the biotechnology century and its workforce
TRANSCRIPT
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Lectures prepared by Christine L. Case
Chapter 2
MIC 2010 Duncan Ross Ph.D.
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Insert Fig CO 2
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The Structure of Atoms
• 2-1 Describe the structure of an atom and its relation to the physical properties of elements.
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The Structure of Atoms
• Chemistry is the study of interactions between atoms and molecules
• The atom is the smallest unit of matter that enters into chemical reactions
• Atoms interact to form molecules
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The Structure of Atoms
• Atoms are composed of – Electrons: negatively charged particles – Protons: positively charged particles – Neutrons: uncharged particles
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The Structure of Atoms
• Protons and neutrons are in the nucleus • Electrons move around the nucleus
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Insert Fig 2.1
Figure 2.1 The structure of an atom.
.
Electron shells
Nucleus
Electron (e−)
Neutron (n0)
Proton (p+)
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Chemical Elements
• Each chemical element has a different number of protons
• Isotopes of an element are atoms with different numbers of neutrons. Isotopes of oxygen:
816O
817O
818O
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Electronic Configurations
• Electrons are arranged in electron shells corresponding to different energy levels
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Insert Table 2.1
Table 2.1 The Elements of Life
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• How does C differ from C? What is the atomic number of each carbon atom? The atomic weight? 2-1
14 6
12 6
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How Atoms Form Molecules
• 2-2 Define ionic bond, covalent bond, hydrogen bond, molecular weight, and mole.
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How Atoms Form Molecules
• Atoms combine to complete the outermost shell
• The number of missing or extra electrons in this shell is known as the valence
• Molecules hold together because the valence electrons of the combining atoms form attractive forces, called chemical bonds, between the atomic nuclei
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Ionic Bonds
• The number of protons and electrons is equal in an atom
• Ions are charged atoms that have gained or lost electrons
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Figure 2.2a Ionic bond formation.
A sodium atom (Na) loses one electron to an electron acceptor and forms a sodium ion (Na+). A chlorine atom (Cl) accepts one electron from an electron donor to become a chloride ion (Cl–).
Sodium ion (Na+)
Sodium atom (electron donor)
Chlorine atom (electron acceptor)
Chloride ion (Cl–)
Loss of electron
Gain of electron
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Ionic Bonds
• Ionic bonds are attractions between ions of opposite charge – One atom loses electrons, and another gains
electrons
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Insert Fig 2.2b
Figure 2.2b Ionic bond formation.
The sodium and chloride ions are attracted because of their opposite charges and are held together by an ionic bond to form a molecule of sodium chloride.
Chloride ion (Cl–)
Sodium ion (Na+)
Sodium chloride molecule Na+ Cl–
NaCl
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Covalent Bonds
• Covalent bonds form when two atoms share one or more pairs of electrons
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Insert Fig 2.3a
Figure 2.3a Covalent bond formation.
Diagram of Atomic Structure Structural Formula Molecular Formula
A single covalent bond between two hydrogen atoms. Hydrogen atom Hydrogen atom Hydrogen molecule
or
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Insert Fig 2.3b
Figure 2.3b Covalent bond formation.
Diagram of Atomic Structure Structural Formula Molecular Formula
Carbon atom Hydrogen atoms
Methane molecule
or
Single covalent bonds between four hydrogen atoms and a carbon atom, forming a methane molecule.
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Hydrogen Bonds
• Hydrogen bonds form when a hydrogen atom that is covalently bonded to an O or N atom is attracted to another N or O atom in another molecule
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Insert Fig 2.4b
Figure 2.4b Hydrogen bond formation in water.
Hydrogen bond
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H2O
2H = 2 × 1 = 2 O = 16 MW = 18 1 mole weighs 18 g
Molecular Weight and Moles • The sum of the atomic
weights in a molecule is the molecular weight
• One mole of a substance is its molecular weight in grams
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• Differentiate an ionic bond from a covalent bond. 2-2
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Learning Objective Chemical Reactions
2-3 Diagram three basic types of chemical reactions.
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Chemical Reactions
• Chemical reactions involve the making or breaking of bonds between atoms
• A change in chemical energy occurs during a chemical reaction
• Endergonic reactions absorb energy • Exergonic reactions release energy
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Synthesis Reactions
• Occur when atoms, ions, or molecules combine to form new, larger molecules
• Anabolism is the synthesis of molecules in a cell
A + B AB Atom, ion,
or molecule A Atom, ion,
or molecule B New molecule
AB
Combines to form
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Decomposition Reactions
• Occur when a molecule is split into smaller molecules, ions, or atoms
• Catabolism is the decomposition reactions in a cell
A + B AB Atom, ion,
or molecule A Atom, ion,
or molecule B New molecule
AB
Breaks down into
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Exchange Reactions
• Are part synthesis and part decomposition
NaCl + H2O NaOH + HCl
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Reversible Reactions
• Can readily go in either direction • Each direction may need special conditions
A + B Water
AB Heat
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• This chemical reaction below is used to remove chlorine from water. What type of reaction is it? 2-3
HClO + Na2SO3 Na2SO4 + HCl
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Important Biological Molecules
• Organic compounds always contain carbon and hydrogen
• Inorganic compounds typically lack carbon
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Inorganic Compounds
• 2-4 List several properties of water that are important to living systems.
