Fig. 5-1 The Structure and Function of Large Biological Molecules Chapter 3.

Fig. 5-1

The Structure and Function of Large Biological Molecules

Chapter 3

Inorganic

• Compounds that do NOT contain carbon

Organic

• Compounds that contain carbon

• Carbon has 4 available electrons for bonding

• All organisms from the smallest bacteria to the largest tree and the most complex animals use the same set of molecules to run their bodies.

Monomers

• Building blocks/units that can be joined together to form larger molecules

Polymer

• Contains more than one molecule/usually several monomers

macromolecules

• Large polymers

HydroxylCHEMICALGROUP

STRUCTURE

NAME OF COMPOUND

EXAMPLE

FUNCTIONALPROPERTIES

Carbonyl Carboxyl

(may be written HO—)

In a hydroxyl group (—OH), ahydrogen atom is bonded to anoxygen atom, which in turn isbonded to the carbon skeleton ofthe organic molecule. (Do notconfuse this functional groupwith the hydroxide ion, OH–.)

When an oxygen atom isdouble-bonded to a carbonatom that is also bonded toan —OH group, the entireassembly of atoms is calleda carboxyl group (—COOH).

Carboxylic acids, or organicacids

Ketones if the carbonyl group iswithin a carbon skeleton

Aldehydes if the carbonyl groupis at the end of the carbonskeleton

Alcohols (their specific namesusually end in -ol)

Ethanol, the alcohol present inalcoholic beverages

Acetone, the simplest ketone Acetic acid, which gives vinegarits sour taste

Propanal, an aldehyde

Has acidic propertiesbecause the covalent bondbetween oxygen and hydrogenis so polar; for example,

Found in cells in the ionizedform with a charge of 1– andcalled a carboxylate ion (here,specifically, the acetate ion).

Acetic acid Acetate ion

A ketone and an aldehyde maybe structural isomers withdifferent properties, as is thecase for acetone and propanal.

These two groups are alsofound in sugars, giving rise totwo major groups of sugars:aldoses (containing analdehyde) and ketoses(containing a ketone).

Is polar as a result of theelectrons spending more timenear the electronegative oxygen atom.

Can form hydrogen bonds withwater molecules, helpingdissolve organic compoundssuch as sugars.

The carbonyl group ( CO)consists of a carbon atomjoined to an oxygen atom by adouble bond.

CHEMICALGROUP

STRUCTURE

NAME OFCOMPOUND

EXAMPLE

FUNCTIONALPROPERTIES

Amino Sulfhydryl Phosphate Methyl

A methyl group consists of acarbon bonded to threehydrogen atoms. The methylgroup may be attached to acarbon or to a different atom.

In a phosphate group, aphosphorus atom is bonded tofour oxygen atoms; one oxygenis bonded to the carbon skeleton;two oxygens carry negativecharges. The phosphate group(—OPO3

2–, abbreviated ) is anionized form of a phosphoric acidgroup (—OPO3H2; note the twohydrogens).

P

The sulfhydryl groupconsists of a sulfur atombonded to an atom ofhydrogen; resembles ahydroxyl group in shape.

(may bewritten HS—)

The amino group(—NH2) consists of anitrogen atom bondedto two hydrogen atomsand to the carbon skeleton.

Amines Thiols Organic phosphates Methylated compounds

5-Methyl cytidine

5-Methyl cytidine is acomponent of DNA that hasbeen modified by addition ofthe methyl group.

In addition to taking part inmany important chemicalreactions in cells, glycerolphosphate provides thebackbone for phospholipids,the most prevalent molecules incell membranes.

Glycerol phosphate

Cysteine

Cysteine is an importantsulfur-containing aminoacid.

Glycine

Because it also has acarboxyl group, glycineis both an amine anda carboxylic acid;compounds with bothgroups are called amino acids.

Addition of a methyl groupto DNA, or to moleculesbound to DNA, affectsexpression of genes.

Arrangement of methylgroups in male and femalesex hormones affectstheir shape and function.

Contributes negative chargeto the molecule of which it isa part (2– when at the end ofa molecule; 1– when locatedinternally in a chain ofphosphates).

Has the potential to reactwith water, releasing energy.

Two sulfhydryl groupscan react, forming acovalent bond. This“cross-linking” helpsstabilize proteinstructure.

