Chapter 3

Carbon Molecules in Cells

The Molecules of Life—From Structure to FunctionA. General

1. Only living cells can synthesize carbohydrates, lipids, proteins, and nucleic acids. 2. These molecules are organic compounds consisting of carbon and one or more additional elements (at least one hydrogen), covalently bonded to one another

Organic Compounds

1. Carbon atoms nearly always form covalent bonds

2. Carbon atoms can bond to each other to form straight chains, branched chains and rings

3. since carbon can form up to 4 single bonds, there are a wide variety of compounds it can form

4. chemists group organic compounds into classes with similar characteristics to make their study easier

Hydrocarbons - the simplest class of organic compounds contain only hydrogen and carbona. they are broken down into three groups based on the types of bonding between the carbon atoms

i. the alkanes are composed of only single bonds between the carbons

- alkanes are also classified as “saturated hydrocarbons”, this means that they are

composed of all single bondsii. the alkenes contain at least one double bond between carbonsiii. the alkynes contain at least one triple bond between

carbons-. Alkenes and alkynes “unsaturated compounds” because their carbons do not have all single bonds

5. Carbon Atoms can Form Rings a. One class of ring hydrocarbons

i. Aromatic Hydrocarbons6. Isomers

a. isomers are compounds with the same chemical formulas but different structures and properties -(ex’s. C4H10O is the formula for 2 isomers; 1-butanol and 2-methyl-1-propanol)

b. different isomers have different properties

C. Naming organic compounds1. the compound name is chosen from a stem that reflects the number of carbons present

a. the stems are: 1carbon – Meth, 2carbons – Eth, 3carbons – Prop, 4carbons – But, 5carbons – Pent, 6carbons – Hex, 7carbons – Hept, 8carbons – Oct, 9 carbons – Non, 10carbons – Dec

2. a suffix is then added to indicate how the carbon atoms are linked to each other

a. the endings can be determined by the class of the compound

-alkanes – “ane”, alkenes – “ene”, alkynes – “yne”, alcohols – “anol”, etc.

3. a prefix can then be added to show if the carbon atoms are arranged in a ring – “cyclo”

4. We name long chain alkenes and alkynes by indicating the location of the double or triple bond within the molecule

a. number the carbon atoms so the first carbon atom in the double bond has the lowest number

b. if there is more than one multiple bond, numberthe position of each multiple bond and use a prefix to indicate the number of multiple bonds

5. Naming Branched Hydrocarbonsa. first, determine the number of carbons in the

longest chain and pick the corresponding stemb. next, number the carbon atoms on that chain so that any branches have the lowest number possiblec. name the attached group (CH3 is called methyl – it is the one we will use)d. if more than one group is attached, the position of each group should be given

i. if the same group is attached more than once, a prefix is used to tell how many

(3,3-dimethylpentane)

6. Names of compounds reflect functional groupsa. Functional groups are atoms or groups of atoms covalently bonded to a carbon backbone; they convey distinct properties, such as solubility and chemical reactivity, to the complete molecule.b. The common functional groups in biological

molecules are: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl

c. see figure 3.5, page 38d. when necessary, the position of the functional

group is noted by counting the carbon number it is on

7. Many biological molecules have “common” names

HYDROXYL

METHYL

CARBONYL

CARBOXYL

AMINO

PHOSPHATE

(alcohol)

(aldehyde;—CHO)

(nonionized;—COOH)

(ionized;—COO–)

(nonionized;—NH2)

(ionized;—+NH3)

(icon for phosphate group)(ketone;

=CO)

Sulfhydryl -SH

CH3

Examples of Functional Groups

Methyl group - CH3

Hydroxyl group - OH

Amino group - NH3+

Carbonyl group -CHO

Carboxyl group - COOH

Phosphate group - PO3-

Sulfhydryl group - SH

D. Representing Organic Molecules1. chemical formulas – show numbers of atoms in the molecule, but does not show the bonds, sizes of atoms or shape of the molecule2. structural formulas – shows arrangement of all atoms and bonds in the molecule, but not the actual shape of the molecule or sizes of atoms and larger molecules can be difficult to draw3. skeletal structure – simply shows arrangement of carbon atoms, does not show actual shape of molecule, or atom sizes and it does not show all atoms or bonds4. space filling model – shows three dimensional shape of molecule and most of the space taken by electrons (relative size), but uses false colors to differentiate between atoms, bonds are not clearly shown and parts of large molecules may be hidden5. A ball-and-stick model depicts bonding of atoms; space-filling models convey a molecule's size and surfaces.6. Larger molecules are best visualized using ribbon models, such as those generated by computer programs.

