The Molecular, Biochemical, and Cellular Basis of Genomic Disease

Question 1

What is molecular disease?

Answer 1

a disease where pathology can be traced back to a single molecular factor (a protein or peptide for instance)

Question 2

What is biochemical genetics?

Answer 2

studies of the phenotypes at the levels of proteins, biochemistry and metabolism

Question 3

List some types of mutations

Answer 3

• point mutations
• Base pair deletions or insertions
• Gene duplications or insertions
• Promoter mutations
• Splice site mutations
• Mobile element insertion
• Expanded repeats

Question 4

How many hemoglobin units does each RBC have?

Answer 4

270,000,000

Question 5

Which chromosome encodes the alpha subunits and which the beta subunits of hemoglobin?

Where is the mutation that causes sickle cell disease located?

Answer 5

Alpha subunits - Chr 16
Beta subunits - Chr 11

amino acid substitution of valine for glutamic acid at amino acid 6 in the beta subunit decreases the solubility of deoxygenated hemoglobin.

Question 6

What symptoms are caused by sickle cell disease?

Answer 6

• hemolytic anemia as RBCs which become permanently sickled are removed from the body by the spleen
• infractions where tissues die from a lack of oxygen due to sickled RBCs occluding capillaries.

Question 7

How can CRISPR be used to treat SCD and beta-thalassemia?

Answer 7

By inactivating the BCL11A enhancer (which controls the transition from fetal hemoglobin to beta-hemoglobin subunit production), in CD34+ (haematopoietic) cells from patients and reinjecting these edited cells back into the body, patients can eliminate vaso-occlusive episodes and become transfusion independent.

Question 8

How can there be more phenotypes (7,000) than genes with phenotype causing mutations (4,000)

Answer 8

Some genes have multiple mutations, so can cause two or more phenotypes

Question 9

What are the four ways a mutation can cause disease?

Answer 9

• loss of function of a protein (beta-thalassemia)
• gain of function of a protein (Hb Kempsey)
• acquisition of a novel property (Hb S)
• Misexpression, either in time (heterochronic) or place (ectopic) (hereditary persistence of fetal hemoglobin/ HPFH)

Question 10

Give examples of a loss of function mutation

Answer 10

• Beta-thalassemia (C to T / Gln39Stop)
• Turner syndrome (loss of X chromosome)
• retinoblastoma (deletions of tumor suppressor genes)

Question 11

Give examples of gain of function mutations

Answer 11

• achondroplasia is caused by mutation in FGFR3 gene.
• Increased production of proteins in Trisomy 21

Question 12

What are the 8 steps at which mutations can disrupt the synthesis or function of a normal protein?

Answer 12

1. transcription
2. translation
3. polypeptide folding
4. post-translational modification
5. Assembly of monomers into a holomeric protein
6. Subcellular localization of monomer or holomer.
7. Cofactor or prosthetic group binding to polypeptide
8. Function of correctly folded assembled and localized protein produced in normal amounts. (Hb Kempsey)

Question 13

What are the five main classes of proteins and give a disease causing protein for each.

Answer 13

Transport - beta globin (SCD)
Cell surface - FGFR3 (achondroplasia)
Nucleus - Rb (retinoblastoma)
Cytoplasm - phenyalanine hydroxylase (PKU)
Organelles - Hexosaminidase A (Tay-Sachs disease)

Question 14

What are the two classifications of proteins based on their expression pattern in the body?

Answer 14

Housekeeping proteins

• present in virtually every cell
• 90% of human mRNA

Tissue specific proteins

• present only in certain cell types (phenylalanine hydroxylase only in liver)
• 10% of human mRNA

Question 15

How does PKU damage the nervous system?

Answer 15

A lack of phenylalanine hydroxylase in the liver causes a build up of phenylalanine throughout the body, which damages the central nervous system and can cause intellectual disabilities if not treated right away.

Question 16

Why do mutations in housekeeping proteins rarely cause observable panoramic pathological changes in patients?

Answer 16

1. If a protein is required for all cells to survive then a lack of it will be lethal meaning no patient. (mutations in Actin or DNA polymerase)
2. If a protein is really important, there will often be genetic redundancy to reduce the effect of any one mutant gene.
3. The expression of a protein may allow heterozygotes with one copy of a LoF gene to survive. (only one copy of hexosaminidase A is sufficient to break down fatty acids and allow for a long life, even though homozygotes for the mutant protein get Tay Sachs disease and die very young)

Question 17

Define Genetic heterogeneity

Answer 17

When any one mutation in multiple genes or loci can lead to a single disease

Question 18

Define pleiotropy

Answer 18

When a single mutation can have multiple effects on phenotype or cause multiple genetic disorders.

Question 19

Define Allelic heterogeneity

how many known mutant alleles in the CFTR gene cause cystic fibrosis?

Answer 19

The occurrence of more than one allele at a locus (SCD and Beta-thalassemia causing mutations in Beta-globin) (COL1A1)

over 1,000 known mutant alleles

Question 20

Define locus heterogeneity

Mutations in how many genes can cause retinitis pigmentosa?

Answer 20

The association of mutations in multiple loci to one clinical phenotype. (hyperphenylalaninemia can be cause either in the PAH gene or the BH₄ gene)

Only one mutant locus in over 100 genes can cause retinitis pigmentosa

Question 21

Clinical or phenotypic heterogeneity

Answer 21

The association of more than one phenotype with mutations at a single locus (PKU, variant PKU, non-PKU hyperphenylalaninemia)

Question 22

Why do cystic fibrosis patients have such variable lung disease expressions?

Answer 22

There are multiple modifier genes which effect how the disease affects the body, which each can have their own alleles and mutations.

• mannose-binding lectin
• glutathione-S-transferase
• tumor necrosis factor-alpha
• transforming growth factor beta 1

Question 23

How many human genes encode enzymes?

Answer 23

over 5,000

Question 24

Define enzymopathy

Answer 24

a metabolic disorder resulting in deficiency or abnormality of a specific enzyme.

Question 25

Deficiency in which two enzymes can cause hyperphenylalaninemia?

What molecule do these enzymes create from Phe?

Answer 25

• Phenylalanine hydroxylase (PAH) and tetrahydrobiopterin (BH₄)
• Tyr which can then be converted to Trp

Question 26

How often does PKU occur in live births?

Answer 26

1 in 2,900 live births

Question 27

What is tested for in a PKU heel-prick screening in newborns?

Answer 27

[Phe]/ [Trp]

Question 28

How does the phenotype of variant PKU and non-PKU hyperphenylalaninemia compare to classic PKU?

Answer 28

variant and non-PKU have a less severe phenotype due to a residual activity of the PAH enzyme.

Question 29

Define compound heterozygote

give an example

Answer 29

When 2 different mutant alleles at the same locus cause a disease.

there are over 400 different PKU causing alleles in the PAH gene

Question 30

Why does a low phenylalanine diet alone in BH₄ mutant still cause hyperphenylalaninemia?

Answer 30

Because BH₄ is needed to convert Phe to Tyr and Trp, so a lack of it will still cause some build up.