UNIT 1: INTRODUCING BIOLOGY Chapter 2: Chemistry of life

UNIT 1: INTRODUCING BIOLOGY Chapter 2: Chemistry of Life   I. Atoms, Ions, and Molecules (2.1)     A. Living things consist of atoms of different elements

1. An atom is the smallest basic unit of matter   2. An element is one type of atom 3. An atom has a nucleus and electrons    

a. The nucleus has protons and neutrons   b. Electrons are in energy levels outside the nucleus    

4. A compound is made of atoms of different elements bonded together       a. Water (H20)   b. Carbon dioxide (CO2) c. Many other carbon-based compounds in living things.

B. Ions form when atoms gain or lose electrons 1. An ion is an atom that has gained or lost one or more electrons a. Positive ions -lost electron(s) b. Negative ions -gain electron(s) 2. Ionic bonds form between oppositely charged ions      

1. A covalent bond forms when atoms share a pair of electrons   a. Multiple covalent bonds b. Diatomic molecules    

2. A molecule is two or more atoms held together by covalent bonds    

A. Life depends on hydrogen bonds in water II. Properties of Water A. Life depends on hydrogen bonds in water   1. Water is a polar molecule a. Polar molecules have slightly charged regions    

b. Nonpolar molecules do not have charged regions      

c. Hydrogen bonds form between slightly positive hydrogen atoms and slightly negative atoms.      

2. Hydrogen bonds are responsible for three important properties of water.       a. High specific heat   b. Cohesion- attraction between molecules of the same substance (because of hydrogen bonds, water is very cohesive)

c. Adhesion- attraction between different substances c. Adhesion- attraction between different substances. Adhesion between water and other charged or polar substances very important force. (responsible for capillary action)      

B. Many compounds dissolve in water       1. A solution is formed when one substance dissolves in another   a. A solution is a homogeneous mixture

b. Solvents dissolve other substances c. Solutes dissolve in a solvent   c. Solutes dissolve in a solvent    

a. Polar solvents dissolve polar solutes 2. “Like dissolves like”   a. Polar solvents dissolve polar solutes b. Nonpolar solvents dissolve nonpolar solutes c. Polar substances and nonpolar substances generally remain separate       

C. Some compounds form acids and bases 1. An acid releases a hydrogen ion when it dissolves in water a. High H+ concentration   b. pH less than 7      

2. A base removes hydrogen ions from a solution. a 2. A base removes hydrogen ions from a solution a. low H+ concentration   b. pH greater than 7      

3. A neutral solution has a pH of 7      

III. Carbon-Based Molecules (2.3) A. Carbon atoms have unique bonding properties 1. Carbon forms covalent bonds with up to four other atoms, including other carbon atoms.      

2. Carbon-based molecules have three general types of structures a. Straight chain   b. Branched chain c. Ring    

1. Monomers are the individual subunits B. Many carbon based molecules are made of many small subunits bonded together       1. Monomers are the individual subunits  2. Polymers are made of many monomers

1. Carbohydrates are made of carbon, hydrogen, and oxygen B. Four main types of carbon-based molecules are found in living things.   1. Carbohydrates are made of carbon, hydrogen, and oxygen     a. Carbohydrates include sugars and starches b.Monosaccharides are simple (single) sugars c. Disaccharides are double sugars

c. Polysaccharides include starches, cellulose, and glycogen         d. Carbohydrates can be broken down to provide energy for cells   e. Some carbohydrates are part of cell structure

(a) Starch: a plant polysaccharide Fig. 5-6 Chloroplast Starch Mitochondria Glycogen granules 0.5 µm 1 µm Amylose Glycogen Amylopectin (a) Starch: a plant polysaccharide (b) Glycogen: an animal polysaccharide

Cell walls Cellulose microfibrils in a plant cell wall Microfibril Fig. 5-8 Cell walls Cellulose microfibrils in a plant cell wall Microfibril 10 µm 0.5 µm Cellulose molecules Glucose monomer

(a) The structure of the chitin monomer. (b) (c) Chitin forms the Fig. 5-10 (a) The structure of the chitin monomer. (b) Chitin forms the exoskeleton of arthropods. (c) Chitin is used to make a strong and flexible surgical thread.

a. Many contain carbon chains called fatty acids 2. Lipids are nonpolar molecules that include fats, oils, and cholesterol   a. Many contain carbon chains called fatty acids b. Fats and oils contain fatty acids bonded to glycerol.    

