Biochm Test Chpt 4 (Test 2 Review)

Front 1

Spatial arrangement =

Back 1

Conformation

Front 2

The native conformation is what?

Back 2

-folded
-the lowest free energy [G]

Front 3

Conformation is primarily stabilized by what 2 things?

Back 3

1. Burying hydrophobic groups in the interior of the molecule
2. Maximizing Hydrogen Binding

Front 4

Describe the structure of a peptide bond?

Back 4

-Always 6 atoms
-Always planar
-2 Carbons at ends can twist

Front 5

Describe the general characteristics of secondary structures?

Back 5

-local 3-D structures
-have a kink
-communication is due to spatial arrangement of AAs

Front 6

Name the two types of secondary structures?

Back 6

1. alpha helix
2. beta sheet

Front 7

Describe the alpha helix?

Back 7

-full turn = 5.4A or 3.6 residues
- "kink" like a hose, (slide says something about proline)

Front 8

Name the 2 types of Beta sheets?

Back 8

1. Parallel
2. Antiparallel

Front 9

Describe a parallel beta sheet?

Back 9

1. All the strands are in the same direction
2. repeats every 6.5
ex.

NH2--------------COOH
NH2--------------COOH
NH2--------------COOH

Front 10

Describe an anti-parallel beta sheet?

Back 10

1.all strands are in opposite directions
2. Repeats every 7 (longer than parallel)

ex.

NH2--------------COOH
COOH-------------NH2
NH2--------------COOH

Front 11

Tertiary is overall what?

Back 11

3-D

Front 12

Describe, generally, tertiary structures?

Back 12

1. 3-D structures
2. involves long range interactions (unlike 2ndary structure, that depends on spatial arrangement of adjacent AAs)

Front 13

Name the 2 major tertiary groups?

Back 13

1. Fibrous (elongated; structural)
2. Globular (enzymes, most proteins, more compact)

Front 14

Name 3 examples of fibrous proteins?

Back 14

1. alpha-keratin
2. collagen
3. silk fibroin

Front 15

Where would you find alpha-keratin?

Back 15

hair, feathers, fingernails, hooves, horns, outer skin

Front 16

Describe the 4 basic characteristics of alpha-keratin?

Back 16

1. Strong
2. RH alpha helix, is it's basic unit, long alpha helices, wraps around itself in left handed fashion
3. LH parallel super helix
(a helix of helices)
4. held together, strength due to, disulfide cross-links

Front 17

Where would you find collagen?

Back 17

tendons, Cartilage, bone

Front 18

Describe 5 basic characteristics of collagen?

Back 18

1. Strong
2. made up of standard and nonstandard proteins
3. has LH helix which is a single strand (this is the alpha CHAIN) (NOT an alpha HELIX)
4. RH superhelix (3 helices)
5. Has novel cross-links

Front 19

Describe 4 basic characteristics of silk fibroin?

Back 19

1. Beta sheets predominate
2. It is fully extended (there is no stretching)
3. There are no cross-links (so it is flexible)
4. it is flat, flexible, and strong

Front 20

Describe 3 points about Globular proteins?

Back 20

1. include enzymes, transport proteins, immunoglobulins
2. 1000s of known structures, and the # doubles every 2 years
3. the 1st structure determined was myoglobulin

Front 21

Myoglobulin is a type of what?

Back 21

Globular protein

Front 22

List 3 features of Myoglobulin?

Back 22

1. Largely alpha-helical
2. has buried hydrophobic groups
3. heme

Front 23

What is a heme?

Back 23

a globular protein

Front 24

What is a motif?

Back 24

-inv. w globular proteins somehow (a 3-D struc)
-collection of secondary structures within a protein
-either alpha or beta

Front 25

What is a Domain?

Back 25

-inv. with globular proteins somehow (a 3-D struc)
-2 polypeptides distinct from eachother but connected by a thin region
-able to move but only relative to one another

Front 26

Hemoglobulin is an example of what?

Back 26

a quaternary structure

Front 27

What levels of structure do all proteins have?

Back 27

primary, secondary, and tertiary

Front 28

What level of structure do only some proteins have?

Back 28

quaternary (3-D rel. of subunits)

Front 29

What kind of structure is quaternary?

Back 29

a 3-D rel. of subunits

Front 30

Domain vs. subunits of quaternary structures?

Back 30

Domains:
-covalent bonds
-same polypeptide w/ different regions

Subunit:
-different polypeptides associated with each unit
-no covalent bonds

Front 31

When will you have a true quaternary structure?

Back 31

-it is a multi-subunit protein
-so only if there is more then one polypeptide

Front 32

What is Denaturation?

Back 32

-a disruption of structure
-does not break bonds
-it changes or disables function
Could be caused by
1. heat
2. chemical (pH, solutes, solvents, detergents)
3. it is reversible sometimes

Front 33

What is Renaturation?

Back 33

1. when denaturation is reversible
2. displays importance of primary structure
3. only occurs when there is a slight denaturation (ex. fever in body)
4. renaturation is spontaneous when denaturation is discontinued

Front 34

What is protein folding?

Back 34

1. it happens to proteins spontaneously in vivo seconds
2. mechanism is not fully understood

Front 35

3 diseases that are the result of protein folding?

Back 35

1. Cystic fibrosis
2. Prion disease
3. Parkinsons

Front 36

Name two proteins that assist folding?

Back 36

1. Molecular chaperones
a. heat-shock proteins (protect folded proteins)
b. chaperonins (helps proteins fold)
c. chaperones related to parkinsons
2. Isomerases

Front 37

How do folded proteins cause parkinsons?

Back 37

cause death of dopamine producing cells in substantia nigra, movement disorders