Chapter 2, Structure of Protein

Question 0

The N-terminal of a peptide chain is written to the (L/R) and the free carboxyl to the (L/R).

Answer 0

N-terminal – Left

free carboxyl – Right

Question 1

Formation of the peptide bond is a _________ reaction, as it entails the loss of a water molecule.

Answer 1

condensation

Question 2

Peptide bonds are examples of amide bonds and cleavage of them requires a molecule of water (hydrolysis). Peptide bonds are considered strong _________ bonds (not easily cleaved).

Answer 2

covalent

Question 3

Peptide bonds can be seen as how many resonance isomers?

Answer 3

2
(C=O double bond with a C-N single bond) or
(C=N double bond with partial charges at NH and O)

Question 4

Describe the rotation around the peptide bond.

Answer 4

There is a restriction of rotation.

Question 5

Describe the polarity and charge of the -C=O and the -NH groups of the peptide bond.

Answer 5

Polar, but uncharged.

Question 6

If you have 10 amino acids attached by peptide bonds, the 8 in the middle would be ________ and the 2 on the ends would be ________.
(charged or uncharged)

Answer 6

8 in the middle - uncharged
2 on the end - charged
*The minimum number of charged will be 2, but the maximum depends on the R groups.

Question 7

Each individual amino acid in a peptide is called a….?

Answer 7

residue

Question 8

Peptides with 10 to 100 amino acid residues are called _________ while those with greater than 100 amino acid residues are called ________.

Answer 8

10-100, polypeptides

>100, proteins

Question 9

What is the largest human protein?

Answer 9

titin

Question 10

Which structure is defined as different types of local confirmations, stabilized by hydrogen bonding?

Give two examples.

Answer 10

Secondary (alpha helix and beta sheets)

Question 11

What is the average length of an alpha helix?

Answer 11

10 residues

Question 12

Naturally occurring alpha helices are coiled in a ______-handed manner with each turn corresponding to how many residues?

Answer 12

Right-handed, 3.6 residues per turn

Question 13

Which structure is the linear sequence of amino acids?

Answer 13

Primary

Question 14

The alpha helix is stabilized by intrachain _________ bonds between the carbonyl of a peptide bond and the -NH of a peptide bond located how many amino acid residues along the polypeptide chain?

Answer 14

hydrogen bonds

four amino acid residues

Question 15

Which amino acid is often known as the “helix breaker” because of it’s size and chemistry which induces distortion in the direction of the helical axis?

Answer 15

Proline (amino and imino acid!)

Question 16

In beta sheets, all peptide bonds participate in hydrogen bonding, which run _________ to the axis of the polypeptide.

Answer 16

perpendicular

Question 17

In beta sheets, separate neighboring polypeptides are aligned in a _________ or ________ orientation.

Answer 17

parallel or anti-parallel

Question 18

Pleating of the beta sheets (accordion folding) serves to optimize inter-chain or intra-chain ________ bonding.

Answer 18

hydrogen

Question 19

Alpha helices and beta sheets are found in what two types of proteins?

Answer 19

fibrous and globular

Question 20

What is the typical length of a beta sheet?

Answer 20

3-10 amino acid residues

Question 21

Non-repetitive secondary structures include bends, forms, and loops which possess a less regular structure relative to alpha helices or beta sheets. Disordered regions can assume a more organized structure upon the binding of a specific ________.

Answer 21

ligand

Question 22

Supersecondary structures, which are referred to as \_\_\_\_\_\_\_\_\_, are protein structures that contain at least 2 adjacent units of secondary structure. Examples include:
Helix-loop-helix
Beta-meander
Beta-barrel
Alpha-helix-hairpin
Beta-hairpin

Answer 22

Motifs

Question 23

Peptide bonds in proteins:

• _________ double-bond character
• Rigid and planar
• ______ configuration
• Polar uncharged

Answer 23

*Partial
*
*Trans
*

Question 24

The folding of the protein domains into a 3-dimensional formation.

Answer 24

Tertiary structure

Question 25

Basic functional and 3-dimensional units of a polypeptide that are constituted from combinations of super-secondary structural motifs to create independently folding, self-stabilizing regions of the polypeptide chain.

Answer 25

Domains

Question 26

Which regions of the gene can domains be associated with?

Answer 26

exons

Question 27

What are the four types of chemical interactions that can cooperate in the stabilization of tertiary structures?

Answer 27

1. Disulfide bonds
2. Hydrophobic interactions
3. Hydrogen bonds
4. Ionic interactions
   * Disulfide are the only covalent bonds

Question 28

The significance of relatively weak noncovalent interactions, is that they allow for both easy _________ and _________ of bonding.

Answer 28

association and disassociation

Question 29

If a protein will remain in the cytoplasm, it will not have this. But if the protein is in the ER, lysosome, membrane, or being secreted, it probably will have this. What are we referring to?

Answer 29

disulfide chains

Question 30

EXTRAcelluar mammalian proteins generally contain disulfide bonds (________), while INTRAcellular proteins contain _________.

Answer 30

EXTRA - cystine

INTRA - cysteine

Question 31

Protein folding is an “all or none” process characterized by _________ transitions.

Answer 31

cooperative

Question 32

Protein folding occurs by what?

Answer 32

progressive stabilization of intermediates

Question 33

Proper folding can also be dependent upon other factors such as surrounding water or lipid molecules or molecular chaperones which are also known as what?

Answer 33

heat shock proteins

Question 34

Protein folding is extremely fast, occurring spontaneously, even in test tubes. What are the problems associated with this?

Answer 34

1. High intracellular protein concentration creates problem of hydrophobic aggregation.
2. Unfolded proteins also susceptible to proteinases.

Question 35

Protein denaturation is caused by the disruption of which structures of the protein?

Answer 35

secondary and tertiary

Question 36

Denatured proteins adopt a confirmation known as a _______ _______. These proteins are usually (soluble/insoluble).

Answer 36

random coil, insoluble

Question 37

The structure of a protein that involves the association of 2 or more polypeptide chains, either identical in sequence, or different, to form a protein complex.

Answer 37

Quaternary structure
(When the tertiary chains come together)
*This is the actual, functional protein

Question 38

What type of structures are found in chromosome and viruses?

Answer 38

Supra-quaternary

Question 39

In hair curling, the keratin molecules are first ________ which ruptures the stabilizing disulfide crosslinks. Then, the addition of ________ agents, reforms the disulfide bonds into their new (curled) position.

Answer 39

• first reduced

* then oxidized

Question 40

The thiol (sulfhydryl) group in cysteine can bind different _________.

Answer 40

metals

Question 41

Protection against intracellular insults offered by:

1. Protein disulfide isomerases
2. Ubiquitin-proteasome… Proteins selected for degradation are tagged with ________, a small globular protein. They are recognized by the cytosolic proteasome, which will initiate their degradation.
3. Chaperones (heat shock proteins)
   a. Prevent premature _________.

Answer 41

2. ubiquitin

3a. folding

Question 42

Unnecessary, damaged, misfolded, or dysfunctional proteins originating from inside the cell are usually degraded by the _________.

Answer 42

proteasome

Question 43

Another class of chaperones, known as _________, are barrel-like structures in which the nascent protein is situated as it folds. The inner wall of this barrel-like structure is actually lined with hydrophobic amino acids. Both of these are known as heat shock proteins.

Answer 43

chaperonins