raw materials and fuel for our bodies i. atoms and...
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• Problem Set #1 will be posted on website tomorrow. • http://www.biology.ucsd.edu/classes/bild10.WI14 • Answers will be posted next Friday. • No Sections or Office Hours this week. Please attend the section of your choice next week and sign in.
Chapter 2: Chemistry
Raw materials and fuel for our bodies
Lecture 2 Outline
I. Atoms and Bonds II. Water III. Acids, Bases, and Buffers IV. Chemistry of Carbon V. Carbohydrates VI. Lipids VII. Proteins VIII. Nucleic Acids
Everything is made of atoms.
q An element is a substance that cannot be broken down chemically into any other substances.
q An atom is a bit of
matter that cannot be subdivided any further without losing its essential properties.
I. Atoms and Bonds
2
Atomic Structure Atomic Numbers
Insert new figure 2.3
25 Elements Found in Your Body and the Big 4
2.2 An atom’s electrons determine how (and whether) the atom will bond with other atoms.
Electron shells
3
Electron Shells
Insert new fig 2-6 Products of bonding!
Molecules
Covalent Bonds
Insert fig 2-9 to right side of slide
Ions and Ionic Bonds
Insert fig 2-10
4
Hydrogen Bonds
Insert fig 2-11
Insert fig 2-12
II. Water
• H20 is a polar molecule attracted to itself. This is the critical factor for all of water’s most important properties.
• Most important molecule for life on Earth.
• Life began in water and evolved here for 3 Billion years before spreading to land.
• Our cells are 70-95% water; we can only survive for 1 week without water.
Properties of Water:
• ICE FLOATS: Solid H20 is ~10% less dense than liquid form. This unusual feature results in a crystal-like matrix of H20 molecules in ice. Insulates water underneath.
• COHESION: Water molecules stay close together due to hydrogen bonding.
• HIGH SPECIFIC HEAT: A great deal of energy is required to break H-bonds to release/vaporize individual molecules.
• EVAPORATIVE COOLING: H20 molecules with highest energy leave water reservoir as vapor, lowering the T of remaining liquid.
• EXCELLENT SOLVENT: Dissolves polar, nonpolar substances and salts.
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2.4 Hydrogen bonds make water cohesive.
Insert fig 2-13
Cohesion
Heat Capacity
6
Why do coastal areas have milder, less variable climates than inland areas?
Low Density as a Solid
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A water-soluble protein
This oxygen is attracted to a slight positive charge on the lysozyme molecule.
This hydrogen is attracted to a slight negative charge on the lysozyme molecule.
(a) Lysozyme molecule in a nonaqueous environment
(b) Lysozyme molecule (purple) in an aqueous environment such as tears or saliva
(c) Ionic and polar regions on the protein’s Surface attract water molecules.
δ+ δ–
7
2.6 Living systems are highly sensitive to acidic and basic conditions.
III. Acids, Bases, and Buffers
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Hydrogen Ions and Hydroxide Ions
Ionized Hydroxide Molecule
OH -
Non-Ionized Water Molecule
H2O O O
H H H
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pH Scale
q The amount of H+ in a solution is a measure of its acidity and is called pH.
q Acids
q Bases
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Blood pH
q Buffers
• can quickly absorb excess H+ ions to keep a solution from becoming too acidic
• can quickly release H+ ions to counteract any increases in OH- concentration
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Four Types of Macromolecules
q Carbohydrates
q Lipids
q Proteins
q Nucleic acids
MACROMOLECULES
IV. Chemistry of Carbon • Whereas H2O is the universal medium for life, C makes up the majority of the cell’s structures. • The C in our bodies ultimately derives from the action of plants. Plants harness the power of sunlight to convert CO2 into Carbon-based macromolecules.
