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PHAR 211 > Basic Concepts > Flashcards

Basic Concepts Flashcards

1
Q

How many cells are in the body?

A

30-40 trillion cells that have a great amount of coordination and specialization

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2
Q

What is the cell cycle?

A

It is the cell division process

G1, S, G1, M, G0

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3
Q

What is G1 in the cell cycle?

A

G1 (Gap 1): Longest phase

Cell growth and preparation for DNA replication

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4
Q

What is the S phase in the cell cycle?

A

Synthesis: DNA replication

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5
Q

What is the G2 phase in the cell cycle?

A

G2 (Gap 2): The cell continues to grow and prepares for mitosis

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6
Q

What is the M phase in the cell cycle?

A

M (Mitosis): Cell growth stops and starts cell division

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7
Q

What is the G0 phase in the cell cycle?

A

G0 (Gap 0): Cell leaves cell cycle and stops dividing

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8
Q

What are the two checkpoints in the cell cycle?

A

G1 and G2 checkpoints

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9
Q

What is the purpose of the G1 checkpoint?

A

Checks for errors in DNA synthesis

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10
Q

What is the purpose of the G2 checkpoint?

A

The cell ensures it is ready for mitosis

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11
Q

What is the restriction point (R)?

A

After this point in the cell cycle, the cell commits to the cyles for division, no additional growth factor required

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12
Q

How many base pairs are found in a DNA molecule?

A

50-250 million base pairs

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13
Q

Are genes evenly dispersed in the chromosome?

A

No, there are regions with 60-120 genes in close proximity called microbands

An average microband has 3-5 million base pairs

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14
Q

What percentage of the human chromosome code for genes?

A

Only 10%, the rest may have important regulatory roles

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15
Q

What are histones?

A

They are a complex of proteins that DNA will wrap around to facilitate super condensation of the chromosomes into a small size that can fit inside the nucleus

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16
Q

What is a gene?

A

A portion of chromosomal DNA sequence required for the production of a polypeptide (protein) or a functional RNA molecules

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17
Q

What are some components of a gene?

A

Coding sequence

Promoters and other regulatory sequences

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18
Q

What are the four types of nucleotides in DNA?

A

Adenosine (A)
Thymine (T)
Guanine (G)
Cytosine (C)

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19
Q

What are the nucleotide pairs?

A

A - T

G - C

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20
Q

Which of the three nucleotides in a codon poses the most significant risk for protein product modification due to a point mutation?

A

If the first and second bases are different, it will result in a completely different amino acid, potentially causing significant changes to structure and function

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21
Q

Do gene mutations always cause disease?

A

No, the impact is either not significant, increased risk, or even reduced risk for disease

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22
Q

What are promoters?

A

DNA sequences that promote gene expression

They are required for DNA transcription (contain RNA polymerase binding site)

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23
Q

How many genes are in the human body?

A

19,000 individual genes in the nuclear DNA genome is a conservative estimate

38 confirmed genes in the mitochondria

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24
Q

What is ENCODE?

A

Encyclopedia of DNA Elements (ENCODE)

This database provides an annotation of functional elements encoded in the human genome. Can tell us about the location, function, and characteristics of genes

25
Q

What are the types of genetic variation in the human genome?

A

These mutations are associated with disease but can also be target for targeted therapy

  • Single nucleotide polymorphisms (SNPs)
  • Copy number variations (CNVs)
  • Insertions and deletions
  • Large scale variations
  • Structural variations
26
Q

How are genetic variations in an individual determined?

A

Determined from a complete sequencing of individual genome

27
Q

What are single nucleotide polymorphisms (SNPs)?

A

Most common type of genetic variation among people (80% of all polymorphisms)

They are small stretched of DNA that differ in only one base

Each individuals, even twins have different SNP patterns (each individual has a unique SNP pattern)

Each gene contains about 5 coding SNPs

28
Q

What is the most pharmaceutically relevant SNP polymorphisms?

A

CYP450 SNPs affect drug metabolism and activity

29
Q

What is the significance of ethnicity in SNPs?

A

SNP frequency is different among different ethnic groups

30
Q

What are copy number variations (CNVs)?

A

It is the variation among people in the number of copies of a particular gene of DNA sequence

Recombination-based and replication-based mechanisms

31
Q

Review slide 22 for a diagram of mutations of CNVs

A
32
Q

What is the impact of a higher copy number frequency for a gene that is associated with drug metabolism?

A

Faster metabolism due to increased translation of protein

33
Q

What are insertions and deletions (INDELs)?

