Glossary of Biochm test Chpt 4 (test 2 review)

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Spatial arrangement =
The native conformation is what?
-the lowest free energy [G]
Conformation is primarily stabilized by what 2 things?
1. Burying hydrophobic groups in the interior of the molecule
2. Maximizing Hydrogen Binding
Describe the structure of a peptide bond?
-Always 6 atoms
-Always planar
-2 Carbons at ends can twist
Describe the general characteristics of secondary structures?
-local 3-D structures
-have a kink
-communication is due to spatial arrangement of AAs
Name the two types of secondary structures?
1. alpha helix
2. beta sheet
Describe the alpha helix?
-full turn = 5.4A or 3.6 residues
- "kink" like a hose, (slide says something about proline)
Name the 2 types of Beta sheets?
1. Parallel
2. Antiparallel
Describe a parallel beta sheet?
1. All the strands are in the same direction
2. repeats every 6.5

Describe an anti-parallel beta sheet?
1.all strands are in opposite directions
2. Repeats every 7 (longer than parallel)


Tertiary is overall what?
Describe, generally, tertiary structures?
1. 3-D structures
2. involves long range interactions (unlike 2ndary structure, that depends on spatial arrangement of adjacent AAs)
Name the 2 major tertiary groups?
1. Fibrous (elongated; structural)
2. Globular (enzymes, most proteins, more compact)
Name 3 examples of fibrous proteins?
1. alpha-keratin
2. collagen
3. silk fibroin
Where would you find alpha-keratin?
hair, feathers, fingernails, hooves, horns, outer skin
Describe the 4 basic characteristics of alpha-keratin?
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
Where would you find collagen?
tendons, Cartilage, bone
Describe 5 basic characteristics of collagen?
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
Describe 4 basic characteristics of silk fibroin?
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
Describe 3 points about Globular proteins?
1. include enzymes, transport proteins, immunoglobulins
2. 1000s of known structures, and the # doubles every 2 years
3. the 1st structure determined was myoglobulin
Myoglobulin is a type of what?
Globular protein
List 3 features of Myoglobulin?
1. Largely alpha-helical
2. has buried hydrophobic groups
3. heme
What is a heme?
a globular protein
What is a motif?
-inv. w globular proteins somehow (a 3-D struc)
-collection of secondary structures within a protein
-either alpha or beta
What is a Domain?
-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
Hemoglobulin is an example of what?
a quaternary structure
What levels of structure do all proteins have?
primary, secondary, and tertiary
What level of structure do only some proteins have?
quaternary (3-D rel. of subunits)
What kind of structure is quaternary?
a 3-D rel. of subunits
Domain vs. subunits of quaternary structures?
-covalent bonds
-same polypeptide w/ different regions

-different polypeptides associated with each unit
-no covalent bonds
When will you have a true quaternary structure?
-it is a multi-subunit protein
-so only if there is more then one polypeptide
What is Denaturation?
-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
What is Renaturation?
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
What is protein folding?
1. it happens to proteins spontaneously in vivo seconds
2. mechanism is not fully understood
3 diseases that are the result of protein folding?
1. Cystic fibrosis
2. Prion disease
3. Parkinsons
Name two proteins that assist folding?
1. Molecular chaperones
a. heat-shock proteins (protect folded proteins)
b. chaperonins (helps proteins fold)
c. chaperones related to parkinsons
2. Isomerases
How do folded proteins cause parkinsons?
cause death of dopamine producing cells in substantia nigra, movement disorders

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