Agenda- 9/25- Honors Biology

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Agenda- 9/25- Honors Biology

• Intro to Chemistry
• Wordsplash- finish for HW

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Honors Biology- 9/26- Block 2

• Bellwork
• Intro to Chemistry
• Atoms, elements, Periodic Table
• Lewis Dot Structures
• Covalent and ionic bonding
• Chemistry practice

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CP Biology- 9/26

• Bellwork
• Intro to Chemistry
• Chemistry Practice

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Composition of Matter

• Atoms
• Basic unit of matter smallest piece of an
  element that keeps its chemical properties
• Matter -
• occupies space and has mass

5
Elements

• Pure substances that cannot be broken down
  chemically

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• Each element has a unique chemical symbol
• 1-2 letters

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Atoms

• Made of subatomic particles
• Protons ()
• Neutrons (0)
• Electrons (-)

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The Nucleus

• Central core
• Consists of protons and neutrons
• Contains most of the mass of the atom

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The Protons

• All atoms of a given element have the same number
  of protons
• Number of protons atomic number
• Most atoms are neutral, which means
• the of protons the of electrons

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The Neutrons

• Isotopes atoms of an element with different of
  neutrons
• Have the same of electrons, so same chemical
  properties
• Radiometric dating (C14) chemotherapy

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Atomic Mass

• Protons and neutrons each have a mass of 1 amu
  (atomic mass unit)
• The approximate atomic mass of protons of
  neutrons

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The Electrons

• Negatively charged high energy particles with
  little or no mass
• Travel at very high speeds at various distances
  (energy levels) from the nucleus

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Bohr Model

• Incorrect but useful basic model of the atom
• Electrons orbit in different energy levels
• First level can hold 2 electrons
• Second level can contain up to 8 electrons
• To be stable, an element needs to have its outer
  (valence) energy level filled
• THIS IS AN OVERLY SIMPLIFIED (and incorrect) VIEW
  OF THE ATOM!!!

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Modern View of the Atom
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Lewis Dot Structure

• Only show electrons involved in bonding (valence
  electrons)
• Drawn top, right, left, and bottom, one at a
  time, then paired

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Agenda- 9/29- CP Biology

• Bellwork
• Chemistry of Life
• 6 most common elements in living things
• Chemical bonding
• Chemistry of water
• Water activities

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Most Common Elements in Living Things
CHNOPS

• Carbon (C) atomic 6
• Hydrogen (H) atomic 1
• Nitrogen (N) atomic 7

• Oxygen (O) atomic 8
• Phosphorous (P) atomic 15
• Sulfur (S) atomic 16

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• A compound
• chemical combination of two or more elements in
  definite proportions
• Chemical formula shows the kind and proportion of
  atoms of each element that occurs in a particular
  compound
• Ex. H2O

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• Molecules- 2 or more atoms bonded together
  chemically (ex. O2, H2O)
• All compounds are molecules not all molecules
  are compounds
• Some molecules are large and complex

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Chemical Formulas

• Subscript number of atoms of each element
• H20
• 2 atoms of hydrogen 1 atom of oxygen
• Coefficients before a formula tell the number of
  molecules
• 3O2
• 3 molecules of oxygen or 6 (3x2) atoms of oxygen

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• Atoms are most stable when their outer most
  energy level is filled
• Number of bonds an atom can make depends on the
  number of valence electrons it has

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Covalent Bonds

• Formed when two atoms share one or more pairs of
  electrons
• Covalent bonds store chemical energy

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How do atoms fill their outermost energy level to
become stable?They can SHARE electrons!
H
H
H
H
Ex the Hydrogen Molecule

• A shared pair of electrons between two atoms a
  COVALENT BOND

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Ionic Bonds

• Some atoms become stable by losing or gaining
  electrons
• Atoms that lose electrons are called positive ions

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• Atoms that gain electrons are called negative
  ions
• Because positive and negative electrical charges
  attract each other ionic bonds form

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Agenda- 9/29

• Bellwork
• Finish Chemistry Start Carbohydrates
• Lab- Carbohydrate Models

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HYDROGEN
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Biological Function of Hydrogen

