Test 2

Question 1

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

Answer 1

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

Question 2

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

Answer 2

Prokaryotes, eukaryotes have introns and exons that affect genome size

Question 3

Horizontal Gene Transfer (HGT)

Answer 3

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

Question 4

Vertical Gene Transfer (VGT)

Answer 4

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

Question 5

Pathogenicity islands

Answer 5

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

Question 6

Gene Family

Answer 6

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

Question 7

How do you determine what an essential gene is?

Answer 7

Something that is found across organisms

Question 8

What types of genes are unique to vertebrates?

Answer 8

Immune or nervous systems

Question 9

50% of the human genome can be classified as:

Answer 9

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

Question 10

How much of the human genome is made of exons?

Answer 10

1%

Question 11

Roughly how many proteins are in the human proteome?

Answer 11

50,000-60,000 proteins

Question 12

Are introns longer or shorter than exons in humans?

Answer 12

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

Question 13

Redundant genes

Answer 13

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

Question 14

scarce mRNA

Answer 14

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

Question 15

abundant mRNA

Answer 15

highly active, usually associated w/specialized function

Question 16

housekeeping gene

Answer 16

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

Question 17

Synonymous mutation

Answer 17

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

Question 18

Nonsynonymous mutation

Answer 18

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

Question 19

positive selection

Answer 19

Non-synon/Synon > 1
make gene better version

Question 20

negative selection

Answer 20

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

Question 21

Low heterozygosity of a gene

Answer 21

can indicate recent selective events

Question 22

Where do most mutations in human genome occur?

Answer 22

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

Question 23

Do synonymous or nonsynonymous mutations accumulate faster?

Answer 23

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

Question 24

Orthologous genes

Answer 24

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

Question 25

Paralogous genes

Answer 25

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

Question 26

Pseudogenes

Answer 26

enough similarity but too many mutations leading to gene inactivation

Question 27

Consensus sequence

Answer 27

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.

Question 28

Codon bias

Answer 28

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

Question 29

Introns late hypothesis

Answer 29

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

Question 30

Introns early hypothesis

Answer 30

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

Question 31

Exon shuffling

Answer 31

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

Question 32

Genome duplication

Answer 32

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

Question 33

Autopolyploidy

Answer 33

results from mitotic or meiotic errors within a species

Question 34

Allopolyploidy

Answer 34

results from hybridization between 2 different but reproductively compatible species

Question 35

Transposable elements

Answer 35

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

Question 36

Gene clusters

Answer 36

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

Question 37

Dispersed gene family

Answer 37

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

Question 38

Ribosomal RNA

Answer 38

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

Question 39

Identical genes

Answer 39

tandemly repeated to form one or more clusters

Question 40

ribosomal DNA (rDNA)

Answer 40

transcriptional units alternate with non-transcribed spacers

Question 41

Non-transcribed spacers

Answer 41

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

Question 42

Nucleolar organizer

Answer 42

region of chromosome carrying genes encoding rRNA

Question 43

Nucleolus

Answer 43

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

Question 44

Crossover fixation

Answer 44

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

Question 45

Unequal crossing over

Answer 45

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

Question 46

Concerted evolution

Answer 46

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

Question 47

Gene conversion

Answer 47

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

Question 48

Satellite DNA

Answer 48

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

Question 49

CsCl gradient ultracentrifugation

Answer 49

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

Question 50

Euchromatin

Answer 50

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

Question 51

In situ hybridization

Answer 51

used to identify the location of highly repetitive DNA

Question 52

Human Minisatellite DNA in DNA Profiling

Answer 52

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

Question 53

Chromosomes

Answer 53

unit of the genome carrying many genes

Question 54

Chromatin

Answer 54

packaged DNA: DNA + proteins

Question 55

Capsid

Answer 55

protein shell, formed by assembly of coat protein

Question 56

Hairpin turn

Answer 56

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

Question 57

Rolling circle

Answer 57

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

Question 58

Terminase

Answer 58

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

Question 59

Bacterial nucleoid

Answer 59

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

Question 60

Nucleoid associated proteins (NAPs)

Answer 60

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

Question 61

Negatively supercoiled

Answer 61

supercoil is unwound, against turn of helix

Question 62

Positively supercoiled

Answer 62

supercoil is tightly wound, with turn of helix

Question 63

Scaffold

Answer 63

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

Question 64

Endoreduplication

Answer 64

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

Question 65

H3 variant

Answer 65

marks where mitotic spindle attaches to centromere

Question 66

CEN element

Answer 66

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

Question 67

CBF3

Answer 67

complex that binds to CDEIII and is essential for centromeric function

Question 68

TRF2

Answer 68

protein that helps form t-loop