Bio 2200 exam 3 james birchler

germinal mutation (germline mutation)

genetic change in reproductive cell that can be passed from parent to offspring

somatic mutation

mutation that happens in a non- reproductive cell

Transition

purine replaces purine or pyrimidine replaces pyrimidine (AT replaces GC)

Transversion

purine replaces pyrimidine or pyrimidine replaces purine (AT replaces CG)

point mutation

affects a single base pair of DNA (transitions or transversions)

missense mutation

single-base mutation results in substitution of one amino acid for another in a protein coding region

nonsense mutation

base pair change of a codon to a nonsense or stop codon, this results in the cessation of protein synthesis

silent mutation

base pair change that alters a codon but the same amino acid is encoded

neutral mutation

base pair change that is neither beneficial nor harmful

frameshift mutation

addition or deletion of a base pair, it shifts the reading frame of mRNA so ribosome incorporates wrong amino acid downstream of mutation

amorphic mutation

loss of function

hypomorphic mutation

partial loss of function

hypermorphic mutation

increase of function

antimorphic mutation

antagonizes wild type, reduces the function of the wild type gene product

neomorphic mutation

gain of function, a mutant gene expressed at a new time and place during development

forward mutation

the normal sequence of a gene is changed to a mutant sequence (normal → mutant)

reverse mutation

mutant is changed back to normal (mutant → normal)

Mutagen

any agent than can induce mutations in DNA

thymine dimers

DNA damage done when uv links together adjacent thymines

specific locus test

mutagenizes normal individuals and mate to a tester stock that has several recessive markers present

replica plating

bacteria colonies are “copy and pasted” to different type of media plates to screen for different phenotypes

Photolyase

breaks the thymine dimer to restore to original state (used for repair of thymine dimers)

AP endonuclease

removes sugar and the phosphate group and leaves a gap (used for repair by glycosylases)

mismatch repair

an enzyme in e coli called adenine methylase puts a methyl group on A residues in the sequence GATC.

excision repair

recognizes thymine dimer and nicks DNA nearby on both sides of the dimer

one gene- one enzyme hypothesis

each gene encodes a specific enzyme

primary structure

a string of amino acids held together by peptide bonds

secondary structure

when proteins form helices and other configurations

tertiary structure

when proteins fold onto itself to make a 3

mutational hotspots

more mutable sites on a gene

intragenic recombination

when mutations are crossed they recombine to produce a normal sequence gene

cis,trans test

a genetic method used to determine whether two recessive mutations that produce the same phenotype belong to the same functional gene (alleles) or to two different genes

Cistron

a segment of DNA or RNA that encodes a specific polypeptide chain or functional RNA molecule

Complementation

a genetic phenomenon where the combination of two different recessive mutations in separate genes produces a normal (wild type) phenotype

Operon

a functional unit of DNA in prokaryotes (bacteria and archaea) that consists of a cluster of related genes controlled and transcribed together from a single promoter

Inducer

the substance that triggers gene expression

Inducible

capable of being formed, activated, or expressed in response to a specific stimulus

Polycistronic

many units of function

polar mutation

a genetic mutation that disrupts the expression of the gene in which it occurs as well as any downstream genes located further along the same transcription unit

Repressor

protein that turns off or reduces gene expression

Cis- acting

only works on one gene, no diffusion because no product

Trans- acting

works on genes other than itself, the product is diffusible (repressor)

Operator

where the regulatory protein binds

Promoter

where RNA polymerase binds to start transcription

negative control

when RNA polymerase is blocked from transcription

positive control

activator protein binds and promotes transcription

constitutive expression

when a gene is not regulated at all

allosteric protein

a protein whose activity is regulated by the binding of an effector molecule at a site other than the protein's active site (known as the allosteric site)

Cis dominant

a genetic term describing an allele or DNA sequence that affects only the genes located on the same continuous piece of DNA (chromosome or plasmid).

catabolite activator protein

also known as cAMP receptor protein (CRP), is a trans-acting regulatory protein that functions as a positive transcription factor in bacteria.

CAP site

specific DNA sequence upstream of a bacterial promoter where the active CAP-cAMP complex binds

Glycosylase

an enzyme critical to the Base Excision Repair (BER) pathway, which fixes damaged DNA

DNA polymerase I

Excises the RNA primers and replaces them with DNA nucleotides

DNA polymerase III

primary replicative enzyme that elongates the new DNA strand. Works in the 5’ to 3’ direction working continuously on the leading strand and discontinuously on the lagging

leading strand

strand is synthesized continuously in the same direction that the replication fork is opening.

lagging strand

strand is synthesized discontinuously in the opposite direction of the moving replication fork. As the fork opens, primase must repeatedly lay down new primers, and DNA polymerase III extends them backwards in Okazaki fragments

single strand binding protein

bind to the single stranded DNA to stabilize them. This prevents the strands from reannealing or forming secondary structures, keeping them accessible as templates

Helicase

Unwinds the double helix. Separates the two parental strands and forms the replication fork

Primase

Synthesizes short RNA primers that provide necessary starting point for DNA polymerase

Okazaki fragments

short, newly synthesized blocks of DNA nucleotides built discontinuously on the lagging template strand.

Nucleotides

monomeric structural subunits

phosphodiester bonds

chemical link established between the 5’ phosphate group and the 3 hydroxyl (OH) group

RNA primer

10 to 12 RNA nucleotides laid down by primase. Since DNA polymerase can only add nucleotides to an existing 3’

Exonuclease

enzymatic activity that cleaves and removes nucleotides

DNA ligase

final glue of the replication process. Seals gaps by creating the final phosphodiester bonds permanently stitching the Okazaki fragments into one unbroken, continuous DNA strand

Diphosphate

when a dNTP is matched and attached to the growing DNA strand, dNA polymerase cleaves off its outer two terminal phosphates as a pyrophosphate molecule. The energetic breaking of these bonds drives the polymerization reaction forward