Definitions Flashcards
1
Q
Glycosidic Bonds
A
Formed when monosaccharides join with a dehydration reaction (water removed)
2
Q
Glycogen
A
A polysaccharide that stores glucose molecules in animal cells
3
Q
Starch
A
A polysaccharide that stores glucose molecules in plant cells
4
Q
Amylopectin
A
Another term for starch
5
Q
Cellulose
A
Main structural component of plant cell walls
Carbohydrate
Made of glucose molecules linked together by a beta 1-4 linkage (which is very strong)
6
Q
Chitin
A
Main structural component of animal cell walls
Carbohydrate
Forms exoskeletons of arthropods
7
Q
Lipids
A
Fats
Used for energy storage
Major component in cell membranes
Steroid hormones important in cell signalling and messenger molecules
8
Q
Fatty acids
A
Long hydrophobic hydrocarbon chains (16-18 carbons) with a carboxyl (COO-) group at one end
9
Q
Unsaturated fatty acids
A
One or more double bonds
10
Q
Saturated fatty acids
A
No double bonds
11
Q
Triglycerides
A
Also known as fats
3 fatty acids linked to a glycerol molecule
Used as storage for fatty acids
Breaking them down yields energy
Insoluble in water
12
Q
Phospholipids
A
Main component of cell membranes
2 non polar Fatty acids joined to a polar head group
13
Q
Glycerol Phospholipids
A
2 non polar fatty acids bound to a glycerol, which is bound to a phosphate group, which is bound to a polar group
14
Q
Sphinogomyelin
A
Only nonglycerol phospholipid found in cell membranes
Polar head group is formed from serine
15
Q
Amphipathic
A
Molecules with a polar (water soluble) end and a non polar (hydrophobic) end
16
Q
Glycolipids
A
Amphipathic
2 hydrocarbon chains and a carbohydrate polar head group
17
Q
Cholesterol
A
Amphipathic
4 hydrophobic hydrocarbon rings and a polar hydroxyl (OH) group
18
Q
Steroid hormones
A
Derivatives of cholesterol, act as chemical messengers
Ex. estrogen, testosterone
19
Q
Nucleic acid
A
Principle informational molecule of the cell
20
Q
Deoxyribonucleic acid
A
Genetic storage material
21
Q
Ribonucleic acid
A
Genetic material with multiple purposes
22
Q
mRNA
A
messanger RNA
carries genetic information copied from the original DNA to the ribosome
read in 5’ to 3’ direction
transport of mRNA out of the nucleus is independent of Ran and does not involve karyopherins
only RNA that does not require transport proteins!
23
Q
rRNA
A
ribosomal RNA
involved in protein synthesis, reads the mRNA and puts the amino acids in the correct order
catalyzes peptide bond formation
24
Q
tRNA
A
transfer RNA
involved in protein synthesis, brings amino acids to ribosome to be coded into proteins and aligns them with corresponding codons on the mRNA template
70-80 nucleotides long and are clover shaped
25
purine
nucleotides that make up DNA and RNA
adenine
guanine
26
pyrimidine
nucleotides that make up DNA and RNA
cytosine
thymine (dna only)
uracil (rna only)
27
nucleoside
nucleotide base linked to sugars
28
2'-deoxyribose
the sugar in dna
29
ribose
the sugar in rna
30
phosphodiester bond
bonds between nucleotides that make up dna/rna
form between 5' phosphate of one nucleotide and the 3' hydroxyl group of another
31
oligonucleotides
polymer of only a few nucleotides
32
polynucleotides
polymer of thousands or millions of nucleotides
rna and dna are polynucleotides
synthesized int he 5' to 3; direction
33
complimentary base pairs
hydrogen bonds between nucleotides:
guanine - cytosine
adenine - thymine (dna)
adenine - uracil (rna)
34
5'-triphosphate
ATP
main form of chemical energy in cells
35
protein
diverse macromolecules
polymers of amino acids
- structural components
- transport and storage of small molecules
- transmit informtaion between cells (protein hormones)
- defence against infection (antibodies)
- enzymes
36
amino acids
consist of an alpha carbon bonded to a carboxyl group and an amino acid group, a hydrogen, and a side chain
4 categories:
- non polar
- polar
- basic
- acidic
20 amino acids
37
peptide bones
joins amino acids
38
polypeptides
chains of hundreds or thousands of amino acids
synthesized from n-terminus to c-terminus
39
n-terminus
an alpha amino group at the end of a polypeptide chain
40
c-terminus
an alpha carboxyl group at the end of a polypeptide chain
41
x-ray crystallography
way to analyze the 3D shape of proteins
used to understand protein folding
42
primary structure of proteins
sequence of amino acids in a chain
43
secondary structure of proteins
many chains of amino acids stuck together that conform to a structure
```
alpha helix
