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Genetics Flashcards

1
Q

Normal human karyotype

A

46 chromosomes - 2n (22 pairs of autosomes and a pair of sex chromosomes)

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2
Q

Chromosome structure

A

Each chromosome consists of a short (p) and long (q) arm joined at the centromere

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3
Q

Telomere

A

Telomere - seal ends of chromosomes and maintain structural integrity (repetitive sequence of thymine)
Telomerase replaces 5’ end of long strand during DNA replication making strand shorter until it can no longer divide

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4
Q

Chromosome classification

A

• centrally = metacentric
• terminal = acrocentric (13,14,15,21,22 - Robertsonian chromosomes)
• intermediate position = submetacentric

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5
Q

Mitosis

A

process by which chromatically separate and divide in to two separate cells
Usually lasts 1 to 2 hours
5 distinct stages: prophase, prometaphase, metaphase, anaphase and telophase

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6
Q

Prophase

A

chromosomes condense, mitotic spindle begins to form, two centrioles begin to form and move to opposite poles (microtubules begin to form from alpha/ beta tubulin)

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7
Q

Prometaphase

A

nuclear membrane disintergrates and chromosomes attach to microtubules by centromeres

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8
Q

Metaphase

A

chromosomes line along equatorial plate of cell to form mature spindle- chromosomes maximally contracted so visible X shape

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9
Q

Anaphase

A

centromere of each chromosome divides longitudinally and 2 daughter chromatids separate to opposite poles of cell

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10
Q

Telophase

A

2 groups of chromatids become surrounded by nuclear membrane

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11
Q

Cytokinesis

A

cell cytoplasm divides to form two new diploid daughter cells

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12
Q

Interphase

A

G1 - chromosomes become thin and extended (variable in length so accounts for change in generation time. Cells that have stopped dividing, e.g. Neurones, arrest in this phase = G0)
S - DNA replication occurs and the chromatin of each chromosome is replicated (homologous pairs replicate in synchrony but 1 of X chromosomes is always late as is inactive X chromosome that forms the sex chromatin which viewed in interphase of female somatic cell)
G2 - chromosomes begin to condense

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13
Q

Importance of mitosis

A

• producing 2 genetically identical daughter cells to parent cell
• growth
• replace dead cells

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14
Q

Clinical relevance of mitosis

A

• detecting chromosomal abnormalities
• categorising tumours as benign or malignant
• grading malignant tumours

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15
Q

Meiosis

A

the process of nuclear division that occurs in final stages of gamete formation

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16
Q

Prophase I

A

chromosomes are already split longitudinally into 2 chromatids joined at centromere. Homologous chromosomes pair (with exception of X and Y in males where pairing only occurs at tip of shorter arms called pseudoautosomal region) and crossing over may occur, exchange of non-sister chromatid alleles.

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17
Q

Metaphase I

A

the nuclear membrane disappears and chromosomes become aligned on the equatorial plane of cell- attached to spindle

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18
Q

Anaphase I

A

chromosomes separate to opposite poles as spindle contracts (independent assortment)

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19
Q

Telophase I

A

each set of haploid chromosomes separated so cleaves to form 2 new daughter gametes (secondary spermatocytes or oocytes)

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20
Q

Meiosis II

A

same as mitotic division to form 4 haploid (n) new daughter gametes (spermatids or ova)- genetically different

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21
Q

Preventing mutations during cell replication/division

A

• genetic material protected in stem cells as rapid cell division occurs in daughter cells not stem cells
• 3 checkpoints: at end of G1 restriction point, needs external growth factor for cell division to continue; in G2 checkpoint looks for damage and unreplicated DNA, can stop cell cycle and kill cell to prevent replication of mutated DNA controlled by P53 but gene for P53 is often mutated in cancer cells leading to uncontrolled cell division; S phase checkpoint by RPA protein itstabilises the replication fork and coordinates repair

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22
Q

3 Main differences between mitosis and meiosis

A
  1. Mitosis = diploid cells, meiosis = haploid cells
  2. Mitosis occurs in somatic cells and early stages of gamete formation, meiosis occurs only at final stage of gametic maturation
  3. Mitosis = one cell division, meiosis = 2 cell divisions
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23
Q

3 cell populations

A

• permanent cells- cells that never divide G0 eg neurones
• Labile cells- cells that constantly divide eg epidermis
• stable cells- spend most of time in G0 but can be induced to re-enter cell cycle eg liver cells

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24
Q

Stopping mitosis

A

Mitotic spindle - taxol or vinca alkaloids (vinblastine, vincristine)
Spindle poles- ispinesib
Anaphase - colchicine-like drugs- form ring structures

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25
Q

Oogenesis

A

mature ova develop from oogonia which themselves originate from primordial germ cells by a process involving 20-30 mitotic divisions that occur in first few months of embryonic life.
By completion of embryogenesis at 8 months of intrauterine life, the oogonia have begun to mature into primary oocytes that undergo meiosis.
At birth, all enter a maturation arrest phase (dictyotene) in which remain suspended until meiosis I is completed at time of ovulation, when a single secondary oocyte is formed that receives most of cytoplasm. Other daughter cell is a polar body (largely consists of nucleus). Meiosis II then occurs (fertilisation can occur) resulting in 2 more polar bodies- meiosis II only completed if fertilisation occurs

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26
Q

Older mothers and non-disjunction

A

Lengthy interval between onset of meiosis and completion accounts for increased incidences of chromosomal abnormalities in offspring of older mothers: damage to cell’s spindle formation and repair mechanisms, leading to non-disjunction

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27
Q

When does meiosis I complete for oogenesis

A

Time of ovulation

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28
Q

When does meiosis II complete for oogenesis

A

Fertilisation

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29
Q

Spermatogenesis

A

at puberty spermatogonia begin to mature into primary spernatocytes which enter meiosis I and emerge as haploid secondary spermatocytes. Then undergo second mitotic division to form spermatids, which develop into mature spermatozoa

