Lecture The Molecules Of Cells Chapter 3 2

The Molecules of Cells
(Chapter 3 in your textbook)

Without water and carbon-based molecules, no life as we know it!

Carbon: The Backbone of Life
• Living organisms consist mostly of carbon-based compounds
Also, H, N, O, P, and S……
• Carbon is unparalleled in its ability to form large, complex, and diverse molecules. Why? Principal source of carbon on Earth?
• Proteins, DNA, carbohydrates, lipids, and other molecules that distinguish living matter are all composed of carbon.

C21H36N7O16P3S

Coenzyme A

• Organic chemistry is the study of compounds that contain carbon.
• Organic compounds range from simple molecules to colossal ones.
Buckminsterfullerene
to

C 60
A “Buckyball”

Methane, CH4
Buckminster Fuller

• Most organic compounds contain hydrogen atoms in addition to carbon atoms.

What properties of carbon make it the element forming the basis for all life?

4 valence e-

The Formation of Bonds with Carbon
• With four valence electrons, carbon can form four covalent bonds with a variety of atoms

• This ability makes large, complex molecules possible.

• In molecules with one or multiple carbons, each carbon bonded by one covalent bond to four other atoms results in a tetrahedral shape.
CH4, methane

• However, when two carbon atoms are joined by a double bond, the atoms joined to the carbons are in the same plane as the carbons.

Name and
Comment

Molecular
Formula

(a) Methane
CH4

(b) Ethane
C2H6

(c) Ethene
(ethylene)
C2H4

Structural
Formula

Ball-andStick Model

Space-Filling
Model

• The electron configuration of carbon gives it covalent compatibility with many different elements.

• The valences of carbon and its most frequent partners
(hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules

What are the valences of C, H, O, and N?

Hydrogen
(valence  1)

Oxygen
(valence  2)

Nitrogen
(valence  3)

Carbon
(valence  4)

Difference in valence electrons and valence?

• Carbon atoms can bond with atoms other than hydrogen. For example:
– Carbon dioxide: CO2

– Urea: CO(NH2)2

Molecular Diversity Arising from Variability in the Carbon Skeleton
• Carbon chains form the skeletons of most organic molecules.
• Carbon chains vary in length, shape, and position of covalent bonds.

Hydrocarbons are organic molecules of only carbon and hydrogen
They are non-polar, and release a relatively large amount of energy in reactions.

(a) Length of carbon molecules

Propane
(C3H8)

Ethane
(C2H6)
A liquefied petroleum LP) gas

(b) Branching of carbon molecules

Butane

2-Methylpropane
(commonly called isobutane and also known as R-600a)

Both molecules are C4H11 and are called isomers

(c) Double bond position
Both C4H8

1-Butene

2-Butene

Butene is acquired by catalytic cracking from crude oil

Catalytic cracking tower at an oil refinery.
Requires a catalyst to separate molecules like benzerne from other hydrocarbons. (d) Presence of rings

Cyclohexane

Benzene

Carbon molecules form ring structures in aqueous solution

Isomers (Greek īsomerēs, having equal share : īso-, iso- + meros, part, share)
• Isomers are compounds with the same molecular formula but different structure and properties.
•

Structural isomers have different covalent arrangements of their atoms.

•

Cis-trans isomers have the same covalent bonds but differ in spatial arrangements.

•

Enantiomers are isomers that are mirror images of each other. (a) Structural isomers

Pentane

2-methyl butane

Both have same molecular formula, C5H12

(b) Cis-trans isomers

cis isomer: The two Xs are on the same side.

trans isomer: The two Xs are on opposite sides.

Can have cis- and trans-isomers only if a double bond is present. Why?

