GH

Question 1

What is a gene, genome, Transcriptome, Proteome, and Exome?

Answer 1

Gene - section of DNA, Genome - all genes in an organism, Transcriptome - all transcripts including spliced ones, as well as structural RNA’s, Proteome - all proteins, Exome

Question 2

Who are the two people who invented Gene sequencing?

Answer 2

Craig venter –> privatised genome sequencing (celera genomic), Francis Collins –> publicly available under the National Human Genome research institute

Question 3

What is the light banding on a Chromatin?

Answer 3

Due to loosely packed/unravelled chromatin, high in euchromatin, high in Guanine and Cytosine, gene dense areas

Question 4

What is the dark banding on the Chromomtin?

Answer 4

Due to tightly packed chromatin, high in heterochromatin, High in Adenine and thymine, gene poor areas

Question 5

Maternal Ancestry

Answer 5

Maternal ancestry traced through mitochondrial DNA variation, has shown that almost all Europeans alive today are descendant of just seven women who lived in different parts of the continent. It was found that all peoples living today originated from a common female individual approximately 148,000 years ago

Question 6

Paternal Ancestry

Answer 6

Paternal ancestry is traced through the Y chromosome as it inherited from father to son. Through paternal sequencing it has been found that there is only minimal variation in the sequence of the y chromosome

Question 7

Haplogroup

Answer 7

A group of people who share the same ancestors, These people act as genetic markers who can be used to trace ancestry and migration

Question 8

How are genes affected by Inherited diseases?

Answer 8

Alter or eliminates normal gene function, protein function and hence cellular tissue and body function

Question 9

How are genes affected by Bacterial infections?

Answer 9

Produces proteins that interfere with normal cellular functions. Cal alter gene expression, can insert genes, affects both genome and proteome

Question 10

How are genes affected by viral infections?

Answer 10

Forces the production of unwanted viral proteins, Interfere with normal cellular functions, Lead to produciton of more virus

Question 11

Chromosome mapping methods?

Answer 11

Amniocentesis –> amniotic fluid surrounding the baby is sampled, Chorionic Villus Sampling - cells of the Chorion/placenta are sampled, Other source of living cells (e.g. leukocytes)

Question 12

Chromosome terminology

Answer 12

Acro - tip, Sub - imperfect/below, Meta - mid, Telo - at the end, P Arm - short arm, Q arm - long arm

Question 13

Telomere pattern

Answer 13

TTAGGG, protect chromosomes from deterioration and fusion with other chromosomes

Question 14

Xp11.2

Answer 14

Chromosome, Arm, region, band, Sub-band

Question 15

Karyotype

Answer 15

Chromosomes ordered by size and banding

Question 16

how many histone make up a nucleosome

Answer 16

8 histones = 1 nucleosome

Question 17

Whats is mendels second law

Answer 17

the law of independent assortment states that alleles at multiple loci assort independantly hence there is a 1:1:1:1 ratio between each gamete however there are some exceptions

Question 18

Concept of linkage

Answer 18

some alleles shoe linkage since they are located on the same chromosome, gene pairs only assort independantly if they are located on different chromosomes or located far apart on the same chromosome

Question 19

Gene mapping by linkage

Answer 19

the probability of crossing over between two genes if roughly proportional to their distance apart on the chromosome,

Question 20

Recombination distance

Answer 20

one map unit = 1% recombination distance = 1m million B.p, two genes are linked if they show <50% recoembinant relative to parental genotypes

Question 21

How is linage studied and tested?

Answer 21

T.h. morgan discovered that linkage can be studied using a test cross where a homozygous recessive trait is corssed with the traits being tested for linkage

Question 22

Epistasis Description

Answer 22

usually involves alleles in one gene masking the phenotypic effects of another gene e.g. coat colour in dogs and blood type in humans e.g. ee is said to be epistatic over B

Question 23

Epistasis in humans Example

Answer 23

Individuals who are hh are blood type O, regardless of the alleles they carry at the ABO locus

Question 24

Pleiotropy

Answer 24

one gene may contribute to more than one visible character

Question 25

Recessive vs. Dominant mutations

Answer 25

recessive mutations affect enzymes, dominant mutations affects structural proteins

Question 26

4 main classes of mutations

Answer 26

Base substitutions (Single base changes caused by rare errors occurring at DNA replication or DNA damage repair) deletions [From 1 bp to megabases (and multiple genes) – shift the reading frame] insertions (From 1bp to megabases (including duplications) – shift the reading frame) Dynamic mutations (Tandem repeats that change size (increase or decrease) following DNA replication)

Question 27

Synonymous (silent) mutations

Answer 27

result when change in coding region does not alter the amino acid sequence

Question 28

missense mutations

Answer 28

Mutations that change amino acid sequence --> Conservative (altered amino acid which sometimes PRESERVES gene function) --> non-conservative (altered amino acids which mostly PREVENTS normal gene function)

