Amino Acids, Peptides, and Protein Structures

Question 1

Specific structure of protein is required for

Answer 1

Presenting a binding site

Creating an active site

Forming a special shape

Question 2

What is Anfinsen’s experiment?

Answer 2

Native 3D protein –> added urea to denature protein and break sulfide bonds –> protein returns to primary sequence –> Remove urea –> protein refolds back to native structure

Question 3

What did Alfinsen’s experiment imply?

Answer 3

Native structure is determined by:

1) sequence (primary structure)
2) Physical and chemical properties of amino acids

Question 4

What are the nonpolar amino acids?

Answer 4

Alanine

Glycine

Valine

Leucine

Isoleucine

Phenylalanine

Tryptophan

Methionine

Proline

Question 5

What force allows peptides to acquire an initial shape?

Answer 5

Hydrophobic effect

Question 6

In soluble proteins, where are the polar and non-polar amino acids located?

Answer 6

Nonpolar are located in the interior

Polar are located on the surface

Question 7

In membrane proteins, where are polar and non-polar amino acids located?

Answer 7

Nonpolar are clutered on the surface of the membrane protein (i.e. in the part that spans the membrane)

Question 8

Which amino acid forms sulfide bonds

Answer 8

Cysteine

Question 9

What are the uncharged, polar amino acids?

Answer 9

Asparagine

Serine

Threonine

Glutamine

Tyrosine

Cysteine

Question 10

Which amino acids have hydroxyl groups that can form a H-bond

Answer 10

Serine

Threonine

Tyrosine

Question 11

Which amino acids have carbonyl and amide groups that can form hydrogen bonds?

Answer 11

Asparagine

Glutamine

Question 12

Which amino acid forms a physiolgoical buffer?

Answer 12

Histidine

Question 13

Basic amino acids carry a __ change, acidic ones carry a __ charge

Answer 13

Basic = positive charge

Acidic = negative charge

Question 14

Peptide bonds are created by __ reactions

Answer 14

Condensation

Question 15

Change from primary to tertiary structure leads to a __ in free energy and is ___

Answer 15

Decrease in free energy = spontaneous reaction

Question 16

Alpha helix is formed by

Answer 16

Hydrogen bonds between peptide-bond carbonyl oxygens and amides

Question 17

In alpha helix, H bonding occurs between

Answer 17

O of carboxy terminus of peptide 1 and H of amino terminus of peptide 5 (n+4)

Question 18

Where are the side chains in an alpha helix?

Answer 18

On the outside

Question 19

What two things can disrupt an alpha helix?

Answer 19

Proline

Positively charged amino acids

Question 20

Beta sheets are stabilized by

Answer 20

H bonds formed between peptide stands

Question 21

Beta bend requires __ amino acids, including

Answer 21

4 amino acids, including

Proline and glycine

Question 22

What is the function of proline in a beta bend?

Answer 22

Forces residue 2 to turn

Question 23

What is the function of glycine in a beta bend?

Answer 23

Allows steric freedom so residue 3 can form a H bond with residue 1

Question 24

What is Leinthal’s paradox?

Answer 24

If protein folding is simply a process of random residue-pairing, it would require a long time

Question 25

What does the formation of secondary structure do?

Answer 25

Greatly reduces the number of possible combinations

Question 26

What are protein motifs?

Answer 26

Super-secondary structural patterns

Question 27

What is the significance of protein motifs?

Answer 27

Makes tertiary folding easier because it decreases residue combinations

Question 28

At what stage do you see the connection of structure and function of proteins?

Answer 28

Secondary structure (super secondary structural patterns)

Question 29

What is the function of alpha-alpha helix motif (aka Helix-loop-helix)

Answer 29

Transcription factors

Channels

Question 30

What is the function of beta-alpha-beta motif

Answer 30

Ligand binding

Question 31

What is the function of beta-meander motif

Answer 31

protein-protein interaction

Question 32

What is the function of the beta-barrel motif

Answer 32

Transporters

Question 33

Domains are built from

Answer 33

Combination of motifs

Question 34

What are the fundamental functional and 3D structural units of proteins

Answer 34

Domains

Question 35

Peptide folding within a domain usually occurs ___ of folding in other domains

Answer 35

Independently

Question 36

What does tertiary folding involve?

Answer 36

Folding of domains and function

Turns loose, domain-formed peptide into a compact, high density protein by rearranging the positions of the domains

Question 37

What interactions are invovled in teritary folding?

Answer 37

Covalent and non-covalent bonds

Question 38

Types of bonds from strongest to weakest

Answer 38

Covalent (disulfide bond)

Ionic

H-bonds

Hydrophobic interactions

Van der Waals