Topic 5 - Synthesis and Fate of Protiens

Question 1

What are post-translational modifications?

Answer 1

Biochemical modifications to a protein that occur after translation of the polypeptide, e.g. glycosylation or phosphorylation.

Question 2

What advantages might there be in the local translation of mRNA?

Answer 2

It is more efficient to move a single mRNA molecule to where the protein that it encodes is needed, and to translate it there, than to transport many proteins from a more distant site. The proteins might interfere with cell function if they were located in the wrong place in a cell.

Question 3

What are miR response elements (MREs)?

Answer 3

Segments of nucleotides in mRNA that act as targets for microRNAs.

Question 4

What is an isoacceptor?

Answer 4

A tRNA molecule that can bind to more than one specific codon.

Question 5

What are aminoacyl tRNA synthases?

Answer 5

Enzymes that are responsible for tRNA charging, i.e. the joining of the appropriate tRNA molecule to its corresponding amino acid. There is one such enzyme for each of the 20 amino acids incorporated into proteins.

Question 6

What is the wobble hypothesis?

Answer 6

An explanation for the fact that that several different codons may encode the same amino acid, because of a lack of requirement for precise base-pairing (wobble) in the third nucleotide of the codon.

Question 7

What is an initiator tRNA (tRNAi)?

Answer 7

A specific tRNA molecule used only for the initiation of translation. Initiator tRNAs in prokaryotes carry the modified amino acid formylmethionine, whereas in eukaryotes they carry methionine. The initiator tRNAs interact with a specific initiation factor before binding to the ribosome.

Question 8

What is elongation factor (EF)?

Answer 8

The term used to describe the ancillary protein that assists with the elongation phase of translation through binding to a charged tRNA. The elongation factor responds to the appropriate pairing of the rRNA anticodon with the mRNA codon by releasing the tRNA amino acid into the ribosome peptide linkage site.

Question 9

What is the Kozak sequence?

Answer 9

A short sequence of ribonucleotides within a eukaryotic mRNA chain, lying upstream from the AUG initiation codon, which assists with translation by directing initiation at the AUG site by the scanning initiation complex.

Question 10

The amino acid is bound to the tRNA via its carboxyl group. What free group is exposed on the amino acid bound to the tRNA, which will form the peptide bond?

Answer 10

The amino group (–NH2) is available to form the peptide bond with the terminal carboxyl group on the growing peptide chain.

Question 11

What is the evolutionary implication of the observation that protein synthesis is catalysed by rRNA?

Answer 11

It suggests that during the early evolution of life, catalysis mediated by RNA preceded catalysis mediated by proteins.

Question 12

What are termination factors (TFs)?

Answer 12

Proteins that bind to actively translating ribosomes at stop codons. These proteins have one surface that specifically recognises stop codons in the mRNA and a region that interacts with the large ribosomal subunit. The tertiary shape of termination factors mimics those of the elongation factor–tRNA complex.

Question 13

What is non-stop decay?

Answer 13

The process whereby eukaryotic mRNAs with no stop codons are degraded in the cell. The stalled mRNA-ribosome complex is recognised and the mRNA targeted for degradation.

Question 14

What is no-go decay?

Answer 14

The process where ribosomes are stalled on an mRNA, usually due to protein binding or secondary structure in the mRNA.

Question 15

What is co-translational folding?

Answer 15

The term used to describe the folding of the newly synthesised polypeptide chain as it is being synthesised on the ribosome, i.e. as it emerges from the tunnel on the ribosome.

Question 16

Where are secreted proteins synthesised within a cell?

Answer 16

They are synthesised on ribosomes located on the endoplasmic reticulum.

Question 17

What is a nuclear localisation signal (NLS)?

Answer 17

A short sequence of amino acid residues within the N-terminal region of a polypeptide chain that is recognised by importin A and targets the polypeptide for transport into the nucleus.

Question 18

What large biomolecules move through the nuclear pore complexes?

Answer 18

Messenger RNAs.

Question 19

What is co-translational localisation?

Answer 19

The term used to describe the first stage in the localisation of a newly synthesised polypeptide to cellular subcompartments or for export from the cell. Proteins destined for certain compartments are actively synthesised across the ER membrane and are processed for downstream destinations.

Question 20

What is glycosylation?

Answer 20

The addition of carbohydrate units to a polypeptide (glycoprotein) or lipid (glycolipid).

