Exam 3 Flashcards
(133 cards)
1
Q
primary gene regulation
A
transcriptional regulation
2
Q
secondary gene regulation
A
post-transcriptional regulation
3
Q
tertiary gene regulation
A
translational regulation
4
Q
quaternary gene regulation
A
protein modification
5
Q
post-transcriptional regulation
A
secondary-quaternary regulation
6
Q
pre-transcriptional regulation
A
regulate the number of gene copies
7
Q
prenatal globin regulation
A
gamma globin produced instead of beta (expression of beta turned off and expression of gamma turned on)
8
Q
postnatal globin regulation
A
beta globin produced instead of gamma (expression of beta turned on and expression of gamma turned off)
9
Q
temporal and spatial regulation of globin
A
temporal: different globins produced at different times (prenatal vs postnatal)
spatial: gamma gene in liver great 12 weeks post-conception, but nonexistent in bone marrow and spleen
10
Q
transcriptional regulation
A
gene is “on” when it’s being transcribed and “off” when transcription is blocked
can also be regulated by controlling how much mRNA is made during transcription
11
Q
post-transcriptional regulation
A
RNA processing
translational control
post-translational control
12
Q
weismann germplasm theory
A
cells destined to become gametes set aside early in development
basic concept correct except theory assumed that once development occurs, the germplasms retains all genetic material while differentiated cells lose genetic material they don’t need
13
Q
steward 1958
A
early cloning experiment to determine whether differentiation involves gene loss
determined that since organism could be cloned from a single cell then the cell must not lose any genetic material during differentiation
14
Q
exceptions to maintaining genetic material
A
gene loss
gene gain
15
Q
gene loss types
A
chromatin diminution
chromosome elimination
cancer cells
16
Q
chromatin diminution
A
loss of segments of chromosme but NOT whole chromosome
roundworm ascaris
17
Q
roundworm ascaris chromatin diminution
A
during early development, the somatic cells lose segments of their chromosomes BUT germline cells retain all genetic material
amount of genome lost depends on species
varies from 25%-85%
18
Q
chromosome elimination
A
entire chromosomes lost (not just segments)
sciarid flies
paramecium and tetrahymena
19
Q
paramecium and tetrahymena
A
form 2 nuclei: micronucleus (inactive and only for reproductive purposes) and macronucleus (active nucleus with genes being expressed – transcription occurring)
20
Q
events of macronucleus growth
A
internal eliminated sequences (IESs) lost and other segments duplicated
21
Q
IES removal process
A
RNA mediated process similar to RNA interference
post-meiotic micronucleus’ entire genome transcribed and compared to old macronucleus genome (that was transcribed before disintegration) to determine which sequences to remove
50,000+ segments removed
22
Q
repeated replication in macronucleus growth
A
repeated replication of DNA without cell division produces a giant nucleus with around 800 copies of the remaining segments of DNA
23
Q
cancer cells
A
many chromosomal changes occur in tumors (including chromosome loss) that make them more viable
24
Q
gene gain
A
increase in number of gene copies
repetitive vs single copy genes
25
repetitive vs single copy genes
some genes normally present in multiple copies
| more copies = more gene product
26
3 types of DNA in eykaryotic genomes
single copy DNA
middle-repetitive DNA
highly-repetitive DNA
27
single copy (unique sequence) DNA
50% of human genes only present once in each genome (twice in each cell bc 1 from each parent)
mRNA (genes coding for proteins)
hybridizes slowly (high Cot value)
28
middle repetitive DNA
around 40% of human genes are moderately repeated with 10-1,000 copies
rRNA and tRNA
29
highly repetitive DNA
around 6% of human genes are highly repeated with up to 100,000 copies
segment length of 5-300 nt
aka "satellite DNA" bc it forms a satellite during CsCl centrifugation
transposable elements and repeated segments of centromere and telomere
usually heterochromatin (inactive genes)
30
gene amplification
```
when DNA segments (or whole genomes) replicated without division
amphibian oocyte
drosophilia
ciliate macronucleus
human liver cells
cancer cells
```
31
amphibian oocyte rRNA genes
rRNA in giant oocyte replicated repeatedly which provides more templates to make ribosome component
gene amplification can be 2,000-1,000,000 fold
32
drosophilia polytene chromosome
some dipteran flies including drosophilia have giant chromosomes in certain larval tissues
drosophilia salivary glands have polytene (many stranded) chromosomes
polytene chromosomes have around 1,000 chromatin strands and show somatic pairing
centromeres in these chromosomes are together at "chromocenter"
33
ciliate macronucleus and gene amplification
when macronucleus is forming from micronucleus, the micronucleus DNA is replicated repeatedly without cell division producing giant nucleus with around 800 copies of remaining segments
34
human liver cells
