Cell Bio Exam 3 - Ch 15

Where does protein synthesis begin?

In the cytoplasm

How do proteins move through the cell?

Diffusion and vesicle transport

What three mechanisms allow proteins to be imported into organelles?

1. Through nuclear pores

2. Across membranes

3. By vesicles

How do signal sequences direct proteins to the correct compartment?

A continuous stretch of amino acids (15-60 AA long) provides signal sequences necessary and sufficient to direct a protein to a destination

How can specific signal sequences be discovered? What method can be used?

Knocking out a signal sequence from a protein could convert it to a different protein, allowing it to redirect to a new area of the cell

What is most important for the function of a signal sequence?

Hydrophobicity or placement of charged amino acids

What is the nuclear pore?

A huge complex of 30 different proteins allowing free movement of small molecules or regulated movement of large molecules

What can freely move in and out of a nuclear pore?

Sugars, amino acids, and salts

What needs help moving through nuclear pores?

mRNA, DNA, proteins

How do proteins get to the nucleus?

They bind specifically through their nuclear localization sequence to nuclear transport receptors to the pores’ cytosolic fibrils

What protein is involved in transcription

RNA polymerase

What is the pathway of a protein getting into the nucleus via nuclear pores?

1. Nuclear protein contains a localization signal recognized by nuclear import receptors

2. Receptor guides proteins to nuclear pore by using cytosolic fibrils

3. When a pore is located, the protein moves through it until nuclear entry triggers cargo release

4. After release, receptors return to cytosol via pores

What conformation is a protein in when moving through the nuclear pore?

Native

How is GTP used for transport?

Transport requires energy in the form of GTP through the action of Ran, which is a GTP binding protein. Ran attaches to the nuclear transport receptor and cargo to re-enter nucleus

For a protein to bind to a nuclear transport receptor, what must dissociate from the receptor?

Ran-GDP

What happens when Ran-GPD dissociates from the receptor?

The binding site is opened

How is the protein released from the import receptor and delivered to the nucleus?

Ran-GTP binds to the receptor and causes the protein to dissociate from the import receptor

What characteristics do mitochondria have that allow them to replicate themselves?

They still have the characteristics of DNA, an inner membrane and respiration from the free living respiratory bacteria they are descended from.

Where are mitochondrial proteins transcribed?

In the nucleus from nuclear DNA

What are mitochondrial proteins translated by?

Cytosolic ribosomes

What mechanisms do mitochondrial proteins use to bind?

They bind through their signal sequence to the receptor in the membrane

Why is a second signal sequence necessary for mitochondrial proteins?

If the protein needs to be sent to a specific destination

How are mitochondrial proteins transported into the mitochondria?

They are first linearlized by chaperones. They move through a protein translocator that needs to that is located on the outside (TOM) and inside (TIM) to enter the organelle. They are refolded to native conformation via chaperones.

Do chloroplasts have more or less extensive DNA than mitochondria? Which of the two has more extensive genes in nuclear DNA?

Chloroplast DNA is more extensive than mitochondrial

Mitochondria have more extensive genes in nuclear DNA

How are chloroplast proteins transported into the organelle?

Analogous to mitochondria except it uses TIC and TOC translocators in the inner and outer membranes

What are the different compartments of the ER and their functions?

Smooth ER = lipid synthesis

Rough ER = protein synthesis

What are the more in depth functions of the Smooth ER?

→ Synthesizing phospholipids, sphingolipids, and steroids

→ Ca²⁺ sequesteration

→ Storage of glycogen on the outside surface

How does the smooth ER have the ability to detoxify the body?

Toxins and drugs that are hydrophobic (cannot be excreted via kidneys) are eliminated via the liver though the metabolism by Cytochrome-P450 (CYP). These toxics/drugs are non polar and non water soluble.

What is hormesis?

Small doses of toxins increase resistance through increasing expression of detox proteins.

What are the more in depth functions of the rough ER?

→ Synthesis of proteins

→ Proteins are able to enter the rough ER while simultaneously being synthesized. Their synthesis begins in the cytosol with no signal sequence. The protein will move into the ER when a signal sequence attaches and finish synthesis.

What determines if a protein will be synthesized in the cytosol or ER?

