Bmb 401 - Amino Acids, Peptides, and Proteins

Peptide bonds link the [… group] of one amino acid to the [… group] of the next amino acid.

alpha-carboxyl; alpha-amino

A […] is when all charges cancel out, so the molecule is neutral.

zwitterion

Amino acids are simple organic compounds containing both a/an […] group and a/an […] group.

carboxyl (-COOH); amino (-NH2)

The amino acid sequence of a peptide chain is written […]-terminus to […]-terminus.

N; C

The isoelectric point formula when there is a basic side chain is […]

pI = 1/2(pk_aamino group + pk_aR group)

The isoelectric point formula when there is a neutral side chain is […]

pI = 1/2(pk_acarboxyl group + pk_aamino group)

The isoelectric point formula when there is an acidic side chain is […]

pI = 1/2(pk_acarboxyl group + pk_aR group)

The N-terminus of a peptide chain is [positively or negatively] charged.

Positively

The pH at which half of the species is deprotonated is called the […]

pK_a

The [1^o, 2^o, 3^o, or 4^o] structure of proteins is the linear sequence of amino acids in a peptide.

1^o

The 1^o structure of proteins is […]

the linear sequence of amino acids in a peptide

The [1^o, 2^o, 3^o, or 4^o] structure of proteins is the local folding of neighboring amino acids. The most common ones are alpha helices and beta pleated sheets.

2^o

The 2^o structure of proteins is […]. The most common ones are […] and […].

the local folding of neighboring amino acids; alpha helices; beta pleated sheets

The [1^o, 2^o, 3^o, or 4^o] structure of proteins is the 3-D shape of a single polypeptide chain.

3^o

The 3^o structure of proteins is […].

the 3-D shape of a single polypeptide chain

The [1^o, 2^o, 3^o, or 4^o] structure of proteins involves interaction between multiple polypeptide chains within a protein complex.

4^o

The 4^o structure of proteins involves interaction between […] within a protein complex.

multiple polypeptide chains

The 1^o structure of proteins is stabilized by […]

peptide bonds

The […] structure of proteins is stabilized by peptide bonds.

1^o

The 2^o structure of proteins is stabilized by […]

hydrogen bonds

The […] structure of proteins is stabilized by hydrogen bonds.

2^o

[…] is when a protein (or nucleic acid) loses its 4^o, 3^o, and 2^o structures sue to breaking of non-covalent interactions.

denaturation

Denaturation is when a protein (or nucleic acid) loses its […] structures due to breaking of non-covalent interactions.

4^o, 3^o, and 2^o

Denaturation is when a protein (or nucleic acid) loses its 4^o, 3^o, and 2^o structures due to […]

breaking of non-covalent interactions

[…] occur when two cysteine molecules are oxidized and create a covalent bond between their thiol groups.

disulfide bridges/bonds

Disulfide bridges/bonds occur when two cysteine molecules are [reduced or oxidized] and create a covalent bond between their […] groups.

oxidized; thiol

[Amino acid] has a rigid cyclic structure and can interrupt 2^o protein structure.

Proline

Proline has a […] structure and can interrupt […] protein structure.

rigid cyclic; 2^o

[…] are clockwise coils around a central axis and are a common [1^o, 2^o, 3^o, or 4^o] protein structure.

alpha-helices; 2^o

[…] are rippled strands that can be parallel or antiparallel and are a common [1^o, 2^o, 3^o, or 4^o] protein structure.

beta sheets; 2^o

This amino acid is [Full Name], [3 Letter Name], [1 Letter Name], [Side Chain Characteristic]

Serine, Ser, S, Polar uncharged aliphatic

This amino acid is [Full Name], [3 Letter Name], [1 Letter Name], [Side Chain Characteristic]

Asparagine, Asn, N, Polar uncharged aliphatic

This amino acid is [Full Name], [3 Letter Name], [1 Letter Name], [Side Chain Characteristic]

Arginine, Arg, R, Polar positively charged aliphatic, basic

This amino acid is [Full Name], [3 Letter Name], [1 Letter Name], [Side Chain Characteristic]

Glycine, Gly, G, Nonpolar aliphatic

This amino acid is [Full Name], [3 Letter Name], [1 Letter Name], [Side Chain Characteristic]

Histidine, His, H, Polar positively charged aromatic, basic

This amino acid is [Full Name], [3 Letter Name], [1 Letter Name], [Side Chain Characteristic]