module 2 Flashcards
1
Q
gene
A
entire nucleic acid sequence that is necessary for the synthesis of a useful RNA molecule or a functional polypeptide
2
Q
distal promotor
A
distant portion of the promoter for a particular gene
region of DNA that may contain additional regulatory elements, often with a weaker influence than the proximal promoter.
3
Q
proximal promotor
A
upstream of the gene that tends to contain primary regulatory elements
approximately 250 base pairs or nucleotides, nts upstream of the transcription start site
4
Q
basal transcription factors
A
Required to assemble the transcription complex TFII(N).
5
Q
regulatory transcription factors
A
regulatory proteins whose function is to activate transcription of DNA by binding to specific DNA sequences
6
Q
enhancer element
A
elements which enhance transcription by helping transcription factors bind to promoter. Activators bind to enhancers.
upstream or downstream
7
Q
activator
A
proteins which may alter chromatin structure or interact with the Mediator or other transcription factors.
8
Q
inducible factor
A
bind to upstream elements that are regulated by an inducer
9
Q
co-activator
A
only found in eukaryotes, localized in nucleus
may alter chromatin structure or interact with tf
10
Q
CpG island
A
areas rich in CG repeats. Methylation of cytosine can inhibit gene expression due to enhanced chromatin compaction by methyl binding proteins
11
Q
methyl binding proteins
A
contain the conserved DNA binding motif methyl-cytosine binding domain
mediating gene silencing via DNA
12
Q
TATA Box
A
located upstream of start site
has consensus sequence
required for transcription of many genes
13
Q
TFIID
A
multi protein complex made of TATA binding proteins
bind to DNA and bend
14
Q
Transcription factor binding elements
A
proteins with DNA binding activity that are involved in the regulation of transcription
15
Q
TFIIB
A
bind to DNA at TFIID
16
Q
TFIIH
A
bind to res of preinitiation complex
phosphorylates the COO- terminal of RNA polymerase
17
Q
RNA Polymerase I
A
Reads Class I genes - rRNA
18
Q
RNA Polymerase II
A
Reads Class II genes (genes encoding proteins)–produces mRNA)
19
Q
RNA Polymerase III
A
tRNA, small rRNA, small viral
RNAs
20
Q
Mediator
A
A multiprotein complex which regulates transcription between activators, coactivators, transcription factors and TFIID.
21
Q
Silencer
A
interact with repressor proteins which block activator/coactivator from interacting with transcription factors or the initiation complex
22
Q
insulator
A
act as boundaries between genes to ensure the “correct” gene gets transcribed
23
Q
wildtype
A
A typical, “normal” form of a given species
24
Q
mutant
A
Organisms that contain one or more mutations
25
Intron
Noncoding DNA
26
Exon
Coding DNA
27
PolA tail
Polyadenylation
part of mRNA processing
28
PABP
recognizes PolyA tail in assembly of mRNA preinitiation complex
29
mGuanine cap
Guanine methylation
5' end cap
Recognition of the 5’ mG cap by eIF4E
30
transcription initiantion/elongation
start of transcription in the nucleus
growing nascent mRNA strand
31
hnRNA
heterogeneous nuclear RNA
encompasses various types and sizes of RNAs found in the eukaryotic cell nucleus
32
mRNA
transported to the cytosol for protein synthesis
messenger RNA
33
Code/sense/codon
double-stranded DNA that carries the translatable code in the 5′ to 3′ direction
34
anti code/antisense/anti-codon
template stand
35
template strand
used in its 3’—> 5’ anti-parallel orientation
used to make RNA
36
HAT/HdAC
part of DNA accessibility
Histone acetyltransferase
transfers an acetyl group to a histone protein allowing euchromatin to form
37
Euchromatin
non condensed chromatin
38
Heterochromatin
condensed (transcriptional inactive) chromatin
39
histone
conserved, small basic (Lys & Arg rich) proteins that condense DNA
40
nucleosome
Octamer of 2 of each of the core histones complexed with 146 bp of DNA
41
zinc finger
small protein structural motif that is characterized by the coordination of one or more zinc ions in order to stabilize the fold
42
helix-loop-helix
found in transcription factors which have DNA binding and protein interaction domains.
