Chapter 9: Genetic Change and Genome Evolution

What is a mutation?

A permanent heritable change in the DNA sequence.

What are the possible effects of mutations?

harmful, beneficial, or neutral

What is the first step in evolution?

The process of genetic change through mutations.

What are two things that mutations can change?

1. structure/function of gene's products

2. regulation of gene's expression

Name the six physical and structural classes of mutations.

Point mutation, insertion and deletion, inversion, duplication, transposition, reversion.

What is a point mutation?

A change in a single nucleotide in the DNA sequence.

What is the difference between a transition and a transversion mutation?

Transition replaces a purine with a purine or a pyrimidine with a pyrimidine; transversion replaces a purine with a pyrimidine or vice versa.

What occurs during an insertion mutation?

One or more nucleotides are added to the DNA sequence; becomes longer

What occurs during a deletion mutation?

One or more nucleotides are removed from the DNA sequence; becomes shorter

What is an inversion mutation?

A fragment of DNA is flipped in orientation relative to the surrounding DNA.

What is a duplication mutation?

A second copy of a DNA sequence is produced, usually adjacent to the original.

What is transposition?

The movement of a sequence fragment (transposon) from one location to another; catalyzed by special enzymes and can involve insertions, deletions, and duplications

What is a reversion mutation?

A mutation that restores a mutated sequence to its original sequence; A-> C -> A

What are the four informational classes of mutations?

Silent mutation, missense mutation, nonsense mutation, frame-shift mutation.

What is a silent mutation?

A mutation that does not change the amino acid sequence of a protein ex. TTT--> TTC is still The

What is a missense mutation?

A mutation that results in an amino acid substitution, affecting the activity of the protein--> can be loss or gain of function

What is a nonsense mutation?

A mutation that changes an amino acid codon into a stop codon, leading to a truncated protein and can genes into pseudogenes

What is a frame-shift mutation?

Insertions or deletions that alter the open reading frame of the DNA sequence; resulting in distorted proteins, premature stop codons or pseudogenes

What can mutations affect in an organism?

Both the genotype and the phenotype.

What is a spontaneous mutation?

A mutation that occurs naturally in the genome without an added mutagens

What is an induced mutation?

A mutation that is caused by external agents known as mutagens; happens due to various chemical/physical agents

______ are rare because of the efficiency of DNA proofreading and repair

spontaneous mutations

What are some causes of spontaneous mutations?

Errors during replication, mobile genetic elements, tautomeric shifts, deamination, formation of apurinic sites and oxidative damage.

What are tautomeric shifts?

Structural isomers of bases that can interconvert, affecting base-pairing properties; results from the relocation of a hydrogen atom within bases

What is deamination of bases by hydrolysis?

The spontaneous conversion of cytosine to uracil and pairs with adenine instead of guanine, altering base-pairing

What are apurinic sites?

Sites in DNA where purines have been spontaneously ejected from DNA by breakage of glycosidic bond, hindering transcription and replication.

What is the key source of reactive oxygen species that cause damage?

metabolic activities of the cell that modify nucleotides ex. hydrogen peroxide, superoxide radicals, hydroxyl radicals

What are mutagens?

Chemical agents or forms of radiation that can damage DNA and induce mutations.

What is the effect of X-rays and gamma rays on DNA?

ionize and break molecules in cells to form free radicals, which break DNA

What is the effect of UV radiation on DNA?

causes the formation of unstable pyrimidine dimers, blocking replication and transcription.

How is a 4-membered cyclobutane ring formed?

excited electrons of carbons 5 and 6 on adjacent pyridines are shared

What is the mechanism of base analog agents?

substitutes "look alike" molecule for normal nitrogenous base during DNA replication --> point mutation ex. caffeine

What is the mechanism of alkylating agents?

adds alkyl group (ex methyl group) to nitrogenous base, resulting in incorrect paring --> point mutation ex. nitrosoguanidine

What is the mechanism of deaminating agents?

removes amino group from nitrogenous base --> point mutation ex, nitrates

What is the mechanism of acridine deviating/intercalating

agents?

inintercalates into DNA ladder between backbones to form a new ring, distorting the helix --> frameshift mutations ex. quinacrine

What does the type of repair mechanism dependent on?

the type of mutation needing repair and extent of damage

What are the two types of DNA repair mechanisms?

Error-proof repair pathways and error-prone repair pathways.

What does error-proof repair pathways include?

methyl mismatch repair, photo reactivation, nucleotide/base excision repair, recombinational repair

What occurs in error-prone repair pathways?

risk of introduced mutations; acts as a final resort, only when damage is so severe that the cell has no other choice but to die

What is methyl mismatch repair?

A repair mechanism that corrects mismatches in DNA based on the methylation status of the parental strand, so that it can contain the proper DNA sequence

What enzyme methylates DNA in E.Coli?

DNA adenine methyltransferase (Dam)

What are the three methyl-directed mismatch repair enzymes?

MutS, MutL and MutH

What is the photoreactivation pathway?

use of light energy alongside enzyme photolysase to cleave cyclobutane ring, returning it to its original state without excising bases

What is nucleotide excision repair?

A process where enzyme UvrABC nuclease recognizes the dimer, cuts out, damaged stretches of DNA, leaving a gap that will be filled by DNA pol 1 and ligase

What are the 4 enzymatic activities of base excision repair pathway?

glycosylase, endonuclease, polymerase, ligase

What does the enzyme glycosylase do?

recognizes specific damaged bases and removing them without breaking the phosphodiester bond, resulting in an AP site

What is an AP site?

apurinic or apyrimidinic site

What occurs during recombinational repair?

a form of strand exchange occurs at shared regions of homologous between DNA molecules, which repairs a double-strand break involving a second chromosome by RecA

What is non homologous end joining (NHEJ)?

A error prone mechanism used to repair DNA that can lead to random insertions and deletions at the damaged site; does not require homology and is carried out by ku and LigD

Why do slow-growing bacteria use the NHEJ mechanism?

they lack a second copy of their chromosome to serve as a repair template, would not have enough time since replication for micro bacterium takes forever

What are some ways foreign DNA can be beneficial for bacteria?

alternative food source, repair for damaged chromosomes, drive genome evolution

What is horizontal gene transfer?

transfer of genetic information from cell to cell, rather from parent to offspring

What are the three mechanisms of horizontal gene transfer? What are the alternative mechanisms?

conjugation, transduction, transformation; membrane vesicles (exo/endocytosis) and nanotubes

What is conjugation?

unidirectional gene transfer of DNA from one bacterium to another via cell-to-cell contact; initiated by sex pilus from donor to recipient cell and requires transferable plasmids

What is oriV and oriT used for?

replicate in non conjugating cells and during DNA transfer, respectively

What is transduction?

bacteriophages accidentally as a result of the phage life cycle carry host DNA from one cell into another; can be generalized (any gene) or specialized (near chromosomal integration site)

What are the steps of transduction?

1. transfusing particles are injected into a cell

2. recombine with host chromosome of newly infected cell

3. become integrated with DNA and change overall genetic makeup of recipient

What is transformation?

The process of importing free DNA into a bacterial cell; involves competent cells extending a type 4 pilus into the cell membrane to access the environment and actively take up free DNA present.

What are transposable elements?

Elements that move from one DNA molecule to another, either within or between chromosomes, play a significant role in genome rearrangements during evolution.

What does enzyme transposase catalyze?

the transfer/copy of the element from one DNA molecule into another

What are the two types if transposable elements bacteria has?

insertion sequence (SIRS) and transposons (antibiotic resistance)

What two mechanisms can transposable elements utilize?

replicative transposition and non-replicative transposition