Computer scientists and Biologists collaborated, using the latest scientific data, to put together a movie of the inside

of a living cell:

http://www.studiodaily.com/main/technique/tprojects/6850.html

A review of the structure and function of a living cell:

OK, now that we know the structures and functions inside different types of

cells, now we need to know:

What makes up those cellular structures??

Carbohydrates, lipids, proteins, and nucleic acids… all

surrounded by water!

Before we can understand how these molecules work together to build a cell, we need to understand some

basic chemistry…

Before we can understand how these molecules work together to build a cell, we need to understand some

basic chemistry…

Chapter 2Essential Chemistry for Biology

Chapter 2Essential Chemistry for Biology

The Flow of Matter…Wait a minute,

WHAT is MATTER?– Matter is anything that occupies space and has

mass.– Matter is found on the Earth in three physical

states:

•Solid •Liquid •Gas

– Matter is composed of chemical elements.

• There are 92 naturally occurring elements on Earth.

– All the elements are listed in the periodic table.

• Four of these make up about 96% of the weight of the human body.

• Trace elements occur in smaller amounts.

Twenty-five elements are essential to life

Each Element consists of one type of Atom– Atoms are composed of subatomic

particles.• A proton is positively charged.• An electron is negatively charged.• A neutron is electrically neutral.

Example: a helium atom

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Electron Arrangement and the Chemical Properties of Atoms– Electrons determine how an atom behaves

when it encounters other atoms.

Copyright © 2007 Pearson Education Inc., publishing as Pearson Benjamin Cummings

–Electrons orbit the nucleus of an atom in specific electron shells.

•The number of electrons in the outermost shell determines the chemical properties of an atom.

Chemical Bonds– Chemical reactions enable atoms to give up or

acquire electrons in order to complete their outer shells.

• These interactions usually result in atoms staying close together.

• The atoms are held together by chemical bonds.

– Three main types of chemical bonds:• Ionic bonds• Covalent bonds• Hydrogen bonds

Stronger bonds

Weaker bonds

Ionic Bonds– When an atom loses or gains electrons,

it becomes electrically charged.• Charged atoms are called ions.• Ionic bonds are formed between oppositely

charged ions.

Covalent Bonds– A covalent bond forms when two atoms

share one or more pairs of outer-shell electrons.

– Water is a compound in which the electrons in its covalent bonds are shared unequally.

• Oxygen is greedy for electrons and keeps their negative charge closer to itself.

• This causes it to be a polar molecule, one with opposite charges on opposite ends.

-

+

What happens when the electrons in a covalent bond are shared unequally?

Covalent bonds where electrons are shared unequally

– The polarity of water results in weak electrical attractions between neighboring water molecules called hydrogen bonds.

Hydrogen Bonds

Covalent bond with unequally shared electrons

Chemical Reactions– Cells constantly rearrange molecules by

breaking and forming chemical bonds.• These processes are called chemical reactions.

– Chemical reactions cannot create or destroy matter,

• They only rearrange it.

Water and Life

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

• Modern life still remains tied to water.• Your cells are composed of 70%–95% water.

– The abundance of water is a major reason Earth is habitable.

Water’s Life-Supporting Properties

– The polarity of water molecules and the hydrogen bonding that results explain most of water’s life-supporting properties:

• Water’s cohesive nature • Water’s ability to moderate temperature• Floating ice• Versatility of water as a solvent

The Cohesion of Water

– Water molecules stick together as a result of hydrogen bonding.

• This is called cohesion.• Cohesion is vital for water transport

in plants.

– Surface tension is the measure of how difficult it is to stretch or break the surface of a liquid.

• Hydrogen bonds give water an unusually high surface tension due to cohesion.

How Water Moderates Temperature

– Because of hydrogen bonding, water has a strong resistance to temperature change.

– Heat and temperature are related, but different.• Heat is an amount of energy. This energy causes

movement of atoms and molecules.• Temperature measures this movement of the atoms

and molecules. http://sv.berkeley.edu/chemicalinteractions/menu.html

– Water can absorb and store large amounts of heat while only changing a few degrees in temperature.

– Water can moderate temperatures.• Earth’s giant water supply causes temperatures

to stay within limits that permit life.• Evaporative cooling removes heat from the

Earth and from organisms.

The Biological Significance of Ice Floating

– When water molecules get cold, they move apart, forming ice.

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

– The density of ice is lower than liquid water.

IceFloats!

– Since ice floats, ponds, lakes, and even the oceans do not freeze solid.

• Marine life could not survive if bodies of water froze solid.

http://majorlycool.com/category/animals/blogid/1

Water as the Solvent of Life– A solution is a liquid consisting of two or

more substances evenly mixed.• The dissolving agent is called the solvent.• The dissolved substance is called the solute.