beta sheet (folded)
```
held together by hydrogen bonds between the peptide bonds
44
tertiary structure
side chains of amino acids interact with different regions of the polypeptide chain
made up of alpha helixes and beta sheets
shape determined by location of hydrophobic and hydrophilic amino acids
(hydrophobic amino acids folded to be on the inside of the protein, and hydrophilic amino acids are on the surface where they interact with water)
45
domain
the basic unit of tertiary structure
46
loop region of a protein
areas where secondary structures of a protein are connected
47
quarternary structure
composed of more than one polypeptide/protein
ex. hemoglobin is composed of 4 polypeptides
48
enzymes
catalysts that increase rate of chemical reactions
do not affect the amount of product, just the speed that you get it
(lowers the transition state/activation energy)
does not get 'used up' by the reaction
49
substrate
the reactants of a chemical reaction involving enzymes
50
transition state
a higher energy state that reactants need to reach before they can make the product
51
activation energy
amount of energy needed to reach the transition state
52
activation site
a site on an enzyme where a specific substrate binds to speed up the reaction
53
enzyme-substrate complex
the result of a substrate that has binded to its substrate
54
lock-and-key model
the substrate fits precisely into the active site
55
induced fit model
structure of both enzyme and substrate is modified after binding to make a perfect fit
56
prosthetic groups
small molecules that bind to proteins that allows them to bind with enzymes
57
coenzymes
small organic molecules that work with enzymes to enhance reaction rates
are not altered by reactions
almost always associated with vitamins
58
NAD+
nicotinamide adenine dinucleotide
a cozenzyme that carries electrons in an oxidation-reduction reaction
accept H+ (proton) and 2 electrons to form NADH
59
NADH
NAD+ plus an H+ proton
carries electrons and donates them to other substrates (this causes it to form NAD+ again)
60
vitamins
contribute part of all of the structure of coenzymes
61
feedback inhibition
the product of a metabolic pathway inhibits an enzyme involved in its own synthesis
a regulatory molecule binds to an enzyme site that is distinct from the catalytic site
changes confirmation of enzyme and prevents substrate from being able to bind to it
a type of allosteric regulation
62
allosteric regulation
controls enzyme activity by binding small molecules to the regulatory sites on enzymes
this results in the structure of enzymes, and thus the activation site to change
63
phosphorylation
a mechanism of enzyme regulation
either stimulates or inhibits the activities of many enzymes
phosphate groups are added to side chain of OH groups of serine, threonine, or tyrosine
64
phospholipid bilayers
2 layers of sheets of phospholipids with the hydrophobic tails facing each other, and the hydrophilic heads facing outwards
proteins are found within this structure
structure makes it selectively permeable
allows cell to control its internal composition
all cells membranes are like this
types of phospholipids, and number of lipids in a membrane varies
65
polar
hydrophilic
66
non polar
hydrophobic
67
mammal cell membranes
has 5 major types of phospholipids
68
animal cell membranes
contain glycolipids and cholesterol
69
membrane fluidity
determined by temperature and lipid composition
cholesteroles and other hormones affect this
unsaturated fats have kinks in their tails an reduces packing and increases fluidity
70
unsaturated fatty acids
have kinks in their tails
71
cholesterol
reduces interaction between fatty acids (comes inbetween)
| and allows membrane to stay fluid at colder temperatures
72
fluid mosaic
our current understanding of the structure of phospholipid bilayers
73
Integral membrane protein
proteins embedded in the lipid bilayer
74
peripheral membrane protein
associated with the cell membrane indirectly
often by interactions with integral membrane proteins
75
transmembrane proteins
goes THROUGH the entire lipid bilayer, with exposed portions on both sides
usually has an apha helix structure and is made of 20-25 nonpolar amino acids
76
beta barrel protein structure
barrel shape made up of beta sheets that have folded into the tube structure
77
selectively permeable membrane
small, nonpolar molecules can diffuse across lipid bilayers
Ex. CO2, O2, H2O
ions and larger uncharged molecules cannot
