Genetics 2153 Review Main Points Chapter 1s3.amazonaws.com/prealliance_oneclass_sample/2lzKvbJ52e.pdf · 2014-06-18 · • Chi-Square (2.5) o allows for scientist to objectively

Genetics 2153 Review Main Points

Chapter 1• Chromosome packing

o DNA wrapped around histone= nucleosomeo Bunch of nucleosomes together= chromatino Chromatin form loops and pack super tightly together forming the chromosome

Double helix

Nucleosomes

Chromatin (solenoid structure)

Tightly condensed Chromatin

Chromosome

• Pairs 1-22 in a human karyotype are the autosomes, pair 23 is the sex chromosome

o Chromosomes same length= XX femaleo Chromosome different length= XY male

• Central dogma of molecular biologyo Francis Cricko Describes flow of hereditary info

o• Lead to changes in allele frequencies in a population over time

o Natural selection : best adapted characteristic increase in a populationo Migration : movement of members between populations alter allele frequencies

Changes because different populationso Mutation : addition of allelic variants increasing diversity of population, serve as “raw material”

of evolutionary change o Random genetic drift: the random change of allele frequencies due to chance in rapidly

mating populations Changes because one population mates a lot

• Probability

o Predicting outcome (diseased child) problemso Predicting phenotype/genotype

Chapter 2• Test cross Unknown genotype with pure breeding

o R- x rr RR x rr

• 100% heterozygous • all dominant phenotype

Rr x rr • 50% heterozygous 50% homozygous recessive• 1:1 ratio of dominant to recessive phenotype

• Both pure breeding crosso GG x gg

F1= all heterozygous F2(self-fertilize hetro)= 1:2:1 genotype; 3:1 phenotype

• Framing a hypothesiso Null- observed values not different from expected; chance aloneo Alternative- observed values are different from expected

• Chi-Square (2.5)o allows for scientist to objectively determine whether results are consistent with expectations or

noto large samples: outcomes predicted by chance have a normal (Gaussian) distribution AKA

“bell-shaped curve”o Outcomes are distributed around the mean(µ), average outcome, and the probability of an

experimental outcome gets smaller the further it is from the mean o Probability of particular outcomes is quantified by a measurement called standard deviation()

Norm distribution• 68.2% fall within 1 of mean• 95.4% fall within 2 of mean

An experimental outcome that is more than 2 from the mean shows a statistically significant difference between the observed and expected outcome

o Chi-square Test Analysis 2 = (O E)2/E

• O= observed values• E= expected values

Probability (P) value is how the test is interpreted• P value is the probability that the results of another experiment of the same size

and structure will deviate as much or more from the expected results by chance.• Low 2 values associate with high P values which indicate chance alone likely

explain deviations• P value is dependent on degrees of freedom, df= # of classes-1• P value<.05=5% hypothesis of chance(null) rejected ( to the right on the chi-

square chart)• P value>.05=5% shows significant deviation between observed and expected

results; hypothesis of chance accepted (to the left on the chi-square chart)• P value=.052< critical value 2> critical value

Accept Null Hypothesis

Reject Null Hypothesis

Data deviations are Data deviations

NOT significant ARE significantDeviations are due to just chance alone

Deviations are not due to chance alone, something else is going on

• Autosomal Dominant Inheritanceo Affected genotype: R-o Not affected by sex: males and females are affected in equal numberso Each affected individual HAS to have at least one affected parento Two unaffected parents CANNOT produce an affected childo Two affected parents MAY produce unaffected childreno Can look at just immediate families, lineage doesn’t mattero Hypercholesterolemia (chromosome 19)

Missing protein to remove cholesterol from blood Heart attack by age 50 1/122 French Canadians

o Huntington Disease (chromosome 4) Progressive mental and neurological damage Neurological disorders by ages 40-70 1/25,000 Caucasians

• Autosomal Recessive Inheritanceo Affected genotype: rro Not affected by sex: males and females are affected in equal numberso Typically affected children have unaffected parentso If affected child is produced by unaffected parent: risk to subsequent children is ¼=25% o If both parents are affected ALL children will be affectedo If the disease is rare, unaffected parents of affected children are likely to be related to one

another; AKA incesto Thalassemia (chromosome 16 or 11)

