Genetics Flashcards
Watson and Crick were responsible for what
Publishing the structure of DNA
What is the TAT of home genetic tests?
how long did it originally take to sequence the entire human genome in 2003?
Turn over time: 12-16 weeks
Originally took 13 years
What is the structure of DNA
double helix: two DNA wound around one another
Nucleotides/base pairs: held together w/ hydrogen bonds
Nucleotides and sugar phosphate backbone: they branch out medially and connects strands
Genes, DNA, nucleotides, chromosomes relationship
Nucleotides make up DNA
DNA makes up genes
Genes are contained in chromosomes
Chromosomes are contained in the nucleus of all cells
genes are
long strands of DNA sequencing
each human cell has _____ chromosomes
23 chromosomes
How many nucleotides do humans have?
Genes?
3 billion nucleotides making about
20,000 genes
Largest chromosome?
Smallest?
Largest: 1 (2,000 bp)
Smallest: 21 (300 bp)
What are the two processes needed to create protein from DNA?
Transcription
Translation
Genes tell you…
which proteins are made
which cells make them
when they are made
Transcription
DNA to mRNA
Does the gene change with transcription
no
We are able to modify the mRNA to some extent prior to translation to create ______ via ______
create similar but non identical proteins
via selective splicing and 3’end formation
DNA makes ______ makes _____
DNA makes RNA, makes proteins
Three ways you control the amount of protein made
1) control how much mRNA is made during transcription
2) turning the gene on or off
3) what alternative splicing is being used
In translation what is used as a template to create protein?
mRNA
What is mRNA read by to create proteins?
ribosomes
Transcription and translation are separated due to what?
the nuclear membrane
Where does transcription occur?
Translation?
Transcription: nucleus
Translation: cytoplasm
Double helix is held together by what?
hydrogen bonds
Hydrogen bonds are what
tight, non-covalent connections btwn strands
What molecule uses DNA as a template, opens the double helix and binds to the _______ to start ______
RNA polymerase uses DNA as a template, opens the double helix and binds to the PROMOTER region on DNA to start TRANSCRIPTION
What is the base pair rules of mRNA
A –> U **instead of T
T –> A
G –> C
Where does RNA polymerase enter the DNA strand?
promoter region
Strength of the promoter decides what?
How much mRNA you get
Initiation stage of transcription
Polymerase attaches to the promoter, it unwinds the DNA at that location, and beings making an RNA transcript from one strand
Elongation stage of transcription
RNA polyermase moves across the DNA molecule synthesizing a strand of RNA. It advances through the gene like this
RNA is going to have the same sequence as which strand and a complimentary sequence to which strand
Identical sequence to non-template strand
Complementary sequence to template strand
Termination stage of transcription
RNA polymerase gets the “stop” signal codon. Polymerase falls off and releases the completed RNA transcript
True or false: in general you’ll have the same completed RNA transcript every time the gene gets copied?
true
mRNA processing: We can regulate gene expression by what?
choosing which exons to keep and which to remove
mRNA processing: Sequencing elements in the gene direct what?
where splicing is going to happen
Introns vs. exons
introns: non-coding
exons: coding
Number and size of introns per gene…
varies greatly
Do alternations in introns alter protein code sequences?
No however they can interfere with how the exons come together therefore indirectly interfering with gene expression
Alternate splicing events allow for what?
Creation of isoforms: slightly different versions of the same proteins
What is the function of tRNA
bing to particular AA and bring that AA to the ribosome to create protein
What are ribosomes made of
RNA and proteins
What is ribosomes job
bind to mRNA and synthesize proteins one AA at a time
Different AA gives proteins different what?
shape and function
What makes up AA’s
amino group, central carbon group, carboxyl R group (what makes aa different from one another)
How are amino acids encoded
non overlapping triplets of nucleotides = codons in mRNA
True or false: there is only one triplet codon combination for each protein
False: the genetic code is redundant. Some aa’s are encoded by more than one triplet
How many aa do we have
20
What is the start codon
AUG
How many stop codons are there
3
Where do ribosomes bind to begin translation, scanning for what?
