1 chapter 3 biological molecules

Chapter 3Biological Molecules

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Carbon Chemistry• Carbon is the Backbone of Biological

Molecules (macromolecules)• All living organisms Are made up of

chemicals based mostly on the element carbon

Figure 4.1

There are 4 types of Biological Macromolecules

Carbohydrates like sugar, starch, chiton, cellulose, potatoes and candy!

Lipids like fat, butter, cream and olive oil (all other oils as well including motor oil)

Proteins like steak, collagen (jello), hair and the machinery that runs your cellular metabolism

Nucleic Acids – these are DNA and RNA which are responsible for storing information about how to build proteins

Carbon Chemistry

• Organic chemistry is the study of carbon compounds

• Carbon atoms can form diverse molecules by bonding to four other atoms or molecules

• Carbon compounds range from simple molecules to complex ones

• Carbon has four valence electrons and may form single, double, triple, or quadruple bonds

How Many?• A single carbon atom can form a maximum

of ___covalent bond(s)?

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

H O N C

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)

Figure 4.4

• The bonding versatility of carbon allows it to form many diverse molecules, including carbon skeletons

(a) Methane

(b) Ethane

(c) Ethene (ethylene)

Molecular Formula

Structural Formula

Ball-and-Stick Model

Space-Filling Model

Name and Comments

Figure 4.3 A-C

• Carbon may bond to itself forming carbon chains• Carbon chains form the skeletons of most

organic molecules• Carbon chains vary in length and shape• The following diagrams show the atoms and

their bonds

H H HH H

HH H H H

H HH H

H H H H

HHHH H

C C C C C

C C C C C C C

CCCCCCCC

(a) Length

(b) Branching

(c) Double bonds

(d) Rings

Ethane Propane

Butane isobutane

1-Butene 2-Butene

Cyclohexane Benzene

H H H HH

Figure 4.5 A-D

So….• Carbohydrates look something like this…

• CH3-CH2-CH2-CH2

Notice that the way the methane is drawn bears no resemblance to the actual shape of the molecule. Methane isn't flat with 90° bond angles. This mismatch between what you draw and what the molecule actually looks like can lead to problems if you aren't careful.

Hydrocarbons

• Hydrocarbons are molecules consisting of only carbon and hydrogen

• Hydrocarbons Are found within many of a cell’s organic molecules

(a) A fat molecule (b) Mammalian adipose cells100 µm

Fat droplets (stained red)

Figure 4.6 A, B

Functional Groups• Functional groups

are the parts of molecules involved in chemical reactions

• They Are the chemically reactive groups of atoms within an organic molecule

• Give organic molecules distinctive chemical properties

Estradiol

Testosterone

Female lion

Male lionFigure 4.9

Macromolecules– Are large molecules composed of smaller

molecules– Are complex in their structures

Figure 5.1

Macromolecules•Most macromolecules are polymers, built from monomers•A monomer is a single unit of a polymer like legos!• Four classes of life’s organic molecules are polymers

– Carbohydrates (include sugars, starches etc)– Proteins– Nucleic acids– Lipids (fats)

• A polymer– Is a long molecule consisting of many

similar building blocks called monomers– Specific monomers make up each

macromolecule– E.g. amino acids are the monomers for

proteins

The Synthesis and Breakdown of Polymers

• Monomers form larger molecules by condensation reactions called dehydration synthesis

• DRAW THIS AND CHECK WITH YOUR GROUP THAT IT IS RIGHT!

(a) Dehydration reaction in the synthesis of a polymer

HO H1 2 3 HO

HO H1 2 3 4

Short polymer Unlinked monomer

Longer polymer

Dehydration removes a watermolecule, forming a new bond

Figure 5.2A

Building up and breaking down

• When you are building a biochemical, you put monomers together and it’s called “DEHYDRATION SYNTHESIS”

• When you break it down to release energy, it is called “hydrolysis”

• Hydro=water lysis=to break• If water is a product, then it’s hydrolysis

• Ex: galactose+glucose = lactose + water

The Synthesis and Breakdown of Polymers

• Polymers can disassemble by– Hydrolysis (addition of water molecules)– DRAW THIS AND COMPARE IT WITH YOUR GROUP TO

MAKE SURE IT’S RIGHT!

