End of Chapter Questions Ch. 3-8

Question 1

When may the terms mutation and polymorphism be used?

Answer 1

Mutation: sudden heritable changes in DNA

Polymorphism: either to indicate non-disease causing change or change with frequency of 1% or higher of general population

Question 2

What kind of mutations do you know according to their origin?

Answer 2

Somatic mutations and Germline mutations

Question 3

Give examples of some physical and chemical mutagens

Answer 3

Physical: UV light, ionizing radiation

Chemical: benzopyrene/other PAH, alkylating agents, aflatoxin, psoralen, fluorescent dyes used in labs, mustard gas

Question 4

Why could a double-stranded DNA break lead to structural chromosomal damage?

Answer 4

Because of the sloppy repair mechanism of non-homologous end joining, large amounts of the genetic code might be deleted

Question 5

What is the difference between the causes leading to polyalanine and polyglutamine diseases?

Answer 5

Polyglutamine (CAG triplets): gain-of-function mutations, replication slippage, expansion

Polyalanine (GCN triplets): loss-of-function mutations, uneven crossing over

Question 6

What is the explanation for the existence of mutational hotspots?

Answer 6

Mutation hot spots have long repeats of CpG, which, if methylated, can see cytosine spontaneously deaminate to thymine, and the base pair would then convert to adenine.

That doesn’t really explain why they exist, but their e-book really didn’t either. Maybe because they are often in promoter regions, so they are so important for survival that any mutation leads to death and cannot be carried on in the genetic code.

Question 7

What is the connection between anticipation and nucleotide repeat mutations?

Answer 7

Anticipation occurs from increasing nucleotide repeat mutations with each generation. The repeat expansion may cause replication slippage, which leads to further repeats being added into the code.

Question 8

Why is SOS repair not found in multicellular organisms?

Answer 8

Because eukaryotes dont have to fight for survival of individual cells; the organism survives unless there is massive cell loss. At the same time, mutations from SOS repair would risk developing tumors in eukaryotic organisms.

Question 9

When does mutation repair take place?

Answer 9

• double-stranded breaks (radio or chemotherapy)
• UV helix distorting damage (UV light)
• mismatches/ insertions/ deletions (replication errors)
• formation of O6-alkyl-guanine (damage from alkylating agents)
• single stranded breaks (ROS)

Not sure if this what they’re referring to, but mutation repair would normally occur during the G1 (“restriction”) checkpoint

Question 10

Give examples of some mutagenicity tests

Answer 10

Ames test (Salmonella with existing histidine mutation.. check for back mutation)

Sister Chromatid Exchange (SCE) - somatic cells have more crossing over with mutagen

Micronucleus test: fragment of DNA broken off that ends up in cytoplasm

Question 11

What could be the consequences of splicing mutations?

Answer 11

Defective protein because an exon could be lost or an intron could be translated

Question 12

What are the causes of aneuploidy and polyploidy?

Answer 12

Aneuploidy: meiotic or mitotic non-dysjunctions

Polyploidy: multiplication of chromosome set due to defects of the microtubules and/or abnormal organization of mitotic spindle

Question 13

What are the main regions of chromosomes?

Answer 13

Centromere
p arm
q arm
Telomere
(not sure what else they really mean)

Question 14

Explain the low incidence of monosomies:

Answer 14

The lack of chromosome is much worsely-tolerated than excess of chromosome. Typically die in utero

Question 15

What is microchimerism, and what is its biological significance?

Answer 15

Mothers retain some cells from their offspring after they’re born. May be responsible for autoimmune disease

Question 16

In what diseases has UPD an etiologic role?

Answer 16

Prader-Willi and Angelman

(UPD is uniparental disomy: instead of one paternal and one maternal chromosome, have a duplication of either paternal or maternal)

Question 17

What are the different positions of chromosomal breakpoints?

Answer 17

?? shitty question
Breakpoints are usually in non coding regions (majority of genome is non coding)

If it is in the coding region, of course the RNA or protein products are altered.

If a break is in the centromere, may result in fusion chromosome

Question 18

What techniques are used for the detection of chromosomal aberrations?

Answer 18

Karyotyping
FISH
CGH (comparative genome hybridization)

Question 19

What are chimerism and mosaicism?

Answer 19

Chimerism: within one organism, different genes due to different original source (absorbed fetal twin etc)

Mosaicism: within one organism, different genes due to same original source (mutation, X inactivation, etc.)

Question 20

What are possible consequences of centric fusion?

Answer 20

Reduction of chromosome # by 1.
May be balanced or unbalanced with some part deleted

Can make a person sterile, produce unviable offspring or Down syndrome offspring.

Question 21

What is the explanation of the higher frequency of first meiotic nondisjunctions?

