PowerPoint Lecture prepared by Dr. Judi Roux,

University of Minnesota Duluth

Chapter 2

Hydrocarbons & Macromolecules

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Learning Outcomes

• Discuss the importance of carbon in living organisms.

• Describe the structure of carbohydrates, proteins, lipids, and nucleic acids and the roles these macromolecules play in cells.

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Carbon, hydrogen, oxygen, and nitrogen make up the bulk of living matter, because they form

MOLECULES

“CHNOPS”CarbonHydrogenNitrogenOxygen

PhosphorusSulfur

P is a major atom in DNA, RNA

S is found in two amino acids that are found in all proteins

Atoms: the fundamental units of an element

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Covalent bonds = join atoms into molecules through electron sharing

In covalent bonds, two atoms share one or more pairs of outer shell electrons, forming molecules

Molecule = specific number of atoms sharing electrons in covalent bonds

MolecularFormula

Electron DistributionDiagram

StructuralFormula

Space-FillingModel

O2

Oxygen

CH4

Methane

H2OWater

Polar covalent bondsin a water molecule

Single bond

Double bond

Nonpolar covalentbonds

Polar covalentbonds

(slightly −)

(slightly +) (slightly +)

H H

H

H

H

H

H H

O O

O

C

O

H H

H2

Hydrogen

Unequal electron sharing creates

polar molecules• A molecule is nonpolar when its covalently bonded

atoms share electrons equally• A molecule is polar when one atom captures more

electrons, most of the time• Atoms gain a partial ionic charge, but• NO atom gains a complete +1 or -1 charge -

Molecules behave as discrete units in water

- Atoms in molecules do not usually dissociate in water -Molecular bonds do not form ions – electrons shared equally

Small molecules dissolve in water when –They contain polar covalent bonds, &/or

They contain an ionic bond

IONIC AND COVALENT BONDS, REVISITED

caffeine glucose aspirinleucine

Large molecules form stable structures in water

Lysozyme, a protein

DNA, a nucleic acid

tRNA bound to a protein

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INTRODUCTION TO ORGANIC COMPOUNDS

INTRODUCTION TO ORGANIC COMPOUNDSLife’s molecular diversity is based on the properties of carbonA carbon atom can form four covalent bonds

• Allowing it to build large and diverse organic compounds

Structuralformula

Methane

H H

H

H H H

H

H

Ball-and-stickmodel

Space-fillingmodel

CC

The 4 single bonds of carbon point to the corners of a tetrahedron.

Carbon atoms

bond covalently to build an infinite number of small to very large molecules

and even “molecular crystals” !

Chemistry for Biology StudentsOrganic chemistry

Chemistry of biological systems

Concerns carbon-containing molecules• Interaction with other elements • E.g., hydrogen

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Life’s molecular diversity is based on the properties of carbon

• Methane and other compounds composed of only carbon and hydrogen are called hydrocarbons.

• Carbon, with attached hydrogens, can form chains of various lengths.

H

H

H

HC

• Electrons sharedequally

• No partial charges• Hydrocarbons arenonpolar

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Hydrocarbons are composed of only hydrogen and carbon

There are an infinite variety of hydrocarbons!Molecules with the same molecular formula but different structures = isomersCan be any lengthCan be branched / unbranched

Can form ringsCan be rigid, flexible, or both- Hydrocarbon chains can bend at single bonds, but are rigid at double & triple bonds

Figure 3.1b-0

Butane

Length: Carbon skeletons varyin length.

Propane 1-Butene 2-Butene

Double bonds: Carbon skeletons may havedouble bonds, which can vary in location.

Double bond

Isobutane Cyclohexane Benzene

Branching: Carbon skeletons maybe unbranched or branched.

Rings: Carbon skeletons may be arranged inrings. (In the abbreviated ring structures, eachcorner represents a carbon and its attachedhydrogens.)

Ethane

A few chemical groups are key to the functioning of biological moleculesThe unique properties of an organic compound depend on

• the size and shape of its carbon skeleton and• the groups of atoms “functional groups” that are

attached to that skeleton.