Structural formula

Ball-and-stick model

Space-filling model

HH

H

H

C

Chapter 5

Biological Molecules

How Do Cells Build Organic Compounds?

A. Four Families of Building Blocks

1. Simple sugars, fatty acids, amino acids, and nucleotides are the four major families of small building blocks (monomers – single units).

2. Monomers can be joined to form larger polymers.

3. simple sugars = carbohydrate monomers fatty acids = lipid monomers amino acids = protein monomers nucleotides = nucleic acid monomers

B. Five Categories of Reactions1. Enzymes are a special class of proteins that mediate five categories of reactions:

a. functional-group transfer from one molecule to anotherb. electron transfer —stripped from one molecule and given to anotherc. rearrangement of internal bonds converts one type of organic molecule to anotherd. condensation (also known as dehydration) makestwo molecules into one by removing a watere. cleavage (or hydrolysis) breaking one molecule into two by adding a water.

2. In a condensation reaction, one molecule is stripped of its H+, another is stripped of its OH–; then the two molecule fragments join to form a new compound and the H+ and OH– form water.

3. Hydrolysis (a type of cleavage reaction) is the reverse: one molecule is split by the addition of H+ and OH– (from water) to the components.

Carbohydrates—The Most Abundant Molecules of Life-3 main types (mono, oligo, poly)-Used in cells for structural materials, transportable forms of energy and energy storage

A. The Simple Sugars (C, H, O usually in a 1:2:1 ratio)1. Monosaccharides—one sugar unit—are the

simplest carbohydrates.2. They are characterized by solubility in water, sweet taste, and several —OH groups.3. Ribose and deoxyribose (five-carbon backbones) are building blocks for nucleic acids.4. Glucose and fructose (six-carbon backbones) are used in assembling larger carbohydrates.5. Other important molecules derived from sugar monomers include glycerol and vitamin C

Structure of glucose Structure of fructose

Short-Chain Carbohydrates1. An oligosaccharide is a short chain of two or more sugar monomers.2. Disaccharides—two sugar units—are the simplest oligosaccharides.

a. Lactose (glucose + galactose) is present in milk.b. Sucrose (glucose + fructose) is a transport form of sugar used by plants and harvested by humans for use in food.c. Maltose (two glucose units) is present in germinating seeds.

3. Oligosaccharides with three or more sugar monomers are attached as short side chains to proteins where they participate in membrane function.

glucose fructose

Sucrose - disaccharide

+ H2O

Complex Carbohydrates1. A polysaccharide is a straight or branched chain of hundreds or thousands of sugar monomers.2. Starch is a plant storage form of energy, arranged as unbranched coiled chains, easily hydrolyzed to glucose units.3. Cellulose is a fiberlike structural material—tough, insoluble—used in plant cell walls.4. Glycogen is a highly-branched chain used by

animals to store energy in muscles and liver.5. Chitin is a specialized polysaccharide with nitrogen attached to the glucose units; it is used as a structural material in arthropod exoskeletons and fungal cell walls.

Cellulose chains Starch chain

Greasy, Oily—Must Be Lipids

-nonpolar, hydrophobic; used in cells for energy storage, structural materials, signaling molecules

A. Lipids are greasy or oily compounds with little tendency to dissolve in water.

1. They can be broken down by hydrolysis reactions.

2. They function in energy storage, membrane structure, and coatings.

Fats and Fatty Acids

1. A fatty acid is a long chain of mostly carbon and hydrogen atoms with a —COOH (carboxyl) group at one end.

2. When they are part of complex lipids, the fatty acids resemble long, flexible tails.

A. Unsaturated fats are liquids (oils) at room temperature because one or more double bonds between the carbons in the fatty acids permits “kinks” in the tails.

B. Saturated fats (triglycerides) have only single C—C bonds in their fatty acid tails and are solids at room temperature.

stearic acid oleic acid linolenic acid

Fats are formed by the attachment of one (mono-), two (di-), or three (tri-) fatty acids to a glycerol.

A. They are a rich source of energy, yielding more than twice the energy per weight basis as

carbohydrates.