Figure 4.7c

(c) Enantiomers…also called stereoisomers
Mirror image isomers
CO2H

H

CO2H

NH2
CH3

NH2

H
CH3

L/S isomer

D/R isomer

(L/S (levo) = left)

(D/R (dextro) = right)

• Enantiomers are important in the pharmaceutical industry, i.e., “The Twins of Drugs”
• Usually only one isomer is biologically active.
R- and S-Thalidomide

phocomelia

• Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules. Figure 4.8

Drug

Condition

Ibuprofen

Pain; inflammation C13H18O2

Albuterol

Effective
Enantiomer

Ineffective
Enantiomer

S-Ibuprofen

R-Ibuprofen

R-Albuterol

S-Albuterol

Asthma

A few chemical groups are key to the functioning of biological molecules
• Distinctive properties of organic molecules depend on the carbon skeleton and on the molecular components attached to it.
• A number of characteristic groups can replace the hydrogens attached to skeletons of hydrocarbons.

The Chemical Groups Most Important in the
Processes of Life
• Functional groups are the components of organic molecules that are most commonly involved in chemical reactions.
• The number and arrangement of functional groups give each molecule its unique properties.

• The six functional groups that are most important in the chemistry of life:
–
–
–
–
–
–

Hydroxyl group
Carbonyl group
Carboxyl group
Amino group
Phosphate group
Methyl group

Will address these functional groups in lab exercise 3.

Functional groups and sex hormones

Estradiol

Testosterone

STOP HERE ON 2 FEB 2015

The Structure and Function of Large Biological
Molecules (Chapter 3, cont. …)
•

All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids •

Macromolecules are large molecules composed of hundreds to thousands of covalently bonded atoms
3D model of a protein called
Porin.
A cell membrane transport protein

Macromolecules are Polymers Built from Monomers
• A polymer is a long molecule consisting of many similar building blocks
• These small building-block molecules are called monomers • Three of the four classes of life’s organic molecules are and three of these are polymers
– Carbohydrates
– Proteins
– Nucleic acids
– Lipids?

The Synthesis and Breakdown of
Polymers
• Polymers are assembled by a process called dehydration.

• Polymers are disassembled to monomers by hydrolysis

The Synthesis and Breakdown of Polymers
(a) Dehydration reaction: synthesizing a polymer
1

2

3

Unlinked monomer

Short polymer
Dehydration removes a water molecule, forming a new bond.

1

2

3

Longer polymer

4

(b) Hydrolysis (from Greek hydro-, meaning "water", and lysis, meaning "separation") : breaking down a polymer
1

2

3

Hydrolysis adds a water molecule, breaking a bond.

1

2

3

4

Carbohydrates serve as fuel and building material
• Carbohydrates include sugars and the polymers of sugars. • The simplest carbohydrates are monosaccharides,
(from Greek monos: single, sacchar: sugar) or single sugars. • Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks.

Sugars
• Monosaccharides have molecular formulas that are usually multiples of CH2O
• Glucose (C6H12O6) is the most common monosaccharide • Monosaccharides are classified by
– The location of the carbonyl group (as aldose or ketose) – The number of carbons in the carbon skeleton

Figure 5.3c

Aldose (Aldehyde Sugar)

Ketose (Ketone Sugar)

Hexoses: 6-carbon sugars (C6H12O6)
Carbonyl group

Glucose

Galactose

Fructose

High-fructose corn syrup is sweeter than its isomer, glucose!

Fructose
Glucose

Glucose

What makes these isomers, and what type of isomers are they?

1
2

6

6

5

5

3
4

4
5

1

3

2

4

1

3

2

6

(a) Linear and ring forms

6
5
4

1
3

2

(b) Abbreviated ring structure

Glucose will form a ring-shaped molecule in aqueous solution.

• Monosaccharides like glucose
• 1. Provide energy for cell function
• 2. Are carbon skeletons for other molecules like amino acids and fatty acids.
Cellular respiration

Formation of Disaccharides
1–4
glycosidic
1 linkage 4

Glucose

Glucose

Maltose

(a) Dehydration reaction in the synthesis of maltose

1–2 glycosidic 1 linkage 2

Glucose

Fructose

(b) Dehydration reaction in the synthesis of sucrose

Sucrose

Is too much sugar bad for you?

