© 2014 Pearson Education, Inc. Carbon & the Molecular diversity of Life The big picture: The subcomponents of biological molecules and their sequence determine

© 2014 Pearson Education, Inc.

Carbon & the Molecular diversity of Life

The big picture:

•The subcomponents of biological molecules and their sequence determine the properties of that molecule.

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


• The atomic number of carbon is 6

• How many valence electrons does it have?


Carbon atoms

• 4 unpaired electrons in valence shell

• Can form up to 4 single covalent bonds

• Can also form double bonds, most commonly with:– Oxygen CO2 O=C=O

– Carbon To create long chains


Organic compounds• A compound containing carbon

• Most, but not all, also contain hydrogen

• Most common elements in organic compounds– Carbon (all)– Hydrogen (most)– Oxygen– Nitrogen– Sulfur– Phosphorus


Figure 3.3

Hydrogen(valence 1)

Carbon(valence 4)

Nitrogen(valence 3)

Oxygen(valence 2)


Shapes of Simple Organic Molecules

• They are 3-dimensional

• When 4 single bonds are formed with a single carbon atom – Angles 109.50

– Tetrahedron


Figure 3.2

Methane

StructuralFormula

MolecularFormula

Space-FillingModel

Ball-and-Stick Model

Name

Ethane

Ethene(ethylene)



Figure 3.4

(a) Length

(b) Branching

(c) Double bond position

(d) Presence of rings

Ethane Propane

Butane BenzeneCyclohexane

1-Butene 2-Butene

2-Methylpropane (isobutane)


• The simplest carbon chain is made of only carbon and hydrogen.

• Hydrocarbon=hydrogen +carbon.

• Hydrogen molecules are attached to the carbon molecules wherever electrons are available for covalent bonding.


• Chemical groups can replace one or more of the hydrogen atoms on the hydrocarbon skeleton.

• They can contribute to the function of the organic molecule by-– Affecting its shape– Being directly involved in chemical reactions


Figure 3.5Chemical Group

Hydroxyl group ( OH)

Compound Name Examples

Alcohol

Ketone

Aldehyde

Methylatedcompound

Organicphosphate

Thiol

Amine

Carboxylic acid,or organic acid

Ethanol

Acetone Propanal

Acetic acid

Glycine

Cysteine

Glycerolphosphate

5-Methyl cytosine

Amino group ( NH2)

Carboxyl group ( COOH)

Sulfhydryl group ( SH)

Phosphate group ( OPO32–)

Methyl group ( CH3)

Carbonyl group ( C O)


Important terms

• Polymer– A long molecule consisting of many similar or

identical building blocks linked by covalent bonds.

• Monomer– The repeating units that serve as the building

blocks of a polymer.

• How are monomers joined together?


Synthesis and Breakdown of Polymers

• Dehydration reaction– Connects monomers– One provides a hydroxyl group (-OH), the other a

hydrogen (-H)– Water is lost

• Hydrolysis– The reverse– Breakage using water– Water attaches a hydroxyl to one molecule,

hydrogen to the other


Figure 3.6a

Unlinked monomerShort polymer

Longer polymer

(a) Dehydration reaction: synthesizing a polymer

Dehydration removesa water molecule,forming a new bond.


Figure 3.6b

(b) Hydrolysis: breaking down a polymer

Hydrolysis addsa water molecule,breaking a bond.


Macromolecules (+ Lipids)• 4 classes of large organic molecules shared by

all living things.– Carbohydrates– Lipids– Proteins– Nucleic acids

• Some do not consider lipids to be true “macromolecules” because– They are not big enough– They are not true polymers


