honors biology ch. 6 chemistry in biology. i.atoms, elements, and bonding -living and nonliving...
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HonorsBiology Ch. 6
HonorsBiology Ch. 6
Chemistry in Biology
Chemistry in Biology
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I. Atoms, Elements, and Bonding
I. Atoms, Elements, and Bonding
- Living and nonliving things are made of atoms.
A.A.ElementElement- pure substance of only 1
type of atom- 98 natural elements- CHNOPS
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The Size of Cells and Their Components
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B. AtomsB. Atoms- smallest unit of matter
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Atomic ModelsAtomic Models
Hydrogen (H) Helium (He)
Nucleus
ElectronElectronShellShell
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B. AtomsB. Atoms- smallest unit of matter
1. Nucleus contains:Charge
Mass - Protonspositive 1
- Neutrons neutral1
2. Electrons negative0
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C. IsotopesC. IsotopesC. IsotopesC. Isotopes- forms of an element with varying
number of neutrons- 12C vs. 14C
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D.D. Compounds and Compounds and BondingBonding
D.D. Compounds and Compounds and BondingBonding- 2 or more elements chemically
bonded1.Covalent Bonds:
- attraction due to shared electrons- ex. water
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Water Is CovalentElectron pair forms covalent bond
Each spends some time w/one, then the other atom
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Oxygen Molecule (O2)Oxygen Molecule (O2)
Oxygen Atom Oxygen Atom
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2.2. Ionic Bonds:Ionic Bonds:2.2. Ionic Bonds:Ionic Bonds:- attraction due to electrons
transferred from one atom to another creating + and - ions
- ex. table salt (NaCl)
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Ionic Bonding in NaClIonic Bonding in NaCl
Sodium can lose 1 electron; Chlorine can gain 1 electron. Sodium becomes a positive ion; Chlorine a negative ion.
Sodium has 1 electron in outer shell;
chlorine has 7.
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Ionic Bonding in NaClIonic Bonding in NaCl
ClCl-- ClCl-- ClCl-- ClCl--
ClCl-- ClCl-- ClCl-- ClCl--
ClCl-- ClCl-- ClCl-- ClCl--
ClCl-- ClCl-- ClCl-- ClCl--
NaNa++ NaNa++ NaNa++
NaNa++ NaNa++ NaNa++
NaNa++ NaNa++ NaNa++
NaNa++
NaNa++
NaNa++
NaNa++ NaNa++ NaNa++ NaNa++
Opposites attract.
Sodiums nestle between chlorines.
Perfectly cubical crystals.
ClCl-- ClCl-- ClCl-- ClCl--
ClCl-- ClCl-- ClCl-- ClCl--
ClCl-- ClCl-- ClCl-- ClCl--
ClCl-- ClCl-- ClCl-- ClCl--
NaNa++ NaNa++ NaNa++
NaNa++ NaNa++ NaNa++
NaNa++ NaNa++ NaNa++
NaNa++
NaNa++
NaNa++
NaNa++ NaNa++ NaNa++ NaNa++
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Some Elements Are Molecular.
Some Elements Are Molecular.
Hydrogen gasOne electron from each hydrogen atom is shared, forming a single covalent bond
Oxygen gasTwo oxygen atoms share four electrons, forming a double bond
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E. Acids, Bases, and pHE. Acids, Bases, and pH1.Acids:
- form H+ ions in solution2.Bases:
- form OH- (hydroxide) ions in solution
3.pH:- measure of how acidic or
basic a solution is- logarithmic scale
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The pH ScaleThe pH Scale
NeutralNeutralpHpH++ = pOH = pOH––
Increasingly AcidicIncreasingly Acidic Increasingly BasicIncreasingly Basic
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14Water
LemonJuice
LimeJuice
StomachAcid
Orange Juice
Coffee
Urine
Vinegar
Blood
SeaWater
BakingSoda
Bleach
Ammonia
OvenCleaner
Hand Soap
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Universal pH Indicator
Universal pH Indicator
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II. WaterII. WaterA.A.Water Is PolarWater Is Polar - water molecules have
positive and negative ends
This results in a partial negative charge on theoxygen and apartial positivecharge onthe hydrogens.
H2O
–
O
H H+ +
Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled closer to oxygen.
