Slide 1

Section 1 of Chapter 2

Chapter 2 Chemistry1

Why study chemistry?A clear understanding of chemistry is essential for the study of physiology.

This is because organ functions depends on cellular functions, which occur as a result of chemical reactions. Watson & Crick first proposed the double helix structure of DNA2DefinitionsBiochemistry = Chemistry of living things

Matter = Anything that has mass and takes up space (Solids, liquids, gasses)Element = Fundamental substance of matter (e.g. Carbon, Hydrogen, Oxygen)Compound = Two or more different elements chemically bonded together (e.g. H2O = water, C6H12O6 = glucose)

Molecule = two or more atoms chemically joined together.

Molecules may be compounds (H2O = water molecule), or Molecules may be of the same element (H2= hydrogen molecule)3Our body consists of 11 bulk elements and 7 trace elements.Hydrogen (H)Oxygen (O)Carbon (C)Nitrogen (N)Sulfur (S)Magnesium (Mg)Sodium (Na)Potassium (K)Calcium (Ca)Chlorine (Cl)Phosphorus (P)Bulk elements make up 99.9% of our body:Trace elements make up less than 0.1% of our body:Cobalt (Co)Zinc (Zn)Manganese (Mn)Iron (Fe)Iodine (I)Copper (Cu)Fluorine (F)Learn each bulk element and trace element along with their atomic symbols shown in parentheses4

All elements are arranged onto a Periodic table5Atoms

Atoms are composted of 3 subatomic particles:Proton carries a single positive chargeNeutron carries no electrical chargeElectron carries a single negative chargeAtoms are the smallest particles of an element that still have the properties of that element.

An atom contains a central nucleus composed of protons and neutrons. Electrons orbit the nucleus.6Subatomic Particles

Atomic Mass:Proton: 1 daltonNeutron: 1 daltonElectron: 0 Electrical Charge: Proton: +1 charge. Electron: -1 charge.Neutron: 0 chargeMost atoms contain equal number of protons and electrons, so an atom contains no overall net charge and is neutral.

7Subatomic Particles

Atomic Number: The number of protons in one atom.

Atomic number identifies an element.Example. The atomic number of oxygen is 8. Oxygen, and only oxygen has 8 protons.Atomic Weight: The sum of protons and neutrons in one atom. Remember, the weight of electrons is negligible.8

Examples of atomic numbers and atomic weightHydrogen has: 1 proton and 1 electron

Atomic number = 1Atomic weight = 1

Carbon has:6 protons, 6 neutrons, and 6 electrons

Atomic number = 6 Atomic weight = 129

Table 2.1 Some Particles of Matter10IsotopesIsotopes are atoms with the same atomic number, but different atomic weights. Isotopes occur because the number of neutrons of an element varies between atoms.Oxygen 16 (O16)Oxygen 17 (O17)Two isotopes of oxygen:protons: 8protons: 8electrons: 8electrons: 8neutrons: 8neutrons: 9Atomic Number:88Atomic Weight:1617*The atomic weight of an element is an average of the isotopes present.11

End of Section 1, Chapter 2Understand the notations on a periodic table. 12Section 2 of Chapter 2Bonding of Atoms

13Properties of electronsElectron Shells: Electrons encircle the nucleus in discrete orbits, called electron shells. Each shell can contain only a fixed number of electrons.Octet rule: Except for the 1st shell, each electron shell holds up to 8 electrons1st shell holds 2 electrons2nd shell holds 8 electrons3rd shell holds 8 electrons* Lower shells are filled first.

14Examples of filling electron shells

HeliumAtomic number = 2Atomic weight = 4(2 electrons fill the 1st electron shell)CarbonAtomic number = 6Atomic weight = 12(The first 2 electrons fill the inner shell, and the remaining 4 electrons are placed the 2nd electron shell).15IonsIons are atoms that readily gain or loose electronsCation: an ion that looses electronsCations are positively charged ions

Anion: an ion that gains electronsAnions are negatively charged ions

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Example of a cationNa+ = Sodium cationSodium (Na)atomic number = 11atomic weight = 23Only 1 lone electron sits in the outer shell. This electron is unpaired and is easily lost, forming the sodium cation.17

Example of an anionChlorine (Cl)atomic number = 17atomic weight = 357 electrons fill the outer shell of chlorine, leaving room for 1 more electron. Chlorine readily accepts one electron, creating the chloride anion.Cl - = Chloride anion18

Na+ + Cl- NaClIonic BondIonic bonds are formed when the oppositely charged particles attract. Figure 2.4 (a) An ionic bond forms when on atom gains and another atom looses electrons, and then (b) oppositely charged ions attract.19

Ionic bonds do not form molecules

Figure 2.4 (c) salt crystal formation occurs because of the ionic bonds of sodium and potassium.Cations & anions attract in all directions, forming organized arrays, such as crystals. They do not form molecules.20

Covalent BondsCovalent bonds are formed when atoms share electrons.Example: A hydrogen molecule (H2) is formed when two hydrogen atoms share their single electron.H + H H221

