Water is nearly tetrahedral; it is bonded, on average to 3.

4 other water molecules; even at 37

C,15% of water molecules are jointed to four others in a short-lived assembly known as a
flickering cluster

Bottom of ocean is permanently 4 C; pressure of water column keeps bottom of ocean under high
pressure and in liquid form

The oxygen is the central atom for the water, and the two electron pairs stick out in a
tetrahedralconfiguration, which is what bonds with the hydrogen

In ice, each water molecule forms four hydrogen bonds to other water molecules, making acrystal
lattice

Hydrogen bonds occur between bases in DNA, between peptide bonds in proteins, and
betweenwater and proteins; sometimes the formation of H-bonds results in specific biochemical
structuressuch as alpha helices

Water competes with biomolecules for H-bonds, and the strength of the H-bond can be increased
by shielding the bond from water; this happens in double helical DNA, where the base-
basehydrogen bonds are within the helix and not exposed to water

Hydrogen bonding occurs in the protein lysozyme, which is in egg whites, and chews up bacteria

The reason the H-bonds can occur between amino acids in a protein (which makes 2ndary
proteinstructure), and not with water, is because the strength of the H-bonds depends on the
localenvironement. If there is a lot of water, the water will form the hydrogen bonds instead.
N-methyl acetamide
in
dioxane
,
tetrachloromethane
and water demonstrates this, since indioxane, it forms the H-bond with itself, but in water, it
makes the H-bond only with water, andthere is little H-bonding with itself.

H-bonds are strongest when the three atoms lie in a straight line; they are about only 1/20
asstrong as a covalent bond, and 0.27 nm in length

larger than the normal covalent bond of 0.1 nm

Water competes for ionic bonds of salts just as it competes for H-bonds; this results in the solvent
properties of water

Salts are highly stable structures, since they have positively charges sitting right next tonegatively
charged ions, but the fact that they dissolve in water and release little heat shows thestrength the
heat of hydration reaction

Outside of DNA has a net negative charge and + ions cluster around it; histones have a net
positive charge (therefore, they must have a large proportion of lysine and arginine); DNAfolding
in chromosomes depends on charge-charge interactions, because the histones neutralizethe
DNA, and the chromosome is 10,000 times shorter than extended DNA, and that amount of
charge would blow up. Thus, folding DNA around nucleosome core particles depends on ionic
bonds.

Even in water, cations and anions are attracted, which is why DNA and histones are attracted
toeach other in aqueous environment. However, if there is a large salt concentration in the
water,the DNA and histones will be less strongly attracted to each other since the ions will get
betweenthe two; this is why separating histones and DNA is done by high salt concentrations.

Proteins consist of many amino acids, which are positively and negatively charged. The
positiveand negative charges depend on the pH; at the pH where there are equal + and

charges whichcancel each other out, this is called the pI, or isoelectric point. At pH=pI, the protein
is leastsoluble, since it is not charged. At higher or lower than pI, the + or

charges accumulate and push away from each other, and are easier to dissolve.

As the salt concentration of water in which protein is dissolved increases, the solubility of the
protein increases, since the salts interact with the protein

Histidine is used a lot in catalysis, because a small change in pH can make it positive or
neutral,activating or deactivating it, since it dissociates at neutral pH, in comparison to the
carboxylic
acid aas which dis
sociate at low pH and arginine and lysine which dissociate at high pHs

Cysteine oxidizes spontaneously to form

Cystine;
the disulfide bonds that cysteine forms withina pp or even between two separate peptides can be
used in protein engineering by reducing the protein to break the bonds, and then curling the
protein and reoxidizing it.

Hydrophobic effect is not because of a large affinity of non-polar molecules, but to prevent
thedisruption of the hydrogen bonds of water

Amphipatic molecules form micelles when thrown in water to remove non-polar regions
fromwater; micelles have a non-polar region in the center; liposomes have an aqueous cavity in
thecenter

The ionization state of a weak acid or base depends on the pH. At pH values below the pKa
thegroup is mostly protonated; at pH values above the pKa, the group is mainly dissociated.
Whenthe pH=pKa, half of the groups are dissociated and half are protonated

Weak acids and bases on biomolecules have similar pKa values to the same groups in water
butnot bound to the biomolecule, but not exactly the same values; this is because on a protein,
the pKa of a group can be changed by the local environment. For example, a carboxyl group on a
protein with a nearby protonated amino group with a plus charge will favor the dissociation of
thecarboxyl group and decrease the pKa (as in the case of serine proteases)

At pH values near neutrality, an amino acid is a zwitterion, and has both a negative and
positivecharge

Amino acids, except for glycine, have optical isomers, L and D. Proteins consist exclusively of L-
amino acids

Peptide bonds have partial double bond character which prevents rotation around the C=N
partialdouble bond; the four atoms C=N, and carboxylic O with partial negative charge, and H
attachedto N, along with alpha carbon are in plane. Rotation of plane occurs around the alpha-
carbon

Residual amino acid backbone is neutral; the proteins charge comes from the side ch
ains and the N and C terminal residues which is negligible

