chemistry in biology

Chemistry in BiologyChapter 6

Chapter 6.1Atoms, Elements, and Compounds

• Matter – anything that occupies space and has a mass.

Atoms, Elements, & Compounds

• Atoms – the simplest particles of en element; the building block of all matter

Structure of Atoms

Structure of AtomsProtons• Positively (+) charged particles • Have mass (1 amu = 1 atomic mass unit)• Located in the nucleus

+

Neutrons• Neutral particles (No charge)• Have mass (1 amu)• Also located in the nucleus

n

Electrons• Negatively (-) charged particles• Mass is negligible (1/1840 amu)• Remain in constant motion in orbitals/shell

Structure of Atoms1. Electrons constantly move around the atom’s nucleus

in energy levels. These energy levels are sometime referred to as shells or orbitals.

2. The electrons (-) are attracted to the protons (+). 3. Atoms contain an equal number of protons and

electrons so the overall charge is ZERO

Elements

• Elements are substances that cannot be broken down chemically into simpler kinds of matter.

Elements in Living Things

o Hydrogen (H)o Carbon (C)

oOxygen (O)oNitrogen (N)

oCalcium (Ca)oMagnesium (Mg)

oSodium (Na)oPotassium (K)

oPhosphorus (P)

The Periodic Table6

C12.011

Atomic Number

Chemical Symbol

Atomic Mass

The Periodic Table• The number of protons in an atom is called the

atomic number.• In an atom, the number of positive protons is

balanced by an equal number of negative electrons. – net electrical charge equals zero

The model to the left represents an atom of which element?

How many electrons must be in the electron shells?

= neutron = proton

Atomically Speaking…

• The mass number of an atom is equal to the total number of protons and neutrons of the atom.

What is the mass number of our carbon atom?

= neutron = proton

The Periodic Table

Practice

• What is the atomic number of potassium? • What is the mass number of potassium? • How many protons does potassium contain? • How many neutrons does potassium contain?

(Mass number – Atomic Number = Neutrons)• How many electron does potassium contain?

19391920

19

Drawing an Atomic Model

1. Find the element’s ATOMIC NUMBER. This determines the number of protons and electrons.

2. Find the MASS NUMBER. Subtract the atomic number from the mass number to determine the number of neutrons.

How many protons, electrons, and neutrons are found in an oxygen atom?

Drawing an Atomic Model

3. Draw the PROTONS and NEUTRONS in the nucleus of the atom.

4. Place the electrons in the correct shell:a. Draw the first shell around the nucleus and place

TWO electrons in the first shell.b. Draw the next shell and place up to

EIGHT electrons in the second shellc. If electrons remain, draw the third shell and place

up to EIGHTEEN electrons in the third shell

Draw the model for an oxygen atom.

Oxygen Example

1. Atomic Number is 8Protons - 8Electrons - 8

2. Mass Number is 16Neutrons – 8 (16-8 = 8)

8 P

8 N

Isotopes

• Isotopes are atoms of the same element that have different numbers of neutrons.

• Isotopes will have different mass numbers (isotopes have the same atomic number)

• Isotopes react the same chemically

= neutron = proton

These two atoms are both carbon atoms. But the atom on the left has 6 neutrons while the atom on the right has 7 neutrons. Because of this, these two atoms are said to be isotopes of one another.

These two atoms are both carbon atoms. But the atom on the left has 6 neutrons while the atom on the right has 7 neutrons. Because of this, these two atoms are said to be isotopes of one another.

Radioactive Isotopes

• Sometimes having too many neutrons can make the nucleus of an atom unstable.– Unstable nuclei decay, or break apart.– Particles (usually neutrons) and energy in the form of

radiation are released.– This radiation can be used to calculate the age

of an object or it can be used in medical treatments such as radiation therapy.

Compounds

• Elements combine to form more complex structures called compounds

• Compounds are represented by their chemical formula– H2O

– CO2

– C6H12O6

- NaCl• (subscripts show how many atoms of each element

are in the compound)

Compounds

1. Each compound has a specific ratio of elements

2. Physically and chemically different from the elements that make up the compounds

3. Cannot be broken down into smaller elements by physical means (may be broken down chemically)

4. Held together by chemical bonds

Chemical Bonds Compounds form because

most atoms are not stable in their natural state.

A partially-filled outermost energy level is not as stable as an energy level that is completely filled with the maximum number of electrons it can hold.

Is this carbon atom stable?