78
channel proteins
transporter
act as open pores across the cell membrane, and can be selectively opened and closed in response to extra cellular signals
79
ion channels
allow passage of inorganic ions
80
carrier proteins
selectively bind and transport small molecules through the cell membrane
undergo conformation changes after binding to specific molecules that open its channel so that molecules can pass
ex. glucose can be transported with carrier proteins
81
passive transport
molecule movement across the membrane is determined by concentration and electrochemical gradients
no ATP required
82
active transport
molecules can be transported against a concentration gradient using energy from the hydrolysis of ATP
83
transcription
mRNA template made from DNA so that proteins can be made outside to nucleus without endangering the DNA
84
translation
tRNA and rRNA bind amino acids together to make polypeptide chains using mRNA template
first step of making proteins
85
gene expression
regulated during translation in both prokaryotic and eukaryotic cells
affects all aspects of cell behaviour and protein acivity
86
codon
3 bases in a row that code for a specific amino acid
codons tell the ribosome what amino acid needs to be attached next
87
aminoacyl rTNA synthestase
enzyme that attaches amino acids to specific tRNAs
20 different enzymes, one for each amino acid
each one recognizes a single type of amino acid, and the tRNA it should attach to
88
codon at 3' end of tRNA
CCA
89
nonstandard codon
wobble
accounts for mistakes in mRNA sequence
each amino acid has multiple codons in case of coding error
90
70S ribosome
bacterial ribosome
91
80S ribosome
eukaryotic ribosome
92
UTRs
untranslated regions
noncoding regions at ends of mRNAs
93
monocistronic
encodes a single protein
common in most eukaryotic mRNAs
94
polycistronic
encodes multiple proteins
each are translated from an independent start site
common in most prokaryotic mRNAs
95
AUG
starting codon for
methionine
translation in both prokaryotes and eukaryotes
96
Shine-Dalgarno sequence
sequence before starting codon in bacterial mRNAs
initiates translation at 5' end of monocistronic mRNAs and at an internal initiation site of polycistronic mRNAs
97
7-methylguanosine cap
found at the 5' end of eukaryotic mRNAs
ribosome scans downstream from this cap to find initiation codon
98
initiation
first stage of translation
methionyl tRNA, mRNA and a specific indicator bind to the small ribosomal subunit
the large ribosomal unit then joins and forms a functional ribosome
99
elongation
connecting the correct amino acids together with peptide bonds in order to form the peptide chain
continues until a stop codon is found
100
termination
a stop codon is found in the mRNA sequence and the chain is translocated into the A site
101
elF
eukaryotic initiation factors
non ribosomal proteins involved in the initiation stage of translation in eukaryotes
102
IRESs
internal ribosome entry sites
areas of eukaryotic mRNAs where translation can initiate without the 5' cap
103
elongation factor
forms a complex with GTP and brings aminoacyl tRNA to the ribosome
correct aminoacyl tRNA needed to synthesize the protein correctly
104
EF-Tu
prokaryotic elongation factor
105
eEF1 alpha
eukaryotic elongation factor
106
P site
peptidyl binding site
initiator methionyl tRNA binds to p site
107
A site
aminoacyl binding site
108
E site
exit binding site
109
decoding center
area in the small ribosomal subunit recognizes correct codon-anticodon base pairs and finds mismatches/mistakes
110
translocation
ribosome moves 3 nucleotides along the mRNA, positioning the next codon in the A site
peptidyl tRNA is translocated from A to P
uncharged tRNA is translocated from P to E
111
stop codon
UAA
UAG
UGA
stops the elongation stage of translation
112
release factors
recognize stop codons and terminates protein synthesis
113
RF1
release factor 1
recognizes stop codons:
UAA
and
UAG
114
RF2
release factor 2
recognizes the stop codons:
UAA
and
UGA
115
eRF1
recognizes all 3 stop codons in eukaryotic cells
116
eRF1
recognizes all 3 stop codons in eukaryotic cells
117
polysome
polyribosome
multiple ribosomes bound to the same mRNA molecule, translating at the same time
118
global translational activity
modulated in response to stress, nutrient availability, and growth factor stimulation
119
ferritin
protein that stores iron
120
RNAi
RNA interference
short double-stranded RNAs is used to block gene expression at the level of translation
