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PHAR211 > Basic Concepts of Personalized Medicine > Flashcards

Basic Concepts of Personalized Medicine Flashcards

1
Q

How many cells are in the human body?

A

30-40 trillion

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2
Q

How many different types of cells are in the human body?

A

over 200 different types
-such as neurons, epithelial cells, RBCs

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3
Q

How many cells die each day?

A

100 billion
-replaced by new cells by cell division
-each division is called a “cell cycle”

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4
Q

What are the phases of the cell cycle?

A

G1 (gap 1): cell grows and prepares for DNA replication
S (synthesis): DNA replication
G2 (gap 2): cell continues to grow and prepare for mitosis
M (mitosis): cell stops growth and starts division
G0 (gap 0): cell has left the cell cycle and stopped dividing

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5
Q

What are the checkpoints in the cell cycle?

A

G1 and G2
-apoptosis starts if anything goes wrong
-G1 checkpoint: DNA synthesis
-G2 checkpoint: preparation for mitosis

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6
Q

What is R (restriction point) of the cell cycle?

A

cell has committed to the cycle for division

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7
Q

How many pairs of chromosomes are in the human body?

A

23 pairs
-complex of a DNA molecule and proteins

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8
Q

What is the structure of a DNA molecule?

A

linear double-stranded (50-250 million base pairs)

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9
Q

How many genes are within the average chromosome?

A

average chromosome contains 2500-5000 genes within 130 million base pairs

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10
Q

Are genes evenly distributed on a chromosome?

A

no, could be clustered
-microband (3-5 million base pairs and 60-120 genes)

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11
Q

What percentage of human chromosomes code for genes? What is the role of the rest of the human chromosomes?

A

10% code for genes
rest play regulating role

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12
Q

What is a gene?

A

a portion of chromosomal DNA sequence required for the production of a protein or a functional RNA molecule
-include the coding sequence and adjacent sequence required for regulation of expression (such as promoters)

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13
Q

What is the size of a gene?

A

varies
-small (1.5 kb) or large (2000 kb)

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14
Q

What is RNA splicing?

A

precursor mRNA –> mRNA

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15
Q

What are the four types of nucleotides in DNA?

A

A, T, G, C
-pairs: AT and GC

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16
Q

What are the four types of nucleotides in mRNA?

A

A, U, G, C
-pairs: AU and GC

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17
Q

Differentiate transcription and translation.

A

transcription: gene –> mRNA
translation: mRNA –> protein

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18
Q

How many genes are expressed in a typical human cell?

A

~15, 000
-expression varies from one cell to another

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19
Q

What is involved in many diseases in regards to genes?

A

gene malfunction

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20
Q

What are promoters?

A

DNA sequences that “promote” gene expression
-required for DNA transcription
-direct the exact place to initiate DNA transcription
-determine when and how a gene is transcribed

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21
Q

Where are promoters located?

A

upstream of genes
-RNA polymerase binding site

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22
Q

What can repress gene transcription?

A

promoter methylation

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23
Q

What is the Human Genome Project?

A

discovered complete DNA sequence of human

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24
Q

Differentiate the nuclear DNA genome and the mitochondrial DNA genome.

A

nuclear:
-22 pairs of autosomes (diploid) and 2 sex chromosomes
- ~ 3 billion base pairs
- ~ 19,000 genes
mitochondrial:
- ~ 17,000 base pairs
- 38 genes

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25
Q

What is ENCODE?

A

encyclopedia of DNA elements
-annotation of functional elements encoded in human genome

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26
Q

What are gene switches?

A

non-gene parts of DNA contributing to diseases
-MS, lupus, RA, Crohns

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27
Q

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

A

single nucleotide polymorphism (SNP)
copy number variations (CNV)
insertions and deletions
large scale variations
structural variations

28
Q

What is the most common type of genetic variation among people?

A

SNP
-80% of known polymorphisms

29
Q

What is an SNP?

A

small stretches of DNA that differ in only one base
-serve to distinguish individual genetic material
-important in understanding the genetic basis of human disease
-relationship with drug response

30
Q

How many SNPs are within each gene?

A

~ 5 coding SNPs

31
Q

What is the effect of an SNP on each of the following regions of a gene:
-non coding
-regulatory
-coding

A

non-coding: no effect
regulatory: change expression level
coding: change protein structure–>may change function

32
Q

What are CNVs?

