How Matter is Organized

Chemistry is the science of the structure and interactions of matter.

all living things consist of matter.

Matter is anything that occupies space.

mass is the amount of matter in any object. weight is the force of gravity acting on matter Does air have matter?

Chemical Elements
Elements are substances that can not be split into simpler substances by ordinary means.
112 elements ( 92 occur naturally ) 26 of naturally occurring elements are in the body represented by chemical symbols ( first 1-2 letters of name )

4 elements form 96 % of the bodys mass

hydrogen, oxygen, carbon and nitrogen

Trace elements are present in tiny amounts

such as copper, tin, selenium & zinc

Structure of Atoms
Atoms are the smallest units of matter that retain the properties of an element Atoms consist of 3 types of subatomic particles protons, neutrons and electrons Nucleus contains protons (p+) & neutrons (neutral charge) Electrons (e-) surround the nucleus as a cloud (electron shells are designated regions of the cloud)

Atomic Number & Mass Number

Atomic number is number of protons in the nucleus. . Mass number is the sum of its protons and neutrons.

Isotopes

Molecule, Element, compound

Molecule= more than one atom existing in union Element= Molecule contains identical atoms Compound: Molecule contains different atoms

IONS: Charged particles

When an atom gains or loses electrons ions are formed Positively charged= cation Negatively charged = anion

 Atom with an unpaired electron in its outmost shell Unstable and highly reactive Can become stable
by giving up electron taking one off another molecule (breaking apart important body molecules)

Free Radicals

 Produced in your body by absorption of energy in ultraviolet light in sunlight, x-rays, by breakdown of harmful substances, & during normal metabolic reactions Linked to many diseases -- cancer, diabetes, Alzheimer, atherosclerosis and arthritis Damage may be slowed with antioxidants such as vitamins C and E, selenium & beta-carotene (precursor to vitamin A)

Free Radicals & Your Health

Chemical Bonds
Bonds hold together the atoms in molecules and compounds An atom with a full outer electron shell is stable and unlikely to form a bond with another atom Octet rule states that biologically important elements interact to produce chemically stable arrangements of 8 electrons in the valence shell. Whether electrons are shared, donated or acquired determines the types of bonds formed

 Atoms share electrons to form covalent bonds Electrons spend most of the time between the 2 atomic nuclei

Covalent Bonds

single bond = share 1pair double bond = share 2 pair triple bond = share 3 pair

Polar Covalent Bonds

Unequal sharing of electrons between atoms. In a water molecule, oxygen attracts the hydrogen electrons more strongly
Oxygen has greater electronegativity as indicated by the negative Greek delta sign.

Ionic Bonds
Positively and negatively charged ions attract each other to form an ionic bond In the body, ionic bonds are found mainly in teeth and bones An ionic compound that dissociates in water into + and - ions is called an electrolyte

The Ionic Bond in Sodium Chloride

Sodium loses an electron to become Na+ (cation) Chlorine gains an electron to become Cl- (anion) Na+ and Cl- are attracted to each other to form the compound sodium chloride (NaCl) -- table salt Ionic compounds generally exist as solids

 Hydrogen bonds are the most important inter molecular force of attraction . Formed by the attraction between slightly positive Hydrogen atom and a slightly negative atom of another element. Too weak to create molecules but creates shapes and stabilizes large molecules like proteins or nucleic acids

Hydrogen bonds

Chemical Reactions
When new bonds form or old bonds are broken Metabolism is all the chemical reactions in the body

Energy and Chemical Reactions

Chemical reactions involve energy changes Law of conservation of energy
energy can neither be created nor destroyed--just converted from one form to another

Reactions that yield energy = Exergonic reactions (Larger to smaller molecules) AB A + B Reactions that require energy to occur= Endergonic reactions (smaller to larger molecules ) A + B AB

Energy Transfer in Chemical Reactions

Chemical reactions usually involve both Human metabolism couples exergonic and endergonic reactions, so that the energy released from one reaction will drive the other.
Glucose breakdown releases energy used to build ATP molecules that store that energy for later use in other reactions

Activation Energy
Atoms, ions & molecules are continuously moving & colliding Activation energy is the collision energy needed to break bonds & begin a reaction Increases in concentration & temperature, increase the probability of 2 particles colliding more particles in a given space as concentration is raised particles move more rapidly when temperature is raised

Catalysts/Enzymes
Normal body temperatures and concentrations are too low to cause chemical reactions to occur Catalysts speed up chemical reactions by lowering the activation energy needed to get it started Catalysts orient the colliding particles properly so that they touch at the spots that make the reaction happen Catalyst molecules are unchanged and can be used repeatedly to speed up similar reactions.