• Covalent bonds in molecules are full of energy
• Ex fat molecules have many hydrogen atoms with
  covalent bonds
• Hydrogen bonds help molecules hold their shapes
• Ex water molecules stick to each other because
  of hydrogen bonds

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Atomic Structure of Hydrogen
1
H
Hydrogen
1.0079
1 first level electron
Helium

• Hydrogen wants to be stable with 2 first level
  electrons

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CARBON
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Biological Function of Carbon

• Carbon forms the backbone of biological
  molecules
• - Ex fat molecules are long chains of carbon
  atoms

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Atomic Structure of Carbon
How many valence electrons?
6
C
Carbon
12.011
4 second level electrons
Neon

• Carbon wants to be stable with 8 second level
  electrons

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Importance of Carbon

• All organic molecules contain 2 or more carbon
  atoms chemically bonded together
• Can make 4 strong covalent bonds because it has 4
  valence (outer) electrons
• Can bond to other Carbon atoms to form rings or
  chains
• Can form millions of large, complex 3-D structures

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The Carbon Cycle
CO2 in Atmosphere
CO2 in Ocean
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Oxygen- atomic number 8
OXYGEN
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Biological Function of Oxygen

• Oxygen is a component of water, which is
  essential for all life.
• Most organisms need oxygen for cellular
  respiration.

C6H12O6 6O2 6CO2 6H2O
HEAT energy
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Atomic Structure of Oxygen
8
O
Oxygen
15.9994
6 second level electrons

• Oxygen wants to be stable with 8 second level
  electrons

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Biological Function of Nitrogen

• Nitrogen is an essential component of protein
  molecules

Amino Acid Molecules
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Biological Function of Sulfur

• Sulfur is a component of some amino acids
• A high Sulfur content in hair causes it to be
  curly

A Sulfur Atom
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Biological Function of Sulfur

• Sulfur is a component of some amino acids
• A high Sulfur content in hair causes it to be
  curly
• Sulfur is the source of energy for deep sea
  bacteria and entire ecosystems

CO2 4H2S O2 CH2O 4S 3H2O
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Phosphorous

• Atomic number 15- how many valence electrons?
• How many bonds can it make?
• Biological importance
• Component of amino acids (which make up proteins)
  and nucleic acids

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Q - What does an atom require to be stable?Q-
Which of these atoms are stable, or nonreactive?

• A - A full set of 8 electrons in the outermost
  energy level

1
2
3
4
5
6
7
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Q Which of these atoms are stable?
Argon
Neon
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Q - Identify the atom for each electron
configuration
A - Oxygen, Argon, Hydrogen, Neon, Nitrogen,
Sulfur, Carbon
1
2
3
4
5
6
7
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The Molecules of Life

• Macromolecules are large molecules composed of
  smaller molecules.
• macro- large
• Three of the classes of lifes organic molecules
  are polymers
• Carbohydrates
• Proteins
• Nucleic acids
• (Lipids are macromolecules, but not polymers)

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Polymers and Monomers

• A polymer is a long molecule consisting of many
  similar building blocks called monomers.
• poly- many mono- one
• Monomers form larger molecules by condensation
  reactions called dehydration synthesis.

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Polymers and Monomers

• Polymers can disassemble by hydrolysis.
• Hydro- water -lysis cutting
• An immense variety of polymers can be built from
  a small set of monomers.

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Carbohydrates
Starch
Glucose
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Lab

• Carbohydrate model building
• Monosaccharide
• Disaccharide
• Dehydration synthesis
• Hydrolysis

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Agenda- 9/30

• Bellwork
• Carbohydrate Notes- types, structure, functions
• Lipids
• Structure, function

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5 Minute Writing

• What does a molecular formula tell you?
• A structural formula?
• How do the molecular formulas of glucose,
  galactose, and fructose compare?
• Their structural formulas?

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Carbohydrates

• Carbohydrates serve as fuel and building material
  and include both sugars and their polymers.
• Monosaccharides (ex. Fructose, glucose,
  galactose)
• Are the simplest sugars (monomers)
• Can be used for fuel
• Can be converted into other organic molecules
• Can be combined into polymers

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Isomers

• Same molecular formula, but different structural
  formula.
• Same of atoms of each element, but different
  physical arrangement

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Carbohydrates

• Disaccharides
• Consist of two monosaccharides
• Are joined by a glycosidic linkage via
  dehydration synthesis

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Carbohydrates

• Polysaccharides are polymers of sugars and serve
  many roles.
• Starch is a polymer made entirely of glucose
  monomers.
• Starch is the major form of energy storage of
  glucose in plants.