(b) Hydrolysis of a polymer

HO 1 2 3 H

HO H1 2 3 4

Hydrolysis adds a watermolecule, breaking a bond

Figure 5.2B

• Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers

• An immense variety of polymers can be built from a small set of monomers

Carbohydrates• Serve as fuel and building material• Include both sugars and their polymers

(starch, cellulose, etc.)• Carbohydrates are either:• Monosaccharides – a single monomer

Disaccharides - two monomers• Polysaccharides – three or more

Sugars

•Monosaccharides–Are the simplest sugars–Can be used for fuel–Can be converted into other organic molecules

–Can be combined into polymers

Monosaccharides• Glucose• Maltose• Sucrose• Fructose

• Note the “ose”

• Examples of monosaccharides

Triose sugars(C3H6O3)

Pentose sugars(C5H10O5)

Hexose sugars(C6H12O6)

H C OH

HO C H

H C OH

HO C H

H C OH

C OC O

H C OH

HO C H

H C OH

H H H H

C C C COOOO

Glyceraldehyde

RiboseGlucose Galactose

Dihydroxyacetone

Ribulose

FructoseFigure 5.3

• Monosaccharides– May be linear– Can form rings

H C OH

HO C H

H C OH

6CH2OH 6CH2OH

(a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5.

O H OO

Figure 5.4

• Disaccharides– Consist of two monosaccharides– Are joined by a glycosidic linkage– a glycosidic bond is a type of covalent

bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate.

– To clarify: Disaccharides are formed when two monosaccharides join together by the dehydration synthesis reaction resulting in a glycosidic bond

Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide.

Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose.Notice that fructose,though a hexose like glucose, forms a five-sided ring.

CH2OH HO

1 41– 4

glycosidiclinkage

1–2glycosidic

linkage

Glucose

Glucose Glucose

Fructose

Maltose

Sucrose

Figure 5.5

Polysaccharides• Polysaccharides (poly = many)

– Are polymers of sugars– Serve many roles in organisms

Storage Polysaccharides• Starch

– Is a polymer consisting entirely of glucose monomers

– Is the major storage form of glucose in plants

Chloroplast Starch

Amylose Amylopectin

(a) Starch: a plant polysaccharideFigure 5.6

• Glycogen– Consists of glucose monomers– Is the major storage form of glucose in animals

Mitochondria Giycogen granules

(b) Glycogen: an animal polysaccharide

Glycogen

Figure 5.6

Structural Polysaccharides

• Cellulose– Is a polymer of glucose and is considered a

fiber! It is indigestible by humans– Cows can digest it because they have four

stomachs

– Has different glycosidic linkages than starch

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

OHOHOH

(a) and glucose ring structures

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

glucose glucose

1 4 41 1

Figure 5.7 A–C

The formulae for both glucose and fructose are identical. How do they differ?

Plant cells

Cell walls

Cellulose microfibrils in a plant cell wall

Microfibril

OHOCH2OH

OCH2OH OH

OH OHO

CH2OHOH

CH2OHOHOOH OH OH OH

OH CH2OH

Glucose monomer

Parallel cellulose molecules areheld together by hydrogenbonds between hydroxyl

groups attached to carbonatoms 3 and 6.

About 80 cellulosemolecules associate

to form a microfibril, themain architectural unitof the plant cell wall.

A cellulose moleculeis an unbranched glucose polymer.

Cellulosemolecules

Figure 5.8

– Is a major component of the tough walls that enclose plant cells

• Cellulose is difficult to digest– Cows have microbes in their stomachs to facilitate this

process

Figure 5.9

• Chitin, another important structural polysaccharide– Is found in the exoskeleton of arthropods– Can be used as surgical thread

(a) The structure of the chitin monomer.

OHHH OH

(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emergingin adult form.

(c) Chitin is used to make a strong and flexible surgical

thread that decomposes after the wound or incision heals.

Figure 5.10 A–C

Lipids• Lipids are a diverse group of

hydrophobic (water fearing) molecules• Lipids

– Are the one class of large biological molecules that do not consist of polymers

– Share the common trait of being hydrophobic

Fats– Are constructed from two types of smaller molecules, a single

glycerol and usually three fatty acids– Vary in the length and number and locations of double bonds

they contain

Fats– Are constructed from two types of smaller molecules, a single

glycerol and usually three fatty acids– Vary in the length and number and locations of double bonds

they contain

Fats• Are constructed from two types of smaller molecules, a single

glycerol and usually three fatty acids

Fats• Vary in the length and number and locations of double

bonds they contain

• Saturated fatty acids (saturated with hydrogen)

– Have the maximum number of hydrogen atoms possible

– Have no double bonds

(a) Saturated fat and fatty acid

Stearic acid

Figure 5.12

• Unsaturated fatty acids– Have one or more double bonds

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12

• Phospholipids– Have only two fatty acids– Have a phosphate group instead of a third fatty

• A hydrogenated fat is more solid - butter

• An unsaturated fat is liquid - oils

• Phospholipid structure– Consists of a hydrophilic “head” and

hydrophobic “tails”

