Biochemistry. Carbon—Backbone of Biological Molecules Although cells are 70–95% water, the rest consists mostly of carbon-based compounds Carbon is unique.

Biochemistry

Carbon—Backbone of Biological Molecules

• Although cells are 70–95% water, the rest consists mostly of carbon-based compounds

• Carbon is unique in its ability to form large, complex, and diverse molecules

• Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds

Organic chemistry-the study of carbon compounds

• Organic compounds range from simple molecules to colossal ones

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

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

• Needs 4 electrons - single, double or triple bonds

• This tetravalence makes large, complex molecules possible - can form long chains or rings

Carbon Molecules• In molecules with multiple carbons, each carbon

bonded to four other atoms has a tetrahedral shape• However, when two carbon atoms are joined by a

double bond, the molecule has a flat shapeMolecularFormula

StructuralFormula

Ball-and-StickModel

Space-FillingModel

Methane

Ethane

Ethene (ethylene)

Carbon Molecules• 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

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)

Carbon Skeleton Diversity

• Carbon is a versatile atom

• Carbon can use its bonds to form an endless diversity of carbon skeletons

• Carbon chains form the skeletons of most organic molecules

LengthEthane Propane

Butane 2-methylpropane(commonly called isobutane)

Branching

Double bonds

Rings

1-Butene 2-Butene

Cyclohexane Benzene

Hydrocarbons

• Hydrocarbons are organic molecules consisting of only carbon and hydrogen

• Many organic molecules, such as fats, have hydrocarbon components

• Hydrocarbons can undergo reactions that release a large amount of energy

Functional Groups• Distinctive properties of organic molecules

depend not only on the carbon skeleton but also on the molecular components attached to it

• Certain groups of atoms called functional groups are often attached to skeletons of organic molecules

• Functional groups are the parts of molecules involved in chemical reactions

• The number and arrangement of functional groups give each molecule its unique properties

Functional Groups• The six functional groups that are most important in the

chemistry of life:– Hydroxyl group– Carbonyl group– Carboxyl group– Amino group– Sulfhydryl group– Phosphate group

Biochemistry: The Molecules of Life

• Within cells, small organic molecules are joined together to form larger molecules

• Macromolecules are large molecules composed of thousands of covalently connected atoms– Carbohydrates– Lipids– Proteins– Nucleic acids

Macromolecules - Polymers• A polymer is a long molecule consisting of many similar

building blocks called monomers• Most macromolecules are polymers, built from monomers• An immense variety of polymers can be built from a small set

of monomers• Three of the four classes of life’s organic molecules are

polymers:– Carbohydrates– Proteins– Nucleic acids

Polymers• Monomers form larger

molecules by condensation reactions called dehydration reactions

• Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction

Short polymer Unlinked monomer

Dehydration removes a watermolecule, forming a new bond

Dehydration reaction in the synthesis of a polymer

Longer polymer

Hydrolysis adds a watermolecule, breaking a bond

Hydrolysis of a polymer

Carbohydrates• Carbohydrates serve as fuel and building material• They include sugars and the polymers of sugars• The simplest carbohydrates are monosaccharides,

or single (simple) sugars• Carbohydrate macromolecules are

polysaccharides, polymers composed of many sugar building blocks

Sugars

• Monosaccharides have molecular formulas that contain C, H, and O in an approximate ratio of 1:2:1

• Monosaccharides are used for short term energy storage, and serve as structural components of larger organic molecules

• Glucose is the most common monosaccharide

• Monosaccharides are classified by location of the carbonyl group and by number of carbons in the carbon skeleton

• 3 C = triose e.g. glyceraldehyde • 4 C = tetrose • 5 C = pentose e.g. ribose, deoxyribose • 6 C = hexose e.g. glucose, fructose, galactose • Monosaccharides in living organisms generally

have 3C, 5C, or 6C:

Monosaccharides

Triose sugars(C3H6O3)

GlyceraldehydeAld

ose

sK

eto

s es

Pentose sugars(C5H10O5)

Ribose

Hexose sugars(C5H12O6)

