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BIOC 2200 > Protein Primary Structure and the Peptide Bond > Flashcards

Protein Primary Structure and the Peptide Bond Flashcards

1
Q

Steric interactions

A
  • Also known as ‘excluded volume’ interactions
  • Two atoms cannot occupy the same region of space
    simultaneously
  • When two atoms are brought very close:
  • electron clouds of atoms overlap
  • Pauli exclusion principle begins to apply
  • Steric interactions allow us to understand many
    conformational properties of molecules (but not all
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2
Q

short-range repulsion has

A

-an exponential dependence on
interatomic distance:

-E (proportional) exp(-r)

(note that it’s only
important at very short
distances)

-similar thinking applies to the conformational behavior of
amino acids (and proteins)

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3
Q

The peptide bond reactions: (2)

A

Water goes on…
hydrolysis

Water comes off…
condensation

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4
Q

The formation of the peptide bond results…

A

in the liberation
of one water molecule per two amino acids condensed.

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5
Q

Hydrolysis is favored thermodynamically in…

A

aqueous media.
But, the rate constant for the hydrolysis reaction is small.

So the reaction is too slow to be accomplished in a living cell
without the aid of enzymes.

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6
Q

Stability and Formation of Peptide Bond:

A

The peptide bond is metastable.

  • That is, the favored reaction at RT° in aqueous solution is
    HYDROLYSIS of the peptide bond
  • But, the uncatalyzed reaction is exceedingly slow.
    Catalysis can occur via acid or base.
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7
Q

Specific catalysis is provided by…

A

proteolytic enzymes
or proteases

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8
Q

The Peptide Bond is…

A
  • Is usually found in the trans conformation
  • Has partial (40%) double bond character
  • Is about 0.133 nm long - shorter than a typical single
    bond but longer than a double bond
  • Due to the double bond character, the six atoms of
    the peptide bond group are always planar!
  • N partially positive; O partially negative
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9
Q

Geometry of Peptide Bond:

A

Linus Pauling proposed that a
peptide bond is most accurately represented as a hybrid of
two contributing structures

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10
Q

the hybrid of two contributing structures has…

A

considerable C-N double bond character
and rotation about the peptide bond is restricted

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11
Q

A resonance hybrid of two forms…

A

The delocalization of (pi) electron orbitals gives the
peptide bond a partial double bond character.

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12
Q

Resonance in the Peptide Bond

A

The peptide group is a rigid, planar structure due to the
resonance interactions which give the peptide bond an
~40% double-bond character.

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13
Q

X-ray studies by Pauling and Corey provided…

A

the structural
basis for our understanding of the peptide group.

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14
Q

The Planar Nature of the
Peptide Bond

A

Six atoms of the peptide group lie in a plane!

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15
Q

Two configurations are possible,
both planar:

A

Trans is the favored configuration particularly with
bulky R groups.

Cis configuration = RARE

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16
Q

Virtually all peptide bonds in proteins have

A

the trans configuration.

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17
Q

The Peptide Bond: So Far (4)

A
  • -electron delocalization over O-C-N fragment
  • Resonance stabilization yields planar structure
  • Adjacent Ca
    atoms are in trans conformation to
    prevent steric hindrance
  • Hydrolysis is thermodynamically favoured
18
Q

The thermodynamic instability of polypeptides requires a…

A

mechanism
other than a straight forward dehydration reaction for their synthesis in
the aqueous medium of the cell.

  • Indeed, coupling to ATP hydrolysis is involved
19
Q

Free amino acids are NOT…

A

used to make
polypeptides / proteins in cells

20
Q

Aminoacyl-RNA’s are…

A

the high energy
intermediates used in biosynthesis of
polypeptides

21
Q

The ribosome has enzymatic activity:

A

promoting
peptide bond formation

22
Q

Polypeptides have ends…

A

or terminals.

  1. Amino
    or “ N”
    terminus
  2. Peptide bond
  3. Carboxyl
    or “ C ”
    terminus
23
Q

In 1902, Emil Fischer proposed that…

A

proteins are long
chains of amino acids joined by amide bonds to which
he gave the name peptide bonds

24
Q

Peptide bond Definition:

A

the special name given to the amide bond
between the a-carboxyl group of one amino acid and
the a -amino group of another

25
Q

Peptide / dipeptide Definition:

A

The product of a reaction in which an amide bond is formed between two
amino acids

-the case of two amino acids,
tripeptide for 3 AAs, tetrapeptide for 4, etc

26
Q

AMINO ACID
RESIDUE
Definition:

A

The portion of the original amino
acid that remains in the peptide

27
Q

OLIGOPEPTIDES Definition:

A

peptides with only a few AA residues

28
Q

POLYPEPTIDES Definiton:

A

long chain peptides with many AA residues

The linear sequence of amino acids within a peptide is written
from N-C, either in 3- or 1- letter code.

29
Q

peptide Definition :

A

the name given to a short polymer of amino acids
joined by peptide bonds; they are classified by the number
of amino acids in the chain

30
Q

dipeptide Definition:

A

a molecule containing two amino acids joined
by a peptide bond

31
Q

tripeptide Definition:

A

a molecule containing three amino acids joined
by peptide bonds

32
Q

polypeptide Definition:

A

a macromolecule containing many amino
acids joined by peptide bonds

33
Q

protein Definition:

A

a biological macromolecule of molecular weight
5000 g/mol of greater, consisting of one or more
polypeptide chains

34
Q

Peptides have…

A

Short polymers of amino acids
* Each unit is called a residue
* 2 residues -dipeptide
* 3 residues -tripeptide
* 12-20 residues - oligopeptide
* many - polypeptide

35
Q

Peptides are…

A

Polyampholites

36
Q

Polypeptides contain…

A

ionizable functions:
amino and carboxy termini and sidechains

37
Q

charge (pH) determines

A

Solubility, structure, function, etc

38
Q

Isoelectric Point Definition:

A

pH at which net charge is 0.

  • I.P. is determined by sequence
39
Q

Proteins are not just…

A

polypeptides.

  • They are polypeptides of defined sequence.
  • Each protein has a defined order of amino acid
    residues.
  • This sequence is referred to as the primary
    structure of the protein.
40
Q

Linear arrays of amino acids can make…

A

a huge number of molecules.

For 100 amino acid protein the number of possibilities are:
20^(100) = 1.27x10^(130)

The total number of atoms in the universe is estimated at
9x10^(78)

41
Q

Enkephalins:

A

Leucine enkephalin
Tyr-Gly-Gly-Phe-Leu
= Y-G-G-F-L

Methionine enkephalin
Tyr-Gly-Gly-Phe-Met
= Y-G-G-F-M

BIOC 2200 (35 decks)

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