Nutrigenomics Flashcards
t/f: RDA has a safety factor built in
true!
RDA is set _______ SD above the mean, meaning that it will meet needs of _____% of the population
1.2 Sd above mean population requirement–> meets 98%
what is the problem with a person eating at the RDA?
maybe eating too much?! could be quite a bit more than what they need to eat
main problem with RDA
not individualized! misses 2% of pop’n and not precise
3 factors that generally affect nutrient requirements
- physical characteristics(sex, life cycle stage, body size)
- lifestyle: PA, smoker?, urban v. rural, etc.
- genetics: gene–> nutrient metabolism
currently main dietetics “diagnostic tools” are what 2 things?
blood profiles and anthropometrics
________ allele determines lipid metabolism
apoE2
apoE2 allele is very responsive to what two lifestyle changes?
soluble fiber intake and physical activity
in the future, what other “diagnostic tool” is probably going to be used in dietetics?
genetic profile
3 genetics implications for dietetics
- tailor nutrient requirements according to genetic profile
- tailor diet therapy
- functional foods for certain genotypes
22 pairs of autosomes are numbered by _________ size
descending
the center of the chromosome is called what? what are the ends called?
centromere
telomeres
karyotype
and appearance of chromosomes in one cell
t/f: all human cells have 46 chromosomes
false! cancer cells often have more or less
the shorter portion of the chromosome off the centromere is labeled as ______, while the longer portion is designated as _______
p=shorter
q=longer
each “arm” of a chromosome is further divided into smaller sections designated by #s. the larger the #, the closer of further to the telomere?
closer!
in a cell, where is there extra nuclear DNA?
small part of genome in the mitochondria
genetics is the study of _________, which are what?
mutations-changes in genomic DNA
two types of mutations
- small scale: mutations in DNA sequence
2. large scale: changes in chromosomal structure, like deletion of a large portion of a chromosome
synonym for small-scale DNA mutation
DNA sequence variants
if a DNA variant is found on less than 1% of population, then it is called _____________, while if its on greater than 1% it is called ____________
mutation for less than 1%
polymorphism=greater than 1%
SNP
single nucleotide polymorphism (single base pair changed)
VNTR
variable number tandem repeats(copies of sequences is abnormal)
what is the “reference” sequence called?
wild-type
INDEL
insertion/deletion polymorphism(missing part of reference sequence)
SNPs are found often in how many versions?
two–> minor and major
minor allele frequency range
> 1%-50%
t/f: SNPs are frequent in the human genome
true! very frequently… at least 1 per every few hundred basepairs
in contrast to SNPs, VNTRs are highly _____________, meaning what?
polymorphic –> many known alleles(not just 2 like with SNPs)
a number of diseases have been implicated to be from VNTRs of how many base pairs?
3 basepair repeats
VNTRs are goof for _____________ studies, while SNPs are good for _____________ studies
VNTR=family-based linkage studies
SNPs=population based association studies(genome-wide associations)
3 major sources of variants (SIT)
- spontaneously: mistakes in replications
- induced: by chemicals or radiation that cause strand breaks
- transposable elements: ancient viruses that could “jump” in the genome
a spontaneous chem rxn can convert adenine to ___________. What are two things that can happen after this?
inosine–> repair mechanism back to adenine
unrepaired—> pairs with cytosine (AT base pair becomes IC base pair)
during DNA replication, an IC base pair will result in what two pairs? ultimate consequence?
I with C and C with G–> AT base pair became a CG base pair in offspring
ENU is a chemical that can react with guanine and adds a __________ to make ___________, which pairs with what?
methyl group–> ethyl guanine which pairs with thymine
what is the difference b/t a coding SNP and non-coding SNP?
coding: changes AA sequence of protein
non-coding: alters amt of protein formed
haplotype
set of SNPs(6-8) that tend to be inherited together
how many haplotypes are thought to occur throughout the population?
3-5
what is the catalog of common SNPs in humans?