Fatty acid (palmitic acid) Fig. 5-11 Fatty acid (palmitic acid) Glycerol (a) Dehydration reaction in the synthesis of a fat Ester linkage (b) Fat molecule (triacylglycerol)

Fat molecule (triacylglycerol) Fig. 5-11b Ester linkage (b) Fat molecule (triacylglycerol)

c. Lipids have several different functions 1). Broken down as a source of energy 2). Make up cell membranes 3). Used to make hormones    

d. Fats and oils have different types of fatty acids   1). Saturated fatty acids 2). Unsaturated fatty acids    

Structural formula of a saturated fat molecule Stearic acid, a Fig. 5-12a Structural formula of a saturated fat molecule Stearic acid, a saturated fatty acid (a) Saturated fat

unsaturated fatty acid Oleic acid, an cis double bond causes bending Fig. 5-12b Structural formula of an unsaturated fat molecule Oleic acid, an unsaturated fatty acid cis double bond causes bending (b) Unsaturated fat

Structural formula of a saturated fat molecule Stearic acid, a Fig. 5-12 Structural formula of a saturated fat molecule Stearic acid, a saturated fatty acid (a) Saturated fat Structural formula of an unsaturated fat molecule Oleic acid, an unsaturated fatty acid cis double bond causes bending (b) Unsaturated fat

e. Phospholipids make up all cell membranes 1). Polar phosphate “head”       1). Polar phosphate “head”   2). Nonpolar fatty acid “tails”

Choline Hydrophilic head Phosphate Glycerol Fatty acids Fig. 5-13 Choline Hydrophilic head Phosphate Glycerol Fatty acids Hydrophobic tails Hydrophilic head Hydrophobic tails (a) Structural formula (b) Space-filling model (c) Phospholipid symbol

Fig. 5-14 Hydrophilic head WATER Hydrophobic tail WATER

3. Proteins are polymers of amino acid monomers       a. Twenty different amino acids are used to build proteins in organisms

b. Amino acids differ in side groups, or R groups   c. Amino acids are linked by peptide bonds    

+H3N Primary Structure Amino end Amino acid subunits 1 5 10 15 20 25 Fig. 5-21a Primary Structure 1 5 +H3N Amino end 10 Amino acid subunits 15 20 25

Fig. 5-21b +H3N Amino end Amino acid subunits Carboxyl end 1 5 10 15 20 25 75 80 85 90 95 105 100 110 115 120 125 Carboxyl end

A ribbon model of lysozyme Fig. 5-19a Groove (a) A ribbon model of lysozyme

Hydrophobic interactions and van der Waals interactions Polypeptide Fig. 5-21f Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Disulfide bridge Ionic bond

d. Proteins differ in the number and order of amino acids   1). Amino acids interact to give a protein its shape   2). Incorrect amino acids change a proteins structure and function      

Protein Types Enzymes Contractile Defensive Hormonal Receptor Sensory Storage Structural Transport

4. Nucleic acids are polymers of monomers called nucleotides       a. Nucleotides are made of sugar, phosphate group, and a nitrogen base.

Nucleotide: Monomer of Nucleic Acids

b. DNA stores genetic information c. RNA builds proteins   c. RNA builds proteins    

Fig. 5-UN2

Fig. 5-UN2a

Fig. 5-UN2b

C6H12O6 + O2 CO2 + H2O CO2 + H2O C6H12O6 + O2 IV. Chemical Reactions (2.4)   A. Bonds break and form during chemical reactions. 1. Reactants are changed during a chemical reaction 2. Products are made by a chemical reactions.     Cellular Respiration Photosynthesis C6H12O6 + O2 CO2 + H2O CO2 + H2O C6H12O6 + O2 reactants products

B. Bond energy is the amount of energy that breaks a bond   1. Energy is added To break bonds 2. Energy is released when bonds form    

C. A reaction is at equilibrium when reactants and products form at the same rate.       CO2 + H2O H2CO3

D. Chemical reactions release or absorb energy   1. Activation energy is the amount of energy that needs to be absorbed to start a chemical reaction.    

2. Exothermic reactions release more energy than they absorb. a. Reactants have higher bond energy than products b. Excess energy is released by the reaction      

3. Endothermic reactions absorb more energy than they release. a. Reactants have lower bond energy than products   a. Energy is absorbed by the reaction to make up the difference.      

A. A catalysts lowers activation energy V. Enzymes (2.5) A. A catalysts lowers activation energy 1. Catalysts are substances that speed up chemical reactions a. Decrease activation energy b. Increase reaction rate      

1. Enzymes are catalysts in living things B. Enzymes allow chemical reactions to occur under tightly controlled conditions.       1. Enzymes are catalysts in living things   a. Enzymes are needed for almost all processes b. Most enzymes are proteins

C. Disruptions in homeostasis can prevent enzymes from functioning. 1. Enzymes function best in a small range of conditions 2. Changes in temperature and pH can break hydrogen bonds. 3. An enzyme’s function depends on its structure      

D. An enzyme’s structure allows only D. An enzyme’s structure allows only certain reactants to bind to the enzyme   1. Substrates 2. Active Site    

E. The lock-and-key model helps illustrate how enzymes function 1. Substrates brought together 2. bonds in substrates weakened