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Molecular Cell Biology > Molecular cell biology uwindsor lecture 2 > Flashcards

Molecular cell biology uwindsor lecture 2 Flashcards

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1
Q

What are proteins composed of?

A

Amino acids linked together with peptide bonds. There is an N-terminus that corresponds to the 5’ end and a C-terminus that corresponds to the 3’ end.

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2
Q

Where is rotation allowed in a polypeptide?

A

No rotation around the C-N peptide bond but rotation is allowed around the a-carbon of an amino acid, phy and psi bonds.

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3
Q

How can different amino acids be grouped?

A

Uncharged, polar, uncharged polar.

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4
Q

What are the different forces that act on polypeptides?

A

Electrostatic interactions, hydrogen bonds and van der waals attractions.

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5
Q

Where are the hydrophilic amino acids in comparison to the hydrophobic ones?

A

Hydrophilic on outside, hydrophobic in core.

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6
Q

Proteins fold according to the confirmation of _____ energy.

A

lowest

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7
Q

How do proteins fold?

A

According to their amino acid sequence, hydrophobic interactions and with the help of chaperone proteins.

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8
Q

What are common secondary protein structures?

A

alpha helix and beta sheets.

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9
Q

Describe the alpha helix.

A

Every amino acid is 1) Hydrogen bonded to the amino acid 4 peptide bonds away.

2) The hydrogen bonds are between the backbone structures s C=O and NH.
3) The hydrophobic backbone is sequestered within the helix.
4) The side chains are oriented outwards.

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10
Q

What is a coiled coil?

A

Two alpha helices coiled around each other to sequester hydrophobic amino acids.

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11
Q

What are the stabilizing forces for the B-sheet dependent on?

A

The backbone.

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12
Q

Describe the basic characteristics of the B-sheet.

A

Two or more parallel or anti-parallel stretches of amino acids.
The H-bonds form between adjacent amino acids (c=o and NH)
Side chains are oriented perpendicular to the sheet.

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13
Q

When there are many B-sheets arranged in either parallel or anti-parallel, what keeps them together?

A

Loop that is not part of the sheet. Generally has inherent pattern, B-turn.

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14
Q

What are the different levels of protein structure?

A

Primary-quaternary.

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15
Q

What is the primary protein structure?

A

The sequence of amino acids.

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16
Q

What is the secondary structure?

A

Common folding patterns such as the a-helix and B-sheet within a protein. The local 3D structure of the protein.

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17
Q

What is the tertiary structure?

A

3D structure of the protein in manner in which the secondary structures are organized relative to each other.

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18
Q

What is the quaternary structure?

A

The 3D structure of the protein complex.

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19
Q

What are protein domains?

A

Modular units in protein that can separate from the protein and still fold properly. The domains confer specific function on the protein, a self-contained activity. Most proteins have multiple domains.

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20
Q

How can domains be identified?

A

Based on functional studies or identified based on sequence similarities to known proteins.

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21
Q

True or false? A given domain on one protein can be found on another.

A

True, proteins that share certain characteristics will have similar domains.

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22
Q

What are protein families?

A

Consist of related proteins. They have the same-ish domains and order of domains. Critical domains are very similar amongst family members. Sometimes it is difficult to find relatedness in protein families based on sequence alone, 3D folding of the protein is often very similar.

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23
Q

What does a highly conserved domain indicate in protein families?

A

That these domains are critical to the function of said proteins.

24
Q

Although the sequence of protein families may differ, especially if speciation occured long ago, what often will remain similar?

A

3D conformation and highly conserved domains.

25
Q

What is thought to be the cause of domains shared in different proteins?

A

Exon shuffling

26
Q

As you go up in evolution, what happens with protein families, namely functional domains?

A

The domains become more complicated and similarity is more greatly shared between closely related species.

27
Q

What are Ig domains used for?

A

Ig domains are found in many proteins and used for interaction/recognition with other proteins.

28
Q

As we go up in evolution, what occurs with proteins?

A

Proteins will have added domains in higher organisms, adopt more abilities or more refined abilities. Multiple proteins will be present that can overlap in function.