Cross-linking ofcysteines in hairproteins maintains thecurliness or straightnessof hair. Straight hair canbe “permanently” curledby shaping it aroundcurlers, then breakingand re-forming thecross-linking bonds.

Acts as a base; canpick up an H+ fromthe surroundingsolution (water, in living organisms).

Ionized, with acharge of 1+, undercellular conditions.

(nonionized) (ionized)

Fig. 5-2

Short polymer

HO 1 2 3 H HO H

Unlinked monomer

Dehydration removes a watermolecule, forming a new bond

HO

H2O

H1 2 3 4

Longer polymer

(a) Dehydration reaction in the synthesis of a polymer

HO 1 2 3 4 H

H2OHydrolysis adds a watermolecule, breaking a bond

HO HH HO1 2 3

(b) Hydrolysis of a polymer

Building of Biological Polymers

Fig. 5-2a

Dehydration removes a watermolecule, forming a new bond

Short polymer Unlinked monomer

Longer polymer

Dehydration reaction in the synthesis of a polymer

HO

HO

HO

H2O

H

HH

4321

1 2 3

(a)

Fig. 5-2b

Hydrolysis adds a watermolecule, breaking a bond

Hydrolysis of a polymer

HO

HO HO

H2O

H

H

H321

1 2 3 4

(b)

Carbohydrates (meaning: water of carbons)

• General Formula (CH2O)

• Examples: monosaccharides, disaccharides, polysaccharides

• Energy Stores: sugars, glycogen, and starches

• Structural Molecules: cellulose and chitin

Monosaccharides

• Simple sugars; usually made up of 3 (triose), 5 (pentose), or 6 (hexose) carbons

• Ribose and deoxyribose are both present in RNA and DNA respectively

Fig. 5-3

Dihydroxyacetone

Ribulose

Ket

ose

sA

ldo

ses

Fructose

Glyceraldehyde

Ribose

Glucose Galactose

Hexoses (C6H12O6)Pentoses (C5H10O5)Trioses (C3H6O3)

Simple sugars: made up of

3 “triose”,

5 “pentose”,or

6 “hexose”

carbons

Major Role of Glucose

• Primary energy source fueling cell metabolism.

Isomers

• Same chemical formula-differ in arrangement of atoms

Disaccharides: Double sugars

• Energy sources and as building blocks for larger molecules

• Formed by joining 2 monosaccharides

• Sucrose: table sugar (glucose + fructose)

• Maltose: malt sugar (glucose + glucose)

• Lactose: milk sugar (glucose + galactose)

• Trehalose: Help protect membranes and proteins from disruption

Fig. 5-5

(b) Dehydration reaction in the synthesis of sucrose

Glucose Fructose Sucrose

MaltoseGlucoseGlucose

(a) Dehydration reaction in the synthesis of maltose

1–4glycosidic

linkage

1–2glycosidic

linkage

Polysaccharides

• Polymers composed of hundreds to thousands of glucose monomers

• 3 important examples: glycogen, starch, and cellulose

• Differ in the molecule’s overall shape in form of the glucose subunit- either alpha glucose or beta glucose and in the bonds between these subunits

Fig. 5-6

(b) Glycogen: an animal polysaccharide

Starch

GlycogenAmylose

Chloroplast

(a) Starch: a plant polysaccharide

Amylopectin

Mitochondria Glycogen granules

0.5 µm

1 µm

Fig. 5-7

(a) and glucose ring structures

Glucose Glucose

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

Fig. 5-7a

(a) and glucose ring structures

Glucose Glucose

Fig. 5-7bc

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

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

Fig. 5-8

Glucosemonomer

Cellulosemolecules

Microfibril

Cellulosemicrofibrilsin a plantcell wall

0.5 µm

10 µm

Cell walls

Fig. 5-9

Cellulose-digesting prokaryotes are found in grazing animals such as this cow.

Fig. 5-10

The structureof the chitinmonomer.

(a) (b) (c)Chitin forms theexoskeleton ofarthropods.

Chitin is used to makea strong and flexiblesurgical thread.

