DNA repair

Chapter 6 - Essential Cell Biology

mutations

permanent change in base sequence of DNA

evolutionary

Mutations are at the base of the _______ process.

Silent mutation

• not deleterious

• exists because of degeneracy of genetic code

third

Degeneracy or redundancy exists in which letter or base?

• known as “wobblie”

High

High or low missense mutations?

aa is the active site of the enzyme

High

High or low missense mutations?

aa goes from negatively charged to positively charged

Low

High or low missense mutations?

aa doesn’t change drastically
e.g.,

Ala → Leu

Nonsense mutations

• substitutes a stop codon for an amino acid

• often deleterious

• proteins synthesized are:

  • mostly shorter

  • often non-functional

Insertions/Deletions

• result in a shift in the reading frame

• not multiple of 3 always cause a shift in reading frame

• almost always deleterious

radiations

Causes of mutations:

• ionizing

• non ionizing

chemical mutagens

Causes of mutations:

• Nucleosides analogs

• Intercalating agents

ionizing radiations

• X and y rays

• used for sterilization

• can cause double-stranded breaks in DNA

• can cause modification in bases (C to U)

nonionizing radiations

UV rays

• NOT strong enough for sterilization

• can cause thymine dimer formation

  • e.g., 2 T’s should bond to A’s, but instead bond to each other

Nucleoside analogs

Introduce mutations by introduction of different base pairs

Intercalating agents

Heterocyclic ring molecules (at least 2 different elements)

• slide between nucleotides

• e.g.,

  • Acridine orange

  • Ethidium bromide

stable

Mutations must occur in ____ states, so that the organism can survive and reproduce.

continually

DNA damage occurs ______ in cells.

temporary

Most DNA damage inside the cell is _______.

Depurination

Common form of DNA damage; Natural process that removes the nitrogenous base of DNA every 30s or so

Deamination

common form of DNA damage; cytosine converted into uracil

Thymine dimers

Occur because of UV radiation; cause two thymine bases to form covalent bonds between each other on the same strand

damage removal

specialized enzymes recognize damaged DNA and cut out the affected section, leaving a small gap in one strand

gap filling

A repair DNA polymerase fills in the missing nucleotides using the undamaged strand as a template

Sealing

DNA ligase seals the remaining break in the sugar-phosphate backbone, restoring the DNA strand

mismatch repair machinery

protects DNA damage beyond the proofreading capability of DNA polymerase

• occurs in one strand

mismatch repair

incorrectly added nucleotide is excised and replaced

• occurs replication

after

Mismatch repair occurs _____ replication.

bacteria (prokaryotes)

Mismatch repair in ________:

• enzymes can detect methylation (new strands are not methylated)

Humans (eukaryotes)

Mismatch repair in ________:

• Exist to detect new strands from the original

• Some versions of colon cancer exists because of abnormal mismatch repair mechanisms

• Humans have two copies of this gene

both

Cancer can only occur if _____copies of genes are mutated.

T

T or F?
Since there are no “back up” strands for single stranded DNA, it is more challenging to repair.

initiation

Homologous end joining:

• A recombination-specific nuclease trims back the 5’ ends at the DNA break, creating 3’ overhangs

strand invasion & synthesis

Homologous end joining:

• one 3’ end invades the undamaged homologous DNA, base-pairs with the matching sequence, and is extended by a repair DNA polymerase

completion

Homologous end joining:

• Newly synthesized DNA re-pairs with its original strand, and the break is fully repaired through additional DNA synthesis and ligation

after

Homologous recombination must happen shortly after DNA was _____.

vicinity

Homologous recombination must happen when newly replicated DNA is in the ________.

Nucleotide excision repair (dark repair)

DNA is cut several ntds upstream and downstream and replaced with correct strand

Direct repair (light repair)

enzyme photolysase, activated by visible light, breaks the thymine dimer