Genomics Flashcards
Define Genomics.
Structural and functional mapping of genomes and their evolution.
Define genetics
The study of heredity
What is a gene?
A sequence of nucleotides that encodes the sequence of amino acids that make up a protein. Or a basic physical and functional unit of heredity.
What is an exon?
a coding region mainly consisting of sections of protein sequences
Define meiosis.
Special cell division for the production of gametes
What is an intron?
non-coding region which is removed during splicing, it can contain regulatory sequences
What is a genotype?
a complete set of genetic material including various variants of genes that they carry
what is a psuedogene?
a non-functional gene
Define heritable
variants passed from variant to offspring
what are mutations?
any heritable change to DNA sequence
Define somatic
things passed to dividing cells in tissues
define germline
things passed from parent to offspring
what is inconsequential when regarding mutation?
it has no net effect
What is consequential when regarding mutation?
has an effect
define pathogenic
associated with a disease
define benign
mot associated with a disease
what is the variance of uncertain significance?
the unknowns
what is a missense mutation?
a single nucleotide that has been substituted for a different one
what is a nonsense mutation?
a single nucleotide that has been substituted for a stop codon
what is an indel?
a deletion or addition
define translocation
abnormalities of chromosomes, added from other codes
define inversions
the reversal of genetic code, a codon but backwards
define mitosis
cell division that results in daughter cells having the same number of chromosomes
what is a large deletion?
removal of over 1000 base pairs
what is a copy number variant?
repetitions of bases
what is genomic bioinformatics?
analysis, storage, annotation and retrieval of genomic data
How can genomics help healthcare?
Genomics has the potential to transform healthcare with more accurate diagnoses of a broader range of diseases with a genetic basis, and allow patients to know their likelihood of developing one of those diseases. It can also track viral infections and variants, tracking gene transfer, and track drug resistance in pathogens.
How is a protein made up?
A sequence of nucleotides that encodes the sequence of amino acids, that make up a protein.
What is the function of histones on a DNA strand?
Histones help package and regulate the DNA strand. There are 8 histones in a nucleosome.
How many pairs of chromosomes are in a DNA strand?
23 pairs
What is the backbone of DNA made up of?
sugary molecules called deoxyribose
What are the 3 DNA base pairs?
A and T, G and C, and T and A. A = adenine, G = guanidine, T = thymine, C = cytosine.
Which base pairs are purines and which are pyrimidines?
A and G = purines, and T and C = pyrimidines
How does DNA make a protein?
The DNA code transcripts to RNA which translates to a protein
Explain what RNA is.
RNA is a single stranded messenger code, which is also known as MRNA
Explain the 3 letter codons in translation
The 3 letter codons make amino acids. AUG is the start code, GGG is the middle code, and the UAG is the stop code. U = uracil
Explain the end of translation and the sequences.
20 amino acids are directly coded in the genome, and each type confers different characteristic to the final protein structure. the four different chains are non-polar (uncharged) side chains, acidic side chains, basic side chains and polar (charged) side chains. If one of the amino acids in the sequence is changed - you could change the function of the protein.
Why are genes not the same?
Due to gain of function mutations, loss of function mutation, lethal mutation, ineffective mutation and alternative gene splicing.
What is alternative gene splicing?
Some genes produce more than one gene product
Name 5 structural proteins.
collagen, elastin, keratin, desmoglein, tubulin
Name 5 functional proteins
Enzymes, ion channels, neurotransmitter receptors, antibodies, active transporters
How do we get extra proteins?
Through alternative gene splicing. Exons coding region mainly containing sections of protein sequences and introns non-coding region, can create more than one protein from one gene. Another way is through post translation modification which changes the structure and function of the final protein. This is created by adding carb parts, lipid parts, modifying AA side chains, and adding chemical regulators.
Explain sexual reproduction in genetic variation
Sexual reproduction causes genetic variant because during meiosis and fertilisation, their is an exchange of genetic material between chromosomes via random crossovers, independent assortment, and random fertilisation. There are trillions of genotypes possible, which are heritable variants that can be passed from parents to offspring.
Explain the causes of genetic variation
The main causes are due to random events and mutagens such as the life of the cell not being able to transfer to offspring, during cell division and mitosis not being able to transfer to offspring. Also, causes like accidental damage to genetic material, inappropriate DNA repair mechanisms, and mutagens.
Explain the difference between a mutation and a variant.
A mutation is any heritable change to DNA sequence, and a variant is the healthcare word for mutation.
Explain the process of missense mutation in a single nucleotide variant
A missense mutation is when a single nucleotide has been substituted for a different one, so the code has been changed. This could specify different AA, so the AA sequence of the resulting protein may change, which could change the function of the protein.
Explain the process of nonsense mutation in a single nucleotide variant
A nonsense is when a single nucleotide has been substituted for a different one, so the code has been changed to a stop codon. Therefore the AA sequence of the resulting protein is truncated.
What is an indel?
The insertions or deletions of a nucleotide, so whether a nucleotide has been added or removed
Name the main types of structural variants
Translocation, inversions, large deletions, copy number variants.
Explain the blood test (PCR) for monogenetic disorders.
Patient gets a blood test, and a DNA sample is taken from the blood, a gene-specific reaction copies the gene. The copies are separated by size, and if there is a gene deletion, the smaller size copy will show up, however you must know the gene involved to do this.
Describe the change in whole genome sequencing.
Whole genome sequencing on a human took 13-15 years and costed billions to do, however with advanced technology today it can be done in a day for less than a grand.
How is whole genome sequencing completed?
A sample is taken, such as blood, then the DNA is extracted from the blood and assessed. The DNA is then placed in a next generation sequencer, which reads DNA letter by letter
Name the 5 types of variants
Pathogenic variants, benign variants, gain of function variants, loss of function variants, and the variance of uncertain significance variants