5’ end scanning, scanning for the AUG start signal
What is the relevance of methionine
Always the first tRNA in translation has methionine as it’s aa
once the first tRNA leaves what happens?
the ribosome steps one codon over, the new tRNA
When does translation end?
And what happens to the protein at this point
When ribosome encounters a stop signal
The full length protein is released
What is a peptide bonds job
bonding one aa to another aa during translation/within the protein
Ribosome carries its own enzyme that catalyzes what?
peptide bond formation (bonds aa’s to another to create protein during translation)
When are introns removed in the whole process?
during mRNA splicing
Changes in DNA affect proteins by changing what three things
Amount
Timing
Function
insertions or deletions of thousands of nucleotides is also called what
Copy number variants (CNV)
True or false CNV are not pathogenic
false they can be but most are not
What is a translocation
rearrangement iwithin a choromosome; there is a piece where they are not supposed to be
Point mutation is a single gene level change or a chromosomal change?
Gene level
sex specific chromosomes generally severe or not?
Not severe in general
Williams DiGeorge syndome is what kind of variant?
chromosomal microdeletion syndrome (thousands of base pairs lost)
Duchenne muscular dystrophy often caused by what?
deletions or duplications that affect one or more exons - single gene change
single base insertion generally causes what
stop to come early
single base deletion generally causes what
extensive aa changes down the line
Single gene changes may cause what type of mutation?
frameshift
What does an in-frame deletion mean
what is an example of one
multiple of three deletions
cystic fibrosis - affects protein folding, wrong shape of protein and it gets stuck
what kind of mutation is cystic fibrosis?
single gene in frame deletion
3 possible consequences of point mutations
silent, nonsense, missense
Silent point mutations
there is genetic variation so sometimes the deletion does not change anything
nonsense point mutation
changes a codon from coding an aa to a STOP codon
Can produce shortened proteins
mRNA often unstable so no protein is made
OFTEN SEVERE consequences bc there is no protein being made when there should be
missense point mutation
Dangerous?
Example?
changes one aa to another
Can be silent or damaging
Ex: sickle cell
Why do missense variants cause problems?
protein function is dependent on their shape - enzymes don’t fit
True or false: genetic diseases are always inherited
False! new mutation/varients exist
In fact most cases of cancer are sporadic
Pairs of chromosomes mean what for genes? Except for what?
that every gene comes in two copies
Except for sex genes
Autosomal dominant: what does an affected individual look like chromosome wise
affected individuals will have one copy with a variant, one copy that is unaffected
What is the chance of an autosomal dominant individual passing it onto their children?
50%
Do autosomal dominant disorders impact relatives?
Yes!
Achondroplaisa (dwarfism) and familial hypercholesterolemia are what kind of genetic conditions?
autosomal dominant
Autosomal recessive: what does an affected individual look like chromosome wise
both copies of the gene have varients
Typically what do the parents of a child with an autosomal recessive phenotype look like
unaffected carrier parents
What is the risk of siblings in an autosomal recessive situation?
Other relatives?
Men or women?
25% to an unborn sibling
Rare for other relatives to have the same condition
Men and women have same risk
Which autosomal pattern has “horizontal transmission”
recessive
Albinism and Spinal muscular atrophy are what kind of genetic conditions?
autosomal recessive
X- linked recessive disorders
boys risk vs girls if mother is a carrier
boys have 50% chance of being affected if their mother is a carrier
50% chance daughter is A CARRIER
50% chance they are nothing
X- linked recessive disorders
boys risk vs girls if father is affected
no chance the son is affected
100% chance daughter will be affected
name x-linked conditions
color blindness, hemoophilia
general thoughts for x linked genes
boys are more likely affected than girls
mothers are often carriers: sons have a 50% chance of being affected
True or false, the majority of CA is hereditary
False!!! only 10-15% majority of cases are sporadic
If the CA is hereditary are most dominant or recessive?
