Lecture 2: Protein Structure and Function, Part II

Question 1

What is protein denaturation?

Answer 1

Protein denaturation is when proteins begin to fold into incorrect shape/ conformation which reduces protein activity

Question 2

What causes protein denaturation?

Answer 2

Protein denaturation is due to cellular stress including increase in heat, extreme pH, and chemicals

Question 3

What is protein aggregation?

Answer 3

when a large number of unfolded/ denatured proteins begin to aggregate and clump within a cell which can diminish cell function and cause disease

Question 4

What causes protein aggregation in a cell?

Answer 4

Protein aggregation is caused by hydrophobic interactions as when proteins unravel, the hydrophobic core will be exposed.
Hydrophobic core will then repel/ hide from water which will cause them to stick together

Question 5

What are chaperones and why are they important?

Answer 5

Chaperones are family of proteins that are used to assist protein folding into the correct shape efficiently and reliable strategy

Question 6

What are the two strategies chaperones can use to help with protein folding?

Answer 6

1st strategy: small tertiary chaperone proteins bind to different spots on one protein to promote correct folding of protein
2nd strategy: Megaproteins that are quaternary will build isolation chamber for proteins to fold inside chamber without aggregating with other proteins

Question 7

What are heat shock proteins (Hsp)?

Answer 7

chaperone proteins that refold proteins that have been denatured

Question 8

Why are heat shock proteins expressed when a cell is exposed to stress?

Answer 8

As an upregulation of proteins and cell is unleashing a defense mechanism

Question 9

Hsp70

Answer 9

• Binds to multiple spots on polypeptide chain
• Tertiary
• Has 2 domains:
  ATP binding domain: bind and hydrolyze ATP
  Substrate binding domain: binding site so protein will bind to specific ligand

Question 10

What is the strategy of Hsp70?

Answer 10

Hsp70 can bind to protein 99% of proteins made in cell and bind to protein as soon as it is translated by ribosome
Hsp70 has ubiquitous expression as it is always around and highly expressed in cells
Hsp70 is binding to ligand that is segment of hydrophobic amino acids and causes segment to extend when rebinding of ATP
Going through cycles of bind, extend, and release of mu;ltiple parts of protein
Segment being extended and stretched, for when that when enough protein is made, it can be folded into correct shape

Question 11

What is Hp60?

Answer 11

• Multisubunit complex that is quaternary structure
• Uses isolation chamber to help protein fold without risk of aggregation

Question 12

What are the four strategies a cell can use to regulate protein activity?

Answer 12

Transcriptional regulation: regulates if gene is transcribed
Post-transcriptional regulation: regulates if mRNA is translated
Post-translational regulation: regulated if protein is active
Protein degradation: regulates if protein is degraded

Question 13

What is protein phosphorylation?

Answer 13

attachment of phosphate group to amino acid side chain which can increase or decrease protein activity

Question 14

What is the role of a kinase and phosphatase in protein phosphorylation?

Answer 14

Kinase: adds phosphate group
Phosphatase: removes phosphate group

Question 15

What happens to proteins that cannot fold properly?

Answer 15

Proteins that cannot fold properly need to be degraded to prevent protein aggregation

Question 16

What is the structure of proteasome?

Answer 16

Proteasome central cylinder core: digests unfolded protein and contains enzymes that cleave peptide bonds
Proteasome cap: unfolds protein for it to become primary structure (linear strand) and binds to polyubiquitin chain

Question 17

What is the function of the proteasome?

Answer 17

multisubunit complex that degrades unneeded or damaged protein within a cell

Question 18

What is ubiquitin?

Answer 18

small protein with tertiary structure attached to other proteins
allows for system of tagging which cell which attach ubiquitin attach to select proteins for degradation

Question 19

C terminus of ubiquitin (last amino translated) performs ….

Answer 19

condensation reaction and will attach to protein with covalent bond to side chain of lysine

Question 20

After attaching ubiquitin to protein, it will form _____ which can be attached to ______ to be tagged for _____

Answer 20

polyubiquitin, lysine residue at position 48 or 63, degradation

Question 21

Why does a cell use proteins E1, E2, E3?

Answer 21

System uses proteins E1, E2, E3 for cell to know to add ubiquitin to which proteins
for degradation

Question 22

E1

Answer 22

Hydrolyzes ATP into AMP + PPi
Binds to free ubiquitin floating in the cytosol
1 or 2 exist

Question 23

E2

Answer 23

Becomes ubiquitylated by E1
Tens exist

Question 24

E3

Answer 24

Our genomes has hundred of genes encoding different types of this protein

Question 25

Steps for ubiquitylation

Answer 25

Step 1: Ubiquitin found all over the cell attached to E1 protein and will signal ubiquitin for protein degradation.
Step 2: Ubiquitin E1 is transferred to E2
Step 3: E2 and E3 form binding site to transfer ubiquitin to target protein, target protein is going to stay bound to E3 and get new E2 repeatedly to produce polyubiquitin chain

Question 26

What happens after polyubiquitin chain is formed?

Answer 26

Ubiquitin binding proteins will bind and escort protein to the proteasome cap. Once reaching the proteasome cap, the protein will be denatured

Question 27

Cysteine

Answer 27

amino acid used to form a covalent bond with ubiquitin on E1 and E2

Question 28

Lysine

Answer 28

amino acid used to form a covalent bond between ubiquitin and the target protein