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Flashcards in Lecture 2 Reading Deck (48):
0

Polypeptide backbone

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

1

What determines the folding of a protein chain?

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

2

Hydrophobic clustering force

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

3

How do most proteins fold up

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

4

Molecular chaperones

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

5

Protein domains

Structural units that fold more or less independently of each other

6

Common folding patterns

Alpha helix and beta sheet

7

Coiled coil

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

8

Different functions of domains

Signaling pathways
Regulation

9

Why do so many proteins form stable conformations

Natural selection

10

What makes up protein families

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

11

Protein folds

Ways in proteins fold up in nature

12

Domain shuffling

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

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Protein modules

A subset of protein domains with versatile structures

14

Protein modules built from

Stable core structure formed from strands of beta sheets

15

Multi domain proteins

Have more than one domain

16

Binding site

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

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Globular proteins

Chain folds up into ball

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Fibrous proteins

Have simple, elongated three d structures

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Intermediate filaments

Component of cytoskeleton

20

Disordered polypeptide chains

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

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What do disordered regions do

Form binding sites
Tether protein domains
Restrict diffusion

22

Disulfide bonds

Disulfide structures. Act as atomic staples rot reinforce favored conformation

23

Advantages of using small subunits to build larger structures

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

24

Rings, tubes and spheres add

Stability

25

Two categories of protein interaction with amino acid side chains

Restricting access to water
Altering reactivity of amino acids

26

Why is regulating water access important?

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

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

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

What does chemical reactivity of protein surface depend on?

Which amino acid side chains are exposed
Their exact orientation to one another

29

Evolutionary tracing purpose

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

30

Evolutionary tracing method

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

Types of protein-protein interfaces

Surface-string interaction
Coiled -coil
Surface-surface

32

Surface-string interaction

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

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Coiled-coil

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

34

Surface-surface interactions

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

35

Antibodies

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

36

Equilibrium constant (k)

Calculates strength of binding

37

How does phosphorylation affect a protein?

Conformational change
Affect bindings, changing activity

Form part of structure that binding sites recognize

38

When are phosphate groups added or removed ?

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

39

What does protein phosphorylation involve

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

Protein kinase

Catalyzes phosphorylation

41

Protein phosphatase

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

42

How are phosphates useful?

They activate and deactivate protein processes

43

How does a kinase work?

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

44

How do GTP-binding proteins work?

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

GTPase activating protein

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

Guanine nucleotide exchange factor

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

47

Proteomics

Research focused on the analysis of large sets of proteins