Microbiology Chapter 9: Genetic Change and Genome Evolution

DNA is a dynamic molecule with sequences that change over generations through ________

Mutations, including single base pair changes, rearrangements, and Gene transfer (interspecies/intraspecies)

The process of ________ is an essential first step of evolution

genetic change

Mutation is defined as a

permanent heritable change in the DNA sequence. may be harmful, beneficial or neutral, facilitate evolutionally change

Mutations fall into different physical and structural classes including:

1. Point mutation

2. Insertion and deletion

3. Inversion

4. Duplication

5. Transposition

6. Reversion

Point mutation is a

change in a single nucleotide.

Transition involves replacing a purine with a different purine (A,G) or a pyrimidine with a different pyrimidine (C, T, U)

Transversion involves replacing a purine for a pyrimidine

Insertion and deletion of one or more nucleotides make the sequence

either longer or shorter than it was originally

Inversion involves

a fragment of DNA being flipped in orientation

Duplication involves

producing a second copy of a sequence right next to the original copy

Transposition involves

movement of a sequence fragment from one location to another. This is catalyzed by special enzymes

Reversion involves

restoring a mutated sequence to its original sequence :)

Mutations are categorized into informational classes based on how they affect the gene product, these include:

1. Silent mutation

2. Missense mutation

3. Nonsense mutation

4. Frame-shift mutation

silent mutation

A mutation that changes a single nucleotide, but does not change the amino acid sequence created. (ex. TTT and TTC are both Phe)

missense mutation

A base-pair substitution that results in a codon that codes for a different amino acid. May decrease or eliminate activity of protein (LOSS OF FUNCTION MUTATION) or opposite (GAIN OF FUNCTION MUTATION)

nonsense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional (truncated) protein. Degraded by cellular proteases

frameshift mutation

mutation that involves the insertion or deletion of a nucleotide in the DNA sequence, shifts the "reading frame", resulting in a distorted protein or premature stop codon.

Mutations can affect both the _______ and ______ of the organism

genotype and phenotype

The genotype of an organism ________

reflects its genome sequences, every mutation causes a change in genotype

The phenotype comprises _____

observable characteristics such as biochemical, morphological, or growth traits

Mutations can be spontaneous or induced, what's the difference?

Spontaneous Mutations occur natural in the genome due to replication error, mitosis, meiosis., mobile genetic elements or transposons.

Induced mutations cause caused by various chemical and physical agents known as mutagens, which increase mutation frequency,

Spontaneous mutations:

rare bc of DNA proofreading/repair efficiency, can arise:

1. Tautomeric shifts in DNA bases that alter base-pairing properties

2. Oxidative deamination of bases

3. Formation of apurinic sites

Damage caused by reactive oxygen species

Tautomeric shifts

occur in chemical structure of bases, involves changing bonding properties of amino and keto groups (moving double bonds). > # mutations

Mutation arising from tautomeric shift of thymine prior to DNA rep:

AT to GC mutation in 1 progeny occurs after the second round of replication

Oxidative deamination of bases

Cytosine spontaneously deaminates to yield uracil, which base-pairs with adenine instead of guanine (-NH2= C-->U)

Formation of apurinic sites

Purines are susceptible to spontaneous Ejection from DNA by breakage of glycosidic bond, which hinders transcription and translation

Damage caused by reactive oxygen species

Cell metabolic activities make reactive oxygen species (ex. H2O2) that can modify nucleotides, which interfere with polymerase function and stop replication or the transcription of affected genes

Mutations can be caused by mutagens

Chemical agents or forms of electromagnetic radiation can cause damage

Chemical agent mutagens:

Base analogs, Base modifiers, Intercalators

electromagnetic radiation

x-rays and gamma rays: break the DNA

UV rays: form pyrimidine dimers

Base analog (ex. caffeine, 5-bromouracil)

substitutes "look-alike" molecule for normal nitrogenous base during DNA replication: point mutation

Alkylating agent (ex. nitrosoguanidine)

Adds alkyl group such as CH3 to nitrogenous base, resulting in incorrect pairing: point mutation

Deaminating agents (ex. nitrous acid, nitrates, nitrites)

removes amino group -NH2 from nitrogenous base: point mutation

Acridine derivative (acridine dyes, quinacrine)

Inserts (intercalates) into DNA ladder between backbones to form new ring, distorting the helix, can cause frameshift mutations

UV-rays

Link to adjacent pyrimidines to each other, as in thymine dimer formation, thereby impairing replication, lethal if not repaired

X-rays and Gamma rays

Ionize and break molecules in cells to form 3 radicals which in turn break DNA: lethal if not repaired

Pyrimidine dimer production

They're susceptible to UV radiation and absorb energy., excited electrons of carbons 5 and 6 on adjacent pyrimidines, then can be shared to form 4-membered cyclobutane ring. Blocks transcription and translation.