Reduced hemoblobin Anemia Bone and spleen enlargement 1/10 in parts of Italy

o *Sickle-cell anemia (chromosome 11) Abnormal hemoglobin Anemia Resistance to malaria 1/625 African-Americans

o Cystic fibrosis (chromosome 7) Defective cell membrane protein Excessive mucus production Digestive and respiratory failure 1/2000 Caucasians

o Tay-Sachs disease (chromosome 15) Missing enzyme causing buildup of fatty deposit in brain disrupting mental development 1/3000 Eastern European Jews

o Phenylketonuria (PKU) (chromosome 12) Missing enzyme causing mental deficiency 1/10,000 Caucasians

• X-Linked Recessive Inheritanceo Affected genotypes: XrXr and XrYo More affected males than females due to hemizygosity(they only need one copy of the bad

chromosome to be affected)

o If a mother is affected, ALL her sons will be affectedo Recessive male x homozygous dominant female: 100% dominant phenotype, all females are

carrierso Recessive male x carrier female: 50% dominant females, 50% recessive females; 50%

dominant males, 50% dominant femaleso Dominant male x homozygous recessive female: 100% dominant carrier females, 100%

recessive males• X-linked Dominant Inheritance

o Affected genotypes: XRX- and XRYo If a father is affected, ALL his daughters will be affectedo Trait appears equally in males and femaleso Congenital hypertrichosis (CGH) (Werewolf Syndrome)

Leads to large increase of hair follicles on body causing tons of body hair everywhere

Chapter 3

Stage of Cell Division # of Chromatids # of Chromosomes

G1 of Mitosis 4 4S of Mitosis 8 4G2 of Mitosis 8 4Prophase of Mitosis 8 4Prometaphase of Mitosis 8 4Metaphase of Mitosis 8 4Anaphase of Mitosis 8 8Telophase of Mitosis (in each cell) 4 4Prophase I of Meiosis 8 4Metaphase I of Meiosis 8 4Anaphase I of Meiosis 8 4Telophase I of Meiosis (each cell) 4 2Prophase II of Meiosis 4 2Metaphase II of Meiosis 4 2Anaphase II of Meiosis 4 4Telophase II of Meiosis (each cell) 2 2

• Cell Cycle:

MITOSIS:- PROPHASE : DNA shortens (chromosomes); spindle apparatus forms; nuclear

membranes disintegrate- PROMETAPHASE : spindle apparatus migrates to opposite poles- METAPHASE : spindle fibers attach to chromosomes and align on metaphase

plate- ANAPHASE : spindle fiber shortens and chromosomes are split- TELOPHASE : nuclear membranes reassemble and spindle fibers disintegrate- CYTOKINESIS : cell divides

MEIOSIS (GERM-LINE CELLS)• PROPHASE I : DNA condenses as tetrads, nuclear envelope and nucleoli

disappear, spindle starts to form, genetic recombination is occurringo LEPOTENE : condensation, spindle formso ZYGOTENE : envelope disappear, synapsiso PACHYTENE : tetrad formation, crossing overo DIPLOTENE : synaptonenial complex dissolves, chiasmao DIAKINESIS : homologous move onto spindle fiber

• METAPHASE I : tetrad on equator, spindle completely formed, genetic recombination is occurring,

• ANAPHASE I : genetic recombination is NOT possible now, tetrads pull apart and chromosomes move toward poles

• TELOPHASE I : chromosomes decondense and nuclear envelope forms around them, each nucleus is haploid

• CYTOKINESIS : two nucleus become their own cell• PROPHASE II: chromosomes condense, nuclear envelope and nucleoli

disappear, spindle is forming• METAPHASE II : chromosomes align on equator, spindle is completely formed• ANAPHASE II : chromosomes split and each chromatid goes toward each pole• TELOPHASE II : chromosomes decondense, surrounded by nuclear envelope• CYTOKINESIS : splits it into four cells

***DNA is halved in both Meiosis I and Meiosis II, ploidy changes from diploid to haploid in meiosis I and stays haploid through meiosis II.

