Class 3 Chemical Components of Cells

Chemical Components of Cells

Molecules in Cells

What molecules are cells made from?
Which elements predominate in the cell?
How are the molecules in the cell built?
What are the interactions within and between the macromolecules?

Approximate Composition of a Bacterial Cell

A bacterial cell is approximately 24% chemicals and 76% water.
The composition of an animal cell is similar.
Nucleic acids make up about 6% of the cell.

Predominant Elements in the Human Body

Four elements (highlighted in red) make up ~99% of the total number of atoms and ~96% of our total weight.
Seven elements (highlighted in blue) represent ~0.9% of our total number of atoms.
Elements shown in green are required in trace amounts.
Molecules in cells are dominated by lighter elements.

Common Elements in Living Organisms

Outermost shells of common elements are not completely filled.
Electrons in these incomplete shells can participate in chemical reactions with other atoms.

Importance of Carbon in Living Systems

Carbon forms stable backbones for molecules due to its stable bonds and ability to build large molecules.
More energy is released when C-C bonds are combusted than when Si reacts with $O_2$ .
Although Si is more abundant in Earth’s crust and can form 4 covalent bonds, C-C bonds are stronger than Si-Si bonds.

Properties of Carbon Molecules

Carbon molecules are soluble in $H<em>2O$ (cells ~70% $H</em>2O$ ).
They can exist as a gas and in circulation.
Combustion byproduct $CO_2$ is given off by one organism to be used by another (respiration, photosynthesis).
Silicon is essentially insoluble after reacting with $O<em>2$ and permanently out of circulation. Quartz is a common form of $SiO</em>2$ .

Additional Essential Elements

N, P, S are also essential.
Trace elements such as Fe, Zn, Mn are vital to many life processes (e.g., Fe in Hemoglobin).

Chemistry of Cells

Based overwhelmingly on carbon compounds.
Depends almost exclusively on reactions that take place in an aqueous environment.

Water and Dissolution

$H_2O$ molecules are attracted to positive or negative charges of ions.
Ions dissolve in the aqueous environment of the cell (hydrophilic).
Small polar molecules also dissolve in the aqueous environment of the cell.

Small Molecules and Macromolecules in the Cell

Subunits:
- Sugar -> Polysaccharide
- Fatty acid -> Fat
- Amino acid -> Protein
- Nucleotide -> Nucleic acid
Water is expelled during the creation of macromolecules

Composition of a Bacterial Cell

70% $H_2O$
30% chemicals:
- Inorganic ions, small molecules (4%)
- Phospholipid (2%)
- DNA (1%)
- RNA (6%)
- Protein (15%)
- Polysaccharide (2%)

Major Families of Organic Molecules

Sugars -> Polysaccharides, glycogen, and starch (in plants)
Fatty acids -> Fats and membrane lipids
Amino acids -> Proteins
Nucleotides -> Nucleic acids

Sugars

Energy sources and subunits of polysaccharides.
In aqueous solution, sugars are usually in cyclic form.

Fatty Acids

Components of cell membranes.
Can have one or two fatty acid tails, such as in phospholipid molecules.
Kinks in chains can result from double bonds.
Also components of triacylglycerol molecules.

Amino Acids

Subunits of proteins.
Have an amino group, carboxyl group, α-carbon, and side chain (R).
Exist in nonionized and ionized forms.
$H<em>2N-C-COOH$ (nonionized form), $H</em>3N-C-COO$ (ionized form)
Proteins make up half the dry mass of a cell.

Nucleotides

Subunits of nucleic acids (DNA and RNA).
Composed of a phosphate group, sugar (ribose or deoxyribose), and a base.

Nucleoside Di- and Tri-phosphates

Carry chemical energy in their phosphoanhydride bonds.
Combine with other groups to form coenzymes (e.g., coenzyme A).
Used as small intracellular signaling molecules (cyclic AMP).

Macromolecules and Covalent Bonds

Atoms share electrons to form molecules via covalent bonds.

Strength of Covalent Bonds

Covalent bonds are strong enough to survive conditions inside cells.
Typical covalent bonds are stronger than thermal energies within the cell by a factor of 100.
Covalent bonds are normally broken only during specific chemical reactions controlled by enzymes.

Formation and Breakdown of Macromolecules

Formed from subunits (monomers) by condensation reactions (energetically unfavorable).
Broken down by hydrolysis (energetically favorable).
Condensation and hydrolysis are reverse reactions.

Condensation and Hydrolysis Reactions

Condensation: two monosaccharides linked by a glycosidic bond, expelling water.
Hydrolysis: water is consumed to break the glycosidic bond.

Peptide Bonds

Two amino acids linked by a peptide bond to form a dipeptide.
Proteins are long polymers of amino acids linked by peptide bonds.
Peptides usually have < 50 amino acids.

Phosphodiester Linkage

Nucleotides joined together by a covalent bond.
3’, 5’- phosphodiester linkage formed between the 3’ and 5’ carbon atoms of adjacent sugar rings (ribose in this example).

Specific Sequences of Subunits

Macromolecules (proteins, nucleic acids, some polysaccharides) contain a specific sequence of subunits.
For proteins with 20 amino acids and a chain length of 200 amino acids, there are $20^{200}$ possible combinations.
For DNA molecules with 4 nucleotides and a length of 10,000 nucleotides, there are $4^{10,000}$ possible combinations.

Debate About Macromolecules

Early 20th-century chemists debated whether proteins, polysaccharides, and other large organic molecules were:
- Discrete particles made of covalently linked atoms,
- Loose aggregations of heterogeneous small organic molecules held together by weak forces.