IV. Chemistry of Carbon, ...
Organic Chemistry: The study of carbon compounds Organic compounds range from simple structures to huge macromolecules:
Plant cells 0.5 µm
Cell walls Cellulose
microfibrils in a plant cell wall
∩ Microfibril
CH2OH
CH2OH OH
OH
O O OH O CH2OH O
O OH
O CH2OH OH
OH OH O
O
CH2OH O
O OH
CH2OH O
O OH
O
O
CH2OH OH CH2OH OH
O OH OH OH OH
O
OH OH CH2OH
CH2OH OH O
OH CH2OH O
O
OH CH2OH OH
β Glucose monomer
O
O
O
O O
O
Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl
groups attached to carbon atoms 3 and 6.
About 80 cellulose molecules associate
to form a microfibril, the main architectural unit of the plant cell wall.
A cellulose molecule is an unbranched β glucose polymer.
OH
OH
O
O OH
Cellulose molecules
Methane
CH4
9
IV. Chemistry of Carbon, ...
• With a VALENCE (# of covalent bonds an atom can form) of 4, carbon is able to simultaneously bond to 4 other elements. This is key to the formation of complex macromolecules.
H O N C
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4)
• This electron configuration gives it covalent compatibility with many different elements.
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• The bonding versatility of carbon
– Allows it to form many diverse molecules, including carbon skeletons
(a) Methane
(b) Ethane
(c) Ethene (ethylene)
Molecular Formula
Structural Formula
Ball-and-Stick Model
Space-Filling Model
H H
H H
H H
H H
H H
H H H H
C
C C
C C
CH4
C2H6
C2H4
Name and Comments
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Molecular Diversity Arising from Carbon Skeleton Variation
• Carbon chains
– Form the skeletons of most organic molecules
– Vary in length and shape
H H H
H H
H H H
H H
H
H H H
H H H H H
H
H
H
H
H
H
H H
H H H H H
H H H H
H H H H
H H
H H
H H H H H
H H
C C C C C
C C C C C C C
C C C C C C C C
C
C C
C C
C
C
C C C
C C
H
H
H
H H H
H
(a) Length
(b) Branching
(c) Double bonds
(d) Rings
Ethane Propane
Butane 2-methylpropane (commonly called isobutane)
1-Butene 2-Butene
Cyclohexane Benzene
H H H H H
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Hydrocarbons
• Molecules consisting of Carbon and Hydrogen.
(a) A fat molecule (b) Mammalian adipose cells 100 µm
Fat droplets (stained red)
• Found in many of the cell’s organic molecules. • Store a great deal of potential energy in their many bonds.
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I. Chemistry of Carbon, ...
• The diversity of products that C can form is due to:
1) Endless geometries possible due to its valency
2) Its ability to bond to a wide variety of functional groups.
• Functional groups are the parts of molecules involved in chemical reactions.
MACROMOLECULES,...
Polymers • Four main classes of biological macromolecules:
Monomers: 1) CARBOHYDRATES (Polysaccharides) SUGARS
2) (LIPIDS - Make up membranes) Glycerol / FAs
3) PROTEINS - Enzymes, etc. Amino Acids
4) Nucleic Acids - DNA, RNA Nucleotides
MACROMOLECULES,...
V. Carbohydrates • Polysaccharides = sugar polymers = (CH2O)n • CH2O = basic formula for Monosaccharides
• Simplest Sugars • Can be used for fuel, converted into other
organic molecules or combined into polymers • Two major purposes of carbohydrates: 1) Store energy (Glycogen in animals; Starch in plants)
2) Provide structural support (Cellulose in plants; Chitin in insects, crustaceans)
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Carbohydrates
q C, H, and O
q Primary fuel for organisms
q Cell structure
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Glucose
q Most carbohydrates— ultimately converted into glucose
q Blood sugar
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Chloroplast Starch
Amylose Amylopectin
1 µm
Starch: a plant polysaccharide
Storage Polysaccharides • STARCH: Comprised entirely of Glucose monomers and is the major form of energy storage in plants
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Mitochondria Giycogen granules
0.5 µm
Glycogen: an animal polysaccharide
Glycogen
Storage Polysaccharides,...
