chemistry in biology
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Chemistry in Biology. Chapter 6. Chapter 6.1 Atoms, 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. Protons - PowerPoint PPT PresentationTRANSCRIPT
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 sometimes 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)oCarbon (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
Atomic Models
• Draw the following atoms in you notebook:– Fluorine – Magnesium– Aluminum
• Bill Nye Atoms– Part 1 - http://
www.youtube.com/watch?v=zbc85dv3ouk – Part 2. http://
www.youtube.com/watch?v=uZ6zR0vu7cU&feature=relmfu
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.
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
• Nitrogen and hydrogen
Ionic Bonding Examples
• Magnesium and Oxygen
• Sodium and Oxygen
Ionic Bonding Examples
• Calcium chloride
Ionic Bonding Examples
Chapter 6.2Chemical Reactions
http://www.youtube.com/watch?v=PlwuxpMh8nk&feature=related (until 3:45/8:00)
Chemical Reactions
• Process by which atoms or groups of atoms in substances reorganize into different substances
• Involve the breaking and reforming of chemical bonds.
• For example – 4 Fe + 3 O2 2 Fe2O3
Physical Change vs. Chemical Change
•Physical change affects appearance, not composition. You have the same substance before and after the physical change.
•A chemical change affects composition. You have a different substance after the chemical change.
o How do you know a chemical change has occurred?o Clues:oProduction of heat or lighto Formation of a solid, liquid, or gas
Chemical Equations
•Scientists often use chemical equations to show what is happening during a chemical change.
C6H12O6 + 6O2 6H2O + 6CO2
•The substances on the left side of the arrow are called the reactants.•They are reacting and are forming the substances on the right side, the products.
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• So the number and types of atoms on each
side of the equation must be balanced. (or 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)
http://www.youtube.com/watch?v=_B735turDoM
For example: 2 H2O2 2 H20 + O2
C6H12O6 + 6 O2 6 CO2+ 6 H20
How to Balance an Equation
• Step 1: Count the number of atoms of each element on both the product and reactant side. You can create a chart to help you.
• Step 2: Determine which atoms are not balanced.
Element Reactant Side Product Side
O
C
How to Balance an Equation
• Step 3: Balance one atom at a time, using coefficients. Start with atoms that appear only once in the reactants and only once in the products. Usually leave Hydrogen atoms followed by Oxygen atoms until last.
• Step 4: After you believe that you have successfully balanced the equation, repeat Step 1, to be certain that mass conservation has been achieved.
• Note: DO NOT Change subscripts in a molecular formula (i.e., 2 NaCl Na2Cl2 )
H2O2 H2 + O2
Na + Cl2 NaCl
Zn + HCL ZnCl2 + H2
Fe + Cl2 FeCl2
Balanced Equation
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• Activation Energy and Enzymes - http://www.sumanasinc.com/webcontent/animations/content/enzymes/enzymes.html • Overview – http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html
• Sucrose Example - http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__enzyme_action_and_the_hydrolysis_of_sucrose.html
• 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
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
http://www.sumanasinc.com/webcontent/animations/content/enzymes/enzymes.html
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 http://www.youtube.com/watch?v=CLHP4r0E7hg&feature=related
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://cc.oulu.fi/~nmrwww/comp_res4.html
Liquid WaterSolid Water (Ice)
• http://www.visionlearning.com/library/module_viewer.php?mid=57
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
• Carbon has FOUR electrons in its outermost shell
• Therefore, carbon can form up to FOUR covalent bonds with other atoms
Organic Chemistry
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- Provide structural support (cell wall)
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 steroids
ProteinsChemical Composition
Composed of Carbon, Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur
Functions in Living Things
Transport substances
Speed up chemical reactions
Hormones
Structural support
Structure
•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