Protein and their 3D structures

Question 1

What is the primary structure for proteins composed of? What is another name for peptide bond?

Answer 1

Polypeptides that consist of amino acids linked by peptide bonds.
Amine bond, another name for peptide bond.

Question 2

What do you call each amino acid in a protein?

Answer 2

A residue

Question 3

What makes polypeptide bonds so unique? Elaborate on the order of functional groups in polypeptide chain. How is the primary structure of a protein written (what comes first?)

Answer 3

Polypeptide bonds have directionality. The amino terminal end is marked as beginning of polypeptide chain. The carboxyl terminal end is at the end of polypeptide chain.
Primary structure is always written from amino terminal to carboxyl terminal (Left to right).

Question 4

Describe the structure of polypeptides in primary structure. what bonds might some of features include?

Answer 4

Polypeptide consists of repeating part called back bone (or main chain) and variable part consisted of distinctive amino acid side chains.
Backbone- hydrogen-bonding potential, because carbonyl and hydrogen atoms are bonded to nitrogen of amine group.

Question 5

How many amino acids do proteins usually consist of? molecular weight of amino acid?

Answer 5

about 50-2000 amino acids. mean molecular weight of amino acid is 110 g mol -1.

Question 6

What kind of bonds can polypeptide chains be cross-linked by? how does it occur? What is the result of the linkage?

Answer 6

Polypeptide can be cross-linked by Disulfide bonds. These bonds form by oxidation of 2 cysteines. 2 linked cysteines by disulfide bonds result in CYSTINE.

Question 7

What is Bovin Insulin? How does it differ from human insulin?

Answer 7

Bovin insulin- Beef insulin 2 polypeptide chain hormone produced in pancreas B cells. Has 3 amino acid residue difference from humans (ALA instead of THR on position 8 and 30; also Val instead of Leu on positon 10) can form 3 disulfide bonds between A and B chain.

Question 8

Describe the features of peptide bonds. is this bond flexible? is it charged?

Answer 8

Peptide bonds are planar. They have partial double bond character because of resonance and thus rotation around bond is prohibited.
Peptide bond is uncharged.

Question 9

what kind of configuration are peptide bonds usually in (trans or cis) ? Why?

Answer 9

Trans configuration to minimize steric clashes between neighboring R groups.

Question 10

which specific bonds allow for some free rotation around peptide bonds? what is the rotation around phi and psi bonds called? what does it do?

Answer 10

Phi and Psi bonds. rotations allowed near N-C alpha bond through phi bond. Rotation allowed for carbonyl bond through psi bond
Th rotation around phi/psi bond is called torsion angle, which determines path of polypeptide chain.

Question 11

What is the Ramachandran Plot?

Answer 11

plot of the most favorable conformation of phi and psi torsional angles.

Question 12

What is the secondary structure of proteins? what are examples present in the secondary structure?

Answer 12

3D structure formed by H-bonds between peptide NH and CO groups of amino acids that are near one another in primary structure.
Ex: alpha helix and Beta sheet

Question 13

Describe the Alpha helix and its features. What kind of bonds stabilize the alpha helix?

Answer 13

Alpha helix- tightly coiled rod like structure with R groups bristling out from axis of helix. Intrachain H-bonds stabilize alpha helix (all backbone CO and NH groups from h-bonds except ones at end of helix)
Most alpha-helices in proteins are right-handed.

Question 14

Besides alpha helices and Beta sheets, what is another structure that is formed in secondary structure of proteins?

Answer 14

Loops and turns which connect one alpha helix to another and are important for enzymes binding to DNA and active site construction.

Question 15

How are Beta sheets stabilized? How does it differ from alpha helix?

Answer 15

Beta sheets are stabilized by H-bond between polypeptide strands (inter H bond). B- sheets formed by adjacent B-strands and its polypeptide is fully extended (unlike alpha helix)

Question 16

What other distinctive features of B sheet apply?

Answer 16

Hydrogen bonds link the strands in B- sheet. The strands of B-sheet may be parallel, antiparallel or mixed. B-sheets can also be flat or adopt twisted conformation.

Question 17

What amino acids may you find in loops and turns?

Answer 17

the amino acids labeled charged, hydrophobic and aromatic residues (phenylalanine, valine, tryptophan, aspartate, glutamate, histidine, asparigine, tyrosine, leucine, isoleucine)

Question 18

How do loops and turns affect Polypeptide chains?

Answer 18

can change direction by making reverse turns, loops.

Question 19

What are coiled-coil proteins? List examples of them.

Answer 19

a superfamily of structural proteins that support cells and tissues. Ex: Alpha-keratin, cytoskeleton proteins and muscle proteins.

Question 20

What is alpha-keratin? what is it used for? How do they interact?

Answer 20

alpha keratin is a structural protein found in wool and hair, composed of 2 right-handed alpha-helices intertwined to form left-handed super helix called coil-coil. The helices interact with ionic bonds or van der waals interactions.

Question 21

Describe the importance, features and function of collagen. how does collagen differ from other structural proteins?

Answer 21

Collagen is a structural protein found in skin, bone, tendons, cartilage, teeth.
consists of 3 intertwined helical polypeptide chains that form superhelical cable. helical polypeptide chains do not contain alpha helices/

Question 22

Which amino acid appears at every third residue in collagen sequence? what is the sequence? What stabilizes the helices in collagen? How do the interwined polypeptide chains interact?

