SBI4U1 Gene Expression, Mutations, Technologies

Spontaneous mutation

Naturally occurring mutations caused by an error in DNA replication

Induced mutation

Caused by mutagens

Transposons

Segments of DNA that can change their position in chromosomes

Class 1 transposons

Transposon is transcribed to RNA, then reverse transcriptase converts RNA into a DNA copy which is inserted into a new location. This increases the number of elements in the genome since the original remains and an additional copy is added

Class 2 transposons

Transposon codes for transposase and uses it to excise itself from its original position and insert it somewhere else. It has ITR sequences which tell transposase when to cut. Once inserted, its DNA is usually duplicated

ITR sequences

Inverted Terminal Repeats found at the ends of class 2 transposons signalling where transposases need to cut

Physical mutagens function

Cause physical changes to DNA structure

Examples of physical mutagens

X rays, UV radiation

Chemical mutagens functions

Molecules which enter nucleus and cause mutations by chemically reacting with DNA

Examples of chemical mutagens

Nitrates (cured meats), gasoline fumes, cigarette smoke

Mechanisms of chemical mutagens causing mutations

Can cause frameshift or substitution mutations, can be incorporated into DNA if they have similar structure to nucleotides, interfere with correct base pairing during replication, may change N base structure through chemical interactions

Germline mutations

Heritable mutations in the DNA of sperm or egg cells

Somatic mutations

Non-heritable mutations in body cells

What are mutations

Changes in the sequence of DNA bases and sources of new alleles

What can mutations result in

Changes to phenotype/genotype existing in natural breeding population

Beneficial mutations

Provide advantages that promote fitness

Silent mutations

Hidden mutations which change DNA without changing coding regions or the amino acid being coded for

Deleterious mutations

May negatively impact fitness

Chromosomal mutations

Change chromosome structure

Frameshift mutations

Deletion/insertion of one or more nucleotides that shifts reading frame

Point mutations

Change in a single nucleotide

Possible outcomes of point mutations

Silent, non-sense, missenseS

Silent point mutations

New codon still codes for same amino acid

Nonsense point mutations

New codon codes for STOP codon

Missense point mutations

New codon codes for different amino acid

Conservative missense mutations

Codes for a different amino acid but polypeptide retains functionality

Non-conservative missense mutations

Codes for a different amino acid and polypeptide loses functionality

Types of chromosomal mutations

Duplication/amplification, deletion, inversion, translocation, inversion

Duplication/amplification mutation

Gene is duplicated

Deletion mutation

Sections of DNA are deleted, chromosomal segments may be lost

Inversion mutation

A sequence of DNA is reversed, so segment is backwards

Translocation mutation

Entire genes or groups of genes are moved to another chromosome

Insertion mutation

Sections of DNA get inserted into another gene on a chromosome, sometimes translocation

Transition substitution point mutation

Substitute purine for purine/pyramidine for pyramidine

Transversion substitution point mutation

Substitute different types (purine for pyramidine)

What is the way a point deletion wouldn’t cause a frame shift mutation

If 3 or multiple of 3 nucleotides of a codon were deleted

Recombinant DNA: HinD III

Bacterial enzyme that can excise viral DNA which entered host genome, these types of enzymes can cut DNA into fragments. This was the birth of genetic engineering biotechnology

Recombinant DNA: Restriction enzymes

Recognize sequences of “recognition site” and cut strand at that location creating restriction fragments which can be recombined

Sticky ends

Nucleotides hanging over after DNA is cut. These ends are easier to recombine

Recombinant DNA: Rejoining fragments

Fragments cut by the same enzymes have the same ends. Sticky ends rejoin through H bonding. DNA ligand rejoins sticky and blunt ends phosphodiester bonds

Competent cells

Healthy cells that can take up foreign plasmids

Recombinant DN: Cloning

Target sequence with desired gene is cut using restriction enzyme, rejoined to a plasmid vector which contains a traceable gene like antibiotic resistance, bacteria take up plasmid and are harvested

Restriction maps

Show position of recognition sites for various restriction enzymes

Gel electrophoresis

Separate proteins by molecular weight or size using electric current

Short Tandem Repeats

Repeated bases 1-6 nucleotides long which are highly variable and can be used to identify individuals

Sanger sequencing

Multiple copies of DNA sequence are denatured forming 2 single strands and are allotted to 1 of 4 batches which contain the template strand, a dideoxynucleotide, deoxyribonucleotides, primer and polymerase. Synthesis proceeds with each batch ending in a specific ddn and sequence can be read with electrophoresis

Dideoxynucleotide

Modified nucleotide lacking 3’ OH group preventing further elongation of DNA strand

PCR

DNA is denatured and cooled to anneal primers bind to target sequence on DNA, then polymerase creates complimentary strand. The cycle is repeated many times leading to millions to billions of copies