AP CHEMISTRY REVIEW – CH. 2 CLIFFS Protons (+), neutrons (0) and electrons

(-) Isotopes – same proton, different

neutron number Ionic bonds vs. covalent bonds (non-

polar covalent and polar covalent) Interaction of electrons determine

bonding

IONIC BONDING

Sharing of valence electrons to create molecules

Non-polar covalent – electrons are shared equally

Polar-covalent – not shared equally (water molecule)

Double and triple bonds

COVALENT BONDING

WATER – POLAR COVALENT

HYDROGEN BONDING Weak bonds between molecules Water molecules display H-bonding

HYDROGEN BONDS

Water and ammonia Water with Water

Water is cohesive - because of hydrogen bonds – because of polarity

Water has surface tension due to cohesion

Water displays capillary action due to adhesion, which allows it to crawl up tubes.

Ice is less dense than water, therefore it floats

Water heats and cools slowly because of high specific heat.

Water is a biological solvent Water has high heat of vaporization

PROPERTIES OF WATER

ACIDS AND BASES pH scale Acids – H+

Bases – OH- (alkaline) Tenfold change – pH 3 is ten times more

acidic than pH of 4

Polymers - Large molecules made by chains of small molecules

Carbohydrates, Lipids, Proteins, Nucleic Acids are all polymers

Organic – contain carbon Inorganic – no carbon (except for CO2) Watch this video Functional groups – pg. 14

ORGANIC MACROMOLECULES

CARBOHYDRATES Mono, di, poly saccharides Glucose and fructose are

monosaccharides Dehydration synthesis yields a

disaccharide – glycosidic linkage Lose water Hydrolysis breaks the bonds Gain water maltose= glucose + glucose Lactose= glucose + galactose Sucrose= glucose + fructose

DEHYDRATION SYNTHESIS

Starches - Carbohydrates stored by plants

Glycogen – Carbohydrates stored by animals in liver and muscle cells. Alpha glucose

Cellulose – forms the cell walls of plants and gives the plant structural support. Beta glucose

Chitin – exoskeletons of arthropods and cell walls of fungi. Beta glucose

STARCH, GLYCOGEN, CELLULOSE

CELLULOSE VS. STARCH

Lipids – Fats, oils, phospholipids, steriods

Nonpolar – they do not dissolve in water Long term energy storage, insulation,

and protection Major component of the cell membrane Glycerol molecule and 3 fatty acid

chains – ester linkage Unsaturated vs. saturated

LIPIDS – DEHYDRATION SYNTHESIS

TRIGLYCERIDE SYNTHESIS

PHOSPHOLIPID STRUCTURE

Amphipathic – hydrophilic head and hydrophobic tails

CHOLESTEROL

Many uses in the cells and are integral in most every process in an organism’s body.

PROTEINS

PEPTIDE BONDING – DEHYDRATION SYNTHESIS

Lose water Dipeptide then

polypeptide Many polypeptides

folded and twisted becomes a functional protein

Primary to tertiary structure

As polypeptide advances in structure, binding sites are formed

POLYPEPTIDE CHAINS – PRIMARY STRUCTURE

SECONDARY STRUCTURE Fibrous proteins

Hydrophobic interactions between amino acids with nonpolar side chains cluster in the core of the pleated sheet or alpha helix.

Disulfide bonds between two cysteine amino acids also occur.

TERTIARY STRUCTURE

Made up of two or more polypeptide chains.

Ex. Collagen and Hemoglobin

QUATERNARY STRUCTURE

PROTEIN STRUCTURES

TYPES OF PROTEINS IN THE BODY1. Structural – keratin, collagen, silk2. Storage – albumin in eggs3. Transport proteins on cell membranes4. Defensive – antibodies5. Enzymes – regulate all chemical rxns.

in the body

Polymers of nucleotides - polynucleotides

Nucleotide – sugar, phosphate group, and nitrogen base

4 nitrogen bases – adenine, guanine, cytosine, thymine

DNA – double helix – deoxyribonucleic acid – deoxyribose sugar

RNA – single strand – ribonucleic acid – ribose sugar

NUCLEIC ACIDS

Single ring Cytosine, thymine and uracil

PYRIMIDINES

Adenine and Guanine Double Ring

PURINES

NUCLEIC ACID STRUCTURE

FLOW OF INFORMATION IN CELLS

Cellular Energetics Bioenergetics – our cells’ ability to release the

energy in glucose, starch, and fat We do this by chemical reactions catalyzed by

enzymes Exergonic reactions vs. endergonic reactions Exergonic – nutrients being oxidized in the

mitochondria Endergonic – plants using CO2 and water to

form sugars Activation energy – energy barrier that must

be broken for exergonic rxns to proceed.

