Chapter 2-3 BiochemistryAP Biology

Why do atoms bond?• Atoms bond because of a difference

in their electronegativity.• Electronegativity is the ability of an

atom to attract electrons.• Electrons determine chemical and

physical properties of atoms.

Nucleus

Types of Bonds• Ionic bonds form when the atoms

electronegativity’s are very different and one has a much stronger pull.

• This generally occurs with metals and nonmetals.

• Covalent bonds happen when both atoms are similar and results in electron sharing.

• This generally occurs with non-metals.

• Covalent bonds come in two forms.• Nonpolar covalent bonds are when

electrons are shared equally.• Polar covalent bonds form when

electrons are shared unequally.• Some electrons spend more time around

the more electronegative atom and a partial charge results.

• Water is an example of a polar molecule.

• Hydrogen bonds generally occur between molecules and with hydrogen atoms and other atoms.

• Positively charged hydrogen atoms weakly bond with the negatively charged area of another atom.

hydrogen

oxygen

Watch water bend!

Water• Water has 5 important properties.• 1. Water is an excellent solvent.• 2. Water has a high specific heat

capacity.• 3. Solid phase is less dense than

liquid phase.

• 4. Water has strong cohesion and high surface tension.

• 5. Water has strong adhesion and capillary action.

Water is an excellent solvent.• Ionic substances are soluble

(dissolve) in water because of the polar water molecules act upon the compounds and separate them into their ions.

• Substances with polar covalent bonds are also affected because they possess a charged pole also.

• Hydrophilic molecules dissolve readily in water.

• Nonpolar covalent molecules do not dissolve in water or are hydrophobic because they lack charged poles.

• Because so many molecules dissolve in water, it is considered the universal solvent.

• A solute is any substance that dissolves in a solvent.

• When the solvent is water, the solution is said to be aqueous.

Water has a high specific heat capacity.• Specific heat is the degree to which

1 gram of a substance changes temperature in response to a gain or loss of heat.

• Since water has a high specific heat, it responds very slowly to temperature changes.

• STOP• Mini-Lab• What will the graph for water look like when

ice is heated until it boils?

• Heat of fusion-energy required to change water from a solid to a liquid.

• Heat of vaporization-energy required to change water from liquid to gas

• It is important to note that in phase change graphs, the line does not change in two places. Why?

Density of Water is Special!

• Water is one of the only substances on Earth in which the solid phase is less dense than the liquid phase!

• Because of this, life can exist in many places.

When winter comes, the ice floats and keeps fish safe.

ICE

Ouch!

If ice was actually denser than water…….

I wish I could get to safer

water below!

• Most substances contract when it converts to its solid form.

• Since water expands when it freezes, it becomes less dense allowing it to float.

• This ability has a profound effect on life on Earth, especially in its beginning stages.

Water has strong cohesion and surface tension.

• Cohesion occurs when like molecules stick together.

• This occurs because of hydrogen bonding.

Cohesion creates surface tension.

Water is very sticky!

Water has strong adhesion and capillary action.

• This results from the attraction of the poles of water molecules to other polar substances.

• This is when molecules that are not alike are attracted, example, water to walls of a test tube, or plant walls

• When you see adhesion, think adhesive, sticky.

Capillarity• This is when water

goes up a small, narrow tube like a plant stem or paper towel.

• Adhesion makes this possible.

Temperature Moderation• Water must gain or lose a

relatively large amount of energy for its temperature to change.

• When water is heated, most of the thermal energy that the water initially absorbs breaks the hydrogen bonds between the molecules.

• When the bonds are broken, the thermal energy is released and increases the motion of the molecules.

• Water’s ability to absorb large amounts of energy helps keep cells at an even temperature despite temperature changes in the environment.

solid liquid

gas

Break bonds

Break bonds

Make bonds

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Organic Compounds• Organic molecules contain carbon.• A carbon atom has 4 electrons in its outer

level which means it can create 4 bonds with any other atoms including itself.

• This makes carbon an excellent backbone for many organic molecules.

• Carbon can even form rings and double and triple bonds!

• Large organic molecules are called macromolecules.

• Most macromolecules are polymers.• Polymers are made of single units

called monomers that are repeated many times.

• An organic molecule’s properties are determined by their functional groups.

Functional Groups• A functional group is a group of atoms that

have specific characteristics.• For example an alcohol is a functional

group that has oxygen and hydrogen attached.