Free Energy and Activation Energy Tutorial

Synthesis Reactions-Anabolism
Two or more atoms, ions or molecules combine to form new & larger molecules All the synthesis reactions in the body together are called anabolism Usually are endergonic because they absorb more energy than they release Example combining amino acids to form a protein molecule

Decomposition Reactions-Catabolism
Large molecules are split into smaller atoms, ions or molecules All decomposition reactions occurring together in the body are known as catabolism Usually are exergonic since they release more energy than they absorb

Inorganic Compounds & Solvents

Most of the chemicals in the body are compounds Inorganic compounds Organic compounds

usually lack carbon & are structurally simple water, salts, acids and bases contain carbon & usually hydrogen always have covalent bonds

pH - measure or acidity/alkalinity pH = - log [H+] acidic < 7 < basic Acids-raise H+ content Bases-lower H+ content: release OH- or accepts H+

Dissociation

1pH unit = 10x difference 1000 as many H+ in a pH of 5 as there are in 8

Buffer-takes up or releases H+ or OH- to prevent changes in pH. In the bicarbonate system, H2CO3 H+ base acceptor, HCO3- acid acceptor
What happens to shells in carbonated drinks? Does Sea Ice Speed Up Ocean Acidification? How does the bicarbonate system work in a blood plasma? In the ocean?

Ocean Acidification: 2, 3

Carbon dioxide concentration in metabolically active cells is much greater than in capillaries, so carbon dioxide diffuses from the cells into the capillaries. About 7% of the CO2 directly dissolves in the plasma. Another 23% binds to the amino groups in hemoglobin. The remaining 70% is transported in the blood as bicarbonate ion.

Concept of pH
pH scale runs from 0 to 14 (concentration of H+ in soln.) pH of 7 is neutral (distilled water) pH below 7 is acidic and above 7 is alkaline

 What is more acid than lemon? In a test of pH levels, a glass of milk was found to have a pH of 6.0. A glass of grape juice had a pH of 3.0. What is the relationship between the pH levels of the milk and grape juice? A The milk is 100 times more acidic than the grape juice B The grape juice is 3 times more acidic than the milk C The milk is 3 times more acidic than the grape juice D The grape juice is 1000 times more acidic than the milk How many more H+s do tomatoes have than bananas? Lemons than milk? Bleach than soap?

Inorganic Acids, Bases & Salts

Acids, bases and salts always dissociate into ions if they are dissolved in water
acids dissociate into H+ and one or more anions bases dissociate into OHand one or more cations salts dissociate into anions and cations, none of which are either H+ or OH-

Acid & bases react in the body to form salts Electrolytes are important salts in the body that carry electric current (in nerve or muscle)

 Most important inorganic compound in living systems, Medium of nearly all chemical reactions Polarity
uneven sharing of electrons makes it an excellent solvent for ionic or polar substances gives water molecules cohesion allows water to moderate temperature changes

Water & Its Properties

Participates as a product or reactant in certain reactions in the body

hydrolysis reactions water is added to a large molecule to separate it into two smaller molecules digestion of food dehydration synthesis reaction two small molecules are joined to form a larger molecule releasing a water molecule

 Most versatile solvent known

Water as a Solvent

polar covalent bonds (hydrophilic vs hydrophobic) its shape allows each water molecule to interact with neighboring ions/molecules

Water dissolves many substances

Water has a high surface tension

Water is wet Water is attracted to itself, and this attraction, due to H bonds is stronger than the attraction to the air above Adhesion and cohesion allow for capillary action water transport in plants Occurs as solid, liquid and gas within normal temperature ranges on Earth

