protein structure

Question 1

what types of forces are involved in forming the 3D shapes of a polypeptide

Answer 1

• mostly noncovalent
• hydrogen bonding
• ionic bonding
• hydrophobic interactions
  
  • less of an interaction, more of an avoidance
• Van der Waal interactions
  disulfide bridges

Question 2

conformation vs configuration

Answer 2

• conformation is around a single bond and can rapidly interconvert
• configuration is how the molecule is arranged and would require bond breaking processes to change

Question 3

disulfide bridges

Answer 3

• formed from the oxidation of the polar SH group of cysteine
• most intracellular proteins do not have disulfide bonds because the cell interior is a reducing environment
• seen in secreted or cell surface proteins

Question 4

Why is protein folding thermodynamically favorable?

Answer 4

• folding decreases entropy, so it isn’t thermodynamically favorable
• the groups interacting with each other lowers delta G
• hydrophobic group have very constrained movement of water around it (low entropy of solvent)
  
  • clustering of hydrophobic regions reduces this

Question 5

define secondary structure of proteins

Answer 5

• local spatial arrangement of main chain (backbone) atoms

Question 6

what type of bonding is involved in secondary structure?

Answer 6

• hydrogen bonding
• formation of secondary structures maximizes H-bonding

Question 7

what are 3 common types of secondary structure

Answer 7

• alpha helix
• beta sheet
• beta turn

Question 8

How are R groups oriented in alpha helices and beta strands

Answer 8

alpha helices:
- r groups protrude outward (perpendicular to helix)
beta strand:
- r groups protrude in opposite directions above and below the plane of the strand

Question 9

loops

Answer 9

• when there are no regular secondar structures
• phi and psi angles aren’t constant for all residues in loops
• not random or disordered - conformation is stable

Question 10

relative positions of H and O participating in alpha helix hydrogen bonding

Answer 10

• Carbonyl oxygens face towards the C-terminus
• amide H face toward N terminus
• bonds are about 3.6 residues apart (one turn around the helix)

Question 11

How do dihedral angles in beta sheets compare to those in alpha helices

Answer 11

• ## angles are much wider in beta sheets

Question 12

why do alpha helices have directional dipole?

Answer 12

• there is a dipole moment across the peptide bonds that align in an alpha helix to create a net dipole
• last few carbonyl oxygens don’t have an amide H to bond to
• last few amine Hs dont have carbonyl O to bond to
• C-terminus is negative
• N-terminus is positive

Question 13

constraints that affect alpha helix stability

Answer 13

• amino acid makeup of the helix
  
  • some more readily conform
  • some are helix breakers
• bulkiness of R groups adjacent to each other in the polypeptide chain
• interactions between R groups near each other in the helix
• charge of amino acids found at helix termini
  
  • neg residues at amino terminus is stabilizing
  • pos residues at carboxy terminus is stabilizing

Question 14

helix breakers

Answer 14

proline
- doesn’t have the flexibly in phi bond
- since the chain reattaches at the animo group, it doesn’t have the amide H to form hydrogen bonds
glycine
- too flexible (dihedral angles don’t hold well)
- makes a coiled structure very different from an alpha helix

Question 15

which amino acids are interacting in an H bond in a beta turn?

Answer 15

• residues 1 and 4

Question 16

why would a beta turn be near the surface of the protein structure rather than buried in the middle

Answer 16

• the turn’s internal 2 aa (proline most common) can form H bonds with water molecules

Question 17

secondary vs tertiary structures

Answer 17

• secondary is interactions between aa’s near eachother on the chain
• tertiary is the overall 3D structure of the polypeptide
• secondary makes up tertiary

Question 18

tertiary structure (and its properties)

Answer 18

• overall 3D structure of polypeptides
• includes interactions between R groups or R groups and backbone atoms
• held together by weak bonds (sometimes disulfide)
• amount of bending (like beta turns) dependent of number and location of residues that facilitate them (ex: proline, glycine)
• burial of hydrohpobic residues takes at least 2 layers of secondary structure

Question 19

why does protein folding reduce entropy

Answer 19

even though there is less movement, the folded state is more stable and requires less energy for the polypeptide to sit in a folded conformation

Question 20

two main groups of tertiary structure

Answer 20

• fibrous proteins
• globular proteins

Question 21

fibrous proteins

Answer 21

• multiple polypeptide chains arranged in long strands or sheets
• mostly for structure, shape, and protection
• usually make of a singly type of repeating secondary structure
  
  • keeps structure relatively simple
• insoluble in water - high concentration fo interior and surface hydrophobic residues
• ex: alpha keratin makes hair, nails, horns, hooves, outer layer of skin

Question 22

globular proteins

Answer 22

• diverse structures and functions
  
  • enzymes, regulatory proteins, chaperones, etc.
• often tightly packed
• percentages of helices and beta sheets depends on the protein

Question 23

motif

Answer 23

• composed of two or more elements of secondary structure and the connections between them
• recognizable folding pattern seen in multiple proteins
• may or may not have independently stable folding or certain function

Question 24

domain

Answer 24

• part of a polypeptide chain that is independently stable and/or move as a single entity relative to other parts of the protein
• seen in multiple proteins
• has a certain function

Question 25

what does it mean for a protein to be intrinsically disordered

Answer 25

• lack ordered structure in solution
  
  • don’t crystalize well if at all
• high density of charged amino acids
• proline common because they disrupt ordered structures
• fully disordered sequences lack sequestered hydrophobic aa
• may become ordered once bound to a substrate

Question 26

quaternary structure

Answer 26

• two or more polypeptides come together