Life Chemistry and Energy 2. Chapter 2 Life Chemistry and Energy Key Concepts 2.1 Atomic Structure...

Life Chemistry and Energy

Chapter 2 Life Chemistry and Energy

Key Concepts

• 2.1 Atomic Structure Is the Basis for Life’s Chemistry

• 2.2 Atoms Interact and Form Molecules

• 2.3 Carbohydrates Consist of Sugar Molecules

• 2.4 Lipids Are Hydrophobic Molecules

• 2.5 Biochemical Changes Involve Energy

Enduring Understanding

2.A. Growth, reproduction, and maintenance of the organization of living systems require free energy and matter. (The concept of free energy will be

discussed in detail during Chapter 6)

Essential Knowledge

2.A.1. All living systems require constant input of energy.

2.A.3. Organisms must exchange matter with the environment to grow, reproduce, and maintain organization.

Assessment

Test of Chapter 2

Word Roots

Like any profession, the study of biology has its own language.

Nouns constructed with components – prefixes and suffixes – of definite purpose and meaning.

What follows may be useful to you in understanding the construction and meaning of scientific vocabulary.

Word Roots

hydro - water; - philos loving; - phobos fearing (hydrophilic: having an affinity for water; hydrophobic: having an aversion to water)

kilo - a thousand (kilocalorie: a thousand calories)

Instructor’s Guide for Campbell/Reece Biology, Seventh Edition

Word Roots

carb - coal (carboxyl group: a functional group present in organic acids, consisting of a carbon atom double-bonded to an oxygen atom and a hydroxyl group)

enanti - opposite (enantiomer: molecules that are mirror images of each other)

hydro - water (hydrocarbon: an organic molecule consisting only of carbon and hydrogen)

Word Roots

iso - equal (isomer: one of several organic compounds with the same molecular formula but different structures and, therefore, different properties)

sulf - sulfur (sulfhydryl group: a functional group that consists of a sulfur atom bonded to an atom of hydrogen)

thio - sulfur (thiol: organic compounds containing sulfhydryl groups)

Word Roots

con - together (condensation reaction: a reaction in which two molecules become covalently bonded to each other through the loss of a small molecule, usually water)

di - two (disaccharide: two monosaccharides joined together)

Word Roots

glyco - sweet (glycogen: a polysaccharide sugar used to store energy in animals)

hydro - water; - lyse break (hydrolysis: breaking chemical bonds by adding water)

macro - large (macromolecule: a large molecule)

meros - part (polymer: a chain made from smaller organic molecules)

Word Roots

mono - single; - sacchar sugar (monosaccharide: simplest type of sugar)

poly - many (polysaccharide: many monosaccharides joined together)

tri - three (triacylglycerol: three fatty acids linked to one glycerol molecule)

Word Roots

bio- life (bioenergetics: the study of how organisms manage their energy resources)

endo- within (endergonic reaction: a reaction that absorbs free energy from its surroundings)

ex- out (exergonic reaction: a reaction that proceeds with a net release of free energy)

Word Roots

kinet- movement (kinetic energy: the energy of motion)

therm- heat (thermodynamics: the study of the energy transformations that occur in a collection of matter)

Word Roots

ana - up (anabolic pathway: a metabolic pathway that consumes energy to build complex molecules from simpler ones)

cata- down (catabolic pathway: a metabolic pathway that releases energy by breaking down complex molecules into simpler ones)

Chapter 2 Opening Question

Why is the search for water important in the search for life?

Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry

Living and nonliving matter is composed of atoms.

Like charges repel; different charges attract.

Most atoms are neutral because the number of electrons equals the number of protons.

Dalton—mass of one proton or neutron (1.7 × 10–24 grams)

Mass of electrons is so tiny, it is usually ignored.

Element—pure substance that contains only one kind of atom

Living things are mostly composed of 6 elements:

Carbon (C) Hydrogen (H) Nitrogen (N)

Oxygen (O) Phosphorus (P) Sulfur (S)

• The number of protons identifies an element.

• Number of protons = atomic number

• For electrical neutrality, # protons = # electrons.

• Mass number—total number of protons and neutrons

A Bohr model for atomic structure—the atom is largely empty space, and the electrons occur in orbits, or electron shells.

Actual atomic structure is far more complicated than the Bohr model - electron clouds, quantum mechanics, electron configurations, etc.

Behavior of electrons

•determines whether a chemical bond will form

•and what shape the bond will have.

Octet rule

•Atoms with at least two electron shells form stable molecules

•So they have eight electrons in their outermost (valence) shells.

Figure 2.1 Electron Shells

Atoms with unfilled outer shells tend to undergo chemical reactions to fill their outer shells.

•Stability attained by sharing electrons with other atoms or by losing or gaining electrons.

•The atoms are then bonded together into molecules.

Concept 2.2 Atoms Interact and Form Molecules

Chemical bond

•An attractive force that links atoms together to form molecules.

There are several kinds of chemical bonds.

Table 2.1 Chemical Bonds and Interactions

Ionic bonds

Ions are charged particle that form when an atom gains or loses one or more electrons.

Cations—positively charged ions

Anions—negatively charged ions

Ionic bonds result from the electrical attraction between ions with opposite charges.

The resulting molecules are called salts.

Figure 2.2 Ionic Bond between Sodium and Chlorine

Ionic attractions are weak, so salts dissolve easily in water.

More about dissolving later…

Covalent bonds

Covalent bonds form when two atoms share pairs of electrons.

• The atoms attain stability by having full outer shells.

• Each atom contributes one member of the electron pair.

Figure 2.3 Electrons Are Shared in Covalent Bonds

Covalent Bonds

http://ibchem.com/IB/ibnotes/full/bon_htm/4.2.htm

Animation – Ionic and Covalent Bonds

http://www.youtube.com/watch?v=QqjcCvzWwww&feature=related

Van der Waals Interactions

Van der Waals interactions• Occur when transiently positive and negative

regions of molecules attract each other

Van der Waals interactions

Molecules with partially negative and positive regions:

• Their electrons are constantly moving• Can be moments when electrons accumulate

by chance in one area of a molecule. • At that moment, a regions of negative charge

is created, and positive region opposite.