B. They are also provide an insulation blanket for animals that must endure cold, harsh temperatures.

C. ex. Triglycerides (3 f.a. tails)

D. body’s main energy reservoir

three fatty-acid tails

glycerol

triglyceride

+ 3H20

C. Phospholipids 1. These are formed by attachment of two fatty acids plus a phosphate group to a glycerol.2. They are the main structural material of membranes where they arrange in bilayers.

two hydrophobic tails

hydrophilic

head

D. Sterols and Their Derivatives1. Sterols have a backbone of four carbon rings but no fatty acid tails.2. Cholesterol is a component of cell membranes in animals and can be modified to form sex hormones (testosterone and estrogen) and vitamin D.3. steroids, hormones, bile salts

Sterol backbone

Cholesterol

E. Waxes 1. They are formed by attachment of long-chain fatty acids to long-chain alcohols or carbon rings.

2. They serve as coatings for plant parts and as animal coverings.

A String of Amino Acids: Protein Primary Structure-most diverse type of biological molecules

A. Proteins function as enzymes, in cell movements, as storage and transport agents, as hormones, as antibodies, and as structural material.

B. Amino Acid Structure 1. Amino acids are small organic molecules with an amino group, a carboxyl group, and one of twenty varying R groups.2. All of the parts of an amino acid molecule are covalently bonded to a central carbon atom.3. see figure 3.17, page 44

Amino group

Carboxyl group

R group

Protein Synthesis

• Peptide bond

– Condensation reaction links amino group of

one amino acid with carboxyl group of next

Water forms as a by-product

Polypeptide Chain Formation1. Primary structure is defined as ordered sequences of amino acids each linked together by peptide bonds to form polypeptide chains.

2. There are 20 kinds of amino acids available in nature.

3. The sequence of the amino acids is determined by DNA and is unique for each kind of protein.

A. shape and function arise from the primary structureB. Fibrous proteins have polypeptide chains organized as strands or sheets; they contribute to the shape, internal

organization, and movement of cells.C. Globular proteins, including most enzymes, have their chains folded into compact, rounded shapes.

How Does a Protein's Final Structure Emerge?

A. Second and Third Levels of Protein Structure

1. Secondary structure refers to the helical coil (as in hemoglobin) or sheetlike array (as in silk) that results from hydrogen bonding of side groups on the amino acid chains.

2. Tertiary structure is the result of folding due to interactions among R groups along the polypeptide chain.

a. adjacent helixes and sheets pack together in structurally stable units called domains

B. Chaperonins are proteins that help other proteins fold correctly

Fourth Level of Protein Structure

1. Quaternary structure describes the complexing of two or more polypeptide chains.

2. Hemoglobin is a good example of four interacting chains that form a globular proteins; keratin and collagen are complex fibrous proteins.

3. Glycoproteins consist of oligosaccharides covalently bonded to proteins; they are abundant on the exterior of animal cells, as cell products, and in the blood.

4. Lipoproteins have both lipid and protein components; they transport fats and cholesterol in the blood.

Tertiary structure

Peptide group

Secondary structure

quaternary structure

Denaturation—How to Undo the Structure

1. High temperatures or changes in pH can cause a loss of a protein’s normal three-dimensional shape (denaturation).

2. Normal functioning is lost upon denaturation, which is often irreversible (for example, a cooked egg).

Why Is Protein Structure So Important?

A. Just One Wrong Amino Acid...1. Alteration of a cell's DNA can result in the wrong amino acid insertion in a polypeptide chain.2. If valine is substituted for glutamate in hemoglobin, the result is called HbS.

B. Sickle-Shaped Cells and a Serious Disorder1. Persons who inherit two mutated genes for the beta chain of hemoglobin can only make HbS.2. The altered hemoglobin causes the red blood cells to be misshapen—sickle-cell anemia, with many

serious body dysfunctions.

Nucleotides and Nucleic Acids

A. The Diverse Roles of Nucleotides1. Each nucleotide consists of a five-carbon sugar (ribose or deoxyribose), a nitrogen-containing base, and a phosphate group.

a. Adenosine phosphates are chemical messengers (cAMP) or energy carriers (ATP).b. Nucleotide coenzymes transport hydrogen atoms and electrons (examples: NAD+ and FAD).

2. Nucleotides also serve as building blocks for nucleic acids (DNA & RNA).

Regarding DNA and the RNAs

1. Nucleic acids are polymers of nucleotides.A. Four different kinds of nucleotides are strung together to form large single or double-stranded

molecules.B. Each strand's backbone consists of joined sugars and phosphates with nucleotide bases projecting

toward the interior from the sugars.

Phosphate

SugarNitrogenous

base

Single strand of DNA or RNA

sugar

phosphateconnected bycovalent bond

base

The two most important nucleic acids are DNA and RNA.

A. DNA is a double-stranded helix carrying encoded hereditary instructions.

1. deoxyribose

2. A to T, C to G

B. RNA is single stranded and functions in translating the code to build proteins.

1. ribose

2. Uracil (U) in place of Thymine (T)