Midterm 1 Vocab Flashcards
(95 cards)
1
Q
Yeast Characteristics
A
-genome around 6000 genes
-32 linear chromosomes
-facultative aerobe
-around 650 species
unicellular
haploid and diploid life cycle phases
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
3
Q
Diploid formation
A
- 2 yeast cells of opposite mating types schmoo together
- cells contact and cell walls dissolve
- plasmogamy
- nuclei fuse (karyogamy)
4
Q
thallus
A
term for bodies of fungi or lichen
5
Q
homothallic
A
sexual reproduction with a single thallus; mates with itself
6
Q
heterothallic
A
sexual reproduction with two different thalli
7
Q
positive selection
A
selects for cells with WT gene copy
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
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
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
11
Q
tetratype (T)
A
both parental and recombinant genotypes present
12
Q
parental ditype (PD)
A
all genotypes the same as parents
13
Q
nonparental ditype (NPD)
A
all genotypes different from parents
14
Q
uniparental inheritance
A
inherited from a single parent (ex. mitochondria)
15
Q
pyruvate dehydrogenase
A
makes acetyl coA
16
Q
PDH kinase
A
adds deactivating phosphate to PDH to regulate
17
Q
PDH kinase inhibitors
A
NAD+, ADP, SH-coA
18
Q
PDH kinase activators
A
NADH, acetyl coA
19
Q
PDH phosphatase
A
removes deactivating phosphate to activate PDH; regulated with calcium
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
21
Q
respirosome
A
physical association of complexes 1, 3, and 4 in the ETC; reduces buildup of ROSs; needed for complex 1 stability
22
Q
brown adipose
A
tissue used to make heat in non-shivering thermogenesis; heat made with uncoupler UCP1
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
24
Q
dinitrophenol
A
uncoupling drug that increases permeability of MIM to H
25
heteroplasmy
multiple different genomes within a single cell
26
twinkle
mtDNA helicase
27
Initiation of mtDNA Replication
- 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
28
rCRS
revised cambridge reference sequence
29
haplogroups
groups of humans based on mtDNA differences
30
mitochondrial eve
hypothetical common ancestor of all human mtDNA
31
TFAM
transcription factor A, mitochondrial; binds DNA without sequence specificity, binds, wraps, and bends DNA for compaction; Recruits POLMRT to promoter to initiate transcription
32
ATAD3
ATPase triple A domain containing proteins; act as scaffold; binds TFAM and ribosomes to improve efficiency of transcription and translation
33
Transcription steps
- HSP and LSP recruit POLRMT
| - mtDNA transcribed into 2 polycistronic transcripts
34
Transcription initiation
- TFAM recruits POLRMT and promoter recognized
| - TFB2M changes POLRMT to induce DNA melting
35
TFB2M
transcription factor B2
36
TEFM
transcription elongation factor, mitochondrial; promotes POLRMT ability to add nucleotides; required for elongation; acts as switch between transcription and replication
37
transcript maturation
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
38
ribozymes
RNA with enzymatic properties
39
S (svedberg) unit
sedimentation velocity per unit gravitational force
40
Transcriptional activators
proteins binding directly to mitochondria mRNA to help recruit ribosome and initiate transcription
41
N-formyl-methionine
mito and bacterial translation start amino acid (instead of methionine in euk.)
