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Atoms
Atomic mass:
Sum of protons and neutrons.
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Atoms
Atomic Number
Number of protons in an atom
Neutral atom
Number of protons = number of electrons
Isotopes
Vary in number of neutrons
Same in atomic number
Vary in atomic mass
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Atoms
Chemical element
Includes all of the isotopic forms of a given
atom
Eg: Element Hydrogen: 3 isotopes
Most common: one proton
Deuterium: one proton, one neutron
Tritium: one proton, two neutrons
Commonly used in research
106 chemical elements
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Elements
Atoms
Orbitals
Chemical bonds:
Interaction of valence electrons
between 2 or more atoms.
# bonds determined by # electrons
needed to complete outer orbital.
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Covalent Bonds
H2
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Covalent Bonds
Polar bonds:
Electrons are shared between two
different atoms.
Electrons may be pulled more toward
more atom.
Oxygen, nitrogen, phosphate pull
Ionic Bonds
Ionic Bonds
(–)
(+)
Na + Cl NaCl
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11p 17p
12n 18n
Na + Cl
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11p 17p
12n 18n
Na + Cl
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11p 17p
12n 18n
Na + Cl
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11p 17p
12n 18n
Na + Cl
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(+) (–)
11p 17p
12n 18n
Na + Cl
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(+) (–)
11p 17p
12n 18n
NaCl
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Hydrophilic:
Formation of hydration spheres.
Polar covalent bonds.
Hydrophobic:
Cannot form hydration spheres.
Nonpolar covalent bonds.
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Hydrogen Bond
Hydrogen forms a
polar bond with
another atom,
hydrogen has a
slight + charge.
Weak attraction
for for a second
electronegative
atom.
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Acid:
Molecule that can release protons (H+).
Proton donor.
Base:
Negatively charged ion that can combine
with H+.
Proton acceptor.
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pH
pH = log _1__
[H+]
Normal pH blood = 7.35 - 7.45.
Buffer:
System of molecules and ions that
act to prevent changes in [H+].
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Organic Molecules
Organic Molecules
Organic Chemistry: deals with
molecules that contain carbon
More than 5 million organic compounds
have been identified
The carbon atom can form bonds with a
greater number of different elements
than any other type of atom
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Functional Groups
Inactive “backbone” to which more
reactive atoms are attached.
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Classes According to
Functional Groups
Ketone and
aldehyde: carbonyl
group
Organic acid:
carboxyl group
Alcohol: hydroxyl
group
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Stereoisomers
Lipids
GR: Lipos=Fat
Diverse group of molecules.
Insoluble in polar solvents (H20).
Hydrophobic (nonpolar)
Consist primarily of hydrocarbon
chains and rings.
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Lipids
Hydrocarbons
Fatty acids
Triglycerides
Ketone Bodies
Phospholipids
Steroids
Prostaglandins
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Hydrocarbons
Fatty acids
Triglycerides
Formed by condensation of glycerol and 3
fatty acids.
Ester bond
Fatty acid consists of hydrocarbon chain with
carboxylic acid end.
May be saturated or unsaturated
Saturated fats:
Mostly animal sources
Mostly solid at room temperature
Unsaturated fats
Mostly plant sources
Mostly liquid at room temperature
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Nutritional considerations
of triglycerides
Also called fat or neutral fat
Stored in adipose cells
Total fat intake should be about 30% of
total energy intake
Saturated fat >10%
Saturated fats are implicated in heart
disease and stroke
Data suggests they promote high blood
cholesterol
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Phospholipids
A number of categories
All contain a phosphate group
Most common
Glycerol (3 carbons)
Fatty Acids on carbon 1 and 2
Phosphate group attached to carbon (and
other polar groups eg.: choline)
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Lecithin
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Phospholipid
Phospholipids
Micelle formation
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Ketone Bodies
Results from the hydrolysis of
triglycerides by adipocytes
Liberates free FA into blood
FA function as an acid in blood
Most FA used as energy source by some
tissues
If not, converted by liver into Ketone
bodies
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Ketone Bodies
4-carbon chunks
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Ketone Bodies
Produced in the rapid breakdown of FA
Low-carbohydrate diets
Uncontrolled Diabetes mellitus
Ketosis: Elevated level of FA in blood
Ketoacidosis: ketosis is high enough to
lower blood ph
Can cause coma, death
Filtered by the kidney
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Steroids
Nonpolar and insoluble in H20.
