hapter 2 The hemistry of Biology
Atoms, Bonds, and Molecules Matter all materials that occupy space and have mass. Matter is composed of atoms Atom simplest form of matter not divisible into simpler substances proton electron ucleus ydrogen ucleus Shells rotons: () subatomic particles eutrons: neutral subatomic particles Electrons: () subatomic particles ucleus (b) 6 protons 6 neutrons 6 electrons arbon proton neutron electron 2
Different Types of Atoms All atoms share the same fundamental structure ucleus Element pure substances with a characteristic number of protons, neutrons, and electrons and predictable chemical behaviors ucleus proton electron 6 protons 6 neutrons 6 electrons ydrogen ucleus arbon Shells proton neutron electron (b) 3
The Major Elements of Life 4
haracteristics of Elements Atomic number number of protons ydrogen Shell Mass number number of protons and neutrons arbon Shell 2 Shell Isotopes variant forms of the same element that differ in the number of neutrons (a) ucleus rbitals Atomic weight average mass numbers of all isotopic forms proton electron ucleus ydrogen Shells Electron orbitals volumes of space surrounding the atomic nucleus where electrons are likely to be found ucleus 6 protons 6 neutrons 6 electrons arbon proton neutron electron 5 (b)
Biologically Important Atoms hemical symbol YDRGE Atomic number hemical name 7 ITRGE 8 XYGE umber f e in Each Energy level a SDIUM p AT. MASS.00 Li a Be Mg Mg 2 MAGESIUM 2p Mg 2 8 2 AT. MASS 24.30 6 ARB 6p c 2 4 AT. MASS 2.0 7p 2 5 e AT. MASS 4.00 B F e Al Si S l Ar 8p S Q 2 6 AT. MASS 6.00 l 7 LRIE p K a Sc Ti V r Mn Fe o i u Zn Ga Gs As Se Br Kr a 2 8 AT. MASS 22.99 Rb s Sr Ba a 20 ALIUM Tc Re Ru s Rh Ir d t 5 SRUS S 6 SULFUR 7p 2 8 7 l K 9 TASSIUM Fr Ra 20p 5p 6p AT. MASS 35.45 9p 2 8 8 2 a AT. MASS 40.08 S 2 8 5 2 8 6 AT. MASS 30.97 AT. MASS 32.06 2 8 8 K AT. MASS 39.0 6
Bonds and Molecules Molecule a chemical substance that results from the combination of two or more atoms ompounds molecules that are combinations of two or more different elements Formula/Mass weight sum of all of the atomic masses of the atoms a molecule contains hemical bonds when 2 or more atoms share, donate, or accept electrons to form molecules and compounds 3 types: covalent, ionic, and hydrogen 7
3 Types of hemical Bonds. ovalent bonds 2. Ionic Bonds 3. ydrogen Bonds 8
3 Types of hemical Bonds. ovalent bonds electrons are shared among atoms ovalent Bonds Single e e 2 p ydrogen atom p p p ydrogen atom ydrogen molecule e e Single bond 8
ovalent Bonds p p 6p 6n p p Methane ( 4 ) 0
ovalent Bonds Double 8p 8p 8n 8n Double Molecular oxygen ( 2 ) Double bond
3 Types of hemical Bonds. ovalent bonds electrons are shared among atoms olar covalent bonds unequal sharing onpolar covalent bonds equal sharing ( ) ( ) 8p p p () () (a) () () (b) 8
3 Types of hemical Bonds 2. Ionic bonds electrons are transferred to one atom forming positively charged cations and negatively charged anions Ionic Bond () ( ) 3
Ionic Bonding a p 2n 7p 8n l (b) a l (a) [a] [l] Sodium atom (a) hlorine atom (l) Sodium 2 hloride (c) (d) Kathy ark Talaro 4
Ionic Bonding al crystals a a l a l a l a a l l l l a a l l p 7p Sodium ion (a ) (cation) hlorine atom (l ) (anion) 5
3 Types of hemical Bonds 3. ydrogen bonds weak bonds between hydrogen and other atoms ydrogen Bond Molecule A Water molecule ydrogen bonds () ( ) o r Molecule B 6
xidationreduction Reactions Energy exchange in cells is a result of the movement of electrons from one molecule to another. xidation the loss of electrons Reduction the gaining of electrons Redox reactions a 2 8 l 2 8 7 a 2 8 l 2 8 8 Reducing agent gives up electrons. xidizing agent accepts electrons. xidized cation Reduced anion 7
