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BMS1. Peptide Bonds (STOCK) > General Information > Flashcards

General Information Flashcards

1
Q

Four organizational levels of protein structure:

A
  1. primary
  2. secondary
  3. tertiary
  4. quaternary
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2
Q

Primary structure

A
  • sequence of amino acids in a protein
  • defined by covalent bonds (including disulfide bridges)
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3
Q

Peptide bonds covalently link amino acids via:

A
  • amide linkages between the α-carboxyl group of one amino acid and the α-amino group of another amino acid.
  • occurs via a loss of water
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4
Q

All amino acid sequences are read from…

A
  • the N- to the C-terminus of the peptide
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5
Q

Peptide bond characteristics (4):

A
  1. partial double-bond character
  2. rigid and planar
  3. uncharged, but polar
  4. trans configurations (except proline, cis 15%)
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6
Q

The -C=O and -NH groups of peptide bonds are …

A
  • polar and involved in hydrogen bonds in alpha helices and beta sheet structures
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7
Q

What angles specify the path of a polypeptide backbone?

A
  • phi and psi angles
  • only two sets of phi and psi angles can be repeted without steric collisions
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8
Q

_____ is the only amino that can cause a cis configuration in a polypeptide chain.

A

Proline

15% of the time

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9
Q

Peptide bonds have trans configurations to minimize:

A

steric hindrance. Orients side chains on opposite sides of the peptide bonds. Proline can cause cis configuration.

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10
Q

Repetitive phi and psi bonds in polypeptide chains aid in the formation of:

A

repetitive secondary structures

  1. alpha helices (coiled chains)
  2. beta sheets (extended chains)
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11
Q

Non-regular and non-repetitive secondary conformations are due to:

A

non-repeating phi and psi angles

  1. coils
  2. turns
  3. loops, etc.
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12
Q

Secondary Structure

A

Local arrangements of the peptide backbone, often defined by H-bonds

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13
Q

Tertiary Structure

A

Arrangement of secondary structure elements into compact domain

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14
Q

Quaternary Structure

A

Arrangement of multiple polypeptide chains in a multi- subunit protein (only in proteins with >1 chain)

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15
Q

Alpha helix dimensions:

A
  1. 3.6 residues / turn
  2. 5.4 Å / turn
  3. 1.5 Å rise / residue
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16
Q

Hydrogen bonding in alpha helices:

A

Residue i forms a hydrogen bond with i + 4.

  • Not all hydrogen bonds are satisfied, but within the body of the helix, every NH group forms a hydrogen bond with a carbonyl oxygen. This neutralizes the polarity of the peptide bond, and stabilizes the entire structure.
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17
Q

In an alpha helix, side chains extend…

A

outward from the helix to avoid interacting sterically with each other

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18
Q

In an alpha helix, all carbonyls extend toward…

A

the C-terminus

creates polarity to helix

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19
Q

Interiors of proteins are largely …

A

repetitive secondary structures

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20
Q

Amino acids that can disrupt an alpha helix:

A
  1. proline (secondary amino group not compatible with right-handed spiral of helix; kinks)
  2. large numbers of charged amino acids (form ionic bonds or repel each other)
  3. amino acids with bulky side chains (Y)
  4. amino acids that branch at beta-carbon (V and I)
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21
Q

Alpha helix characteristics:

A
  1. right-handed
  2. C=O point to C-terminus (dipole)
  3. H-bonds (between C=O and H-N; residue i and residue i+4)
  4. 3.6 residues / turn
  5. 5.4 Å / turn
  6. 1.5 Å rise / residue
22
Q

Hydrophobic helices:

A
  1. hydrophobic (nonpolar) sidechains
  2. typically go through lipid bilayer
23
Q

Polar helices:

A
  1. typically charged side chains
  2. exposed to solvents (intracellular and extracellular)
24
Q

Amphipathic helices:

A
  1. a mixed pattern of polar residues, hydrophobic residues, and charged residues.
  2. Can have polar faces and non-polar faces.
25
Q

In alpha helices, hydrogen bonding is:

A
  • between the peptide-bond carbonyl oxygens and amide hydrogens that are part of the polypeptide backbone (i and i + 4 residues H-bond)
  • parallel
26
Q