42
aminoacyl tRNA synthetase
enzyme responsible for adding amino acids to tRNA
43
pleiotropy
one gene mutation has many different effects; ex. tRNA mutations could produce different phenotypes each translation
44
electrophoretic effect
transport based on voltage potential
45
PAM
presequence translocase associated motor; uses ATP hydrolysis to pull preprotein into matrix
46
mia
protein in MIM that forms transient disulfide bonds with preprotein
47
Erv1
enzyme that oxidizes mia by passing electrons to cytochrome C
48
SAM
sorting and assembly machinery
49
fractionate
separate mitochondria from rest of cell for analysis
50
OSCP
oligomycin sensitivity conferring protein
51
MICOS
mitochondrial contact site and cristae organizing system; anchors mitochondrial membranes together
52
DnaJ
Complex unit that embeds in MOM, tethering MIM and MOM together
53
MIB
SAM + MICOS; mito intermembrane space bridging complex
54
mfn1
GTPase involved in mito fusion
55
mfn2/f201p
mito fusion GTPase; fuzzy onion (due to phenotype in spermatid formation of fruit flies)
56
OPA1
optic atrophy; involved in inner membrane fusion
57
Drp1
dynamin related protein; in fission
58
Dynamins in membrane fission
- dynamin forms helical polymer
- dynamin oligomer constricts in presence of GTP
- dynamin catalyzes fission upon GTP hydrolysis
- eventually membranes winched apart
59
importance of fission and fusion
- mitos can have specialized functions in different parts of the cell
- involved in mito quality control
60
mitofilin/mic60
Transmembrane protein part of larger MIB complex involved in crista junction formation
61
E1
activator of ubiquitination
62
E2
conjugation activity during ubiquitination
63
E3
Ligates ubiquitin onto mito proteins (parkin)
64
PINK1
PTEN induced kinase 1; accumulates when membrane potential abnormal and phosphorylates parkin; levels controlled by PARL at normal membrane potentials
65
Parkin
tags mfn1 for ubiquitnation; prevents unhealthy mito fusing with a healthy one; mutations cause parkinson's
66
archaezoan
primitive euk evolved from archaea; often used to describe host at time of endosymbiosis
67
PFOR
pyruvate ferridoxin oxidoreductase; converts pyruvate into CO2, acetyl coA, and reduced ferredoxin
68
ferredoxin
Accepts electrons from hydrogenase to produce hydrogen gas
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hydrogenase
oxidizes ferredoxin to make hydrogen
70
Driving forces of endosymbiosis
- reducing levels of toxic oxygen
- syntropy (host uses symbiont waste products)
- mutually beneficial energy metabolism
71
hydrogen hypothesis
theory that need for hydrogen by the host drove the endosymbiosis and development of mito
72
TACK superphylum
Archaea group with homologs of ESPs
- crenactins in korearchaeota, aigararchaeota
- distant tubulin in thanarchaeota
73
Ras-GTPases
euk proteins involved in cytoskeleton dynamics and phagocytosis
74
inside out model of nucleus evolution
-theory of nucleus evolution based on membrane blebs forming to associate more with endosymbiont resulted in the double membrane of the eukaryotic nucleus
75
group 2 introns
self-catalytic ribozymes implicated as a driving factor in the development of the nucleus
76
IEP
intron encoded protein; encoded by group 2 introns; has maturase, DNA binding, nuclease, and reverse transcriptase activity
77
Domestication of group 2 intron
Host has adapted methods to regulate introns (ex. spliceosome, low IEP production, etc.)
78
Mitochondrial cross
cross where both parents contribute mtDNA
79
segregational petities
show mendellian inheritance
80
vegetative petities
show non-mendellian inheritance
81
vegetative
non-sexual/mitotic
82
neutral petities
all progeny WT; lack mtDNA
83
suppressive petities
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
hypersuppressive
>95% petite progeny
85
panmixis model
mitos fuse and mtDNA randomly mixes in yeast zygote; homoplasmy happens by chance
86
stochastically assorted
asymmetric distribution initially favours asymmetry later in distribution
87
oli
oligomycin; inhibits ATP synthase
88
cap
chloramphenicol; inhibits mito protein synthesis
89
DAPI
DNA specific fluorescent dye
90
Ytal10p-GFP
transmembrane MIM protein; able to populate all parts of membrane over time
91
Tom6p-GFP
outer membrane protein distributed throughout cell after 3-4 hours
92
mdm
mitochondria distribution and morphology mutants
93
mmm
maintenance of mito morphology mutants
94
ERMES
ER-mito encounter structure
95
Dnm1
yeast version of Drp1
