Exam 1

What is the role of Ran-GTP in nuclear transport?

To bind to importin causing it to release the protein with the NLS

If you put an NES on a protein that normally resides in the cytoplasm, where will it go?

stays in the cytoplasm

What does GEF do?

Helps a GTP binding protein exchange a GDP for a GTP

What does importin bind?

Protein with an NLS

What lines the nuclear pore?

FG-NUPs

How do you turn Ran-GTP off?

By hydrolyzing the GTP

When Ran has GTP bound is it active or inactive?

Active

Where is the Ran GEF

nucleus

What is special about tyrosine

it can be phosphorylated

how do proteins enter the nucleus

through the nuclear pore interacting with importin

if a sequence of codons is ATG AAC GCT what is the corresponding strand of mRNA

UACUUGCCA

Ran GTPase

GTPase (molecular switch) which functions in the regulation of nuclear import and export.

what coat is on vesicles traveling to the plasma membrane

clathrin

what coats are associated with arf

clathrin and copI

GDI

GDP dissociation inhibitor

what does v-snare interact with?

t-snare

where will a protein with an NLS end up

inside nucleus

what coat is on vesicles leaving the ER

copII

what coat is on vesicles going to ER

copI

what does RabGTP interact with

tethering protein

what is the role of snare proteins?

pull membranes near each other and exclude water

where will a protein with an ER signal sequence end up

starts in ER, goes to golgi, then is secreted.

where is a v-snare located?

on the vesicle

AP2

adapter protein interacting with cargo receptors and clathrin

what coated vesicle has Sar1 in it

copII

where will a protein with an ER signal sequence and a stop transfer sequence end up?

starts in ER, goes through golgi, ends up in plasma membrane

what coat is on vesicles budding from plasma membrane

clatherin

how does Rab get back to its original membrane

the GDI dissociation inhibitor binds, keeps it in GDP form and brings it back to membranr

what role does RanGTP play

nuclear import and export

where is the specificity found for the vesicle going to the correct target membrane

Rab protein

what GTP binding protein is involved in the vesicle pinching off

dynamin

what does AP2 need to bind to be open so that it can bind cargo receptors?

PIP2

glycosylation

addition of sugar

where will a protein with an ER signal sequence and an NES end up

starts in ER, secreted

cannot go to the cytoplasm if it has an ER sequence.

what ribosome is a protein with a KDEL sequence transcribed on

ER associated ribsome

where will a protein with a KDEL sequence end up

cytoplasm (no ER signal sequence to get it translated on ER associated ribosome)

what is the role of the trans golgi network

"post office" sorting and shipping of proteins

If the mRNA codon is UAG, then what is its complimentary tRNA anticodon?

AUC

If the tRNA anticodon is CGC, then what is the amino acid?

Alanine (GCG)

Many chromosome mutations result when chromosomes fail to separate properly during ___________.

meiosis

If a frameshift mutation from exposure to radiation caused a segment of RNA to change from AUC to UAG, what would happen to the protein during translation?

it would stop

Where does translation take place?

cytoplasm

What amino acid would pair up with the beginning DNA bases TAC?

Met

During what phase of the cell cycle does DNA make a copy of itself?

S-phase of Interphase

If a sequence of codons on DNA is A-T-G-A-A-C-G-G-T, what is the corresponding strand of mRNA?

U-A-C-U-U-G-C-C-A

If exposure to radiation caused a segment of DNA to change from TTC to TTT, what would happen to the protein during translation?

nothing

Where does DNA replication take place?

in the nucleus

Name three things that could cause DNA mutation?

Ionizing radiation Carcinogenic chemicals High heat Certain viruses

Euchromatin

loosely packed chromatin more likely to have gene expression

How does acetylation affect chromatin structure? gene expression?

Open chromatin Upregulation

Small RNA that causes specific mRNA to be degraded

siRNA

What type of methylation is only repressive?

DNA methylation

heterochromatin

closed chromatin less likely to have gene expression

What enzyme promotes removal of acetylation from histones?

Histone deacetylases (HDACs)

Small RNA that inhibits protein translation degrades mRNA

microRNA

Complex that adds methyl groups to H3 K9 or K27

Polycomb repressive complex

DNA wrapped around histones

nucleosome

What does histone methylation do to gene expression?

It depends. It may activate or repress transcription.