• Three sources of genetic variability

•

o Asymmetrico Oogonium(one circle): diploido Primary oocyte(one circle): diploido Secondary oocyte(two circles): haploid each circle (four circles): three polar

bodies (haploid) degrade and do not form functional eggs, one ovum (haploid) forms into functional egg

•o Symmetric o Spermagonium(one circle): diploido Primary spermatocyte(one circle):

diploido Secondary spermatocytes(two circles):

haploid each circleo Spermatids(four circles): haploid each

circleo Sperm: mature haploid male gametes

Chapter 4•

*VARIABLE(INCOMPLETE) PENETRANCE: same genotype, but some do not show the corresponding phenotype (examples: Breast cancer – BRCAI gene 80% chance; Polydactyly; retinoblastoma(retina cancer)

*VARIABLE EXPRESSIVITY: same genotype expresses different degrees or magnitudes of phenotype (examples: Waardenburg syndrome – diff combo of symptoms – graying, hearing loss, eye color, etc.; Neurofibromatosis – shwann cells develop into tumors; Holoprosencephaly – forebrain doesn’t develop into two lobes)

*VARIABLE PENETRANCE AND EXPRESSIVITY: same genotype, but some do not show corresponding phenotype and some show different degrees of the corresponding phenotype

• Epistatic interactionso An allele at one gene modifies or prevent the expression of an allele on another geneo Minimum of 2 genes required; usually participate in the same pathwayo Epistasis is readily detected among progeny of dihybrid crosses involving genes with both

dominant and recessive alleles

TYPE: RATIO: EXAMPLE: DESCRIPTION:

NO INTERACTION 9:3:3:1

FLY EYE COLOR: (RED:BROWN:VERMILLION:WHITE

)(B-V-):(bbV-):(B-vv):(bbvv)

Normal expected dihybrid test cross

COMPLEMENTARY GENE INTERACTION

9:7SWEET PEA FLOWER COLOR

(PURPLE:WHITE)(C-P-): (C-pp; ccP-; ccpp)

Mutation of either genes produces a mutant phenotype (white). In order to be wildtype (purple) it

must have both genes.

DUPLICATE GENE INTERACTION

15:1BEAN FLOWER COLOR

(PURPLE:WHITE)(P-R-; P-rr; ppR):(pprr)

Only homozygous recessive has mutant allele. Both dominant

alleles can switch on the pigment gene.

DOMINANT GENE INTERACTION

9:6:1SQUACH FRUIT SHAPE (DISK:SPHERE:LONG)

(A-B-):(A-bb or aaB-):(aabb)

All Dominant produces 1 phenotype (A-B-). One Dominant

and one Recessive produces another phenotype (aaB- or A-

bb). And aabb produces another phenotype.

RECESSIVE EPISTASIS 9:3:4LABRADOR RETRIEVER COAT

(BLACK:CHOCOLATE:GOLDEN) (B-E-):(bbE-):(B-ee or bbee)

Recessive alleles mask/reduce the expression of the other alleles

DOMINANT EPISTASIS 12:3:1

FOXGLOVE FLOWER COLOR (WHITE:DARK RED:LIGHT RED)(D-W- or ddW-):(D-ww):(ddww)

Dominant allele masks the expression of another allele.

Having the dominant allele for white flowers (W-) will produce white flowers even if dominant allele for red (D-) is present.

DOMINANT SUPPRESSION 13:3CHICKEN FEATHER COLOR

(WHITE:COLORED)(C-I- or ccI- or ccii):(C-ii)

Dominant gene suppresses another dominant gene

• WILSONo Thought DNA was hereditary materialo Observed that sperm and egg both have same # of chromosomes during reproduction

• GRIFFITHo Rough and smooth pneumonia with ratso RII lived, SIII died, heat-killed SIII+living RII diedo Discovered there was a transformation factor

• AVERY, MCLEOD, MCCARTYo Discovered DNA was the transformation factor by deleting lipids, polysaccharides, proteins,

RNA, and DNA to find out what kept the mouse alive; DNA did.• WATSON AND CRICK

o Figured out the double helix structure• CAIRNS

o Reported first evidence of bacterial origins of replication; theta structure• HERSHEY AND CHASE

o Demonstrated that DNA is responsible for bacteriophage infection of bacteria• MESELSON AND STAHL

o Used cesium chloride to test models of replication; figured out it was semi-conservative with use of heavy and light nitrogen

• HUBERMAN & RIGGSo Pulse-chase labelingo 1st evidence of bidirectional replication

• MEISCHNERo DNA isolated from nuclei of WBCo “nuclein”

• BLACKBURN, GREIDER, & SZOSTAK

o Teleomeres and how they work• SUTTON & BOVERI

o Parallels between chromosomes->gametes and gene inheritance

• Replication Fork

• PCR

o Requires Double stranded DNA template with target sequence Supply of four dNTPs Heat-stabled DNA polymerase 2 different single stranded DNA primers Buffer solution

o Steps Denaturation: DNA heated ~95˚C and separates Primer annealing: temp reduced to ~45-68˚C to allow primers to hybridize to their

complementary sequences in target DNA Primer extension: temp raised to 72˚C to allow Taq polymerase to synthesize DNA

o Primers provide a starting point for Taq polymerase to add nucleotideso Amplified DNA fragments are separated from rxn mixture by gel electrophoresis and visualized

by ethidium bromide stainingo VNTRs(each allele produces a PCR fragment of a different length) can be detected through