Van der Waals Interactions

Van der Waals interactions

COMMON MISCONCEPTION

The simplified models of the atom electron shells, and covalent bonding can be confusing if you take them too literally. Please understand that:

• Atoms do not have defined surfaces.• Electrons do not travel in planetary orbits

around the nucleus of the atom.• Shared electron pairs are not paired spatially

in covalent bonds.• Electron shells represent energy levels rather

than the position of electrons.

Student Misconceptions

Carbon

•Carbon atoms have four electrons in the outer shell

•Can form single covalent bonds with four other atoms.

Figure 2.4 Covalent Bonding (Part 1)

Figure 2.4 Covalent Bonding (Part 2)

Properties of molecules are influenced by characteristics of the covalent bonds:

•Orientation—length, angle, and direction of bonds between any two elements are always the same.

Example: Methane always forms a tetrahedron.

Video 2.1 Methane: A three-dimensional model

Video 2.2 Starch: A three-dimensional model

• Strength and stability—covalent bonds are very strong; it takes a lot of energy to break them.

• Multiple bonds

Single—sharing 1 pair of electrons

Double—sharing 2 pairs of electrons

Triple—sharing 3 pairs of electrons

Degree of sharing electrons is not always equal.

•Let’s review the implications of this in terms of • Electronegativity• Hydrogen bonds• Specific heat capacity• Polar and nonpolar covalent bonds• Cohesion and adhesion• Heat of vaporization• Solvent

Degree of sharing electrons is not always equal.

•Electronegativity—the attractive force that an atomic nucleus exerts on electrons

• It depends on the number of protons and the distance between the nucleus and electrons.

Table 2.2 Some Electronegativities

• If two atoms have similar electronegativities, they share electrons equally; a nonpolar covalent bond.

• If atoms have different electronegativities, electrons tend to be near the most attractive atom; a polar covalent bond

Hydrogen bonds

• Attraction between the δ– end of one molecule and the δ+ hydrogen end of another molecule forms hydrogen bonds.

• Special kind of interactive force of attraction between a hydrogen atom, H, and the nonbonding electrons of a second, very electronegative F, O, or N

Hydrogen bonds

• Do not involve the sharing or transfer of electrons.

• Relies on the attraction of partial opposite charges.

• Important in the structure of DNA and proteins.

Hydrogenbonds

Hydrogen bonds

• Can occur between different molecules as long as there are areas of partial opposite charges.

Figure 2.5 Hydrogen Bonds Can Form between or within Molecules

Hydrogen bonds

• Are weak bonds; roughly 1/20th the strength of a typical covalent bond.

• Are fleeting; they form and break with slight changes in the system’s energy.

• Have a collective strength, as you see in the formation of water ice.

Hydrogen bonds

“The bond lengths give some indication of the bond strength. A normal covalent bond is 0.96 Angstroms, while the hydrogen bond length is 1.97 A.”

http://www.elmhurst.edu/~chm/vchembook/161Ahydrogenbond.html

Hydrogen bonds

•At 0oC, water becomes locked into a crystalline lattice with each molecule bonded to the maximum of four partners.

Hydrogen bonds

•Remember – bond length of hydrogen bonds is roughly twice as much as typical covalent bond

Hydrogen bonds

•Resulting lattice structure finds molecules farther apart. As a result, the same amount of mass occupies more volume.

Hydrogen bonds

•Water ice is approximately 10% less dense that liquid water.

• Since ice floats in water, Life can exist under

the frozen surfaces of lakes and polar seas

• So why is this oddity important to life?

If ice sank, eventually all ponds, lakes, and even the ocean would freeze solid from bottom up.

During the summer, only the upper few inches of the ocean would thaw.

Instead, the surface layer of ice insulates liquid water below, preventing it from freezing and allowing lifeto exist under the frozen surface.

Hydrogen bonds

• Hydrogen bonds make possible water’s properties:

• freezing point,• cohesion and adhesion,• plus its ability to dissolve many

substances.

• Weak bonds like the hydrogen bond are vital in many biological processes

Animation – Hydrogen Bonds

Animation – Molecular Water

Video- Hydrogen Bonds

http://www.youtube.com/watch?v=cgiNk94XyaI

Animation – Hydrogen Bonds

http://www.youtube.com/watch?v=LGwyBeuVjhU

Animation – Basilisk Lizard

http://www.youtube.com/watch?v=Spc9r4CHRDo&feature=related

Students often believe that a hydrogen bond can occur between atoms in the same manner as ionic or covalent bonds instead of as a strong, yet transient attraction.

COMMON MISCONCEPTIONS

Weak bonds play important roles in the chemistry of life, despite the transient nature of each individual bond.

• The compelling example of the gecko, able to walk on ceilings because of the van der Waals interactions between the ceiling and the hairs on the gecko’s toes.

• Strong and weak bonds are both important in the chemistry of life. Can you think of any examples?

Water molecules form multiple hydrogen bonds with each other—this contributes to high specific heat capacity.

A lot of heat is required to raise the temperature of water—the heat energy breaks the hydrogen bonds.

In organisms, presence of water shields them from fluctuations in environmental temperature.

Water moderates air temperature

• By absorbing heat from air that is warmer and releasing the stored heat to air that is cooler

Why can water absorb or release relatively large amounts of heat with only a slight change in its own temperature?

Distinguish Between Heat and Temperature

Heat Is a measure of the total amount of kinetic

energy due to molecular motion

Temperature Measures the intensity of heat due to the

average kinetic energy of molecules.

Atoms and molecules have kinetic energy, the energy of motion, because they are always moving.

•Faster that a molecule moves, the more kinetic energy that it has.

•As the average speed of molecules increases, a thermometer will record an increase in temperature.

Heat and temperature are related, but not identical.

FYI: There is no measure of cold in science – all objects have heat energy until the object is at absolute zero.

•Heat passes from the warmer object to the cooler until the two are the same temperature.

•Molecules in the cooler object speed up at the expense of kinetic energy of the warmer object.

•Ice cubes cool a drink by absorbing heat as the ice melts.

Biology measure temperature on the Celsius scale (oC).

•At sea level, water freezes at Oo C and boils at 100o C.

•Human body temperature averages 37o C.

