Lecture 11 Flashcards by she ign

Point mutations is a – level base substitution

DNA

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replace DNA base with the same chemical property

purine–> purine

transitions

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replace DNA base from different chemical
property
purine –> pyrimidine

transversions

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one or more DNA nucleotides are added

base insertions

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one or more DNA nucleotides are deleted

base deletions

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Base substitutions in coding regions is – level

amino acid

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change mRNA nucleotide but same aa

silent mutation

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change mRNA nucleotide change aa

missense mutation

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change mRNA nucleotide –> stop codon

nonsense mutation

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altered aa is in the same aa group

conservative missense mutation

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altered aa is in a different aa group

non-conservative missense mutation

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DNA damage is unavoidable and arise by – of chemical bonds in DNA

spontaneous cleavage

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DNA damage can occur via – chemicals in the environment

genotoxic

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DNA damage can occur via certain by-products of normal –

cellular metabolism

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DNA damage can occur via environmental agents such as – and -

UV light and ionizing radiation

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DNA damage can occur via – induced by DNA pol during replication

copying errors

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inside the cell is - environment

reducing

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deamination of a cytosine base, converts it into a

uracil

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deamination of a common modified base 5-methyl cytosine, converts it to a –

thymine

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depurination can release – and – from a DNA strand

guanine and adenine

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depurination can a – mutation

deletion

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common type of damage caused by UV light

thymine dimers

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thymine dimers interfere with – and –

DNA replication and RNA transcription

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cells use – to fix DNA regions containing chemically modified bases that distort the normal shape of DNA locally

nucleotide excision repair

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determine potential mutagens

Ames test

base analog of thymine that can bind with guanine

5-bromouracil (enol tautomer)

intercalating agents that can cause mutations include

proflavin, ehtidium, and acridine orange

first line of defense in preventing mutations is

DNA polymerase

proofreading depend on the -- of some DNA pol

3'--> 5' exonuclease activity

when an incorrect base is incorporated during DNA synthesis, the 3' end is transferred to the -- where the incorrect misfired base is removed

exonuclease site

-- methylates A residues of 5'GATC3' sequence

E. coil dam methylase

methylation marks the -- therefore the mismatch repair system can distinguish the newly synthesized strands

template strands

-- enables replication to proceed across DNA damage

translesion DNA synthesis

in photoreactivation, -- breaks thymine dimers

DNA photolyase

methyl group removal by -- is an example of direct reversal of DNA damage

methlytransferase

besides DNA pol, cells have other repair systems called -- for preventing mutations due to copying errors and exposure to mutagens

DNA excision-repair systems

many cancers arise from a loss of one of --

DNA repair systems

base excision repair removes damaged bases by a specific

glycosylase

Because a G-T mismatch is almost always caused by a chemical conversion (deamination) -- the repair system "knows" to remove the -- and replace it with --

5-methyl C --> T | remove T and replace with C

-- is recognized by a DNA glycosylase and flips out the thymine base out of the helix cuts it away from the sugar-phosphate backbone

G-T mismatch

-- an endonuclease specific for the 5' end of the baseless site cuts the DNA backbone

APEI

another endonuclease called -- which is associated with DNA pol beta removes the deoxyribose phosphate

AP lyase

-- fill the gaps which are sealed by DNA in base excision repair systems

DNA pol beta

in nucleotide excision repair, a complex of -- and -- proteins slide along the surface of a double stranded DNA molecule looking for any distortions of the double helix.

XP-C and 23B

complex of XP-C and 23B recruits then recruits the general transcription factor --, whose helicase subunits partially unwind the double helix.

TFIIH

After TFIIH is recruited, -- then bind to the complex and further unwind and stabilize the helix until a bubble of ~25 bases is formed.

XP-G and RPA proteins

After a bubble is formed, --(now acting as an endonuclease) and --, a second nuclease, cut the damaged strand on each side of the lesion.

XP-G and XP-F

during nucleotide excision repair, the DNA fragment with damaged bases is released and --

degraded to mononucleotides

Lastly, the gap is filled by --, and the remaining nick is sealed by DNA ligase during nucleotide excision repair

DNA polymeraseδ/ε

error -- homologous recombination

free

error -- DNA end joining

prone

error- free homologous recombination: double strand DNA break forms in the --

chromatids

error-free homologous recombination: double strand break activates -- which leads to the activation of a set of exonucleases that remove nucleotides at the break creating single-stranded 3' ends

ATM kinase

error-free homologous recombination: in a BRCA1 and BRCA2 dependent process, -- polymerizes on single-stranded DNA with free 3' ends to form a nucleoprotein filament

RAD51

error-free homologous recombination: -- conducts a homology search on the duplex DNA sequence in the sitter chromatid

RAD51 nucleoprotein filament

after finding a homology, the RAD51 nucleoprotein filament invades the duplex to form a -- in which the single-stranded 3' end is base-paired to the complementary strand on the homologous DNA strand.

joint molecule

error-free homologous recombination: DNA pol elongates the 3' end of the -- (using the complementary sequences on the sister chromatid as a template)

damaged DNA

error-free homologous recombination: When sufficiently long, this repaired 3' end of the damaged DNA -- with the single-stranded end of the other damaged strand.

pairs

error-free homologous recombination: Any remaining gaps are filled in by DNA polymerase and DNA ligase, regenerating a -- double helix in which an entire segment has been regenerated.

wild-type

The predominant mechanism of double-strand break repair in multicellular organisms.

error-prone repair by enjoining

error-prone repair by enjoining: nvolves rejoining the -- of two DNA molecules.

nonhomologous ends

error-prone repair by enjoining: Even if joined DNA fragments come from the same chromosome, the repair process results in loss of several base pairs at --(mutations).

the joining point

error-prone repair by enjoining: -Sometimes broken ends from different chromosomes are accidentally joined together, leading to -- of pieces of DNA from one chromosome to another.

translocation