Chemistry/Biochemistry - Carl Schurz High School

Chemistry/Biochemistry Chapters 2 -5 Mr. Volkening Elements and Compounds Matter is made up of elements An element is a substance that cannot be broken down to other substances by chemical reactions A compound is a substance consisting of two or more elements in a fixed ratio A compound has characteristics different from those of its elements 2011 Pearson Education, Inc. Elements and Compounds

Matter is made up of elements An element is a substance that cannot be broken down to other substances by chemical reactions A compound is a substance consisting of two or more elements in a fixed ratio A compound has characteristics different from those of its elements 2011 Pearson Education, Inc. Atomic Number and Atomic Mass Atoms of the various elements differ in number of subatomic particles An elements atomic number is the number of protons in its nucleus

An elements mass number is the sum of protons plus neutrons in the nucleus Atomic mass, the atoms total mass, can be approximated by the mass number 2011 Pearson Education, Inc. Covalent Bonds A covalent bond is the sharing of a pair of valence electrons by two atoms In a covalent bond, the shared electrons count as part of each atoms valence shell 2011 Pearson Education, Inc.

Figure 2.11-3 Hydrogen atoms (2 H) Hydrogen molecule (H2) A molecule consists of two or more atoms held together by covalent bonds A single covalent bond, or single bond, is the sharing of one pair of valence electrons A double covalent bond, or double bond, is the sharing of two pairs of valence electrons 2011 Pearson Education, Inc.

Figure 2.12 Name and Molecular Formula (a) Hydrogen (H2) (b) Oxygen (O2) (c) Water (H2O) (d) Methane (CH4) Electron Distribution

Diagram Lewis Dot Structure and Structural Formula SpaceFilling Model In a nonpolar covalent bond, the atoms share the electron equally In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally

Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule 2011 Pearson Education, Inc. Figure 2.13 O + H

H H2O + Ionic Bonds Atoms sometimes strip electrons from their bonding partners An example is the transfer of an electron from sodium to chlorine After the transfer of an electron, both atoms have charges A charged atom (or molecule) is called an ion

2011 Pearson Education, Inc. Figure 2.14-2 Na Sodium atom Cl Chlorine atom + Na+

Sodium ion (a cation) Cl Chloride ion (an anion) Sodium chloride (NaCl) Hydrogen Bonds A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom In living cells, the electronegative partners are usually oxygen or nitrogen atoms

2011 Pearson Education, Inc. Molecular Shape and Function A molecules shape is usually very important to its function A molecules shape is determined by the positions of its atoms valence orbitals In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes 2011 Pearson Education, Inc. Figure 2.17b

Space-Filling Model Ball-and-Stick Model Hybrid-Orbital Model (with ball-and-stick model superimposed) Unbonded Electron pair Water (H2O)

Methane (CH4) (b) Molecular-shape models Concept 2.4: Chemical reactions make and break chemical bonds Chemical reactions are the making and breaking of chemical bonds The starting molecules of a chemical reaction are called reactants The final molecules of a chemical reaction are called products 2011 Pearson Education, Inc. Chapter 3

Water Overview: The Molecule That Supports All of Life Water is the biological medium on Earth All living organisms require water more than any other substance Most cells are surrounded by water, and cells themselves are about 7095% water The abundance of water is the main reason the Earth is habitable 2011 Pearson Education, Inc.

Concept 3.1: Polar covalent bonds in water molecules result in hydrogen bonding The water molecule is a polar molecule: the opposite ends have opposite charges Polarity allows water molecules to form hydrogen bonds with each other Animation: Water Structure 2011 Pearson Education, Inc. Figure 3.2 Hydrogen

bond + + Polar covalent bonds + +

1. n PrevNext 2.Mon, Jul 11, 2011 ext Surface tension is a measure of how hard it is to break the surface of a liquid Surface tension is related to cohesion 2011 Pearson Education, Inc.