As we review each macromolecule

• Monomer

• Polymer

• Type of bond that links the monomers together

• Basic structure

• Example

• Function


Carbohydrates

• Monomer- simple sugar, monosaccharide

• Disaccharide- 2 simple sugars linked together

• Polysaccharide- many simple sugars linked together


• Monosaccharides– Contain a carbonyl group (C=O) and multiple

hydroxyl groups (-OH)– Vary in the length of the carbon skeleton and

position of the carbonyl group– All have chemical formulas that are multiples of

CH2O, ex. Glucose is C6H12O6

– Names end in “ose”– Used as fuel


Figure 3.7

GlyceraldehydeAn initial breakdown

product of glucose in cellsRibose

A component of RNA

Triose: 3-carbon sugar (C3H6O3) Pentose: 5-carbon sugar (C5H10O5)

Hexoses: 6-carbon sugars (C6H12O6)

Energy sources for organismsGlucose Fructose


• Sugars can exist in both a linear and ring form

• Equilibrium favors the ring form.

• Notice the convention for naming the carbon atoms.


Figure 3.8

(a) Linear and ring forms

(b) Abbreviated ring structure


• Two monosaccharides are linked by a covalent bond through a dehydration reaction.

• The resulting linkage is called a glycosidic linkage.


Figure 3.9-1

Glucose Fructose


Figure 3.9-2

1–2glycosidic

linkage

Glucose

Sucrose

Fructose


Polysaccharides

• 2 functions– Storage- sugars for later use– Structural- building material


Storage

• Plants– Starch

• Polymer of glucose

• Mostly unbranched

• Most animals also have enzymes to break it down so it can be a food source


Figure 3.10a

Starch granulesin a potato tuber cell

Starch (amylose)

Glucosemonomer


• Animals– Glycogen

• Also a polymer of glucose

• Extensive branching

• Stored in liver and muscles

• Stores for only 1 day


Figure 3.10b

Glycogen granulesin muscletissue

Glycogen


Figure 3.10

Starch granulesin a potato tuber cell

Cellulose microfibrilsin a plant cell wall

Glycogen granulesin muscletissue

Cellulosemolecules

Hydrogen bondsbetween —OH groups(not shown) attached tocarbons 3 and 6

Starch (amylose)

Glycogen

Cellulose

Glucosemonomer


Structural

• Cellulose– Plant cell walls– Never branched– Different from starch because of presence of 2 ring

forms of glucose• Cellulose α glucose

• Starch β glucose


Figure 3.11

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

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

(a) and glucose ring structures

Glucose Glucose


• Cellulose polymers lie parallel and can form hydrogen bonds with neighboring polymers

• Creates cable-like microfibrils


Figure 3.10c


Cellulosemolecules

Hydrogen bondsbetween —OH groups oncarbons 3 and 6

Cellulose


Figure 3.10ca



Lipids

• No true monomers

• Not big enough to be considered “macro”

• Share one important trait– They are all hydrophobic (due to hydrocarbons)

• 3 biologically important lipids– Fats– Phospholipids– Steroids


Fats

• Composed of– Glycerol (1)– Fatty acids (3)

• Linkage is called an “ester bond” and it is a covalent bond between a hydroxyl group and a carboxyl group

• What kind of reaction is used in the synthesis of a fat?


Figure 3.12

(b) Fat molecule (triacylglycerol)

Glycerol

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

Ester linkage

Fatty acid(in this case, palmitic acid)


Saturated vs. Unsaturated

• Are there any carbon double bonds within the hydrocarbon chains of the fatty acids?– Yes- unsaturated– No- saturated


Figure 3.13

(a) Saturated fat (b) Unsaturated fat

Structuralformula of asaturated fatmolecule

Structuralformula of anunsaturated fat molecule Space-filling

model ofstearic acid,a saturatedfatty acid

Space-fillingmodel of oleicacid, an unsaturatedfatty acid Double bond

causes bending.


Phospholipids

• Differ from fats in that there are only 2 fatty acids

• The third hydroxyl group of the glycerol molecule bonds to a phosphate

• The phosphate is negatively charged AND other small polar molecules can be attached to the phosphate. Both of these things make the phosphate end. . . Hydrophilic!


Figure 3.14ab

(a) Structural formula (b) Space-filling model

Choline

Phosphate

Glycerol

Fatty acids

Hyd

rop

hili

c h

ead

Hyd

rop

ho

bic

tai

ls


• Where in a cell might you find phospholipids?