Figure 8.6

(a) Exergonic reaction: energy released, spontaneous

(b) Endergonic reaction: energy required, nonspontaneous

Reactants

EnergyProducts

Progress of the reaction

Amount of energy

released(G 0)

ReactantsEnergy

Products

Amount of energy

required(G 0)

Progress of the reaction

Fre

e e

nerg

yFre

e e

nerg

y

Figure 8.8b

Adenosine triphosphate (ATP)

Energy

Inorganicphosphate

Adenosine diphosphate (ADP)

(b) The hydrolysis of ATP

How the Hydrolysis of ATP Performs Work

• The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP

• In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction

• Overall, the coupled reactions are exergonic

© 2011 Pearson Education, Inc.

Figure 8.9

Glutamicacid

Ammonia Glutamine

(b)Conversionreactioncoupledwith ATPhydrolysis

Glutamic acidconversionto glutamine

(a)

(c)Free-energychange forcoupledreaction

Glutamicacid

GlutaminePhosphorylatedintermediate

GluNH3 NH2

Glu GGlu = +3.4 kcal/mol

ATP ADP ADP

NH3

Glu Glu

PP i

P iADP

GluNH2

GGlu = +3.4 kcal/mol

Glu GluNH3 NH2ATP

GATP = 7.3 kcal/molGGlu = +3.4 kcal/mol

+ GATP = 7.3 kcal/mol

Net G = 3.9 kcal/mol

1 2

Enzymes Lower activation energy Specificity Active site binds substrate in lock and

key fit – enzyme/substrate complex Induced fit – when enzyme changes its

shape to accommodate substrate Enzymes are not used up in the reaction Do not work alone – need co-enzymes

like vitamins, iron, and magnesium

Figure 8.13

Course ofreactionwithoutenzyme

EA

withoutenzyme EA with

enzymeis lower

Course ofreactionwith enzyme

Reactants

Products

G is unaffectedby enzyme

Progress of the reaction

Fre

e en

erg

y

Figure 8.14

Substrate

Active site

Enzyme Enzyme-substratecomplex

(a) (b)

Figure 8.15-3

Substrates

Substrates enter active site.

Enzyme-substratecomplex

Enzyme

Products

Substrates are heldin active site by weakinteractions.

Active site canlower EA and speedup a reaction.

Activesite is

availablefor two new

substratemolecules.

Products arereleased.

Substrates areconverted toproducts.

12

3

45

6

Factors affecting reaction rates

1. Temperature Increasing temp. increasing rxn rate Too much heat can damage the

enzyme – denature most human enzymes work at 37

degrees Celsius2. pH3. Enzyme concentration4. Substrate concentration

Figure 8.16

Optimal temperature fortypical human enzyme (37°C)

Optimal temperature forenzyme of thermophilic

(heat-tolerant)bacteria (77°C)

Temperature (°C)(a) Optimal temperature for two enzymes

Rate

of

reacti

on

Rate

of

reacti

on

120100806040200

0 1 2 3 4 5 6 7 8 9 10pH

(b) Optimal pH for two enzymes

Optimal pH for pepsin(stomachenzyme)

Optimal pH for trypsin(intestinal

enzyme)

Enzyme Regulation Allosteric regions on an enzyme can be

bound by inhibitors or activators Allosteric sites are subject to feedback

inhibition – where the product inhibits the rxn.

Competitive inhibition – when the allosteric inhibitor binds the active site of the enzyme

Non-competitive inhibition – when the inhibitor binds another site on the enzyme leading to a conformational change in the active site

Figure 8.17

(a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition

Substrate

Activesite

Enzyme

Competitiveinhibitor

Noncompetitiveinhibitor

Figure 8.19

Regulatorysite (oneof four)

(a) Allosteric activators and inhibitors

Allosteric enzymewith four subunits

Active site(one of four)

Active form

Activator

Stabilized active form

Oscillation

Non-functionalactive site

Inactive formInhibitor

Stabilized inactiveform

Inactive form

Substrate

Stabilized activeform

(b) Cooperativity: another type of allosteric activation

Figure 8.21

Active siteavailable

Isoleucineused up bycell

Feedbackinhibition

Active site ofenzyme 1 isno longer ableto catalyze theconversionof threonine tointermediate A;pathway isswitched off. Isoleucine

binds toallostericsite.

Initial substrate(threonine)

Threoninein active site

Enzyme 1(threoninedeaminase)

Intermediate A

Intermediate B

Intermediate C

Intermediate D

Enzyme 2

Enzyme 3

Enzyme 4

Enzyme 5

End product(isoleucine)

Video on Enzymes

• Watch this video