Storage Polysaccharides
• Starch, a storage polysaccharide of plants, consists entirely of glucose monomers
• Plants store surplus starch as granules within chloroplasts and other plastids
• Animals store the polysaccharide glycogen in liver and muscle cells.

Chloroplast

Starch granules
Amylopectin

Amylose

(a) Starch:
1 m a plant polysaccharide
Mitochondria

Glycogen granules

Glycogen
(b) Glycogen:
0.5 m an animal polysaccharide

Structural Polysaccharides
• The polysaccharide cellulose is a major component of the tough wall of plant cells and the most abundant organic compound on
Earth.

• Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ.

Figure 5.7b

1

4

(b) Starch: 1–4 linkage of  glucose monomers

1

4

(c) Cellulose: 1–4 linkage of  glucose monomers

Cellulose microfibrils in a plant cell wall

Cell wall

Microfibril

10 m
0.5 m

Cellulose molecules  Glucose monomer • Enzymes that digest starch by hydrolysis hydrolyze cellulose
• Cellulose in human food passes through the digestive tract as insoluble fiber

• Benefits of insoluble fiber?

• Some microbes use enzymes to digest cellulose
• Many herbivores, from cows to termites, have symbiotic relationships with these microbes

• Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods
(C8H13O5N)n

• Chitin also provides structural support for the cell walls of many fungi

Lipids are a diverse group of hydrophobic macromolecules • Lipids are the one class of large biological molecules that do not form polymers.

• The unifying feature of lipids is having little or no affinity for water….HIGHLY NON POLAR
MOLECULES…LIPIDS ARE HYDROPHOBIC!

• Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds

• The most biologically important lipids are fats, phospholipids, and steroids

FIRST step in the formation of a Fat Molecule

Fatty acid
(in this case, palmitic acid)

Glycerol
(a) One of three dehydration reactions in the synthesis of a fat

Figure 5.10b

Ester linkage (formed linkage of a carboxyl and hydroxyl group)

(b) Fat molecule….also known as a triglyceride

• Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats that are non-polar

• Fatty acids vary in length (number of carbons) and in the number and locations of double bonds

• Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds

• Unsaturated fatty acids have one or more double bonds (a) Saturated fat

- Solid at room temperature

Structural formula of a saturated fat molecule Space-filling model of stearic acid, a saturated fatty acid

(b) Unsaturated fat
-liquid at room temperature

Structural formula of an unsaturated fat molecule Space-filling model of oleic acid, an unsaturated fatty acid Cis double bond causes bending.

• Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen
• Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds
• Peanut butter and margarine are examples of products formed from hydrogenated fats.

Functions of fats in animals
• The principal function of fats is energy storage.
• Humans and other mammals store their fat in adipose cells. • Adipose tissue also cushions vital organs and insulates the body.

Phospholipids
• In a phospholipid, two fatty acids and a phosphate group are attached to glycerol
• The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head

Hydrophilic head
Hydrophobic tails
(a) Structural formula

Choline

Phosphate
Glycerol

Fatty acids

(b) Space-filling model

Hydrophilic head Hydrophobic tail WATER

WATER

Steroids
• Steroids are lipids characterized by a carbon skeleton consisting of four fused rings
• Cholesterol, an important steroid, is a component in animal cell membranes

Proteins include a diversity of structures, resulting in a wide range of functions
• The most diverse in form and function, and most numerous of biological macromolecules….1000’s!
• Proteins account for more than 50% of the dry mass of most cells.
• Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances.

Enzymatic proteins

substrate
Enzyme

-

Function: Selective acceleration of chemical reactions

-

Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules without changing the enzyme.

Storgae: Storage Proteins
Function: Storage of amino acids
Example: Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo.

Ovalbumin

Amino acids for embryo

Cellular Communication: Hormonal proteins
Function: Coordination of an organism’s activities
Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration

High blood sugar

Insulin secreted Normal blood sugar

Cellular Communication: Receptor proteins
Function: Response of cell to chemical stimuli

Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells.