OHHH2OCovalent Bonds of waterWater consist of oxygen covalently bonded to two hydrogen atoms.Structural Formula: depicts the covalent bonds of a molecule as lines.Molecular Formula: is a shorthand notation for representing molecules.22Types of covalent bondsA Single Bond occur when two atoms share one pair of electronsA Double Bond occurs when atoms are joined by two pairs of electrons

A Triple Bond occurs when atoms are joined by three pairs of electrons

Two oxygen atoms joined by a double bond.Oxygen joined to two hydrogen atoms by single bondsA Carbon atom joined to hydrogen by a single bond and to nitrogen by a triple bond.23Nonpolar covalent bondsNonpolar covalent bonds occur when the atoms share the electrons equally, so the molecule has no overall charge.

Two hydrogen atoms share their electrons equally. Thus, the hydrogen molecule has no overall charge and is nonpolar.24

Slightly negative endSlightly positive endPolar covalent bondsPolar bonds have an unequal distribution of electrons.

Water is a polar molecule because the oxygen atom (with 8 protons) tends to pull the electrons away from hydrogen. The oxygen end has a slight negative charge, while the hydrogen end has a slight positive charge.One portion of the atom has a higher affinity for electrons than the rest of the molecule (electronegative).25

Hydrogen bondsOccur when the slightly positive (hydrogen) end of a polar molecule weakly attracts to the slightly negative end of another molecule.Hydrogen Bonds:Form weak bonds at room temperature, but are strong enough to form ice

Stabilize large proteins, DNA, and RNA

End of Section 2, Chapter 226section 3 of chapter 2

chemical reactions27Chemical ReactionsReactants (starting chemicals) are on the left Products are on the rightSynthesis Reaction joins molecules togetherA + B AB

Decomposition Reaction breaks chemical bonds AB A + B

Exchange Reaction reactants are swapped AB + CD AC + BD

Reversible Reaction products can also yield reactants A + B AB28

activation energy: energy required to start a reaction

A catalyst reduces the amount of energy needed to initiate a reaction.

Catalysts increase the rate of reactions, but are not consumed by the reaction- reusable

29Acids, Bases, and Salts

Electrolytes are substances that dissociate in water to release ions.Example: NaCl Na+ + Cl-30Bases- electrolytes that absorb H+ from water, or electrolytes that dissociate to release hydroxide ions (OH-) in waterExamples: NaOH Na+ + OH-

Acids - electrolytes that dissociate to release protons (H+) in waterExample: HCl H+ + Cl-Salt electrolyte formed by the reaction between an acid and baseAcid + Base Salt + water HCl + NaOH NaCl + H2OExample:31acid and base concentrationspH pH measures the concentration of hydrogen ions [H+] in a solution.

As pH decreases, [H+] increases = solution is more acidicpH0714acidic property increasingalkaline property increasingneutral32

Small changes in pH reflect large changes in [H+]

change of 1 pH = 10 fold change in [H+]change of 2 pH = 100 fold change in [H+]change of 3 pH = 1000 fold change in [H+] 33Blood contains several buffers

Buffer = resists changes to pHBlood

Average blood pH = 7.35 - 7.45

Acidosis = blood pH less than 7.3Symptoms include fatigue, disorientation, and difficulty breathing.

Alkalosis = blood pH greater than 7.5Symptoms include agitation and dizziness34Chemical components of cellsOrganic Vs. Inorganic MoleculesOrganic moleculesCompounds with carbonMay form macromoleculesIncludes proteins, carbohydrates, lipids, nucleic acids

Inorganic moleculesCompounds that lack Carbon (exception is CO2)Usually dissociate in water35End of Section 3, Chapter 2Inorganic Substances

Water (H2O)2/3 of weight in a personTransports gasses, nutrients, wastes, hormones, ect.

Oxygen (O2)Used in cellular respiration

Carbon Dioxide (CO2)Waste of metabolic reactions

Inorganic SaltsNa+, Cl-, K+, Ca2+, HCO3-, PO42-36

Section 4, Chapter 2Organic Molecules37Organic MoleculesMolecules that contain carbonOrganic SynthesisSmall molecules (monomers) join together to form larger molecules (polymers)

Monomerportion of a polymer38Atomic Number of Carbon = 62 electrons in 1st shell4 electrons in 2nd shell

Empty space for covalent bondingNote there are 4 empty spaces in the 2nd shell available for covalent bonds.Covalent Bonds formed by Carbon C612.0139

Carbon can form 4 covalent bondsCarbon to Carbon bonds can form long chainsCarbon can also form double or even triple bondshydrocarbonExamples of covalent bonds formed by carbon 40Large organic molecules, called polymers consist of repeating subunits, called monomers.

