6: Protein Fundamenals 2

Question 1

what is post-translational modificaion of proteins?

Answer 1

covalent and enzymatic modification of proteins following protein biosynthesis (transcription and translation)

covalent - forming new covalent bond or cleaving existing bond (including peptide bond)

Question 2

what is the significance of post-translational modification of proteins?

Answer 2

what happens to proteins after they’re made determines protein function

Question 3

what can PTMs affect?

Answer 3

• stability
• localization
• inactivation
• activation
• interactions
• protein conformation

Question 4

how does phosphorylation modify a protein?

Answer 4

attachment of phosphate to a serine, threonine, or tyrosine amino acid residue
- can promote or inhibit protein interactions
- kinases add phosphate
- phosphatases remove phosphate

Question 5

impact of glycosylation on a protein

Answer 5

attaches a sugar group to an amino acid residue
- can promote protein stability and localization of proteins

Question 6

how does lipidation modify a protein?

Answer 6

attaches a lipid group to an amino acid residue
- lipidation can target proteins to membranes by acting like membrane anchors

Question 7

how does acetylation/methylation modify a protein?

Answer 7

alters charge or provides a binding site for other proteins
- important in regulation of histones (chromatin)

Question 8

how does ubiquitination modify a protein?

Answer 8

addition of ubiquitin protein to a lysine residue
- targets protein for degradation (destruction)

Question 9

how/why are there so many more protein species in the cell than encoded in the genome?

Answer 9

one gene can give rise to a series of related proteins

how?
- alternative splicing of mRNAs
- post translational modifications (PTMs)
- specific proteolysis

Question 10

what is proteolysis?

Answer 10

enzymatic process that produces two or more peptides from one protein (breaks apart)
- allows different parts to the protein to have differential localization and function (each section has a different function)

Question 11

what is the effect of a conformational change?

Answer 11

a conformational change is when proteins change their shape in response to environment or other factors
(each different protein shape is a different conformation)
- affects protein interactions with other molecules

Question 12

conformational change: effect of phosphorylation-induced change

Answer 12

protein structure changes from bent to extended conformation through phosphorylation –> causes activity (DNA binding)
- can make some proteins inactive and some active

Question 13

conformational change: effect of ligand-induced change

Answer 13

binding of heme to a protein causes conformational change in protein
Ex. formation of an alpha helix (without ligand binding, there is a loop instead)

Question 14

what are conformational changes caused by?

Answer 14

• post-translational modification
• substrate/ligand binding
• electrochemical changes

Question 15

how are membrane proteins associated with the cell membrane?

Answer 15

N and C terminus can be in either intracellular and extracellular
- integral (thru the whole membrane) or peripheral (anchored)

Question 16

characteristics of transmembrane domains

Answer 16

• typically alpha helices
• contain about 20 amino acid residues
• hydrophobic

Question 17

what are the two types of membrane insertion of a transmembrane protein?

Answer 17

1) polypeptide has a terminal ER signal sequence and an internal stop-transfer sequence.
- ER signal sequence attaches the polypeptide to the membrane. The polypeptide migrates into the lumen.
- stop-transfer sequence stops the movement of the polypeptide towards the ER lumen

2) polypeptide only has an internal start-transfer sequence.
- start-transfer sequence is not on the end of the polypeptide
- everything after the start-transfer sequence gets moved into the lumen of the ER.

Question 18

transmembrane proteins: G-Protein Coupled Receptors (GPCRs)

Explain what they are and what they do.

Answer 18

• the most important widespread receptor in the cell: has many functions (many transmembrane domains)
• ligand binding domain –> extracellular
• enzymatic binding is intracellular
• function: interacts with other proteins and signals what happens when a ligand binds
• how? ligand will bind, GPCR will shift and change conformation, it will do something cytoplasmically, and then something happens inside the cell.

Question 19

transmembrane proteins: ion channels

explain what they are and what they do

Answer 19

• central pore is formed by tetramers/monomers with 4 domains.
• ligands can bind on extra or intracellular side, or not at all
• the amino acids that line the pore determine selectivity and controls which ions can pass through the pore

Question 20

transmembrane proteins: voltage-gated ion channels

explain what they are and what they do

Answer 20

• changes in voltage open/close an ion channel (or the “gate” at the bottom of the channel)
• triggered by differences in voltage across the membrane

Question 21

transmembrane proteins: transporters

explain what they are and what they do

Answer 21

• similar to ion channels but move larger molecules (like drugs)
• mostly present as dimers (two of the same molecule linked together)

Question 22

how does an ABC transporter work?

Answer 22

• ATP binding cassette (ABC) transporters have a region that binds ATP and a substrate
• uses ATP energy to transport drugs in and out of the cell

Question 23

what are the major protein classes as drug targets?

Answer 23

• GPCR
• transporter
• ion channel
• enzymes
• transcription factors
• tubulin