Chapter 5: Inorganic Compound

Inorganic compound

An inorganic compound can be considered as a compound that does not contain a carbon-to-

hydrogen bond, also called a C-H bond. Moreover, inorganic compounds tend to be minerals or
geologically-based compounds that do not contain carbon-to-hydrogen bonds. Not all, but most inorganic
compounds contain a metal. That said, there are countless compounds that fall under the realm of
inorganic. In fact, the majority of all compounds in this universe are inorganic in nature. For this reason,
inorganic compounds have an overwhelming amount of applications and practical uses in the real world.
Since most of the compounds in this world are inorganic, these compounds can take on a host of forms
and possess many different characteristics.

Acid Base Balance

Your blood needs the right balance of acidic and basic (alkaline) compounds to function properly. This is
called the acid-base balance. Your kidneys and lungs work to maintain the acid-base balance. Even slight
variations from the normal range can have significant effects on your vital organs. Acid and alkaline levels
are measured on a pH scale. An increase in acidity causes pH levels to fall. An increase in alkaline
causes pH levels to rise.

When the levels of acid in your blood are too high, it’s called acidosis. When your blood is too
alkaline, it is called alkalosis. Respiratory acidosis and alkalosis are due to a problem with the lungs.
Metabolic acidosis and alkalosis are due to a problem with the kidneys.

Electrolutes

Electrolytes are minerals in your body that have an electric charge. They are in your blood, urine,
tissues, and other body fluids. Electrolytes are important because they help

 Balance the amount of water in your body

 Balance your body's acid/base (pH) level

 Move nutrients into your cells

 Move wastes out of your cells

 Make sure that your nerves, muscles, the heart, and the brain work the way they should

Sodium, calcium, potassium, chloride, phosphate, and magnesium are all electrolytes. You get them from
the foods you eat and the fluids you drink.
The levels of electrolytes in your body can become too low or too high. This can happen when the amount
of water in your body changes. The amount of water that you take in should equal the amount you lose. If
something upsets this balance, you may have too little water (dehydration) or too much water
(overhydration). Some medicines, vomiting, diarrhea, sweating, and liver or kidney problems can all upset
your water balance.
Organic Compound

An organic compound is defined as any compound whose molecules contain carbon and hydrogen
( also known as ” hydrocarbons” ) or compound that is the derivative of it. The branch of science which deals
with the scientific study of structure, properties and reactions of hydrocarbons and their derivatives is known
as organic chemistry.

The general characteristics of Organic Compounds include:

 Can be isolated as well as prepared in laboratory

 Comprise almost 90% of all known compounds.

 Mostly built up of only three elements- carbon, hydrogen and oxygen. Other elements like halogen,
nitrogen as well as phosphorous are also present but to a lesser extent.

 Possess complex structures and high molecular weights

 Their properties are decided by certain active atom or

group of atoms known as the functional group.

 They are mostly insoluble in water but soluble in organic

solvents.

 They are combustible in nature

 Chemical reactions involving organic compounds

proceed at slower rates.

Characteristics due to Presence of Covalent Bonds

Importance of Organic Compounds

 Organic compounds are important because all living

organisms contain carbon.

 While carbohydrates, proteins and fats, the basic structures of life, are organic compounds

 They are the basic components of many of the cycles that drive the earth. For example,
the carbon cycle that includes the exchange of carbon between plants and animals in photosynthesis
and cellular respiration.

 Organic compounds combine with metals to form organometallic compounds. These

compounds are important industrially. They are used as catalysts, promoters, analysers as well as
stabilizers.

Protein

Proteins are biological polymers composed of amino acids. Amino acids, linked together by peptide

bonds, form a polypeptide chain. One or more polypeptide chains twisted into a 3-D shape form a protein.
Proteins have complex shapes that include various folds, loops, and curves. Folding in proteins happens
spontaneously. Chemical bonding between portions of the polypeptide chain aid in holding the protein
together and giving it its shape. There are two general classes of protein molecules: globular proteins and
fibrous proteins. Globular proteins are generally compact, soluble, and spherical in shape. Fibrous
proteins are typically elongated and insoluble. Globular and fibrous proteins may exhibit one or more of
four types of protein structure. 
Four Types of Protein Structure

1. Primary Structure

Primary Structure describes the unique order in which amino acids are linked together to form a protein.
Proteins are constructed from a set of 20 amino acids. Generally, amino acids have the following
structural properties:

