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Cell Biology > Lecture 2 Reading > Flashcards

Lecture 2 Reading Flashcards

0
Q

What determines the folding of a protein chain?

A

Weak noncovalent Bonds
H bonds, electrostatic attractions, van der waals attractions. The combined strength of these bonds determines stability of folded shape.

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1
Q

Polypeptide backbone

A

Repeating sequence of atoms along the core of the polypeptide chain. Attached to repetitive chain are side chains.

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2
Q

Hydrophobic clustering force

A

Has a central role in determining shape of protein. Distribution of polar and nonpolar amino acids. Nonpolar cluster in interior.

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3
Q

How do most proteins fold up

A

Into one stable conformation that can change slightly when the protein interacts with other molecules in the cell.

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4
Q

Molecular chaperones

A

Assist in protein folding. Bind to partly folded polypeptide chains and help them progress along most energetically favorable folding pathway.

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5
Q

Protein domains

A

Structural units that fold more or less independently of each other

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6
Q

Common folding patterns

A

Alpha helix and beta sheet

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7
Q

Coiled coil

A

Stable alpha helix structure, firms when two alpha helices have most of their nonpolar side chains on one side, so they can twist around each other with three side chains facing inward

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8
Q

Different functions of domains

A

Signaling pathways

Regulation

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9
Q

Why do so many proteins form stable conformations

A

Natural selection

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10
Q

What makes up protein families

A

Each family member has an amino acid sequence and a 3d conformation that resembles those of other family members

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11
Q

Protein folds

A

Ways in proteins fold up in nature

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12
Q

Domain shuffling

A

Many large proteins have evolved through the joining of oreexsiting domains in new combinations

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13
Q

Protein modules

A

A subset of protein domains with versatile structures

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14
Q

Protein modules built from

A

Stable core structure formed from strands of beta sheets

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15
Q

Multi domain proteins

A

Have more than one domain

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16
Q

Binding site

A

Any region of a proteins surface that can interact with another molecule thorough sets of noncovalent bonds

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17
Q

Globular proteins

A

Chain folds up into ball

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18
Q

Fibrous proteins

A

Have simple, elongated three d structures

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19
Q

Intermediate filaments

A

Component of cytoskeleton

20
Q

Disordered polypeptide chains

A

Rubber elastic mesh work that allows for flexibility of skin, for example

21
Q

What do disordered regions do

A

Form binding sites
Tether protein domains
Restrict diffusion

22
Q

Disulfide bonds

A

Disulfide structures. Act as atomic staples rot reinforce favored conformation

23
Q

Advantages of using small subunits to build larger structures

A

Needs only small amt of genetic info
Assembly and disassembly readily controlled
Synthesis errors avoided more frequently

24
Q

Rings, tubes and spheres add

A

Stability

25
Q

Two categories of protein interaction with amino acid side chains

A

Restricting access to water

Altering reactivity of amino acids

26
Q

Why is regulating water access important?

A

Water molecules form hydrogen bonds that can compete with ligands for sites on protein surface. A ligand will form tighter h bonds and electrostatic interactions with a protein if water molecules are kept away.

27
Q

How can clustering of neighboring polar amino acid chains alter the reactivity if these amino acids?

A

If protein folding forces together a bunch of negative side chains against their will, this will make a more attractive site for something that is positively charged. Amino acid chains that are normally not reactive will become reactive when they interact with one another through h bonds, so they can make or break covalent bonds

28
Q

What does chemical reactivity of protein surface depend on?

A

Which amino acid side chains are exposed

Their exact orientation to one another

29
Q

Evolutionary tracing purpose

A

Identify sites in a protein’s domain that are most crucial to the domain’s function.

30
Q

Evolutionary tracing method

A

Amino acids that are unchanged, or nearly unchanged, when all of the known family members are mapped onto a model of the three d structure of one family member. Most invariant positions often cluster on protein surface. Cluster generally corresponds to binding site.

31
Q

Types of protein-protein interfaces

A

Surface-string interaction
Coiled -coil
Surface-surface

32
Q

Surface-string interaction

A

Portion of surface of protein contacts an extended loop of polypeptide chain on a second protein

33
Q

Coiled-coil

A

When two alpha helices, one from each protein pair together. Seen in gene regulatory proteins

34
Q

Surface-surface interactions

A

Precise matching of one rigid surface to another. Extremely specific.

35
Q

Antibodies

A

Immunoglobulins, produced by immune system in response to foreign molecules, bind to target molecules, either inactivate molecule or mark it for destruction.

36
Q

Equilibrium constant (k)

A

Calculates strength of binding

37
Q

How does phosphorylation affect a protein?

A

Conformational change
Affect bindings, changing activity

Form part of structure that binding sites recognize

38
Q

When are phosphate groups added or removed ?

A

In response to signals that specify change in a cells state.

39
Q

What does protein phosphorylation involve

A

Enzyme catalyzed transfer of terminal phosphate group of ATP molecule to hydroxy ply group in do serine , threonine, or tyrosine side chains of the proteins

40
Q

Protein kinase

A

Catalyzes phosphorylation

41
Q

Protein phosphatase

A

Catalyzes the reverse reaction of phosphate removal, or de phosphorylation.

42
Q

How are phosphates useful?

A

They activate and deactivate protein processes

43
Q

How does a kinase work?

A

It transfers a phosphate group from an ATP molecule to an amino acid side chain of a target protein

44
Q

How do GTP-binding proteins work?

A

Phosphate is not attached directly to protein. It’s par of a guanine nucleotide GTP. This binds tightly to a class of proteins known as GTP-binding proteins. Proteins regulated in this way are in their active conformations with GTP bound. Loss of phosphate group when bound GTP is hydrolyzed to GDPin a reaction catalyzed by protein itself. In its GDP bonus state protein is inactive. Aka as GTPases.

45
Q

GTPase activating protein

A

Regulatory protein that controls whether GTP or GDP is bound. GAP will bind to a protein and induce it to hydrolyzed its bound GTP

46
Q

Guanine nucleotide exchange factor

A

Binds to GDP bound protein and causes it to release its GDP. Site is immediately filled by GTP. Activates protein.

47
Q

Proteomics

A

Research focused on the analysis of large sets of proteins

Cell Biology (35 decks)

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