1.

Introduction to Biochemistry & Functional

Module 2 /

Groups
 Provide a general overview of biochemistry based on component parts.
Describe molecular orbitals.
Characterize functional groups.
 Recognize chiral centers

Cell Theory
Every cell on Earth belongs to one of two categories:

1. Prokaryotic cells
2. Eukaryotic cells
Prokaryotic cells were the first cells to appear on our planet. All prokaryotes
alive today are unicellular (one-celled), and include bacteria (singular form is
"bacterium") and archaea (singular form is "archaean"). Prokaryotes are small
cells that don't have a nucleus or membrane-bound organelles.

Eukaryotic cells appeared after prokaryotes. The main difference between the
two is that eukaryotes have a central control structure, called
the nucleus (plural form is "nuclei"), where DNA is housed. In prokaryotes,
the main DNA molecule (bacterial chromosome) is present in a region called
the nucleoid, but the nucleoid lacks a surrounding membrane. Smaller DNA
molecules called plasmids can be also found in prokaryotes. Prokaryotic
DNA is circular, in contrast to the linear structure of eukaryotic DNA.
Both eukaryotic and prokaryotic cells have a cell or plasma membrane,
which surrounds and defines the inner environment of the cell. The cell
membrane is made of a phospholipid bilayer containing a variety of proteins
and additional components. The cell membrane is responsible for mediating
interactions between the cell and its environment and permits certain
molecules to enter the cell.

Typical Animal Cell (Eukaryotic) Bacteria Cell (Prokaryotic)

 Note: these images are not drawn to scale. A typical
eukaryotic cell is 10 times bigger than the typical
prokaryotic cell.
Prokaryotic cells have a simpler structure than eukaryotic cells, and they range
in diameter from 0.1 to 5.0 µm (micrometers). Most prokaryotes have a
protective layer called the cell wall that is made of peptidoglycan, which is a
combination of polysaccharides and amino acids. Although eukaryotic plant
cells also have a cell wall, it has a different molecular structure. Prokaryotes,
like prokaryotic cells, also have a cell membrane and cytoplasm. Many
prokaryotes also have external appendages such as a flagellum. The
cytoplasm contains the DNA and the ribosomes, where protein synthesis
takes place. Several types of RNA are involved in the process of protein
synthesis, and ribosomal RNA (rRNA) is the main component of ribosomes.
Ribosomes can be found free from membranes, but they bind to membranes
when synthesizing exported proteins. Both prokaryotes and eukaryotes have
ribosomes, but they are different.
Eukaryotic cells have internal membrane bound compartments, called
organelles, that perform specialized functions for the cell. These
compartments and their functions are as follows:

Organelle Function

nucleus Contains DNA in the form of chromosomes.

smooth endoplasmic reticulium Site of lipid synthesis

 Organelle Function

rough endoplasmic reticulium First part of the protein secretory pathway

golgi Part of the protein secretory pathway.

Mitochondria Site of energy production

Lysosome Destruction of unwanted material.

Comparison of cell sizes

Rela
tive sizes of cells and their contents. Notice that the scale shown is logarithmic.

Information flow in Living Organisms

The repository of genetic information in all organisms in a double stranded
polymer called DNA. The DNA contains all of the information required for the
cell to function, encoded in the order of four nucleotide bases, A, G, C, or T. In
order for this information to be utilized it is necessary to copy the sequence of
bases from DNA to RNA in a process called transcription. RNA differs from
DNA in several key points: i) it is usually a single stranded molecule, ii) the T
base in DNA is replaced by U. There are many functinally different RNA
molecules. A class of RNA molecules, called mRNA (messenger RNA) are
utilized by ribosomes to generate proteins, in this case the sequence of the
nucleobases in the mRNA are translated to a sequence of amino acids in the
protein.

Most viruses, which are technically not living because they cannot reproduce
on their own, also utilize DNA as their genetic material. Some viruses use
RNA. Some viruses copy the RNA directly to new RNA molecules when new
viruses are made. Other viruses, called retroviruses, copy the RNA first to
DNA (retro, or backwards) and then back to RNA. One of the more notable
retroviruses is the HIV (human immunodeficiency virus) that causes acquired
immunodeficiency syndrom (AIDS).

Understanding biochemistry requires that you understand the basic functions

of the cell, the differences between eukaryotic and prokaryotic cells, and
fundamental features of genetics. Take the following ungraded quiz to
determine whether you need to review this material.

checkpoint
Cell Biology and Genetic Background
Ribosomes

are the site of photosynthesis are the site of protein synthesis are never bound to

membranes replicate DNA

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Introduction to Biochemistry
 Overview of Central

Themes in Biochemistry. Simple building blocks, such as amino acids, are used to generate complex biochemical

structures, such as proteins. Proteins play diverse roles in the cell, including structural, transport, and catalysis. The

information for the generation of such complex structures is encoded in nucleic acids. The flow of this information is

regulated in a complex fashion. The entire process is fueled by metabolic processes that generate energy from organic

energy sources and use this energy to synthesize complex molecules.

Chemical Bonding and Biochemical

Structures
The elements that are commonly found in biochemical molecules are among
the most abundant on earth, this includes carbon, oxygen, nitrogen, sulfur,
and phosphorous.

Atoms are made up of subatomic particles: protons, neutrons, and electrons.

