Chapter 2 The Chemistry of Biology 1 Atoms, Bonds, and Molecules Matter - all materials that occupy space and have mass. Matter is composed of atoms Nucleus Atom - simplest form of matter not divisible into simpler substances Protons: (+) subatomic particles Neutrons: neutral subatomic particles Electrons: (-) subatomic particles 1 proton 1 electron Hydrogen Shells Nucleus proton Nucleus 6 protons 6 neutrons Carbon 6 electrons neutron electron (b) 2 Different Types of Atoms All atoms share the same fundamental structure Element - pure substances with a characteristic number of protons, neutrons, and electrons and predictable chemical behaviors Nucleus 1 proton 1 electron Hydrogen Shells Nucleus proton Nucleus (b)
6 protons 6 neutrons Carbon 6 electrons neutron electron 3 The Major Elements of Life 4 Characteristics of Elements Atomic number number of protons Mass number number of protons and neutrons Isotopes variant forms of the same element that differ in the number of neutrons Atomic weight average mass numbers of all isotopic forms Electron orbitals volumes of space surrounding the atomic nucleus where electrons are likely to be found Shell Hydrogen Shell 2 Shell 1 Carbon Orbitals (a) Nucleus 1 proton 1 electron Hydrogen Shells Nucleus proton Nucleus (b) 6 protons 6 neutrons Carbon 6 electrons neutron electron 5 Biologically Important Atoms Chemical symbol H HYDROGEN N Atomic number
1 7 NITROGEN O Chemical name 8 OXYGEN 7p 1p Number Of e in Each Energy level Mg 12 C MAGNESIUM H 6 25 H 1 11 12p Li Be Na Mg K Ca Rb Sr 24 AT. MASS 24.30 AT. MASS 12.01 Ti V Cr C N O
F Ne AT. MASS 16.00 Al Si P S Cl Ar Cl c 282 Sc B Mn Fe Co Ni Tc Ru Rh Pd Cu 17 CHLORINE Zn Ga Gs As Se Br Kr 17p Na 281 Ca AT. MASS 22.99 CALCIUM Cs K
PN SO Q 26 6p Mg SODIUM 11p He AT. MASS 14.00 AT. MASS 1.00 Na 8p N CARBON P 15 PHOSPHORUS Ba Re Os Ir Fr 16 Cl SULFUR Pt 287 Ra 15p 20p Ca 19p S AT. MASS 35.45 19 POTASSIUM 20 16p S
P 2882 285 AT. MASS 40.08 AT. MASS 30.97 286 AT. MASS 32.06 K 2881 AT. MASS 39.10 6 Concept Check: If two atoms have the same number of protons and electrons but different numbers of neutrons, they would be A. Different elements B. Isotopes of the same element C. Ions of the same element D. Orbitals of the same element 7 Bonds and Molecules Molecule - a chemical substance that results from the combination of two or more atoms Compounds - 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 Chemical bonds - when 2 or more atoms share, donate, or accept electrons to form molecules and compounds 3 types: covalent, ionic, and hydrogen 8 3 Types of Chemical Bonds Covalent Bonds 1. Covalent bonds electrons are shared among atoms Polar covalent bonds unequal sharing Nonpolar covalent bonds equal sharing Single Double 9 Covalent Bonds + H e H e H2 e 1p
1p Hydrogen atom + 1p + Hydrogen atom H Molecular oxygen (O2) O O Double bond H Single bond 1p+ H C H H 8p+ 8n e H H + Hydrogen molecule H 8p+ 8n 1p + C 1p+ 6p+ 6n 1p+ H H Methane (CH4) 1p+ 10 Polarity () () O H 8p+ H O 1p+ (+)
