3-D Structure of Proteins

Question 1

What is the primary organization of proteins?

Answer 1

Amino acid sequence + disulfide bonds

Question 2

What is the secondary organization of proteins?

Answer 2

Regular recurring arrangements of adjacent amino acids

Question 3

What is the tertiary organization of proteins?

Answer 3

Arrangement of the total protein, the complete 3D structure

Question 4

What is the quaternary organization of proteins?

Answer 4

The arrangement of multiple protein subunits

Question 5

When a protein is denatured, what bonds aren’t broken?

Answer 5

Disulfide bonds

Peptide bonds

Question 6

What is a domain, with regards to proteins?

Answer 6

A contiguous region with a distinct function

Question 7

What are some examples of protein domains?

Answer 7

DNA binding
Transmembrane
Calcium binding

Question 8

Peptide bonds and disulfide bonds are both which type of bond?

Answer 8

Covalent

Question 9

Peptide bonds are ___ and ___.

Answer 9

Planar and rigid

Question 10

Which amino acid acts as the “oxidative stress sensor”?

Answer 10

Cysteine

Question 11

What are the 3 major secondary structure types in proteins?

Answer 11

Alpha helix
Beta pleated sheet
Beta turn

Question 12

In alpha helices, where do the peptide bonds align?

Answer 12

Along the long axis

Question 13

In alpha helices, where are the R groups?

Answer 13

Sticking out of the sides

Question 14

Each turn in alpha helices uses about how many amino acids?

Answer 14

About 3.6

Question 15

How are alpha helices stabilized?

Answer 15

Lots of hydrogen bonding

Question 16

Which amino acid is generally a “helix breaker”?

Answer 16

Proline

Question 17

What things are alpha helix destabilizers?

Answer 17

• A string of several basic or acidic amino acids
• A string of several amino acids with bulky side groups
• Amino acids 3-4 residues apart which cannot interact
• Proline residues
• A string of glycine residues

Question 18

How are beta pleated sheet chains arranged?

Answer 18

May be in parallel or anti-parallel fashion

Question 19

What is beta pleated sheet?

Answer 19

Extended arrangement of polypeptides

Question 20

What hold the adjacent chains together in beta pleated sheet?

Answer 20

Hydrogen bonds

Question 21

Beta turns contain which amino acid?

Answer 21

Proline

Question 22

In which conformation is proline found in beta turn?

Answer 22

The cis conformation

Question 23

What converts proline from the trans to the cis conformation?

Answer 23

Proline isomerase

Question 24

What are the two major groups of protein tertiary structure?

Answer 24

Globular

Fibrous

Question 25

Are fibrous proteins primarily water soluble or insoluble?

Answer 25

Water insoluble

Question 26

Which group of proteins (globular or fibrous) are structural proteins?

Answer 26

Fibrous proteins

Question 27

How are fibrous proteins usually arranged?

Answer 27

In long chains or sheets

Question 28

What are classic examples of right-handed alpha helix?

Answer 28

alpha and beta keratin

Question 29

Where is alpha and beta keratin found?

Answer 29

Hair Nails Feather etc.

Question 30

What type of amino acids are found in alpha and beta keratin?

Answer 30

Many hydrophobic amino acids

Question 31

What is a protofilament?

Answer 31

2-stranded superhelix

Question 32

How do alpha and beta keratin crosslink?

Answer 32

Via disulfide links

Question 33

To create a perm, what bonds are broken and then reformed?

Answer 33

Disulfide bonds

Question 34

How many types of keratin are there in the skin?

Answer 34

At least 18

Question 35

Cytokeratins can be diagnostic for what?

Answer 35

Tumors

Question 36

Most enzymes and protein hormones are what type of protein?

Answer 36

Globular proteins

Question 37

Which structure is more complex in globular proteins than in fibrous proteins?

Answer 37

Secondary structure

Question 38

What shape do globular proteins take on, due to the multiple arrangements of folding?

Answer 38

"spherical"

Question 39

What are the 4 bond types found in the tertiary structure?

Answer 39

Hydrogen bonds Ionic bonds Hydrophobic interactions Van der Waals forces

Question 40

What occurs in an H+ bond?

Answer 40

An electronegative atom (Usually O or N) acts as a Hydrogen acceptor

Question 41

What is an ionic bond?

Answer 41

Attraction between oppositely charged atoms

Question 42

What are hydrophobic interactions?

Answer 42

Forces that hold nonpolar regions together

Question 43

What are van der Waals forces?

Answer 43

Weak attractions resulting from transient dipole formation

Question 44

What proteins assist in folding or assembling subunits of a new protein?

Answer 44

Chaperone proteins

Question 45

What are the most famous chaperone proteins?

Answer 45

Heat shock proteins

Question 46

What causes prion diseases?

Answer 46

Improper folding of PrP protein

Question 47

What is Scrapie?

Answer 47

Spongiform encephalitis found in sheep

Question 48

What is kuru?

Answer 48

Human spongiform disease found in the Fore tribe of New Guinea

Question 49

What is Creutzfeldt-Jacob disease?

Answer 49

Sporadic, hereditary degenerative neurologic disease

Question 50

What causes cystic fibrosis?

Answer 50

Defective protein folding

Question 51

Which protein is missing an amino acid leading to cystic fibrosis? Which amino acid is missing?

Answer 51

Chloride channel protein is missing Phe-508

Question 52

When is quaternary structure found in proteins?

Answer 52

Only if the protein has more than one protein subunit

Question 53

What are some huge proteins with quaternary structure?

Answer 53

Pyruvate dehydrogenase Ribosomes RNA polymerase

Question 54

What is the best way to study protein structure?

Answer 54

Via x-ray crystallography

Question 55

What things will denature the secondary-quaternary structure of proteins?

Answer 55

Heat pH extremes Detergents Organic solvents (alcohol, acetone, urea)

Question 56

How can the primary protein structure be broken?

Answer 56

Boiling in a strong acid or base

Question 57

What things can cleave proteins at specific dipeptide sites?

Answer 57

Proteases

Question 58

What chemical can be used to reduce disulfide bonds?

Answer 58

Beta-Mercaptoethanol (BME)

Question 59

Tertiary structure is dictated by what?

Answer 59

Primary structure