General Information

Question 1

Four organizational levels of protein structure:

Answer 1

1. primary
2. secondary
3. tertiary
4. quaternary

Question 2

Primary structure

Answer 2

• sequence of amino acids in a protein
• defined by covalent bonds (including disulfide bridges)

Question 3

Peptide bonds covalently link amino acids via:

Answer 3

• amide linkages between the α-carboxyl group of one amino acid and the α-amino group of another amino acid.
• occurs via a loss of water

Question 4

All amino acid sequences are read from…

Answer 4

• the N- to the C-terminus of the peptide

Question 5

Peptide bond characteristics (4):

Answer 5

1. partial double-bond character
2. rigid and planar
3. uncharged, but polar
4. trans configurations (except proline, cis 15%)

Question 6

The -C=O and -NH groups of peptide bonds are …

Answer 6

• polar and involved in hydrogen bonds in alpha helices and beta sheet structures

Question 7

What angles specify the path of a polypeptide backbone?

Answer 7

• phi and psi angles
• only two sets of phi and psi angles can be repeted without steric collisions

Question 8

_____ is the only amino that can cause a cis configuration in a polypeptide chain.

Answer 8

Proline

15% of the time

Question 9

Peptide bonds have trans configurations to minimize:

Answer 9

steric hindrance. Orients side chains on opposite sides of the peptide bonds. Proline can cause cis configuration.

Question 10

Repetitive phi and psi bonds in polypeptide chains aid in the formation of:

Answer 10

repetitive secondary structures

1. alpha helices (coiled chains)
2. beta sheets (extended chains)

Question 11

Non-regular and non-repetitive secondary conformations are due to:

Answer 11

non-repeating phi and psi angles

1. coils
2. turns
3. loops, etc.

Question 12

Secondary Structure

Answer 12

Local arrangements of the peptide backbone, often defined by H-bonds

Question 13

Tertiary Structure

Answer 13

Arrangement of secondary structure elements into compact domain

Question 14

Quaternary Structure

Answer 14

Arrangement of multiple polypeptide chains in a multi- subunit protein (only in proteins with >1 chain)

Question 15

Alpha helix dimensions:

Answer 15

1. 3.6 residues / turn
2. 5.4 Å / turn
3. 1.5 Å rise / residue

Question 16

Hydrogen bonding in alpha helices:

Answer 16

Residue i forms a hydrogen bond with i + 4.

• Not all hydrogen bonds are satisfied, but within the body of the helix, every NH group forms a hydrogen bond with a carbonyl oxygen. This neutralizes the polarity of the peptide bond, and stabilizes the entire structure.

Question 17

In an alpha helix, side chains extend…

Answer 17

outward from the helix to avoid interacting sterically with each other

Question 18

In an alpha helix, all carbonyls extend toward…

Answer 18

the C-terminus

creates polarity to helix

Question 19

Interiors of proteins are largely …

Answer 19

repetitive secondary structures

Question 20

Amino acids that can disrupt an alpha helix:

Answer 20

1. proline (secondary amino group not compatible with right-handed spiral of helix; kinks)
2. large numbers of charged amino acids (form ionic bonds or repel each other)
3. amino acids with bulky side chains (Y)
4. amino acids that branch at beta-carbon (V and I)

Question 21

Alpha helix characteristics:

Answer 21

1. right-handed
2. C=O point to C-terminus (dipole)
3. H-bonds (between C=O and H-N; residue i and residue i+4)
4. 3.6 residues / turn
5. 5.4 Å / turn
6. 1.5 Å rise / residue

Question 22

Hydrophobic helices:

Answer 22

1. hydrophobic (nonpolar) sidechains
2. typically go through lipid bilayer

Question 23

Polar helices:

Answer 23

1. typically charged side chains
2. exposed to solvents (intracellular and extracellular)

Question 24

Amphipathic helices:

Answer 24

1. a mixed pattern of polar residues, hydrophobic residues, and charged residues.
2. Can have polar faces and non-polar faces.

