Introduction To Biochemistry, Chirality, & Functional Groups

Biochemistry (Open + Free)
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Muhammad Awais (/jcourse/webui/myaccount/edit.do?user=ststa.2022@gmail.com)
[ S IG N OU T ] ( / JC OU R S E/ W E BU I/ L O G OU T. D O ?
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Module 1 - Introduction and Water Structure Search

This course is not led by an instructor
1. Introduction to Biochemistry, Chirality, & Functional

Groups
Learning Objectives
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
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membrane-bound organelles. context=4c2
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 also be 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
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

Relative 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 functionally 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
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.
Show Inner Orbits
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 1st 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
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2 2 2
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3
C 1s 2s 2p 4 3×sp2 + pz or 4× sp
N 1s2 2s2 2p3 3 (4 when protonated) 3×sp2 + pz or 4× sp3
O 1s2 2s2 2p4 2 (3 when protonated) 3×sp2 + pz or 4× sp3
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 sp orbitals from an s orbital
2
and two p orbitals. The three sp orbitals all lie in the same plane and are 120o from each other. The bottom section
2
show the generation of four sp orbitals from an s orbital and three p orbitals. The resultant sp orbitals form a
3 3
tetrahedron, with an angle of 109o between each orbital.
Visualizing Molecules in 3D with JSMol (JMol)

An important component of understanding the function of biological molecules is to
understand the spatial organization of interacting molecules. There are many software
packages that can be used to accomplish this. JSMol is used in this course because it can be
embedded into web pages. It is also possible to run JSMol in a stand-alone configuration,
independent of a web-browser. You can learn more about JSMol by visiting the following
Web site: jmol.sourceforge.net (http://jmol.sourceforge.net/)
JSMol is a very powerful software package and we will only use some of its functionality in
this course. You can learn more about how to use JSMol by visiting the following tutorial
guide: JSMol Tutorial (http://www.andrew.cmu.edu/user/rule/jsmol/jsmol_tutorial.html)
Two useful commands are:
Action Command (PC)
Rotate molecule Left mouse
Zoom Center mouse wheel
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. Planar
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
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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
Important 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(/jcourse/wo
(/jcourse/webui/syllabus/module.do? 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.
2D structural models of examples from the selected functional group appear in the right
panel.
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.
PROPERTIES FUNCTIONAL GROUPS
Non-Polar
? Choose Example:
This location will contain a brief description of the
?
Polar functional group you select.
?
Neutral
?
Charged
?
Hydrophilic
?
Hydrophobic
?
Amphipathic
Review
Did I Get This
Bonding and Functional Groups
Most (but not all) of the important functional groups on biological molecules
contain oxygen and(or) nitrogen and are acidic.
contain oxygen and a phosphate.
contain nitrogen and a phosphate.
contain oxygen and(or) nitrogen and are polar.
contain oxygen and(or) nitrogen and are nonpolar.
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Introduction To Biochemistry, Chirality, & Functional Groups

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Biochemistry (Open + Free)

Muhammad Awais (/jcourse/webui/myaccount/edit.do?user=ststa.2022@gmail.com)

Module 1 - Introduction and Water Structure Search

1. Introduction to Biochemistry, Chirality, & Functional

Provide a general overview of biochemistry based on component parts.

Describe molecular orbitals.

Characterize functional groups.

Recognize chiral centers.

Every cell on Earth belongs to one of two categories:

Typical Animal Cell (Eukaryotic) Bacteria Cell (Prokaryotic)

Note: these images are not drawn to scale. A typical eukaryotic

nucleus Contains DNA in the form of chromosomes

smooth endoplasmic reticulium Site of lipid synthesis

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

Information flow in Living Organisms

Cell Biology and Genetic Background

are the site of photosynthesis

are the site of protein synthesis

are never bound to membranes

Reset this Activity

Chemical Bonding and Biochemical Structures

Show Inner Orbits

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

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

Visualizing Molecules in 3D with JSMol (JMol)

Two useful commands are:

Action Command (PC)

Rotate molecule Left mouse

Zoom Center mouse wheel

Chirality of Chloro-Fluoro Methane

Chirality of Chloro-Fluoro-Bromo Methane

Is it possible to superimpose one molecule on to

Reset this Activity

Functional Group Tutorial

Bonding and Functional Groups

contain oxygen and(or) nitrogen and are acidic.

contain oxygen and a phosphate.

contain nitrogen and a phosphate.

contain oxygen and(or) nitrogen and are polar.

contain oxygen and(or) nitrogen and are nonpolar.

Reset this Activity

(http://creativecommons.org/licenses/by-nc-sa/3.0/)Unless otherwise noted this work

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