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Flashcards in Nov 6 Deck (41):
1

Influenza is a/an ___ virus who’s genome is primarily ___
a) RNA/proteins coding regions
b) RNA/ncDNA
c) DNA/proteins coding regions
d) DNA/ncDNA

a) RNA/proteins coding regions

2

TRUE/FALSE
Transposons are ‘selfish DNA’ elements that can circularize, self-replicate and are transmitted between cells via conjugation

FALSE
plasmids

3

How many ___ are described in a synteny
plot w/ 3 perpendicular lines?
a) duplications/2
b) deletions/3
c) inversions/3
d) inversions/2

c) inversions/3

4

What is slippage?

mutation which leads to either a trinucleotide or dinucleotide expansion or contraction during DNA replication

5

Mononucleotide repeats often lead to...

slippage

6

What nucleotide repeats are most common?

AT

7

Short nucleotide repeats are as frequent as would be expected by chance? What about longer repeats?

very few

8

Genomes with more coding DNA sequences (CDS) are generally more ___ biased

GC

9

Free-living bacteria more ___ biased than pathogens
and endosymbionts

GC

10

Why is there mutational bias for G --> A and C --> T?

Melting of G-C bond slower than A-T, so faster replication and transcription

11

Highly expressed genes present
a) lagging strand
b) leading strand
c) both

b) leading strand

12

What nucleotide occurs more frequently on the leading strand of a bacterial chromosome?

G

13

What percentage of the eukaryotic genome is protein-coding genes?

1.5%

14

TRUE/FALSE
Eukaryotic genomes do NOT have mobile genetic elements

FALSE

15

Mononucleotide repeats are most
problematic in all but which of these genomic
motifs?
a) exons
b) rRNA
c) introns
d) plasmid origin of replication

c) introns

16

Which are expressed?
a) introns
b) exons

b) exons

17

How are new proteins made without generating new genes?

Modular protein structures shuffled

18

TRUE/FALSE
Recombination in introns does NOT change reading frame

TRUE

19

Introns arose
a) early
b) late
c) unknown

c) unknown

20

What is a reason for why introns may have arose early?

parsimony-->no known bacteria today have spliceosomal introns

21

What is the difference btw conservative and non-conservative transposable elements?

conservative- cut and paste
non-conservative- copy and paste

22

Transposable elements are found in
a) bacteria
b) eukaryotes
c) both

c) both

23

What is the path of retrotransposons?

DNA-->RNA-->cDNA

24

What is the most common type of retrotransposon?

autonomous LINE/L1 elements

25

What do nonautonomous SINE elements rely on for motility?

L1 protein products

26

What is a benefit of retrotransposons?

can aid in shuffling genes and nuclear material within a single generation

27

What are 3 costs of retrotransposons?

1) generally ‘selfish’ because they don’t help host
2) can disrupt protein coding genes
3) homologous regions can cause ectopic recombination

28

What is ectopic recombination?

Recombination at non-homologous loci

29

What mechanism helps manage transposons?

RNA interference (RNAi)

30

What is the difference btw synonymous and non-synonymous mutations? Which is more common?

synonymous- amino acid change, frequent
non-synonymous- no amino acid change, RARE

31

Which codon position has the greatest mutation rate?

3rd>2nd>1st

32

At what codon position do synonymous and non-synonymous mutations occur?

synonymous- 3rd and 2nd
non-synonymous- 2nd and 1st

33

What is relaxed selection?

weakening or removal of a source of selection that had been important in the maintenance of one or more traits

34

What is the usual cause of synonymous mutation?

drift

35

What allows for non-synonymous mutation?

relaxed (tolerance) selection or novel benefit

36

What does Ka/Ks pairwise comparison examine?

synonymous mutation-->Ks
non-synonymous mutation-->Ka
pairwise comparisons for types of selection

37

What is the difference btw purifying selection and positive selection?

purifying selection- selection for conservation of
ancestral state
positive selection- selection for beneficial, derived
state

38

What is the type of selection if:
a) Ka/Ks > 1
b) Ka/Ks~=1
c) Ka/Ks < 1

a) Ka/Ks > 1-->positive selection
b) Ka/Ks~=1-->neutrality
c) Ka/Ks < 1--> negative selection

39

Average Ka/Ks for antibiotic resistance gene antR in 20 E. coli strains is 0.7 while for the ribosomal protein rpsL it is 0.3
a) rpsL > antR purifying sel
b) antR > rpsL purifying sel
c) equal positive sel
d) equal purifying sel

a) rpsL > antR purifying sel

40

What is a haplotype block?

combination of alleles at adjacent loci on a chromosome that are inherited together

41

How can haplotype blocks reveal newly emerged
positively selected genes?

after many generations of selection for a new mutation, high haplotype diversity is seen around the ancestral allele and low haplotype diversity is seen around the selected allele