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Winter P1 > Pharm 737 Exam 1 > Flashcards

Pharm 737 Exam 1 Flashcards

1
Q

What is a Genome?

A

All the genetic Material (DNA) of an organism.

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2
Q

What are Genetics?

A

The study of single genes and its effects. (Cystic Fibrosis, Huntington’s disease)

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3
Q

What are Genomics?

A

The study of all the genes in the genome, including their interactions with environmental factors. (Heart Disease, asthma)

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4
Q

What are Pharmacogenetics?

A 
The study of genetic influences on an individuals reponse to drugs. 
 - The analysis of a specific gene, or group of genes, may be used to predict responses to a specific drug or class of drugs.
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5
Q

What are Pharmacogenomics?

A

The study of all genes collectively that influence drug responses, and how genome-wide analysis may be used to identify such genes in the search for novel drug targets and/or key determinants of drug reactions.

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6
Q

Define SNP and describe how the variants effect drug discovery.

A

SNP - Single Nucleotide Polymorphism variant, they allow more personalized medicine, but as the SNP variants are generally more specific, they result in slowed drug discovery, but bypass drug trial and error period.

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7
Q

What is the therapeutic window and how is it used to calculate safety of a drug?

A

Area between dosage value where Toxic effects of a drug occur and minimum effective dosage, the broader the window the more safe the drug, a small window means very toxic side effects.

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8
Q

What is the significance of Mendelian Inherited Diseases?

A

There are 1200 genes that are currently identified as causing human diseases/traits exhibit inherited phenotype

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9
Q

What is a Transcriptome?

A

The full range of RNA molecules expressed by an organism or present in a cell at a given time.

Changes in the transcriptional activity contributes to a disease.

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10
Q

What is a Proteome?

A

The entire set of proteins expressed by a genome, organism, cell or tissue at a certain time. It is constantly changing since proteins are continually being newly synthesized, modified and degraded. Also species and cell-state dependent.

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11
Q

What is the Epigenome?

A

The epigenome is a series of chemical compounds that can tell the genome what to do.

Epigenomics is the study of changes in the regulation of gene activity and expression that ARE NOT dependent on gene sequence.

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12
Q

What is the purpose of Systems Biology?

A

To connect the molecular characteristics of a disease with pharmacogenomics to deliver a personalized therapy option to a patient.

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13
Q

What is the importance of Simple Viral and Bacterial Genomes?

A

This is an untapped resource of raw genomic material

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14
Q

What is the importance of Ancestral Genomics?

A

Can be used to track the evolution of genomes, duplication events and similarities.

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15
Q

Describe the ENCODE project

A

ENCyclopedia Of DNA Elements

International collaboration of research groups funded by the National Human Genome Research Institute.

Goal is to build a list of functional elements in human genome.

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16
Q

What is the importance of the interpretation of shared characteristics?

A

Determining traits that mammals have gained and lost through evolution

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17
Q

What are the five stages that drugs undergo in the body?

A 
Absorption
Distribution
Target Interaction
Metabolic Processing
Excretion from the body
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18
Q

How prevalent are genetic factors when it comes to variation in drug response between individuals?

A

20-95 percent

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19
Q

What genes are important for pharmacokinetic properties of drugs? Pharmacodynamics?

A

Those for drug metbolizing enzymes and drug transporters.

Those for enzymes, receptors, and ion channels.

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20
Q

What are SNPs and how common are they?

A

Single Nucleotide Polymorphisms, they occurr in at least 1% of the population

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21
Q

Define Haplotype

A

A group of alleles that are rarely separated by recombination (generally inherited together)

Human haplotypes are 60,000 base pairs in size and contain 60 SNPs that travel as a group

Haplotypes are better predictors of drug responsiveness than single, isolated SNPs

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22
Q

What is a Missence SNP?

A

Characterized by changes of amino acids, with about half of such changes occurring in coding sequences.

Can result in the alteration of protein function and is the cause of most monogenetic disease.

