Theme 3 & 4 Applied Lectures Flashcards
lactose
- a sugar common in milk and other dairy products
- can serve as primary energy source
- composed of glucose and galactose
lactase
a beta-galactosidase
hydrolyzes lactose to the monosaccharides glucose and galactose
- present on absorptive enterocyte cells in microvilli
what has to happen for galactose to be broken down and used?
it has to be converted into glucose through an enzyme pathway involving galactokinase, gal-1-P uridyltransferase and UDP-gal epimerase
lactase production by the body throughout the life of a person
- production decreases significantly after weaning
- 65% of humans have decreased ability to digest lactose after weaning
mutations that keep the lactase gene permanently on
- those whose ancestors domesticated cattle for dairy (N. Africa, Middle East and on to Europe)
- random mutations in MCM6 regulatory gene enhances LCT transcription (recruits transcription factors for lactase transcription)
- more in pastoralist populations, less is non-pastoralist populations in the above mentioned areas
lactase non-persistance
most people w lactase non-persistance retain some lactase activity and can include varying amounts of lactose in their diet w/o any problems
lactose intolerance
individuals BORN with the inability to express the lactase gene that codes for the lactase proteins = a congenital lactase deficiency
- results: people will have little to no lactase in their SI and bacteria in LI try to break down lactose (ferment, producing gas, bloating) preventing water from being reabsorbed (diarrhea)
congenital lactase deficiency
in normal people, LCT gene on chromosome 2 codes for the lactase enzyme
- LCT gene mutations in coding region of gene cause congenital lactase deficiency
- mutations/changes often result in production of polypeptides that are too short
galactosemia
= galactose in the blood
- individuals that are born without enzymes needed for galactose processing
- caused by mutations in GALT, GALE and GALK1 genes on chromosomes 9 which result in altered AAs or proteins that are too short
results: toxic accumulation of galactose which can lead to organ and tissue damage (for tissues that depend on glucose)
type I galactosemia
a problem w gal-1-P uridyltransferase resulting in galactosemia
type II galactosemia
a problem w galactokinase resulting in galactosemia
type III galactosemia
a problem w UDP-gal epimerase resulting in galactosemia
galactosemia symptoms
- jaundice caused by inappropriate secretion of bile
- enlarged liver
- kidney damage
- should do DNA test to determine if lactose intolerance or galactosemia
treatment for lactose intolerance
- avoid consuming lactose
- pre treated milk with purified lactase to break glucose into galactose
treatment for galactosemia
- omitting galactose consumption in diet
- more serious due to long term, permanent damage
Elie Metchnikoff
developed the original hypothesis for bacteria
- milk fermented w lactic acid was able to inhibit growth of certain bacteria in intestines (by lowering pH of intestinal env’t)
- observed populations in rural Europle that lived on fermented milk were expectionally long lived
- theory: consuming fermented milk might feed lactic-acid bacteria and suppress growth of harmful bacteria
microbes and diary products
fermentation is required to produce many dairy products: a result of lactic acid bacteria that consume carbohydrates in milk (break down the lactose into glucose and galactose, producing lactic acid as a product)
- the acid precipitates in milk and can hinder growth of harmful bacteria
microbial B-galactosidase
- present in food forms active form in duodenum, a study involving fecal samples, maybe presence of beta-galactosidase enhances lactose absorption in lactase deficient individuals
the effect of pH on beta-galactosidase activity
low pH environment decreases enzyme activity in duodenum, but B-galactosidase can still survive in pH of 4
- also consuming yogurt itself increases pH of stomach bc of its buffering capacity
probiotics and lactose intolerance
- microorganisms assoc w beneficial effects to humans often found in fermented milk products and OTC freeze dried bacteria (lactobascillus and bifidobacterium are most common)
- helps modify microbiome of colon: people are able to ingest lactose w/o symptoms
epigenetics
changing gene expression without changing the genetic sequence (changes by covalent changes to the molecule)
= “above the genome”
how are signals detected by cells