• Drunk Bear

• Drunk Squirrel

How are polymers made and broken?

• Monomers link together in a condensation (dehydration) reaction.

• When two monomers combine, water is released.

• When polymers are broken, it is called a hydrolysis reaction.

• Water is broken into two parts and breaks the bonds that holds the monomers together.

Energy Currency• Life processes require energy.• This energy is available to life in the

form of a compound called ATP.• ATP has three phosphates on the

molecule and when one phosphate is broken off, energy is released.

Carbohydrates• A monomer of a carbohydrate is

called monosaccharide.• A monosaccharide is a simple

sugar.• Two forms of glucose alpha and

beta differ simply by the reversal of the H and OH groups.

• Two monosaccharides form a disaccharide.

• A disaccharide is made by glycosidic linkage.

• During this process, a water molecule is lost.

• A polysaccharide is a complex molecule composed of three or more monosaccharides formed by glycosidic linkage.

• What are some carbs?

Cellulose is an unbranched polymer of glucose with linkages that are chemically very stable. Glycogen and starch are polymers

of glucose, with branching at carbon 6 (see Figure 2.9).

Important Carbohydrates• Starch (alpha-glucose) is the principal

energy storage molecule in plant cells.• Glycogen (alpha-glucose) is the major

energy storage molecule in animal cells.• Cellulose (Beta-glucose) serves as a

structural molecule in the walls of plant cells and is a major component of wood.

• Chitin (Beta-glucose) is a polymer similar to cellulose.

• Chitin serves as a structural molecule in the walls of fungus cells and in the exoskeletons of insects, other arthropods and mollusks.

• It is important to note that alpha-glucose linkages are easily digested by humans and other animals but only specialized organisms can digest Beta-glucose linkages.

Layers of cellulose fibrils, as seenin this scanning electron micro-graph, give plant cell walls greatstrength.

Within these potato cells, starchdeposits (colored purple in thisscanning electron micrograph) have a granular shape.

The dark clumps in this electron micrograph are glycogendeposits in a monkey liver cell.

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Lipids• Lipids are large, non- polar molecules

that are nearly insoluble in water but highly soluble in nonpolar substances like ether or chloroform.

• There are 3 major classes of lipids.

Types of Lipids• A triglyceride is composed of three

molecules of fatty acids joined to an alcohol called glycerol.

• Fatty acids are unbranched carbon chains that make up most lipids.

Glycerol(an alcohol)

3

3Fatty acidmolecules

Triglyceride

Triglycerides• Fatty acids vary in structure with the number of

carbons and placement of single and double covalent bonds.

• Single bonds in fatty acids mean all the available spaces are taken up by hydrogen atoms so they are called saturated fatty acids.

• As a result, saturated fatty acids pack together more tightly, have higher melting temperatures, and are usually solid at room temperature.

Palmitic acid

Carbon

Oxygen

Hydrogen

• The double bond in a fatty acid creates a bend at the bond slightly spreading the triglyceride apart.

• This means there are available bonds so this is called unsaturated fatty acids.

• Monounsaturated fats have one double bond while polyunsaturated fats have two or more double bonds.

• Unsaturated fatty acids are looser because of the space the double bond gives so they have lower melting temperatures and are usually liquid at room temperature.

Linoleic acid

Phospholipids• Phospholipids are made from two fatty

acids connected to the glycerol backbone and a phosphate group.

• The two fatty acid “tails” are hydrophobic and the “head” is hydrophilic and oriented to the outside.

• These form the basis for all cell membrane structures.

Choline

Phosphate

Glycerol

Hydrocarbonchains

Hydrophilichead

Hydrophobictail

• Hydrophilic-water-loving, molecules dissolve in water

• Hydrophobic-water-fearing, molecules do not dissolve in water

Steroids• Steroids are characterized by a

backbone of four linked carbon rings.

• Examples of steroids include cholesterol (a component of cell membranes) and certain hormones, including testosterone and estrogen.

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Proteins• Proteins are organic compounds

made from monomers called amino acids.

• There are 20 different amino acids.• The differences between the amino

acids are their R groups.

• Two amino acids bond to form a dipeptide.• In a condensation reaction, two amino

acids form a covalent bond called a peptide bond.

• Long chains of amino acids are called polypeptides.

• What are some proteins?

• Proteins can be grouped according to their functions.