• 2-5 Define acid, base, salt, and pH.
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Water
• Inorganic • Polar molecule • Solvent
– Polar substances dissociate, forming solutes
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Insert Fig 2.4a
Figure 2.4a Hydrogen bond formation in water.
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Insert Fig 2.5
Figure 2.5 How water acts as a solvent for sodium chloride (NaCl).
Sodium chloride crystal
Sodium ion dissolved in water
Chloride ion dissolved in water
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Water
• H+ and OH− participate in chemical reactions
R—R′ + H2O → R—OH + H—R′
Maltose + H2O → Glucose + Glucose
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Maltose + H2O → Glucose + Glucose
Glucose C6H12O6
Glucose +C6H12O6
Total C12H24O12
Maltose C12H22O11
The difference is:
Water
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Insert Fig 2.4b
Figure 2.4b Hydrogen bond formation in water.
Hydrogen bond
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Insert Fig 2.6
Figure 2.6 Acids, bases, and salts.
Acid Base Salt
HCl NaCl NaOH
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Acids
• Substances that dissociate into one or more H+
HCl → H+ + Cl−
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Insert Fig 2.6a
Figure 2.6a Acids, bases, and salts.
Acid
HCl
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Bases
• Substances that dissociate into one or more OH−
NaOH → Na+ + OH−
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Insert Fig 2.6b
Figure 2.6b Acids, bases, and salts.
Base
NaOH
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Salts
• Substances that dissociate into cations and anions, neither of which is H+ or OH−
NaCl → Na+ + Cl−
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Insert Fig 2.6c
Figure 2.6c Acids, bases, and salts.
Salt
NaCl
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Acid-Base Balance
• The amount of H+ in a solution is expressed as pH
• pH = −log[H+] • Increasing [H+] increases acidity • Increasing [OH−] increases alkalinity • Most organisms grow best between pH 6.5
and 8.5
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Insert Fig 2.7
Figure 2.7 The pH scale.
pH scale
Stomach acid
Lemon juice
Grapefruit juice
Wine Tomato juice
Urine Milk Pure water
Seawater
Milk of magnesia
Household ammonia
Household bleach
Oven cleaner Limewater Basic solution
Neutral solution
Acidic solution
Human blood
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• Why is the polarity of a water molecule important? 2-4
• Antacids neutralize acid by the following reaction. Identify the acid, base, and salt. 2-5
Mg(OH)2 + 2HCl → MgCl2 + H2O
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Structure and Chemistry
• The chain of carbon atoms in an organic molecule is the carbon skeleton
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Structure and Chemistry
• Functional groups are responsible for most of the chemical properties of a particular organic compound
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Organic Compounds
• 2-8 Identify the building blocks of carbohydrates. • 2-9 Differentiate simple lipids, complex lipids, and
steroids. • 2-10 Identify the building blocks and
structure of proteins. • 2-11 Identify the building blocks of nucleic
acids. • 2-12 Describe the role of ATP in cellular
activities. •
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Polymers
• Monomers join by dehydration synthesis or condensation reactions
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Carbohydrates
• Cell structures and energy sources • Consist of C, H, and O with the formula
(CH2O)n
• Monosaccharides are simple sugars with three to seven carbon atoms
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Carbohydrates
• Disaccharides are formed when two monosaccharides are joined in a dehydration synthesis
• Disaccharides can be broken down by hydrolysis
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Lipids
• Primary components of cell membranes • Consist of C, H, and O • Are nonpolar and insoluble in water
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Simple Lipids
• Fats or triglycerides • Contain glycerol and fatty acids; formed by
dehydration synthesis
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Ester linkage
Molecule of fat (triglyceride)
Figure 2.9c Structural formulas of simple lipids.
Palmitic acid (C15H31COOH) + (saturated)
H2O
H2O Stearic acid (C17H35COOH) + (saturated)
cis configuration
Oleic acid (C17H33COOH) + (unsaturated)
H2O
Molecule of fat (triglyceride)
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Simple Lipids
• Saturated fat: no double bonds • Unsaturated fat: one or more double bonds in
the fatty acids – Cis: H atoms on the same side of the double bond – Trans: H atoms on opposite sides of the double
bond
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Insert Fig 2.9c Insert Fig 2.9c
Palmitic acid (C15H31COOH) + (saturated)
Ester linkage
Molecule of fat (triglyceride)
H2O
H2O Stearic acid (C17H35COOH) + (saturated)
cis configuration
Oleic acid (C17H33COOH) + (unsaturated)
H2O
Figure 2.9c Structural formulas of simple lipids.
