Lecture 1.2: mutation + single gene

Question 1

1) Define polymorphism
2) Is this its only defining characteristic?

Answer 1

1) Two or more versions of an allele, with each comprising at least 1% of the population
2) Yes

Question 2

Define locus and what it looks like when it’s large or small

Answer 2

locus” (Latin for location) is a segment of DNA occupying a particular position or location on a chromosome (plural “loci”)
May be large – a segment with many genes
May be tiny – one base in the DNA code

Question 3

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Answer 3

Alternative versions of a locus on the DNA code are called “alleles”
Changes between alleles result from mutation

Question 4

The most common version (accounting for more than 50%) is called the “wild type” or “common allele”
Alternative to this are the “mutant” or “variant” alleles

Question 5

1) Define genotype
2) Define phenotype

Answer 5

1) The genetic material in a person – in a specific locus the two alleles occupying that locus on two homologues
2) The expressed physical traits of the genotype

Question 6

1) Define mutation
2) Will it always effect fitness to the envt?
3) What mediates it?

Answer 6

1) Random change to the DNA structure
2) May or not effect fitness to the environment
3) Selection

Question 7

List the Categories of mutation (largest to smallest by size)

Answer 7

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Question 8

1) Define chromosomal mutation and its outcome

Answer 8

1) Mutation accounting for all or most of a chromosome
Most always leads to disease or death

Question 9

1) define Regional or subchromosomal mutations
2) Define gene mutation. Is it always a big deal?

Answer 9

1) The middle ground between gene mutation and chromosomal
2) Alteration of involving substitution, deletion, or insertion of DNA – from single nucleotide to arbitrary limit of 100kb
Can be benign or a “big deal”

Question 10

1) Our cells make what from DNA?
2) The alterations that wind up on the _________ strand are the mutations we are talking about

Answer 10

1) RNA
2) protein
3) The DNA mutation has to be carried over to RNA and translated into the protein in order to create a phenotypic difference

Question 11

True or false: Some mutations occur in DNA or RNA only – and sometimes there’s no change in the protein!

Answer 11

True

Question 12

What questions should you ask to figure out if a change in DNA structure will correspond w a change in protein?

Answer 12

1) Does the mutation occur in a coding segment?
2) Does it substantively change the codon?
3) Does the change in polypeptide composition change the function of the protein?

Question 13

1) Define Single Nucleotide Polymorphisms (SNPs)
2) What does it usually have?
3) Where do most occur?

Answer 13

1) Multiple versions of nucleotide base at single location “substitution
2) Usually has but two alleles
3) Non-coding portions of DNA

Question 14

1) More than 100K ________ SNP’s have been discovered
2) Half of these do not alter the amino acid sequence (called “________________”)
3) Those that alter amino acid sequence are “________________”

Answer 14

1) exonic
2) synonymous
3) nonsynonymous

Question 15

List 2 significant changes caused by Single Nucleotide Polymorphisms (SNPs)

Answer 15

1) Altering or introducing a stop codon
2) Altering a splice site where introns/exons are altered

Question 16

1) How many base pairs can Indels (Insertion / deletion polymorphisms) occur in?
2) How many alleles do most “simple” indels have? What does this mean?
3) What is another type of indel besides “simple”? What are these?

Answer 16

1) as few as one base pairs, and as many as ~1000
2) Two; basically, the presence or absence of the inserted/deleted segment
3) “Microsatellite”; have multiple short repeats of the inserted segment

Question 17

1) Give an example of a microsatellite indel
2) What does this make? What are these called?

Answer 17

1) Instead of a single instance of TGT, you see TGTTGTTGTTGTTGT
2) Many different alleles, depending upon how many repeats there are. Called STR polymorphisms
(“short tandem repeat”; tandem means “length”)

Question 18

1) What can be unique and used to identify individuals and families
2) Microsatellite loci are known to researchers and number in the _____________

Answer 18

1) Microsatellite indels
2) thousands

Question 19

What is involved in DNA fingerprinting?

