genes and genomes Flashcards
how is genomics possible?
next-generation sequencing
How is genomics possible
computational capacity
Definition of a gene
the DNA sequence required to synthesize a product (protein or RNA) important for the function of a cell
Three regions of a gene
- coding sequence
- transcribed, non-coding sequences
- Regulatory sequences
Methods for finding genes(2)
- look for DNA sequences that are usually found in or near genes
- look for molecules produced by genes( RNA, protein)
Steps in identifying gene products
- Isolate cytoplasmic RNA and make a copy DNA (cDNA) of this RNA using reverse transcriptase
- Sequence these cDNAs
- Compare the sequence of these cDNAs with the genome sequence of the organism
Using RNA to make cDNA cannot
show what the encoded gene product does
Genome size in viruses and prokaryotes, but not in eukaryotes
gene numbers correlate with genome size
Gene number variation
varies less than DNA content
Largest portion of the human genome
transposons and not actual coding sequences
Life of the retrovirus
viral RNA changes into DNA and inserts into the host genome
what do retroviruses evolve into when they become defective
retrotransposons
Determine function of new gene: Compare
compare sequence of the gene product to sequences of gene products with known functions
Comparing function of new gene example
CDK
Determine function of new gene: test tube
isolate its products and determine what process this product is able to perform in a test tube
Test tube function of new gene example
hemoglobin binding oxygen
Determine function of new gene: make a mutation
Make a mutation in the gene and see what happens
make a mutation function of new gene example
Tbx5 specifies forelimbs
Determine function of new gene: over express
overexpress the gene and see the effect it has on the organism
How do mutations arise
spontaneously
What do spontaneous mutations over time create
evolution
What is antibiotic-resistant cells considered?
mutations
difference in the DNA called
polymorphism
difference on just one nucleotide
single nucleotide polymorphism
What is the effect of most mutations
does not actually affect the expression or activity of genes
Each germline generation has more
mutations
Error in replication
caused by mismatch mutations
High energy x-rays can lead to
chromosome rearrangements
transposons can jump into genes and
disrupt them
When does misalignment happen?
during meiosis
What can misalignment lead to?
large scale chromosomal alterations
abnormal segregation of chromosomes(nondisjunction) can. lead to
abnormal chromosome numbers
Trisomy 21
copy number variation
Alleles
genes that have different DNA sequences
What do mutations in the regulatory sequences effect?
rates, location, timing of transcription
What do mutations in the coding sequences effect?
amount or activity of a gene product
Silent mutation
does not change the amino acid produced
nonsense mutation
STOP codon
missense conservative
changes amino acid but not super different
missense nonconservative
changes amino acid to a very different one
Frameshift
insertions and deletions can cause these
What happens when DNA polymerase fiinds an incorrect nucleotide?
exonuclease activity removes. the incorrect nucleotide and replaces it
When can mutations in DNA be removed?
replication or repaired postreplication
