genetics save me

define genetics

the study of heredity, and how genes are encoded, replicated, expressed, and evolved.

epistasis

a gene (epistatic) masks/inhibits the phenotype of another gene (hypostatic)

polygenic inheritance

multiple genes affect a single trait

Labrador retriever coat color involves two genes:

• 𝐵 allows black pigment (bb = brown pigment).

• 𝐸 allows pigment deposition in fur (ee prevents deposition → yellow coat).

Consider the cross 𝐵𝑏𝐸𝑒 × 𝐵𝑏𝐸𝑒.

• (a) What phenotypic ratio (black : brown : yellow) is expected in the

𝐹2?

• (b) Which genotype class demonstrates epistasis, and which gene is

epistatic?

a) 9:3:4

b) ee shows epistasis, E locus is epistatic

Holliday model

Double-strand break model

Theta replication

Rolling replication

inversion loops

when a chromosome fragment is flipped 180

• paracentric does NOT include the centromere. results in a dicentric chromatid (2 centromeres) and an acentric chromatid (no centromere). usually nonviable.

• pericentric includes the centromere, goes around it. results in 2 nonviable recombinant gametes, nonrecombinant with pericentric inversion, and a normal nonrecombinant gamete.

chromosome/DNA counting

DNA replication doubles chromatids, not chromosome number, until they split

What is a Barr body, and how does X‑chromosome inactivation create

mosaicism in heterozygous females?

Inactivated X chromosomes. If females have two X’s, they will delete one (human dosage compensation). If X has different genomes, it will make a mosaic across cells (think calico cats)

complete dominance

one allele completely masks the other

incomplete dominance

neither allele is completely dominant, blend

codominance

both alleles are fully expressed and neither masks the other, patches

lethal alleles

cause death before birth usually

In the human ABO system, the relationship between 𝐼𝐴 and 𝐼𝐵 alleles is:

A. Complete dominance (𝐼𝐴 > 𝐼𝐵) B. Complete dominance (𝐼𝐵 > 𝐼𝐴) C.

Codominance (𝐼𝐴 = 𝐼𝐵) D. Incomplete dominance

C. codominance 𝐼𝐴 = 𝐼𝐵

transition mutation

purine to purine, or pyrimidine to pyrimidine

transversion mutation

purine to pyrimidine, or pyrimidine to purine

insertions/deletions

cause frameshift mutations if less than 3 bases are inserted/deleted

forward mutation

wild type gene to mutant gene

reverse mutation

mutant gene to wild type gene

missense

new codon → new amino acid

nonsense

new codon → STOP codon

silent

new codon → no change in amino acid

tautomeric shifts

hydrogen atoms switch across base

strand slippage

• newly synthesized strand loops out and causes addition

• template strand loops out and causes deletion

unequal crossing over

homologous chromosomes misalign during crossing over, one product has an insertion and the other has a deletion

depurination

loss of a purine base from a nucleotide leads to base substitution, will often incorporate A into the empty spot

incorporated error

an initial wrong nucleotide placed opposite of the template from mispairing

replicated error

a later, fixed mutation of an incorporated error that survives repair and acts as a template

Which statement correctly compares ultraviolet and ionizing radi-

ation?

A. UV commonly causes pyrimidine dimers, whereas ionizing radiation

can generate free radicals and double-strand breaks.

B. UV mainly causes double-strand breaks, whereas ionizing radiation

mainly causes pyrimidine dimers.

C. Both types of radiation are mutagenic only because they increase tran-

scription.