Answer 19

Microsatellite indels

Question 20

1) Mobile Element Insertion Polymorphisms consist of what? Give examples
2) What happens to these? What is this called?
3) What is this process called? What is it similar to?

Answer 20

1) Repetitive elements (think Alu and LINE)
2) Transcribed into RNA, then reverse transcribed back into the DNA code, but at a different locus; retrotranscription
3) Insertion (i.e. transposition); processed pseudogenes

Question 21

1) What are Copy Number Variants?
2) What are the largest of these called?
3) The allelic variation comes from what?

Answer 21

1) Up to hundreds of thousands of base pairs long
2) “segdups” (segmental duplications)
3) The number of copies

Question 22

Regarding copy number variants:
1) True or false: The larger the number of copies inserted, the more variation
2) If these do include genetic material, what can they do? Why is this a big deal?

Answer 22

1) True
2) Alter gene dosage; it’s like giving yourself multiple copies of a given gene

Question 23

Give an example of a copy number variant

Answer 23

Down syndrome

Question 24

1) Define inversion polymorphism
2) When does it often happen?

Answer 24

1) A portion of the sequence is “flipped around”
2) During recombination
(recombination is the same thing as “crossing over”)

Question 25

1) What are the two general types of inversion polymorphisms?
2) What can inversion polymorphisms result in?

Answer 25

1) Pericentric (includes centromere) vs paracentric (doesn’t)
2) Duplication or deletion of DNA located between regions of homology, causing genetic disease

Question 26

List some origins of mutations

Answer 26

1) DNA replication
2) DNA repair
3) DNA recombination
4) Chromosome segregation

Question 27

What are mutations called when they happen in the gametes? What about in the body?

Answer 27

Germline; somatic

Question 28

1) Many chromosome mutations are produce a change in the number of what?
2) What is this caused by?
3) What does this result in? Maternal or paternal?
4) In what chromosomes is this nearly always lethal? Why?

Answer 28

1) Chromosomes
2) Chromosome missegregation during meiosis I or II
3) Aneuploidy; maternal or paternal (often maternal)
4) autosomal; “gene dosing”

Question 29

1) Give 3 examples of regional mutations. When do all of these predominantly happen?
2) Give an example of where this can happen

Answer 29

1) Large duplications, deletions, or inversions; during recombination
2) At spontaneous breaks in the DNA

Question 30

Single gene mutations:
Include base pair substitution, indels, can occur in what two ways?

Answer 30

1) During DNA replication
2) After failure to repair damaged DNA

Question 31

1) Between 10,000 and 1 million nucleotides are damaged per ___________ per _____________.
2) Give 3 reasons for nucleotide damage

Answer 31

1) per cell per day
2) Spontaneous processes in the cell, reactions with chemical mutagens in the environment, exposure to UV or ionizing radiation

Question 32

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1) “Inserting a base other than the correct complementary one” is the definition of what?
2) How often do these errors in base pairs occur?

Answer 32

1) DNA replication errors
2) 1: 10 million
3) !Repair enzymes recognize which strand contains the incorrect base and replaces it with proper one –DNA proofreading!

Question 33

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Answer 33

Of these 99.9% are resolved by DNA proofreading
That puts the number are less than one error per cell division

Question 34

Mick
1) Single nucleotide substitution or “point mutation” may lead to one of what two mutations?

Answer 34

1) “Missense mutation” or “nonsense mutation”

Question 35

Mick
1) When mutations alter the genetic code in a “minor way” they fall into the first category of missense, though they need not always result in change in function of the protein
2) What may be wrong with the protein?

Answer 35

1)
2) The protein may work properly, may be unstable and rapidly degraded, or may not localize in the right spot in the cell

Question 36

Mick
1) What type of nucleotide substitution mutation disrupt the code enough that the protein is unusable?
2) What does this frequently occur due to?

Answer 36

1) Nonsense mutations
2) Premature or otherwise altered “stop” codon

Question 37

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Question 38

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Question 39

What part of RNA transcription do errors happen during?
What are the 2 classes of mutation here? Describe each

Answer 39

Splicing:
1) Introns must be excised and exons spliced together
-This requires nucleotide sequences at 5’ donor site and 3’ acceptor site
-Splicing can be disrupted or broken if mutations occur in either one
2) Base substitutions may also create alternative donor-acceptor sites for splicing

Question 40

What can both kinds of mutation during splicing affect?