Convenient unit of measurement of heat energy is the calorie (cal).

•One calorie is the amount of heat energy necessary to raise the temperature of one g of water by 1oC.

In biology, the kilocalorie (kcal), is even more convenient.

•A kilocalorie is the amount of heat energy necessary to raise the temperature of 1000g (1 kilogram or kg) of water by 1oC.

Another common energy unit, the joule (J), is equivalent to 0.239 cal.

Water has a relatively high specific heat

The specific heat of a substance

• Is the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1ºC Absorbing heat energy will increase temperature Releasing heat energy will decrease temperature

Water has a high specific heat compared to other substances.

•Example: ethyl alcohol has a specific heat of 0.6 cal/g/oC

Less energy required to get a temperature increase in alcohol

•Specific heat of iron is 1/10th that of water.

Due to high specific heat, water resists changes in temperature

•Takes relatively more heat energy to speed up its molecules

Or, water absorbs or releases a relatively large quantity of heat for each degree of change

Water’s high specific heat is due to hydrogen bonding between each molecule of water

•Must absorb heat to break the hydrogen bonds

•Because so much energy must first be used to break hydrogen bonds…

Less energy is actually available to move the molecules faster – to increase its kinetic energy and therefore its temperature.

When enough energy is added, enough bonds break…

•That’s when a liquid may change its state of matter – liquid to gas.

Heating Curve of Water

It takes a lot of energy to force a change of water’s state of matter – solid to liquid to gas.

Why? Goes back to hydrogen bonds – added energy goes first to breaking hydrogen bonds before water can be evaporated.

Environmental significance of high specific heat

Water’s high specific heat

• allows water to minimize temperature fluctuations to within limits that permit life.

Ever notice how it is cooler near at a beach?

• Large bodies of water can absorb a large amount of heat from the sun in daytime and during the summer, while warming only a few degrees.

• At night and during the winter, the warm water will warm cooler air.

• Therefore, ocean temperatures and coastal land areas have more stable temperatures than inland areas.

High specific heat impact individual organisms

• Organisms are mostly water.

• Water moderates changes in temperature better than if composed of a liquid with a lower specific heat.

Transformation of a substance from a liquid to a gas known as vaporization

•Molecules now move fast enough to overcome the attraction of other molecules in the liquid.

•Even in a low temperature liquid (low average kinetic energy), some molecules are moving fast enough to evaporate.

•Heating a liquid increases the average kinetic energy and increases the rate of evaporation.

Heat of vaporization

Quantity of heat a liquid must absorb for 1 gram of it to be converted from a liquid to a gas.

• Water has a relatively high heat of vaporization.• About 580 cal of heat to evaporate 1g of water at room

temperature.• That’s double the heat of vaporization of alcohol or

ammonia.

Why? I’ll tell you why!

Water’s many more hydrogen bonds must be broken before it can evaporate.

So why is a high heat of vaporization important to biology?

Heat of Vaporization

Observe same quantities of water and isopropyl alcohol poured onto tables as a thin film.

What did you see?

The alcohol evaporated much faster than the water.

What does this say about alcohols heat of vaporization?

As a liquid evaporates, the surface of the liquid that remains behind cools - evaporative cooling.

•Is due to water’s high heat of vaporization.

•Allows water to cool a surface.

•Cooling happens because the most energetic molecules are the most likely to evaporate, leaving the lower kinetic energy molecules behind.

So why is evaporative cooling important to biology?

Remember, water has a high heat of vaporization—a lot of heat is required to change water from liquid to gaseous state.

Thus, evaporation has a cooling effect on the environment.

Sweating cools the body—as sweat evaporates from the skin, it transforms some of the adjacent body heat.

Hydrogen bonds also give water cohesive strength, or cohesion—water molecules resist coming apart when placed under tension.

• Bonding of a high percentage of the molecules to neighboring molecules

• Due to hydrogen bonding

•Permits narrow columns of water to move from roots to leaves of plants.

Helps pull water up through the microscopic vessels of plants

Water conducting cells

100 µm

Cohesion and formation of a meniscus

Animation - Cohesion Transport

http://www.youtube.com/watch?v=Ns4vrocF99s

Surface tension

Related to cohesion, it is a measure of the force necessary to break the surface of a liquid.

Water has greater surface tension that most liquids.

The Solvent of Life

Water is a versatile solvent due to its polarity.

It can form aqueous solutions:

• Solution A liquid that is a completely homogeneous

mixture of two or more substances

• Aqueous solution A solution in which water is the solvent

• Solvent Dissolving agent

The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them.

Negative

oxygen regions

of polar water molecules

are attracted to sodium

cations (Na+).

+Cl –

Na+Positive hydrogen regions

of water molecules cling to chloride anions

(Cl–).

–Na+

The Solvent of Life

Each dissolved ion is surrounded by a sphere of water molecules, a hydration shell.

Eventually, water dissolves all the ions, resulting in a solution with two solutes, sodium and chloride.

The Solvent of Life

Polar molecules are water soluble because they can form hydrogen bonds with water.

Even large molecules, like proteins, can dissolve in water if they have ionic and polar regions.

The Solvent of Life

Water can also interact with polar molecules such as proteins.

This oxygen is

attracted to a slight

positive charge on the

lysozyme molecule.

This oxygen is attracted to a slight

negative charge on the lysozyme molecule.

(a) Lysozyme molecule

in a nonaqueous

environment

(b) Lysozyme molecule (purple)

in an aqueous environment

such as tears or saliva

(c) Ionic and polar regions on the protein’s

Surface attract water molecules.

