ch8 - bacterial genetics

genetic change in bacteria

genetic changes are inevitable in any organism

• all living organisms have to evolve with time to survive

organisms adapt to changing environments

• natural selection occurs thru mutations and it favors those with greater fitness

• some mutations can make it better…

• how bacteria adjust to new circumstances

  • regulation of gene expression: in diff environment and diff carbon/food sources, they can express diff genes for that source

    • lactose: bacteria will make the enzyme to break down lactose and allow b to live in the presence of lactose

  • genetic change (ch8)

    • change in organism’s DNA alters genotype

    • allows it to survive when there’s mutations in the genotype of the DNA

    • this will then change the phenotype

  • may change observable characteristics, or phenotype

    • also influenced by environmental conditions

mechanisms of genetic change in bacteria

mutation: change in base sequence of DNA

• if you have a sequence of DNA and during the process an A is changed to a C (ATCGTA vs CTCGTA)

  • occurs during process of DNA replication

horizontal gene transfer: acquisition of DNA (plasmid)

• where the bacteria can acquire extrachromosomal dna like plasmid

• one with and one without it

• extra dna extra genes on it

• when it divides all of its progeny will have that…

  • antibotic reistance genes example

  • once it acquires it itll be resistant and all offsprings will be resistant

spontaneous mutations

occur randomly in absence of a mutagen (chemical or source) → mutants (resultant organism)

• mutation rate: between 10^-4 and 10^-12 for a given gene

mutations passed to progeny

• types of mutations that can be passed on to offspring if it occurs

  • ?ex. lactose intolerant vs tolerant

• if a mutation did occur, where would it have to occur to be passed down to next gen in humans

  • ?only the ones in the (what are these) germ cells will be passed on

  • in bacteria they only have one which is the chromosome and it can be passed on to offspring

mutations can occur from

• base substitutions

• deletion or addition of nucleotides

• transposable elements

spontaneous mutations - base substitution

most common

• ?because it occurs thru DNA replication

• incorrect nucleotide incorporated during DNA synthesis in the strand

• point mutation: a single base pair is substituted for another

spontaneous mutations - 3 possible outcomes of point mutations

silent mutation

• same amino acid, no observable change in protein

  • no change in amino acid even tho the dna changed bcuz of the redundancy of genetic code

    • cysteine example

missense mutation

• different amino acid

• resulting protein may be only partially functional (leaky mutation)

• if it’s a very imp amino acid the enzyme may not be functional at all

nonsense mutation

• stop codon produced

• yields shorter protein

• may or may not be functional depending on how short they are

• what happens when this is in your rna?

  • mRNA rbs aug……uga………….uga

    • when rbs gets to the nonsense mutation of uga, it stops even though the whole protein hasnt been translated

    • therefore, the protein may not be functional especially if its closer to the beginning

    • if its near the end it might not be as critical

spontaneous mutations - deletion or addition of nucleotides

a lot more lethal than point mutations bcuz they shift translational reading frame → frameshift mutations

• affects all amino acids downstream and they wont be the correct amino acid bcuz of how the mRNA reads it after deletion or addition

• the fat cat ate the rat → the fa cat ate the rate → theafat cat ate the rat

• produces totally different protein or very rarely generates stop codons

  • truncated protein?

• open reading frames

  • have to start from correct one to produce correct protein

  • read in 3s

• will not produce correct protein

spontaneous mutations - transposons

jumping genes

• DNA pieces that can move spontaneously from one location to another (transposition)

  • small pieces that can cut themselves and put themselves anywhere

  • can go from one organism to the other

• can inactivate gene → knockout mutations

  • gene product generally non-functional

  • ?when it inserted itself, the gene is inactivated bcuz the protein is no longer functional, the characteristic it produces wont be there and it will never be able to produce anymore

• ?simplest is insertion sequence (IS)

  • encodes only transposase enzyme, inverted repeats

  • knows what dna is part of transposon bcuz of inverted repeats

• composite transposons

  • include one or more genes

  • can confer antimicrobial resistance

  • what will?..it will be resistant to whatever resistant gene is encoded in the transposon

induced mutations

result from outside influence

• mutagen (chemical that can induce mutation to occur): agent that induces DNA change

  • 2 types: chemical, radiation

induced mutations - chemical mutagens

nitrous acid: changes cytosine to uracil by the removal of ?NHH amino group

• base-pairs with adenine instead of guanine

• C G (U) A A T?

intercalating agents: insert between adjacent bases

• create space between bases → extra base added to fill space

  • addition mutation

• ethidium, bromine, acridine, chloroquine

  • mutations can lead to tumors and to potential carcinogen

induced mutations - radiation

two type

ultraviolet irradiation: causes thymine dimers in DNA

• covalent bonds between adjacent thymine bases

  • A T-T A C G T

• causes stalling or replication and transcription

  • is this strand is used as a template, it wont know how to interpret the thymine dimer and will stall

