individual correlated with the  presence or absence of a particular chromosome  

∙ X and Y Sex Chromosomes

o Male and female sexes in humans and many (but not all)  other animals is determined by the X and Y chromosomes  o Heterogametic sex – has two different sex chromosomes,  for example, x and y  

 Males has XY sex chromosomes

 Hemizygous – only has one copy of a gene  

o Homogametic sex – has two of the same sex  

chromosomes, for example xx  

 Females have XX sex chromosomes  

∙ Sex Linked Pattern of Inheritance  

o In Mendel’s reciprocal crosses it did not matter which trait  was present in the male parent and which in the female  parent – progeny phenotype ratios were the same  

o Thomas Hunt Morgan found an exception to this rule – the  Drosphilia white gene  

 The Y chromosome, which specifies male files, does  not have a copy of the white gene on it  

 The X chromosome does  

∙ Sex Linked Traits in Human Populations  

o The genes that confer these traits are on the X  

chromosome  

o Since human males, only have one copy of the X  chromosome, they don’t have a second copy of any X linked gene to compensate for a mutant allele  

∙ How to tell if a pedigree indicates sex linked inheritance o Most of the affected individuals are males

o The mother of the affected individual is a carrier (trait is on

the mother’s side of the family)

∙ Nondisjunction  

o In nondisjunction, two chromosomes fail to separate from  

each other during meiosis  

o One cell gets two copies, while the other cell gets zero

∙ Major Concepts

o The cell cycle includes a synthesis (S) phase where the  chromosomes are duplicated and mitosis (M) phase when  the chromosomes are separated to two new cells

o Mitosis produces identical diploid somatic cells  o Meiosis consists of one replication of the chromosomes, but two divisions of the nucleus  

 Therefore, four haploid cells are produced because of crossing over, none of them are identical  

o Random alignment of bivalents in meiosis I is the reason  for independent assortment of traits on non-homologous  chromosomes  

o Chromosomes are a compact way of storing DNA  o The extreme condensation of the metaphase chromosome  is necessary to avoid chromosome breakage during cell  division

o The centromere and telomeres are essential for  chromosome segregation and stability  

o Sex linked genes can be identified by their patterns of  inheritance  

o Not all animals use the XY system of sex determination

Chapter 4

∙ Review Concepts

o Locus – physical location of a gene on a chromosome o Homologous pairs of chromosomes often contain  alternative forms of a given gene (alleles)

o Alleles of genes segregate at meiosis I with their  homologous chromosomes

o Alleles of different genes assort independently into  gametes if they are unlinked  

∙ Random Alignment of non-homologous chromosomes in  metaphase I cause independent assortment of genes

∙ Linkage

o Genes can be linked (inherited together) if they are located in close proximity on the same chromosome 

o Crossing over of homologous chromosomes in prophase I of meiosis causes gene combinations to recombine and  produce different allele combinations than the parental  types  

 AKA Recombination 

∙ Recombination is caused by crossing over

o Chromosome breakage and re-joining that happens  between genes

∙ Linkage, Recombination, and Genetic Maps

o Genes have well-defined positions along a chromosome  (called a locus) 

o Linkage is estimated by the frequency of recombination  50% of recombination frequency is unlinked (same as independent assortment)

o Frequency of recombination serves as a measure of genetic distance between genes and allows us to construct genetic maps  

 Ex. The positions of genes along chromosomes  

 1% recombination = 1 map unit (cM – centiMorgan) ∙ Linked Alleles

o Two Basic Configurations  

 Cis (or coupling) configuration, where the wild type  alleles are on one chromosome and the mutant  

alleles are on the other chromosome  

 Trans (repulsion) configuration, where each  

chromosome has one wild type and one mutant allele

∙ Gametes produced in meiosis have alleles in either a parental or  a recombinant form

∙ Linkage

o Parental types are the allele combos that match the  parent’s chromosomes

 In linkage problems, these will always be the most  common types 

o Recombinant types are allele combos produced by crossing over  

 In linkage problems, these are the least common  types 

o Genes are unlinked if ½ parental and ½ non-parental   This is the expectation for independent assortment  o Recombination frequency = number recombinant/total  ∙ Recombination

o Recombination between linked genes occurs at the same  frequency in cis or trans configuration

o Recombination frequency is specific to gene pair  o Recombination frequency increases with increased  distances between genes

o Maximum genetically observable frequency of  

recombination between any two genes is 50%  

 At that point, complete mixing (independent  

assortment) has occurred due to multiple crossover  events  

∙ Genetic Maps

o Genetic maps are diagrams that show the location of every gene on every chromosome  

o Genetic maps allow researchers to locate and identify the  genes responsible for diseases and mutant phenotypes

∙ Recombination frequencies are used to construct genetic maps o Gene mapping methods use recombination frequencies  between alleles in order to determine the relative distances between them  

o The higher the recombination frequencies the further the  distance between genes  

o Distance measurement  

 1 map unit = 1 percent recombination  

 1 map unit = 1 cenitMorgan (cM)

∙ Ordering genes using recombination frequencies  

o When there is <10% recombination between two genes,  the genes are pretty close together 

 Therefore it is unlikely there have been any double  crossovers between the two  

o Map distances of <10 can be added to get the total map  distance between two genes  

∙ Physical distance is not always correlated with map distance o Observed recombination value is an underestimate of the  cross-over frequency

o Sometimes no crossing over occurs  

o Heterochromatin has much less crossing over than  euchromatin

∙ Double Crossing Over

o If a double cross-over occurs between two genes,  

recombination (of those two genes) will not occur 

o Double cross-overs can be seen in three-point (three gene)  crosses

 Two exchanges taking place between genes, with  

both involving the same pair of chromatids  

∙ Mapping Genes using three factor crosses

o Three factor crosses allow the order of genes on a  

chromosome to be determined  

o Map distances between genes can also be calculated using three factor cross data