the env’t influences what genes are expressed
- signal received by cell
- receptors on target cell bind signal
- a simple transduction cascade can lead to short or long term responses in the target cell
short term vs long term responses
short term: modify immediate processes (metabolic)
- can include post translational protein modifications
long term: modifications of gene expression and/or development
methyl donors
any molecules that can give up a methyl group, often obtained through diet
epigenome
altered genome that can happen above the genome, which causes gene expression to change
- chemical genome modifications that occur along the genome that change gene activity without altering the DNA sequence
epigenetic mechanisms
essential for normal dev’t, cell differentiation and involved in human diseases
- modifications of histone tails
- DNA methylation
- chromatin remodelling
- packaging of DNA around nucleosomes
epigenomics
studying the epigenetic modifications across and individuals entire genome
factors affecting epigenetic mechanisms
- age
- diet
- drugs/pharmaceuticals
- development
- environmental chemicals
abnormal epigenomes of cancer cells
- cancer cells can have lower levels of methylation: can increase expression of genes that promote cell growth
- can also have higher levels of methylation: can decrease expression of genes needed to keep growth or repair of DNA in check or initiate programmed cell death due to damaged DNA
Agouti gene in mice
2 mice can be genetically identical but one is yellow and obese and the other is brown:
- Agouti gene codes for protein that signals for melanocytes to switch from producing black to yellow pigment
- when the gene is expressed, it is paired with genes that regulate metabolism etc so mouse is obese; also modifications of CpG islands
gene regulation in Agouti mice
- normal mice (brown) are healthy and agouti genes are kept off due to DNA methylation
- yellow obese mice: agouti genes are not methylated and leads to yellow colour since genes are kept on and other genes are under methylated, the mice develop tumours; mice are also predisposed to cancer and diabetes
- methyl sources are diet derived
supplementing methyl groups to pregnant yellow agouti mouse
in a pregnant mouse where agouti gene is active:
- supplementation of methyl groups produces more brown and healthy mice where the agouti gene is silenced
- when not supplemented, agouti gene is mostly expressed and mice are yellow, unhealthy
- can have blends of brown and yellow mice resulting in mottled mice depending on the amount of maternal methyl supplementation from food
sources of methyl donors
vitamin B12, choline, folic acid
are identical twins really identical
when twins are young, they experience similar things, but as they grow up are are exposed to different environments, they can end up with different characteristics
ex. smoking = heavier set eyes, more wrinkles, frown lines
comparison of DNA methylation in identical twins as they age
chromosomal mapping reveals differential methylation in twins
- 3yo twins show similar methylation
- 50 yo twins show abundant changes in methylation (regions of over and under methylation)
- they showed 4x as many differentially expressed genes
- older twins also show differences in histone acetylation
- they showed 4x as many differentially expressed genes
factors influencing our epigenome
changing lifestyles conditions: dietary, exercise, exposure to toxins (smoking etc)
epigenetic drift
failure to transmit epigenetic info through successive cell divisions or maintaining them in differentiated cells
- internal factors accumulate with aging
Canadian Longitudinal Study on Aging
Dr. Parminder Raina
- measures epigenetic markers in a large cohort of 50,000 Canadians
- microarray approach to measure epigenome of subjects over time
Human Epigenome Project
international research connecting epigenetics to disease
- there is a link between expression of HDAC (histone deacetylases) and cancer (HDAC inhibitors would suppress tumour genes, could prevent cancer cells from turning on the cells that the want)
the laser beam experiment
- used fluorescent labels to make metaphase chromosomes blue and microtubules yellow
- at the start of anaphase, photobleached a section of the microtubules to mark them
- predicted that bleached region would disappear once the chromosomes began to move
however, photobleached section remained visible - concludes that microtubules shorted at kinetochore end
how do microtubules move chromosomes during mitosis?
