fundamental molecular biology Flashcards
mutations are usually dominant/recessive
recessive
mutations are usually silent or advantageous/ deleterious
deleterious
what is a mutation
a change in the genetic material of a virus or cell
what process are mutations essential for and why
evolution - new genetic material creates variation which is needed for evolution
which mutations are heritable
mutations which arise in the germ line
which mutations are not heritable
mutations which arise in the soma
describe germ line cell mutations in terms of mutation rate and heritability
they have a low mutation rate
the mutations are passed on to the next generation
describe somatic cell mutations in terms of mutation rate and heritability
they have high mutation rate
the mutations are not heritable (genetic dead end)
what are germ line cells
Cells that become gametes are referred to as germ line cells
what are somatic cells
any biological cell forming the body of an organism, any cell other than a gamete, germ cell, gametocyte or undifferentiated stem cell.
name some origins of mutation
replication and repair errors
DNA damaging agents - mutagens
give examples of mutagens (DNA damaging agents)
by products of metabolism - ROS
ionizing radiation
UV light
DNA damage – repair =??
mutation
DNA repair works to lower what
net mutation rate
mutation rate increases with decreasing/increasing rate of repair
decreasing
mutation rate increases with decreasing/increasing DNA damage
increasing
describe what happens to DNA when exposed to UV light
exposure to UV light causes thymine dimers to form (covalent bonding between thymine bases) which lead to frameshift mutations. RNA polymerase can’t access the DNA to make mRNA
what is Xeroderma pigmentosum
a condition where thymine dimers cannot be repaired. it is caused by mutations in excision repair machinery causing extreme UV light sensitivity.
what happens when someone with Xeroderma pigmentosum is exposed to UV light
basal cell carcinoma
metastatic malignant melanoma
squamous cell carcinoma
what are induced mutations
mutations that are brought on by mutagens
can all mutagens damage DNA
yes
can all mutagens cause cancer
yes
what are the 4 categories of chemical mutagens
- base modifiers
- base analogues
- intercalating agents
- deaminating agents
what is a base modifier
a chemical mutagen that reacts directly with nucleotide bases altering their structure and causing point mutations
give an example of a base modifier
EMS
what are base analogues
chemical mutagens that have very similar structures to DNA bases and cause point mutations
give an example of a base analogue
5BU
what are intercalating agents
chemical mutagens that can insert themselves between successive bases in DNA which causes a frameshift mutation
give as example of an intercalating agent
arcidine dyes
what is a deaminating agent
they cause point mutations (substitutions) for example by converting cytosine to uracil.
give an example of a deaminating agent
nitrous acid
what are the 4 types of chromosome mutation
inversion
translocation
duplication
deletion
what are the 3 types of point mutation
insertion
deletion
substitution
most random mutations affect important/unimportant regions
unimportant - between genes, between exons
in which regions are mutations not silent
if they affect key functional residues (protein coding regions) or regulatory regions (gene expression/translation)
why are mutations usually silent
because exons take up such little space in the genome the mutations very rarely fall in them. most of the genome is empty space
what are the 3 possible consequences of point substitution mutations
missense
nonsense
silent
what are conservative mutations
when the amino acid produced after mutation has a very similar structure to the amino acid in the absence of the mutation (polar aa –> polar aa)
what are non conservative mutations
when the amino acid produced from the mutated area has a completely different structure to the amino acid in the absence of the mutation (polar aa –> non polar aa)
what is a point mutation
a mutation affecting only one base pair
what is a frameshift mutation
a mutation that causes a change in the reading frame (insertions and deletions)
what is a missense mutation
when a mutation causes a different amino acid to be made
what is a nonsense mutation
when a mutation causes an early stop codon so the resulting polypeptide chain is cut short and often results in a non functional protein
what do rare recessive mutations require to affect phenotype
inbreeding - in order to get a person who is homozygous - these mutations have high incidence in isolated communities
what are the 4 conditions caused by mutations in the albinism pathway
- albinism
- alkaptonuria
- cretinism
- phenylketonuria
what causes albinism
a mutant tyrosinase enzyme cannot convert tyrosine –> melanin so melanin is absent or in very little quantities
what are the symptoms of albinism
lack of melanin form skin, hair and eyes
what are the 4 oculocutaneous albinism genes
oca1
oca2
oca3
oca4
what do mutations in the oca1 gene result in
mutation in tyrosinase enzyme - severe albinism
what do mutations in the oca2 gene result in
mutation in P protein (tyrosinase helper) - mutants have mild albinism
what do mutations in the oca3 gene result in
mutation in tyrosine related gene - mutants have weak albinism
what do mutations in the oca4 gene result in
mutation in tyrosinase helper protein - mutants have mild albinism
mutations in which oca genes result in weak/mild albinism
oca2
oca3
oca4
which oca gene causes severe albinism
oca1
what is alkaptonuria an what causes it
recessive condition
sufferers have black urine
it is caused by a mutation on chromosome 3 which encodes mutant homogentisate 1,2 -dioxygenase which results in homogentisic acid (HA) NOT being converted to maleylacetoacetic acid. HA is expelled in the urine
what is phenylketonuria and what causes it
recessive condition
mutation causing enzyme phe hydroxylase being unable to convert phenylalanine to tyrosine.
