Biol121 Lecture 10-11 Midterm 2 Review

Mosaic nature of genomes

Microbial genomes are Mosaic--> full of genomic islands, inversions, deletions, as a result of heavy horizontal gene transfer, recombination, mutagenics and DNA repair strategies

Genetic Islands

Large insertions of sequence

Plasmids

Extrachromosomal DNA, circular--> important for bacterial adaptation to changing environments, has its own original of replication, transferred by transformation and conjugation

Vertical gene transfer

From mother to daughter cells through cell division, differs from horizontal gene transfer that occurs in prokaryotes

Transformation Discovery

Discovered with Steprotococcus pneumoniae by Griffith(mice strains), Mice with rough strain and heat killed smooth strain dies, like if the mice was just infected with live smooth strain.

Transformation

Uptake of DNA directly from the environment, cells need to be competent, cell membrane need to be permeable DNA.

Gram Positive Bacteria(Transformation)

Requires translocasome, secretes competent factors, buildup of competent factors allows assembly of translocasome, which can take up foreign DNA

Gram Negative bacteria(Transformation)

Stress(lack of nutrients) induces competence, increased ability for cells to take up foreign DNA.

Conjugation

transfer of DNA from one bacterium to another, through cell to cell contact,

Type IV secretion system(Conjugation system): F Factor transmission, recipient cell recieves copy of F-factor and becomes F+, where the recipient is always F-, basically a "female" cell becomes "male".

Conjugation(cont.)

Rolling Circle Replication--> Single strand of plasmid DNA nicked, new strand displaces old strand(No specifics need to be known)

Transduction

Bacteriophages carry host DNA from one cell to another, occurs accidentally. Sometimes Bacterial DNA is packaged into viral capsid before cell lysis.

Something to understand about the different Phage lifecycles:

Lytic cycle

The bacteriophage uses the host cell's resources to create viral genomes and capsid proteins, which then assemble into new bacteriophages. The host cell then dies, releasing the new bacteriophages to infect other cells.

Lysogenic cycle

The bacteriophage's genome integrates into the host cell's DNA, where it's replicated and passed on to new cells. The host cell isn't killed, and the bacteriophage is copied along with the host cell's DNA

Generalized Transduction

can transfer any gene from donor to recipient(can occur during lytic cycle). Basically for this, original bacterial DNA not fully degraded due to some error, and can accidentally be taken up by bacteriophages during cell lysis--> goes and infects other bacteria

Specialized Transduction

Can only transfer a few closely linked genes between cells, occurs during lysogeny(lysogenic cycle). Basically bacteriophage accidentally take up some bacterial DNA along with phage DNA that integrated into bacterial chromosome, when lysing cell-->goes and infects other bacteria

Restriction Endonucleases

Degrade foreign DNA in recipient cell, plasmids can exist, incorporate into chromosomal DNA by recombination, cuts at palindormic sequences

Bacterial DNA methylation

Methylation protects DNA at restriction/palindromic sites(preventing self nucleation/destruction). Foreign DNA without methylation is destroyed, unless foreign DNA is bacterial and methylated

CRISPR

Bacteria cut up viral DNA, and insert some pieces into their own genome

Interesting: This is how they discovered CRISPR, viral DNA was being stored in "spacer" regions of the CRISPR DNA array, so bacteria could remember past viruses.

Mutant

Direct offspring of a normal member of a species, but contains mutations, generates new variants.

Mutation

Heritable changes in the nucleic acid bases in genome of organism, takes time to change, provide novel functions, can become fixed in populations

spontaneous mutation

Errors in DNA replication, occur at a very low rate 1/1000000

Induced mutations

Caused by mutagens, occur at a rate of about 1/1000-->1/100000, way better than spontaneous rate. Chemical-->carcinogens, Physical--> radiation Biological-->transposon insertion(jumping genes)

Point mutation

change in a single base

Silent-->Does not change amino acid

Nonsense--> Produces a stop codon

Missense-->Leads to amino acid change

Frameshift mutation

Insertions or deletions that disrupt the reading frame, not a multiple of 3 and therefore can lead to major changes in polypeptide downstream of mutation, most severe type of mutation.

Physical Mutagen-->Radiation

Causes the formation of toxic oxygen radicals, causes pyrmidine dimerization(Specifically Two thymines-hence called thymine dimer), prevent replication and transcription

Something you don't need to know but: oxygen radicals--> Caused by leaking electrons reacting with oxygen in ETC

Chemical Mutagen-Base Analogs

Similar structure to natural bases, incorporated during DNA replication, leads to point mutation--> Incorrect base pairing.

Difference between Base Analogs and DNA modifying agents--> DNA modifiers-->literally modify DNA, Base Analogs, replace bases, alter pairing characteristics

Chemical Mutagen-DNA modifying agent

Changes base structure by adding groups and pairing characteristics

example: methylguanine pairs with A/T instead of C.

Another example--> Intercalating agent--> used in cancer treatments, inserts itself between base pairs, damaging DNA, causing cell death.

Mobile Genetic Elements

Transposons--> Jumping genes, can hop from one place in DNA to another, transposition, widely used as a mutagen in molecular genetics

Transposition process

Transposase cuts DNA at inverted repeat sequences at both ends of transposable elements and target sequence of DNA, ligates transposable element with target DNA

Replicative transposition

Transposable element copied, one copy remiains in original site.

Non-replicative tranposition

Transposable element jumps from one site to another

Ames Test

Ability of a chemical substance to cause mutations, or strength of a mutagen tested(commonly used to determine carcinogenic substances)

Ames test steps/summary

1) Use a bacterial mutant that cannot synthesize an amino acid, gene is broken

2)Plate bacteria on defined medium(without histidine), and with mutagen chemical

3) Cells might retain inability to produce amino acid, or some might be able to produce it again and appear on plate, because of reversion mutation

4) More colonies=stronger mutagen.

DNA Repair-Proofreading

DNA polymerase III 3'-5' exonuclease activity removes mismatches during DNA replication

Photoreactivation

photoylyase enzyme, binds to pyrimidine dimer caused by radiation and breaks it apart

Excision repair

Most common damage/mismatch repair mechanism

"Cut, copy, and paste"

1) Enzyme removes damaged base or string of nucleotides

2)DNA polymerase copies template to replace excised strand

3)DNA ligase seals nicks to give intact, repaired DNA

Nucleotide excision repair

recognizes damage that causes DNA structure distortion, usually replaces bulky DNA damage, and repairs a larger section of damaged DNA

Base Excision repair

Repairs bases that don't distort DNA structure

Methyl Mismatch repair

Repairs mismatches missed by proofreading

SOS system

SO much damage, Save our souls, LexA represses SOS geens, RecA activated by DNA damage to inactivate LexA to activate SOS genes. Utilizes DNA mutases-->Can repair DNA rapidly, but generate numerous mutations

Lex-->Lose

Rec-->Reactivate

Non-Homologous End joining

Fixes double strand breaks, which are super bad for bacteria, (does not require homology-->essentially no template required), Ku proteins bind broken endsm ligases also help to fix break.