Unlike alpha helix, beta sheets are:

A
  1. composed of two or more polypeptide chains
  2. almost fully extended
  3. H-bonds are perpendicular to the polypeptide backbone
27
Q

The three perpendicular planes of beta sheets:

A
  1. plane of strands
  2. plane of hydrogen bonds
  3. plane of side chains
28
Q

Dimension of Beta-sheet:

A
  • about 3.5 Å / residue
29
Q

Two types of Beta Sheets:

A
  1. Parallel
  2. Antiparallel
30
Q

Parallel Beta Sheets

A
  1. hydrophobic (N-N-N-N-N-N-N)
  2. buried in protein interior
  3. N-termini line up with one another, C-termini line up with one another

(N=nonpolar)

31
Q

Antiparallel Beta Sheets

A
  1. amphipathic (N-P-N-P-N-P)
  2. N-terminal and C-terminal ends alternate
  3. one face hydrophobic, one face polar.
  4. Polar face is on surface, and hydrophobic face buried on interior.
32
Q

Beta sheet hydrogen bond and side chains:

A
  1. side chains perpendicular to sheet (above and below)
  2. hydrogen bonds parallel to sheet
33
Q

Turns and loops are:

A

secondary structures, just not as regular/repetitive as helices and sheets.

34
Q

Turns and loops largely make up:

A
  • the surface of proteins
35
Q

Turns and loop are often the sites of:

A
  • functional residues/binding sites (since turns and loops compose the surface of globular proteins)
  • Alpha helices and beta sheets provide scaffold for these loops and turns
36
Q

Approximately ___% of an average globular protein is organized into repetitive structures such as the alpha helix and/or beta sheet.

A

50%

The remainder is made up of nonrepetitive loops, turns, and coils.

37
Q

Helix-loop-Helix Motif

A

loop can be large or small

38
Q

Beta-hairpin Motif

A

antiparallel sheets

39
Q

Greek Key Motif

A
  • a fold of a large antiparallel beta hairpin.
  • Fold over a long beta strand.
  • Create really common and stable structures. This fold is in immunoglobulins.
40
Q

Beta-Alpha-Beta Motif

A
  • connect two parallel beta strands in a beta sheet.
  • Loop through amphipathic helix.
41
Q

Five forces that stabilize protein structure:

A
  1. Hydrophobic Interactions
  2. van der Waals Interactions (very small, due to tight packing of residues)
  3. Hydrogen Bonds (inter- or intrachain or with water)
  4. Ionic Interactions (between positively and negatively charged side chains)
  5. Disulfide Bridges (covalent bond between cysteines)
42
Q

Domains are:

A
  • the fundamental functional and 3-D structural units of polypeptides
  • 100-300 amino acids
43
Q

Domain cores are built from:

A
  • combinations of super-secondary structural elements (motifs)
  • Folding of a domain occurs independently of the folding of other domains in a protein
44
Q

Typical weight of a single domain:

A
  • 10-30 kDA
45
Q

Folds of proteins consisting of all alpha proteins:

A
  • mostly alpha helices
  • all perpendicular orientations or all parallel orientations.
46
Q

Folds of proteins consisting of all beta proteins:

A
  • usually have little bits and pieces of helices
  • core of protein made of anti-parallel beta strands
47
Q

Folds of proteins consisting of both alpha and beta proteins:

A
  • parallel beta sheet usually connected by alpha helices.
  • Can wrap around in barrel or go around in a flat sheet.
48
Q

Subunits of quaternary structures are held together via:

A
  • non-covalent interactions
    • H-bonds
    • ionic bonds
    • hydrophobic interactions, etc.
  • subunits may function independently or cooperatively (i.e. hemoglobin)
49
Q

Isoforms:

A
  • proteins that perform the same function but have different primary structures
  • If the isoform protein is an enzyme, then it is referred to as an isozyme
50
Q

Native conformation:

A
  • the functional, fully-folded protein structure
  • determined by primary structure (AA sequence)
  • AA interactions guide secondary, tertiary, and sometimes quaternary structure
51
Q

Protein chaperones assist with:

A

the proper folding of many species of proteins

BMS1. Peptide Bonds (STOCK) (1 decks)

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