Dominant
What does hereditary CA syndroms not being fully penetrant mean
people can have the mutation and NOT get CA however their risk for developing it is high
BRCA1 and 2 account for what % of all cases of breast CA
5%
HBOC
recessive or dominant
Hereditary breast and ovarian CA
Dominant
What does a BRCA 1 or 2 mutation mean for an individual
they have an increased lifetime risk of breast cancer (85% instead of average 12% risk)
Cystic fibrosis recessive or dominant?
recessive
Mutation in CFTR gene causes what
Cystic fibrosis
two symptoms of cystic fibrosis you wouldn’t have thought of
Pancreatic insufficeincey, male infertility
PT implications for cystic fibrosis
chest PT, reduced bone density, kyphosis (due to barrel chest), muscle atrophy, myalgia, OA
Mitral valve prolapse plus retinal detachment plus disproportionately long arms/legs could mean what?
Marfan syndrome
What are some things that would signal HBOC
HBOC: hereditary breast and ovarian cancer
Premenopausal breast cancer
Multiple individuals w/ breast or ovarian in the same blood lineage over generations
Someone with multiple primary CA’s
Man with breast CA
If you suspect HBOC what should you do
refer patient to genetic counselor
Value of genetic testing
determine risk
offer genetic testing
identify other at risk family members who should be aware of their risk
Offer info, surveillance or treatment if positive
The kind of genetic testing you get depends on what?
what variant is suspected
Ex: chromosomal vs. gene sequencing
What is gene sequencing
reading the nucleotides in a gene to determine if there are variants
Sanger vs. Next gen sequencing
Sanger: slow (one gene at a time) gold standard, high cost
Nex Gen: rapid, multiple genes simultaneously “shot gun/masively parallel”
What is next gen sequencing used in
Whole exome sequencing (WES) and whole genome sequencing WGS
Pathogenic or likely pathogenic variant (LPV) gives what result
positive
No faimilial vairant, a benign variant, or likely benign variant gives what result
negative
What is a true negative result in regards to a mutation found in family
you have the gene your sister does not, she has the same risk as the general population NOT zero
What does a benign variant tell you about risk
not harmful, risk is not increase, no altered management/screening
What does a LBV tell you
likely benign variant: no risk, no alternation in management/screening
What do you do with a variant of uncertain significance treatment wise
hardest to counsel on we don’t act on knowing this: no testing other people, does not reduce or increase risk
Different labs still “weigh” evidence somewhat differently
Leads to potentially different classification for the same variant
Multigene testing is much more common than single: looks at a set of genes most likely to be involved in the condition
Ex: familial CA, autism, intellectual disabilities
What does WES stand for
Whole exome sequencing
Sequences all of the protein-coding regions (1.5%) of the human genome
Whole exome sequencing (WES)
True or false: WES has a low diagnosis yield
false: very high diagnostic yield because the WES looks at the coding regions of the human genome and 85% of pathogenic variants are in exons
limitations of NGS therefore WES or WGS (whole genome sequencing)
does not detect all types of variant bc some are found in the non-coding regions, not all exons are targeted, carrier status not reported, incidental findings common
Labs are required to report certain findings in WES
you look at WGS if WES is uninformative
Limitations of WGS
tons of variation, which ones are important? Will find variations of unknown significance, unexpected/didn’t want to know disease
Not all insurance companies cover WGS, its hard to say you got consent to test for EVERY genetic disorder
Some information is not reported when its not interpreted to affect the pts health
Benefits of WGS
identify new mutations, carrier screening, pharmacogenomics, disease identification possibly before symptoms, more cost effective than one gene at a time
Genetic information non-disrimination act
protects insurance from discriminating based on genetic info
but there are limitations
Is hereditary cancer a single gene disorder
yes!
is DMD chromosomal change or single gene disorder?
single gene disorder