= neutron = proton = electron

• Atoms become more stable by losing electrons or attracting electrons from other atoms

• This results in the formation of chemical bonds

Chemical Bonds

Two Ways to Bond

CovalentBonds

(electrons are shared)

Ionic Bonds(attraction of a charged atom)

Chemical BondsCovalent Bond Ionic Bond

A chemical bond that forms when electrons are SHARED

Example: water

An atom can gain or lose an electron to make a stable energy level. This atom is called an ion and is now charged.

An ionic bond is electrical attraction between two oppositely charged atoms.

Example: sodium chloride

Covalent Bonds

Ionic Bond

Covalent Bonding Examples

• Hydrogen and Chlorine

Covalent Bonding Examples

• Carbon and Hydrogen

Ionic Bonding Examples

• Magnesium and Iodine

• Sodium and Oxygen

Ionic Bonding Examples

Chapter 6.2Chemical Reactions

Chemical Reactions

• Process by which atoms or groups of atoms in substances reorganize into different substances

• Chemical bonds are broken or formed

• For example –

4 Fe + 3 O2 2 Fe2O3

Reactants and Products

Chemical Equation:C6H12O6 + O2 CO2 + H20

(Glucose and oxygen react to form carbon dioxide and water)

Reactants (starting substances):C6H12O6 + O2

Products (substances formed):CO2 + H20

Balanced Equation• According to the principle of conservation of

mass, matter cannot be created or destroyed• The number of atoms of each element on the

reactant side must equal the number of atoms of the same element on the product side

For example:

2 H2O2 2 H20 + O2

C6H12O6 + 6 O2 6 CO2+ 6 H20

Energy of Reactions

• Activation Energy – minimum amount of energy needed to start a chemical reaction; energy needed for reactants to form products

Energy of Reactions

Endothermic

Energy-Absorbing Reaction Energy-Releasing Reaction

Products

Products

Activation energy

Activation energy

Reactants

Reactants

Exothermic

Enzyme Tutorials• http://www.northland.cc.mn.us/biology/Biology1111/animations/enzyme.html• http://www.phschool.com/science/biology_place/labbench/lab2/temp.html• http://bcs.whfreeman.com/thelifewire/content/chp06/0602001.html• http://www.sumanasinc.com/webcontent/animations/content/enzymes/enzymes.

html

• http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html

• http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__enzyme_action_and_the_hydrolysis_of_sucrose.html

Enzymes

• Most chemical reactions proceed slowly since the activation energy is high

• A catalyst is a substance that lowers the activation energy needed to start a chemical reaction

• Enzymes are biological catalysts; enzymes are proteins

Enzymes

How Enzymes Work

1. Reactants, called substrates, bind to specific enzymes; the site where enzymes bind is called the active site

2. Once the substrate binds to the active site, it changes shape and forms the enzyme-substrate complex

3. The substrates react to form new products; the enzyme-substrate complex helps to break and form bonds

Example of Enzyme Reaction

http://blog.poolcenter.com/print.asp?articleid=6072

Another View of Enzymes

EnzymesMany factors can affect enzyme activity such as:

– pH– Temperature– Concentration of substrates

Chapter 6.3Water & Solutions

Water’s Polarity• Water molecules are formed by

covalent bonds between 2 hydrogens and 1 oxygen atom

• Since the electrons are more strongly attracted to the oxygen, the electrons spend more time near the oxygen nucleus

• The unequal distribution of electrons gives oxygen a slight negative charge

• Molecules with an unequal distribution of charges are polar molecules – they have oppositely charged regions

Slight Negative Charge

Slight Positive Charge

Water’s Polarity and Hydrogen Bonds• The two water molecules are

brought together, their polar ends attract each other

• This attraction between water molecules is called hydrogen bonding

• It is a weak bond between the hydrogen of one atom and the oxygen of another

• A water molecule can hydrogen bond with three other water molecules

Hydrogen Bonding in Water

http://commons.wikimedia.org/wiki/File:3D_model_hydrogen_bonds_in_water.jpg

Properties of WaterWater is the UNIVERSAL SOLVENT

• Because water is polar, it can dissolve many substances

• For example, NaCl

http://www.mhhe.com/physsci/chemistry/essentialchemistry/flash/molvie1.swf

Properties of Water

Water Expands When It Freezes

• Because of hydrogen bonding, water molecules separate when freezing and water becomes less dense

• Extremely important for marine organisms

http://expertvoices.nsdl.org/polar/2009/02/03/teaching-about-snowflakes-a-flurry-of-ideas-for-science-and-math-integration/http://cc.oulu.fi/~nmrwww/comp_res4.html

