Organization of eukaryotic genomes

Question 1

… orders of magnitude difference from smallest to the largest eukaryotic genome

Answer 1

5

Question 2

Describe the genome of Encephalitozoon cuniculi

Answer 2

2.9 X 106 bp

Question 3

Describe the genome of Homo sapiens

Answer 3

6 X 109 bp

Question 4

Describe the genome of Paris japonica

Answer 4

1.5 X 1011 bp

Question 5

Every human cell has … of DNA packaged into a sphere …

Answer 5

2m, 1 x 10-5m across

Question 6

The combined length of DNA in a human is … the diameter of our solar system

Answer 6

4x

Question 7

Every body has … cells

Answer 7

~ten trillion

Question 8

Each one of us has
… km of DNA

Answer 8

~2 x 10^10

Question 9

Describe the packaging of DNA

Answer 9

• naked DNA is packaged into nucleosomes
• into chromatin fibres
• into topologically associated domains
• into an individual chromosome
• in the nucleus

Question 10

DNA encodes every component needed to…

Answer 10

build, operate, maintain, and reproduce an organism.

Question 11

What are the two main delineations of the eukaryotic genome?

Answer 11

• transcribed into RNA
• not transcribed

Question 12

What are the two main delineations of transcribed DNA?

Answer 12

• protein coding genes (1%)
• non-coding genes (3%)

Question 13

Describe the transcribed sequences that form protein coding genes

Answer 13

mRNA

Question 14

Describe the transcribed sequences that form non-coding genes

Answer 14

• tRNA
• rRNA
• snRNA
• snoRNA
• lncRNA
• siRNA

Question 15

Describe the major delineations of the non-transcribed DNA

Answer 15

• structural
• non-structural

Question 16

Describe the structural elements of DNA

Answer 16

• telomeres
• centromeres

Question 17

Describe the major delineations of the non-structural DNA

Answer 17

• unique (35%)
• repetitive (50%)

Question 18

Describe the unique DNA

Answer 18

• CNE
• non-conserved non coding elements

Question 19

CNE

Answer 19

conserved non-coding elements

Question 20

Describe the repetitive DNA segments

Answer 20

• satellite DNA
• retrotransposons
• LINEs
• SINEs

Question 21

Describe a protein coding RNA

Answer 21

• 5’ Cap and UTR
• CDS
• 3’UTR
• polyA tail

Question 22

Describe protein coding DNA

Answer 22

exons separated by introns

Question 23

Describe the relationship between gene number and bp length

Answer 23

Normally distributed

Question 24

The average CDS … bp

Answer 24

~1,000

Question 25

Longest CDS (Titin)

Answer 25

~90,000 bp

Question 26

The average gene ... bp

Answer 26

~20,000

Question 27

Longest gene (dystrophin)

Answer 27

- ~2.2 million bp - CDS = 14,000bp - 16hrs to transcribe

Question 28

Modal exon length

Answer 28

~ 111bp (37 codons)

Question 29

nucleosome

Answer 29

1 DNA packaging unit

Question 30

It takes ...bp of DNA to wrap twice around a nucleosome + ...bp spacer each side (...bp total)

Answer 30

147, 33, 213

Question 31

of all exons shorter than 213bp

Answer 31

~90%

Question 32

Only ... of human genes have only 1 exon

Answer 32

5%

Question 33

... of human genes have 2 or more exons

Answer 33

95%

Question 34

... exons is most common number

Answer 34

4

Question 35

Dystrophin has ... exons

Answer 35

79

Question 36

Titin has ... exons

Answer 36

363

Question 37

Describe the average human gene

Answer 37

- 4 exons - 1000bp CDS - 20,000bp genomic footprint - 95% intron

Question 38

Protein coding genes are ...

Answer 38

not uniformly distributed on chromosomes

Question 39

What is the function of the centromere?

Answer 39

attach chromosomes to spindle

Question 40

Describe the centromere

Answer 40

- region of chromosome that links pair of sister chromatids - where spindle fibers attach via kinetochores in mitosis - usually one per chromosome - 5 million bp long in humans - mostly composed of α-satellites - 10% of the genome

Question 41

α-satellites

Answer 41

171bp repeats

Question 42

What is the function of the telomeres?

Answer 42

protect chromosome ends from degradation

Question 43

Describe the telomeres

Answer 43

- at both ends of each chromosome - ~10,000 bp - thousands of repeats of “TTAGGG” - 3’ Single strand overhang which invades the double helix to form a T-loop - 1% of the genome

Question 44

Regions next to telomeres tend to have ...

Answer 44

higher gene density

Question 45

Describe the relationship between telomeres and recombination

Answer 45

Sub-telomeric regions most frequently exchanged during recombination

Question 46

Describe “satellite” DNA

Answer 46

- 1–6 bp simple tandem repeats - 3% of the genome

Question 47

What causes satellite DNA?

Answer 47

DNA replication errors

Question 48

What percentage of the genome is DNA replication errors?

Answer 48

3%

Question 49

Describe DNA replication errors

Answer 49

- slippage and realignment - misalignment

Question 50

Describe the two possibilities of misalignment post-extension

Answer 50

- +1 repeat mutation: 12-repeat allele after subsequent DNA replication - -1 repeat mutation: 10-repeat allele after subsequent DNA replication

Question 51

What is one method of DNA rescue?

Answer 51

DNA mismatch repair

Question 52

List some retrotransposons

Answer 52

- LTRs - LINEs - SINEs

Question 53

Describe retrotransposon formation

Answer 53

- formation of ribonuceloprotein complices undergo reverse transcription and integration - then transcribed and translated

Question 54

Describe retrotransposons

Answer 54

- encode proteins that facilitate retrotransposition - kept inactive by RNAi - older ones mostly mutated and thus inactive - ~47% of your genome

Question 55

Describe LTRs

Answer 55

gag and pol type genes

Question 56

Describe LINEs and SINEs

Answer 56

encode reverse transcriptase and other proteins

Question 57

Describe the average human gene

Answer 57

- 4 exons encoding an 1000 bp long mRNA - footprint of the gene is 20,000bp long ~30% of an average gene is LINEs, SINEs, and SSRs