Figure 3.14

(a) Structural formula (b) Space-filling model

Hydrophilichead

(d) Phospholipid bilayer

(c) Phospholipid symbol

Hydrophobictails

Choline

Phosphate

Glycerol

Fatty acids

Hyd

rop

hil

ic h

ead

Hyd

rop

ho

bic

tai

ls


Steroids

• Carbon skeleton of 4 fused carbon rings

• Distinguished by the attached chemical groups

• Cholesterol is an example– Common component of animal cell membranes– Other important steroids are synthesized from it


Figure 3.15


Proteins

• Proeios- “first” or “primary”

• Play a roll in almost everything a cell does

• 50% of dry mass of most cells


Protein functions include:

– Speeding up chemical reactions (enzymes)– Defense– Storage– Transport– Cellular communication– Movement– Structural support


Figure 3.16a

Enzymatic proteins

Storage proteins

Defensive proteins

Transport proteins

Enzyme

Function: Selective acceleration of chemical reactions

Function: Storage of amino acids

Example: Digestive enzymes catalyze thehydrolysis of bonds in food molecules.

Ovalbumin Amino acidsfor embryo

Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo.

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.

Function: Transport of substances

Transportprotein

Cell membrane

Antibodies

BacteriumVirus

Function: Protection against disease

Example: Antibodies inactivate and help destroy viruses and bacteria.


Figure 3.16b

Hormonal proteins

Contractile and motor proteins

Receptor proteins

Structural proteins

Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration.

Function: Coordination of an organism’s activities

Normalblood sugar

Highblood sugar

Insulinsecreted

Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles.

Function: Movement

Muscle tissue

Actin Myosin

30 m Connective tissue 60 m

Collagen

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 afibrous framework in animal connective tissues.

Function: Support

Signaling molecules

Receptorprotein

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

Function: Response of cell to chemical stimuli


• Monomer- amino acid

• Polymer- polypeptide (unbranched)

• Linkage- peptide bond, a covalent bond between an amino group and a carboxyl group (What kind of reaction?)

• Protein definition=– A biologically functional molecule that consists of

one or more polypeptides folded and coiled into a specific 3-dimensional structure.


Amino acids

• 20 amino acids

• All have a common structure– α carbon in the center– 4 partners

• Hydrogen

• Amino group

• Carboxyl group

• R group (Think “R” = “the rest”)


Figure 3.UN04

Side chain (R group)

Carboxylgroup

Aminogroup

carbon


R Groups

• Unique to each amino acid

• Often ionized at the pH found in cells (=7.2)

• Chemical and physical properties determine the characteristics of the amino acid and its role in a polypeptide


R groups (also called side chains) can be:

• Nonpolar: hydrophobic

• Polar: hydrophilic

• Electrically charged: hydrophilic– Acidic– Basic


Figure 3.17a

Nonpolar side chains; hydrophobicSide chain (R group)

Glycine (Gly or G)

Alanine (Ala or A)

Methionine (Met or M)

Phenylalanine (Phe or F)

Leucine (Leu or L)

Isoleucine (le or )

Tryptophan (Trp or W)

Proline (Pro or P)

Valine (Val or V)


Figure 3.17b

Polar side chains; hydrophilic

Serine (Ser or S)

Threonine (Thr or T)

Tyrosine (Tyr or Y)

Asparagine (Asn or N)

Cysteine (Cys or C)

Glutamine (Gln or Q)


Figure 3.17c

Aspartic acid (Asp or D)

Glutamic acid (Glu or E)

Arginine (Arg or R)

Lysine (Lys or K)

Histidine (His or H)

Electrically charged side chains; hydrophilic

Acidic (negatively charged)

Basic (positively charged)


Polypeptides

• Amino acids linked in a non-branching polymer by peptide bonds through a dehydration reaction.