• GLYCOGEN: Comprised entirely of Glucose monomers and is the major form of energy storage in animals.
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Cellulose
Plant cells 0.5 µm
Cell walls Cellulose microfibrils
in a plant cell wall
∩ Microfibril
CH2OH
CH2OH OH
OH
O O
OH O CH2OH
O O
OH O
CH2OH OH
OH OH O
O
CH2OH O
O OH
CH2OH
O O
OH
O
O
CH2OH OH
CH2OH OH O OH OH OH OH
O
OH OH
CH2OH
CH2OH OH
O
OH CH2OH
O O
OH CH2OH OH
β Glucose monomer
O
O
O
O
O
O
Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl
groups attached to carbon atoms 3 and 6.
About 80 cellulose molecules associate
to form a microfibril, the main architectural unit of the plant cell wall.
A cellulose molecule is an unbranched β glucose polymer.
OH
OH
O
O OH
Cellulose molecules
– Is a major component of the tough walls that enclose plant cells
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Cellulose, ...
• Not digestible by humans. Cows and termites possess symbiotic bacteria that break down cellulose into glucose monomers for energy utilization by their hosts.
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Structural Polysaccharides
• CELLULOSE: Also made with Glucose monomers BUT uses Glucose enantiomer.
(c) Cellulose: 1– 4 linkage of β glucose monomers
H O
O
CH2OH
H OH H
H
OH OH H
H
HO 4
C
C
C
C
C
C
H
H
H
HO
OH
H
OH
OH
OH
H
O
CH2OH
H H
H
OH
OH H
H
HO 4 OH
CH2OH
O
OH
OH
HO 4 1
O
CH2OH
O
OH
OH
O
CH2OH
O
OH
OH
CH2OH
O
OH
OH
O O
CH2OH
O
OH
OH
HO 4 O 1
OH
O
OH OH O
CH2OH
O
OH
O OH
O
OH
OH
(a) α and β glucose ring structures
(b) Starch: 1– 4 linkage of α glucose monomers
1
α glucose β glucose
CH2OH
CH2OH
1 4 4 1 1 • STARCH: all monomers “right-side up”.
• CELLULOSE: every other monomer is upside down.
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• another important structural polysaccharide
– Is found in the exoskeleton of arthropods
– Can be used as surgical thread
(a) The structure of the chitin monomer.
O
CH2OH
OH H
H OH
H
NH
C
CH3
O
H
H
(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging
in adult form.
(c) Chitin is used to make a strong and flexible surgical
thread that decomposes after the wound or incision heals.
OH
Chitin
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MACROMOLECULES,...
Polymers • Four main classes of biological macromolecules:
Monomers: 1) CARBOHYDRATES (Polysaccharides) SUGARS
2) (LIPIDS - Make up membranes) Glycerol / FAs
3) PROTEINS - Enzymes, etc. Amino Acids
4) Nucleic Acids - DNA, RNA Nucleotides
MACROMOLECULES,...