Glucose Galactose

Dihydroxyacetone

Ribulose

Fructose

Monosaccharides• Monosaccharides serve as a

major fuel for cells and as raw material for building molecules

• The monosaccharides glucose and fructose are isomers– They have the same chemical

formula– Their atoms are arranged

differently

• Though often drawn as a linear skeleton, in aqueous solutions they form rings Glucose Fructose

Monosaccharides

• In aqueous solutions, monosaccharides form rings

Linear andring forms

Abbreviated ringstructure

Monosaccharides: Hexoses

H H H H H

H

OH OH

OH O

OH H

OH O

CH2OH

Ribose

Pentoses (5-carbon sugars)

Deoxyribose

H H 4

5

1

3 2

4

5

1

3 2

CH2OH

Monosaccharides: Pentsoses

Disaccharides• A disaccharide is formed when a dehydration reaction joins two

monosaccharides• Disaccharides are joined by the process of dehydration synthesis• This covalent bond is called a glycosidic linkage

Glucose

Maltose

Fructose Sucrose

Glucose Glucose

Dehydrationreaction in thesynthesis of maltose

Dehydrationreaction in thesynthesis of sucrose

1–4glycosidic

linkage

1–2glycosidic

linkage

Disaccharides

• Lactose = Glucose + Galactose• Maltose = Glucose + Glucose• Sucrose = Glucose + Fructose• The most common disaccharide is

sucrose, common table sugar• Sucrose is extracted from sugar cane and

the roots of sugar beets

Polysaccharides• Complex carbohydrates are called polysaccharides

• They are polymers of monosaccharides - long chains of simple sugar units

• Polysaccharides have storage and structural roles

• The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages

(a) Starch

(b) Glycogen

(c) Cellulose

Storage Polysaccharides - Starch

• Starch, a storage polysaccharide of plants, consists entirely of glucose monomers

• Plants store surplus starch as granules within chloroplasts and other plastids

Chloroplast Starch

1 µm

Amylose

Starch: a plant polysaccharide

Amylopectin

Storage Polysaccharides - Glycogen

• Glycogen is a storage polysaccharide in animals

• Humans and other vertebrates store glycogen mainly in liver and muscle cells

Mitochondria Glycogen granules

0.5 µm

Glycogen

Glycogen: an animal polysaccharide

Structural Polysaccharides• Cellulose is a major

component of the tough wall of plant cells

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

• The difference is based on two ring forms for glucose: alpha () and beta ()– Polymers with alpha

glucose are helical

– Polymers with beta glucose are straight

a Glucose

a and b glucose ring structures

b Glucose

Starch: 1–4 linkage of a glucose monomers.

Cellulose: 1–4 linkage of b glucose monomers.

Cellulose • Enzymes that digest starch by

hydrolyzing alpha linkages can’t hydrolyze beta linkages in cellulose

• Cellulose in human food passes through the digestive tract as insoluble fiber

• Some microbes use enzymes to digest cellulose

• Many herbivores, from cows to termites, have symbiotic relationships with these microbes

Cellulosemolecules

Cellulose microfibrilsin a plant cell wall

Cell walls Microfibril

Plant cells

0.5 µm

Glucosemonomer

Lipids• Lipids are the one class of large biological molecules

that do not form polymers• Utilized for energy storage, membranes, insulation,

protection• Greasy or oily substances• The unifying feature of lipids is having little or no

affinity for water - insoluble in water • Lipids are hydrophobic becausethey consist mostly

of hydrocarbons, which form nonpolar covalent bonds

Fats• The most biologically important lipids are fats,

phospholipids, and steroids• Fats are constructed from two types of smaller molecules:

glycerol and fatty acids• Glycerol is a three-carbon alcohol with a hydroxyl group

attached to each carbon• A fatty acid consists of a carboxyl group attached to a long

carbon skeleton

Dehydration reaction in the synthesis of a fat

Glycerol

Fatty acid(palmitic acid)

Fatty Acids• A fatty acid has a long hydrocarbon chain with a

carboxyl group at one end.

