Basic Concepts Flashcards
How many cells are in the body?
30-40 trillion cells that have a great amount of coordination and specialization
What is the cell cycle?
It is the cell division process
G1, S, G1, M, G0
What is G1 in the cell cycle?
G1 (Gap 1): Longest phase
Cell growth and preparation for DNA replication
What is the S phase in the cell cycle?
Synthesis: DNA replication
What is the G2 phase in the cell cycle?
G2 (Gap 2): The cell continues to grow and prepares for mitosis
What is the M phase in the cell cycle?
M (Mitosis): Cell growth stops and starts cell division
What is the G0 phase in the cell cycle?
G0 (Gap 0): Cell leaves cell cycle and stops dividing
What are the two checkpoints in the cell cycle?
G1 and G2 checkpoints
What is the purpose of the G1 checkpoint?
Checks for errors in DNA synthesis
What is the purpose of the G2 checkpoint?
The cell ensures it is ready for mitosis
What is the restriction point (R)?
After this point in the cell cycle, the cell commits to the cyles for division, no additional growth factor required
How many base pairs are found in a DNA molecule?
50-250 million base pairs
Are genes evenly dispersed in the chromosome?
No, there are regions with 60-120 genes in close proximity called microbands
An average microband has 3-5 million base pairs
What percentage of the human chromosome code for genes?
Only 10%, the rest may have important regulatory roles
What are histones?
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
What is a gene?
A portion of chromosomal DNA sequence required for the production of a polypeptide (protein) or a functional RNA molecules
What are some components of a gene?
Coding sequence
Promoters and other regulatory sequences
What are the four types of nucleotides in DNA?
Adenosine (A)
Thymine (T)
Guanine (G)
Cytosine (C)
What are the nucleotide pairs?
A - T
G - C
Which of the three nucleotides in a codon poses the most significant risk for protein product modification due to a point mutation?
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
Do gene mutations always cause disease?
No, the impact is either not significant, increased risk, or even reduced risk for disease
What are promoters?
DNA sequences that promote gene expression
They are required for DNA transcription (contain RNA polymerase binding site)
How many genes are in the human body?
19,000 individual genes in the nuclear DNA genome is a conservative estimate
38 confirmed genes in the mitochondria
What is ENCODE?
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
What are the types of genetic variation in the human genome?
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
How are genetic variations in an individual determined?
Determined from a complete sequencing of individual genome
What are single nucleotide polymorphisms (SNPs)?
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
What is the most pharmaceutically relevant SNP polymorphisms?
CYP450 SNPs affect drug metabolism and activity
What is the significance of ethnicity in SNPs?
SNP frequency is different among different ethnic groups
What are copy number variations (CNVs)?
It is the variation among people in the number of copies of a particular gene of DNA sequence
Recombination-based and replication-based mechanisms
Review slide 22 for a diagram of mutations of CNVs
What is the impact of a higher copy number frequency for a gene that is associated with drug metabolism?
Faster metabolism due to increased translation of protein
What are insertions and deletions (INDELs)?
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
What are the five categories of INDELs?
- 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
What are the three primary outcomes following a DNA mutation?
- No impact
- Causes harm (most likely)
- Improvement in function (least likely)
What are Large-scale variations in the DNA sequence?
Large portions of DNA repeated or missing for no known reasons in healthy people
Found in 225 loci in human genome
What is a pharmaceutical consideration for Large-scale variations in the DNA sequence?
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
What are Structural variations in the DNA sequence?
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
What are some examples of structural variations of chromosomes?
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)
What is the Philadelphia chromosome?
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
What are the basic technologies in developing personalized medicine?
- Molecular diagnostics, especially SNP genotyping
- The “omics” (used to identify targets, diagnosis, treatments, and patient stratification)
- Bioinformatics (computer analysis of large data sets)
What is molecular diagnosis?
Detect specific DNA sequences that may or may not be associated with diseases
ex. SNPs, CNVs, Insertions, Deletions, Duplications, Rearrangements
What are some examples of the “omics” studies?
- Genomics (comprehensive DNA study)
- Transcriptomics (comprehensive mRNA study)
- Proteomics (comprehensive protein study)
- Metabolomics (comprehensive study of sugars, lipids, amino acid found in sample)
Why are metabolomics relatively rarely conducted?
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
What is the difference between genetics and genomics?
Genetics: look at a single gene
Genomics: look at all genes as an entire system (mapping, sequencing, and functional analysis of the genome)
What is transcriptomics?
Study of transcriptomes (RNA sequences) and their functions
Review slide 39 for alternative splicing
What is proteomics?
Study of proteomes and their functions
Proteome: entire proteins expressed in a cell, tissue, or organism
Review slide 41 for the process involved in proteomics experiment
What is the difference between bottom-up and top-down proteomics?
bottom-up proteomics: digest proteins and study smaller portions of protein
Top-down proteomics: entire protein put into mass spectrometry device for analysis
What is metabolomics?
Study of metabolites within cells, tissues or organisms (closer to phenotype)
What is glycomics?
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
What is lipidomics?
Study of pathways and networks of cellular lipids in biological systems
What is bioinformatics?
Computational approaches to analyze, manage, and store biological data
What are biomarkers?
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
What is systems biology and medicine?
It involves the computational modelling of complex biological systems
ex. cross-talk between multiple genes that can increase risk of ovarian cancer
What is the central principle of conventional medicine?
Universal drug targets general disease (no stratification)
