CHAPTER 3

The Molecules of Life

Did you know?

Organic Molecules

• A cell is mostly water.

– The rest of the cell consists mostly of carbon-based molecules.

– Organic chemistry is the study of carbon compounds.

– An organic compound must contain Carbon! Note that there are some inorganic compounds that also contain carbon, but these lack hydrogen. An example is CO2. Another way to determine if a carbon containing compound is organic is to decide if it is found in living tissue.

Carbon Chemistry

• Carbon is a versatile atom.

• Carbon has the atomic number of 6.

• How many valence electrons available for covalent bonding does it have______?

– Carbon can share its electrons with other atoms to form up to ________ covalent bonds.

• ___ single bond(s)

• ____ double bond(s)

• ___ triple bond(s)

• Carbon can use its bonds to

– Attach to other carbons.

– Form an endless diversity of carbon skeletons in many shapes as shown below.

Carbon Chemistry

• The simplest organic compounds are hydrocarbons.

– These are organic molecules containing only carbon and hydrogen atoms.

– The simplest hydrocarbon is methane (shown below)

Carbon Chemistry

Carbon Chemistry

• Larger hydrocarbons are used in our bodies and elsewhere.

– Are the main molecules in the gasoline we burn in our cars.

– The hydrocarbons of fat molecules provide energy for our bodies.

• Each type of organic molecule has a unique three-dimensional shape that defines its function in an organism.

– The molecules of your body recognize one another based on their shapes.

Carbon Chemistry

• The unique properties of an organic compound depend not only on its carbon skeleton but also on the atoms attached to the skeleton.

– These atoms are called functional groups.

Hydroxyl: -OH alcoholsCarbonyl: -CO aldehydes & ketonesCarboxyl: -COOH aka carboxylic acidsAmino: -NH2 aminesPhosphate: -PO4 phosphates

Carbon Chemistry

Memorize the names, chemical formula, where they are found and the structure of the parts.

Phosphate Group

Found in amino acids and used in energy storage in ATP!

-OH -CO

-COOH

-NH2-PO4

Giant Molecules from Smaller Building Blocks

• On a molecular scale, many of life’s molecules are gigantic.

– Biologists call them macromolecules.

• macro = large

– Examples: carbohydrates, proteins, lipids, the nucleic acids - & RNA DNA

Giant Molecules from Smaller Building Blocks

• Most macromolecules are polymers.

– Polymers are made by stringing together many smaller molecules called monomers.

– Cells link monomers to build polymers by dehydration reactions.

Note that water has been lost when the polymer is formed this is what makes it a “dehydration reaction”

• Organisms also have to break down macromolecules.– Cells do this by a process called hydrolysis.

• Hydro = water, lysis = split/destroy

Note that water has been split to create break apart the polymer into smaller subunits such as monomers.

Breaking down large molecules

Biological Molecules

• There are four categories of large molecules in cells:

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic acids

Carbohydrates

• Carbohydrates include:

– Small sugar molecules in soft drinks

– Long starch molecules in pasta and potatoes

Monosaccharides

• Monosaccharides are simple sugars.

– Examples:

• Glucose is found in sports drinks.

• Fructose is found in fruit.

• Honey contains both glucose and fructose.

• The monosaccharides glucose, fructose and galactose are isomers.

– They have the same formula, but their atoms are arranged differently.

L-Dopa (watch and take notes!)

Isomers (watch and take notes!)

Monosaccharides

• In aqueous solutions, monosaccharides form rings.

• Monosaccharides are the main fuel that cells use for cellular work.

Monosaccharides

Disaccharides

• A disaccharide is a double sugar.

– It is constructed from two monosaccharides.

• Disaccharides are joined through a dehydration reaction.

Disaccharides

• Lactose is another type of disaccharide.

– Some people have trouble digesting lactose, a condition called lactose intolerance.

Disaccharides

• The most common disaccharide is sucrose, common table sugar.

– It consists of a glucose linked to a fructose.– Sucrose is extracted from sugar cane and the roots

of sugar beets.• The United States is one of

the world’s leading markets for sweeteners.

– The average American consumes about 64 kg of sugar per year.

Disaccharides

Polysaccharides

• Complex carbohydrates are called polysaccharides.

– They are long chains of sugar units.

– They are polymers of monosaccharides.

Polysaccharides

• One familiar example of a polysaccharide is starch.

– Plant cells store starch for energy.

– Potatoes and grains are major sources of starch in the human diet.

Polysaccharides

• Animals store excess sugar in the form of a polysaccharide called glycogen.

– Glycogen is similar in structure to starch.

• Cellulose is a structural component of plant cells and is the most abundant organic compound on Earth.

– It forms cable-like fibrils in the tough walls that enclose plants.

– It is a major component of wood.

– It is also known as dietary fiber.

Polysaccharides

• Most animals cannot derive nutrition from fiber.