Signaling molecules Receptor protein Movement: Contractile and motor proteins
Function: Movement
Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles. Actin

Muscle tissue

100 m

Myosin

Defensive Proteins
Function: Protection against disease
Example: Antibodies inactivate and help destroy viruses and bacteria.

Antibodies

Virus

Bacterium

Transport Proteins
Function: Transport of substances
Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes.

Transport protein Cell membrane

Structural Proteins
Function: Support
Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues.

Collagen

Connective tissue 60 m

Polypeptides
• Polypeptides are unbranched polymers built from the same set of 20 amino acids.
• A protein is a biologically functional molecule that consists of one or more polypeptides.
• All polypetides are not proteins but all proteins are (made of) polypeptides.

Amino Acid Monomers of
Polypeptides
• Amino acids are organic molecules with carboxyl and amino groups
Amino acids differ in their properties due to differing side chains, called R groups

Usually in form of NH3+ in pH of cells asymmetric carbon?

Amino group

Carboxyl group

Nonpolar side chains: Hydrophobic Amino Acids

Side chain

Glycine
(Gly or G)

Methionine
(Met or M)

Alanine
(Ala or A)

Valine
(Val or V)

Phenylalanine
(Phe or F)

Leucine
(Leu or L)

Tryptophan
(Trp or W)

Isoleucine
(Ile or I)

Proline
(Pro or P)

Polar side chains: Hydrophilic Amino Acids

Serine
(Ser or S)

Threonine
(Thr or T)

Cysteine
(Cys or C)

Tyrosine
(Tyr or Y)

Asparagine
(Asn or N)

Glutamine
(Gln or Q)

Amino Acid Polymers
• Amino acids are linked by peptide bonds.
• A polypeptide is a polymer of amino acids.
• Polypeptides range in length from a few to many thousand monomers.
• Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)

A peptide is short chain of amino acids

Dehydration

Peptide bond

New peptide bond forming
Side
chains

Backbone

Amino end
(N-terminus)

Peptide bond Carboxyl end
(C-terminus)

Protein Structure and Function
• A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape

• The sequence of amino acids determines a protein’s threedimensional structure
• A protein’s structure determines its function

Antibody bindings to a flu virus protein

Four Levels of Protein Structure
• Primary
• Secondary

• Tertiary
• Quaternary.

Figure 5.20a

Primary structure
Amino
acids

The primary structure of a protein is its unique sequence of amino acids

Primary structure is determined by inherited genetic information

Amino end

Primary structure of transthyretin

Carboxyl end

Secondary structure
Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain

 helix

 pleated sheet

Hydrogen bond
 strand, shown as a flat arrow pointing toward the carboxyl end

Hydrogen bond

Spider silk is a “pleated sheet” protein and spider silk has greater tensile strength than steel.

Tertiary structure is determined by interactions among various side chains (R groups)

Hydrogen bond Hydrophobic interactions and van der Waals interactions Disulfide bridge Ionic bond

Polypeptide backbone Heme
Iron
 subunit
Red blood cells

 subunit

 subunit

 subunit

Quaternary structure results

Hemoglobin

when a protein consists of multiple polypeptide chains

Sickle-Cell Disease: A Change in
Primary Structure
• A slight change in primary structure can affect a protein’s structure and ability to function.
• Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin.

Sickle-cell hemoglobin

Normal hemoglobin

Primary
Structure
1
2
3
4
5
6
7

Secondary and Tertiary
Structures

Quaternary
Structure

Function
Molecules do not associate with one another; each carries oxygen. Normal hemoglobin  subunit



Red Blood
Cell Shape



10 m




1
2
3
4
5
6
7

Exposed hydrophobic region

Sickle-cell hemoglobin 
 subunit


Molecules crystallize into a fiber; capacity to carry oxygen is reduced. 