as the chromosome tracks over the spindle fiber, it breaks down the spindle fiber into tubulin subunits from the plus end to the minus end
Johnson and Rao Experiments
tries to find
Johnson and Rao Experiments
tries to find where chemicals that regulate the cell cycle are found
- cell fusion of an M phase and interphase cell
prediction: interphase cell will enter M phase
results: chromosomes of interphase cell condense, signalling the start of M phase
conclusion: M phase cytoplasm contains a regulatory molecule that induces M phase in interphase cells - a heterocarbon was produced when the 2 cells fused together
- these experiments were not run for a long duration
Markert and Masui Experiments
tries to find where chemicals that regulate the cell cycle are found
- micro injection of cytoplasm of M-phase cell and interphase cell into frog oocyte
Prediction: 1 or both oocytes will begin M phase
results: in cell injected w M phase cytoplasm, the oocyte began M phase recognized by early mitotic spindle dev’t
proteo onco genes
aren’t damaging to health until turned on
Ronald Lebby at Standford University
trying to use vaccines and drugs to treat cancer cells
- most chemo drugs don’t distinguish between regular cells and cancer cells, and infusing cells throughout the whole body to prevent cancer cells from migrating to other parts of the body
shape of cancer cells compared to normal cells
- large and variably shaped nuclei
- many dividing cells, disorganized arrangement
- variation in size and shape
- loss of normal features
characteristics of normal cell division
normal cells exhibit:
- anchorage dependance
- density-dependant inhibition
anchorage dependance
normal cells anchor to dish surfaces and divide, remaining in the confines of the dish
density-dependent inhibition
normal cells stop dividing when they have formed a complete single layer
- if some cells are scraped away, remaining cells divide to fill the gap and then stop once they contact one another
characteristics of cancer cell division
cancer cells continue dividing beyond a single layer, forming a clump of overlapping cells
- they do not exhibit anchorage dependance or density-dependant inhibition
- they divide faster than normal cells
- uncontrolled cell division
- cell cycle is not regulated
- cell cycle checkpoints are disrupted
- can have extra chromosomes, some deleted
anti-tumor agents
combat growth of cancer cells
anti-microtubule agents
- Vincristine (from rosy periwinkle)
- Taxol (from Pacific Yew tree’s bark)
- – these plant fibers inhibit spindle fiber formation resulting in disruption of mitosis
Steve Jobs
- had a rare form of pancreatic cancer (not aggressive) and was hesitant to go through regular chemo
- had genome sequenced and identified section of genes associated with his rare cancer and allowed us to have microchip detection of cancer
- Pim 1 Biomarker for cancer research
- Afinitor drug
- Pancreatic cancer immunotherapy: immune T-cells manipulation to seek and destroy cancer cells which we are doing trials of right now at McMaster
liquid biopsy
early cancer detection method
MPF
mitotic promoting factor
- cyclin and CDK pushes cell into mitosis
the human genome project
- sequence was publised in Feb 2001 done by a collaboration of lots of labs
genomics
- the scientific field that sequences, interprets and compares whole genomes
- the genome is the complete DNA sequence
- provides a list of the genes present in an organism and their function
functional genomics
examines when those genes are expressed and how their products interact
scientists do not know the function of more than ___ genes in the human genome
don’t know the function of 1/3 of the genes
TUFs
many sequences are Transcripts of Unknown Function (TUFs) bc their role in the cell is unknown
- genes for microRNA are more common than previously thought
why do humans have so few genes
- a surprising observation because eukaryotes have such complex morphology and behaviour and do not to appear to have a large number of genes
- scientists expected that humans would have 100,000 genes, instead we have about 21,000 genes
- alternative splicing hypothesis proposes that eukaryotes do not require large amounts of distinct genes bc it creates different proteins from the same gene!
Dr. Tallulah Andrews
- completed her undergrad in Bioinformatics at Mac under Dr. Brian Golding and Dr. Dushoff
- both look at big data that happens in bio and interpreting them in computer forms
- works at wellcome trust sanger institute and studies systems biology, genetics and bioinformatics
- research focuses on analysis of single-cell RNASeq data and putting that info into computers
Wellcome Sanger institute
in London, first noted for their studying of DNA sequencing
- study mutations in cancer cells
- has identified over 600 mutations in cancerous cells
applying genomics to understand cancer
- using our understanding of genomics to understand cancer
- can compare gene expression in normal vs cancerous cells and see why there might be overgrowth
- human genome proj has revealed common sets of genes that are mutated in cancerous cells where >120 mutations may be involved
Genome Canada
coordinates regional, national and international genome projects in canada and provides a lot of their funding since 2000
- many people want to have customized medicine (ex. Steve Jobs)
- looking at cancer from a cellular/molecular level and trying to find preventative measures
- explains how a person’s genetic makeup affects why he or she responds to pharmaceutical drugs (how one drug works for some and not for others)
Mike Stratton
head of Sanger institute
- when you’ve had cancer that’s a result of genetics, do you choose to have kids
- sequencing human genome of people with cancer looking for differences b/w cancer and normal cells and these differences are the mutations