– Grazing animals survive on a diet of cellulose because they have prokaryotes in their digestive tracts that can break down cellulose.

Polysaccharides

• Simple sugars and double sugars dissolve readily in water.

– They are hydrophilic, or “water-loving.”

Polysaccharides

Low-Carb Diets

• In recent years, “low-carb diets” and “no carb diets” have become popular.

– Are these diets healthy?

– But consumers need to be wary of products boasting that they are “low-carb” because they can be unhealthy.

Lipids

• Lipids are hydrophobic.

– They do not mix with water.

– Examples: fats and steroids

Fats

Fats

• Dietary fat consists largely of the molecule triglyceride.

– Triglyceride is a combination of glycerol and three fatty acids.

• Fats perform essential functions in the human body:

1. Energy storage

2. Cushioning

3. Insulation

Fats

• Unsaturated fatty acids– Have less than the maximum number of

hydrogens bonded to the carbons.• Saturated fatty acids

– Have the maximum number of hydrogens bonded to the carbons.

Fats

• Most animal fats have a high proportion of saturated fatty acids, which can be unhealthy.

– Example: butter

• Most plant oils tend to be low in saturated fatty acids.

– Example: corn oil

Fats

• Not all fats are unhealthy.

– Fats perform important functions in the body and are essential to a healthy diet.

– Are no fat diets healthy?

Fats

Steroids

• Steroids are very different from fats in structure and function.

– The carbon skeleton is bent to form four fused rings.

• Cholesterol is the “base steroid” from which your body produces other steroids.

– Example: sex hormones

Figure 3.17

Steroids

• Synthetic anabolic steroids are controversial.

– They are variants of testosterone.

• Some athletes use anabolic steroids to build up their muscles quickly.

– However, these substances can pose serious health risks.

– Testicle shrinkage, Addiction, Growth of Breasts (in men), Facial Hair (in women) Reduced Sexual Function, Baldness & Skin Conditions, Infertility, Halted Growth (in teens) High Blood Pressure, Liver Damage, Pain, Psycosis, Heart Attack, Death and more!

Steroids

Proteins

• A protein is a polymer constructed from amino acid monomers.

• Proteins perform most of the tasks the body needs to function.

Structural Proteins

Storage Proteins

Contractile Proteins

Transport Proteins

Defensive Proteins

Receptor Proteins

Enzymes

Hormonal Proteins

Sensory Proteins

Protein Videos

• Information on many important proteins below.

• I encourage you to watch those we do not get to in class online for more information!

Gene Regulatory Proteins

The Monomers: Amino Acids

• All proteins are constructed from a common set of 20 kinds of amino acids.

• Each amino acid consists of

1. A central carbon atom bonded to four covalent partners.

2. A side group that is variable among all 20.

Proteins as Polymers

• Cells link amino acids together by dehydration reactions.

– The resulting bond between them is called a peptide bond.

• Your body has tens of thousands of different kinds of protein.

– The arrangement of amino acids makes each one different.

Proteins as Polymers

• Primary structure

– The specific sequence of amino acids in a protein

Proteins

• A slight change in the primary structure of a protein affects its ability to function.

– The substitution of one amino acid for another in hemoglobin causes sickle-cell disease.

Proteins

Protein Shape

• Proteins have four levels of structure.

Protein Structure Introduction

Primary Protein Structure

Secondary Protein Structure

Tertiary Protein Structure

Quaternary Protein Structure

What Determines Protein Structure?

• A protein’s shape is sensitive to the surrounding environment.

– Unfavorable temperature and pH changes can cause a protein to unravel and lose its shape.

– This is called denaturation.

Nucleic Acids

• Nucleic acids are information storage molecules.

– They provide the directions for building proteins.

• There are two types of nucleic acids:

– DNA, deoxyribonucleic acid

– RNA, ribonucleic acid DNA

• The genetic instructions in DNA

– Must be translated from “nucleic acid language” to “protein language.”

Nucleic Acids

• Nucleic acids are polymers of nucleotides.

Nucleic Acids

• Each DNA nucleotide has one of the following bases:

– Adenine (A)

– Guanine (G)

– Thymine (T)

– Cytosine (C)

Nucleic Acids

• Nucleotide monomers are linked into long chains.

– These chains are called polynucleotides, or DNA strands.

– A sugar-phosphate backbone joins them together.

DNA and RNA Structure

Nucleic Acids

• Two strands of DNA join together to form a double helix.

Nucleic Acids

• RNA, ribonucleic acid, is different from DNA.

– Its sugar ribosehas an extra OH group.

– It has the base uracil (U) instead of thymine (T).

Nucleic Acids

Evolution Connection:DNA and Proteins as Evolutionary Tape Measures• Evolutionary relationships between organisms can

be assessed.

– Molecular genealogy extends to relationships between species.

– Biologists use molecular analysis of DNA and protein sequences for testing evolutionary hypotheses.

Figure 3.30