• Functional groups are particular groupings of atoms that give organic molecules particular properties

For example:

The sex hormones testosterone and estradiol (a type of estrogen) differ only in the groups of atoms highlighted in the following figure:

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Testosterone Estradiol

Functional Groups - Attached to hydrocarbon backbones

- Groups of atoms that react

H

Cells make a huge number of large molecules from a particular set of small molecules

The four main classes of biological molecules:

lipids carbohydrates

proteins and nucleic acids

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LIPIDS

Lipids• are water insoluble (hydrophobic, or water-fearing)

compounds,• are important in long-term energy storage,• consist mainly of carbon and hydrogen atoms linked

by nonpolar covalent bonds.• form aggregates.

Any hydrocarbon is a “lipid” if it is hydrophobic

Lipids vary a great deal in structure and function.

Biological MacromoleculesLipids

• Composed mostly of carbon and hydrogen

• Hydrophobic molecules

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Biological Macromolecules

Three types of lipids:

Fats: glycerol and three fatty acid tails• Store energy

Steroids: four fused carbon rings • Cholesterol and sex hormones

Phospholipids: glycerol molecule, two fatty acid tails, and a phosphate group

• Component of cell membranes

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Fats, also called triglycerides

• Are lipids whose main function is energy storage

• Consist of glycerol linked to three fatty acids

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

H2O

H HHH

OHOH OH

H

HOC O

C C C

Fatty acid

Glycerol

H HH

H H

CH2

O O O

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

CH2

CH2

CH2

CH2

CH2

CH2

CH

CH

CH2

CH2

CH2

CH2

CH2

CH2

CH3

C C C OOO

C C C

H

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3.1 Nutrients: MacronutrientsFats• Energy storage molecules

• Act as a cushion and insulator for skin & other organs

• Consist of a glycerol attached to fatty acid tails• Essential fatty acids: cannot be made in the body

(e.g., omega-3 and omega-6)

Saturated fats Unsaturated fats

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3.1 Nutrients: Macronutrients

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3.1 Nutrients: Macronutrients

Saturated fats• Fatty acid carbons

bound to as much hydrogen as possible

• Lack double bonds

• Solid at room temperature

• Most animal fats are saturated

Unsaturated fats• Fewer hydrogens bound

to carbons

• Contain double bonds• Kinks in the tails

• Liquid at room temperature

• Most plant fats (oils) are unsaturated or polyunsaturated

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3.1 Nutrients: MacronutrientsFats

• Hydrogenation • Process of adding hydrogen atoms to unsaturated fat

to make it a solid

• Trans fats • Produced by incomplete hydrogenation

• Double bonds are flat and not kinked

• May be linked to increased health risks• Clogged arteries• Heart disease • Diabetes

3.10 Phospholipids and steroids are important lipids with a variety of functions

• Phospholipids are the major component of all cell membranes.

• Phospholipids are structurally similar to fats.• Fats contain three fatty acids attached to glycerol.• Phospholipids contain two fatty acids attached to

glycerol.

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Phosphategroup

Glycerol

Hydrophilic heads

Hydrophobic tails

Symbol for phospholipid

Water

Water

3.10 Phospholipids and steroids are important lipids with a variety of functions

• Phospholipids cluster into a bilayer of phospholipids.

• The hydrophilic heads are in contact with• the water of the environment and • the internal part of the cell.

• The hydrophobic tails cluster together in the center of the bilayer.

3.10 Phospholipids and steroids are important lipids with a variety of functions

• Steroids are lipids in which the carbon skeleton contains four fused rings.

• Cholesterol is• a common component in animal cell membranes

and• a starting material for making steroids, including sex

hormones.