An aqueous solution

An aqueous solution

The slight negative charge of the oxygen in a water molecule attracts it to the positive charge of the Na+ ion.

The slight positive charge of the hydrogen atoms in a water molecule attracts them to the negative charge of the Cl- ion.

As the water molecules surround the ions of NaCl they become dissolved in the water!

A Group Challenge:

• Based on the information of how NaCl becomes dissolved in water, can you figure out:– Why carbohydrates, proteins, and nucleic

acids can dissolve in water?– Why lipids (fats and oils) cannot dissolve in

water?

Acids, Bases, and pH

– Acid• A chemical

compound that donates H+ ions to solutions.

– Base • A compound that

accepts H+ ions and removes them from solution.

Chapter 3

The Molecules of Life

Organic Molecules– A cell is mostly water.

• The rest of the cell consists mostly of carbon-based molecules called organic molecules.

Carbon Chemistry– Carbon is a versatile atom.

• It has four electrons in an outer shell

that holds eight.• Carbon can share its electrons with other

atoms to form up to four covalent bonds.

– Each type of organic molecule has a unique three-dimensional shape that defines its function in an organism.

• The molecules of your body recognize one another based on their shapes.

Shape defines function!

Giant Molecules from Smaller Building Blocks

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

• Biologists call them macromolecules.• Examples: DNA, carbohydrates, proteins

– Most macromolecules are polymers.• Polymers are made by stringing together many

smaller molecules called monomers.• Cells link monomers by dehydration reactions.

Monomer - means “one” unit

Monomer - means “one” unitDimer - means “two” units

Monomer - means “one” unitDimer - means “two” unitsPolymer - means “many” units

– Organisms also have to break down macromolecules.

• Cells do this by a process called hydrolysis.

Monomer - means “one” unitDimer - means “two” unitsPolymer - means “many” units

Monomer - means “one” unitDimer - means “two” units

Monomer - means “one” unit

Biological Molecules– There are four categories of large molecules in

cells:

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Biological Molecules– There are four categories of large molecules in

cells:

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Biological Molecules– There are four categories of large molecules in

cells:

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

short

sugarmolecules

L-O-N-Gstarchmolecules

Monosaccharides

– Monosaccharides are simple sugars.• Glucose is found in sports drinks.• Fructose is found in fruit.

short

sugarmolecules

Monomer - means “one” unit

OR

Abbreviated structure

Monosaccharides are the main fuel that cells use to do work.

Disaccharides– A disaccharide is a double sugar.

• It is constructed from two monosaccharides.

– Disaccharides are joined through a dehydration reaction.

Monomer - means “one” unitDimer - means “two” units

– Lactose is another type of disaccharide.• Some people have trouble digesting lactose, a

condition called lactose intolerance.

– The most common disaccharide is sucrose, common table sugar.

• It consists of a glucose linked to a fructose.• Sucrose is extracted from sugar cane and the roots of

sugar beets.

– The United States is one of the world’s leading markets for sweeteners.

• The average American consumes about 64 kg of sugar per year.

PolysaccharidesMonomer - means “one” unitDimer - means “two” unitsPolymer - means “many” units

– Complex carbohydrates are called polysaccharides.

• They are long chains of sugar units.

• They are polymers of monosaccharides.

An aqueous solution

Remember this??

– Simple sugars and double sugars dissolve readily in water.

• They are hydrophilic, or “water-loving.”

OR

Abbreviated structure

Slight negative charge of oxygen in water and sugar molecules

are attracted to

Slight positive charges of hydrogen in water and sugar molecules.

I LoveYou!

Where are carbohydrates in a cell?

In the cytosol as an energy source

In the cell wall as cellulose

In amyloplasts in plants as starch (organelle not shown)

Biological Molecules– There are four categories of large molecules in

cells:

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

small

sugarmolecules

L-O-N-Gstarchmolecules

Biological Molecules– There are four categories of large molecules in

cells:

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

–fats

–steroids

–Lipids are hydrophobic.•They do not mix with water

Fats

Functions: energy storage, cushioning, insulation

Fats are formed by linking fatty acids onto a glycerol molecule by dehydration reactions

– Dietary fat consists largely of the molecule triglyceride.

• Triglyceride is a combination of glycerol and three fatty acids.

No charge! Cannot interact with water! (hydrophobic)

Run Away!

– Unsaturated fats• Have less than the maximum number of hydrogens

bonded to the carbons.

– Saturated fats • Have the maximum number of hydrogens bonded to

the carbons.

(double and triple bonds)

(all single bonds)

– Most animal fats have a high proportion of saturated fatty acids, which can be unhealthy.