(a) 1p+ H H (+) (+) (+) (b) 11 3 Types of Chemical Bonds 2. Ionic bonds electrons are transferred to one atom forming positively charged cations and negatively charged anions Ionic Bond (+) () 12 Ionic Bonding 2 1 Na 17p 18n 11p 12n + + Cl 1 2 NaCl crystals (a) (b) Sodium atom (Na) Na Cl Chlorine atom (Cl) [Na]+ [Cl] 1 Na 1 Sodium Na Cl
Chloride Na Cl 1 Na (d) Kathy Park Talaro 1 Cl 2 1 H Cl 2 1 2 2 Na 2 O 1 Na 1 11p H 1 Na 1 Cl 2 1 Cl2 (c) Cl 2 2 2 1 Cl Cl
Na 1 2 2 17p Sodium ion (Na1) Chlorine atom (Cl2) (cation) (anion) 2 13 3 Types of Chemical Bonds 3. Hydrogen bonds weak bonds between hydrogen and other atoms H Molecule A H H 1 Hydrogen Bond Water molecule 1 O (+) 2 Hydrogen bonds 1 H () O or 1 1 2 H O 2 H 1 H N
H O O 1 H H 2 O H 1 1 Molecule B 14 14 Concept Check: Molecules where atoms share electrons contain A. Covalent Bonds B. Ionic Bonds C. Hydrogen Bonds 15 Oxidation-Reduction Reactions Energy exchange in cells is a result of the movement of electrons from one molecule to another. Oxidation the loss of electrons Reduction the gaining of electrons Redox reactions 1 Na 28 1 Reducing agent gives up electrons. Cl 28 7 Oxidizing agent accepts electrons. Na 28 Oxidized cation 2 Cl 28 8 Reduced anion 16 Chemical Shorthand Reactants - molecules starting a reaction Products - substances left by a reaction Synthesis reaction - the reactants bond together in a manner that produces an entirely new molecule S + O2
SO2 Decomposition reaction - the bonds on a single reactant molecule are broken to release two or more products 2H2O2 2H2O + O2 Exchange reaction - the reactants trade portions between each other and release products that are combinations of the two HCl + NaOH NaCl + H2O 17 Solutions Solution a mixture of one or more substances called solutes, dispersed in a dissolving medium called a solvent 2 1 1 2 NaCl crystals Solutes Na & Cl + Na 1 Na Cl Cl 1 Na 11p 1 2 H Cl 2 1 H O 1 Na 1 Na 1 Cl 2
Cl Cl 2 1 Solvent H2O 2 2 Cl 1 Cl 1 2 Na Cl 2 2 Na 1 Na 1 2 2 17p 2 18 Sodium ion (Na1) (cation) Chlorine atom (Cl2) (anion) - Aqueous Solutions Hydrophilic molecules - dissolve in water Hydrophobic molecules - repel water Amphipathic molecules - have both hydrophilic and hydrophobic properties Hydrogen Oxygen Water molecules
19 pH 0 1 M hy dr oc hl 2. or 0 ic 2. aci ac 3 d id 2. lem spri 4 on ng v 3. ine ju w 0 g ice at er re ar d 3. w in 5 e s 4. aue 2 r k b r 4. eer aut 6 ac 5. id 0 r c h a in ee se 6. 0 yo gu rt 6. 6 co w 7. 0 's d m 7. istil ilk 4 l hu ed 8. ma wa t 0 se n b er 8. aw lood a 4 so ter di um
9. bi 2 ca bo rb ra on x, at al e ka lin 10 e so .5 ils m ilk of m 11 ag .5 ne ho si a us eh 12 o ld .4 am lim ew m on 13 at ia er .2 ov en cl ea 1 M ne po r ta ss iu m hy dr ox id e 0. 1 Acidity, Alkalinity, and the pH Scale Ionization of H2O releases hydrogen ions [H+] and hydroxyl ions [OH ] pH scale ranges from 0 to 14, expresses the concentration of H+ ions pH is the negative logarithm of the concentration of H+
