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Simple Genomes Set 1 > Midterm 1 Vocab > Flashcards

Midterm 1 Vocab Flashcards

1
Q

Yeast Characteristics

A

-genome around 6000 genes
-32 linear chromosomes
-facultative aerobe
-around 650 species
unicellular
haploid and diploid life cycle phases

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2
Q

Yeast haploid life cycle

A
  • mother cell starts to bud
  • bud grows and splits off
  • bud scar left behind
  • after many divisions, cell covered in bud scars and can no longer divide
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3
Q

Diploid formation

A
  • 2 yeast cells of opposite mating types schmoo together
  • cells contact and cell walls dissolve
  • plasmogamy
  • nuclei fuse (karyogamy)
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4
Q

thallus

A

term for bodies of fungi or lichen

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5
Q

homothallic

A

sexual reproduction with a single thallus; mates with itself

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6
Q

heterothallic

A

sexual reproduction with two different thalli

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7
Q

positive selection

A

selects for cells with WT gene copy

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8
Q

Determining Mating type: testing for secreted pheromones

A
  • seed plate with sensitive strain of yeast
  • mating factor diffuses from filter paper patch of an unknown mating type
  • lawn grows
  • dark “halo” around sensitive cells of the opposite mating type that are stopped in G1
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9
Q

Determining mating type: crossing with known types

A
  • agar streaked with yeast cells on rich media w/ a selectable marker
  • test crosses with strains of known mating types
  • incubate
  • replica plate onto media lacking uracil and lysine
  • use phenotype to determine query strain
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10
Q

Isolating haploids

A
  • collect asci
  • use enzymes to open asci and release the ascospores
  • separate ascospores onto agar
  • replica plate onto media lacking lysine and onto media lacking uracil
  • use phenotypes to score tetrad
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11
Q

tetratype (T)

A

both parental and recombinant genotypes present

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12
Q

parental ditype (PD)

A

all genotypes the same as parents

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13
Q

nonparental ditype (NPD)

A

all genotypes different from parents

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14
Q

uniparental inheritance

A

inherited from a single parent (ex. mitochondria)

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15
Q

pyruvate dehydrogenase

A

makes acetyl coA

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16
Q

PDH kinase

A

adds deactivating phosphate to PDH to regulate

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17
Q

PDH kinase inhibitors

A

NAD+, ADP, SH-coA

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18
Q

PDH kinase activators

A

NADH, acetyl coA

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19
Q

PDH phosphatase

A

removes deactivating phosphate to activate PDH; regulated with calcium

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20
Q

Reactions catalyzed by PDH

A
  • removal of pyruvate carboxyl group
  • remaining 2C molecule oxidized and NAD+ reduced
  • coenzyme A attached via sulfer atom to make acetyl coA
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21
Q

respirosome

A

physical association of complexes 1, 3, and 4 in the ETC; reduces buildup of ROSs; needed for complex 1 stability

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22
Q

brown adipose

A

tissue used to make heat in non-shivering thermogenesis; heat made with uncoupler UCP1

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23
Q

UCP mechanism

A
  • long chain FA anions trapped by hydrophobic interactions of long tails in their symporter
  • oscillates back and forth
  • unable to dissociate, so only H transported
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24
Q

dinitrophenol

A

uncoupling drug that increases permeability of MIM to H

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25
Q

heteroplasmy

A

multiple different genomes within a single cell

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26
Q

twinkle

A

mtDNA helicase

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27
Q

Initiation of mtDNA Replication

A
  • twinkle binds Ori H, and unwinds short DNA section
  • POLRMT initiates transcription from LSP; provides 3’ primer to start synthesis
  • twinkle passes TAS
  • new strand displaces parental H-strand, making D-loop; coated in mtSSB
  • pol gamma replicates DNA
  • ori L displaced and forms stem loop; primer made on stem loop, and H-strand replicated
  • RNase H removes primer
  • DNA ligase repairs backbone
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28
Q

rCRS

A

revised cambridge reference sequence

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29
Q

haplogroups

A

groups of humans based on mtDNA differences

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30
Q

mitochondrial eve

A

hypothetical common ancestor of all human mtDNA

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31
Q

TFAM

A

transcription factor A, mitochondrial; binds DNA without sequence specificity, binds, wraps, and bends DNA for compaction; Recruits POLMRT to promoter to initiate transcription

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32
Q

ATAD3

A

ATPase triple A domain containing proteins; act as scaffold; binds TFAM and ribosomes to improve efficiency of transcription and translation

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33
Q

Transcription steps

A
  • HSP and LSP recruit POLRMT

- mtDNA transcribed into 2 polycistronic transcripts

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34
Q

Transcription initiation

A
  • TFAM recruits POLRMT and promoter recognized

- TFB2M changes POLRMT to induce DNA melting

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35
Q

TFB2M

A

transcription factor B2

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36
Q

TEFM

A

transcription elongation factor, mitochondrial; promotes POLRMT ability to add nucleotides; required for elongation; acts as switch between transcription and replication

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37
Q

transcript maturation

A

endonuceotytic exision of mt-tRNA releases mRNAs and rRNAs

  • tRNA punctuation model
  • RNase P binds 5’ side of tRNA transcript, RNase 2 binds 3’ end
  • other transcripts released
  • 3’ adenylation completes stop codon
  • rRNAs join with proteins to make ribosomes
  • tRNAs associate with amino-acyl tRNA synthetase
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38
Q

ribozymes

A

RNA with enzymatic properties

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39
Q

S (svedberg) unit

A

sedimentation velocity per unit gravitational force

40
Q

Transcriptional activators

A

proteins binding directly to mitochondria mRNA to help recruit ribosome and initiate transcription

41
Q

N-formyl-methionine

A

mito and bacterial translation start amino acid (instead of methionine in euk.)