CH2CHCH2

C O C O

Phosphate

Glycerol

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

Fatty acids

(c) Phospholipid symbol

Hydrophilichead

Hydrophobictails

hi li c

CH2 Choline+

Figure 5.13

N(CH3)3

• The structure of phospholipids– Results in a bilayer arrangement found in cell

membranes

Hydrophilichead

Hydrophobictail

Figure 5.14

Steroids• Steroids

– Are lipids characterized by a carbon skeleton consisting of four fused rings

– Examples are hormones such as estrogen and testosterone

• One steroid, cholesterol– Is found in cell membranes– Is a precursor for some hormones

H3C CH3

Figure 5.15

Proteins• Proteins have many structures, resulting in a wide

range of functions• Proteins do most of the work in cells and act as

enzymes. Enzymes are proteins.• Proteins are made of monomers called amino

• An overview of protein functions

Table 5.1

• Enzymes– Are a type of protein that acts as a catalyst, speeding up

chemical reactions

Substrate(sucrose)

Enzyme (sucrase)

Glucose

Fructose

3 Substrate is convertedto products.

1 Active site is available for a molecule of substrate, the

reactant on which the enzyme acts.

Substrate binds toenzyme.

4 Products are released.Figure 5.16

Polypeptides• Polypeptides

– Are polymers (chains) of amino acids

• A protein– Consists of one or more polypeptides

• Amino acids– Are organic molecules possessing both carboxyl

and amino groups– Differ in their properties due to differing side chains,

called R groups– YOU MUST REMEMBER THIS!

Twenty Amino Acids• 20 different amino acids make up proteins

H3N+ C CO

H3N+ C

CH3 CH3

CH3CH2

CH2CH2

H3N+ C

Nonpolar

Glycine (Gly)Alanine

(Ala)Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

Tryptophan (Trp) Proline (Pro)

Figure 5.17

OH CH3

H3N+ C

C CH3N

Electricallycharged

–O O

C CH3N

O– O

C CH3N

C NH2+

C CH3N

Serine (Ser) Threonine (Thr)Cysteine

(Cys)Tyrosine

(Tyr)Asparagine

(Asn)Glutamine

Acidic Basic

Aspartic acid (Asp)

Glutamic acid (Glu)

Lysine (Lys) Arginine (Arg) Histidine (His)

Amino Acid Polymers

• Amino acids– Are linked by peptide bonds

• Again, building proteins is dehydration synthesis and breaking proteins is hydrolysis

• Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure and secondary structure which is present in their native state

Protein Conformation and Function

• A protein’s specific conformation (shape) determines how it functions

Four Levels of Protein Structure

• Primary structure– Is the unique sequence

of amino acids in a polypeptide

Figure 5.20–

Amino acid

subunits

+H3NAmino

oCarboxyl end

GlyProThrGlyThr

GluSeuLysCysProLeu

MetVal

ValLeu

AspAlaValArgGly

SerPro

SerProPheHisGluHis

GluValValPheThrAla

AspSer

GlyProArg

ArgTyrThr

lleAla

LeuSer

ProTyrSerTyrSerThr

ValVal

ThrAsnProLysGlu

ThrLys

SerTyrTrpLysAlaLeu

GluLleAsp

O C helix

pleated sheetAmino acid

subunitsNCH

N HO C

O CH C R

• Secondary structure– Is the folding or coiling of the polypeptide into a

repeating configuration– Includes the helix and the pleated sheet– Be sure that you can identify what this structure looks

Figure 5.20

• Tertiary structure– Is the overall three-dimensional shape of a polypeptide– Results from interactions between amino acids and R

groups

CH2 NH3+ C-O CH2

CH2SSCH2

Hydrophobic interactions and van der Waalsinteractions Polypeptid

ebackbone

Hyrdogenbond

Ionic bond

Disulfide bridge

• Quaternary structure– Is the overall protein structure that results from the

aggregation of two or more polypeptide subunits

Polypeptidechain

Collagen

Chains

ChainsHemoglobin

IronHeme

Review of Protein Structure

+H3NAmino end

Amino acidsubunits

Sickle-Cell Disease: A Simple Change in Primary Structure

• Sickle-cell disease– Results from a single amino acid

substitution in the protein hemoglobin

Fibers of abnormalhemoglobin deform cell into sickle shape.

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin A

Molecules donot associatewith oneanother, eachcarries oxygen.Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen

10 m 10 m

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin SMolecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced.

subunit subunit

1 2 3 4 5 6 7 3 4 5 6 721

Normal hemoglobin

Sickle-cell hemoglobin . . .. . .

Figure 5.21

Exposed hydrophobic

region

Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu

What Determines Protein Conformation?