2 3 Acidic 4 [H+] Increasing acidity 5 6 7 Neutral 8 9 10 [OH] 11 Increasing basicity 12 13 14 Basic (alkaline) 20 pH and Ion Concentration 21 Concept Check: If solution A has a pH of 2 and solution B has a pH of 4, which of the following is true? A. Solution A has 2 times more H+ ions than solution B B. Solution B has 2 times more H+ ions than solution A C. Solution A has 10 times more H+ ions than solution B D. Solution B has 10 times more H+ ions than solution A E. Solution A has 100 times more H+ ions than solution B 22 The Chemistry of Carbon and Organic Compounds Organic chemicals compounds containing carbon bonded to hydrogens Carbon is the fundamental element of life Contains 4 atoms in its outer orbital Can form single, double, or triple covalent bonds Can form linear, branched, or ringed molecules 23 The Versatility of Bonding in Carbon Linear C C H C 1 H C C C C
C C C C C C C C C C C C C H Branched C O C 1 O C O C C C C N C 1 N C N C C C 1 C C C C C C 1 C C C Ringed C C C C
C C C C C C C C C C (a) N C 1 N C N (b) C C C 24 Functional Groups of Organic Compounds Accessory molecules that bind to organic compounds TABLE 2.3Representative Functional Groups and Organic Compounds That Contain Them Formula of Functional Group R* O H Name Can Be Found in Hydroxyl Alcohols, carbohydrates Carboxyl Fatty acids, proteins, organic acids Amino Proteins, nucleic acids O R C OH H
Confer unique reactive properties on the whole molecule R C NH2 H O R Ester C O Lipids R H R C SH Sulfhydryl Cysteine (amino acid), proteins Carbonyl, terminal end Aldehydes, polysaccharides Carbonyl, internal Ketones, polysaccharides H O R C H O R C C O R O P OH OH Phosphate DNA, RNA, ATP
25 Macromolecules Biochemicals are organic compounds produced by living things Macromolecules: large compounds assembled from smaller subunits Monomer: a repeating subunit Polymer: a chain of monomers 4 Biological Macromolecules: Carbohydrates, Lipids, Proteins, Nucleic Acids 26 Biological Macromolecules 27 Carbohydrates Sugars and polysaccharides General formula (CH2O)n Aldehydes and ketones H O Aldehyde group H C1 C1 6 H C2 OH CH2OH HO C3 H H H C4 OH H C5 OH H C6 H O 5 H O
H 4 1 HO OH OH H 3 H H 2 OH OH H C2 OH HO C3 H HO C4 H H C5 OH H C6 O C2 O HO C3 H H C4 OH H C5 OH
CH2OH 5 O HO H H 4 OH H 1 OH 3 H H Glucose C1 H 6 H OH 2 OH H C6 OH H Ketone group O 6 HOCH2 OH 5 H 2 H 4 OH HO CH 2OH 1 3 H H Galactose
Fructose 28 Carbohydrates Saccharide: simple carbohydrate Monosaccharide: 3-7 carbons Disaccharide: two monosaccharides Polysaccharide: five or more monosaccharides O O O O Monosaccharide O Disaccharide O O O O O O CH2 O O O O CH 2 O O O Polysaccharide 29 Carbohydrates Subunits linked by glycosidic bonds C C C C O H OH C 1 C OH H C C O C O H C
C C C C O C H C O C C C (a) 6 Dehydration synthesis: loss of water in a polymerization reaction H2 O C CH2OH O C 5 H H H H 1 C 1 C4 C4 H O HO OH HO 2 3 C C H OH Glucose 1 6 CH2OH O C 5 H H 1C OH H OH 2 3 C C H OH 6
CH2 OH C5 O H H H H 1C C4 C4 OH H O HO 2 3 C C H OH Glucose 6 CH2 OH O C 5 H OH H 2 3 C C H 1 H C 1 H2 O OH OH Maltose (b) 6 CH2OH C O 5 H H 4 C OH HO 3 C H 6 CH2OH 6 O C CH2OH O 5 H
H H 1 C 1 C5 C4 H OH H HO 2 3 OH H 4 C C C OH H OH Glucose 1 OH C OH CH2OH 3 C 1 H 2 H 1C 2 6 H C OH O 1 H2 O CH2OH O C 5 OH H 1(b) C 1 OH H H 3 2 C C H OH H2 O CH2OH O C5 H H 4 C OH 3