Figure 3.4 Waters high specific heat can be traced to hydrogen bonding Heat is absorbed when hydrogen bonds break Heat is released when hydrogen bonds form The high specific heat of water minimizes temperature fluctuations to within limits that permit life 2011 Pearson Education, Inc. Floating of Ice on Liquid Water

Ice floats in liquid water because hydrogen bonds in ice are more ordered, making ice less dense Water reaches its greatest density at 4C If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth 2011 Pearson Education, Inc. Water: The Solvent of Life A solution is a liquid that is a homogeneous mixture of substances A solvent is the dissolving agent of a solution The solute is the substance that is dissolved

An aqueous solution is one in which water is the solvent 2011 Pearson Education, Inc. Hydrophilic and Hydrophobic Substances A hydrophilic substance is one that has an affinity for water A hydrophobic substance is one that does not have an affinity for water Oil molecules are hydrophobic because they have relatively nonpolar bonds A colloid is a stable suspension of fine particles in a liquid

2011 Pearson Education, Inc. Acids and Bases An acid is any substance that increases the H+ concentration of a solution A base is any substance that reduces the H+ concentration of a solution 2011 Pearson Education, Inc. Figure 3.10 +

H+ H H+ H+ OH + OH H H+ H+ H+ Acidic solution

Increasingly Acidic [H+] > [OH] pH Scale 0 1 Battery acid 2 Gastric juice, lemon juice 3

Vinegar, wine, cola 4 Tomato juice Beer Black coffee 5 6 OH

OH + H H+ OH OH OH H+ H+ H+ Neutral [H+] = [OH] 8

OH OH H+ OH OH OH OH + H Basic solution

Increasingly Basic [H+] < [OH] Neutral solution OH 7 Rainwater Urine Saliva Pure water Human blood, tears

Seawater Inside of small intestine 9 10 Milk of magnesia 11 Household ammonia 12 13 Household bleach

Oven cleaner 14 Buffers The internal pH of most living cells must remain close to pH 7 Buffers are substances that minimize changes in concentrations of H+ and OH in a solution Most buffers consist of an acid-base pair that reversibly combines with H+ 2011 Pearson Education, Inc.

Figure 3.UN04 Ice: stable hydrogen bonds Liquid water: transient hydrogen bonds Figure 3.UN08 Chapter 4 Carbon Overview: Carbon: The Backbone of Life Living organisms consist mostly of carbon-based

compounds Carbon is unparalleled in its ability to form large, complex, and diverse molecules Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds 2011 Pearson Education, Inc. Concept 4.1: Organic chemistry is the study of carbon compounds Organic chemistry is the study of compounds that contain carbon Organic compounds range from simple molecules to colossal ones

Most organic compounds contain hydrogen atoms in addition to carbon atoms 2011 Pearson Education, Inc. Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms Electron configuration is the key to an atoms characteristics Electron configuration determines the kinds and number of bonds an atom will form with other atoms 2011 Pearson Education, Inc.

The Formation of Bonds with Carbon With four valence electrons, carbon can form four covalent bonds with a variety of atoms This ability makes large, complex molecules possible In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape However, when two carbon atoms are joined by a double bond, the atoms joined to the carbons are in the same plane as the carbons 2011 Pearson Education, Inc. Figure 4.3

Name and Comment Molecular Formula (a) Methane CH4 (b) Ethane C2H6 (c) Ethene (ethylene)

C2H4 Structural Formula Ball-andStick Model Space-Filling Model Figure 4.5 (c) Double bond position (a) Length

Ethane Propane (b) Branching Butane 1-Butene 2-Butene (d) Presence of rings 2-Methylpropane

(isobutane) Cyclohexane Benzene Hydrocarbons Hydrocarbons are organic molecules consisting of only carbon and hydrogen Many organic molecules, such as fats, have hydrocarbon components Hydrocarbons can undergo reactions that release a large amount of energy 2011 Pearson Education, Inc.

Concept 4.3: A few chemical groups are key to the functioning of biological molecules Distinctive properties of organic molecules depend on the carbon skeleton and on the molecular components attached to it A number of characteristic groups can replace the hydrogens attached to skeletons of organic molecules 2011 Pearson Education, Inc. The Chemical Groups Most Important in the Processes of Life Functional groups are the components of

organic molecules that are most commonly involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties 2011 Pearson Education, Inc. Chapter 5 Macromolecules The Chemical Elements of Life: A Review The versatility of carbon makes possible the great diversity of organic molecules

Variation at the molecular level lies at the foundation of all biological diversity 2011 Pearson Education, Inc. Overview: The Molecules of Life All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids Macromolecules are large molecules composed of thousands of covalently connected atoms Molecular structure and function are inseparable

2011 Pearson Education, Inc. Concept 5.1: Macromolecules are polymers, built from monomers A polymer is a long molecule consisting of many similar building blocks These small building-block molecules are called monomers Three of the four classes of lifes organic molecules are polymers Carbohydrates Proteins Nucleic acids 2011 Pearson Education, Inc.