Liquid WaterSolid Water (Ice)

Properties of WaterWater is COHESIVE and ADHESIVE

Because of hydrogen bonding, – Water is attracted to other water molecules – this

is called COHESION– Water is attracted to other surfaces – this is called

ADHESION

Cohesion

Cohesion Causes Surface Tension

Adhesion

Adhesion (Capillary Action)

http://discovermagazine.com/2003/mar/featscienceofhttp://www.sciencebuddies.org/science-fair-projects/project_ideas/PlantBio_p033.shtml

Mixtures

• two or more substances which are combined so that each substance keeps its own chemical identity.– Water combines to form many types of mixtures

Mixtures

• Mixtures can be classified as – Homogeneous – a combination of substances that is

uniform throughout or – Heterogeneous – a combination of substances that are

physically distinct from one another

Homogenous Mixtures

• Same uniform appearance

• Same composition throughout

• Examples– Sugar water– Salt water– Water and vinegar– Air in the atmosphere

Homogeneous Mixture• Solutions are a

homogeneous mixture• There are two components

of solution:– Solvent – a substance in

which another substance is dissolved

– Solute – the substance that is dissolved

Heterogeneous Mixture

• Visibly different substances

• Components remain distinct

• Examples – – Vinegar and oil– Salad (lettuce,

vegetables, croutons, etc.)

– Sand and water

Acids and Bases

WATERH2O

ACIDS BASES

Substances that release H+ ions when dissolved

in water

Substances that release OH- ions when dissolved

in water

pH ScaleH2O H+ + OH-

•pH scale – measurement system used to indicate the concentration of H+ ions in a solution

•pH scale ranges from 0-14• pH 7 is neutral and the concentration of H+ ions and OH- ions is equal

• Acids – any compound that forms H+ ions in solution; contain pH values less than 7 (the lower the pH values, the higher the acidity)

• Bases – a compound that produces hydroxide ions (OH-) in solution; contain lower concentrations of H+ ions than water and have pH value greater than 7

•Buffers • weak acids or bases that can react with strong acid or bases to prevent sudden

changes in pH

• For example, to buffer a strong acid, you would add a weak base

Chapter 6.4

The Building Blocks of Life

Organic Chemistry

• Organic compounds are those containing CARBON

• Life forms are carbon-based and therefore considered organic

Macromolecules

• Macromolecules – large molecules that form from joining smaller molecules together– The smaller molecules are called monomer– The larger molecules are called polymers

• Four biologically important macromolecules:– Carbohydrates– Lipids– Proteins– Nucleic acids

Macromolecules

Monomer – smaller molecule

Polymer – larger molecule formed by joining together smaller molecules

Biological MacromoleculesGroup Function

Carbohydrates - Store Energy

Lipids - Store energy- Provide cellular barriers

Proteins - Transport substances- Speed up reactions-Provide structural support-Make hormones

Nucleic Acids Store and communicate genetic information

CarbohydratesChemical Composition•Made of Carbon, Hydrogen , and Oxygen

•Ratio of 1:2:1 (# of C atoms: # of H atoms: # of O atoms)Or (CH2O)2

Functions in Living Things

•ENERGY!• Structural support (cellulose in plant cell walls or chitin in animal shells)

Structure• Monomers may be small carbohydrates like glucose or sucrose. These monomers are called monosaccharide

• The monomers join to form large polymer called polysaccharides

Examples

Sucrose – table sugar

Cellulose – support of plant cell walls

Chitin – rigid support for animal shells (ex. lobster)

LipidsChemical Composition

• Made of Carbon, Hydrogen, and Oxygen

• Higher ratio of Hydrogen to Carbon

Functions in Living Things

ENERGY storage

Provide barriers for cell (cell membranes)

Protective layersStructure

Composed of several fatty acids attached to glycerol

Examples

Fats

Waxes – protective coating on leaves

Oils

Biological steriods

ProteinsChemical Composition

Composed of Carbon, Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur

Functions in Living Things

Transport substances

Speed up chemical reactions

Hormones

Structural supportStructure

•Monomers of proteins are amino acids

• The monomers, amino acids, join to form long chains of proteins

Examples

Enzymes – speed up chemical reactions

Nucleic AcidsChemical Composition

Composed of Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus

Functions in Living Things

Store genetic information

Structure

• Smaller monomers, called nucleotides, join together to form long polymers, DNA and RNA

Examples

DNA – stores genetic information

RNA – copies and transmit genetic information; help to make proteins