INTRODUCTION TO BIOCHEMISTRY

Biochemistry is the science in which chemistry is applied to the study of living organisms and the atoms and
molecules which comprise living organisms. Take a closer look at what biochemistry is and why the science is
important.

What Is Biochemistry?

Biochemistry is the study of the chemistry of living things. This includes organic molecules and their chemical
reactions. Most people consider biochemistry to be synonymous with molecular biology.

What Types of Molecules Do Biochemists Study?

The principal types of biological molecules or biomolecules are:

 carbohydrates
 lipids
 proteins
 nucleic acids

Many of these molecules are complex molecules called polymers, which are made up of monomer subunits.
Biochemical molecules are based on carbon.

What Is Biochemistry Used For?

 Biochemistry is used to learn about the biological processes which take place in cells and organisms.
 Biochemistry may be used to study the properties of biological molecules, for a variety of purposes. For
example, a biochemist may study the characteristics of the keratin in hair so that a shampoo may be
developed that enhances curliness or softness.
 Biochemists find uses for biomolecules. For example, a biochemist may use a certain lipid as a food additive.
 Alternatively, a biochemist might find a substitute for a usual biomolecule. For example, biochemists help to
develop artificial sweeteners.
 Biochemists can help cells to produce new products. Gene therapy is within the realm of biochemistry. The
development of biological machinery falls within the realm of biochemistry.

What Does a Biochemist Do?

Many biochemists work in chemistry labs. Some biochemists may focus on modeling, which would lead them to work
with computers. Some biochemists work in the field, studying a biochemical system in an organism. Biochemists
typically are associated with other scientists and engineers. Some biochemists are associated with universities and
they may teach in addition to conducting research. Usually, their research allows them to have a normal work
schedule, based in one location, with a good salary and benefits.

What Disciplines Are Related to Biochemistry?

Biochemistry is closely related to other biological sciences that deal with molecules. There is considerable overlap
between these disciplines:

 Molecular Genetics
 Pharmacology
 Molecular Biology
 Chemical Biology

Carbohydrates or saccharides are the most abundant class of biomolecules. Carbohydrates are used to store energy,
though they serve other important functions as well. This is an overview of carbohydrate chemistry, including a look
at the types of carbohydrates, their functions, and carbohydrate classification.
List of Carbohydrates Elements

All carbohydrates contain the same three elements, whether the carbohydrates are simple sugars, starches, or
other polymers. These elements are:

 carbon (C)
 hydrogen (H)
 oxygen (O)

Different carbohydrates are formed by the way these elements bond to each other and the number of each type of
atom. Usually, the ratio of hydrogen atoms to oxygen atoms is 2:1, which is the same as the ratio in water.

What Is a Carbohydrate?

The word "carbohydrate" comes from the Greek word sakharon, which means "sugar". In chemistry, carbohydrates
are a common class of simple organic compounds. A carbohydrate is an aldehyde or a ketone that has additional
hydroxyl groups. The simplest carbohydrates are called monosaccharides, which have the basic structure (C·H2O)n,
where n is three or greater. Two monosaccharides link together to form a disaccharide. Monosaccharides and
disaccharides are called sugars and typically have names ending with the suffix -ose. More than two monosaccharides
link together to form oligosaccharides and polysaccharides.

In everyday usage, the word "carbohydrate" refers to any food that contains a high level of sugars or starch. In this
context, carbohydrates include table sugar, jelly, bread, cereal, and pasta, even though these foods may contain other
organic compounds. For example, cereal and pasta also contain some level of protein.

Functions of Carbohydrates

Carbohydrates serve several biochemical functions:

 Monosaccharides are a fuel for cellular metabolism.

 Monosaccharides are used in several biosynthesis reactions.
 Monosaccharides may be converted into space-saving polysaccharides, such as glycogen and starch. These
molecules provide stored energy for plant and animal cells.
 Carbohydrates are used to form structural elements, such as chitin in animals and cellulose in plants.
 Carbohydrates and modified carbohydrates are important for an organism's fertilization, development,
blood clotting and immune system function.