hemical Shorthand Reactants molecules starting a reaction roducts substances left by a reaction Synthesis reaction the reactants bond together in a manner that produces an entirely new molecule S 2 S 2 Decomposition reaction the bonds on a single reactant molecule are broken to release two or more products 2 2 2 2 2 2 Exchange reaction the reactants trade portions between each other and release products that are combinations of the two l a al 2 8
Solutions Solution a mixture of one or more substances called solutes, dispersed in a dissolving medium called a solvent al crystals a a l l l a a a l a l a l l l l a Solutes a & l Solvent 2 p 7p Sodium ion (a ) (cation) hlorine atom (l ) (anion) 9
Aqueous Solutions 20 ydrophilic molecules dissolve in water ydrophobic molecules repel water Amphipathic molecules have both hydrophilic and hydrophobic properties l ydrogen xygen Water molecules a
Acidity, Alkalinity, and the p Scale Ionization of 2 releases hydrogen ions [ ] and hydroxyl ions [ ] p scale ranges from 0 to 4, expresses the concentration of ions p is the negative logarithm of the concentration of p 0 2 3 4 5 6 7 8 9 0 2 3 4 Acidic [ ] eutral [ ] Basic (alkaline) Increasing acidity Increasing basicity 2
p and Ion oncentration 22
The hemistry of arbon and rganic ompounds rganic chemicals compounds containing carbon bonded to hydrogens arbon is the fundamental element of life ontains 4 atoms in its outer orbital an form single, double, or triple covalent bonds an form linear, branched, or ringed molecules 23
The Versatility of Bonding in arbon Linear Branched Ringed (a) (b) 24
Functional Groups of rganic Accessory molecules that bind to organic compounds ompounds TABLE 2.3 Representative Functional Groups and rganic ompounds That ontain Them Formula of Functional Group ame an Be Found in R* R ydroxyl arboxyl Alcohols, carbohydrates Fatty acids, proteins, organic acids onfer unique reactive properties on the whole molecule R R 2 R Amino Ester roteins, nucleic acids Lipids R S Sulfhydryl ysteine (amino acid), proteins R arbonyl, terminal end Aldehydes, polysaccharides R arbonyl, internal Ketones, polysaccharides R hosphate DA, RA, AT 25
Macromolecules Biochemicals are organic compounds produced by living things Macromolecules: large compounds assembled from smaller subunits Monomer: a repeating subunit olymer: a chain of monomers 4 Biological Macromolecules: arbohydrates, Lipids, roteins, ucleic Acids 26
Biological Macromolecules 27
arbohydrates Sugars and polysaccharides General formula ( 2 ) n Aldehydes and ketones 2 3 4 5 6 Aldehyde group 6 2 5 4 3 2 2 3 4 5 6 6 2 5 4 3 2 2 3 4 5 6 Ketone group 6 2 5 4 3 2 2 Glucose Galactose Fructose 28
arbohydrates Saccharide: simple carbohydrate Monosaccharide: 37 carbons Disaccharide: two monosaccharides olysaccharide: five or more monosaccharides Monosaccharide Disaccharide 2 2 olysaccharide 29
arbohydrates Subunits linked by glycosidic bonds (a) 2 Dehydration synthesis: loss of water in a polymerization reaction (b) 4 4 6 6 2 5 3 2 Glucose 6 2 5 3 2 6 2 5 3 2 Glucose 2 4 5 4 3 2 2 4 6 6 2 5 3 2 2 5 3 2 2 2 5 3 2 Maltose 6 4 5 6 4 2 4 3 2 2 2 (c) Glucose Fructose Sucrose (d) 4 6 2 5 4 3 2 Galactose 6 2 5 3 2 Glucose 4 6 2 2 5 5 ( b ) 4 3 2 3 2 Lactose ( b ) ( b ) 6 2 30
arbohydrates Functions cell structure, adhesion, and metabolism 2 2 2 2 2 5 5 5 4 b 4 b 4 b 4 b 4 a 4 a 4 a 3 2 3 2 3 2 2 2 bonds 6 6 6 6 2 5 4 Branch Branch 3 2 point 6 5 4 3 2 (a) ellulose (b) Starch 3
Lipids Long or complex, hydrophobic, chains Triglycerides, phospholipids in membranes, steroids like cholesterol Functions Triglycerides energy storage hospholipid major cell membrane component Steroids cell membrane component 32
Triglycerides: 3 fatty acids bound to glycerol Triglycerides are used for energy storage ould be saturated or unsaturated Fatty acids Triglycerides almitic acid, a saturated fatty acid 2 Linolenic acid, an unsaturated fatty acid 33
