DNA and Genetics

what defines recombination

an event in which one bacterium donates DNA to another bacterium- type of genetic transfer

what is the end result of recombination

a new strain of DNA different from both the donor and the original strain

what are the extrachromosomal DNA in bacteria called

plasmids

what does it mean to be recombinant

be an organism who’s genes contain any genes originated from another organism

what is horizontal gene transfer

any transfer of DNA that results in organisms acquiring new genes that did not come directly from parent organisms

what is vertical gene transfer

acquiring genes from parent organisms during reproduction

what are plasmids

small, circular pieces of DNA that contain their own origin of replication

how do plasmids replicate

independently of the bacterial chromosome, due to containing their own origin of replication

besides plasmids, what else is prevalent in the transfer of genetic information between bacterial cells

chromosomal fragments

what is an importance difference between chromosomal fragments and plasmids in terms of how they replicate

fragments must integrate themselves into the bacterial chromosome in order to be replicated

* whereas plasmids have its own mode of replication

what is required for conjugation

the attachment of two related species and the formation of a bridge that can transport DNA

what entails of transformation

the transfer of naked DNA, requires no special vehicle

what entails of transduction

the transfer of DNA from one bacterium to another via a bacterial virus

what mode(s) of horizontal gene transfer are direct

conjugation

what mode(s) of horizontal gene transfer are indirect

* transformation
* transduction

what denotes a gram-negatives cells role in conjugation

its fertility factor- called F factor. Either F+ (has the factor) or F- (lacks the factor)

what is the F+ gram-negative cells role in conjugation

to grow a sex pilus that attaches to the F- cell, pulling them closer together so DNA can be exchanged across this ‘bridge’

what is conjugation

the horizontal transfer of genetic information between two cells via a sex pilus

what happens in gram-positive cell conjugation

an opening between two adjacent cells is created and genetic information is replicated and passed across from one cell to the other

what does it mean to say that conjugation is a conservative process

the donor bacterium generally retains (converses) a copy of the genetic material being transferred

what are the two modes of conjugation for the conjugative plasmid of E. coli

* Transfer of the F plasmid
* Transfer of chromosomal DNA (also called high-frequency recombination \[Hfr\])

what happens in transfer of the F plasmid in conjugative plasmids (specially the E. coli species)

the F+ cell makes a copy of its F factor and transmits it to a recipient F- cell, the cell is thereby changed into a F+ cell and is capable of initiating conjugation with other F- cells

what happens in transfer of chromosomal DNA \[Hfr\] in conjugative plasmids (specially the E. coli species)

the plasmid becomes integrated into the F+ donor chromosome, which becomes replicated, then begins to transfer to the recipient cell.

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Meaning, some of the chromosomal genes get transferred to the recipient (plasmid genes may or may not be transferred)

what type of conjugation is this

F factor transfer

what type of conjugation is this

Hfr transfer

whats the importance of conjugation in a biomedical since

special (R) plasmids or R factors, that have genes for resisting antibiotics and other drugs are commonly shared among bacteria through conjugation

what is transformation

the nonspecific acceptance of small DNA fragments from the surrounding environment by a bacterial cell

what is transformation facilitated by

special DNA-binding proteins on the cell wall that capture DNA from the surrounding medium

what does it mean to be ‘competent’ in terms of horizontal gene transfer

that a cell is capable of accepting free DNA from their environment

what happens after DNA is taken in during transformation

the new DNA is transported into the cytoplasm where some of it is inserted into the bacterial chromosome

due to transformation requiring to special accessories how can this process be utilized in recombinant DNA technology

foreign genes from a completely unrelated organism can be inserted into a plasmid and introduced to a competent cell

adding foreign genes to a completely unrelated organism during recombinant DNA transformation technology is called what if it occurs in Eukaryotes

transfection

what does it mean to be a genetic vector- viruses can serve as these

it means to be entity that can bring foreign DNA into a cell

what is transduction

the process by which a bacteriophage serves as the carrier of DNA from a donor cell to a recipient cell

what are the two versions of transduction

* Generalized
* Specialized

what occurs in generalized transduction

random fragments of disintegrating host DNA are taken up by the phage during assembly. Meaning, virtually any gene from the bacterium can be transmitted through this means

what occurs in specialized transduction

a highly specific part of the host genome is regularly incorporated into the virus. This specifically is explained by the prior existence of a temperate prophage inserted in a fixed site on the bacterial chromosome. When activated, the prophage DNA separates from the bacterial chromosome, carrying a small segment of host genes with it

whats the biomedical importance of transduction in certain virulent strains of bacteria

these strains produce toxins with profound physiological effects. As it turns out this toxicity arises from the presence of bacteriophage genes that have been introduced during transduction.

