Download BIOCHEMISTRY Class Notes Summary Table of Contents 1.0

BIOCHEMISTRY
Class Notes Summary
Table of Contents
1.0
Inorganic and Organic Compounds
2.0
Monomers and Polymers
3.0
Dehydration (Condensation) Synthesis
4.0
Hydrolysis Reaction
5.0
Organic Compounds
5.1
Carbohydrates
5.11 Monosaccharides
5.12 Dissacharides
5.13 Polysaccharides
1.0
5.2
Lipids
5.21 Triglycerides
5.22 Phospholipids
5.23 Wax
5.24 Steroids
5.3
5.4
Proteins
Nucleic Acids
Inorganic and organic compounds.
In chemistry there are inorganic and organic compounds. Inorganic compounds are not
made from and do not come from living organisms. Organic compounds make up or
come from living organisms. For example, a rock is an inorganic compound composed of
inorganic elements. Whereas, a piece of wood is made of organic compounds because
there piece of wood once came from a live tree. All organic compounds must contain
carbon, hydrogen and oxygen. Some organic compounds such as proteins and nucleic
acid also contain nitrogen.
The we are covering now state in order to understand the concept that the fundamental
life processes of plants and animals depend on a variety of chemical reactions that occur
in specialized areas of the organisms cells, students must know that most macromolecules
(carbohydrates, lipids, proteins and nucleic acids) in cells and organisms are synthesized
from a small collection of simple precursors. Basically what this standard is stating is
that large molecules (polymers, or macromolecules) are composed of small molecules
called monomers.
2.0
Monomers and Polymers
A monomer is made of one subunit.
A polymer is made of 3 or more monomers.
Monomers and polymers are made and broken down by two chemical reactions,
dehydration (condensation) and hydrolysis.
3.0
Dehydration (Condensation) Synthesis
Polymers are formed by condensation (dehydration) reactions. This type of reaction can
be recognized because water is formed as a product. Dehydration reaction build large
molecules (macromolecules or polymers) from small molecules (precursors or
monomers).
Figure 1: Condensation ( Dehydration) Reaction
During dehydration water is formed by the removal of a hydrogen from one monomer and
the removal of a hydroxyl (-OH) from another monomer. The hydrogen and hydroxyl
bonds together to form water H2O. For every two monomers joined 1 water is produced.
So if 6 monomers are joined to form 1 polymer, 5 waters are produced.
4.0
Hydrolysis Reaction
Macromolecules or polymers are broken down into precursors or monomers by hydrolysis
reaction. This type of reaction uses water to split large molecules into small molecules polymers into monomers.
Figure 2: Hydrolysis Reaction
Hydrolysis split polymers or macromolecules by inserting a hydrogen on one monomer
and a hydroxyl (-OH) on another.
5.0
Organic Compounds
All living organisms are made of organic compounds. There are four types of organic
compounds; carbohydrates, lipids, proteins, and nucleic acids. All organic compounds
contain carbon - C, hydrogen - H, and oxygen - O. Proteins and nucleic acids also have
nitrogen - N. Carbohydrates provide a quick sources of energy. Lipids can be used to
store energy, water proofing and are found in hormones. Proteins provides the building
materials for growth and repair. Nucleic acids store genetic information.
5.1
Carbohydrates
Carbohydrates are sugars and not all of them are sweet. Carbohydrates provide a
quick source of energy. In carbohydrates the ration of hydrogen to oxygen is two
to one, 2:1. Meaning for every oxygen there are two hydrogen. Carbohydrates are
divided into three groups; monosaccharides, disaccharides and polysaccharides.
The prefix and roots of the words give you a clue to their meaning. Mono = one,
di = two and poly three or more. Saccharide = sugar. So monosaccharide are
made of one sugar molecule, disaccharides are made of two sugar molecules and
poly saccharides are made of many (in the hundreds) sugar molecules.
5.11
Monosaccharides
A monosaccharide is a simple six carbon sugar molecules. There are three
types of monosaccharides, glucose, fructose, and galactose. They all have
the same chemical or molecular formula C6H12O6. Monosaccharides are
isomers, meaning they have the same chemical formula but different
structural formula. In the structural formula of monosaccharides the atoms
are arranged differently giving each monosaccharide its own unique
properties.
glucose
fructose
galactose
Glucose is the main source of energy for plants and animals. All provide energy
but glucose gives the most energy. Glucose is produced by green plants during
photosynthesis. Fructose the sweetest of all monosaccharides is found in fruits.
Galactose is found in milk and milk products such as cheese. Monosaccharides
are the precursors for all other carbohydrates.
5.12
Disaccharides
Disaccharides are formed by dehydration (condensation) reaction.
Remember dehydration removes a hydrogen and a hydroxyl (-OH) to form
water as a by-product.
C6H12O6
+ C6H12O6
C12H24O12
- H2O
C12H22O11 +
monosaccharide monomer
monosaccharide monomer
Condensation forms water from monomers
H2O
Disaccharides all have the same chemical or molecular formula, C12H22O11.