Carbohydrate Classification

Three characteristics are used to classify monosaccharides:

 number of carbon atoms in the molecule

 location of the carbonyl group
 the chirality of the carbohydrate

aldose - monosaccharide in which the carbonyl group is an aldehyde

ketone - monosaccharide in which the carbonyl group is a ketone

triose - monosaccharide with 3 carbon atoms

tetrose - monosaccharide with 4 carbon atoms

pentose - monosaccharide with 5 carbon atoms

hexose - monosaccharide with 6 carbon atoms

aldohexose - 6-carbon aldehyde (e.g., glucose)

aldopentose - 5-carbon aldehyde (e.g., ribose)

ketohexose - 6-carbon hexose (e.g., fructose)

A monosaccharide is D or L depending on the orientation of the asymmetric carbon located furthest from the
carbonyl group. In a D sugar, the hydroxyl group is on the right the molecule when written as a Fischer projection. If
the hydroxyl group is on the left of the molecule, then it is an L sugar.

Lipids are a diverse group of fat-soluble biological molecules. Each major type has distinct properties and is found in
certain locations.

Triacylglycerols or Triglycerides

The largest class of lipids goes by different names: triacylglycerols, triglycerides, glycerolipids, or fats.

 Location: Fats are found in many places. One well-known form of fat is found in human and animal tissue.
 Function: The primary function of fats is energy storage. Some animals, such as polar bears, can live off
their fat stores for months at a time. Fats also provide insulation, protecting delicate organs and generating
warmth.

 Example: Margarine, a butter substitute, is made from vegetable oils and sometimes animal fats (typically
beef tallow). Most margarines have a fat content of about 80 percent.

Steroids

All steroids are hydrophobic molecules derived from a common four fused carbon ring structure.

 Location: Cellular membrane, digestive system, endocrine system.

 Function: In animals, many steroids are hormones, which enter cells and initiate specific chemical
reactions. These hormones include the androgens and estrogens, or sex hormones, along with
corticosteroids such as cortisol, which is produced by stress. Other hormones exist as part of various
organisms' cellular structures, adding fluidity to cellular membranes.
 Example: The most common steroid is cholesterol. Cholesterol is a precursor for making other steroids.
Other examples of steroids include bile salts, estrogen, testosterone, and cortisol.

Phospholipids

Phospholipids are derivatives of triglycerides that consist of a glycerol molecule with two fatty acids, a phosphate
group on the third carbon, and often an additional polar molecule. The diglyceride portion of a phospholipid is
hydrophobic, while the phosphate is hydrophilic.

 Location: Cell membrane.
 Function: Phospholipids form the basis of cellular membranes, which play a significant role in regulating
homeostasis.
 Example: Phospholipid bilayer of the cellular membrane.
  Proteins are very important molecules in our cells and are essential for all living organisms. By weight,
proteins are collectively the major component of the dry weight of cells and are involved in virtually all cell
functions.
 Each protein within the body has a specific function, from cellular support to cell signaling and cellular
locomotion. In total, there are seven types of proteins, including antibodies, enzymes, and some types
of hormones, such as insulin.
 While proteins have many diverse functions, all are typically constructed from one set of 20 amino acids. The
structure of a protein may be globular or fibrous, and the design helps each protein with their
particular function.
 In all, proteins are absolutely fascinating and a complex subject. Let's explore the basics of these essential
molecules and discover what they do for us.

Antibodies

Antibodies are specialized proteins involved in defending the body from antigens (foreign invaders). They can travel
through the bloodstream and are utilized by the immune system to identify and defend against bacteria, viruses, and
other foreign intruders. One way antibodies counteract antigens is by immobilizing them so they can be destroyed
by white blood cells.

Contractile Proteins

Contractile proteins are responsible for muscle contraction and movement. Examples of these proteins include actin
and myosin.

Enzymes

Enzymes are proteins that facilitate biochemical reactions. They are often referred to as catalysts because they speed
up chemical reactions. Enzymes include lactase and pepsin, which you might hear of often when learning about
specialty diets or digestive medical conditions.

Lactase breaks down the sugar lactose found in milk. Pepsin is a digestive enzyme that works in the stomach to break
down proteins in food.

Hormonal Proteins

Hormonal proteins are messenger proteins which help to coordinate certain bodily activities. Examples include
insulin, oxytocin, and somatotropin.