Continuous process so many mitotic divisions leading to new dominant mutations due to consequences of DNA copy errors in interphase (s)

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30
Q

Numerical chromosomal abnormalities

A

loss or gain of one or more chromosomes (aneuploidy) or the addition of one or more complete haploid components (polyploidy). Loss of a single chromosome - monosomy

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31
Q

Trisomy

A

presence of an extra chromosome eg downs syndrome is presence of additional 21 chromosome. Usually caused by failure of separation of one of pairs of homologous chromosomes during anaphase I or less often when sister chromatids fail to separate in anaphase II- non-disjunction

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32
Q

Trisomy conditions

A

Patau syndrome (trisomy 13)
Edward’s syndrome (trisomy 18)
1st trimester miscarriage (trisomy 16)
Down’s syndrome (trisomy 21)

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33
Q

Monosomy

A

absence of a single chromosome. For an autosome, usually not carried to full term. Turner syndrome - lack of X or Y chromosome resulting in 45,X karyotype. Can be caused by non-disjunction or anaphase lag (loss of chromosome during anaphase)

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34
Q

Polyploidy

A

cells contain multiple of the haploid number of chromosomes
Triploidy (69) can be caused by failure of maturation meitotic division in an ovum or sperm(eg retention of polar body or diploid can be caused by fertilisation of an ovum by 2 sperm (dispermy)
2 paternal = swollen placenta/ 2 maternal = small placenta - not carried to term

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35
Q

Down syndrome

A

• learning problems
• short stature
• characteristic facial appearance
• congenital heart disease
Additional 21 chromosome (trisomy)
47, XX/XY +21

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36
Q

Mosaicism

A

the presence in an individual or tissue of 2 or more cell lines that differ in the genetic constitution but are derived from a single zygote. Usually results from non-disjunction in early embryo mitotic division or can exist if a new mutation arises in a somatic or early germline cell division. Germline/ gonadal mosaicism = duchenne muscular dystrophy

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37
Q

Chimerism

A

the presence in an individual of 2 or more genetically distinct cell lines derived from more than one zygote. Dispermic chimeras - result of double fertilisation whereby 2 sperm fertilise 2 ova and the resulting 2 zygotes fuse to form one embryo (if different sex, XX/XY karyotype so hermaphroditism). Blood chimeras - exchange of cells, via the placenta, between non-identical twins in utero

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38
Q

robertsonian translocation

A

results from the breakage of 2 acrocentric chromosomes (13, 14,15, 21 and 22) at or close to their centromeres with subsequent fusion of their long arms - centric fusion. The short arms are lost so the total chromosome number is reduced to 45. (No gain or loss of genetic material as short arms only code for rRNA). Can predispose to birth of babies with Down syndrome as a result of embryo inheriting 2 normal 21 chromosomes and a translocation chromosome involving a 21 chromosome

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39
Q

dosage sensitive

A

Genes are dosage sensitive (normal dose is 2)- deletion or duplication causes an imbalance, causing a disease

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40
Q

deletion

A

loss of part of a chromosome and results in monosomy for that segment. Large deletion - Wolf-Hirschhorn and cri du chat. Submicroscopic microdeletions- Prader-Willi and Angelman syndrome

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41
Q

Insertion

A

when a segment of one chromosome becomes inserted into another

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42
Q

Inversion

A

a two-break rearrangement when a segment is reversed in position. If involves centromere, pericentric inversion. If only one arm, paracentric inversion- results in recombinant chromosomes (acentric cannot undergo mitotic division. Dicentric are unstable during cell division)

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43
Q

Ring chromosomes

A

when a break occurs on each arm of a chromosome leaving two ‘sticky’ ends on the central portion that reunite as a ring. The two distal fragments are lost so if an autosome, serious effects

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44
Q

Isochromosome

A

loss of one arm with duplication of the other as centromere divided transversely not longitudinally (eg 2 long X chromosome arms = Turner syndrome)

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45
Q

Duplication

A

section is copied

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46
Q

Translocation

A

the transfer of genetic material from one chromosome to another. A reciprocal translocation is formed when a break occurs in each of 2 chromosomes with the segments being exchanged to form 2 new derivative chromosomes- a Robertsonian translocation is when the breakpoints are located at, or close to, the centromeres of 2 acrocetric chromosomes. Segregation at meiosis: they can segregate to generate significant chromosome imbalance leading to early pregnancy loss or birth of an infant with multiple abnormalities. Problems arise at meiosis as they cannot pair normally to form bivalents- instead form a cluster called a pachytene quadrivalent. When they separate they can:
1. If alternate chromosomes segregate, the gamete will carry a normal/ balanced haploid complement
2. If adjacent chromosomes segregate together, the gamete will acquire an unbalanced chromosome complement, leading to non-disjunction at fertilisation
3. 3 chromosomes can segregate to one gamete with only one chromosome in the other gamete. - tertiary trisomy

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47
Q

Balanced translocation

A

no gain or loss of DNA (same number of genes just swapped), so healthy human

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48
Q

Unbalanced translocation

A

loss or gain of DNA, causing a disease

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49
Q

Mosaicism

A

the presence in an individual or tissue of 2 or more cell lines that differ in the genetic constitution but are derived from a single zygote. Usually results from non-disjunction in early embryo mitotic division or can exist if a new mutation arises in a somatic or early germline cell division

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50
Q

Example of condition caused by Gondal mosaicism

A

duchenne muscular dystrophy

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51
Q

Chimerism

A

presence in an individual of 2 or more genetically distinct cell lines derived from more than one zygote.

