Gene Mutations I and II

Question 1

Polymorphism meaning?

Answer 1

Natural variation in gene,DNA, Chromosome that has no adverse affects to the organism.

Benefit - population
Benefit evolution

natural variations in a gene, DNA sequence, or chromosome that have no adverse effects on the individual and…
occur with fairly high frequency in the general population.

Beneficial – Evolution

Question 1

What is a Mutation? When occurs? Effect?

Answer 1

Change in genome, spontaneously, polymorphism

1. Change in the genome - can occur spontaneously
2. Produces genetic variation (polymorphism)

3.Gene mutation = change within a single gene
- One allele is mutated, to become another allele

4.Some mutations are point mutations, change in a single nt pair

Question 2

Allele meaning?

Answer 2

Allele = one of a number of alternative forms of the same gene or same genetic locus

Question 3

Mutation Nomenclature:

for
Bases, Deletion, Insertion, Amino Acids

Answer 3

5162 G –> A
5162= base position
G = orignal base
A = replacement base

Deletion: 197delAG
Insertion: 2552insT

R197G
R= Original Amino Acid
197 = AA position
G= Replacement AA

Question 4

Wild type vs Mutant:

Answer 4

Wild-type: STANDARD GENOTYPE/PHENOTYPE
- Wild-type = found in nature or in the laboratory STOCK of the organism

Mutant: ALTERED genotype or phenotype (due TO MUTATION )

Question 5

Origins of Mutations:

INDUCED VS SPONTANEOUS
Which one is the ultimate source of genetic variation? rate

Answer 5

1. Induced = Treatment with Mutagen
2. Spontaneous = Absence of mutagen
   - Spontaneous mutations - ultimate source of genetic
   variation
   (DNA replication/repair).
   - Rate is low - one cell in 10^5 - 10^8

Question 6

What are Mutagens? how they effect?

Answer 6

Mutagens cause mutations - greater dose, more mutations

A mutagen is a CHEMICAL or PHYSICAL AGENT capable of INDUCING CHANGES in DNA called mutations

Question 7

define mutagenesis?

Answer 7

the production of genetic mutations.

Question 8

TYPE SOF MUTATIONS: POINT MUTATIONS
2? What are they?

Answer 8

Two main types:

1. Base substitutions: one base pair is replaced by another
   - Transition: replacement of a base by another base of the same chemical category (Purine ->Purine e.g. A ->G) or (Pyrimidine->Pyrimidine e.g. C ->T)
   - Transversion: replacement of a base by another base of a different chemical category (Purine ->Pyrimidine e.g. A ->C) or (Pyrimidine->Purine e.g. C ->A)
2. Base insertions/deletions (indel): Insertion or deletion of nt pairs

Question 9

Types of Base Substiutions:

Answer 9

Base substitutions: one base pair is replaced by another

1. • Transition: replacement of a base by another base of the same chemical category (Purine ->Purine e.g. A ->G) or (Pyrimidine->Pyrimidine e.g. C ->T)
2. Transversion: replacement of a base by another base of a different chemical category (Purine ->Pyrimidine e.g. A ->C) or (Pyrimidine->Purine e.g. C ->A)

Question 10

Types of Base Insertions/Deletions (indel):

Answer 10

Base insertions/deletions (indel):

Insertion or deletion of nt pairs

Question 11

TYPES PF MUTATIONS = Point mutations at

***AT PROTEIN LEVEL (Protein coding part of a gene) =4

Answer 11

1. Synonymous mutation – Codon change results in same AA (degeneracy of genetic code)
2. Missense mutation (conservative/non) – Change in AA (to chemically similar
   AA/chemically different AA - affects protein structure and function!!)
3. Nonsense mutation – Codon for one AA changed to STOP codon (premature
   termination of translation – affects protein function e.g. inactive proteins)
4. Frameshift mutation – Indel (AA sequence downstream of mutation changed – loss of normal protein structure and function)

Question 12

AMINO ACID CLASSIFICATIONS

NON POLAR -

POLAR -

ELECTRICALLY CHARGED- ACID VS BASIC

Answer 12

NON POLAR - Glycine, alanine, valine, leucine, isoleucine, methionine, tryptophan, phenylalanine, proline