The Solvent of Life

Glucose molecules have polar hydroxyl (OH) groups in them and these attract the water to them. When sugar is in a crystal the molecules are attracted to the water and go into solution. Once in solution the molecules stay in solution at least in part because they become surrounded by water molecules. This layer of water molecules surrounding another molecule is called a hydration shell.

http://staff.jccc.net/pdecell/chemistry/hydrophilic.html

Dissolving leads to a hydration shell which bounds up water molecules – fewer free water molecules, less osmotic potential (more on osmosis in later chapter)

http://staff.jccc.net/pdecell/chemistry/hydrophilic.html

When a sucrose molecule is in water, it is immediately surrounded by water molecules. The sucrose has hydroxyl groups that have a slight negative charge. The positive charge of the oxygen found in the water molecule binds with the sugar. As the hydration shell forms around the sucrose molecule, the molecule is shielded from other sugar molecules so the sugar crystal does not reform.

http://www.bioinquiry.vt.edu/bioinquiry/water/waterpaid/waterhtmls/chem8.html

Assuming two solutions of the same molar concentration, one of glucose, the other of sucrose

Glucose, being a smaller molecule with therefore relatively greater surface area than sucrose, will bound up more water molecules.

http://www.bioinquiry.vt.edu/bioinquiry/water/waterpaid/waterhtmls/chem8.html

Any polar molecule can interact with any other polar molecule through hydrogen bonds.

Hydrophilic (“water-loving”)—in aqueous solutions, polar molecules become separated and surrounded by water molecules

Nonpolar molecules are called hydrophobic (“water-hating”); the interactions between them are hydrophobic interactions.

Figure 2.6 Hydrophilic and Hydrophobic

Water: exists in nature as three states of matter

Water: exists in nature as three states of matterConcept 2.2 Atoms Interact and Form Molecules

Chapter 2 Opening Question

Why is the search for water important in the search for life?

Overview

Three-quarters of the Earth’s surface is submerged in water.

The abundance of water is the main reason the Earth is habitable.

Water is most unusual

• Only pure substance that exists naturally as a gas, liquid and solid.

• Less dense as a solid than a liquid, unlike almost all other chemicals. Explains why ice floats.

Water is the molecule that supports all of life

• Water is the biological medium here on Earth.

• All living organisms require water more than any other substance.

Liquids essential to biochemistry because…

• Biochemical reactions need a liquid medium.• In a liquid, molecules can dissolve and

chemical reactions can occur.

• Liquid not stable; it can transport chemical from place to place within a cell, organism, or ecosystem. Imagine trying to transport vital nutrients

within a solid or a gas.

Water is the best liquid

• The best solvent – it dissolves just about everything.

• Helps maintain the shape of enzymes – essential catalysts of biochemistry – no shape, no chemistry.

• If water wasn’t the essential liquid, if another liquid could take its place, why haven’t we seen it in any life forms?

Ammonia! Ammonia!

AP TIP

You should be able to describe the properties of water and why these properties are important to life.

Functional groups—small groups of atoms with specific chemical properties

•Confer these properties to larger molecules, e.g., polarity.

•One biological molecule may contain many functional groups.

•Attachments that replace one or more hydrogen atoms to the carbon skeleton.

•Behave consistently from one organic molecule to another.

Basic structure of testosterone (male hormone) and estradiol (female hormone) is identical.

Estradiol

Testosterone

Female lion

Male lion

Both are steroids with four fused carbon rings, but have different functional groups attached to the rings.

Estradiol

Testosterone

Female lion

Male lion

These functional groups then interact with different targets in the body.

Estradiol

Testosterone

Female lion

Male lion

Male and female mallards

Male and female peacocks

Male and female sage grouse

Six functional groups are important in the chemistry of life:

• Hydroxyl• Carbonyl• Carboxyl• Amino• Sulfhydryl• Phosphate

All are hydrophilic and increase the solubility of organic compounds in water.

-OH, a hydrogen atom forms a polar covalent bond with an oxygen atom, which forms a polar covalent bond to the carbon skeleton. Because of these polar covalent bonds,

hydroxyl groups improve the solubility of organic molecules.

Hydroxyl group

Organic compounds with hydroxyl groups are alcohols and their names typically end in -ol.

Hydroxyl group

>Carbonyl consists of an oxygen atom joined to the carbon skeleton by a double bond. If the carbonyl group is on the end of the

skeleton, the compound is an aldelhyde.

Carbonyl group

If not, then the compound is a ketone. Isomers with aldehydes versus ketones have

different properties.

Carbonyl group

-Carboxyl COOH consists of a carbon atom with a double bond to an oxygen atom and a single bond to a hydroxyl group. Compounds with carboxyl groups are

carboxylic acids.

Carboxyl group

Acts as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the dissociation of hydrogen as an ion (H+).

Carboxyl group

-NH2 consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton. Organic compounds with amino groups are

amines.

Amino group

Acts as a base because ammonia can pick up a hydrogen ion (H+) from the solution.

Amino acids, the building blocks of proteins, have amino and carboxyl groups.

Amino group

-SH consists of a sulfur atom bonded to a hydrogen atom and to the backbone. This group resembles a hydroxyl group in

shape.

Sulfhydryl group

Organic molecules with sulfhydryl groups are thiols.

Sulfhydryl groups help stabilize the structure of proteins.

Sulfhydryl group

-OPO32- consists of phosphorus bound to four

oxygen atoms (three with single bonds and one with a double bond). Connects to the carbon backbone via one of its

oxygen atoms.

Phosphate group

Anions with two negative charges as two protons have dissociated from the oxygen atoms.

One function of phosphate groups is to transfer energy between organic molecules.

Phosphate group

ATP (adenosine triphosphate) is a type of nucleotide that is the cell’s primary energy transferring molecule

Phosphate group

Figure 2.7 Functional Groups Important to Living Systems (Part 1)

Figure 2.7 Functional Groups Important to Living Systems (Part 2)

AP TIP

You should be able to identify the functional groups most common in biological molecules and explain the characteristics that each functional group confers on molecules.

Macromolecules

• Most biological molecules are polymers (poly, “many”; mer, “unit”), made by covalent bonding of smaller molecules called monomers.

• Proteins: Formed from different combinations of 20 amino acids

• Carbohydrates—formed by linking similar sugar monomers (monosaccharides) to form polysaccharides

• Nucleic acids—formed from four kinds of nucleotide monomers

• Lipids—noncovalent forces maintain the interactions between the lipid monomers

Polymers are formed and broken apart in reactions involving water.