Protons and neutrons are at the center of the atom and have a mass of 1
atomic mass unit (a.m.u) each. Each proton has a positive charge (+1), while
neutrons are neutral (they carry no charge). Each electron has a negative
charge (-1) and zero mass. Two atoms that differ by the number of neutrons
are called isotopes of the same element.

One characteristic of the atoms of the major elements is that they are able to
form molecules through formation of covalent bonds with other atoms.
 Covalent bonds
(definition)
Covalent bonds represent the sharing of the electrons
(negatively charged subatomic particles between atoms.) The
number of covalent bonds that can form is dictated by the
number of unpaired electrons in the outer valence shell of the
atom.

Each atom in a molecule will complete its outer shell of electrons, which is 2
for hydrogen, and 8 for second row elements (e.g. C, N and O). The valence
shells for each of the biologically relevant elements are highlighted in the
periodic table below.

Only the valence shells are shown. The six shaded elements have unpaired electrons and readily form covalent bonds.

The electron shells are divided into atomic orbitals. Each atomic orbital holds
at most 2 electrons. The s orbital is spherically symmetric. The three p orbitals
(px, py, pz) are bi-lobed, have a defined direction in space, and hold a total of 6
electrons. The 1st shell consists of the 1s orbital, and can hold 2 electrons. the
2nd shell contains the 2S and the 2Px, 2Py, and 2Pz orbitals and can thus hold 8
electrons. The 3rd shell contains the 3S, 3Px, 3Py, 3Pz, and the five 3d orbitals.
Since the 3d orbitals are very high in energy, it is reasonable to consider that
the 3rd shell really contains 8 electrons as well. For most elements that are
found in biological systems it is sufficient to consider the 1 st shell, the 2nd shell,
and the 3S and 3P orbitals as the third shell

Atom Electronic Configuration Number of bonds Hybrid Orbitals

H 1s1 1

C 1s2 2s2 2p2 4 3×sp2 + pz or 4× sp3

N 1s2 2s2 2p3 3 (4 when 3×sp2 + pz or 4× sp3

protonated)
 Atom Electronic Configuration Number of bonds Hybrid Orbitals

O 1s2 2s2 2p4 2 (3 when 3×sp2 + pz or 4× sp3

protonated)

S 3s23p4 2 (usually)

P 3s23p3 5

Carbon, nitrogen, and oxygen, usually form hybrid orbitals, that show a
mixture of s and p character, e.g. sp3 hybrid orbitals, as dicussed below.

Generation of

Hybrid Atomic Orbitals. The top section shows the generation of three sp2 orbitals from an s orbital and two p

orbitals. The three sp2 orbitals all lie in the same plane and are 120o from each other. The bottom section show the
generation of four sp3 orbitals from an s orbital and three p orbitals. The resultant sp 3 orbitals form a tetrahedron,

with an angle of 109o between each orbital.

Covalent bonds indicate the sharing of electrons between atoms. Usually
two half-filled orbitals combine to form the bond. Hence hydrogen forms one
bond while carbon forms four.

Chirality
When a molecule cannot be superimposed on its mirror image, it is said to be
chiral. Biochemical processes are often able to distinguish between chiral
molecules, thus it is important to be able to identify if a compound is chiral or
not. Carbon, when sp3 hybridized, is tetrahedral. If the four groups attached to
the carbon are different, then the molecule containing that carbon is chiral,
and the carbon itself is refereed to as a chiral center. Planer groups, such as
carbon hybridized as sp2, are not chiral, because the plane of the molecule
forms a mirror plane within the molecule itself, thus the mirror images are
identical.
learn by doing

Chirality of Chloro-Fluoro Methane

Instructions: Chloro-fluoro methane and its mirror image are shown below.
Please answer the question using these two structures.

How many different groups are attached to the central carbon atom?

 
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learn by doing

Chirality of Chloro-Fluoro-Bromo Methane

Instructions: One hydrogen has been replaced by bromine (colored purple).
One form of the molecule is shown on the left and it's mirror image is on the
right. Use these two structures to answer the question on the right.

Is it possible to superimpose one molecule on to its mirror image?

 
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Functional Groups
 I

mportant Functional Groups in Biochemistry. Alkanes and benzene aromatic rings do not contain polar atoms

(e.g. N and O), and therefore do not interact with water, a polar solvent. Consequently they usually leave the aqueous

phase. This hydrophobic behavior is very important in the self-assembly of many biochemical structures, such as

proteins and membranes. The remaining compounds have some polar atoms and thus interact with water to a greater

extent. Imidazole is found in the amino acid Histidine and plays an important role in the catalytic activity of many

enzymes. The guanidinium group is found on the amino acid arginine and the indole group is found in the amino acid

tryptophan.
Functional Group Tutorial
learn by doing

Functional Groups Activity

In the activity below, the radio buttons on the extreme left let you select a
property and hilight the functional groups that exhibit the selected property.
The [?] buttons display the definition of each of the properties.
The FUNCTIONAL GROUPS column shows the names and chemical
structure of important functional groups in biology.
 Select any one of these functional groups to see it's properties
and to view examples of this group.
 The pull-down menu allows you to select different chemicals
that contain the selected functional group.
 The functional groups are hilighted in both the 2D structure and
the 3D Jmol.
Recognizing these functional groups where they appear in larger structures
and knowing what properties they exhibit will provide you with insight into
their function within these larger structures.