The Synthesis and Breakdown of Polymers A dehydration reaction occurs when two monomers bond together through the loss of a water molecule Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction Animation: Polymers 2011 Pearson Education, Inc. Figure 5.2

(a) Dehydration reaction: synthesizing a polymer 1 2 3 Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond.

1 2 3 4 Longer polymer (b) Hydrolysis: breaking down a polymer 1 2

3 Hydrolysis adds a water molecule, breaking a bond. 1 2 3 4 Concept 5.2: Carbohydrates serve as

fuel and building material Carbohydrates include sugars and the polymers of sugars The simplest carbohydrates are monosaccharides, or single sugars Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks 2011 Pearson Education, Inc. Sugars- names end in -ose Monosaccharides have molecular formulas that are usually multiples of CH2O Glucose (C6H12O6) is the most common

monosaccharide Monosaccharides are classified by The location of the carbonyl group (as aldose or ketose) The number of carbons in the carbon skeleton 2011 Pearson Education, Inc. Figure 5.3 Aldoses (Aldehyde Sugars) Ketoses (Ketone Sugars) Trioses: 3-carbon sugars (C3H6O3) Glyceraldehyde

Dihydroxyacetone Pentoses: 5-carbon sugars (C5H10O5) Ribose Ribulose Hexoses: 6-carbon sugars (C6H12O6) Glucose Galactose

Fructose Figure 5.4 1 2 6 6 5 5

3 4 4 5 1 3 6 (a) Linear and ring forms 6 5

4 1 3 2 (b) Abbreviated ring structure 2 4 1 3

2 A disaccharide is formed when a dehydration reaction joins two monosaccharides This covalent bond is called a glycosidic linkage Animation: Disaccharide 2011 Pearson Education, Inc. Figure 5.5 14 glycosidic 1 linkage 4

Glucose Glucose Maltose (a) Dehydration reaction in the synthesis of maltose 12 glycosidic 1 linkage 2 Glucose

Fructose (b) Dehydration reaction in the synthesis of sucrose Sucrose Polysaccharides Polysaccharides, the polymers of sugars, have storage and structural roles The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages 2011 Pearson Education, Inc.

Storage Polysaccharides Starch, a storage polysaccharide of plants, consists entirely of glucose monomers Plants store surplus starch as granules within chloroplasts and other plastids The simplest form of starch is amylose 2011 Pearson Education, Inc. Glycogen is a storage polysaccharide in animals Humans and other vertebrates store glycogen mainly in liver and muscle cells 2011 Pearson Education, Inc.

Structural Polysaccharides The polysaccharide cellulose is a major component of the tough wall of plant cells Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ The difference is based on two ring forms for glucose: alpha () and beta () Animation: Polysaccharides 2011 Pearson Education, Inc. Figure 5.8b Cell wall

10 m Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods Chitin also provides structural support for the cell walls of many fungi 2011 Pearson Education, Inc. Figure 5.9 The structure of the chitin monomer

Chitin forms the exoskeleton of arthropods. Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. Concept 5.3: Lipids are a diverse group of hydrophobic molecules Lipids are the one class of large biological molecules that do not form polymers The unifying feature of lipids is having little or no affinity for water Lipids are hydrophobic becausethey consist

mostly of hydrocarbons, which form nonpolar covalent bonds The most biologically important lipids are fats, phospholipids, and steroids 2011 Pearson Education, Inc. Fats Fats are constructed from two types of smaller molecules: glycerol and fatty acids Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon A fatty acid consists of a carboxyl group attached to a long carbon skeleton 2011 Pearson Education, Inc.

Figure 5.10a Fatty acid (in this case, palmitic acid) Glycerol (a) One of three dehydration reactions in the synthesis of a fat Fatty acids vary in length (number of carbons) and in the number and locations of double bonds Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds

Unsaturated fatty acids have one or more double bonds Animation: Fats 2011 Pearson Education, Inc. Figure 5.11 (a) Saturated fat Structural formula of a saturated fat molecule

Space-filling model of stearic acid, a saturated fatty acid (b) Unsaturated fat Structural formula of an unsaturated fat molecule Space-filling model of oleic acid, an unsaturated fatty

acid Cis double bond causes bending. The major function of fats is energy storage Humans and other mammals store their fat in adipose cells Adipose tissue also cushions vital organs and insulates the body 2011 Pearson Education, Inc. Phospholipids In a phospholipid, two fatty acids and a phosphate group are attached to glycerol