• 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, – Monounsaturated (one double bond)– Polyunsaturated (more than one double bond)

• H can be added to unsaturated fatty acids using a process called hydrogenation

• The major function of fats is energy storage

Stearate Oleate

Fats• Fats separate from water because water molecules form

hydrogen bonds with each other and exclude the fats

• In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride

Glycerides

• Glycerol + 1 fatty acid = monoglyceride Glycerol + 1 fatty acid = monoglyceride

• Glycerol + 2 fatty acids = diglyceride Glycerol + 2 fatty acids = diglyceride

• Glycerol + 3 fatty acids = triglyceride (also Glycerol + 3 fatty acids = triglyceride (also called triacylglycerol or “fat”.)called triacylglycerol or “fat”.)

Ester linkage

Fat molecule (triacylglycerol)

Saturated Fats• Fats made from saturated fatty acids are called saturated

fats

• Most animal fats are saturated

• Saturated fats are solid at room temperature

• A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits

Saturated fat and fatty acid.

Stearic acid

Unsaturated Fats• Fats made from unsaturated fatty acids are called

unsaturated fats

• Plant fats and fish fats are usually unsaturated

• Plant fats and fish fats are liquid at room temperature and are called oils

Unsaturated fat and fatty acid.

Oleic acid

cis double bondcauses bending

Fat Sources

• Most animal fats contain saturated fatty acids and tend to be solid at room temperature

• Most plant fats contain unsaturated fatty acids. They tend to be liquid at room temperature, and are called oils.

Phospholipids• In phospholipids, two of the –OH groups on glycerol are joined to

fatty acids. The third –OH joins to a phosphate group which joins, in turn, to another polar group of atoms.

• The phosphate and polar groups are hydrophilic (polar head) while the hydrocarbon chains of the 2 fatty acids are hydrophobic (nonpolar tails).

Structural formula Space-filling model Phospholipid symbol

Hydrophilichead

Hydrophobictails

Fatty acids

Choline

Phosphate

Glycerol

Hyd

rop

ho

bic

tai

lsH

ydro

ph

i lic

hea

d

Phospholipids

Micelle

Phospholipid bilayer Water

Water

Water Lipid head (hydrophilic)

Lipid tail (hydrophobic)

Phospholipids• When phospholipids are added to water, they orient so that the

nonpolar tails are shielded from contact with the polar H2O may form micelles

• Phosopholipids also may self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior

• The structure of phospholipids results in a bilayer arrangement found in cell membranes

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• Testosterone and estrogen function as sex

hormones

Proteins• Proteins have many structures, resulting in a

wide range of functions• They account for more than 50% of the dry

mass of most cells• Protein functions

– Structural support / storage / movement - fibers – Catalysis - Enzymes– Defense against foreign substances–

Immunoglobulins– Transport – globins, membrane transporters– Messengers for cellular communications -

hormones

Proteins• A protein is composed of one or more polypeptides that

performs a function• A polypeptide is a polymer of amino acids joined by

peptide bonds to form a long chain• Polypeptides range in length from a few monomers to

more than a thousand• Each polypeptide has a unique linear sequence of amino

acids• A protein consists of one or more polypeptides which are

coiled and folded into a specific 3-D shape. • The shape of a protein determines its function.

Amino Acids• Amino acids are monomers of polypetides

• They composed of a carboxyl group, amino group, and an “R”Group

• Amino acids differ in their properties due to differing side chains, called R groups

• Cells use 20 amino acids to make thousands of proteins

Aminogroup

Carboxylgroup

carbon

O

O–

H

H3N+ C C

O

O–

H

CH3

H3N+ C

H

C

O

O–

CH3 CH3

CH3

C C

O

O–

H

H3N+

CH

CH3

CH2

C

H

H3N+

CH3

CH3

CH2

CH

C

H

H3N+ C

CH3

CH2

CH2

CH3N+

H

C

O

O–

CH2

CH3N+

H

C

O

O–

CH2

NH

H

C

O

O–

H3N+ C

CH2

H2C

H2N C

CH2

H

C

Nonpolar

Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

C

O

O–

Tryptophan (Trp) Proline (Pro)