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52
Q

Dispermic chimeras

A

result of double fertilisation whereby 2 sperm fertilise 2 ova and the resulting 2 zygotes fuse to form one embryo (if different sex, XX/XY karyotype so hermaphroditism)

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53
Q

Blood chimeras

A

exchange of cells, via the placenta, between non-identical twins in utero

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54
Q

DNA composition

A

nucleic acid is a long polymer of nucleotides (each composed of a nitrogenous base, deoxyribose, and a phosphate molecule) with phosphodiester bonds between 3’ and 5’ carbons on adjacent sugars
• purine bases: guanine, adenine. Pyrimidine bases: cytosine, thymine, uracil
• 2 anti-parallel chains in a double helix joined by hydrogen bonds between complementary bases- a purine always pairs to a pyrimidine: G&C (3 hydrogen bonds) and A&T (2 hydrogen bonds)

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55
Q

DNA semiconservative replication

A

allows replication and self-repair
1. Helix unwound by topoisomerase and strands separated by DNA helicase breaking hydrogen bonds
2. Single stranded binding (SSB) protein coat the strand to prevent team taking or snapping back together and exposed bases act as a template for free DNA nucleotides to bond to by complementary base pairing
3. Primate enzyme synthesises a short RNA primer
4. DNA polymerase joins nucleotides together by forming phosphodiester bonds in 5’ to 3’ direction. Replication fork= leading strand synthesised in continuous process. Lagging strand synthesised in Okazaki fragments which are then joined by DNA ligase
5. DNA replication progresses in both directions from points of origin to form replication bubbles which fuse to form 2 identical daughter molecules
6. (RNAse H recognises RNA primers bound to the DNA template and hydrolyses them and DNA polymerase can fill in the gaps)

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56
Q

Which enzyme unwinds DNA helix

A

Topoisomerase

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57
Q

Which enzyme breaks hydrogen bonds

A

DNA helipads

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58
Q

Which enzyme synthesises short RNA primer

A

Primate enzyme

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59
Q

Which enzyme joins together nucleotide bases

A

DNA polymerase

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60
Q

Which enzyme joins Okazaki fragments

A

DNA ligase

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61
Q

Which enzyme hydrolyses RNA primers

A

RNAse H

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62
Q

Coiling of DNA

A

DNA is coiled around a histone to form nucleosomes (8 histone proteins)
Tertiary coiling of nucleosomes forms chromatin fibres that form long loops which coil further- the solenoid model. Chromatin condenses into visible aggregates (chromosomes)

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63
Q

Who suggested dna structure

A

Watson and Crick in 1953 based on X-ray diffraction studies

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64
Q

Telomere

A

seal ends of chromosomes and maintain structural integrity (repetitive sequence of thymine)
Telomerase replaces 5’ end of long strand during DNA replication making strand shorter until it can no longer divide

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65
Q

Degenerate but unambiguous

A

amino acids coded for by more than one codon but each codon is specific to one amino acid

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66
Q

Almost universal

A

same in all organisms apart from fewer than 10 exceptions

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67
Q

Non-overlapping

A

Each nucleotide is only read once

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68
Q

Telomerase

A

replaces 5’ end of long strand during DNA replication making strand shorter until it can no longer divide

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69
Q

Nuclear DNA sequence

A

genes, unique single copy (code for polypeptides), multigene families (arisen through gene duplication eg alpha and beta globin gene), classic gene families (high sequence homology eg numerous copies of genes coding for rRNA), gene superfamilies (limited sequence homology but functionally related)

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70
Q

Extragenic DNA

A

tandem repeat, satellite, minisatellite, telomeric

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71
Q

Mitochondrial DNA

A

2 rRNA genes and 22 tRNA genes

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72
Q

RNA

A

Single-stranded molecule that forms an alpha helix and is relatively short
Contains uracil instead of thymine and ribose instead of deoxyribose

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73
Q

mRNA

A

formed by transcription of DNA and allows flow of genetic material from nucleus to ribosome. Consists of a leader sequence (with a guanosine cap) at the 5’ end, a coding region and a trailer sequence at the 3’ end with a poly(A) tail

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74
Q

tRNA

A

single-stranded 3D RNA (clover -shaped formed by hydrogen bonds) that carries amino acids to ribosomes during translation through base pairing the anticodon with the codon of mRNA
- at least 20 types

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75
Q

rRNA

A

folded RNA which forms aggregates with ribonuclease proteins in ribosomes. Contains many loops and exhibit extensive base pairing in the regions between loops. It has enzymatic properties that catalyse the formation of peptide bonds between amino acids

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76
Q

Allele

A

alternative form of a gene at a specific locus

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77
Q

Law of uniformity

A

when 2 homozygotes with different alleles are crossed, all of the offspring in the F1 generation are identical and heterozygous

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78
Q

Law of segregation

A

each person possesses 2 genes for a particular characteristic, only one of which can be transmitted at any one time

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79
Q

Law of independent assortment

A

(Mendel’s 2nd law) = members of different gene pairs separate to offspring independently of one another

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80
Q

Genome

A

all the genes and non-coding DNA in the body

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81
Q

3 types of genome

A
  1. Germline - genome in the sperm/eggs. Passed from parent to child- heritable
  2. Somatic - genome found in every other tissue. Not heritable
  3. Mitochondrial - found only within the mitochondria. Heritable
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82
Q

Non-coding DNA

A

promoter sequence (transcription factors binds), introns, enhancers, terminators

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83
Q

Phenotype

A

the physical or behavioural characteristics of an organism that results from the interaction between its genotype and environment

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84
Q

Mutagenesis

A

an alteration to the genomic code by exposure to a substance- mutation. Can be in the womb or post natal eg in carcinogenesis, exposure to radiation

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85
Q

Teratogenesis

A

a damaging effect on embryonic/ fetal development by exposure to a substance eg virus causing cell death, toxin interrupting blood supply. Some teratogens are also mutagens. Teratogens eg smoking, alcohol

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86
Q

Monogenic

A

caused by a single gene mutation

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87
Q

Somatic

A

disease causing mutations are found in the affected tissue (cancer)

