Protein maturation, Point mutations, DNA repair, & HGT

Most proteins need to

fold

Proteins may undergo

chemical modification, or cleavage

Proteins can translocated...

translocated into the periplasmic space

Proteins may be

secreted outside of the cell entirely

Mutations can be caused by __ or __

intrinsic processes (spontaneous) or external mutagens (induced)

Spontaneous mutations

caused by mistakes in the process of DNA replication

Induced mutation

caused by exposure to mutagens - chemical agents or radiation; mutagens exposure can increase the rate of mutation more than 1000-fold

chemical mutagens:

nucleoside analogs, modifying agents, intercalating agents

Nucleotides analog

are structurally similar to normal nucleotide bases and can be incorporated into DNA during replication. These base analogs induce mutations bec. they often have different base-pairing rules than the bases they replace

Modifying agents

modify normal DNA bases, resulting in different base-pairing rules deaminates GC base pair to an AT

Intercalating agents

slide between the stacked nitrogenous bases of the DNA double helix, distorting the molecule and creating atypical spacing between nucleotide base pairs. This results in DNA polymerase either skipping several nucleotides (creating a deletion) or inserting extra nucleotides (creating an insertion) -> frameshift mutation

- shorten words
- bc
- own interpretation

Silent mutation

due to degeneracy of the genetic code, a point mutation will commonly result in the same amino acid being incorporated into the resulting polypeptide despite the sequence change

Missense mutation

results in a different amino acid being incorporated into the resulting polypeptide. The effect of a missense mutation depends on how chemically different the new amino acid is from the wild-type amino acid and location

Nonsense Mutation

converts a codon encoding an amino acid (a sense codon) into a stop codon (a nonsense codon); this results in shortened proteins typically not functional

Frameshift mutation

results from insertion or deletion of 1 or 2 base pairs in the coding region of gene; can change every amino acid after the point of the mutation. The new reading frame may also include a stop codon before the end of the coding sequence; resulting proteins nearly always nonfunctional

Conditional mutants only have

phenotype under some conditions

Auxotrophic mutants are

unable to make a specific biomolecule - eg amino acid

how does Ames Test work?

two test tubes 1 control and other with mutagen, look at how much grows

What does it Ames test prove?

looks at how the end result is metabolized by the rat liver enzymes

The Ames Test

is a method that uses bacteria for rapid, inexpensive screening of the
carcinogenic potential of new chemical compounds. Measures the mutation rate associated with
exposure to the compound, which, if elevated, may indicate that exposure to this compound is
associated with greater cancer risk. Because many chemicals are not directly mutagenic but are
metabolized to mutagenic forms by liver enzymes, rat liver extract is commonly included at the
start of this experiment to mimic liver metabolism.

Proofreading

promptly corrected by DNA polymerases through proofreading.
If an incorrect base has been added, the enzyme makes a cut to release the
wrong nucleotide and a new base is added.

Mismatch Repair

shortly after the replication machinery has moved. The
enzymes involved in this mechanism recognize the incorrectly added nucleotide,
excise it, and replace it with the correct base.

Nucleotide excision repair

enzymes remove the pyrimidine
dimer and replace it with the correct
bases. Enzyme cuts the sugar-
phosphate backbone several bases
upstream and downstream of the
dimer, and the segment of DNA
between these two cuts is then
enzymatically removed. DNA pol I
replaces the missing nucleotides with
the correct ones and DNA ligase
seals the gap in the sugar-phosphate
backbone.

Direct repair

occurs through the
process of photoreactivation in the
presence of visible light. An enzyme
called photolyase recognizes and
breaks apart the thymine dimers,
allowing the thymines to again
correctly base pair with the adenines
on the complementary strand.

Horizontal gene transfer

= transfer of genes from one
independent, mature
organism to another

what a transposable element is

DNA sequence that have the ability to change their position within a genome
diversity

transformation

Uptake of naked DNA by a competent
cell followed by incorporation of the DNA into the recipient
cell’s genome

transduction

Viruses that infect bacteria
(bacteriophages) may also move short pieces of
chromosomal DNA from one bacterium to another in a
process called transduction
- chromosomal DNA from the infected host bacterium is
accidentally packaged into the phage head during phage
assembly

lytic phage

mediate generalized transduction

lysogenic phage

mediate specialized transduction

transduction phage-mediated

transfer of genetic material

Conjugation

DNA is directly transferred from one prokaryote to another by means of a conjugation pilus, which brings the organisms into contact with one another
- DNA transfer by direct cell-cell contact

F plasmid also called

Fertility factor
- in ecoli the genes encoding the ability to conjugate are on bacterial plasmid

F +

DONOR = cells with F plasmid and F pilus (conjugation)

F -

recipient cells = cells lacking an F plasmid and F pilus

F plasmid integration results

in Hfr cell

Hfr cells can

transfer genomic material but usually not the entire F plasmid

F plasmids carry

other genes from the bacterial chromosome

High frequency of recombination

seen when recipient F - cells receive genetic information from Hfr cells through conjugation

The integrated F plasmid

may also be imprecisely excised from the chromosome, producing an F plasmid that carries with it some chromosomal DNA adjacent to the integration site
-high transfer of certain donor chromosomal genes