BIOCHEMISTRYthe chemistry of life

Chpt. 3

Matter, energy &

organization

1. Water2. Carbon compounds3. Molecules of life

WATER

The molecules that make you you are NOT water…

(Proteins, Carbohydrates, Lipids & Nucleic Acids) why then is water important for

life? Why will you die w/out it?

• Somehow, it has properties that other molecules don’t… properties that are vital for life.

• But what is it about a water molecule that makes it so special???

• LET’s FIND OUT TODAY!!!!

Water molecule? Or…

A: WATER IS A POLAR MOLECULE… it has a partial positive & partial negative side to it… call them “poles”.

This gives it some unique properties.

Polarity means separation of + & - charges

• Oxygen is a more electronegative element than hydrogen- it’s pull on the electrons is greater.

• The shared electrons spend more time around the OXYGEN than they do around the HYDROGENS.

• OXYGEN is partially -• HYDROGENS are partially

+

Water is formed viapolar covalent bondsbetween the hydrogenand oxygen atoms.

Oxygen gasIs O=O

This happenswhen one atom is moreelectronegativethan anotherin the covalentbond.

Because of it’s polarity… water is a great solvent!

• Sugars• Proteins• Ionic

compoundsex. Table salt

(Na+Cl-)

Polar substances will readily dissolve in water.

Watch the salt disappear…IT’S MAGIC!!!

No matter what the charge is on the solute, it can be completely surrounded by water molecules. The partially negative OXYGEN is attracted to the positive ion OR the partially positive HYDROGENS are attracted to the - Cl

Salt crystals dissolve in water when Na+ and Cl- ions are separated and

surrounded by water

The polarity of water makes hydrogen bonding possible

• A HYDROGEN Bond extends from the + hydrogen atom in one molecule to the partially negative atom in another molecule (N, O, S).

• N (nitrogen) O (oxygen) and S (sulfur) are all electroneg.

• Shown as a dotted line. Hydrogen bonds are weak bonds that hold water molecules together or to other charged substances.

This results in COHESION between water molecules.

(water-water H bonds)

• Jesus lizard • Water Strider

The high surface tension of water allows for these two miracles. Increased habitat for organisms. Water resists being pulled apart from other water molecules.

Surface tension is molecules resisting being pulled apart because of their

hydrogen bonds!

BIOLOGICAL MOLECULES LIKE DNA ARE HELD TOGETHER

BECAUSE OF HYDROGEN BONDS

ADHESION attractive force between unlike polar

substances Adhesion of water

molecules to the xylem

in these Giant Sequoia trees

lets it rise 275 ft.by capillary action.

Capillarity or capillary action is the rising of water up small tubes w/out the use of Energy (this happens in XYLEM tubes).

TRANSPIRATION

• When water climbs through Xylem tubes in plants, from soil to the roots to the leaves to the atmosphere this is called transpiration.

• A continuous water chain is “yanked” up w/ each evaporated water molecule from the leaf.

• This is called the COHESION-TENSION MODEL and it explains how plants transport water and minerals without using any ATP/energy.

BECAUSE OF IT’S HYDROGEN BONDS, WATER IS A GREAT

TEMPERATURE MODERATOR

Where would you like to be on a hot day?Water absorbs energy into it’s HYDROGENBONDS before it starts gaining energy itself.Important for life/cells which are 90% water.Helps to maintain homeostasis.

Water is excellent at preventing temperature swings (getting too hot or

too cold under normal circumstances)because it has an extremely high SPECIFIC HEAT.

=‘s the amount of energy needed to change 1 g of the substance by 1

degree celcius.

WATER BOILS AT A HIGHER TEMPERATURE THAN ALCOHOL. WHY?

Water is MOREpolar & has morehydrogen bonds.

Because of hydrogen bonding WATER IS LESS

DENSE AS A SOLID…• Hydrogen bonding

between water molecules at low energy levels places them farther apart than as a liquid or gas.

• This means ice (solid water) floats.

• An important reality for aquatic organisms.

RECAP OF THE PROPERTIES OF WATER THAT MAKE IT ESSENTIAL FOR LIFE

1. Polarity: good solvent.

2. Hydrogen Bonding: surface tension,cohesion, adhesion, capillarity.

3. Hydrogen Bonding: temperature moderation & expands upon freezing.

THE WATER LAB1. Magic Salt Disappearing Trick Sprinkle a spoon-full of salt into a beaker/glass of water. Stir it around and make

it “disappear”. Where did it go? How do you explain this using your knowledge of water chemistry?

2. Drops on a PennyPlace as many drops of water on the face of a penny as you can without them spilling over the side. Explain how you can make this snow-globe shaped dome at the top!

3. Can you Break these BondsTake two flat pieces of glass (microscope slides work well) and hold them flat sides together. Pull them apart. Now put a film of water between them and try to pull them apart. Can you? Explain what’s going on.

4. Rainbow Tree SimulationTake a piece of chromatography paper and use a vis-à-vis (water soluble ink) marker to draw a line near the bottom of the strip that is horizontal to the paper. Put the paper in a shallow cup of water with the end of the paper w/ the line in the water. The water should be lower than the drawn line. Watch as water creeps up the paper and see what it does to the ink!!!! Explain this in terms of cohesion and adhesion.