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88
Q

Malformation

A

intrinsic issue with development of an organ or tissue eg congenital heart disease. Commonly genetic

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89
Q

Deformation

A

extrinsic factors impinge upon development of an organ eg compression from womb due to no amniotic fluid (due to no kidneys in baby so no urine), blood clot leading to loss of limb. Less commonly genetic

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90
Q

Minor malformation

A

more than 2, consider underlying genetic condition

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91
Q

Major malformation

A

consider underlying genetic condition

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92
Q

Teratogens mechanism

A

Affects development of tissues not genes

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93
Q

Splice site

A

codes in DNA to move a portion of RNA. Second most common section for mutations

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94
Q

Major histocompatibility complex

A

located on chromosome 6
• group of genes that code for proteins found on the surfaces of cells that help the immune system recognize foreign substances

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95
Q

DNA repair

A

• mismatch repair
• DNA base excision

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96
Q

Dual excision

A

a short section of single stranded DNA (25ish nucleotides) containing the lesion is removed

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97
Q

Micro satellite instability

A

condition that arises when a mutation develops in the mismatch repair genes so the cell can no longer repair errors (insertions or deletions) leading to an increased mutation rate

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98
Q

Proband

A

individual of interest on pedigree drawing
Indicated by an arrow

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99
Q

Pedigree chart: square

A

Male

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100
Q

Pedigree chart: circle

A

Female

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101
Q

Pedigree chart: diamond

A

Gender unknown

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102
Q

Pedigree chart: diagonal line through symbol

A

Person deceased

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103
Q

Pedigree chart: brackets around a symbol and a dashed line

A

Adopted

104
Q

Pedigree chart: P in symbol

A

Pregnant

105
Q

Pedigree chart: 2 lines from same symbol

A

Non-identical twins

106
Q

Pedigree chart: 2 lines from same symbol with horizontal line joining

A

Identical twins

107
Q

Pedigree chart: triangle

A

Pregnancy loss eg miscarriage, still birth, elective abortion

108
Q

Pedigree chart: line through connecting line

A

Estranged

109
Q

Pedigree chart: number in symbol

A

Multiple of same gender and generation

110
Q

Pedigree chart: shaded in symbol

A

Affected by disease

111
Q

Pedigree chart: half shaded symbol

A

Carrier of disease

112
Q

Percentage of DNA that is coding

A

1.5%
20000-22000 genes coding for proteins in humans

113
Q

Autosomal dominant inheritance

A

manifests in the heterozygous state (tends to be toxic gain-of-function variants) eg toxic mRNA molecule in cell which is too long and doesn’t break down so poisons the cell

Usually multiple generations affected

Transmission by individuals of both sexes to both sexes

Males + females affected in equal proportions (but can be more common in one sex eg breast cancer)

114
Q

What causes variety in frequency of genetic disorders

A

environment (eg sickle cell disease and malaria), isolation and cultural differences
Carrier frequency for recessive conditions varies by population

115
Q

Autosomal inheritance

A

Inheritance of a trait or disorder by a gene on an autosome- usually more than one gene

116
Q

Pleiotropy

A
  • A single gene that may give rise to 2 or more apparently unrelated effects eg tuberous sclerosis affects learning difficulties, a facial rash (adenoma sebaceum), epilepsy or subungual fibromas
117
Q

Variable expressivity

A

dominant disorders can show variation from person to person

118
Q

Penetrance

A

percentage of individuals who have a certain genetic variant who develop a condition because of it

119
Q

Age-related penetrance

A

percentage of individuals with a genetic variant who develop a condition at a given age- important for diagnosis and preventative measures

120
Q

Reduced penetrance

A

individuals with a heterozygous gene mutation that show very few abnormal clinical features, may be due to modifying effects of other genes and interaction of gene with environmental factors.

121
Q

Non-penetrance

A

no features of a disorder

122
Q

Recurrence risk

A

an affected person has 50% chance of having an affected child (for each pregnancy)

123
Q

Homozygosity- autosomal dominant

A

may be more/less severely affected or have an earlier age of onset

124
Q

Anticipation

A

onset of the disease occurs at an earlier stage in offspring than parents or disease occurs with increasing severity in subsequent generations. As a result of the expansion of unstable triplet repeat sequences- larger sequence, more severe

125
Q

De novo mutations

A

newly arised mutation- the disease causing genetic variant occurs in either the sperm or the egg, or during early embryo cell division (in zygote). An unaffected parent has a child with an autosomal dominant condition- not inherited- mutation in germline (more common in sperm due to more cell divisions so mutations more likely)

Associated with increased age of the father as a result of large number of mitotic divisions male gametes undergo

126
Q

Co-dominance

A

two allelic traits that are both expressed in the heterozygous state eg blood group

127
Q

Autosomal recessive inheritance

A

manifest when mutant allele is homozygous. Heterozygous individuals are carriers but unaffected. (Tends to be loss of function gene eg loss of function of enzyme)

Usually one generation affected

Parents can be related (consanguineous)

Males + females affected in equal proportions (but can be more common in one sex eg breast cancer)

128
Q

Carrier frequency

A

If 2 carriers, 25% chance of being affected. If not affected, 2/3 chance of being a carrier (if have affected sibling)

129
Q

Consanguinity

A

the rarer the recessive trait, the greater the frequency of related parents (consanguinity)- increase chance of recessive conditions

130
Q

Pedigree chart: double line between symbols

A

Married but related

131
Q

Pseudodominace

A
  • if an homozygous and heterozygous have offspring, 50% chance of being affected
132
Q

Locus heterogeneity

A

conditions due to mutations in more than one gene/ same condition by different gene mutations

133
Q

Genocopies

A

disorders with same phenotype from different loci

134
Q

Compound heterogeneity

A

two different mutations at the same locus causing the disease as both genes non-functional so same as Homozygosity