Insulin regulates glucose metabolism by controlling the blood-sugar concentration. Oxytocin stimulates contractions
during childbirth. Somatotropin is a growth hormone that stimulates protein production in muscle cells.

Structural Proteins

Structural proteins are fibrous and stringy and because of this formation, they provide support for various body parts.
Examples include keratin, collagen, and elastin.

Keratins strengthen protective coverings such as skin, hair, quills, feathers, horns, and beaks. Collagens and elastin
provide support for connective tissues such as tendons and ligaments.

Storage Proteins

Storage proteins store amino acids for the body to use later. Examples include ovalbumin, which is found in egg
whites, and casein, a milk-based protein. Ferritin is another protein that stores iron in the transport protein,
hemoglobin.

Transport Proteins
Transport proteins are carrier proteins which move molecules from one place to another around the body.
Hemoglobin is one of these and is responsible for transporting oxygen through the blood via red blood cells.
Cytochromes are another that operate in the electron transport chain as electron carrier proteins.

Amino Acids and Polypeptide Chains

Amino acids are the building blocks of all proteins, no matter their function. Most amino acids follow a particular
structural property in which a carbon (the alpha carbon) is bonded to four different groups:

 A hydrogen atom (H)

 A Carboxyl group (-COOH)
 An Amino group (-NH2)
 A "variable" group

Of the 20 amino acids that typically make up proteins, the "variable" group determines the differences among the
amino acids. All amino acids have the hydrogen atom, carboxyl group, and amino group bonds.

Amino acids are joined together through dehydration synthesis to form a peptide bond. When a number of amino
acids are linked together by peptide bonds, a polypeptide chain is formed. One or more polypeptide chains twisted
into a 3-D shape forms a protein.

Protein Structure

We can divide the structure of protein molecules into two general classes: 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 types of protein structure. 

There are four levels of protein structure: primary, secondary, tertiary, and quaternary. These levels are distinguished
from one another by the degree of complexity in the polypeptide chain.

A single protein molecule may contain one or more of these protein structure types. The structure of a protein
determines its function. For example, collagen has a super-coiled helical shape. It is long, stringy, strong, and
resembles a rope, which is great for providing support. Hemoglobin, on the other hand, is a globular protein that is
folded and compact. Its spherical shape is useful for maneuvering through blood vessels.

In some cases, a protein may contain a non-peptide group. These are called cofactors and some, such as coenzymes,
are organic. Others are an inorganic group, such as a metal ion or iron-sulfur cluster.

Protein Synthesis

Proteins are synthesized in the body through a process called translation. Translation occurs in the cytoplasm and
involves the translation of genetic codes into proteins.

The gene codes are assembled during DNA transcription, where DNA is transcribed into an RNA transcript. Cell
structures called ribosomes help translate the gene codes in RNA into polypeptide chains that undergo several
modifications before becoming fully functioning proteins.

Nucleic Acid Facts

If you're taking general chemistry, organic, or biochemistry, you'll need to understand some basic concepts about
nucleic acids, the polymers used to code the genetic information of organisms. Here are some quick nucleic acid facts
to get you started:

 Nucleic acids are the molecules that code the genetic information of 
  The two nucleic acids used in the repair, reproduction and protein synthesis are deoxyribonucleic acid (DNA,
shown) and ribonucleic acid (RNA).

 DNA and RNA are polymers made up of monomers called nucleotides.

 A DNA molecule is a double helix made up of two strands of polymers that are complementary to each other,
but not identical. Hydrogen bonding holds the base pairs of the two strands together.
 RNA is used to direct the production of proteins by the cell.

DNA vs RNA
Transcription
Translation
10 RNA Facts
10 DNA Facts

The Differences Between DNA and RNA

DNA stands for deoxyribonucleic acid, while RNA is ribonucleic acid. Although DNA and RNA both carry genetic
information, there are quite a few differences between them. This is a comparison of the differences between DNA
versus RNA, including a quick summary and a detailed table of the differences.

Summary of Differences Between DNA and RNA

1. DNA contains the sugar deoxyribose, while RNA contains the sugar ribose. The only difference between
ribose and deoxyribose is that ribose has one more -OH group than deoxyribose, which has -H attached to
the second (2') carbon in the ring.

