Proteins

and nucleic acids (lecture 3 4):

We slowly move closer to the molecules that make up a cell. Everything in biology is
based on carbon chemistry, because carbon can form 4 covalent bonds, and
therefore can form an infinite variety of molecules, covered in organic chemistry.
The default molecule has only C-C and C-H bonds, e.g. the molecule octane, which
you can find in gasoline. Whenever something else is attached to carbon, we call it a
functional group. Important functional groups are: Hydroxyl, Amino, and Carboxyl.

R stands for the rest of the molecule (can be anything, but must start with a C).

Humans are made up of water, large molecules, ions and small molecules. Babies
have the highest water content, as you get older you dry up more and more. We
usually call proteins, nucleic acids and carbohydrates macromolecules, because they
can form large polymers.

Advantage of biochemical unity: we can obtain energy from eating and digesting
other organisms.

Two very common chemical reactions in metabolism:
Condensation: formation of a polymer linked by covalent bonds, releasing one water
molecule with each monomer added. This reaction is anabolic, requires energy
input. Examples are DNA replication, protein synthesis, making of starch.
Hydrolysis: Breaking of covalent bonds with the help of water to transform a
polymer into its constituent monomers. This reaction is catabolic, releases energy.
Example: digestion of food molecules for energy generation.

Organisms consist of 100s of different lipids, 5 nucleotides forming RNA and DNA,
1000s of different sugars, and 10000-30000 different proteins from bacteria to
humans (and really much more if all modifications and isoforms are counted).

Proteins:

Proteins are the machines that do all of the work in a cell: build structures like hair,
replicate DNA, catalyze metabolic reactions, transport materials inside cells and
across the membrane, etc.

Proteins are made of amino acids, which are ionized at neutral pH.

There are 20 amino acids, which are classified according to the properties of their
side chains: nonpolar, hydrophobic amino acids; polar amino acids; charged amino
acids. Peptide bond formation (a condensation reaction) occurs between the
carboxyl group of one amino acid and the amino group of the next amino acid
generating a peptide backbone consisting of NCCNCCNCCNCC repetitions (in this

example there are four amino acids covalently bonded. An amino acid always starts
with an amino group [N-terminus] and ends with a carboxyl group [C-terminus]).

Amino acids are abbreviated with a three letter code or a one letter code: proline =
Pro = P

The number of amino acids used and the sequence in which they are arranged
(covalently bonded to each other) is called the primary structure. The primary
structure determines all the properties of the resulting protein.

There is an unimaginably large amount of possible different ways amino acids can
be arranged in a large protein. Even for a small 100 amino acid protein, there are
more possibilities than atoms in the universe; enough for billions of years of further
evolution!

As the polypeptide backbone consists of single covalent bonds, it is pretty flexible
(rotation about the single bonds is possible, full rotation for the C-C bond, less so for
the N-C bond). This allows polypeptides to fold into proteins. This occurs in two
steps. First, hydrogen bonds form within the polypeptide backbone between the O
of a carboxyl group and the H of an amino group. This can give rise to exactly two
secondary structures that form very quickly after a polypeptide has been made: the
alpha-helix and the beta-pleated sheet. Note that these hydrogen bonds do not
involve the side chains at all!

In the alpha-helix, hydrogen bonds form in the direction of the helix, generating a
stable rod-like structure. Side chains point outwards, away from the helix. In the
beta-pleated sheet, hydrogen bonds form within the plane of the sheet, generating a
stable sheet. Side chains point away from the plane, up or down. There are no
obvious rules, where youll find alpha helices and beta sheets within a protein.
Protein structure determination is the only way to confirm the presence or absence
of secondary structures within a protein.

Important for many structural proteins is the coiled coil, which are two alphahelices wrapped around each other. Hydrophobic amino acids at every 4th position
generates a band of hydrophobicity running along the length of the alpha-helix and
slowly rotating around it. Hydrophobic interaction then ensures that two such
alpha-helices come together just at that band resulting in the coiled coil (exactly like
a rope that consists of intertwined strands). This structure occurs in proteins giving
strength to tendons, hair, feathers

Proline is a unique amino acid, because the side chain is covalently bonded to both
the C and the N atom of the peptide backbone. This generates a kink in the peptide
because the ring prevents free rotation of the N-C bond. Also, the backbone
hydrogen bond cannot form, because the backbone N lacks a hydrogen. Therefore
formation of secondary structures (alpha helix, beta pleated sheet) is impossible. A
proline is often the last amino acid of an alpha helix.