135
Q

Allelic polymorphism

A

When more than one allele can be found for a given gene within the normal population

136
Q

Locus heterogeneity

A

An allele is one of a number of alternative forms of the same gene found at the same genetic locus

137
Q

Allelic/mutational heterogeneity

A

Lots of different mutations in one gene cause a condition eg cystic fibrosis

138
Q

Cystic fibrosis

A

• most common recessive condition affecting Northern European population
• incidence of ~ 1 in 2500
• carrier frequency 1/25
• F508 mutation in CFTR gene on 7q31.2
• over 1000 mutations (mutational heterogeneity)
• standard carrier testing detects top 29 mutations (~90%)
• sweat testing (salt levels in babies sweat) = diagnostic test (not genetic analysis)

139
Q

Neurofibromatosis type 1 (NF1)

A

• Dominant disorder
• Most affected people only have skin signs (café-au-lait macules and neurofibromas)
• Small % have epilepsy and learning problems
• Different seventy of symptoms with same genetic variant (variable expressivity)

140
Q

X-linked inheritance

A

The pattern of inheritance shown by genes that are located on either of the sex chromosomes

X chromosomes = X-linked
Y chromosome = Y-linked or holandric inheritance

141
Q

Male-male transmission

A

in a family shows condition is not X- linked

142
Q

Duchenne muscular dystrophy

A

affected men (mostly)
• mutation in the dystrophin gene on the X chromosome
• absence of dystrophin protein in skeletal muscle
• limb weakness in males
• eventual use of a wheelchair
• Raised serum creatine kinase CK

143
Q

Gondal mosaicism

A

de novo mutation only found in the ovary, not in blood DNA of mother. No Clinical test for this. Could offer a prenatal test (amniocentesis)

144
Q

X-linked recessive inheritance

A

a trait determined by a gene carried on the X chromosome and usually manifests only in males (a male with a mutant allele on his single X chromosome is hemizygous)
• transmitted by usually healthy heterozygous female carriers to affected males, as well as by affected males to their obligate carrier daughters (consequent risk to male grandchildren - diagonal pattern of transmission)
• male cannot transmit an X-linked trait to his son as receives Y sex chromosome
• for a carrier female, each son has a 50% chance of being affected and each daughter has a 50% chance of being a carrier
• many diseases eg Duchenne muscular dystrophy transmitted via female carriers or new mutations as males rarely survive to reproductive age

145
Q

Variable expression

A

in several X-linked disorders heterozygous females have a mosaic phenotype with a mixture of features of the normal and mutant alleles. Due to random process of X-inactivation

146
Q

Females affected with X-linked recessive disorders can be due to:

A

Homozygosity
Skewed x-inactivation
Numerical x-chromosome abnormalities
X-autosome translocations

147
Q

Skewed x-inactivation/ lyonisation

A

Lyonisation (random X-inactivation) = female cells randomly inactivate one of their X chromosomes during embryogenesis. If through chance, the healthy X chromosome is inactivated more than the mutated X chromosome in a given tissue it will cause disease. Skewed X inactivation - 80% of cells show preferential inactivation of one X chromosome (should be 50:50), can do on blood or affected tissue eg muscle

148
Q

Numerical x-chromosome abnormalities

A

if only has one X chromosome and it is mutated eg Turner syndrome

149
Q

X-autosome translocations

A

if breakpoint of translocation disrupts gene on X chromosome female can be affected

150
Q

Barr body

A

transcriptionally inactive X chromosome

151
Q

X-linked dominant inheritance

A

both males and females (generally less severely) are affected
• Affected males can transmit the disorder to their daughters but not sons
• eg hypophosphatemia (vitamin D-resistant rickets) - affected with short stature

152
Q

Examples of X-linked dominant inheritance

A

Rett syndrome or Alport’s syndrome

153
Q

Non-Mendelian inheritance

A

a disease not explained by a dominant, recessive or x-linked mode of inheritance.

154
Q

SNP

A

single nucleotide polymorphism: a genomic variant at a single base position in the DNA

155
Q

Multi factorial inheritance

A

the risk of the condition in relatives of an affected individual is much higher than in the general population
• the incidence of the condition is greatest amongst relatives of the most severely affected patients
• risk is greatest for first degree relatives and decreases for more distant relatives
• if more than one affected close relative then the risks for other relatives are increased

156
Q

Liability

A

genetic risk interacting with environmental exposure- can be considered as a single entity. Continuous normal distribution- a threshold exists above which the disease occurs

157
Q

GWAS (genetic wise association)

A

based on SNPs genetic sequencing to see if certain SNPs are more common in healthy or diseased population to identify location of genetic variation causing disease- can then tell risk- association between genotypes and phenotypes

158
Q

Somatic mosaicism

A

certain issues have genetic variant and some do not
• Not inherited
• can form cancer after exposure to a mutagen (mutation occurs in stem cell within a tissue). More serve genetic changes occur as tumour grows and progresses
• can cause a developmental disorder (localised overgrowth) for autosomal dominant genes

159
Q

Mitochondrial disease

A

16.5kB mitochondrial chromosome- mtDNA and some genes on chromosome 1 code for respiratory enzymes
• Mitochondrial DNA has a higher rate of spontaneous mutation that nuclear DNA
• mitochondria produce energy in form of ATP- symptoms occur due to a lack of energy to drive cellular functions

• greater proportion of mutant mitochondria in a cell/tissue the more likely there is to be disease
• only ova large enough to contain significant numbers of mitochondria so all mitochondria derived from mother
• some ova can contain more mutated mitoxhrobdria than others in same female so offspring affected differently
• male with a mitochondrial disease cannot have an affected child

