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Genetics and genomes > W8LECT - GENETICS OF BIOLOGICAL PROCESSES > Flashcards

W8LECT - GENETICS OF BIOLOGICAL PROCESSES Flashcards

1
Q

Make a schematic diagram of Genetics of biological processes

A
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2
Q

I. GENETICS OF DEVELOPMENT
1. What are the 6 features of Mammalian embryo development:

A
  1. characterized by regulative mechanisms of lineage segregation
  2. cell specification
  3. combination of carefully orchestrated gene expression networks
  4. signaling pathways
  5. epigenetic marks
  6. defines specific developmental stages
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3
Q

I. GENETICS OF DEVELOPMENT
2. What happen in Early phase of embryonic development?

A
  • in early embryogenesis, Oct4, Nanog, and Sox2 confer pluripotency and are required for the formation of the inner cell mass
  • Gastrulation: NODAL FGF8, the SNAI group of zinc finger transcription factors, the T- box transcription factor EOMES, and the basic helix- loop-helix transcription factors, MESP1 and MESP2
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4
Q

I. GENETICS OF DEVELOPMENT
3. How is Somitogenesis regulated?

A

Somitogenesis is regulated by oscillating expression of Notch signaling pathway

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5
Q

I. GENETICS OF DEVELOPMENT
4. What is Somitogenesis?

A

It is the process through which the paraxial mesoderm that flanks the notochord undergoes segmentation in the cranio-caudal axis to form somites, which eventually give rise to the axial skeleton, skeletal muscles and associated tissues

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6
Q

I. GENETICS OF DEVELOPMENT
5. What are the 3 features of The Notch signaling pathway?

A

1.Maintenance of an oscillating protein gradient (called the segmental clock)
2. Establish the polarity of somites
3. Ligand identity controls Notch activity

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7
Q

I. GENETICS OF DEVELOPMENT
6. What happen if there are Loss-of-function mutations in any of the Notch signaling pathway genes?

A
  1. Notch signaling pathway genes that are part of the segmentation clock lead to one of the types of spondylocostal dysostosis
    * Scoliosis (spinal deformity)
    * Dwarfism
    * Congenital heart diseas
    * nodules on the upper lip
    * generalized enamel hypoplasia,
    * and gemination of the crown of tooth
  2. loss-of-functional mutations in MESP2 lead to spondylothoracic dysostosis
  3. Both of which are skeletal dysplasias characterized by contiguous segmentation defects of the vertebrae.
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8
Q

I. GENETICS OF DEVELOPMENT - Developmental potencies – Epigenetic modification
7A. Green, red, blue and purple circles represent which level of differentiation?

A
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9
Q

I. GENETICS OF DEVELOPMENT - Developmental potencies – Epigenetic modification
7B. Green, red, blue and purple circles represent which epigenetic conditions?

A
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10
Q

I. GENETICS OF DEVELOPMENT
8A. Based on this figure, what are the intrinsic factors?

A
  1. Asymmetric division
  2. Uneven distribution of receptors, transcription factors
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11
Q

I. GENETICS OF DEVELOPMENT
8B. Based on this figure, what are the extrinsic factors?

A
  1. Morphogens = Signalling molecules
  2. Cell-cell interactions
  3. Cell-matrix interactions
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12
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
9A. What are the characteristics of morphogens?

A
  1. Direction of development is influenced by concentration
    gradients
  2. Oocyte or embryo origin
  3. Soluble factors
  4. Induce: Transcription factors
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13
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
9B. What are the molecules of morphogens?

A
  1. Hedgehog protein family
  2. TGFβ family (BMP)
  3. WNT family (Drosophila Wingless mutation)
  4. FGF
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14
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
10A. Concentration gradient of a morphogen is information carrier
=> T/F?

A

True!

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15
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
10B. Give an example to explain that Concentration gradient of a morphogen is information carrier

A

Mesoderm differentiation
- Morphogen: Activin (TGF family)

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16
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
11. What are the 3 features of Sonic hedgehog gene?

A
  1. Coding a morphogen (signaling molecule)
  2. Expressed in notochord and later in central cells of the ventral neural tube
  3. Involved in the development of central nervous system, muscles and limbs and in lateralization
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17
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
12. What is Allele heterogeneity?

A

The presence of different variants at a single gene locus that cause the same or similar phenotypic expressions of a disease.

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18
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
13A. How does Sonic hedgehog involve in the development of central nervous system?

A
  • Central cells of ventral neural tube express “sonic hedgehog” protein
  • Due to the concentration gradient of sonic hedgehog every cell know who they are and where they are
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19
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
13B. What happen if we have Small amount of sonic hedgehog?