Water = good evaporative coolant

Heat of vaporization is also high
amount of heat needed to change from liquid to gas evaporation of water from the skin removes large amount of heat

B/c it takes a lot of energy to change water from a liquid to a gas, it takes energy with it Heat capacity is high
can absorb a large amount of heat with only a small increase in its own temperature large number of hydrogen bonds in water bonds are broken as heat is absorbed instead of increasing temperature of water large amount of water in body helps lessen the impact of environmental changes in temperature

 Major component of lubricating fluids within the body mucus in respiratory and digestive systems synovial fluid in joints serous fluids in chest and abdominal cavities
organs slide past one another

Water as a Lubricant

Ice floats
Water has a high freezing point and lower density as a solid than a liquid

Chemical Reactions
energy causes rearrangement of e-'s and new bonds, new compounds are formed, E can be force of collision, heat, electricity etc. reactants yield product(s) Balanced equations (energy cannot be created or destroyed). Balance the following equations: CH4 + O2 CO2 + H2O CuO + NH3 Cu + H2O + N2 NH3 + O2 NO + H2O

CH4 + 2O2 = CO2 + 2H2O 3CuO + 2NH3 = 3Cu + 3H2O + N2 4NH3 + 5O2 = 4NO + 6H2O

 Mixtures-- combination of substances in which the individual components retain their own properties

solutions-- or more substances is distributed evenly in another substance

solution=solvent(H2O)+solute(dissolvedparticles)

suspension-- particles of materials temporarily mixed together (blood) colloid-- particles larger than solution, smaller than suspension (cytosol)

are

Chemistry Tutorial
The Biology Project: http://www.biology.arizona.edu/biochemistry /tutorials/chemistry/main.html

 Properties of carbon atoms forms bonds with other carbon atoms produce large, stable molecules with many different shapes (rings, straight or branched chains) Many functional groups can attach to carbon skeleton esters, amino, carboxyl, phosphate groups (Table 2.5) Very large molecules called macromolecules (polymers if all monomer subunits are similar)

Carbon & Its Functional Groups

 The properties of different biological molecules depend on certain characteristic groupings of atoms called functional groups. If you know the properties of some of the functional groups, you will be able to quickly look at many simple biological molecules and get some idea of their solubility and possible identity. The names of the six most important functional groups are: Hydroxyl Carbonyl Carboxyl Amino Sulfhydryl Phosphate

Hydroxyl
Two functional groups containing oxygen, the hydroxyl and carbonyl groups, contribute to water solubility. Hydroxyl groups have one hydrogen paired with one oxygen atom (symbolized as -OH). Hydroxyl groups are not highly reactive, but they readily form hydrogen bonds and contribute to making molecules soluble in water. Alcohols and sugars are "loaded" with hydroxyl groups.

Genistein and daidzein, two phytoestrogens from legumes

Notice that the only difference between these two molecules is the additional hydroxyl (-OH) group on genistein. Both are typical isoflavones. Genistein, however, is considerably more estrogenic than daidzein; chemists attribute this to the influence of the additional hydroxyl group. The hydroxyl groups are important for binding to estrogen receptors.

Carbonyl
Carbonyl groups have one oxygen atom doublebonded to a carbon atom (symbolized as -C=O). Like hydroxyl groups, carbonyl groups contribute to making molecules water-soluble. All sugar molecules have one carbonyl group, in addition to hydroxyl groups on the other carbon atoms.
Aldehyde groups, where the C=O group is at the end of an organic molecule. A hydrogen atom is also located on the same carbon atom. Keto groups, where the C=O group is located within an organic molecule. All sugars have either a keto or an aldehyde group.

 Carbonyl -COH C3H6O aldehyde = end (propanol) ketone = inside (acetone)

 Carboxyl groups are weak acids, dissociating partially to release hydrogen ions.The carboxyl group (symbolized as COOH) has both a carbonyl and a hydroxyl group attached to the same carbon atom, resulting in new properties.
Carboxyl groups frequently ionize, releasing the H from the hydroxyl group as a free proton (H+), with the remaining O carrying a negative charge. Molecules containing carboxyl groups are called carboxylic acids and dissociate partially into H+ and COO.
Carboxyl groups are common in many biological molecules, including amino acids and fatty acids.

