Lesson 3The Chemical Building Blocks of Life

January 21, 2015

Carbon: The Framework of Biological Molecules

• In the previous lectures we discussed the basic principles of chemistry– All substances that has mass and occupies space is

called matter– Matter is composed of extremely small particles called

atoms– An atom is made of electrons, protons, and neutrons– The composition of an atom and its arrangement of

subatomic particles gives it certain characteristics

Carbon: The Framework of Biological Molecules

• We also discussed the basic principles of chemistry– The elements of the periodic table exhibit a

pattern of chemical properties that repeats every 8 elements (octet rule)

– The octet rule is related to the number of electrons in the outer shell (valence electrons)

– Atoms interacting with other atoms are called molecules. This interaction is held together by chemical bonds

Chemical Bond Strength

BondStrength

Carbon: The Framework of Biological Molecules

• We discussed the basic principles of chemistry– Carbon is the most abundant element in living

organisms

• This lecture will discuss the science of carbon chemistry and how these carbon based chemicals play a vital role in all life

Organic Chemistry

• Organic chemistry is the study of carbon based molecules– The framework of biological molecules consists

mainly of carbon atoms bonded to either oxygen, nitrogen, sulfur, phosphorus, hydrogen, or other carbon atoms

– Due to carbon having four valence electrons, it is capable of forming four bonds

– Molecules that consist only of carbon and hydrogen atoms are called hydrocarbons

Hydrocarbons

• The covalent bonds between hydrogen and carbon atoms are high-energy bonds– High-energy bonds store a considerable amount of

energy• Because of the energy level of the bonds,

hydrocarbons make excellent fuel

• Gasoline is abundant in hydrocarbons– Can anyone name a hydrocarbon????

Hydrocarbons

Functional Groups

• In most biological molecules, carbon binds to more than a hydrogen atom– Oxygen, nitrogen, sulfur, phosphorus, or other

carbon atoms• When carbon binds to atoms other than

hydrogen, the arrangement of atoms that it binds to are called functional groups

Functional Groups

• The electronegativity between carbon and hydrogen are similar so the electrons between hydrocarbons are evenly distributed between the atoms

• But because the atoms in most functional groups have different electronegativities than carbon, they exhibit regions of partial positive or negative charge

Common Functional Groups

Functional Groups

• Functional groups have definite chemical properties that they retain regardless of where they occur– Hydroxyl (OH) and Carbonyl (C=O) are polar– Carboxyl (COOH), Phosphate (PO4), and Amino

(NH2) participate in hydrogen bonding because of their electronegativities

Isomers

• Isomers—organic molecules that have the same molecular or empirical formula but exist in different forms– Empirical formulas are the numerical arrangement

of atoms in a molecule– Examples of an empirical formula are C6H12O6

(Glucose) and C2H4O (Ethanol)

• There are different kinds of isomers

Isomers

• Structural isomers—isomers where there is a structural difference in the carbon skeleton between to molecules (2-D)

Structural Isomer

Isomers

• Structural isomers—isomers where there is a structural difference in the carbon skeleton between to molecules (2-D)

• Stereoisomers—isomers that have the same carbon skeleton but differ in how the functional groups are attached to the skeleton in space (3-D)

Stereoisomers

• The enzymes in biological systems usually only recognize a single, specific stereoisomer

• Enantiomers—stereoisomers that are mirror images of one another

• A compound is said to be chiral if it has a mirror image of itself and can not be superimposed on one another

Enantiomers

Chirality

*Non-sumperimposable images*

Chirality

• Chiral compounds are characterized by their effect on polarized light

• Polarized light travels in a path through a single plane but chirality affects the way light travels through this plane– Chiral molecules rotate this plane either to the right

(dextro) or to the left (levo)– Therefore we label the two forms of a chiral molecule

either dextrorotatory and levorotatory

• Can you denote a chiral molecule solely based on its empirical formula?

• Many distinct molecules in living organisms are comprised of long chains of atoms– Some molecules are composed of thousands of atoms linked

to one another (macromolecules)

• Biological macromolecules can be divided into four distinct groups– Carbohydrates, Nucleic Acids, Proteins, and Lipids

• All organisms contain these four macromolecules as their basic components

Carbohydrates

• Carbohydrates—are defined as molecules that contain carbon, hydrogen, and oxygen at a ratio of 1:2:1– Due to the presence of the Carbon-Hydrogen

bonds, which releases energy when oxidized (loss of electrons), are considered good energy-storage molecules

– Sugars are the most important energy-storage molecules• But they also serve other purposes

Monosaccharides

• Simplest form of a carbohydrate– Glyceraldehyde is the simplest form of a

monosaccharide (C3H6O3).• Serves as an energy intermediate in glycolysis

– Five-carbon sugars, ribose and deoxyribose serve as the back bone for nucleic acids• Ribose makes up RNA and deoxyribose makes up DNA

– Six-carbon sugars play a central role in energy storage• Empirical formula is C6H12O6

Monosaccharides

• Most important six carbon monosaccharide is glucose. Glucose is the principle energy-storing sugar– Contains seven energy-storing carbon-hydrogen

bonds

• Six-carbon sugars may exist in a straight chain conformation but when dissolved in water it converts into a ring conformation

In water (aqueous environment)

• Ring closure results in two structural isomers of glucose being formed– Alpha-glucose– Beta-glucose

• Structures differ only in the position of the -OH molecule on the 1 carbon

Critical Thinking

• Glucose is not the only sugar with the empirical formula C6H12O6. Fructose and Glucose both contain the same empirical formula. How is this possible?