29
Q

What do assembly factors do?

A

Often aid in the formation of complex biological structures.

30
Q

What do assembly factors aid with in insulin?

A

Proteolytic cleavage of proinsulin. (Cut connecting peptide, leaving two-chain insulin)

31
Q

How do proteins interact together and with other macromolecules?

A

Non-covalent bonding

32
Q

What does surface conformation determine in proteins?

A

What the protein will interact with and determines its activity.

33
Q

What are the different binding interfaces that proteins use?

A

Surface-string: Surface is secondary structure, string is linear sequence.
Helix-Helix: Coiled-coil, sequester hydrophobic amino acids.
Surface-Surface: Interaction of two different secondary structures.

34
Q

What part of antibodies interacts with specific epitopes?

A

Two domains, a constant domain and a variable domain, both of the light chain.

35
Q

What leads to antibody diversity?

A

Hyper-variable loops.

36
Q

What do enzymes do?

A

Catalyze reactions.

37
Q

What do multienzyme complexes help in what concerns cell metabolism?

A

Increase the rate.

38
Q

What is negative regulation?

A

When the product of an enzymatic reaction, or steps of reactions, can inhibit the pathway when there is a sufficiency of the substrate.

39
Q

What do kinases do?

A

Add a phsophate group.

40
Q

What do phosphatases do?

A

Remove a phosphate group.

41
Q

How do kinases work?

A

Bind to ATP and to substrate, and transfers phosphate to substrate. Can only add to certain amino acids. (Ser, tyr, thr for this class)

42
Q

What does the additon of phosphate, or removal, do to a protein?

A

Induces a conformational change, which changes protein activity (surface conformation which is related to its chemistry).

43
Q

What are the different parts of the Src protein kinase?

A 
Squiggle domain (for embedding in lipid-bilayer)
SH3, SH2 and kinase domains.
44
Q

How does the Src kinase work?

A

When off, SH3 is bound to polypeptide chain, SH2 is bound to a phosphate and tyrosine is blocking active site of kinase domain. When active, the phosphate is removed from SH2, SH3 binds to an activating ligand and the tyrosine is autophosphorylated leaving the kinase active site open.

45
Q

How do GTPases cycle between their active and inactive state?

A

When bound to GTP, it is in an active state, when GTP is hydrolyzed, it becomes GDP bound and inactive, the loss of GDP is favoured but a slow reaction, the replacement of with GTP is a fast reaction.

46
Q

What does GAP do?

A

Favours the hydrolysis of GTP and therefore the GDP state.

47
Q

What does GEF do?

A

Favours the exchange of GDP for GTP, therefore favours the GTP state.

48
Q

What are GTPases?

A

Proteins that bind and hydrolyze GTP. They are ubiquitous cell regulators.

49
Q

The GTPase can be active when bound to GDP and GTP, how is this possible?

A

When bound to either GDP or GTP, the GTPase has a different conformation and binds to different proteins. GAP, or GTPase activating protein, favours the GDP bound state and its active state in terms of hydrolysis activity. GEF favours the GTP bound state and the active state in terms of cell regulation.

50
Q

What is an example of regulation of proteins based on covalent addition of proteins?

A

Ubiquitination

51
Q

How is ubiquitin added to a protein, notably at the lysine residue?

A

E1 binds to ubiquitin which becomes charged. Then binds to E2 and trasnfers ubiquitin to it. E1 leaves. E3 then binds to E2 and protein to transfer ubiquitin to target protein. The amount of ubiquitin addedis absed on which types of E2-E3 are covalently attached.

52
Q

What does polyubiquitination of a protein cause?

A

Protein degradation.

53
Q

What is E1?

A

ubiquitin activating enzyme.

Transfers charged ubiquitin to E2.

54
Q

What is E2?

A

ubiquitin conjuguation enzyme. Finds E3.

55
Q

What is E3?

A

Diverse group of proteins, ubiquitin ligase. Binds specific protein and E2 in specific site.

Molecular Cell Biology (9 decks)

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