Molecular Weight of Hemoglobin

Hemoglobin's molecular weight is 68,000 daltons.
1 dalton is nearly equal to the mass of a hydrogen atom (= 1 g/mol).

Ultracentrifuge and Macromolecules

Svedberg’s invention of the ultracentrifuge settled the debate about whether macromolecules exist.
If proteins were aggregates of smaller molecules, they would appear as a smear of molecules of different sizes when sedimented.
Results supported the theory that proteins are true macromolecules.

Macromolecules and Noncovalent Bonds

Polysaccharides, proteins, nucleic acids are built from covalent bonds.
Noncovalent bonds specify the precise shape of a macromolecule.
Noncovalent bonds allow a macromolecule to bind other selected molecules.

Assembly of Macromolecular Complexes

Covalent bonds allow small organic molecules to join together to form macromolecules.
Macromolecules can assemble into large macromolecular complexes via noncovalent bonds.

Ribosomes and Endoplasmic Reticulum

Some ribosomes are free in the cytosol; others are attached to membranes of the ER.

Noncovalent Interactions within Macromolecules

Amino acids within a polypeptide chain can be hydrogen-bonded to each other.

Noncovalent Interactions between Macromolecules

Weak noncovalent bonds have less than 1/20th the strength of a strong covalent bond.
They are strong enough to provide binding only when many of them are formed simultaneously.

Shape and Conformation of Macromolecules

Most proteins and many RNA molecules fold into a three-dimensional shape, or conformation.
Shape/conformation is directed mostly by a multitude of weak, noncovalent, intramolecular bonds.
Disruption of conformation affects biological activity.

Binding Through Noncovalent Interactions

A protein can bind to another protein through noncovalent interactions on the surface of each molecule.
In the aqueous environment of a cell, many individual weak interactions cause proteins to recognize each other specifically and form a tight complex.
Electrostatic attractions between complementary positive and negative charges.

Noncovalent Bonds and Molecular Binding

Macromolecule A randomly encounters other macromolecules (B, C, and D).
Surfaces of A and B, and A and C, are a poor match, forming only a few weak bonds that thermal motion rapidly breaks apart.
Surfaces of A and D match well, forming enough weak bonds to withstand thermal jolting; they therefore stay bound to each other.

Molecular Motion and Diffusion

Molecules in the cell are in constant motion due to thermal energy.
Molecules diffuse inside the cell but constantly collide with other molecules, resulting in a “random walk.”
Smaller molecules diffuse through cell cytosol more rapidly.
Proteins and other large macromolecules diffuse through cytosol more slowly.
Noncovalent interactions between macromolecules are facilitated by their close proximity in the cell and by many random collisions.

Types of Noncovalent Interactions

Hydrogen bonds
Electrostatic interactions
Van der Waals interactions
Hydrophobic effect
Individually weak, but collectively strong.

Hydrogen Bonds

Hydrogen bonds between urea and $H_2O$ molecules.
Hydrogen bonds between the bases in DNA.
$H_2O$ molecules joined together in a hydrogen-bonded lattice.

Hydrogen Bonds in Water

Due to polarization, two adjacent $H_2O$ molecules can form a hydrogen bond.
Slight positive charge on hydrogen is attracted to the slight negative charge of oxygen.
Oxygen is more electronegative than hydrogen, resulting in electronegative and electropositive regions in the $H_2O$ molecule.

Hydrogen Bond Donors and Acceptors

In cells, hydrogen bonds commonly form between molecules containing oxygen or nitrogen.
The atom bearing the hydrogen is the H-bond donor.
The atom that interacts with the hydrogen is the H-bond acceptor.
Hydrogen bonds are important noncovalent bonds for many biological molecules.
Hydrogen is often sandwiched between two electronegative atoms (O or N).
Hydrogen bonds have ~1/20 the strength of a covalent bond.

Electrostatic Interactions

An enzyme that binds a positively charged substrate will often have a negatively charged amino acid side chain at the binding site.
Partially charged groups on polar molecules in close proximity can have electrostatic interactions.

Van der Waals Interactions

Dipole–dipole interactions: partial positive side of a molecule attracts the partial negative side of another molecule.
Induced dipole–induced dipole interactions: attraction between transient induced dipoles.
Dipole–induced dipole interactions: permanent dipole in one molecule induces a transient dipole in another molecule through momentary distortion of electron clouds.

Hydrophobic Effect

Nonpolar hydrocarbons do not form hydrogen bonds and are generally insoluble in $H_2O$ .
Hydrophobic molecules contain many nonpolar bonds and are usually insoluble in $H_2O$ .
Hydrocarbons, which contain many C-H bonds, are especially hydrophobic.

Spontaneous Hydrophobic Interactions

Hydrophobic interactions are spontaneous processes, resulting in an increase in the entropy of the Universe (ΔS_{univ} > 0).

Clustering of Hydrophobic Molecules

Hydrophobic molecules, such as benzene, tend to cluster together in aqueous solutions.
Clustering is called the hydrophobic effect.
The hydrophobic effect is powered by the increase in entropy of water when hydrophobic molecules come together.
The hydrophobic effect is a powerful organizing force in biological systems, such as membranes.

Entropy and the Hydrophobic Effect

Nonpolar solute molecules are driven together in water not primarily because they have a high affinity for each other, but because, when they do associate, they release ordered water molecules around nonpolar molecules (e.g., benzene) into bulk water, which increases the entropy of the system.
Higher entropy is achieved, leading to increased stability. Molecules are in constant motion due to thermal energy.