Genomics Exam 1

What is cloning?

An exact duplication of DNA

List the ways nucleic acids can be chemically mutated

-Methylation of bases -Deamination of bases (5-methylcytosine to thymine and usually goes uncorrected)

Define the term polycistronic

-Multiple genes, especially if needed expressed at the same time -To do this a SNP would be located in the promoter region

How many chromosomes are in humans?

-22 pairs of autosomes; one pair of sex chromosomes (X, Y) -23 pairs or 46 chromosomes in "normal" somatic human cells

What is p53 and why are mutations to this gene and protein correlated with a higher cancer rate?

-A DNA binding protein that recognizes DNA damage and signals to stop the cell cycle from entering S phase -P53 mutations permit cancer to grow and have resistance to chemotherapy and radiation

What is a gene?

-A DNA segment that contributes to a phenotype/function -Codes for an RNA product

Genomic Markers

-A measurable DNA and/or RNA characteristic that is an indicator of normal biologic processes, pathogenic processes, and/or response to therapeutic or other interventions -Can measure expression, function, regulation

What is PCR?

-A method to duplicate DNA in the test tube -Real time PCR: a method that used a fluorescent dye to indicate when enough DNA double helical copies have been made

What are multigene proteins?

-A protein that has multiple subunits from multiple genes -Hemoglobin has an alpha and a beta gene, plus a gamma gene expressed during development and a delta gene that upregulates at high altitude

Lynch Syndrome

-Also called hereditary non-polyposis colorectal cancer (HNPCC) -MLHL, MSH2, MSH6, PMS2, EPCAM

Explain how mutations to the Shine-Dalgarno sequence could affect expression?

-Can decrease protein synthesis for a gene -This would prevent the RNA from being translated into a protein

What is Favism?

-Caused by a glucose-6-phosphate dehydrogenase deficiency, which is a genetically inherited trait -Fava beans contain divicine which produces H2O2 which can cause hemolytic anemia in G6PD deficient individuals

How are genetic tests done?

-Clinical setting and home kits -Sample types of blood, saliva, cheek cells

Non-Small Cell Lung Cancer (NSCLC)

-Crizotinib: kinase inhibitor -Indicated when anaplastic lymphoma kinase (ALK) or ROS1-positive

What information is available with genetic testing?

-DNA sequence, amino acid sequence, SNPs, possible disease likelihoods, possible unique reactions to drugs -Can test stuff like lactose intolerance, caffeine consumption, sickle cell anemia, tay-sachs, Zellweger syndrome -Can search for variants in a patient's DNA

How do you get G6PDD?

-Defect of the enzyme glucose-6-phosphate dehydrogenase -X-linked recessive (mostly males get it from mother who was either carrier or had disorder, females only get it if their father had the disorder and their mother was at least a carrier) -Caused by a SNP in an exon

Clinical Pharmacogenomics

-Developing processes for: ordering, reporting, and interpreting pharmacogenomic tests -Testing can be preemptive (proactive) or reactive

What is the effect of consanguinity on recessive disorders?

-Doubled if parents are first cousins to about 3-5% -High increase with inbreeding

Biomarkers examples

-Examples: DNA sequence, gene expression -Specific biomarker: prostate specific antigen (PSA)

What is G6PDD?

-G6P is part of the oxidative phase of the pentose phosphate pathway -It produces 2 NADPH so if there is a G6PDD then we get no NADPH -NADPH is the essential molecule needed by the red blood cell that is only available to those cells from the pentose phosphate pathway

Autosomal dominant diseases

-Huntington's disease -marfan's disease

Variation is the rule

-Is the RULE not the exception -Essential for survival -Some are disadvantageous, some advantageous, some neutral

Mitochondrial disorders

-Leber's syndrome -leigh syndrome -mitochondrial myopathy

Cystic Fibrosis

-Mutation G551D in CFTR gene leads to impaired chloride channel function -Ivacaftor indicated for patients with CFTR G551D mutation

Why do mutations to signaling systems cause both metabolic concerns and vulnerability to cancers?

-PKA mutations: lead to altered expression -RAS: leads to cancer

What are histones? What are the subunits? What role do they play in the chromosome?

-Proteins that bind DNA -8 histone subunits in the histone core (H2A, H2B, H3, H4) and 1 holding the DNA to the histone core (H1) -This makes up the structure and composition of a chromosome

What is genetic anticipation?

-Severity of dominant mutations increases through generations -Ex: Huntington's disease

What is DNA fingerprinting?