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Carbohydrates

• 2. Glycogen consists of glucose monomers and is
  the major storage form of glucose in animals.

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Carbohydrates

• 3. Cellulose is also a polymer of glucose, but it
  has different glycosidic linkages than glycogen.

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Carbohydrates

• Cellulose is a major component of the tough walls
  that enclose plant cells (structural).

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Carbohydrates

• Humans lack the enzyme cellulase that can break
  down cellulose.

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Carbohydrates

• What animals can break the bonds that combine
  glucose monomers into the cellulose polymer by
  using cellulase?

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Carbohydrates

• Cows have microbes in their stomachs to break
  down cellulose (via hydrolysis).

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Carbohydrates

• 4. Chitin is another important structural
  polysaccharide
• It is found in the exoskeleton of arthropods and
  in the cell walls of fungi (structural).
• It can be used as surgical thread.

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Carbohydrates
Starch
Glucose
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Carbohydrates Which elements? In what ratio?

• C, H, O
• Ratio of HO of 21
• Carbo- refers to Carbon
• Hydrate- refers to the ratio of HO (21, like
  water)
• Functions
• Short-term energy storage
• Structural (cell walls, exoskeletons)

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5 Minute Writing

• What are the functions of carbohydrates (2)? Of
  fats?
• What are some foods that are high in fat?
• Whats the difference between saturated and
  unsaturated fats? Why does it matter?

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Lipids Fatty Acids
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Lipids
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Lipids

• Lipids
• the one class of large biological molecules that
  do not consist of polymers.
• share the common trait of being hydrophobic.
• Several functions
• Long term energy storage
• Insulation
• Waterproof coatings
• Component of membranes

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Lipids

• Fats are constructed from two types of smaller
  molecules, a single glycerol and usually three
  fatty acids.
• How do the C, H, O
• Ratios compare to
• carbohydrates?
• Lots of C H
• A few O atoms

Figure 5.11
(b) Fat molecule (triacylglycerol)
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Lipid Models- Fats

• Complete the model building activity.

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Agenda- 10/1- Honors Biology

• Bellwork
• Lipids- structure and function
• Nucleic Acids- structure and function
• DNA coloring, reading, and questions

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Bellwork
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Lipids

• Fats are constructed from two types of smaller
  molecules, a single glycerol and usually three
  fatty acids.
• How do the C, H, O
• Ratios compare to
• carbohydrates?
• Lots of C H
• A few O atoms

Figure 5.11
(b) Fat molecule (triacylglycerol)
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Lipids

• Fatty acids vary in the number and locations of
  double bonds they contain.
• Saturated- no double bonds
• Unsaturated- at least one double bond

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Lipids

• Saturated fatty acids
• Have the maximum number of hydrogen atoms
  possible
• saturated with hydrogen atoms
• Have no double bonds between carbon atoms

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Lipids

• Unsaturated fatty acids have one or more double
  bonds (unsaturated with hydrogen atoms)

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Phospholipids

• Phospholipids found in cell membranes.
• Have only two fatty acids (the hydrophobic
  tails).
• Have a phosphate group instead of a third fatty
  acid (the hydrophilic head).

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Phospholipids

• The structure of phospholipids results in a
  bilayer arrangement found in cell membranes.

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Steroids

• Steroids are lipids characterized by a carbon
  skeleton consisting of four fused rings.
• One steroid, cholesterol
• Is found in cell membranes
• Is a precursor for some hormones (like
  Testosterone)

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The Structure of Nucleic Acids

• Nucleic acids consist of monomers called
  nucleotides.
• Nitrogen base
• Pentose sugar
• 5 carbons
• Phosphate group
• Contain what elements?
• C, H, O, N, P
• Function
• carry the genetic code

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The Structure of Nucleic Acids

• Nucleic acids, therefore, exist as polymers
  called polynucleotides.