POLAR - serine, threonine, cystine, tyrosine, asparagine, glutamine

ELECTRICALLY CHARGED-

ACID: apartic acid, Glutamic acid
BASIC: lysine, arginine, histidine

Question 13

Transitions vs Transversions

Answer 13

TRANSITIONS
1. Purine to Purine
A - G
G - A

2. PYRIMIDINE
   T - C
   C - T

TRANSVERSIONS
1. PURINE TO PYRAMIDINE
A-C
A-T
G-C
G-T

2. PYRIMIDINE TO PURINE
   C-A
   C-G
   T-A
   T-G

Question 14

Consequences of mutations within genes;
Types of Mutations at DNA level, Results at molecular level

NO MUTATION

TRANSITION OR TRANSVERSION

INSERTION OR DELETION

Answer 14

NO MUTATION: wild type
- Codons specify wild type protein

TRANSITION OR TRANSVERSION

1. Synonymous mutation: Altered codon specifies the same A acid.
2. Missense mutation (conservative):
   Altered codon specifies a chemically similar amino acid
3. Missense Mutation (NONCONSERVATIVE):
   Altered codon specifies a chemically dissimilar amino acid.
4. Nonsense mutation: Altered codon signals chain termination (STOP CODON)

INSERTION OR DELETION:
1. Frameshift mutation:

Question 15

POINT MUTATION DO NOR ALWAYS HAVE PHENOTYPIC EFFECT:

Answer 15

Other than silent mutations, usually the least severe mutations in a protein coding gene result from missense mutations, but some missense mutations can be very deleterious…

Question 16

Mutations can alter pre-mRNA Splicing
HOW? WHAT THE STEPS?

Answer 16

1. Whole exon can be deleted as result of mutations in splice
   signals,
   e.g. Exon Skipping

2.Part of exon can be deleted as a result of mutations in normal splice signals cryptic splice site selection (sequences resembling normal splice signals)

Question 17

Abnormal Splicing of b-globin
RNA in patients with b
thalassaemia (Mild to severe
anaemia)

Answer 17

Abnormal Splicing of b-globin
RNA in patients with b
thalassaemia (Mild to severe
anaemia)

PG 19

Question 18

Different single-base mutations cause different splicing defects & disease:

WHAT ARE THEY? = 3

Answer 18

1. Exon skipping
2. Cryptic splice-site selection
3. New splice site created

Question 19

Wild type:

which way for Wild type and mutant?

Forward vs Reverse Mutation?

Answer 19

1. Forward Mutation – alters WT
   (Changes WT into a Mutant Phenotype)

Wildtype -> Mutant

2.Reverse Mutation – get WT
(Restores the WT phenotype)

Wildtype <- Mutant

Question 20

Explain Reverse Mutations:

Answer 20

Exact reversion (true or genotypic) gives the wild type DNA sequence

Equivalent reversion gives a different DNA sequence, but the wild type AA sequence.

“reversion” is usually used to indicate reappearance of parental phenotype in a mutant organism caused,

Change in nt sequence to give back wild-type AA sequence, but not wild-type nt sequence…

Question 21

Explain Suppressor mutation:

Answer 21

1. “hides” the effect of another mutation.
2. Distinct to exact reversion in which the mutated site changes back to original WT sequence.
3. Occurs at a site distinct from the site of the original mutation.
4. Double Mutant - Possesses original and suppressor mutation
   but WT phenotype.
5. Two classes Intragenic and Intergenic

Question 22

Intragenic vs Intergenic Supressor

Answer 22

both classes of Supressor mutation:

1. Intragenic suppressor – mutation occurs in the gene
   containing the original forward mutation

… Might change a second nucleotide in the same codon.
…Might also work by suppressing a frameshift mutation

2. Intergenic suppressor – mutation occurs in a gene other than the one containing the original mutation that it supresses

Question 23

action of an intergenic suppressor mutation,

Answer 23

steps

Question 24

Base substitution?

Answer 24

changes the base of a single DNA nucleotide

Question 25

transition?

Answer 25

Base substitution in which a purine replaces a purine or a pyrimidine replaces pyrimidine.

