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BIOC192 > Lecture 5 - Protein Strucute > Flashcards

Lecture 5 - Protein Strucute Flashcards

1
Q

When amino acids are bonded together in a peptide of protein, they are referred to as…

A

… amino acid residues

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2
Q

How are the amino acid residues in a polypeptide chain numbered?

A

From the amino terminus to the carboxy terminus

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3
Q

How many chains do proteins have

A

Anywhere from one to several chains
- proteins with one chain are the most common variety

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4
Q

Because proteins are mostly globular, the main chain must….

A

Be able to form a more compact shape and be able to double back

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5
Q

Globular proteins will be mainly comprised of..

A

Primarily a-helix, B-helix structure and turns

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6
Q

How ,any levels of protien structure

A
  • 4
  • primary, secondary, tertiary and quanternary
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7
Q

All proteins have….
Some proteins have…..

A

All proteins have primary, secondary and tertiary structure
Some proteins have quanternary structure

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8
Q

Primary structure

A

The linear sequence of amino acids that make up the polypeptide

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9
Q

Secondary structure

A
  • the 3D arrangement of a protein chain over a short stretch of adjacent amino acid residues
  • includes a-helices and b-sheets
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10
Q

Tertiary structure

A
  • the 3D structure of a complete protein chain
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11
Q

Quanternary structure

A
  • interchain packing and structure for a protien that contains multiple polypeptide chains (e.g haemoglobin)
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12
Q

The protein main chain and side chains atoms have bond which can…. And are somewhat….

A

The protein main chain and side chains atoms have binds which can rotate and are somewhat flexible

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13
Q

The main chain atoms in a protein are

A

N
Ca
C’

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14
Q

Bond angle between N and Ca is called

A

phi

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15
Q

Bond angle between Ca and C’ are called

A

Psi

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16
Q

Bong angles take on values ranging from

A

0 to +/- 180*

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17
Q

The chain angle between ‘ and N is called

A

w (omega)

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18
Q

W (omega) bond have the angle..

A

Very close to either 180 or 0

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19
Q

Main chain bond angles

A
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20
Q

Phi angle

A

Rotation around the N-Ca bond

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21
Q

Psi angle

A

Rotation angle around the Ca-C’

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22
Q

Omega

A
  • rotation angle around the peptide bond
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23
Q

Main chain angles in the polypeptide shown

A

180

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24
Q

Phi-phi restrictions

A

Phi-Phi angles have restrictions in their values because of steric hinderance

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25
Q

What collision results form phi rotation

A

O-O collision

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26
Q

Phi rotation can lead to

A

O-O collision

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27
Q

Psi rotation can lead to collisions of

A

NH-NH

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28
Q

Psi rotation can lead to

A

NH-NH collisions

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29
Q

O-O collisions result from

A

Phi rotation

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30
Q

NH-NH collisions result from

A

Psi rotation

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31
Q

Steric hinderance between the hydrogen on the amide nitrogen and the carbonyl oxygen

A
32
Q

What is w - omega

A
  • third main chain angle
  • angle of rotation around the peptide bond
33
Q

Most peptide bonds are cis/trans

A

Trans

34
Q

Angle of omega bond for a trans peptide bond

A
  • w is about 180
  • Ca atoms are found on opposite sides of the peptide bond
35
Q

Steric crowding is increased for cis/trans peptide bonds

A

Cis

36
Q

Bond angle of cis peptide omega bond angle

A
  • in a cis peptide bond, the Ca atoms are found on the same side of the peptide bond, w is about 0
37
Q

Once formed, the peptide bond angle usually does/does not rotate very much

A

Does not rotate very much

38
Q

The combination of all the ____ and ____ around all of the ___ in a ___ leads to its overall ____ ____, which in turn, leads to the arrangement of all the side chains in the protien, which in turn leads to its function

A

The combination of all the rotations and twists around all the bonds in a protien leads to its overall 3D structure, which in turn, leads to the arrangement of all the side chains in the protien, which in turn leads to its function

39
Q

Two canonical structures that are protien secondary structures

A

B-strand/B-sheet
a-helix

40
Q

Strucutre of the a-helix

A
  • the main chain spirals around the central axis like a spiral staircase
  • no covalent interaction (hydrogen bond) between the carbonyl of residue “n” and the N-H of residue “n+4”
  • hydrogen bonds help stabilise the a-helix structure
  • slightly positive charge on the hydrogen
  • slightly negative charge on the oxygen
41
Q