42
Q

aminoacyl tRNA synthetase

A

enzyme responsible for adding amino acids to tRNA

43
Q

pleiotropy

A

one gene mutation has many different effects; ex. tRNA mutations could produce different phenotypes each translation

44
Q

electrophoretic effect

A

transport based on voltage potential

45
Q

PAM

A

presequence translocase associated motor; uses ATP hydrolysis to pull preprotein into matrix

46
Q

mia

A

protein in MIM that forms transient disulfide bonds with preprotein

47
Q

Erv1

A

enzyme that oxidizes mia by passing electrons to cytochrome C

48
Q

SAM

A

sorting and assembly machinery

49
Q

fractionate

A

separate mitochondria from rest of cell for analysis

50
Q

OSCP

A

oligomycin sensitivity conferring protein

51
Q

MICOS

A

mitochondrial contact site and cristae organizing system; anchors mitochondrial membranes together

52
Q

DnaJ

A

Complex unit that embeds in MOM, tethering MIM and MOM together

53
Q

MIB

A

SAM + MICOS; mito intermembrane space bridging complex

54
Q

mfn1

A

GTPase involved in mito fusion

55
Q

mfn2/f201p

A

mito fusion GTPase; fuzzy onion (due to phenotype in spermatid formation of fruit flies)

56
Q

OPA1

A

optic atrophy; involved in inner membrane fusion

57
Q

Drp1

A

dynamin related protein; in fission

58
Q

Dynamins in membrane fission

A
  • dynamin forms helical polymer
  • dynamin oligomer constricts in presence of GTP
  • dynamin catalyzes fission upon GTP hydrolysis
  • eventually membranes winched apart
59
Q

importance of fission and fusion

A
  • mitos can have specialized functions in different parts of the cell
  • involved in mito quality control
60
Q

mitofilin/mic60

A

Transmembrane protein part of larger MIB complex involved in crista junction formation

61
Q

E1

A

activator of ubiquitination

62
Q

E2

A

conjugation activity during ubiquitination

63
Q

E3

A

Ligates ubiquitin onto mito proteins (parkin)

64
Q

PINK1

A

PTEN induced kinase 1; accumulates when membrane potential abnormal and phosphorylates parkin; levels controlled by PARL at normal membrane potentials

65
Q

Parkin

A

tags mfn1 for ubiquitnation; prevents unhealthy mito fusing with a healthy one; mutations cause parkinson’s

66
Q

archaezoan

A

primitive euk evolved from archaea; often used to describe host at time of endosymbiosis

67
Q

PFOR

A

pyruvate ferridoxin oxidoreductase; converts pyruvate into CO2, acetyl coA, and reduced ferredoxin

68
Q

ferredoxin

A

Accepts electrons from hydrogenase to produce hydrogen gas

69
Q

hydrogenase

A

oxidizes ferredoxin to make hydrogen

70
Q

Driving forces of endosymbiosis

A
  • reducing levels of toxic oxygen
  • syntropy (host uses symbiont waste products)
  • mutually beneficial energy metabolism
71
Q

hydrogen hypothesis

A

theory that need for hydrogen by the host drove the endosymbiosis and development of mito

72
Q

TACK superphylum

A

Archaea group with homologs of ESPs

  • crenactins in korearchaeota, aigararchaeota
  • distant tubulin in thanarchaeota
73
Q

Ras-GTPases

A

euk proteins involved in cytoskeleton dynamics and phagocytosis

74
Q

inside out model of nucleus evolution

A

-theory of nucleus evolution based on membrane blebs forming to associate more with endosymbiont resulted in the double membrane of the eukaryotic nucleus

75
Q

group 2 introns

A

self-catalytic ribozymes implicated as a driving factor in the development of the nucleus

76
Q

IEP

A

intron encoded protein; encoded by group 2 introns; has maturase, DNA binding, nuclease, and reverse transcriptase activity

77
Q

Domestication of group 2 intron

A

Host has adapted methods to regulate introns (ex. spliceosome, low IEP production, etc.)

78
Q

Mitochondrial cross

A

cross where both parents contribute mtDNA

79
Q

segregational petities

A

show mendellian inheritance

80
Q

vegetative petities

A

show non-mendellian inheritance

81
Q

vegetative

A

non-sexual/mitotic

82
Q

neutral petities

A

all progeny WT; lack mtDNA

83
Q

suppressive petities

A

mutant phenotypes dominate over WT; have deletions in mtDNA so size made up by replicating whatever’s left until around the same size as WT

84
Q

hypersuppressive

A

> 95% petite progeny

85
Q

panmixis model

A

mitos fuse and mtDNA randomly mixes in yeast zygote; homoplasmy happens by chance

86
Q

stochastically assorted

A

asymmetric distribution initially favours asymmetry later in distribution

87
Q

oli

A

oligomycin; inhibits ATP synthase

88
Q

cap

A

chloramphenicol; inhibits mito protein synthesis

89
Q

DAPI

A

DNA specific fluorescent dye

90
Q

Ytal10p-GFP

A

transmembrane MIM protein; able to populate all parts of membrane over time

91
Q

Tom6p-GFP

A

outer membrane protein distributed throughout cell after 3-4 hours

92
Q

mdm

A

mitochondria distribution and morphology mutants

93
Q

mmm

A

maintenance of mito morphology mutants

94
Q

ERMES

A

ER-mito encounter structure

95
Q

Dnm1

A

yeast version of Drp1

Simple Genomes Set 1 (1 decks)

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