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Complex Lipids
• Contain C, H, and O + P, N, or S • Membranes are made of phospholipids
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Figure 2.9ab Structural formulas of complex lipids.
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Steroids
• Four carbon rings with an –OH group attached to one ring
• Part of membranes
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Insert Fig 2.11
Figure 2.11 Cholesterol, a steroid.
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Proteins
• Are essential in cell structure and function • Enzymes are proteins that speed chemical
reactions • Transporter proteins move chemicals across
membranes • Flagella are made of proteins • Some bacterial toxins are proteins
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Amino Acids
• Proteins consist of subunits called amino acids
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Insert Fig 2.12
Figure 2.12 Amino acid structure.
Side group Amino
group
Carboxyl group
Generalized amino acid
Cyclic side group
Tyrosine
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Peptide Bonds
• Peptide bonds between amino acids are formed by dehydration synthesis
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Insert Fig 2.14
Figure 2.14 Peptide bond formation by dehydration synthesis.
Glycine Alanine
Dehydration synthesis
Peptide bond
Glycylalanine (a dipeptide)
Water
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Levels of Protein Structure
• The primary structure is a polypeptide chain
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Peptide bonds
Figure 2.15a Protein structure.
(a) Primary structure: polypeptide strand
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Levels of Protein Structure
• The secondary structure occurs when the amino acid chain folds and coils in a regular helix or pleats
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Insert Fig 2.15b
Hydrogen bond
(b) Secondary structure: helix and pleated sheets (with three polypeptide strands)
Helix
Pleated sheet
Disulfide bridge
Figure 2.15b Protein structure.
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Levels of Protein Structure
• The tertiary structure occurs when the helix folds irregularly, forming disulfide bridges, hydrogen bonds, and ionic bonds between amino acids in the chain
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Insert Fig 2.15c
(c) Tertiary structure: folded helix and pleated sheet
Hydrogen bond
Disulfide bridge (between cysteine molecules)
Ionic bond
Details of bonds associated with tertiary structure
Hydrophobic interaction
Polypeptide strand
Figure 2.15c Protein structure.
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Insert Fig 2.15 Insert Fig 2.15a
Peptide bonds
(a) Primary structure: polypeptide strand
Hydrogen bond
(b) Secondary structure: helix and pleated sheets (with three polypeptide strands) Helix
Pleated sheet
Disulfide bridge
(c) Tertiary structure: folded helix and pleated sheet
(d) Quaternary structure: two or more polypeptides in their folded states
Hydrogen bond
Disulfide bridge (between cysteine molecules)
Ionic bond
Details of bonds associated with tertiary structure
Hydrophobic interaction
Polypeptide strand
Figure 2.15 Protein structure.
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Nucleic Acids • Consist of nucleotides • Nucleotides consist of
– Pentose – Phosphate group – Nitrogen-containing (purine or pyrimidine) base
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DNA
• Deoxyribonucleic acid • Has deoxyribose • Exists as a double helix • A hydrogen bonds with T • C hydrogen bonds with G
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Insert Fig 2.16
Figure 2.16 The Structure of DNA.
Phosphate Sugar Adenine (A) Thymine (T) Sugar Phosphate
Adenine nucleotide
The carbon atoms in the sugars are identified by adding a marker, ’ (for example, 5’, pronounced “5-prime”). This differentiates them from the carbon atoms in the nucleo-bases, such as Thymine.
Adenine and Thymine (as well as Cytosine and Guanine, not shown here) are nitrogenous bases or nucleobases.
Hydrogen bonds
Individual DNA nucleotides are composed of a deoxyribose sugar molecule covalently bonded to a phosphate group at the 5’ carbon, and to a nitrogen-containing base at the 3’ carbon. The two nucleotides shown here are held together by hydrogen bonds.
Sugars
Phosphates Sugar-phosphate backbone
The sugar-phosphate backbone of one strand is upside down, or antiparallel, relative to the backbone of the other strand.
DNA double helix
DNA’s double-helical, ladder-like form is made up of many nucleotides base pairs forming the rungs, and the repeating sugar-phosphate combination, forming the backbone.
Thymine nucleotide
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RNA
• Ribonucleic acid • Has ribose • Is single-stranded • A hydrogen bonds with U • C hydrogen bonds with G
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Insert Fig 2.17
Figure 2.17 A uracil nucleotide of RNA.
Phosphate
Uracil (U)
Ribose
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ATP
• Adenosine triphosphate • Has ribose, adenine, and three phosphate
groups
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Insert Fig 2.18
Figure 2.18 The structure of ATP.
Phosphates
Adenosine
Ribose
Adenine
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ATP
• Is made by dehydration synthesis • Is broken by hydrolysis to liberate useful
energy for the cell
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• Which can provide more energy for a cell and why: ATP or ADP? (2-12)