 A carbon (the alpha carbon) bonded to the four groups below:

 A hydrogen atom (H)
 A Carboxyl group (-COOH)
 An Amino group (-NH2)
 A "variable" group or "R" group

2. Secondary Structure
Secondary Structure refers to the coiling or folding of a polypeptide chain that gives the protein its 3-D
shape. There are two types of secondary structures observed in proteins. One type is the alpha (α)
helix structure. This structure resembles a coiled spring and is secured by hydrogen bonding in the
polypeptide chain. The second type of secondary structure in proteins is the beta (β) pleated sheet. This
structure appears to be folded or pleated and is held together by hydrogen bonding between polypeptide
units of the folded chain that lie adjacent to one another.
3. Tertiary Structure
Tertiary Structure refers to the comprehensive 3-D structure of the polypeptide chain of a protein. There
are several types of bonds and forces that hold a protein in its tertiary structure. 
4. Quaternary Structure
Quaternary Structure refers to the structure of a protein macromolecule formed by interactions between
multiple polypeptide chains. Each polypeptide chain is referred to as a subunit. Proteins with quaternary
structure may consist of more than one of the same type of protein subunit. They may also be composed
of different subunits. Hemoglobin is an example of a protein with quaternary structure. Hemoglobin, found
in the blood, is an iron-containing protein that binds oxygen molecules. It contains four subunits: two
alpha subunits and two beta subunits.
Carbohydrate
Carbohydrates are the sugars, starches and fibers found in fruits, grains, vegetables and milk
products. Though often maligned in trendy diets, carbohydrates — one of the basic food groups — are
important to a healthy diet.
Carbohydrates provide fuel for the central nervous system and energy for working muscles. They
also prevent protein from being used as an energy source and enable fat metabolism, according to Iowa
State University.

Also, "carbohydrates are important for brain function," Smathers said. They are an influence on
"mood, memory, etc., as well as a quick energy source." In fact, the RDA of carbohydrates is based on
the amount of carbs the brain needs to function.

Lipids

Lipids are molecules that contain hydrocarbons and make up the building blocks of the structure
and function of living cells. Examples of lipids include fats, oils, waxes, certain vitamins (such as A, D, E
and K), hormones and most of the cell membrane that is not made up of protein. Lipids are not soluble in
water as they are non-polar, but are thus soluble in non-polar solvents such as chloroform.

The functions of lipids include storing energy, signaling, and acting as structural components
of cell membranes.[4][5] Lipids have applications in the cosmetic and food industries as well as
in nanotechnology.[6]

Nucleic Acid

Nucleic acid, naturally occurring chemical compound that is capable of being broken down to

yield phosphoric acid, sugars, and a mixture of organic bases (purines and pyrimidines). Nucleic acids are
the main information-carrying molecules of the cell, and, by directing the process of protein synthesis,
they determine the inherited characteristics of every living thing. The two main classes of nucleic acids
are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the master blueprint for life
and constitutes the genetic material in all free-living organisms and most viruses. RNA is the genetic
material of certain viruses, but it is also found in all living cells, where it plays an important role in certain
processes such as the making of proteins.

Nucleic acids are molecules that store and transmit hereditary information and energy in living
things. They are believed to be the first biomolecules to support life as it is typically defined.

Enzyme as Catalyst

Enzymes are proteins that have a specific function. They speed up the rate of chemical reactions
in a cell or outside a cell. Enzymes act as catalysts; they do not get consumed in the chemical reactions
that they accelerate. Why do cells need a catalyst? Cells use a lot of energy! There are thousands of
reactions that take place in cells and these require energy. Since energy is always limiting in a living cell,
cells have adopted enzymes as a way to conserve energy. Insufficient energy is a barrier to initiating the
reaction. Only when there is a sufficient amount of energy, can the reactant overcome the energy barrier
and proceed to form a product. This is called the activation energy.

How do catalysts speed up chemical reactions? In biological systems, the energy required to make a
reaction go is stored primarily in the bonds that make up adenosine triphosphate (ATP). Specifically, the
energy is stored in the bonds between phosphate groups and the nucleotide, adenosine. Energy (~7
kcal/mole) is released when one of the phosphate bonds in ATP to form adenosine diphosphate (ADP) is
broken. This is equivalent to the amount of energy in a peanut. A catalyst lowers the barrier for the
activation energy. For example, ethanol is metabolized into acetaldehyde by the enzyme, alcohol
dehydrogenase. In the absence of ADH, the rate of the reaction would be less than 0.000006 (or 6 x 10-6)
µmoles/L per minute. While in the presence of ADH, the reaction rate is 2700 µmoles/L per minute. That’s
an acceleration of more than 4500 million times!