•Condensation—removal of water links monomers together

•Hydrolysis—addition of water breaks a polymer into monomers

Figure 2.8 Condensation and Hydrolysis of Polymers (Part 1)

Figure 2.8 Condensation and Hydrolysis of Polymers (Part 2)

Concept 2.3 Carbohydrates Consist of Sugar Molecules

Carbohydrates

• Source of stored energy

• Transport stored energy within complex organisms

• Structural molecules that give many organisms their shapes

• Recognition or signaling molecules that can trigger specific biological responses

nn OHC )( 2

Monosaccharides are simple sugars.

Pentoses are 5-carbon sugars

Ribose and deoxyribose are the backbones of RNA and DNA.

Hexoses (C6H12O6) include glucose, fructose, mannose, and galactose.

Figure 2.9 Monosaccharides (Part 1)

Figure 2.9 Monosaccharides (Part 2)

Monosaccharides are covalently bonded by condensation reactions that form glycosidic linkages.

Sucrose is a disaccharide.

Oligosaccharides contain several monosaccharides.

Many have additional functional groups.

They are often bonded to proteins and lipids on cell surfaces, where they serve as recognition signals.

Polysaccharides are large polymers of monosaccharides; the chains can be branching.

Starches—a family of polysaccharides of glucose

Glycogen—highly branched polymer of glucose; main energy storage molecule in mammals

Cellulose—the most abundant carbon-containing (organic) biological compound on Earth; stable; good structural material

Figure 2.10 Polysaccharides (Part 1)

Video 2.3 Cellulose: A three-dimensional model

AP TIP

You should be able to describe structure and function of carbohydrates.

You should be able to explain how polysaccharides for energy storage differ from structural polysaccharides.

Concept 2.4 Lipids Are Hydrophobic Molecules

Lipids are hydrocarbons (composed of C and H atoms); they are insoluble in water because of many nonpolar covalent bonds.

When close together, weak but additive van der Waals interactions hold them together.

Lipids

• Store energy in C—C and C—H bonds

• Play structural role in cell membranes

• Fat in animal bodies serves as thermal insulation

Triglycerides (simple lipids)

Fats—solid at room temperature

Oils—liquid at room temperature

They have very little polarity and are extremely hydrophobic.

Triglycerides consist of:

• Three fatty acids—nonpolar hydrocarbon chain attached to a polar carboxyl group (—COOH) (carboxylic acid)

• One glycerol—an alcohol with 3 hydroxyl (—OH) groups

Synthesis of a triglyceride involves three condensation reactions.

Figure 2.11 Synthesis of a Triglyceride

Fatty acid chains can vary in length and structure.

Saturated fatty acids – hydrocarbon chains contain only single carbon-carbon bonds; they have the maximum number of hydrogen atoms (hence saturated).

Unsaturated fatty acids – hydrocarbon chains contain one or more double bonds. Results in kinks in the chain and prevents molecules from packing together tightly.

Figure 2.12 Saturated and Unsaturated Fatty Acids (Part 1)

Figure 2.12 Saturated and Unsaturated Fatty Acids (Part 2)

Video 2.4 Palmitic acid and linoleic acid: A three-dimensional model

Fatty acids are amphipathic; they have a hydrophilic end and a hydrophobic tail.

Phospholipid—two fatty acids and a phosphate compound bound to glycerol.

•Phosphate group has a negative charge, making that part of the molecule hydrophilic.

Figure 2.13 A Phospholipids

Figure 2.13 B Phospholipids

In an aqueous environment, phospholipids form a bilayer.

The nonpolar, hydrophobic “tails” pack together and the phosphate-containing “heads” face outward, where they interact with water.

Biological membranes have this kind of phospholipid bilayer structure.

Concept 2.4 Lipids are Hydrophobic Molecules

AP TIP

You should be able to describe structure and function of lipids.

You should be able to explain how lipids form biological membranes and describe why the degree of saturation in the fatty acid tail affects the structure of lipids.

Overview

The living cell Is a miniature factory where thousands of

reactions occur Converts energy in many ways

Overview

Some organisms Convert energy to light, as in bioluminescence

Figure 8.1

Overview

Graphic Organizer for Concept 2.5

Concept 2.5 Biochemical Changes Involve Energy

Chemical reactions occur when atoms have enough energy to combine, or change, bonding partners.

sucrose + H2O glucose + fructose

(C12H22O11) (C6H12O6) (C6H12O6)

reactants products

Metabolism—the sum total of all chemical reactions occurring in a biological system at a given time

Metabolic reactions involve energy changes.

A metabolic pathway has many steps That begin with a specific molecule and end with

a product That are each catalyzed by a specific enzyme

Enzyme 1 Enzyme 2 Enzyme 3

A B C D

Reaction 1 Reaction 2 Reaction 3

Startingmolecule

Product

Animation – Overview of Metabolic or Biochemical Pathways

http://highered.mcgraw-hill.com/olc/dl/120070/bio09.swf

Two basic types of metabolism:

• Anabolic reactions

• Catabolic reactions

Metabolic Pathways

Catabolic pathways release energy by breaking down complex molecules into simpler

compounds. Energy stored in the chemical bonds is released. A major pathway of catabolism is cellular

respiration, in which the sugar glucose is broken down in

the presence of oxygen to carbon dioxide and water.

Metabolic Pathways

Anabolic pathways Build complicated molecules from simpler ones Consume energy; require energy input and

capturing of some of that energy in newly formed chemical bonds.

Also called biosynthetic pathways. The synthesis of protein from amino acids is an

example of anabolism. The energy released by catabolic pathways can

be stored and then used to drive anabolic pathways.

All forms of energy can be considered as either:

• Potential—the energy of state or position, or stored energy

• Kinetic—the energy of movement (the type of energy that does work) that makes things change

Energy can be converted from one form to another.

Chemical energy is a form of potential energy stored in

molecules because of the arrangement of their atoms.

Breaking or making chemical bonds – covalent or ionic – requires the release or absorption of energy during a chemical reaction

Chemical reactions can be classified as either exergonic or endergonic based on free energy.

Figure 2.14 Energy Changes in Reactions (Part 1)

Figure 2.14 Energy Changes in Reactions (Part 2)

An exergonic reaction Proceeds with a net release of free energy

and is spontaneous – negative ∆G

Reactants

Products

Energy

Progress of the reaction

Amount ofenergyreleased (∆G <0)

(a) Exergonic reaction: energy released

An exergonic reaction The greater the decrease in free energy, the

greater the amount of work that can be done

Reactants

Products

Energy

For the overall reaction of cellular respiration: C6H12O6 + 6O2 -> 6CO2 + 6H2O

G = −686 kcal/molReactants

Products

Energy

The products have 686 kcal less free energy than the reactants.