VI. Lipids • Three main types of lipids: 1) FATS = Glycerol + 3 Fatty Acids
2) PHOSPHOLIPIDS = Spontaneously form membranes
3) STEROIDS = Skeleton consists of 4 fused carbon rings
• Macromolecule but NOT a polymer (no covalent bonds) • Share the common trait of being HYDROPHOBIC
VI. Lipids, ... 1) FATS = Glycerol + 3 Fatty Acids
(b) Fat molecule (triacylglycerol)
H H H H
H H H H H H H H H
H H H O
H O H C
C
C
H
H OH
OH
H
H H
H H
H H H H
H H H H H H
H
H C C C C C C C C C
C C
C C
C C C
Glycerol
Fatty acid (palmitic acid)
H H
H
H
H H H H
H H
H H
H H H H H
H H H
H H H H H H H H H H H H H H H H
H
H H H H H H H H H H H H H H H H
H H H H H H H H H H H H H H
H H H H H H H H H H H H H H H H
H H H H H H H H H H H H H H H
HO
O O
O
O C
C
C C C C C C C C C C C C C C C C C
C
C C C C C C C C C C C C C C C C
C C C C C C C C C C C C C C C O
O
(a) Dehydration reaction in the synthesis of a fat Ester linkage
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Fatty Acids
• Saturated:
– Have the maximum number of hydrogen atoms possible
– Have no double bonds
(a) Saturated fat and fatty acid
Stearic acid
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• Unsaturated:
– Have one or more double bonds
– Causes kinks in tail resulting in looser packing
(b) Unsaturated fat and fatty acid cis double bond causes bending
Oleic acid
Fatty Acids, ... VI. Lipids, ... 2) PHOSPHOLIPIDS
• Have only TWO Fatty Acids, with a P group replacing third FA
CH2
O P O O O
CH2 CH CH2 O O
C O C O
Phosphate
Glycerol
(a) Structural formula (b) Space-filling model
Fatty acids
(c) Phospholipid symbol
Hyd
roph
obic
tails
Hydrophilic head
Hydrophobic tails
–
Hyd
roph
ilic
head
CH2 Choline +
Figure 5.13
N(CH3)3
• Consist of a Hydrophilic head and two Hydrophobic tails
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Phospholipids
Hydrophilic head
WATER
WATER
Hydrophobic tail
• Spontaneously form lipid bilayers due to amphipathic nature of lipid molecules. Found in all cell membranes.
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VI. Lipids, ... 3) STEROIDS
• Lipids characterized by a C skeleton with 4 fused rings
• Cholesterol: A steroid important in cell membranes and acts as a precursor to some sex hormones.
HO
CH3
CH3
H3C CH3 CH3
MACROMOLECULES,...
Polymers • Four main classes of biological macromolecules:
Monomers: 1) CARBOHYDRATES (Polysaccharides) SUGARS
2) (LIPIDS - Make up membranes) Glycerol / FAs
3) PROTEINS - Enzymes, etc. Amino Acids
4) Nucleic Acids - DNA, RNA Nucleotides
Proteins are bodybuilding macromolecules.
VII. Proteins
Amino Acids
q Twenty different amino acids
q Strung together to make proteins
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2.16 A protein’s function is influenced by its three-dimensional shape.
q Peptide bonds
Primary Structure
q The sequence of amino acids
Secondary Structure
q Hydrogen bonding between amino acids
q The two most common patterns:
• twist in a corkscrew-like shape
• zig-zag folding
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Tertiary Structure
q Folding and bending of the secondary structure
q Due to bonds such as hydrogen bonds or covalent sulfur-sulfur bonds.
Quaternary Structure
q When two or more polypeptide chains are held together by bonds between the amino acids on the different chains.
q Hemoglobin
Take-home message 2.14
q Unique combinations of 20 amino acids give rise to proteins, the chief building blocks of physical structures that make up all organisms.
q Proteins perform myriad functions, from assisting chemical reactions to causing blood clotting to building bones to fighting microorganisms.
Nucleic acids are macromolecules that store information.
VIII. Nucleic Acids
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2.20 DNA holds the genetic information to build an organism.
Insert new fig 2-46
Two Types of Nucleic Acids
q Deoxyribonucleic acid (DNA)
q Ribonucleic acid (RNA)
q Both play central roles in directing the production of proteins.
Insert fig 2-45 to right
2.21 RNA is a universal translator, reading DNA and directing protein production.
Insert fig 2-47
RNA differs from DNA in three important ways.
q The sugar molecule of the sugar-phosphate backbone
q Single-stranded
q Uracil (U) replaces thymine (T)
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Take-home message 2.21
q RNA acts as a middleman molecule—taking the instructions for protein production from DNA to another part of the cell where, in accordance with the RNA instructions, amino acids are pieced together into proteins.
Building Blocks of Life
Reading: Chapter 2 For Next Week: Chapter 3 (Architecture of the Cell) Problem set #1 will be posted on the website tomorrow PS#1 will form basis of discussion sections next week PS#1 answers posted next Friday
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