Chapter 4 Lecture Videos

Question 1

What are the four most common types of secondary structure?

Answer 1

alpha helices, beta conformation, beta turns, random coil

Question 2

Random coils

Answer 2

don’t have repeating bond angles, but are not necessarily “unstructured”

Question 3

Secondary Structure

Answer 3

describes the spatial arrangement of backbone atoms (everything but side chains) in a specific segment of a polypeptide chain (adjacent to each other)

Question 4

Stability of alpha helices conformation?

Answer 4

most stable conformation for a polypeptide chain

Question 5

What hold together alpha helices?

Answer 5

-held together by hydrogen bonds between carbonyl oxygen and amino hydrogen
- successive h-bonds between n and n+4 residues stabilize the alpha helix

Question 6

Structure of alpha helices?

Answer 6

• one turn of helix = 3.6 residues
• condensed structure (tightly packed)
• no space down center, side chains project outwards

Question 7

How do side chains affect the stability of an alpha helix?

Answer 7

They can stabilize or destabilize the helix
- alanine is ideal for alpha helices
- proline (too restricted) and glycine (too flexible) are bad for alpha helices

Question 8

How can we stabilize the ends of helices where there are fewer hydrogen bonds?

Answer 8

• helices have overall polarity bc n-term is positive and c-term is negative
• negative charges are found @ n-term and positive charged residues are found @ c-term

Question 9

Structure of beta conformation?

Answer 9

more extended and takes on a zigzag shape
- side chains project above and below the plane of the backbone

Question 10

What contains all the “information” necessary to dictate the protein’s final structure?

Answer 10

the polypeptide sequence

Question 11

What does protein stability refer to?

Answer 11

the ability of a protein to maintain its native conformation
- native conformation has the lowest free energy

Question 12

What is a beta strand?

Answer 12

a polypeptide chain in the beta conformation

Question 13

What forms a beta sheet?

Answer 13

a beta strand interacting with other beta strands
- can be made out of parallel (out-of line h-bonds) or antiparallel (in-line h-bonds) strands

Question 14

Beta Turns

Answer 14

• provide a tight 180 degree turn that is ideal for connecting adjacent strands
• 4 amino acids, first and fourth amino acids h-bond to each other

Question 15

Type 1 beta turn

Answer 15

uses proline for a tight turn

Question 16

Type 2 beta turn

Answer 16

uses glycine at position 3

Question 17

Tertiary structure

Answer 17

refers to the entire three dimensional arrangement of all atoms in a natively folded protein
- includes backbone atoms and side chains

Question 18

What are the four major classes of tertiary structure?

Answer 18

• fibrous proteins
• globular proteins
• membrane proteins
• intrinsically disordered proteins

Question 19

Structure of fibrous proteins

Answer 19

• contain repeating helical structure
  -classified by having a highly repetitive 2 prime structural elements

Question 20

Role of fibrous proteins?

Answer 20

• often serving structural roles, providing strength, and/or flexibility
• frequently insoluble (enriched in hydrophobic residues)(contain repeating helical structure)
• Example: Alpha-keratin and collagen

Question 21

Alpha-Keratin Protein

Answer 21

• strong, super twisted coiled-coils
• bundles held together by disulfide bonds (the more disulfide the stronger)
• only found in mammals (provides strong tissue for a variety of functions)

Question 22

What is the most abundant protein in mammals?

Answer 22

collagen

Question 23

Collagen

Answer 23

• part of connective tissue, provides strength and flexibility
• unique left-handed helix, packed into a triple coil
• repeating sequence of Gly-Pro-Hyp (Hydroxyproline)

Question 24

Globular Proteins

Answer 24

• have more variety in residues and structure
• constitute most cellular proteins
• ex. myoglobin
• may contain a combination of various 2 prime structural elements

Question 25

Myoglobin

Answer 25

• O2 binding protein
• first protein crystallized
• 8 alpha helices connected via loops or beta turns
• protein core is filled with hydrophobic groups

Question 26

Protein motifs or folds

Answer 26

folding patters involving two or more 2 prime structural elements

Question 27

Protein Domain

Answer 27

-implies an independently stable part of the protein
- often have a specialized function
- can be “clipped off” and still maintain function

Question 28

Intrinsically Disordered Proteins

Answer 28

• some proteins are entirely or partially intrinsically disordered
• intrinsically disordered regions lack a hydrohphobic core and contain no recognizable 2 prime structural elements

Question 29

What do intrinsically disordered proteins do?

Answer 29

often involved in facilitating protein-protein interactions, act as scaffolds

Question 30

Quaternary Structure

Answer 30

-encompasses the three-dimensional structure of proteins containing more than one polypeptide chain
- aka: a protein complex, multi-subunit protein, oligomer, multiuser

Question 31

Subunit

Answer 31

• a single chain within the protein complex
• often abbreviated with greek letters

Question 32

Protein folding

Answer 32

proteins can unfold then spontaneously refold

Question 33

Stepwise protein folding

Answer 33

• local secondary structure folds first
• long-range connections happen second
• driven by thermodynamics to the lowest free energy conformation

Question 34

Conformation

Answer 34

the arrangement in space of its constituent atoms which determine the overall shape of the molecule

Question 35

Native conformation

Answer 35

-a proteins functional/ normal/ stable conformation
-has the lowest free energy

Question 36

Phi Angle (circle w/ vertical line)

Answer 36

torsion angle between the nitrogen and the alpha carbon

Question 37

Psi Angle (pitchfork lookin thang)

Answer 37

torsion angle between the alpha carbon and the carbonyl carbon

Question 38

Multimer/ Oligomer

Answer 38

a protein with a quaternary structure

Question 39

Denaturation

Answer 39

the unfolding or breaking up of a protein, modifying its standard three-dimensional structure

Question 40

Renaturation

Answer 40

the reconstruction of a protein to its original form especially after denaturation

Question 41

What forces drive protein folding?

Answer 41

• entropy: hydrophobic forces
• enthalpy: h-bonds, van der waals, disulfide, peptide bonds

Question 42

steady-state

Answer 42

intermediate concentrations are equal