Figure 3.10c

Biological Macromolecules:Carbohydrates Proteins Nucleic Acids

Macromolecules

Large organic molecules comprise living organisms:

They are made by linking together smaller molecules called monomer subunits

In organic chemistry, such a larger molecule is called a polymer of these smaller monomers

Living systems make macromolecules = polymers of certain types of monomers

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Cells make most of their large molecules by joining smaller organic molecules into chains called polymers

H

OH H

OH

H OH

Unlinked monomer

Dehydration reaction

Longer polymer

Short polymer

OH H

H OH

Unlinked monomer

Dehydration reaction

Short polymer

H2O

Polymers are broken down to monomers by the reverse process, hydrolysis

H

H2O

OH

H OHOH H

Hydrolysis

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CARBOHYDRATES

Biological Macromolecules

Carbohydrates

• Molecules of carbon,oxygen, and hydrogen(CH2O)

• Major source of energyfor cells

• Made of sugar subunits• Monosaccharide: 1 sugar• Disaccharides: 2 sugars• Polysaccharide: many sugars

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The monosaccharides glucose and fructose are isomers

• That contain the same atoms but in different arrangements

• Both form rings when dissolved in water

C

C

C

C

C

C

C

C

C

C

H

H

H

H

H

H

H H

H

H

H

HO

H

H

H

C

O

HO

OH

OH

OH

OH OH

OH

OH

C O

OH

Glucose Fructose

Figure 3.4c

Structuralformula

Abbreviatedstructure

Simplifiedstructure

Polysaccharides are long chains of sugar units

Polysaccharides are macromolecules, polymers composed of thousands of monosaccharides.

• Polysaccharides may function as• storage molecules or• structural compounds.

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Starch granules ina potato tuber cell Starch

Glycogen granulesin muscletissue

Cellulose microfibrilsin a plant cell wall

Cellulosemolecules Hydrogen bonds

Cellulose

Glycogen

Glucosemonomer

PROTEINS

Proteins have a wide range of functions and structuresProteins are

• involved in nearly every dynamic function in your body and

• very diverse, with tens of thousands of different proteins, each with a specific structure and function, in the human body.

The types of proteins made by a cell determine what type of organism is made – goldfish, mushroom, rabbit, pine tree, snake, etc.

Genes determine what types of proteins a particular living system can make.

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Proteins have a wide range of functions and structures

Probably the most important role for proteins is as enzymes, proteins that

• serve as catalysts – “speed up” reactions and• regulate virtually all chemical reactions within cells.

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Proteins have a wide range of functions and structures

Other types of proteins include• transport proteins embedded in cell membranes,

which move sugar molecules and other nutrients into your cells,

• defensive proteins, such as antibodies of the immune system,

• signal proteins such as many hormones and other chemical messengers that help coordinate body activities,

Proteins have a wide range of functions and structures

Other types of proteins include (continued)• receptor proteins, built into cell membranes, which

receive and transmit signals into your cells,• contractile proteins found within muscle cells,• structural proteins such as collagen, which form the

long, strong fibers of connective tissues, and• storage proteins, which serve as a source of amino

acids for developing embryos in eggs and seeds.

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Biological MacromoleculesProteins

• Made of carbon, oxygen, hydrogen, and nitrogen and some sulfur

Amino acid subunits• 20 different amino acids• Joined by peptide bonds• Different amino acid

combinations = different properties for proteins

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Aminoacids

+H3NAmino end

Peptide bondsconnect aminoacids.

Alphahelix

Secondary structuresare maintained byhydrogen bondsbetween atoms

of thebackbone.

Beta pleated sheet

Tertiary structure isstabilized by interactionsbetween R groups.

Polypeptides are associatedinto a functional protein.

TERTIARY STRUCTURE

PRIMARY STRUCTURE

QUATERNARYSTRUCTURE

Two types ofSECONDARY STRUCTURES

At the molecular level

Form = Function

Protein shape determinesall its functions = 3o &/or 4o structure

Note:Primary Structure – type &position of amino acids inthe chain – determinesprotein shape!

Tertiary & Quaternary Structure aligns functional groups on amino acid side chains,

- allowing the protein to interact with other chemicals and proteins

NUCLEIC ACIDS

NUCLEIC ACIDS

Nucleic acids are information-rich polymers of nucleotides

• Nucleic acids such as DNA and RNA encode the types of proteins made by a cell, and thus control the metabolism and functions performed by a cell

• Stretches of a DNA molecule called genes program the amino acid sequences of proteins

Nucleic acids are polymers of nucleotides

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are composed of monomers called nucleotides.

