systems to cells part 2 Flashcards
how could we go about finding a gene for a trait e.g. cystic fibrosis - what do we need to do this
we need:
- the trait segregating in large families
- the trait needs to behave as a mendelian, single gene trait
- genetic differences across the genome (SNPs)
when gene mapping what are the 3 milestones towards finding a single gene responsible for a trait
- phenotype
- small chromosomal region
- single gene
when you get down to a region of the chromosome in gene mapping how many genes are usually in the this region
usually around 50
what are mendels 2 laws
law of segregation
law of independent assortment
what is the law of segregation
alleles of a given locus separate into different gametes during meiosis
what is the law of independent assortment
when homologous pairs of chromosomes orient independently of each other at the metaphase plate of meiosis 1
probability of inheriting an allele at one locus is independent of inheriting an allele at a second locus
the allele a gamete receives from one gene doesn’t influence the allele received for another gene
if genes are close to each other, are we likely to get parental or recombinant genotypes in a dihybrid cross
more parental because the genes will have strong linkage
what is the difference between parental and recombinant genotypes
- a parental genotype is the same as one of the parents - a combination of alleles inherited from parents
- a recombinant genotype is different to both of the parent genotypes - a different combination of alleles than possessed by the parents
the .…….. is blind to what a gene is
spindle
how can pieces of the same chromosome segregate independently
we get homologous recombination (crossover) at meiosis 1
what is crossing over
crossing over generates gametes with recombinant genotypes
this enables alleles at different loci on the same chromosome to be re-associated
by creating new genotypes it creates genetic diversity in the population
give 2 characteristics about crossing over sites on chromosomes
they are fairly randomly distributed
they occur 1-2 times per chromosome in each meiosis
the further away genes are on a chromosome, the greater/lower the probability of crossing over
greater
what is the recombination frequency
the measure of the distance between 2 genes
how do we calculate recombination frequency
no. recombinants/ total no. chromosomes or total offspring
if we have independently segregating genes what is our RF value likely to be
RF=50%
no. parental = no. recombinants
what happens to recombination frequency as genes get closer together on the same chromosome
the recombination frequency decreases RF = <50% and the parental dominate
when mendel was studying peas he looked at dihybrid crosses where the genes of interest were very close/far
far apart - saw recombination
if our RF <5% what does this tell us about the genes
they must be linked on the same chromosome
we see linkage is genes are between ………… of the genome
1.6%
1% recombination = 1 ??
centi morgan (cm)
genetic distance = ???
physical distance
1 centi morgan = …. bp
1 million
1 million bp = …… genes
6
what is the maximum observaleb RF
50% = 50cm
1.6% genome = ……. bp
50 million
define linkage
when alleles of nearby loci tend to be inherited together
what is a haplotype
a chromosome
we inherit one chromosome from each parent each with a different combination of ………..
alleles/polymorphisms
crossing over generates new haplotypes but blocks of ……..… remain
old ones
describe the inheritance of a causative allele (allele that causes a trait)
- lots of SNPs will be located around the causative allele
- recombination will occur and some of these SNPs will be lost
- the SNPs very close to the causative allele will be inherited by descendants due to linkage
- the chromosome is passed on containing the causative mutation and the tightly linked SNPs
- these SNPs will feature in every person with the causative allele
- using this knowledge we can try to determine where a causative locus is - if we know where SNPs are located we can estimate where the disease locus is likely to be
what is the only chromosome that never recombines
y chromosome
how can you be a descendant of someone and not be related to them
parts of haplotypes are lost during recombination so you may no longer share common sequence
how many SNPs does one person have
> 10,000
genetic linkage results in random/non-random segregation
non-random
……. are generally linked to a trait locus and all those with the trait will have the same ones
SNPs
why has most genetic analysis so far been on traits like cystic fibrosis
it is caused by a single gene
large effect size - if you have the allele you have the trait
little to no environmental effect
runs in families in clear mendelian patters/ratios
we can find a gene that explains all the variability
give examples of 2 traits that are not inherited in clear mendelian pattern
- complex trait like diabetes, depression etc
- quantitative traits like height etc
why do some trait not follow simple mendelian patterns
there could be multiple genes involved
there could be no genetic basis
if genes are involved they may only affect the risk of developing the trait, it is not necessarily pre-determined
environmental factors can also have a role
what is heritability
the contribution of genetics to a trait under current conditions
what is grave’s disease
an autoimmune disorder that leads to hyperthyroidism (overactivity of the thyroid)
why are identical twins good for studying genetics
because they have the same genetics and they are generally exposed to the same environment unless separated
when looking at the heritability of a trait we need to separate the genes from the environment - how can we do this with twins
identical twins - same genes, same environment
fraternal twins - different genes. same environment
heritability = identical twin trait probability id the other has it - fraternal twin probability of trait if other has it x2
for huntington’s disease what is the probability that if one twin is affected the other will be too and what is the estimate of heritability
identical twins - 100%
fraternal twins - 50%
estimate of heritability 100-50 x2 = 100%
what would be better than looking at fraternal twins but isn’t necessarily ethical
separating identical twins at birth - they would have same genes but different environment
what does 40% heritability mean
for a population:
- 40% of the risk is attributable to genetics
- 60% of the risk is non-genetic
what is a gwas
a genome-wide association study (GWAS) is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait.
