Cell Biology Chapter 4 Notes

I. Proteins
A. Protein Function/Structure:
1. Proteins have a plethora of functions in the cell—work like machines.
2. Comprised of chains of amino acids.
3. The shape of the protein dictates its function (Figure 4-9).
4. Amino acid side chains are important to protein shape and function (see Figure 4-2)
5. There are 4 levels of protein structure: 1o , 2o , 3o , and 4o .
6. Protein shape/structure is maintained by a combination of covalent and non-covalent bonds.
B. Protein primary (1o ) structure.
1. Primary structure = the sequence of amino acids
2. Primary structure dependent upon covalent bonds (peptide bonds) formed during translation.
3. Primary structure (i.e., sequence of amino acids) regulates higher levels of protein structure.
4. Chain of amino acids is ‘polar’ because it has two differently-charged ends (N + and COO-).
5. Amino acids are distinguished from each other by the chemical composition of their side
chains (‘R groups’ attached to the central carbon).
a.) Chemical composition depends upon side chain polarity.
1.) Polar and non-polar amino acid side chains (Figure 4-3).
b.) Chemical composition also depends upon side chain size.
1.) Small side chains = glycine; large side chains = tryptophan, tyrosine and
phenylalanine.
2.) See handout from another text book.
3.) Additional information about side chain chemistry:
i.) Histadine can be charged or uncharged dependent upon its immediate location
ii.) Proline has a side chain that covalently bonds with the protein backbone,
generating a bend in the protein.
iii.) Serine, threonine and tyrosine have terminal –OH groups on their side chains.
iv.) Methionine and Cysteine contain sulfur atoms, but only cysteine has a terminal
sulfhydryl group that is reactive.

NOTE: M e mori ze the a mi no ac i ds and t he ir s i de cha ins !! !

C. Higher levels of protein structure are mostly maintained by noncovalent bonds.
1. Ionic interactions: + and – charged amino acids.
2. Hydrogen bonds
3. Van der Waalls
4. Hydrophobic interactions
a.) A cluster of hydrophobic side chains don’t want to be in the polar hydrophilic regions.
D. Protein secondary (2o ) structure.
1. Secondary structure = local or regional structure/shape
2. Secondary structure maintained by H bonds between atoms in the protein backbone (i.e., not
between atoms of amino acid side chains).
3. Secondary structure can contribute to protein function.
a.) leucine zipper proteins (see figure 4-16 below).
b.) transmembrane-spanning regions (see figures 4-15 and 11-24 below).
4. two general kinds of secondary structures:
a.) α helices

Figure 4-10

1.) Hydrogen bonds between atoms in the backbone.

2.) 3.6 amino acids per turn.
3.) Amino acid side chains stick out from helix like ‘lollipops’.
4.) Side chains can influence the formation of an α-helix—specifically proline side
chains as no α-helices can exist where proline is present.
5.) Some information about function might be discerned from knowing the side chains
present in an α- helix.
i.) Helix wheel projection (looking ‘down’ on a helix) enables one to ‘see’ if amino
acids with a particular chemical character (polarity and/or size) are located on one
side of the helix versus the other side.
ii.) Amphipathic helices can result if one side of the helix is non-polar and the other
is polar.
Figure 4-16

Figure 4-15 Figure 11-24

b.) β-strands
1.) Hydrogen bonds between atoms in the backbone.
2.) Amino acid side chains alternate up and down from plane of the strand.
3.) Side chains can influence the formation of an β-strand—specifically proline side
chains as no β-strand can exist where proline is present.
4.) Produce a very rigid, pleated local structure.
5.) β-strands align side-by-side to make “β-sheets”.

Figure 4-10 Figure 4-17

i.) Can be parallel or anti-parallel (Figure 4-17)