• N-terminus: the amino end of a polypeptide

• C-terminus: the carboxyl end of a polypeptide


Figure 3.18

New peptidebond forming

Peptide bond

Side chains

Back-bone

Amino end (N-terminus)

Carboxyl end(C-terminus)

Peptide bond


To be clear . . .

• A polypeptide is NOT a protein

• A protein is one or more polypeptides precisely twisted, coiled and folded into a unique shape.

• The sequence of amino acids determines this shape

• The shape determines how it functions


• Function depends on the protein’s ability to recognize and bind with other molecules.

• The binding requires an exact match between the protein and the other molecule.

• Like puzzle pieces or a lock and key.


Figure 3.20

Antibody protein Protein from flu virus


4 Levels of Protein Structure

• Primary

• Secondary

• Tertiary

• Quaternary


Primary

• The sequence of amino acids

• The primary structure then controls the secondary and tertiary structures .


Figure 3.21aPrimary structure

Amino end

Carboxyl end

Primary structure of transthyretin

125

95

90

100105110

120

115

80

70 60

85

75

6555

504540

2530

35

20 15

1051

Amino acids


Secondary

• Coiled or folded patterns that result from hydrogen bonds between parts of the polypeptide backbone NOT the R-groups.

• 2 types– α helix– Β pleated sheet


Figure 3.21ba

Secondary structure

Hydrogenbond

pleated sheet

helix

Hydrogen bond

strand


Tertiary

• The overall shape of the polypeptide resulting from interactions between the side chains (R-groups)


Interactions contributing to tertiary structure

– Hydrophobic interactions• Amino acids with nonpolar (hydrophobic) side chains

get moved to the inner core away from water, then van der Waals interactions hold them together.

– Hydrogen bonds• Between polar side chains

– Ionic bonds• Between positively and negatively charged side chains

– Disulfide bridges• Covalent bond between the sulfur of 2 cysteine

monomers


Figure 3.21d

Hydrogenbond

Disulfidebridge

Polypeptidebackbone

Hydrophobicinteractions andvan der Waalsinteractions

Ionic bond


Figure 3.21bb

Tertiary structure

Transthyretinpolypeptide


Quaternary

• The overall protein structure that results from the aggregation of polypeptide subunits.


Figure 3.21bc

Quaternary structure

Transthyretinprotein


Figure 3.21b

Secondarystructure

Tertiarystructure

Quaternarystructure

Transthyretinpolypeptide

Transthyretinprotein

pleated sheet

helix


Figure 3.21f

HemeIron

subunit

subunit

subunit

subunitHemoglobin


Figure 3.22a

subunit

FunctionQuaternaryStructure

Secondaryand TertiaryStructures

PrimaryStructure

Normal hemoglobin

Molecules do notassociate with oneanother; each carriesoxygen.

1

234567

No

rmal


Figure 3.22aa

5 m


Figure 3.22b

subunit

FunctionQuaternaryStructure


PrimaryStructure

Sickle-cell hemoglobin

Exposed hydro-phobic region

Molecules crystallizedinto a fiber; capacity tocarry oxygen is reduced.

1234

567

Sic

kle-

cell


Figure 3.22ba

5 m


Figure 3.22

subunit

subunit

Function Red Blood CellShape

QuaternaryStructure


PrimaryStructure

Normal hemoglobin

Sickle-cell hemoglobin

Exposed hydro-phobic region

Molecules crystallizedinto a fiber; capacity tocarry oxygen is reduced.

Molecules do notassociate with oneanother; each carriesoxygen.

12

345

67

12

345

67

No

rmal

Sic

kle-

cell

5 m

5 m


Protein structure depends on:

• Primary sequence of amino acids

• AND

• pH

• Salt concentration

• Temperature

• Other environmental factors


Denaturation

• When environmental conditions are changed, the chemical bonds and interactions are destroyed .

• The protein unravels.

• Without its native shape, it is no longer functional.


Figure 3.23-2

Normal protein Denatured protein


Nucleic Acids

• Two types– DNA (deoxyribonucleic acid)– RNA (ribonucleic acid)

• Function: Store, transmit, and help express hereditary information.

