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CHAPTER 2Small Molecules: Structure and Behavior
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Atoms: The Constituents of Matter Matter is composed of atoms with positively
charged nuclei of protons and neutrons surrounded by negatively charged electrons.
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Main Elements Found in Living Organisms
Figure 2.1
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Isotopes of an element differ in numbers of neutrons
Figure 2.2 Some isotopes are unstable and are termed radioactive. Some isotopes are unstable and are termed radioactive. These radioisotopes are useful for many purposes.These radioisotopes are useful for many purposes.
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Electrons are distributed in shells of orbitals
Each orbital contains a max of 2 electrons
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Orbital Shell Representations for Several Atoms Figure 2.5
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Interaction of atoms via sharing of electrons generates molecules via bonding
Table 2.1
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Figure 2.6
Covalent Bonds
Covalent bonds form when two atomic nuclei share one or more pairs of electrons. They have spatial orientations that give molecules three-dimensional shapes
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Covalent Bonds
Figure 2.7
Combining electrons in all the orbitals in a particular level often occurs.
sp3 bonds of carbon are the combination of the 2s orbital and the 3 2p orbitals to form 4 sp3 orbitals which each have a single electron that is shared with the single electron in H’s 1s orbital
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Table 2.2
Table 2.2
table 02-02.jpg
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Chemical Bonds: Linking Atoms Together Nonpolar covalent bonds form when the
electronegativities of two atoms are approximately equal
Polar covalent bond in which one end is + and the other is – forms when atoms with strong electronegativity (such as oxygen) bond to atoms with weaker electronegativity (such as hydrogen)
Hydrogen bonded to a strongly electronegative atom can be donated to a H-bond
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Polarity in bonding
Figure 2.8
figure 02-08.jpg
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Table 2.3
Table 2.3
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Ionic bonds
Figure 2.10
Complete gain/loss of electron to form a charged species
Oppositely charged ions then interact electrostatically
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Hydrogen bonds Hydrogen bonds form between a + hydrogen
atom in one molecule and a – nitrogen, oxygen or sulfur atom in another molecule or in another part of a large molecule.
figure 02-09.jpg
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Polar solvents dissolve ionic & polar substances
Figure 2.11
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Polar & Non-polar Molecules Nonpolar molecules do not interact directly
with polar substances. They are attracted to each other by very weak bonds called van der Waals forces.
Van der Waals forces are the weak sharing of electons between orbitals of molecules
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Water: Structure and Properties Water’s molecular structure and capacity to
form hydrogen bonds give it unusual properties significant for life.
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Water: Structure and Properties Cohesion of water molecules results in a high
surface tension. Water’s high heat of vaporization assures cooling when it evaporates.
Solutions are substances dissolved in water. Concentration is the amount of a given substance in a given amount of solution. Most biological substances are dissolved at very low concentrations.
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Chemical Reactions: Atoms Change Partners
In chemical reactions, substances change their atomic compositions and properties. Energy is either released or added. Matter and energy are not created or destroyed, but change form.
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Acids, Bases, and the pH Scale Acids are substances that donate hydrogen ions.
Bases are those that accept hydrogen ions. The pH of a solution is the negative logarithm of
the hydrogen ion concentration. pH=-log[H+] Values lower than pH 7 indicate an acidic
solution. Values above pH 7 indicate a basic solution
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pH Scale
Figure 2.18
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Acids, Bases, and the pH Scale Buffers are systems of weak acids and bases that
limit the change in pH when hydrogen ions are added or removed.
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The Properties of Molecules Molecules vary in size, shape, reactivity,
solubility, and other chemical properties. Functional groups make up part of a larger
molecule and have particular chemical properties.
The consistent chemical behavior of functional groups helps us understand the properties of the molecules that contain them.
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Functional Groups
Figure 2.20 – Part 1
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Functional Groups
Figure 2.20 – Part 2
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Isomers
Optical Isomers Figure 2.21
•Optical isomers•rotate plain polarized light in opposite directions
•Structural isomers•Differ in position of functional groups
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CHAPTER 3Macromolecules: Their Chemistry and
Biology
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Macromolecules: Giant Polymers Macromolecules are formed by covalent
bonds between monomers and include polysaccharides, proteins, and nucleic acids.
Lipids are crucial biomolecules, but are not considered ‘macromolecules’
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Table 3.1
table 03-01.jpg
Fatty Acid TriglyceridePhospholipid
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Macromolecules: Giant Polymers Macromolecules have specific three-
dimensional shapes. Different functional groups give local sites on
macromolecules specific properties.
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Condensation Reactions
Monomers are joined by condensation reactions. Hydrolysis reactions break polymers into monomers.
Joining of monomers is typically called polymerization
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Proteins: Polymers of Amino Acids Functions of proteins include support,
protection, catalysis, transport, defense, regulation, and movement. They sometimes require an attached prosthetic group.
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Proteins: Polymers of Amino Acids Twenty amino acids are found in proteins. Each consists of an amino group, a carboxyl
group, a hydrogen, and a side chain bonded to the carbon atom.
