BioPhysics Cheat Sheet Part 2

CHNOPS is an acronym for the elements most commonly found in living cells
(pronounced chi-nops, with a short i as in “chip” and a short o as in “top”).

The individual smaller molecules that are chained together are called
residues. When the residues are all identical, the polymer is called a homopolymer.

A hydrocarbon is a molecule made of only hydrogen and carbon.

Carbon atoms have four valence electrons to share. Therefore, in a

molecule, carbon atoms will form four covalent bonds with other atoms

A functional group is a specific group of atoms within a molecule that confers

certain characteristics to that molecule.

A hydroxyl group is an oxygen atom with one hydrogen atom covalently attached.
BioPhysics Cheat Sheet Part 2

A carbonyl group is carbon atom with a double covalent bond to an oxygen

atom.

A carboxyl group is a type of carbonyl group. We discuss it here in a section of

its own because it is so common in biomolecules.

A phosphate group is a phosphorous atom with four oxygen atoms attached.

Nucleic acids serve a variety of functions in living things. Here we review only
the most major roles they play.

The primary structure of nucleic acids is the specific nucleotide sequence

making up the polymer.

A cell is a pouch or sack of biomolecules that is (or was) alive.

A cell is the smallest unit of an organism that can be considered alive.

Cell theory says (1) all living things are made of cells and (2) all cells come
from preexisting cells.

Cell theory was formally developed in 1839 by M. J. Schleiden and T. Schwann.

An organism can be single cellular, that is, made up of a single cell (like an
amoeba) or multicellular (like people).

All cells are surrounded by a lipid bilayer membrane that encloses and contains
the contents of the cell.
BioPhysics Cheat Sheet Part 2

The cell membrane is also called the plasma

membrane.

A receptor is a molecule in the membrane (such as a protein, glycoprotein,

glycolipid, or carbohydrate) that has at least a portion of itself on the surface of
the membrane.

Some cells have a protective layer on the outside surface of the membrane
called a cell wall. Cell walls are commonly found in plants and many prokary-
otes such as bacteria, but are not usually found in animal cells.

DNA is perhaps the largest and certainly the most significant of structures
inside the cell.

Cells contain many fibrous structures which together are called the cytoskeleton.

There are three

types of cytoskeleton fibers, classified according to their size and shape: micro-
tubules, intermediate filaments, and microfilaments.

A ribosome is a complex of structural proteins, enzymes, and ribosomal RNA (rRNA).

The endoplasmic reticulum (ER) is a network of folded membranes found inside

eukaryotic cells

The nucleus is an approximately spherical membrane-bound (membrane-

surrounded) organelle near the center of eukaryotic cells

The nucleus is surrounded by a double membrane called the nuclear envelope

or nuclear membrane.

One of the larger organelles in the endomembrane system is the Golgi appara-
tus, also called the Golgi complex or Golgi body.

Vesicles are small, approximately spherical lipid bilayer containers. They typically
result from a portion of some larger membrane structure budding out and being
pinched off. In the process of budding out and being pinched off, various mole-
cules (proteins, etc.) become trapped inside the vesicle.

Chloroplasts are organelles found in the cells of plants and a few other eukary-
otes
BioPhysics Cheat Sheet Part 2

When a protein is folded into its correct shape, it is said to be in its native state.
The native state can include one or a small number of conformations that are
involved in the natural functioning of the protein. When a protein is unfolded,
so that it is no longer in its native state, we say that it is denatured.
BioPhysics Cheat Sheet Part 2

Five of the 20 major amino acids have side chains that carry a charge (ionize) at
physiological pH.
BioPhysics Cheat Sheet Part 2

At least a half-dozen of the 20 major amino acids contain uncharged polar,

hydrophilic side chains. These side chains will tend to face toward the outside
of the protein in an aqueous environment.

Nonpolar amino acid side chains are a source for the hydrophobic effect.

Two of the major amino acids contain sulfur. One in particular, cysteine, con-
tains a sulfur atom at the end of its functional group with only a small hydrogen
atom attached.

Membranes are lipid bilayers in which the majority of the bilayer (the inside)
is very hydrophobic, with a layer of charged and polar hydrophilic groups mak-
ing up both surfaces of the membrane.

The polypeptide backbone requires a good deal of flexibility in order for a

polypeptide to fold up into a globular protein.

There are two very common secondary structural motifs that occur throughout
protein structures. One is called the alpha helix and the other is called the beta
sheet.

The alpha helix is a secondary structure in which the polypeptide chain forms
a right-handed helical shape.

The beta sheet (denoted as b sheet and also called beta pleated sheet) is the
second most common secondary structure found in proteins.