121
siRNA
small interfering RNAs
produced from double-stranded RNAs by the nuclease dicer
pair with their targets and induce cleavage of the mRNA
122
miRNA
microRNAs
transcribed by RNA polymerase II, then cleaved by nucleases Drosha and Dicer
1000 miRNAs in mammals
each target up to 100 different mRNAs
123
RISC
RNA-induced silencing complex
represses translation and targets the mRNA for degradation by stimulating deadenylation
124
miRNA
microRNAs
transcribed by RNA polymerase II, then cleaved by nucleases Drosha and Dicer
1000 miRNAs in mammals
each target up to 100 different mRNAs
up to one half of protein coding genes are regulated by miRNAs
important in embryonic development
play a role to cancer and other diseases
125
RISC
RNA-induced silencing complex
represses translation and targets the mRNA for degradation by stimulating deadenylation
126
modificated initiation factors
effects overall translational activity instead of targeting translation of specific mRNAs
127
chaperones
proteins that facilitate folding of other proteins
catalysts that assist the self assembly process
do not become part of the folded protein
stabilize unfolded or partially folded polypeptides
128
Hsp
Heat-shock proteins
Expressed in cells subjected to high temperatures
a type of chaperone that stabilize and facilitate refolding of proteins that have been partially denatured
129
Hsp70
Stabilize polypeptide chains during tranlsation and transport by binding to short hydrophobic segments
Found in both prokaryotic and eukaryotic cells
130
chaperonin
Consists of subunits arranged in two stacked rings to form a double-chambered structure
Folding of proteins takes place here
Isolates proteins from cytosol and other unfolded proteins
131
chaperonin
Consists of subunits arranged in two stacked rings to form a double-chambered structure
Folding of proteins takes place here
Isolates proteins from cytosol and other unfolded proteins
132
Protein misfolding diseases
Mutations and deformations caused by misfolded proteins
133
Cystic fibrosis
Mutation that results in the deletion of one amino acid that leads to improper folding of protein CFTR
134
CFTR protein
Transports Cl- ions across epithelial cell membranes
135
Alzheimers Disease
Associated with 2 aggrigate types of misfolded proteins in brain tissue
```
neurofibrillary tangles (misfolded tau proteins)
amyloid plaques (aggregates of misfolded amyloid-beta protein)
```
136
Parkinson's Disease
Associated with aggregation of misfolded proteins
137
Type 2 Diabetes
Associated with aggregation of misfolded proteins
138
Amyloids
Fibrous aggregates caused by misfolded proteins
characterized by beta-sheet structures when the protein is not supposed to be in this shape
139
prions
misfolded proteins that can self-replicate
140
Scrapie
Disease in sheep caused by prions
141
Mad Cow Disease
Disease caused by prions
142
Creutzfeldt-Jakob disease
Disease caused by prions
143
Kuru
Disease caused by prions
144
PDI
protein disulfide isomerase
catalyzes disulfide bond formation
abundant in the ER, where the oxidizing environment allows S--S linkages
145
peptidyl prolyl isomerase
catalyzes isomerization of peptide bonds that involve proline residues
146
Proteolysis
Cleavage of a polypeptide chain removes portions such as the initiator methionine from the n-terminus
147
signal sequences
sequence of amino acids that target the new protein for transport to a specific destination
148
signal sequences
sequence of amino acids that target the new protein for transport to a specific destination
149
signal peptidase
A membrane protease that cleaves off signal sequences
150
signal peptidase
A membrane protease that cleaves off signal sequences
151
glycosylation
adds carbohydrate chains to proteins to form glycoproteins
starts in the ER before translation is complete
152
glycoproteins
Proteins with carbohydrate chains attached
The carbohydrate plays important roles in:
protein folding in the ER
targeting proteins for transport
and recognition sites in cell-cell interactions
153
N-linked glycoproteins
glycoprotein where the carbohydrate is attached to the nitrogen atom in the side chain of asparagine
154
O-linked glycoproteins
glycoprotein where the carbohydrate is attached to the oxygen atom in the side chain of serine/threonine
155
dolichol phosphate
a lipid carrier
156
N-myristoylation
a type protein modification where lipids are added
myristic acid (fatty acid) attached to an N-terminal glycine