1. DNA is a double-stranded molecule while RNA is a single stranded molecule.

2. DNA is stable under alkaline conditions while RNA is not stable.
3. DNA and RNA perform different functions in humans. DNA is responsible for storing and
transferring genetic information while RNA directly codes for amino acids and as acts as a messenger
between DNA and ribosomes to make proteins.
4. DNA and RNA base pairing is slightly different since DNA uses the bases adenine, thymine, cytosine, and
guanine; RNA uses adenine, uracil, cytosine, and guanine. Uracil differs from thymine in that it lacks a
methyl group on its ring.
 5. DNA and RNA base pairing is slightly different since DNA uses the bases adenine, thymine, cytosine, and
guanine; RNA uses adenine, uracil, cytosine, and guanine. Uracil differs from thymine in that it lacks a
methyl group on its ring.

Comparison of DNA and RNA

While both DNA and RNA are used to store genetic information, there are clear differences between them. This table
summarizes the key points:

Comparison DNA RNA

Name DeoxyriboNucleic Acid RiboNucleic Acid

Function Long-term storage of genetic information;
transmission of genetic information to make
other cells and new organisms.
Used to transfer the genetic code from the nucleus to
the ribosomes to make proteins. RNA is used to
transmit genetic information in some organisms and
may have been the molecule used to store genetic
blueprints in primitive organisms.

Structural B-form double helix. DNA is a double- A-form helix. RNA usually is a single-strand helix
Features stranded molecule consisting of a long chain of consisting of shorter chains of nucleotides.
nucleotides.

Composition of deoxyribose sugar ribose sugar

Bases and phosphate backbone phosphate backbone
Sugars adenine, guanine, cytosine, thymine bases adenine, guanine, cytosine, uracil bases

Propagation DNA is self-replicating. RNA is synthesized from DNA on an as-needed

basis.

Base Pairing AT (adenine-thymine) AU (adenine-uracil)

GC (guanine-cytosine) GC (guanine-cytosine)

Reactivity The C-H bonds in DNA make it fairly stable,
plus the body destroys enzymes that would
attack DNA. The small grooves in the helix
also serve as protection, providing minimal
space for enzymes to attach.
The O-H bond in the ribose of RNA makes the
molecule more reactive, compared with DNA. RNA
is not stable under alkaline conditions, plus the large
grooves in the molecule make it susceptible to
enzyme attack. RNA is constantly produced, used,
degraded, and recycled.

Ultraviolet DNA is susceptible to UV damage. Compared with DNA, RNA is relatively resistant to
Damage UV damage.

Which Came First?

While there is some evidence DNA may have occurred first, most scientists believe RNA evolved before DNA. RNA
has a simpler structure and is needed in order for DNA to function. Also, RNA is found in prokaryotes, which are
believed to precede eukaryotes. RNA on its own can act as a catalyst for certain chemical reactions.

The real question is why DNA evolved, if RNA existed. The most likely answer for this is that having a double-
stranded molecule helps protect the genetic code from damage. If one strand is broken, the other strand can serve as a
template for repair. Proteins surrounding DNA also confer additional protection against enzymatic attack.

Unusual DNA and RNA

While the most common form of DNA is a double helix. there is evidence for rare cases of branched DNA, quadruplex
DNA, and molecules made from triple strands. Scientists have found DNA in which arsenic substitutes for
phosphorus.
Double-stranded RNA (dsRNA) sometimes occurs. It is similar to DNA, except thymine is replaced by uracil. This
type of RNA is found in some viruses. When these viruses infect eukaryotic cells, the dsRNA can interfere with normal
RNA function and stimulate an interferon response. Circular single strand RNA (circRNA) has been found in both
animals and plants. At present, the function of this type of RNA is unknown.

Steps of Transcription From DNA to RNA

DNA or deoxyrubonucleic acid is the molecule that codes genetic information. However, DNA can't directly order a
cell to make proteins. It has to be transcribedinto RNA or ribonucleic acid. RNA, in turn, is translated by cellular
machinery to make amino acids, which it joins together to form polypeptides and proteins

Overview of Transcription

Transcription is the first stage of the expression of genes into proteins. In transcription, an mRNA (messenger RNA)
intermediate is transcribed from one of the strands of the DNA molecule. The RNA is called messenger RNA because
it carries the "message," or genetic information, from the DNA to the ribosomes, where the information is used to
make proteins. RNA and DNA use complementary coding where base pairs match up, similar to how the strands of
DNA bind to form a double helix.