Reactants

Products

Energy

An endergonic reaction Is one that absorbs free energy from its

surroundings and is nonspontaneous

Energy

Products

Amount ofenergyreleased (∆G>0)

Reactants

(b) Endergonic reaction: energy required

An endergonic reaction stores energy in molecules; G is positive.

Energy

Products

Reactants

If cellular respiration releases 686 kcal, then photosynthesis, the reverse reaction, must require an equivalent investment of energy.

Energy

Products

Reactants

For the conversion of carbon dioxide and water to sugar, G = +686 kcal/mol.

Figure 8.6

Energy

Products

Reactants

Equilibrium and Metabolism

Reactions in a closed system Eventually reach equilibrium and can do no

(a) A closed hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium.

∆G < 0 ∆G = 0

Should a cell reach equilibrium, when G = 0, THAT CELL IS DEAD!

(a) A closed hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium.

∆G < 0 ∆G = 0

Cells in our body Experience a constant flow of materials in and

out, preventing metabolic pathways from reaching equilibrium.

(b) An open hydroelectric system. Flowing water keeps driving the generator because intake and outflow of water keep the system from reaching equlibrium.

∆G < 0

Metabolic disequilibrium is one of the defining features of life.

Cells maintain disequilibrium because they are open systems.

The constant flow of materials into and out of the cell keeps metabolic pathways from ever reaching equilibrium.

A cell continues to do work throughout its life.

An analogy for cellular respiration

(c) A multistep open hydroelectric system. Cellular respiration is analogous to this system: Glucoce is brocken down in a series of exergonic reactions that power the work of the cell. The product of each reaction becomes the reactant for the next, so no reaction reaches equilibrium.

∆G < 0

Some reversible reactions of respiration are constantly “pulled” in one direction, as the product of one reaction does not accumulate but…

becomes the reactant in the next step.

Sunlight provides a daily source of free energy for photosynthetic organisms.

Nonphotosynthetic organisms depend on a transfer of free energy from photosynthetic organisms in the form of organic molecules.

Let’s double check if you fully grasp the concept of energy, and especially potential energy.

• Potential energy is not a substance or fuel that is somehow stored in matter.

• Potential energy is associated with an object’s ability to move to a lower-energy state, thus releasing some of the potential energy.

The laws of thermodynamics apply to all matter and energy transformations in the universe.

First law: Energy is neither created nor destroyed.

Second law: Disorder (entropy) tends to increase. • When energy is converted from one form to

another, some of that energy becomes unavailable for doing work.

• That “lost” energy contributes to disorder or entropy.

First law of thermodynamics Energy can be transferred and transformed. Energy cannot be created or destroyed.

First law of thermodynamics The first law is also known as the principle of

conservation of energy Total energy in a system before a

transformation must equal the total energy in the system after the transformation

First law of thermodynamics Plants do not produce energy; they transform

light energy to chemical energy Animals eat other organisms and catabolize

complex nutrient molecules into simple compounds, such as H2O and CO2

Quantity of energy does not change, but the quality of energy does change

An example of energy conversion

First law of thermodynamics: Energy can be transferred or transformed but Neither created nor destroyed. For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetah’s movement in (b).

Chemicalenergy

No process is 100% efficient in using potential energy to do work

During every transfer or transformation of energy, some energy is converted to heat,

which is the energy associated with the random movement of atoms and molecules

Energytotal = Energywork + Energylost as heat

Heat can still do work

A system can use heat to do work only when

there is a temperature difference that results in heat flowing from a warmer location to a cooler one.

a.k.a a temperature gradient

If temperature is uniform, as in a living cell, heat can only be used to warm the organism.

Inherent inefficiency in energy transformations leads us to the second law of thermodynamics

Energy transfers and transformations make the universe more disordered due to this loss of usable energy.

Cue the cheetah

According to the second law of thermodynamics Every energy transfer or transformation

increases the disorder of the universe.

Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.

Heat co2

According to the second law of thermodynamics Cheetah breaks down – catabolizes –

relatively more complex sugar molecules into simple CO2 and H2O.

Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.

Heat co2

We needed a better way to conceptualize the second law of thermodynamics and the disorder of the universe

Hence the concept of entropy

Entropy

• Quantity used as a measure of disorder or randomness.

• The more random a collection of matter, the greater its entropy.

• Let’s update the cheetah

• Every energy transfer or transformation increases the disorder (entropy) of the universe.

Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder (entropy) of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.

Heat co2

• Entropy increases because as the cheetah runs, it adds heat to its surroundings and releases simple by-products from the breakdown of complex chemicals

Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder (entropy) of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.

Heat co2

The universe the cheetah lives in is a closed system (so far as we know).

Second law requires that the disorder or entropy of any closed system always increases.

Therefore, if there is at one point a decrease in entropy, there must also be somewhere an increase in entropy.

If the second law of thermodynamics requires an increase in disorder, what form may that disorder take?

•Catabolism breaks complex molecules into simpler ones, increasing disorder (entropy)

•Each catabolic reaction will also release heat energy, increasing disorder (entropy)

•So there are two types of entropy• Material• Thermal

The Second Law of Thermodynamics

Combustion of the fuel releases heat, thereby increasing entropy. Automobiles convert only 25% of the energy in gasoline into motion; the rest is lost as heat.

C8H18 + O2 CO2 + H2O + heat

There is both an increase in disorder materially – octane to carbon dioxide and water – and thermally – the release of heat energy

Here’s another way of defining entropy

Entropy is measured by the number of distinguishable arrangements by the particles of matter The fewer the number of distinguishable

arrangements, the lower the entropy The more distinguishable arrangements,

the greater the entropy

An to illustrate distinguishable arrangements ..a card trick

How many possible five card hands can be dealt in poker?

Each of the 2,598,960 five-card hands are a distinguishable arrangement

When happens when the number of cards is halved to 26?

With 26 cards, only 65,780 five card arrangements can be made.