• Structural Proteins-keratin, collagen, silk• Storage Proteins-casein, ovalbumin, zein• Transport Proteins-hemoglobin, facilitated

transport• Defensive Proteins-antibodies• Enzymes

Protein Structure• The primary structure of a protein

describes the order of amino acids.• The secondary structure of a protein

is a 3 dimensional shape that results from hydrogen bonding.

• This produces spirals or a folded plane like a pleated sheet. (fibrous proteins)

• The tertiary structure includes additional three-dimensional shaping and often dominates the structure of globular proteins.

• The shaping is increased by additional hydrogen bonding, ionic bonding, the hydrophobic effect and disulfide bonds.

• The quaternary structure describes a protein that is assembled from two or more separate peptide chains.

• Hemoglobin for example consists of four peptide chains that are held together by hydrogen bonding.

• Under normal cellular conditions, the primary structure of a protein determines how it folds into its particular three-dimensional shape.

• Structure also depends on physical and chemical conditions of the environment.

• Adverse conditions can weaken the bonding and is known as denaturation.

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Enzymes are a special kind of protein.• In order for a chemical reaction to take place, the

reacting molecules must first collide with sufficient energy to trigger the formation of new bonds. (Activation energy)

• Many reactions require the presence of a catalyst to accelerate the rate of reaction so it occurs within an appropriate span of time.

• Enzymes are a protein that acts as a catalyst by lowering the activation energy required for a reaction to take place.

• Chemical reactions that occur in biological systems are referred to as metabolism.

• Breakdown of substances is called catabolism.

• Formation of new products is called anabolism or synthesis.

• Enzymes work to accelerate either catabolism or anabolism by acting upon a specific substrate.

Types of Reactions• Exergonic reactions release energy

when complete.• Endergonic reactions absorb energy

when complete.• Many metabolic processes use

coupling which pairs both reactions together.

• Enzymes are substrate specific and can only act upon one specific item under the correct conditions.

• An enzyme remains unchanged during the chemical reaction and doesn’t take actual part in the process. It is not used up.

• Enzymes can catalyze a reaction in both the forward and reverse directions.

• Most enzymes are named after their substrate and the ending is changed to –ase.

• The induced-fit model describes how enzymes work.

Induced-Fit Model• Within the enzyme there is an active

site in which the substrate readily reacts because of its shape.

• The interaction of the substrate and the enzyme causes the enzyme to change shape.

• The new position places the substrate molecules into a position favorable to their reaction.

Effects on Enzymes• Temperature-raising or lowering

temperature can cause an enzyme to malfunction

• Most enzymes are particularly adapted to the temperature conditions of the organism it works in.

• A change in pH can decrease the ability of an enzyme to function.

• A foreign chemical or metal can decrease the ability of an enzyme to function.

• The presence of co-factors (non-protein helpers) influence enzymes by donating or accepting electrons. (vitamins)

• Some metals increase an enzyme’s function (Iron, magnesium)

• The amount of ATP present in the system affects enzyme function.

• ATP is made via phosphorylation and broken via hydrolysis.

Enzyme Regulation• Enzymes have two binding sites-one

active and one allosteric.• Allosteric sites are for allosteric

factors.• An allosteric activator binds to the

enzyme and induces the active form.• An allosteric inhibitor binds to the

enzyme and induces the inactive form.

Inhibition• In feedback inhibition, the end product

of the reactions acts as an allosteric inhibitor, shutting down the enzyme.

• In competitive inhibition, the substance mimics the substrate and occupies the active site displacing the real enzyme and not allowing the reaction to occur.

• In noncompetitive inhibition, a substance binds to the allosteric site and changes the shape of the enzyme, stopping its ability to work.

• Many toxins and antibiotics are this type of inhibitor.

• Cooperativity is different in which the enzyme becomes more receptive to additional substrate molecules after one substrate attaches to the active site.

• This is common with enzymes with quaternary structure like hemoglobin.

• How does aspirin work?• Use what we’ve learned about

enzymes to fully explain your answer.

• Include important vocabulary terms and a diagram if necessary.

• Include specific information, do not be general!

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Nucleic Acids• Nucleic acids are large and complex

organic molecules that store important information in the cell.

• RNA stores and transfers information to make proteins.

• DNA contains information that is essential for cell activities.

• Both RNA and DNA are composed of monomers called nucleotides.

• A nucleotide has 3 components: a phosphate group, a sugar and a nitrogen base.

What are some of the differences between DNA and RNA?