Answer 21

Ova stay stuck in first meiotic division (prophase diplotene) until maturation/ovulation, where they become stuck in meiosis II (metaphase). Since so much time is left in meiosis I, can be more than 40 years, there is more time for some damage to occur.

Question 22

What is the purpose of dosage compensation?

Answer 22

Equalization of gene expression between males and females, despite the fact that females have 2 X and males have X. So females undergo X inactivation (lyonization) to form Barr bodies

Question 23

What could be an evolutionary explanation for imprinting?

Answer 23

Conflict of Parental Interests Theory: father has more drive to have more active, resource-using proliferative genes to encourage survival of his offspring, while the mother has more interest in keeping the child’s needs modest because she is more likely having to feed and provide for the child, and needs to save her resources.

Question 24

What is a differentially methylated cluster?

Answer 24

Stretches of DNA in genome that have different DNA methylation patterns compared to other samples
(just from wikipedia, as far as I know they never taught this either)

Question 25

What molecular alterations are in the background of epigenetic changes?

Answer 25

DNA (cytosine) methylation

Histone acetylation, methylation, phosphorylation, ubiquitination, etc.

Question 26

Why can CpG dinucleotides be mutation hot spots?

Answer 26

Methylated C -> T via demination. Then T matches with A.

To have methylated cytosines within CpG islands is frequently pathological, and inhibits tumor suppressor genes

Question 27

What is the role of non-coding RNA in X inactivation?

Answer 27

In the X chromosome to be inactivated, in its XIC (X inactivation center), there is a XIST gene (X inactivation specific transcript) that codes for a large non-coding RNA that is a major effector of the X inactivation process

Question 28

What mechanisms can cause Angelman syndrome?

Answer 28

• Maternal Deletion
• Wrong imprinting
• UBE3A mutation (UBE3A normally only active from the maternal allele on Chromsome 15; this is partially responsible for differences between Angelman and Prader-Willi)
• Paternal UPD

Question 29

What is the histone code?

Answer 29

The pattern of epigenetic modifications on histones which influences the expression of genes

(part of the epigenetic code)

Question 30

What are the CpG islands and what is their epigenetic significance?

Answer 30

CpG islands are areas with higher than normal CpG frequency that are also less methylated than normal. They are more frequent in promoter regions, which explains why increased methylation would be a problem.

If they are located in promoter regions of tumor suppressor genes, methylation can allow for tumor formation.

Question 31

What is chromatin remodeling?

Answer 31

Modification of chromatin architecture to either allow or block off access of condensed DNA from the mechanisms that transcribe DNA to RNA.

It’s performed by histone modifications (acetylation/ decetylation etc)

Question 32

Describe Mendel’s principles!

ugh

Answer 32

Classical Mendelian inheritance: no environmental influence, 2 alleles that can be autosomal dominant, recessive, co-dominant, X-linked dominant or X-linked recessive, or Y linked. These are relatively more simple “monogenic” forms of inheritance of traits.

• Law of Segregation (the “First Law”) - two alleles for a heritable character separate from each other during gamete formation and end up in different gametes.
• Law of Independent Assortment (the “Second Law”), aka “Inheritance Law” - separate genes for separate traits are passed independently of one another from parents to offspring.
• Law of Dominance (the “Third Law”) - recessive alleles will always be masked by dominant alleles. So, a cross between a homozygous dominant and homozygous recessive will always express the dominant phenotype, while still having a heterozygous genotype.

Question 33

Define the following terms! — gene, allele, multiple allelism

Answer 33

• Gene: DNA sequence coding for functional products (various RNA)
• Allele: member of a pair of genes; a variant form of a gene
• Multiple allelism: Certain genes with more than 2 different alleles; more than 2 phenotypes are possible (e.g. AB0 blood group) “many possible alleles in the wild”

Question 34

Define the following terms! dominance, recessivity, codominance, complex or compound heterozygotes

Answer 34

• Dominance: phenotype visible even in heterozygous form
• Recessive: phenotype only visible in homozygous form
• Codominance: both alleles are manifested phenotypically in heterozygotes, e.g. AB0 blood group
• Complex/Compound heterozygotes: technically heterozygote for a recessive disease, yet both alleles cause the disease in a different way (e.g. multiple CFTR mutations in 1 person)

Question 35

Define the following terms!

locus heterogeneity, allele heterogeneity

Answer 35

• Locus heterogeneity: several different gene locus mutations -> same phenotype (e.g. deafness)
• Allele heterogeneity: mutations within the same gene locus cause similar symptoms/diseases (e.g. FGFR3 achondroplasia, hypochondroplasia, tanatophoroplasia)

Question 36

Which phenomena interfere with the classical application of Mendel’s principles in the case of monogenic diseases?