Question 26

Transversion

Answer 26

base substitution in which a purine replaces pyrimidine or a pyrimidine replaces a purine

Question 27

Insertion vs deletion

Answer 27

insertion: addition of one or more nucleotides deletion: deletion of of one or more nucleotides

Question 28

frameshift mutation:

Answer 28

insertion or deletion that alters the reading frame of a gene

Question 29

in-frame deletion or insertion:

Answer 29

deletion or insertion of a multiple of 3 nucleotides that DOES NOT alter the reading frame

Question 30

expanding trinucleotide repeats:

Answer 30

repeated sequence of 3 nucleotides (trinucleotide) in which the number of copies of the trinucleotide increases

Question 31

forward vs reverse mutation:

Answer 31

forward mutation: changes the wild type phenotype to a mutant phenotype reverse mutation: changes a mutant phenotype back to the wild-type phenotype

Question 32

missense mutation

Answer 32

changes a sense codon into a different sense codon, resulting in the incorporation of a different amino acid in the protein

Question 33

nonsense mutation:

Answer 33

changes a sense codon into a nonsense codon; causing premature termination of translation

Question 34

Silent mutation:

Answer 34

changes a sense codon into a synonymous codon, leaving unchanged the amino acid sequence of the protein

Question 35

Neutral mutation:

Answer 35

changes the AA sequence of a protein without altering its ability to function

Question 36

Loss-of-function mutation vs Gain of function mutation:

Answer 36

Loss-of-function mutation: causes a complete or partial loss of function Gain of function mutation: causes the appearance of a new trait or function or causes the appearance of a trait in inappropriate tissue or at an inappropriate time.

Question 37

Lethal mutation:

Answer 37

causes premature death

Question 38

supressor mutation:

Answer 38

suppresses the effect of an earlier mutation at a different site

Question 39

Intragenic suppressor mutation vs Intergenic suppressor mutation:

Answer 39

Intragenic suppressor mutation: supresses the effect of an earlier mutation within the SAME gene Intergenic suppressor mutation: suppresses the effect of an earlier mutation in ANOTHER gene

Question 40

Explain Gain of function mutation: mutant vs wild type

Answer 40

Protein or Gene product has enhanced function or a new function eg Tumour formation, mutation in gene that encodes a receptor for a growth factor, mutated receptor may stimulate growth all the time even in absence of the growth factor Wildtype Inactive --> Active Mutant Always Active

Question 41

Understanding Conditional Mutations:

Answer 41

Mutant phenotype only seen under CERTAIN CONDITIONS usually associated with PROTEIN FOLDING eg at elevated temperatures …eg. dominant heat-sensitive lethals of Drosophila

Question 42

Understanding Somatic and Germinal Mutation

Answer 42

Mutations can occur in somatic cells or in germinal cells 1. Somatic cells: cells of the body (non-reproductive cells) 2. Germinal cells: give rise to gametes, so DNA is passed to next generation

Question 43

Understanding Somatic Mutation and Cancer...

Answer 43

Cancer cells: - control of cell division lost - movement of these cells through the body Mutation in genes that control cell division can lead to cancer

Question 44

Detecting mutations: WHY AND HOW?

Answer 44

Why? - To understand mutation events - To obtain mutants in a particular biological process How? - Use systems where a mutation will cause a change in phenotype

Question 45

Detecting Recessive Mutations in Humans: 3

Answer 45

1. Only see mutant phenotype in homozygote - (Both alleles must be mutant in order for the mutant phenotype to be observed) 2. Mutation may have been present for generations before phenotype seen 3. X-linked recessive mutations are expressed more frequently in males - (need to inherit only a single copy of the mutant allele to display the trait)

Question 46

Haemophilia? Expression on X and Y Chr.s?

Answer 46

Haemophilia: failure in blood clotting - Mutant allele on X chromosome (Xa) - Males carrying mutant allele (Xa Y) express phenotype

Question 47

Understanding mutation rate? How to calculate?