high levels of phenylalanine leads to high levels of phenylpyruvic acid which leads to progressive brain dysfunction dues to it acting as a neurotoxin
treatment – low phenylalanine diet
what is cretinism
recessive condition
mutation causes tyrosine not to be converted into thyroxine which causes mental retardation
what happens to substrate and product levels when enzymes fail to function
substrate level builds up and there is a lack of product
which of the albinism pathway conditions is caused by lack of product
albinism
which of the albinism pathway conditions is caused by build up of substrate
alkaptonuria
phenylketonuria
cretinism
what is the genotype
the internally encoded inheritable information (the DNA)
what is the phenotype
the outward physical manifestation of the organism - anything that is an observable function, structure or behaviour
what is epigenetics
changes dues to gene expression rather than changes in genetic code
what affects phenotypes
gene products - proteins
what determines dominance/recessiveness
it is determine by how the pool of products (protein) of the 2 alleles functions in a heterozygote
most recessive/dominant mutations are GAIN OF FUNCTION
dominant - more of a normal function or gain of a new function
most recessive/dominant mutations are LOSS OF FUNCTION
recessive
what are null alleles
completely non functioning allele - no protein is produced
describe the yellow pigment in fruit flies
WT and heterozygotes convert yellow pigment to black
homozygous recessive mutants cannot convert pigment
why are most mutations recessive
it is easier to damage something than to make it work better or differently
how could a recessive condition be treated by gene therapy
by introducing a WT copy of the gene
how could a dominant condition be treated by gene therapy
inactivating the gene - stopping the new function
what is incomplete dominance
when the heterozygote has an intermediate phenotype
what are oncogenes
genes which transfer cells into tumour cells
give examples of conditions caused by autosomal recessive mutations
albinism
alkaptonuria
cretinism
phenylketonuria
give examples of conditions caused by autosomal dominant mutations
achondroplasia
Huntington’s disease
what is achondroplasia
the most common form of dwarfism caused by an autosomal dominant mutation
what causes achondroplasia
achondroplasia is caused by an autosomal dominant mutation. It is caused by one of 2 point mutations in the gene for the FGFR3 receptor which is a transmembrane protein kinase
what happens in achondroplasia sufferers by comparing sufferers and non sufferers
NORMAL
FGF is a signalling protein which binds to FGFR receptor
this causes phosphorylation by kinases which results in the molecules of the receptor coming together
this conformation of the receptor inhibits limb growth
ACHONDROPLASIA
We see phosphorylation and the molecules of the receptor coming together in the absence of the FGF signal
the mutant receptor is locked in a more active state so limbs do not grow normally
doe the achondroplasia mutation confer the same function as the wild type but more of it or does it result in a new function
the same function but more of it - in WT limb growth is inhibited, just not all the time
of those affected with achondroplasia, how many have a parent with achondroplasia
20%
80% of the achondroplasia mutations are generated in the parents germline as ……………………………….
de novo mutations
what are de novo mutations
from new mutations - arise during our lifetime - we all get approximately 200 de novo mutations
what do two heterozygous parents for achondroplasia give offspring in ratios of
normal and achondroplasia children in a 1:2 ratio. would be 1:3 but homozygous embryos for achondroplasia die in utero
from this we can infer that achondroplasia shows incomplete dominance since homozygous and heterozygous people show different phenotypes
give an example of an autosomal dominant condition that results in gain of new function
huntiinton’s disease
what does huntington’s disease cause
causes progressive neurodegeneration
- loss of limb control
does huntington’s disease show complete or incomplete dominance
complete
if huntington’s is a dominant lethal mutation then how is it present in the population
because it is late onset - doesn’t start till 30-50s
does the huntington’s phenotype skip generations
no - child of affected parent has 50% chance of being affected
what mutation causes huntington’s disease
it is caused by an autosomal dominant mutation in the HDD1 gene which encodes the huntingtin protein
the mutation is found in the glutamine triplet in DNA which causes the glutamine section to repeat (microsatellite), expanding the genome. the large polyglutamine tract formed is toxic in some neurons
what is ncRNA
non coding RNA that does not code for proteins but do code for other functional RNA
what 2 things do genes encode for (as well as all the other things it contains LINEs, LTRs etc)
mRNA which codes for proteins
ncRNA which codes for other functional RNA
what methods could we use to find a protein coding gene
proteomics - look for protein and work back to sequence on DNA
transcriptomics - look for mRNA and work back to sequence
look at DNA sequence directly - predict exons, ORF (open reading frame), start/stop codon - use homology
how to find an ncRNA gene
look for RNA using transcriptomics and work back to find gene sequence
look at sequence directly - predict exons and use homology
what percentage of RNA is coding and non coding
coding - 4%
non-coding - 96%
what are LINES
long interspersed nuclear elements
what are SINEs
short interspersed nuclear elements
what are transposons
DNA that can translocate
what are LTRs
long terminal repeats
what can indicate the function of a gene
where ii is expressed - organ
when it is expressed - age
inactivate the gene - knockout, CRISPR, RNAi tech
activate the gene - over expression
find mutations in the population and study them
study other genomes and look for homology
what are taste receptors
proteins found on the cell surface of the tongue, lungs and gut and affect taste perception
what genomes is the human genome closely related to which can be tested ethically? (model organisms)
mouse fly worm yeast e.coli
what are orthologs
genes in different species that evolved from a common ancestral gene and normally retain the same function. they can be used to infer roles in other species where iit is not ethical to study them
what are paralogs
genes resulting from gene duplications, probably with diverged role or function
the more closely related species are, the more genes are .…………….. and may have similar/identical roles
conserved
in distantly related species less of the genome is …………….and may have similar/related roles
conserved
provide the percentage of orthologs of human diseases in mice, flies, worms, yeast
mice - 90%
fly - 70-80%
worm - 60-70%
yeast - 30-40%
human CDK1/yeast cdc2 homology spiel
47% identity in protein sequence between yeast and human gene. a pair of genes that have very similar sequences and the same function.