PCR• Restriction enzymes: cut the DNA at restriction sequence

o Sticky ends: can attach to another DNAo Blunt ends: nothing else can attach

Chapter 10• Sickle cell disease

o Autosomal recessiveo Caused by a single base pair substitution in the β-globin geneo Affects hemoglobin’s ability to carry oxygeno Hemoglobin’s most common form(HbA): tetramer with 2 protein chains with α- and β-globin;

each protein in hemoglobin carries one iron-containing molecule of heme which reversibly binds to oxygen

o Walter Noel: first patient,o Ernest Iron: Doctoro Elongated RBCso Reduced blood flow= Muscle painso βAβA

normal RBCs normal susceptibility to malaria

o βAβS

co-dominant β-globin some bad RBCs in high altitudes (incomplete dominance) resistant to malaria mild SCD symptoms

o βSβS

all bad RBCs anemic resistant to malaria

• SOUTHERN BLOTTING: Edwin Southern; DNA transfer• NORTHERN BLOTTING: RNA transfer• WESTERN BLOTTING: protein transfer

o βAβA furthest downo βAβS two bandso βSβS highest up

• Gel electrophoresiso Well at (-) end, DNA moves to (+) end (DNA is negatively charged)

o Bigger pieces go further on gel than smaller pieceso Circular DNA goes further than linear o More (-) DNA goes furthero More supercoiled goes further

the gel will slower longer molecules what determines the difference in electrophoretic mobility of mRNA molecules? – length

Chapter 11Chromosome Structure

• Bacterial Chromosomes Are Simple in Organization o Bacterial and Archaeal Chromosomes

Bacterial genomes may consist of a single circular chromosome or multiple chromosomes that may be linear or circular

The single or, in those few species with more than one chromosome, largest chromosome carries essential genes

• Required for reproduction, gene expression, and normal metabolic activities Also carry multiple copies of one or more plasmids

• Extra-chromosomal DNA molecules • Not part of the bacterial genome • Carry non-essential genes

o Not needed by bacteria in completion of their normal processes Chromosomes are densely packed to form a small region called the nucleoid

• Efficient organization of the chromosome into a series of tight loops makes this region remarkably small

o Bacterial Chromosome Compaction Twofold:

• Proteins help organize the DNA into loops that pack them into the nucleoid • The circular DNA undergoes supercoiling

Two major groups of proteins: • Small nucleoid-associated proteins• DNA bending that contributes to folding and condensation of chromosomes • Structural maintenance of chromosome (SMC) proteins:

o Attach directly to the DNA o Holding it in coils or V-shapes to form large nucleoprotein complexes

Supercoiling • Negative

o Predominant o Twists DNA in the opposite direction to the helical twist

• Positive o In a few archaea species o Twist the same direction o Primarily hyperthermophiles

Live in very high temperature and specialized topoisomerase induce positive supercoiling to provide additional stability against the degradation effects of high heat that might otherwise denature the duplex by destabilizing the hydrogen bonds

• Topoisomerases o Partial unwind supercoiled DNA to relieve torsional stresses that could

result form “over-winding” • Eukaryotic Chromosomes Are Organized as Chromatin

o With regard to chromosomes, the most significant differences between eukaryotic and bacterial cells are the presence of multiple pairs of chromosomes in the eukaryotic nucleus and the organization of eukaryotic DNA into chromatin

o Chromatin: the complex containing DNA and proteins that combine to form eukaryotic chromosomes

o Chromatin Composition Half DNA and half protein by weight Half the proteins are histone proteins:

• Five small, basic proteins that are positively charged and bind tightly to negatively charged DNA

• Remain proteins are nonhistone proteins that perform a variety of tasks Histones

• Principal agents in chromatin packaging • H1, H2A, H2B, H3, and H4 • Two molecules each of four histones – H2A, H2B, H3, and H4 – join together to

form an octameric nucleosome o A span of DNA approximately 146 bp long wraps around each

nucleosome core particles; which is the first level of DNA condensation and compacts the DNA about sevenfold

o The 146 bp of DNA wrapped around a core particle is called core DNA Structure

• Beads-on-a-string o Least condensed state as 10-nm fiber o Beads= nucleosomes o String= linker DNA