Polysaccharide Structure Biological function

Location in the organism

Glycogen Branched alpha-1,4- linkages

Temporary energy stores in animals

Liver, muscle cells

Starch 1,4 alpha linkages

Stored energy in plants

Leaves, roots

Cellulose Unbranched chain of 1,4 beta linkages

Structural material in plants

Plant cell walls

Chitin 1,4 beta linkages + amino group

Structural material in arthropods and fungi

Exoskeleton, fungi cell walls

LIPIDS

• Group of organic compounds with an oil, greasy, or waxy consistency

• Insoluble in water and tend to be water-repelling• High proportion of carbon-hydrogen with small

proportion of oxygen (some contain P and N)• Excellent way to store energy; yield more than

twice the energy of carbohydrates• Types of lipids: fatty acids, waxes, triglycerides,

phopholipids, steroids

Fig. 5-11

Fatty acid(palmitic acid)

Glycerol

(a) Dehydration reaction in the synthesis of a fat

Ester linkage

(b) Fat molecule (triacylglycerol)

Fig. 5-11a

Fatty acid(palmitic acid)

(a) Dehydration reaction in the synthesis of a fat

Glycerol

Fig. 5-11b

(b) Fat molecule (triacylglycerol)

Ester linkage

Type of Lipid Structure Biological Function Location in the organism

Fatty acid Simplest Monomer -----------------

Waxes Long alcohol chain + 3 fatty acids

Waterproofing Leaves, fruits, skin, feathers, hair

Triglycerides One glycerol + 3 fatty acids

Insulation Seeds, under skin, protect organs

Phospholipids Saturated/unsaturated fatty acid + glycerol

Main component of cell membranes

Cell membranes

Glycolipid 3rd C of glycerol bonded to carbohydrate chain

Attached to carbohydrate; cell-cell communication

Cell membranes

Steroid Continuous carbon ring

Chemical messengers/hormones

Cell membranes

Fig. 5-12

Structuralformula of asaturated fatmolecule

Stearic acid, asaturated fattyacid

(a) Saturated fat

Structural formulaof an unsaturatedfat molecule

Oleic acid, anunsaturatedfatty acid

(b) Unsaturated fat

cis doublebond causesbending

Fig. 5-12a

(a) Saturated fat

Structuralformula of asaturated fatmolecule

Stearic acid, asaturated fattyacid

Fig. 5-12b

(b) Unsaturated fat

Structural formulaof an unsaturatedfat molecule

Oleic acid, anunsaturatedfatty acid

cis doublebond causesbending

Fig. 5-13

(b) Space-filling model(a) (c)Structural formula Phospholipid symbol

Fatty acids

Hydrophilichead

Hydrophobictails

Choline

Phosphate

Glycerol

Hyd

rop

ho

bic

tai

lsH

ydro

ph

ilic

hea

d

Fig. 5-13ab

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

Fatty acids

Choline

Phosphate

Glycerol

Hyd

rop

ho

bic

tai

lsH

ydro

ph

ilic

hea

d

Fig. 5-14

Hydrophilichead

Hydrophobictail WATER

WATER

Fig. 5-15

CHOLESTEROL, A STEROID

Amino acids

• Are the basic units from which proteins are made

• Plants can manufacture all the amino acids they require from simpler molecules

• Animals must obtain a certain number of ready-made amino acids from their diet

• The order of aa directed by the order of nucleotides in DNA

Fig. 5-17a

Nonpolar

Glycine (Gly or G)

Alanine (Ala or A)

Valine (Val or V)

Leucine (Leu or L)

Isoleucine (Ile or I)

Methionine (Met or M)

Phenylalanine (Phe or F)

Tryptophan (Trp or W)

Proline (Pro or P)

AMINO ACIDS

Fig. 5-17b

Polar

Asparagine (Asn or N)

Glutamine (Gln or Q)

Serine (Ser or S)

Threonine (Thr or T)

Cysteine (Cys or C)

Tyrosine (Tyr or Y)

Peptidebond

Fig. 5-18

Amino end(N-terminus)

Peptidebond

Side chains

Backbone

Carboxyl end(C-terminus)

(a)

(b)

MAKING A POLYPEPTIDE CHAIN

PROTEINS

• Are large complex molecules that are made of smaller monomer units, amino acids, and linked together through dehydration reactions

• 20 different amino acids• Make up more than 50% of the dry weight of

animals and bacteria• Structural proteins make up hair, finger nails,

silk, covering of viruses, and forms tendons and cartilage

• Soluble proteins in the body fluids of animals include antibodies

Fibrous proteins

• Water insoluble

• Very tough physically; may be supple or stretch

• Parallel polypeptide chains in long fibers or sheets

• FUNCTION: structural role of cells/organisms

contractile (myosin,actin)