One difference between DNA and RNA is that RNA uses uracil in place of the thymine used in DNA. RNA polymerase
mediates the manufacture of an RNA strand that complements the DNA strand. RNA is synthesized in the 5' -> 3'
direction (as seen from the growing RNA transcript). There are some proofreading mechanisms for transcription, but
not as many as for DNA replication. Sometimes coding errors occur.

Differences in Transcription

There are significant differences in the process of transcription in prokaryotes versus eukaryotes.

 In prokaryotes (bacteria), transcription occurs in the cytoplasm. Translation of the mRNA into proteins also
occurs in the cytoplasm. In eukaryotes, transcription occurs in the cell's nucleus. mRNA then moves to the
cytoplasm for translation.
 DNA in prokaryotes is much more accessible to RNA polymerase than DNA in eukaryotes. Eukaryotic DNA
is wrapped around proteins called histones to form structures called nucleosomes. Eukaryotic DNA is packed
to form chromatin. While RNA polymerase interacts directly with prokaryotic DNA, other proteins mediate
the interaction between RNA polymerase and DNA in eukaryotes.
 mRNA produced as a result of transcription is not modified in prokaryotic cells. Eukaryotic cells modify
mRNA by RNA splicing, 5' end capping, and addition of a polyA tail.

Key Takeaways: Steps of Transcription

 The two main steps in gene expression are transcription and translation.
 Transcription is the name given to the process in which DNA is copied to make a complementary strand of
RNA. RNA then undergoes translation to make proteins.
 The major steps of transcription are initiation, promoter clearance, elongation, and termination.

Steps of Transcription

Transcription can be broken into five stages: pre-initiation, initiation, promoter clearance, elongation, and
termination:

Pre-Initiation
The first step of transcription is called pre-initiation. RNA polymerase and cofactors (general transcription factors)
bind to DNA and unwind it, creating an initiation bubble. This space grants RNA polymerase access to a single strand
of the DNA molecule. Approximately 14 base pairs are exposed at a time.

Initiation

The initiation of
transcription in
bacteria begins
with the binding of
RNA polymerase to
the promoter in
DNA. Transcription
initiation is more
complex in
eukaryotes, where a
group of proteins
called transcription
factors mediates
the binding of RNA
polymerase and the
initiation of
transcription.

The next step of

transcription is called promoter clearance or promoter escape. RNA polymerase must clear the promoter once the
first bond has been synthesized. Approximately 23 nucleotides must be synthesized before RNA polymerase loses its
tendency to slip away and prematurely release the RNA transcript.
One strand of DNA serves as the template for RNA synthesis, but multiple rounds of transcription may occur so that
many copies of a gene can be produced.

Termination

Termination is the final step of transcription. Termination results in the release of the newly synthesized mRNA from
the elongation complex. In eukaryotes, the termination of transcription involves cleavage of the transcript, followed
by a process called polyadenylation. In polyadenylation, a series of adenine residues or poly(A) tail is added to the
new 3' end of the end of the messenger RNA strand.

Chemical Reactions

This is a collection of important chemical reactions you may encounter in a chemistry class or in the lab.

Citric Acid Cycle

The Citric Acid Cycle is also known as the Krebs Cycle or Tricarboxylic Acid (TCA) Cycle. It is a series of chemical
reactions that takes place in the cell that breaks down food molecules into carbon dioxide, water, and energy.
Narayanese,

Chemiluminescence Reaction - TCPO

Chemiluminescence Reaction

Saponification (Soap) Reaction

Saponification involves the hydrolysis of an ester to form an alcohol and the salt of a carboxylic acid. Anne
Helmenstine

Translation

Translation is the initial step in the production of proteins by the cell. Translation uses the product of transcription,
mRNA, as the template for constructing a sequence of polypeptides. This is done according to the genetic code. Each
mRNA base signifies a series of three amino acids. The amino acids join to form polypeptides, which are modified to
become proteins.

Translation is done by the ribosomes in a cell's cytoplasm. There are four stages of translation: activation, initiation,
elongation, and termination. These steps describe the growth of the amino acid chain.