A

variation among people in the number of copies for a particular gene or DNA sequence
-source of genetic diversity
-recombination based and replication based mechanisms

33
Q

What is the predominant mechanism for genome evolution?

A

gene duplication and exon shuffling

34
Q

What are some CNVs association with diseases?

A

cancer
autism
lupus
autoimmune disorders
stroke

35
Q

What are insertions and deletions?

A

insertion or deletion of small pieces of DNA
-alternative form of natural genetic variation

36
Q

What are the five categories of INDELs?

A

insertion or deletion of single base pairs
expansions by only one base pair
multi-base pair expansions (2-15 repeats)
transposon insertions (inserting mobile elements)
random DNA sequence insertions or deletions

37
Q

What are large scale variations?

A

large portions of DNA repeated or missing for no known reasons in healthy persons
-may underlie disease susceptibility

38
Q

What are structural variations?

A

kilobase to megabase-sized deletions, duplications, insertions, inversions, and complex combinations of rearrangements
-genome structural changes are involved

39
Q

What are hot spots?

A

regions with a lot of variation and often associated with genetic disorders and diseases
-ex: short arm of chromosome 1

40
Q

What are the types of structural variations?

A

deletion
duplication
paracentric inversion
balanced translocation
unbalanced translocation

41
Q

What is molecular diagnosis?

A

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

42
Q

Which studies are involved in the “omics”?

A

genomics
transcriptomics
proteomics
metabolomics

43
Q

What is genomics?

A

mapping, sequencing and functional analysis of the genome

44
Q

Is genomics the same as genetics?

A

no, they are different
-genetics: look at a single gene
-genomics: look at all genes as an entire system

45
Q

Differentiate genetics vs genomics.

A

genetics
-study of heredity
-specific gene
-function and composition of a single gene
genomics
-study of entirety
-entire genome
-address all genes and their relationships

46
Q

What is transcriptomics?

A

study of transcriptomes an their functions

47
Q

What is a transcriptome?

A

complete set of RNA transcripts produced by the genome

48
Q

What are the technologies used in transcriptomics?

A

RNA-Seq and microarray

49
Q

Differentiate between an exon and an intron.

A

exon: a portion of a gene that encodes amino acids
intron: a portion of a gene that does not encode amino acids

50
Q

What is proteomics?

A

study of proteomes and their functions

51
Q

What is a proteome?

A

entire proteins expressed in a cell, tissue or organism

52
Q

What are the technologies used in proteomics?

A

2D SDS-PAGE
liquid chromatography
mass spectroscopy

53
Q

What is metabolomics?

A

study of metabolites within cells, tissues or organisms
-less or non-invasive and closely linked to phenotype of diseases

54
Q

What are metabolites?

A

proteins
lipids
sugars
nucleotides

55
Q

What are some applications of metabolomics?

A

biomarker identification
drug safety screens

56
Q

What is glycomics?

A

identify the structure and function of the complete set of glycans produced in a given cell or organism and identify all the genes that encode glycoproteins

57
Q

What is lipidomics?

A

study of pathways and networks of cellular lipids in biological systems

58
Q

What are the technologies utilized in lipidomics?

A

LC
HPLC
NMR
MALDI-MS

59
Q

What is bioinformatics?

A

computational approaches to analyze, manage and store biological data
-meeting point for computer science and molecular biology
-analytical method for the “omics”

60
Q

What are biomarkers?

A

a biological molecule found in the blood, other body fluids, or tissues that is a sign of a normal or abnormal process, or of a condition or disease
-used to see how well the body responds to a treatment for a disease or condition

61
Q

What is systems biology and systems medicine?

A

computational modeling of complex biological systems
biology of interacting networks
facilitate the development of personalized medicine
apply the systems biology technology to medicine

62
Q

What is the systems approach?

A

P4 medicine
-predictive
-preventative
-personalized
-participatory

63
Q

What is conventional medicine?

A

empirical therapies and mechanism-based therapies
-developed as universal drugs for a certain disease
-diseases with multiple therapies: up to physician experience and preference

64
Q

What is conventional medicine associated with?

A

lack of efficacy and adverse effects

65
Q

What is evidence-based medicine?

A

highest level of evidence from multiple RCTs
-address a particular clinical problem
evidence-based guidelines may not be suitable for personalized medicine

PHAR211 (16 decks)

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