for unknown reason, liver cells undergo a round or 2 of replication without cell division (making polyploid cell)
cells contain 2-4x normal # of chromosomes
35
cancer cells and gene amplification
tumor cells routinely amplify specific genes that are related to cell division
oncogenes turned on (gene gain) and tumor supressor genes turned off (gene loss)
36
who found genes involved in lactose catabolism
jacob and monod in 1961
37
lac operon
contains 3 genes adjacent to each other that are necessary for lactose catabolism
transcribed as polycistronic message (if 1 turned on, all turned on)
38
structural genes on lac operon
z: beta-galactosidase
y: lactose permease
a: transacetylase
39
beta-galactosidase
cleaves lactose
40
lactose permease
facilitates lactose entry into cell
41
transacetylase
removes tag along toxin that enters with lactose by action of lactose permease
42
promoter (P)
RNA polymerase holoenzyme binding site
not transcribed
cis-acting
43
operator (O)
where repressor protein binds
| when repressor is bound, RNA polymerase is prevented from binding to promoter
44
repressor (i)
protein coding sequence that produces repressor protein
| trans-acting (protein diffuses and can act on different DNA strand than the one it came from)
45
CAP binding site
catabolite activator protein (CAP) binding site
~60 nt upstream from transcription start site
binding of cAMP to CAP stimulates it to bind to CAP binding site
CAP binding facilitates binding of RNA polymerase to promoter
46
negative control in the lac operon
when lactose isn't present, transcription of 3 genes is negligible (neg control because there is something that normally turns gene expression off)
presence of repressor protein prevents transcription from occurring
47
"normal state" of lac operon
no lactose
| repressor makes protein that binds to operator and prevents RNA polymerase from binding to promoter
48
lac operon when lactose is present
allolactose (lactose isomer) binds allosterically to repressor which prevents it from binding the operator so RNA polymerase can bind promoter and transcription occurs
49
I+
normal repressor
50
I-
mutant repressor that doesn't make repressor
51
Is
mutant that makes repressor that always binds operator (even when lactose is present) so transcription never occurs
52
O+
normal operator
53
O-
mutant operator that repressor can't bind to
54
P+
normal promoter
55
P-
mutant promoter that RNA polymerase can't bind to
56
z+
makes functioning beta-galactosidase
57
z-
makes no functional beta-galactosidase
58
y+
makes functional lactose permease
59
y-
makes no functional lactose permease
60
lactose paradox question
allolactose must bind to repressor protein for it to detach but allolactose is made when lactose is brought into cell by lactose permease but lactose permease only present when transcription is on
question: how can transcription ever be turned on if lactose can't be brought in to make allolactose?
61
lactose paradox solution
"escape" synthesis occurs when repressor dissociates
no protein can bind forever so when it dissociates enough z and y is produced so that when cell encounters lactose enough lactose can be brought up and converted to allolactose to induce operon
62
positive control in lac operon
when glucose and lactose are present, the cell prefers to use glucose
when glucose is present cAMP levels are low so no cAMP-CAP complex to facilitate RNA polymerase binding
when glucose levels are low cAMP levels are high so cAMP-CAP complex present and facilitates RNA polymerase binding which turns on transcription
pos control bc event involved (presence of cAMP) facilitates transcription
63
conditions for transcription to occur
negative control must be inactivated and positive control must be activated
64
how does cAMP-CAP complex facilitate RNA polymerase binding
CAP recruits RNA polymerase by interacting with a few amino acids on RNA polymerases alpha chain CTD and causes them to bind to promoter which causes whole RNA polymerase to bind to promoter
65
transcriptional control in eukaryotes similarities to prokaryotes
presence of promoter and controlling sequences upstream from structural gene
66
transcriptional control in eukaryotes differences from prokaryotes
don't have polycistronic messages
don't usually see clusters of functionally related genes turned on by turning on transcription of single RNA -- functionally related genes often scattered across genome
67
enhancers in eukaryotes
may be 10-1,000s of nt away from gene or even on different chromosome
specific transcription factors bind to it and other may bind near promoter which enhances binding of RNA polymerase to promoter (turning on gene)
68
similarities between binding proteins in eukaryotes
zinc fingers
helix-turn-helix
leucine zipper
helix-loop-helix
69
repressors in eukaryotes
proteins can bind to sites near promoter and interfere with RNA polymerase binding (similar to prokaryotes)
can also interact directly with RNA polymerase to prevent transcription
70
mRNA inactivation by protein binding
protein can bind to specific mRNA and block its translation
