protein structure

Question 1

What are proteins?

Answer 1

Proteins are linear polymers of amino acids joined
by peptide bonds.

Question 2

What is the smallest protein length? What is the average protein length? What is the largest known protein?

Answer 2

The smallest proteins are ~40 amino acids in
length. The “average” protein is ~300-400 amino acids in
length. The largest known protein is the muscle protein titin: ~30,000 amino acids!

Question 3

What is the specific sequence of amino acids in a
protein called?

Answer 3

The specific sequence of amino acids in a protein is
called the protein’s primary structure.

Question 4

Do linear polymers of amino acids form straight
rod-like structures?

Answer 4

No, but fold into definite 3-D structures
depending on the sequence of amino acids.

Question 5

What determines the functions of a protein?

Answer 5

The functions of a protein are determined by :
-its overall shape (i.e., specific folding pattern driven by amino acid sequence)
-the distribution throughout that overall shape of the amino acid side chains with their distinctive chemical properties.

Question 6

What are the two major classes of amino acid side
chains?

Answer 6

Hydrophilic and Hydrophobic.

Question 7

What is the charge distribution of hydrophilic side
chains?

Answer 7

They have a polar electronic charge distribution.

Question 8

What is the charge distribution of hydrophobic side
chains?

Answer 8

They have a non-polar charge distribution.

Question 9

What is the hydrophobic effect?

Answer 9

Water molecules surrounding hydrophobic molecules dispersed in water
adopt a constrained, cage-like organization (low entropy).
If hydrophobic molecules coalesce, constrained water molecules is reduced, and this net increase in entropy
ultimately drives the formation of separate hydrophobic and aqueous phases.

Question 10

What type of interactions favor the coalescence of
hydrophobic molecules?

Answer 10

Weak non-covalent van der Waals intermolecular
interactions.

Question 11

What is the “Oil drop” model of protein folding?

Answer 11

It is a model that takes into account the hydrophobic
and hydrophilic side chains of amino acids and their
interactions in an aqueous solution.

Question 12

What determines the overall shape of the molecule?

Answer 12

specific, local, structural interactions, called secondary
and tertiary, determine the path of the peptide “backbone”
through space and hence, the overall shape of the molecule.

Question 13

What dictates protein structure and function?

Answer 13

The amino acid sequence

Question 14

What is the relationship between DNA and protein
function?

Answer 14

DNA indirectly determines protein function through
its determination of the amino acid sequence.

Question 15

How do amino acids link together? (Process)

Answer 15

The amino acids of a polypeptide are attached to their neighbors by covalent bonds known as a peptide bonds. Each bond forms in a dehydration synthesis (condensation) reaction. The carboxyl group of the amino acid chain reacts with the amino group of an incoming amino acid, releasing a molecule of water. The resulting bond between amino acids is a peptide bond

Question 16

What is the directionality of amino acids in a protein
chain?

Answer 16

it has two ends that are chemically distinct from one another. At one end, the polypeptide has a amino group, and this end is called the amino terminus (or N-terminus). The other end, which has a carboxyl group, is known as the carboxyl terminus (or C-terminus).

Question 17

What is the secondary structure of polypeptides?

Answer 17

local conformations of the
peptide chain backbone.

Question 18

What are the two major peptide chain backbone
conformations?

Answer 18

Alpha-helix and beta-sheet.

Question 19

What is the basis for the alpha-helix and beta-sheet
structures?

Answer 19

H-bonding between peptide bond carbonyl O atoms
on one amino acid residue and amino group
hydrogens on a different amino acid residue.

Question 20

What drives the periodicity of the alpha-helix
structure?

Answer 20

The tilted axis of H-bonds, which drives a periodicity
of 3.6 monomers per turn. (or 36aa per 10 turns)

Question 21

What determines the surface properties of an
alpha-helix?

Answer 21

side-chains

Question 22

What is the gross structure of an alpha-helix?