Matter, energy &

organization

1. Water2. Carbon compounds3. Molecules of life

II. CARBON COMPOUNDSORGANIC COMPOUNDS are:

• Molecules formed by the actions of living things.

• Molecules containing CARBON & HYDROGEN.

• Molecules with a carbon backbone-carbon atoms covalently bonded to other carbon atoms & to other elements as well.

• The other clusters of atoms attached to the carbon backbone are called functional groups.

• Ex. Alcohol functional group

Organic molecules must be made of carbon. Why carbon?

• Abundance on Earth.• Makes 4 covalent bonds because

2 electrons in first shell and 4 in the 2nd shell… needs 4 more e-

• Versatility of carbon allows for complex shapes & arrangements

-Straight chains-Branched chains-Rings

• Single, double, or triple bonds too!!!!

Carbon (atomic #6)

some carbon compounds

Glycogen

benzeneglucose

Ethyne

GLUCOSE

FUNCTIONAL GROUPSare clusters of atoms attached to the

carbon skeleton that influence the properties of the molecules they compose.

FUNCTIONAL GROUPS:know this for the SAT subject

test• Hydrogen (-H)polar or nonpolar; involved in condensation and hydrolysis.

• Amino (-NH2)Basic; involved in peptide bonds

• Phosphate (-H2PO4)acid; links nucleotides; energy carrier group

ENERGY• Methyl (-CH3)

nonpolar, makes molecules hydrophobicCONTROL OF GENE EXPRESSION• Carboxyl (-COOH)

acidic (carboxylic acids)

BESIDES WATER…WHAT MOLECULE IS INVOLVED IN ALL CHEMICAL

REACTIONS???

THIS IS THE ENERGY MOLECULE ASSISTING “coupled to” ALL BIOCHEMICAL REACTIONS???

ATP adenosine tri-phosphate

• Energy molecule• Energy is stored in

the bonds between the phosphate groups.

• Energy is released when the phosphate-phosphate bond is broken!!!!!

ATP --> energy + ADP + Pi

Adenosine TRI phosphate can be brokendown into Adenosine DI phosphate…When this happens, energy is released to power ENDERGONIC reactions.

NAD+ + H+ + e- + e- = NADH

WHAT TYPES OF MOLECULES ARE LIVING THINGS MADE

OUT OF ???(hint: there’s 4 categories)

THERE ARE 4 TYPES OF LARGE MOLECULES… each is made from specific kind

of smaller, “building block” .

1. PROTEIN2. CARBOHYDRATES3. NUCLEIC ACIDS4. LIPIDS(POLYMERS)

1. amino acids2. glucoses3. nucleotides4. glycerol + fatty

acids(MONOMERS)

Monomers & Polymers

MONOMERS are simple molecules “chemical building blocks” used to construct larger carbon compounds called POLYMERS.

Ex. Nucleotides form DNA amino acids form PROTEIN

How do we build polymers from monomers?

How do we break down polymers into monomers?

CONDENSATION REACTION (dehydration synthesis)

BUILDS LARGER MOLECULESmonomer in, water out-

you get a polymer!!!

HYDROLYSIS or DISSOCIATION

splitting of a polymer by adding a water molecule.

- Means “to CUT w/ water”.

Macro-molecule(polymer)

Chemical building

block(monomer)

carbohydrates

simple sugars

(ex. glucose)

proteins Amino acids(20 types)

lipids Glycerol & fatty acids

nucleic acids(DNA, RNA)

Nucleotides(A,T,G,C)

#1 CARBOHYDRATE functions:

1. Short term energy storage &

2. Provide structure for cell walls

Plants- Starch ex.amyloseAnimals- glycogen

cellulose

CARBOHYDRATES• Made of C, H, & O.• Ratio is 1 Carbon:2 hydrogens:1 Oxygen• The number of carbons varies.• Can exist as monomers or polymers.

1. Monosaccaride (single sugar)ex. Glucose- metabolized to make ATP

Fructose- fruit sugar Galactose- milk sugar

2. Disaccharide (double sugar) ex. Sucrose = fructose + glucose Maltose = glucose + glucose Lactose = galactose + glucose

3. Polysaccharide (3 or more) ex. Glycogen = millions of glucoses in animal cells

Starch = millions of glucoses in plant cellsCellulose = millions of glucoses in plant cell

walls

ISOMERS are molecules with the same molecular

formula but different shapes.

•C 6 H 12 O6

• Glucose (used for cell energy)

• Fructose (fruit sugar)

• Galactose (milk sugar)

#2 LIPIDS FUNCTIONS:1)long-term, light weight, energy storage

2) communication & 3) structure

phospholipid

Steroid- hormone

phospholipid bilayer ofCell membrane

#2

#3

#1 triglyceride

LIPIDS are:large, nonpolar, organic

molecules that don’t dissolve in water.

• C,H, 0 but with a higher ratio of carbons & hydrogen than carbohydrates.