H3C

Figure 5.17

S

O

O–

Amino Acids

O–

OH

CH2

C C

H

H3N+

O

O–

H3N+

OH CH3

CH

C C

HO–

O

SH

CH2

C

H

H3N+ C

O

O–

H3N+ C C

CH2

OH

H H H

H3N+

NH2

CH2

O

C

C C

O

O–

NH2 O

C

CH2

CH2

C CH3N+

O

O–

O

Polar

Electricallycharged

–O O

C

CH2

C CH3N+

H

O

O–

O– O

C

CH2

C CH3N+

H

O

O–

CH2

CH2

CH2

CH2

NH3+

CH2

C CH3N+

H

O

O–

NH2

C NH2+

CH2

CH2

CH2

C CH3N+

H

O

O–

CH2

NH+

NH

CH2

C CH3N+

H

O

O–

Serine (Ser) Threonine (Thr)Cysteine

(Cys)Tyrosine

(Tyr)Asparagine

(Asn)Glutamine

(Gln)

Acidic Basic

Aspartic acid (Asp)

Glutamic acid (Glu)

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

Amino Acids

Amino Acids and Peptide Bonds

• Two amino acids can join by condensation to form a dipeptide plus H2O.

• The bond between 2 amino acids is called a peptide bond.

Protein Conformation and Function• A functional protein consists

of one or more polypeptides twisted, folded, and coiled into a unique shape

• The sequence of amino acids determines a protein’s three-dimensional conformation

• A protein’s conformation determines its function

• Ribbon models and space-filling models can depict a protein’s conformation

A ribbon model

Groove

Groove

A space-filling model

Four Levels of Protein Structure• The primary structure of a protein is its unique sequence of amino

acids

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

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

• Quaternary structure results when a protein consists of multiple polypeptide chains

Amino acidsubunits

pleated sheet

helix

Levels of Protein Structure

51

Interactions that Contribute to a Interactions that Contribute to a Protein’s ShapeProtein’s Shape

51 51 51

52

Enzymes as Catalysts• To increase reaction rates:

– Add Energy (Heat) - molecules move faster so they collide more frequently and with greater force.

– Add a catalyst – a catalyst reduces the energy needed to reach the activation state, without being changed itself. Proteins that function as catalysts are called enzymes.

Reactant

Product

CatalyzedUncatalyzed

Product

Reactant

Activationenergy

Activationenergy

En

erg

y su

pp

lied

En

erg

y re

leas

ed

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Activation Energy and Catalysis

Enzymes Are Biological Catalysts• Enzymes are proteins that carry out most catalysis in living

organisms.• Unlike heat, enzymes are highly specific. Each enzyme

typically speeds up only one or a few chemical reactions.• Unique three-dimensional shape enables an enzyme to

stabilize a temporary association between substrates.• Because the enzyme itself is not changed or consumed in

the reaction, only a small amount is needed, and can then be reused.

• Therefore, by controlling which enzymes are made, a cell can control which reactions take place in the cell.

Substrate Specificity of Enzymes• Almost all enzymes are globular proteins with one or more active sites on their surface.• The substrate is the reactant an enzyme acts on• Reactants bind to the active site to form an enzyme-substrate complex.• The 3-D shape of the active site and the substrates must match, like a lock and key• Binding of the substrates causes the enzyme to adjust its shape slightly, leading to a

better induced fit.• When this happens, the substrates are brought close together and existing bonds are

stressed. This reduces the amount of energy needed to reach the transition state.

Substate

Active site

Enzyme

Enzyme- substratecomplex

1 The substrate, sucrose, consistsof glucose and fructose bonded together.

Bond

Enzyme

Active site

The substrate binds to the enzyme, forming an enzyme-substrate complex.

2

H2O

The binding of the substrate and enzyme places stress on the glucose-fructose bond, and the bond breaks.

3

Glucose Fructose

Products are released, and the enzyme is free to bind other substrates.

