Lecture 2 Reading

Question 0

What determines the folding of a protein chain?

Answer 0

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

Question 1

Polypeptide backbone

Answer 1

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

Question 2

Hydrophobic clustering force

Answer 2

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

Question 3

How do most proteins fold up

Answer 3

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

Question 4

Molecular chaperones

Answer 4

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

Question 5

Protein domains

Answer 5

Structural units that fold more or less independently of each other

Question 6

Common folding patterns

Answer 6

Alpha helix and beta sheet

Question 7

Coiled coil

Answer 7

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

Question 8

Different functions of domains

Answer 8

Signaling pathways

Regulation

Question 9

Why do so many proteins form stable conformations

Answer 9

Natural selection

Question 10

What makes up protein families

Answer 10

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

Question 11

Protein folds

Answer 11

Ways in proteins fold up in nature

Question 12

Domain shuffling

Answer 12

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

Question 13

Protein modules

Answer 13

A subset of protein domains with versatile structures

Question 14

Protein modules built from

Answer 14

Stable core structure formed from strands of beta sheets

Question 15

Multi domain proteins

Answer 15

Have more than one domain

Question 16

Binding site

Answer 16

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

Question 17

Globular proteins

Answer 17

Chain folds up into ball

Question 18

Fibrous proteins

Answer 18

Have simple, elongated three d structures

Question 19

Intermediate filaments

Answer 19

Component of cytoskeleton

Question 20

Disordered polypeptide chains

Answer 20

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

Question 21

What do disordered regions do

Answer 21

Form binding sites
Tether protein domains
Restrict diffusion

Question 22

Disulfide bonds

Answer 22

Disulfide structures. Act as atomic staples rot reinforce favored conformation

Question 23

Advantages of using small subunits to build larger structures

Answer 23

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

Question 24

Rings, tubes and spheres add

Answer 24

Stability

Question 25

Two categories of protein interaction with amino acid side chains

Answer 25

Restricting access to water

Altering reactivity of amino acids

Question 26

Why is regulating water access important?

Answer 26

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.

Question 27

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

Answer 27

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

Question 28

What does chemical reactivity of protein surface depend on?

Answer 28

Which amino acid side chains are exposed

Their exact orientation to one another

Question 29

Evolutionary tracing purpose

Answer 29

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

Question 30

Evolutionary tracing method

Answer 30

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.

Question 31

Types of protein-protein interfaces

Answer 31

Surface-string interaction
Coiled -coil
Surface-surface

Question 32

Surface-string interaction

Answer 32

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

Question 33

Coiled-coil

Answer 33

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

Question 34

Surface-surface interactions

Answer 34

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

Question 35

Antibodies

Answer 35

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

Question 36

Equilibrium constant (k)

Answer 36

Calculates strength of binding

Question 37

How does phosphorylation affect a protein?

Answer 37

Conformational change
Affect bindings, changing activity

Form part of structure that binding sites recognize

Question 38

When are phosphate groups added or removed ?

Answer 38

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

Question 39

What does protein phosphorylation involve

Answer 39

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

Question 40

Protein kinase

Answer 40

Catalyzes phosphorylation

Question 41

Protein phosphatase

Answer 41

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

Question 42

How are phosphates useful?

Answer 42

They activate and deactivate protein processes

Question 43

How does a kinase work?

Answer 43

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

Question 44

How do GTP-binding proteins work?

Answer 44

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.

Question 45

GTPase activating protein

Answer 45

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

Question 46

Guanine nucleotide exchange factor

Answer 46

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

Question 47

Proteomics

Answer 47

Research focused on the analysis of large sets of proteins