VARIABILITY AND CHANGES OF GENETIC INFORMATION I

Question 1

WHAT IS GENETIC VARIATION?

Answer 1

differences in the sequence of DNA among individuals

Question 2

WHAT DOES GENETIC VARIABILITY ARISE FROM?

Answer 2

mutations and polymorphisms

Question 3

WHAT IS A MUTATION?

Answer 3

permanent heritable change that occurs in DNA sequences either due to mistakes when the DNA is copied or as the result of environmental factors such as UV light
-frequency of <1% (rare genetic variants)

Question 4

WHAT ARE POLYMORPHISMS?

Answer 4

the inheritance of a trait controlled by a single genetic locus with 2 alleles, in which the least common allele has a frequency of about >1%
-most common type of polymorphism involves variation at a single nucleotide
EG: HAIR COLOUR

Question 5

WHAT INCREASES THE RISK OF A GENE MUTATION WITHIN A CHILD?

Answer 5

age of the father

Question 6

WHAT INCREASES THE RISK OF A CHROMOSOMAL ABORNOMALITY IN A CHILD?

Answer 6

age of both parents, mainly the mother
father = 50 yrs
mother = 35 yrs

Question 7

HOW COMMON ARE CHANGES IN THE GENOME?

Answer 7

very frequent, however the majority has no effect and we are not even aware of them unless
they cause a genetic disease (only then they become clinically significant)

Question 8

WHAT IS ALLELIC HETEROGENEITY?

Answer 8

different mutations at the same gene locus leads to the same or very similar phenotypes
-several mutations for one gene (each leading to an abnormal phenotype)
-gene problem

Question 9

WHAT IS LOCUS / NON-HETEROGENEITY?

Answer 9

a mutation at multiple loci are capable of producing the same phenotype
-neighborhood problem - various genes

Question 9

DEFINE WILD TYPE

Answer 9

the phenotype of the typical form of a species as it occurs in nature

Question 10

WHAT IS A SINGLE NUCLEOTIDE POLYMORPHISM?

Answer 10

DNA sequence variation occurring when a single nucleotide in the genome differs between members of a species or paired chromosomes in an individual
-occur in the coding and non-coding (1/1000 bp) parts of genome
-commonly known as a point mutation = change of one single nucleotide (base) anywhere in the genome (90%)
-usually with no effect or small effect (effects the predisposition to individual disorders)

Question 11

HOW DO POLYMORPHISMS WITH AN INCREASED NUMBER OF COPIES DIFFER?

Answer 11

alleles differ in the number of repeats

Question 12

NAME AND EXPLAIN THE 5 TYPES OF POLYMORPHISMS WITH INCREASED NUMBER OF COPIES.

Answer 12

MICROSATELLITES / SHORT TANDEM REPEATS (STR) = occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other
-repeats of 2-5bp, frequently CA bases or GATA bases, usually di / tri / tetra nucleotide
-usually in introns, accessible regions
-unique to each family
-used as molecular markers in forensic science

MINISATELLITE / VARIABLE NUMBER TANDEM REPEATS (VNTR) = tract of repetitive DNA in which certain DNA motifs (ranging in length from 10 – 100 base pairs) are typically repeated 5-50 times.
-occur in telomeres and sub-telomeric regions of genome

CLASSICAL SATELLITES = repeated units of 100s / 1000s of nucleotides
-main component of functional centromeres and form the main structural constituent of heterochromatin
-variability is without phenotypic effect

COPY NUMBER VARIATION (CNV) = sections of the genome are repeated and the number of repeats in the genome varies between the individuals in the human population
-type of structural variation
-DNA segments greater than 1000bp long but less than 5mb
-segments can include several genes
-changes the biggest amount of genome

INDEL VARIANT = insertion or deletion of bases in the genome of an organism
-measure from 1-10,000bp long
-usually only have 2 alleles
-important for microdeletion and microduplication syndromes, evolutionary significance on gene duplication

Question 13

WHAT ARE THE IMPACTS OF INSERTIONS, DELETIONS, INVERSIONS, AMPLIFICATION OF SINGLE NUCLEOTIDES TO WHOLE DNA SEGMENTS?