-Southern blots are a way to look at only pieces of interest with DNA probe -Unique RFLP pattern for a specific DNA

Describe how to make a cDNA

-Take RNA from the cell and mRNA reflects sequence of gene without introns, only looking at exon portion of the gene (this is the cDNA) -Can define where in the chromosome we have the gene

What is the largest pharmacogenomics consideration a pharmacist must make?

-The difference between males and females -Estrogen not given to men, testosterone not given to women

Why would mutations in the mismatch repair (MMR) enzyme system be associated with higher cancer rates?

-The loss of MMR allows for a significant number of spontaneous mutation to go uncorrected. -A significant number of cancers are associated with mutations of enzymes in these pathways. -Specifically, nonpolyposis colorectal cancer is associated with mutations in these pathways

X-linked dominant diseases

-fragile X syndrome -rett syndrome

X-linked recessive diseases

-hemophilia -fabry disease -G6PPD -lesch-nyhan

Prader-Willi Syndrome

-mutation in proximal part of chromosome 15 coming from the father -due to no expression of gene 2

Angleman Syndrome

-mutation in proximal part of chromosome 15 coming from the mother -due to no expression of gene 1

Autosomal recessive diseases

-sickle cell -cystic fibrosis -tay-sachs

Y-linked dominant diseases

-wyer syndrome -Y chromosome infertility

In humans, how many chromosomes do we have?

23 pairs, 46 total, during S phase we have 92 chromosomes going into M phase and then separate into the daughter cells

Histone Core

8 histone proteins

What are microarrays

A chip that has DNA sequences covalently attached and can be used to evaluate which genes are expressed

How do the bases pair up in the double helix and how does the cell know when a mismatch takes place?

A:T (11 A) and C:G (10.8), other combos can hydrogen bond but the distance will be different and be recognized as incorrect

Pharmacogenomics

Defined as a field of research that studies how a person's genes affect how that person responds to medications

A nonsense mutation

AKA early termination mutation; caused by the creation of stop codon before completely reading the code for a protein

Hereditary breast cancer

BRCA1 and BRCA2

How is the DNA analyzed?

Break the cells open, cut up the DNA with specific endonucleases, type II restriction endonucleases are used for these techniques

What is the molecular basis of this disorder?

Change in AA creates problems and creates defects in enzymes

What are trisomys?

Change in chromosome number/size causes disability/disease

What is mtDNA?

Circular, commonly have more than one nearly identical DNA molecule, can divide inside of the cell, can merge together to make larger mitochondria

Ortholog (Orthologue)

separated by a speciation event; same protein in different species

How are chromosomes condensed, especially when that are inactive?

Coil up histones and make them into loops, fold the loops and creates thickness of chromosome, especially during meta phase prior to cell division when DNA is doubled in number

How mutations in histone, methylases, and acylases affect gene expression?

DNA is negatively charged, histones are positively charged. Methylation and acylations of histones neutralizes the charges on histones and regulates the release of DNA from those histones

Why does Favism cause hemolytic anemia?

Fava beans can interfere with the glutathione reaction which inhibits the ability to reduce and eliminate peroxides which reacts with the double bonds in the unsaturated fatty acid tails of the membranes, making the membranes rigid and easy to break causing hemolysis

Paralog (Paralogue) Examples

Heme containing proteins of cytochrome P450 and myoglobin

Ortholog (Orthologue) Examples

Human insulin and bovine insulin

Homolog (homologue)

Sequences or structures that are related to each other by descent from a common ancestral sequence or structure are homologues. All members of a gene family are homologues

Li-Fraumeni Syndrome (LFS)

Mutations in TP53 gene, CHEK2 gene

Why would mutations to introns affect protein synthesis?

Mutations in these sequences may lead to retention of large segments of intronic DNA by the mRNA, or to entire exons being spliced out of the mRNA. These changes could result in production of a nonfunctional protein.

How does X-inactivation affect symptom level in females?

Occurs very early in life, inactivation is random, wide implications for X-linked disorders

How do we know that DNA is the molecule that carries genetic information?

Phosphate containing molecule and not a sulfur containing molecule. Phosphorus is a permanent component of DNA, but only a transient component of Proteins. Sulfur is a permanent component of proteins but sulfur is not part of the structure of DNA

Which drugs should not be given to a patient that is G6PDD?

Primaquine

What is the "upstream region" of a gene?