D. Neither type of radiation changes DNA directly.

A

repair pathway for pyrimidine dimer

nucleotide excision repair, removes bulk and fills with polymerase + ligase

nucleotide excision repair

strands are separated and section of DNA with the bulky lesion is removed, polymerase fills in gap and ligase seals it

repair pathway for O^6 methyl guanine

direct repair restores it to original guanine structure

direct repair

does not replace mistake, but fixes it to its original form

repair pathway for uracil from cytosine deamination

base excision repair removed the damaged base using glycosylase

base excision repair

a modified base is removed, and the whole nucleotide is replaced

repair pathway for mismatch after replication

mismatch repair corrects the mismatched base that escaped proofreading

mismatch repair

corrects incorrectly inserted nucleotides that escape proofreading by DNA polymerase during replication

transposable element

DNA sequences that move in the genome and often cause mutations

flanking direct repeat

staggered cut is made into DNA, transposable element inserts itself but there are gaps. polymerase fills in the gaps to make the repeats

replicative transposition

copy/paste

nonreplicative transposition

cut/paste

retrotransposons

transpose through an mRNA intermediate and copied back into DNA (reverse transcription)

restriction enzymes

recognize specific nucleotide strands in DNA and make double-stranded cuts at the sequences. makes sticky/blunt ends that can combine fragments

CRISPR-Cas9

modifies genomes

• Cas 9 and sgRNA combine to make an effector complex

• this associates with PAM sequence (target) and unwinds the DNA

• pairs with complementary sequence

• Cas protein cleaves DNA

• nonhomologous end joining (NHEJ) or homology directed repair (HDR)

nonhomologous end joining (NHEJ)

CRISPR repair, joins ends and introduces duplications or deletions that cause frameshifts

homology directed repair (HDR)

CRISPR repair, repairs by inserting donor DNA

western blot

separates proteins by mass using anitbodies

cloning vectors

bacteria, have an origin of replication, 1+ selectable markers, and recognition sites for 1+ restriction enzymes

plasmid vectors

ecoRI cuts plasmid to insert a foreign DNA segment, sticky ends join

expression vector

has an operon sequence that allows the DNA to be transcribed and translated, can turn on/off the sequenced gene

LacZ gene

screens for bacteria with recombinant plasmids. Foreign DNA is inserted into the partial lacZ gene.

• nonrecombinant OG plasmids: blue, intact lacZ

• recombinant: white, disrupted lacZ

• no plasmid: not grown

Sanger sequencing

reads DNA sequences

• sequences have dNTPs added on, but there’s no 3’OH

• fragments terminated by ddNTPs

• reads fragments from shortest to longest

PCR

DNA amplification

requires: template DNA, primers (3’OH end), thermostable polymerase, dNTPs, buffer

• denaturation separates strands

• annealing lets primers bind to complementary sites

• extension copies from primers and grows

• grows 2^n from the starting molecule

• repeat

Illumina sequencing

accurate short reads

• fluorescently tagged dNTPs are added onto the primer

• tag is excised with a labor and fluoresces.

• read by a computer

• tag/reversible terminator removed, and repeated

PacBio HiFi

long reads with high accuracy

• emits light

Nanopore

very long reads, portable field use

• electrical current

GWAS

tests markers (SNP) to find associations with a trait, can detect diseases caused by complex interactions

• SNP can be causal or tag a nearby causal variant

linkage disequilibrium

nearby variants are likely inherited together often by chance

RNA sequencing

can detect sequences without prior probe designs, way more useful, reads expressed RNAs

• makes cDNA from mRNA, broken into fragments, amplification adaptors are added and undergo PCR. assembled into RNA transcripts

DNA microarray

hybridization to predesigned probes

orthologs

genes in different species descended from a common ancestral gene.

paralogs

related genes produced by duplication within a lineage

synteny

neighboring genes retained in the same order across genomes.

C-value paradox

genome size does not scale with organism complexity

map based sequencing

detailed genetic and physical maps to align sequenced fragments (not really used)

shotgun sequencing

uses sequencing overlap to align sequenced fragments, overlap creates clones

X-linked recessive inheritance

• sons receive X from mother and Y from father

• daughters recieve X from both

• affected father passes mutant X to all daughters and Y to all sons

linked genes

• largest classes are parentals

• coupling: dominant alleles together

• repulsion: dominant alleles on opposite homologs

• <50%

meiotic nondisjunction

failure of sister chromatids or homologous chromosomes separating before fertilization, zygote starts with abnormal chromosome number

mitotic nondisjunction

failure of sister chromatids or homologous chromosomes separating after fertilization, only descendent cells carry change

• affect larger fraction of the body