Chapter 6: Cellular Respiration

 Cellular Respiration

Cellular respiration is the set of reactions that produces ATP. ATP, quite possibly the most
talked about molecule in biology, is our energy currency.
Cellular respiration uses glucose to produce the ATP our body needs to perform
essential functions. I am going to treat this as an overview article and I will do separate, more detailed
articles on each part.
Cellular respiration can be divided into three parts: glycolysis, the citric acid cycle and electron
transport chain. This article will give you the basics in order to better understand the more detailed stuff.
And believe me, cellular respiration can get pretty complicated.
Cellular respiration is the process of oxidizing food molecules, like glucose, to carbon dioxide
and water.

C6H12O6 + 6O2 + 6H2O → 12H2O + 6 CO2

The energy released is trapped in the form of ATP for use by all the energy-consuming activities of the
cell.

The process occurs in two phases:

 glycolysis, the breakdown of glucose to pyruvic acid

 the complete oxidation of pyruvic acid to carbon dioxide and water

In eukaryotes, glycolysis occurs in the cytosol. (Link to a discussion of glycolysis). The remaining
processes take place in mitochondria

Anaerobic Respiration

Anaerobic respiration is the process of creating energy without the presence

of oxygen. Sometimes the body can’t supply the muscles with the oxygen it needs to create energy –
such as in a sprinting situation. Without the process of anaerobic respiration there may be no energy
supplied to muscles in times of high demand.

Fermentation

Fermentation, chemical process by which molecules such as glucose are broken down

anaerobically. More broadly, fermentation is the foaming that occurs during the manufacture
of wine and beer, a process at least 10,000 years old. The frothing results from the evolution of carbon
dioxide gas, though this was not recognized until the 17th century. French chemist and
microbiologist Louis Pasteur in the 19th century used the term fermentation in a narrow sense to describe
the changes brought about by yeasts and other microorganisms growing in the absence of air
(anaerobically); he also recognized that ethyl alcohol and carbon dioxide are not the only products of
fermentation.

Lactic Acid

Lactic acid is mainly produced in muscle cells and red blood cells. It forms when the body breaks
down carbohydrates to use for energy when oxygen levels are low. Times when your body's oxygen level
might drop include:

 During intense exercise

 When you have an infection or disease

A test can be done to measure the amount of lactic acid in the blood.

Alcohol Fermentation

Alcohol fermentation, also known as ethanol fermentation, is the anaerobic pathway carried out
by yeasts in which simple sugars are converted to ethanol and carbon dioxide. Yeasts typically function
under aerobic conditions, or in the presence of oxygen, but are also capable of functioning under
anaerobic conditions, or in the absence of oxygen. When no oxygen is readily available, alcohol
fermentation occurs in the cytosol of yeast cells. Let's explore the process of alcohol fermentation then
see what it means for yeasts and for humans.

Photosynthesis

Photosynthesis is the process by which plants, some bacteria and some protistans use the
energy from sunlight to produce glucose from carbon dioxide and water. This glucose can be converted
into pyruvate which releases adenosine triphosphate (ATP) by cellular respiration. Oxygen is also formed.

Photosynthesis may be summarised by the word equation:

carbon dioxide + water glucose + oxygen

The conversion of usable sunlight energy into chemical energy is associated with the action of the green
pigment chlorophyll.

Chlorophyll is a complex molecule. Several modifications of chlorophyll occur among plants and other
photosynthetic organisms. All photosynthetic organisms have chlorophyll a. Accessory pigments absorb
energy that chlorophyll a does not absorb. Accessory pigments include chlorophyll b (also c, d, and e in
algae and protistans), xanthophylls, and carotenoids (such as beta-carotene). Chlorophyll a absorbs its
energy from the violet-blue and reddish orange-red wavelengths, and little from the intermediate (green-
yellow-orange) wavelengths.

