Biochemistry

Chapter 3

• Life on Earth began in water and evolved there for 3 billion years

WATER AND LIFE

– Our cells are composed of 70%–95% water

• The abundance of water is a major reason Earth is habitable

Objectives:

• Describe the structure of a water molecule

• Explain how water’s polar nature affects its ability to dissolve substances

• List properties of water that result from hydrogen bonding

Water’s biological properties stem from it’s chemical

structure

(–)

O

(–)

(+)(+)

H H

OH H

Structural formula

Space-filling model

o

o

oo o

o

o

o

o

oδ+ δ+

δ-

Electron-energy-level formula

o

o

o

o

oo

oo

oo

Oxygen

HydrogenHydrogen

δ+δ+

δ- Oxygen is moreelectronegativethan hydrogen

Water is a polar molecule

Water is a polar compound

• In a water molecule oxygen exerts a stronger pull on the shared electrons than hydrogen

- O is more electronegative than H

• If electrons are shared unequally in a covalently bonded molecule, a polar molecule is created

• The charged regions on water molecules are attracted to the oppositely charged regions on nearby molecules– This attraction forms weak bonds called hydrogen bonds

Water’s polarity leads to hydrogen bonding and other unusual

properties

Hydrogen bond{

Hydrogen bonds make liquid water have the following

properties• good solvent• cohesive and adhesive properties• surface tension• maintains stable temperature• density of ice supports aquatic life

• Solutes whose charges or polarity allow them to stick to water molecules dissolve in water–They form aqueous solutions

1. Water is a versatile solvent

Ions in solution

Salt crystal

Cl–

Na+

Cl–

–

– –

–

Na+

+

+

+

+

–

Water’s polar nature makes it an effective solvent of other polar or ionic substances like

- ionic compounds (NaCl)- sugars- some proteins

2. Cohesion – strong tendency of H2O molecules to stick together

3. Adhesion – H2O molecules stick to substances with charged surfaces

• Capillarity – tendency for H2O molecules to rise in a narrow tube by both adhesive and cohesive forces against the force of gravity

Capillarity: Cohesion of Water

– Forces of cohesion and adhesion help pull water molecules up to the tops of tall trees

– Vital for water transport in plants

Microscopic tubes

4. Surface tension• Because water is cohesive, it is more attracted to other water molecules than to air molecules

•Thus, surface water molecules experience a greater pull downwards not counterbalanced by pull upwards

Surface tension - causes round water droplets- supports the weight of water stridersInsects can walk on water due to surface tension created by cohesive water molecules

Like no other common substance, water exists in nature in all three physical states

–solid–liquid–gas

• It takes a lot of energy to disrupt hydrogen bonds– Therefore, water is able to absorb a great deal of heat energy without a large increase in temperature (high specific heat)

– As water cools, a slight drop in temperature releases a large amount of heat

5. Water’s hydrogen bonds moderate temperature

Hydrogen bonding in water leads to

high specific heat

and

high heat of vaporization

– A water molecule takes a large amount of energy with it when it evaporates (high heat of vaporization: 540 cal/g H2O)– This leads to evaporative cooling

Because of H-bonds, it takes more heat energy to raise the

temperature of water

• Heat of fusion: ~80 cal needed to melt 1 g of H2O (ice)

• Heat of vaporization: 540 cal needed to vaporize 1 g of H2O

• Large heat capacity of water: helps large bodies of water (oceans) to have a stable temperature

• When water molecules get cold, they move apart, forming ice

The Biological Significance of Ice Floating

– A chunk of ice has fewer molecules than an equal volume of liquid water

• The density of ice is lower than liquid water – ice floats

Hydrogen bond

Liquid water

Hydrogen bondsconstantly break and re-form

Ice

Stable hydrogen bonds

Water molecules are at their closest at 4°C

Water Benzene

• Since ice floats, ponds, lakes, and even the oceans do not freeze solid– Marine life could not survive if bodies of water froze solid

Objectives

• Define organic compounds• Explain why carbon forms so many different compounds

• Define functional group and explain its significance

• Compare a condensation reaction (dehydration synthesis) with hydrolysis

Life’s molecular diversity is due to properties of C

• Organic molecules are made in cells, and contain C

• After H2O, C compounds most prevalent in cells

• A variety of organic molecules contribute to life’s structural and functional diversity

• Over 2 million organic compounds (C)