GWASs typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major human diseases, but can equally be applied to any other genetic variants and any other organisms.
used to identify loci contributing to complex traits
when doing a gwas do we sample a population or a family
population - they can look at >100,00 0 people
……. can be used to test for association with disease alleles
SNPs
if SNPs are not associated in the population what do we see
the state of one SNP does not influence the state of the other - the SNPs are not associated in the population - the SNPs are very far apart
if SNPs area associated in the population what do we see
the 2 SNPs are very close together and the state of one SNP influences the other - they are in a common haplotype block in the population
if two SNPs are linked and the state of one SNP confers disease what do we see
because there is linkage we will see a higher frequency of the linked SNP in those with the disease SNP - the other SNP behaves as though it is genetically linked to the pre-disposing SNP
we can find loci contributing to complex risks even if multiple genes contribute. each genes contributes a …. ……. and so we need …………. numbers
small risk huge
what are association statistics important for
determining if a SNP is linked to an allele
what is the method of association analysis
- collect large population sample
- separate into trait and no trait groups taking care to match the groups for other features that have a genetic component e.g. age, sex, ethnicity
- genotype 100,000 SNPs in each person
- check the population is in hardy Weinberg equilibrium
- determine if the allele frequency of each SNP is different between groups
- if there is a difference, check to see if it is statistically significant
do practice calculations
khan academy
how can we determine is there is a significant difference between allele frequencies
chi squared test - if there is a significant difference then the more frequent allele in the trait group is associated with the trait
analysing SNPs for association is very prone to what and what extra measure do we take to avoid these
multiple testing and false positives
p value threshold is lowered to p<5x10-8 - decreases the chance of a false positive
why were many early gwas prone to false positives
because there were too few people in the study and the stats were less well understood so the p-value threshold was higher
groups were also not well matched for other features that have a genetic components
why were early gwas also prone to finding nothing
too few participants in studies meant only SNPs associated with large effects could be found
a SNP on which gene is associated with autism
CDH10 - this could shed light on the development of autism and possible therapies
where were the most highly associated SNPs for autism found
between CDH9 and CDH10
how can SNP gwas results be effectively displayed
in manhattan plots - the number of dots highlight the strength of the association and the position on the chromosome is also shown
what are the hallmarks of diabetes
fat distribution, obesity, hepatic lipid metabolism –> insulin resistance –> hyperglycaemia
autoimmune B cell dysfunction, low insulin synthesis, low insulin secretion –> insulin deficiency –> hyperglycaemia
what are the 3 variations of diabetes
T1D, T2D, MODY
T1D and MODY are normally diagnosed in …….. people whereas T2D is normally diagnosed in ……….. people
younger
older
what does MODY stand for and what is it
monogenic onset diabetes in the young
it is a very rare mendelian trait and often misdiagnosed as T1D or T2D
there are multiple versions with a different mutated gene in each
the two most common mutations affect GCK and HNF1A
what does GCK encode and what does the MODY mutation cause
glucokinase which is responsible for catalysing the first step in glycolysis (glucose –> glucose-6-phosphate)
the mutation is recessive showing loss of function
glucose becomes trapped in cells as it is still being taken up but not being metabolised in glycolysis
what does HNF1A encode and what dies the MODY mutation cause
a transcription factor that drives expression of certain genes in the endoderm, including GLUT1 and 2
the mutation is recessive showing strong loss of function
what % of diabetes cases does T1D account for and what % of the population does it affect
10% of cases
0.5% of the population
what is T1D
an autoimmune disease that destroys the pancreatic B cells
the immune system destroys pancreatic B cells due to expression of insulin as self antigen
what has genetic testing of t1D involved
looking at candidate genes chosen based on biology
gwas to search for risk loci
several gwas wee carried out - the HLA (human leukocyte antigen) region was implicated early. this encodes the major histocompatibility complex which regulates the immune system