Answer 22

Straight rod.

Question 23

What links two adjacent beta-strands in a
beta-sheet?

Answer 23

H-bonds.

Question 24

What determines the interactions of a beta-sheet
with other parts of the protein?

Answer 24

Amino acid side chains protruding above and below
the plane of the sheet.

Question 25

Beta-sheet strands can be _________ or ___________.

Answer 25

parallel
antiparallel

Question 26

What is the difference between secondary and
tertiary structure?

Answer 26

Secondary structure is local, while tertiary structure
is the overall conformation of the polypeptide.

Question 27

What mediates interactions between different parts
of a protein and between the protein and its ligand
GDP?

Answer 27

Amino acid side chains.

Question 28

What are the types of non-covalent bonds that drive
interactions among amino acids in a protein? (4)

Answer 28

-H-bonds among peptide backbone carbonyl and amino groups
-H-bonds between amino acid side chains with polar side chains
-ionic bonds between positively charged (basic) and negatively charged (acidic) side chains
-van der Waals interactions among hydrophobic side chains.

Question 29

What is the covalent bond interaction that can be
important in protein structure?

Answer 29

The side chain of the amino acid cysteine contains
a sulfhydryl group that can form covalent S-S
(disulfide) bonds with other cysteine side chains

Question 30

What are motifs of protein structure?

Answer 30

Combinations of secondary structures forming
distinct local 3D structure.

Question 31

What motif is involved in protein:protein interactions?

Answer 31

coiled-coil motif

Question 32

What is a Ca++-binding motif?

Answer 32

EFhand/helix-loop-helix motif

Question 33

What is a motif that is common in transcription factors: binds to DNA/RNA?

Answer 33

Zinc-finger motif

Question 34

What is the difference between a motif and a
domain in protein structure?

Answer 34

Motifs are generally small, local structures that do
not contain a sufficient number of structure-maintaining bonds to hold the motif in its
characteristic 3-D shape if it is cut away from the
rest of the protein, while domains are larger than
motifs and contain a sufficient number of bonds to
hold the domain in its characteristic shape if it is cut
away from the rest of the protein.

Question 35

What is a heptad repeat?

Answer 35

It is a repeating pattern of amino acids in protein
structure that is commonly represented as
HxxHxxxHxxHxxxH, where H represents a
hydrophobic amino acid and x represents any
amino acid.

Question 36

What is the significance of the rest of the protein in
relation to motifs and domains?

Answer 36

The rest of the protein contributes to the stability of
a motif, but contributes little to the stability of a
domain.

Question 37

What are domains in protein structure?

Answer 37

Domains are structurally independent entities,
although covalently-joined to the rest of the protein.

Question 38

What are the four major structural classes of protein?

Answer 38

-Fibrous protein
-Globular protein
-Integral membrane protein
-Intrinsically disordered protein

Question 39

What is a intrinsically disordered protein?

Answer 39

Proteins (or protein segments) that exist as random coils under physiological conditions.
May adopt a specific secondary/tertiary structure upon binding to a well-structured partner protein.

Question 40

True or False: Similar domains cannot be found in diverse proteins, and also as multiple
similar copies within any given protein.

Answer 40

False
Similar domains can be found in diverse proteins, and also as multiple
similar copies within any given protein.

Question 41

Domains (HA1 and HA2) are held together by ________ bonds. The three identical two-protein
subunits are held together by ___________ bonds.

Answer 41

non-covalent
non-covalent

Question 42

True or False: Multimeric proteins can contain any number of identical or different polypeptides

Answer 42

True

Question 43

What are supramolecular complexes?

Answer 43

Large “molecular machines” made up of multiple distinct proteins,
each of which may itself contain multiple subunits.
(They are not stable and fall apart when the job is done).

Question 44

True or False: Evolution is to maintain the function of the protein, not the aa sequence.

Answer 44

True