• C is the structural backbone of all organics

• Versatile and stable atom• Can bond to 4 other atoms covalently

• Bonds with other C atoms to form chains and rings

• Allows formation of many different necessary compounds

Carbon Chemistry

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

A carbon atom forms four covalent bonds- it joins other C atoms to form chains or rings

Structuralformula

Ball-and-stickmodel Space-filling

model

• The simplest organic compounds are hydrocarbons (containing only C and H)

Structuralformula

Ball-and-stickmodel

• Larger hydrocarbons

– Gasoline (mixture of different hydrocarbons)

• The hydrocarbons of fat molecules provide energy for our bodies

• Carbon can use its bonds to– Attach to other carbons– Form an endless diversity of carbon skeletons

Carbon skeletons may -vary in length

- be branched or unbranched

- have double bonds, which

can vary in location

- be arranged in rings

Cyclohexane Benzene

1-Butene 2-Butene

Butane Isobutane

Ethane Propane

Isomers• Molecules with the same chemical formula but different structures

• May have very different properties

Butane Isobutane

(C4H10)

The unique properties of an organic compound depend on- its carbon skeleton - other groups of atoms attached to the skeleton called functional groups- functional groups are the sites of chemical reaction

Some common functional groups

Hydroxyl group Carbonyl group Amino group Carboxyl group

Found in alcoholsand sugars

Found in sugars Found in amino acids and urea in urine (fromprotein breakdown)

Found in aminoacids, fatty acids, and some vitamins

ketone aldehyde

• On a molecular scale, many of life’s molecules are gigantic – macromolecules

• Most complex macromolecules (polymers) are made of many smaller basic repeating units (monomer)

Giant molecules from smaller building blocks

Examples: proteins, DNA, carbohydrates

Four major groups of organic molecules

Polymers are made of smaller identical units or monomers

Polymer MonomerProtein Amino acidPolysaccharide MonosaccharideDNA/RNA Nucleotide

Monomers join to form polymers

Combining 2 monomers to form a larger molecule often releases H & O forming H2O –Condensation Reaction/Dehydration Synthesis

• Breaking down a polymer to its constituent monomers uses water–Hydrolysis (the opposite of dehydration synthesis/condensation)

Cells link monomers to form polymers by dehydration synthesis/condensation reaction

Unlinked monomerShort polymer

Removal ofwater molecule

Longer polymer

1

1

2

2

3

3 4

Addition ofwater molecule

1

1

2

2

3

3 4

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

4

Objectives

• Define carbohydrate, monosaccharide, disaccharide and polysaccharide

• Discuss their significance to living organisms

1. Carbohydrates

• Contains C plus H & O in the same ratio as water, 2H:O

• Include– Sugars– Starches– Cellulose

• Suffix for many carbohydrates is ‘-ose’

1. Monosaccharides (= single sugar molecules)

• Monomers that make up carbohydrates– single sugar molecules

• General formula: (CH2O)n

• Two common monosaccharides:glucose & fructose– Both are C6H12O6

– Differ in structural arrangement = isomers

Honey contains both glucose and fructose

Glucose and fructose are isomers

Glucose Fructose

Both represented by C6H12O6

ketonealdehyde

• Many monosaccharides form rings, as shown here for glucose

Linear and ring structures Ring structure

1. Main fuel for cellular work

- Carbon rings contain energy

C6H12O6 6CO2 + 6H2O releases 686 kcal/mol

2. Raw material for synthesis of other materials

The Importance of Sugars

2. Disaccharides (= two sugar molecules)

• Formed by joining 2 monosaccharides

• Some important disaccharides:– Lactose = glucose & galactose– Sucrose = glucose & fructose– Maltose = glucose & glucose

• Disaccharides are formed by the process of dehydration synthesis

Glucose Glucose

Maltose

• Sucrose is extracted from sugar cane and sugar beets

• Simple sugars and double sugars dissolve readily in water

– They are hydrophilic, or “water-loving”

3. Polysaccharides (multiple sugar

molecules)• Large, complex carbohydrates

• Polymers of 100s or 1000s of monomers, arranged in long chains

• Energy storage or structural component – Starch & glycogen- Cellulose

Storage Polysaccharides

• Starch– polymer of glucose– stored by plants– Potatoes and grains are major sources of starch in the human diet

• Glycogen– also a polymer of glucose– stored by animals– similar to starch

• Cellulose is the most abundant organic compound on Earth

– It forms cable-like fibrils in the tough walls that enclose plant cells

– It is a major component of wood– It is also known as dietary fiber

Structural Polysaccharide

(a) StarchGlucose monomer

(b) Glycogen

(c) Cellulose

Cellulosemolecules

Starch & Glycogen: digested by animals and humans

Cellulose: can’t be digested by humans; digested by termites and ruminants

• Most animals cannot derive nutrition from fiber

– How do grazing animals survive on a diet of cellulose?