Polymers and Monomers

Example: Starch is a polysaccharide composed of many glucose molecules (monosaccharides) joined together.Monosaccharide (simple sugars)Disaccharides (double sugars)

Polysaccharides(complex carbohydrates)MonomerPolymerAmino AcidsProteins

Fatty Acids + Glycerol Fats**Not truly a polymer

NucleotidesNucleic Acids

major organic macromolecules of the cell42Simple carbohydrates = sugarsMonosaccharidesDisaccharides

Complex CarbohydratesAlso called PolysaccharidesComposed of several simple carbohydratesCarbohydrates

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monosaccharidesTwice as many Hydrogen as Oxygen atomsExample: Glucose (C6H12O6)44

disaccharides2 monosaccharides bonded togetherExamples of disaccharides45

polysaccharide

Built of simple carbohydrates

46Starch easily digested

Cellulose- Plant polysaccharide, indigestible by humans

Glycogen storage form of energy, synthesized by liver

examples of polysaccharides

Glycogen47LIPIDSIncludes: Fats, Phospholipids, and Steroids48Fats (Triglycerides)1 glycerol + 3 fatty acid moleculesBuilding blocks of fats

nonpolar moleculesThey are soluble in oils, but insoluble in water49Fatty Acids1. Carboxyl end2. Hydrocarbon chain

Carboxylgroup50Fatty AcidsSaturated = all single carbon to carbon bonds

Unsaturated = one or more carbon to carbon double bonds

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Glycerol MoleculeOH (in red) represents sites of fatty acid attachments52

Triglyceride (fat)1 glycerol3 fatty acidsUnsaturated fat53PhospholipidsBuilding Blocks of phospholipids:1 glycerol molecule2 fatty acid molecules1 phosphate groupPhospholipids are modified triglycerides

54PhospholipidsBuilding Blocks of phospholipids:1 glycerol molecule2 fatty acid molecules1 phosphate groupPhospholipids are modified triglycerides

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Polar region (hydrophilic)Nonpolar region(hydrophobic)Phospholipids

56Types of SteroidsCholesterol

Sex HormonesTestosteroneEstrogenProgesterone

End of section 4, Chapter 2SteroidsConnected rings of carbon atoms

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Section 5, Chapter 2Organic molecules

ProteinsProteins have many functions:

Proteins provide structural material.

They are a source of energy.

Some act as chemical messengers (hormones, neurotransmitters).

Many proteins are receptors.

Most enzymes are proteins.59

Synthesis reaction involving an enzymeEnzymes catalyze reactions (increases rate), but are not consumed by the reaction (reusable).Proteins: enzymesProteins: amino acidsAll amino acids consists of:An amino group (-NH2)

A Carboxyl Group (-COOH)

A single Carbon atom

An R group (R = rest of the molecule)1 of 20 possible R groups = determines amino acid

Amino groupCarboxyl groupR groupAmino Acid

20 amino acids determined by 20 possible R groupsPeptide BondsAmino Acids are joined by peptide bonds

Dipeptide = 2 amino acids joined by peptide bond

Polypeptide = several amino acids joined by peptide bond

Peptide bond (red) joins two amino acids.

Dipeptide: two amino acids joined together

Polypeptide: several amino acids joined together

Primary structure is the amino acid sequence of a polypeptide chainA proteins shape, or conformation, determines its function. Therefore, its important to understand a proteins shape at 4 levels.4 Levels of Protein Structure

Secondary Structure Shapes within local regions of polypeptides Includes coils (alpha helix) & folds (pleated sheets) Secondary structures are stabilized by Hydrogen bonding.Red dots indicatehydrogen bonding4 Levels of protein structureTertiary Structure includes the three-dimensional folding of a polypeptide

The tertiary structure is the highest level for proteins consisting of just one polypeptide.

4 Levels of protein structureQuaternary Structure The quaternary structure is the three-dimensional shape of proteins consisting of two or more polypeptides

4 Levels of protein structureHemoglobin = protein with 4 polypeptide chains

Example of a protein4 Levels of protein structureConformationComplex 3 dimensional fold of a protein

Conformation determines a proteins function

DenatureTreatment that alters the shape of a protein to make it nonfunctional

Heat, pH changes, radiation, certain chemicals may denature proteinsProtein Structure Deoxyribonucleic Acid (DNA)Double stranded polynucleotide

Ribonucleic Acid (RNA)Single-stranded polynucleotideNucleic acids: overviewNucleic AcidsIncludes DNA and RNAGenetic informationConsists of monomers, called nucleotidesRNAContains the sugar ribose (ribonucleic acid)RNA is a single-stranded nucleic acid.Transcribes DNA for protein synthesisRNA also may act as an enzyme

DNADNA contains a sugar, called deoxyribose (deoxyribonucleic acid)Double-stranded helixEncodes genetic information for protein synthesis.74NucleotidesNucleotides are the monomers of Nucleic Acids

3 Components of a Nucleotide5 Carbon Sugar (S)Nitrogenous Base (B)Phosphate Group (P)

RNASugar = ribose

DNASugar = deoxyribose

RNA

Single polynucleotide strand

DNA

2 polynucleotide strands stabilized by Hydrogen bonds Strands are anti-parallelH bondsAntiparallel

Summary of organic compounds

end of chapter 2