A

They are small pieces of DNA that can be inserted or deleted from a DNA sequence

Likely to have a major impact on humans, including health and susceptibility to diseases

More potentially dangerous than CNVs due to risk of frameshift mutations which can completely disrupt downstream translation into protein

34
Q

What are the five categories of INDELs?

A
  • Insertions or deletions of single base pairs
  • Expansions by only one base pair
  • Multi-base pair expansions of 2-15 repeats (can be more than 15 in some cases)
  • Transposon insertions (insertions of mobile elements, introduction of new proteins to DNA sequence, can help with adaptation)
  • Random DNA sequence insertions or deletions
35
Q

What are the three primary outcomes following a DNA mutation?

A
  1. No impact
  2. Causes harm (most likely)
  3. Improvement in function (least likely)
36
Q

What are Large-scale variations in the DNA sequence?

A

Large portions of DNA repeated or missing for no known reasons in healthy people

Found in 225 loci in human genome

37
Q

What is a pharmaceutical consideration for Large-scale variations in the DNA sequence?

A

If a target sequence for a gene therapy is in a hotspot for LCVs, then HCPs need to ensure patient has desired sequence in their genome

38
Q

What are Structural variations in the DNA sequence?

A

Extremely common in humans

Involves kb to Mb sized deletions, duplications, insertions, and inversions (much more significant impact than any other genetic variation)

These often occur in hotspots that are regions with lots of variation and are often associates with genetic disorders and diseases

39
Q

What are some examples of structural variations of chromosomes?

A

Review slide 29

  • Deletion
  • Duplication
  • Paracentric inversion (centromere is not involved, no impact on mitosis)
  • Pericentric inversion (centromere is involves, significant impact on mitosis)
  • Balanced translocation (two chromosomes swap genetic material)
  • Unbalanced translocation (one chromosome donates genetic material, while the other chromosomes accepts genetic material)
40
Q

What is the Philadelphia chromosome?

A

It is an example of balanced translocation

Involves chromosomes 8 and 22

Results in the generation of two fusion gene

Changed chromosome 22 (BCR-ABL) is associated with leukemia

41
Q

What are the basic technologies in developing personalized medicine?

A
  • Molecular diagnostics, especially SNP genotyping
  • The “omics” (used to identify targets, diagnosis, treatments, and patient stratification)
  • Bioinformatics (computer analysis of large data sets)
42
Q

What is molecular diagnosis?

A

Detect specific DNA sequences that may or may not be associated with diseases

ex. SNPs, CNVs, Insertions, Deletions, Duplications, Rearrangements

43
Q

What are some examples of the “omics” studies?

A
  • Genomics (comprehensive DNA study)
  • Transcriptomics (comprehensive mRNA study)
  • Proteomics (comprehensive protein study)
  • Metabolomics (comprehensive study of sugars, lipids, amino acid found in sample)
44
Q

Why are metabolomics relatively rarely conducted?

A

Metabolomics study sugars, lipids, amino acids, and nucleotides. These structures are non-linear and have branching structures. This branched structure introduces complexity to sequencing, and by extention cost

45
Q

What is the difference between genetics and genomics?

A

Genetics: look at a single gene
Genomics: look at all genes as an entire system (mapping, sequencing, and functional analysis of the genome)

46
Q

What is transcriptomics?

A

Study of transcriptomes (RNA sequences) and their functions

47
Q

Review slide 39 for alternative splicing

A
48
Q

What is proteomics?

A

Study of proteomes and their functions

Proteome: entire proteins expressed in a cell, tissue, or organism

49
Q

Review slide 41 for the process involved in proteomics experiment

A
50
Q

What is the difference between bottom-up and top-down proteomics?

A

bottom-up proteomics: digest proteins and study smaller portions of protein

Top-down proteomics: entire protein put into mass spectrometry device for analysis

51
Q

What is metabolomics?

A

Study of metabolites within cells, tissues or organisms (closer to phenotype)

52
Q

What is glycomics?

A

A type of study that helps identify the structure and function of the complete set of glycans produced in a a given cell or organisms and identify all the genes that encode glycoproteins

53
Q

What is lipidomics?

A

Study of pathways and networks of cellular lipids in biological systems

54
Q

What is bioinformatics?

A

Computational approaches to analyze, manage, and store biological data

55
Q

What are biomarkers?

A

Biomarkers are determined from “omics” studies

A biological molecule found in blood, other body fluids, or tissues that is a sign of a normal or abnormal process

56
Q

What is systems biology and medicine?

A

It involves the computational modelling of complex biological systems

ex. cross-talk between multiple genes that can increase risk of ovarian cancer

57
Q

What is the central principle of conventional medicine?

A

Universal drug targets general disease (no stratification)

58
Q
A

PHAR 211 (18 decks)

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