Study Guide Flashcards
what was the 1 gene hypothesis? did it turn out to be correct?
hypothesis: genes make proteins - one gene = one protein
not correct - 1 gene codes for at least 10 proteins and with alternative splicing - one gene encodes for multiple RNAs
SNPs and other mutations were thought to be the sole cause of human variation, was this assumption correct?
FALSE - humans have minimal gene variation, variation is dt gene regulation and the epigenome
how much of the human genome is protein coding? how much is retroviral?
4% protein coding
10% retroviral
in what people and country does most of the variability in the human genome still reside?
San Bushmen of East Africa
how are mitochondrial DNA and Y chromosome DNA different and how are they used in migration studies?
comparing the mtDNA ‘age’ with the number of mutations on the Y chromosome, the time frame and direction of migration can be determined. mtDNA allows us to estimate the age of a species
what did the story about Koko and her cat suggest about human behavior?
??
what are the 3 main problems with trying to determine the cause vs correlation in genetic dz with genetic studies like the GWAS?
chance (variant mb found by random chance)
linkage (study bias - variant is next to the dz causing segment but does nothing on its own)
stratification (an ethnic group has concentration of the variant and the disease but they aren’t linked)
what is the first point of control and how does it work?
- chromatin: histone methylation, target sites of histone methylation are cytidines which exist as CG (CpG, areas w/lots are called CpG islands); methylation of CpG regulates transcription; histone acetylation stops further condensing of DNA which encourages active transcription
what does methylation do? what does demethylation do?
generally methylation upregulates transcription and demethylation inhibits transcription
what groups modify histones?
methyl, acetyl and phosphate groups modify histones
what is the second point of control and how does it work?
- transcription - promoters CCATT and TATA boxes, all in protein coding genes, exon shuffling, enhancers (transcription factors bind to enhancer regions)
what is the third point of control and how does it work?
- translation - RNA transport (exportins); importins and exportins are regulated by GTPases called Ran
what is the fourth point of control and how does it work?
- post-translation into cytoplasm - cap/tail communication
what is the fifth point of control and how does it work?
- post-translation modification
TATA and CCATT boxes are examples of what?
promoter regions
what is exon shuffling and which part (exon or intron) remains as a section of the mRNA?
EXONS
molecular mechanism for the formation of new genes, it is a process through which two or more exons from different genes can be brought together ectopically or the same exon can be duplicated to create a new exon-intron structure
what are enhancers? what is the role of enhancer regions?
enhancers - short (50-1500 bp) region of DNA that can only be bound by proteins (activators) to increase the likelihood that transcription of a particular gene
what are the 3 major types of molecular groups that modify histones and cause epigenetic effects?
methyl
acetyl
phosphate
which epigenetic marker can attach to DNA directly?
METHYLATION
when looking at a cartoon or ideogram of a chromosome, how can you tell the locus from the gene? (know the abbreviations for each; for instance is EPO the gene or the locus? look at slide 7 lecture 3)
the locus is marked by “p” or “q” followed by a number
genes are marked by acronyms given by their discoverer
so EPO is the gene
what are DNA marker alleles? are they necessarily involved in the transcription or biologically active?
any gene or allele that is associated with a specific chromosome and can be used to identify the chromosome or to locate other genes or alleles
they are not necessarily directly involved in transcription or biologically active
what is the difference btw the genotype and phenotype?
genotype - combination of alleles a person has
phenotype - any observable trait, expressed by genotype
what are the 5 basic modes of inheritance?
autosomal dominant autosomal recessive x-linked recessive x-linked dominant mitochondrial
describe autosomal dominant inheritance
the locus is on an autosomal chromosome (1-22) and only one mutant allele is required for expression of the phenotype
describe autosomal recessive inheritance
the locus is on an autosomal chromosome and both alleles must be mutant alleles to express the phenotype
describe x-linked recessive
locus is on the X chromosome and both alleles must be mutant alleles to express the phenotype in females, men can have the dz with only 1 copy of the gene
describe x-linked dominant inheritance
the locus is on the X chromosome and only mutant allele is required for expression of the phenotype in females
describe mitochondrial inheritance
locus is on the mitochondrial chromosome
describe the pedigree pattern with an AD dz
how common are AD dz? how common are AD dz traits?
AD dzs will be in all generations; if females and males affected equally it is autosomal
AD dzs are rare
AD dz traits are common
describe pedigree pattern with AR dz
how common are AR dzs? how common are AR dz traits?