C and N atoms of peptide bond do not have formal charges and are not further protonated or
deprotonated at any pH; the O has a partial

charge and the N has a partial + charge

Peptide bond is very stable and does not hydrolyze as do ether bonds. Only enzymes can
cleavethem

Alpha helix, beta sheet,

collagen helix

linear helix created by three peptide chains wrappedaround each other and limited flexibility,
beta turns

conformations adapted when peptide chainhas to sharply change direction in a folded protein

almost always have proline to force the turnand/or glycine, which bc of its small side chain has
larger flexibility

Alpha helices such as wool can absorb water and are flexible; beta sheets such as silk do
notabsorb water and are not flexible

Proline
has two configurations because of its ring structure

trans (94%) and cis (6%). All other amino acids are almost always trans (99.95%)

Examples of protein structure:

prealbumin
: B-sheet is dominant 2 structure; two B-sheets areadjacent and form a dimer, which is tertiary
structure. Two identical subunits= quaternarystructure

Cytochrome C
= monomer, so no quaternary structure, and no common motifs can be seen. It hasa prosthetic
heme group in the center

Lysozyme has groove for substrate; composed of many B-sheets

Myoglobin is dominantly a-helix; hemoglobin is tetramer of four myoglobin-like subunits whichis

quaternary structure; bee venom called
melittin
normally has the non-polar side chainsdistributed evenly throughout, but when in contact with a
lipid membrane, it forms an alpha-helixtype structural motif, so that the side chains of half the
helix are non-polar and all on one side sothat they can bind to the membrane of the target and
destroy it; the other side is positivelycharged. The melittin forms a tetramer, and makes a large
hold in the membrane.

Some proteins have two or more globular regions but on a single peptide chain

and these are

domains

Troponin C
has such domains; in between domains are usually the binding site of substrates, since there is a
gap between the two globular regions

Ribonuclease
has four disulfide bonds between cysteins

has a B-sheet center, and histidinesholding a metal (zinc)

Because disulfide bonds are so prominent in protein structure, reducing them will destroy
thedisulfide bonds and denature the proteins. Some common reducing agents used to denature
proteins are
urea, B-mercaptoethanol
(HOCH2CH2SH), and
guanidine hydrochloride
(seestructure before exam)

Additional motifs are being identified, many of which are combinations of the well known
motifs,such a
B-barrel
, which is a B-sheet wrapped into a cylinder,
B-a-B Loop
,
a-a Corner
, and
twisted B-sheet
. B-barrel example is
green fluorescence protein
which oxidizes and fluorescesspontaneously, and can be injected into animals and make them
green

Protein folding would be too slow if random, which suggests that the primary structure
includesinformation that guides folding

Some proteins such as

insulin
do not spontaneously refold if they are denatured. This is true in proteins that have undergone
posttranslational modification
. To help such proteins fold areother proteins called
chaperone proteins

Immunoglbulins: tetramer including four polypeptides, two subunits of two equivalent

polypeptides; each pp is composed of two or more flexible domains that helps for binding
toantigens and interacting with cell membranes and membrane bound proteins which
requireflexibility. The quaternary structure is not well defined, as with hemoglobin which has a
tetramer structure. The dimains have

Serine proteases are used to hydrolyze other proteins and cut them in two. It involves
asparticacid and histidine residues along with serine, which is called the
catalytic triad
. Because the pKaof serine is very high, it almost never dissociates, so the aspartic acid induces
the histidine toremove the hydrogen from the OH group of serine. Serine becomes negatively
charged and readyto covalently bond with the protein needing to be cut, thus causing hydration
rxn that would chopit in two

Only aromatic amino acids absorb light in the UV range, so it can be used to determine
proteinconcentration. In addition, tryptophan (Trp, W) can be used in protein fluorescence
experiments

After protein is formed, it undergoes posttranslational modification, and some of the aas are
changed. Proline can be changed into
hydroxyproline

without the hydroxyl group, the prolineis not stable, and since it is used in connective tissue,
scurvy results. Glutamate can be changedinto
carboxyglutamate
which has an extra carboxyl group on the terminal carbon, and binds tocalcium well, and is used
in blood clotting. In addition, hydroxyl groups in serine can be phosphorylated to make
phosphoserine
to regulate the enzyme.

Flavoproteins are involved in ox/red and have a prosthetic flavin nucleotide in the center that isnot
covalently bound

Zymogens
are the inactive precursor of the active enzyme, and they are self-inhibiting, with alength of the pp
covering the active site. Other activating enzymes, usually serine proteases comeand cleave the
pp so that the active site is exposed. This cleavage is irreversible, so other inhibiting proteins are
needed to inactivate it after this. In the blood coagulation cascade, eachfactor (XII, XI, X, IX,
prothrombin, etc) are zymogens that become activated into (XIIa, XIa, Xa,IXa, thrombin, etc) and
activate the next zymogen in the chain. Each of these activated factors areserine proteases.
Maintaining enzymes initially in a zymogen form is important for manyenzymes such as
chymotrypsin, since they do not eat out of control.

Other than zymogens, there exist other ways to regulate enzymes: 1. Allosteric binding sites
(i.e.feedback inhibition), 2. Regulation by covalent modification, 3. Induction or repression of
enzyme synthesis