RR5

Question 1

What’s a genome?

Answer 1

Entirety of an organism’s hereditary information. Usually DNA (except some viruses).

Question 2

True or False? “Genomes only contain coding sequences”

Answer 2

False. It’s mostly non-coding DNA.

Question 3

True or False? “Genome size is an indicator of organism complexity”

Answer 3

False. (Humans have less bases than tulips.) The differences are mostly due to non-coding regions.

Question 4

What’s the difference between introns and intergenic regions?

Answer 4

Introns are found within the coding sequence (gets removed) while intergenic regions are between two separate genes.

Question 5

What’s a gene?

Answer 5

Nucleic acid sequence required for the synthesis of a product (protein, DNA, RNA). They are transcribed.

Question 6

What are the different parts of a gene?

Answer 6

Exons: Coding region, ORF. Start to end codon. // Control regions: promoters, regulators // Introns: separate exons, are spliced during mRNA synthesis, UTR

Question 7

What’s a transcription unit?

Answer 7

The combination of all exons (no control, no intron) that gets transcribed into RNA.

Question 8

True or False? “The same gene will always be read and processed the same way”

Answer 8

False. Genes can be spliced differently leading to isoforms (multiple forms of a protein). (An exon might not get transcribed, etc.)

Question 9

What’s the difference between “solitary” and “gene family” genes?

Answer 9

Solitary: appears once, single-copy gene
Gene family: related genes that come are duplicates, multiple copies of a solitary gene.

Question 10

True or False? “Proteins with similar functions have completely different amino acid sequences”

Answer 10

False. It’s common that similar sequences are observed if they carry the same task.

Question 11

Describe BLAST (protein sequence similarity test)

Answer 11

Both proteins are aligned so that identical residues are at the same position.

Question 12

True or False? “Protein numbers and DNA length vary just as much between species”

Answer 12

False. Protein number is much more consistent.

Question 13

What’s the point of duplicating genes in the genome.

Answer 13

They can either evolve a new function or get degraded (no need for two genes doing the same job).

Question 14

True or False? “Comparing proteins among species can suggest evolutionary relationships.”

Answer 14

True.

Question 15

What are ortholog proteins?

Answer 15

Same proteins, different species (homolog trait, speciation)

Question 16

What are paralog proteins?

Answer 16

Similar proteins, same species.

Question 17

What are the two types of SSRs?

Answer 17

minisatellite DNA and microsatellite DNA

Question 18

What’s minisatellite DNA?

Answer 18

Usually in centromeres/telomeres, 20-50 repeats (each 14-100 bp)

Question 19

What’s microsatellite DNA?

Answer 19

Sometimes in transcription unit, goes up to 600bp (each repeat is 1 to 4 bp).

Question 20

Describe backward slippage during replication of repeats

Answer 20

Polymerase can slip as replication happens which ultimately adds an extra repeat: can lead to toxic proteins and aggregates (Huntington’s disease).

Question 21

True or False? “Each individual has a different amount of SSRs (the actual repeats themselves”

Answer 21

True. It can be amplified by PCR and studied in DNA fingerprinting (paternity or criminal Id)

Question 22

What are transposable elements (TEs)

Answer 22

Sequence of genes that can move around the genome. Can cause mutations.

Question 23

Name two major types of TEs

Answer 23

Transposons and Retrotransposons

Question 24

What’s the difference between transposons and retrotransposons?

Answer 24

Transposons cut and paste while retrotransposons copy and paste.

Question 25

How were TEs first discovered?

Answer 25

Bu studying the color formation pattern of corn (which didn’t adhere to Mendel’s teachings).

Question 26

Describe how transposons duplicate differently

Answer 26

(Requires a transposase to catalyze its insertion) If they jump to a region that hasn’t replicated yet, an extra copy is generated in the resulting daughter chromosome (assuming it started somewhere replication had already occurred).

Question 27

What is an effect of TE moving around?

Answer 27

Recombination, exon shuffling, new genes.

Question 28

How do LTR function as TE?

Answer 28

Similar to retroviruses, they can code for reverse transcriptase and integrase (essentially the same as transposase). (LTR is the repeat region being moved)

Question 29

What’s the difference between LTRs and LINEs/SINEs?

Answer 29

Unlike LTRs, the repeats are AT-rich. The protein region contains ORF1/ORF2 (both for LINE, only ORF1 for SINE).

Question 30

True or False? “During their motion, transposons and LINEs can bring adjacent genes sometimes”

Answer 30

True. For LINEs, it happens if there’s a stronger poly(A) tail signal nearby. For transposons, it happens when a gene is between two TE.