AR dzs will skip generations; if females and males affected equally it is autosomal
AR dzs are rare
AR dz traits are common
describe pedigree of mitochondrial inheritance pattern
mitochondrial inheritance cannot come from Dad, can affects male and female offspring
all offspring of an affected female are affected
all offspring of an affected male but unaffected female are not affected
what are the characteristics of X-linked dominant diseases? can they be transmitted father to son? can they be transmitted father to daughter?
X-linked dominant dzs are 2x common in females than males
cannot be transmitted father to son but can be transmitted father to daughter b/c he contributes the second X
males and females can be affected by X-linked dominant dzs
why can males get X-linked recessive dzs w/just 1 mutated allele?
males only have 1 X chromosome
have to have mom who is heterozygous for mutated X
what is the difference btw a missense mutation and a nonsense mutation?
missense - single base change in the gene that leads to a change in the codon that encodes for the amino acid, effect depends on which base was substituted in
nonsense - base change that results in a “stop codon” which results in a short and completely inactivate protein/enzyme, severe dz is likely
what is the difference btw a gain-of-function and a loss-of-function mutation? is one less troublesome than the other?
loss-of-function: cause a vital or protective protein to become non-functional in the cell (loss of tumor suppressors lead to cancer)
gain-of-function: a mutation occurs when either a completely new enzyme is produced in a cell, or more commonly, the enzyme is overproduced (proto-oncogenes become oncogenes)
why is consanguinity important in clinical medicine, even though it is rare amongst Americans?
marrying w/in 1st degree relatives - leads to increased rate of AR dzs
(although 50% of marriages are consanguineous)
why it is called fragile X syndrome and what determines its severity?
MC cause of mental retardation dt #of CGG repeats # of CGG repeats determines severity
what is the epigenetic significance of X chromosome inactivation and what is a barr body? Do barr bodies form when autosomal chromosomes are imprinted (as for instance in AS and PWS)?
significance is that through inactivation of a singular X chromosome females don’t make double the products conferred by genes
a barr body is a female X chromosome that is rendered inactive
barr body formation occurs in early divisions of cells and is called lyonization (when fertilized egg will become male or female phenotype)
what is the general clinical characteristic of inherited mitochondrial dzs?
neuropathies and/or myopathies
what is the difference btw penetrance, incomplete penetrance and variability?
penetrance - degree to which the phenotype is expressed
incomplete penetrance - some genes are expressed to varying degrees; when individuals with the genotype for dz do not express it phenotypically
variability - how bad the dz is when it is expressed
what is the recurrence risk and how is it calculated
multiple the penetrance by either 25% or 50% depending on if dz is AR or AD, respectively
what is pleitropy? is Marfan syndrome an example?
pleiotropy - single mutation that affects multiple organ systems
YES MARFAN’S IS AN EX - AD mutation in fibrillin which causes issues in many organ systems (1/10,000)
what is anticipation? what does it imply will occur in each subsequent generation of a family carrying a mutation causing a dz characterized by anticipation?
pattern of inheritance in which individuals in the most recent generations of a pedigree develop a dz at an earlier age or with greater severity than do those in the earlier generations (Huntington’s dz). usu due to gradual expansion of trinucleotide repeat polymorphisms w/in or near a coding region
how are the bands of a chromosome striped for a karyotype? what are the 3 types of bands that appear after staining?
GLEMSA staining reveals (=). (+) or variable bands
how many BPs have to be involved in a deletion or duplication to be grossly detectable on a karyotype without using special immunofluroescent stains? if the deletion is smaller than this number can a FISH study be used to detect it?
difference >4 Mbp can be see on karyotyping
<4 Mbp requires detection by FISH
what is the main cause of numerical chromosome abn?
meiotic nondisjunction dt spindle fibers behaving badly
proper name and characteristics for trisomy 21?
Down’s syndrome
MC autosomal trisomy
ALL risk, decreased fertility, mental retardation, protruding large tongue, flat nose and face, eye changes, shorter fifth finger, gap btw 1st and 2nd toes, GI defects
proper name and characteristics for trisomy 18?
Edward’s syndrome
AVSD, PDA
hand, foot malformations, low set ears and micrognathia (small jaw)
proper name and characteristics of trisomy 13?
Patau syndrome
polydactyly, cleft palate, microphthalmia, microcephaly, cardiac and renal defects - both which lead to early death (dt cardiac defects)
why aren’t there any autosomal autosomies?
incompatible with life
what is the karyotyping and characteristics for Kleinfelter’s syndrome?
