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BIOL 322 Genetics > Exam 1 - Chp 3: Genome Structure, Organization, and Variation > Flashcards

Exam 1 - Chp 3: Genome Structure, Organization, and Variation Flashcards

1
Q

How do genetic variation and evolution relate?

A

Evolution produces variation and variation causes evolution

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2
Q

What is the most common cause of evolutionary change in the genome?

A

Natural selection

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3
Q

What is the purpose of polyacrylamid gel electrophoresis?

A

Identify protein variation according to size and charge

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4
Q

What are restriction endonucleases?

A

Enzymes that cut specific sequences on DNA

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5
Q

How can restrictions enzymes (endonucleases) be used to determine if DNA differs?

A

If fragments are similar correlates to if the DNA sequences are similar since restriction enzymes target specific sequences

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6
Q

How is dideoxyribose different from deoxyribose and ribose?

A

There is no hydroxyl (OH) group on the 3’ carbon

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7
Q

What effect does the lack of a hydroxyl (OH) group on the 3’ carbon mean for dideoxynucleotides?

A

No other nucleotides can be added to the dideoxynucleotide once it has been adding to a DNA sequence

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8
Q

What are two benefits to Sanger Sequencing?

A

Runs in 20-150 minutes
Can sequence around 700 bases

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9
Q

What are two cons to Sanger sequencing?

A

It is only good for short sequences, like a single gene
The first 1-30 bases sequences are relatively unreliable

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10
Q

Know what Sanger Sequencing is

A

Described on page 13 of “BIOL322_Exam1”

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11
Q

What are two benefits of Roche 454 sequencing

A

Sequences up to 700 bp fragments
Can do 1 billion bases in 3 days

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12
Q

What are two cons of Roche 454?

A

Produces short reads
individual sequence runs are expensive

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13
Q

What are four pros of Illumina sequencing?

A

Sequences up to 20 billion bases in 1-2 days
Sequences using 50-300 base long fragments
Has high yield with low cost per sequence
Sequences multiple fragments at once

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14
Q

What is massive parallel sequencing/next gen sequencing?

A

Sequencing multiple DNA fragments at the same time; Illumina sequencing is an examples

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15
Q

What are two bonds of Illumina sequencing?

A

Upfront costs are more expensive
Requires larger DNA sample

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16
Q

What is direct sequencing?

A

When DNA is cut into specific fragments that are inserted into vectors and the vectors are amplified. Then, inserts are sequenced and the sequence is assembled using fragment overlaps.

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17
Q

What is shotgun sequencing?

A

When DNA is cut into random fragments that are amplified, then sequenced. The, the sequence is assembled using fragment overlaps.

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18
Q

How does direct sequencing differ from shotgun sequencing?

A

The fragments of DNA are larger and specific
Utilizes vectors for application process

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19
Q

What are reads in terms of analyzing a DNA sequence?

A

The short sequences produced by fragments of the DNA that were created during sequencing process

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20
Q

What are contigs in terms of analyzing a DNA sequence?

A

Genes found from overlap in reads

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21
Q

What are scaffolds in terms of analyzing a DNA sequence?

A

Contigs pieced together to form a chromosome

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22
Q

What are the three key steps of annotation after assembling a genome?

A

1) Scan for ORFs
2) Scan upstream of start codon (ATG) to find transcription start site and control regions
3) BLAST (computer program) genes to look for orthologs

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23
Q

What are orthologs?

A

Genes in different species that evolved from a common ancestral gene

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24
Q

Is genome size correlated with organismal complexity?

A

Loosely?

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25
What are two reasons for keeping unused genes?
May need to recall it Less energy to keep than get rid of
26
What are pseudogenes?
a gene that resembles functional genes (was a functional gene) but have inactivating mutations and no function
27
What organisms most commonly lose genome size and why?
Endosymbionts and parasites because they have access to genetic products from their host
28
What causes the largest increase in genome size?
Polyploidization
29
What is polyploidy?
Having multiple copies on a chromosome
30
What is horizontal gene transfer?
Transfer of DNA from one organism to another
31
What are four causes of genome expansion?
Horizontal gene transfer Polyploidization Gene duplication Gene family expansion
32
What are plasmids?
Small pieces of circular DNA found in prokaryotes?
33
What is the bacterial genome structure?
A closed circular DNA molecule known as their chromosome
34
What is chromatin?
A complex of nucleosomes and DNA that forms higher order structures to form chromosomes
35
What is a nucleosome?
A complex of 8 positively charged proteins that compromise the nucleosome
36
What does Histone 1 do?
It is separate from the 8 histones that make up the nucleosome and works with the nucleosome to regulate chromatin folding
37
What is a chromosome?
Highly condensed chromatin; condenses in metaphase
38
How many chromosome pairs do humans have? Total chromosomes?
23; 46
39
What is the G-banding pattern of the human genome?
Geisma stain make dense part of chromosome appear darker
40
What is heterochromatin?
Chromatin that is densely packed
41
What is euchromatin?
Chromatin that is less dense, typically protein coding region
42
What is endosymbiosis?
The theory that mitochondria and chloroplast arose from an ancestral eukaryotic cell absorbing/consuming a bacterium
43
Did the mitochondria or chloroplast come first based on endosymbiosis?
Mitochondria
44
What is a telomere?
A repetitive DNA sequence that caps the end of a chromosome
45
What is the p-arm of the chromosome?
The shorter arm
46
What is the q-arm of a chromosome?
The longer arm?
47
What is a centromere?
where chromosomes attach during metaphase
48
What are sister chromatids?
Chromosomes in a pair that are exact copies of one another created by DNA replication
49
What are homologous chromosomes?
Two pairs of chromosomes in a diploid organism that has the same structure, size, and gene arrangement, bur different alleles
50
What is a locus?
The location of a gene on a chromosome
51
What is a genetic map?
An atlas of positions of genes in a genome
52
How do more complex genomes compare in the number of protein coding genes and noncoding protein genes?
More complex genomes tend to have more protein coder genes, but a higher percentage of their genes are noncoding
53
In what cells must mutations occur to to be passed down to offspring?
Germline cells
54
What are gremlin cells?
Cells that produce eggs and sperm (gametes)
55
What are paralogs?
Genes created via gene duplication with slightly altered functions within the same genome
56
What is a base substitution?
A mutation where a base in the DNA sequence is not what it should have been according to the original sequence
57
What is a base deletion?
A base in the sequence is missing → causes a frame shift mutation
58
What is a base insertion?
An extra base is added in the sequence → causes frameshift mutation
59
What is copy number variation (CNV)?
A block of DNA sequence is duplicated and repeated multiple times in a row; very impactful
60
What are gene families?
Similar genes related based on the structure of their protein domain (basically, paralogs)
61
What is the primary genetic source of variation between species?
A base change
62
In what comparison is gene family diversification see most commonly?
Comparison of different species
63
What is redundancy and an example?
More than one version of the same information; paralogs
64
What is robustness and an example?
Alternate routes/system for same outcome; different molecular pathways to achieve same goal
65
What is the C-value paradox?
States that genome size is not correlated with biological complexity which is untrue and based on outliers
66
What is a karyotype?
An individuals complete set of chromosomes

BIOL 322 Genetics (9 decks)

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