The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head 2011 Pearson Education, Inc. Hydrophobic tails Hydrophilic head Figure 5.12 Choline Phosphate

Glycerol Fatty acids Hydrophilic head Hydrophobic tails (a) Structural formula (b) Space-filling model (c) Phospholipid symbol Figure 5.13

Hydrophilic head Hydrophobic tail WATER WATER Steroids Steroids are lipids characterized by a carbon skeleton consisting of four fused rings Cholesterol, an important steroid, is a

component in animal cell membranes Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease 2011 Pearson Education, Inc. Concept 5.4: Proteins include a diversity of structures, resulting in a wide range of functions Proteins account for more than 50% of the dry mass of most cells Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign

substances 2011 Pearson Education, Inc. Figure 5.15-a Enzymatic proteins Defensive proteins Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules. Function: Protection against disease

Example: Antibodies inactivate and help destroy viruses and bacteria. Antibodies Enzyme Virus Bacterium Storage proteins Transport proteins Function: Storage of amino acids

Function: Transport of substances Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes. Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo. Transport protein Ovalbumin

Amino acids for embryo Cell membrane Figure 5.15a Enzymatic proteins Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules. Enzyme

Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life Animation: Enzymes 2011 Pearson Education, Inc. Polypeptides Polypeptides are unbranched polymers built from the same set of 20 amino acids A protein is a biologically functional molecule that consists of one or more polypeptides

2011 Pearson Education, Inc. Amino Acid Monomers Amino acids are organic molecules with carboxyl and amino groups Amino acids differ in their properties due to differing side chains, called R groups 2011 Pearson Education, Inc. Figure 5.16 Nonpolar side chains; hydrophobic Side chain (R group)

Glycine (Gly or G) Alanine (Ala or A) Methionine (Met or M) Isoleucine (Ile or I) Leucine (Leu or L)

Valine (Val or V) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P) Polar side chains; hydrophilic Serine

(Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Electrically charged side chains; hydrophilic Tyrosine (Tyr or Y) Asparagine (Asn or N)

Glutamine (Gln or Q) Basic (positively charged) Acidic (negatively charged) Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine

(Lys or K) Arginine (Arg or R) Histidine (His or H) Protein Structure and Function A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape 2011 Pearson Education, Inc.

Figure 5.18a Groove (a) A ribbon model The sequence of amino acids determines a proteins three-dimensional structure A proteins structure determines its function 2011 Pearson Education, Inc. Four Levels of Protein Structure The primary structure of a protein is its unique sequence of amino acids

Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain Tertiary structure is determined by interactions among various side chains (R groups) Quaternary structure results when a protein consists of multiple polypeptide chains Animation: Protein Structure Introduction 2011 Pearson Education, Inc. Figure 5.21 Sickle-cell hemoglobin Normal hemoglobin

Primary Structure 1 2 3 4 5 6 7 Secondary and Tertiary Structures

Quaternary Structure Function Molecules do not associate with one another; each carries oxygen. Normal hemoglobin subunit

Red Blood Cell Shape 10 m 1 2 3 4 5

6 7 Exposed hydrophobic region Sickle-cell hemoglobin Molecules crystallize into a fiber; capacity to carry oxygen is reduced.

subunit 10 m What Determines Protein Structure? In addition to primary structure, physical and chemical conditions can affect structure Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel

This loss of a proteins native structure is called denaturation A denatured protein is biologically inactive 2011 Pearson Education, Inc. Concept 5.5: Nucleic acids store, transmit, and help express hereditary information The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene Genes are made of DNA, a nucleic acid made of monomers called nucleotides 2011 Pearson Education, Inc.

The Roles of Nucleic Acids There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA provides directions for its own replication DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis Protein synthesis occurs in ribosomes 2011 Pearson Education, Inc.

The Components of Nucleic Acids Nucleic acids are polymers called polynucleotides Each polynucleotide is made of monomers called nucleotides Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups The portion of a nucleotide without the phosphate group is called a nucleoside 2011 Pearson Education, Inc. DNA and Proteins as Tape Measures of Evolution

The linear sequences of nucleotides in DNA molecules are passed from parents to offspring Two closely related species are more similar in DNA than are more distantly related species Molecular biology can be used to assess evolutionary kinship 2011 Pearson Education, Inc.

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