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Table 3.2 – Part 1
table 03-02a.jpg
Amino Acids
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table 03-02bc.jpgAmino Acids
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Proteins: Synthesis
Amino acids are covalently bonded together by peptide linkages or peptide bond
Chemically this is an amide bond
Each amino acid is called a residue
Reaction proceeds leaving the amino terminus of the 1st aa and the carboxyl terminus of the last aa unmodified (free)
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Proteins: Structure Polypeptide chains of proteins are folded into
specific three-dimensional shapes There are 4 levels of structure
Primary (1o) – amino acid sequence Secondary (2o) – localized structures of adjacent residues Tertiary (3o) – folding of units of secondary structure Quaternary – association of multiple individual proteins
(subunits) to form a functional complex
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H-bonds stabilize 2o structures
Protein Structure
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3.5 – Part 2
Figure 3.5 – Part 2Protein Structure
Covalent bonds (disulfide bridges), H-bonds & ionic bonds (salt bridges) stabilize 3o and 4o structures
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Figure 3.3
figure 03-03.jpg
The SH groups of cysteine residues The SH groups of cysteine residues can form disulfide bridges that link can form disulfide bridges that link distant regions of proteins togetherdistant regions of proteins together
Protein Structure
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3.7
Figure 3.7
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Proteins: Structure
• Chemical interactions important for binding of proteins to other molecules. • H-bonds• Van der Waals
interactions• Ionic interactions
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Proteins: Structure Proteins can be
denatured heat, acid, or
chemicals Loss of tertiary
and secondary structures and biological function.
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Proteins: Structure Proper folding of proteins is critical for their function Chaperonins assist protein folding
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Carbohydrates: Sugars and Sugar Polymers• Monosaccharides
• 3-carbons – trioses• 5-carbons - pentoses• 6-carbons – hexoses
• Disaccharides• Two monosaccharides
• Maltose• Sucrose• Lactose
• Oligosaccharide• <10 glycoside residues
• Polysaccharide• >10 glycoside residues
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Carbohydrates: Structures
Hemiacetal forms
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Carbohydrates Structure
Glyceraldehyde
4 carbon sugar is erythrose
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Carbohydrates Structure figure 03-12b.jpg
Isomers
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Carbohydrate Polymerization
Glycosidic linkages may have either or orientation in spaceNumbering of bond refers to carbon position of hemiacetal ring
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Carbohydrate polymerization
Figure 3.14 – Part 1An unbranched polysaccharide
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Carbohydrate polymerization
Figure 3.14 – Part 2Branched chain polysaccharides
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Carbohydrates modified sugars• Chemically modified
monosaccharides• Phosphates, • Acetyl groups• Sulfates• Amino groups
• Derivative of glucosamine polymerizes to form the polysaccharide chitin• Used as the basis of
arthropod exoskeletons• Proteoglycans &
Glycoproteins• Proteins with attached
carbohydrates• Heparin sulfate• Chondroitin sulfate
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Nucleic Acids: Informational Macromolecules
• In cells, DNA is the hereditary material. DNA and RNA play roles in protein formation.
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Nucleotide Structures
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Nucleotides – The Sugars
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Nucleotides – The Bases
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Nucleosides – Sugar + Base
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Nucleotide – Nucleoside + Phosphates
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Nucleic Acids – Polymers of Nucleotides
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Nucleic Acid Structure
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Nucleic Acids Complementary Base Pairing
A-T or U G-C Watson-Crick Pairing
Specificity Fidelity of DNA replication Fidelity of transcription Fidelity of any nucleic acid-nucleic acid
interaction ie. mRNA – tRNA Hybridization
Our manipulation of nucleic acids
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16S rRNA Secondary Structures
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tRNA Secondary Structure
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DNA Double Helix
Figure 3.18
Major Groove
Minor Groove
Spacing of base-pairs – 3.4ÅHelix diameter ~ 20Å10 base-pairs per helical turn
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DNA – The Genetic Material Genes
Coding sequences Regulatory sequences
Genes encode proteins Information flow DNA RNA protein Central Dogma
DNA sequences
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Nucleic Acids: Manipulation Molecular Biology
• DNA amplification – PCR• DNA cloning – gene isolation and
identification• DNA sequencing – gene characterization• DNA-RNA & DNA-DNA hybridization – Gene
Chips
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Lipids Fatty Acids
Triglycerides Phospholipids
Steroids Steroid hormones Retinoids
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Fatty Acids
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Triglyceride Formation
Figure 3.19
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Phospholipids:
• Phospholipids have a hydrophobic hydrocarbon “tail” and a hydrophilic “head” group.
• Head group• Phosphate connection• Base
• Choline• Ethanolamine
• Sugar• Inositol
• Amino acid• Serine
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Lipid Bilayer Formation
Figure 3.22
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Steroid Lipids:• Carotenoids trap light energy in green plants. β-Carotene
can be split to form vitamin A (retinol), a lipid vitamin.
All-trans retinol
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Steroid Lipids
Figure 3.24