Answer 22

Glycine appears at every 3rd residue.

Sequence- gly-pro-pro is very common

Question 23

What stabilizes the helices in collagen? How do the intertwined helical polypeptide chains interact? what is unique about super helical table?

Answer 23

Steric repulsion of pyrrolidine rings of proline stabilize helices in collagen. The intertwined polypeptide chains interact through H-bonds. The interior of super helical cable is crowded and only glycine can fit in interior.

Question 24

Describe examples of how defects in collagen structure leads to pathological conditons (osteogenesis, scurvy?)

Answer 24

Osteogenesis imperfecta, (brittle bone disease) occurs when a mutation results in substitution of another amino acid in place of glycine.
Hydroxyproline- modified version of proline (OH replaces hydrogen) is important for stabilizing collagen, Vitamin C is required to form hydroxyproline. Lack of Vit C, results in scurvy.

Question 25

what are prions? What kind of disease may include prions?

Answer 25

misfolded proteins that can mutate and polymerize; Mad cow disease (caused by prion infectious agent, communicable)

Question 26

What is the tertiary structure of proteins?

Answer 26

The spatial arrangement of amino acids that are far apart in primary structure and to the pattern of disulfide bond formation.

Question 27

What are the principles of tertiary structure? Who illustrates them? What is in the interior of globular proteins? Exterior?

Answer 27

Globular proteins, like MYOGLOBIN form 3D structures.
These globular proteins are compact, little or no empty space in interior of globular proteins.
Interior of globular proteins- hydrophobic amino acids
Exterior- charged and polar amino acids.

Question 28

What are motifs and domains in a polypeptide sequence.

Answer 28

Motifs- (super secondary structure) combinations of secondary structure found in many proteins
Domains- proteins with 2 or more similar or identical compact structures.

Question 29

what are subunits? what is the quaternary structure? describe how dynamic quaternary structure is?

Answer 29

subunits- multiple polypeptide chains. Quatenary structure happens when multiple protein subunits join together and squeeze into one major complex. Exl: Hemoglobin
Quaternary structure can be simply 2 identical polypeptide chains or complex made of dozens of different polypeptide chains.

Question 30

which part of proteins structure dictates multi-dimensional structure of individual proteins?

Answer 30

primary sequence of amino acids

Question 31

List the process for protein structure in order.

Answer 31

1. Primary structure- sequence of amino acids
2. Secondary- regular pattern of H-bonding between NH and CO groups (contained within peptide backbone, alpha helices, beta sheets)
3. Tertiary- R group interactions from distant parts of poly peptide (highest level order of a polypeptide)
4. Quaternary- multiple polypeptides associate

Question 32

Describe the Anfinsen experiment,

Answer 32

Anfinsens placed Enzyme ribonuclease (degrades RNA) in solution with urea and B- mercaptoethanol. Urea destroyed all noncovalent bonds, while B-mercapto destroyed disulfide bonds. Hence, ribonuclease denatured (enzyme displayed no enzymatic activity. ) When urea and B-mercapto slowly removed, enzymes regain its structure and its activity, and ribonuclease is renatured (attain its normal state)

Question 33

What specific substance breaks disulfide bonds?

Answer 33

B-mercaptoethanol breaks down disulfide bonds.

Question 34

What part of the protein contains information required for polypeptide chain to fold into functional protein and defined 3D structure? what is function of ribonuclease?

Answer 34

Primary structure.

Ribonuclease- hydrolyze RNA, fold on itself and assist in protein folding .

Question 35

How does protein folding occur? What process?

Answer 35

protein folding occurs by cumulative selection. partially correct folding intermediates are retained because they are slightly more stable that unfold regions.

Question 36

What kind of medical conditions may arise due to misfolding of proteins? list examples.

Answer 36

Amyloidosis- diseases that result from formation of protein aggregates called amlyoid fibril and plaques. this abnormal protein (amylodisis)
Ex: Alzheimer disease is an example of amyloidosis

Question 37

What are the 2 states of prions? how does this affect the cell?

Answer 37

infectious neurological diseases are caused by infectious proteins called prions.
Prion can be one alpha-helix (PrP) and B-sheet rich (PrP^SC)
pRp^SC forms aggregates that disrupt function.

Question 38

What are the different levels of structure of proteins?

Answer 38

s

Question 39

Distinguish between noncovalent and covalent levels of structure of protein.

Answer 39

t

Question 40

How is a peptide bond formed? What is the directionality of peptide bond?

Answer 40

s

Question 41

What is the special property of cysteine amino acids ?

Answer 41

s

Question 42

Which bonds in peptide allow freedom of rotation around them?

Answer 42

b

Question 43

What does Ramachandran plot tell you about peptide bond rotation?

Answer 43

s

Question 44

What are the two major secondary structures of a peptide?

Answer 44

s

Question 45

What is the basis for the disorder “osteogenesis imperfecta”?

Answer 45

n

Question 46

What is the role of vitamin C (ascorbate) in human health? What conditions result due to a lack
of vitamin C?

Answer 46

d

Question 47

How is the three-dimensional structure of proteins attained? Where does the information for
protein folding reside?

Answer 47

s