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Molec and Cell > Chapter 3: Proteins > Flashcards

Chapter 3: Proteins Flashcards

1
Q

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

A

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

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2
Q

What are the two secondary structures of proteins?

A

alpha helices + beta sheets

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3
Q

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

A

every <4 amino acids

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4
Q

About how far apart are beta sheets?

A

~0.7 nm

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5
Q

What level of protein structure do domains typically occur as?

A

tertiary

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6
Q

What is a typical domain size in AAs?

A

40-350 AA

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7
Q

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

A

domain

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8
Q

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

A

modules

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9
Q

What function does the Kringle module complete?

A

protein-protein interactions

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10
Q

What function does the immunoglobulin module complete?

A

antigen OR other protein/moleucle recognition

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11
Q

What function does the fibronectin type 3 module complete?

A

cell-to-cell interactions

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12
Q

What is the common function of an SH2 domain?

A

recognizes P-Tyrosine

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13
Q

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

A

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

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14
Q

What regions are the complementary structure of proteins sourced from?

A

R-regions of amino acids

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15
Q

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

A

weaker; allow for dynamic growth/shrinkage

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16
Q

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

A

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

17
Q

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

A

The cell environment is reductive; easily cleaved

18
Q

What is critical for the correct folding of insulin?

A

connecting peptide

19
Q

What are 2 defining characteristics of phosphates?

A
  1. very large
  2. very negatively charged
20
Q

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

A
  1. specificity pocket
  2. p-Tyrosine pocket
21
Q

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

A
  1. SH3
  2. SH2
  3. kinase domain
22
Q

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

A
  1. SH3
  2. SH2
  3. kinase domain
23
Q

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

A

performs phosphorylating catalytic activity

24
Q

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

A

binds to the activating ligand with specificity

25
Q

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

A

recognizes p-Tyr molecules attached to other specific molecules

26
Q

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

A

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

27
Q

what happens when Src kinase protein activity increases excessively?

A

summed apoptosis signals decrease –> induces tumorgenesis

28
Q

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

A

NeF protein (negative regulatory factor protein)

29
Q

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

A

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

30
Q

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

A

GDP removed –> replaced with new GTP

31
Q

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

A

adds directionality to natural movement

32
Q

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

A

Trimeric S protein

33
Q

What is the trimeric S protein?

A

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

34
Q

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

A

ACE2 PD domain

Molec and Cell (18 decks)

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