| ferritin synthesis
71
ferritin
ferritin: intracellular iron-storing molecule
increased iron concentration in cells means more ferritin necessary
also found in low concentration in plasma
72
ferritin synthesis and inactivation by protein binding
regulated by iron regulatory protein (IRP) binding to iron response element (IRE) on ferritin mRNA
binding of IRP to IRE prevents small ribosomal subunit from scanning for initiator AUG codon (turns of translation)
in presence of iron, IRP doesn't bind to IRE so translation occurs
other proteins bind to 3' UTR and act as translation repressors
73
IRP
iron regulatory protein
IRP1 and IRP2
IRP1 in presence of iron becomes inactive (doesn't bind to IRE)
IRP2 in presence of iron is degraded
74
IRE
iron regulatory element
found on 5' UTR
sequence on ferritin mRNA
75
miRNAs and siRNAs
can down regulate translation process
may come from processing of intron RNA or mRNA UTRs
some transcribed as larger RNA that can be processed to produce more than 1 miRNA/siRNA then RNase called dicer converts large molecules into double stranded short RNA molecules
around 20-26 nt long
seem to be involved in regulation of ~1/3 of all human genes
1,000+ discovered in humans and 1.5 million+ discovered in arabidopsis
76
miRNA
microRNA
77
siRNA
small interfering RNA
78
how to miRNAs and siRNAs regulate translation
1 strand of RNA binds to protein called argonaut and complex is called RNA induced silencing complex (RISC)
RISC then binds to 3' UTR of an mRNA
if complementary base pairing is precise (siRNA) it stimulates cleavage of mRNA
if complementary base pairing is not precise (miRNA) it inhibits translation
79
other function of small RNAs (miRNA/siRNA)
inhibition of transcription
80
hunting for miRNAs
genes for these small, non-transcribed RNAs are difficult to find because cells/organisms that lack miRNA may not have a clear phenotype
in caenorhabditis elegons there is miRNA redundancy so when knocking out 1 miRNA, it may only produce a phenotype when worm is under physical stress
81
epigenetics definition
study of heritable changes in gene expression that don't change DNA sequence
82
examples of epigenetic changes
methylation
histone modification
non-coding RNA (ncRNA) associated gene silencing
83
historic example of epigenetics
children born during Dutch famine have increased rates of coronary heart disease and obesity
84
methylation
addition of methyl group at the 5-carbon of the cytosine ring resulting in 5-methylcytosine
85
DNA methyltransferases (DNMTs)
family of enzymes responsible for adding methyl groups
86
types of DNMTs
DNMT1
DNMT3a
DNMT3b
87
DNMT1
copies methylation pattern after DNA replication (maintenance methylase)
88
DNMT3a and DNMT3b
create new DNA methylation patterns
89
types of histone modification
```
methylation
phosphorylation
acetylation
ubiquitylation
sumoylation
```
90
noncoding RNA (ncRNA)
functional RNA molecule that is transcribed but not translated
91
x-chromosome inactivation (XCI)
example of large intergenetic non-coding RNA (lincRNA)
92
nuclear membrane (nuclear envelope)
separates nucleus from cytoplasm
double membrane with pores
continuous with ER and has all characteristics of the ER (including attached ribosomes)
2 membranes have same phospholipid bilayer structure as plasma membrane
93
perinuclear space
name of space between 2 nuclear membranes
94
nuclear lamina
network of fibrous proteins called lamina right inside nuclear membranes
proteins form tertiary and quaternary structure (coiled coil and higher order structure)
lamina binds to inner nuclear membrane and to chromatin (H2A and H2B histones) at the ends of the chromosomes
95
lamins
type of intermediate filament protein
| may be used in regulation
96
nuclear pore complex
allows for entry/exit of macromolecules, polar molecules, and ions
small, uncharged molecules can easily diffuse across phospholipid bilayer
97
nuclear pore structure
joins inner and outer nuclear membranes
each pore includes numerous proteins called nucleoporins (up to 50 in vertebrates)
made up of 8 protein structures in radial symmetry around the central channel
central ring and a ring on both the cytosolic and nuclear sides of the pore
protein filaments extend outward from the 2 surface rings
98
types of entry and exit into/out of nucleus
passive
| active
99
passive diffusion
smaller proteins (20-40 kd) and small molecules can freely pass through open pores in either direction by simple diffusion
100
active transport
macromolecules (larger proteins and RNAs) and ribonucleoprotein particles (preribosomal subunits) must be actively transported into/out of nucleus through pores
101
proteins that must enter nucleus through active transport
```
made in cytoplasm
those involved in DNA and RNA metabolism
histones
DNA and RNA polymerases
replication enzymes
transcription factors
RNA processing enzymes
many others
```
102
proteins that leave nucleus through active transport
RNAs made by transcription
103
protein entry/exit
protein destined to enter nucleus marked with nuclear localization signal (NLS) which is recognized by a nuclear transport receptor (protein)