10 m

What Determines Protein Structure?
• In addition to primary structure, physical and chemical conditions can affect structure.
• Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel. • This loss of a protein’s native structure is called denaturation. • A denatured protein is biologically inactive.

tu

Normal protein

Denatured protein

But, could we renature a fried egg?

STOP ON 4 FEB 2015

Nucleic Acids Store, Transmit, and Help Express
Hereditary Information
• The amino acid sequence of a polypeptide is programmed by a unit of inheritance called the gene.
• Genes are made of DNA (deoxyribonucleic acid), and a nucleic acid made of monomers is called a nucleotide.

gene

encoded nucleic acid

polypeptide

What Nucleic Acids Do
• There are two types of nucleic acids
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
• DNA provides directions for its own replication.
• DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis.

DNA

1 Synthesis of mRNA mRNA

NUCLEUS
CYTOPLASM

Figure 5.25-2

DNA

1 Synthesis of mRNA mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of mRNA into cytoplasm Figure 5.25-3

DNA

1 Synthesis of mRNA mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of mRNA into cytoplasm Ribosome

3 Synthesis of protein

Polypeptide

Amino acids The Components of Nucleic Acids
• Nucleic acids are polymers called polynucleotides. • Each polynucleotide is made of monomers called nucleotides.

Sugar-phosphate backbone

5 end
5C

3C
Nucleoside
Nitrogenous base 5C

1C
5C
3C
3 end
(a) Polynucleotide, or nucleic acid

Phosphate group (b) Nucleotide

3C
Sugar
(pentose)

The Structure of DNA and RNA Molecules
• RNA molecules usually exist as single polypeptide chains.
• DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix.

5

3

Sugar-phosphate backbones Hydrogen bonds

Base pair joined by hydrogen bonding 3

5

(a) DNA

Base pair joined by hydrogen bonding

(b) Transfer RNA

Note Uracil substituting for Thymine in RNA.

Watson and Crick proposed the double-helical structure of DNA in 1953.
My Dear Michael,
Jim Watson and I have probably made a most important discovery. We have built a model for the structure of des-oxy-ribosenucleic-acid (read it carefully) called D.N.A. for short. You may remember that the genes of the chromosomes — which carry the hereditary factors — are made up of protein and D.N.A. ………
These two and one more won the
Nobel Prize in Physiology or
Medicine in 1962

Lots of love,
Daddy

• The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C)
• This is called complementary base pairing
One strand of DNA

ATTCGCAGCT =

Sequence of 2nd complimentary strand of DNA

???????

• Complementary pairing can also occur between two RNA molecules or between parts of the same molecule
• In RNA, thymine is replaced by uracil (U) so A and U pair

•
One strand of RNA

AUUCGCAGCU =

Sequence in 2nd strand of RNA

???????

DNA and Proteins as a Tape Measures of Evolution
• The linear sequence of nucleotides in DNA molecules are passed from parents to offspring.
• Two closely related species are more similar in DNA than are more distantly related species.
• Molecular biology can be used to assess evolutionary kinship. -

Genome-wide variation from one human being to another can be up to
0.5% (99.5% similarity)

-

Chimpanzees are 96% to 98% similar to humans, depending on how it is calculated.

-

Cats have 90% of homologous genes with humans, 82% with dogs,
80% with cows, 79% with chimpanzees, 69% with rats and 67% with mice. -

Cows are 80% genetically similar to humans.

-

The fruit fly (Drosophila) shares about 60% of its DNA with humans.

-

About 60% of chicken genes correspond to a similar human gene.

The Human Genome Project (HGP)
- In 1990, the National Institutes of
Health (NIH) and the Department of
Energy joined with international partners in a quest to sequence all
3 billion letters, or base pairs, in the human genome.
- In April 2003, researchers successfully completed the Human Genome Project, under budget and more than two years ahead of schedule.

- The Human Genome Project has already fueled the discovery of more than
1,800 genes responsible for diseases.
- There are now more than 2,000 genetic tests for human conditions.

http://www.youtube.com/watch?v=nhoEvAY0ToM