RNA that acts as a scaffold for other protein complexes

lncRNA

LncRNA involved in X inactivation Binds HDACs. polycomb proteins DNA methylases

Xist

histones

allow for packaging of the nucleus, of the DNA in the nucleus

multinucleated cells

muscle, protozoa, fungus, parasite, cancer cells

nucleosome

DNA wrapped around histones

Remodelling complexes

move histone location to change nucleosome packaging

CPG island

when methylated, gene expression is prevented

DNA region that contains many copies of a cytosine base followed by a guanine base; often found near transcription start sites in eukaryotic DNA. The cytosine bases in CpG islands are commonly methylated when genes are inactive but are demethylated before the initiation of transcription.

SWI/SNF complex

Part of chromatin remodeling, if lost cannot inactivate genes in heterochromatin and cells become undifferentiated

histone acetyltransferase

adds a cell group to histone proteins and allows for opening of chromatin, allowing for RNA Pol to bind

to turn off a gene

condense chromatin by methylating cytosines to prevent binding

acetylation of histones

Unwinds DNA, adds actyl group- changes shape = genes turned ON

histone methyltransferase

Enzyme modifies histones by transfering 1 to 3 methyl groups to histone tails (lysine OR arginine residues)

methylation of DNA

methyl groups are added to certain nucleotides in genomic DNA in order to repress a gene

acetylation is mediated by

histone acetyltransferases (HATs) and histone deacetylases (HDACs)

methylation is mediated by

histone methyltransferases and histone demethylases

Why are calico cats always female?

the genotype involves 2 X chromosomes; XB and Xb

Where does splicing occur?

nucleus in spliceosome

RNA polymerase II

transcribes mRNA

what direction is mrna synthesized

5' to 3'

RNA polymerase that moves left to right uses which DNA strand as a template?

bottom

RNA polymerase that moves right to left uses which DNA strand as a template?

top

GTFs required by eukaryotic RNA pol II

TBP/TFIID TFIIB TFIIE TFIIH

speckles

contain components of spliceosome

RNA export factor

shuttles rna to cytoplasm to be translated

Central Dogma of Molecular Biology

DNA -> RNA -> Protein

exocytosis

vesicles fuse with the plasma membrane, releasing their contents into the extracellular fluid

So if we have our protein and it has an ER signal sequence on it, and that's the only signal sequence that's on it. What happens?

t's made in the ER, moves through the Golgi and then is secreted.

constitutive exocytosis

substance constantly delivered to membrane default pathway all you need is ER signal sequence

regulated exocytosis

• operates in cells specialized for secretion • membrane fusion occurs only in response to an extracellular signal • proteins aggregate at membrane until signalled to release

Synaptotagmin

binds calcium which causes it to interact with snare complex and promote vesicle fusion

complexin

binds to the snare complex and slows the interaction of synaptotagmin (prevents spontaneous exocytosis)

snare complex

This is a cytosolic membrane protein that promotes fusion of vesicles with target membranes

receptor-mediated endocytosis

The movement of specific molecules into a cell by the inward budding of membranous vesicles containing proteins with receptor sites specific to the molecules being taken in; enables a cell to acquire bulk quantities of specific substances. ex) cholesterol endocytosis

Cholesterol Endocytosis

1. inside cell, clathrin coat is shed/released due to PIP2 conversion to PIP

2. Vesicle delivered to early endosome

3. Low pH in endosome/lysosome causes release of LDL from its receptor

4. Early endosome matures to late endosome

5. Late endosome fuses with lysosome

6. Lysosomal enzymes hydrolyze and remove cholesterol from LDL

1. Cholesterol produced in liver

2. interacts with other proteins to make an LDL

3. a cell will have an LDL receptor on the plasma membrane and LDL will interact with this receptor

4. clathrin mediated vesicle forms to bring vesicle inside

5. clathrin is uncoated and fuses with endosome

6. LDL comes off of receptor due to acidity of endosome

7. receptor brought back to a recycling endosome and then brought back to plasma membrane to pull in more LDL

what signal does LDL receptor need

ER signal sequence and stop transfer sequence

what signal sequence is needed for constitutive secretion

ER signal sequence

proteins destined for lysosomes are made on

ER associated ribosomes

what ribosomes are generally used to make proteins degraded by the proteasome

cytoplasmic

the cytoplasmic side of a transmembrane protein remains on the cytoplasmic side. T/F

t

high blood cholesterol could be due to

mutation of LDL receptor so it cannot bind AP2 mutation in ER signal sequence so not recognized by SRP deletion of stop transfer sequence of LDL receptor

why do the enzymes used in lysosomes not break down organelles/macromolecules when they are being made?

enzymes only function at low pH