Summary: primary structure is just the sequence of amino acids, with each amino
acid linked to the next by peptide bonds. Some stretches of this polypeptide fold into
an alpha-helix or beta-pleated sheet (secondary structure), or remain unfolded at
this first stage of folding.

Tertiary structure finishes the folding of a polypeptide, and is mediated by side
chain interactions.

Four types of interaction contribute to tertiary structure formation: ionic bonds,
hydrogen bonds, disulfide bonds, and hydrophobic interactions, all of them typically
between amino acid side chains in the interior of the protein.

Curling/Uncurling your hair: reduce/break disulfide bonds in keratin; then shape
hair as you wish; finally oxidize/reform disulfide bonds to keep hair in new shape.
In the keratin protein, you find coiled coils forming through hydrophobic interaction
as discussed above, and additionally, you find disulfide bonds between alpha-helices
to provide additional strength.

Hydrophobic interactions are the most important determinant of protein
folding/tertiary structure, because stretches of hydrophobic amino acids
automatically rearrange towards the interior of a protein (away from water),
whereas hydrophilic amino acids rearrange to be on the outside interacting with
water.

Important: primary structure (peptide bond formation) requires energy,
secondary/tertiary folding releases energy, i.e. occurs automatically

Quaternary structure indicates several polypeptides interacting to form a bigger
protein complex, e.g. hemoglobin consists of four individual polypeptides, the
coiled-coil keratin consists of three alpha-helices. Many proteins, however, consist
of only one polypeptide, that is, they are fully folded after tertiary structure
formation.

The importance of the amino acid sequence (primary structure) for folding and
function can be demonstrated in multiple ways: First, a single amino acid mutation
in the protein hemoglobin changes the shape (also called conformation) of
hemoglobin, and this results in a shape change of red blood cells (sickled), because
red blood cells contain only hemoglobin. Second, a typical protein sufficiently
diluted in watery solution denatures at high temperature (unfolds), but will
renature (refold), when the temperature is lowered. This is evidence that the
primary structure is sufficient for protein folding, or in other words, all the
information about protein folding and function is encoded by the primary structure.

Protein turnover: proteins have a half-life ranging from minutes to weeks (average
about 2 days).

Protein turnover is very important, because proteins often get damaged: fever, pH
change (lemon juice in milk changes the protonation state of COOH and NH3 groups;
milk proteins precipitate, same happens in cheese production), other chemical
changes.
Example: egg becomes hard by boiling because proteins denature, and get all
entangled when they try to renature.

Chaperones help proteins to fold properly after synthesis or after stress-related
unfolding.

Nucleic acids:

Nucleotides make RNA and DNA, and serve functions in signaling and energy
storage as monomers. A nucleotide is made up of a 5-carbon sugar, a nitrogenous
base and a phosphate group. 4 nucleotides in RNA: cytosine, uracil (pyrimidines);
guanine, adenine (purines). In DNA uracil is replaced by thymine. DNA lacks the
hydroxyl group at carbon-2 (deoxyribose).

Nucleotides polymerize via phosphodiester linkages (another condensation
reaction), with the 3 hydroxyl group of the polymer forming a covalent bond with
the 5 phosphate group of the incoming nucleotide (5 and 3 refers to the position of
the carbon atom, where the functional group is attached). This means that a long
RNA/DNA molecule always starts with a 5 phosphate group and ends with a 3
hydroxyl, we say, polymerization occurs in 5 to 3 direction.

DNA is made of two antiparallel strands held together by hydrogen bonds between
the bases. Purine bases can only pair with pyrimidine bases, and more specifically,
guanine (G) with cytosine (C), and adenine (A) with thymine (T). G-C forms three
hydrogen bonds, and is therefore more stable than A-T, which forms two hydrogen
bonds. DNA is a double helix with the sugar-phosphate backbone on the outside and
the bases on the inside arranged like rungs on a ladder. The double-helical structure
resulting from two strands being wound around each other has a major groove and
a minor groove. In the major groove, the two sugar-phosphate backbones are more
widely spaced allowing DNA-binding proteins to recognize the bases in the interior.
This is very important for transcription factors, restriction enzymes etc, which
recognize a unique DNA sequence. The overall DNA sequence of a genome carries
the genetic information. Basepairing and the double helical structures makes DNA
much more stable than RNA.

RNA came first in evolution, because it can store and execute information. RNA can
work like an enzyme catalyzing certain reactions, because it can fold into
complicated 3D structures similar to proteins. The folding occurs because
nucleotide bases within the same macromolecule pair via hydrogen bonds (in

contrast to DNA, where nucleotide bases of different macromolecules pair). A

particularly important RNA structure found in many mRNAs is the stem-loop
structure, which contributes to the regulation of mRNA function.