• Example: butter

– Most plant oils tend to be low in saturated fatty acids.

• Example: corn oil

Saturated Fatty Acids: Too much of a good thing can be bad

WHY are too many saturated fats unhealthy?

– Not all fats are unhealthy.• Some fats perform important functions in the

body and are essential to a healthy diet.

• Phospholipids form a two-layered membrane, the phospholipid bilayer.

Special Lipid: Phospholipids

Negative charge interacts with water!(hydrophilic)

No charge! Cannot interact with water!(hydrophobic)

Water!

Other Lipids: Steroids– Steroids are very different from fats in structure

and function.• The carbon skeleton is bent to form four fused rings.

– Cholesterol is the “base steroid” from which your body produces other steroids.

• Example: sex hormones

Cholesterol is a key componentof cellular membranes…

– Synthetic anabolic steroids are controversial.

• They are variants of testosterone.

Where are lipids in a cell?

In the all membranes as phospholipids

In the smooth ER where lipids are synthesized

Triglycerides (Ex: fat in animal cells, seed oils in plant cells) stored in cytoplasm (not shown)

Biological Molecules– There are four categories of large molecules in

cells:

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

–fats

–steroids

–Lipids are hydrophobic.•They do not mix with water

Biological Molecules– There are four categories of large molecules in

cells:

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Proteins– A protein is a polymer constructed from

amino acid monomers.– Proteins perform most of the tasks the

body needs to function.

Structural Proteins

Storage Proteins

Contractile Proteins

Transport Proteins

Defensive Proteins

Receptor Proteins

Enzymes

Hormonal Proteins

Sensory Proteins

Gene Regulatory Proteins

Structure of an Amino Acid

Structure of an Amino Acid

Run Away!

I LoveYou!

The Monomers:

Amino Acids– All proteins are

constructed from a common set of 20 kinds of amino acids.

– Some fear water (hydrophobic)

– Some love water (hydrophilic)

Structure givesFunction!

Proteins as Polymers– Cells link amino

acids together by dehydration reactions.

• The resulting covalent bond between them is called a peptide bond.

– Your body has tens of thousands of different kinds of protein.

• The arrangement of amino acids makes each one different.

Structure gives Function!!

Protein Shape

– Proteins have four levels of structure.

• Primary 1st level• Secondary 2nd level• Tertiary 3rd level• Quaternary 4th level

– Primary structure• The specific sequence of amino acids in a

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.

Protein Shape

– Primary structure held together by covalent bonds

– Secondary structure held together by hydrogen bonds

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

– This happens by disrupting the hydrogen bonds that hold together the shape of a protein.

– This is called denaturation.

– If the shape unfolds, the function is destroyed…

A protein’s shape is sensitive to the surrounding environment

The Plasma Membrane:A Fluid Mosaic of Lipids and

Proteins

– The membranes of cells are composed mostly of:

• Lipids• Proteins

Copyright © 2007 Pearson Education, Inc. publishing as Pearson Benjamin Cummings

– The lipids belong to a special category called phospholipids.

– Phospholipids form a two-layered membrane, the phospholipid bilayer.

– Most membranes have specific proteins embedded in the phospholipid bilayer.

– This behavior leads to the description of a membrane as a fluid mosaic:

• Molecules can move freely within the membrane.

• A diversity of proteins exists within the membrane.

Membrane phospholipids and proteins can drift about in the plane of the membrane

Where are proteins in a cell?

In the all membranes as integral membrane proteins

Everywhere!! Proteins are enzymes, and structural, transport, receptor, regulatory, contractile proteins, etc, and perform most of the functions of a cell!

Biological Molecules– There are four categories of large molecules in

cells:

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Biological Molecules– There are four categories of large molecules in

cells:

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

DNA, deoxyribonucleic acid

RNA, ribonucleic acid

Nucleic Acids– Nucleic acids are information storage

molecules.• They provide the directions for building

proteins.

Transcription

Translation

– Nucleic acids are polymers of nucleotides.

I LoveYou!

Nucleic acids are hydrophilic!

– Each DNA nucleotide has one of the following bases:

– Nucleotide monomers are linked into long chains.

• These chains are called polynucleotides, or DNA strands.

• A sugar-phosphate backbone joins them together.

– Two strands of DNA join together to form a double helix.

– RNA, ribonucleic acid, is different from DNA.

• Its sugar has an extra OH group.• It has the base uracil (U) instead of thymine (T).

Where are nucleic acids in a cell?DNA is in the nucleus, mitochondria, and chloroplasts

RNA is in the nucleus, mitochondria, chloroplasts, cytosol, and ribosomes!