Genetics (Bio 304)

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a mutant allele that produces no functional gene product; usually inherited as a recessive trait. Results in a loss-of-function mutation.
e.g. A gene effects the construction of an enzyme, rendering it defunct.

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null allele

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condition in which a single mutation causes multiple phenotypic effects
e.g. cat w/ gene mutation for blue irises and deafness

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pleiotropy

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The frequency (expressed as a percentage) with which individuals of a given genotype manifest at least some degree of a specific mutant phenotype associated w/ a trait

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penetrance

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The degree of range in which a phenotype for a given trait is expressed

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expressivity

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a reciprocal exchange of chromosome segments which results in the reshuffling of alleles between homologs; always occurs in the TETRAD STAGE (prophase 1)

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crossover/recombination

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gamete consisting wholly of one or the other parent’s genetic information

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parental/non-crossover gamete

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gamete consisting of both parental information

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recombinant/crossover gamete

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proportional to the distance between two genes, that is the interlocus distance; the larger the RF, the further apart

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recombinant frequency (RF)

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recombinant frequency (RF) equation

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(#recomb. progeny pheno.1 + #recomb. progeny pheno.2)/total # progeny

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genes that are part of the same chromosome

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linkage

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a group of genes located on a chromosome (essentially, a group of linked genes); theoretically the number of linkage groups corresponds to the haploid number of chromosomes

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linkage group

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the inhibition of crossover events by a crossover event in a nearby region of the chromosome

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interference

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Calculate # of polygenes

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1/(4^n)

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Calculate interference

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Coefficient of Correlation= observed DCO/expected DCO

I = 1 - CoC

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all chromosomes belong to complete haploid sets

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euploidy

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the loss or gain of one or more chromosomes, but not a complete set

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aneuploidy

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more than two sets of chromosomes present

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polyploidy

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paired homologs fail to disjoin during segregation, disrupting the normal distribution of chromosomes into gametes

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nondisjunction

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absence of a single chromosome from an otherwise diploid genome (2n – 1)

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monosomy

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the gain of one extra chromosome (2n + 1)

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trisomy

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human autosomal trisomy 21

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Down syndrome (trisomy 21)

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contains genes that are dosage sensitive in trisomy, and which are responsible for classic phenotypic expression

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Down syndrome critical region

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(trisomy 13) 47 chromosome karyotype; D group

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Patau syndrome (trisomy 13)

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trisomy 18 - E group, phenotype = reduced life expectancy, low-set/malformed ears, elongated skulls, webbed neck, congenital dislocation of hips, receding chin

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Edwards syndrome (trisomy 18)

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the addition of one or more extra sets of chromosomes, identical to the normal haploid complement of the same species

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autoploidy

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the combination of chromosome sets from different species may occur as a consequence of hybridization

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alloploidy

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the loss of a a piece of DNA when a chromosome breaks in one or more places

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chromosomal deletion/deficiency

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lost from an end of chromosome

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terminal deletion

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more rare than deletions; may be formed when crossing over (misalignment during synapsis, especially between tandemly repeated regions

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chromosomal duplication

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a segment of chromosome is turned around 180 degrees within a chromosome; thus, an inversion does not involve a loss of genetic information, but rather rearranges the linear gene sequence

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chromosomal inversion

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the centromeres IS included in the inverted segment

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pericentric

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the centromeres is NOT part of the rearranged chromosome segment (pAracentric = chromosome Absent)

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paracentric inversion

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pairing between one inverted chromosome and one normal homolog through the formation of an inversion loop

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inversion heterozygotes

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the product of a single crossover between _____________ produces two parental chromatids and two recombinant chromatids. When this occurs within a _____________ two chromatids are produced, both of which contain duplications and deletions of chromosome segments:

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nonsister chromatids

paracentric inversion

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lacking a centromeres; moves randomly to one pole or other, or may be lost

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acentric

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has two centromeres and is therefore pulled in two directions, creating a ‘tug-of-war' At some point, it will usually break, so that one part goes to each gamete

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dicentric chromatid

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the movement of a chromosomal segment to a new location in the genome

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chromosomal translocation

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the exchange of segments between two nonhomologous chromosomes

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reciprocal translocation

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a form of chromosomal aberration in which breaks occur in the short arms of two acrocentric chromosomes and the long arms of these chromosomes fuse at the centromeres. Also called centric fusion.