Question 29

nonsense mutations

Answer 29

result in an amino acid being replaced with a stop codon, causing a premature halt to translation and formation of truncated protein

Question 30

Notation for mutations

Answer 30

DNA level --> g. = genomic, m. = mitochondrial, c. = coding DNA, n. = non-coding DNA RNA level --> r. = RNA Protein level --> p. = protein

Question 31

Format of notation

Answer 31

"“Prefix” “Position” “Reference base”> “New base” Exceptions - at DNA-level, with a “g.” prefix, starting with a number referring to the nucleotide affected example: g.76A>T - at RNA-level, with an r. prefix in lower-case, starting with a number referring to the nucleotide affected example: r.76g>c - at Protein level, three letter abbreviation for the amino acid affected, position number then new amino acid example: p.Thr26Pro"

Question 32

nonsense mutations notation note

Answer 32

These mutations are named with the three-letter abbreviation for the wild type amino acid – then the position number – then a Ter or *, signifying the stop codon

Question 33

insertion mutation notation note

Answer 33

“prefix”“positions_flanking”“ins”“inserted_sequence”

Question 34

deletions mutation notation note

Answer 34

Deletions are named by listing the nucleotide number of the first deleted nucleotide - del (short for deletion) --> “prefix”“position(s)_deleted”“del”

Question 35

Briefly explain phenlylketonuria

Answer 35

Metabolic disorder, in clasic PKU --> phenylalanine hydroxylase (PAH) which breaks down the phenylalanine, most common mutation is a missense mutation of p.Arg408Trp, hence without PAH phenylalanine accumulates in body tissues

Question 36

about 50% of untreated infants of PKU have the following symptoms

Answer 36

Vomiting, irritability, eczma like rash, a mousy odour to the urine

Question 37

subtle signs of of Nervous system problems

Answer 37

incresed muscle tone, more active muscle tendon reflexes

Question 38

Other commonly noted features in untreated children of PKU include:

Answer 38

Microcephaly (small head), Prominent cheek and upper jaw bones with widely spaced teeth, Poor development of tooth enamel, Decreased body growth

Question 39

later severe brain symptoms of PKU

Answer 39

Cognitive impariment, seizures

Question 40

Brief overview of Thalassemia

Answer 40

Group of heterogenous blood disorders where one of the globin chains of haemoglobin has not been synthesised correctly --> usually due to a deletion that blocks protein production

Question 41

α-thalassemia

Answer 41

involves the α globin chain --> HBA 1 or HBA2 gee is affected, Main regions: , South East Asia, Eastern Mediterranean, Africa, the Pacific islands and New Zealand (Maori)

Question 42

β-thalassemia

Answer 42

involves the the β globin chain --> HBB gene is affected with 400 mutations documented, Main regions: Middle East, Mediterranean, Africa, Indian Subcontinent, Central and South East Asia and the Caribbean

Question 43

Hemoglobin description

Answer 43

it’s a tretramer of two alpha and two beta subunits. The subunits change to suit the gas carrying needs of embryo, fetus and adult.

Question 44

alpha and beta globin genes

Answer 44

there are 4 alpha globin genes (2 on each copy of chromosome 16) and 2 beta globin genes (1 on each copy of chromosome 11)

Question 45

Thalassemia screening

Answer 45

Traditional methods include: hematologic testing of red blood cell indices, peripheral blood smear, supravital stain to detect RBC inclusion bodies, and qualitative and quantitative haemoglobin analysis * Diagnostic/Confirmatory test --> e.g. mutations in genes of interest

Question 46

Alpha thalassemia

Answer 46

No treatment is effecttive for Hb barts hydrops fetalis --> however, HbH disease, occasional RBC's transfusions may be neededduring hemolytic or aplastic crises

Question 47

Beta thalassemia major

Answer 47

* Regular transfusions correct the anaemia, suppress erythropoiesis, and inhibit increased GIT absorption of Iron * The only available definitive cure is bone marrow transplantation from a matched family of cord blood transplantation from a related donor

Question 48

Beta thalassemia intermedia

Answer 48

Symptomatic therapy based on splenectomy in most affected individuals, sporadic red cell transfusions in some, folic acid supplementation and iron chelation

Question 49

Thalassemia facts

Answer 49

"* Most thalassemia heterozygotes have mild symptoms and are undiagnosed due to incomplete dominance * - Thalassemia major affected babies are normal at birth but become anemic between 3 – 18 months and die "

Question 50

Thalassemia stats on types

Answer 50

* Beta thalassemia is the most common form in Australia because of the high number of people migrated from Mediterranean countries * Alpha thalassemia has also increased due to the large amount of migration from Asia