A

Sensory neuron

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20
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
13C. What happen if we have medium amount of sonic hedgehog?

A

motor neuron

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21
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
13D. What happen if we have lots of amount of sonic hedgehog?

A

motor neuron

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22
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
14. What happen if there are Mutants without sonic hedgehog?

A

Mutants without sonic hedgehog have no motor neurons and die.

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23
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
15. What does sonic hedgehog separate?

A

Sonic hedgehog separates eyes

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24
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
16. What does lower hedgehog singing result in?

A

Cyclopia

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25
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
17. What are the features of Homeobox genes?

A
  1. Hox genes (homeobox sequence)
  2. 60 AA, helix-turn-helix structure proteins
  3. Positional information – longitudinal axis
  4. Max. 13 box
  5. Spatial colinearity
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26
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
18. What are the characteristics of Synpolydactyly type II, HOXD13 mutation?

A
  1. Coding triplet repeats
  2. Polyalanine disorder
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27
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
19. What are the features of the cyclopia?

A
  • Lower hedgehog singing results in cyclopia.
  • Interactions between morphogens and HOX genes: mutations in SHH and HOXD: holoprosencephaly.
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28
Q

I. GENETICS OF DEVELOPMENT - Governing molecules I.
19. Somatic cells acquire mutations throughout ___

A

the course of an individual’s life

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29
Q

II. GENETICS OF SEX
1. Make a schematic diagram of SEX DETERMINATION?

A
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30
Q

II. GENETICS OF SEX
2. Describe male sex determination

A
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31
Q

II. GENETICS OF SEX
3. SRY is a conventional transcription factor
=> T/F?

32
Q

II. GENETICS OF SEX
4. Make a schematic diagram to describe Y-Chromosome

33
Q

II. GENETICS OF SEX - ABNORMALITIES OF SEXUAL DEVELOPMENT
5. What is the cause of abnormalities of sex reversion?

A

abnormal crossing-over during male gametogenesis (meiosis I)

34
Q

II. GENETICS OF SEX - ABNORMALITIES OF SEXUAL DEVELOPMENT
6. What are the features of sex reversion in both male and female?

A
  1. 46 XX male
    - SRY is transferred to chromosome
  2. 46 XY female
    - SRY is lost from Y chromosome
35
Q

II. GENETICS OF SEX
7. What are the features of Androgen insensitivity syndrome?

A
  1. X-linked recessive hereditary disease
  2. XY genotype
  3. normal serum testosterone level
  4. female external sexual characteristics
  5. sterile
  6. testosterone receptor mutation
36
Q

II. GENETICS OF SEX
8A. What are the symptoms of Androgen insensitivity syndrome?

A
  1. Anosmia (lack of sensing smell)
  2. hypogonadotrop- hypogonadism
  3. Delayed puberty
  4. Treated with hormone replacement therapy
37
Q

II. GENETICS OF SEX
8B. What are the genetic features of Androgen insensitivity syndrome?

A
  1. Mutations in KAL1 gene (among others)
  2. X chromosome, PAR1
  3. Encodes a cell adhesion protein which has a role in neuronal migration
  4. Part of these stem cells migrate to the olfactory nerve, another part to the hypothalamus during development.
  5. No gonadotropin-releasing hormone (GHRH): failure in gonadal differentiation
38
Q

II. GENETICS OF SEX
9. What are the genetic features of Congenital adrenal hyperplasia (CAH)

A
  • CYP21A2 mutation
  • male genitals in the case of girl babies,in male babies, an enlarged penis, slow rate of weight gain, weight loss, dehydration (dehydration),
    male pattern hair and deep voice (virilisation) in female patients)
39
Q

III. ONCOGENETICS
1. How does cancer arise from DNA mutations in cells

40
Q

III. ONCOGENETICS
2. Describe Cancer as a genetic disorder

A
  1. In our lives, there is about 40% chance of developing cancer of any type
  2. Tumors are in only <10% of Mendelian inheritance, but the GENOTYPE (genetic background) AFFECTS OUR OVERALL CANCER RISK (complex trait/disease).
  3. A multi-stage process; characterized by accumulation of somatic mutations, derived from one cell (clonality).
41
Q

III. ONCOGENETICS
3. Describe Tumor evolution

A
  • On average, each cancer genome carries four or five driver mutations, which provide cancer cells with a selective advantage.
  • Only 5% of tumors studied had no identified driver aberrations.
  • Many cancers exhibited hallmarks of genomic catastrophes called chromoplexy (17.8% of tumours) and chromothripsis (22.3%), which result in major structural changes to the genome.
42
Q