Answer 40

The functionality of the end-product protein

Question 41

Frameshift mutations: When the insertion / deletion number of nucleotides is not a multiple of three, what happens?

Answer 41

Everything downstream is messed up

Question 42

1) What makes dynamic mutations unique?
2) What may these mutations involve?

Answer 42

1) In most cases, once a mutation occurs it is stable when transmitted from one generation to the next; in dynamic mutations, the mutation changes from generation to generation
2) Amplification in a simple nucleotide repeat sequence

Question 43

Dynamic mutation:
Often the wild type allele is polymorphic with varying number of tandem repeats, however, the _____________ expands as it is passed down in some families, causing abnormalities of gene expression

Answer 43

number

Question 44

Where will mutation persist in mosaicism?

Answer 44

In the descendants of that cell

Question 45

1) Define placental mosaicism
2) Define somatic mosaicism
3) Define germline mosaicism
4) When does segmental mosaicism occur? Give an example

Answer 45

1) In the extraembryonic tissue but not in baby
2) In the body and not gametes
3) In the germline only
4) Only part of the body is affected; neurofibromatosis 1

Question 46

True or false: Mosaicism might and will occur due to X-inactivation

Answer 46

True

Question 47

List 4 different types of mosaicism

Answer 47

1) Placental
2) Somatic
3) Germline
4) Segmental

Question 48

1) Define frequency (in the medical sense)
2) ______________ is sometimes used to refer to the frequency of mutations per se

Answer 48

1) Frequency of mutations per disease locus per generation is considered
2) “Genetic load”

Question 49

How do you track the rate of disease-causing gene mutations: what 3 things make the frequency traceable?

Answer 49

1) You have to look at incidence of new cases not present in mom or dad
2) Disease has to be caused by single mutation
3) Has to be evident in baby

Question 50

Mick
1) What kind of mutation is achondroplasia? What does this mean?
2) Is it dominant or recessive? What does this mean?

Answer 50

1) Gain of function mutation; altered gene product has new function
2) Autosomal dominant; when you’ve got it, you display it

Question 51

Mick
1) Is achondroplasia a missense or nonsense mutation? Describe where it comes from
2) De novo mutation in germ line of one parent
Happens almost exclusively in the paternal side because DNA in sperm has undergone far more replication cycles than DNA in the ova
Greater opportunity for de novo errors due to the sheer number of replications

Answer 51

1) Missense mutation resulting from substitution of G > A or G > C, resulting in the substitution of one Glycine for Arginine
2)

Question 52

What are the clinical features of achondroplasia? What is it the most common form of?

Answer 52

Age at onset: prenatal
Rizomelic short stature
Megalocephaly
Spinal cord compression
Most common cause of human
dwarfism

Question 53

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achondroplasia

Answer 53

FGFR3 protein is transmembrane tyrosine kinase receptor that binds to fibroblast growth factors
Binding of growth factors here, in endochondral bone, regulates proliferation of chondrocytes

Question 54

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Answer 54

When mutated, constitutive activation of FGFR3 inappropriately inhibits chondrocyte proliferation in the growth plate
Leads to shortening of the long bones
Abnormal differentiation of other bones

Question 55

List complications of achondroplasia

Answer 55

Delayed motor development secondary to combination of hypotonia, hyperextensible joints (not in elbows), mechanical difficulty balancing large heads
Less common: foramen magnum stenosis leading to brainstem compression
Midface hypoplasia can cause dental crowding, OSA, and otitis media
Hydrocephalus can result from narrowing of jugular foramina

Question 56

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Answer 56

Dx can usually be made with radiograph or clinically
Management involves anticipating and treating complications

Question 57

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Answer 57

Meets conditions for tracking disease present mutations
This is a single point mutation disease
It always shows up when present; To have such a clear-cut cause is extremely uncommon

Question 58

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Achondroplasia:
1) What do is the risk of inheritance in subsequent children of unaffected parents?
2) How about offspring of affected individual?

