lecture 7

Question 1

what are protein domains

Answer 1

• distinct, stable, structural units that often have arrogated functions and fold as independent compact units
• they can move as a single entity with respect to the entire protein
• one domain is typically made of a single stretch of primary sequence
• proteins have one or more domains

Question 2

Discuss the protein domains in Src Protein Kinase

Answer 2

• contains 4 functional domains each with a different function
• Src protein kinase is one protein
• each domain is made from a single stretch of primary sequence
• contains elements of secondary structures

Question 3

why are some proteins intrinsically disordered

Answer 3

Functional importance
- binding
- tethering
- scaffolding
- flexibility

Question 4

What affect do non covalent bonds have on proteins

Answer 4

• they help proteins fold and maintain their structure

Question 5

List the types of non- covalent interactions that help proteins fold and maintain shape

Answer 5

• Van Der Waal interactions
• electrostatic interactions
• hydrophobic interactions
• hydrogen bonds

Question 6

How do covalent bonds help stabilize proteins?

Answer 6

• primarily achieved through disulfirame bonds which are formed between 2 cysteine residues
• they do not form in cytosol because it has a high concentration of reducing agents

Question 7

Disulfide bonds

Answer 7

• are very strong
• can make proteins like keratin very tough

Question 8

where is keratin found

Answer 8

• hair and nails

Question 9

what are the 4 representations of protein conformations?

Answer 9

1. Backbone: shows the backbone
2. Ribbon: shows the backbone and emphasizes secondary structure
3. Wire: shows backbone and emphasizes side chain
4. Space filing: provides contour map of surface

Question 10

What are the two major groups of protein

Answer 10

• fibrous protein
• globular protein

Question 11

Fibrous proteins

Answer 11

• possesses property that give strength and/or flexibility- important for structural functions
• example: a-keratin, silk, elastin, collagen

Question 12

globular proteins

Answer 12

• roughly spherical in shape and often contain several types of secondary structures
• example: myoglobin, lysozyme, cytochrome

Question 13

a coiled coil composed of two a-keratin chains is

Answer 13

left handed

Question 14

silk has small

Answer 14

small r groups

Question 15

Why is fibroin rich in Ala and Gly

Answer 15

• permits close packing of B-sheets and interlocking arrangements of R groups
• also participates in van der waal interactions which help stabilize stacked structures

Question 16

why are globular proteins structurally diverse

Answer 16

diverse functions:
- enzymes
- motor proteins
- regulatory proteins

Question 17

What native state

Answer 17

• in general, all molecules of a given protein species adopt the same 3D conformations despite the countless folding possibilities
• usually (but not always) the most stable state (lowest energy) of a folded protein

Question 18

why are only few of many possible polypeptide chains useful

Answer 18

• most proteins do not fold into stable proteins, others may be harmful to the cell by causing unwanted interactions
• even small changes can dramatically affect a proteins function (sickle cell anemia)

Question 19

If the Glu from hemoglobin a was mutated to another amino acid, which amino acid would be most likely to result in a preservation of the function of the hemoglobin?

Answer 19

• aspartic acid because they are both negatively charged (acidic)

Question 20

Protein denaturation

Answer 20

• destruction of the native structure by breaking weak bonds responsible for secondary and tertiary structures

Question 21

what does the term abrupt mean

Answer 21

• transition from folded to unfolded state

Question 22

what are the common causes of protein denaturation

Answer 22

• changes in temperature
• extreme pH
• detergents or organic solvents
• urea or guanidinium chloride
• reducing agent

Question 23

what are chaperone proteins

Answer 23

• many proteins can fold without any additional help
• some rely on chaperone proteins which help with the folding process through various mechanism
• for example: formation of isolation chambers to prevent polypeptide chains from aggregating with either other molecules or itself in the cytoplasm
• may also bind to hydrophobic residues of nascent polypeptides preventing unwanted associations with other hydrophobic residues

Question 24

what are some diseases that arise as a result of misfiled proteins

Answer 24

• alzheimer’s disease
• huntingtons disease
• creutzfeldt-jakob disease
• “mad cow” disease

Question 25

Describe the Chris Anfinsen refolding experiment

Answer 25

- starts in a native state and added urea and mercapto-ethanol - this protein is forced into an unfolded state (inactive) and disulfide cross links reduce to yield cys residues - removal of urea and mercapto-ethanol - disulfide cross links are correctly reformed and protein goes back to its native state

Question 26

What is the Anfinsen dogma? Is this true for all proteins?

Answer 26

- The 3D structure of a protein is is determined only by its protein amino acid sequence - this is generally true only for small proteins (some must fold during protein synthesis (translation) and some may need the help of chaperones)