III. ONCOGENETICS
4. What is germline mutation?

A

A change in the DNA sequence that can be inherited from either parent

43
Q

III. ONCOGENETICS
5. What is Somatic mutation?

A
  • A change in the DNA sequence in cells other than sperm or egg
  • The mutation is present in the cancer cell and its offspring, but not in the patient’s healthy cells
44
Q

III. ONCOGENETICS
6. What are differences between germline and somatic mutation in relation to cancer?

A
  • Most cancer is the result of acquired, or somatic, mutations that occur in a cell.
  • Cancers that occur because of somatic mutations are referred to as sporadic cancers.
  • Somatic mutations are often caused by environmental and lifestyle
  • Cancers caused by germline mutations are called hereditary cancers and account for 5-10% of all cancers.
45
Q

III. ONCOGENETICS
7. What are sporadic cancers?

A
  • Cancers that occur because of somatic mutations
46
Q

III. ONCOGENETICS
8. What are hereditary cancers?

A

Cancers caused by germline mutations are called hereditary cancers and account for 5-10% of all cancers.

47
Q

III. ONCOGENETICS
9. Describe somatic tumor formation

A
  • Multistep carcinogenesis, a series of successive mutations, some of which contribute to tumour growth/persistence (evolutionary advantage
    => these are driver mutations (x)
  • Other sequence changes occur randomly, but play no role in tumour evolution (passanger mutations)
48
Q

III. ONCOGENETICS
10. Describe hereditary/germline tumorigenesis

A
  • Germline mutations are inherited and present in all cells of the body
  • Tumor formation can affect multiple organs (tumor syndromes)
  • The first step of multistep tumor formation is already given, less time is needed
    +) usually appears at a younger age
    +) but it is ‘only’ a predisposition, the occurrence of further mutations is not a matter of course: inherited variation often influences the type of mutations that occur later
    +) often a distinctive ‘final’ mutation spectrum and distinctive pathological/biological presentation - the possibility of individual therapy
49
Q

III. ONCOGENETICS
11. What is the Importance of DNA changes in human cancer?

A
  1. Only 5 –10% of cancer cases have a clear hereditary component
  2. e.g. BRCA1 and BRCA2 in breast cancer
  3. Even in those cases where susceptibility is clearly inherited, somatic changes are required for cancer to develop
50
Q

III. ONCOGENETICS
12. What are driver and passenger mutation?

A
  1. Driver mutation: confers a selective growth advantage
  2. Passenger mutation: has no effect on the fitness of a clone
51
Q

III. ONCOGENETICS
13. The majority of cancer is caused by germline mutations.
=> T/F?

A

FALSE!
=> The majority of cancer is caused by somatic mutations.

52
Q

III. ONCOGENETICS
13. Usually several mutations are needed for tumor development.
=> T/F?

53
Q

III. ONCOGENETICS
14. What are the features of Driver mutations?

A
  • Many protein-coding driver mutations occur in single-site ‘hotspots’.
  • The most frequently mutated sites were well- studied hotspots in cancer genes
54
Q

III. ONCOGENETICS
15. Give the Typical timelines of tumor development

A
  • In colorectal adenocarcinoma, for example, it were find APC mutations to have the highest odds of occurring early, followed by KRAS, loss of 17p and TP53, and SMAD4
  • Whole-genome duplications occur after tumors have accumulated several driver mutations, and many chromosomal gains and losses are typically late.
55
Q

III. ONCOGENETICS
16A. What are the 3 types of most commonly mutating driver genes of tumors?

A
  1. Oncogenes
  2. Tumor suppressor genes
  3. Mutator genes
56
Q

III. ONCOGENETICS most commonly mutating driver genes of tumors
16B. What are the features of oncogenes?

A

Dominant mutations, usually somatic

57
Q

III. ONCOGENETICS - most commonly mutating driver genes of tumors
16C. What are the features of Tumor suppressor genes?

A

recessive mutation in cellular level, but they often result in a dominantly inherited predisposition

58
Q

III. ONCOGENETICS - most commonly mutating driver genes of tumors
16C. What are the features of Mutator genes?

A
  • play a role in DNA repair, germline and somatic mutations.
  • Dominantly inherited predisposition or AR tumorigenic syndrome may be caused
59
Q

III. ONCOGENETICS
17. In Oncogenes and tumor suppressors, what can the uncontrolled growth be caused by?

A
  • a gain-of-funtion mutation of a proto-oncogene, which leads to an oncogene
    or
  • a loss-of-function mutation of a tumor suppressor gene.
    => The loss-of-function mutations are more common than the gain of function mutations, even if both alleles are mutated.
60
Q