the structure of the binding cleft of HLA DBQ1 determines what antigenic peptides are bound and presented to the immune system
insulin is presented and seen as non self
T1D is the only organ specific autoimmune disease not to show a strong ……… bias
sex - most autoimmune diseases are more common in females
what does T1D therapy involve
injections of recombinant human insulin
describe the heritability of T1D
the probability of a twin having the disease if the other has it is:
- identical - 20-40%
- fraternal - 6%
it has been found that there are ……………….. risks that are the same for multiple autoimmune diseases
pre-disposable
why is early diagnosis of T1D difficult
because clinical signs are only evident after development of the disease
how could we improve early diagnosis of T1D
genotyping could identify high risk children 2-5yrs before development of T1D
are there environmental factors for T1D
yes
it is thought that an …………… infection early in life could lead to multiple immune challenges which could cause T1D
enterovirus
what % of diabetes cases does T2D account for and what % of the population does it affect
90%
6% of the population
one of the biggest health problems globally
describe the heritability of T2D
the probability of a twin having the disease if the other has it is:
- identical - 70%
- fraternal - 20-30%
there is some extent of heritability but this extent is unclear because there are also definite environmental factors
what is the biggest risk factor for T2D
obesity
how may T2D genes affect behaviour
may affect food intake, fat accumulation, metabolism, BMI, glycaemic traits, liver processes, B cell responses/survival
how much of the T2D risk has been explained using gwas
6% - the identified risk alleles feed into the same endophenotypes which are found in several different metabolic diseases e.g. B cell dysfunction, fat distribution, hepatic fluid metabolism and increased adiposity
what is the strongest risk variant of T2D
the TCF7L2 gene which encode a transcription factor and acts in pancreatic B cells
where are the majority of T2D risk variants found and what does this mean
ncRNA - the current idea is that these are regulating sites e.g. TF binding sites, meaning T2D would be a regulatory disorder
what is the odds ratio
the odds for carriers of risk alleles divided by the odds of non-carriers of risk alleles
look at odds ratio calcs
notes and khan academy
what does an odds ratio of one mean
the allele has no affect on the probability of having the disease
what does the odds ratio supply
the relative risk - this can be misleading
what can be more informative than relative risk
absolute risk/incidence frequency
risk = cases/total
do most T2D carry the TCF7L2 risk allele
no
what environmental factors increase T2D risk
movement to a higher calorie diet
westernised lifestyle
movement of native populations to urban settings
what is the polygenic risk score
it considers the population of variants together to look at individual people
it gives a percentile score which relates to relative risk of disease
it can be used to give preventative measures to those of high risk, however, for T2D this would be a lifestyle change and a PRS is generally not enough to motivate people
is PRS reliable
not it is not very accurate or reliable so it is more effective when combined with tests for other factors
this has been effective for stroke and heart disease but PRS doesn’t enhance predictive risk of T2D
is T2D predestined by genes alone
no
it is part heritable part non-genetic
can heritability change with the environment
yes
how many genes have alleles that contribute to T2D risk
100s if not 1000s
what is the new theory for T2D risk
omni-genetic - whole genome contribution - not a single part
what causes the mortality associated with diabetes, the disease itself or the associated conditions
the associated conditions
what is diabetes now classified as
a global epidemic due to the increase in prevalence of T2D
what conditions has diabetes caused increased mortality and morbidity in
- CVD
- PVD - peripheral vascular diseases - narrowing of the blood vessels that carry blood to leg and arm muscles the most common cause of which is atherosclerosis
- renal dysfunction - poor kidney function that may be due to reduced kidney perfusion which can be caused by high blood pressure
- neural dysfunction - loss of feeling in limbs
- blindness - caused by high blood glucose concentration around the retina
- vascular endothelial dysfunction - problems with blood vessels that supply our essential organs
what is atherosclerosis
build up pf plaque inside the artery walls, reducing the flow of blood to the tissues resulting in reduced nutrient and oxygen transport
what modifiable factor can prevent or delay the onset of diabetes
physical activity - an type of activity increases ATP use - increasing intensity drives fat burning