Carboxylic Acids

 Nitrogen in biological molecules usually occurs in the form of basic amino groups.Nitrogen is another abundant element in biological molecules. Having a valence of 3, nitrogen normally forms three covalent bonds, either single, double, or triple bonds. Amino groups (-NH2) are common functional groups containing nitrogen. Amino groups are basic, and often become ionized by the addition of a hydrogen ion (H+), forming positively charged amino groups (NH3+).

Amino Group

 Sulfur is found mainly in proteins in the form of sulfhydryl groups or disulfide groups.Like oxygen, sulfur typically has a valence of 2, although it can also have a valence of 6, as in sulfuric acid. Sulfur is found in certain amino acids and proteins in the form of sulfhydryl groups (symbolized as SH). Two sulfhydryl groups can interact to form a disulfide group (symbolized as -S-S-).

Sulfhydryl

Phosphate Groups
In biological molecules, phosphorus occurs mainly in the form of acidic phosphate groups. Phosphorus normally has a valence of 5. Its most common functional group in organic molecules is as a phosphate group (symbolized as OPO32-). Phosphorus is covalently paired to 4 oxygen atoms in phosphate groups: one P=O bond and three P-Obonds.

Importance of Functional Groups in Biology

Function Groups Practice

Match the columns
1. 2.

3.
4.

5.
6.

Types of Organic compounds

Four major groups of organic compounds, necessary for life are: polymers monomers____ Carbohydrates monosacchrides Lipids fatty acids Proteins amino acids Nucleic acids nucleotides

Carbohydrates
Diverse group of substances from C, H, and O
ratio of one carbon atom for each water molecule (carbohydrates means watered carbon) glucose is 6 carbon atoms and 6 water molecules (H20)

Main function is to produce energy 3 sizes of carbohydrate molecules monosaccharides disaccharides polysaccharides

Mono saccharides
one sugar

Called simple sugars Contain 3 to 7 carbon atoms (CH2O)n We can absorb only 3 simple sugars without further digestion in our small intestine
glucose found in syrup or honey fructose found in fruit galactose found in dairy products

Disaccharides (two)
Formed by combining 2 monosaccharides by dehydration synthesis (releases a water molecule) Name of bond= Glycosidic bond
sucrose = glucose & fructose

Condensation Rxn & Dehydration Synthesis

2 Condensation & Hydrolysis QT Mov

Disacchrides of distinction
glucose + fructose = sucrose glucose + glucose = maltose glucose + galactose = lactose

Polysaccharides
> 100s of monomers by dehydration synthesis In animals

(many)

Glycogen: glucose polymer, found in liver & skeletal muscle, when blood sugar level drops, liver hydrolyzes glycogen to create and release glucose into the blood

Polysaccharide

 Formed from C, H and O 18-25% of body weight Hydrophobic fewer polar bonds because of fewer oxygen atoms insoluble in water Combines with proteins for transport in blood Lipoproteins Three functional classes: Storage lipid: -Triglycerides: Common body fat. Regulatory lipid: - Steroids: act as hormone - Eicosanoids: hormones Structural lipid: Phospholipids: Cell membrane Glycolipids: Cell membrane

Lipids = fats, oils, steroids, waxes

Triglycerides
Fats composed of a single glycerol molecule and 3 fatty acid molecules
three-carbon glycerol molecule is the backbone

Very concentrated form of energy

9 calories/gram compared to 4 for proteins & carbohydrates our bodies store triglycerides in fat cells if we eat extra food

Triglyceride Formation
Triglycerides = three fatty acids attached by dehydration synthesis to one molecule of glycerol by an ester bond
Figure 2.15

 Determined by the number of single or double covalent bonds in fatty acid Saturated fats contain single covalent bonds and are covered with hydrogen atoms----lard Unsaturated are not completely covered with hydrogen---safflower oil, corn oil Polyunsaturated fats contain even less hydrogen atoms----olive and peanut oil

Saturation of Triglycerides

Regulatory lipids: Steroids

Formed from 4 rings of carbon atoms joined together Common steroids sex hormones, bile salts, vitamins & cholesterol Cholesterol found in animal cell membranes starting material for synthesis of other steroids Which is most soluble in water?