• Higher levels of chromatin compaction o 10-nm is not observed under normal cellular conditions o 30-nm fiber is observed

6 times more condensed Forms when the 10-nm fiber coils into a solenoid structure, with 6-

8 nucleosomes per turn and histone H1 stabilizing the solenoid Exist during interphase and becomes maximally condensed during

metaphase of mitosis o Higher Order Chromatin Structure

Interphase chromosomes have variably sized loops of 30-nm fibers that form a 300-nm fiber

• With continued condensation, the chromatin loops form sister chromatids • In metaphase, chromosome condensation reaches its zenith, resulting in

chromosomes that are easily visualized by microscopy

Chromosome scaffold • Filamentous nonhistone protein framework that gives chromosomes their shape• Provides shape, strength, and support

Chromatin loops of 20 to 100 kb are anchored to the chromosome scaffold by non-histone proteins at sites called MARs (matrix attachment regions)

The radial loop-scaffold model predicts that the chromatin loops gather into rosette-like structures and are further compressed by nonhistone proteins

• 1. Chromatin is anchored at MARs • 2. Nonhistone proteins organize chromatin loops into rosettes • 3. Rosettes are compressed in metaphase chromosomes

o Metaphase chromatin is compacted 250-fild compaction of the already condensed 300-nm fiber

Plays a critical role in two distinctive features of eukaryotic genetics • Allows for efficient separation of chromosomes at anaphase • The chromatin looped formed during condensation play a role in the regulation of

gene expression • Larger loops have more active transcription than small loops

o Nucleosome Distribution and Synthesis During Replication The presence of nucleosome on chromosomes raises several questions about DNA

replication• Are old nucleosomes lost during replication? • Are new nucleosomes synthesized during replication? • Do old nucleosomes stay intact, so that nucleosomes are composed of either old

histone proteins entirely or new histone proteins entirely? • Whether or not nucleosomes stay intact, how are nucleosomes distributed to the

sister chromatids? o Old histones are retained either as dimers, tetramers, or individual

molecules, that most nucleosomes present after replication are at least partially assembled from old nucleosome components, and that most nucleosomes contain some newly synthesized histone protein dimers

Nucleosomes and replication • As the replication fork passes, nucleosomes break down into component parts

o H3-H4 tetramers immediately re-associate randomly with one of the sister chromatids

o H2A-H2B dimers disassemble and are re-assembled from both old and new histones

• Chromosome Regions Are Differentiated by Banding o When chromosome condensation reaches a maximum at metaphase cytogeneticists can

distinguish the chromosome microscopically based on size, shape, and banding pattern o Chromosome bands appear light or dark when chromosomes are treated with specific dyes and

stains o Chromosome Structure and Banding Patterns

Chromosome arms: centromeres divide chromosomes into segments of unequal length • Short arm= p arm • Long= q arm

Chromosome shape • Metacentric • Sub-metacentric • Acrocentric: satellite • Telocentric: no p arm

Karyotypes • Ordered photographic display of a complete set of chromosomes for a species

o Grouped into homologous pairs in descending order of size o Sex chromosomes are identified separately

• Uses: o Allows for recognition of abnormalities in chromosome number or

structure o Extra or missing chromosomes can be easily identified or rearrangements

(insertions, deletions, etc.) o Tracing evolutionary history

Banding techniques • Human banding

o G (Giemsa) banding: used to create lightly and darkly stained bands in a different pattern on each type of human chromosome

o Heterochromatin and Euchromatin Euchromatin

• Actively expressed genes and less condensed during interphase Heterochromatin

• Fewer expressed genes and remained condensed during interphase • Facultative

o Exhibits variable levels of condensation, related to levels of transcription • Constitutive

o Permanently condensed o Found in centromeres and telomeres o Composed primarily of repetitive DNA sequence

o Centromere Structure Repetitive DNA sequences in centromeres facilitate kinetochore proteins and spindle

microtubule binding Carbon and Clarke found centromeres of yeast has slightly different sequences, called

CEN sequences (centromeric DNA) • Three elements: CDE I, II, III • Highly repetitive and constitutively heterochromatic

o In Situ Hybridization Uses molecular probes, labeled with fluorescence or radioactivity, to detect their target

sequences First generation: 32P FISH: Fluorescent In Situ Hybridization

• Use molecular probes labeled with compounds that emit fluorescent light when excited by UV or visible light