160
Q

Homoplasmy

A

All mitochondria in cell have same genetic code

161
Q

Heteroplasmy

A

certain proportion of mitochondria in a cell has genetic variant

162
Q

Imprinting disorders

A

2 copies of every gene- for certain genes either the maternal or paternal copy is ‘switched off’ - imprinted genes due to methylation of DNA
• disease can be caused when imprinting is altered or genes are switched on/off inappropriately
• deletion of active gene leads to disease
• eg Prader-Willi syndrome- deletion of male paternal gene at chromosome 15p, floppy baby, learning problems, obesity. Angelman syndrome - deletion of female paternal gene at chromosome 15p, below average size, epilepsy, learning problems

163
Q

Leber’s optic neuropathy

A

mutations in mitochondrial DNA which encode complex 1 (mitochondrial enzyme for generating ATP)
• gradual onset of painless visual loss- thinning of optic nerve
• males much more likely to be affected than females

164
Q

Mutation

A

heritable alteration or change in the genetic material
Can arise through exposure to mutagenic agents eg radiation/ benzopyrene (product of incomplete combustion of hydrocarbons, it is a DNA-adduct so reacts with bases to form a bulky group disrupting replication, or spontaneously through errors in DNA replication and repair

Ionising radiation: can damage bases, causes breaks in phosphate backbone
UV : damaged bases- forms thymine dimers

165
Q

Single nucleotide variants

A

change of one nucleotide (wild-type) to another nucleotide (mutant).

166
Q

Substitution mutation

A

replacement of a single nucleotide by another.
• most common type
• transition = replaced by same type of nucleotide (pyrimidine or purine) eg G and A or C and T
• transversion = replaced by other type of nucleotide
• transitions are more common than transversions

167
Q

Transition mutation

A

replaced by same type of nucleotide (pyrimidine or purine) eg G and A or C and T

168
Q

Transversion mutation

A

replaced by other type of nucleotide

169
Q

Silent/ synonymous mutations

A

the mutation does not alter the polypeptide product of the gene due to genetic code for some amino acids being degenerate. Usually substitution mutation

170
Q

Types of non synonymous mutations

A

Missense
Nonsense
Frameshift

171
Q

Deletion mutation

A

the loss of one or more nucleotides. Causes a frameshift and larger deletions may result in partial or whole gene deletions and may arise through unequal crossover between repeat sequences

172
Q

Insertion mutation

A

the addition of one or more nucleotides into a gene. Causes a frameshift.

173
Q

Missense mutation

A

single base-pair substitution can result in coding for a different amino acid and synthesis of an altered protein (a nonconservative substitution occurs if amino acid is chemically dissimilar so it leads to a reduction or loss of biological activity. A conservative substitution is the replacement with a chemically similar amino acid, and may have no functional effect.)

174
Q

Nonsense mutation

A

-a substitution that leads to a STOP codon, resulting in termination of translation, producing non-functional polypeptides. mRNA containing premature termination codons are frequently degraded by nonsense-mediated decay. Loss-of-function variant

175
Q

Frameshift mutation

A

a mutation involving insertion or deletion of nucleotides that are not a multiple of 3, disrupts reading frame so amino acid sequence is subsequently altered. Loss-of-function variant

176
Q

Splicing mutations

A

mutations of the highly conserved splice donor (GT) and splice acceptor (AG) sites usually result in different splicing. Can result in loss of coding sequence (exon skipping) or retention of intronic sequence (leading to frameshift mutations)- intron translated into protein. Loss-of-function variant

177
Q

Canonical splice sites

A

GT
AG

178
Q

Splice acceptor site

A

CGAT

179
Q

Copy number variants

A

deletion or duplication of a segment of chromosome. Can affect single exon or hundreds of genes. Deletions more likely harmful than duplications

180
Q

Trinucleotide repeat expansion

A

if triplet repeats expand in non-coding parts above a certain threshold RNA can’t be broken down, causing disease eg >30 CAG causes Huntingdon’s diseases. Forms an elongated, toxic mRNA which resists degradation

181
Q

Out-of-frame mutation

A

leads to formation of premature STOP codon. Nonsense-mediated decay. More likely to cause disease

182
Q

STOP codons

A

UAA
UAG
UGA

183
Q

In-frame mutations

A

multiple of 3 nucleotides. Lose/gain single amino acid can have few effects

184
Q

Variant is pathogenic if

A

• a de novo variant is more likely to be causing a medical condition
• The variant is found in several people in the family who have the disease (positive segregation)
• Absence if SNV from ‘healthy’ populations
• Computational tools predict damaging effect

185
Q

Variant is benign if

A

• variant is found in an unaffected parent
• Variant is found commonly in healthy populations
• Computational tools predict variant has no effect on gene function

186
Q

Trio testing

A

(testing parents) is important as variant inherited from a normal parent unlikely to be causal- de novo mutation instead. Compared to database of similar ancestry
Different genetic variants may need different tests to detect

187
Q

Comparative genetic hybridisation

A

can detect CNVs involving single exons (like ELISA test)
Exome = exons plus some splice sites (miss non-coding variants and trinucleotide repeats)
Genome = exons, promoters/enhancers, splice sites, trinucleotide repeats (can also detect CNVs)

188
Q

American college of medical genetics criteria (ACMG)

A

Pathogenic variant
Likely pathogenic variant
Variant of uncertain significance
Likely benign variant
Benign variant

189
Q

Why is genome sequencing the most comprehensive test

A

Genome gives more data than exomes but might miss mosaic changes (in blood) that exomes can detect as DNA is sequenced fewer times. Exomes don’t detect changes in non-coding regions

190
Q

Chorionic villous sampling

A

taking a sample of trophoblastic cells adjacent to placenta to aid genetic screening

191
Q

Exome

A

exons plus some splice sites (miss non-coding variants and trinucleotide repeats)

192
Q

Genome

A

exons, promoters/enhancers, splice sites, trinucleotide repeats (can also detect CNVs)

193
Q

Nonsense-mediated decay

A

mRNA containing premature termination codons are frequently degraded

194
Q

P53 gene

A

• DNA damage detected- initiate repair mechanisms
• Pause cell cycle until repair is carried out
• Halt cell cycle if DNA not repaired
• Apoptosis- command cell to commit suicide if DNA damage not repaired