Promoter/enhancer regions that can change expression and change concentration of protein product with no effect on the activity of the protein

Mutations in JAK2 (V617F)

Risk of essential thrombocytopenia

What are introns?

Sequencing of DNA that are not a part of our genetic code they are inserted between segments of exons, made up of DNA similar to viruses and must be removed to express proteins, some self-splice some need removed by snRNPs

What is alternate splicing?

Splicing genes to give more than one protein

How is genetic testing done?

Take a sample from blood or salvia

cDNA

complimentary DNA, made by reverse transcription of mRNA (mature) to create a cDNA library

GAA -- GAC

conservative missense mutation

Phylogeny

The evolutionary history of a molecule (such as a gene or a protein), or even a species and the relationship between such entities

TGA -- TGG

run on non-sense mutation

Explain how mutations to the upstream regions of a gene, or the associated proteins affect gene expression

The upstream regions contain the promoter and enhancer sites

How does mutations in topoisomerases, methylases, and acylases affect gene expression?

Topoisomerases are needed to unwind DNA

Biomarkers

Used as an indicator of a biological state

What are restriction endonucleases?

Used to chop up (restrict) foreign DNA

Point mutation

a change of one location

Conservative mutation

a change to the gene product causes only a small effect such as switching a glutamate for an aspartate, both are acid amino acids

Duplication mutation

a piece of DNA is abnormally copied one or more times

SNP

a single change to a nucleic acid base

Mutation

a variant that occurs less than 1% of the time in the population

Nucleosome

about 200 base pairs of DNA and 9 histone proteins

Insertion mutation

addition of one or more nucleic acid bases to the DNA sequence

Histones

basic proteins that bind DNA

SNP in a stop codon

cause a run on non-sense mutation

A run-on mutation

caused by a mutation in a stop codon leading to a longer than normal protein

SNP in an exon could

change an amino acid or introduce an early stop codon

A missense mutation

changes an amino acid

SNPs in the upstream region could

decrease expression of the protein

GAA -- GA

deletion, frame shift non-sense mutation

CAG -- TAG

early termination nonsense mutation

Trisomy 21

extra copy chromosome 21- Down's syndrome (usually from mother)

Trisomy X

extra copy of X chromosome in females: behavioral defects, learning disabilities, delayed motor skills

XXY

extra copy of X in males: sterility, gynecomastia

XYY

extra copy of Y in males: hyperactivity, learning difficulties

Trisomy 13

extra copy of chromosome 13- severe retardation, death, hand deformity

Trisomy 18

extra copy of chromosome 18 - microcephaly, clenched hands and overlapping fingers

SNP at an exon-intron junction could

fail to remove an intron and cause a non-sense mutation

CNV

gene that occur more than once on the same chromosome in the genome and sometimes change in the number of copies

"Reverse genetics"

identification of atypical amino acids helped to identify mutations at the DNA and mRNA level which lead to different drug responses

GAA -- GAAA

insertion, frame shift non-sense mutation

Deletion mutation

loss of one more nucleic acid bases to the DNA sequence

Frameshift mutation

loss of reading frame due to an insertion of deletion mutation

Paralog (Paralogue)

separated by a gene duplication event; similar proteins in same species

Wild-type

most common allele in a population

De Novo Mutation

new mutations that occurred in this individual

DNA

no oxygen at position 2 of ribose ring, uracil is replaced by thymidine

Silent mutation

no physical change is created

GAG -- GTG

non-conservative missense mutation

Inherited Mutation

occurred in a previous generation and was passed to the offspring

Centromere

point of attachment of duplicated chromosome after S phase until separation in M phase

SNP at an intron-exon junction could

remove an exon between two introns

Repeat expansion

repeated sections of DNA increase the number of repeats

Telomeres

repetitive DNA caps on the ends of chromosomes to protect them from degradation

VNTR

repetitive sequences of DNA outside the gene

Microsatellites

short repeats of less than 5 bases that occur in the DNA

CTG -- TTA

silent mutation

What is genetic imprinting?

the genetic defect differs when it comes from one parent verse another

Heterozygous:

the pair of chromosomes has different alleles

Homozygous

the pair of chromosomes has the same alleles

Allele

the specific version of a variable form of the same gene

RNA

there is an oxygen at position 2, and no methyl group at position 5 when using uridine

Polymorphism

two or more variations of the same DNA section

Sequence homology

two sequences that came from the same ancestral sequence

Genomic Library

using radio labeled cDNA probes to identify which fragments contain a gene