DNA damage is repaired before it becomes a heritable mutation. The type used and when depends on:

The type of mutation needing repair and the extent of damage

DNA repair is divided into two types:

1. Error-proof repair pathways: prevent mutations, do not introduce

2. Error-prone repair pathways: risk introducing mutations

Error-proof repair pathways

1. Methyl mismatch repair, 2. photoreactivation, 3. nucleotide excision repair, 4. base excision repair, and 5. recombinational repair

Error-prone repair pathways

Operate only when damage is so severe that the cell has no other choice but to die

Methyl mismatch repair

Uses methyl on parent strand to differentiate between new strand since they're not immediately methylated. Parental strand should contain proper DNA sequence

Repair proteins and genes are called Mut because _____

A bacterial strain with a high mutation rate is called a ______

a high mutation rate results in strains that are defective in one of these proteins,

mutator strain

In E coli., _______ methylates the palindromic sequence GATC to produce GAmeTC

Methyl directed ismatch repair enzymes are_________

DNA adenine methyltransferase (Dam). MutS, MutL, and MutH.

Photoreactivation

The enzyme photolyase binds to the pyrimidine dimer with light energy and cleaves the cyclobutane ring linking 2 adjacent, damaged nucleotides. Activated by lower energy wavelength of light (visible). Damages repaired without cell removal

Nucleotide excision repair

UvrABC nuclease recognizes dimer, cleaves and removes short section of DNA including dimer, leaves behind gap filled by DNA Pol. I and ligase

Base excision repair

specialized enzymes recognize and remove specific damaged bases without breaking phosphodiester bonds, reulting in an AP site.

AP site

apurinic or apyrimidinic, recognized by AP nuclease that cleaves the phosphodiester backbone. Allows DNA Pol I to synthesize a replacement strand containing proper base

Replacement of damaged base requires a succession of 4 enzymatic activities

Glycosylase, Endocuclease, Polymerase, Ligase

NTPs = Nucleoside triphosphates

Recombinational repair

A form of strand exchange occurs at shared regions of homolog between DNA molecules. Single strand segment of undamaged daughter strand can be used to replace gap in damaged daughter strand (carried out by RecA) Recombination repair works on any damage that causes gaps during replication.

Nonhomologours end joining (NHEJ)

Found in slow growing bacteria (Myco. tuberculosis & Bacillus) and Eukaryotes. Another copy of chromosome isnt' present for homologous recombination carried out by Ku and LigD.

Why is NHEJ error prone?

because it doesn't require homology. May cause loss or addition of a few nucleotides or even the joining of two previously unlinked DNA molecules

Taking up foreign DNA can be beneficial.

•Imported DNA can be used as an alternative food source (C, N, P)

•Repair damaged chromosomes (homologous recombination)

•Drive genome evolution (new genes=new functions)

Gene Transfer by Conjugation

unidirectional gene transfer of DNA from one bacteria to another, requires cell-to-cell contact. Initiated by special pilus protruding from donor cell. pilus component of type IV secretion system (T4SS), Can transfer DNA to cells different or same species, even different domains

Conjugation requires the presence of special

transferable plasmids, contain all genes needed for pilus formation & dna export.

Ex) Fertility (F) factor in E coli.

Begins with donor cell (F+ cell) contact with recipient (F- cell)

oriV and oriT

oriV: used to replicate in nonconjugating cells

oriT: used to replicate during DNA transfer

Gene Transfer by Phase Transduction

process where bacteriophages carry host DNA from one cell to another. Occurs accidentally bc of phage life cycle

2 types of phage transduction

1. Generalized transduction: can transfer any gene from donor to recipient cell

2. Specialized transduction: can transfer only genes near chromosomal integration site of bacteriophage.

Transducing particles in generalized transduction are the

phages that carry host DNA. When injected its DNA into a cell, no new phages are made

The hijacked host DNA can recombine/exchange, with sequences in host chromosome of newly infected cell

which changes genetic makeup of recipient.

Specialized Transduction: prophase

chromosome with integrated phage genome produced by site-specific recombination, flanked by chimeric att sites called attL and attR. Called "chimeric" because each one is half made from bacterial and phage att sites

Transformation is the process of

Cells capable of taking foreign DNA from environment are referred to as

importing free DNA into the bacterial cell, competent. Ex) vibrio cholerae Gram- extends a type IV pilus, actively takes up free DNA in enviro

role of type IV pilus in trnasformation for V.cholerae

pilus spans inner and outer membranes to access enviro. PilA- major pilin protein

Most prevalent means of transferring genes from one cell to another? alternatives?

conjugation, transduction, and transformation. alts are membrane vesicles & nanotubes

Human GI tract ideal for exchange of _____

__________ allow for close contact between living organisms, a requirement for _________

GI tract contains many phage that can mediate _______, important site of the transfer of ______

genetic information between diverse species. hIgh-density mixed-species biofilms, conjugation, transduction, antibiotic resistance genes

transposable elements

move from 1 DNA molecule to another, exist in all life forms, move within and between chromosomes, incapable of existing outside larger DNA molecule, contribute to genome rearrangements during evolution, include gene that encodes transposase. An enzyme that catalyzes transfer of the element from one DNA to another

2 types Transposable elements

- Insertion sequences (IS): simple, have transposase gene flanked by short inverted-repeat sequences, targets of transposase enzymes - Transposons: mobile elements that carry other genes with those req. for transposition, encodes for antibiotic resistance proteins.

Basic transposition and the origin of target site duplication

Enzymes that catalyze transposition generate duplications in the target site by ligating the ends of the insertion element to the long ends of a staggered cut at the target DNA site.

Transposition is the process

moving a transposable element within or between DNA molecules. Transposase randomly select a possible target sequence to move insertion sequence

Transposable elements transpose by one of two mechanisms:

Replicative transposition or Nonreplicative transposition