• Monomer: nucleotide


Terms to know

• Chromosome: a single long DNA molecule

• Gene: A specific nucleotide sequence of DNA that codes for a specific amino acid sequence

• A chromosome may be composed of >100 genes.


Structure of Nucleic Acids

• Monomer: nucleotide

• Polymer: poly nucleotide

• Nucleotide = nucleoside (nitrogenous base + 5 carbon sugar) + 1 or more phosphates

• Nitrogenous (nitrogen-containing) as in “acid vs. base” not as in “foundation”. The N tends to take up H+ from solution acting as a base.


Figure 3.26b

(b) Nucleotide

Phosphategroup Sugar

(pentose)

Nitrogenousbase

Nucleoside


2 types of nitrogenous bases

• Pyrimidine- One 6-member ring of C and N– Cytosine– Thymine (only in DNA)– Uracil (only in RNA)

• Purine- 6-member ring fused to a 5-member ring– Adenine– Guanine


Figure 3.26c

Nitrogenous bases

Pyrimidines

Cytosine (C) Thymine(T, in DNA)

Uracil(U, in RNA)

Purines

Adenine (A) Guanine (G)


Sugars

• Deoxyribose-DNA

• Ribose- RNA


Figure 3.26d

Sugars

Deoxyribose (in DNA) Ribose (in RNA)


• Then a phosphate is added at the 5´ carbon of the sugar.

• Note: The “prime” symbol ´ distinguishes the sugar carbon from the nitrogenous base carbon.


Figure 3.26b

(b) Nucleotide


(pentose)

Nitrogenousbase

Nucleoside


Polynucleotide

• Nucleotides joined by phosphodiester linkage

• The sugars of the nucleotides are linked into a sugar phosphate backbone.


Figure 3.26aSugar-phosphate backbone(on blue background)

(a) Polynucleotide, or nucleic acid

(b) Nucleotide

5 end

3 end

5C

5C

3C

3C


(pentose)

Nitrogenousbase

Nucleoside


• Note: polynucleotides have directionality much like proteins

• Each end is different– 5énd-phosphate attached to 5Ć– 3énd- OH attached to 3Ć


Figure 3.26

Sugar-phosphate backbone(on blue background)

(a) Polynucleotide, or nucleic acid

(b) Nucleotide

(c) Nucleoside components

5 end

3 end

5C

5C

3C

3C


(pentose)

Nitrogenousbase

Nucleoside

Nitrogenous bases

Pyrimidines

Cytosine (C) Thymine(T, in DNA)

Uracil(U, in RNA)

Purines

Adenine (A) Guanine (G)

Sugars

Deoxyribose (in DNA) Ribose (in RNA)


DNA

• 2 polynucleotide strands that run antiparallel

• Think of a two way street– One strand 5´to 3´ – One strand 3´to 5´

• The 2 strands are held together by hydrogen bonds.


Figure 3.27a

(a) DNA

Sugar-phosphatebackbones

5

5

3

3 Base pair joinedby hydrogen bonding

Hydrogen bonds


• Only certain bases will bond together

• A-T

• G-C

• This allows 2 identical strands to be made

• Form follows function


RNA

• Only a single strand, but it can fold on itself

• No thymine so. . .

• A-U


Figure 3.27b


(b) Transfer RNA

Hydrogen bonds

Base pair joinedby hydrogen bonding


Figure 3.27

(a) DNA


5

5

3

3

(b) Transfer RNA


Hydrogen bonds



Evidence for common ancestry

• More common DNA sequences= more closely related


For Monday’s QuizMacromolecules plus lipids

To know:

•Monomers

•Polymers

•Linkages

•Basic structure

•Function

•Examples


Figure 3.UN06


Figure 3.UN06a


Figure 3.UN06b

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© 2014 Pearson Education, Inc. Carbon & the Molecular diversity of Life The big picture: The subcomponents of biological molecules and their sequence determine