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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

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Biology 101 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
Q

What are two reasons for keeping unused genes?

A

May need to recall it
Less energy to keep than get rid of

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26
Q

What are pseudogenes?

A

a gene that resembles functional genes (was a functional gene) but have inactivating mutations and no function

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27
Q

What organisms most commonly lose genome size and why?

A

Endosymbionts and parasites because they have access to genetic products from their host

28
Q

What causes the largest increase in genome size?

A

Polyploidization

29
Q

What is polyploidy?

A

Having multiple copies on a chromosome

30
Q

What is horizontal gene transfer?

A

Transfer of DNA from one organism to another

31
Q

What are four causes of genome expansion?

A

Horizontal gene transfer
Polyploidization
Gene duplication
Gene family expansion

32
Q

What are plasmids?

A

Small pieces of circular DNA found in prokaryotes?

33
Q

What is the bacterial genome structure?

A

A closed circular DNA molecule known as their chromosome

34
Q

What is chromatin?

A

A complex of nucleosomes and DNA that forms higher order structures to form chromosomes

35
Q

What is a nucleosome?

A

A complex of 8 positively charged proteins that compromise the nucleosome

36
Q

What does Histone 1 do?

A

It is separate from the 8 histones that make up the nucleosome and works with the nucleosome to regulate chromatin folding

37
Q

What is a chromosome?

A

Highly condensed chromatin; condenses in metaphase

38
Q

How many chromosome pairs do humans have? Total chromosomes?

A

23; 46

39
Q

What is the G-banding pattern of the human genome?

A

Geisma stain make dense part of chromosome appear darker

40
Q

What is heterochromatin?

A

Chromatin that is densely packed

41
Q

What is euchromatin?

A

Chromatin that is less dense, typically protein coding region

42
Q

What is endosymbiosis?

A

The theory that mitochondria and chloroplast arose from an ancestral eukaryotic cell absorbing/consuming a bacterium

43
Q

Did the mitochondria or chloroplast come first based on endosymbiosis?

A

Mitochondria

44
Q

What is a telomere?

A

A repetitive DNA sequence that caps the end of a chromosome

45
Q

What is the p-arm of the chromosome?

A

The shorter arm

46
Q

What is the q-arm of a chromosome?

A

The longer arm?

47
Q

What is a centromere?

A

where chromosomes attach during metaphase

48
Q

What are sister chromatids?

A

Chromosomes in a pair that are exact copies of one another created by DNA replication

49
Q

What are homologous chromosomes?

A

Two pairs of chromosomes in a diploid organism that has the same structure, size, and gene arrangement, bur different alleles

50
Q

What is a locus?

A

The location of a gene on a chromosome

51
Q

What is a genetic map?

A

An atlas of positions of genes in a genome

52
Q

How do more complex genomes compare in the number of protein coding genes and noncoding protein genes?

A

More complex genomes tend to have more protein coder genes, but a higher percentage of their genes are noncoding

53
Q

In what cells must mutations occur to to be passed down to offspring?

A

Germline cells

54
Q

What are gremlin cells?

A

Cells that produce eggs and sperm (gametes)

55
Q

What are paralogs?

A

Genes created via gene duplication with slightly altered functions within the same genome

56
Q

What is a base substitution?

A

A mutation where a base in the DNA sequence is not what it should have been according to the original sequence

57
Q

What is a base deletion?

A

A base in the sequence is missing → causes a frame shift mutation

58
Q

What is a base insertion?

A

An extra base is added in the sequence → causes frameshift mutation

59
Q

What is copy number variation (CNV)?

A

A block of DNA sequence is duplicated and repeated multiple times in a row; very impactful

60
Q

What are gene families?

A

Similar genes related based on the structure of their protein domain (basically, paralogs)

61
Q

What is the primary genetic source of variation between species?

A

A base change

62
Q

In what comparison is gene family diversification see most commonly?

A

Comparison of different species

63
Q

What is redundancy and an example?

A

More than one version of the same information; paralogs

64
Q

What is robustness and an example?

A

Alternate routes/system for same outcome; different molecular pathways to achieve same goal

65
Q

What is the C-value paradox?

A

States that genome size is not correlated with biological complexity which is untrue and based on outliers

66
Q

What is a karyotype?

A

An individuals complete set of chromosomes

BIOL 322 Genetics (9 decks)

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