define co-dominance
contributions from both homozygous parents are present in the offspring phenotype e.g. red and white spot flowers
ancestor calculation
look in notes
if there is a new generation every 25 years, how many ancestors does one have after 500 years
2^20
if there is a new generation every 25 years, how many ancestors does one have after 1000 years
2^40
what is a polymorphism
common genetic differences between people
what percentage of identity do humans generally show at sequence level
99.5%
what is a microsatellite
repeating sequence of DNA that is 2-6bp long with 5-200 repeats - huntington’s
what is a minisatellite
repeating sequences of DNA that are 10-100bp long with 10-1500 repeats
provide a practical application for microsatellites
DNA fingerprinting
provide a practical application for minisatellites
paternity testing because they occur in family groups
what are indels
insertions and deletions in the genome which can vary in size
how can indels have an effect on proteins
they can result in frameshift mutations if they occur in the ORF of a protein coding gene
apart from proteins what other parts of the genome are effected by indels
ncRNA and regulatory regions
why are most indels silent
because they occur outside the coding region
what are CNVs
copy number variants - they are chromosomal deletions or duplications that involve large stretches of DNA which can span many genes
are CNVs inherited or de novo
they can be both
how long ar CNVs
500- 1 million bp long
why don’t all CNVs have an effect
they often occur in unimportant parts of the genome so are silent but they can have drastic effects if the sections duplicated or deleted involve important genes
what are SNPs
single nucleotide polymorphism -a substitution of a single nucleotide that occurs at a specific position in the genome where each variation is present to some appreciable degree within a population e.g. >1%
what % of the population have rare SNPs
between 1 and 4.9%
what % of the population have common SNPs
5% allele frequency or more
if SNPs occur in the OFR what are the 3 possible outcomes
missense - different amino acid
nonsense - early stop codon
silent - same amino acid
can SNPs affect ncRNA
yes if they occur in those regions
can SNPs affect regulatory regions of the genome
yes, if they occur there
what is the affect of most SNPs
silent or they occur outside of genes
every how many bp does a common SNP occur
every 100bp approximately - common variant among the population
do many SNPs have an effect
no most are silent but those within a gene or regulatory region can have a role in disease by affecting a gene’s function
what are point mutation
mutations that only affect a single base - insertion, deletion, substitution
what is a private point mutation
a de novo mutation - we each get around 200 of these
what is the frequency of a fairly common point mutation
allele frequency is less than 1% - variant
what is the allele frequency of a very common point mutation
allele frequency greater then 1% - polymorphism
most SNPs only have two alleles but for a single SNP there can be up too 4 different alleles, why is this
because there are only options of A, T, C, G
how can eye colour have more than 4 colours if there are only 4 bases for a polymorphism
eye colour involves interactions between more than one gene so there are a greater number of polymorphism combinations
how do you calculate allele frequency
no. allele of interest/total no. alleles
if we have a two allele system what equation can we use to describe their frequency
p+q=1 where p and q are the frequencies of allele one and two respectively
what is evolution
the change in allele frequency of a gene pool over time
why are most new mutations lost in the gene pool
they are either detrimental or cause no advantage - soo the organisms either dies or does not pass on the mutation to offspring
what is the hardy Weinberg equilibrium
the equilibrium predicts that the allele and genotype frequencies in a population will remain constant from one generation to the next - there is no evolution
p^2 +2pq +p^2=1
if the equation equals 1 then the population is in hardy Weinberg
when is a population considered to be in hardy Weinberg equilibrium
when the observed genotype frequencies equal the expected genotype frequencies
Are most SNPs in hardy Weinberg
yes they are, there is no evolution because there is no change in frequency
what are the 5 conditions for a population to be in hardy Weinberg equilibrium
- random mating
- large population
- no change in allelic frequency due to mutation
- no immigration or emigration (no gene flow)
- no natural selection
what are the differences in the TAS2R38 taste receptor caused by
SNPs - there are 3 SNPs that are strongly linked
what is epistasis
interaction of genes that are not alleles, in particular the suppression of the effect of one such gene by another
what is epigenetics
changes caused by gene expression