Answer 47

Mutation Rate: Number of mutations per unit of time (eg cell divisions or generations) Calculation: No. mutational events / No. cell divisions

Question 48

Understanding mutation Frequency? How to calculate:

Answer 48

How often a mutant is found in a population? No. Mutants / Size of Population

Question 49

Understanding Mutation Frequency (Single Genes) examples corn vs humans

Answer 49

Mutations are rare events Corn 1 x 10^-6 to 500 x 10^-6 mutations per gamete Humans 1 x 10^-6 mutations per gamete

Question 50

Strategies to Improve Success when Hunting for Mutants? 2

Answer 50

1. Mutagens: Agents that increase the frequency of mutation 2. Selective systems: Methods to identify mutants easily from a large population

Question 51

Understanding Selective Systems:

Answer 51

Methods to "select" mutants Must be able to: - Identify mutants clearly - Subject a large number of individuals to - selection (mutants are rare)

Question 52

What are Biochemical Mutants? Prototroph vs Auxotroph

Answer 52

Biochemical Mutants: Microorganisms Prototroph: able to grow on a simple medium Auxotroph: requires additional nutrients to grow - Selection of auxotrophs by inability to grow on minimal medium (eg mutation disrupts ability to synthesize one or more biomolecules)

Question 53

1940 Beadle and Tatum's work with Neurospora crassa

Answer 53

Beadle and Tatum's work with Neurospora crassa is a classic experiment in genetics that helped establish the "one gene, one enzyme" hypothesis. Here it is in very simple dot points: - **Organism Used:** Neurospora crassa, a type of bread mold. - **Objective:** To understand how genes control the production of enzymes. - **Steps:** - They exposed Neurospora crassa to radiation to induce mutations. - Each mutation affected a specific gene. - They observed the effects of these mutations on the mold's ability to grow on different nutrient media. - **Key Finding:** - Mutations resulted in the loss of specific enzymes needed for nutrient synthesis. - For example, one mutation prevented the mold from making an enzyme to produce a specific nutrient. - **Conclusion:** - Each gene in the mold's DNA coded for a specific enzyme. - Mutations in genes led to the loss of corresponding enzymes, affecting the mold's ability to grow on certain nutrients. - **Hypothesis:** - "One gene, one enzyme" - Each gene controls the production of a specific enzyme. - **Significance:** - This experiment laid the foundation for our understanding of the relationship between genes and enzymes, advancing the field of molecular biology. In simple terms, Beadle and Tatum's work with Neurospora crassa showed that genes are responsible for making specific enzymes, and mutations in genes can lead to the loss of these enzymes, affecting the organism's abilities. This discovery had a significant impact on our understanding of genetics and biochemistry.

Question 54

Explain Resistance selection:

Answer 54

E. coli resistance to bacteriophage T1 Sensitive cells are lysed, do not form colonies (a) Resistant cells form a colony (b) - stable, genuine mutants

Question 55

Origin of Resistant cells:

Answer 55

Understanding the nature of mutation, 1943: Knew phage caused E. coli death, but also knew that a small percentage of colonies did not die - they became resistant & were stable & genuine mutants. BUT, didn’t know HOW! Did the presence of the bacteriophage T1 induce a physiological change in the E. coli that caused resistance? OR Were the mutant E. coli formed spontaneously, but randomly in time?

Question 56

Origin of resistant cells

Answer 56

1, Physiological change 2. Random mutation

Question 57

Origin of resistant cells: FLUCTUATION TEST

Answer 57

1. “Fluctuation Test” of Luria & Delbrük, second scenario correct. 2. Inoculated 20 small cultures & grew to 108 cells/mL 3. At same time inoculated 1 large culture & grew to 108 cells/mL 4. Took 20 individual cultures & 20 samples from large culture & plated in presence of phage. 5. 20 individual cultures - showed high variation (“fluctuation”) in number of resistant colonies: from 0 to 107 per plate. 6. 20 samples from large culture had much less variation - from 14 - 26 resistant colonies per plate.

Question 58

ORIGIN OF RESISTANT CELLS BEST EXPLANATION:

Answer 58

Best explanation = mutations occurred randomly in time: early mutations gave higher number of resistant cells (more generations of descendants). Later mutations gave fewer resistant cells. Hence, resistant cells are selected by environmental agent (e.g. phage), rather than produced by it. Can existence of mutants in a population before selection be demonstrated directly? Replica plating technique (1952) Grew cells on a master plate of nonselective media & colonies transferred to a series of selective media plates

Question 59

SUMMARY

Answer 59

1. Mutations can be detected by phenotype using appropriate crosses, & pedigree analysis 2. Mutations are rare 3. Mutation is a random process. Any allele in any cell can mutate at any time! 4. Mutagens increase the number of mutants 5. Mutations are useful in research 6. Selective systems aid in screening for mutants present in a population