2C OH 2OH C CH 1 H Sucrose Fructose (c) 6 CH2OH O C 5 H H HO H 1 C 1 C4 C4 OH H CH HO H 3 2 C C H OH (d) Galactose 1 6 CH2OH O C 5 H H 1C OH H OH 3 2 C C H OH Glucose 6 CH2OH O C 5 H HO H 1(b) C O C4 C4 OH H H H 3
2 C C H OH Lactose 6 30 Carbohydrates Functions cell structure, adhesion, and metabolism CH2OH H OH CH2OH H OH O O H H H H H1 H 1H 4 1 O 4 OH 4 H 1 O 4 OH OH H H OH H H O O O H H H H O O H OH CH2OH H OH CH2OH 6 6 6 CH2OH CH2OH CH2OH 5 5 5 O O O H H H H H H H H H 4 1 4 1
4 1 O O O O OH H OH H OH H 3 H 2 OH 3 H 2 OH 3 H 2 OH 6 CH2OH 5 O H H H 4 1 OH H Branch O Branch 2 3 point O H O H 6 C OH 5 O H H H 4 1 O OH H H bonds 3 H (a) Cellulose (b) Starch 2 OH 31
Lipids Long or complex, hydrophobic, C - H chains Triglycerides, phospholipids in membranes, steroids like cholesterol Functions Triglycerides energy storage Phospholipid major cell membrane component Steroids cell membrane component 32 Triglycerides: 3 fatty acids bound to glycerol Triglycerides are used for energy storage Could be saturated or unsaturated Fatty acids 1 O C HO Triglycerides H H H H H H H H H H H H H H H C C C C C C C C C C C
C C C C H H H H H H H H H H H H H H H H Palmitic acid, a saturated fatty acid 2 O C HO H H H H H H H H H H H H H H H
H H C C C C C C C C C C C C C C C C C H H H H H H H H H H H H Linolenic acid, an unsaturated fatty acid 33 Phospholipids: glycerol with 2 fatty acids and a phosphate group Bilayers of phospholipids form membranes Variable alcohol group Phosphate R O O P O2
O HCH H HC O O C CH Charged head Polar lipid molecule Glycerol Polar head Nonpolar tails O O C HCH HCH HCH HCH Tail Double bond Creates a kink. HCH HCH HCH HCH HCH HCH HCH HCH HCH HC HC HCH HCH HCH HCH HCH HCH HCH HCH H HCH HCH HCH HCH HCH HCH 1 Phospholipids in single layer HCH HCH HCH HCH HCH Fatty acids (a) Water Water Water H
2 Phospholipid bilayer (b) 34 Membrane Lipids Glycolipid Phospholipids Cholesterol is inserted into the phospholipid bilayer Cell membrane Protein Site for ester bond with a fatty acid Cholesterol HO H C Globular protein CH2 CH2 H2C C C CH3 H2 HC C CH2CH H2C CH Cholesterol CH CH3 C HC CH2C H2 CHCH3 CH2 CH2 CH2 CH CH3 CH3 35 Concept Check: Triglycerides that have double bonds in their fatty acids are best described as A. Saturated B. Unsaturated C. Phospholipids D. Cholesterol
36 Proteins Predominant molecules in cells Monomer amino acids 20 Polymer peptide, polypeptide, protein Subunits linked by peptide bonds Fold into very specific 3-D shapes Functions support, enzymes, transport, defense, movement 37 Amino Acids Amino acids are the monomers that make up a protein polymer 38 Formation of a Peptide Bond Amino acids are attached through peptide bonds to form proteins Bond forming H H N O H C C R1 OH H H O N H C R1 R2 H N C H H C C H H
H C N O H R2 N OH C N O C H C R3 C H R4 N H N OH O R4 H C R3 H H O C H C H OH C O H + 3H2O C O 39 Protein Structure Primary Structure
