Chapter 4 Protein structure 1 of 3
Amino acids are linked via a condensation reaction
Here amino acids within the peptide are called "amino acid residues" because only the residual atoms remain.
The definition of chiral molecule
A chiral molecule is molecule with a non-superposable mirror image. L-amino acids D-amino acids
Which amino acid side chains may oxidize to for disulfide bonds?
Cys
Which amino acid side chains contain sulfur?
Cys Met
Disulfide bond is form by two of which amino acid?
Cysteine
Which of the 20 amino acids that form proteins is most likely to be present with its side chain in a mixture of ionization states near physiological pH?
His
What you need to know for the amino acids
When given the name, the three letter code, or the one letter code be able to know which group it belongs to. If it is one of the charged amino acid, know whether it is positively or negatively charged in physiological condition, pH7.4.
What is the net charge on the following peptide at pH 9.5? Lys-Ala-Glu-Gln-Cys-Ile
-2
What is the net charge on the following peptide at pH 6.5? Lys-Ala-Glu-Gln-Cys-Ile
0
Which amino acid side chains carry negative charges?
Asp, Glu
What is the net charge on the following peptide at pH 7.0? Arg-Ile-His-Gly-Cys-Asn
+1
4 charged amino acids
Aspartate (Asp) - Glutamate (Glu,E) - Lysine ( Lys ,k) + Arginine (Arg, R) +
Which amino acid side chains are non-polar?
Ala
Which amino acid side chains are hydrophobic?
Ala Ile Leu Met Phe Try Tyr Val
7 Hydrophobic amino acids
Alanine (Ala,A) Valine (Val, V) Phenylalanine ( Phe, F) Tryptophan (Try, W) Leucine (Leu, L) Isoleaucine ( IIe,I) Methionine (Met,M)
Which amino acid side chains carry positive charges?
Arg, His, Lys
Disulfide bonds facilitate crosslinking
Disulfide bonds can form intra-strand crosslinks When a protein contains more than one polypeptide chain, disulfide bonds can also form inter-chain crosslinks.
Charged amino acids
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The two types peptidases
Exopeptidase: Chew the peptides from the ends Endopeptidase: Cuts peptides in the middle
Which amino acid side chains are achiral?
Gly
All but one of the amino acids are chiral
Glycine
Glycine side chain
Glycine doesn't have much of a side chain thus is hard to define Gly is the simplest amino acid. Side chain = H
The reason glycine is not considered to a chiral molecules is because
It doesn't have four distinct groups coming off of the C-alpha
We use what amino acids?
L-amino acids
Which amino acid would most likely be found in the internal core of a globular protein?
Leu
Which of the amino acids listed below are positively charged at physiological pH7.4?
Lysine
What effect do hydrophobic and hydrophilic portions of proteins have on protein folding?
Nonpolar portions of the molecule associate with one another on the interior of the protein (opposite within cell membranes)
What type of covalent bonds are responsible for holding together the amino acids?
Peptide bonds
Which amino acid side chains are contain aromatic groups?
Phe *Hydrophobic Tyr *Hydrophobic Try *Polar
Amino acids are linked by peptide bonds to form a polypeptide
Polypeptides have many amino acid residues.
Which amino acid side chains contain reactive aliphatic hydroxyl groups?
Ser Thr
Which amino acid side chains are polar but uncharged?
Ser, Thr, Asn, Gln
Some amino acid side chain act like weak acids
Some amino acid side chain act like weak acids
Amino acids
There are 20 unique amino acids that make up proteins in general. Each of the 20 different amino acids has a different R group. Otherwise, the amino acid structure is the same!
Polar Amino Acids
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Which amino acid side chains have multiple chiral carbons?
Thr
7 Polar Amino Acids
Threonine (Thr,T) Tyrosine (Tyr,y) Serine (Ser,S) Cysteine (Cys, C) Glutamine (Gln,Q) Histidine (His, H) Asparagine (Asn, N)
Which amino acid side chains are aliphatic?
Val, Leu, Ile, Met, Pro
Amino acids are linked?
Via condensation reaction By peptide bonds to form a polypeptide
Proteins are
polymers of amino acids