Now suppose those cards are atoms?

With fewer atoms, few distinguishable arrangements can be made, the lower the entropy.

But then of course, if you increased the number of atoms in each arrangement, from 5 to 10

You get 5,311,735 distinguishable arrangements – fewer atoms but larger molecules – entropy is increased!

Second law of thermodynamics

• Requires increasing entropy from any closed system

• Isolated from its surroundings, lacking any input of additional energy, the closed system will (eventually) increase its entropy

• All things will fall apart

For a process to occur on its own, without outside help in the form of energy input, it must increase the entropy of the universe.

In other words, the process must be spontaneous

Spontaneous processes need not occur quickly.

•Some spontaneous processes are instantaneous, such as an explosion.

•Some are very slow, such as the rusting of an old car.

A spontaneous change is a change that has a tendency to occur without been driven by an external influence

e.g. the cooling of a hot metal block to the temperature of its surroundings

A non-spontaneous change is a change that occurs only when driven

e.g. forcing electric current through a metal block to heat it

The Second Law of ThermodynamicsConcept 2.5 Biochemical Changes Involve Energy

So, another way to state the second law of thermodynamics is

•for a process to occur spontaneously, it must increase the entropy of the universe

•You will see that spontaneous processes are absolutely vital to biological processes

Diffusion and facilitated diffusion Osmosis and dissolution Evolution

Let’s describe the second law mathematically S = entropy ∆S = change in entropy A spontaneous process will be a positive or

negative ∆S?positive

Enthalpy is the total potential energy of a system

H – the total enthalpy (in biological systems, equivalent to energy)

Enthalpy – the energy and matter within a system that may be exchanged with its surroundings.

Entropy is that fraction of enthalpy that cannot be used to do work – it is always lost to increasing disorder

So the amount of energy in any system that can do work is approximately the difference between the two

Total entropy change

entropy change of system

entropy change of surroundings

Dissolving

disorder of solution

disorder of surroundings

• must be an overall increase in disorder for dissolving to occur

The Second Law of ThermodynamicsThe Second Law of Thermodynamics

Biological Order and Disorder

Now for the apparent paradox of life…

Don’t living systems increase order, violating the second law of thermodynamics?

Living systems are open systems that absorb energy—light or chemical energy – in the form of organic molecules

and release heat and metabolic waste products such as urea or CO2 to their surroundings.

Living systems create ordered structures from less ordered starting materials.

The structure of a multicellular body is organized and complex.

Example: amino acids are ordered into polypeptide chains

But living systems must use energy to maintain order.

And, in using energy to maintain order an organism takes in organized forms of

matter and energy from its surroundings and replaces them with less ordered forms.

Example: an animal consumes organic molecules as food and catabolizes them to low-energy carbon dioxide and water.

So what is the answer to the paradox?

While they can increase order locally and temporarily, there is an unstoppable trend toward randomization of the entire universe.

“Living things preserve their low levels of entropy throughout time, because they receive energy from their surroundings in the form of food.”

Entropy in Biology,

Jayant Udgaonkar

“They gain their order at the expense of disordering the nutrient they consume.”

Entropy in Biology,

Jayant Udgaonkar

“Dust thou art, and unto dust thou shalt return" (Genesis 3:19)

Death is the inevitable result of increasing molecular entropy

The entropy of a particular system, such as an organism, may decrease as long as

the total entropy of the universe—the system plus its surroundings—increases.

Think of organisms as islands of low entropy in an increasingly random universe.

The evolution of biological order is perfectly consistent with the laws of thermodynamics.

Now how does entropy relate to evolution?

Over evolutionary time, complex organisms have evolved from simpler ones.

How does this happen?

Second law of thermodynamics makes certain that a sequence of DNA cannot be maintained forever.

•Eventually it must fall to disorder and increase its entropy

•Small random changes in the DNA sequence is inevitable

Sometime those changes – mutations – lead to changes in a gene

which leads to different proteins being produced,

which leads to different traits, which allows natural selection to determine

the advantageous traits, and so on and so on.

Evolution therefore does not violate the second law of thermodynamics

Individuals and entire species are merely temporary and isolated examples of decreasing entropy

Entropy drives the processes of evolution, osmosis, diffusion and other spontaneous processes

Not a directed process; there is no goal Evolution is inevitable

Let’s check your understanding of entropy using this model of osmosis.

Assume the dialysis bag contains a saline solution.

It is surrounded by pure water.

Which direction will the water tend – into or out of the bag?

Water will tend to go into the bag

Osmosis requires water move from an area of high concentration – outside – to an area of low concentration until equilibrium is reached.

Now explain what happens in terms of entropy.

First, we recognize the bag is an open system

Second, we know there will be a net flow of water into the bag

Third, we know this will be spontaneous

By definition, this will increase entropy in the beaker/bag system

But wait..there’s more!

Salt water has greater entropy than pure water

Na+ and Cl- ions are spread out through the solution, creating greater disorder

Pure water is just water molecules bumping into other water molecules

Entropy will seek equilibrium until ∆S = 0

Solutions have more distinguishable particles

With a solute(s), you can see more combinations between molecules of solute(s) and solvent, than just solvent

1. If we freeze water, disorder of the water molecules decreases , entropy decreases

( -ve S , -ve H)

2. If we boil water, disorder of the water molecules increases , entropy increases (vapour is highly disordered state)

( +ve S , +ve H)

Biological Order and DisorderBiological Order and Disorder

System in Dynamic EquilibriumSystem in Dynamic Equilibrium

A + B C + D

Dynamic (coming and going), equilibrium (no net change)

• no overall change in disorder

S 0 (zero entropy change)

Biological Order and DisorderBiological Order and Disorder

Is the second law of thermodynamics responsible for time?

Well, not really. Second law and entropy do not require time in the equations, however…

Second does imply a direction of time All things must move toward a more

disordered state Known as Time’s Arrow

Zero entropy13.7 billions years ago

Constantly increasing entropy in Universe

Figure 2.15 The Laws of Thermodynamics (Part 2)

Figure 2.15 The Laws of Thermodynamics (Part 3)

If a chemical reaction increases entropy, its products are more disordered or random than its reactants.