4

The Catalytic Cycle Of An Enzyme

Conformational Change and Enzyme Activity• In addition to primary structure, physical and chemical conditions can

affect conformation

• Alternations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel

• This loss of a protein’s native conformation is called denaturation

• A denatured protein is biologically inactive

Denaturation

Renaturation

Denatured proteinNormal protein

Effects of Temperature and pH• Each enzyme has an optimal temperature in

which it can function

Optimal temperature for enzyme of thermophilic

Rat

e o

f re

actio

n

0 20 40 80 100Temperature (Cº)

(a) Optimal temperature for two enzymes

Optimal temperature fortypical human enzyme

(heat-tolerant) bacteria

Effects of Temperature and pH– Each enzyme has an optimal pH in which it can function

Figure 8.18

Rat

e o

f re

actio

n

(b) Optimal pH for two enzymes

Optimal pH for pepsin (stomach enzyme)

Optimal pHfor trypsin(intestinalenzyme)

10 2 3 4 5 6 7 8 9

Nucleic Acids (DNA/RNA)

• Nucleic acids store and transmit hereditary information

• The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene

• Genes are made of DNA, a nucleic acid

The Roles of Nucleic Acids• 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

• Protein synthesis occurs in ribosomes

NUCLEUS

DNA

CYTOPLASM

mRNA

mRNA

Ribosome

Aminoacids

Synthesis ofmRNA in the nucleus

Movement ofmRNA into cytoplasmvia nuclear pore

Synthesis of protein

Polypeptide

The Structure of Nucleic Acids• Nucleic acids are

polymers called polynucleotides

• Each polynucleotide is made of monomers called nucleotides

• Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group

• The portion of a nucleotide without the phosphate group is called a nucleoside

5 end

3 end

Nucleoside

Nitrogenousbase

Phosphategroup

Nucleotide

Pentosesugar

Nucleotide Monomers• Nucleotide monomers are made

up of nucleosides and phosphate groups

• Nucleoside = nitrogenous base + sugar

• There are two families of nitrogenous bases: – Pyrimidines have a single six-

membered ring– Purines have a six-membered ring

fused to a five-membered ring

• In DNA, the sugar is deoxyribose• In RNA, the sugar is ribose

Nitrogenous bases

Pyrimidines

Purines

Pentose sugars

CytosineC

Thymine (in DNA)T

Uracil (in RNA)U

AdenineA

GuanineG

Deoxyribose (in DNA)

Nucleoside components

Ribose (in RNA)

Nucleotide Polymers• Nucleotide polymers are linked

together, building a polynucleotide• Adjacent nucleotides are joined by

covalent bonds that form between the –OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

• These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages

• The sequence of bases along a DNA or mRNA polymer is unique for each gene

The DNA Double Helix• A DNA molecule has two

polynucleotides spiraling around an imaginary axis, forming a double helix

• In the DNA double helix, the two backbones run in opposite 5´ to 3´ directions from each other, an arrangement referred to as antiparallel

• One DNA molecule includes many genes

• The nitrogenous bases in DNA form hydrogen bonds in a complementary fashion: A always with T, and G always with C

Sugar-phosphatebackbone

3 end5 end

Base pair (joined byhydrogen bonding)

Old strands

Nucleotideabout to beadded to anew strand

5 end

New strands

3 end

5 end3 end

5 end

ATP• Adenosine triphosphate (ATP), is the primary energy-

transferring molecule in the cell • ATP is the “energy currency” of the cell• ATP consists of an organic molecule called adenosine

attached to a string of three phosphate groups• The energy stored in the bond that connects the third

phosphate to the rest of the molecule supplies the energy needed for most cell activities

ATP

• ATP (adenosine triphosphate)– Is the cell’s energy shuttle– Provides energy for cellular functions

O O O O CH2

H

OH OH

H

N

H H

O

NC

HC

N CC

N

NH2Adenine

RibosePhosphate groups

O

O O

O

O

O

-- - -

CH

ATP• Energy is released from ATP when the terminal phosphate bond

is broken

P

Adenosine triphosphate (ATP)

H2O

+ Energy

Inorganic phosphate Adenosine diphosphate (ADP)

PP

P PP i