Answer 13

quantitative structural changes of different degrees
-various alleles with the presence or absence of a segment or variability in the number of segment copies
-various effects as some can be pathological, some cause predispositions and some do nothing

Question 13

WHAT ARE INSERTIONS AND DELTIONS ALSO KNOWN AS?

Answer 13

frameshift mutations
-the mutation can alter the translational reading frame of the gene, it can lead to the formation of a new stop codon and the production of a protein with loss of function

Question 14

WHAT CAN MUTATIONS IN PROMOTOR REGIONS CAUSE?

Answer 14

can effect gene expression
-lead to impaired binding of transcription factors
-decreased affinity of RNA polymerase and reduced transcription

(both of the above are essential for transcription and translation of gene into protein)

Question 15

WHAT CAN MUTATIONS WITHIN THE EXON / INTRON BOUNDARY CAUSE?

Answer 15

interfere with the process of splicing

EG: TAY-SACHS DISEASE
arises due to the autosomal (chromosome 15) recessive mutations in the beta hexosaminidase A gene which cause the intron between exon 12-13 to not be removed - causes defect in the beta hexosaminidase A enzyme and the accumulation of the GM2 (as a result of build up of galactose) ganglioside (fat) within nerve cells in the brain and spinal cord leading to toxicity
-beta hexosaminidase A usually breaks galactose down into glucose in breast milk as an energy supply for the baby
-most common type is infantile tay-sachs disease which becomes apparent around 3-6 months with the baby unable to carry out typical motor functions

Question 16

WHAT ARE INTERSPERSED REPETITIVE SEQUENCES?

Answer 16

identical or nearly identical DNA sequences that are scattered throughout the genome as a result of transposition or retro-transposition events
-repeat sequences are dispersed throughout the genome and non-adjacent

Question 16

WHAT ARE THE 2 CLASSES OF MOBILE ELEMENTS?

Answer 16

CLASS I / RETROTRANSPOSONS = replication through RNA intermediate by reverse transcription
-a new copy of a DNA sequence is then inserted into another place in the genome
(COPY AND PASTE)

LINE:
-long interspersed nuclear elements - L1 sequences
- transcribed into mRNA and translated into a protein that acts as a reverse transcriptase, which can make a DNA copy of the LINE RNA that can be integrated into genome
-100,000 truncated and 4,000 full length L1 sequences in human genome

SINE:
- short interspersed nuclear elements
- Alu sequences (repetition inserted into different locations on genome) are the most common
- non coding mobile elements
-100 to 700bp long
-transcribed into tRNA or rRNA by RNA polymerase III

LTR:
- long terminal repeats
- identical sequences of DNA that repeat hundreds or thousands of times found at either end of retrotransposons or pro-viral DNA formed by reverse transcription of retroviral RNA
-endogenous retrovirus

CLASS II / DNA TRANSPOSONS = “jumping genes” - are DNA sequences that move from one location in the genome to another using the enzyme DNA transposase
(CUT AND PASTE)

-45% of human genome consists of these mobile elements

Question 17

WHAT ARE THE TYPES OF MUTATIONS DEPENDING ON ORIGINS?

Answer 17

SPONTANEOUS = endogenous causes (errors in replication, spontaneous lesions, transposable genetic elements and reactive oxygen species)

INDUCED = exogenous causes (mutagens), ionizing radiation

Question 18

WHAT ARE THE 2 MUTATION CLASSES OF CELLS?