Nucleotides have three parts:1. a five-carbon sugar called ribose in RNA and

deoxyribose in DNA,2. a phosphate group, and3. a nitrogenous base.

Sugar

Phosphategroup

Nitrogenousbase

(adenine)

Nucleic acids are polymers of nucleotides

A nucleic acid polymer, a polynucleotide, forms from the nucleotide monomers when the phosphate of one nucleotide bonds to the sugar of the next nucleotide by dehydration reactions.

This produces a repeating sugar-phosphate backbone with protruding nitrogenous bases.

DNA polynucleotide

A

C

T

G

T

Sugar-phosphate backbone

Phosphate groupNitrogenous base

SugarA

C

T

G

T

Phosphategroup

O

O–

OO P CH2

H3C C

C

C

CN

C

N

H

H

O

O

C

O

O

H

C H H

H

C

H

Nitrogenous base(A, G, C, or T)

Thymine (T)

Sugar(deoxyribose)

DNA nucleotide

DNA nucleotide

DNA and RNA are polymers of nucleotidesDNA is a nucleic acid made of long chains of nucleotide monomers

DNA has four kinds of nitrogenous bases• A, T, C, and G

CC

C

CC

C

O

N

C

H

H

ONH

H3C

H H

H

H

N

N

N

H

OC

H HN

H C

N

N N

N

C

CC

C

H

H

N

N

H

C

CN

C HN

CN

H C

O

H

H

Thymine (T) Cytosine (C) Adenine (A) Guanine (G)

PurinesPyrimidines

DNA and RNA are the two types of nucleic acids

The amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance known as a gene.

Genes consist of DNA (deoxyribonucleic acid), a type of nucleic acid.

DNA is inherited from an organism’s parents.

DNA provides directions for its own replication.

DNA programs a cell’s activities by directing the synthesis of proteins.

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DNA forms a “double helix”Hydrogen bonds between bases hold two strands togetherEach base pairs with a complementary partner

• A with T, and G with C

G C

T A

A T

G

G

C

C

A T

GC

T A

T A

A T

A T

G C

A T

O

O

OH–O

P

O O–O

PO

OO

P– O

– O OP

OO

O

OH

H2C

H2C

H2C

H2C

O

O

O

O

O

O

O

O

PO–

O–

O–

O–

OH

HO

O

O

O

P

P

P

O

O

O

O

O

O

O

O

T A

G C

C G

A T

CH2

CH2

CH2

CH2

Hydrogen bond

Basepair

Ribbon model Partial chemical structure Computer model

RNA, by contrast is a single-stranded polynucleotide

and contains uracil rather than thymine

Nitrogenous base (A, G, C, or U)

Phosphategroup

O

O–

OO P CH2

HC

C

C

CN

C

N

H

H

O

O

C

O

O

H

C H H

OH

C

H

Uracil (U)

Sugar(ribose)

KeyHydrogen atomCarbon atomNitrogen atomOxygen atom

Phosphorus atom

Biological Macromolecules

Types of nucleic acids

RNA • For protein synthesis• Ribose sugar & uracil bas

DNA• Stores genetic information• Deoxyribose sugar & thymine base• Double helix structure

• Sugar-phosphate backbone• Rungs of nitrogen base pairs

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Recap:

Monomers & Polymers:

• Carbohydrates

• Proteins

• Nucleic Acids

Aggregates:

Lipids – any hydrophobic hydrocarbon

Macromolecules act like “machines” as well as “building blocks”

Protein binding: Interleukin Receptor http://www.youtube.com/watch?feature=player_detailpage&v=Ms_ehUVvKKk 2014 Fall YouTube

Virus infecting bacterium YouTube http://www.youtube.com/watch?feature=player_detailpage&v=41aqxcxsX2w

Kinesin motor protein carrying a lysosome along a microtubule https://www.youtube.com/watch?feature=player_embedded&v=y-uuk4Pr2i8