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Robertsonian translocation

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the transmission of genetic information to offspring through the cytoplasm rather than through the nucleus; usually from only one parent

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extranuclear inheritance

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mutations in chloroplasts seem to be passed on only from one parent (usually the maternal chloroplast, but not always)

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chloroplast DNA

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contain a distinctive genetic system, where mutations are passed through the cytoplasm

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mitochondrial DNA

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variation in the genetic content of organelles

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heteroplasmy

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makes cuts to relax super coiling

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DNA gyrase

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an RNA polymerase that synthesizes a short RNA segment on the DNA template, which enables DNA synthesis

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primase

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proteins, such as DnaB and DnaC, that denature the double helix by breaking H-bonds

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helicase

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the uninterrupted synthesis the replicon in the leading strand

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continuous synthesis

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the synthesis of the lagging strand, which requires multiple initiation pts

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discontinuous synthesis

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uninterrupted synthesis (5’-3’)

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leading strand

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synthesizes multiple sections from 5’-3’, requires binding of Okazaki fragm.

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lagging

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DNA seqhences on the lagging strand with RNA primers in between each. these primers are eventually removed

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Okazaki fragments

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catalyses the formation of the phosphodiester bond which seals the nick between discount. synthesized strands allowing for continuity

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DNA ligase

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(5’-3’ direction) works in vitro; first to be isolated, and appeared to degrade DNA as well as synthesize it

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DNA polymerase I

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(5’-3’) no exonuclease activity… fewer in # than DNA polymerase III

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DNA polymerase III

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detection of a mismatched nucleotide (in the 3’-5’ direction) and excision of erroneous base via holoenzyme

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proofreading

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degradation of the DNA strand

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exonuclease

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reflection of the length of DNA that is synthesized by an enzyme before it dissociates from the template

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processivity

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ends of eukaryotic chromosomes, which protect against nucleases and preserve the integrity and stability of the chromosome

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telomeres

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unique enzyme containing a piece of RNA, allowing it to serve as both guide and template for reverse transcription

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telomerase

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base pairs in 3’s

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triplet code

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group of 3 ribonucleotides that codes for an amino acid

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codon

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each triplet specifies only one amino acid

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unambiguous (wrt genetic code)

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an amino acid may be specified by more than one codon (18/20, this is the case)

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degenerate (wrt genetic code)

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the contiguous sequence of nucleotides encoding a polypeptide

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reading frame

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the “start” codon for synthesis

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initiator codon (AUG)

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the “stop” codon for synthesis

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terminator codon (UAG, UAA, UGA)

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enzyme which synthesizes RNA on a DNA template

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RNA polymerase

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the complex, active format an enzyme

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holoenzyme

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DNA sequences in the 5’ region that is a point of binding, and therefore denaturing of the strand via polymerase, as well as the point at which transcription begins

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promoter

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point at which transcription actually begins

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transcription start site

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sequence adjacent to the gene itself

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cis-acting element

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molecules that bind to DNA elements

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trans-acting factor

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an important element of termination, the unique sequence of nt’s in the termination region causes a newly formed tanscript to fold back on itself and form H-bonds

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RNA hairpin secondary structure

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5’ capping, 3’ adenylation (AAAAA tail), and splicing prior to translation

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RNA processing

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responsible for all mRNA’s, snRNA’s

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RNA polymerase II (eukaryotes)

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a cis-acting core promoter that promotes denaturation

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TATA box

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proteins that facilitate transcription

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transcription factors –

general transcription factors (TFIIA, TFIIB, etc.) – mandatory for RNA polymerase II transcription
specific transcription factors – influence efficiency/rate – influence efficiency/rate

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those mods w/in RNA processing ^

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post-transcriptional modification

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the 5’ cap added during post trans-modification

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7mG cap

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3’ adenylation (see above)

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poly-A tail/ polyadenylation

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the nuclear macromolecule complex within which splicing reactions occur to remove introns from pre-mRNA

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spliceosome

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abundant species of small RNA molecules ranging in size from 90 to 400 nucleotides that in association with proteins form RNP particles known as snRNPs or snurps. Located in the nucleoplasm, snRNAs have been implicated in the processing of pre-mRNA and may have a range of cleavage and ligation functions