Question 21

What are lectins?

Answer 21

The general term used to describe a class of adhesion molecules that bind glycosyl (i.e. carbohydrate) chains (and therefore the proteins they are attached to). Calreticulin is an example of a lectin.

Question 22

What is the glycocalyx?

Answer 22

A tangled layer on the outside of the cell formed by the carbohydrate groups that are attached to many of the proteins and lipids that comprise the membrane. The glycocalyx has an important role in recognition and adhesion.

Question 23

What is axonal transport?

Answer 23

The movement of organelles and proteins along the microtubular network in the axons of neuronal cells. (T5P2)

Question 24

What is vesicular transport?

Answer 24

The mechanism by which molecules are ferried between the membrane-bound compartments of a cell, or between these compartments and the plasma membrane.

Question 25

What are transport vesicles?

Answer 25

Vesicles that pinch off from one compartment and diffuse, or are more often actively transported, to another compartment, where they fuse and discharge their cargo.

Question 26

Give one example of a membrane molecule, that you have already encountered, that can facilitate transport of proteins from the cytosol across a membrane.

Answer 26

Signal recognition factor (ER-SRF), which recognises the signal sequence on membrane and secreted proteins, interacts with a transport channel for transfer of the translating polypeptide across the ER membrane (Figure 3.1). You may also have identified the TOM–TIM complex on mitochondria (Figure 2.1) or components of the nuclear pore complex (Figure 2.2).

Question 27

What are signal patches?

Answer 27

Sequences of amino acids within a polypeptide chain that are recognised by (for example) chaperone proteins, which promote transport to the correct cellular compartment.

Question 28

What are sorting receptors?

Answer 28

Membrane proteins of the endosome that help sort proteins for their correct cellular compartment.

Question 29

What is the basolateral domain?

Answer 29

The area of the cell membrane facing the extracellular matrix and adjacent cells, in contradistinction to the apical domain.

Question 30

What are secretory vesicles?

Answer 30

Vesicles that release hormones, cytokines and small signalling molecules from cells.

Question 31

What is constitutive secretion?

Answer 31

One of the two basic types of exocytosis carried out by all cells and which transfers molecules from the Golgi network to the outer surface of the cell.

Question 32

What is regulated secretion?

Answer 32

Secretion that occurs in response to specific conditions, signals or biochemical triggers, and is the process underlying the release of cytokines, hormones, neurotransmitters and other small signalling molecules, such as histamine.

Question 33

What is endocytosis?

Answer 33

The process by which cells internalise molecules from the outside. It includes pinocytosis, the uptake of small soluble molecules in vesicles, and phagocytosis, the internalisation of large insoluble particles.

Question 34

What is phagocytosis?

Answer 34

The process by which bacteria, cell debris and other larger items are internalised by cells.

Question 35

What are caveolae?

Answer 35

Flask-shaped invaginations of the cell membrane, and the vesicles that are derived from them, which are surrounded by the protein caveolin. Receptors located in caveolar membranes bind their specific ligand, and endocytosis then follows. Caveolae also function to transfer molecules from one side of a cell to the other or between the cell surface and the large endosomal compartment called the caveosome.

Question 36

What is the ubiquitin-mediated pathway?

Answer 36

The protein degradation pathway by which proteins that are to be degraded are tagged with chains of ubiquitin by ubiquitin ligases.

Question 37

What is ubiquitin?

Answer 37

A small, highly conserved protein that is attached to proteins through the action of ubiquitin ligases and targets them for degradation in the proteasome.

Question 38

What is a proteasome?

Answer 38

A large multisubunit protease. A component of the ubiquitin-mediated pathway for protein degradation. The proteasome is a barrel structure into which proteins are placed for degradation. The process yields short peptide chains, which are further degraded by cellular proteases.

Question 39

Explain macroautophagy

Answer 39

Process by which defunct macromolecules are taken up directly from the cytosol by lysosomes (by invagination of the lysosomal membrane) and broken down.

Question 40

What is chaperone-mediated autophagy?

Answer 40

A mechanism by which defunct proteins are directed to lysosomes (for degradation) by binding to chaperones.

Question 41

What are lysosomal storage diseases?

Answer 41

A group of conditions in which a lysosomal enzyme is defective, resulting in the progressive accumulation of undegraded biomolecules. Many of these conditions produce nerve cell death.