CAS BI 108 Chapter Notes - Chapter 3: Peptide Synthesis, Tryptophan, Threonine

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Chapter 3- Proteins (Part 2)
You will also have to learn:
(1) the basic structure of amino acids (alpha-carbon, R-group, -NH3+, -CO2-)
(2) Hydrophilic amino acids have R-groups that contains O and/or N
(3) Hydrophobic amino acids have R-groups that DO NOT contain O and/or N.
Unfortunately, (3) in the previous paragraph is a bit of a lie; tyrosine has an oxygen and
tryptophan has a nitrogen. Proline looks like it has a nitrogen, but this is actually the
backbone nitrogen and does not count. I will not try to trick you by asking whether
tyrosine, tryptophan or proline are hydrophilic or hydrophobic.
These 20 amino acids are incorporated into peptides by the ribosome during peptide
synthesis, which is a process called “translation.” Amino acids are often modified after
translation. The most common modification is phosphorylation, which most often occurs
on the –OH group of serine, threonine or tyrosine.
Proteins: Primary Structure, Secondary Structure, Tertiary Structure and
Quaternary Structure
“Primary structure” for proteins refers to the amino acid sequence.
“Secondary structure” refers to the shape adopted by the amino acid backbone, where
two shapes are
common: the “α-helix” and the “β-strand,” which are discussed at greater length below
“Tertiary structure” refers to the folded three-dimensional structure of a peptide.
“Quaternary structure” refers to how multiple subunits fit together when proteins exist as
multi-meric units.
The α-Helix
Let’s talk more about the α-helix, which resembles a DNA helix, except it is made up of
the amino acid backbone and it is a single chain, whereas DNA is a double helix (two
chains) of nucleotides. The α-helix is right-handed, with ~3.5aa/turn and 5.4Å/turn. (The
symbol Å refers to “Angstrom,” who was a Swedish physicist, and an Å is 10-10
meters.) In an α-helix, every amide-hydrogen (-N-H) forms a hydrogen bond with a
carbonyl-oxygen (C=O), which is a crucial interaction that helps to hold the α-helix
together. Every amide-hydrogen (-N-H) points in the same direction (down in the slide),
while every carbonyl-oxygen (C=O) points in the opposite direction (up in the slide). An
α-helix resembles a cylinder, and when viewed end-on, it resembles a circle with the
amino acid R-groups protruding outward. It takes ~2 turns of the helix (~7aa) to get
back to the original position for an R-group.
But what do I have to know? The α-helix:
(1) looks like a cork screw (side view)
(2) is right-handed (just like DNA)
(3) has all (-C=O) pointing in the same direction (up)
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