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snRNA

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generation of different protein molecules from the same pre-mRNA by incorporation of a different set and order of exons into the mRNA product

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alternative splicing

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adapts genetic info present as specific triplet codons in mRNA to their corresponding amino acids

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transfer RNA (tRNA)

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three nt’s (ribo) complementary to the codon

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anticodon

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triplet of nt’s that codes for an amino acid

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codon

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mods by enzymatic cleavage, or the addition of phosphate groups, carbohydrate chains, or lipids

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posttranslational modifications

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changes in the nucleotide sequence that appear to have no cause

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spontaneous mutation

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mutations that result from extraneous factors

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induced mutation

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those occurring in any cell in the body except germ cells

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somatic mutation

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those occurring in the gametes

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germ-line mutation

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mutations that result from extraneous factors

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induced mutation

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mods by enzymatic cleavage, or the addition of phosphate groups, carbohydrate chains, or lipids

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posttranslational modifications

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a change of one base pair to another in a DNA molecule

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point mutation

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same as point mutation

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base substitution mutation

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a point mutation that changes a triplet, resulting in a new triplet which codes for a different amino acid in the protein product

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missense mutation

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a point mutation that results in a new triplet being a STOP codon

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nonsense mutation

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alteration of a codon that does not change the encoded amino acid

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silent mutation

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a purine replacing a purine, and in the same way, pyrimidine to pyrimidine (e.g., A>G, both purines)

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transition

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A purine replacing a pyrimidine, or vice versa

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transversion

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one that reduces or eliminates the function of the gene product

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loss-of-function mutation

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one that results in a complete loss of function

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null mutation

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results in a gene product with an enhanced or new functions

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gain-of-function mutation

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Most common in regions containing repeated sequences; skipped or copied sequences (deletions or insertions) due to misalignment during replication

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replication slippage

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agents with the potential to damage DNA and cause mutations

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mutagen

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donate an alkyl group such as methyl CH3 or ethyl CH3CH3, to amino or keto groups in nt’s; base-pairing affinities are altered, and transition mutations result

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alkylating agent

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chemical species consisting of two identical pyrimidines; major result of UV radiation is the creation of pyrimidine dimers, which distort DNA conformation and inhibit normal replication

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pyrimidine dimer

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radiation energetic enough to produce ions and other high-energy particles; also capable of breaking phosphodiester bonds, disrupting the integrity of chromosomes, and producing a variety of chromosomal aberrations, such as deletions, translocations, and chromosomal fragmentation

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ionizing radiation

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uses any of many strains of salmonella typhimurium which have been selected for their ability to reveal the presence of specific types of mutations (e.g. base-pair subs, frameshift mutations); these mutations affect the bacterium’s ability to synthesize histidine (his-) and therefore require histidine for growth. (See hw #6, problem 4)

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Ames test

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after proofreading, mismatch repair may be activated; this detects alterations, removes incorrect nucleotides, and inserts the correct nt’s; HOWEVER, the special problem encountered is how to differentiate between the correct template strand and the altered strand. Recognizes unmethylated strand as newly synthesized strand. Mechanism is described in full on page 422.

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mismatch repair

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responds after damaged DNA has escaped repair and failed to be completely replicated

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postreplication repair

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light-induced repair of damage caused by exposure to ultraviolet light. Associated with an intracellular enzyme sysem

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photoreactivation repair

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“cut-and-paste” system; corrects damage to nitrogenous bases created by spontaneous hydrolysis or by agents that chemically alter them

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base excision repair

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(NER) repairs “bulky” lesions in DNA that alter or distort the double helix, such as the UV-induced pyrimidine dimers discussed previously

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nucleotide excision repair

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a rare recessive genetic disorder that predisposes individuals to severe skin abnormalities and cancers; lost ability to undergo NER, and as a result, individuals suffering from XP who are exposed to the UV radiation in sunlight exhibit reactions that range from initial freckling and skin ulceration to the development of skin cancer

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xeroderma pigmentosum (XP)

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specialized pathway activated and responsible for reattaching two broken DNA strands. Defects in this pathway are associated with X-ray hypersensitivity and immune deficiency

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double-strand break (dsb) repair