Question 25

In alpha helices, hydrogen bonding is:

Answer 25

* between the peptide-bond carbonyl oxygens and amide hydrogens that are part of the polypeptide backbone (i and i + 4 residues H-bond) * parallel

Question 26

Unlike alpha helix, beta sheets are:

Answer 26

1. composed of two or more polypeptide chains 2. almost fully extended 3. H-bonds are perpendicular to the polypeptide backbone

Question 27

The three perpendicular planes of beta sheets:

Answer 27

1. plane of strands 2. plane of hydrogen bonds 3. plane of side chains

Question 28

Dimension of Beta-sheet:

Answer 28

* about 3.5 Å / residue

Question 29

Two types of Beta Sheets:

Answer 29

1. Parallel 2. Antiparallel

Question 30

Parallel Beta Sheets

Answer 30

1. hydrophobic (N-N-N-N-N-N-N) 2. buried in protein interior 3. N-termini line up with one another, C-termini line up with one another (N=nonpolar)

Question 31

Antiparallel Beta Sheets

Answer 31

1. amphipathic (N-P-N-P-N-P) 2. N-terminal and C-terminal ends alternate 3. one face hydrophobic, one face polar. 4. Polar face is on surface, and hydrophobic face buried on interior.

Question 32

Beta sheet hydrogen bond and side chains:

Answer 32

1. side chains perpendicular to sheet (above and below) 2. hydrogen bonds parallel to sheet

Question 33

Turns and loops are:

Answer 33

secondary structures, just not as regular/repetitive as helices and sheets.

Question 34

Turns and loops largely make up:

Answer 34

* the surface of proteins

Question 35

Turns and loop are often the sites of:

Answer 35

* functional residues/binding sites (since turns and loops compose the surface of globular proteins) * Alpha helices and beta sheets provide scaffold for these loops and turns

Question 36

Approximately \_\_\_% of an average globular protein is organized into repetitive structures such as the alpha helix and/or beta sheet.

Answer 36

50% The remainder is made up of nonrepetitive loops, turns, and coils.

Question 37

Helix-loop-Helix Motif

Answer 37

loop can be large or small

Question 38

Beta-hairpin Motif

Answer 38

antiparallel sheets

Question 39

Greek Key Motif

Answer 39

* a fold of a large antiparallel beta hairpin. * Fold over a long beta strand. * Create really common and stable structures. This fold is in immunoglobulins.

Question 40

Beta-Alpha-Beta Motif

Answer 40

* connect two parallel beta strands in a beta sheet. * Loop through amphipathic helix.

Question 41

Five forces that stabilize protein structure:

Answer 41

1. Hydrophobic Interactions 2. van der Waals Interactions (very small, due to tight packing of residues) 3. Hydrogen Bonds (inter- or intrachain or with water) 4. Ionic Interactions (between positively and negatively charged side chains) 5. Disulfide Bridges (covalent bond between cysteines)

Question 42

Domains are:

Answer 42

* the fundamental functional and 3-D structural units of polypeptides * 100-300 amino acids

Question 43

Domain cores are built from:

Answer 43

* combinations of super-secondary structural elements (motifs) * Folding of a domain occurs independently of the folding of other domains in a protein

Question 44

Typical weight of a single domain:

Answer 44

* 10-30 kDA

Question 45

Folds of proteins consisting of all alpha proteins:

Answer 45

* mostly alpha helices * all perpendicular orientations or all parallel orientations.

Question 46

Folds of proteins consisting of all beta proteins:

Answer 46

* usually have little bits and pieces of helices * core of protein made of anti-parallel beta strands

Question 47

Folds of proteins consisting of both alpha and beta proteins:

Answer 47

* parallel beta sheet usually connected by alpha helices. * Can wrap around in barrel or go around in a flat sheet.

Question 48

Subunits of quaternary structures are held together via:

Answer 48

* non-covalent interactions * H-bonds * ionic bonds * hydrophobic interactions, etc. * subunits may function independently or cooperatively (i.e. hemoglobin)

Question 49

Isoforms:

Answer 49

* proteins that perform the same function but have different primary structures * If the isoform protein is an enzyme, then it is referred to as an isozyme

Question 50

Native conformation:

Answer 50

* the functional, fully-folded protein structure * determined by primary structure (AA sequence) * AA interactions guide secondary, tertiary, and sometimes quaternary structure

Question 51

Protein chaperones assist with:

Answer 51

the proper folding of many species of proteins