(there are too many)

Answer 36

• Expressivity: variable “gene strength,” “variable expressivity”
• Penetrance: dominant diseases don’t always occur in heterozygotes, “incomplete penentrance”
• Anticipation: younger generations gets the disease earlier (Huntington’s disease)
• Compound heterozygotes: heterozygote with 2 defective recessive allels, still has disease
• Pleiotropy: 1 gene codes for many different things, wide array of effects
• Heterogeneity: opposite of pleiotropy; 1 trait affected by many genes
• de novo mutations: correlated to age of parents
• Modifier genes: some genes affect expression of other genes
• Heterozygote advantage
• Influence of sex
• Influence of environment
• Lethal/sublethal genes
• Phenocopy: environmental change causes a change in a trait that mimics genetic alteration

Question 37

Describe the meaning and give examples: the age and the sex influence the manifestation of some diases

Answer 37

Age: mutation occurs in germline of parent, usually the father because of repeated spermatogonia divisions. Example: most autosomal dominant disease, for example achondroplasia

Sex: an autosomally inherited trait is expressed more in one of the sexes, e.g. baldness more in males, or precocious puberty also more in males due to higher testosterone than in females

Question 38

How has the discovery of oligogenic inheritance pattern affected our view of the monogenic inheritance? Give examples!

Answer 38

Oligogenic inheritance: some hereditary disease is significantly influenced by modifier genes where the modifier genes are also polymorphic and have variable effects.

Examples: cystic fibrosis, polycystic kidney disease both have quite a bit of variation in how they are expressed

Question 39

What are the classical monogenic inheritance patterns?

Answer 39

AD, AR, XD, XR, Y-linked

Question 40

What types of genes are usually mutated in the case of AD and AR diseases? Give examples for each type!

Answer 40

AD: normally genes for structural proteins (e.g. Marfans), regulatory proteins (e.g. CACNA1S in malignant hyperthermia), receptors (e.g. achondroplasia, familial hypercholesterolemia), and proto-oncogenes (e.g. germline mutation of K-Ras, causes Noonan syndrome and myeloid leukemia; and RET mutation for tyrosine kinase receptor related to MEN2A and FMTC )

AR: normally for enzymes (e.g. PKU), elements of hemoglobin (e.g. sickle cell anemia), or tumor suppressor genes (e.g. RB). The regulatory protein of CFTR is abnormally AR.

Question 41

Does the environment influence the manifestation of diseases following monogenic inheritance patterns?

Answer 41

In some monogenic diseases yes: the “ecogenic” inheritable diseases. No symptoms of the disease until some environmental change

e.g. Porphyria, G6PD deficiency, pharmacogenetic diseases

Question 42

Describe the inheritance and the manifestation of tumors and pharmacogenetic diseases with respect to the environmental effects!

Answer 42

Tumors: even AR inherited tumor suppressor defects usually develop tumors in every generation (vertical family tree) due to environmental knock-out of the healthy dominant allele

Pharmacogenetic diseases: ecogenetic diseases; no symptoms until take some medication that the body cannot handle normally due to genetic mutation (e.g. G6PD deficiency/Favism)

Question 43

What is the role of RNAs in cytoplasmic inheritance?

Answer 43

Maternal RNAs are stored in the oocyte and can influence the formation of diseases; part of the epigenetic state of the zygote
(may be mRNA, non-coding RNA, etc.)

Question 44

What kinds of dose compensation mechanisms are known?

Answer 44

X chromosome random inactivation (lyonization, Barr body formation)

X inactivation is the only one occuring in humans, but some strategies of other species:

• Twice as much transcription in those with a single X genotype
• Half as much transcription in both X’s of XX genotype

Question 45

What is the supposed role of skewed X inactivation in the development of autoimmune diseases?

Answer 45

Possibly autoimmune diseases develop because sometimes in certain tissues more paternal X is inactivated than maternal, or vice versa. When the thymus and immune tolerance are developing, maybe they are using the X chromosome that is not activate in other tissues. So then the immune system starts to see those cells with the other X as foreign

Question 46

Based on pedigree analysis how can we distinguish the X linked dominant inheritance from the autosomal dominant one?

Answer 46

They both affect every generation but in XD:

• Females affected twice as often as males
• Affected males cannot transmit the disease to their sons, but always transmit them to their daughters
• From affected women, 50% of their offspring are affected - no regard to gender
• May not be visible in pedigree, but women usually have milder symptoms due to the other X and mosaicism, inactivation of the defective X

Question 47

What are homo- and heteroplasmy?

Answer 47

Homoplasmy: cell cytoplasm contains the same normal or same mutant mitochondria

Heteroplasmy: cell cytoplasm contains combination of normal and mutant mitochondria.

Question 48

What can be the consequences of maternal heteroplasmy?

Answer 48

It’s variable, depending on how many mutated mitochondria were passed into her ovum.

Mitochondrial diseases normally affect regions with high energy needs, like the nervous system

Question 49

What do you know about the genetics of pre-eclampsia?