If an ER signal peptide emerges from the ribosome, then SRP binds. If no signal peptide is present, the protein will be synthesized in the cytosol.

Does the binding of SRP slow down or speed up translation?

Slow down

What happens after SRP binds to the ribosome synthesizing the protein?

1. SRP binds to the SRP receptor at the start of protein synthesis in cytosol.

2. The ribosome binds a translocator which causes the ribosome to lose affinity for SRP. SRP is released for reuse.

3. Translation speeds up again while the protein being synthesized is translocated to the ER.

Are ER proteins in their conformation shape?

No, it is linearlized. Chaperone proteins allow it to take its native shape in the ER using ATP.

What happens to the signal peptide once the mature, soluble protein is in the ER?

It is cleaved off and broken down

Why do membrane proteins stay in the membrane?

They have an affinity for the protein translocator. The hydrophobic stop-transfer sequence and ER signal sequence present on the protein move to the translocator together. When the stop-transfer sequence enters the translocator, a mature single-pass transmembrane protein is left.

What allows double pass transmembrane proteins to be in the membrane of ER?

The protein has a hydrophobic stop and start transfer sequence that have an affinity for the translocator. When the stop-transfer sequence enters the translocator, the protein stays in the membrane without the translocator.

What are some examples of multiple transmembrane domain proteins?

G-protein coupled receptor

Voltage-gated Na+ channel

What are transport vesicles?

Vesicles that carry soluble proteins, membrane proteins, and lipids between compartments of a cell.

How are vesicles moved to transport material?

They can be moved by motor proteins along the cytoskeleton or by microtubles (nerves)

Where do synthesized proteins/lipids go after the ER?

Golgi apparatus

How do proteins/lipids move through the golgi?

Cis cisterna → medial cisterna → trans cisterna

What happens to the membranes of transport vesicles when they encounter a membrane?

It becomes apart of the plasma membrane and releases its inner contents

What is vesicle budding on the ER driven by?

The assembly of a protein coat using clatherin or coatamer

What does clatherin/coatamer do?

They physically pull on cargo attached to the cell membrane to form a vesicle

What facilitates the pinching off of a vesicle from the membrane?

Dynamin

Depending on target location, what protein coats can be used for transport vesicles?

1. Clatherin → between golgi and plasma membrane

2. COP → between ER and golgi

What proteins facilitate the vesicle targeting and attaching to target membrane>

1. Rab → cognition, complement shape/charge

2. Tethering → “docking” to target membrane

3. SNARE → v-SNARE/t-SNARE pull vesicle to membrane

Which SNARE protein is present on the vesicle vs target membrane?

v-SNARE is present on the vesicle. t-SNARE is present on the target membrane.

What direction do Rab proteins move vesicles?

From golgi to target cell

What protein is vesicle fusion dependent on?

SNARE

When the plasma membrane is the target cell, secretory vesicles are released via exocytosis. What two kinds of secretion can occur?

1. Constitutive: automatic release at the same rate (ex: mucus)

2. Regulated: delay of docking and fusion until stimuli is present (ex: neurotransmitters/insulin)

Can GFP be used on live or dead cells to visualize protein movement?

Live

What are two types of endocytosis?

1. Phagocytosis: cell eating, uptake of particles

2. Pinocytosis: cell drinking, uptake of small molecules

Is pinocytosis about water?

NO

How do cells get water?

Aquaporins

Where do materials taken up by phagocytosis, pinocytosis or derived from autophagosomes go?

They are digested by lysosomes

How does receptor-mediated endocytosis relate to endosomes?

The acidic environment of endosomes causes receptors to release and by reused.

Difference between LDL and HDL

LDL brings cholesterol from body tissues to arteries.

HDL removes cholesterol from tissues, removing excess.

Where does lipid/protein recycling occur?

Plasma membrane

Lysosomes acidic environment

pH 5

Contain acid hydrolases to digest molecules and the enzymes cannot work in a neutral environment. The cytosol is 100x less acidic than the lysosomal environment.

What happens if lysosomes are non functional?

Build up of undigested molecules could lead to life threatening diseases. Some genetic mutations may cause hydrolytic enzymes to be nonfunctional and causes diseases like Tay-Sachs.