Eicosanoids
Lipid type derived from a fatty acid called arachidonic acid
prostaglandins = wide variety of functions
modify responses to hormones contribute to inflammatory response prevent stomach ulcers dilate airways regulate body temperature influence formation of blood clots

leukotrienes = allergy & inflammatory responses

Structural lipids
Phospholipids: Glycerol+ fatty acids + phosphate Part of cell membrane. Ex. Lecithin. Glycolipid: Glycerol+ fatty acid+ sugar chain. Part of cell membrane surface.

Chemical Nature of Phospholipids

amphi pathic
head tails

Lipid Behavior in Various Environments

How do phospholipids behave In an oil spill? Submerged in water? In a living cell?

Lipoproteins
What determines the density of lipoproteins?

Nucleic acids are chains of nucleotides

Three types: DNA, RNA, ATP Function: Storage of genetic information and energy Nucleotides are composed of: sugar, phosphate,nitrogenous base
Sugar = deoxyribose (DNA) or ribose (RNA & ATP) DNA Bases = adenine, thymine, cytosine, guanine RNA bases = adenine, uracil, cytosine, guanine Base Pairing: A-T, G-C or A-U. Held together by hydrogen bonds

DNA Structure
Huge molecules containing C, H, O, N and phosphorus Each gene of our genetic material is a piece of DNA that controls the synthesis of a specific protein A molecule of DNA is a chain of nucleotides Nucleotide = nitrogenous base (A-G-T-C) + pentose sugar + phosphate group

RNA Structure
Differs from DNA single stranded ribose sugar not deoxyribose sugar uracil nitrogenous base replaces thymine Types of RNA within the cell, each with a specific function messenger RNA ribosomal RNA transfer RNA

 Temporary molecular storage of energy as it is being transferred from exergonic catabolic reactions to cellular activities

Adenosine Triphosphate (ATP)

muscle contraction, transport of substances across cell membranes, movement of structures within cells and movement of organelles

Consists of 3 phosphate groups attached to adenine & 5-carbon sugar (ribose)

Formation & Usage of ATP

Hydrolysis of ATP (removal of terminal phosphate group by enzyme -- ATPase) releases energy leaves ADP (adenosine diphosphate) Synthesis of ATP enzyme ATP synthase catalyzes the addition of the terminal phosphate group to ADP energy from 1 glucose molecule is used during aerobic respiration to create 36 to 38 molecules of ATP

Amino Acid Structure

Central carbon atom Amino group (NH2) Carboxyl group (COOH) Hydrogen Side chains (R groups) vary between amino acids

Proteins
Contain carbon, hydrogen, oxygen, and nitrogen Constructed from combinations of 20 amino acids. Levels of structural organization
primary, secondary and tertiary shape of the protein influences its ability to form bonds

Which Amino Acids are hydrophobic? How do you know?

Which Amino Acids are alkaline? Why?

Formation of a peptide Bond

Dipeptides formed from 2 amino acids joined by a covalent bond called a peptide bond dehydration synthesis
Polypeptides chains formed from 10 to 2000 amino acids.

Levels of Structural Organization

Primary is unique sequence of amino acids Secondary is alpha helix or pleated sheet folding Tertiary is 3-dimensional shape of polypeptide chain Quaternary is relationship of multiple polypeptide chains

 Primary is unique sequence of amino acids Secondary is alpha helix or pleated sheet folding Tertiary is 3-dimensional shape of polypeptide chain Quaternary is relationship of multiple polypeptide chains
Protein Folding Tutorial: Protein folding in Water

The four levels of protein configuration

Bonds of protein Structure

Hydrogen bond forms the secondary structure Disulfide bonds stabilize the tertiary structure of protein molecules Disulfide bond between 2 polypeptide chains create quaternary structure

Protein Denaturation
Function of a protein depends on its ability to recognize and bind to some other molecule Hostile environments such as heat, acid or salts will change a proteins 3-D shape and destroy its ability to function
raw egg white when cooked is vastly different

Glycoprotein and Proteoglycan

Proteins exist in combination with sugar. Glycoprotein: Protein + sugar chain. Found in cell membrane. Serve as surface proteins. Proteoglycan: Protein + sugar chain. Also present in cell membrane. Can have enzymatic activity.