43
leucine zip
important sequence motif facilitating protein–protein interactions
sequence-specific DNA-binding proteins that regulate transcription
44
monocistronic
one promotor
one gene
eukaryotes
45
polycistronic
one promotor
many proteins
prokaryotes
46
epigenetic
Heritable gene regulation that does not involve
changes in the DNA code
47
structural gene
gene that codes for the amino acid sequence of a protein (such as an enzyme) or for a ribosomal RNA or transfer RNA
48
ubiquitin
histone modification
small regulatory protein that regulates turnover of proteins
49
acylation
post-translational modification of proteins via the attachment of functional groups through acyl linkages
50
sumoylation
covalent attachment of SUMO family f proteins to lysine of a specific target via enzymatic cascade
51
microRNA
controls gene expression mainly by binding with messenger RNA (mRNA) in the cell cytoplasm
52
half-life
time at which the amount of message produced has been reduced to one half the starting value
53
Hoagland & Zmaecnick
proposed that The code was transcribed from DNA onto RNA
54
Gamow
proposed that In order to make 20 different amino acids from 4 different nucleotides would require that a minimum of 3 nucleotides must be present since 42 = 16 and 43 = 64
55
redundant
a different sequence may specify the same amino acid, e.g. serine is coded by 6 different
codons
56
wobble base
the first 2 nucleotides of the codon and anticodon interact tightly, the 3rd is looser
57
non-standard nucleotide
wobbles base references this on tRNA
tRNA 5’ base is paired to the codon 3’ base.
Referred to as the degenerate base.
58
shine/Delgarno
sequence signals recognition of start site by ribosome (16 S of the 30 S Subunit)
59
Kozac sequence
AUG
60
formyl-methione
initiation of protein synthesis from bacterial and organellar genes
61
30S, 50S, 70S
70s is final complex for prokaryotes
30s&50S subunit
62
40S
60S
80S
eukaryotes
40s and 60s subunits
63
IFS 1
binds with IFS 3 and both bind to 30s subunit
64
IFS 2
binds with fmet containing anticodon, once binding occurs IF3 released
65
IFS 3
fidelity function in the initiation of translation, inducing the dissociation of fMet-tRNAfMet from 30S initiation complexes containing a non-canonical initiation triplet in place of a canonical initiation triplet
66
elF4E
Recognition of the 5’ mG cap
67
elF4G
cap-binding protein which, in synergy with proteins such as the helicase eIF4A and the scaffolding protein eIF4G, binds to mRNA, allowing the recruitment of ribosomes and translation initiation
68
elf4A
unwinds during Assembly of the mRNA Preinitiation Complex
69
amino-acyl "a-site"
Anticodon of tRNA binds to mRNA codon
turns into p site
70
peptidyl transferase "p-site"
turns into e site
71
exit channel "e-site"
Release and exit of the deacylated tRNA from E and reloading new acylated- tRNA at the “A” site
72
ribosome
site of peptide bond synthesis; made of rRNA and Protein
73
EF-tu
escorts next t-RNA to Aminoacyl Domain
74
EF-G
energy release drives the movement of the Ribosome complex to the next codon
changes gtp to gdp
75
release factors
proteins used in the place of tRNA.
76
reading frame
correct identification and translocation at
each codon
77
frame shift
insertion or deletion of nucleotide bases in numbers that are not multiples of three
78
biosynthesis
refers to the making of proteins and their modifications through the ER and Golgi.
79
trafficking
refers to the targeting and transport of proteins to specific cellular organelles.
80
signal peptidase
enzyme which cleaves the signal peptide from the growing nascent peptide chain.
81
disulfide isomerase
enzyme that catalyzes the formation and shuffling of disulfide bonds. Needed for unfolding
82
proteasome
specialized structures that degrade misfolded proteins
83
glycosyltransferase
enzymes that add an oligosaccharide chain to a protein
84
SER
synthesises many lipids such as cholesterol, and other molecules such as steroids and hormones for use inside the cell and for export outside of the cell
85
RER
The N-terminal of the nascent polypeptide
encodes a signal peptide which directs the
Ribosome to the RER
86
signal sequence
on the N-terminal
87
signal recognition particle
binds to the recognition sequence.
88
SRP receptor
SRP binds to
GTP binds to after SRP bind to SRP receptor, causes release of SRP
89
translocon
term for the protein channel where
the ribosome attaches and inserts nascent strand
90
integral protein
different functional characteristics based upon
structural insertion in the membrane
91
binding protein
help chaperon the new peptide into the ER lumen.
