Chapter 4 Lecture Videos Flashcards

1
Q

What are the four most common types of secondary structure?

A

alpha helices, beta conformation, beta turns, random coil

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2
Q

Random coils

A

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

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3
Q

Secondary Structure

A

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

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4
Q

Stability of alpha helices conformation?

A

most stable conformation for a polypeptide chain

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5
Q

What hold together alpha helices?

A

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

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6
Q

Structure of alpha helices?

A
  • one turn of helix = 3.6 residues
  • condensed structure (tightly packed)
  • no space down center, side chains project outwards
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7
Q

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

A

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

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8
Q

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

A
  • 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
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9
Q

Structure of beta conformation?

A

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

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10
Q

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

A

the polypeptide sequence

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11
Q

What does protein stability refer to?

A

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

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12
Q

What is a beta strand?

A

a polypeptide chain in the beta conformation

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13
Q

What forms a beta sheet?

A

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

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14
Q

Beta Turns

A
  • 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
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15
Q

Type 1 beta turn

A

uses proline for a tight turn

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16
Q

Type 2 beta turn

A

uses glycine at position 3

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17
Q

Tertiary structure

A

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

18
Q

What are the four major classes of tertiary structure?

A
  • fibrous proteins
  • globular proteins
  • membrane proteins
  • intrinsically disordered proteins
19
Q

Structure of fibrous proteins

A
  • contain repeating helical structure
    -classified by having a highly repetitive 2 prime structural elements
20
Q

Role of fibrous proteins?

A
  • often serving structural roles, providing strength, and/or flexibility
  • frequently insoluble (enriched in hydrophobic residues)(contain repeating helical structure)
  • Example: Alpha-keratin and collagen
21
Q

Alpha-Keratin Protein

A
  • 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)
22
Q

What is the most abundant protein in mammals?

23
Q

Collagen

A
  • part of connective tissue, provides strength and flexibility
  • unique left-handed helix, packed into a triple coil
  • repeating sequence of Gly-Pro-Hyp (Hydroxyproline)
24
Q

Globular Proteins

A
  • have more variety in residues and structure
  • constitute most cellular proteins
  • ex. myoglobin
  • may contain a combination of various 2 prime structural elements
25
Myoglobin
- O2 binding protein - first protein crystallized - 8 alpha helices connected via loops or beta turns - protein core is filled with hydrophobic groups
26
Protein motifs or folds
folding patters involving two or more 2 prime structural elements
27
Protein Domain
-implies an independently stable part of the protein - often have a specialized function - can be "clipped off" and still maintain function
28
Intrinsically Disordered Proteins
- some proteins are entirely or partially intrinsically disordered - intrinsically disordered regions lack a hydrohphobic core and contain no recognizable 2 prime structural elements
29
What do intrinsically disordered proteins do?
often involved in facilitating protein-protein interactions, act as scaffolds
30
Quaternary Structure
-encompasses the three-dimensional structure of proteins containing more than one polypeptide chain - aka: a protein complex, multi-subunit protein, oligomer, multiuser
31
Subunit
- a single chain within the protein complex - often abbreviated with greek letters
32
Protein folding
proteins can unfold then spontaneously refold
33
Stepwise protein folding
- local secondary structure folds first - long-range connections happen second - driven by thermodynamics to the lowest free energy conformation
34
Conformation
the arrangement in space of its constituent atoms which determine the overall shape of the molecule
35
Native conformation
-a proteins functional/ normal/ stable conformation -has the lowest free energy
36
Phi Angle (circle w/ vertical line)
torsion angle between the nitrogen and the alpha carbon
37
Psi Angle (pitchfork lookin thang)
torsion angle between the alpha carbon and the carbonyl carbon
38
Multimer/ Oligomer
a protein with a quaternary structure
39
Denaturation
the unfolding or breaking up of a protein, modifying its standard three-dimensional structure
40
Renaturation
the reconstruction of a protein to its original form especially after denaturation
41
What forces drive protein folding?
- entropy: hydrophobic forces - enthalpy: h-bonds, van der waals, disulfide, peptide bonds
42
steady-state
intermediate concentrations are equal