• Human: 24 different fluorophores• Chromatin Structure Influences Gene Transcription

o Chromosome Territory During Interphase Boveri first observed that chromosomes are not evenly distributed within the nucleus and

suggested that the variation in position might be related to gene activity Cremer and Cremer investigated the arrangement of chromosomes in the nucleus

during interphase and found that chromosomes are partitioned into their own chromosome territories: domain of a single chromosome

• Don’t leave till M phase • Move, twist, and turn within their territories during transcription and DNA

replication • Anchored by centromeres • Inter-chromosomal domains exist between the territories (like hallways)

o Movement of proteins, enzymes, and RNA molecules

Chapter 12

Gene Mutation, DNA Repair, and Homologous Recombination • Mutations are Rare and Occur at Random

o Every organism carries mutant alleles, whether they manifest in distinct phenotypes or not o Individuals acquire one to four new mutations each generations o Mutations are rare o Mutation Frequency

Measured by the number of times mutation alter a particular gene Is defied and investigated differently in sexually reproducing diploids Defined as the number of mutational events in a given gene over a defined period of

time Dominant mutations are easier to detect than recessive mutations and are easier to

study Three essential conclusions can be drawn:

• Mutation frequencies are low in all genomes o Genome stability is paramount and mutations contribute slowly to

inherited diversity • Gene mutation frequencies differ considerably among organisms

o Genomes may have variable levels of tolerance for mutations and that mutation repair efficiency may vary among organisms

• Mutation frequencies among different genes of a single species show variation o There are intrinsic DNA sequence variable that lead to different mutation

rates among the genes in a genome Variation:

• Larger genomes= higher mutation frequencies• Hotspots of mutation

o Individual genes or regions of genomes where mutations occur much more often than average

o Derive form specific characteristics of the genes or DNA sequence involved; like larger gene size

o The Fluctuation Test Designed by Luria and Delbruck to test if mutations occur randomly or adaptively

• Began with 20 small cultures of bacteria derived from a mother culture • All reached final concentration • All exposed to same concentration of bacteriophage • All produced different numbers of bacteriophage-resistant colonies

o Mutations occur at random • Gene Mutations Modify DNA Sequence • Mutations May Be Induced by Chemicals or Ionizing Radiation

o Induced Mutations Produced by interactions between DNA and physical, chemical, or biological agent that

generates damage resulting in mutation (called mutagens)o Mutagens

Use types od sequence changes Sometimes exotic or rare, but often present in the everyday life of an organism Important study for public and safety as it is for advancing our understanding if the

biological basis of mutation and repair o Chemical Mutagens

Nucleotide Base Analogs • Base analog is a chemical compound with a structure similar to a DNA nucleotide • Can pair with normal nucleotides and polymerases cannot tell them apart from

normal nucleotides Deaminating Agents

• Removes amino groups from nucleotide bases• Deamination of adenine produces hypoxanthine which can mis-pair and lead to

A-T to G-C base-pair substitutions Alkylating Agents

• Added bulky adducts (methyl and ethyl) that interfere with DNA base pairing and distort the DNA double helix

Oxidative Reactions• Chemical process of electron transfer by addition of an oxygen atom or removal

of a hydrogen atom • Can lead to tranversion mutation

Hydroxylating Agent • Add hydroxyl groups to a recipient compound • Can cause to transition mutation

Intercalating Agents • Fit between DNA base pairs • Distort the DNA duplex that leads to DNA nicking that is repaired results in added

or lost nucleotides o Radiation-Induced DNA Damage

Photoproducts • UV irradiation alter DNA nucleotides by inciting the formation of additional bonds

that form aberrant structures • Pyrimidine dimers

o Produced by the formation of one or two additional covalent bonds between adjacent pyrimidine nucleotides

• Thymine dimer o Two covalent bonds joining 5 and 6 carbons of adjacent thymines

• If not repaired cause replication disruption because complementary As of the new DNA strand cant form H-bonds with the dimerized Ts

o Replication stallso Translesion DNA synthesis fill in the gaps left by stalled DNA synthesis

Controlled by specialized polymerases that can replicate across gaps that lack proofreading activity so they are error-prone

Other radiation • X-rays and radioactive materials

o Breaks in single-stranded or double-stranded DNA Can block DNA replication

o The Ames Test Mimics what happens when animals are exposed to chemicals; it test the chemicals and

their breakdown products for mutagenic potential Bacteria are exposed to experimental compounds in the presence of mammalian liver

enzymes • Ingested chemicals are transport to the liver to be broken down by enzymes • Salmonella typhumurium is used that carry various types of mutations interfering

with their ability to synthesize histidine The bacteria are exposed to the chemical to be tested, plus an extract of purified liver

enzymes, and plated on medium lacking histidine Results:

