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Chapter 13: Genes and Genomes - Coggle Diagram
Chapter 13: Genes and Genomes
Illumina next-generation sequencing
slides: attach short DNA sequences, synthesize complementary strand using fluroescently labelled nucleotides (each nucleotide is a different color)
5 billion 150bp reads
1500Gb (600x guman genome)
possible to sequence the genome of any organism very cheaply
Gene
Definition of a gene: the DNA sequence required to synthesize a product (protein or RNA) important for cell function
Definition of genome: ALL the DNA in a gamete (in all the chromosomes of a haploid cell) (complete set of genetic material in an organism)
Structure of a gene
Transcribed region: includes protein coding region (introns and exons) and ends at termination region
Regulatory region: includes promoter and enhancer
METHODS FOR FINDING GENES
Look for DNA sequences that are usually found in, or near, genes
DNA Sequences in genes can be broadly classified as
coding sequence (i.e. sequence that ACTUALLY PRODUCES FUNCTIONAL PRODUCT)
transcribed, non-coding sequences: transcribed into RNA but doesn't do anything (i.e. introns)
Regulatory sequence (not transcribed)
Look for molecules that are produced by genes (RNA, protein)
To find gene in DNA sequence: look for TATA box, start codon, splice sites, stop codon
computer program predicts where gene is
Identifying gene products
1) Isolate cytoplasmic RNA and make a DNA copy (cDNA) of this RNA using reverse transcriptase
2) Sequence these cDNAs
3) Compare the sequence of these cDNAs with the genome sequence of the organism
TELLS YOU if the gene you predicted really makes a product
cDNA represents EXONS (NOT INTRONS)
Types of genome sequences
noncoding RNA
dispersed repeat: present at multiple sites of genome
Tandem repeat: sequences repeated next to each other
Simple sequence repeat: short repeats next to each other
Genome size varies widely between organisms
no correlation with complexity of organism
Gene number correlates with genome size in VIRUSES/PROKARYOTES, NOT IN EUKARYOTES
Gene number varies less than DNA content
What explains variation in genome size?
Genome size varies because the amount of DNA WITHIN genes and BETWEEN genes varies, intron length varies too
prokaryotes: genes are densely packed in genome so gene # correlates with genome size
eukaryotes:
genes are separated by LARGER distances
human genome is mostly retroransposons: short, repeated sequence with no function "junk DNA"
Retrotransposons are nonfunctional: derivatives of viruses
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duplicate copies of functionally important genes
How to determine the function of a new gene
Compare the sequence of the gene to the sequences of genes with known functions
Isolate its product and determine what process this product is able to perform in a test tube
Over-express the gene in a transgenic organism and see what effect it has on the organism
Make a mutation in the gene and see what happens
CRISPR-Cas9
Cas9 endonuclease enzyme is guided by sgRNA to a region of RNA complementary to the target genome you want to mutate
cleavage causes the mutation
can also edit the gene by adding an edited DNA sequence as a template to fill in genome that had been cleaved