Lecture 3

Question 1

What is the functional unit of the cell?

Answer 1

Proteins

Question 2

What are proteins?

Answer 2

Polymers of amino acids.

Question 3

How are amino acids distinguished from one another?

Answer 3

Their side chains (R-groups)

Question 4

Describe the kinds of R-groups

Answer 4

Non-polar (R is just C and H), polar uncharged (contains OH or SH), polar charged acidic (COO-), and polar charged basic (NH3+)

Question 5

Name the unique characteristics of Cysteine and Tyrosine

Answer 5

Cysteine can form disulfide bonds and Tyrosine can be post-translationally modified by phosphorylation

Question 6

What are peptide bonds?

Answer 6

They covalently link amino acid backbones

Question 7

What dictates the folding of amino acid chains?

Answer 7

The primary structure of the protein

Question 8

What drives the folding of proteins?

Answer 8

Hydrophobic associations- they want to move away from water.

Question 9

What kinds of bonds occur between R-groups of amino acids?

Answer 9

Covalent and ionic bonds, hydrophobic associations, and hydrogen bonds.

Question 10

What kind of side chain would form a covalent bond?

Answer 10

Cysteine-Cysteine (rare)

Question 11

What kind of side chain would form ionic bonds?

Answer 11

A positive to a negative side chain

Question 12

What kind of side chain would form hydrophobic associations?

Answer 12

Non-polar-Non-polar

Question 13

What kind of side chain would form hydrogen bonds?

Answer 13

Polar uncharged-Polar uncharged

Question 14

Name the factors that affect protein folding patterns and function

Answer 14

pH, temperature, ionic concentration and composition, and other cofactors

Question 15

What is the function of a chaperone protein?

Answer 15

They assist in the folding of proteins or target misfolded proteins for degredation

Question 16

What are the secondary functions of chaperone proteins?

Answer 16

They assemble multi-unit proteins, transport unfolded polypeptides to specific organelles, and target misfolded proteins for degredation

Question 17

Where does transcription occur?

Answer 17

In the nucleus

Question 18

Where does translation occur?

Answer 18

It starts on free ribosomes in the cytoplasm

Question 19

What dictates the primary sequence of amino acids?

Answer 19

DNA

Question 20

Describe proteolytic activation

Answer 20

When an inactive protein must be cleaved in order for it to be activated

Question 21

Why are inactive proteins stored to be used instead of creating new active ones as we need them?

Answer 21

Translation is too slow

Question 22

What is the inactive form of insulin?

Answer 22

Proinsulin

Question 23

Where are sorting signals generally found?

Answer 23

At the N-terminus

Question 24

What are the 3 mechanisms for moving proteins amongst compartments?

Answer 24

Nuclear import, protein translocators, and transport vesicles

Question 25

Describe nuclear import

Answer 25

Soluble folded proteins are made in the cytoplasm and translated through NPC; requires NLS to be recognized by importins

Question 26

Describe protein translocators

Answer 26

They transport unfolded proteins across the bilayer of the ER or mitochondria

Question 27

Describe transport vesicles

Answer 27

They transport proteins made at the rough endoplasmic reticulum to the golgi which then sends them back or to lysosomes or the plasma membrane for export.

Question 28

What does cotranslational mean?

Answer 28

Proteins destined for anywhere in the endomembrane system begin at the rough endoplasmic reticulum

Question 29

What does post-translational mean?

Answer 29

The translation completes in the cytoplasm

Question 30

Where is the signal sequence (SS) found on a protein destined for the endomembrane system?

Answer 30

The SS is found near the N terminus

Question 31

What is the function of a signal sequence?

Answer 31

It directs the ribosome/mRNA/translating protein to dock at the rough endoplasmic reticulum

Question 32

What is a signal recognition particle (SRP)?

Answer 32

It reads the signal sequence (SS) and binds N terminal SS to stop translation

Question 33

Where does SRP dock?

Answer 33

To the translocon on the cytoplasmic surface of the ER at the SRP receptor

Question 34

What is translocation?

Answer 34

It is ATP-dependant movement of the peptide into the lumen of the ER

Question 35

What are the two mechanisms of membrane insertion?

Answer 35

There are proteins with an N terminal SS coupled with a stop transfer sequence and proteins with only a start transfer sequence anywhere in the protein

Question 36

How are multipass proteins made?

Answer 36

The proteins have alternating start and stop transfer sequences

Question 37

What is post-translational import?

Answer 37

When a protein is localized to its destination afer translation has completed.

Question 38

For which organelles are proteins imported post-translationally?

Answer 38

Mitochondria, peroxisome, chloroplast, and the nucleus

Question 39

What is the localization signal for mitochondria called?

Answer 39

The transit sequence

Question 40

What is the default compartment in the mitochondria if only a transit sequence is present?

Answer 40

The matrix

Question 41

What do TIM and TOM stand for?

Answer 41

Translocase of the inner membrane and translocase of the outer membrane

Question 42

What is Hsp70?

Answer 42

Heat shock protein 70- a chaperone that prevents fully translated proteins from folding

Question 43

Where is the N terminal transit sequence bound?

Answer 43

A receptor at TOM

Question 44

What drives protein translocation in the mitochondria?

Answer 44

As part of cellular respiration, there is a voltage difference across the mitochondrial inner membrane that provides energy; ATP hydrolysis also helps