• Number of revertants from his- to his+ are assayed for each treatment or control • Compound is mutagenic shown by a significant increase in the reversion rate

Chapter 13 Chromosome Aberrations and Transposition

• Nondisjunction Leads to Changes in Chromosome Number

o Nondisjunction: A process of failed chromosome and sister chromatid disjunction that can result in

abnormalities of chromosome number o Euploidy and Aneuploidy

The number of chromosomes contained in a nucleus and the relative size and shape of each chromosome are species-specific characteristics, but neither parameter is directly associated with the complexity of the organism

Euploid:• The euploid number of chromosomes of an individual is the number of complete

sets (n, 2n, 3n) Aneuploid:

• If cells contain a number of chromosomes that is not euploid • Occurs when one or more chromosomes are lost or gained relative to the normal

euploid number o Chromosome Nondisjunction

Applies to the failure of homologous chromosomes or sister chromatids to separate as they normally do during cell division

Somatic cells • It can result in one daughter cell with an extra chromosome (2n+1) and the other

missing one chromosome (2n-1) • The relatively poor survival of these cells normally limits their number is animals

Germ-line cells • Produces aneuploidy gametes and can lead to the production of aneuploidy

zygotes • Nondisjunction is meiosis I (but can occur in meiosis II) results form failure of

homologs to separate; the gametes produced are either n+1 or n-1 which assumes only one chromosome pair is affected

o Fusion of these gametes with normal (n) gametes produces trisomic (2n+1) or monosomic (2n-1)

In Meiosis II • Results in the failure of sister chromatids to separate normally • Only two of the four will be affected

o n+1 and n-1 o Aneuploidy in Humans

Humans are enormously sensitive to gene dosage changes and aneuploids usually do not survive

Only trisomies of chromosome 13,18, and 21 are seen in newborn infants and no autosomal monosomies are observed

Multiple forms of sex-chromosome trisomies, and one type of sex-chromosome monosomy occur

• Those found in newborns infants are known to occurs in humans • Half of all conceptions spontaneously abort during the first trimester • About half of these pregnancies carry abnormalities of chromosome number or

structure Trisomy 21 (Down syndrome)

• Link between the risk of trisomy 21 and maternal age • A small number of genes on chromosome 21 are responsible for the cognitive

disabilities and heart abnormalities that are principal symptoms o A portion is called DSCR (Down Syndrome Critical Region) which is

correlated with the majority of symptoms • DYRK

o Candidate gene known to produce dosage-sensitive learning defects in mice and flies

o Major contribution to Down Syndrome Turner Syndrome

• A monosomy of X chromosome in which there is one X chromosome but no second sex chromosome

• The XO embryos, the single copy of the gene SHOX, which is inactivated by dosage compensation, is insufficient to direct normal development

• The haploinsufficiency of this gene plays a central role in producing the symptoms of the syndrome

o Reduced Fertility in Aneuploidy In the case of trisomy, chromosome segregation in meiosis is disturbed because three

homologous chromosomes rather than two are aligning at synapsis and segregating during anaphase I

• Either trivalent synapsis or bivalent and univalent arrangement but there is no mechanism to divide three chromosomes equally at anaphase I

• Meiosis results in two chromosomes moving to one pole and one chromosome moving to the other

o Upon completion of meiosis, half of the gametes are haploid for the chromosome; but the remaining gametes contain two copies

The gamete with an extra chromosome will produce trisomic progeny that are unlikely to survive

• A 1:1 ratio of haploid (normal) to diploid (abnormal) gametes has been observed in numerous experimental organisms

o This circumstance results in a form of semi-sterility, a reduction – but not complete elimination – of fertility

o Mosaicism Which different cells of the organism contain differently functioning X chromosomes It can develop through mitotic nondisjunction early in embryogenesis and is one of many

kinds of chromosome abnormalities that occur in newborn infants • 25-30% of Turner syndrome cases occur in females that are mosaic, with some

45, XO cells and some 46, XX • Some Turner syndrome individuals carry 47, XXX cells too

o This kind of mosaicism is usually derived from mitotic nondisjunction in 46, XX zygote