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23
Q

What is a nonsense SNP?

A

Introduce a stop codon with the same consequences as Missence SNPs (alteration in protein function, cause of monogenetic disease)

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24
Q

How many SNPs does the human genome have? Which are most prevalent, where do they occur, and how do they effect us?

A

3 million, distributed randomly

Occur in both coding and non-coding regions, with 2 out of every 3 involving the replacement of cytosine (C) with thymine (T). Some have no effect on cell function but may predispose people to a disease or impact how they respond to certain drugs.

25
Q

What is TSC and what do they do?

A

The SNP Consortium (HapMap Project)

A partnership of scientists from Canada, China, Japan, Nigeria, UK and US that seeks to determine the frequency of certain SNPs in three major world populations.

Goal is to make a public resource that researchers can use to find genes associated with disease and pharmaceutical response in humans.

26
Q

How is pharmacogenetic testing prior to drug therapy limited?

A

Largely to specialized drugs such as chemotherapy agents

27
Q

What is GWAS?

A

Genome Wide Associated Study is a study of many common genetic variants in individuals to determine if any variant is associated with a trait.

28
Q

What are nucleotide subunits composed of?

A

Sugar-phosphate molecule with a nitrogen containing side group, or base, attached to it.

29
Q

What are the activated precursors in RNA synthesis?

A

Ribonucleotide triphosphates

30
Q

What direction does the chain grow in RNA synthesis?

A

5’ to 3’

31
Q

What are the start and stop sites for transcription?

A

Start - ATG

Stop - TAA

32
Q

List 4 important transcriptional co-regulators

A
  1. Mediator complexes
  2. Histone chaperone complexes
  3. Histone modifying enzyme complexes
  4. ATP-dependent chromatin remodeling complexes
33
Q

What is Euchromatin

A

Euchromatin is uncondensed and is considered “good” chromatin (ideal for replication)

34
Q

What is Heterochromatin

A

heterochromatin is condensed and not favorable for replication (repressing or silencing)

35
Q

Describe how transcription is modulated

A

DNA bound activator protein upstream from enhancer sequence attracts proteins to promoter region that activate RNA polymerase. The DNA can loop around its self to facilitate the interaction of proteins that activate RNA polymerase.

Active repressors can bind to operator sequences near the promoter and interfere with RNA polymermase binding to the promoter.

36
Q

Describe the general process of Translation

A

Amino acids are transported to the ribosome by tRNA (20 different tRNA molecules total, one for each amino acid), tRNA anti-codons find their RNA complement and peptide bonds form between amino acids to form a peptide, with translation stopping once the stop codon has been reached.

37
Q

What is Chromatin?

A

A nucleoprotein complex that causes condensation and organization of DNA. Strings of nucleosomes compose the primary structural unit while nucleosome interactions provide a secondary level of compaction.

38
Q

Describe a histone octamer

A

The 8 protein coplex found at the center of a nucleosome, consisting of 2 copies of each core protein (H2A, H2B, H3, and H4)

39
Q

Describe CRMs and their impact on cells

A

Cis Regulators Modules regulate gene expression in cells and are activated by transcription factors which in turn recruit co-regulators which deposit/or remove crucial histone modifications.

As a results, only half of the 25,000 protein-coding genes of the mammalian genome are expressed in any given cell.

40
Q

Describe Epigenetics.

A

Heritable traits that aren’t linked to changes in the DNA sequence (changes caused by external or environmental factors)

41
Q

Describe DNA methylation of the human genome

A

Methyl groups added to DNA at CpG sites, with the pattern being determined during embryogenesis (and getting passed over to differentiating cells).

In humans, 3-5% of DNA cytosine is methylated, and this methylation occurs almost exclusively at cytosines that are followed by a Guanine-CpG dinucleotide (5’CpG3’). The process is performed by DNA methyltransferase, and is heritable, reversible, and often used as a therapeutic target. Methylation on the human genome is not uniform.