Polar Covalent Bonds in a Water Molecule
Polar Covalent Bonds in a Water Molecule
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II. WaterII. Water
Hydrogenbonds
+
+
H
H+
+
–
–
––
Hydrogen Bonds between Water Molecules
Hydrogen Bonds between Water Molecules
A.A.Water Is PolarWater Is Polar - hydrogen bonds form
between water molecules
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A.Water Is PolarA.Water Is Polar- polarity gives special properties
OO
OO
HH
HH
HHHH
++
++
++
––
––
++
++
Hydrogen Bonds
Hydrogen Bonds
How Polarity Makes Water Behave Strangely (3:52)
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- solvent of life
Negative oxygen regions of polar water molecules are attracted to sodium
ions (Na+). +
+
+
+Cl –
–
–
–
–
Na+
Positive hydrogen regions
of polar water molecules cling to chloride ions (Cl–).
+
+
+
+
–
–
–
–
–
–Na+
Cl–
A Crystal of Table Salt Dissolving in Water
A Crystal of Table Salt Dissolving in Water
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- strong cohesion and adhesionWater surface tension
Water is transported great heights up the stem.
Water conducting cells
100 µm
Cohesion among Water MoleculesCohesion among Water Molecules
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- strong cohesion and adhesion
Meniscus
Meniscus Capillarit
yCapillarit
y
Adhesion among Water Molecules
Adhesion among Water Molecules
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- high specific heat- good evaporative coolant
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- less dense when frozen
Liquid waterHydrogen bonds
constantly break and re-form
IceHydrogen bonds are stable
Hydrogenbond
Ice: Crystalline Structure and Floating
Barrier
Ice: Crystalline Structure and Floating
Barrier
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III. Organic CompoundsIII. Organic Compounds - Living organisms are made up of
organic compounds.
A.Major Differences Between:Living vs.Nonliving
Systems Systems
complex simplecompounds compoundshigh energy low energy
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- All organic compounds contain carbon.- Exceptions: CO2, CO, CaCO3
- Carbon can form 4 covalent bonds.
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- Carbon based molecules form chains, branched chains, rings, etc.
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Chlorophyll AChlorophyll A Chlorophyll BChlorophyll B
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Buckminsterfullerene
Buckminsterfullerene
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B. 4 Classes of Organic Compounds:
B. 4 Classes of Organic Compounds:1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic Acids
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IV. CarbohydratesIV. Carbohydrates- contain C, H, O (1:2:1) - include sugars, starches, cellulose - used for energy storage and to
build cell walls - names usually end in "-ose"
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A. Monosaccharides:A. Monosaccharides:- single (simple) sugar
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A. Monosaccharides:A. Monosaccharides:- single (simple) sugar - C6H12O6, C5H10O5
- ex. glucose (source of energy in cells), fructose (fruit sugar), galactose
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B.Disaccharides:B.Disaccharides:- double sugar
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B.Disaccharides:B.Disaccharides:- double sugar - C12H22O11
- ex. sucrose (table sugar), lactose (milk sugar)
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C. Polysaccharides :C. Polysaccharides :
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C. PolysaccharidesC. Polysaccharides- many sugars1. Starch
- Made of many 10 - 1000 glucose molecules
- in plants (potatoes, grains) - Glycogen: animal starch
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Storage polysaccharides of plants and animals
Storage polysaccharides of plants and animals
Mitochondria Glycogen granules
Chloroplast
Starch
AmyloseAmylopectin
1 m
0.5 m
Starch: a plant polysaccharideGlycogen: an animal polysaccharide
Glycogen
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2. Cellulose:2. Cellulose:
- long starch chains bonded side by side
- very strong - found in the plant cell walls
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The Arrangement of Cellulose in Plant Cell
Walls
The Arrangement of Cellulose in Plant Cell
Walls
Cellulosemolecules
Plant cells
0.5 m
Cell walls
Cellulose microfibrils in a plant cell wall
Microfibril
CH2OH
CH2OH
OH
OH
OO
OHOCH2OH
OO
OHO
CH2OH OH
OH OHO
O
CH2OH
OO
OH
CH2OH
OO
OH
O
O
CH2OHOH
CH2OHOHOOH OH OH OH
O
OH OH
CH2OH
CH2OH
OHO
OH CH2OH
OO
OH CH2OH
OH
Glucose monome
r
O
O
O
O
O
O
Parallel cellulose molecules areheld together by hydrogen
bonds between hydroxylgroups attached to carbon
atoms 3 and 6.
About 80 cellulosemolecules associateto form a microfibril, themain architectural unitof the plant cell wall.
A cellulose moleculeis an unbranched glucose polymer.