Answer 18

SOMATIC = aging (accumulation of various small mutation) or tumours (mutation of proliferation gene)
-occur in non-germline tissue
-non-heritable

GAMETIC = present in egg or sperm and infects all cells in off spring
-heritable
-cause cancer family syndrome

Question 18

EXPLAIN CHROMOSOMAL MUTATIONS

Answer 18

results from a structural chromosomal aberration
-double stranded breaks in DNA, loss or gain of chromosomal segment or abnormal rearrangement of segment
-submicroscopic and microscopic deletion or duplication of larger segments (>kb, CNV)
-interstitial deletion/duplication – when a part of chromosome deletions/duplicates in-between telomeres

Question 19

EXPLAIN GENOME MUTATIONS

Answer 19

change in number of chromosomes, chromosomal abnormalities

POLYPLOIDY = multiplication of haploid chromosome set (triploidy, tetraploidy)

ANEUPLOIDY = one chromosome missing or in addition (monosomy, trisomy)

EUPLOIDY = one or more complete set of chromosomes

Question 20

WHAT IS A POINT MUTATION?

Answer 20

mutation which affects a single nucleotide base pair

Question 21

WHAT IS A GENE MUTATION?

Answer 21

results from a permanent alteration in the DNA sequence that makes up a gene, such that the sequence differs from what is commonly found

Question 22

WHAT IS A SYNONYMOUS MUTATION?

Answer 22

substitution of one nucleotide base for another in an exon of a gene coding for a protein, such that the produced amino acid sequence is not changed

TRANSITION = purine for purine / pyrimidine for pyrimidine

TRANSVERSION = purine for pyrimidine / pyrimidine for purine

-these processes are possible due to the degenerative nature of genetic code
-can also occur outside of coding sequences

EG: CHRISTMAS DISEASE
Hemophilia B = A->G in promoter of gene for anti-hemophylic factor IX - this prevents transcription factor (which is for clotting) from binding -> decrease in the amount of product)

Question 23

WHAT IS A NON-SYNONYMOUS / MISSENSE MUTATION?

Answer 23

point / substitution mutation in which a single nucleotide change results in a codon that code for a different amino acid
EG: SICKLE CELL
-GAG -> GTG = glu -> val = HbA -> HbS in the beta globin gene causing sickle shape of RBC
-occurs in exon coding region

Question 24

WHAT IS A NONSENSE MUTATION?

Answer 24

point mutation in a sequence of DNA that results in a premature stop codon and a truncated, usually non-functional protein product

EG: NEUROFIBROMATOSIS
NF1 gene (tumor suppressor gene)
CGA -> TGA
arg -> stop
-cancer occurs

Question 25

WHAT IS AN ELONGATION MUTATION?

Answer 25

point mutation that changes a stop codon into an amino acid coding triplet
EG: ALPHA GLOBIN
UAA -> UAC
STOP -> Tyrosine
-abnormal protein hemoglobin

Question 26

WHAT IS A FRAMESHIFT MUTATION?

Answer 26

is a genetic mutation caused by indels (insertions or deletions) of a number of nucleotides in a DNA sequence that is not divisible by three

EG: ABO BLOOD GROUPS
deletion GTG -> single bp deletion at the ABO locus alters the reading frame
= allele A -> allele O
EG: Tay Sachs
4bp insertion-> frameshift leading to the origin of premature stop codon = deficiency of enzyme hexosaminidase A

EG: mutations in rRNA and tRNA genes can lead to errors in cellular translation

Question 26

GIVE EXAMPLES OF CHEMICAL MUTAGENS

Answer 26

ALKYLATING AGENTS = methylation -> error in base pairing→ point Mutation

NITRIC ACID = base deamination -> error in base pairing

ACRIDINE DYES = insertions -> frameshift mutations

NUCLEOTIDE BASE ANALOGS = structural similarity eg. bromouridine - an analogue of thymidine
- transition - purine for purine, pyrimidine for pyrimidine transversion - purine for pyrimidine and vice versa

POLYCYCLIC AROMATIC HYDROCARBONS = cigarettes

Question 27

GIVE EXAMPLES OF PHYSICAL MUTAGENS

Answer 27

UV RADIATION = form pyrimidine dimers T=T, C=C, T=C => replication defects, interfere with transcription