Energy Absorption and Reactivation

The activation energy of a chemical reaction is kind of like that “hump” you have to get over to get
yourself out of bed. Even energy-releasing (exergonic) reactions require some amount of energy input to
get going, before they can proceed with their energy-releasing steps. This initial energy input, which is
later paid back as the reaction proceeds, is called the activation energy and is abbreviated \text E_{\text
A}EAstart text, E, end text, start subscript, start text, A, end text, end subscript.

Activation energy

Why would an energy-releasing reaction with a negative ∆G need energy to proceed? To understand this,

we need to look at what actually happens to reactant molecules during a chemical reaction. In order for

the reaction to take place, some or all of the chemical bonds in the reactants must be broken so that new

bonds, those of the products, can form. To get the bonds into a state that allows them to break, the

molecule must be contorted (deformed, or bent) into an unstable state called the transition state. The

transition state is a high-energy state, and some amount of energy – the activation energy – must be
added in order for the molecule reach it. Because the transition state is unstable, reactant molecules don’t

stay there long, but quickly proceed to the next step of the chemical reaction.

In general, the transition state of a reaction is always at a higher energy level than the reactants or

products, such that \text E_{\text A}EAstart text, E, end text, start subscript, start text, A, end text, end

subscript always has a positive value – independent of whether the reaction is endergonic or exergonic

overall. The activation energy shown in the diagram below is for the forward reaction

(reactants \rightarrow→right arrow products), which is exergonic. If the reaction were to proceed in the

reverse direction (endergonic), the transition state would remain the same, but the activation energy

would be larger. This is because the product molecules are lower-energy and would thus need more

energy added to reach the transition state at the top of the reaction “hill.” (An activation energy arrow for

the reverse reaction would extend from the products up to the transition state.)

Reaction coordinate diagram for an exergonic reaction. Although the products are at a lower energy level

than the reactants (free energy is released in going from reactants to products), there is still a "hump" in

the energetic path of the reaction, reflecting the formation of the high-energy transition state. The

activation energy for the forward reaction is the amount of free energy that must be added to go from the

energy level of the reactants to the energy level of the transition state.

The source of activation energy is typically heat, with reactant molecules absorbing thermal energy from

their surroundings. This thermal energy speeds up the motion of the reactant molecules, increasing the

frequency and force of their collisions, and also jostles the atoms and bonds within the individual

molecules, making it more likely that bonds will break. Once a reactant molecule absorbs enough energy

to reach the transition state, it can proceed through the remainder of the reaction.
Activation energy and reaction rate

The activation energy of a chemical reaction is closely related to its rate. Specifically, the higher the

activation energy, the slower the chemical reaction will be. This is because molecules can only complete

the reaction once they have reached the top of the activation energy barrier. The higher the barrier is, the

fewer molecules that will have enough energy to make it over at any given moment. 

[Why do some molecules have more energy than others?]

Many reactions have such high activation energies that they basically don't proceed at all without an input

of energy. For instance, the combustion of a fuel like propane releases energy, but the rate of reaction is

effectively zero at room temperature. (To be clear, this is a good thing – it wouldn't be so great if propane

canisters spontaneously combusted on the shelf!) Once a spark has provided enough energy to get some

molecules over the activation energy barrier, those molecules complete the reaction, releasing energy.

The released energy helps other fuel molecules get over the energy barrier as well, leading to a chain

reaction.

Most chemical reactions that take place in cells are like the hydrocarbon combustion example: the

activation energy is too high for the reactions to proceed significantly at ambient temperature. At first, this

seems like a problem; after all, you can’t set off a spark inside of a cell without causing damage.

Fortunately, it’s possible to lower the activation energy of a reaction, and to thereby increase reaction

rate. The process of speeding up a reaction by reducing its activation energy is known as catalysis, and

the factor that's added to lower the activation energy is called a catalyst. Biological catalysts are known

as enzymes, and we’ll examine them in detail in the next section.

Independent Reaction

After the energy from the sun is converted and packaged into ATP and NADPH, the cell has the
fuel needed to build carbohydrate molecules. The carbohydrate molecules made will have a backbone of
carbon atoms. Where does the carbon come from? The carbon atoms used to build carbohydrate
molecules comes from carbon dioxide, which diffuses into the leaves through the stomata. The Calvin
cycle is the term used for the reactions of photosynthesis that use the energy stored by the light-
dependent reactions to form glucose and other carbohydrate molecules.
Carbon Fixation

The assimilation of carbon into organic compounds is the result of a complex series of

enzymatically regulated chemical reactions—the dark reactions. This term is something of a misnomer,
for these reactions can take place in either light or darkness. Furthermore, some of the enzymes involved
in the so-called dark reactions become inactive in prolonged darkness; however, they are activated when
the leaves that contain them are exposed to light.