Globular Proteins

• Easily water soluble• Tertiary structure critical to function• Polypeptide chains folded into a spherical

shape• Catalytic: enzymes, -ase• Regulatory: hormones• Transport: hemoglobin• Protective: anti-bodies

Fig. 5-20

Antibody protein Protein from flu virus

Fig. 5-21

PrimaryStructure

SecondaryStructure

TertiaryStructure

pleated sheet

Examples ofamino acidsubunits

+H3N Amino end

helix

QuaternaryStructure

Fig. 5-21a

Amino acidsubunits

+H3N

Amino end

25

20

15

10

5

1

Primary Structure

Polypeptide

Fig. 5-21b

Amino acidsubunits

+H3N Amino end

Carboxyl end125

120

115

110

105

100

95

9085

80

75

20

25

15

10

5

1

Secondary structure

Polypeptides become folded in various ways; maintained with hydrogen bonds between neighboring CO and NH groups

Example: alpha- keratin

Beta- silk protein

Fig. 5-21c

Secondary Structure

pleated sheet

Examples ofamino acidsubunits

helix

Fig. 5-21d

Abdominal glands of thespider secrete silk fibers

made of a structural proteincontaining pleated sheets.

The radiating strands, madeof dry silk fibers, maintain

the shape of the web.

The spiral strands (capturestrands) are elastic, stretching

in response to wind, rain,and the touch of insects.

Fig. 5-21e

Tertiary Structure Quaternary Structure

Tertiary structure: precise folding creates a 3 dimensional arrangement of the active “R” groups

Fig. 5-21f

Polypeptidebackbone

Hydrophobicinteractions andvan der Waalsinteractions

Disulfide bridge

Ionic bond

Hydrogenbond

Fig. 5-21g

Polypeptidechain

Chains

HemeIron

Chains

CollagenHemoglobin

ENZYMES

• Efficient catalyst- shapes very specific• Decreases the activation energy needed for reactions

to occur• For each chemical reaction that occurs in an

organism, a specific enzyme is required (Not consumed in the reaction)

• Standard suffix –ase; name of enzyme is given according to its substrate and kind of reaction it catalyzes

• Rate of the reaction can be regulated by temperature, pH and substrate concentration

Denaturing of Proteins

• Strong acids & alkalis: disrupt ionic bonds and result in coagulation of the protein

• Heavy metals: may disrupt ionic bonds• Heat & Radiation: cause disruption of the

bonds in the protein through energy provided to the atoms

• Detergents & Solvents: form bonds with the non-polar groups in the protein, thereby disrupting hydrogen bonding

NUCLEIC ACIDS DNA and RNA

• Largest organic molecule made by organisms• Nucleotides are the basic units of both DNA and

RNA– A nucleotide has three parts sugar,

phosphate, and a nitrogen-containing base•DNA nucleotides: Deoxyribose sugar,

phosphate and nitrogenous bases (adenine, guanine, cytosine, thymine)

•RNA nucleotides: ribose sugar, phosphate, and nitrogenous bases (adenine, guanine, cytosine, uracil)

5' end

5'C

3'C

5'C

3'C

3' end

Polynucleotide, nucleic acid

(b) Nucleotide

Nucleoside

Nitrogenousbase

3'C

5'C

Phosphategroup Sugar

(pentose)

Purines

Guanine (G)Adenine (A)

Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)

Nitrogenous bases Pyrimidines

Ribose (in RNA)Deoxyribose (in DNA)

Sugars

Nucleotide components: sugars

DNA Sugar-phosphatebackbones

3' end

3' end

3' end

3' end

5' end

5' end

5' end

5' end

Base pair (joined byhydrogen bonding)

Old strands

Newstrands

Nucleotideabout to beadded to anew strand

Types of nucleic acids• Adenosine phosphate -ATP: energy carrier

• Nucleotide coenzymes- NAD, NADP, FAD: transport of protons (H), electrons from one reaction site to another

• Nucleic acids-DNA & RNA: storage, transmission, translate of genetic information

– DNA: contains instructions for primary structure of proteins (located in the nucleus of a cells)

– RNA: carries the instructions from the nucleus to the cytoplasm where proteins are assembled at the ribosomes

DNA vs. RNA

Structure of DNA