– Bacteria in their digestive tracts can break down cellulose

Various types of molecules, including non-sugars, taste sweet because they bind to “sweet” receptors on the tongue

(Equal,Nutrasweet)(Sweet and Low)(Splenda)

• A protein (polymer) is constructed from amino acids (monomers)

Proteins

• Basic building material of all living things

• In addition to C, H, and O, proteins contain N, S and other elements

• Very complex molecules– They are the most elaborate of life’s molecules

– The arrangement of amino acids makes each one different

• cellular structure • movement • storage• defensive/protective• transport• signal • toxins • chemical catalysts or enzymes (-ase)

Proteins: Most structurally and functionally diverse of

life’s molecules

Examples of four types of proteins

(a) Structural proteins

(b) Storageproteins

(c) Contractile proteins

(d) Transport proteins

Amino Acids• Monomers that make up proteins

• 20 different amino acids

• Can be arranged in any order to form complex polypeptides that are 1000’s of amino acids long

• All proteins are constructed from a common set of 20 kinds of amino acids

• Protein diversity is based on different arrangements of amino acids

The Monomers: Amino Acids

Carboxyl (acid)groupAmino

group

• Each amino acid consists of– A central carbon atom bonded to four covalent partners

– A side group that is variable among all 20

Aminogroup

Carboxylgroup

Sidegroup

(a)

Sidegroups(b)

Leucine Serine

(hydrophobic) (hydrophobic)

Each amino acid has specific properties

Leucine (Leu)

Serine (Ser) Cysteine (Cys)

HYDROPHILICHYDROPHOBIC

Carboxylgroup

Aminogroup

Sidegroup

Sidegroup

Amino acid Amino acid

Dehydrationsynthesis

Sidegroup

Sidegroup

Peptide bond

• Cells link amino acids together by dehydration synthesis

Proteins as Polymers

– The resulting bond between them is called a peptide bond

Forming Longer Peptides

• Dipeptide = two amino acids linked

• Polypeptide = many amino acids linked

• Proteins can be formed from one or several polypeptides

• Protein molecules are formed through condensation reactions/dehydration synthesis

Primary structure

– Is determined by the specific sequence of amino acids in a protein

1 510 15

20253035

4045

5055

6065

70

75 80 85

9095

100

105110 115

120125

129

Amino acid

Importance of Shape

• 3D shape of proteins is very important– determines function

• A single amino acid difference may critically change the protein

• A slight change in the primary structure of a protein affects its ability to function– The substitution of one amino acid for another in hemoglobin causes sickle-cell disease

(a) Normal red blood cell Normal hemoglobin

12 3

4 56

7. . . 146

(b) Sickled red blood cell Sickle-cell hemoglobin

2 314 5

67. . . 146

A protein’s shape determines its function

A protein loses its specific function when its polypeptides unravel

Example: A protein, like lysozyme, consists of polypeptide chains folded into a unique shape

• A protein’s shape is sensitive to the surrounding environment

What Determines Protein Structure?

–Unfavorable temperature and pH changes can cause a protein to unravel and lose its shape

–This is called denaturation

Linus Pauling

Winner of Nobel Prize in Chemistry (1954) and of Nobel Peace Prize (1963)

He made important contributions to the understanding of protein structure and function

3. LIPIDS, includes fats, oils and waxes

• These are insoluble in water – hydrophobic

• Contain C and H, smaller proportion of O

• Not true polymers, more complex than carbohydrates

• Energy rich storage materials

• Good for energy storage due to many C-H bonds

A. Fats = Triglycerides

• Also called neutral fats• Backbone is glycerol, a 3 carbon alcohol

• With 3 fatty acids attached =triglyceride

• Fatty acids – are chain like molecules with 14-22 carbon atoms

– the three fatty acids in a triglyceride can be the same or different

Fats (Triglycerides)- Fat = glycerol + 3 fatty acids

- Fatty acids: ~15 C atoms, -COOH group

Fatty acid

Dehydration synthesis linking a fatty acid to glycerolGlycerol

Saturated & Unsaturated Fats• Saturated – fatty acids contain only

single bonds

• Saturated fatty acids have no double bonds between the carbon atoms of the fatty acid chain and are thus

fully saturated with hydrogen atoms.