Answer 49

Not much

Autosomal genes are related, and so paternal genes are also important even though men will never experience pre-eclampsia.

Question 50

What are the characteristics of the inheritance of precocious puberty?

Answer 50

There are different types of precocious puberty, but the one they mentioned in the e-book says it is an autosomal gene mutation of Leutinizing Hormone Receptor (LRH), inducing increased testosterone synthesis. This mainly affects men.

The e-book does not clearly state it’s autosomal dominant, but that’s what https://ghr.nlm.nih.gov/ says

Question 51

Which genes can escape the X inactivation?

Answer 51

The pseudoautosomal regions (PAR1 and PAR2), especially the XIC (X inactivation center) that codes for genes that perform X inactivation

Question 52

What are the differences amongst the symptoms of a carrier woman, if the X-linked gene encodes a soluble or a cell-bound product?

Answer 52

Soluble: effect is “averaged” between the two X’s, the gene product is probably reduced but not symptomatic (e.g. hemophilia, soluble clotting factors)

Cell-bound: due to mosaicism, any region that primarily has the healthy X inactivated may be locally affected (e.g. a sweat gland disease, hypohydrotic ectodermal dysplasia)

Question 53

What kind of oncogene activation mechanisms do you know?

Answer 53

1. Point mutations (e.g. H-Ras, Gly12Val point mutation; hyperactive Ras stimulates cell cycle)
2. Gene amplification (e.g. HER2 amplification)
3. Chromosome translocations [e.g. t(9;22)]
4. Epigenetic changes (oncogene hypomethylation, tumor suppressor hypermethylation)

Question 54

What is LOI?

Answer 54

Loss of Imprinting

Normally, colon epithelial cells only express the paternal allele for IGF2 and imprint the maternal allele. In colon tumors, this maternal imprinting is lost and maternal allele also becomes active.

(note this is what the lecture says, while the e-book has it the opposite way with maternal/ paternal. I think the lecture is right, checked an article)

Question 55

What is the function of care taker and gatekeeper genes?

Answer 55

Gatekeepers: classic tumor suppressors (e.g. RB and p53)

Caretakers: DNA repair genes, aka mutator genes (e.g. MLH1 and MSH2 mismatch repair genes)

Question 56

What do you know about the iPS cells?

Answer 56

iPS = induced pluripotent stem cell

Adult unipotent cells are reprogrammed to de-differentiate into pluripotent stem cells

Originally used pluripotency factors that included an oncogene (cMYC), so they were not safe to use, but now that has been resolved

Now the problem is the epigenetic code is altered and still not understood

Question 57

What is sonic hedgehog and what is its effect based on?

Answer 57

SHH is a morphogen with a role in differentiation of the neural tube and separation of the eyes

Its effect is based on its concentration. In low concentrations, the neural tube stem cells form sensory neurons (dorsally), while in high concentration they form motor neurons (ventrally)

The effect of sonic the hedgehog is based on his ability to go real fast, jump, and to spindash (hold down and press B repeatedly)

Question 58

What is the role of HOX genes?

Answer 58

HOX (homeobox) genes regulate early steps of embryonic development (in particular the cranio-caudal and the limb proximo-distal spatial axes) via a transcription factor cascade. Most important regulators of development, aka “master regulator” genes. 60 codons long.

Question 59

What is the role of SRY and RSPO1?

Answer 59

SRY: male-determining factor on the Y chromosome. Encodes TDF (testis determining factor) - a protein that opens up DNA to allow classical transcription factors to initiate sequences related to male gender

RSPO1: the less-mentioned “female sex determining gene.” If it is mutated, an XX person can form a male phenotype. Produces a soluble ligand that competes with WNT4, triggering the beta catenin pathway.

Question 60

Give an example of epigenetic changes related to carcinogenesis!

Answer 60

Loss of imprinting of maternal IGF2 allele in colon cancer

Hypomethylation of p16 in 40% of colon cancers

Histones: Tumor suppressor genes normally interact with histone deacetylase complex (HDAC) to prevent them from being made into heterochromatin, but if they are already mutated then they can’t prevent their own suppression

Some liver tumors may have hypomethylation of N-Ras oncogene

Question 61

Explain the Knudson’s hypothesis!

Answer 61

Tumor suppressor genes have a recessive pattern, needing homozygous recessive alleles in order for a tumor to form. Thus they need a “double hit” - both healthy alleles need to be mutated.

The first hit allele may be inherited from the germline, such as in the case of retinoblastoma. Then, the second hit of a somatic mutation would also be much more likely to occur.

Question 62

Why is somatic recombination not regarded as an epigenetic mechanism?

Answer 62

The DNA splicing actually changes the genomic code of the B and T cells that undergo somatic recombination; whereas epigenetic mechanisms are only modifications of how the genome is expressed without actually changing the code.