§ Parallel beta sheets (B in figure)
i. Neighboring polypeptide chains run in the same direction.
ii. A lot of amino acids looping from one strand to another.
§ Antiparallel beta sheets (A in figure)
i. Neighboring polypeptide chains run in opposite directions.
6.) Some information about function might be discerned from knowing the side chains
present in a β-strand and/or sheet.
i.) Can have a hydrophobic side and a hydrophilic side on the same sheet
ii.) Can have one side positively charged and the other side negatively charged.
iii.) β-sheets can pass thru a membrane in the form of a β-barrel (see figure 11-25).
7.) Potential Exam questions:
i.) In the string of amino acids, leucine and serine amino acids alternate. This region
of a protein is known to form a beta sheet. Is there anything you can discern
about the function of this region of this protein? One side is polar and the other is
hydrophobic. It is possible that this protein transverses the membrane to form a
pore in which the leucine amino acid side chains are facing toward the fatty acid
tails of the phospholipids and the serine side chains facing the polar environment
of the extracellular space?
ii.) The following amino acid sequence is known to form an alpha helix: Ser-Pro-Tyr-
Gly-Leu-Val- Ala-Val-Ala-Met-Leu-Ile-Gly-Ile-Val-Ala-Gly-Met-Gly- Leu-Cys-
Thr-Arg). Use the helix wheel projection to assess whether there’s anything
‘remarkable’ or unusual about this alpha helix. The helix has 17 hydrophobic
amino acids in a row and therefore may transverse a cell membrane as an alpha
helix.
E. Protein tertiary (3o ) structure.
1. Tertiary structure = overall 3D structure/shape
2. Tertiary structure maintained mostly by non-covalent bonds between atoms in the protein’s
amino acid side chains.
3. Tertiary structure can also be maintained by one special type of covalent bond: a disulfide
bond (Figure 4-29).
a.) Formed in a non-reducing environment (e.g., the extracellular space, certain intracellular
compartments) between terminal sulfhydryl groups on cysteine side chains within the
same protein or between different proteins.
1.) Interchain: two –SH groups from two different proteins.
2.) Intrachain: two –SH groups from two different cyteine side chains in the same
protein.
b.) Helps to stabilize a favored protein conformation.
4. Tertiary structure is critical for protein function.
F. Proteins can be grouped into families based upon similar structures and/or functions.
1. Once a protein has evolved a stable conformation and has useful properties, it is multiplied or
replicated within a genome (on an evolutionary time scale).
2. The structure could be modified over time to enable it to perform new functions.
3. Groups of proteins in which all of the proteins in the family have similar:
a.) Shapes or conformations.
b.) Amino acid sequences.
c.) Functions.
4. Ex. Of protein families: See Figure 4-21.
G. Protein quaternary (4o ) structure.
1. Quaternary structure is the overall shape of a complex of proteins (i.e., multiple proteins).
2. Quaternary structure is generally maintained by non-covalent interactions between atoms in
the participating proteins’ side chains, although some covalent bonds between cysteine side
chains can contribute to quaternary structure.
G. Protein Function Regulation
1. Proteins can and are made in inactive forms —activity can and is regulatable.
2. There are common mechanisms used to activate or deactivate proteins:
a.) Binding of a molecule (ion like Ca+ or another protein) acts as a switch to turn a protein
on or off.
1.) Why does binding alter the protein? SHAPE CHANGE!
2.) Protein activity regulation via binding:
i.) Active site binding
ii.) Allosteric binding
b.) Protein phosphorylation.
1.) Covalently attaching a phosphate group to an amino acid side chain.
2.) Phosphate groups are very negatively charged so addition of a phosphate group can
drastically change the shape (and therefore the activity) of a protein.
3.) Phosphate groups can be added to amino acid side chains that have terminal hydroxyl
groups (serine, threonine and tyrosine, from smallest to largest).
4.) Phosphate comes from ATPà ADP.
5.) This reaction is reversible.
6.) Enzymes that help the procedure occur:
 i.) Protein Kinases catalyze the phosphorylation reaction (transfer of phosphate group
from ATPà -OH group of the protein).
ii.) Protein Phosphatases catalyze the de-phosphorylation reaction (removal of
phosphate group from the amino acid side chain).
7.) Depending on the protein and its function either phosphorylation or
dephosphorylation can activate
or deactivate it.
c.) GTP binding and subsequent
hydrolysis to GDP.
1.) GTP binding proteins = ‘G-
proteins’– proteins that bind GTP
and hydrolyze it to GDP.
2.) When GTP is bound, the protein is
activated.
3.) G proteins have the ability to
hydrolyze GTPà GDP; they do this slowly.
4.) Therefore, this ‘reaction’ is reversible—GTP binding/hydrolysis acts as an on/off
switch (respectively).
5.) Hydrolysis of GTPà GDP results in protein inactivation.
i.) Helper proteins (GAPs—GTPase activating proteins) expedite the hydrolysis
reaction.
6.) GDP-bound G proteins are always inactive (i.e., turned off).
7.) The GDP needs to be released so that the G protein can be re-activated at some point
in the future.
i.) Helper proteins (GEFs—Guanine nucleotide exchange factors, orGNRPs—
Guanine nucleotide releasing proteins) expedite the release of GDP and its
exchange for GTP.
ii.) This process is aided by the fact that GTP is at a higher concentration inside the
cell than GDP.

Figure 4-42