CpG is methylated in non-promoter regions and un-methylated in promoter region (methylation in promoter region correlates with silencing)

42
Q

In histone modification, acetylation and deacetylation are regulated by…

A

Histone acetyltransferases (HATs) and Histone Deacetylases (HDACs)

43
Q

How do HATs work?

A

HATs catalyze the transfer of the acetyl moiety from acetyl-CoA to the amino group of histone lysine residues, resulting in acetylated lysine and CoA.

Positively charged histones are neutralized and their interaction with the negatively charged DNA is decreased.
In general, this increases gene expression.

44
Q

What can acetlyation regulate in DNA?

A

DNA replication, histone deposition and DNA repair

45
Q

What is the result of lysine acetylation?

A

More opened euchromatin state which is more accessible to transcription factors

46
Q

What are two primary disease examples in humans resulting from histone modifications? Describe each disease.

A

Coffin-Lowry Syndrome:
>Genetic disorder characterized by mental retardation and head/facial abnormalities
>X-linked dominant genetic trait
>results from mutations in the RSK2 gene (histone phosphorylation)

Rubinstein-Taybi Syndrome:
>Short stature, intellectual disability, distinctive facial features, and broad thumbs and first toes
>results from mutations in CREB-binding protein (histone acetylation)

47
Q

Describe Chain Termination

A

Also known as the di-deoxy method, or Sanger sequencing.

Relies on ability of DNA polymerase to incorporate nucleotide analogs while synthesizing template driven DNA

48
Q

Describe the Shotgun sequencing method.

A

Used in human genome sequencing and involves the fragmentation of larger DNA strands into manageable chunks.

49
Q

Describe Pyrosequencing and why it’s so useful.

A

Unlike Sanger sequencing, this type relies on the detection of pyrophosphate release on nuecleotide incorporation rather than on chain termination.

This method is accurate and fast, easily automated, eliminates the need for primer and nucleotide labeling, as well as the need for gel electrophoresis.

50
Q

Explain RT-PCR

A

Reverse Transcriptase-Polymerase Chain Reaction is used to determine whether a particular type of mRNA is present.

The mRNA is converted to ds-cDNA using reverse transciptase and RNase H, followed by the addition of a primer and the completion of the second strand using DNA Taq polymerase.

The target DNA is denatured and two sets of primers added which hybridize to opposite ends of the target sequence. Addition of Taq polymerase to the denatured DNA causing each strand to synthesize its complement.

51
Q

Describe RNA-Seq

A

Long RNAs converted into cDNA fragments by RNA/DNA fragmentation. Sequencing adaptors added to each cDNA fragment. A short sequence is obtained from each cDNA through high-throughput sequencing. Sequence reads are aligned with the reference genome and classified as exonic reads, junction reads or poly(A) end-reads. These three reads are used to generate base-resolution expression profiles for each gene.

52
Q

What is CHIP-seq

A

Chromatin Immunoprecipitation Sequencing, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.

53
Q

Explain why RNA expression odes not always reflect protein levels

A

Translational control, degradation and turnover

54
Q

What does Functional Proteomics Encompass?

A

Post-translational modifications
Protein-Protein and Protein- Ligand Interactions
Sequence structure-function relationships

55
Q

Describe Metabolomics

A

New field that uses systematic determination of metabolite levels in the metabolome and their changes over time as a consequence of stimuli

56
Q

Define Metabolome

A

The complete set of small-molecule metabolites found within a biological sample

57
Q

Define Metabolites

A

Intermediates and products of metabolism (antibiotics, pigments, carbs, fatty acids, amino acids, etc.)

58
Q

What is the purpose of Systems Biology?

A

To connect the molecular characteristics of a disease with pharmacogenomics to deliver a personalized therapy option to a patient.

59
Q

Describe transgenic mice

A

Mice with germ-line transformations that involve the insertion of genes into the reproductive cells of an organism, which permanently alters the individual and all offspring (transgenic)

Used to study the functions of specific genes in development or disease processes

Winter P1 (8 decks)

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