human genome module Flashcards
what does SNP stand for an what is it
a single nucleotide polymorphism, are single nucleotide sites in the DNA that commonly vary within populations
why did they sequence the human genome
identify all human genes, and their roles.
analyze genetic variation between humans.
sequence the genomes of several model organisms used in genetics.
develop new sequencing techniques and
computational analyses.
to share genome information with scientists and the general public as fast as possible.
how many base pairs and genes does the human genome have
6 billion base pairs and around 20,000 genes
what were some of the key findings of the human genome
There are fewer genes than expected
Less than 2% of our genome codes for proteins
The genome is dynamic
We still don’t know what many of our
protein-coding genes do
Most human genes are related to those of
other animals
All humans are 99.9% similar at sequence
level
how much of genome actually codes for proteins
less than 2 percent
how common are SNPs, in numbers
one in every 300 bases
where do our SNPs come from
they come mostly from our parents but as we develop we form some unique to us
what are the three types of SNP
linked, non coding and coding
why are most SNPs harmless
they are harmless as they fall outside of the coding regions of DNS
whats a linked SNP.
an SNP located close to a gene but not in coding or regulatory sequences, are inherited but have no effect on the protein.
whats causitive SNP
and SNP that is located in the gene sequence, either coding or non coding
whats a non coding SNP
one that is in the regulation sequence, changes where, when and how much protein produced. Likely to not do much but based on the nature of the variation may alter the regulation of the protein production.
whats a coding SNP
these are in the exon, these may change the amino acid sequence. Could potentially be problematic and code for early termination. But likely wont cause a large scale change due to redundancy of the genetic code.
whats an STR
a short tandem repeat
whats an inDel
small insertion or deletion mutations
whats the second most common varient type
SNP is first, inDel is 2nd
what can inDels cause
can cause reading frame shift if the amount of bases deleted is not a multiple of 3. and the mutation is in the exon region
what does STR stand for
short tandem repeats
what is an STR
STRs are repeats of 2-5
nucleotides, found in specific
regions of genome
how do STRs provide a genetic fingerprint
each person inherits two alleles from their biological parents. these alleles can have different lengths of STR at the same site. the mother may have 8 CAG repeats and father only 3, so the person is 3,8 at STR 1.
why does STR work for fingerprints
because the likely hood of two different people having the same STR lengths at 20 different sites is slim to none.
whats CNV stand for
copy number varients
what is a CNV
this is a large section of DNA, over 500 base pairs that are present in different amounts with reference to the human genome.
how do we do comparative genomics and explain the process
we do it in a process called aligning, this is when we line up two sequences of DNA and mark each point where the sequences are the same.
what does conserved mean
it means things that are the same in the genomes of two separate species.
things that differ in two different species genomes could be what
could potentially be encoding for the organisms specific biology.
what can we learn about an organsism by comparing its genome
What sort of genes they have
§ How differences between species arise
§ Relationships between species
DNA from dead things can remain in the environment, why might it be hard to compare this DNA with human genome
DNA degrades and is masked by more modern DNA
DNA bases are also modified as they degrade,
sometimes changing the sequence.
how much DNA do we share with the neanderthal
for non africans we share 2-4 %
why don’t most africans share DNA with neanderthal
because the homo sapiens that evolved in africa never migrated out of africa to go interbreed with the neanderthal
whats the amount of DNA shared between Melanesian and denisovans
4-6%
mutations that can be inherited are called
germline mutations
what causes a somatic mutation
damage to DNA by UV, radiation or chemicals or incorrect copying of DNA
how many mutations in our genome do we develop ourselves as a fetus
60
what affects the outcome of a mutation on the phenotype
the location of it in the human genome, environmental factors( diet and toxin exposure), other genes (background genes)
whats a loss of function mutation
A mutation that might break a gene to cause it to not work as well as normal, or not work at all.
why are loss of functions generally recessive
because there are two copies of each gene. if one is defective, its defects can be covered by the normal gene on the other chromosome.
whats a gain of function mutation
when a mutation causes a gene to work too well, or to do something unexpected.
why are gain of functions generally dominant
Gain of function mutations are often dominant, because having an allele that works too well or does something novel, will not be replaced by the normal copy of the gene.
whats polygenic disorder
involve several genes acting together or
environmental factors interacting with genes.
whats monogenic disorder
a disease caused by one set of alleles
why do most genetic disorders not follow a straightforward inheritance pattern
Polygenic disorders involve several genes acting together or environmental factors interacting with genes.
for most diseases, having a disease related variation means what
not necessarily anything, having a disease related variation does not mean youll get the disease
why does getting a disease variation not mean youll get the disease
because most diseases are combinations of genotype and environment
most genes are what not what
probabilistic not determinalistic
how do we get information about a gene from its phenotype
by studying organisms that are naturally mutant for a gene, or creating our own mutations. using this we can figure out how mutations lead to phenotype change and learn what that gene is supposed to do.
what is genetic screening and how can we do it
genetic screening is when we increase the rate of mutation, then select a phenotype of interest, then sequence the genome to identify the mutation. the mutation rate can be increased through increased interbreeding or inducing mutations with mutagens.
what is transgenesis
Take a gene you are interested in, copy it and insert it into another organism
whats a targeted mutation
Deliberately break a particular gene to see what happens
what study does genetic screening, transgenesis and targeted mutation create
these makeup functional molecular genetics.
whats a model organism
Model organisms are ones that can be easily raised in a controlled environment and are easy to manipulate genetically. these organisms also sharing large amounts of genes with humans
why does transgenesis work
because the DNA code is universal, so
what is a transgene
a gene that we have taken from one organism and put into the next
transgenesis method? 5 steps
1: isolate gene interested in
2: insert into male pronucleus or fertilised egg
3: reimplant egg into parent organism
4: if successful, all resulting cells should contain that gene
5: screen offspring for transgene
whats one way of carrying out a target mutation
CRISPR-Cas9
method of CRISPR
make a guide RNA that binds to gene of interest, combine RNA and Cas9 protein, insert this complex, the complex enters the nucleus binding to the DNA at the point complementary to the RNA, the CRISPR makes a cut at the target site, the DNA will then try to repair itself
in CRISPR what are the two ways the DNA can repair itself,
with or without a template of that DNA
what happens when DNA repairs without template after CRISPR
DNA repair enzymes try to patch up the cut.
v This often results in errors as there is no template to read from.
v Small InDels are created at the target site,
the gene is potentially disrupted, or mutated (a).
what happens when there is a template for DNA to repair itself after CRISPR
if there is a template the correct gene will be reinserted by the DNA enzymes
what are 3 ways we can fix germline mutation
3 parent babies, Pre-implantation genetic diagnosis, and CRISPR gene-edited babies
whats 3 parent babies
where the faulty
gene is on the mitochondrial DNA,
nuclear transfer to a donor egg can be
used.
whats preimplantation genetic diagnosis
in families with an identified risk, IVF
can be used to make embryos from the
parents’ eggs and sperm. These
embryos can be tested before
implantation, and only healthy embryos
implanted.
