Protein Structures

Question 1

Why proteins are workhorse of the cell

Answer 1

• several functions such as structural stability and expression of genetic info
• able to fulfill several functions bc of diversity in structure

Question 2

Structure determines function

Answer 2

• many forms to fulfill several functions
• structural versatility from different combination of 20 amino acids allowing it to be diverse
• lipifs and carbohydrates may also be added to function as elements of cell membrane/ cell signaling
• no common pattern to describe general structure of protein hence structural hierarchy system is used

Question 3

Limited conformation

Answer 3

• in secondary structure peptide C-N cannot easily rotate restricting possible protein conformation
• in teritary common folding motifs observed despite being different proteins bc used as basis to organize protein

Question 4

4 levels structure

Answer 4

Primary - linear sequence
Secondary - localized conformation of polypeptide backbone
Tertiary - 3D conformation including side chains
Quaternary - more than one peptide chain to form a complex

Question 5

Primary structure provide info on protein evolution

Answer 5

• amino acid sequence that closely resemble one another
  -ubiquitin is present in most eukryotes it is highly conserved indicating it is essential for function

Question 6

Secondary structure partial double bond

Answer 6

Carbonyl carbon has double bond but electron delocalization of pi electrons merge to give partial double bond character and restricts rotation

Question 7

Alpha helix

Answer 7

Carbonyl oxygen (C=O) pf each residue form bond with backbone of NH group 4 residues away
Van der waals

Question 8

Beta sheet

Answer 8

H bond with neighbor strands
Parallel - same direction
Antiparallel - opposite direction strands more stable bc of direct interaction which makes H bond to form easily

Question 9

Hydrophobic effect in tertiary

Answer 9

Driven by entropy > maximize entropy of water molecules
Non polar - inside
Polar - mostly exterior but some can H bind with other polar inside
Charged - surface interact with water

Question 10

Protein folding not a random process

Answer 10

• trial and error too long and energy costly
• stepwise folding
• some proteins can adopt more than one conformation
  
  • change in cellular condition, oxidation, binding partner can favor conformations

Question 11

Domains as evolutionary sink

Answer 11

Conserved sequence give rise to same folding pattern = may have same molecular lineage
Sequence can be different but same folding pattern

Question 12

Domains more accurate than primary sequence

Answer 12

Essential structure function element proteins are conserved rather than amino acid residues
- tolerable substituions can still result in the same folding bc of same IMFAs

Question 13

Globular

Answer 13

Backbone fold in itself, compact spherical molecule
Proteins that need to be soluble when traveling through bloodsteam
Myoglobin hormones enzymes

Question 14

Fibrous

Answer 14

Polypeptide in long strands or sheets
Structural support shape external protection

Question 15

Quaternary structure modular design

Answer 15

• mix and match to create functional protein which diversifies function and customization of protein for specific function
• cost effective when damaged bc only one sub unit needs to be replaced

Question 16

Regulatory mechanism in hemoglobin

Answer 16

• binding of first O2 is the hardest but after this affinity for O2 binding is increased making it easier for them to bind
• orientation doesnt encourage O2 binding

Question 17

Improper folding

Answer 17

Aggregation
Misfolding
Refolding

Question 18

Aggregation

Answer 18

Non polar exposed to aq solvent
Natural tendency of hydrophobic effect

Question 19

Protein misfolding

Answer 19

Not recognized as functional protein
Candidate for elimination and degradation
Lose proteins that have a function to fulfill in the body

Question 20

Refolding

Answer 20

Possible if caused by natural process but not always accurate
If caused by disease they aggregate or degrade

Question 21

Molecular chaperone

Answer 21

Bind to unfolded polypeptide to prevent improper association of exposed hydrophobic segment
Induce refolding of misfolded protein
Ensure fidelity of protein

Question 22

Hsp 70

Answer 22

Beta barrel wrap that primes for proper folding inside the barrel
Provides protective shelter while synthesis to avoid exposure

Question 23

Groel/groes

Answer 23

Chaperonin forms closed chambers where protein folds
Unfolded protein enter chamber and groes serve as cap
Conformation of chaperonin and protein change
2 subunits for efficiency
- top and bottom portion fold protein