If there are fewer products than reactants, the disorder is reduced; this requires energy to achieve.

As a result of energy transformations, disorder tends to increase.

•Some energy is always lost to random thermal motion (entropy).

Metabolism creates more disorder (more energy is lost to entropy) than the amount of order that is stored.

Example:

•The anabolic reactions needed to construct 1 kg of animal body require the catabolism of about 10 kg of food.

Life requires a constant input of energy to maintain order.

AP TIP

You should be able to predict the outcome of endergonic and exergonic reactions

You should be able to discuss the significance of the second law of thermodynamics.

Answer to Opening Question

One way to investigate the possibility of life on other planets is to study how life may have originated on Earth.

An experiment in the 1950s combined gases thought to be present in Earth’s early atmosphere, including water vapor. An electric spark provided energy.

Complex molecules were formed, such as amino acids. Water was essential in this experiment.

Figure 2.16 Synthesis of Prebiotic Molecules in an Experimental Atmosphere (Part 1)

Figure 2.16 Synthesis of Prebiotic Molecules in an Experimental Atmosphere (Part 2)

Life Chemistry and EnergyCGI Video Summation

Inner Lives of a Cell – Full version with musical score

We have reviewed the basics of biological molecules. This video shows those biological molecules in action. Can you, in your mind’s eye, see the bonds, the interactions?

http://www.youtube.com/watch?v=zrXykvorybo

Life Chemistry and EnergyPractice Questions

Atomic structure

The element magnesium has an atomic number of 12 and a mass number of 24. Working in pairs, and using the Bohr model for atomic structure, draw a magnesium atom.

Once you have drawn your magnesium atom, answer the following questions:

1. How many protons and neutrons are in the nucleus? How many electrons are in this atom?

2. Is the magnesium atom likely to bond with other atoms? Why or why not?

Take a few minutes to discuss, and then present your drawing and answers to the class.

Select the false statement about elements:

a. An element contains only one kind of atom.

b. Isotopes are variants of an element with additional neutrons in the nucleus.

c. Atoms of different elements can have the same number of protons.

d. All the atoms of a particular element contain the same number of protons.

e. Carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur are the main elements found in living organisms.

Chemical bonds

Working in pairs, compare the following bonds with respect to their basis of interaction and strength:

• Ionic• Covalent• Hydrogen

Draw an example of each type of bond.

Which of the following statements about water is false?

a. Water helps to prevent dramatic changes in body temperature because it has a high heat capacity.

b. Sweating cools the body because water has a high heat of vaporization.

c. Not counting bones, water makes up about 70% of the weight of your body.

d. During condensation, the addition of water breaks a polymer into monomers.

e. Molecules with polar covalent bonds are attracted to water.

Carbohydrates

Working in pairs or small groups, discuss the polysaccharides starch, glycogen, and cellulose. In your discussion, consider the following questions:

1. Where are these polysaccharides found?

2. What biological role does each polysaccharide play?

3. What do these molecules have in common?

4. How do these molecules differ?

Present your answers to the class.

Carbohydrates

a. can have the same chemical formula, but distinct chemical properties and different biological roles.

b. such as polysaccharides are formed when monosaccharides are ionically bonded by condensation reactions.

c. are made of carbon, hydrogen, and oxygen.

d. are always linear, unbranched molecules.

e. Both a and c

Triglycerides

Working individually, compare saturated and unsaturated fatty acids with respect to the following characteristics:

1. Presence of double bonds between carbon atoms in the hydrocarbon chain

2. Ability to pack tightly together

3. State of lipid at room temperature

4. Melting point of lipid

5. Typical source

Compare your answers with your classmates and discuss.

Which of the following statements about phospholipids is false?

a. The phosphate functional group and glycerol form the hydrophobic head of a phospholipid.

b. A phospholipid has two fatty acids whereas a triglyceride has three fatty acids.

c. Phospholipids are amphipathic (i.e., they have two opposing chemical properties).

d. The phosphate functional group and glycerol form the hydrophilic head of a phospholipid.

e. Biological membranes are characterized by a phospholipid bilayer structure.

Chemical reactions

Working in pairs, consider the following chemical reaction and answer the questions below:

glucose + galactose lactose + water

1. Is this a condensation or hydrolysis reaction?

2. What are the reactants? What are the products?

3. Is this an anabolic or catabolic reaction?

4. Is energy required or released?

Which of the following statements about energy is false?

a. Exergonic reactions release energy.

b. The energy released in anabolic reactions is often used to drive catabolic reactions.

c. Potential energy is stored energy.

d. Endergonic reactions require energy

e. Kinetic energy is the energy of movement.

Science, Technology and Society

• While waiting at an airport, Neil Campbell once overheard this claim:

– “It’s paranoid and ignorant to worry about industry or agriculture contaminating the environment with their chemical wastes. After all, this stuff is just made of the same atoms that were already present in our environment.”

• How would you counter this argument?

Review – Online Quiz by Campell/Reece

http://www.hbwbiology.net/quizzes-ap-review-main.htm

2. You are studying a cellular enzyme involved in breaking down fatty acids for energy. Looking at theR groups of the amino acids in the following figures, what amino acids would you predict to occur in the parts of the enzyme that interact with the fatty acids? *

a. non-polar

b. polar

c. electrically charged

d. polar and electrically charged

e. all of these

Practice Problems

The 20 Amino Acids of Proteins

The 20 Amino Acids of Proteins (cont.)

• Let’s begin with the condensation reaction that lead to the 1-4 glycosidic linkage

Scientific Inquiry

• Repeated many times results in a polysaccharide known as starch

Scientific Inquiry

• Hydrolysis breaks the glycosidic linkages, leaving behind glucose monomers, reinserting a water molecule

Note one hydrogen bonds with the oxygen of carbon-1; the remaining hydroxyl group OH bonds with the carbon 4

Scientific Inquiry

• If hydrochloric acid used to break glycosidic linkages..

The hydrogen will bond with carbon-1, as before, but the chlorine Cl- will bond with the carbon-4, resulting in only one glucose monomer, not two

Scientific Inquiry

Life Chemistry and Energy 2. Chapter 2 Life Chemistry and Energy Key Concepts 2.1 Atomic Structure...

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