HapMap!
epigenetics
changing phenotypes without changing genotype(affecting whether gene will be transcribed or not)
3 components of chromatin
- DNA
- histone proteins
- non-histone proteins
components of a nucleosome
146 base pairs (2 superhelical turns)+ core of 8 histones
____________ of the tail amino ends of histones is thought to play a key role in expression of genes because histones do what?
acetylation of histones b/c histones regulate shape and conformation of DNA
2 enzymes involved in histone acetylation
HAT(histone acetyl transferase)
HDAC(histone deactylase)
acetylation by HAT causes what to happen to DNA?
causes to uncoil from histones and is accessible for transcription
function of HDAC
deactylases the histones, causing DNA to coil and become unaccessible for transcription
1 method to modify DNA
methylation
3 methods to modify histones
- methylation
- acetylation
- biotinylation
some examples of changes in phenotype
longevity, resistance to disease, behavior, physical appearance, stress response!
methylation of what portion of the DNA affects transcription of exon?
the promotor region of the gene(Not exons themselves)
t/f: HAT and HDAC can be affected by diet
true!
cur cumin can reduce activity of _________, and reduce transcription of pro___________ genes
HAC–> fewer pro inflammatory chromatin
what other diet factor has been shown to reduce HAC activity?
calorie restriction
nutrigenomics v. nutrigenetics
nutrigenetics: how genes affect metabolism of nutrients(ex. gene makes absorption of certain nutrients lower)
nutrigenomics: how food + nutrients can affect phenotype(expression of genes)
Vitamin ______________ binds to RARC on gene is an example of nutrigenomics
A retinol(but not epigenetic!)
genomics
studying the gene sequences and variations in genetic material
transcriptonomics
studying how much mRNA of each type there are
proteinonomics
how much of each type of protein is expressed in each cell
metabolonomics
study of how much of reaction intermediates there are, which can affect how body handles nutrients and health
in order to do genetic testing, we can sample what two things?
WBC(but a pain); cheek swab inside… both can extract DNA
PCR stands for what?
polymerase chain rxn
what is a PCR used for?
amplifying # of copies of specific region of DNA in order to produce enough DNA to be adequately tested
t/f: there can be a DNA variant between paired chromosomes
true!
how many alleles (except last set for me) does a person have?
two for each gene
difference b/t DNA sequencing and genotyping
DNA sequencing: looking for new DNA variants
genotyping: identifying what variant a person has based on already known variants
most routine DNA sequencing has what two steps?
- PCR: amplify # of copies of gene
2. Sanger sequencing
what is the beginning of a sequence labeled as? end?
5’–> 3’
what is the relationship b/t the 2 DNA strands called/
reverse complementarity
you need to add 2 _______________s at the beginning of the PCR procedure to define what regions to amplify
2 PCR primers around each exon desired to amplify
1st step of PCR is _____________, attained by applying ___________, which breaks ___________
denaturation—> apply heat which breaks H bonds b/t DNA base pairs
2nd step of PCR is _____________ at a lower temp, allowing H bonds to form between __________s and DNA
annealing b/t primers and DNA strands(one for each)
3rd step of PCR is ____________ that adds nucleotides to the _____ end of the strand
elongation by DNA polymerase to 3’ end
the # of DNA molecules ___________ in each round of PCR
doubles
elongation during Sanger sequencing by a primer + polymerase will be terminated when a ________ is added. why?
ddNTP–> dideoxy so cannot attach another phosphate
products of electrophoresis will be separated by ____________ because why? how does this help genome sequencing?
separated by size b/c smaller strands will move through electrified capillary tube faster–> laser will read fluoresecently colored peaks, giving the sequence of nitrogenous bases
what if there are two color peaks in the same position in an electropherogram?
means ind. is heterozygous for that gene…
exome
all protein coding genes in a genome(about 1% of total genome)
what does “alignment” mean in DNA testing?
during whole exome testing, exome is compared to reference sequences from human genome project… if differences, may indicate DNA variants
most DNA variants known to be responsible for disease are found in ___________ sequences
coding
t/f: we can determine if a non-coding sequence will have a functional effect
false(at least right now)
if known DNA variants already exist and are defined, is PCR needed?
nope! just genotyping of that particular region
what is the biggest benefit of genotyping?
much much cheaper than whole-genome or whole-exome sequencing
GWAS stands for what?
genome wide associated studies that look for genetic variation across the entire genome(huge amount of SNPs)
what are two concerns about genetic testing?
- privacy: info used v. person like employer/health care company
- health care delivery: who pays? who should get tested? which discipline should take charge/counsel patients? (genetic counselors? nutritionists?) will we create “worried well”?
gene with high __________ implies that person with that gene will likely get disease
penetrance
most autosomal dominant genes cause ________% penetrance for disease
100
___________ and _______________ of gene variant determines who should be tested
prevalence and effective prevention/txt
consumer centered model of genetic testing + problems
consumer contacted private testing labs(no involvement of clinician)
**problem: don’t understand penetrants, no follow-up
what are the other models for genetic testing?
health care practitioner model(clinician involved) esp with serious genetic issues
public health model