Answer 58

1) Same odds you started with (small) since you’re not a carrier
2) 50%

Question 59

1) Define homozygous
2) Define heterozygous
3) Define compound heterozygous
4) Define hemizygous and give an example

Answer 59

1) Having a pair of identical alleles
2) Having two different alleles – one mutant and one wild type
3) Having two mutant alleles
4) Only one allele (MC a male with the mutant allele on single X chromosome)

Question 60

What terms don’t apply to mitochondrial DNA?

Answer 60

Homozygous, heterozygous, compound heterozygous, hemizygous

Question 61

What type of disorder did Mendel observe? Define this
2) Autosomal recessive
Autosomal dominant
X-linked

Answer 61

1) Single-gene disorder: One determined primarily by the alleles at a single locus; follow the typical patterns
2)
3) Serious ones effect 1 in 300 neonates and cause 7% of pediatric hospitalizations

Question 62

1) What does expressivity refer to?
2) When is expressivity variable?

Answer 62

1) Severity of expression
2) When persons with the same genotype have different severity of symptoms

Question 63

When frequency of expression is less than 100% - in other words, when at least someone with the genotype completely fails to demonstrate disease – it is said to show what kind of penetrance?

Answer 63

“reduced” or “incomplete”

Question 64

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Question 65

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Answer 65

Single-gene disorders have classic inheritance patterns
To trace them, first ask about family hx of pt – summarized in a pedigree shown before
Especially early and lethal disease makes this difficul

Question 66

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Answer 66

Affected individual being studied is the “proband”
First degree = mom / dad, brother / sister, children
Second degree = grandma / grandpa, uncle / aunt, nephew / niece, and half-siblings

Question 67

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Answer 67

Third degree = first cousins. . . And so on, taking further steps on family tree
“Isolated case” occurs only in the proband
If new case is shown to occur due to new mutation, this is a “sporadic” case

Question 68

Regarding mendelian inheritance, what 2.5 factors matter the most?

Answer 68

1) Is the disease on an autosome or a sex chromosome?
2) Is the disease dominant or recessive?
-Remember, dominant is expressed with just one allele and recessive needs both
½) Were mom and dad homozygotes or heterozygotes?

Question 69

List the 3 general rules for autosomal gene mendelian inheritance

Answer 69

1) Transmission of autosomes is your classic Punnett square transmission
2) A mutant allele in a heterozygous parent has a 50% chance of being passed on to baby
3) Baby’s sex does not matter

Question 70

What are the general rules for X-linked mendelian inheritance?

Answer 70

1) Males give their Y chromosome to all their sons, so they give no X-linked genes to male heirs
2) Males give their X chromosome to all their daughters, so they always pass X-linked genes to their female heirs

Question 71

What comes exclusively from mom because sperm don’t pass this along?

Answer 71

Mitochondrial DNA

Question 72

When all mom’s babies have the disease, it’s probably ____________________.

Answer 72

Mitochondrial

Question 73

Define dominant and recessive

Answer 73

Dominant: The disease is present if the patient has just one copy of the dominant allele
Recessive: The disease is only present if both the patient’s alleles are present

Question 74

When do you see recessive disease?
When do you see the dominant gene?

Answer 74

1) Homozygotes, hemizygotes, compound heterozygotes
Never in (regular) heterozygotes!
2) Homozygotes AND heterozygotes

Question 75

A disease demonstrates “incomplete dominance” when ________________ dominant individuals suffer more severely from autosomal dominant disease than their _______________ counterparts

Answer 75

homozygous; heterozygous

Question 76

1) Autosomal recessive inheritance shows up in who?
2) Why?

Answer 76

1) Only in homozygous recessive individuals with two mutant alleles – no heterozygotes
2) Generally, the mutant allele is reducing or eliminating the function of the gene product. . . Often loss-of-function

Question 77

autosomal recessive disorders
1) The most common type of transmission is from what group?
2) True or false: as long as both mom and dad have the recessive gene somehow, they can make a baby with the recessive phenotype

Answer 77

1) Heterozygous carriers
2) True

Question 78

1) Define consanguinity
2) What does it increase the chance of?
3) What does finding it suggest?

