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Molecular Biology of the Gene > Test 2 > Flashcards

Test 2 Flashcards

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1
Q

True or False: Minimum gene number and size requirement are not related to organism complexity

A

False
The more complex, the higher minimum gene number AND size required

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2
Q

Gene size is proportional to gene number in prokaryotes or eukaryotes?

A

Prokaryotes, eukaryotes have introns and exons that affect genome size

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3
Q

Horizontal Gene Transfer (HGT)

A

transfer of DNA from one cell to another without cell division (same generation)

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4
Q

Vertical Gene Transfer (VGT)

A

transfer of DNA from one cell to another utilizing cell division (across generations)

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5
Q

Pathogenicity islands

A

segments of DNA that are present in pathogenic bacterial genomes but absent in nonpathogenic relatives (acquired via HGT)

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6
Q

Gene Family

A

Multiple copies of gene type but with slight variations (expression, function, etc.) that are similar enough to become family

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7
Q

How do you determine what an essential gene is?

A

Something that is found across organisms

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8
Q

What types of genes are unique to vertebrates?

A

Immune or nervous systems

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9
Q

50% of the human genome can be classified as:

A

repetitive DNA (transposons, introns, telomeres, centromeres, satellite sequences, etc.)

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10
Q

How much of the human genome is made of exons?

A

1%

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11
Q

Roughly how many proteins are in the human proteome?

A

50,000-60,000 proteins

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12
Q

Are introns longer or shorter than exons in humans?

A

Introns are longer in humans compared to plants that have smaller genes with shorter introns

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13
Q

Redundant genes

A

When there are two or more copies of a single gene, can lead to mutations in either that might not have detectable effects

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14
Q

scarce mRNA

A

large number of individual mRNA species, each present in very few copies per cell (most genes)

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15
Q

abundant mRNA

A

highly active, usually associated w/specialized function

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16
Q

housekeeping gene

A

high abundance, genes with standard or needed functions (ex. actin)
Important b/c measuring activity of genes need to make sure gene are not changing due to stress or other factors so a housekeeping gene will be used as a reference to see if activity level is stable

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17
Q

Synonymous mutation

A

mutation within a coding region that does NOT alter the amino acid sequence (aka silent mutation)

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18
Q

Nonsynonymous mutation

A

mutation within a coding region that DOES alter the amino acid sequence

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19
Q

positive selection

A

Non-synon/Synon > 1
make gene better version

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20
Q

negative selection

A

Non-synon/Synon < 1
changes/disrupt function of gene

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21
Q

Low heterozygosity of a gene

A

can indicate recent selective events

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22
Q

Where do most mutations in human genome occur?

A

Most likely to be in a regulatory element since exons are only 1% of human genome

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23
Q

Do synonymous or nonsynonymous mutations accumulate faster?

A

Synonymous mutations, since they don’t change function so it can be passed on easier vs nonsynonymous mutations that DO change function and can make it harder to pass the gene on

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24
Q

Orthologous genes

A

related genes in different species that have the same function. Made by speciation

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25
Q

Paralogous genes

A

related genes in same species, not same function. Made by gene duplication

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26
Q

Pseudogenes

A

enough similarity but too many mutations leading to gene inactivation

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27
Q

Consensus sequence

A

Blast sequences against all other sequences to compare similarity, calculated by taking the most common base at each position, can help determine how long its been since divergence.

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28
Q

Codon bias

A

higher usage of one codon to encode for an amino acid in where there are several synonymous codes

29
Q

Introns late hypothesis

A

earliest genes did not contain introns, later added to some genes
Evidence: similar genes in closely related organisms have new introns in new locations

30
Q

Introns early hypothesis

A

genes originated as interrupted structures, those now without introns have lost them in evolution
Evidence: similar genes in distant organisms have similar locations; introns usually break up protein sub-domains

31
Q

Exon shuffling

A

hypothesis that genes evolved by recombination of various exons encoding functional protein domains

32
Q

Genome duplication

A

when polyploidization increases the chromosome number by a multiple of 2 (not common in animals)

33
Q

Autopolyploidy

A

results from mitotic or meiotic errors within a species

34
Q

Allopolyploidy

A

results from hybridization between 2 different but reproductively compatible species

35
Q

Transposable elements

A

tend to increase in copy number when introduced to a genome, kept in check by negative selection and transposition regulation elements