Critical Thinking

Our taste buds can discern the difference between them!!!! *Structure Determines Function*

Disaccharides

• Glucose circulates throughout the human body in a monosaccharide form. In most other organisms, it needs to be in a form that is not readily metabolized to be transported

• Organisms convert glucose into a disaccharide which are two monosaccharide molecules joined together

Dissaccharides

• Disaccharides serve as effective reservoirs of glucose b/c the enzymes that metabolize glucose cannot break the dissaccharide bonds

Polysaccharides

• The linkage of multiple monosaccharides results in the formation of polysaccharides

• These polymers can serve either as storage molecules (starch and glycogen) or can act as structural components (cellulose)

• The difference between the polymers is solely based on how the monosaccharides are linked together– Alpha or beta glucose linkages– Which carbon is bound to the carbon atom of another

monosaccharide

Branched Chain

Unbranched Chain

Structural

Energy Carriers

Polysaccharide

• Chitin-structural material found in arthropods and fungi– Polymer of N-

acetylglucosamine– When cross-linked, it

forms a tough resistant surface material (exoskeleton)

N-acetyl groups instead of -OH

Carbohydrates

• Carbohydrates’ structural differences between the monomeric sugars and how they bind to one another can affect the function of the polysaccharides

Nucleic Acids

• All the biological processes of a cell are carried out by a large number of proteins– No two proteins are alike. Each contain a specific

sequence of amino acids. Their sequence determines their shape, conformation, and function.

– The information necessary to produce the correct protein sequence is encoded in the DNA (deoxyribonucleic acid)

Nucleic Acids

• DNA—(deoxyribonucleic acid) molecule in which hereditary information is passed from one generation to the next

• DNA is comprised of nucleic bases bound to sugar/phosphate moieties– Purines (Adenine and Guanine) are double ring structures– Pyrimidines (Thymine and Cytosine) are single ring

structures• The purines and pyrimidines base pair with one

another (AT and GC). They are said to be base complementary.

Nucleic Acids

Nucleic Acids

• DNA is arranged in a double helical shape

Nucleic Acids

• RNA—molecule have multiple roles in living cells. One of which is providing the framework for protein synthesis– Purines (Adenine and Guanine) are double ring

structures– Pyrimidines (Uracil and Cytosine) are single ring

structures

• Single-stranded molecule

Central Dogma

DNA

RNA

Protein

Transcription

Translation

Nucleic Acids

• DNA encodes the necessary information needed to produce and assemble proteins

• RNA is synthesized from the DNA and provides the framework for protein production (transcription). This type of RNA is called messenger RNA

• The RNA sequence is read and based on its arrangement, will produce a corresponding protein (translation)

Proteins

• The most diverse group of macromolecules; both chemically and functionally

• Proteins have a varied array of functions within the cell (structure determines function)

Protein Functions

1. Enzymes catalyze reactions2. Transporter proteins move chemicals into and out

of cells3. Integral part of cell structures such as walls,

membranes, and cytoplasmic components4. The defend the body against foreign molecules5. They aid in cell motility6. They help regulate other functions in the cell7. They can act as storage molecules

Protein Composition

• Amino acids are the building blocks of proteins– Proteins are polymers of amino acids

– 20 different amino acids

– Amino acids are linked through peptide bonds (carboxyl and amino groups form this linkage)

– The 20 amino acids are grouped into different chemical classes based on their structure

Amino Acids

Protein Structure

• Proteins are held together via peptide bonds. – The carboxyl group of

one amino acid bonds with an amine group of another amino acid

– This bond results in the loss of H20

Amino Acid 1 Amino Acid 2

Protein Structure

• The arrangement of amino acids in a protein determines its structure, which in turns determines its function

• The structure of proteins is usually discussed in terms of a hierarchy of four levels– Primary, secondary, tertiary, quatenary

• Primary structure refers to its amino acid sequence

• Secondary structure results from the hydrogen bonding of amino acids near each other

• Tertiary Structure refers to the shape of the globular protein and how it folds on itself

• When two or more polypeptide chains associate to form a functional protein, how they are arranged in respect to one another is the Quaternary structure

One Hemoglobin Protein