Genome structure and the language of genetics

Viruses

infectious particles comprised of a genome surrounded by a protein coat

Viral genomes

• 2000 bp to 1 million bp of RNA or DNA

• Circular, linear or segmented

• Single stranded, double stranded

• invade the genomes of other organisms

RNA viruses

• have RNA genomes (single or double-stranded)

• They use host machinery to translate their genes and further infection

DNA viruses

• have DNA genomes (single or double-stranded)

• They use host machinery to transcribe and translate their genes

Retroviruses

• have RNA or DNA genomes

• They insert their genome into the host genome and use host machinery to transcribe and translate genesc

Types of viruses: RNA viruses, DNA viruses, and retroviruses
Which viral group is most oncogenic (causes cancer)?
A) DNA viruses
B) RNA viruses
C)Retroviruses

A) DNA viruses
C)Retroviruses

Genes

are DNA sequences that encode information for functional* products.

Intron splice signals

• have known function in
  the regulation of genes

• contain the regulatory information for their own splicing, guides excising the intron from the mRNA is located in the intron itself

• Second, serve as sites for cis-regulatory evolution by slowing down translation

What organisms contain introns?
A) Eukaryotes
B) Archea
C) Bacteria
D) Viruses
E) All of the above

E) All of the above

Non-spliceosomal introns

• are technically self-splicing ribozymes: RNA molecules that can catalyze their own excision

• found throughout all domains of life and viruses

• Neither Group I or Group II introns rely on ribonuclearproteins

Group I introns

• require GTP for the energy to do their splicing

• differ in their specific splicing mechanism which results in a linear or circular intron

Group II introns and spliceosomal introns

• require the adenine at the 3’ end and form a lariat

• Because of the similarities in mechanism, it is assumed that spliceosomal introns evolved from this intron

Cis-regulatory sequences (promoter)

located on the same DNA (chromosome) as the DNA they are controlling

Trans-regulatory sequences (enhancer)

located on a different chromosome/piece of DNA, typically proteins

Long segmental duplications

can be on the same or different chromosomes

short segmental duplications

sequential repeats like Simple repeats (SSRs), simple tandem repeats (STRs), Satellites

Satellite DNA

• are relatively small tandemly repeating sequences that can repeat for millions of base pairs

• expands typically though complex local chemical interactions in the DNA, repeating the same sequence often causes strange self interactions that can lead to either deletion or duplication

• make up the telomeric repeats, centromeric repeats, and other important chromosome structures

Class 1: Retrotransposons (TE DNA)

• “Copy and paste”

• transcribed into mRNA, reverse transcribed into DNA, then integrated back into the genome elsewhere, creating a new copy

• related and can evolve into one another, the only real difference is the viral protein coat is missing here

Class 2:DNA transposons (TE DNA)

“Cut and paste”

Transposons

• can be ‘domesticated’ by the host genome to serve new functions

• neutral to the host genome they reside in

Do 2 different individuals from the same species have the same banding patterns on their chromosomes?
a) Yes
b) No
c) I don’t know

a) Yes

What percentage of our genomes differ?
a. ~ <0.5%
b. ~ 1.5%
c. ~ 17%
d. ~ 50%
e. ~ 85%

b. ~ 1.5%

Single Nucleotide Polymorphisms (SNPs)

• sometimes called SNV (variant))

• Typically caused by errors in DNA replication ( differ by 1 base pairs)

• Sometimes by environmental damage

Copy Number Variants (CNVs)

• Some are very short (eg. Trinucleotide repeat).

• Most are very long, containing >1 gene (Average size in humans is ~20Kbp)

• Typically caused by errors in recombination (meiosis and DNA repair or in mitosis and die)

What type of mutation is likely to lead to a LOF (or null) allele?
An allele that prevents the activity of a gene is referred to as a LOSS OF FUNCTION (LOF) allele.
a. Intergenic (between gene) SNP
b. Intergenic CNV
c. Intergenic indel
d. Intragenic (within gene) SNP
e. Intragenic indel

c. Intergenic indel

Frameshifts

caused by Indels in coding sequences that results in altered protein reading frames, or introduce a stop codon