IONIZING RADIATION = direct effect (DNA break, chromosomal aberration) and indirect (ionization of molecules)

Question 28

GIVE EXAMPLES OF BIOLOGICAL MUTAGENS

Answer 28

VIRUSES = the viral nucleic acid integrates into the genome of host cell

Question 29

EXPLAIN MUTATION HOTSPOTS

Answer 29

mutation frequencies vary significantly along nucleotide sequences such that mutations often concentrate at certain positions called hotspots
-mutation hotspots (12x more likely to become mutated)
-C≡G
-CpG islands can mutate during replication
-Transition of cytosine
-gene mutations increase with paternal age
-chromosomal mutations increase with maternal age

Question 30

WHAT IS A DYNAMIC MUTATION?

Answer 30

progressive base amplification (triplet repeats)
-the probability of expression of a mutant phenotype is a function of the number of copies of the mutation
-the replication product of a dynamic mutation has a different likelihood of mutation than its predecessor
-unstable, heritable
-origin through premutation in a previous generation

EG:
FRAGILE X = CGG in UTR
HUNTINGTONS = CAG in EXON
FREIDREICH ATAXIA = GAA in INTRON
MYOTONIC DYSTROPHY = CTG in UTR

Question 31

WHAT ARE INDIRECT MUTAGENS?

Answer 31

Chemical compounds which start to be reactive only after metabolic activation in organism

Question 32

WHAT ARE PHENOTYPIC CONSEQUENCES OF MUTATIONS?

Answer 32

LOSS OF GENE PRODUCT FUNCTION = metabolic defects because of change in enzymes, usually recessive character

GAIN OF NEW, ABNORMAL FUNCTION OR ABNORMAL PROTEIN = usually dominant/codominant character

DOMINANT - NEGATIVE MUTATION (antimorphic) = abnormal protein inhibits normal protein, occurs in heterozygotes

Question 32

WHAT IS A REPLICATION CLIP?

Answer 32

DNA chain or DNA polymerase accidentally forms a loop during replication -> small duplication

if template strand detaches -> small deletion

Question 33

WHAT OCCURS DURING UNEQUAL CROSSING OVER?

Answer 33

aberrant recombination; large deletion/duplication

Question 34

WHAT OCCURS DURING UNEQUAL EXCHANGE NETWEEN MISALIGNED SISTER CHROMATIDS?

Answer 34

breaks and exchange between sister chromatids –

microdeletion syndrome

Question 35

EXPLAIN THE DIFFERENT TYPES OF DELETIONS

Answer 35

3 / MULTIPLE OF 3 BASES = 3bp deletion in cystic fibrosis
-1 amino acid is missing -> delta F 508 = phenylalanine is missing)

LARGE DELETIONS WITHIN A GENE = Duchenne muscular dystrophy -> huge deletion in the dystrophin gene

TOTAL GENE DELETION = X-linked ichtyosis has a complete deletion of the steroid sulphatase gene

WHOLE GENE DUPLICATION = Charcot-marie tooth -> there is a tandem duplication of a gene segment between repetitive sequences. Duplication of genes -> increase dose of product
(one of the gene encodes for components of myelin in the PNS) = there is a progressive loss of muscle tissue and touch sensation

Question 36

WHAT ARE NON SYNONYMOUS MUTATIONS?

Answer 36

missense, nonsense, elongation
-worst type of mutations
-coding mutations

Question 37

WHAT ARE SYNONYMOUS MUTATIONS?

Answer 37

silent, RNA translation issues
-coding mutations

Question 38

WHAT ARE THE NON-CODING MUTATIONS?

Answer 38

promoter, splicing, interaction issues

Question 39

WHAT IS THE FUNCTION OF AN UNTRANSLATED REGION?

Answer 39

provides stability to the transcript