associated with the inner face of the plasma membrane
157
prenylation
a type protein modification where lipids are added
prenyl groups are attached to sulfur in the side chains of cysteine near the c-terminus
these proteins are involved in control of cell growth and differentiation
158
Rasoncogene proteins
Proteins responsible for many human cancers
159
palmitoylation
a type protein modification where lipids are added
palmitic acid (a fatty acid) is added to the sulfur in the side chains of internal cysteine residues
involved in association of some proteins with the cytosolic face of the plasma membrane
160
GPI anchors
a type protein modification where lipids are added
glycosylphosphatidylinositol anchors
lipids linked to oligosaccharides
glycolipids are added to the c-terminus carboxyl groups
anchor proteins to the external plasma membrane
161
Protein Regulation
Via activities, or the amounts of proteins
- regulation by small molecules
- phosphorylation and other modifications
- protein-protein interactions
162
Ras proteins
Rasoncogene proteins
Proteins responsible for up to 25% of human cancers
caused by small difference in protein conformatoin resulting in ras being able to interact with its target molecule, which signals the cell to divide
cancer = cells dividing out of control
163
Protein Regulation
Via activities, or the amounts of proteins
164
regulation by small molecules
small molecules bind to enzymes to change their conformation.
common in controlling metabolic pathways by feedback inhibition
165
protein kinases
transfer phosphate groups from ATP to the hydroxyl groups of side chains of serine, threonine, or tyrosine
often components of signal transduction pathways
can transmit a signal from the cell surface to target proteins in the cell, resulting in changes in call behavior in response to environmental stimuli
involved in DNA repair
166
protein phosphatases
reverses phosphorylation
catalyze hydrolysis of phosphorylated amino acids
167
epinephrine
signals the breakdown of glycogen to glucose-1-phosphate, providing energy for increased muscular activity
168
glycogen phosphorylase
enzyme that catalyzes the breakdown of glycogen for energy for muscle activity
regulated by protein kinase
169
protein-protein interactions
many proteins consist of multiple subunits, interactions between them can regulate protein activity
170
protein ubiquitylation
regulates protein kinases
controls endocytosis and vesicle trafficking
171
Ran GAP
Ran GTPase-activating protein
associated with nuclear pore complexes and is required for import of proteins
separates a Pi off of GTP, turning it to GDP
172
ubiquitin-proteasome pathway
major pathway of protein degradation in eukaryotes
ubiquitin is attached to the amino group of the side chain of a lysine residue
173
ubiquitin
highly conserved in all eukaryotes
attach to old or disfunctional proteins to signal them for deconstruction
tend to regulate proteins that control fundamental cell processes
174
polyubiquinated proteins
recognized and degraded by large protease complex called the proteasome
175
proteasome
large protease complex
176
proteolysis
Degradation of old or defective proteins by the proteasome
177
lysosomes
membrane-enclosed organelles that contain digestive enzymes, including proteases
digest extra cellular proteins taken up by endocytosis and help in turnover of organelles and proteins
178
autophagy
Act of digesting and recycling non nessesary parts of a cell's self
Activates during times of nutrient starvation
Recycles molecules from non essential proteins and organelles and use them for necessary processes
Vesicles called autophagosomes enclose small areas of cytoplasm or organelles then fuse with the lysosome
major role in developmental processes that involve extensive tissue remodeling
like insect metamorphosis
179
Autophagosomes
Vesicles that form inside a cell and bring the parts of a cell to its own lysosome to recycle non nessesary parts during starvation
180
Autophagosomes
Vesicles that form inside a cell and bring the parts of a cell to its own lysosome to recycle non nessesary parts during starvation
181
nuclear envelope
seperates the nuclear contents from the cytoplasm
controls traffic of proteins and RNAs
critical role in regulating gene expression
- 2 nuclear membranes
- underlying nuclear lamina
- nuclear pore complexes
182
nuclear pore complexes
regulates traffic of proteins and RNAs into and out of the nucleus