All have cholesterol as precursor.
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Prostaglandins
Prostaglandins:
Fatty acid with cyclic hydrocarbon
group.
Derived from arachidonic acid.
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Prostaglandins
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Carbohydrates
Carbohydrates
Supply energy
Glucose
Complex carbohydrates
Provide structural support
cellulose
Part of plasma membrane
Monomer: monosaccarides
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Carbohydrates
Monosaccharide: the “simple sugars”
Pentoses (5-carbons):
Ribose: in RNA
Deoxyribose: in DNA
Hexoses (6-carbons):structural isomers
Glucose, fructose and galactose
Characteristics
Soluable
Sweet
Alcoholic fermentation
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Glucose
Also called :
Dextrose
Transportable in the blood
Blood glucose
C6H12O6
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Fructose
Fruit sugar
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Galactose
C6H12O6
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Carbohydrates
Disaccharide:
2 monosaccharides joined covalently.
Sucrose
Glucose and fructose
Maltose
Glucose and glucose
Lactose
Glucose and galactose
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Disaccharides
Characteristics
Sweet
Soluable
Can be fermented
Formation: called condensation
Requires an enzyme
Removal of molecule of water
Also called dehydration synthesis
Formation of a covalent bond
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Formation of Disaccharides
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Hydrolysis
Reverse of dehydration synthesis.
Digestion reaction.
H20 molecule split.
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Carbohydrates
Polysaccharides:
Many monosaccharides joined covalently.
General formula: (C6H10O5)n
Characteristics:
Devoid of taste
Do not form solutions
Iodine test
Iodine +starch+blue
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Polysaccarides
Kinds:
Starch
Glucose subunits
branched
Dextrins
Glycogen (animal starch)
Glucose subunits
Branched
Cellulose
Glucose subunits
Long, unbranched chains
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Proteins
General Information:
GR: proteios=first rank
~50% of the organic material of the
body
Functions
Structural:
Cell structures, CTs
Functional:
Enzymes, hormones, Hb, etc!
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Proteins
Protein Structure
Large molecules (polymers)
composed of amino acid sub-units
(monomers).
Amino Acid structure
H
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Proteins
20 different standard amino acids.
Based on the properties of the
functional group
E.g.:
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Proteins
Dehydration synthesis:
Amino end of one amino acid
combines with hydroxyl group of
carboxylic end of another amino acid.
Peptide bond:
Bond between two adjacent amino
acids.
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Peptide bond
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Proteins
Dipeptide: 2 amino acids
Tripeptide: 3 amino acids
Polypeptide: many amino acids
Number of amino acids varies
Up to 100 aa
Protein
Over 100aa
Great variety!
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Protein structure
Four structural levels
Primary structure
Based on amino acid sequence
Amino acid sequence determined by DNA
Secondary structure
Based on hydrogen bonding between close aa
Tertiery structure
3-D shape
Quaternary structure
Only in proteins with 2 or more polypeptide
chains
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Secondary structures
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Tertitary structure
Tertiary structure
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Quaternary Structure
Number of
polypeptide
chains
covalently
linked
together.
Insulin,
hemoglobin
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Conjugated proteins
Protein combined with another type of
molecule
Glycoproteins: carbohydrate with protein
Membranes, hormone
Lipoproteins: Lipid and protein
Membranes, blood plasma
Hemoproteins: iron and protein
Hemoglobin, cytochromes
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Nucleic Acids
Nucleic Acids
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Nucleotides
Structure of a nucleotide: 3 subunits
Pentose sugar
Phosphate group
Nitrogenous base
Purines: two rings
Guanine
Adenine
Pyrimidines: one ring
Cytosine
Thymine
Uricil
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Nucleotide Structure
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Nitrogenous Bases
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DNA
Huge molecules with simple structure
Big time data storage!
Structure
Nucleotides
Pentose sugar: Deoxyribose
Bases:
Purines: G and A
Pyrimidines: C and T
Form double-stranded helix
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DNA
Nucleotide strands: 2
Sugar-phosphate backbone
Bases stick out
Bases bond to each other
Base pairing:
A–T
G–C
Called law of complementary base pairing
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Nitrogenous Bases
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DNA
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RNA
Means by which DNA directs cellular activities
Structure
Pentose sugar: ribose
Bases: uracil (not thymine)
Single stranded
Three main types
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
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DNA vs RNA