36
Q

Gene clusters

A

group of adjacent genes that are identical or related (physically next to one another on chromosome)

37
Q

Dispersed gene family

A

Genes that are placed within the same family that are located on different chromosomes

38
Q

Ribosomal RNA

A

increased demand in cell, evolved to have multiple copies
Genes in genome (identical copies of one another) clustered together that when translated are made into rRNA

39
Q

Identical genes

A

tandemly repeated to form one or more clusters

40
Q

ribosomal DNA (rDNA)

A

transcriptional units alternate with non-transcribed spacers

41
Q

Non-transcribed spacers

A

shorter repeating units whose number and length vary (repetitive but not identical)

42
Q

Nucleolar organizer

A

region of chromosome carrying genes encoding rRNA

43
Q

Nucleolus

A

denser region that stains darker b/c high transcriptional activity in region

44
Q

Crossover fixation

A

hypothesis on how identical repeats are maintained
consequence of unequal crossing over, allows mutation in one member of tandem cluster to spread through whole cluster –> continuous expansion and contraction of the number of genes in the cluster

45
Q

Unequal crossing over

A

hypothesis on how identical repeats are maintained
results from error in pairing and crossing over. one recombinant with deletion of genetic material and one with duplication

46
Q

Concerted evolution

A

hypothesis on how identical repeats are maintained
two or more related genes evolve together as if they were single locus

47
Q

Gene conversion

A

if one gene mutated, cell will use other copy to do replication to maintain original sequence

48
Q

Satellite DNA

A

short repeating DNA sequences, no coding function, do not interrupt coding sequences = not introns

49
Q

CsCl gradient ultracentrifugation

A

Release DNA into solution and add CsCl and spin for hours, DNA will form band with certain density within density gradient (DNA ~1.7, RNA bottom, proteins top) DNA will have two bands upon closer inspection, and lower smaller band is satellite DNA

50
Q

Euchromatin

A

most of the genome in interphase nucleus. Contain most of active or potentially active DNA. less tightly coiled than heterochromatin

51
Q

In situ hybridization

A

used to identify the location of highly repetitive DNA

52
Q

Human Minisatellite DNA in DNA Profiling

A

Differences in individuals on restriction fragments that contain short repeated sequences or using PCR

53
Q

Chromosomes

A

unit of the genome carrying many genes

54
Q

Chromatin

A

packaged DNA: DNA + proteins

55
Q

Capsid

A

protein shell, formed by assembly of coat protein

56
Q

Hairpin turn

A

when single stranded DNA or RNA can loop back on itself and bind ot itself, leaving a ring/hoop region at end where DNA/RNA remains unpaired

57
Q

Rolling circle

A

genome replication mechanism, circular DNA helix is nicked, outer layer starts to unravel, DNA polymerase starts to replicate missing DNA but it cut off, creating copies of the genome ot insert into the capsid

58
Q

Terminase

A

enzyme cleaving multimers using hydrolysis of ATP to provide energy to translocate DNA into empty viral capsid starting with cleaved end

59
Q

Bacterial nucleoid

A

where genome is contained, multiple loops compacted by nucleoid associated proteins

60
Q

Nucleoid associated proteins (NAPs)

A

associated with packaging DNA (–> gene expression) function in nucleoid architecture, domain topology, and gene regulation

61
Q

Negatively supercoiled

A

supercoil is unwound, against turn of helix

62
Q

Positively supercoiled

A

supercoil is tightly wound, with turn of helix

63
Q

Scaffold

A

DNA loops around and attaches to scaffold at matrix attachment regions (sequences of DNA that attach to scaffold). no sequence conservation, unsure of how it signals DNA to attach at those points
1 scaffold = 1 chromosome

64
Q

Endoreduplication

A

large chromosomes with many dna strands produced by successive replication of synapsed diploid pair of chromosomes replicas do not separate

65
Q

H3 variant

A

marks where mitotic spindle attaches to centromere

66
Q

CEN element

A

protein complex known as kinetochore allows a plasmid to segregate correctly at mitosis

67
Q

CBF3

A

complex that binds to CDEIII and is essential for centromeric function

68
Q

TRF2

A

protein that helps form t-loop

69
Q
A

Molecular Biology of the Gene (2 decks)

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