Key properties of the a-helix

A

-3.6 residues/turn; 5.5A rise/turn; d=1.5A residue
- spiral is right handed
- side chains point out from the helix axis; help stabilise the a-helix
- stabilising hydrogen bond, 3-7kcal/mol or 12-28kj/mol
- some residues are ‘helic breakers’ e.g glycine, proline
- helic dipole exists, positive at N-terminus

42
Q

Which way do the side chains point in an a-helix

A

Outwards

43
Q

Energy in a-helix hydrogen bonds

A
  • 3-7 kcal/mol
  • 12-28 kj/mol
44
Q

a-helix rotations

A
45
Q

Which residues are considered “helix breakers”

A
  • glycine
  • proline
46
Q

Do a-helixes have dipoles

A

Yes
Positive at N-terminus

47
Q

Helix dipole depiction

A
48
Q

Helix wheel

A

-3.6 residues/turn
-one full turn is 360*
- in an a-helix each amino acid side chain is separated by 100*

49
Q

B-structure

A

• Stretches of residues with a more
extended structure than the a-helix.
• Each section of B structure is called a
B-strand
• Hydrogen-bonding occurs between
adjacent chains (strands)
• Adjacent chains can often form a B-
sheet, ≥ two B-strands
• 2 to 10 strands per sheet
• Average strand length contains ~ 6
amino acid residues
• Each strand may have up to 15
residues
• Two types of hydrogen bonding
interaction in a B-sheet:

50
Q

each seaction of B strucutre os called a

A

B strand

51
Q

Hydrogen bonding occurs between

A

Adjacent chains (strands)

52
Q

Adjacent chains can often form

A

B-sheet

53
Q

How many stands per B-sheet

A

2-10

54
Q

How many amino acid residues in the average B-strand

A

6 amino acid residues

55
Q

How many residues can a B-stand have

A

15

56
Q

Two types of hydrogen bonding interaction in a B-sheet

A

Antiparallel: strands run in the opposite direction
- hydrogen bonding pattern is optimal (vertical)

Parallel: strands run in the same direction
- hydrogen bonds are zig zagged

57
Q

B-pleated sheet

A
  • extended
  • pleated
58
Q

B-sheet vs B-strand

A
  • sheets not planar, pleated with R-handed twist
59
Q

B- strucutre location of side chains

A
  • side chains point above and below the sheet
60
Q

Any NP-P-NP-P* stretch of residues commonly will form a

A

B-strand

61
Q

B-structure in silk

A
  • model sequence is (-Gly-Ser-Gly-Ala-Gly-Ala-) n
  • all from one sheet is interdigitate with ala from other sheet
  • silks from different species have different interdigitating groups and have differing physical properties
62
Q

What is needed to form globular proteins

A

Turns

63
Q

Structure of turns

A

Often short and hair pin like

64
Q

How many residues are involved in turns

A

3 or 4

65
Q

Almost __% of residues are involved in turns

A

300

66
Q

High amounts of ____ and ____ in turns

A

Gly and pro

67
Q

Turns often have an H-bon across _____

A

Width

68
Q

Which types of turns are very common

A

Type 1 and type 2

69
Q

How many types of turns are there

A

16

70
Q

Features of glycine good for turns but not helies

A
  • small side chains make glycine very flexible. It has a lot of conformational freedom.
71
Q

What makes proline good for turns and bad for helicies

A
  • proline is too rigid for helices but has a built-in turn because of the bonding between the R-group and the amino group
72
Q

Why are protein structures challegenign to display clearly

A
  • there are lots of atoms
  • detailed internal cavities
  • complicated shapes
  • all the elements of protein structure
    • a-helix, b-stands, turns, loops
73
Q

Protein display structure

A
  • helices shown as spirals (or cylinders)
  • strands shown as arrows, pointing form N to C
  • turns and random coil, shown as loops or rope like stretches
74
Q

Protien structure shorthand

A
75
Q

Protein short hand advantages

A
  • easily visualise the main chain path of protein
  • identify elements of secondary strucutre
  • allows an appreciation of proteins as 3D objects
  • allows comparison to other proteins

BIOC192 (38 decks)

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