Secondary Structure Tertiary Structure Amino acids 1 The primary structure is a series of amino acids bound in a chain. Amino acids display small charged functional groups (red symbols). 2 The secondary structure develops when CO and NH groups on adjacent amino acids form hydrogen bonds. This action folds the chain into local configurations called the helix and -pleated sheet. Most proteins have both types of secondary structures. Primary structure -pleated sheet N N H O C C C C O Secondary structure N H N C O Detail of hydrogen bond Disulfide bond 3 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 three-dimensional molecule. Depending on the protein, this may be the final functional state. S S Tertiary structure Quaternary Structure O C helix Projected 3-dimensional shape (note grooves and projections) 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. Image courtesy RCSB Protein Data Bank, www.pdp.org Quaternary structure 40 Nucleic Acids DNA and RNA Nucleotide monomer DNA deoxyribonucleic acid A,T,C,G nitrogen bases Double helix Function hereditary material RNA ribonucleic acid A,U,C,G nitrogen bases Function organize protein synthesis N base Pentose sugar Phosphate (a) A nucleotide, composed of a phosphate, a pentose sugar, and a nitrogen base (either A,T,C,G, or U) is the monomer of both DNA and RNA. Backbone Backbone P DNA D A T P R P D C G P A D P R P D G C P C D P
R P D T A P G D P R P D A T P C D P R P D P U D P RNA C G H bonds D P A R P (b) In DNA, the polymer is composed of (c) In RNA, the polymer alternating deoxyribose (D) and is composed of phosphate (P) with nitrogen bases (A,T,C,G) alternating ribose (R) attached to the deoxyribose. DNA almost and phosphate (P) always exists in pairs of strands, oriented attached to nitrogen 41 so that the bases are paired across the bases (A,U,C,G), but central axis of the molecule. it is usually a single strand.
Nucleotide Components HOCH2 O DNA Nucleotides: Deoxyribose C, G, A or T H H HOCH2 O OH H H H H H H OH H OH OH Deoxyribose Ribose (a) Pentose sugars H H N N RNA Nucleotides: OH N N H N Ribose C, G, A or U O N H N H H H O H H
N O H H H H N O H N H N N H Guanine (G) (b) Purine bases H N H Adenine (A) H3C N N N O H N H H H Thymine (T) Cytosine (C) Uracil (U) (c) Pyrimidine bases O 42 Double Helix of DNA DNA is formed by two very long polynucleotide strands linked along their length by hydrogen bonds
Backbone strands Base pairs O O O T D A D Hydrogen O bonds P O O P C D G O P O D D O P O O T A D O P 43 DNA Passing on the Genetic Message Each strand is copied Replication is guided by base pairing End result is two separate double strands Cells Events in Cell Division Events in DNA Replication A
T C G A T G C H-bonding severed G New bases A T G C Two single strands T C G A T G C Two double strands A T A T C G C G A T A T G C G C
44 ATP: The Energy Molecule of Cells Adenosine triphosphate Nucleotide - adenine, ribose, three phosphates Function - transfer and storage of energy NH2 N 7 5 9 N 4 3 N 8 O O P O O O P O O O P O CH2 O 6 1 2 N O OH OH Adenosine Adenosine diphosphate (ADP) Adenosine triphosphate (ATP) 45 Concept Check: Which of the following is TRUE about RNA? A. It is a double stranded molecule B. It contains the sugar deoxyribose C. It contains the nitrogenous base Uracil D. It holds the genetic information E. All of the above are true 46
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