  • cell will die if not repaired or it will continue which results? in a SOS response calling in a less specific dna polymerase which puts in any base pair and it will move on

    • deletion mutation two T to one base pair

x rays

• cause breaks and alteration in DNA

• can cause cells to die severing the two strands of the dna molecule

• double-strand breaks

  • often lethal

repair of damaged dna

repair is critical

• if not repaired → lead to cell death or cancer in animals

repair ensure integrity of dna

• repair of base substitution

  • proofreading by dna polymerase

  • dna polymerase makes very few mistakes which is why its 10^#

  • mismatch repair

repair of damaged dna - mismatch repair

1. the wrong nucleotide is incorporated during DNA synthesis

2. near the site of the mismatched base, an enzyme cuts the sugar-phosphate backbone of the unmethylated strand

3. an enzyme degrades a short stretch of the strand that had the error

4. dna polymerase synthesizes a new stretch, incorporation the correct nucleotide

5. dna ligase joins the 3’ end and of the newly synthesized segments to the original strand

repair of thymine dimers - photoreactivation

several methods to repair damage from UV light

• light repair

  • enzymes use energy from light to break covalent bond of thymine dimer

  • only found in some bacteria

• thymine dimer distorts the DNA molecule

• an enzyme uses visible light to break the covalent bond of the thymine dimer, restoring the DNA to its original state

repair of thymine dimers - excision repair

several methods to repair damage from UV light

• dark repair

  • enzyme removes damage

  • dna polymerase, dna ligase repair

• thymine dimer distorts the DNA molecule

• an enzyme removes the damaged section by cutting the DNA backbone on either side of the thymine dimer

• the combined actions of DNA polymerase and DNA ligase fill and seal the gap after the bond is broken

when repair mechanisms are defective or missing

xeroderma pigmentosum

• genetic disorder → inability to repair damaged dna caused by UV light → skin carcinoma

• exposure to sunlight is limited or forbidden

  • cuz if they are exposed it could lead to thymine dimer and potential skin carcinoma

mechanisms of horizontal gene transfer

genes naturally transferred by three mechanisms

1. transformation: naked DNA uptake by bacteria

2. transduction: bacterial DNA transfer by viruses

3. conjugation: dna transfer during cell-to-cell contact

transformation

acquisition of ?what is it: naked dna

discovered by Frederick Griffith while working with Streptococcus pneumoniae

S. pneumoniae existed in 2 forms

• smooth in appearance

  • encapsulated, virulent form

  • bcuz of the capsule, it prevents the bacteria from going thru phagocytosis → more likely to cause disease

• rough in appearance

  • nonencapsulated, avirulent form

  • white blood cells will engulf and destroy them cuz theres no capsule

??the living non encapsulated cells acquire the dene from the dead cell

• when it dies everything goes to environment and it was picked up by the nonE gene to have a capsule

• acquire dna from heat killed encapsulated () and incorporate it to their genome

transduction - formation of transducing particle

bacterial DNA transferred from donor to recipient via a bacterial virus (bacteriophage)

• result from mispackaging of bacterial DNA during viral replication

1. a bacteriophage attaches to a specific receptor on a host cell

2. the phage dna enters the cell. the empty phage coat remains on the outside of the bacterium

3. enzymes encoded by the phage genome cut the bacterial DNA into small pieces

4. phage nucleic acid is replicated and coat proteins synthesized

5. during construction of viral particles, bacterial dna can mistakenly enter a protein coat. this creates a transducing particle that carries bacterial dna instead of phage dna

• stored in the head, can include virus/disease?

• the viral dna is released

• part of dna is inserting to phage head and when the head carries dna from donor to recipient and will combine with recipient and divide with it ?

• donor to recipient by bacterial phase

process of transduction

1. a transducing particle attaches to a specific receptor on a host cell

2. the bacterial dna is injected into a cell

3. the injected bacterial dna integrates into the chromosome by homologous recombination

4. bacteria multiply with new genetic material. replaced host dna is degraded

cont. conjugation

dna transfer between bacterial cells

• mediated by a conjugative plasmid (F factor)

• requires direct contact between cells via a sex pilus

• cells must be of opposite mating types

  • F+ donor cell

    • carries plasmid for fertility factor

  • F- recipient cell

    • does not carry a plasmid

the mobile gene pool

consists of extrachromosomal DNA

• plasmids, transposons, genomic islands, phage DNA

  • very common

  • confer some advantage to bacterium

plasmids

self-replicating

R plasmids

• confer resistance to antimicrobial medication and heavy metals (mercury and arsenic)