Question 51

Thalassemia new treatment

Answer 51

Switching on fetal globin genes to treat adults with thalassemia, In Beta thalassemia γ globin can partner with α globin in place of the defective β globin Downside is that there is a need to switch on many transcription factors which may affect other systems

Question 52

Sickle cell Anemia Overview

Answer 52

RBC mutation on the left is due to mutant allele of the haemoglobin subunit (HBB gene; same as Thalassemia, but with different outcome) Blood Disease affecting people with ancestors from Africa; Mediterranean countries such as Greece, turkey and Italy; the arabian peninsula; india; and Spanish speaking regions in south America, central America, and parts of the Caribbean

Question 53

Sickle Cell Anemia Mutation

Answer 53

The Beta chain of human haemoglobin has a single amino acid substitution (HbS allele) causing fibre formation compared to the wild type heterotramer (HbA) à “S= sickle cell” --> p.Glu6Val (non conservative subtitution)

Question 54

Sickle cells diagnosis method and screening

Answer 54

* Diagnosis is done by blood screening for deformed RBC’s using a microscope & quantitative haemoglobin analysis (electrophoresis) * Included in newborn screening * Management is based on prevention of crisis * Outlook is good if routinely checked

Question 55

Malaria and HbS

Answer 55

Malarial parasite grow poorly in RBC’s of both homozygous HbS/HbS and heterozygous HbS/Hb+ carriers --> As a direct consequence, the frequency of the HbS alleles in population that are exposed to malaria is maintained at high levels through NATURAL SELECTION

Question 56

Heterozygous advantage

Answer 56

The relatively high frequency of disease associated alleles causing reduced fitness on homozygotes (e.g. sickle cell anemia in Africans) --> This is explained by assuming that heterozygotes (Aa) have a greater fitness than either of the homozygotes (AA or aa)

Question 57

Hemachromatosis description

Answer 57

caused by mutations in HFE gene (high Fe or Iron) --> The two most common mutations found in Europeans are missense mutations designated Cys282Tyr (Cysteine to Tyrosine --> most cases of hereditary hemachromatosis) and His63Asp (Histidine to Aspartic Acid)

Question 58

Mechanis of development of Hemachromatosis

Answer 58

The exact mechanism for development of hemochromatosis is not known, but mutant HFE does not bind properly to transferrin receptors --> Important for transcriptional regulation of Hepcidin – master Iron regulatory hormone in the body

Question 59

Symptoms of Hemachromatosis

Answer 59

body absorbs and stores too much Iron --> Extra iron in body builds up in organs and damages them, without treatment these organs can fail since body has no way of excreting iron --> Healthy people only absorb a proportion of protein associated iron conteined in food however HM affected people absorbs almost all protein associated iron

Question 60

Compound heterozygotes

Answer 60

if an individual has two differnet allales, both of which are defective, they are said to be compound heterozygotes --> Compound heterozygotes of recessive disorders are usually affected by disease

Question 61

How could a child with Cystic fibrosis be produced by a couple if only one of them is a carrier?

Answer 61

(1) Mosaic – blood sample came back normal, reproductive tissues may be producing gametes with affected sequence variants (2) De novo - occurrence during embryogenensis, a new sequence variant occurred and was not corrected

Question 62

Alpha Thalassemia Table

Answer 62

Silent carrier -α/αα 1 of 4 α-globin genes mutated. Silent carriers, typically have no symptoms. α-Thalassemia trait (Minor) --α/-α 2 of 4 α-globin genes mutated. Individuals have mild anaemia, cells can still produce some normal haemoglobin. Haemoglobin H (HbH) --/-α 3 of 4 α-globin genes mutated. Mild to moderate anaemia. may require treatment with blood transfusions (either intermittently or on a regular basis), an enlarged spleen and jaundice (yellowing) of the eyes and skin. Haemoglobin Barts hydrops fetalis (Hb Barts) syndrome --/-- 4 of 4 α-globin genes mutated. Severe form of α-Thalassemia where excess fluid builds up in the developing baby due to severe anaemia and the baby usually does not survive long after birth.

Question 63

Beta Thalassemia Table

Answer 63

β-Thalassemia trait (minor) β/β° or β/β+ 1 of 2 faulty β-globin genes mutated. May have lifelong mild anaemia. β-Thalassemia intermedia Milder variant of β+/β+ or β°/β+ 2 of 2 faulty β-globin genes mutated. Milder version of β-Thalassemia. Causes mild to moderate anaemia. Symptoms may appear in early childhood or later in life and blood transfusions may be required. Other symptoms include slow growth and bone changes. β-Thalassemia major β°/ β°, β°/β+ or β+/β+ 2 of 2 faulty β-globin genes mutated. More severe form of β-thalassemia. Children develop life-threatening anaemia within the first year of life and require regular blood transfusions throughout their life. Other symptoms may include failure to thrive, jaundice (yellowing) of the eyes and skin, enlarged spleen, bone changes and developmental delay.