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The Structure of Nucleic Acids

• The nitrogenous bases
• Pyrimidines- Cytosine, Thymine (DNA), and Uracil
  (RNA)
• Purines - Adenine and Guanine

• Pyrimidines
• single ring

• Purines
• double ring

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The Structure of Nucleic Acids

• The Base Pair Rule
• In DNA,
• A pairs with T
• C pairs with G
• In RNA,
• A pairs with U
• C pairs with G

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The Structure of Nucleic Acids

• The pentose sugars
• Deoxyribose (in DNA)
• Ribose (in RNA)
• How do these two sugars differ in structure?

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The Structure of Nucleic Acids

• The DNA double helix consists of two antiparallel
  nucleotide strands.

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Nucleic Acids- Function

• DNA
• Transfers genetic material from one generation to
  the next
• Carries the code for proteins, which determine an
  organisms characteristics
• RNA
• Carry genetic information from the DNA in the
  nucleus to the ribosomes, where proteins are made

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5 Minute Writing

• What elements are found in carbohydrates and
  lipids? In proteins?
• What functional groups have we seen so far?
• What are some functions of proteins?

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Carbohydrates
Starch
Glucose
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Lipids
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Agenda- 10/02- Honors Biology

• Bellwork- none- quiz instead
• Proteins- structure and function (frameworks 1.2,
  1.3, 1.4)
• Organic molecules graphic organizer
• Water (if time)

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Proteins

• Functions
• Structural
• Can act as a biological catalyst to speed up
  chemical reactions (enzymes)
• Movement and transport
• Storage of amino acids
• And more!

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Proteins

• Proteins have many structures, resulting in a
  wide range of functions.

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Polypeptides

• Polypeptides are polymers of amino acids.
• A protein consists of one or more polypeptides.

A generalized amino acid
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Amino Acid Monomers

• Amino acids
• Organic molecules with both carboxyl (-COOH) and
  amino (-NH2) groups.
• They differ in their properties due to differing
  side chains, called R groups.

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Amino Acids
Amino group
Carboxyl group
General structure
Serine
Alanine
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Amino Acid Monomers

• 20 different amino acids make up proteins
• There are lots of different proteins made from
  those 20 amino acids (just like there are lots of
  words made from just 26 letters)

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Amino Acid Polymers

• Amino acids are linked by peptide bonds.
• Bond between carboxyl and amino groups
• Peptide bonds polypeptides

OH
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Amino Acids Proteins
Amino acids
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Sickle-Cell Disease is a simple change in primary
structure an amino acid substitution in
hemoglobin.
Fibers of abnormalhemoglobin deform cell into
sickle shape.
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Organic Macromolecules
Molecule Function Elements Monomer/ Subunits




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5 Minute Writing

• What do enzymes do?
• Why are enzymes important to cells?
• What does the equation below mean?
• 2 H2O2 2 H2O O2

catalase
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Agenda- 10/03- Honors Biology

• Bellwork
• Properties of water
• Water mini-lab
• Ticket to leave

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Water- a Polar Molecule

• Polar uneven sharing of electrons
• Results in a SLIGHT charge on each end of the
  molecule
• This leads to properties of water that are very
  important to living things

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Water Hydrogen Bonds

• Hydrogen bonding is responsible for many of
  waters properties.
• Cohesion attraction between molecules of the
  same substance (surface tension)

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Water Hydrogen Bonds

• Hydrogen bonding is responsible for many of
  waters unique properites
• Adhesion attraction between molecules of
  different substances (capillary action)

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Hydrogen Bonds in Ice

• Due to hydrogen bonding, ice is less dense than
  water, so it floats
• This is VERY unusual!! Most compounds are more
  dense in the solid form!

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• Dissociation of water
• Water molecule breaks apart into two ions of
  opposite charge
• H2O ? H (hydrogen ion) OH- (hydroxide ion)
• H H2O ? H3O (hydronium ion)

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Acids

• Number of hydrogen ions in solutions is greater
  than the number of hydroxide ions (pH lt 7)
• HCl ? H Cl-

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Bases

• Number of hydroxide ions in solution is greater
  than the number of hydrogen ions (pH gt 7)
• NaOH ? Na OH-

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pH Scale

• logarithmic scale comparing the concentrations of
  H and OH- ions in a solution
• ranges from 0 to 14
• 7 is neutral

• Each pH is 10X stronger than next
• e.g. ph 1 is 10 times stronger than pH 2

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Buffers

• Control of pH is very important
• Most enzymes function only within a very narrow
  pH
• Control is accomplished with buffers made by the
  body
• Buffers keep a neutral pH (pH 7)

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• Buffers neutralize small amounts of either an
  acid or base added to a solution
• Complex buffering systems maintain the pH values
  of your bodys many fluids at normal and safe
  levels

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Water a universal solvent

• Solution, solute, solvent
• Water can dissolve polar and ionic molecules and
  ions.