hospholipids: glycerol with 2 fatty acids and a phosphate group Bilayers of phospholipids form membranes Variable alcohol group hosphate Double bond reates a kink. Tail R 2 harged head Glycerol Water olar lipid molecule olar head onpolar tails hospholipids in single layer Water Water (a) Fatty acids 2 hospholipid bilayer (b) 34
Membrane Lipids hospholipids Glycolipid holesterol is inserted into the phospholipid bilayer ell membrane rotein Site for ester bond with a fatty acid 2 2 2 3 holesterol Globular protein holesterol 2 2 2 3 2 2 3 2 2 2 35 3 3
roteins redominant molecules in cells Monomer amino acids 20 olymer peptide, polypeptide, protein Subunits linked by peptide bonds Fold into very specific 3D shapes Functions support, enzymes, transport, defense, movement 36
Amino Acids Amino acids are the monomers that make up a protein polymer 37
Formation of a eptide Bond Amino acids are attached through peptide bonds to form proteins Bond formin g R 2 R 4 R R 3 R 2 R 4 3 2 R R 3 38
rotein Structure rimary Structure The primary structure is a series of amino acids bound in a chain. Amino acids display small charged functional groups (red symbols). Amino acids rimary structure Secondary Structure Tertiary Structure 2 3 The secondary structure develops when and groups on adjacent amino acids form hydrogen bonds. This action folds the chain into local configurations called the a helix and b pleated sheet. Most proteins have both types of secondary structures. The tertiary structure forms when portions of the secondary structure further interact by forming covalent disulfide bonds and additional interactions. From this emerges a stable threedimensional molecule. Depending on the protein, this may be the final functional state. bpleated sheet a helix Secondary structure Disulfide bond S S Detail of hydrogen bond Quaternar y Structure 4 The quaternary structure exists only in proteins that consist of more than one polypeptide chain. Shown here is a model of the cholera toxin, composed of five separate polypeptides, each one shown in a different color. Tertiary structure rojected 3dimensional shape (note grooves and projections) Image courtesy RSB rotein Data Bank, www.pdp.org Quaternary structure 39
ucleic Acids DA and RA ucleotide monomer DA deoxyribonucleic acid A,T,,G nitrogen bases Double helix Function hereditary material RA ribonucleic acid A,U,,G nitrogen bases Function organize protein synthesis hosphate (a) A nucleotide, composed of a phosphate, a pentose sugar, and a nitrogen base (either A,T,,G, or U) is the monomer of both DA and RA. Backbone D D D D D D entose sugar A G T A base DA bonds (b) In DA, the polymer is composed of alternating deoxyribose (D) and phosphate () with nitrogen bases (A,T,,G) attached to the deoxyribose. DA almost always exists in pairs of strands, oriented so that the bases are paired across the central axis of the molecule. T G A T G D D D D D D RA U A G A Backbone R R R R R R (c) In RA, the polymer is composed of alternating ribose (R) and phosphate () attached to nitrogen bases (A,U,,G), but it is usually a single strand. 40
ucleotide omponents 2 2 DA ucleotides: Deoxyribose, G, A or T RA ucleotides: Ribose, G, A or U Deoxyribose Ribose (a) entose sugars Adenine (A) Guanine (G) (b) urine bases 3 Thymine (T) ytosine () (c) yrimidine bases Uracil (U ) 4
Double elix of DA DA is formed by two very long polynucleotide strands linked along their length by hydrogen bonds Backbone strands Base pairs D D T A D ydrogen bonds G D D A T D 42
DA assing on the Genetic Each strand is copied Replication is guided by base pairing End result is two separate double strands Message Events in ell Division ew bases ells Events in DA Replication A A G bonding severed A G T G T T Two single strands T A G G T Two double strands A T A T G G A G T A G T 43
AT: The Energy Molecule of ells Adenosine triphosphate ucleotide adenine, ribose, three phosphates Function transfer and storage of energy 2 2 7 8 9 5 6 4 3 2 Adenosine Adenosine diphosphate (AD) Adenosine triphosphate (AT) 44