• Carbon-Hydrogen bonds store energy.

• Monomers of LIPIDS are:

1) glycerol & 2) fatty acid(s)

FATTY ACIDS

2 SIDES:An unbranched carbon chain

(12-28 carbons) at one end

That is HYDROPHOBIC water fearing

And a -COOH carboxyl group at the other end

That is HYDROPHILLIC water loving

Waterfearing

Waterloving

COMPLEX LIPIDS

TRIGLYCERIDE3 fatty acids + 1 glycerol

Saturated ones have a high melting points & solid at room temperature- shortening.

Unsaturated ones have lower melting points, are liquid at room temp and are found in plant seeds and fruits.

saturated vs. unsaturated Saturated means each carbon is

“full of hydrogens”. BAD FOR YOUR HEALTH(beware of hydrogenated products

like margarine, shortening and CRISCO)

Unsaturated means the carbons have some double bonding and fewer hydrogens.

Best = polyunsaturated fatsThese may lower your cholesterol!!!

GOOD FOR YOU

PHOSPHOLIPIDSTwo fatty acids joined by a

molecule of glycerol.A double layer of

phospholipids provide a stable and effective barrier for cells.

WAXESLong fatty acid joined to a

long alcohol chain. Highly waterproofProtective coating in plants

and animals.

STEROIDS

• Four fused carbon rings with various functional groups attached.

• Not made of fatty acids.

• Many animal hormones are steroids.

• Ex. Cholesterol, testosterone, progesterone etc.

#3) NUCLEIC ACIDS function is to store and transmit genetic information and use that information to direct

the synthesis of new protein

DNA

RNA

NUCLEOTIDES are the basic building block of Nucleic Acids

NUCLEOTIDE STRUCTURE:All contain a 1. sugar (ribose or deoxyribose) a2. phosphate… & a 3. nitrogen containing base .- Adenine- Cytosine- Guanine- Thymine (Uracil in RNA

nucleotides)

DNA’s sugar is DEOXYRIBOSERNA’s sugar is RIBOSE

DNA… stores genetic information.

• THE sugars and phosphates make the “uprights” of the ladder.

(joined by covalent bonds)• The nitrogenous bases make

the “rungs” of the ladder.(joined by hydrogen bonds)• STORES information used in

the manufacture of proteins.• RNA molecules are assembled

based on a “gene” (1 side of DNA)

Two polymer chains, twisted ladder, spiral staircase, double helix

RNA does the work of building proteins!!!

• mRNA is the messenger (directions)

• tRNA brings the amino acids (transfer RNA)

• rRNA builds the RIBOSOME (huge enzyme where the polypeptide chains are built)

#4) PROTEINS provide structure & hormonal control and they transport materials like oxygen or materials across

cell membranes.

PROTEINSPOLYPEPTIDE

• organic compounds made of carbon, hydrogen, and nitrogen.

• Ex. Skin, muscles, hair, enzymes, and some hormones.

• Made from Amino Acids joined by PEPTIDE bonds.

• 20 types• AMINO ACIDS consist of: a central CARBON w/ 4 fun groups 1. hydrogen -H 2. amino group -NH2 3. carboxylic acid -COOH 4. R group (variable x 20)

Amino Acid(monomer)

4 levels of STRUCTURE OF PROTEINSare due to interactions of the amino acids.

1) PRIMARY STRUCTUREAmino acid chain (peptide bonds)2) SECONDARY STRUCTUREAlpha helix, Beta pleated sheet(due to hydrogen bonds)3) TERTIARY STRUCTURE3-D clump (R group interactions)4) QUATERNARY STRUCTURETwo or more 3D proteins.

ENZYMES• Are catalytic PROTEINS• Names end in -ase.• Biological Catalyst• Lower the amount of required

activation energy to start RXN.• Thus… speeds up reactions!

• Unlike inorganic catalysts which are consumed in the RXN, enzymes are RECYCLED

(don’t get used up).

Enzymes are catalytic proteins… the protein’s unique primary sequence & the environment of

the solution (pH, salts, polarity) results in a unique tertiary globular structure or shape of the

protein.

• The SUBSTRATE fits into the ACTIVE SITE of the enzyme.

• Shape dependent- very specific• LOCK & KEY model means

one enzyme works w/ one substrate.

• INDUCED FIT model says the enzyme “hugs” the substrate once it binds.

• Ex. CATALASE breaks HYDROGEN PEROXIDE into WATER and OXYGEN

TemperatureEffects rate Of RXN.

Think about kinetic energy.

• Work best under specific conditions of temperature, pH, and salt concentration.

• High temperature or changes in pH, solvent polarity, or Salt concentration can DENATURE the enzyme (now it won’t work)

• DENATURE = CHANGE SHAPE

Which enzyme works best at acidic pH?

• Ubiquitous!• they are

everywhere• every reaction

has a specific enzyme to catalyse it!

3 DIGESTIVE ENZYMES

• Amylase- breaks carbs to sugar

• Peptidase- breaks peptide bonds… breaks proteins down into amino acids.

• Lipase- breaks lipids apart.