Answer 78

1) Descended from the same ancestor
2) Increases the chance of baby getting mutant allele for obvious reasons
3) Finding consanguinity suggests (but does not prove) that a disease may be autosomal recessive

Question 79

1) What is consanguinity more common as? Why?
2) Give an example

Answer 79

1) A factor in very rare disease; bc it is less likely that two random people will carry a rare allele
2) Xeroderma pigmentosum

Question 80

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Answer 80

Typically seen in siblings and potential offspring of the proband – not in parents, offspring, or other relatives
Why would this be?
Usually, males and females equally affected
Parents of affected child are asymptomatic carriers
Recurrence risk for each sib is about 25%

Question 81

1) Define Sex-influenced Autosomal Recessive (side-note)
2) Give an example

Answer 81

1) Autosomal disease that varies in its severity in males and females
2) Hereditary hemochromatosis is autosomal recessive phenotype, causing increased levels of iron, that is 5-10 times more common in males
Males and females have different penetrance

Question 82

1) Define hemochromatosis
2) What is its penetrance and expressivity?
3) What inheritance pattern does it have?

Answer 82

1) Disease of iron overload resulting in mutation of the HFE gene
2) Incomplete penetrance and variable expressivity
3) Autosomal recessive inheritance pattern

Question 83

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Answer 83

Age at onset: 40-60
Early: Fatigue, arthralgia, abd pain, impotence / decreased libido
Late findings: hyperpigmentation (bronzing), DM, cirrhosis, hepatomegaly, cardiomyopathy

Question 84

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Answer 84

*Pt’s with cirrhosis have 10-30% chance of hepatocarcinoma even after treatment
Labs:
Elevated serum transferrin iron saturation
Elevated serum ferritin
Dx: genetic testing
Tx: Phlebotomy!

Question 85

Mick 67
1) Body stores of iron determined by what?
2) What regulates these stores?
3) Whar

Answer 85

1) dietary absorption from enterocytes in small intestine and release of iron from macrophages that phagocytize RBC’s
2) Regulated by iron response hormone, hepcidin, which is synthesized in the liver and released to block further iron absorption when supplies are good
3) Mutant HFE inhibits hepcidin signaling – disinhibiting enterocytes and macrophages to release iron

Question 86

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Answer 86

Most patients homozygous for Cys282Tyr (cystine / tyrosine) mutation, but can be compound heterozygous for Cys282Tyr/His63Asp (Histidine / aspartate)

Question 87

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Answer 87

Homozygosity does not always lead to dz
Penetrance is in question and may vary from 10% to 70% depending on how disease is defined
Organ damage
Elevated biomarkers

Question 87

What is the sex difference in penetrance for hemochromatosis?

Answer 87

Females have lower iron intake, lower etoh use, increased iron loss through menstruation, so women usually do not develop sx until after menopause

Question 88

1) Autosomal Dominant Inheritance risk and severity is determined by what?
2) Achondroplasia as an example is incompletely dominant, because it is usually fatal when homozygous

Answer 88

1) Whether trait is pure dominant and by whether one or both parents are affected

Question 89

Highlights
Autosomal Dominant Inheritance
1) In what generations does the phenotype usually appear?
2) True or false: Each affected person has an affected parent. Explain your answer and list any exceptions.
3) Any child of affected heterozygous parent has ____% chance of having disease
4) Who are equally likely to give it to children of either sex: males, females, or both?

Answer 89

1) In every generation
2) True; exceptions are due to incomplete penetrance, variable expressivity, and new mutations
3) 50%
4) Males and females equally likely to give it to children of either sex

Question 90

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Question 91

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Question 92

1) Lineage of __ is easy, but there are almost no genes here
2) For sex linked dz then, we look to the ____ chromosome

Answer 92

1) Y
2) X

Question 93

What are the possibilities for males and females for X-linked disease?

