Comp Exam

nondisjunction in meiosis I results in

no normal gametes (trisomic or monosomic) after fertilization

nondisjunction in meiosis II results in

normal, trisomic, or monosomic gametes after fertilization

phases of mitosis

prophase, metaphase, anaphase, telophase

mitosis results in

diploid cells and 2 genetically identical cells

phases of meiosis

Prophase 1, Metaphase 1, Anaphase 1, Telophase 1, Prophase 2, Metaphase 2, Anaphase 2, Telophase 2

meiosis results in

4 haploid daughter cells

allelic heterogeneity

different mutations in the same gene produce the same phenotype

locus heterogeneity

similar phenotypes due to mutations in different genes

phenotypic heterogeneity

multiple phenotypic effects from the same condition (many forms/organs affected)

penetrance

percentage of individuals with a particular genotype that actually displays the phenotype associated with the genotype (number of affected individuals/number of individuals with genotype \= % penetrance)

chance of having affected child (reduced penetrance)

likelihood of transmitting allele x penetrance

incomplete dominance

more severe in homozygotes (FH)

codominant inheritance

both alleles expressed in heterozygotes (AB blood type)

somatic mosaicism

mutation arises from mitotic errors after fertilization and propagates through multiple tissues or organs (segmental expression)

germline/gonadal mosaicism

the presence of a mutation in a germline cell of an unaffected individual, can result in multiple siblings affected

sex-limited inheritance

a pattern of inheritance in which phenotypic expression is limited to one sex but not x-linked

sex-influenced inheritance

the sex of an individual influences the expression of a phenotype that is not limited to one sex or the other

sex-linked inheritance

inheritance of a gene that is carried on a sex chromosome

x-linked recessive

males \> females; no male to male transmission

X-linked dominant

females \> males; females can be more mildly affected due to X-inactivation

X-inactivation

one copy of X turned off early in development, usually by chance; skewed X-inactivation can lead to expression of an XLR trait in a female

post-inactivation selection

may occur to inactivate mutant X

pseudoautosomal region

segments of X + Y where crossing over happens in male meiosis, mutations in these regions look autosomal (ex. SHOX), escapes inactivation in women to maintain haplosufficiency

central dogma

DNA -\> RNA -\> protein

pyrimidines

C + T

purines

G + A

direction of transcription

5' to 3'

introns

intervening sequence between protein-coding sequence

exons

protein-coding sequences, remain present in final mature RNA after splicing

genome length

3.2x10^9 bp (haploid)

how much of genome is protein-coding

1-2% (15,000-20,000 bp)

repetitive sequences

DNA sequences that are present in many copies in the genome; short tandem repeats, interspersed repeats

alternative splicing

splicing of introns in a pre-mRNA that occurs in different ways, leading to different mRNAs that code for different proteins or protein isoforms; increases the diversity of proteins

unambiguous code

each codon codes for a single amino acid

degenerative code

amino acids can be encoded for by different codons

non-overlapping code

each base in the sequence is read only once, bases do not overlap

missense mutation

a base-pair substitution that results in a codon that codes for a different amino acid (proline \> leucine)

nonsense

stop codon, ends protein early

silent mutation

a mutation that changes a single nucleotide, but does not change the amino acid created (SNP)

splice site mutation

mutation at a point where coding and non-coding regions meet in a section of DNA, gain/lose splice site

regulatory mutation

affect the regulation of gene expression; may inappropriately active or inactive expression of a gene

insertions and deletions

additions or losses of nucleotide pairs in a gene; can shift frame if not in multiple of 3

triplet repeat expansion

a spontaneous error that can arise during replication involving regions of chromosomes that contain highly repetitive regions; triplet or trinucleotide repeats (CAG, CTG, CGG etc) become massively expanded creating a tandemly repeated cluster of three nucleotides

inversion

a mutation involving a piece of a chromosome that breaks off and reattaches in reverse orientation

translocation

mutation in which one part of one chromosome breaks off and attaches to another

deletion and duplication

piece extra/missing of chromosome

transition mutation

purine to purine or pyrimidine to pyrimidine

transversion mutation

purine to pyrimidine or vice versa

methylation

addition of methyl group to CpG site that suppresses gene activity and expression

demethylation

removal of methyl group in CpG site that generally activates transcriptional activity