III. ONCOGENETICS
18. What is the difference between Proto-oncogene and Oncogene?

A
  1. Proto-oncogene
    - Def.: genes that regulate cell division => Normal cell division
  2. Ocogene
    - Def: mutated or over-expressed proton-oncogene
    => Uncontrolled cell division leading to tumor formation
61
Q

III. ONCOGENETICS
19. Give an of Point mutations (Oncogenic mutations)

A
  • Mutations in the Ras genes (Hras, Nras, Kras) are the most frequent oncogenic mutations
  • Gly12Val point mutation in the Ras genes
    → the ability of the active Ras protein to hydrolyze GTP decreases
    → signalling is continuously active, independently of the external ligands
    → proliferation ↑
62
Q

III. ONCOGENETICS
20. What are the features of Loss of heterozygosity?

A
  • The main cause tumor suppression is the LOH = loss of heterozygosity.
  • The most common mutations in tumors affect:
    +) the RAS oncogene
    +) the P53 tumor suppressor gene (they occur in > 60% of all cancers).
63
Q

III. ONCOGENETICS
21. What is Knudson two hits hypothesis?

64
Q

III. ONCOGENETICS
22. What are the features of TP53 Tumor Suppressor Gene?

A
  • The tumor suppressor p53 is found mutated in roughly 60% of human cancers!
  • Inheritance of one mutant p53 allele results in the Li-Fraumeni syndrome, in which a rare form of cancer develops in several tissues
  • Tumors arise when the 2nd allele is mutated, so the trait is inherited as autosomal recessive
65
Q

III. ONCOGENETICS
23A. What are the features of Retinoblastoma Tumor Suppressor, RB?

A
  • Retinoblastoma is the most common eye tumor in children; surgery and radiation is effective (90%
  • 2 forms of Retinoblastoma: unilateral and bilateral.
66
Q

III. ONCOGENETICS
23B. Retinoblastoma Tumor Suppressor, RB
=> What are the features of unilateral Retinoblastoma

A
  • Unilateral, sporadic retinoblastoma develops in children with no family history
67
Q

III. ONCOGENETICS
23C. Retinoblastoma Tumor Suppressor, RB
=> What are the features of Bilateral Retinoblastoma

A

Bilateral, hereditary retinoblastoma is the paradigm of Alfred Knudson’s two- hit mutation model, stating two mutations are required for RB development

68
Q

III. ONCOGENETICS
24A. What are the features of Mutator genes?

A
  • Cancer is caused by mutations, so factors that increase mutation rate will increase cancer rate.
  • Many environmental factors (carcinogens) also cause DNA damage or mutations, that can lead to cancer
69
Q

III. ONCOGENETICS
24B. Give examples of Mutator genes that would increase mutation rate?

A

BRCA1 and BRCA2

70
Q

III. ONCOGENETICS
25. How can Chromosome translocation result in chimeric protein?

A
  • Philadelphia chromosome = t(9;22)
  • BRC-ABL fusion – increased tyrosine-kinase activity
  • CML and ALL
  • Medication: Gleevec
    (Imatinib)
71
Q

III. ONCOGENETICS
25. Epigenetics
=> What is happening here?

72
Q

III. ONCOGENETICS
26. Epigenetics
=> What is happening here?

A
  1. Epigenetic inactivation
  2. Epigenetic depression
73
Q

III. ONCOGENETICS
27. What are the features of LOI (Loss of imprinting)?

A
  • Oncogenes
    – e.g. IGF2 (insulin-like
    growth factor = somatomedin A)
  • In normal cells only the paternal allele is expressed.
  • In colon cancer the maternal allele is expressed, as well.
  • relationship between oncogenes and epigenetics
74
Q

III. ONCOGENETICS
28. What is the role of DNA oncoviruses?

A

DNA oncoviruses (e.g. human papilloma virus (HPV) typically cause cancer by inactivating p53 and Rb, thereby inhibiting the function of these tumor suppressors.

75
Q

III. ONCOGENETICS
29. Give an example of DNA oncoviruses

A

HPV: infects the mucosa and underlying progenitor cells. Depending on the subtype of the virus cervix or head and neck cancer risk increases.

76
Q

III. ONCOGENETICS
30. Describe Genetic heterogeneity in cancer evolution

A

Tumour heterogeneity :
- existence of subpopulations of cells, with distinct genotypes and phenotypes
- divergent biological behaviours, within a primary tumor and its metastases, or between tumours of the same histopathological subtype (intra- and inter- tumour, respectively).

Genetics and genomes (19 decks)

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