Klinefelter’s syndrome - 47XXY - intersexed
hypogonadism, but ultimately normal appearing males
what is the karyotyping and characteristics for Turner’s syndrome?
Turner’s - 45X - females missing all or part of the X chromosome
short stature, ovarian dysgenesis and neurocognitive problems
what is the karyotyping and characteristics of “Alien 3 syndrome”?
47XYY - normal but tall stature
through which mechanism is the Philadelphia chromosome formed? what is its significance in terms of dzs it is most associated with? know how it will read on a karyotype (what are the Philadelphia chromosome number)?
Philadelphia chromosome is formed by reciprocal translocation of chromosomes 9 and 22 associated with CML numbers are (t9;22)
can partial monosomies occur? what would the karyotype of Down’s syndrome caused by a partial monosomy read?
yes they can occur
Down’s w/partial monosomy would read as 47XX or 47XY
cri-du-chat results from what abn? does the patient’s voice improve as they age?
caused by deletion of short arm of chromosome 5 leading to abn larynx development
most develop normal larynx and voice after 2 yo
what is Angelman syndrome? what is its significance?
Angelman syndrome - microdeletion of maternal chromosome 15
happy children who are ataxic and epileptic
what is prader-willi syndrome and what is its significance?
PWS - microdeletion in paternal chromosome 15
children who are voraciously hungry and present as floppy babies
what is a ring chromosome and what is its significance? how will it read on a karyotype?
ring chromosome forms when a deletion occurs on both tips of a chromosome and the remaining chromosomal ends fuse together - often resulting in a monosomy
karyotype reading - r = ring chromosome, t = translocation, i = isochromosome
in which dz is the translocation described in cri-du-chat and what is it associated with?
t(9;22) - associated with the Philadelphia chromosome and CML
what are isochromosomes and are they seen in the autosomes of live pts?
chromosome divides along the axis perpendicular to its normal axis of division resulting in 2 copies of 1 chromosome but not copy of the other
autosomal isochromosomes are incompatible with life, most observed in live births will involve the X chromosome
in the Overkalix studies, it was found that nutritional influences and subsequent epigenetic markers could be transmitted to future generations - when it is thought that these epigenetic effects are imprinted onto the fetus’ of women?
when can the influence be acquired by transmission by the males?
are these the only time epigenetic effects can potentially be acquired by a person and transmitted to future generations?
epigenetic effects are imprinted into women when mother is in utero (what your grandmother ate, drank, was exposed to, affects you)
epigenetic effects are imprinted into males at any time b/c they continually make sperm
these are not the only 2 times that epigenetic effects can potentially be acquired by a person and subsequently be passed down
did studies performed in mice demonstrate that CA causing heritable changes were not a result from a sequence change in DNA itself? were these mice PG or PG and in the 3rd TM when sprayed with pesticides? this suggests what about epigenetic change and when they can take place?
yes - epigenetic changes, not changes to DNA
unclear what TM the mice were in
suggests epigenetic changes can take place at any time
know the major reasons gene therapy did not work well
therapeutic DNA must remain functional and cells with it must be long lived and stable
pts must undergo multiple rounds of gene therapy
immune response may be severe and make it difficult to repeat gene therapy b/c of immune cell memory
problems with vectors
won’t work with multigene disorders
MC dzs are dt multiple genes and would be hard to tx w/gene therapy
infecting gene via virus into humans can potentially cause a severe immune response to virus or virus could revert to causing an infection
what is iRNA?
interference RNA- inhibits gene expression or translation by neutralizing targeted mRNA
iRNA is a process w/in living cells that moderates the activity of their genes aka co-suppression/posttranscriptional gene silencing/quelling
has an important role in defending cells against parasitic and viral nucleotide sequences
can iRNA be passed to subsequent generations?
yes - reason iRNA is such a big deal b/c it implies DNA is not the only form of inheritance
what are knock-down situations? how do they work? what do they tell you about a gene? what is the most effective modality for performing knock-down studies?
expression of one or more genes is reduced through genetic modification or a reagent such as short DNA or RNA
can help identify the components necessary for a particular cellular process or event such as cell division
can be used to test the effect of mutated genes
iRNA is the most effective modality for performing knock-down studies
who was George price and what was his contribution to genetics?
a population geneticist, he contributed the Price equation and 2 other things to genetics - it determined how a gene or trait changes in frequency in the population over time
