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Smith for final Flashcards

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Biology 101 flashcards
1
Q

What is the start codon?

A

AUG

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2
Q

What are the stop codons?

A

UAA UAG UGA

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3
Q

Describe cox1 in the human mitochondrial genome

A

intact and continuous

polycistronic transcript

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4
Q

What does continuous mean in terms of genes?

A

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

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5
Q

Describe cox1 in the mushroom mitochondria genome

A

has 19 introns

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6
Q

Describe cox1 in diplonema

A

fragmented and distributed over 9 different chromosomes

trans-splicing puts them together

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7
Q

Describe cox1 in diplonema

A

fragmented and distributed over 9 different chromosomes

trans-splicing puts them together

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8
Q

Describe cox1 in Selaginella

A

exons are not in order

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9
Q

What is trans-splicing?

A

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

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10
Q

What is the Davd’s definition of a gene?

A

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

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11
Q

Name a few ways genes can be organized

A

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

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12
Q

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

A

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

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13
Q

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

A

twintrons…an intron inside and intron

have to take the inner one out first

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14
Q

In general does complexity scale with gene number?

A

yes

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15
Q

Does gene number scale with genome size?

A

no

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16
Q

What does it mean to be functional?

A

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

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17
Q

What was the overall goal of the ENCODE project?

A

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

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18
Q

What were the goals of the Human Genome Project?

A

the DNA sequence of all chromosomes

annotation of the genes on those chromosomes

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19
Q

What were the goals of the ENCODE project?

A 
discover which regions are transcribed
locate and characterize all regulatory elements
chromatin modifications
uncover DNA methylation patterns 
locate RNA editing sites
20
Q

What were some important results of ENCODE?

A

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

21
Q

What were some important results of ENCODE?

A

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

22
Q

What was ENCODE’s definition of functional?

A

anything that’s transcribed

23
Q

What is epigenetics?

A

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

24
Q

Is DNA methylation found across the 3 domains of life?

A

yes

25
Q

How do bacteria use DNA methylation?

A

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

26
Q

What is a DNA modification?

A

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

27
Q

Name some organisms with non-standard genetic codes

A

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

28
Q

Describe RNA editing in Selaginellla

A

Cs get post-transcriptionally edited to Us

requires many extra proteins, very expensive and wasteful

29
Q

Describe RNA editing in Trypanosomes

A

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

30
Q

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

A

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

31
Q

Name 5 categories of differences in genome architecture

A 
size
structure 
content
modifications
embellishment
32
Q

What is conversion?

A

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

33
Q

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

A

context
frequency
bias

34
Q

What happens to mutations in an effectively large population?

A

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

35
Q

What happens to mutations in an effectively small population?

A

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

36
Q

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

A

skeletal DNA hypothesis

37
Q

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

A

selfish DNA hypothesis

38
Q

Explain the mutational hazard hypothesis

A

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

39
Q

Explain the mutational hazard hypothesis

A

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

40
Q

What is blastn?

A

searching nucleotides vs nucleotides

41
Q

What is tblastx?

A

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

42
Q

What is blastp?

A

amino acid sequence against known amino acid sequences

43
Q

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

A

coverage
type of hits
score and E-value

44
Q

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

A

coverage
type of hits
score and E-value

45
Q

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

A

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

46
Q

What is a barcode?

A

a standard gene that you use to compare organisms

Genetics (5 decks)

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