Enzymes
Enzymes are protein molecules that act as catalysts by lowering Activation Energy Enzyme = apoenzyme + cofactor
Apoenzymes are the protein portion Cofactors are nonprotein portion
may be metal ion (iron, zinc, magnesium or calcium) may be organic molecule derived from a vitamin

Enzymes usually end in suffix -ase and are named for the types of chemical reactions they catalyze How Enzymes Work Enzyme Tutorial Enzyme Catalysis

Enzyme Functionality
Highly specific
acts on only one substrate
active site versus induced fit

Very efficient

speed up only one reaction

Under nuclear control Co-factors first bind to the enzyme = enzyme activated

speed up reaction up to 10 billion times faster

Enzyme Structure Interactions

Lock and Key: shape and active site of enz is only compatible w/ substrate, forming substrate enzyme complex -enz reused but are eventually decomposed=constant synthesis -usually end in "ase" and take name of substrate

Factors Affecting Enzyme Action

Temperature: 40oC, denaturation Enzyme Saturation Concentration of substrate pH pepsin ( gastric protease) pH 2 trypsin (pancreatic protease) pH 8

Saturation

Cofactors
Cofactors can aid how enzyme works. If they are organic, then they are coenzymes these are enzyme activators Allosteric & Cofactors inhibitors activators Competitive

Pharmacological Enzyme Inhibitors Allosteric Regulation Biochemical Pathway Competitive vs Noncompetitive Inhibitors

 Competitive vs Noncompetitive Inhibitors

In this animation, the enzyme is olive, the substrate is green, the competitive inhibitor is red and the products A & B are yellow and blue. The enzyme has binding site into which either the substrate or the competitive inhibitor may fit. Which product, A or B, would most likely be a competitive inhibitor?

 The enzyme has 2 binding sites, one for the substrate (the active site) and the other for the allosteric activator (the regulatory site). Allosteric Activation
Nerve gas permanently blocks pathways involved in nerve message transmission, resulting in death. Penicillin, the first of the "wonder drug" antibiotics, permanently blocks the pathways certain bacteria use to assemble their cell wall components.

Examples of Enzyme function

Ethylene levels cause changes in the production of different enzymes, allowing fruits to ripen. In eukaryotic cells the mRNA transcript undergoes a series of enzyme regulated modifications. The enzyme RNA-polymerase reads the DNA molecule in the 3' to 5' direction and synthesizes complementary mRNA molecules that determine the order of amino acids in the polypeptide. ATP Synthase DNA polymerase, ligase, RNA polymerase, helicase and

topoisomerase,

Positive Feedback
Amplification occurs when the stimulus is further activated, which in turn initiates an additional response that produces system change

Lactation in mammals Onset of labor in childbirth Ripening of fruit Blood clotting

Estrogen & Progesterone in Female System

Negative Feedback/ Feedback Inhibition

When the product is in abundance, it binds competitively with its enzyme's active site; as the product is used up, inhibition is reduced and more product can be produced. In this way the concentration of the product is always controlled within a certain range.

Operons in gene regulation

Temperature regulation in animals Plants response to water limitations

1
2 3 4 5 6

A
B C D E F

Animations: Microbiology: BioTopics Contents: What is an Enzyme: Lipid Behavior in Various Environments Organic Molecules Interactive Animations for Biochemical Processes Biology Project Chemistry Tutorial Chemistry Target Practice Importance of Functional Groups Functional groups Matching Identify the Biomolecules Matching "Hot Potatoes" Practice matching exercises Factors that affect the rate of Chemical Reactions with Alka Seltzer Properties of Water Properties of Water & Transpiration Enzyme Specificity Tutorial Enzyme Kinetics Animation Water Potential Quiz

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