Chapter 3: Proteins

Question 1

What do protein chaperones do? why do they need to do this?

Answer 1

encourage proper protein folding; allows for different conformations/independent from cytosolic concentrations

Question 2

What are the two secondary structures of proteins?

Answer 2

alpha helices + beta sheets

Question 3

How often do H bonds occur between amino acids in an alpha helix?

Answer 3

every <4 amino acids

Question 4

About how far apart are beta sheets?

Answer 4

~0.7 nm

Question 5

What level of protein structure do domains typically occur as?

Answer 5

tertiary

Question 6

What is a typical domain size in AAs?

Answer 6

40-350 AA

Question 7

This is a specific portion of a protein that has known functions (whether that be catalytic, spacing, etc.)

Answer 7

domain

Question 8

This is a specific subset of domians that are considered to be “genetically mobile”; can be found in many other proteins performing the same function

Answer 8

modules

Question 9

What function does the Kringle module complete?

Answer 9

protein-protein interactions

Question 10

What function does the immunoglobulin module complete?

Answer 10

antigen OR other protein/moleucle recognition

Question 11

What function does the fibronectin type 3 module complete?

Answer 11

cell-to-cell interactions

Question 12

What is the common function of an SH2 domain?

Answer 12

recognizes P-Tyrosine

Question 13

Why are non-covalent bonds much more common between protein-protein/polypeptide-polypeptide interactions?

Answer 13

allow protein conformational changes without being “irreversible” like covalent bonding

Question 14

What regions are the complementary structure of proteins sourced from?

Answer 14

R-regions of amino acids

Question 15

The bonds between many actin modules to form actin fibers are usually ___? why?

Answer 15

weaker; allow for dynamic growth/shrinkage

Question 16

The bonds within a collagen fiber tend to be _____ than the bonds within actin fibers. why?

Answer 16

stronger; used as structural support/should not be easily altered

Question 17

Why can’t disulfide bonds exist easily within the cell?

Answer 17

The cell environment is reductive; easily cleaved

Question 18

What is critical for the correct folding of insulin?

Answer 18

connecting peptide

Question 19

What are 2 defining characteristics of phosphates?

Answer 19

1. very large
2. very negatively charged

Question 20

What are the two “pockets” found within the SH2 domain of a protein?

Answer 20

1. specificity pocket
2. p-Tyrosine pocket

Question 21

What are 3 notable domains found in Src-type protein kinases?

Answer 21

1. SH3
2. SH2
3. kinase domain

Question 22

What are 3 notable domains found in Src-type protein kinases?

Answer 22

1. SH3
2. SH2
3. kinase domain

Question 23

what is the function of a kinase domain in a Src-type protein kinase

Answer 23

performs phosphorylating catalytic activity

Question 24

What is the function of an SH3 domain in a Src-type protein kinase?

Answer 24

binds to the activating ligand with specificity

Question 25

What is the function of an SH2 domain in a Src-type protein kinase?

Answer 25

recognizes p-Tyr molecules attached to other specific molecules

Question 26

What happens to the kinase domain after SH3 binds to the activating ligand in Src-type kinase?

Answer 26

catalytic region of kinase domain becomes stabilized enough to self-phosphorylate --> activates kinase

Question 27

what happens when Src kinase protein activity increases excessively?

Answer 27

summed apoptosis signals decrease --> induces tumorgenesis

Question 28

What protein does the HIV virus produce inside an infected cell to influence SRC kinase?

Answer 28

NeF protein (negative regulatory factor protein)

Question 29

What are the steps of what HIV does in a cell?

Answer 29

produces NeF --> NeF interacts w/ SH3 --> Src kinase hyperactivity --> decreased apoptosis signals --> cell reproduces virus longer

Question 30

What do GTP binding proteins do after GTP hydrolysis takes place?

Answer 30

GDP removed --> replaced with new GTP

Question 31

What does the addition of ATP to motor proteins (kinesin) do to their activity?

Answer 31

adds directionality to natural movement

Question 32

What is the name of the SARS-Cov-2 spike protein?

Answer 32

Trimeric S protein

Question 33

What is the trimeric S protein?

Answer 33

a homodimer that has up (active) and down (inactive) states

Question 34

The up conformation of the trimeric S protein allows binding to which human receptor?

Answer 34

ACE2 PD domain