Gynandromorphs • Occurs in fruit flies, butterflies, and moths producing a sexually ambiguous

phenotype • Sex morphology is female on one half of the body and male on the other half • Develops as a consequence of mitotic nondisjunction early in development

• Changes in Euploidy Results in Various Kinds of Polyploidy o Polyploidy

The presence of three or more sets of chromosomes in the nucleus of an organisms Polyploids whose karyotype is comprised of chromosomes derived from a single species

are designated autopolyploids Polyploids with chromosome set from two or more species are called allopolyploidy

o Autopolyploidy and Allopolyploidy Three mechanisms that lead to Autopolyploidy

• Multiple fertilizations o Fertilization of an egg by more than one haploid pollen grain result in a

zygote that is triploid (3n) or higher o It a rare event because most sexually reproducing plants have elaborate

mechanisms to prevent fertilization of an egg by more than a single pollen grain

• Mitotic nondisjunction

o Occurring in sex stem cells can result in chromosome doubling o These cells divide by mitosis before entering meiosis, and mitotic

nondisjunction double the number of chromosomes from 2n to 4n • Meiotic nondisjunction

o It can produce a diploid gamete instead of a haploid gamete o It is similar to the mitotic nondisjunction mechanism, except that the break

down in disjunction affects the products of a single meiosis Allopolyploidy

• Carry multiple sets of chromosomes that originated in different species, and can result in a hybrid offspring that is infertile because the chromosome sets are not homologous

o Chromosome nondisjunction in these hybrids leads to cells with double the number of chromosomes so that now each chromosome has a homolog from pairing, and the hybrid is fertile

o Consequences of Polyploidy Occur in nature and are also produced by human manipulation Three main consequences

• Fruit and flower is increase • Fertility is decreased, particularly in odd-numbered polyploids (3n, 5n, etc.)

o Odd number of chromosomes cannot be evenly divided at the first meiotic division

o This result is an unequal distribution of chromosomes that makes almost all of the resulting gametes nonviable

• Hybrid vigor o More rapid growth, increased fruit and flower production, and improved

resistance to disease occur in polyploids o Increase in heterozygosity relative to diploids that comes about when

inbred lines are crossed and is the basis of additional growth vigor o Reduced Recessive Homozygosity

The pattern of single-gene inheritance in polyploids differs from that in diploids with respect to the proportions of dominant and recessive phenotypes from certain crosses

This difference is tied directly to the additional number of gene copies in polyploidy genomes (they have more than two alleles for each gene)

Recessive phenotype are produced only in individuals that are homozygous for that allele

• This occurs much less frequently in polyploids then in normal diploids o Polyploidy and Evolution

Evolution of polyploidy is a sudden, dramatic event that can lead to the development of a new species over a span of just one or two generations

More than half of all flowering plant species are derived from ancestors that evolved by polyploidy

Allopolyploids are reproductively isolated from each parent Polyploidy produces gene duplication that relaxes natural selection constraints on

duplicated copes of the genes • Chromosome Breakage Leads to Inversion and Translocation of Chromosomes

o Sometimes chromosome breakage leads to reattachment of the wrong broken ends o Reattachment in the wrong orientation leads to chromosome inversion o Reattachment to non-homologous chromosome leads to chromosome translocation o As long as no critical genes or regulatory regions are mutated by chromosome breakage, and

as long as dosage-sensitive genes are retained in their proper balance, heterozygous carriers of chromosome inversion or chromosome translocation may experience no phenotypic abnormalities

o Chromosome Inversion

Paracentric • The centromere is outside of the inverted region

Pericentric • The centromere is within the inverted region

Inversion heterozygotes • Have one normal and one inverted homolog • May experience no genetic or phenotypic abnormalities

o Chromosome Translocation Occur when broken ends of non-homologous chromosomes are reattached Translocation heterozygotes

• One normal copy and one translocated copy of each chromosome, may be normal in phenotype if no genes are disrupted by the breakage and reattachment events

• May experience samisterility die to segregation abnormalities Three types:

• 1. Unbalanced translocations o Arise from a chromosome break and subsequent reattachment to a non-

homologous chromosome in a one-way event; that is, a piece of one chromosome is translocated to a non-homologous chromosome and there is no reciprocal event

• 2. Reciprocal balanced translocations o Produced when breaks occur on two non-homologous chromosome and

the resulting fragments switch places when they are reattached • 3. Robertsonian translocation (chromosome fusion)

o Involves the fusion of two non-homologous chromosomes o One consequence is the reduction of chromosome number