104
nuclear localization signal (NLS)
short amino acid sequence that marks protein destined to enter nucleus
sequences may be consecutive amino acids or bipartite
105
karyopherins
example of nuclear transport receptor
importins
exportins
bind to protein to be imported/exported and cross nuclear pore with that protein
106
Ran proteins
GTP binding proteins that regulate entry/exit of other proteins into/out of nucleus
GTP can be hydrolyzed to GDP and P by enzyme on cytosolic side of nuclear membrane
Ran GAP
Ran GEF
107
Ran GAP
Ran GTPase-activating protein
cytosolic side
hydrolyzes GTP --> GDP + P
therefore Ran-GDP in high concentration outside nucleus
108
Ran GEF
Ran Guanine Nucleotide Exchange Factor
nuclear side
exchanges GDP bound to Ran for GTP
therefore Ran-GTP in high concentration inside nucleus
109
protein import process
begins with binding of importin to nuclear localization sequence of "cargo" protein (protein to be imported)
complex binds to nuclear filaments on outside of nuclear pore and importin-cargo complex transported through pore
once inside nucleus, Ran-GTP binds to the importin and bidning displaces cargo and releases it inside the nucleus
Ran-GTP-importin complex then transported back through a pore to the outside where Ran-GAP hydrolyzes GTP to GDP releasing the importin to be reused
Ran-GDP transported by its own transport mechanisms back into nucleus where it will be quickly converted into Ran-GTP by Ran GEF by replacing GDP with GTP
110
RNA entry/exit process
active process
111
tRNA entry/exit
Ran-GTP dependent importins/exportins transport
112
rRNA entry/exit
Ran-GTP dependent importins/exportins transport
113
snRNA entry/exit
Ran-GTP dependent importins/exportins transport
those that are part of snRNPs (used in splicing) transported out of nucleus, associate with protein, then completed snRNPs transported back into nucleus as a result of nuclear localization signals on protein
114
mRNA entry/exit
do not require Ran
| transported by other proteins
115
organization within the nucleus
not a homogenous material and chromosomes are not randomly distributed in the nucleus
shows organization and compartmentalization
116
organization of chromatin during interphase
heterochromatin (2 types)
| euchromatin
117
heterochromatin
condensed during interphase
constitutive heterochromatin
facultative heterochromatin
118
constitutive heterochromatin
never transcribed
always condensed in all cells
satellite DNA
centromere DNA
119
facultative heterochromatin
condensed in some tissues or at some times but may be decondensed in other tissues or at other times
transcriptionally active DNA is decondensed)
120
euchromatin
not condensed during interphase
121
localization within the nucleus
certain features and processes are not randomly distributed in the nucleus but are instead localized to an area
122
chromatin localization
patterns vary with tissues, organisms, and time but distribution is not random in the nucleus
123
localization of replication
visualizing DNA synthesis using bromodeoxyuridine and fluorescent antibodies show that DNA synthesis occurs in discrete clusters
124
localization of splicing
splicing machinery is found in clusters in the nucleus
125
nucleolus
site of 45S pre-rRNA transcription and processing and where ribosomes are assembled
NOT membrane enclosed
126
NOR
nucleolar organizer region
nucleolus formed by tandemly repeated genes for the 45 S pre-rRNA
humans - genes are on 13, 14, 15, 21, and 22 (acrocentric chromosomes)
nucleolus forms around NOR
127
45S pre-rRNA transcription and cleavage
RNA polymerase I transcribes 45S pre-rRNA and while still in the nucleolus it is cleaved into 18S, 5.8S, and 28S rRNAs (including removal of spacers - ETS and ITS)
128
what composes the 45S pre-rRNA gene
18S, 5.8S, and 28S rRNAs
external transcribed spacer (ETS)
internal transcribed spacer (ITS)
untranscribed spacers between 45S genes
129
rRNA chemical modifications
modified while still in nucleolus
| especially methylation
130
snoRNAs and snoRNPs
small nucleolar ribonuclear proteins
protein/RNA complexes
catalyze cleavage and chemical modification reaction
snoRNA components of snoRNPs include RNAs that cleave the 45S pre-rRNA and RNAs that recognize specific base sequences that are to be methylated
131
5S rRNA
transcribed outside nucleolus by RNA polymerase III but are assembled into ribosomes in nucleolus
132
rProteins
proteins of ribosome made like all other proteins (transcribed by RNA polymerase II and then transcript translated in cytoplasm)
must then enter nucleus through pore
133
ribosome assembly and transport
ribosomal proteins begin to aggregate with 45S pre-rRNA before its transcription is finished
more than half bound before rRNA is completely cleaved
when proteins have bound, the 40S preribosomal subunit (with 18S rRNA) and 60S preribosomal subunit (with 28S, 5.8S, and 5S rRNAs) are exported from nucleus through nuclear pores where they become mature 40S and 60S ribosomal subunits ready to take part in translation