channels for small polar molecules, ions, and macromolecules
large, made of 30 proteins (nucleoporins)
8 subunits organized around a large central channel
183
outer nuclear membrane
phospholipid bilayers that are only permeable to small nonpolar molecules
continuous with the ER
184
inner nuclear membrane
phospholipid bilayers that are only permeable to small nonpolar molecules
has integral proteins, including ones that bind to the nuclear lamina for stabilization
185
space between inner and outer nuclear membranes
connected with the lumen of the ER
186
nuclear lamina
fiberous mesh that provides structural support to the nuclear envelope
consists of fiberous proteins (lamins) and other proteins
187
lamins
a class of intermediate filament proteins that associate to form higher order structures (lamina)
bind to inner membrane proteins such as emerin, LBR, and chromatin
188
lamin dimer
alpha-helical regions of lamins wind around each other to form a coilerd coil
associate with each other to form the lamina
189
LBR
lamin B receptor
inner membrane protein
190
emerin
inner membrane protein
191
LINC protein complexes
connect the lamina to the cytoskeleton of the cell
192
passive diffusion
small molecules pass freely in either direction through pore complexes
no ATP needed
193
selective transport
proteins and RNAs selectively transported through pore complexes
requires ATP
194
nuclear localization signals
amino acid sequences on proteins that must enter the nucleus
195
nuclear transport receptors
recognize nuclear localization signals
196
NLS
nuclear localization signals
amino acid sequences on proteins that must enter the nucleus
197
nuclear transport receptors
recognize NLS
198
importins
receptors that recognize NLS and carry proteins through the nuclear pore complex
bind to the NLS of a protein then to the nuclear pore proteins and the complex is transported across the membrane
work in conjunction with GTP-binding protein Ran
Ran controls direction of movement
GTP/Ran binds to the importin and brings it back outside the nucleus
199
NES
nuclear export signals
amino acid sequence that targets for transport out of the nucleus
200
exportins
recognizes NES and direct protein transport to the cytoplasm
201
karyopherins
family of nuclear transport receptors
most importins and exportins fall into this family
202
exportins
recognizes NES and direct protein transport to the cytoplasm
form stable complexes with cargo proteins in association with Ran/GTP in the nucleus
In the cytoplasm, cargo protein disassociates from complex when GTP hydrolyzes and into Ran/GDP
203
karyopherins
family of nuclear transport receptors
most importins and exportins fall into this family
204
RNP
ribonucleoprotein complexes
Transports RNA to the cytoplasm
karyopherin exportins transport tRNA, rRNA, and miRNA
205
RNP
ribonucleoprotein complexes
Transports RNA to the cytoplasm
karyopherin exportins transport tRNA, rRNA, and miRNA
206
snRNA
small nuclear RNA
_____
initially exported from the nucleus by exportin Crm1
in the cytoplasm, snRNA associate with proteins to form snRNP, which is recognized by an importin and brought back into the nucleus
function within the nucleus
207
snRNA
small nuclear RNA
initially exported from the nucleus by exportin Crm1
in the cytoplasm, snRNA associate with proteins to form snRNP, which is recognized by an importin and brought back into the nucleus
function within the nucleus
208
snoRNA
small nuclear RNA
guide RNA to direct specific base modifications of pre-rRNA
2 families associate with different proteins, which catalyze ribose methylation or pseudouridine formation
have sequences complementary to 18S or 28S rRNA, including the sites of base modification
```
function in pre-rRNA processing
form complexes with proteins, forming snoRNPs, which function similar to spliceosomes on pre-mRNA
```
associated with nucleoli
function within the nucleus
209
protein transport regulation
regulation of import and export of transcription factors controls gene expression
- proteins associate with cytoplasmic proteins and mask their NLS, causing proteins to remain in the cytoplasm
- phosphorylation of transcription factors can interfere with import
210
chromatin
bundles of genetic information
highly condensed during mitosis to form compact metaphase chromosomes
loose and distributed throughout the nucleus during interphase
chromatin stays within distinct regions of the nucleus
211
chromosomes