92
heat shock protein
refold the protein (ATP) and targeting sequence is cleaved from protein, aka binding protein
93
carrier
pass trait to offspring
94
chaperone
proteins that guide proteins along the proper pathways for folding
95
stop-transfer anchor sequence
signals the channel to stop importing into the ER and to translocate the peptide through the channel proteins into the membrane
96
signal-anchor sequence
initiate the translocation of the following polypeptide segments
97
clathrin
A fibrous lattice protein made of triskelion that forms on the cytosolic face of the membrane pulls the membrane into pits to form vesicles
98
oligosaccaryl transferase
atalyzes the addition of glycans to selected Asn residues within nascent polypeptides in the lumen of the endoplasmic reticulum.
99
N- glycosidic bond
asparagine
100
O- glycosidic bond
threonine or serine
101
COP-I
Recovers Retrograde Transport
102
COP II
Delivers Anteriograde Transport
103
Glycosylphosphotidyl inositol
posttranslational modification of proteins with a glycolipid and is used ubiquitously in eukaryotes and most likely in some Archaea
104
GPI anchor
acting as receptors, transporters, and adhesion molecules
105
transamidase
enzymes that add the protein to a lipid
106
anterio transport
vesicles released from trans-Golgi Recticulum for export to membrane
107
retrograde transport
Vesicles from the RER transported to
the cis-Golgi Recticulum - Network
108
cis RER/Golgi
protein travels from here to trans to excrete
109
trans RER/Golgi
receiver that collects from the cis Golgi only its most refined fraction for later distribution to specific locations throughout the cell
110
M6P
transporting proteins from the Golgi complex and cell surface to the lysosome
111
M6P receptor
bind to M6P-containing lysosomal acid hydrolases and transport them from the Golgi to the endosomal–lysosomal system
112
lysosome storage disease
malfunction of the lysosome mechanism
Enzyme wont break down material
Problem with export after breakdown
113
t-snares
mediate vesicle fusion
associated with nerve terminal membranes
114
complexin
acts as both an inhibitor and a facilitator of synaptic vesicle fusion and neurotransmitter release
115
syntaxin
essential component of the presynaptic exocytotic fusion machinery in the brain and interacts with several other proteins
116
fusion-pore opening
cells fuse lipid bilayers and target proteins from one cellular compartment to the next in membrane trafficking
117
endosome
vesicles formed from endocytosis which contain recycled proteins, and foreign materials like bacteria which will be degraded
118
receptor mediated endocytosis
means to import macromolecules from the extracellular fluid
119
receptor mediated exocytosis
specific for substances recognized by a cell-surface receptor
secretion of large molecules
120
triskelion
clathrin forms triskelion shape
involved in coating membranes that are endocytosed from the plasma membrane and those that move between the trans-Golgi network and endosomes
121
nuclear pore complex
Proteins which form a basket-like complex which extends into cytoplasm and nucleoplasm
122
importin
proteins which direct proteins into the nucleus
123
exportin
proteins that direct RNA out as complexes with
protein
124
ran-GTP
support formation of complexes containing an export receptor and cargos such as RNAs, RNPs or proteins that are destined for export
125
ran-GDP
binds either GTP or GDP and shuttles between the nucleus and cytoplasm
126
RCC1
Regulates Nuclear Envelope Formation, Spindle Formation and Nuclear Transport
127
Ran GDP binding protein
molecular switch, converting between the active GTP-bound and inactive GDP-bound conformations.
128
NLS
Amino acid sequences which direct a protein to import into the nucleus.
129
NES
Amino acid sequences which direct a protein out of the nucleus
130
Ran-GAP
causes their local release and assembly into nuclear pore complexes, the fusion of vesicles to form a double membrane, and the restarting of nuclear transport.
131
Ran-GEF
modulating nuclear import and export of proteins
132
matrix stimulating factor
recognizes the sequence and binds (ATP dependent) or Heat Shock Protein (HSP) delivers
133
matrix targeting sequence
short peptide, about 15–70 amino acids long, bearing positively charged basic residues, that directs the transport of a protein to the mitochondria.
134
Tom receptor
required for the import of proteins into the organelle
135
Tom channel
allows movement of proteins through this barrier and into the intermembrane space of the mitochondrion
136
intermembrane space targetting
nucleotide phosphorylation
137
sequence
primary structure of a biological macromolecule
138
Tic receptor
mediates the import of the vast majority of nuclear-encoded plastid proteins from the cytoplasm
139
Hsp60
maintains protein homeostasis.
140
Pex5
peroxisome associating factor
141
CHAP
chaperone, HSP
142
DTM
Docking/translocating Machinery
