Genomics Flashcards
What is the role of genomics in healthcare?
Genomics has the potential to transform healthcare with more accurate diagnosis of a broader range of diseases with a genetic basis and to allow patients to know their likelihood of developing one of these diseases.
What is genomics?
The structural and functional mapping of genomes and their evolutions
What is a gene?
A sequence of nucleotides that encodes the sequence of amino acids that make u a protein
What is a chromatin?
Consists of DNA and protein found inside the nucleus of a cell
How many histones are there in a nucleosome?
8
What are the function of histones in a nucleosome?
The histones help package and regulate the DNA in the chromatin
What is DNA made of?
A sugar called deoxyribose
How does DNA form the ‘rungs’ of the classic ladder shape?
The rungs are base pairs which weakly bond together.
They form a code which cells follow to make proteins
What are the two different types of nucleotides?
Purines (A and G)
Pyrimidines (T and C or U in RNA)
What are the matches in base pairs?
A always pairs with T (or U in RNA)
G always pairs with C
How does DNA make RNA?
Through a process called Transcription
How does DNA make proteins?
Through a process called Translation
What is the first stage of transcription?
A gene is a continuous string of nucleotides, containing a region that codes for an RNA molecule.
This region begins with a promotor and ends in a terminator
What is the second stage of transcription?
The promotor region of a gene functions as a recognition site for RNA to bind.
This is where the majority of gene expression is controlled by either permitting or blocking access to this site by the RNA
What is the third stage of transcription?
Binding causes the DNA helix to unwind, open and then elongate in which the RNA slides along the template DNA strand.
What is the fourth stage of transcription?
As the complementary bases pair up, the RNA links nucleotides to the three prime ends of the growing RNA molecule.
What is the final stage of transcription?
Once the terminator portion of the gene reaches the messenger, the RNA transcript is complete and the RNA, DNA and messenger RNA transcript dissociate from each other.
What are exons?
A region in the messenger RNA made during transcription.
They code for a protein.
What are introns?
A region in the messenger RNA made during transcription.
They are non-coding sections.
What is intron splicing?
Where the non-coding introns are removed and modified and either a 5-prime or 3-prime poly tail is added
What happens in order for translation to begin?
Intron splicing which removes the intron segments and joins adjacent exons to produce a mature messenger RNA strand, leaving the nucleus through a nuclear pore, entering the cytoplasm.
What are 3 letter codons involved in translation?
AUG
GGG
UAG
What does UAG code for in translation?
UAG is the ‘stop’ codone that stops translation.
What does AUG code for in translation?
An amino acid called Methionine
What does GGG code for in translation?
An amino acid called Glycine
What are 4 types of characteristics in a final protein structure?
- Non-polar side chains
- Acidic side chains
- Alkali side chains
- Polar side chains
What do amino acids do for the final protein?
The amino acids do different jobs. If you change one of the amino acids in the sequence, then you could change the function of the protein.
How many genes are there roughly in the human body?
~ 21,000 genes
What are the 4 different types of mutation a gene can mutate into?
- Gain of function mutations
- loss of function mutations
- lethal mutations
- ineffective mutations
What is alternative gene splicing?
A process that causes genes to produce more than one protein
What are the two main groups of proteins?
Structural and functional types
What are 3 structural protein types?
Collagen
Elastin
Keratin
What are 3 functional protein types?
Enzymes
Ion channels
Neurotransmitter receptors
What process allows us to make changes to the structure and function of the final protein?
Translational modification
What are the 4 steps in the process of translational modification?
- adding carbohydrate parts
- adding lipid parts
- modifying AA side chains
- adding chemical regulators
What is a pseudogene?
non-functional genes
‘damaged’ gene sequence
What are some key features of pseudogenes?
They either do not produce proteins or it is non-functional
They lack key regulatory regions
Premature stop codon
Partially deleted gene sequence
What are the two types of sexual reproduction?
Meiosis
Mitosis
What is meiosis?
special cell division for production of gametes.
What causes genetic variation?
Meiosis and Mitosis
What are mutagens?
accidental damage to the genetic material
What are examples of mutagens?
pollutants/environmental triggers (chemicals, smoke)
Viral insertions
Ultraviolet light
Radiation
What are different effects from genetic mutations
Inconsequential (no net effect)
Consequential (has an effect) (mild-lethal)
What are the main categories of variants?
loss/gain function variant
Benign (not associated with disease)
Pathogenic (associated with disease)
Variants of uncertain significance (the unkowns)
What is a Missense Mutation?
A single nucleotide has been substituted for a different one. The code has been changed so that they could specify a different AA, which may change its function.
What is a Nonsense Mutation?
A single nucleotide has been substituted for a different one. The code has been changed to STOP codon so that AA sequence is truncated.
What are indels?
Insertions and deletions
where a nucleotide is added or removed.
How do indels affect a coding sequence?
Change in the reading frame
Change in the amino acid sequence
Change the function of resulting protein
What causes Cystic Fibrosis?
🔺F508 deletion mutation in the CFTR gene on chromosome 7 can cause cystic fibrosis.
What are translocations?
Chromosomal abnormalities
What are inversions?
Reversal of genetic coding region
What are copy number variants?
Deletion or duplication of coding region
How do you test for genetic mutations (cystic fibrosis as an example)?
Take a sample of DNA (e.g. from blood)
Use gene-specific reactions to ‘copy’ the gene (PCR)
Separate the ‘copies’ by size
If there is a gene deletion the smaller copy will show up.
What are the benefits for new sequencing technology?
Much more rapid
Highly automated
Relatively inexpensive
What is Bioinformatics?
Analysis, storage, annotation and retrieval of genomic data.