195
Q

Tumour suppressor genes

A

code for proteins that carry out DNA repair, slowing the cell cycle, signalling apoptosis
A normal gene maintains constant rate of cell division so prevents tumour formation
Hypermethylation of DNA can occur preventing a transcription factor binding, meaning the gene is not transcribed and so leading to uncontrolled cell division
A mutation can produce non-functional polypeptides
Must inherit 2 mutated alleles as it is recessive

196
Q

Oncogenes

A

proto-oncogenes stimulate a cell to divide when growth factors attach to a cell membrane receptor which activates genes that cause DNA replication and mitosis
Oncogenes can become permanently activated-
• receptor protein activated, even when no growth factor
• oncogene may code for a growth factor that is produced in excessive amounts
Results in excessive cell division
Only inherit 1 mutated allele as dominant
Cancer cells have decreased methylation causing activation of genes that promote cellgrowth, loss of imprinting and chromosome instability (highly active = more likely to mutate)

197
Q

Therapeutic drugs targeting DNA replication

A

Inhibitors of nucleotide synthesis
DNA polymerase inhibitors
DNA template damaging agents
Inhibitors of DNA topoisomerase

198
Q

From genome sequence can infer:

A

• age, ethnicity, sexuality, reconstruct facial appearance
• Can use Y chromosome genetic markers to connect surnames to people
De-identification → criminal activity/ genomic inference → discrimination

199
Q

Newborns genome project

A

proposed to undertake genome sequencing at birth to screen for a greater range of treatable genetic disorders- population screening
• as don’t understand genetic variants, babies would require further testing
• May not develop disease, penetrance; variability; unfounded anxiety

200
Q

Predicative genetic testing

A

• individual without symptoms requests test for highly penetrant genetic variant causing a disease
• Autosomal dominant neurological conditions
• In mentally competent adults this can be seen to promote their autonomy provided no evidence of coercion by a third party
• For children (under 16) UK guidelines, under Gillick competence, are to only perform diagnostic tests in children or for conditions in which preventive treatment is required eg child bowel cancers. Parental anxiety is often main reason for requests. A non-competent child cannot make an autonomous decision so should not have presymptomatic tests

201
Q

Direct to consumer testing

A

• saliva sample
• Uses SNP ChIP, less commonly exome sequencing
• Rarely any clinical input and no consideration of family history
• Negative doesn’t mean zero risk- means you have no elevated risk compared to general population
• Associated with dustress due to lack of clinical advice; could result in inappropriate management or screening; can increase healthcare costs through additional referrals needed to manage direct to consumer results

202
Q

SNP microarray

A

uses known nucleotide sequences as probes to hybridise with the tested DNA sequences, allowing qualitative and quantitative single nucleotide polymorphisms analysis through signal detection

203
Q

Current issues for newborn genome sequencing

A

• what conditions to screen for?
• how to deal with adult onset genetic conditions?
• how reliable are genetic variants in predicting disease onset in these contexts?
• What if untreatable conditions are diagnosed?

204
Q

Advantages of screening

A

• informed choice
• Improved understanding
• Early treatment when available
• Reduction in births of affected homozygotes

205
Q

Ethical considerations of screening

A

• attendant risk and awareness of prenatal diagnosis may create a sense of guilt, especially if decision involves possible pregnancy termination (prognosis of disease cannot be stated with certainty due to variability or reduced penetrance or if hope of a treatment developed)
• pressure to participate causing mistrust and suspicion
• stigmatisation of carriers (social, insurance, employment)- discrimination
• irrational anxiety in carriers
• inappropriate reassurance if test is not 100% sensitive
• Confidentiality?
• Short circuits natural selection

206
Q

Invasive prenatal diagnosis

A

(amniocentesis)
Ending a pregnancy affected by familial genetic condition- but what is defined as a serious condition, perspectives of clinicians and patients vary
People with objectively ‘severe’ disease still report a good quality of life not a cause of suffering- many disagreed with prenatal testing for their condition

207
Q

Non-invasive prenatal diagnosis

A

(testing free fetal DNA extracted from maternal serum)- no increased risk of miscarriage, trisomy screening, bespoke sequencing for single gene disorders (usually paid for privately)

208
Q

Advantages of prenatal diagnosis

A

potential to facilitate autonomy by increasing information available to pregnant women;
more cost efffective than invasive tests

209
Q

Disadvantages of prenatal screening

A

potential to increase number of terminations;
increased chance of terminating healthy pregnancy;
equity of access;
screen out disabilities eg Downs Syndrome

210
Q

Preimplantation genetic testing

A

routine NHS procedure for genetic conditions before IVF- downplays risk of IVF

211
Q

Potential to select based on physical traits using PGT;

A

Genetic variants identified in GWAS as being associated with height, IQ, athleticism are used to select embryos- PGT-P (polygenic risk scores)

Tests for polymorphisms (likelihood of traits) not genetic variants that cause disease

212
Q

Methods of chromosome analysis:

A

Any tissue with living nucleated cells that undergo division can be used eg most commonly lymphocytes, skin, bone marrow
1. Sample added to a small volume of nutrient medium containing phytohemagglutinin which stimulates T lymphocytes to divide
2. Cells cultured in sterile conditions at 37°C for 3 days then colchicine added to each mixture (prevents spindle formation so cells arrested during metaphase when chromosomes maximally condensed)
3. Hypotonic saline added causing blood cells to lyse and results in spreading of chromosomes which are then fixed, mounted on a slide and stained.