what are transposons

‘jumping genes’ another means of genetic transfer that have the distinction of shifting from one part of the genome

what is the overall effect of transposons

they can be beneficial or adverse

what are some examples of effects of transposons

* changes in traits such as colony morphology, pigmentation, and antigenic characteristics
* replacement of damaged DNA
* the intermicrobial transfer of drug resistance (in bacteria)

what does it mean for a bacteria to be a ‘wild type’

a microorganism that exhibits a natural, nonmutated characteristic

what does it mean for a bacteria to be a ‘mutant strain’

if the microorganism bears a mutation

what is a spontaneous mutation

a random change in the DNA arising from errors in replication that occur randomly

what are induced mutations

mutations that result from exposure to mutagens

what are mutagens

physical or chemical agents that interact with DNA in a disruptive manner.

* Ex: radiation (UV, X rays), certain chemicals

what is a point mutation

the addition, deletion, or substitution of single bases

what is a missense mutation

any change in the code that leads to placement of a different amino acid

what are some of the results of a missense mutation

* create a faulty, nonfunctional (or less functional protein)
* produce a protein that functions in a different manner
* cause no significant alteration in protein function

what is a nonsense mutation

changes a normal codon to a stop codon

what is a silent mutation

a mutation that alters a base but does not change the amino acid and thus has no effect

what is a back mutation

when a gene that has undergone mutation reserves back (through mutation) to its original base composition

what is a frameshift mutation

a mutation when one or more bases are inserted into or deleted from a newly synthesized DNA strand

what is a single nucleotide polymorphism (SNP)

a mutation in which only a single nucleotide is altered

how are most DNA mutations repaired

through the use of enzymatic systems specialized for finding and fixing defects

what is the only thing that can restored DNA that has been damaged by ultraviolet radiation

photoactivation- or light repair

what is excision repair

refers to a series of enzymes that can cut out and remove the incorrect bases and add the correct ones

what are restriction endonucleases

they come from bacterial cells. And function to recognize foreign DNA and are capable of breaking the phosphodiester bonds between adjacent nucleotides on both strands of DNA, leading to a break in the DNA strand

how are restriction endonucleases used in a lab setting

the enzymes can be used be cleave DAN at desired sites and are necessary for the techniques of recombinant DNA technology

what are palindromes

sequences of DNA that are identical when read from the 5’ to 3’ direction on one strand and the 5’ to 3’ direction on the other strand

what does heating a DNA strand do

causes the two strands to separate

what does cooling a DNA strand do

causes the two strands to rejoin

are endonucleases usually named

by combining the first letter of the bacterial genus, the first two letters of the species, and the endonuclease number

what are restriction fragments

pieces of DNA produced by restriction endonucleases

what gives rise to restriction fragment length polymorphisms (RELPs)

differences in the cutting pattern of specific restriction endonucleases, resulting in restriction fragments of differing lengths

what is the function of ligase

to seal the sticky ends of DNA together by rejoining the phosphate-sugar bonds cut by endonucleases

what is the function of reverse transcriptase (RT)

converts RNA into DNA

what can complementary DNA (cDNA) be made from

messenger, transfer, ribosomal, and other forms of RNA

what is the importance of cRNA being made from various forms of RNA

it provides a means of synthesizing eukaryotic genes from mRNA transcripts

what is the role of primers (specifically in PCR)

they serve as landmarks to indicate where DNA amplification will begin

what are the 3 repetitive cycles of PCR

* denaturation
* priming
* extension

what is DNA profiling

a pattern of restriction enzyme fragments that is unique for an individual organism

what is DNA sequencing

determining the exact order of nucleotides in a fragment of DNA. Most commonly done using the Sanger dideoxy sequencing method

what causes DNA fragments to move through gel electrophoresis

the phosphate groups in DNA give the entire molecule an overall negative charge, which causes the DNA to move toward the positive pole in the gel

what are sequence maps

a sequencing technique that give an exact order of bases in a plasmid, a chromosomes, or an entire genome

what are genomics

the systematic study of an organisms genes and their functions

what are proteomics

the study of an organisms complement of proteins and functions mediated by the proteins

what are metagenomics

the study of all the genomes in a particular ecological niche, as opposed to individual genomes from single species

what is metabolomics

the study of the complete complement of small chemicals present in a cell at any given time. Provides a snapshot of the physiological state of the cell and the end products of its metabolism