unfortunately most diabetics are physically inactive
barriers to exercise need to be reduced
why does exercise help with diabetes
hyperglycaemia results in - glucose toxicity - vascular endothelial dysfunction exercise results in - increased ATP consumption - substrate utilisation switches to carbohydrate with increasing intensity
what is thought to be a barrier to exercise compliance
people lack time, access and interest
prescription of exercise modality, intensity and duration
we need to find ways to allow people to engage with physical activity and make it easily accessible
T2D is characterised by reduced insulin sensitivity what are the acute and chronic responses of exercise
acute - hyperglycaemia --> euglycaemia (normal blood glucose) - improved insulin sensitivity chronic - blood glucose control
at rest and postprandially, glucose transport into muscle is via …… which is modulated by …………. being released, allowing transport of glucose into cells. this is the insulin dependent/independent effect
GLUT4
insulin
dependent
what is insulin independent glucose uptake
muscle contraction can modulate GLUT4
how is muscle contraction of benefit for T1D and T2D
muscle contraction can modulate GLUT4 uptake to muscle cells and the effect lasts for hours
what lasts longer muscle contraction uptake of GLUT4 or insulin dependent uptake
insulin dependent effect last longer than the muscle contraction (insulin independent effect)
other than insulin injection what is the only other glycaemic control that T1D get
muscle contraction
what are the effects of moderate intensity aerobic exercise on diabetics
during exercise, unlike healthy individuals where liver glucose production is matched peripheral glucose uptake, diabetics use more than is produced, reducing blood sugar during exercise
the effect last between 24-72 hours
what are the effects of high intensity exercise on diabetics
high intensity exercise can cause hyperglycaemia due to catecholamine induced glycogen breakdown
the effect last 1-2 hours
may be sensitive to duration of intensity exercises
how does resistance exercise affect diabetics
little of no data available on single bouts of resistance in diabetes
benefits have been shown in pre-diabetes (blood glucose elevated during fasting)
it can lower blood glucose for up to 24 hours and it responds to both volume and intensity
what are the current exercise recommendations
150 min per week
- moderate aerobic activity 2-3 times per week - has metabolic impact for up to 72 hours
- resistance exercise - metabolic impact for up to 24 hours
- increased muscle mass/strength for enhanced insulin independent affect
what is a novel strategy to help those where time is an issue exercise
HIIT - high intensity interval training - might have the same effect as longer duration moderate intensity activity
exercise isn’t enough, its all about energy balance what is meant by this
the balance between food intake and basal metabolism, thermic of food, physical activity, thermogenesis
what is basal metabolisms
energy required at rest by endothermic animals
what is the thermic effect of food
a reference to the increase in metabolic rate that occurs after ingestion of food
what is physical activity
an body movement that works muscles and requires more energy than resting
what is thermogenesis
the process of heat production -energy loss by heat production
what we eat is important as well - what substrate is favoured at rest ATP generation
fatty acids
high …………. content foods increase blood glucose and should be avoided
carbohydrate
apart from the amount of carbohydrates in our food what else do we need to consider about them
type (amylose (straight chain) vs. amylopectin (branched)) - amylopectin more easily digested than amylose
preparation (cooking time or method) - frying is bad
processed vs fresh
- trans fatty acids are found in energy dense foods
- processed foods with long shelf lives are hard to break down
a low carbohydrate diet is ineffective without ……… restriction to maintain energy balance
calorie
define concomitant
naturally accompanying or associated with
what are the concomitant conditions associated with obesity
- hyperlipidaemia - elevated levels of lipids/lipoproteins in blood - can lead to endothelial dysfunction and atherosclerosis
- hypertension - increased blood pressure
- cancer
- orthopaedic issues - bones and muscles
- asthma - respiratory condition marked by spasms in the bronchi causing breathing difficulties
give examples of some nutritional supplements and their effects
caffeine, ketone bodies, green tea - can be consumed as part of healthy diet - some people take them as weight loss pills but this is dangerous and generally doesn’t work
other than supplements what other things are used for weight loss
synthetic amines and neoprene belts
