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1. Subatomic particles and compounds.
2. Water and some important properties
3. pH scale
4. Carbon chemistry, alkanes
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• Essential elements of life.• Subatomic
particles of an atom.• Compounds.
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(a) Nitrogen deficiency(b) Iodine deficiency
(Goiter)
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Simplified models of an Atom
4
Nucleus
(a) (b)
In this even more simplifiedmodel, the electrons areshown as two small bluespheres on a circle around thenucleus.
Cloud of negativecharge (2 electrons)
Electrons
This model represents theelectrons as a cloud ofnegative charge, as if we hadtaken many snapshots of the 2electrons over time, with eachdot representing an electron‘sposition at one point in time.
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• H2O: H atoms partial (+) charge, O atoms partial (-) charge. Water is POLAR, and attracts other polar molecules.
• Polarity allows water to form weak H bonds with other polar substances…this is what makes H20 a great solvent.
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 more toward oxygen.
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Van der Waals Interactions
– Occur when transiently positive and negative regions of molecules attract each other
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Hydrogenbond
–
+
+ +
+
–
– –
H
HO
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Liquid water:transient hydrogenbonds
Ice: stable hydrogen bonds
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• Cohesion- tendency of molecules to stick together. Ex: H20 evap. from a leaf.
• Adhesion- tendency to stick to other substances.
• Capillary Action• High Specific Heat-Is the amount of heat
that must be absorbed or lost for 1 gram of that substance to change its temperature by 1ºC
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• Water moderates air temperatureWater moderates air temperature• By absorbing heat from air that is warmer By absorbing heat from air that is warmer
and releasing the stored heat to air that is and releasing the stored heat to air that is coolercooler
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• Water has a high specific heat which allows Water has a high specific heat which allows it to minimize temperature fluctuations to it to minimize temperature fluctuations to within limits that permit lifewithin limits that permit life– Heat is absorbed when hydrogen bonds Heat is absorbed when hydrogen bonds
breakbreak– Heat is released when hydrogen bonds Heat is released when hydrogen bonds
formform
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Acids and Bases
• Dissociation of water molecules leads to acidic and basic conditions that affect living organisms
• Organisms must maintain homeostasis in the pH of their internal and external environments
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Effects of Changes in pH• Water can dissociate Into hydronium ions
(H+ or H3O+) and hydroxide (OH-) ions• Changes in the concentration of these ions
Can have a great affect on pH in living organisms
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H
Hydroniumion (H3O+)
H
Hydroxideion (OH–)
H
H
H
H
H
H
+ –
+
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• 1-14• Towards pH of 1= Acidic.• Towards pH of 14 = Basic (alkaline)• pH of 7 = neutral.• Acids have a higher concentration of H+
ions, bases have a higher concentration of OH- ions. (Hydroxide)
• Difference of strength of 5 to 4, etc. (10x) ….ie: diff of 3 to 6 is?
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• Covalent: sharing of electrons; compounds held together by the sharing.
• Ionic: taking of electrons; compounds held together by oppositely charged ions.
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Covalent Bonding• A molecule
– Consists of two or more atoms held together by covalent bonds
• A single bond– Is the sharing of one pair of valence
electrons
• A double bond– Is the sharing of two pairs of valence
electrons
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Biological molecules recognize and interact with each other with a specificity based on molecular shape
Molecules with similar shapes can have similar biological effects
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(a) Structures of endorphin and morphine
(b) Binding to endorphin receptors
Naturalendorphin
Endorphinreceptors
Morphine
Brain cell
Morphine
Natural endorphin
KeyCarbonHydrogen
NitrogenSulfurOxygen
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• Six elements essential to life?• Covalent vs. Ionic bond?• Why is water a POLAR molecule?• Cohesion vs. Adhesion?• pH scaled• Chemical vs. Structural formula
• Carbon chemistry
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• Carboxyl Group• Amino Group• Hydroxide Group• Carbonyl Group• Sulfhydryl Group• Phosphate Group
NH2
OH
COOH
C=O
S-H
PO4
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Fig. 4-10c
STRUCTURE
EXAMPLE
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Carboxyl
Acetic acid, which gives vinegar its sour taste
Carboxylic acids, or organic acids
Has acidic propertiesbecause the covalent bond between oxygen and hydrogen is so polar; for example,
Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion).
Acetic acid Acetate ion
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Fig. 4-10d
STRUCTURE
EXAMPLE
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Amino
Because it also has a carboxyl group, glycine is both an amine anda carboxylic acid; compounds with both groups are called amino acids.
Amines
Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms).
Ionized, with a charge of 1+, under cellular conditions.
(ionized)(nonionized)
Glycine
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Fig. 4-10e
STRUCTURE
EXAMPLE
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Sulfhydryl
(may be written HS—)
Cysteine
Cysteine is an important sulfur-containing amino acid.
Thiols
Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure.
Cross-linking ofcysteines in hairproteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breakingand re-forming thecross-linking bonds.
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Fig. 4-10f
STRUCTURE
EXAMPLE
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Phosphate
In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes.
Glycerol phosphate
Organic phosphates
Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates).
Has the potential to react with water, releasing energy.
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Fig. 4-10g
STRUCTURE
EXAMPLE
NAME OFCOMPOUND
FUNCTIONALPROPERTIES
Methyl
5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group.
5-Methyl cytidine
Methylated compounds
Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes.
Arrangement of methyl groups in male and female sex hormones affectstheir shape and function.
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GENERAL TERMINOLOGY:
•Monomer(S)•Polymer(S)•Isomer(s)
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