C3 

Chapter 1: The Introduction to Cell Biology

Cell

the smallest structural and functional unit of an organism, typically microscopic and
consisting of cytoplasm and a nucleus enclosed in a membrane. Microscopic organisms
typically consist of a single cell, which is either eukaryotic or prokaryotic

Cell Theory

 Cell theory is the historic scientific theory, now universally accepted, that living organisms are
made up of cells, that they are the basic structural/organizational unit of all organisms, and that all cells
come from pre-existing cells. Cells are the basic unit of structure in all organisms and also the basic unit
of reproduction. With continual improvements made to microscopesover time, magnification technology
advanced enough to discover cells in the 17th century. This discovery is largely attributed to Robert
Hooke, and began the scientific study of cells, also known as cell biology. Over a century later, many
debates about cells began amongst scientists. Most of these debates involved the nature of cellular
regeneration, and the idea of cells as a fundamental unit of life. Cell theory was eventually formulated in
1839. This is usually credited to Matthias Schleiden and Theodor Schwann. However, many other
scientists like Rudolf Virchow contributed to the theory. It was an important step in the movement away
from spontaneous generation.

Cell Types

Prokaryotes

Prokaryotes are the simpler and older of the two major types of cells.
Prokaryotes are single-celled organisms. Bacteria and archaebacteria are
examples of prokaryotic cells.

Prokaryotic cells have a cell membrane, and one or more layers of

additional protection from the outside environment. Many prokaryotes have a cell
membrane made of phospholipids, enclosed by a cell wall made of a rigid sugar.
The cell wall may be enclosed by another thick “capsule” made of sugars.

Many prokaryotic cells also have cilia, tails, or other ways in which the cell
can control its movement.

Eukaryotes
 Eukaryotic cells are thought to be the most modern major cell type. All
multicellular organisms, including you, your cat, and your houseplants, are
eukaryotes. Eukaryotic cells seem to have “learned” to work together to create
multicellular organisms, while prokaryotes seem unable to do this.

Eukaryotic cells usually have more than one chromosome, which contains
large amounts of genetic information. Within the body of a multicellular
organism, different genes within these chromosomes may be switched “on” and
“off,” allowing for cells that have different traits and perform different functions
within the same organism.

Eukaryotic cells also have one or more internal membranes, which has led
scientists to the conclusion that eukaryotic cells likely evolved when one or more
types of prokaryote began living in symbiotic relationships inside of other cells.

Organelles with interior membranes found in eukaryotic cells typically include:

 For animal cells – Mitochondria, which liberate the energy from sugar
and turn it into ATP in an extremely efficient way.
Mitochondria even have their own DNA, separate from the cells’ nuclear
DNA, which gives further support for the theory that they used to be
independent bacteria.
 For plant cells – Chloroplasts, which perform photosynthesis, making
ATP and sugar from sunlight and air.
Chloroplasts also have their own DNA, suggesting that they may have
originated as photosynthetic bacteria.
 Nucleus – In eukaryotic cells, the nucleus contains the essential DNA
blueprints and operating instructions for the cell.
The nuclear envelope is thought to provide an extra layer of protection
for the DNA against toxins or invaders which might damage it.
It is unknown whether the nucleus might also have been an
endosymbiotic prokaryote at one time, or whether its membrane simply
evolved as an extra layer of protection for the cell’s DNA.
 Endoplasmic reticulum – This complex internal membrane is a major
site of protein creation for cells. The evolutionary origin of the
endoplasmic reticulum is not known.
 Golgi apparatus – This internal membrane complex can be thought of
like the endoplasmic reticulum’s “post office.” It receives proteins from
the ER, packages and “labels” them by attaching sugars as needed, and
then ships them off to their final destinations!
  Others – Many eukaryotic cells can create temporary internal membrane
“sacs,” called “vacuoles,” to store waste, or to package important
materials.
Some cells, for example have special vacuoles called “lysosomes” which
are full of corrosive substances and digestive enzymes. Cells simply
dump their “trash” into lysosomes, where the harsh environment breaks
them down into simpler components that can be re-used!

Cell Organelles