Rider Biology 1.4–1.5 — Nucleus, Ribosomes, ER & Proteasomes

What is the nucleoplasm?

The material filling most of the nucleus that contains DNA, RNA, and accessory proteins.

What does the nucleoplasm contain?

DNA, RNA, and accessory proteins.

How many chromosomes does Rider say human DNA is divided into?

46 chromosomes.

About how long would human DNA be if stretched into one continuous strand?

About 2 meters.

About how wide is the nucleus in Rider's example?

Roughly 10 micrometers.

Why does Rider describe the nucleoplasm as "organized chaos"?

It is extremely crowded with DNA and proteins, but the cell must still access the correct genes when needed.

What is the nucleolus?

A dense region inside the nucleus where ribosomes are assembled.

Is the nucleolus surrounded by its own membrane?

No.

What two main components are assembled to make ribosomes in the nucleolus?

rRNA and ribosomal proteins.

What does rRNA stand for?

Ribosomal RNA.

What happens to mature ribosomes after they are assembled?

They leave the nucleus and function in the cytosol or on the endoplasmic reticulum.

Why may the nucleolus become larger in a very busy cell?

The cell needs to make more ribosomes to produce more proteins.

What is the nuclear envelope?

The double membrane that surrounds the nucleus.

How many membranes make up the nuclear envelope?

Two: an outer membrane and an inner membrane.

What is the main job of the nuclear envelope?

To protect the nucleus and help control what enters and leaves it.

What is laminin in Rider's nucleus section?

A tightly woven protein network that supports and shapes the inner surface of the nuclear membrane.

What is the main job of laminin around the nucleus?

To help support and maintain the shape of the nuclear envelope.

What are nuclear pores?

Controlled openings in the nuclear envelope that regulate transport into and out of the nucleus.

Why are nuclear pores important?

They control which molecules can enter or leave the nucleus.

What is an importin?

A transport protein that carries selected molecules into the nucleus.

What is an exportin?

A transport protein that carries selected molecules out of the nucleus.

What does NLS stand for?

Nuclear localization signal.

What does an NLS tell the cell?

That a molecule should be transported into the nucleus.

What does NES stand for?

Nuclear export signal.

What does an NES tell the cell?

That a molecule should be transported out of the nucleus.

Which transport protein recognizes an NLS?

An importin.

Which transport protein recognizes an NES?

An exportin.

What happens to newly made mRNA in the nucleus?

It is exported through nuclear pores so ribosomes can use it to make proteins.

What does mRNA stand for?

Messenger RNA.

What is the main job of mRNA?

To carry genetic instructions from DNA to ribosomes.

Can some proteins have both an NLS and an NES?

Yes.

Why might a protein have both an NLS and an NES?

So it can move into or out of the nucleus depending on which signal is active.

What is Ran?

A protein that helps control transport through nuclear pores.

What molecule is Ran usually bound to inside the nucleus?

GTP.

What molecule is Ran usually bound to outside the nucleus?

GDP.

What does GTP stand for?

Guanosine triphosphate.

What does GDP stand for?

Guanosine diphosphate.

Which carries more energy, GTP or GDP?

GTP.

What does Ran-GTP help indicate?

That the molecule is on the inside of the nucleus.

What does Ran-GDP help indicate?

That the molecule is outside the nucleus.

What happens to Ran's GTP after Ran leaves the nucleus?

It is converted to GDP.

What is a nucleoid in a prokaryotic cell?

The region containing the cell's chromosome without a surrounding membrane.

Do prokaryotic cells have a membrane-enclosed nucleus?

No.

What shape is the main chromosome of most prokaryotic cells?

Large and circular.

What is a plasmid?

A small additional circular DNA molecule found in some prokaryotic cells.

What kinds of useful genes can plasmids carry?

Genes such as those for toxins or antibiotic resistance.

Can plasmids spread from one bacterial cell to another?

Yes.

What is the main job of a ribosome?

To make proteins.

What does a ribosome read to make a protein?

mRNA.

What process converts an mRNA sequence into an amino acid sequence?

Translation.

What does tRNA stand for?

Transfer RNA.

What is the job of tRNA?

To bring amino acids to the ribosome.

What does rRNA do in a ribosome?

It forms an important structural and functional part of the ribosome.

What are the two main parts of a ribosome?