CpG islands

DNA regions rich in C residues adjacent to G residues; these regions are where methylation of cytosine usually occurs, typically in promoters

euchromatin

less condensed form of eukaryotic chromatin that is available for transcription (eu go girl)

heterochromatin

highly condensed chromatin

types of heterochromatin

constitutive: Y chromosome and centromere

faculative: X chromosome (f for female)

why does x-inactivation happen

dosage compensation

XIST

X-inactivation specific transcript gene; codes for functional RNA that coats inactive X and initiates shutdown

recombination is more likely to occur between genes that are

far apart on the chromosome

steps of PCR

denaturing DNA strands, annealing primers, elongation by Taq polymerase

what is PCR used for

create large quantities of DNA to perform testing on (prior to sequencing) or used to detect certain disease on its own (repeat primed PCR)

repeat primed PCR

used to detect triplet repeat expansions (e.g. FX in FMR1), uses repeat region primers

microarray

a grid of DNA segments of known sequence that is used to test and map DNA fragments

what is microarray used for

del/dup analysis, differences in gene expression (tumor profiling), SNPs

Sanger sequencing

uses modified nucleotides w/o 3' hydroxyl groups; can incorporate into DNA strand but result in chain termination --\> fluorescence used to determine resulting sequence

next gen sequencing

use millions of overlapping small sequences, computers align and merge data for analysis; reads one base at a time; get shorter reads + more data

fragile X syndrome gene and mechanism

FMR1 gene; CGG repeats in 5' UTR

fragile X syndrome symptoms

intellectual disability, autism, long face w big ears, macro-orchidism

premutation carriers of FX at risk for

POF, tremor/ataxia

repeat ranges for FX

normal: 2-44

intermediate: 45-54

premutation: 55-200

full mutation: \>200

Huntington's disease gene and mechanism

HTT gene; repeats of CAG in exon 1

repeat ranges for HD

normal:

HD exhibits

anticipation; esp when paternally inherited

HD symptoms

involuntary movements (chorea), mood/behavioral changes, cognitive impairment; symptom onset in 30s-50s w/ 15-20 year course

myotonic dystrophy type 1 gene and mechanism

DMPK; CTG repeats in 3' UTR

myotonic dystrophy type 1 symptoms

progressive muscle weakness beginning in face, myotonia (can't relax muscles after contraction), cataracts, cardiac conduction disease

congenital form can have hypotonia, clubfoot, breathing difficulties, ID/DD

myotonic dystrophy repeat ranges

normal: 5-37

minimally affected: 44-180

congenitally affected: \>750

myotonic dystrophy exhibits

maternal anticipation, nearly 100% penetrance by age 50

what tests are best to detect repeat expansion disorders

sanger/repeat primed PCR

why is C--\>T a common mutation

C is often methylated, can then be deaminated into T

base excision repair

DNA repair that first excises modified bases and then replaces the entire nucleotide (fixes single strand break)

nucleotide excision repair

a nuclease cuts out and replaces damaged stretches of DNA (fixes single strand break)

mismatch repair

special enzymes fix incorrectly paired nucleotides (fixes replication errors)

homologous recombination repair

uses sister chromatid to repair break (fixes double strand break)

nonhomologous end joining

brings together 2 ends of DNA fragments to repair double-stranded breaks, quick and dirty (error prone)

common features of DNA repair disorders

rare, multisystem, AR, premature aging, photo- and radio-sensitivity, early onset malignancy, shortened lifespan

Cockayne syndrome mechanism

defective NER

Cockayne syndrome symptoms

photosensitivity, growth and mental deficits, premature aging

ataxia telangiectasia mechanism

ATM gene (AR), faulty double stranded break repair, homologous repair

ataxia telangiectasia symptoms

ataxia, dysarthria, impaired coordination, neuropathy, telangiectasias, malignancy

CMMRD mechanism

AR Lynch genes, faulty mismatch repair

CMMRD symptoms

childhood malignancy, NF-like symptoms

Bloom syndrome mechanism

AR in BLM gene, faulty double strand repair and homologous recombination, excessive sister chromatid exchanges lead to chromosome breakage

Bloom syndrome symptoms

growth defects, cancer predisposition, skin pigmentation, sun sensitivity, male infertility

xeroderma pigmentosum mechanism

faulty NER

XP symptoms

sun sensitivity, malignant lesions, predisposition to skin cancers, ocular sensitivity and neoplasm, neuro symptoms in 20% associated with premature aging (neurodegeneration)

duchenne gene and mechanism

DMD gene; XLR; largest known gene; typically caused by large deletions; disrupt reading frame; 1/3 de novo

DMD symptoms

progressive muscle weakness

unremarkable at birth, present at 2-5 years

delayed walking, abnormal gait, toe-walking, gower sign, pseudohypertrophy of calf muscle, wheelchair by 10y

elevated CK

dilated cardiomyopathy in 90%

death due to respiratory failure

DMD carriers

can have cardiomyopathy or some muscle weakness (due to skewed X inactivation)

DMD treatment strategies

upregulate utrophin (similar function to dystrophin), introduce mini dystrophin, read through stop codons, exon skipping

becker muscular dystrophy

same gene as duchenne but later onset and slower progression; due to in-frame mutations

marfan syndrome gene

FBN1