There are three types of disaccharides; sucrose, lactose and maltose.
Sucrose is table sugars produces from sugar cane or sugar beet. Sucrose
is formed from glucose plus fructose. Lactose is found in milk and milk
products. Lactose is formed from glucose plus galactose. Maltose is a
grain sugar found in grains, such as wheat and barley, and grass. Maltose
is formed from two molecules of glucose. Notice that all disaccharides
contain glucose.
Disaccharides are broken down into their precursors (monosaccharide) by
hydrolysis reaction.
One water molecule is with the help of an enzyme gives one hydrogen to
one monosaccharide and a hydroxide to the other monosaccharide so water
is used to split the disaccharide into two monosaccharides.
5.13
Polysaccharides
Polysaccharides are many monosaccharides linked together to form very
long chains. Since the molecular formula is very complex, you are not
required to know them. Polysaccharides are also formed by dehydration
reaction. Remember for every monosaccharide that is linked to another
monosaccharide one water is formed. So if 5 monosaccharides are linked
together 4 water molecules are produced.
If 50 monosaccharides are linked together 49 water molecules are
produced. If 200 monosaccharides are linked together 199 water
molecules are produced.
Get the picture, for the total number of monosaccharides linked substrate
one from the total to get the number of water produced.
So if you are given a problem to calculate the chemical formula of a
polysaccharide to the following: add the chemical formulas together and
subtract the total number of water to get the chemical formula of a
polysaccharide.
For example: A polysaccharide is formed from 11 molecules of
monosaccharides, calculate the chemical formula of the polysaccharide.
C6H12O6
C6H12O6
C6H12O6
C6H12O6
C6H12O6
C6H12O6
C6H12O6
C6H12O6
C6H12O6
C6H12O6
+ C6H12O6
C66H132O66
- H20O10
C66H112O56
monosaccharide monomers
subtract out 10H2O (to subtract change it to H20O10
The chemical formula is C66H112O56
Polysaccharides are broken down into monosaccharides by hydrolysis
reaction. Water is used with the help of an enzyme to split the
polysaccharide into its monosaccharide precursors. You can figure out
how many water molecules are need to split a polysaccharide.
For example. Using the above chemical formula of a polysaccharide, C66H112O56
- the chemical formula of a monosaccharide is C6H12O6
- divide the 6 from carbon of the monosaccharide into the 66 carbon of the
polysaccharide and you get 11
- so the polysaccharide was made from 11 monosaccharides
- subtract 1 from 11 and you get the number of water molecules needed to split
C66H112O56 into its monosaccharide precursors.
- 10 water molecules are needed.
There are three types of polysaccharides; starch, cellulose, and glycogen.
Starch is produced by plants to store energy. There are two forms of starch
one is a highly branched carbon chain and the other is a long unbranched
carbon chain. Examples of plants the produce starch are potatoes, rice,
and corn. Cellulose is also produced by plants. Cellulose gives plant
strength, support and rigidity. Remember plants don’t have skeletons.
Cellulose enables a plant to stand upright. Cellulose are long straight
chains of carbon. Note, humans can not digest cellulose. To do so we
would need an extra stomach and special bacteria like cows. But cellulose
is good for human because it acts as roughage to clean out the intestines
like a scrub brush. The crunchy sound you hear in fruit or vegetables is
the sound of cellulose breaking. Glycogen is found only in animal and is
also used to store energy. Glycogen is a high branched chain of carbons.
Its is store between the muscle cells. The liver can break down glycogen
to provide energy. However if an animal ever reach this point it must be
starving and out of fat reserves.
5.2
Lipids
Lipids are organic molecules that store large amounts of energy. Lipids can
provide up to 4 times the amount of energy as a carbohydrate, but they take longer
to breakdown. A special property of lipid is they are insoluble in water, meaning
they do not dissolve in water. There are four types of lipids; triglycerides,
phospholipids, wax, and steroids.
5.21
Triglycerides
Triglycerides are made of 3 fatty acid tails attached to a glycerol head.
The fatty acid tails are long chains of carbon and hydrogen with a carboxyl
group (-COOH) at one end. The fatty acid tails are hydrophobic. Hydro =
water and phobic = fear, so hydrophobic literally means fear of water.
Hydrophobic molecules are not attracted to water so they are non polar.
The glycerol head is a short three carbon molecule with one hydroxyl
group (-OH) per carbon. It is the fatty acid tails that make triglycerides
insoluble in water.
There are two types of triglycerides; oil and fat. Oil is a liquid at room
temperature and is produced by plants. Fat is a solid at room temperature
and is produced by animals.
You may be familiar with the terms saturated fat and unsaturated fat.
Saturated fat is a fatty acid molecule saturated with hydrogen. The
hydrogen forms single bonds with the carbon forming straight chains.
