1. Variation Mutations DNA repair

2. Variation Variation is any difference between organisms Variation
Non-heritable Heritable
- Recombination
- Mutations

3. Mutations (H. de Vries, 1901)
Mutations are permanent changes in the genetic material.

4. Classification of mutations
By inheritance:
Somatic (occur in body cells)
Germinal (occur in gametes)
By expression in a heterozygote:
Dominant
Recessive

5. By effect on a wild-type (the most common phenotype):
Forward (wild-type → mutant (new) phenotype)
Reverse (mutant phenotype → wild-type)
Suppressor (mutant phenotype → wild-type)
4. By effect on phenotype:
Lethal
Morphological
Biochemical etc.

6. 5. By causes:
Spontaneous (result from abnormalities in cellular processes)
Induced (caused by environmental agents)
6. By effect on fitness:
Beneficial
Neutral
Harmful
7. By effect on genome:
Single-gene (small changes in DNA structure that occur within a particular gene)
Chromosome (changes in chromosome structure)
Genome (changes in chromosome number)

7. Mutagens Mutagens are agents that can cause mutations. Physical
Ionizing radiation (X rays, gamma rays)
UV light
Chemical
Base analogous (bromouracil, aminopurine)
Alkylating agents (ethyl methanesulfonate, nitrogen mustard)
Deaminating agents (nitrous acid, nitrites)
Intercalating agents (acridine dyes, proflavin, ethidium bromide)
Dioxins etc.
Biological
Mobile genetic elements
Viruses

8. Gene mutations Base-pair substitutions A transition: A↔G, T↔C
A gene mutation is a permanent change in the DNA sequence that makes up a gene.
Base-pair substitutions
A transition: A↔G, T↔C
A transversion: A↔C, A↔T, G↔C, G↔T
Insertions of nucleotides
Deletions of nucleotides
Intragenic inversion
Dynamic mutations (trinucleotide repeat expansion)
frameshift mutations

9. Missense mutations cause a codon to code for a different amino acid
Nonsense mutations change an amino acid codon into a stop codon
Silent (same-sense) mutations do not alter the amino acid sequence of the polypeptide because of redundancy in the genetic code

10. Mechanisms of Mutation Induction
1. Errors in DNA replication
2. Tautomeric shift (the spontaneous isomerization of a nitrogen base to an alternative hydrogen-bonding form, possibly resulting in a mutation)
3. Base-analogue-induced mutagenesis
4. Deamination
5. Depurination
6. Formation of pyrimidine dimers
7. Alkylation
8. Intercalating agents
9. Breaking of phosphodiester bonds

11. DNA repair DNA repair is correction of DNA damages Types of Repair:
Direct repair
Excision Repair
Recombinational repair
SOS-repair

12. Direct repair
These systems act directly on damaged nucleotides, converting each one back to its original structure (reversing).
DNA polymerase proofreading
Photoreactivaton is a process that directly reverses pyrimidine dimers by the action of the enzyme photolyase. This enzyme mechanism requires visible light.
Repair of alkylation damage by the special methyltransferases.
Nicks can be repaired by a ligase.
Repair of AP-sites by base-insertion enzymes (insertases).

13. Excision repair
The damage is repaired by excision and replacing it with new DNA synthesized using the complementary strand as template
Excision repair of modified bases
Excision repair of pyrimidine dimers
Mismatch repair

14. Steps of excision repair:
Damage recognition
Damage excision
DNA repair synthesis
DNA ligation

15. Excision repair of modified bases
Modified or damaged base is removed by a DNA glycosylase
AP-deoxyribose is then released by AP endonuclease and phosphodiesterase
Missing nucleotide replaced by DNA polymerase
The nick is sealed by DNA ligase

16. Excision repair of pyrimidine dimers (prokaryotic cells)
UvrABC endonuclease complex (excinuclease) recognizes the DNA damage.
Excinuclease cuts the damaged strand at two sites separated by 12 or 13 bases.
Helicase UvrD unwinds the damaged region.
DNA polymerase I fills the gap.
DNA ligase seals the nick.

17. DNA mismatch repair Proteins MutS и MutL binds to a mismatched bp
Endonuclease MutH cleaves the error strand
Helicase separates the strands
Exonuclease removes the error strand
DNA polymerase fills the gap
DNA ligase seals the nick

18. Recombinational repair
This pathway allows a damaged chromosome to be repaired using a sister chromatid or a homologous chromosome as a template.

19. SOS-repair SOS-repair occurs when cells are overwhelmed by DNA damages
This is induced by RecA binding to ssDNA.
RecA protein mediates proteolytic cleavage of LexA protein. LexA is a repressor of 43 genes involved in DNA repair.
Transcription of umuC and umuD genes are activated.
Protein complex UmuCD serves as DNA polymerase that can operate on damaged or imperfect DNA templates.
This is error-prone replication.