Amino Acids, Peptides, Proteins Flashcards

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1
Q

Stereochemistry

A

The stereochemistry of the a-carbon is L for all chiral
amino acids in eukaryotes. (carbohydrates are D-config).
All chiral amino acids except cysteine have (S)
configuration and all amino acids are chiral except for
Glycine.

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2
Q

Amphoteric

A

Amino acids can act as a base or an acid.

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3
Q

pKa

A

The pH at which half of the species is deprotonated;
[HA] = [A-
].

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4
Q

Dipeptide:

A

2 residues

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5
Q

Tripeptide:

A

3 residues

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6
Q

Oligopeptides:

A

Less than 20 residues

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7
Q

Polypeptides:

A

Greater than 20 residues

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8
Q

Formation of a Peptide bond

A

Forming a peptide bond is a dehydration reaction. The
nucleophilic amino group of one amino acid attacks the
electrophilic carbonyl group of another amino acid.

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9
Q

Amide Bonds

A

The C-N bond of a peptide bond. Rigid due to resonance.

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10
Q

Breaking peptide bonds

A

Breaking a peptide bond is a hydrolysis reaction.

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11
Q

1° Structure:

A

Linear sequence of amino acids in a peptide. Stabilized by
peptide bonds. The AA sequence is written N-terminus to Cterminus. N-terminus is POSITIVELY charged due to –NH3
+.

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12
Q

2° Structure:

A

The local structure of neighboring amino acid. Is stabilized
by hydrogen bonding between amino groups and
nonadjacent carboxyl groups.

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13
Q

a-helices:

A

: A common 2° structure. Clockwise coils around a central axis.

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14
Q

b-pleated

sheets:

A

A common 2° structure. Rippled strands that can be parallel

or antiparallel.

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15
Q

The effects of proline on secondary structure

A

Can interrupt secondary structure because of its rigid cyclic structure

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16
Q

3° Structure:

A

3-D shape of a single polypeptide chain, and is
stabilized by hydrophobic interactions, acid-base
interactions, H-bonds, and disulfide bonds.

17
Q

Hydrophobic

Interactions

A

Push hydrophobic R groups to the interior or a
protein, which increases entropy of the surrounding
water molecules and creates a negative Gibbs free
energy.

18
Q

Disulfide Bonds:

A

Occur when two cysteine molecules are oxidized and
create a covalent bond between their thiol groups.
This forms cystine.

19
Q

4° Structure

A

The interaction between peptides in proteins that

contain multiple subunits

20
Q

Conjugated Proteins

A

Proteins with covalently attached molecules.

21
Q

Prosthetic Group

A

The attached molecule in a conjugated protein. Can
be a metal ion, vitamin, lipid, carbohydrate, or
nucleic acid

22
Q

Denaturation:

A

The loss of 3-D structure. Caused by heat or solute

concentration.