∙ Strategy for analyzing three factor crosses 

o 1. Identify the most common classes

 These are the parental (non-recombinant) classes

o 2. Identify the next most common classes  

 These are the result of single crossovers  

o 3. Identify the two rarest classes  

 These are the result of double crossover  

∙ Double cross-over results in exchanged of the middle pair of two  alleles 

o Key to solving the order of genes in a three factor cross:  The gene that is exchanged in the double crossover  class = the middle gene

∙ Identifying the gene in the middle (“odd man out” shortcut) o Once you have identified the double crossover class, look  for the gene that does not match the parentals

 That is the gene in the middle  

∙ Result of single crossovers in a triple heterozygote ∙ Determining map distances in a three factor cross o 1. Write the genes in the correct order  

o 2. Group the reciprocal crosses (they will have similar  frequencies)

o 3. Add up the single and double recombinants for each  class

o 4. Divide by the total to get the map distance

o 5. Make a map  

∙ Double strand break model for recombination 

o 1. Double strand break  

o 2. Strand invades – involves base pairing, and therefore  homology  

o 3. New DNA is synthesized to fill in the gap  

o 4. Breakage and re-joining resolves the Holliday junctions

o 5. Crossover between A and B results  

∙ Double Strand Break Repair 

o 1. Double strand break  

o 2. Strand tries to invade – DNA synthesis occurs, but strand is kicked back out

o 3. Double strand break is repaired

o No crossover between A  

∙ Challenges with mapping human genes

o Most genes that cause genetic disease are rare, and are  observed in only a small number of families  

o Most mutant genes are recessive and not detectable in the  heterozygotes  

o Number of offspring is pretty small

 Segregation can’t be detected in single sibships (the  siblings of a set of parents)

o Experimenters can’t perform test crosses

∙ Genetic polymorphisms can be used to map human traits  o Polymorphism – a genetic difference that is relatively  common in a population  

o Most of these polymorphisms do not cause any disease or  particular trait  

 But, they can be linked to disease causing alleles  o Polymorphisms provide convenient genetic markers on  each of the chromosomes  

∙ SNP – Single Nucleotide Polymorphism  

o SNPs are instances in which a single nucleotide site differs  from one individual to the next  

 Each individual has a specific assortment of SNPs  o SNPs are the most common form of genetic difference  between people  

o SNP maps are being compiled to associate SNPs with  disease states and genetic risk  

 Most diseases are affected by multiple genes –  

patterns of SNPs can be used to identify them  

o SNPs are also used to type and track populations of wild  animals  

o Single Nucleotide Polymorphisms – a single base variation  between two otherwise identical DNA sequences  

 Most SNPs occur in the non-coding regions between  genes  

 More thatn 3 million SNPs are common in the human  population

∙ A DNA microarray has >10,000 DNA probes (short DNA  sequences) representing the genome stuck to it  

o In the case of a SNP chip, the DNA sequences will  

correspond to common SNPs found in the human  

population  

o Traditionally cheaper and faster

∙ Restriction Enzymes

o Restriction enzymes are proteins that cut DNA at specific  sequences

o Restriction fragment length polymorphism (RFLP) is a  single base variation between two otherwise identical DNA  sequences that causes a change in a restriction site  

o When DNA from a restriction digest is run on a gel, the  resulting sizes of the DNA fragments can be seen  

∙ Simple sequence repeats (SSRs)

o Simple sequence repeats are another type of DNA  

polymorphism  

o SSRs are tandemly repeated short DNA sequences  common in the human genome  

o Exact length of each SSR varies from person to person  o There are a lot of SSRs in the human genome  

o Simple sequence repeats are alleles that differ in the  number of copies of a short, repeated nucleotide sequence  o Simple sequence repeats (SSRs) are another type of DNA  polymorphism  

 Depending on the number of repeats in an SSR,  

length of a DNA fragment between two restriction  

sites can be different  

o SSR variability is very common

 Most individuals are heterozygous at any given  

position

∙ Genes can be mapped using DNA polymorphisms as phenotypes o When human DNA is run on a gel, the SSR or RFLP  becomes a visible phenotype for each individual and can  be mapped in the same way  

o Importantly, presence of certain SSRs or RFLPs correlate  with disease states, allowing the mapping and  

identification of disease genes in human populations  

∙ DNA polymorphisms can be used to map disease genes o The locations of many different DNA polymorphisms in the  human genome are known

o There are many diseases and traits for which the  

underlying genetic causes are unknown  

o Many projects are currently underway to find disease  genes that show linkage to specific DNA polymorphisms  ∙ Major Concepts 

o Genes are linked if they are in close proximity on the same  chromosome  

o Linked genes do not undergo independent assortment  o Frequency of recombination is a measure of the genetic  distance between genes, and it used to order or “map”  genes on chromosomes  

o Three factor crosses are used to order genes on  

chromosomes and to determine the location of newly  isolated mutations  

 Use the “odd man out” strategy for solving three  

factor crosses

o Recombination is thought to occur by a “break and repair”  mechanism  

o Recombination occurs in meiosis and results in new  combinations of alleles  

o The human genome is really variable  

 Most variations are polymorphisms: SNPs, RFLPs,  

SSRs

o DNA polymorphisms are phenotypes that can be used to  map genes, just like visible phenotypes  

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