• Protein conformation Depends on the physical and chemical conditions of the protein’s environment

• Temperature, pH, etc. affect protein structure

•Denaturation is when a protein unravels and loses its native conformation(shape)

Denaturation

Renaturation

Denatured protein

Normal protein

Figure 5.22

The Protein-Folding Problem

• Most proteins– Probably go through several intermediate states on their way

to a stable conformation – Denaturated proteins no longer work in their unfolded

condition– Proteins may be denaturated by extreme changes in pH or

temperature

• Chaperonins– Are protein molecules that assist in the proper folding of

other proteins

Hollowcylinder

Chaperonin(fully assembled)

Steps of ChaperoninAction: An unfolded polypeptide enters the cylinder from one end.

The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide.

The cap comesoff, and the properlyfolded protein is released.

Correctlyfoldedprotein

Polypeptide

Figure 5.23

• X-ray crystallography– Is used to determine a protein’s three-dimensional

structure

X-raydiffraction pattern

Photographic filmDiffracted X-

raysX-ray

source

CrystalNucleic acid Protein

(a) X-ray diffraction pattern(b) 3D computer modelFigure 5.24

Nucleic Acids• Nucleic acids store and transmit

hereditary information• Genes

– Are the units of inheritance– Program the amino acid sequence of

polypeptides– Are made of nucleotide sequences on

The Roles of Nucleic Acids

• There are two types of nucleic acids– Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)

Deoxyribonucleic Acid

• DNA– Stores information for the synthesis of

specific proteins– Found in the nucleus of cells

DNA Functions– Directs RNA synthesis (transcription)– Directs protein synthesis through RNA (translation)

Synthesis of mRNA in the nucleus

Movement of mRNA into cytoplasm

via nuclear pore

Synthesisof protein

NUCLEUSCYTOPLASM

Ribosome

AminoacidsPolypeptide

Figure 5.25

The Structure of Nucleic Acids

• Nucleic acids– Exist as polymers called

polynucleotides– Nucleic acids are polymers of

nucleotides

(a) Polynucleotide, or nucleic acid

5’ end

3’ endOH

Figure 5.26

• Each polynucleotide– Consists of monomers called nucleotides– Sugar + phosphate + nitrogen base

Nitrogenousbase

Nucleoside

O P CH2

3’CPhosphate

group Pentosesugar

(b) NucleotideFigure 5.26

Nucleotide Monomers• Nucleotide monomers

– Are made up of nucleosides (sugar + base) and phosphate groups

(c) Nucleoside componentsFigure 5.26

Uracil (in RNA)U

Ribose (in RNA)

Nitrogenous bases Pyrimidines

CytosineC

Thymine (in DNA)T

AdenineA

GuanineG

Purines

OHOCH2

Pentose sugars

Deoxyribose (in DNA)Ribose (in RNA)OHOH

Uracil (in RNA)U

3’OH H

3’ 2’

Nucleotide Polymers• Nucleotide polymers

– Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

DNA nucleotides

Be sure that you can recognize a single strand of DNA

Can you do this?

• In DNA, A always pairs with T and G always pairs with C

• Therefore, can you tell me what the compliment of this is?

• AGTACTG

• TCATGAC

• A specific stretch of DNA that programs the amino acid sequence of a polypeptide is a gene

• The sequence of bases along a nucleotide polymer– Is unique for each gene

The DNA Double Helix• Cellular DNA molecules

– Have two polynucleotides that spiral around an imaginary axis

– Form a double helix

– Check this out

• The DNA double helix– Consists of two antiparallel nucleotide strands

3’ end

Sugar-phosphatebackbone

Base pair (joined byhydrogen bonding)

Old strands

Nucleotideabout to be added to a new strand

3’ end

5’ end

Newstrands

3’ end

5’ end

Figure 5.27

A,T,C,G• The nitrogenous bases in DNA

– Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)

– RNA substitutes Uracil for Thymine

DNA and Proteins as Tape Measures of Evolution

• Molecular comparisons – Help biologists sort out the

evolutionary connections among species

The Theme of Emergent Properties in the Chemistry of

Life: A Review• Higher levels of organization

– Result in the emergence of new properties

• Organization– Is the key to the chemistry of life

Large biologicalmolecules

Functions Components Examples

Carbohydrates

Lipids

Proteins

Nucleic acids

Dietary energy;storage; plantstructure

Long-termenergy storagefats;hormonessteroids

Enzymes, structure,storage, contraction,transport, and others

Informationstorage

Monosaccharides:glucose, fructoseDisaccharides:lactose, sucrosePolysaccharides:starch, cellulose

Fats triglycerides;Steroidstestosterone,estrogen

Lactasean enzyme,hemoglobina transport protein

DNA, RNA

Monosaccharide

Components ofa triglyceride

Amino acid

Nucleotide

Fatty acid

Glycerol

Aminogroup

Carboxylgroup

Sidegroup

Phosphate

Figure UN3-2

1 chapter 3 biological molecules

diverse molecules

parts of molecules

simple molecules

carbon skeletons

cells organic molecules

carbon chemistrycarbon

single carbon atom

bonding versatility

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