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Glycolysis

 Glycolysis is the metabolic process that serves as the foundation for both aerobic and anaerobic cellular respiration.
In glycolysis, glucose is converted into pyruvate. Todd Helmenstine

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Nylon Synthesis - General Reaction

 This is the general reaction for the polymerization of nylon as a result of condensation polymerization of dicarboxylic
acid and diamine. Calvero, Public Domain License

10 RNA Facts

RNA or ribonucleic acid is used to translate instructions from DNA to make proteins in your body. Here are 10
interesting and fun facts about RNA.

1. Each RNA nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate.

2. Each RNA molecule typically is a single strand, consisting of a relatively short chain of nucleotides. RNA can
be shaped like a single helix, a straight molecule, or may be bet or twisted upon itself. DNA, in comparison, is
double-stranded and consists of a very long chain of neucleotides.
3. In RNA, the base adenine binds to uracil. In DNA, adenine binds to thymine. RNA does not contain thymine
— a uracil is an unmethylated form of thymine capable of absorbing light. Guanine binds to cytosine in
both DNA and RNA.
4. There are several types of RNA, including transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal
RNA (rRNA). RNA performs many functions in an organism, such as coding, decoding, regulating, and
expressing genes.
5. About 5% of the weight of a human cell is RNA. Only about 1% of a cell consists of DNA.
6. RNA is found in both the nucleus and cytoplasm of humans cells. DNA is only found in the cell nucleus.
7. RNA is the genetic material for some organisms which don't have DNA. Some viruses contain DNA; many
only contain RNA.
8. RNA is used in some cancer gene therapies to reduce the expression of cancer-causing genes.
9. RNA technology is used to suppress the expression of fruit ripening genes so that fruits can remain on the
vine longer, extending their season and availability for marketing.
10. Friedrich Miescher discovered nucleic acids ('nuclein') in 1868. After that time, scientists realized there were
different types of nucleic acids and different types of RNA, so there is no single person or date for the
discovery of RNA. In 1939, researchers determined RNA is responsible for protein synthesis. In 1959, Severo
Ochoa won the Nobel Prize in Medicine for discovering how RNA is synthesized.

10 Interesting DNA Facts

DNA or deoxyribonucleic acid codes for your genetic make-up. There are lots of facts about DNA, but here are 10 that
are particularly interesting, important, or fun.

Key Takeaways: DNA Facts

 DNA is the acronym for deoxyribonucleic acid.

 DNA and RNA are the two types of nucleic acids the code for genetic information.
 DNA is a double-helix molecule built from four nucleotides: adenine (A), thymine (T), guanine (G), and
cytosine (C).
 Even though it codes for all the information that makes up an organism, DNA is built using only four
building blocks, the nucleotides adenine, guanine, thymine, and cytosine.
 Every human being shares 99% of their DNA with every other human.
 If you put all the DNA molecules in your body end to end, the DNA would reach from the Earth to the Sun
and back over 600 times (100 trillion times six feet divided by 92 million miles).
 A parent and child share 99.5% of the same DNA.
 You have 98% of your DNA in common with a chimpanzee.
 If you could type 60 words per minute, eight hours a day, it would take approximately 50 years to type
the human genome.
 DNA is a fragile molecule. About a thousand times a day, something happens to it to cause errors. This could
include errors during transcription, damage from ultraviolet light, or any of a host of other activities. There
are many repair mechanisms, but some damage isn't repaired. This means you carry mutations! Some of the
mutations cause no harm, a few are helpful, while others can cause diseases, such as cancer. A new
technology called CRISPRcould allow us to edit genomes, which might lead us to the cure of such mutations
as cancer, Alzheimer's and, theoretically, any disease with a genetic component.
 Scientists at Cambridge University believe humans have DNA in common with the mud worm and that it is
the closest invertebrate genetic relative to us. In other words, you have more in common, genetically
speaking, with a mud worm than you do with a spider or octopus or cockroach.
 Humans and cabbage share about 40-50% common DNA.
 Friedrich Miescher discovered DNA in 1869, although scientists did not understand DNA was the genetic
material in cells until 1943. Prior to that time, it was widely believed that proteins stored genetic
information.