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Solutions

• A solution is a mixture in which 2 or more
  substances are uniformly distributed
• Aqueous solutions (water) are universally
  important to living things

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• Solute is the substance dissolved in the solution
• Solvent is the substance in which the solute is
  dissolved
• Water is the universal solvent

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Water Mini-Lab

• Go to each station (4)
• Read the scenario. Figure out a way to determine
  the properties of water.
• Any stations that arent finished today are
  homework (this is one of the few labs that can be
  done at home!)

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Agenda 10/06- Honors Biology

• Bellwork- next slide
• Enzyme structure and function
• Chemical Reactions
• Enzyme Lab
• HW- write a lab procedure to test the affect of
  temperature on enzyme activity

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Protein Conformation and Function

• A proteins specific conformation (shape)
  determines how it functions.
• Two models of protein
• conformation

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Four Levels of Protein Structure

1. Primary structure (1º)
2. Secondary structure (2º)
3. Tertiary structure (3º)
4. Quaternary structure (4º)

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Four Levels of Protein Structure

1. Primary structure is the unique sequence of amino
   acids in a polypeptide.

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• 2. Secondary structure is the folding or coiling
  of the polypeptide into a repeating configuration
  (due to hydrogen bonds).
• It includes the ? helix and the ? pleated sheet.

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• 3. Tertiary structure is the overall
  three-dimensional shape of a polypeptide due to
  attractions between alpha and beta helices.
• It results from interactions between amino acids
  and R groups.

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• 4. Quaternary structure is the overall protein
  structure that results from the aggregation of
  two or more polypeptide subunits.

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Quaternary structure is what determines a
proteins specific function.
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Energy and Chemical Reactions

• Living things undergo thousands of chemical
  reactions as part of the life process

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Chemical Reactions

• A process that changes one set of chemicals into
  another set of chemicals
• C6H12O6 6O2 6CO2 6H2O energy
• Reactants Products
• Chemical reactions involve breaking bonds in
  reactants and forming new bonds in products.

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• Most chemical reactions require energy to begin
• The amount of energy needed to start the reaction
  is called activation energy

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• Certain chemical substances (catalysts) reduce
  the amount of activation energy required
• Biological catalysts are called enzymes

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• Enzymes are an important class of catalysts in
  living organisms
• Mostly protein
• Thousands of different kinds
• Each specific for a different chemical reaction

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Enzyme Structure

• Enzymes work on substances called substrates
• Substrates must fit into a place on an enzyme
  called the active site
• Enzymes are reusable!

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Enzymes
4 Products are released.
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Enzymes

• Because of their shape, enzymes provide a more
  efficient site for a chemical reaction to occur.
• They DO NOT cause a reaction to occur- the
  reactions happen anyway, but MUCH more slowly.
• Enzymes increase the rate at which a chemical
  reaction takes place by reducing the activation
  energy.

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• When the physical or chemical nature of the
  environment of a protein changes, denaturation
  can occur.
• If this happens, a protein unravels and loses its
  shape, and therefore its function.

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• What are some specific physical or chemical
  changes that can occur in the environment of a
  protein?
• Alcohol
• pH
• Reducing agents
• Heat
• Heavy metals

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• What are some specific physical or chemical
  changes that can denature a protein?
• Alcohol
• pH
• Reducing agents
• Heat
• Heavy metals

Heat can remove all noncovalent bonds in a
protein H-Bonds, ionic bonds (salt bridges), van
der Waals forces.
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Pre-Lab

• Read the entire lab!
• Follow the steps of the pre-lab.
• Using the pre-lab technique, write a procedure
  you could use to test the effect of temperature
  on enzyme activity.
• This needs to be in a numbered, step-by-step
  list.