OH
OH
O
OOH
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Starch and Cellulose Structures
Starch and Cellulose Structures
Cellulose: 1– 4 linkage of glucose monomers
H O
O
CH2OH
HOH H
H
OH
OHH
H
HO
4
C
C
C
C
C
C
H
H
H
HO
OH
H
OH
OH
OH
H
O
CH2OH
HH
H
OH
OHH
H
HO
4 OH
CH2OH
O
OH
OH
HO41
O
CH2OH
O
OH
OH
O
CH2OH
O
OH
OH
CH2OH
O
OH
OH
O O
CH2OH
O
OH
OH
HO4
O1
OH
O
OH OHO
CH2OH
O
OH
O OH
O
OH
OH
and glucose ring structures
Starch: 1– 4 linkage of glucose monomers
1
glucose glucose
CH2OH
CH2OH
1 4 41 1
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V. LipidsV. Lipids- fats, oils, waxes, steroids - not soluble in water - more energy (calories) in lipids
than in carbohydrates- energy storage, insulation, cell
membrane, coatings, and many hormones
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Triglycerides
Triglycerides
GlycerolGlycerol
3 Fatty Acids .
3 Fatty Acids .
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Lipid Structure Lipid Structure
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Animal fat
Animal fat
Vegetable oil
Vegetable oil
Saturated vs. UnsaturatedFatty Acids
Saturated vs. UnsaturatedFatty Acids
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Carcinogenic
Carcinogenic
‘Natural’‘Natural’
What Are Trans Fatty Acids?
What Are Trans Fatty Acids?
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Phospholipid Bilayer
Phospholipid Bilayer
Cell MembraneCell Membrane
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Steroids
Steroids
CholesterolCholesterol
EstradiolEstradiol Testosterone
Testosterone
Progesterone
Progesterone
AldosteroneAldosteroneCortisolCortisol
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VI. Proteins:VI. Proteins:- the most abundant and varied of
organic compounds- contain C, H, N, O (S)
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A. Types of ProteinA. Types of Protein1.Structural:
- keratin (hair, fingernails)- collagen
2.Contractile:- actin and myosin (muscle)
3.Pigments:- melanin (in skin, hair, iris)
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4.Hormones:- regulate body functions (insulin)
5.Antibodies:- fight disease
6.Enzymes:- amylase (in saliva), lactase
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B. Structure of ProteinsB. Structure of Proteins- very complex
1. Amino Acids- building blocks of proteins
- 20 different amino acids- proteins contain between
50 - 2000 amino acids
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2. Peptide Bond2. Peptide Bond- joins 2 amino acids - polypeptide: many amino acids
Peptide Bond
Peptide Bond
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3. Levels of Protein Structure3. Levels of Protein Structure
Primary Structur
e
Primary Structur
e
Secondary
Structure
Secondary
Structure
Tertiary Structur
e
Tertiary Structur
e
Quaternary
Structure
Quaternary
Structure
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3. Levels of Protein Structure3. Levels of Protein Structurea) Primary Structure:
- sequence of amino acids
b) Secondary Structure:- helix or pleated sheet
c) Tertiary Structure:- amino acids interact to form the polypeptide into a 3 dimension shape
d)Quaternary Structure:- 2 or more tertiary polypeptides
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C. Enzymes C. Enzymes - protein catalysts- speed up chemical reactions- each enzyme catalyzes only one
specific substrate- most function at a specific
temperature and pH
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C. Enzymes C. Enzymes
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C. Enzymes C. Enzymes
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VII. Nucleic AcidsVII. Nucleic Acids- 2 major types:
A.DNA- contains
hereditary information (genes) - double helix
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VII. Nucleic AcidsVII. Nucleic Acids- 2 major types:
A.DNA- contains hereditary
information (genes) - double helix
B. RNA- controls protein synthesis - single helix
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Information Flow:
Information Flow:
DNA
RNA
Protein
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TheTheTheThe
EndEndEndEnd
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ƒ2-6Chapter
2 65
NaCl Dissolved by WaterNaCl Dissolved by Water
NaCl is ionicly bonded
NaCl is ionicly bonded
Water is polar and charged
Water is polar and charged
O sticks to Na+
O sticks to Na+
H sticks to Cl-
H sticks to Cl-
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Universal pH Indicator
Universal pH Indicator
pH 4.0
pH 5.0
pH 6.0
pH 7.0
pH 8.0
pH 9.0
pH 10.0
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Information Flow:Information Flow:DNA RNA ProteinDNA RNA Protein