Answer 93

1) Male is hemizygous for mutant allele
2) Female is heterozygous with one wild-type dominant allele, homozygous with mutant allele, or a compound heterozygote

Question 94

1) True or false: Genes on X chromosomes are distributed unequally to males and females
2) True or false: X inactivation is normal and ubiquitous in females. Explain your answer.

Answer 94

1) Genes on X chromosomes are distributed unequally to males and females
2) X inactivation is normal and ubiquitous in females; this equalizes gene dose between both human sexes

Question 95

True or false: Two female heterozygotes with the same disease may have very different presentations for this reason because their mosaicism will vary

Answer 95

True

Question 96

Mick
1) What two ways can you get hemophilia A?
2) What is the expressivity?
3) What is it linked to?

Answer 96

1) Intrachromosomal recombination and Movable element insertion
2) Variable expressivity
3) X-linked

Question 97

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Question 98

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Question 99

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Answer 99

Age at onset: infancy to adulthood
Bleeding
Hemarthroses
Hematoma

Question 100

Mick slide 84

Answer 100

Factors in the clotting cascade are present in circulation at all times, though inactive
Sequentially activated, they form fibrin clot
Factors VIII and IX in particular amplify this cascade in order to form fibrin clot
Deficiency in these are caused by hemophilia A or B respectively
Mutations in F VIII and F IX genes account for each of these

Question 101

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Answer 101

Dx by identifying low factor VIII in presence of normal von Willebrand factor
Treated with factor replacement therapy

Question 102

Hemophilia A:
1) What is its well-defined pattern?
2) Expressed in all __________ who receive it and disease is limited to _____________.
3) Who do those with the disease inherit the disease from?

Answer 102

1) X-linked recessive
2) males; males
3) Either mom or dad

Question 103

True or false: In X-linked disease, male does not give the allele it to all his daughters, and doesn’t give it to any of his sons

Answer 103

False; Male gives the allele it to all his daughters (though they won’t show the phenotype) and none of his sons

Question 104

X-linked recessive: Affected females occur under what two circumstances?

Answer 104

1) Female could be homozygous for the disease. . . So so unlikely, though
2) More commonly, female is a “manifesting heterozygote”

Question 105

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Answer 105

More commonly, female is a “manifesting heterozygote”
This could occur under some circumstances of X inactivation
Usually, this process occurs at random
If skewed X inactivation occurs – the choice of which X to terminate is made early on in development when there is a fewer number of cells – the presence of the mutant allele may proliferate at a higher rate

Question 106

X-linked dominant:
From an affected male, all of his ___________ would have it, and none of his _____________–

Answer 106

daughters; sons

Question 107

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X-linked dominant: male lethality

Answer 107

These rare conditions have odd transmission patterns due to their extreme lethality in males
Boy’s don’t have it because the fitness in this disease is zero

Question 108

Give an example of X-linked dominant male lethality and what it looks like in females

Answer 108

Rett syndrome: Normal development in females for 6 months – then speech, coordination, hand movement is lost

Question 109

Give and describe an example of X-linked dominant with Male Sparing (an exception to the rule)

Answer 109

X-inked epilepsy and cognitive impairment
Asymptomatic at birth until second year of life
Seizures, regression of development with mild to severe cognitive dysfunction
Males are completely unaffected

Question 110

X-linked dominant with Male Sparing (an exception to the rule)

Answer 110

One theory:
Females with disease are mosaic for protocadherin 19, a cell surface protein in the brain, due to random X inactivation
Males have uniform surface protein and no disease

Question 111

X-linked dominant Pointers:
1) Affected males with normal mates have no affected _________ and no normal ____________.
2) Both male and female offspring of female carriers have ____% risk of inheriting the phenotype
Affected females are roughly twice as common as affected males, but they typically have milder expression of the phenotype

Answer 111

1) sons; daughters
2) 50%

Answer 112

RNA and protein made in a cell have DNA from nucleus
Mitochondrial genome has 37 genes that make 13 subunits of enzymes involved in oxidative phosphorylation as well as ribosomal RNAs and transfer RNAs required for making these enzymes