some human chromosomes are rich in transcribed genes, whereas others contain very few genes
gene-rich chromosomes tend to be located in the center of the nucleus, and gene-poor chromosomes near the edges
212
chromosome territory
descrete area in the nucleus where chromosomes tend to occupy
213
euchromatin
decondensed and transciptionally-active genetic informatoin
distributed throughout the nucleus
214
heterochromatin
highly condensed and not trsncribed
| often associated with the nuclear envelope or periphery of the nucleolus
found at the edges
215
TADS
topologically associating domains
how genomes are divided
regions with a domain interact frequently with one another, but only rarely with regions in other domains
216
LADs
lamina-associated domains
chromosomes associated with the nuclear lamina
genes within LADs are generally transcriptionally repressed - LADs are heterochromatin
217
NADs
nucleolus-associated domains
chromosomes associated with the nucleolus
DNA sequences found in NADs substantially overlap with those in LADs
NADs are heterochromatin
218
LADs
lamina-associated domains
chromosomes associated with the nuclear lamina
genes within LADs are generally transcriptionally repressed - LADs are heterochromatin
DNA sequences found in LADs substantially overlap with those in NADs
219
NADs
nucleolus-associated domains
chromosomes associated with the nucleolus
NADs are heterochromatin
DNA sequences found in NADs substantially overlap with those in LADs
220
replication factories
large complexes where DNA replication occurs
221
transciption factories
clustered sites where transcription occurs
contain newly synthesized RNA
coregulated genes from different chromosomes may be transcribed in the same factory
222
nuclear bodies
organelles within the nucleus that concentrate proteins and RNAs for specific processes
not enclosure by membranes
dynamic structures maintained by protein-protein and protein-RNA interactions
223
nucleolus
involved in rRNA synthesis and ribosome production
actively growing mammal cells have 5-10 million ribosomes that must be synthesized each time the cell divides
224
RNA polymerase I
unit in the nucleolus that transcribes 5.8S, 18S, and 28S rRNAs
yields a 45S ribosomal precursor RNA
225
RNA polymerase III
unit outside the nucleolus that transcribes and catalyzes the 5S rRNA
226
nucleolar organizing regions
SLIDE 86 ??
227
nucleoli
3 regions, the all represent the progressive stages of rRNA transcription, processing, and ribosome assembly
have over 300 proteins and 200 snoRNAs
228
spacer DNA
seperates clusters of tandemly repeated rRNA genes
229
45S pre-rRNA
____
primary transcript of rRNA genes in higher eukaryotes
processed via a series of cleavages and substantial base modification
- addition of methyl groups to bases and ribose residues
- conversion of uridine to pseudouridine
230
snoRNP
complexes that function similar to spliceosomes on pre-mRNA
231
snoRNP
complexes that function similar to spliceosomes on pre-mRNA
232
polycomb proteins
repress transcription of genes via methylation of histone H3 lysine 27 residues
some contain clusters of repressed domains from different chromosomal regions
233
cajal bodies
involved in assembly of snRNPs and other RNA-protein complexes
play a role in assembly of telomerase
promotes assembly of the RNA-protein telomerase complex and facilitates its delivery to the telomeres
enzyme for RNA methylation (fibrillarin) is found in cajal bodies
234
scaRNA
RNA specific to cajal bodies
related to snoRNA, and similarily serve as guides to direct ribose methylation and pseudouridylation of snRNA
235
telomerase
replicates the ends of chromosomal DNA
| prevents aging -> the shorter the telomeres, the older you are
236
speckles
after assembly and maturation in cajal bodies, snRNPs are transported here
speckles contain splicing factors
recruited to actively transcribed genes where pre-mRNA processing occurs
237
NTF2
A protein involved in export and important proteins to and from the nucleus.
In both processes, it binds to Ran/GDP, and brings it back into the nucleus from the cytoplasm through the nuclear pore complex (NPC)
With export, the Ran/GDP is attached to an exportin
238
Ran/GEF
Located in the nucleus
Removes GDP from Ran, and adds a GTP to form Ran/GTP
This is a process in both protein import and export used to reuse the Ran for transporting exportin/importin out of the nucleus
239
adhesion proteins
link components of the extracellular matrix to each other and to attach to cells