A large subunit and a small subunit.

Which is larger, a eukaryotic or prokaryotic ribosome?

A eukaryotic ribosome.

Do prokaryotic and eukaryotic ribosomes perform the same basic job?

Yes, both translate mRNA into protein.

What does the A site of a ribosome do?

It is the arrival site for the next amino acid-carrying tRNA.

What does the P site of a ribosome do?

It holds the growing peptide or protein chain.

What does the E site of a ribosome do?

It is the exit site for empty tRNAs.

Put the ribosome sites in the order a tRNA moves through them.

A site → P site → E site.

What is the endoplasmic reticulum, or ER?

A membrane-enclosed network that surrounds the nucleus and helps process proteins and make other molecules.

Why is rough ER called "rough"?

It has ribosomes attached to its surface.

Does smooth ER have ribosomes attached?

No.

What do free ribosomes generally make?

Proteins destined for the cytosol, nucleus, peroxisomes, mitochondria, and chloroplasts in plant cells.

What do rough ER-bound ribosomes generally make?

Proteins destined for the Golgi, lysosomes, plasma membrane, or outside the cell.

What is a signal sequence?

A short part of a new protein that tells the cell the protein should enter the ER.

What does SRP stand for?

Signal recognition particle.

What does SRP do?

It recognizes a signal sequence and guides the ribosome to the ER.

What is a translocon?

A pore in the ER membrane through which a new protein enters the ER.

What happens after the ribosome docks at the translocon?

The growing protein is fed into the inside of the ER.

What is signal peptidase?

An enzyme that removes the signal sequence from the new protein.

What happens to many proteins inside the ER?

They are chemically processed and helped to fold properly.

Where are proteins often sent after processing in the ER?

To the Golgi apparatus in vesicles.

What is a vesicle?

A small membrane-bound bubble used to transport materials.

What is one major job of smooth ER?

To make lipids and other biomolecules.

What important ion is stored inside the ER?

Calcium, Ca2+.

Why does the ER store calcium?

So it can release calcium into the cytosol when the cell needs it.

Why are calcium bursts especially important in muscle cells?

They help control muscle activity.

What is the calcium-storing ER in muscle cells called?

Sarcoplasmic reticulum.

What is a proteasome?

A large protein machine that destroys old, damaged, or incorrectly made proteins.

How is a proteasome different from a ribosome?

A ribosome makes proteins; a proteasome destroys proteins.

What is ubiquitin?

A small protein label that marks other proteins for destruction.

Which enzymes attach ubiquitin labels to proteins?

E1, E2, and E3 enzymes.

What do E1 and E2 mainly do in ubiquitin tagging?

They help prepare and transfer ubiquitin.

What does E3 mainly do in ubiquitin tagging?

It recognizes and grabs the protein that should be destroyed.

Why are several ubiquitin molecules often attached to one protein?

To clearly mark that protein for destruction by the proteasome.

What does the proteasome do first when a ubiquitin-tagged protein enters?

It recognizes the tag, removes the ubiquitin, and unfolds the protein.

What happens to ubiquitin after it is removed?

It can be reused.

What happens inside the proteasome core?

The unfolded protein is cut into small peptide fragments.

What are proteases?

Protein-cutting enzymes.

About how large are the peptide fragments described by Rider after proteasome cutting?

About 7 or 8 amino acids long.

What happens to those peptide fragments afterward?

Cytoplasmic proteases break them down into individual amino acids.

What can the recycled amino acids be used for?

They can be reused by ribosomes to build new proteins.

Scenario: A new protein has an NLS. Where should it go?

Into the nucleus.

Scenario: A new protein has an NES. Where should it go?

Out of the nucleus.

Scenario: You find lots of Ran-GTP in an area. Are you more likely inside or outside the nucleus?

Inside the nucleus.

Scenario: You find lots of Ran-GDP in an area. Are you more likely inside or outside the nucleus?

Outside the nucleus.

Scenario: A ribosome is making a protein that begins with an ER signal sequence. What happens next?

SRP recognizes the signal sequence and guides the ribosome to the ER.

Scenario: A protein is destined to be secreted outside the cell. Which ribosomes will usually make it?

Ribosomes bound to the rough ER.

Scenario: A protein will stay in the cytosol. Which ribosomes will usually make it?

Free ribosomes.