Saturated fatty acids of fats can nestle closely together, forming solid
lumps at room temperature. Unsaturated fatty acids have double bonds
between the carbons so few hydrogens can bond. Oils have mostly
unsaturated fatty acids. The double bond in the unsaturated fatty acid
produces kinks in the fatty acid chains. The kinks keep the oil molecules
apart so oil is a liquid at room temperature. Oils can be converted to a fat
by breaking the double bonds between carbons and replacing them with
single bonds and adding hydrogens. This type of oil is called
hydrogenated oil and is used to make margarine.
Saturated fats can be used by the body to make cholesterol. Cholesterol
comes in two forms bad cholesterol which cause plaque in the arteries, and
good cholesterol which is needed for proper cellular functions. So people
who must keep control of the cholesterol levels should avoid foods with
saturated fats.
5.22
Phospholipids
There is another type of lipid called phospholipids. Phospholipids are
similar to fats or oils except that only two fatty acid tails are attached to
the glycerol backbone. The third position on the glycerol is occupied by a
polar head composed of phosphate group (-PO4) which is usually attached
to a nitrogen containing functional group. The phosphate group is
negatively charged and the nitrogen containing group is positively charged.
The glycerol head with its phosphate is polar and hydrophilic. Philic
means to love, so hydrophilic literally means water loving. The fatty acid
tails are non polar and hydrophobic. Hydro = water and phobic = fear, so
hydrophobic literally means fear of water. Hydrophobic molecules are not
attracted to water and hydrophilic molecules are attracted to water. This
gives phospholipids it unique reaction in water that is important in cell
membrane function.
5.23
Wax
Wax are chemically similar to fats. They are very saturated, making them
solid at normal outdoor temperatures. Wax is made of 2 fatty acid tails
attached to an alcohol chain. Again the fatty acid tails make them
insoluble in water. The main function of wax is waterproofing and
forming protective layers. Wax is found on the leaves and stems of plants,
in mammal fur and ears, and on an insects exoskeleton.
5.24
5.3
Steroids
Steroids are made of 4 carbon rings attached to different functional groups.
This makes them look chemically different from other lipids. Steroids are
classified as lipids because they are insoluble in water. Remember
insoluble means it will not dissolve in water. Cholesterol, testosterone,
and estrogen are examples of steroids. Steroids are found in hormones,
nerve tissue and poisons.
Proteins
Proteins provide the structural materials for growth and repair. Proteins are
macromolecules made of amino acids. There are 22 different kinds of amino
acids. An amino acid is made of 3 components: a carboxyl group (COOH), an
amine group (NH3) and a R-group.
The R-group is a variable group, meaning it varies or is different for each type of
amino acid. It is the R-group that gives each amino acid its distinctive properties.
Depending of the R-group some amino acids are hydrophilic and polar so are
soluble in water and others are hydrophobic with non polar R-groups making
them insoluble in water.
Amino acids with sulfur in its R-group (cysteine) can bond with other amino acid
that have a cysteine R-group linking two proteins together. This bonds are called
disulfide bridges. The linked proteins will bend at each disulfide bridge. A visual
example of disulfide bridges is hair. Straight hair have few disulfide bridges.
Naturally curly hair has many disulfide bridges. When a person gets a perm to
make their hair curly, them are chemically causing disulfide bridges to form. If a
person has a perm to make curly hair straight, they are breaking the natural
disulfide bridges.
Proteins have many functions such as: providing structural materials for growth
and repair, function in movement because muscle are made of protein structures
called actin and myosin, proteins function in defense via antibodies in blood,
proteins store glycogen in mammal, and finally proteins can act as enzymes which
speed up or start chemical reactions.
The amino acids of proteins are joined by the nitrogen in the amino group bonding
to the carbon in the carboxyl group of another amino acid. These bonds are called
peptide bond. Joined amino acids are also called peptide. So peptide is another
word for protein. Dipeptide is two amino acids joined. Polypeptide is a long chain
of amino acids joined together.
Proteins are highly organized molecules that can have up to four levels of
structure. The primary structure is the sequence of amino acid that make up the
protein. This is the first structure that is coded and produced from DNA. In the
secondary structure hydrogen bonds causes the protein molecules to form a helix
(like a coiled spring). Example are hair, subunits of hemoglobin. In the tertiary
structure proteins can assume complex 3- dimensional shapes. Basically the
secondary structure has folded on itself. The quaternary structure is the grouping
(aggregation) of 2 or more tertiary structures. To understand the structures of a
protein try this: take a piece of bendable wire, when the wire is straight it
represents the primary structure. Now twist the wire around a pencil and slide it
off when done, you have the secondary structure. Take the secondary structure
and fold it into a ball creating the tertiary structure. If you have different colors of
wire, the quaternary structure would be the combining of different color of tertiary
structures.
The exact type, position, and number of amino acids bearing specific R-groups
determines the 3-dimensional shape of the protein which in turn determines its
biological function.
5.4
Nucleic Acids
Nucleic acids store and carries genetic information for cellular structures and
functions. Nucleic acids are made of nucleotides. There are two types of nucleic
acids, DNA and RNA. DNA stands for deoxyribose nucleic acid and RNA stands
for ribose nucleic acid. We will learn more about nucleic acids later.
End of Summary