Unsaturated fat is a fat or fatty acid in which there is at least one double bond within the fatty acid chain.

A fat molecule is monounsaturated if it has one double bond, and polyunsaturated if it contains more than one double bond

Fats and Oils• Triglyceride that is solid at room temperature = fat; liquid = oil

• Most animal fats have a high proportion of saturated fatty acids– Example: butter, lard

• Most plant oils tend to be low in saturated fatty acids– Example: corn oil, olive oil

• Fats perform essential functions• in the human body:

– Energy storage– Cushioning – Insulation

B. Phospholipids

• Glycerol and 1 or 2 fatty acids plus phosphorous

• Usually contain nitrogen• Phosphorous & nitrogen are usually absent in neutral fats

• Very polar –one end hydrophobic, one hydrophilic

• Primary component of cell membranes

Phospholipid

Hydrophilic head

Hydrophobic tail

Glycerol

Fatty acid

Amphipathic Nature of Phosposlipids

• They are both hydrophilic and hydrophobic

• The “head” is a negatively charged phosphate group

• The two ‘tails’ are hydrophobic hydrocarbon chains

• Hydrophobic forces cause the ‘tails’ to congregate together

• Common amphiphilic substances are soaps and detergents

• One fatty acid linked to alcohol

• More hydrophobic than fats

• Wax coating on fruits and insects prevent them from drying out

C. Waxes

D. Steroids• Lipids whose molecules contain 4 rings of carbon atoms

• Cholesterol– A component of animal cell membranes

– The precursor molecule from which many other steroids are formed

• Sex hormones• Anabolic steroids

A Cholesterol Molecule

Cholesterol

Testosterone A type of estrogen

Synthetic anabolic steroids are controversial

– They are variants of testosterone

– Some athletes use them to build up their muscles quickly

– They can pose serious health risks

– Side affects include: breast development in men, shrinking of testicles

4. Nucleic Acids

• Two kinds : DNA & RNA– DNA records the instructions– RNA reads them & carries them out

• How cells know what to manufacture and when

• Made of smaller molecules linked together = nucleotides

The monomers of nucleic acids are nucleotides

• Nucleotides have 3 parts: – a 5 carbon sugar– a phosphate group

– a nitrogen base

• DNA contains the sugar deoxyribose, RNA contains ribose

• DNA bases: A, T, G, C RNA bases: A, U, G, C

Nucleotide

Sugar-phosphatebackbone

Nucleotides link to form a polynucleotide

BaseSugar

Phosphate

Each DNA nucleotide has one of the following bases

Thymine (T) Cytosine (C)

Adenine (A) Guanine (G)

Basepair

DNA Two polynucleotides or strands of DNA twist around each other in a double helix

DNA

-Adenine (A) always pairs with thymine (T)

- Guanine (G) always pairs with Cytosine (C)

Base Pairing• ‘A’ pairs with ‘T’

– joined by 2 hydrogen bonds

• ‘C’ pairs with ‘G’– joined by 3 hydrogen bonds

RNA Consists of a single polynucleotide with four kinds of nitrogenous bases (A, U, G, C)

RNA is different from DNA– Made of a single poly- nucleotide

– Its sugar has an extra OH group (ribose)

– It has the base uracil (U) instead of thymine (T)

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

Phosphategroup

Uracil (U)

Sugar (ribose)

ATP & ADP

• Not nucleic acids, but nucleotides with additional phosphate groups–Sugar, ribose, bound to base, adenine, and phosphates

• ATP transfers energy within the cell

• When ATP is converted back to ADP, it releases energy the cell can use for metabolism

The Structure of ATP

Energy

Adenosine Adenosine

ATP is formed from ADP– causes storage of energy in chemical bonds

- ATP is broken down to ADP, accompanied by the release of energy

Phosphate transferred to othermolecules

Enzymes• A special group of proteins- speed up chemical reactions in cells- are neither consumed nor affected by the reaction themselves

• Substrate – molecule acted on by enzyme

• Active site – part of the enzyme that bonds substrate

• Act by weakening other bonds– Lowers the activation energy

• Action is very specific: lock & key

Coenzymes

• Some enzymes have a part that is not a protein = coenzyme

• May aid in bonding the active site

• Some vitamins are coenzymes

• Enzymes can function over and over again

Enzyme(sucrase)

Active site

FructoseGlucose

Substrate(sucrose)

Enzyme available with empty active site

1

Substrate binds to enzyme

Substrate isconverted toproducts

Productsare released

1

2

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