Smith for final

Question 1

What is the start codon?

Answer 1

AUG

Question 2

What are the stop codons?

Answer 2

UAA UAG UGA

Question 3

Describe cox1 in the human mitochondrial genome

Answer 3

intact and continuous

polycistronic transcript

Question 4

What does continuous mean in terms of genes?

Answer 4

goes from start to stop codon without anything in between i.e. introns

Question 5

Describe cox1 in the mushroom mitochondria genome

Answer 5

has 19 introns

Question 6

Describe cox1 in diplonema

Answer 6

fragmented and distributed over 9 different chromosomes

trans-splicing puts them together

Question 7

Describe cox1 in diplonema

Answer 7

fragmented and distributed over 9 different chromosomes

trans-splicing puts them together

Question 8

Describe cox1 in Selaginella

Answer 8

exons are not in order

Question 9

What is trans-splicing?

Answer 9

exons located in distant regions or even on different strands or chromosomes are transcribed separately and they joined together key is transcribed separately

Question 10

What is the Davd’s definition of a gene?

Answer 10

A continuous, discontinuous, or fragmented nucleotide sequence encoding a biologically functional molecule, such as a protein, tRNA or rRNA

Question 11

Name a few ways genes can be organized

Answer 11

tight-knit groups
genes within genes
overlapping start/stop codons
genes all alone with lots of noncoding DNA
different strands i.e. point in different directions

Question 12

Give an example of a weird gene in Selaginella’s chloroplast genome

Answer 12

Has a gene with an intron and the intron contains another gene

Question 13

Give an example of a weird gene in Euglena’s (unicellular alga) chloroplast genome

Answer 13

twintrons…an intron inside and intron

have to take the inner one out first

Question 14

In general does complexity scale with gene number?

Answer 14

yes

Question 15

Does gene number scale with genome size?

Answer 15

no

Question 16

What does it mean to be functional?

Answer 16

crucial to the survival of the organism
removing it causes major loss of fitness or death
sequence is essential

Question 17

What was the overall goal of the ENCODE project?

Answer 17

To uncover all functional elements in the human genome, particularly those outside genes

Question 18

What were the goals of the Human Genome Project?

Answer 18

the DNA sequence of all chromosomes

annotation of the genes on those chromosomes

Question 19

What were the goals of the ENCODE project?

Answer 19

discover which regions are transcribed
locate and characterize all regulatory elements
chromatin modifications
uncover DNA methylation patterns 
locate RNA editing sites

Question 20

What were some important results of ENCODE?

Answer 20

75% of the genome is transcriptionally active
8.5% involves transcription factor binding
thousands of new regulatory sites
400 000 transcriptional enhancers
70 000 promoters
80% is associated with at least one biochemical function

Question 21

What were some important results of ENCODE?

Answer 21

75% of the genome is transcriptionally active
8.5% involves transcription factor binding
thousands of new regulatory sites
400 000 transcriptional enhancers
70 000 promoters
80% is associated with at least one biochemical function
5% of the genome is methylated
96% of CpGs are methylated

Question 22

What was ENCODE’s definition of functional?

Answer 22

anything that’s transcribed

Question 23

What is epigenetics?

Answer 23

the study of heritable information that doesn’t involve changes in the DNA sequence

Question 24

Is DNA methylation found across the 3 domains of life?

Answer 24

yes

Question 25

How do bacteria use DNA methylation?

Answer 25

methylate their own DNA so that it doesn't get cut by restriction enzymes

Question 26

What is a DNA modification?

Answer 26

significant genetic alteration that is not apparent or obvious given the primary DNA sequence alone

Question 27

Name some organisms with non-standard genetic codes

Answer 27

vertebrate mitochindrial invertebrate mitochindrial i.e. starfish, c elegans yeast mitochondrial chloroplast of dinoflagellate diplonema, both mitochondrial AND nuclear

Question 28

Describe RNA editing in Selaginellla

Answer 28

Cs get post-transcriptionally edited to Us | requires many extra proteins, very expensive and wasteful

Question 29

Describe RNA editing in Trypanosomes

Answer 29

maxi circles have genes are transcribed mini circles are also transcribed, they are guide RNAs bind to machinery that inserts and deletes Us from the RNA transcripts of the genes on the maxi circles

Question 30

Describe cox1 of humans, mushrooms, diploma, selaginella and trypanosomes

Answer 30

humans- nonstandard code mushrooms- nonstandard code diplonema- nonstandard code and RNA editing selaginella- exons out of order and C to U editing trypanosomes- non-standard code and indel of Us

Question 31

Name 5 categories of differences in genome architecture

Answer 31

``` size structure content modifications embellishment ```

Question 32

What is conversion?

Answer 32

its a type of recombination, one region copies itself onto another

Question 33

Name 3 things you need to consider when thinking about mutations altering genomes

Answer 33

context frequency bias

Question 34

What happens to mutations in an effectively large population?

Answer 34

natural selection is efficient beneficial mutations are fixed deleterious mutations are lost

Question 35

What happens to mutations in an effectively small population?

Answer 35

natural selection is not as efficient there is random genetic drift neutral and slightly deleterious mutations have a better chance of being fixed

Question 36

What is an example of an adaptive hypothesis on genome evolution?

Answer 36

skeletal DNA hypothesis

Question 37

What is an example of a non-adaptive hypothesis on genome evolution?

Answer 37

selfish DNA hypothesis

Question 38

Explain the mutational hazard hypothesis

Answer 38

high mutation rates and large population sizes lead to less embellished genomes

Question 39

Explain the mutational hazard hypothesis

Answer 39

high mutation rates and large population sizes lead to less embellished genomes ie mutation rate and effective population size drive genome evolution

Question 40

What is blastn?

Answer 40

searching nucleotides vs nucleotides

Question 41

What is tblastx?

Answer 41

nucleotide sequence in all 6 reading frames against nucleotide database in all 6 reading frames

Question 42

What is blastp?

Answer 42

amino acid sequence against known amino acid sequences

Question 43

What 3 things do you need to take into consideration when blasting a sequence?

Answer 43

coverage type of hits score and E-value

Question 44

What 3 things do you need to take into consideration when blasting a sequence?

Answer 44

coverage type of hits score and E-value

Question 45

When should you use an amino acid sequence instead of a DNA sequence to make a phylogeny?

Answer 45

when the relationships are broad (amino acid sequence will have fewer differences i.e. won't be saturated)

Question 46

What is a barcode?

Answer 46

a standard gene that you use to compare organisms