213
Q

Chromosome G-banding

A

treated with typsin to denature protein content and then stained with a DNA binding dye (Giemsa) to give a pattern of light and dark bands (400-500 bands per set)

Each band = 6-8 Mbp

214
Q

Metaphase spreads

A

counting number of chromosomes

215
Q

Idiogram

A

chromosome banding pattern

216
Q

Fluorescence in-situ hybridisation (FISH)

A

can be used to detect and characterise subtle chromosome abnormalities: DNA probe is labeled with a fluorochrome which after hybridisation allows it to be visualised using a fluorescence microscope

217
Q

Types of FISH probes:

A

• centromic probes- consist of repetitive DNA sequences found in and around centromere (useful for aneuploidy syndromes)
• chromosome specific unique-sequence probes - specific for a particular locus (useful for deletions and duplications)
• whole-chromosome paint probes - a mix of probes to fluoresce an entire chromosome (useful for translocations)

218
Q

Euchromatin

A

stains lightly and consists of actively expressed genes

Increased acetylation of histones

219
Q

Heterochromatin

A

stains darkly and is made up largely of inactive, unexpressed, repetitive DNA

Increased methylation if DNA

220
Q

Inaccessible gene

A

Decreased acetylation
Increased methylation
More condensed
Heterochromatin
No access to TF
Inactive

221
Q

Accessible gene

A

Increased acetylation
Decreased methylation
Less condensed
Euchromatin
Access to TF
Active

222
Q

Epigenetics

A

How environmental influences, such as diet, stress and toxins, can subtly alter the genetic inheritance of an organism’s offspring, without changes to the DNA base sequence

223
Q

Epigenome

A

the second layer of chemical tags that cover DNA and histones, and so determines the shape of the DNA-histone complex
It is flexible so can be reversed
It is independent so occurs in different forms at different areas of the DNA

224
Q

Epigenetic imprinting

A

only inherit one working copy of a gene as one copy is epigenetically silenced through increased methylation of DNA during formation of oocytes and sperm
If a loss of imprinting- overproduction of proteins due to 2 active copies of gene

225
Q

Acetylation of histones

A

acetyl groups can be added to lysine amino acids on histone proteins- lysine has a positively charged R group, which forms ionic bonds with the negatively charged phosphate backbone of DNA
Acetylation to lysine residues removes the positive ion and removes a bond between the histone protein and DNA so the complex is less condensed -TF and RNA polymerase can bind more easily so gene transcribed and expressed
Deacetylation returns lysine to its positively charged state which has a stronger attraction to the DNA molecule and inhibits transcription

226
Q

Methylation of DNA

A

methyl groups can be added to a C atom on a cytosine base within
sequences with multiple C and G bases
The addition of methyl groups prevents the TF binding and attracts proteins that condense the complex by inducing deacetylation of histones so gene is not transcribed

227
Q

Penetrance

A

An index of the proportion of individuals with a gene mutation who show it

228
Q

Haploinsufficiency

A

Where a diploid organism only has a single functional copy of a gene (the other is inactive due to a mutation) and the single functional gene does not produce enough gene product to bring about a wild-type phenotype , resulting in disease

229
Q

When is anticipation seen

A

Trinucleotide repeat disorders

230
Q

ACMG Criteria

A

The American College of Medical Genetics and Genomics are used for the interpretation of sequence variants in Mendelian disorders. Variants are classified into five categories: pathogenic, likely pathogenic, uncertain significance (VUS), likely benign and benign.

231
Q

Down Syndrome

A

A congenital condition caused by trisomy 21 (an extra copy of all or part of chromosome 21).

232
Q

Edward’s syndrome

A

A congenital condition caused by trisomy 18 (an extra copy of all or part of chromosome 18).

233
Q

Eugenics

A

pseudoscience that promotes the improvement of a species or race by means of selecting for particular inherited characteristics.

234
Q

Hemizgous

A

term used to describe the genotype of a male with an X-linked trait (because males only have one X chromosome).

235
Q

Lyonisation

A

process of inactivation of one of the X chromosomes in females

236
Q

Patau syndrome

A

A congenital condition caused by trisomy 13 (an extra copy of all or part of chromosome 13).

237
Q

Polymorphism

A

The presence of two or more variant forms of a specific genetic sequence in the genome. The sequences may vary by only a single nucleotide (called a single-nucleotide polymorphism) or may involve longer stretches of DNA.

238
Q

Recurrence risk

A

statistic that estimates the probability that a condition present in one or more family members will recur in another relative in the same or future generations.

239
Q

Imprinting

A

1 parental allele expressed, other suppressed by epigenetics

240
Q

Prophase

A

Nuclear membrane: starts disintegrating
Spindle fibres: centrosome microtubules move to poles

241
Q

Prometaphase

A

Nuclear membrane: dissolves
Spindle fibres: form and attach

242
Q

Telophase

A

Nuclear membrane: reforms
Spindle fibres: disintegrate

243
Q

Assortative mating

A

Choose mates with similar or dissimilar phenotypes

244
Q

Knudson multiple hit hypothesis

A

> ## 2 defective alleles for disease eg cancer

245
Q

What is southern blotting used for

A

DNA

246
Q

What is northern blotting used for

A

RNA

247
Q

What is western blotting used for

A

Proteins

248
Q

What type of genetic condition is Huntington’s disease

A

Autosomal dominant

249
Q

What are the 3 genetic mechanisms for Down syndrome

A

Gamete non-disjunction
Robertsonian translocation
Mosaic

250
Q

What is the major genetic mechanism responsible for Prader-Willi syndrome

A

Micro-deletion of the parental chromosome

251
Q

What is a reciprocal translocation

A

Transfer of genetic material between 2 non-homologous chromosomes caused by break points in each

252
Q

Pleiotropy

A

A condition where a single mutation causes more than one observable phenotypic effect

253
Q

Example of a pleiotropy condition

A

Phenylketonuria

254
Q

What is the transcriptome

A

Composed of all RNA present in a cell

255
Q
  1. Where does alternative splicing producing different gene products occur?
A

IN mRNA

IMMS (6 decks)

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